From d245065045941bd382b02edd47c0dc2b5676596c Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 27 Sep 2022 17:23:11 -0400
Subject: [PATCH 001/221] adding basic socketio webserver for gui

---
 refl1d/webserver.py | 67 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 refl1d/webserver.py

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
new file mode 100644
index 00000000..7dee2fe2
--- /dev/null
+++ b/refl1d/webserver.py
@@ -0,0 +1,67 @@
+# from .main import setup_bumps
+
+from aiohttp import web
+import socketio
+from pathlib import Path
+import json
+from copy import deepcopy
+
+from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit
+
+FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
+FITTER_DEFAULTS = {}
+for fitter in FITTERS:
+    FITTER_DEFAULTS[fitter.id] = {
+        "name": fitter.name,
+        "settings": dict(fitter.settings)
+    }
+
+# set up mutable state of fitters:
+fitter_settings = deepcopy(FITTER_DEFAULTS)
+active_fitter = "amoeba"
+
+sio = socketio.AsyncServer(cors_allowed_origins="*")
+app = web.Application()
+static_dir_path = Path(__file__).parent / 'webview'
+sio.attach(app)
+
+async def index(request):
+    """Serve the client-side application."""
+    # redirect to static built site:
+    return web.HTTPFound('/static/index.html')
+    
+@sio.event
+async def connect(sid, environ):
+    print("connect ", sid)
+    sio.enter_room(sid, "situation")
+    await sio.emit("fitter-defaults", FITTER_DEFAULTS, to=sid)
+    await sio.emit("fitter-settings", fitter_settings, to=sid)
+    await sio.emit("fitter-active", active_fitter, to=sid)
+
+@sio.on("fitter-active")
+async def new_fitter_active(sid, data):
+    # using global state here:
+    global active_fitter
+    active_fitter = data
+    await sio.emit("fitter-active", data, room="situation")
+
+@sio.on("fitter-settings")
+async def new_fitter_settings(sid, data):
+    global fitter_settings
+    fitter_settings.update(data)
+    await sio.emit("fitter-settings", fitter_settings, room="situation")
+
+# async def get_sessions(sid):
+#     return web.Response(text=json.dumps(list(sessions)), content_type='application/json')
+
+@sio.event
+def disconnect(sid):
+    print('disconnect ', sid)
+
+app.router.add_static('/static', static_dir_path)
+# app.router.add_static('/static', os.path.join(currdir, 'webview'))
+app.router.add_get('/', index)
+
+
+if __name__ == '__main__':
+    web.run_app(app)

From 4242336fe742138662c6c99f17112361fc44d725 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 27 Sep 2022 17:26:44 -0400
Subject: [PATCH 002/221] initial commit of web gui for refl1d

---
 refl1d-web-gui/README.md                      |  29 +++
 refl1d-web-gui/index.html                     |  13 ++
 refl1d-web-gui/package.json                   |  18 ++
 refl1d-web-gui/src/App.vue                    | 175 +++++++++++++++
 .../src/assets/refl1d-icon_256x256x32.png     | Bin 0 -> 54618 bytes
 refl1d-web-gui/src/components/FitOptions.vue  | 210 ++++++++++++++++++
 refl1d-web-gui/src/fitter_defaults.ts         |  62 ++++++
 refl1d-web-gui/src/main.js                    |   6 +
 refl1d-web-gui/vite.config.js                 |  15 ++
 9 files changed, 528 insertions(+)
 create mode 100644 refl1d-web-gui/README.md
 create mode 100644 refl1d-web-gui/index.html
 create mode 100644 refl1d-web-gui/package.json
 create mode 100644 refl1d-web-gui/src/App.vue
 create mode 100644 refl1d-web-gui/src/assets/refl1d-icon_256x256x32.png
 create mode 100644 refl1d-web-gui/src/components/FitOptions.vue
 create mode 100644 refl1d-web-gui/src/fitter_defaults.ts
 create mode 100644 refl1d-web-gui/src/main.js
 create mode 100644 refl1d-web-gui/vite.config.js

diff --git a/refl1d-web-gui/README.md b/refl1d-web-gui/README.md
new file mode 100644
index 00000000..e8949d5e
--- /dev/null
+++ b/refl1d-web-gui/README.md
@@ -0,0 +1,29 @@
+# refl1d-web-gui
+
+This template should help get you started developing with Vue 3 in Vite.
+
+## Recommended IDE Setup
+
+[VSCode](https://code.visualstudio.com/) + [Volar](https://marketplace.visualstudio.com/items?itemName=Vue.volar) (and disable Vetur) + [TypeScript Vue Plugin (Volar)](https://marketplace.visualstudio.com/items?itemName=Vue.vscode-typescript-vue-plugin).
+
+## Customize configuration
+
+See [Vite Configuration Reference](https://vitejs.dev/config/).
+
+## Project Setup
+
+```sh
+npm install
+```
+
+### Compile and Hot-Reload for Development
+
+```sh
+npm run dev
+```
+
+### Compile and Minify for Production
+
+```sh
+npm run build
+```
diff --git a/refl1d-web-gui/index.html b/refl1d-web-gui/index.html
new file mode 100644
index 00000000..030a6ff5
--- /dev/null
+++ b/refl1d-web-gui/index.html
@@ -0,0 +1,13 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <link rel="icon" href="/favicon.ico" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Vite App</title>
+  </head>
+  <body>
+    <div id="app"></div>
+    <script type="module" src="/src/main.js"></script>
+  </body>
+</html>
diff --git a/refl1d-web-gui/package.json b/refl1d-web-gui/package.json
new file mode 100644
index 00000000..0d0651c3
--- /dev/null
+++ b/refl1d-web-gui/package.json
@@ -0,0 +1,18 @@
+{
+  "name": "refl1d-web-gui",
+  "version": "0.0.0",
+  "scripts": {
+    "dev": "vite",
+    "build": "vite build --outDir ../refl1d/webview --emptyOutDir",
+    "preview": "vite preview --port 4173"
+  },
+  "dependencies": {
+    "bootstrap": "^5.2.1",
+    "socket.io-client": "^4.5.2",
+    "vue": "^3.2.38"
+  },
+  "devDependencies": {
+    "@vitejs/plugin-vue": "^3.0.3",
+    "vite": "^3.0.9"
+  }
+}
diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
new file mode 100644
index 00000000..4abda4f5
--- /dev/null
+++ b/refl1d-web-gui/src/App.vue
@@ -0,0 +1,175 @@
+<script setup lang="ts">
+import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
+import { onMounted, ref, shallowRef } from 'vue';
+import { api } from './server_api';
+import { io, Socket } from 'socket.io-client';
+import FitOptions from './components/FitOptions.vue';
+// import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
+const FITTER_DEFAULTS = {};
+
+const REFLECTIVITY_PLOTS = [
+  "Fresnel",
+  "Log Fresnel",
+  "Linear",
+  "Log",
+  "Q4",
+  "SA"
+] as const;
+type ReflectivityPlotEnum = typeof REFLECTIVITY_PLOTS;
+type ReflectivityPlot = ReflectivityPlotEnum[number];
+
+const reflectivity_type = ref<ReflectivityPlot>("Linear");
+const connection_id = ref("");
+const connection = ref<Socket | null>(null);
+const connected = ref(false);
+const menuToggle = ref(null);
+const fitOptions = ref(null);
+const fitter_settings = shallowRef(structuredClone(FITTER_DEFAULTS));
+const fitter_defaults = shallowRef(FITTER_DEFAULTS);
+const active_fitter = ref('amoeba');
+
+function set_reflectivity(refl_type: ReflectivityPlot) {
+  reflectivity_type.value = refl_type;
+}
+
+function load_model_path(path: string) {
+
+}
+
+function connect() {
+  const socket = io('http://localhost:8080', {
+    reconnectionAttempts: 10
+  });
+  connection.value = socket;
+  socket.on('connect', () => {
+    console.log(socket.id);
+    connected.value = true;
+  });
+
+  socket.on('fitter-settings', (payload) => {
+    fitter_settings.value = payload;
+  });
+  socket.on('fitter-defaults', (payload) => {
+    fitter_defaults.value = payload;
+  });
+  socket.on('fitter-active', (payload) => {
+    active_fitter.value = payload;
+  });
+  socket.on('disconnect', (payload) => {
+    console.log("disconnected!", payload);
+    connected.value = false;
+  })
+}
+
+function disconnect() {
+  connection.value?.disconnect();
+  connected.value = false;
+}
+
+function openFitOptions() {
+  fitOptions?.value?.open();
+}
+
+function get_sessions() {
+  fetch('http://localhost:8080/get_sessions');
+}
+
+function updateActiveFitter(fitter_name) {
+  connection.value?.emit("fitter-active", fitter_name);
+}
+
+function updateActiveSettings(new_settings) {
+  connection.value?.emit("fitter-settings", new_settings);
+}
+
+onMounted(() => {
+  const menuToggleButton = new Button(menuToggle.value);
+  connect();
+});
+</script>
+
+<template>
+  <div class="h-100 d-flex flex-column">
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark p-2">
+      <div class="container-fluid">
+        <div class="navbar-brand">
+          <img src="./assets/refl1d-icon_256x256x32.png" alt="" height="36" class="d-inline-block align-text-middle">
+          Refl1D
+        </div>
+        <button ref="menuToggle" class="navbar-toggler" type="button" data-bs-toggle="collapse"
+          data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false"
+          aria-label="Toggle navigation">
+          <span class="navbar-toggler-icon"></span>
+        </button>
+        <div class="collapse navbar-collapse" id="navbarSupportedContent">
+          <ul class="navbar-nav me-auto mb-2 mb-lg-0">
+            <li class="nav-item dropdown">
+              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+                aria-expanded="false">
+                Session
+              </a>
+              <ul class="dropdown-menu">
+                <li><a class="dropdown-item" href="#" @click="connect">New</a></li>
+                <li><a class="dropdown-item" href="#" @click="disconnect">Disconnect</a></li>
+                <li><a class="dropdown-item" href="#" @click="reconnect">Existing</a></li>
+              </ul>
+            </li>
+            <li class="nav-item dropdown">
+              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+                aria-expanded="false">
+                File
+              </a>
+              <ul class="dropdown-menu">
+                <li><a class="dropdown-item" href="#">Open</a></li>
+                <li><a class="dropdown-item" href="#">Save</a></li>
+                <li>
+                  <hr class="dropdown-divider">
+                </li>
+                <li><a class="dropdown-item" href="#">Quit</a></li>
+              </ul>
+            </li>
+            <li class="nav-item dropdown">
+              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+                aria-expanded="false">
+                Fitting
+              </a>
+              <ul class="dropdown-menu">
+                <li><a class="dropdown-item" href="#">Start</a></li>
+                <li><a class="dropdown-item" href="#">Stop</a></li>
+                <li>
+                  <hr class="dropdown-divider">
+                </li>
+                <li><a class="dropdown-item" href="#" @click="openFitOptions">Options...</a></li>
+              </ul>
+            </li>
+            <li class="nav-item dropdown">
+              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+                aria-expanded="false">
+                Reflectivity
+              </a>
+              <ul class="dropdown-menu">
+                <li v-for="plot_type in REFLECTIVITY_PLOTS" :key="plot_type">
+                  <a :class="{'dropdown-item': true, active: (plot_type === reflectivity_type)}" href="#"
+                    @click="set_reflectivity(plot_type)">{{plot_type}}</a>
+                </li>
+              </ul>
+            </li>
+          </ul>
+          <div class="d-flex">
+            <div id="connection_status" :class="{'btn': true, 'btn-outline-success': connected, 'btn-outline-danger': !connected}">
+              {{(connected) ? 'connected' : 'disconnected'}}</div>
+
+          </div>
+        </div>
+      </div>
+    </nav>
+  </div>
+  <FitOptions ref="fitOptions" :fitter_defaults="fitter_defaults" :fitter_settings="fitter_settings"
+    :active_fitter="active_fitter" @active-fitter="updateActiveFitter" @active-settings="updateActiveSettings"/>
+</template>
+
+<style scoped>
+div#connection_status {
+  pointer-events: none;
+}
+</style>
diff --git a/refl1d-web-gui/src/assets/refl1d-icon_256x256x32.png b/refl1d-web-gui/src/assets/refl1d-icon_256x256x32.png
new file mode 100644
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diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
new file mode 100644
index 00000000..e226b4c2
--- /dev/null
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -0,0 +1,210 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+// import { Modal } from 'bootstrap';
+import { Modal } from 'bootstrap/dist/js/bootstrap.esm';
+import { isArray } from '@vue/shared';
+
+const props = defineProps({
+  fitter_defaults: {
+    type: Object,
+    default: {}
+  },
+  fitter_settings: {
+    type: Object,
+    default: {}
+  },
+  active_fitter: {
+    type: String,
+    default: 'amoeba'
+  }
+});
+
+const emit = defineEmits<{
+  (e: 'close'): void
+  (e: 'update', value: Object): void
+  (e: 'active-fitter', value: string): void
+  (e: 'active-settings', value: Object): void
+}>();
+
+const dialog = ref(null);
+const isOpen = ref(false);
+
+const FIT_FIELDS = {
+  'starts': ['Starts', 'integer'],
+  'steps': ['Steps', 'integer'],
+  'samples': ['Samples', 'integer'],
+  'xtol': ['x tolerance', 'float'],
+  'ftol': ['f(x) tolerance', 'float'],
+  'alpha': ['Convergence', 'float'],
+  'stop': ['Stopping criteria', 'string'],
+  'thin': ['Thinning', 'integer'],
+  'burn': ['Burn-in steps', 'integer'],
+  'pop': ['Population', 'float'],
+  'init': ['Initializer', ["eps", "lhs", "cov", "random"]],
+  'CR': ['Crossover ratio', 'float'],
+  'F': ['Scale', 'float'],
+  'nT': ['# Temperatures', 'integer'],
+  'Tmin': ['Min temperature', 'float'],
+  'Tmax': ['Max temperature', 'float'],
+  'radius': ['Simplex radius', 'float'],
+  'trim': ['Burn-in trim', 'boolean'],
+  'outliers': ['Outliers', ["none", "iqr", "grubbs", "mahal"]]
+}
+
+const active_fitter = ref('amoeba');
+// work with a copy of the fitter definitions, which will
+// still get used as defaults
+
+// make another working copy for editing:
+const active_settings = ref({});
+
+let modal: Modal;
+
+onMounted(() => {
+  modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
+});
+
+function close() {
+  modal?.hide();
+}
+
+function open() {
+  // copy the active_fitter from the server state:
+  active_fitter.value = props.active_fitter;
+  changeActiveFitter();
+  modal?.show();
+}
+
+const fit_names = computed(() => Object.keys(props.fitter_defaults));
+
+function changeActiveFitter() {
+  active_settings.value = structuredClone(props.fitter_settings[active_fitter.value]?.settings);
+}
+
+// watch(isOpen, (newState, oldState) => {
+//   if (newState == true && modal) {
+//     modal.show();
+//   }
+//   else {
+//     modal.hide();
+//   }
+// })
+
+// watch(() => props.fitter_settings, (newState, oldState) => {
+//   // fit_names.value = Object.keys(newState);
+// })
+
+function process_settings() {
+  return Object.fromEntries(Object.entries(active_settings.value).map(([sname, value]) => {
+    const field_type = FIT_FIELDS[sname][1];
+    let processed_value = value;
+    if (field_type === 'integer') {
+      processed_value = Math.round(Number(value));
+    }
+    else if (field_type === 'float') {
+      processed_value = Number(value);
+    }
+    else if (field_type === 'boolean') {
+      // probably unnecessary if it is bound to a checkbox
+      processed_value = Boolean(value);
+    }
+    return [sname, processed_value];
+  }))
+}
+
+function save() {
+  const new_settings = {};
+  new_settings[active_fitter.value] = {settings: process_settings()};
+  emit('active-settings', new_settings);
+  emit('active-fitter', active_fitter.value);
+  close();
+}
+
+function reset() {
+  active_settings.value = structuredClone(props.fitter_defaults[props.active_fitter].settings);
+}
+
+function validate(value, field_name) {
+  const field_type = FIT_FIELDS[field_name][1];
+  if (isArray(field_type) || field_type === 'boolean') {
+    // there's no way to get an incorrect option.
+    return true;
+  }
+  const float_value = Number(value);
+  if (isNaN(float_value)) {
+    return false;
+  }
+  if (field_type === 'integer' && parseInt(value, 10) != float_value) {
+    return false;
+  }
+  return true;
+}
+
+const anyIsInvalid = computed(() => {
+  return Object.entries(active_settings.value).some(([sname, value]) => !validate(value, sname));
+})
+
+defineExpose({
+  close,
+  open
+})
+</script>
+
+<template>
+  <div ref="dialog" class="modal fade" id="fitOptionsModal" tabindex="-1" aria-labelledby="fitOptionsLabel"
+    :aria-hidden="isOpen">
+    <div class="modal-dialog">
+      <div class="modal-content">
+        <div class="modal-header">
+          <h5 class="modal-title" id="fitOptionsLabel">Fit Options</h5>
+          <button type="button" class="btn-close" @click="close" aria-label="Close"></button>
+        </div>
+        <div class="modal-body">
+          <div class="container">
+            <div class="row border-bottom">
+              <div class="col">
+                <div class="form-check" v-for="fname in fit_names.slice(0,3)" :key="fname">
+                  <input class="form-check-input" v-model="active_fitter" type="radio" name="flexRadio" :id="fname"
+                    :value="fname" @change="changeActiveFitter">
+                  <label class="form-check-label" :for="fname">
+                    {{props.fitter_defaults[fname].name}}
+                  </label>
+                </div>
+              </div>
+              <div class="col">
+                <div class="form-check" v-for="fname in fit_names.slice(3)" :key="fname">
+                  <input class="form-check-input" v-model="active_fitter" type="radio" name="flexRadio" :id="fname"
+                    :value="fname" @change="changeActiveFitter">
+                  <label class="form-check-label" :for="fname">
+                    {{props.fitter_defaults[fname].name}}
+                  </label>
+                </div>
+              </div>
+            </div>
+            <div class="row p-2">
+              <div class="row p-1" v-for="(value, sname, index) in active_settings" :key="sname">
+                <label class="col-sm-4 col-form-label" :for="'setting_' + index">{{FIT_FIELDS[sname][0]}}</label>
+                <div class="col-sm-8">
+                  <select v-if="isArray(FIT_FIELDS[sname][1])" v-model="active_settings[sname]" class="form-select">
+                    <option v-for="opt in FIT_FIELDS[sname][1]">{{opt}}</option>
+                  </select>
+                  <input v-else-if="FIT_FIELDS[sname][1]==='boolean'" class="form-check-input m-2" type="checkbox" v-model="active_settings[sname]" />
+                  <input v-else :class="{'form-control': true, 'is-invalid': !validate(active_settings[sname], sname)}" type="text" v-model="active_settings[sname]" /></div>
+              </div>
+            </div>
+          </div>
+        </div>
+        <div class="modal-footer">
+          <button type="button" class="btn btn-secondary" @click="reset">Reset Defaults</button>
+          <button type="button" class="btn btn-primary" :class="{disabled: anyIsInvalid}" @click="save">Save Changes</button>
+        </div>
+      </div>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+.form-check label {
+  user-select: none;
+}
+</style>
\ No newline at end of file
diff --git a/refl1d-web-gui/src/fitter_defaults.ts b/refl1d-web-gui/src/fitter_defaults.ts
new file mode 100644
index 00000000..2f2d638a
--- /dev/null
+++ b/refl1d-web-gui/src/fitter_defaults.ts
@@ -0,0 +1,62 @@
+export const FITTERS = {
+    dream: {
+      name: "DREAM",
+      settings: {
+        "samples": 10000,
+        "burn": 100,
+        "pop": 10,
+        "init": "eps",
+        "thin": 1,
+        "alpha": 0.01,
+        "outliers": "none",
+        "trim": false,
+        "steps": 0
+      }
+    },
+    lm: {
+      name: "Levenberg-Marquardt",
+      settings: {
+        "steps": 200,
+        "ftol": 1.5e-08,
+        "xtol": 1.5e-08
+      }
+    },
+    amoeba: {
+      name: "Nelder-Mead Simplex",
+      settings: {
+        "steps": 1000,
+        "starts": 1,
+        "radius": 0.15,
+        "xtol": 1e-06,
+        "ftol": 1e-08
+      }
+    },
+    de: {
+      name: "Differential Evolution",
+      settings: {
+        "steps": 1000,
+        "pop": 10,
+        "CR": 0.9,
+        "F": 2.0,
+        "ftol": 1e-08,
+        "xtol": 1e-06
+      }
+    },
+    mp: {
+      name: "MPFit",
+      settings: {
+        "steps": 200,
+        "ftol": 1e-10,
+        "xtol": 1e-10
+      }
+    },
+    newton: {
+      name: "Quasi-Newton BFGS",
+      settings: {
+        "steps": 3000,
+        "starts": 1,
+        "ftol": 1e-06,
+        "xtol": 1e-12
+      }
+    },
+  }
\ No newline at end of file
diff --git a/refl1d-web-gui/src/main.js b/refl1d-web-gui/src/main.js
new file mode 100644
index 00000000..e629d700
--- /dev/null
+++ b/refl1d-web-gui/src/main.js
@@ -0,0 +1,6 @@
+import { createApp } from 'vue'
+import 'bootstrap/dist/css/bootstrap.min.css';
+// import './style.css'
+import App from './App.vue'
+
+createApp(App).mount('#app')
diff --git a/refl1d-web-gui/vite.config.js b/refl1d-web-gui/vite.config.js
new file mode 100644
index 00000000..40c640c2
--- /dev/null
+++ b/refl1d-web-gui/vite.config.js
@@ -0,0 +1,15 @@
+import { fileURLToPath, URL } from 'node:url'
+
+import { defineConfig } from 'vite'
+import vue from '@vitejs/plugin-vue'
+
+// https://vitejs.dev/config/
+export default defineConfig({
+  plugins: [vue()],
+  base: '',
+  resolve: {
+    alias: {
+      '@': fileURLToPath(new URL('./src', import.meta.url))
+    }
+  }
+})

From f17d0bfb580d5f3c1b166c240bed7544f8b0ee58 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 27 Sep 2022 17:30:19 -0400
Subject: [PATCH 003/221] update title and favicon

---
 refl1d-web-gui/index.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/index.html b/refl1d-web-gui/index.html
index 030a6ff5..1c749da0 100644
--- a/refl1d-web-gui/index.html
+++ b/refl1d-web-gui/index.html
@@ -2,9 +2,9 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
-    <link rel="icon" href="/favicon.ico" />
+    <link rel="icon" href="./src/assets/refl1d-icon_256x256x32.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Vite App</title>
+    <title>Refl1D</title>
   </head>
   <body>
     <div id="app"></div>

From 419c34c7a4479575c118277bd4dc06018a5dd9c4 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:06:00 -0400
Subject: [PATCH 004/221] adding mathjax

---
 refl1d-web-gui/index.html | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/refl1d-web-gui/index.html b/refl1d-web-gui/index.html
index 1c749da0..c58c76fe 100644
--- a/refl1d-web-gui/index.html
+++ b/refl1d-web-gui/index.html
@@ -4,6 +4,9 @@
     <meta charset="UTF-8" />
     <link rel="icon" href="./src/assets/refl1d-icon_256x256x32.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <script type="text/javascript" async
+      src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTML">
+    </script>
     <title>Refl1D</title>
   </head>
   <body>

From 99fb4d1e25acffbed753e0cde478a3a49643cc16 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:06:22 -0400
Subject: [PATCH 005/221] adding plotting libraries

---
 refl1d-web-gui/package.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/refl1d-web-gui/package.json b/refl1d-web-gui/package.json
index 0d0651c3..0beb3186 100644
--- a/refl1d-web-gui/package.json
+++ b/refl1d-web-gui/package.json
@@ -8,6 +8,8 @@
   },
   "dependencies": {
     "bootstrap": "^5.2.1",
+    "mpld3": "^0.5.8",
+    "plotly.js": "^2.14.0",
     "socket.io-client": "^4.5.2",
     "vue": "^3.2.38"
   },

From 6d16a2beb8789bd397c486163b961698b635d2c3 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:07:29 -0400
Subject: [PATCH 006/221] move component-specific listener registration on
 socket to components, add fileBrowser

---
 refl1d-web-gui/src/App.vue | 119 ++++++++++++++++++++-----------------
 1 file changed, 64 insertions(+), 55 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 4abda4f5..1c81adc8 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -1,11 +1,15 @@
 <script setup lang="ts">
 import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
-import { onMounted, ref, shallowRef } from 'vue';
+import { onMounted, ref, shallowRef, VNodeRef } from 'vue';
 import { api } from './server_api';
 import { io, Socket } from 'socket.io-client';
 import FitOptions from './components/FitOptions.vue';
+import DataView from './components/DataView.vue';
+import ModelView from './components/ModelView.vue';
+import PanelTabContainer from './components/PanelTabContainer.vue';
+import FileBrowser from './components/FileBrowser.vue';
+import SummaryView from './components/SummaryView.vue';
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
-const FITTER_DEFAULTS = {};
 
 const REFLECTIVITY_PLOTS = [
   "Fresnel",
@@ -19,73 +23,71 @@ type ReflectivityPlotEnum = typeof REFLECTIVITY_PLOTS;
 type ReflectivityPlot = ReflectivityPlotEnum[number];
 
 const reflectivity_type = ref<ReflectivityPlot>("Linear");
-const connection_id = ref("");
-const connection = ref<Socket | null>(null);
 const connected = ref(false);
-const menuToggle = ref(null);
-const fitOptions = ref(null);
-const fitter_settings = shallowRef(structuredClone(FITTER_DEFAULTS));
-const fitter_defaults = shallowRef(FITTER_DEFAULTS);
-const active_fitter = ref('amoeba');
+const menuToggle = ref<HTMLButtonElement>();
+const fitOptions = ref<typeof FitOptions>();
+const fileBrowser = ref<typeof FileBrowser>();
+const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) =>  {});
+const file_picker = ref<HTMLInputElement>();
 
 function set_reflectivity(refl_type: ReflectivityPlot) {
   reflectivity_type.value = refl_type;
 }
 
-function load_model_path(path: string) {
+// Create a SocketIO connection, to be passed to child components
+// so that they can do their own communications with the host.
 
-}
+const socket = io('', {
+  // this is mostly here to test what happens on server fail:
+  reconnectionAttempts: 10
+});
+socket.on('connect', () => {
+  console.log(socket.id);
+  connected.value = true;
+});
 
-function connect() {
-  const socket = io('http://localhost:8080', {
-    reconnectionAttempts: 10
-  });
-  connection.value = socket;
-  socket.on('connect', () => {
-    console.log(socket.id);
-    connected.value = true;
-  });
-
-  socket.on('fitter-settings', (payload) => {
-    fitter_settings.value = payload;
-  });
-  socket.on('fitter-defaults', (payload) => {
-    fitter_defaults.value = payload;
-  });
-  socket.on('fitter-active', (payload) => {
-    active_fitter.value = payload;
-  });
-  socket.on('disconnect', (payload) => {
-    console.log("disconnected!", payload);
-    connected.value = false;
-  })
-}
+socket.on('disconnect', (payload) => {
+  console.log("disconnected!", payload);
+  // connected.value = false;
+})
 
 function disconnect() {
-  connection.value?.disconnect();
+  socket.disconnect();
   connected.value = false;
 }
 
-function openFitOptions() {
-  fitOptions?.value?.open();
+function selectOpenFile() {
+  if (fileBrowser.value) {
+    fileBrowserSelectCallback.value = (pathlist, filename) => {
+      socket.emit("load_model_file", pathlist, filename);
+    }
+    fileBrowser.value.open();
+  }
+  // const path = prompt("full path to file:");
+  // if (path != null) {
+  //   let defaulted_path = (path == '') ? '/home/bbm/dev/refl1d-modelbuilder/ISIS_GGG/GGG_GdIG_MultiFit.py' : path;
+  //   socket.emit("load_model_file", defaulted_path);
+  // }
+  // file_picker.value?.click();
 }
 
-function get_sessions() {
-  fetch('http://localhost:8080/get_sessions');
+function load_model_path(event: Event) {
+  console.log(event);
+  const { files } = event.target;
+  console.log(files);
+  // socket.emit("load_model_file", files[0]);
+  window.testevent = event;
 }
 
-function updateActiveFitter(fitter_name) {
-  connection.value?.emit("fitter-active", fitter_name);
-}
 
-function updateActiveSettings(new_settings) {
-  connection.value?.emit("fitter-settings", new_settings);
+function openFitOptions() {
+  fitOptions.value?.open();
 }
 
 onMounted(() => {
   const menuToggleButton = new Button(menuToggle.value);
-  connect();
 });
+
 </script>
 
 <template>
@@ -103,7 +105,7 @@ onMounted(() => {
         </button>
         <div class="collapse navbar-collapse" id="navbarSupportedContent">
           <ul class="navbar-nav me-auto mb-2 mb-lg-0">
-            <li class="nav-item dropdown">
+            <!-- <li class="nav-item dropdown">
               <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 Session
@@ -113,14 +115,14 @@ onMounted(() => {
                 <li><a class="dropdown-item" href="#" @click="disconnect">Disconnect</a></li>
                 <li><a class="dropdown-item" href="#" @click="reconnect">Existing</a></li>
               </ul>
-            </li>
+            </li> -->
             <li class="nav-item dropdown">
               <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 File
               </a>
               <ul class="dropdown-menu">
-                <li><a class="dropdown-item" href="#">Open</a></li>
+                <li><a class="dropdown-item" href="#" @click="selectOpenFile">Open</a></li>
                 <li><a class="dropdown-item" href="#">Save</a></li>
                 <li>
                   <hr class="dropdown-divider">
@@ -142,7 +144,7 @@ onMounted(() => {
                 <li><a class="dropdown-item" href="#" @click="openFitOptions">Options...</a></li>
               </ul>
             </li>
-            <li class="nav-item dropdown">
+            <!-- <li class="nav-item dropdown">
               <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 Reflectivity
@@ -153,22 +155,29 @@ onMounted(() => {
                     @click="set_reflectivity(plot_type)">{{plot_type}}</a>
                 </li>
               </ul>
-            </li>
+            </li> -->
           </ul>
           <div class="d-flex">
-            <div id="connection_status" :class="{'btn': true, 'btn-outline-success': connected, 'btn-outline-danger': !connected}">
+            <div id="connection_status"
+              :class="{'btn': true, 'btn-outline-success': connected, 'btn-outline-danger': !connected}">
               {{(connected) ? 'connected' : 'disconnected'}}</div>
 
           </div>
         </div>
       </div>
     </nav>
+    <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
   </div>
-  <FitOptions ref="fitOptions" :fitter_defaults="fitter_defaults" :fitter_settings="fitter_settings"
-    :active_fitter="active_fitter" @active-fitter="updateActiveFitter" @active-settings="updateActiveSettings"/>
+  <FitOptions ref="fitOptions" :socket="socket" />
+  <FileBrowser ref="fileBrowser" :socket="socket" title="Load Model File" :callback="fileBrowserSelectCallback" />
+  <input ref="file_picker" type="file" multiple="false" id="file_picker" style="display:none;" @change="load_model_path" />
 </template>
 
-<style scoped>
+<style>
+html, body, #app {
+  height: 100%;
+}
+
 div#connection_status {
   pointer-events: none;
 }

From c9d6582be3d787a76ca0686ab3b73d7cfa33c54c Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:08:21 -0400
Subject: [PATCH 007/221] interact directly with the socket, registering
 listeners and performing GET requests

---
 refl1d-web-gui/src/components/FitOptions.vue | 117 +++++++++----------
 1 file changed, 55 insertions(+), 62 deletions(-)

diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
index e226b4c2..2bb1f22b 100644
--- a/refl1d-web-gui/src/components/FitOptions.vue
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -1,33 +1,17 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
-// import { Modal } from 'bootstrap';
+import { ref, onMounted, computed, shallowRef } from 'vue';
 import { Modal } from 'bootstrap/dist/js/bootstrap.esm';
-import { isArray } from '@vue/shared';
-
-const props = defineProps({
-  fitter_defaults: {
-    type: Object,
-    default: {}
-  },
-  fitter_settings: {
-    type: Object,
-    default: {}
-  },
-  active_fitter: {
-    type: String,
-    default: 'amoeba'
-  }
-});
+import type { Socket } from 'socket.io-client';
 
-const emit = defineEmits<{
-  (e: 'close'): void
-  (e: 'update', value: Object): void
-  (e: 'active-fitter', value: string): void
-  (e: 'active-settings', value: Object): void
-}>();
+const props = defineProps<{socket: Socket}>();
 
-const dialog = ref(null);
+type FitSetting = { name: string, settings: object };
+const dialog = ref<HTMLDivElement>();
 const isOpen = ref(false);
+const fitter_defaults = shallowRef<{ [fit_name: string]: FitSetting }>({});
+const fitter_settings = shallowRef<{ [fit_name: string]: FitSetting }>({});
+const fitter_active = ref<string>("amoeba");
+const fitter_active_local = ref("amoeba");
 
 const FIT_FIELDS = {
   'starts': ['Starts', 'integer'],
@@ -51,17 +35,35 @@ const FIT_FIELDS = {
   'outliers': ['Outliers', ["none", "iqr", "grubbs", "mahal"]]
 }
 
-const active_fitter = ref('amoeba');
-// work with a copy of the fitter definitions, which will
-// still get used as defaults
-
 // make another working copy for editing:
+// const active_settings = ref<{ name: string, settings: object}>({name: "", settings: {}});
 const active_settings = ref({});
 
+props.socket.on('fitter_settings', () => {
+  props.socket.emit('get_last_message', 'fitter_settings', (payload) => {
+    fitter_settings.value = payload;
+  });
+});
+props.socket.on('fitter_defaults', () => {
+  props.socket.emit('get_last_message', 'fitter_defaults', (payload) => {
+    fitter_defaults.value = payload;
+  });
+});
+props.socket.on('fitter_active', () => {
+  props.socket.emit('get_last_message', 'fitter_active', (payload) => {
+    fitter_active.value = payload;
+  });
+});
+
+props.socket.emit('subscribe', 'fitter_settings');
+props.socket.emit('subscribe', 'fitter_defaults');
+props.socket.emit('subscribe', 'fitter_active');
+
 let modal: Modal;
 
 onMounted(() => {
   modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
+
 });
 
 function close() {
@@ -69,35 +71,22 @@ function close() {
 }
 
 function open() {
-  // copy the active_fitter from the server state:
-  active_fitter.value = props.active_fitter;
+  // copy the  fitter_active_local from the server state:
+  fitter_active_local.value = fitter_active.value;
   changeActiveFitter();
   modal?.show();
 }
 
-const fit_names = computed(() => Object.keys(props.fitter_defaults));
+const fit_names = computed(() => Object.keys(fitter_defaults?.value));
 
 function changeActiveFitter() {
-  active_settings.value = structuredClone(props.fitter_settings[active_fitter.value]?.settings);
+  active_settings.value = structuredClone(fitter_settings.value[fitter_active_local.value]?.settings) ?? {};
 }
 
-// watch(isOpen, (newState, oldState) => {
-//   if (newState == true && modal) {
-//     modal.show();
-//   }
-//   else {
-//     modal.hide();
-//   }
-// })
-
-// watch(() => props.fitter_settings, (newState, oldState) => {
-//   // fit_names.value = Object.keys(newState);
-// })
-
 function process_settings() {
   return Object.fromEntries(Object.entries(active_settings.value).map(([sname, value]) => {
     const field_type = FIT_FIELDS[sname][1];
-    let processed_value = value;
+    let processed_value: any = value;
     if (field_type === 'integer') {
       processed_value = Math.round(Number(value));
     }
@@ -114,19 +103,19 @@ function process_settings() {
 
 function save() {
   const new_settings = {};
-  new_settings[active_fitter.value] = {settings: process_settings()};
-  emit('active-settings', new_settings);
-  emit('active-fitter', active_fitter.value);
+  new_settings[fitter_active_local.value] = { settings: process_settings() };
+  props.socket.emit("publish", "fitter_settings", new_settings);
+  props.socket.emit("publish", "fitter_active", fitter_active_local.value);
   close();
 }
 
 function reset() {
-  active_settings.value = structuredClone(props.fitter_defaults[props.active_fitter].settings);
+  active_settings.value = structuredClone(fitter_defaults.value[fitter_active_local.value].settings) ?? {};
 }
 
 function validate(value, field_name) {
   const field_type = FIT_FIELDS[field_name][1];
-  if (isArray(field_type) || field_type === 'boolean') {
+  if (Array.isArray(field_type) || field_type === 'boolean') {
     // there's no way to get an incorrect option.
     return true;
   }
@@ -164,19 +153,19 @@ defineExpose({
             <div class="row border-bottom">
               <div class="col">
                 <div class="form-check" v-for="fname in fit_names.slice(0,3)" :key="fname">
-                  <input class="form-check-input" v-model="active_fitter" type="radio" name="flexRadio" :id="fname"
-                    :value="fname" @change="changeActiveFitter">
+                  <input class="form-check-input" v-model="fitter_active_local" type="radio" name="flexRadio"
+                    :id="fname" :value="fname" @change="changeActiveFitter">
                   <label class="form-check-label" :for="fname">
-                    {{props.fitter_defaults[fname].name}}
+                    {{fitter_defaults[fname].name}}
                   </label>
                 </div>
               </div>
               <div class="col">
                 <div class="form-check" v-for="fname in fit_names.slice(3)" :key="fname">
-                  <input class="form-check-input" v-model="active_fitter" type="radio" name="flexRadio" :id="fname"
-                    :value="fname" @change="changeActiveFitter">
+                  <input class="form-check-input" v-model="fitter_active_local" type="radio" name="flexRadio"
+                    :id="fname" :value="fname" @change="changeActiveFitter">
                   <label class="form-check-label" :for="fname">
-                    {{props.fitter_defaults[fname].name}}
+                    {{fitter_defaults[fname].name}}
                   </label>
                 </div>
               </div>
@@ -185,18 +174,22 @@ defineExpose({
               <div class="row p-1" v-for="(value, sname, index) in active_settings" :key="sname">
                 <label class="col-sm-4 col-form-label" :for="'setting_' + index">{{FIT_FIELDS[sname][0]}}</label>
                 <div class="col-sm-8">
-                  <select v-if="isArray(FIT_FIELDS[sname][1])" v-model="active_settings[sname]" class="form-select">
+                  <select v-if="Array.isArray(FIT_FIELDS[sname][1])" v-model="active_settings[sname]" class="form-select">
                     <option v-for="opt in FIT_FIELDS[sname][1]">{{opt}}</option>
                   </select>
-                  <input v-else-if="FIT_FIELDS[sname][1]==='boolean'" class="form-check-input m-2" type="checkbox" v-model="active_settings[sname]" />
-                  <input v-else :class="{'form-control': true, 'is-invalid': !validate(active_settings[sname], sname)}" type="text" v-model="active_settings[sname]" /></div>
+                  <input v-else-if="FIT_FIELDS[sname][1]==='boolean'" class="form-check-input m-2" type="checkbox"
+                    v-model="active_settings[sname]" />
+                  <input v-else :class="{'form-control': true, 'is-invalid': !validate(active_settings[sname], sname)}"
+                    type="text" v-model="active_settings[sname]" />
+                </div>
               </div>
             </div>
           </div>
         </div>
         <div class="modal-footer">
           <button type="button" class="btn btn-secondary" @click="reset">Reset Defaults</button>
-          <button type="button" class="btn btn-primary" :class="{disabled: anyIsInvalid}" @click="save">Save Changes</button>
+          <button type="button" class="btn btn-primary" :class="{disabled: anyIsInvalid}" @click="save">Save
+            Changes</button>
         </div>
       </div>
     </div>

From 0fef02c53b3e2ea5cb48759535a730e03da42d49 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:08:40 -0400
Subject: [PATCH 008/221] add minimal style.css

---
 refl1d-web-gui/src/main.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/main.js b/refl1d-web-gui/src/main.js
index e629d700..acc9741a 100644
--- a/refl1d-web-gui/src/main.js
+++ b/refl1d-web-gui/src/main.js
@@ -1,6 +1,6 @@
 import { createApp } from 'vue'
 import 'bootstrap/dist/css/bootstrap.min.css';
-// import './style.css'
+import './style.css'
 import App from './App.vue'
 
 createApp(App).mount('#app')

From beb31da22965c743500856a925d723a7ac581373 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:09:06 -0400
Subject: [PATCH 009/221] add minimal style.css

---
 refl1d-web-gui/src/style.css | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 refl1d-web-gui/src/style.css

diff --git a/refl1d-web-gui/src/style.css b/refl1d-web-gui/src/style.css
new file mode 100644
index 00000000..230b64b8
--- /dev/null
+++ b/refl1d-web-gui/src/style.css
@@ -0,0 +1,3 @@
+html, body, #app {
+    height: 100%;
+}
\ No newline at end of file

From 2acf6cd6a6b7f85f8cc8d3e41ce0bc576de0135f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:10:51 -0400
Subject: [PATCH 010/221] adding view components

---
 refl1d-web-gui/src/components/DataView.vue    |  60 +++++++++
 refl1d-web-gui/src/components/FileBrowser.vue | 119 ++++++++++++++++++
 refl1d-web-gui/src/components/ModelView.vue   |  58 +++++++++
 .../src/components/PanelTabContainer.vue      |  66 ++++++++++
 refl1d-web-gui/src/components/SummaryView.vue |  78 ++++++++++++
 5 files changed, 381 insertions(+)
 create mode 100644 refl1d-web-gui/src/components/DataView.vue
 create mode 100644 refl1d-web-gui/src/components/FileBrowser.vue
 create mode 100644 refl1d-web-gui/src/components/ModelView.vue
 create mode 100644 refl1d-web-gui/src/components/PanelTabContainer.vue
 create mode 100644 refl1d-web-gui/src/components/SummaryView.vue

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
new file mode 100644
index 00000000..9acd83a6
--- /dev/null
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -0,0 +1,60 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import Plotly from 'plotly.js/src/core';
+import type { Socket } from 'socket.io-client';
+
+const title = "Reflectivity";
+const plot_div = ref<HTMLDivElement>();
+
+const props = defineProps<{
+  socket: Socket,
+  visible: Boolean
+}>();
+
+props.socket.on('plot_update_ready', () => {
+  props.socket.emit('get_plot_data', 'linear', (payload) => {
+
+    let theory_traces = [];
+    let data_traces = [];
+    for (let model of payload) {
+      for (let xs of model) {
+        theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: {width: 2}});
+        data_traces.push({ x: xs.Q, y: xs.R, mode: 'markers', name: xs.label + ' data' });
+      }
+    }
+
+    const layout = {
+      xaxis: {
+        title: {
+          text: '$Q (Å^{-1})$'
+        },
+        type: 'linear',
+        autorange: true
+      },
+      yaxis: {
+        title: {text: 'Reflectivity'},
+        exponentformat: 'e',
+        showexponent: 'all',
+        type: 'log',
+        autorange: true
+      }
+    };
+
+    Plotly.newPlot("plot_div", [...theory_traces, ...data_traces], layout);
+
+    // mpld3.draw_figure("plot_div", payload);
+  });
+});
+
+defineExpose({
+  title
+});
+</script>
+
+<template>
+  <div class="container h-100">
+    <div ref="plot_div" id="plot_div">
+
+    </div>
+  </div>
+</template>
diff --git a/refl1d-web-gui/src/components/FileBrowser.vue b/refl1d-web-gui/src/components/FileBrowser.vue
new file mode 100644
index 00000000..73638c82
--- /dev/null
+++ b/refl1d-web-gui/src/components/FileBrowser.vue
@@ -0,0 +1,119 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Modal } from 'bootstrap/dist/js/bootstrap.esm';
+import { Socket } from 'socket.io-client';
+import { emitValidationErrors } from 'mapbox-gl/dist/mapbox-gl-unminified';
+
+const props = defineProps<{
+  socket: Socket,
+  title: string,
+  callback: (pathlist: string[], filename: string) => void
+}>();
+
+const emit = defineEmits<{
+  (e: 'selected', pathlist: string[], filename: string): void
+}>();
+
+const dialog = ref<HTMLDivElement>();
+const isOpen = ref(false);
+const pathlist = ref(["/", "home", "bbm", "dev", "refl1d-modelbuilder"]);
+const subdirlist = shallowRef<string[]>([])
+const filelist = shallowRef<string[]>([])
+const chosenFile = ref("");
+
+let modal: Modal;
+onMounted(() => {
+  modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
+});
+
+function close() {
+  modal?.hide();
+  isOpen.value = false;
+}
+
+function open() {
+  modal?.show();
+  isOpen.value = true;
+  setPath();
+}
+
+function subdirClick(subdir: string) {
+  pathlist.value.push(subdir);
+  setPath();
+  props.socket.emit("get_dirlisting", pathlist.value, ({ files, subfolders }) => {
+
+  })
+}
+
+function setPath(new_pathlist?: string[]) {
+  if (new_pathlist !== undefined) {
+    pathlist.value = new_pathlist;
+    chosenFile.value = "";
+  }
+  props.socket.emit("get_dirlisting", pathlist.value, ({ files, subfolders }) => {
+    subdirlist.value = subfolders.sort();
+    filelist.value = files.sort();
+  })
+}
+
+function chooseFile() {
+  props.callback(pathlist.value, chosenFile.value);
+  close();
+}
+
+defineExpose({
+  close,
+  open
+})
+</script>
+
+<template>
+  <div ref="dialog" class="modal fade" id="fileBrowserModal" tabindex="-1" aria-labelledby="fileBrowserLabel"
+    :aria-hidden="isOpen">
+    <div class="modal-dialog modal-lg">
+      <div class="modal-content">
+        <div class="modal-header">
+          <h5 class="modal-title" id="fileBrowserLabel">{{title}}</h5>
+          <button type="button" class="btn-close" @click="close" aria-label="Close"></button>
+        </div>
+        <div class="modal-body">
+          <div class="container border-bottom">
+            <nav aria-label="breadcrumb">
+              <ol class="breadcrumb">
+                <li v-for="(pathitem, index) in pathlist" :key="index" class="breadcrumb-item">
+                  <a href="#" @click="setPath(pathlist.slice(0, index+1))">{{pathitem}}</a>
+                </li>
+              </ol>
+            </nav>
+          </div>
+          <div class="container border-bottom">
+            <h3>Subdirectories:</h3>
+            <div class="row row-cols-3">
+              <div class="col overflow-hidden" v-for="subdir in subdirlist" :key="subdir">
+                <a href="#" @click="subdirClick(subdir)" :title="subdir">{{subdir}}</a>
+              </div>
+            </div>
+          </div>
+          <div class="container border-bottom">
+            <h3>Files:</h3>
+            <div class="row row-cols-3">
+              <div class="btn col overflow-hidden border" :class="{'btn-warning': filename === chosenFile}" v-for="filename in filelist" :key="filename" @click="chosenFile = filename">
+                {{filename}}
+              </div>
+            </div>
+          </div>
+          <div class="modal-footer">
+            <button type="button" class="btn btn-secondary" @click="close">Cancel</button>
+            <button type="button" class="btn btn-primary" :class="{disabled: chosenFile==''}" @click="chooseFile">OK</button>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+  .active {
+    background-color: light
+  }
+</style>
\ No newline at end of file
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
new file mode 100644
index 00000000..c5741b57
--- /dev/null
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -0,0 +1,58 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import type { Socket } from 'socket.io-client';
+import mpld3 from 'mpld3';
+
+const title = "Profile";
+const plot_div = ref<HTMLDivElement>();
+
+const props = defineProps<{
+  socket: Socket,
+  visible: Boolean
+}>();
+
+onMounted(() => {
+  props.socket.on('plot_update_ready', () => {
+    if (props.visible) {
+      fetch_and_draw();
+    }
+  });
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_profile_plot', (payload) => {
+    console.log(payload, plot_div.value);
+    payload.width = plot_div.value?.clientWidth ?? 640;
+    payload.height = plot_div.value?.clientHeight ?? 480;
+    // delete payload.width;
+    // delete payload.height;
+    console.log(payload, plot_div.value);
+    mpld3.draw_figure("profile_div", payload);
+  });
+}
+
+watch(() => props.visible, (value) => {
+  if (value) {
+    fetch_and_draw();
+  }
+});
+
+defineExpose({
+  title
+});
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1">
+    <div class="flex-grow-1" ref="plot_div" id="profile_div">
+
+    </div>
+  </div>
+</template>
+
+<style scoped>
+  svg {
+    width: 100%;
+  }
+</style>
\ No newline at end of file
diff --git a/refl1d-web-gui/src/components/PanelTabContainer.vue b/refl1d-web-gui/src/components/PanelTabContainer.vue
new file mode 100644
index 00000000..c94085a7
--- /dev/null
+++ b/refl1d-web-gui/src/components/PanelTabContainer.vue
@@ -0,0 +1,66 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef, Component } from 'vue';
+import type { Socket } from 'socket.io-client';
+import { Tab } from 'bootstrap/dist/js/bootstrap.esm';
+
+type PanelComponent = Component & { title: string };
+
+const tabTriggers = ref<HTMLAnchorElement[]>([]);
+const panelComponents = ref<PanelComponent[]>([]);
+const panelContainers = ref<HTMLDivElement[]>([]);
+const panelVisible = ref<boolean[]>([]);
+
+const props = defineProps<{
+  socket: Socket,
+  panels: PanelComponent[]
+}>();
+
+let triggers: Tab[] = [];
+
+function activateTab(index) {
+  triggers?.[index].show();
+  panelContainers.value.forEach((el, i) => {
+    if (i === index) {
+      el.classList.add('active');
+      panelVisible.value[index] = true;
+    }
+    else {
+      el.classList.remove('active');
+      panelVisible.value[index] = false;
+    }
+  });
+}
+
+onMounted(() => {
+  for (let triggerEl of tabTriggers.value) {
+    let tabTrigger = new Tab(triggerEl);
+    triggers.push(tabTrigger);
+  }
+  if (triggers.length > 0) {
+    activateTab(0);
+  }
+});
+</script>
+
+<template>
+  <ul class="nav nav-tabs">
+    <li class="nav-item" v-for="(panel, index) in props.panels" :key="index">
+      <a ref="tabTriggers" class="nav-link" href="#" @click="activateTab(index)">{{panelComponents[index]?.title}}</a>
+    </li>
+  </ul>
+  <div class="tab-content d-flex flex-column flex-grow-1">
+    <div ref="panelContainers" class="tab-pane flex-column flex-grow-1" v-for="(panel, index) in props.panels"
+      :key="index">
+      <component :is="panel" :socket="props.socket" ref="panelComponents" :visible="panelVisible[index]"></component>
+    </div>
+  </div>
+</template>
+
+<style scoped>
+.tab-content>.tab-pane {
+  display: none;
+}
+.tab-content>.tab-pane.active {
+  display: flex !important;
+}
+</style>
\ No newline at end of file
diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
new file mode 100644
index 00000000..1190b097
--- /dev/null
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -0,0 +1,78 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import type { Socket } from 'socket.io-client';
+
+const title = "Summary";
+
+const props = defineProps<{
+  socket: Socket,
+  visible: Boolean
+}>();
+
+const parameters = shallowRef<{
+  name: string,
+  value01: number,
+  value_str: string,
+  min: string,
+  max: string
+}[]>([]);
+
+const parameters_old = [{
+  name: 'background',
+  value01: 0.75,
+  value_str: '1.7e-6',
+  min: '1e-11',
+  max: '1e-6'
+}];
+
+onMounted(() => {
+  props.socket.on('plot_update_ready', () => {
+    if (props.visible) {
+      fetch_and_draw();
+    }
+  });
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_parameters', (payload) => {
+    console.log(payload);
+    parameters.value = payload;
+  });
+}
+
+watch(() => props.visible, (value) => {
+  if (value) {
+    fetch_and_draw();
+  }
+});
+
+defineExpose({
+  title
+});
+
+</script>
+        
+<template>
+  <div class="container flex-grow-1">
+    <div class="row border-bottom py-1">
+      <div class="col-2">Fit Parameter</div>
+      <div class="col-6"></div>
+      <div class="col-2">Value</div>
+      <div class="col-1">Minimum</div>
+      <div class="col-1">Maximum</div>
+    </div>
+    <div class="row" v-for="param in parameters" :key="param.name">
+      <div class="col-2">{{param.name}}</div>
+      <div class="col-6"><input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model="param.value01"/></div>
+      <div class="col-2">{{param.value_str}}</div>
+      <div class="col-1">{{param.min}}</div>
+      <div class="col-1">{{param.max}}</div>
+    </div>
+  </div>
+</template>
+    
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file

From 2a3bc2fd1525b39aa74f2bc9e2730a6be193dfc0 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:14:47 -0400
Subject: [PATCH 011/221] fix missing oversampling argument

---
 refl1d/probe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/probe.py b/refl1d/probe.py
index 4bdb363b..d0c4b390 100644
--- a/refl1d/probe.py
+++ b/refl1d/probe.py
@@ -1647,7 +1647,7 @@ def __init__(self, xs: Optional[Tuple]=None,
                        mp: optional_xs=None,
                        pm: optional_xs=None,
                        pp: optional_xs=None,
-                       name=None, Aguide=BASE_GUIDE_ANGLE, H=0):
+                       name=None, Aguide=BASE_GUIDE_ANGLE, H=0, oversampling=None):
         if any([mm, mp, pm, pp]):
             if xs is not None:
                 warnings.warn("a cross-section is directly specified - xs argument will be ignored")

From 8b8191760fcbf11475f9de2ed6d42ac341a1f5c1 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 07:15:31 -0400
Subject: [PATCH 012/221] add methods to webserver to support parameter view,
 profile view and data view

---
 refl1d/webserver.py | 215 +++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 191 insertions(+), 24 deletions(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 7dee2fe2..0f613dca 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -1,12 +1,18 @@
 # from .main import setup_bumps
 
+from typing import Any, Dict, List
+from datetime import datetime
 from aiohttp import web
+import numpy as np
+import asyncio
 import socketio
-from pathlib import Path
+from pathlib import Path, PurePath
 import json
 from copy import deepcopy
 
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit
+from bumps.serialize import to_dict
+import refl1d.fitproblem, refl1d.probe
 
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
 FITTER_DEFAULTS = {}
@@ -17,14 +23,45 @@
     }
 
 # set up mutable state of fitters:
-fitter_settings = deepcopy(FITTER_DEFAULTS)
-active_fitter = "amoeba"
+# fitter_settings = deepcopy(FITTER_DEFAULTS)
+# active_fitter = "amoeba"
 
 sio = socketio.AsyncServer(cors_allowed_origins="*")
 app = web.Application()
 static_dir_path = Path(__file__).parent / 'webview'
 sio.attach(app)
 
+# class TopicManager:
+#     topics: Dict[str, Any] = {}
+
+#     def subscribe(self, sid: str, topic: str):
+#         sio.enter_room(sid, topic)
+
+#     def unsubscribe(self, sid: str, topic: str):
+#         sio.leave_room(sid, topic)
+
+#     def get(self, topic: str):
+#         return self.topics.get(topic, None)
+
+#     async def publish(self, topic: str, message):
+#         timestamp = datetime.now().timestamp()
+#         self.topics[topic] = {"message": message, "timestamp": timestamp}
+#         await sio.emit("message-available", timestamp, room=topic)
+
+# topicManager = TopicManager()
+
+# use context storage: within the aiohttp app, see 
+# class TopicData(TypedDict):
+#     message: Any
+#     timestamp: float
+
+# topic_buffers: Dict[str, TopicData] = {}
+
+topics: Dict[str, Dict] = {}
+app["topics"] = topics
+app["problem"] = {"fitProblem": None, "filepath": None}
+problem = None
+
 async def index(request):
     """Serve the client-side application."""
     # redirect to static built site:
@@ -33,35 +70,165 @@ async def index(request):
 @sio.event
 async def connect(sid, environ):
     print("connect ", sid)
-    sio.enter_room(sid, "situation")
-    await sio.emit("fitter-defaults", FITTER_DEFAULTS, to=sid)
-    await sio.emit("fitter-settings", fitter_settings, to=sid)
-    await sio.emit("fitter-active", active_fitter, to=sid)
-
-@sio.on("fitter-active")
-async def new_fitter_active(sid, data):
-    # using global state here:
-    global active_fitter
-    active_fitter = data
-    await sio.emit("fitter-active", data, room="situation")
-
-@sio.on("fitter-settings")
-async def new_fitter_settings(sid, data):
-    global fitter_settings
-    fitter_settings.update(data)
-    await sio.emit("fitter-settings", fitter_settings, room="situation")
-
-# async def get_sessions(sid):
-#     return web.Response(text=json.dumps(list(sessions)), content_type='application/json')
+
+@sio.event
+async def load_model_file(sid: str, pathlist: List[str], filename: str):
+    from bumps.cli import load_model
+    path = Path(*pathlist, filename)
+    app["problem"]["fitProblem"] = load_model(str(path))
+    await sio.emit("plot_update_ready", True)
+
+def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
+    fresnel_calculator = probe.fresnel(substrate, surface)
+    Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
+    Q, R = theory
+    assert isinstance(FQ, np.ndarray)
+    if len(Q) != len(probe.Q):
+        # Saving interpolated data
+        output = dict(Q = Q, theory = R, fresnel=np.interp(Q, probe.Q, FQ))
+    elif getattr(probe, 'R', None) is not None:
+        output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, theory = R, fresnel = FQ)
+    else:
+        output = dict(Q = probe.Q, dQ = probe.dQ, theory = R, fresnel = FQ)
+    output['label'] = label
+    return output
+
+def get_probe_data(theory, probe, substrate=None, surface=None):
+    if isinstance(probe, refl1d.probe.PolarizedNeutronProbe):
+        output = []
+        for xsi, xsi_th, suffix in zip(probe.xs, theory, ('--', '-+', '+-', '++')):
+            if xsi is not None:
+                output.append(get_single_probe_data(xsi_th, xsi, substrate, surface, suffix))
+        return output
+    else:
+        return [get_single_probe_data(theory, probe, substrate, surface)]
+
+@sio.event
+def get_plot_data(sid: str, view: str = 'linear'):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    result = []
+    for model in fitProblem.models:
+        theory = model.reflectivity()
+        probe = model.probe
+        result.append(get_probe_data(theory, probe, model._substrate, model._surface))
+        # fresnel_calculator = probe.fresnel(model._substrate, model._surface)
+        # Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
+        # Q, R = theory
+        # assert isinstance(FQ, np.ndarray)
+        # if len(Q) != len(probe.Q):
+        #     # Saving interpolated data
+        #     output = dict(Q = Q, R = R, fresnel=np.interp(Q, probe.Q, FQ))
+        # elif getattr(probe, 'R', None) is not None:
+        #     output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, fresnel = FQ)
+        # else:
+        #     output = dict(Q = probe.Q, dQ = probe.dQ, R = R, fresnel = FQ)
+        # result.append(output)
+    return to_dict(result)
+
+@sio.event
+def get_profile_plot(sid: str):
+    import mpld3
+    import matplotlib.pyplot as plt
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    for model in iter(fitProblem.models):
+        model.plot_profile()
+    return mpld3.fig_to_dict(plt.gcf())
+
+@sio.event
+def get_parameters(sid: str):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if fitProblem is None:
+        return []
+    raw_parameters = fitProblem._parameters
+    parameters = []
+    for rp in raw_parameters:
+        p = {}
+        low, high = (v for v in rp.prior.limits)
+        p['min'] = VALUE_FORMAT.format(nice(low))
+        p['max'] = VALUE_FORMAT.format(nice(high))
+        p['value_str'] = VALUE_FORMAT.format(nice(rp.value))
+        p['value01'] = rp.prior.get01(rp.value)
+        p['name'] = rp.name
+        parameters.append(p)
+    return to_dict(parameters)
+
+@sio.event
+async def set_parameter01(sid: str, parameter_name: str, parameter_value01: float):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if fitProblem is None:
+        return
+    parameter_matches = [p for p in fitProblem._parameters if p.name == parameter_name]
+    if len(parameter_matches) < 1:
+        return
+    parameter = parameter_matches[0]
+    new_value  = parameter.prior.put01(parameter_value01)
+    nice_new_value = nice(new_value, digits=VALUE_PRECISION)
+    parameter.value = nice_new_value
+    await sio.emit("plot_update_ready", True)
+    return new_value
+
+@sio.event
+async def subscribe(sid: str, topic: str):
+    sio.enter_room(sid, topic)
+    last_timestamp = topics.get(topic, {}).get("timestamp", None)
+    if last_timestamp is not None:
+        await sio.emit(topic, last_timestamp, to=sid)
+
+@sio.event
+def unsubscribe(sid: str, topic: str):
+    sio.leave_room(sid, topic)
+
+@sio.event
+async def publish(sid: str, topic: str, message):
+    timestamp = datetime.now().timestamp()
+    topics[topic] = {"message": message, "timestamp": timestamp}
+    await sio.emit(topic, timestamp, room=topic)
+
+@sio.event
+def get_last_message(sid: str, topic: str):
+    # this is a GET request in disguise -
+    # emitter must handle the response in a callback,
+    # as no separate response event is emitted.  
+    return topics.get(topic, {}).get("message", None)
+
+@sio.event
+def get_dirlisting(sid: str, pathlist: List[str]):
+    # GET request
+    # TODO: use psutil to get disk listing as well?
+    subfolders = []
+    files = []
+    for p in Path(*pathlist).iterdir():
+        if p.is_dir():
+            subfolders.append(p.name)
+        else:
+            files.append(p.resolve().name)
+    return dict(subfolders=subfolders, files=files)
+
+app.on_startup.append(lambda App: publish('', 'fitter_defaults', FITTER_DEFAULTS))
+app.on_startup.append(lambda App: publish('', 'fitter_settings', deepcopy(FITTER_DEFAULTS)))
+app.on_startup.append(lambda App: publish('', 'fitter_active', 'amoeba'))
 
 @sio.event
 def disconnect(sid):
     print('disconnect ', sid)
 
 app.router.add_static('/static', static_dir_path)
-# app.router.add_static('/static', os.path.join(currdir, 'webview'))
 app.router.add_get('/', index)
 
+VALUE_PRECISION = 6
+VALUE_FORMAT = "{{:.{:d}g}}".format(VALUE_PRECISION)
+
+def nice(v, digits=4):
+    """Fix v to a value with a given number of digits of precision"""
+    from math import log10, floor
+    if v == 0. or not np.isfinite(v):
+        return v
+    else:
+        sign = v/abs(v)
+        place = floor(log10(abs(v)))
+        scale = 10**(place-(digits-1))
+        return sign*floor(abs(v)/scale+0.5)*scale
+    
 
 if __name__ == '__main__':
     web.run_app(app)

From 5fbca59d0efd6a07b320171fe14bbf9fba15ec84 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:31:49 -0400
Subject: [PATCH 013/221] fix bug in assigning visible status

---
 refl1d-web-gui/src/components/PanelTabContainer.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/components/PanelTabContainer.vue b/refl1d-web-gui/src/components/PanelTabContainer.vue
index c94085a7..da38a4e5 100644
--- a/refl1d-web-gui/src/components/PanelTabContainer.vue
+++ b/refl1d-web-gui/src/components/PanelTabContainer.vue
@@ -22,11 +22,11 @@ function activateTab(index) {
   panelContainers.value.forEach((el, i) => {
     if (i === index) {
       el.classList.add('active');
-      panelVisible.value[index] = true;
+      panelVisible.value[i] = true;
     }
     else {
       el.classList.remove('active');
-      panelVisible.value[index] = false;
+      panelVisible.value[i] = false;
     }
   });
 }

From c5ce0daf80a66fad3a6fccfda93d238f5bed930f Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:32:41 -0400
Subject: [PATCH 014/221] prevent re-render on active slider, and send
 parameter updates to server

---
 refl1d-web-gui/src/components/SummaryView.vue | 51 ++++++++++++++++---
 1 file changed, 44 insertions(+), 7 deletions(-)

diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index 1190b097..2aa2a9bd 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -1,22 +1,37 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref, onMounted, watch, onUpdated, computed, shallowRef, nextTick } from 'vue';
 import type { Socket } from 'socket.io-client';
 
 const title = "Summary";
+const active_parameter = ref("");
 
 const props = defineProps<{
   socket: Socket,
   visible: Boolean
 }>();
 
-const parameters = shallowRef<{
+type parameter_info = {
   name: string,
   value01: number,
   value_str: string,
   min: string,
-  max: string
+  max: string,
+  active?: boolean,
+  value01_local?: number
+}
+
+const parameters = ref<{
+  name: string,
+  value01: number,
+  value_str: string,
+  min: string,
+  max: string,
+  active?: boolean,
+  value01_local?: number,
 }[]>([]);
 
+const parameters_local = ref<parameter_info[]>([]);
+
 const parameters_old = [{
   name: 'background',
   value01: 0.75,
@@ -34,12 +49,28 @@ onMounted(() => {
 });
 
 function fetch_and_draw() {
-  props.socket.emit('get_parameters', (payload) => {
-    console.log(payload);
-    parameters.value = payload;
+  props.socket.emit('get_parameters', (payload: parameter_info[]) => {
+    // console.log(payload);
+    const pv = parameters.value;
+    payload.forEach((p,i) => {
+      if (!(pv[i]?.active)) {
+        pv.splice(i, 1, {...p, value01_local: p.value01});
+      }
+    });
+    pv.splice(payload.length);
   });
 }
 
+function onMove(param) {
+  props.socket.emit('set_parameter01', param.name, param.value01_local);
+}
+
+async function onInactive(param) {
+  param.active = false;
+  console.log("change");
+  fetch_and_draw();
+}
+
 watch(() => props.visible, (value) => {
   if (value) {
     fetch_and_draw();
@@ -63,7 +94,13 @@ defineExpose({
     </div>
     <div class="row" v-for="param in parameters" :key="param.name">
       <div class="col-2">{{param.name}}</div>
-      <div class="col-6"><input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model="param.value01"/></div>
+      <div class="col-6">
+        <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="param.value01_local"
+        @mousedown="param.active=true"
+        @input="onMove(param)"
+        @mouseup="onMouseup"
+        @change="onInactive(param)"/>
+      </div>
       <div class="col-2">{{param.value_str}}</div>
       <div class="col-1">{{param.min}}</div>
       <div class="col-1">{{param.max}}</div>

From c129d1ee9eeddb33aff2bea6db57ac8dfcb5c486 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:33:21 -0400
Subject: [PATCH 015/221] update existing plot if already created (preserves
 zoom)

---
 refl1d-web-gui/src/components/DataView.vue | 34 ++++++++++++++++++----
 1 file changed, 29 insertions(+), 5 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index 9acd83a6..d70729c9 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -5,13 +5,22 @@ import type { Socket } from 'socket.io-client';
 
 const title = "Reflectivity";
 const plot_div = ref<HTMLDivElement>();
+const plot = ref(null);
 
 const props = defineProps<{
   socket: Socket,
-  visible: Boolean
+  visible: boolean
 }>();
 
-props.socket.on('plot_update_ready', () => {
+onMounted(() => {
+  props.socket.on('plot_update_ready', () => {
+    if (props.visible) {
+      fetch_and_draw();
+    }
+  });
+});
+
+function fetch_and_draw() {
   props.socket.emit('get_plot_data', 'linear', (payload) => {
 
     let theory_traces = [];
@@ -40,10 +49,25 @@ props.socket.on('plot_update_ready', () => {
       }
     };
 
-    Plotly.newPlot("plot_div", [...theory_traces, ...data_traces], layout);
-
+    if (plot.value) {
+      const update = {
+        x: [...theory_traces.map((t) => t.x), ...data_traces.map((t) => t.x)],
+        y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],       
+      }
+      Plotly.update(plot_div.value, update);
+    }
+    else {
+      plot.value = Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
+    }
+    // console.log(plot.value);
     // mpld3.draw_figure("plot_div", payload);
   });
+}
+
+watch(() => props.visible, (value) => {
+  if (value) {
+    fetch_and_draw();
+  }
 });
 
 defineExpose({
@@ -52,7 +76,7 @@ defineExpose({
 </script>
 
 <template>
-  <div class="container h-100">
+  <div class="container d-flex flex-grow-1">
     <div ref="plot_div" id="plot_div">
 
     </div>

From ed12693bea24635a4d2486f23f57269127dc287d Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:33:54 -0400
Subject: [PATCH 016/221] clear profile plot before redraw

---
 refl1d-web-gui/src/components/ModelView.vue | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index c5741b57..8878cf5e 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -8,7 +8,7 @@ const plot_div = ref<HTMLDivElement>();
 
 const props = defineProps<{
   socket: Socket,
-  visible: Boolean
+  visible: boolean
 }>();
 
 onMounted(() => {
@@ -26,13 +26,15 @@ function fetch_and_draw() {
     payload.height = plot_div.value?.clientHeight ?? 480;
     // delete payload.width;
     // delete payload.height;
-    console.log(payload, plot_div.value);
-    mpld3.draw_figure("profile_div", payload);
+    /* Data Parsing Functions */
+    // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+    mpld3.draw_figure("profile_div", payload, false, true);
   });
 }
 
 watch(() => props.visible, (value) => {
   if (value) {
+    console.log('visible', value);
     fetch_and_draw();
   }
 });

From 4ee68cf24b4c1e5960ce4b1d66917f41d994e996 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:34:56 -0400
Subject: [PATCH 017/221] create new figure for each profile plot draw, and
 update model after parameter change

---
 refl1d/webserver.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 0f613dca..9bffff37 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -130,6 +130,7 @@ def get_profile_plot(sid: str):
     import mpld3
     import matplotlib.pyplot as plt
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    fig = plt.figure()
     for model in iter(fitProblem.models):
         model.plot_profile()
     return mpld3.fig_to_dict(plt.gcf())
@@ -164,6 +165,7 @@ async def set_parameter01(sid: str, parameter_name: str, parameter_value01: floa
     new_value  = parameter.prior.put01(parameter_value01)
     nice_new_value = nice(new_value, digits=VALUE_PRECISION)
     parameter.value = nice_new_value
+    fitProblem.model_update()
     await sio.emit("plot_update_ready", True)
     return new_value
 

From 3a51ebec80f5bd344f3c58bb47e3496de4444171 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:35:16 -0400
Subject: [PATCH 018/221] add second panel to right of first

---
 refl1d-web-gui/src/App.vue | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 1c81adc8..59ebb8e3 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -166,7 +166,14 @@ onMounted(() => {
         </div>
       </div>
     </nav>
-    <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
+    <div class="flex-grow-1 d-flex flex-row">
+      <div class="flex-grow-1 d-flex flex-column">
+        <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
+      </div>
+      <div class="flex-grow-1 d-flex flex-column">
+        <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
+      </div>
+    </div>
   </div>
   <FitOptions ref="fitOptions" :socket="socket" />
   <FileBrowser ref="fileBrowser" :socket="socket" title="Load Model File" :callback="fileBrowserSelectCallback" />

From 2d263df5192d319c9f17cc56103006186a4bd1af Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 30 Sep 2022 16:35:43 -0400
Subject: [PATCH 019/221] set min-height so panels can shrink in height

---
 refl1d-web-gui/src/style.css | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/refl1d-web-gui/src/style.css b/refl1d-web-gui/src/style.css
index 230b64b8..a2b25da4 100644
--- a/refl1d-web-gui/src/style.css
+++ b/refl1d-web-gui/src/style.css
@@ -1,3 +1,7 @@
 html, body, #app {
     height: 100%;
+}
+
+.flex-column {
+    min-height: 0;
 }
\ No newline at end of file

From 7a8d644ed027638386bea3ecbc4cf95118c0bd07 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:32:28 -0400
Subject: [PATCH 020/221] separate local_str and local value so sliders can
 work independently of updates

---
 refl1d-web-gui/src/components/SummaryView.vue | 56 +++++++------------
 1 file changed, 21 insertions(+), 35 deletions(-)

diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index 2aa2a9bd..cf139ece 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -17,28 +17,11 @@ type parameter_info = {
   min: string,
   max: string,
   active?: boolean,
-  value01_local?: number
 }
 
-const parameters = ref<{
-  name: string,
-  value01: number,
-  value_str: string,
-  min: string,
-  max: string,
-  active?: boolean,
-  value01_local?: number,
-}[]>([]);
-
-const parameters_local = ref<parameter_info[]>([]);
-
-const parameters_old = [{
-  name: 'background',
-  value01: 0.75,
-  value_str: '1.7e-6',
-  min: '1e-11',
-  max: '1e-6'
-}];
+const parameters = ref<parameter_info[]>([]);
+const parameters_local01 = ref<number[]>([]);
+const parameters_localstr = ref<string[]>([]);
 
 onMounted(() => {
   props.socket.on('plot_update_ready', () => {
@@ -53,16 +36,20 @@ function fetch_and_draw() {
     // console.log(payload);
     const pv = parameters.value;
     payload.forEach((p,i) => {
+      parameters_localstr.value[i] = p.value_str;
       if (!(pv[i]?.active)) {
-        pv.splice(i, 1, {...p, value01_local: p.value01});
+        pv.splice(i, 1, p);
+        parameters_local01.value[i] = p.value01;
       }
     });
     pv.splice(payload.length);
+    parameters_local01.value.splice(payload.length);
+    parameters_localstr.value.splice(payload.length);
   });
 }
 
-function onMove(param) {
-  props.socket.emit('set_parameter01', param.name, param.value01_local);
+function onMove(param_index) {
+  props.socket.volatile.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
 }
 
 async function onInactive(param) {
@@ -84,25 +71,24 @@ defineExpose({
 </script>
         
 <template>
-  <div class="container flex-grow-1">
+  <div class="">
     <div class="row border-bottom py-1">
-      <div class="col-2">Fit Parameter</div>
+      <div class="col-3">Fit Parameter</div>
       <div class="col-6"></div>
-      <div class="col-2">Value</div>
-      <div class="col-1">Minimum</div>
-      <div class="col-1">Maximum</div>
+      <div class="col-1">Value</div>
+      <div class="col-1">Min</div>
+      <div class="col-1">Max</div>
     </div>
-    <div class="row" v-for="param in parameters" :key="param.name">
+    <div class="row px-1" v-for="(param, index) in parameters" :key="param.name">
       <div class="col-2">{{param.name}}</div>
-      <div class="col-6">
-        <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="param.value01_local"
+      <div class="col-4">
+        <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="parameters_local01[index]"
         @mousedown="param.active=true"
-        @input="onMove(param)"
-        @mouseup="onMouseup"
+        @input="onMove(index)"
         @change="onInactive(param)"/>
       </div>
-      <div class="col-2">{{param.value_str}}</div>
-      <div class="col-1">{{param.min}}</div>
+      <div class="col-1 mr-2">{{parameters_localstr[index]}}</div>
+      <div class="col-1 mr-2">{{param.min}}</div>
       <div class="col-1">{{param.max}}</div>
     </div>
   </div>

From 09ccaca68b444e3fe7f2ac52411679cb77858090 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:33:16 -0400
Subject: [PATCH 021/221] clean up styling

---
 refl1d-web-gui/src/App.vue | 30 ++++++++++++------------------
 1 file changed, 12 insertions(+), 18 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 59ebb8e3..de3f26b2 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
-import { onMounted, ref, shallowRef, VNodeRef } from 'vue';
+import { onMounted, ref } from 'vue';
 import { api } from './server_api';
 import { io, Socket } from 'socket.io-client';
 import FitOptions from './components/FitOptions.vue';
@@ -27,7 +27,7 @@ const connected = ref(false);
 const menuToggle = ref<HTMLButtonElement>();
 const fitOptions = ref<typeof FitOptions>();
 const fileBrowser = ref<typeof FileBrowser>();
-const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) =>  {});
+const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
 const file_picker = ref<HTMLInputElement>();
 
 function set_reflectivity(refl_type: ReflectivityPlot) {
@@ -71,15 +71,6 @@ function selectOpenFile() {
   // file_picker.value?.click();
 }
 
-function load_model_path(event: Event) {
-  console.log(event);
-  const { files } = event.target;
-  console.log(files);
-  // socket.emit("load_model_file", files[0]);
-  window.testevent = event;
-}
-
-
 function openFitOptions() {
   fitOptions.value?.open();
 }
@@ -92,10 +83,10 @@ onMounted(() => {
 
 <template>
   <div class="h-100 d-flex flex-column">
-    <nav class="navbar navbar-expand-lg navbar-dark bg-dark p-2">
+    <nav class="navbar navbar-expand-lg navbar-dark bg-dark">
       <div class="container-fluid">
         <div class="navbar-brand">
-          <img src="./assets/refl1d-icon_256x256x32.png" alt="" height="36" class="d-inline-block align-text-middle">
+          <img src="./assets/refl1d-icon_256x256x32.png" alt="" height="24" class="d-inline-block align-text-middle">
           Refl1D
         </div>
         <button ref="menuToggle" class="navbar-toggler" type="button" data-bs-toggle="collapse"
@@ -166,22 +157,25 @@ onMounted(() => {
         </div>
       </div>
     </nav>
-    <div class="flex-grow-1 d-flex flex-row">
-      <div class="flex-grow-1 d-flex flex-column">
+    <div class="flex-grow-1 row">
+      <div class="col d-flex flex-column">
         <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
       </div>
-      <div class="flex-grow-1 d-flex flex-column">
+      <div class="col d-flex flex-column">
         <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
       </div>
     </div>
   </div>
   <FitOptions ref="fitOptions" :socket="socket" />
   <FileBrowser ref="fileBrowser" :socket="socket" title="Load Model File" :callback="fileBrowserSelectCallback" />
-  <input ref="file_picker" type="file" multiple="false" id="file_picker" style="display:none;" @change="load_model_path" />
+  <input ref="file_picker" type="file" multiple="false" id="file_picker" style="display:none;"
+    @change="load_model_path" />
 </template>
 
 <style>
-html, body, #app {
+html,
+body,
+#app {
   height: 100%;
 }
 

From d281661d62091fbfdc0ac03f2957e1c6de4d477d Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:34:41 -0400
Subject: [PATCH 022/221] make get_plot_data awaitable

---
 refl1d-web-gui/src/components/DataView.vue | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index d70729c9..fe3636f0 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -1,11 +1,12 @@
 <script setup lang="ts">
+/// <reference types="@types/plotly.js" />
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import Plotly from 'plotly.js/src/core';
 import type { Socket } from 'socket.io-client';
 
 const title = "Reflectivity";
-const plot_div = ref<HTMLDivElement>();
-const plot = ref(null);
+const plot_div = ref<HTMLDivElement | null>(null);
+const plot = ref<HTMLDivElement>();
 
 const props = defineProps<{
   socket: Socket,
@@ -21,8 +22,10 @@ onMounted(() => {
 });
 
 function fetch_and_draw() {
-  props.socket.emit('get_plot_data', 'linear', (payload) => {
-
+  props.socket.emit('get_plot_data', 'linear', async (payload) => {
+    if (plot_div.value === null) {
+      return
+    }
     let theory_traces = [];
     let data_traces = [];
     for (let model of payload) {
@@ -49,15 +52,15 @@ function fetch_and_draw() {
       }
     };
 
-    if (plot.value) {
-      const update = {
+    if (plot.value !== undefined) {
+      const trace_updates = {
         x: [...theory_traces.map((t) => t.x), ...data_traces.map((t) => t.x)],
         y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],       
       }
-      Plotly.update(plot_div.value, update);
+      await Plotly.update(plot_div.value, trace_updates);
     }
     else {
-      plot.value = Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
+      plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
     }
     // console.log(plot.value);
     // mpld3.draw_figure("plot_div", payload);
@@ -76,7 +79,7 @@ defineExpose({
 </script>
 
 <template>
-  <div class="container d-flex flex-grow-1">
+  <div class="">
     <div ref="plot_div" id="plot_div">
 
     </div>

From 425a9ed73e3ed750de15735f72b6333b5c2c14ef Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:36:57 -0400
Subject: [PATCH 023/221] add animation loop, only call for new profile plot
 after finished retrieving one

---
 refl1d-web-gui/src/components/ModelView.vue | 36 ++++++++++++++-------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index 8878cf5e..c9611191 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -1,10 +1,11 @@
 <script setup lang="ts">
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
-import type { Socket } from 'socket.io-client';
+import { Socket } from 'socket.io-client';
 import mpld3 from 'mpld3';
 
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
 
 const props = defineProps<{
   socket: Socket,
@@ -12,26 +13,38 @@ const props = defineProps<{
 }>();
 
 onMounted(() => {
-  props.socket.on('plot_update_ready', () => {
+  props.socket.on('plot_update_ready', ({ message, timestamp }) => {
     if (props.visible) {
-      fetch_and_draw();
+      draw_requested.value = true;
     }
   });
+  window.requestAnimationFrame(draw_if_needed);
 });
 
 function fetch_and_draw() {
   props.socket.emit('get_profile_plot', (payload) => {
-    console.log(payload, plot_div.value);
-    payload.width = plot_div.value?.clientWidth ?? 640;
-    payload.height = plot_div.value?.clientHeight ?? 480;
-    // delete payload.width;
-    // delete payload.height;
-    /* Data Parsing Functions */
-    // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-    mpld3.draw_figure("profile_div", payload, false, true);
+    if (props.visible) {
+      let plotdata = { ...payload };
+      console.log(plotdata, plot_div.value);
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 32;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 32;
+      // delete payload.width;
+      // delete payload.height;
+      /* Data Parsing Functions */
+      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+      mpld3.draw_figure("profile_div", plotdata, false, true);
+    }
   });
 }
 
+function draw_if_needed(timestamp: number) {
+  if (draw_requested.value) {
+    draw_requested.value = false;
+    fetch_and_draw();
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
 watch(() => props.visible, (value) => {
   if (value) {
     console.log('visible', value);
@@ -48,7 +61,6 @@ defineExpose({
 <template>
   <div class="container d-flex flex-grow-1">
     <div class="flex-grow-1" ref="plot_div" id="profile_div">
-
     </div>
   </div>
 </template>

From 94e3f9703ef9a6839db7c24e6fe0b225de3c06fa Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:37:18 -0400
Subject: [PATCH 024/221] messages will be sent with timestamps

---
 refl1d-web-gui/src/components/FitOptions.vue | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
index 2bb1f22b..7e7c5457 100644
--- a/refl1d-web-gui/src/components/FitOptions.vue
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -41,17 +41,17 @@ const active_settings = ref({});
 
 props.socket.on('fitter_settings', () => {
   props.socket.emit('get_last_message', 'fitter_settings', (payload) => {
-    fitter_settings.value = payload;
+    fitter_settings.value = payload?.message;
   });
 });
 props.socket.on('fitter_defaults', () => {
   props.socket.emit('get_last_message', 'fitter_defaults', (payload) => {
-    fitter_defaults.value = payload;
+    fitter_defaults.value = payload?.message;
   });
 });
 props.socket.on('fitter_active', () => {
   props.socket.emit('get_last_message', 'fitter_active', (payload) => {
-    fitter_active.value = payload;
+    fitter_active.value = payload?.message;
   });
 });
 

From da7410228eaa8c7bcc2538ecb3de7506457425e8 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:37:39 -0400
Subject: [PATCH 025/221] add types for plotly

---
 refl1d-web-gui/package.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/refl1d-web-gui/package.json b/refl1d-web-gui/package.json
index 0beb3186..92dbbbe9 100644
--- a/refl1d-web-gui/package.json
+++ b/refl1d-web-gui/package.json
@@ -14,6 +14,7 @@
     "vue": "^3.2.38"
   },
   "devDependencies": {
+    "@types/plotly.js": "^2.12.5",
     "@vitejs/plugin-vue": "^3.0.3",
     "vite": "^3.0.9"
   }

From 1e9b86d38125331328ab120826157a4f9def67da Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 16:41:25 -0400
Subject: [PATCH 026/221] send timestamp with messages from topics

---
 refl1d/webserver.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 9bffff37..caf82ca4 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -126,14 +126,19 @@ def get_plot_data(sid: str, view: str = 'linear'):
     return to_dict(result)
 
 @sio.event
-def get_profile_plot(sid: str):
+async def get_profile_plot(sid: str):
     import mpld3
     import matplotlib.pyplot as plt
+    import time
+    print('queueing new profile plot...', time.time())
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     fig = plt.figure()
     for model in iter(fitProblem.models):
         model.plot_profile()
-    return mpld3.fig_to_dict(plt.gcf())
+    dfig = mpld3.fig_to_dict(plt.gcf())
+    plt.close(fig)
+    # await sio.emit("profile_plot", dfig, to=sid)
+    return dfig
 
 @sio.event
 def get_parameters(sid: str):
@@ -183,7 +188,7 @@ def unsubscribe(sid: str, topic: str):
 @sio.event
 async def publish(sid: str, topic: str, message):
     timestamp = datetime.now().timestamp()
-    topics[topic] = {"message": message, "timestamp": timestamp}
+    topics[topic] = {"message": message, "timestamp": f"{timestamp:.6f}"}
     await sio.emit(topic, timestamp, room=topic)
 
 @sio.event
@@ -191,7 +196,7 @@ def get_last_message(sid: str, topic: str):
     # this is a GET request in disguise -
     # emitter must handle the response in a callback,
     # as no separate response event is emitted.  
-    return topics.get(topic, {}).get("message", None)
+    return topics.get(topic, {})
 
 @sio.event
 def get_dirlisting(sid: str, pathlist: List[str]):

From 1a5c8733553c2ef503b3a4819fdbf98ce7e20e98 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 17:37:29 -0400
Subject: [PATCH 027/221] give profile plot div unique id so it can be used
 wherever it is (even if 2 model views present in the DOM)

---
 refl1d-web-gui/package.json                 |  2 ++
 refl1d-web-gui/src/components/ModelView.vue | 20 +++++++++++---------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/refl1d-web-gui/package.json b/refl1d-web-gui/package.json
index 92dbbbe9..e55f50eb 100644
--- a/refl1d-web-gui/package.json
+++ b/refl1d-web-gui/package.json
@@ -11,10 +11,12 @@
     "mpld3": "^0.5.8",
     "plotly.js": "^2.14.0",
     "socket.io-client": "^4.5.2",
+    "uuid": "^9.0.0",
     "vue": "^3.2.38"
   },
   "devDependencies": {
     "@types/plotly.js": "^2.12.5",
+    "@types/uuid": "^8.3.4",
     "@vitejs/plugin-vue": "^3.0.3",
     "vite": "^3.0.9"
   }
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index c9611191..0787e1d2 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -1,12 +1,14 @@
 <script setup lang="ts">
+/// <reference types="@types/uuid"/>
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
 import mpld3 from 'mpld3';
 
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
 const draw_requested = ref(false);
-
+const plot_div_id = ref(uuidv4());
 const props = defineProps<{
   socket: Socket,
   visible: boolean
@@ -26,21 +28,21 @@ function fetch_and_draw() {
     if (props.visible) {
       let plotdata = { ...payload };
       console.log(plotdata, plot_div.value);
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 32;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 32;
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
       // delete payload.width;
       // delete payload.height;
       /* Data Parsing Functions */
       // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure("profile_div", plotdata, false, true);
+      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
     }
   });
 }
 
 function draw_if_needed(timestamp: number) {
   if (draw_requested.value) {
-    draw_requested.value = false;
     fetch_and_draw();
+    draw_requested.value = false;
   }
   window.requestAnimationFrame(draw_if_needed);
 }
@@ -60,13 +62,13 @@ defineExpose({
     
 <template>
   <div class="container d-flex flex-grow-1">
-    <div class="flex-grow-1" ref="plot_div" id="profile_div">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
     </div>
   </div>
 </template>
 
 <style scoped>
-  svg {
-    width: 100%;
-  }
+svg {
+  width: 100%;
+}
 </style>
\ No newline at end of file

From a8daa06185e05904c2f7eb4636da24bfd4ff8062 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 17:37:58 -0400
Subject: [PATCH 028/221] add typings for DataView (Plotly)

---
 refl1d-web-gui/src/components/DataView.vue | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index fe3636f0..6f4fdf54 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -1,12 +1,12 @@
 <script setup lang="ts">
 /// <reference types="@types/plotly.js" />
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
-import Plotly from 'plotly.js/src/core';
+import * as Plotly from 'plotly.js/lib/core';
 import type { Socket } from 'socket.io-client';
 
 const title = "Reflectivity";
 const plot_div = ref<HTMLDivElement | null>(null);
-const plot = ref<HTMLDivElement>();
+const plot = ref<Plotly.PlotlyHTMLElement>();
 
 const props = defineProps<{
   socket: Socket,
@@ -26,8 +26,8 @@ function fetch_and_draw() {
     if (plot_div.value === null) {
       return
     }
-    let theory_traces = [];
-    let data_traces = [];
+    let theory_traces: Plotly.Data[] = [];
+    let data_traces: Plotly.Data[] = [];
     for (let model of payload) {
       for (let xs of model) {
         theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: {width: 2}});
@@ -35,7 +35,7 @@ function fetch_and_draw() {
       }
     }
 
-    const layout = {
+    const layout: Partial<Plotly.Layout> = {
       xaxis: {
         title: {
           text: '$Q (Å^{-1})$'
@@ -57,7 +57,7 @@ function fetch_and_draw() {
         x: [...theory_traces.map((t) => t.x), ...data_traces.map((t) => t.x)],
         y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],       
       }
-      await Plotly.update(plot_div.value, trace_updates);
+      await Plotly.update(plot_div.value, trace_updates, layout);
     }
     else {
       plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);

From be83fef2e217aa82568389ee898325e8661bf926 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 17:38:23 -0400
Subject: [PATCH 029/221] improve layout of Summary table

---
 refl1d-web-gui/src/components/SummaryView.vue | 30 ++++++++++++-------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index cf139ece..84dedaef 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -73,23 +73,31 @@ defineExpose({
 <template>
   <div class="">
     <div class="row border-bottom py-1">
-      <div class="col-3">Fit Parameter</div>
-      <div class="col-6"></div>
-      <div class="col-1">Value</div>
-      <div class="col-1">Min</div>
-      <div class="col-1">Max</div>
+      <div class="col-2">Fit Parameter</div>
+      <div class="col-5"></div>
+      <div class="col-5">
+        <div class="row">
+          <div class="col-4">Value</div>
+          <div class="col-4">Min.</div>
+          <div class="col-4">Max</div>
+        </div>
+      </div>
     </div>
-    <div class="row px-1" v-for="(param, index) in parameters" :key="param.name">
-      <div class="col-2">{{param.name}}</div>
-      <div class="col-4">
+    <div class="row align-items-center px-1" v-for="(param, index) in parameters" :key="param.name">
+      <div class="col-2 border-bottom">{{param.name}}</div>
+      <div class="col-5">
         <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="parameters_local01[index]"
         @mousedown="param.active=true"
         @input="onMove(index)"
         @change="onInactive(param)"/>
       </div>
-      <div class="col-1 mr-2">{{parameters_localstr[index]}}</div>
-      <div class="col-1 mr-2">{{param.min}}</div>
-      <div class="col-1">{{param.max}}</div>
+      <div class="col-5">
+        <div class="row">
+          <div class="col-4">{{parameters_localstr[index]}}</div>
+          <div class="col-4">{{param.min}}</div>
+          <div class="col-4">{{param.max}}</div>
+        </div>
+      </div>
     </div>
   </div>
 </template>

From 5cc8b441062fb7bbc698519d3b84d63cc08d6f3f Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 21:50:36 -0400
Subject: [PATCH 030/221] node id starting with number causes issue with CSS
 selectors... prepend uuid with div-

---
 refl1d-web-gui/src/components/ModelView.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index 0787e1d2..1c4c7b85 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -8,7 +8,7 @@ import mpld3 from 'mpld3';
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
 const draw_requested = ref(false);
-const plot_div_id = ref(uuidv4());
+const plot_div_id = ref(`div-${uuidv4()}`);
 const props = defineProps<{
   socket: Socket,
   visible: boolean

From c5625a0dfe04c90d59c982fbd9e6d7d692257f8a Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 21:51:06 -0400
Subject: [PATCH 031/221] make data plot full height

---
 refl1d-web-gui/src/components/DataView.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index 6f4fdf54..7fdc63ce 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -79,8 +79,8 @@ defineExpose({
 </script>
 
 <template>
-  <div class="">
-    <div ref="plot_div" id="plot_div">
+  <div class="container d-flex flex-grow-1">
+    <div class="flex-grow-1" ref="plot_div" id="plot_div">
 
     </div>
   </div>

From a0518969d7ee9cc5ba29df69cb7ca4a3d2ef77de Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Mon, 3 Oct 2022 21:55:45 -0400
Subject: [PATCH 032/221] allow dbl-click to choose file

---
 refl1d-web-gui/src/components/FileBrowser.vue | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/refl1d-web-gui/src/components/FileBrowser.vue b/refl1d-web-gui/src/components/FileBrowser.vue
index 73638c82..a302b397 100644
--- a/refl1d-web-gui/src/components/FileBrowser.vue
+++ b/refl1d-web-gui/src/components/FileBrowser.vue
@@ -16,7 +16,8 @@ const emit = defineEmits<{
 
 const dialog = ref<HTMLDivElement>();
 const isOpen = ref(false);
-const pathlist = ref(["/", "home", "bbm", "dev", "refl1d-modelbuilder"]);
+// const pathlist = ref(["/", "home", "bbm", "dev", "refl1d-modelbuilder"]);
+const pathlist = ref(["/", "Users", "bbm", "dev", "refl1d-modelbuilder"]);
 const subdirlist = shallowRef<string[]>([])
 const filelist = shallowRef<string[]>([])
 const chosenFile = ref("");
@@ -97,14 +98,16 @@ defineExpose({
           <div class="container border-bottom">
             <h3>Files:</h3>
             <div class="row row-cols-3">
-              <div class="btn col overflow-hidden border" :class="{'btn-warning': filename === chosenFile}" v-for="filename in filelist" :key="filename" @click="chosenFile = filename">
+              <div class="btn col overflow-hidden border" :class="{'btn-warning': filename === chosenFile}"
+                v-for="filename in filelist" :key="filename" @click="chosenFile = filename" @dblclick="chosenFile=filename;chooseFile()">
                 {{filename}}
               </div>
             </div>
           </div>
           <div class="modal-footer">
             <button type="button" class="btn btn-secondary" @click="close">Cancel</button>
-            <button type="button" class="btn btn-primary" :class="{disabled: chosenFile==''}" @click="chooseFile">OK</button>
+            <button type="button" class="btn btn-primary" :class="{disabled: chosenFile==''}"
+              @click="chooseFile">OK</button>
           </div>
         </div>
       </div>
@@ -113,7 +116,7 @@ defineExpose({
 </template>
 
 <style scoped>
-  .active {
-    background-color: light
-  }
+.active {
+  background-color: light
+}
 </style>
\ No newline at end of file

From f349f14e4f1fa011a1babecf3997dd7cf87a7b63 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 4 Oct 2022 09:16:15 -0400
Subject: [PATCH 033/221] send full fit_settings on update

---
 refl1d-web-gui/src/components/FitOptions.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
index 7e7c5457..f7296865 100644
--- a/refl1d-web-gui/src/components/FitOptions.vue
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -102,7 +102,7 @@ function process_settings() {
 }
 
 function save() {
-  const new_settings = {};
+  const new_settings = structuredClone(fitter_settings.value);
   new_settings[fitter_active_local.value] = { settings: process_settings() };
   props.socket.emit("publish", "fitter_settings", new_settings);
   props.socket.emit("publish", "fitter_active", fitter_active_local.value);

From 330aaa83103d31cc060a70cef685cdd970526967 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:48:50 -0400
Subject: [PATCH 034/221] adding icon in a supported size for favicon (48x48)

---
 refl1d-web-gui/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/index.html b/refl1d-web-gui/index.html
index c58c76fe..ddd28ef3 100644
--- a/refl1d-web-gui/index.html
+++ b/refl1d-web-gui/index.html
@@ -2,7 +2,7 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
-    <link rel="icon" href="./src/assets/refl1d-icon_256x256x32.png" />
+    <link rel="icon" href="./src/assets/refl1d-icon_48x48x32.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <script type="text/javascript" async
       src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTML">

From 8dc75969584f4fde95be6b688903f9d854601edb Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:48:59 -0400
Subject: [PATCH 035/221] adding icon in a supported size for favicon (48x48)

---
 .../src/assets/refl1d-icon_48x48x32.png          | Bin 0 -> 4071 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 refl1d-web-gui/src/assets/refl1d-icon_48x48x32.png

diff --git a/refl1d-web-gui/src/assets/refl1d-icon_48x48x32.png b/refl1d-web-gui/src/assets/refl1d-icon_48x48x32.png
new file mode 100644
index 0000000000000000000000000000000000000000..dfaa7415fcd18deb2253bc3c4015cc8aa264ac58
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From 55a8886e539758ba272e79e2e865f0d1a651b890 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:55:59 -0400
Subject: [PATCH 036/221] import Component as type

---
 refl1d-web-gui/src/components/PanelTabContainer.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/components/PanelTabContainer.vue b/refl1d-web-gui/src/components/PanelTabContainer.vue
index da38a4e5..b64044f3 100644
--- a/refl1d-web-gui/src/components/PanelTabContainer.vue
+++ b/refl1d-web-gui/src/components/PanelTabContainer.vue
@@ -1,5 +1,6 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef, Component } from 'vue';
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import type { Component } from 'vue';
 import type { Socket } from 'socket.io-client';
 import { Tab } from 'bootstrap/dist/js/bootstrap.esm';
 

From c70f5917da6bde0a35a92cefc0bcd343ad37ea5d Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:56:15 -0400
Subject: [PATCH 037/221] pass all settings back to server, not just active one

---
 refl1d-web-gui/src/components/FitOptions.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
index 7e7c5457..566ef923 100644
--- a/refl1d-web-gui/src/components/FitOptions.vue
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -102,7 +102,7 @@ function process_settings() {
 }
 
 function save() {
-  const new_settings = {};
+  const new_settings = structuredClone(fitter_settings);
   new_settings[fitter_active_local.value] = { settings: process_settings() };
   props.socket.emit("publish", "fitter_settings", new_settings);
   props.socket.emit("publish", "fitter_active", fitter_active_local.value);

From f7b5020208d354f1257e2efbd9a84aa602dc6163 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:57:09 -0400
Subject: [PATCH 038/221] add new method to get seriallized model

---
 refl1d/webserver.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index caf82ca4..57ada8ec 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -26,6 +26,7 @@
 # fitter_settings = deepcopy(FITTER_DEFAULTS)
 # active_fitter = "amoeba"
 
+# sio = socketio.AsyncServer(cors_allowed_origins="*", serializer='msgpack')
 sio = socketio.AsyncServer(cors_allowed_origins="*")
 app = web.Application()
 static_dir_path = Path(__file__).parent / 'webview'
@@ -68,7 +69,7 @@ async def index(request):
     return web.HTTPFound('/static/index.html')
     
 @sio.event
-async def connect(sid, environ):
+async def connect(sid, environ, data=None):
     print("connect ", sid)
 
 @sio.event
@@ -125,6 +126,12 @@ def get_plot_data(sid: str, view: str = 'linear'):
         # result.append(output)
     return to_dict(result)
 
+@sio.event
+async def get_model(sid: str):
+    from bumps.serialize import to_dict
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    return to_dict(fitProblem)
+
 @sio.event
 async def get_profile_plot(sid: str):
     import mpld3

From f8e657d379d311045d3c85fb1d5ba1c34d8e8008 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:58:00 -0400
Subject: [PATCH 039/221] adding new component to visualize serialized model
 tree

---
 .../src/components/ModelInspect.vue           | 101 ++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 refl1d-web-gui/src/components/ModelInspect.vue

diff --git a/refl1d-web-gui/src/components/ModelInspect.vue b/refl1d-web-gui/src/components/ModelInspect.vue
new file mode 100644
index 00000000..61962d9e
--- /dev/null
+++ b/refl1d-web-gui/src/components/ModelInspect.vue
@@ -0,0 +1,101 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef, nextTick } from 'vue';
+import JsonViewer from 'vue-json-viewer';
+import { getDiff } from 'json-difference';
+import type { Socket } from 'socket.io-client';
+
+// from https://github.com/microsoft/TypeScript/issues/1897#issuecomment-1228063688
+type json =
+    | string
+    | number
+    | boolean
+    | null
+    | json[]
+    | { [key: string]: json };
+
+const title = "Model";
+const active_parameter = ref("");
+
+const props = defineProps<{
+  socket: Socket,
+  visible: Boolean
+}>();
+
+const modelJson = ref<json>(null);
+window.model = modelJson;
+
+onMounted(() => {
+  props.socket.on('plot_update_ready', fetch_and_draw);
+});
+
+function fetch_and_draw() {
+  if (props.visible) {
+      props.socket.emit('get_model', (payload: json) => {
+        const diff = getDiff(modelJson.value, payload);
+        for (let [path, oldval, newval] of diff.edited) {
+          const {target, parent, key} = resolve_diffpath(modelJson.value, path);
+          console.log({target, parent, key}, oldval, newval);
+          // trigger reactive update;
+          if (key instanceof Number) {
+            parent.splice(key, 1, newval);
+          }
+          else {
+            parent[key] = newval;
+          }
+        }
+        // modelJson.value = Object.assign({}, modelJson.value, payload);
+        // console.log(modelJson);
+      });
+    }
+}
+
+watch(() => props.visible, (value) => {
+  if (value) {
+    props.socket.emit('get_model', (payload: json) => {
+      modelJson.value = payload;
+    });
+  }
+});
+
+function* traverse(o: object, path: string[]=[]) {
+    for (var i of Object.keys(o)) {
+        const itemPath = path.concat(i);
+        yield [i,o[i],itemPath,o];
+        if (o[i] !== null && typeof(o[i])=="object") {
+            //going one step down in the object tree!!
+            yield* traverse(o[i],itemPath);
+        }
+    }
+}
+
+function resolve(o: object, path: string[] = []) {
+  let target = o;
+  for (let pfrag of path) {
+    target = target[pfrag];
+  }
+  return target;
+}
+
+const ARRAY_PATH_RE = /^([0-9]+)\[\]$/;
+function resolve_diffpath(o: object, diffpath: string) {
+  const pathitems = diffpath.split('/');
+  let target = o;
+  let parent = null;
+  let key = null;
+  for (let pathitem of pathitems) {
+    const array_path = pathitem.match(ARRAY_PATH_RE);
+    parent = target;
+    key = (array_path) ? Number(array_path[1]) : pathitem;
+    target = target[key];
+  }
+  return {target, parent, key};
+}
+
+defineExpose({
+  title
+});
+</script>
+
+<template>
+  <JsonViewer :value="modelJson" />
+</template>
\ No newline at end of file

From 59c061521f42435fb42cc88f623a48a664b1fa92 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:58:21 -0400
Subject: [PATCH 040/221] adding support for json viewer for ModelInspect panel

---
 refl1d-web-gui/package.json | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/refl1d-web-gui/package.json b/refl1d-web-gui/package.json
index e55f50eb..b71bb585 100644
--- a/refl1d-web-gui/package.json
+++ b/refl1d-web-gui/package.json
@@ -8,11 +8,13 @@
   },
   "dependencies": {
     "bootstrap": "^5.2.1",
+    "json-difference": "^1.8.2",
     "mpld3": "^0.5.8",
     "plotly.js": "^2.14.0",
     "socket.io-client": "^4.5.2",
     "uuid": "^9.0.0",
-    "vue": "^3.2.38"
+    "vue": "^3.2.38",
+    "vue-json-viewer": "^3.0.4"
   },
   "devDependencies": {
     "@types/plotly.js": "^2.12.5",

From de938af65923a5300ebc5adf0da933089c755260 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 08:59:07 -0400
Subject: [PATCH 041/221] add definition of global to support old-style
 plotly.js libs

---
 refl1d-web-gui/vite.config.js | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/refl1d-web-gui/vite.config.js b/refl1d-web-gui/vite.config.js
index 40c640c2..1502e210 100644
--- a/refl1d-web-gui/vite.config.js
+++ b/refl1d-web-gui/vite.config.js
@@ -11,5 +11,10 @@ export default defineConfig({
     alias: {
       '@': fileURLToPath(new URL('./src', import.meta.url))
     }
+  },
+  define: {
+    // By default, Vite doesn't include shims for NodeJS/
+    // necessary for segment analytics lib to work
+    global: {},
   }
 })

From 2695eeaee561cd469926b85f09e034aac1cff771 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 11:54:49 -0400
Subject: [PATCH 042/221] use shared list of panels

---
 refl1d-web-gui/src/App.vue | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index de3f26b2..fabdfc6a 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -1,7 +1,6 @@
 <script setup lang="ts">
 import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
 import { onMounted, ref } from 'vue';
-import { api } from './server_api';
 import { io, Socket } from 'socket.io-client';
 import FitOptions from './components/FitOptions.vue';
 import DataView from './components/DataView.vue';
@@ -9,6 +8,7 @@ import ModelView from './components/ModelView.vue';
 import PanelTabContainer from './components/PanelTabContainer.vue';
 import FileBrowser from './components/FileBrowser.vue';
 import SummaryView from './components/SummaryView.vue';
+import ModelInspect from './components/ModelInspect.vue';
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
 
 const REFLECTIVITY_PLOTS = [
@@ -22,13 +22,19 @@ const REFLECTIVITY_PLOTS = [
 type ReflectivityPlotEnum = typeof REFLECTIVITY_PLOTS;
 type ReflectivityPlot = ReflectivityPlotEnum[number];
 
+const panels = [
+  {title: 'Reflectivity', component: DataView},
+  {title: 'Parameters', component: SummaryView},
+  {title: 'Profile', component: ModelView},
+  {title: 'Model', component: ModelInspect}
+];
+
 const reflectivity_type = ref<ReflectivityPlot>("Linear");
 const connected = ref(false);
 const menuToggle = ref<HTMLButtonElement>();
 const fitOptions = ref<typeof FitOptions>();
 const fileBrowser = ref<typeof FileBrowser>();
 const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
-const file_picker = ref<HTMLInputElement>();
 
 function set_reflectivity(refl_type: ReflectivityPlot) {
   reflectivity_type.value = refl_type;
@@ -159,17 +165,15 @@ onMounted(() => {
     </nav>
     <div class="flex-grow-1 row">
       <div class="col d-flex flex-column">
-        <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
+        <PanelTabContainer :panels="panels" :socket="socket" />
       </div>
       <div class="col d-flex flex-column">
-        <PanelTabContainer :panels="[DataView, ModelView, SummaryView]" :socket="socket" />
+        <PanelTabContainer :panels="panels" :socket="socket" />
       </div>
     </div>
   </div>
   <FitOptions ref="fitOptions" :socket="socket" />
   <FileBrowser ref="fileBrowser" :socket="socket" title="Load Model File" :callback="fileBrowserSelectCallback" />
-  <input ref="file_picker" type="file" multiple="false" id="file_picker" style="display:none;"
-    @change="load_model_path" />
 </template>
 
 <style>

From a8f1cd7976e54307fe7d7ffe52b117e242eb13df Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 12:00:04 -0400
Subject: [PATCH 043/221] Set title from parent element, rather than from child
 in tab panel

---
 refl1d-web-gui/src/components/DataView.vue     | 3 ---
 refl1d-web-gui/src/components/ModelInspect.vue | 3 ---
 refl1d-web-gui/src/components/ModelView.vue    | 4 ----
 refl1d-web-gui/src/components/SummaryView.vue  | 4 ----
 4 files changed, 14 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index 7fdc63ce..03cc72ce 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -73,9 +73,6 @@ watch(() => props.visible, (value) => {
   }
 });
 
-defineExpose({
-  title
-});
 </script>
 
 <template>
diff --git a/refl1d-web-gui/src/components/ModelInspect.vue b/refl1d-web-gui/src/components/ModelInspect.vue
index 61962d9e..81cff302 100644
--- a/refl1d-web-gui/src/components/ModelInspect.vue
+++ b/refl1d-web-gui/src/components/ModelInspect.vue
@@ -91,9 +91,6 @@ function resolve_diffpath(o: object, diffpath: string) {
   return {target, parent, key};
 }
 
-defineExpose({
-  title
-});
 </script>
 
 <template>
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index 1c4c7b85..08442d54 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -54,10 +54,6 @@ watch(() => props.visible, (value) => {
   }
 });
 
-defineExpose({
-  title
-});
-
 </script>
     
 <template>
diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index 84dedaef..d89a0f32 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -64,10 +64,6 @@ watch(() => props.visible, (value) => {
   }
 });
 
-defineExpose({
-  title
-});
-
 </script>
         
 <template>

From aa3cb5b18dc1e376948583d22c834015b34fffcc Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 12:01:25 -0400
Subject: [PATCH 044/221] typing updates

---
 refl1d-web-gui/src/components/DataView.vue | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index 03cc72ce..c4267323 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -26,11 +26,11 @@ function fetch_and_draw() {
     if (plot_div.value === null) {
       return
     }
-    let theory_traces: Plotly.Data[] = [];
-    let data_traces: Plotly.Data[] = [];
+    let theory_traces: (Plotly.Data & {x: number, y: number})[] = [];
+    let data_traces: (Plotly.Data & {x: number, y: number})[] = [];
     for (let model of payload) {
       for (let xs of model) {
-        theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: {width: 2}});
+        theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
         data_traces.push({ x: xs.Q, y: xs.R, mode: 'markers', name: xs.label + ' data' });
       }
     }
@@ -44,18 +44,18 @@ function fetch_and_draw() {
         autorange: true
       },
       yaxis: {
-        title: {text: 'Reflectivity'},
+        title: { text: 'Reflectivity' },
         exponentformat: 'e',
         showexponent: 'all',
         type: 'log',
         autorange: true
-      }
+      },
     };
 
     if (plot.value !== undefined) {
       const trace_updates = {
         x: [...theory_traces.map((t) => t.x), ...data_traces.map((t) => t.x)],
-        y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],       
+        y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],
       }
       await Plotly.update(plot_div.value, trace_updates, layout);
     }

From eef0e5220a36b89fffc054dcd440b099e9dfc536 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 12:02:20 -0400
Subject: [PATCH 045/221] cleanup

---
 .../src/components/ModelInspect.vue           | 52 +++++++++----------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelInspect.vue b/refl1d-web-gui/src/components/ModelInspect.vue
index 81cff302..9014b54d 100644
--- a/refl1d-web-gui/src/components/ModelInspect.vue
+++ b/refl1d-web-gui/src/components/ModelInspect.vue
@@ -21,8 +21,7 @@ const props = defineProps<{
   visible: Boolean
 }>();
 
-const modelJson = ref<json>(null);
-window.model = modelJson;
+const modelJson = ref<json>();
 
 onMounted(() => {
   props.socket.on('plot_update_ready', fetch_and_draw);
@@ -31,20 +30,19 @@ onMounted(() => {
 function fetch_and_draw() {
   if (props.visible) {
       props.socket.emit('get_model', (payload: json) => {
-        const diff = getDiff(modelJson.value, payload);
+        const old_model: json = modelJson.value as Record<string, any>;
+        const new_model: json = payload as Record<string, any>;
+        const diff = getDiff(old_model, new_model);
         for (let [path, oldval, newval] of diff.edited) {
-          const {target, parent, key} = resolve_diffpath(modelJson.value, path);
-          console.log({target, parent, key}, oldval, newval);
+          const {target, parent, key} = resolve_diffpath(old_model, path);
           // trigger reactive update;
-          if (key instanceof Number) {
+          if (typeof(key) === 'number' && Array.isArray(parent)) {
             parent.splice(key, 1, newval);
           }
           else {
             parent[key] = newval;
           }
         }
-        // modelJson.value = Object.assign({}, modelJson.value, payload);
-        // console.log(modelJson);
       });
     }
 }
@@ -57,31 +55,31 @@ watch(() => props.visible, (value) => {
   }
 });
 
-function* traverse(o: object, path: string[]=[]) {
-    for (var i of Object.keys(o)) {
-        const itemPath = path.concat(i);
-        yield [i,o[i],itemPath,o];
-        if (o[i] !== null && typeof(o[i])=="object") {
-            //going one step down in the object tree!!
-            yield* traverse(o[i],itemPath);
-        }
-    }
-}
+// function* traverse(o: object, path: string[]=[]) {
+//     for (var i of Object.keys(o)) {
+//         const itemPath = path.concat(i);
+//         yield [i,o[i],itemPath,o];
+//         if (o[i] !== null && typeof(o[i])=="object") {
+//             //going one step down in the object tree!!
+//             yield* traverse(o[i],itemPath);
+//         }
+//     }
+// }
 
-function resolve(o: object, path: string[] = []) {
-  let target = o;
-  for (let pfrag of path) {
-    target = target[pfrag];
-  }
-  return target;
-}
+// function resolve(o: object, path: string[] = []) {
+//   let target = o;
+//   for (let pfrag of path) {
+//     target = target[pfrag];
+//   }
+//   return target;
+// }
 
 const ARRAY_PATH_RE = /^([0-9]+)\[\]$/;
 function resolve_diffpath(o: object, diffpath: string) {
   const pathitems = diffpath.split('/');
   let target = o;
-  let parent = null;
-  let key = null;
+  let parent: object = o;
+  let key: number | string = "";
   for (let pathitem of pathitems) {
     const array_path = pathitem.match(ARRAY_PATH_RE);
     parent = target;

From 7e4f5a7e95f7d26c94847f69a2f292ed7c5226d5 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 12:02:53 -0400
Subject: [PATCH 046/221] get title from props instead of from child components

---
 refl1d-web-gui/src/components/PanelTabContainer.vue | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/refl1d-web-gui/src/components/PanelTabContainer.vue b/refl1d-web-gui/src/components/PanelTabContainer.vue
index b64044f3..06563338 100644
--- a/refl1d-web-gui/src/components/PanelTabContainer.vue
+++ b/refl1d-web-gui/src/components/PanelTabContainer.vue
@@ -1,19 +1,18 @@
 <script setup lang="ts">
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
-import type { Component } from 'vue';
+import type { DefineComponent, Component } from 'vue';
 import type { Socket } from 'socket.io-client';
 import { Tab } from 'bootstrap/dist/js/bootstrap.esm';
 
-type PanelComponent = Component & { title: string };
+// type PanelComponent = DefineComponent<{socket: Socket, visible: boolean}, any>;
 
 const tabTriggers = ref<HTMLAnchorElement[]>([]);
-const panelComponents = ref<PanelComponent[]>([]);
 const panelContainers = ref<HTMLDivElement[]>([]);
 const panelVisible = ref<boolean[]>([]);
 
 const props = defineProps<{
   socket: Socket,
-  panels: PanelComponent[]
+  panels: {title: string, component: unknown}[],
 }>();
 
 let triggers: Tab[] = [];
@@ -46,13 +45,13 @@ onMounted(() => {
 <template>
   <ul class="nav nav-tabs">
     <li class="nav-item" v-for="(panel, index) in props.panels" :key="index">
-      <a ref="tabTriggers" class="nav-link" href="#" @click="activateTab(index)">{{panelComponents[index]?.title}}</a>
+      <a ref="tabTriggers" class="nav-link" href="#" @click="activateTab(index)">{{panels[index]?.title}}</a>
     </li>
   </ul>
   <div class="tab-content d-flex flex-column flex-grow-1">
     <div ref="panelContainers" class="tab-pane flex-column flex-grow-1" v-for="(panel, index) in props.panels"
       :key="index">
-      <component :is="panel" :socket="props.socket" ref="panelComponents" :visible="panelVisible[index]"></component>
+      <component :is="panel.component" :socket="props.socket" :visible="panelVisible[index]"></component>
     </div>
   </div>
 </template>
@@ -61,6 +60,7 @@ onMounted(() => {
 .tab-content>.tab-pane {
   display: none;
 }
+
 .tab-content>.tab-pane.active {
   display: flex !important;
 }

From 86eccae1c28336f965f94a6e4d131045a8e95e45 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 17:36:53 -0400
Subject: [PATCH 047/221] support serialization of MixedExperiment

---
 refl1d/experiment.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/refl1d/experiment.py b/refl1d/experiment.py
index 8779fccb..a2944f50 100644
--- a/refl1d/experiment.py
+++ b/refl1d/experiment.py
@@ -638,6 +638,7 @@ def penalty(self):
 
 assert isinstance(Experiment, Fitness)
 
+@schema(init=False)
 class MixedExperiment(ExperimentBase):
     """
     Support composite sample reflectivity measurements.
@@ -663,6 +664,13 @@ class MixedExperiment(ExperimentBase):
     profiles can be accessed from the underlying experiments
     using composite.parts[i] for the various samples.
     """
+    name: str
+    ratio: List[Union[float, Parameter]]
+    samples: Optional[List[model.Stack]]
+    probe: Union[Probe, PolarizedNeutronProbe]
+    coherent: bool
+    interpolation: float
+
     def __init__(self, samples=None, ratio=None, probe=None,
                  name=None, coherent=False, interpolation=0, **kw):
         self.samples = samples
@@ -675,7 +683,7 @@ def __init__(self, samples=None, ratio=None, probe=None,
         self._substrate = self.samples[0][0].material
         self._surface = self.samples[0][-1].material
         self._cache = {}
-        self._name = name
+        self.name = name if name is not None else probe.name
 
     def update(self):
         self._cache = {}

From a36a5d333daa9da27a641bd2c6055d00a36efb91 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 17:37:22 -0400
Subject: [PATCH 048/221] don't store inflections as part of state, as they are
 derived from dz etc.

---
 refl1d/mono.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/mono.py b/refl1d/mono.py
index 289673b9..f3a7a510 100644
--- a/refl1d/mono.py
+++ b/refl1d/mono.py
@@ -117,7 +117,7 @@ class FreeInterface(Layer):
     interface: Par
     dz: List[Union[float, Par]]
     dp: List[Union[float, Par]]
-    inflections: List[Any]
+    # inflections: List[Any]
 
     def __init__(self, thickness=0, interface=0,
                  below=None, above=None,

From 2824a8433b7c4d4f5778146663e45f1f6dc6f974 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 17:38:18 -0400
Subject: [PATCH 049/221] fix Material class serialization - need to store
 input formula

---
 refl1d/material.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/refl1d/material.py b/refl1d/material.py
index 7e2dc0e8..3389a2d5 100644
--- a/refl1d/material.py
+++ b/refl1d/material.py
@@ -219,7 +219,7 @@ class Material(Scatterer):
     formula_natural_density: Union[float, Literal[None]]
     density: Parameter
     value: Parameter
-    fitby: Union[Literal['bulk_density', 'number_density', 'natural_density', 'relative_density', 'cell_volume']] = 'bulk_density'
+    fitby: Literal['bulk_density', 'number_density', 'natural_density', 'relative_density', 'cell_volume'] = 'bulk_density'
     use_incoherent: bool = False
 
     def __init__(self, formula=None, name=None, use_incoherent=False,
@@ -229,6 +229,7 @@ def __init__(self, formula=None, name=None, use_incoherent=False,
                                              natural_density=formula_natural_density)
         self.formula_density = formula_density
         self.formula_natural_density = formula_natural_density
+        self.formula = formula
         self.name = name if name is not None else str(self._formula)
         self.density = Parameter(name=self.name + " density")
 

From 8c95a69535b328d3bb90c7093d5fa026fe484a9d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 5 Oct 2022 17:39:52 -0400
Subject: [PATCH 050/221] minor cleanup on web components

---
 refl1d-web-gui/src/App.vue                 | 2 +-
 refl1d-web-gui/src/components/DataView.vue | 2 --
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index fabdfc6a..c65cddbb 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
 import { onMounted, ref } from 'vue';
-import { io, Socket } from 'socket.io-client';
+import { io } from 'socket.io-client';
 import FitOptions from './components/FitOptions.vue';
 import DataView from './components/DataView.vue';
 import ModelView from './components/ModelView.vue';
diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index c4267323..f91ba7cd 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -62,8 +62,6 @@ function fetch_and_draw() {
     else {
       plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
     }
-    // console.log(plot.value);
-    // mpld3.draw_figure("plot_div", payload);
   });
 }
 

From c22ece85f58c83d23951f0cec0d9d7cfb78c5c55 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 6 Oct 2022 15:05:37 -0400
Subject: [PATCH 051/221] add mime type hints to files to be served as static

---
 refl1d/webserver.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 57ada8ec..96989a9a 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -10,6 +10,15 @@
 import json
 from copy import deepcopy
 
+import mimetypes
+mimetypes.add_type("text/css", ".css")
+mimetypes.add_type("text/html", ".html")
+mimetypes.add_type("application/json", ".json")
+mimetypes.add_type("text/javascript", ".js")
+mimetypes.add_type("text/javascript", ".mjs")
+mimetypes.add_type("image/png", ".png")
+mimetypes.add_type("image/svg+xml", ".svg")
+
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit
 from bumps.serialize import to_dict
 import refl1d.fitproblem, refl1d.probe
@@ -215,7 +224,8 @@ def get_dirlisting(sid: str, pathlist: List[str]):
         if p.is_dir():
             subfolders.append(p.name)
         else:
-            files.append(p.resolve().name)
+            # files.append(p.resolve().name)
+            files.append(p.name)
     return dict(subfolders=subfolders, files=files)
 
 app.on_startup.append(lambda App: publish('', 'fitter_defaults', FITTER_DEFAULTS))

From 96269bd191669cbc6cf324afd0bb1f59f1415d15 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 6 Oct 2022 15:59:14 -0400
Subject: [PATCH 052/221] send local file path to client

---
 refl1d/webserver.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 57ada8ec..0123a366 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -245,4 +245,5 @@ def nice(v, digits=4):
     
 
 if __name__ == '__main__':
-    web.run_app(app)
+    app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
+    web.run_app(app)
\ No newline at end of file

From f216af7706104ea1feb5e2c65f547142dbea0dda Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 6 Oct 2022 16:00:15 -0400
Subject: [PATCH 053/221] retrieve local file path from server, to populate
 file browser

---
 refl1d-web-gui/src/components/FileBrowser.vue | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/components/FileBrowser.vue b/refl1d-web-gui/src/components/FileBrowser.vue
index a302b397..58936ad5 100644
--- a/refl1d-web-gui/src/components/FileBrowser.vue
+++ b/refl1d-web-gui/src/components/FileBrowser.vue
@@ -16,8 +16,8 @@ const emit = defineEmits<{
 
 const dialog = ref<HTMLDivElement>();
 const isOpen = ref(false);
-// const pathlist = ref(["/", "home", "bbm", "dev", "refl1d-modelbuilder"]);
-const pathlist = ref(["/", "Users", "bbm", "dev", "refl1d-modelbuilder"]);
+const pathlist = ref(["/"]);
+// const pathlist = ref(["/", "Users", "bbm", "dev", "refl1d-modelbuilder"]);
 const subdirlist = shallowRef<string[]>([])
 const filelist = shallowRef<string[]>([])
 const chosenFile = ref("");
@@ -25,6 +25,13 @@ const chosenFile = ref("");
 let modal: Modal;
 onMounted(() => {
   modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
+  props.socket.on('local_file_path', () => {
+    props.socket.emit('get_last_message', 'local_file_path', ({message: new_pathlist, timestamp}) => {
+      console.log(new_pathlist);
+      pathlist.value = new_pathlist;
+    });
+  });
+  props.socket.emit('subscribe', 'local_file_path');
 });
 
 function close() {

From 5d9673b1d3471bff2e3cff71109044a8840044bb Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 7 Oct 2022 14:05:13 -0400
Subject: [PATCH 054/221] change event names to be more consistent with
 existing wx gui

---
 refl1d-web-gui/src/App.vue                    |  1 +
 refl1d-web-gui/src/components/DataView.vue    | 13 ++---
 .../src/components/ModelInspect.vue           | 48 +++++++++----------
 refl1d-web-gui/src/components/ModelView.vue   |  2 +-
 refl1d-web-gui/src/components/SummaryView.vue | 21 ++++----
 refl1d/webserver.py                           |  5 +-
 6 files changed, 44 insertions(+), 46 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index c65cddbb..fe12a4b9 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -47,6 +47,7 @@ const socket = io('', {
   // this is mostly here to test what happens on server fail:
   reconnectionAttempts: 10
 });
+
 socket.on('connect', () => {
   console.log(socket.id);
   connected.value = true;
diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index f91ba7cd..ec1e0432 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -14,20 +14,21 @@ const props = defineProps<{
 }>();
 
 onMounted(() => {
-  props.socket.on('plot_update_ready', () => {
-    if (props.visible) {
-      fetch_and_draw();
-    }
+  props.socket.on('update_parameters', () => {
+    fetch_and_draw();
   });
 });
 
 function fetch_and_draw() {
+  if (!props.visible) {
+    return
+  }
   props.socket.emit('get_plot_data', 'linear', async (payload) => {
     if (plot_div.value === null) {
       return
     }
-    let theory_traces: (Plotly.Data & {x: number, y: number})[] = [];
-    let data_traces: (Plotly.Data & {x: number, y: number})[] = [];
+    let theory_traces: (Plotly.Data & { x: number, y: number })[] = [];
+    let data_traces: (Plotly.Data & { x: number, y: number })[] = [];
     for (let model of payload) {
       for (let xs of model) {
         theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
diff --git a/refl1d-web-gui/src/components/ModelInspect.vue b/refl1d-web-gui/src/components/ModelInspect.vue
index 9014b54d..524ab44f 100644
--- a/refl1d-web-gui/src/components/ModelInspect.vue
+++ b/refl1d-web-gui/src/components/ModelInspect.vue
@@ -6,12 +6,12 @@ import type { Socket } from 'socket.io-client';
 
 // from https://github.com/microsoft/TypeScript/issues/1897#issuecomment-1228063688
 type json =
-    | string
-    | number
-    | boolean
-    | null
-    | json[]
-    | { [key: string]: json };
+  | string
+  | number
+  | boolean
+  | null
+  | json[]
+  | { [key: string]: json };
 
 const title = "Model";
 const active_parameter = ref("");
@@ -23,28 +23,26 @@ const props = defineProps<{
 
 const modelJson = ref<json>();
 
-onMounted(() => {
-  props.socket.on('plot_update_ready', fetch_and_draw);
-});
+props.socket.on('update_parameters', fetch_and_draw);
 
 function fetch_and_draw() {
   if (props.visible) {
-      props.socket.emit('get_model', (payload: json) => {
-        const old_model: json = modelJson.value as Record<string, any>;
-        const new_model: json = payload as Record<string, any>;
-        const diff = getDiff(old_model, new_model);
-        for (let [path, oldval, newval] of diff.edited) {
-          const {target, parent, key} = resolve_diffpath(old_model, path);
-          // trigger reactive update;
-          if (typeof(key) === 'number' && Array.isArray(parent)) {
-            parent.splice(key, 1, newval);
-          }
-          else {
-            parent[key] = newval;
-          }
+    props.socket.emit('get_model', (payload: json) => {
+      const old_model: json = modelJson.value as Record<string, any>;
+      const new_model: json = payload as Record<string, any>;
+      const diff = getDiff(old_model, new_model);
+      for (let [path, oldval, newval] of diff.edited) {
+        const { target, parent, key } = resolve_diffpath(old_model, path);
+        // trigger reactive update;
+        if (typeof (key) === 'number' && Array.isArray(parent)) {
+          parent.splice(key, 1, newval);
+        }
+        else {
+          parent[key] = newval;
         }
-      });
-    }
+      }
+    });
+  }
 }
 
 watch(() => props.visible, (value) => {
@@ -86,7 +84,7 @@ function resolve_diffpath(o: object, diffpath: string) {
     key = (array_path) ? Number(array_path[1]) : pathitem;
     target = target[key];
   }
-  return {target, parent, key};
+  return { target, parent, key };
 }
 
 </script>
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index 08442d54..e71ecfd5 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -15,7 +15,7 @@ const props = defineProps<{
 }>();
 
 onMounted(() => {
-  props.socket.on('plot_update_ready', ({ message, timestamp }) => {
+  props.socket.on('update_parameters', ({ message, timestamp }) => {
     if (props.visible) {
       draw_requested.value = true;
     }
diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index d89a0f32..87261c80 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -24,18 +24,20 @@ const parameters_local01 = ref<number[]>([]);
 const parameters_localstr = ref<string[]>([]);
 
 onMounted(() => {
-  props.socket.on('plot_update_ready', () => {
-    if (props.visible) {
-      fetch_and_draw();
-    }
+  props.socket.on('update_parameters', () => {
+    fetch_and_draw();
   });
 });
 
 function fetch_and_draw() {
+  if (!props.visible) {
+    // do nothing if not visible
+    return
+  }
   props.socket.emit('get_parameters', (payload: parameter_info[]) => {
     // console.log(payload);
     const pv = parameters.value;
-    payload.forEach((p,i) => {
+    payload.forEach((p, i) => {
       parameters_localstr.value[i] = p.value_str;
       if (!(pv[i]?.active)) {
         pv.splice(i, 1, p);
@@ -54,14 +56,11 @@ function onMove(param_index) {
 
 async function onInactive(param) {
   param.active = false;
-  console.log("change");
   fetch_and_draw();
 }
 
 watch(() => props.visible, (value) => {
-  if (value) {
-    fetch_and_draw();
-  }
+  fetch_and_draw();
 });
 
 </script>
@@ -83,9 +82,7 @@ watch(() => props.visible, (value) => {
       <div class="col-2 border-bottom">{{param.name}}</div>
       <div class="col-5">
         <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="parameters_local01[index]"
-        @mousedown="param.active=true"
-        @input="onMove(index)"
-        @change="onInactive(param)"/>
+          @mousedown="param.active=true" @input="onMove(index)" @change="onInactive(param)" />
       </div>
       <div class="col-5">
         <div class="row">
diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 9a26d82f..a683b775 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -86,7 +86,8 @@ async def load_model_file(sid: str, pathlist: List[str], filename: str):
     from bumps.cli import load_model
     path = Path(*pathlist, filename)
     app["problem"]["fitProblem"] = load_model(str(path))
-    await sio.emit("plot_update_ready", True)
+    await sio.emit("update_model", True)
+    await sio.emit("update_parameters", True)
 
 def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
     fresnel_calculator = probe.fresnel(substrate, surface)
@@ -187,7 +188,7 @@ async def set_parameter01(sid: str, parameter_name: str, parameter_value01: floa
     nice_new_value = nice(new_value, digits=VALUE_PRECISION)
     parameter.value = nice_new_value
     fitProblem.model_update()
-    await sio.emit("plot_update_ready", True)
+    await sio.emit("update_parameters", True)
     return new_value
 
 @sio.event

From a3f266b5e44938bab177fb474d6993cb81783807 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 7 Oct 2022 16:29:00 -0400
Subject: [PATCH 055/221] include intensity and background in probe plottable
 data, for calculating Q4 view

---
 refl1d/webserver.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index a683b775..9230b1af 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -98,7 +98,7 @@ def get_single_probe_data(theory, probe, substrate=None, surface=None, label='')
         # Saving interpolated data
         output = dict(Q = Q, theory = R, fresnel=np.interp(Q, probe.Q, FQ))
     elif getattr(probe, 'R', None) is not None:
-        output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, theory = R, fresnel = FQ)
+        output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, theory = R, fresnel = FQ, background=probe.background.value, intensity=probe.intensity.value)
     else:
         output = dict(Q = probe.Q, dQ = probe.dQ, theory = R, fresnel = FQ)
     output['label'] = label

From 645d763d6515f59f05a411e815781e80c583cc3b Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 7 Oct 2022 16:29:34 -0400
Subject: [PATCH 056/221] move reflectivity plot types to DataView, and
 implement view switcher

---
 refl1d-web-gui/src/App.vue                 |  16 ---
 refl1d-web-gui/src/components/DataView.vue | 107 ++++++++++++++++++---
 2 files changed, 92 insertions(+), 31 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index fe12a4b9..fa3e67be 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -11,17 +11,6 @@ import SummaryView from './components/SummaryView.vue';
 import ModelInspect from './components/ModelInspect.vue';
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
 
-const REFLECTIVITY_PLOTS = [
-  "Fresnel",
-  "Log Fresnel",
-  "Linear",
-  "Log",
-  "Q4",
-  "SA"
-] as const;
-type ReflectivityPlotEnum = typeof REFLECTIVITY_PLOTS;
-type ReflectivityPlot = ReflectivityPlotEnum[number];
-
 const panels = [
   {title: 'Reflectivity', component: DataView},
   {title: 'Parameters', component: SummaryView},
@@ -29,17 +18,12 @@ const panels = [
   {title: 'Model', component: ModelInspect}
 ];
 
-const reflectivity_type = ref<ReflectivityPlot>("Linear");
 const connected = ref(false);
 const menuToggle = ref<HTMLButtonElement>();
 const fitOptions = ref<typeof FitOptions>();
 const fileBrowser = ref<typeof FileBrowser>();
 const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
 
-function set_reflectivity(refl_type: ReflectivityPlot) {
-  reflectivity_type.value = refl_type;
-}
-
 // Create a SocketIO connection, to be passed to child components
 // so that they can do their own communications with the host.
 
diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index ec1e0432..fdb8ab7d 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -6,6 +6,7 @@ import type { Socket } from 'socket.io-client';
 
 const title = "Reflectivity";
 const plot_div = ref<HTMLDivElement | null>(null);
+const draw_requested = ref(true);
 const plot = ref<Plotly.PlotlyHTMLElement>();
 
 const props = defineProps<{
@@ -13,12 +14,70 @@ const props = defineProps<{
   visible: boolean
 }>();
 
+const REFLECTIVITY_PLOTS = [
+  "Fresnel",
+  "Log Fresnel",
+  "Linear",
+  "Log",
+  "Q4",
+  "SA"
+] as const;
+type ReflectivityPlotEnum = typeof REFLECTIVITY_PLOTS;
+type ReflectivityPlot = ReflectivityPlotEnum[number];
+const reflectivity_type = ref<ReflectivityPlot>("Log");
+
+
 onMounted(() => {
   props.socket.on('update_parameters', () => {
-    fetch_and_draw();
+    draw_requested.value = true;
   });
+  window.requestAnimationFrame(draw_if_needed);
 });
 
+function generate_new_traces(model_data, view: ReflectivityPlot) {
+  let theory_traces: (Plotly.Data & { x: number, y: number })[] = [];
+  let data_traces: (Plotly.Data & { x: number, y: number })[] = [];
+  switch (view) {
+    case "Log":
+    case "Linear": {
+      for (let model of model_data) {
+        for (let xs of model) {
+          theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
+          data_traces.push({ x: xs.Q, y: xs.R, /*error_y: {type: 'data', array: xs.dR, visible: true},*/ mode: 'markers', name: xs.label + ' data' });
+        }
+      }
+      break;
+    }
+    case "Log Fresnel":
+    case "Fresnel": {
+      for (let model of model_data) {
+        for (let xs of model) {
+          const theory = xs.theory.map((y, i) => (y / (xs.fresnel[i])));
+          const R = xs.R.map((y, i) => (y / (xs.fresnel[i])));
+          theory_traces.push({ x: xs.Q, y: theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
+          data_traces.push({ x: xs.Q, y: R, mode: 'markers', name: xs.label + ' data' });
+        }
+      }
+      break;
+    }
+    case "Q4": {
+      // Q4 = 1e-8*Q**-4*self.intensity.value + self.background.value
+      for (let model of model_data) {
+        for (let xs of model) {
+          const {intensity, background} = xs;
+          const Q4 = xs.Q.map((qq) => (1e-8*Math.pow(qq, -4)*intensity + background));
+          const theory = xs.theory.map((t, i) => (t / Q4[i]));
+          const R = xs.R.map((r, i) => (r / Q4[i]));
+          theory_traces.push({ x: xs.Q, y: theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
+          data_traces.push({ x: xs.Q, y: R, mode: 'markers', name: xs.label + ' data' });
+        }
+      }
+      break;
+    }
+  }
+  return {theory_traces, data_traces};
+}
+
 function fetch_and_draw() {
   if (!props.visible) {
     return
@@ -27,14 +86,16 @@ function fetch_and_draw() {
     if (plot_div.value === null) {
       return
     }
-    let theory_traces: (Plotly.Data & { x: number, y: number })[] = [];
-    let data_traces: (Plotly.Data & { x: number, y: number })[] = [];
-    for (let model of payload) {
-      for (let xs of model) {
-        theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
-        data_traces.push({ x: xs.Q, y: xs.R, mode: 'markers', name: xs.label + ' data' });
-      }
-    }
+    // console.log(payload);
+    const { theory_traces, data_traces } = generate_new_traces(payload, reflectivity_type.value)
+    // let theory_traces: (Plotly.Data & { x: number, y: number })[] = [];
+    // let data_traces: (Plotly.Data & { x: number, y: number })[] = [];
+    // for (let model of payload) {
+    //   for (let xs of model.data) {
+    //     theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
+    //     data_traces.push({ x: xs.Q, y: xs.R, mode: 'markers', name: xs.label + ' data' });
+    //   }
+    // }
 
     const layout: Partial<Plotly.Layout> = {
       xaxis: {
@@ -42,22 +103,27 @@ function fetch_and_draw() {
           text: '$Q (Å^{-1})$'
         },
         type: 'linear',
-        autorange: true
+        // autorange: true
       },
       yaxis: {
         title: { text: 'Reflectivity' },
         exponentformat: 'e',
         showexponent: 'all',
+        // type: (/^(Log|Q4)/.test(reflectivity_type.value)) ? 'log' : 'linear',
         type: 'log',
-        autorange: true
+        // autorange: true
       },
     };
 
     if (plot.value !== undefined) {
+      console.log('update');
       const trace_updates = {
         x: [...theory_traces.map((t) => t.x), ...data_traces.map((t) => t.x)],
         y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],
       }
+      // if (["Log", "Linear"].includes(reflectivity_type.value)) {
+      //   trace_updates.error_y = [...theory_traces.map((t) => null), ...data_traces.map((t) => t.error_y.array)]
+      // }
       await Plotly.update(plot_div.value, trace_updates, layout);
     }
     else {
@@ -66,16 +132,27 @@ function fetch_and_draw() {
   });
 }
 
-watch(() => props.visible, (value) => {
-  if (value) {
+function draw_if_needed(timestamp: number) {
+  if (draw_requested.value && props.visible) {
     fetch_and_draw();
+    draw_requested.value = false;
   }
-});
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+// watch(() => props.visible, (value) => {
+//   if (value) {
+//     fetch_and_draw();
+//   }
+// });
 
 </script>
 
 <template>
-  <div class="container d-flex flex-grow-1">
+  <div class="container d-flex flex-column flex-grow-1">
+    <select v-model="reflectivity_type" @change="fetch_and_draw">
+      <option v-for="refl_type in REFLECTIVITY_PLOTS" :key="refl_type" :value="refl_type">{{refl_type}}</option>
+    </select>
     <div class="flex-grow-1" ref="plot_div" id="plot_div">
 
     </div>

From adb73e45c1f1989f0c81069f786a2c9c41ca3e6a Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 7 Oct 2022 16:52:38 -0400
Subject: [PATCH 057/221] add TODO for generating view plots in python

---
 refl1d/webserver.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 9230b1af..b9532412 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -116,6 +116,8 @@ def get_probe_data(theory, probe, substrate=None, surface=None):
 
 @sio.event
 def get_plot_data(sid: str, view: str = 'linear'):
+    # TODO: implement view-dependent return instead of doing this in JS
+    # (calculate x,y,dy.dx for given view, excluding log)
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     result = []
     for model in fitProblem.models:

From 7b197fdd45be428603f3f9f97625fad195fdfc49 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Fri, 7 Oct 2022 16:53:15 -0400
Subject: [PATCH 058/221] simplify plotly plotting to use just Plotly.react,
 and add uirevision to persist zoom level between parameter updates

---
 refl1d-web-gui/src/components/DataView.vue    | 34 ++++---------------
 refl1d-web-gui/src/components/FileBrowser.vue |  1 -
 2 files changed, 7 insertions(+), 28 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index fdb8ab7d..82768ea5 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -43,7 +43,7 @@ function generate_new_traces(model_data, view: ReflectivityPlot) {
       for (let model of model_data) {
         for (let xs of model) {
           theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
-          data_traces.push({ x: xs.Q, y: xs.R, /*error_y: {type: 'data', array: xs.dR, visible: true},*/ mode: 'markers', name: xs.label + ' data' });
+          data_traces.push({ x: xs.Q, y: xs.R, error_y: {type: 'data', array: xs.dR, visible: true}, mode: 'markers', name: xs.label + ' data' });
         }
       }
       break;
@@ -88,47 +88,27 @@ function fetch_and_draw() {
     }
     // console.log(payload);
     const { theory_traces, data_traces } = generate_new_traces(payload, reflectivity_type.value)
-    // let theory_traces: (Plotly.Data & { x: number, y: number })[] = [];
-    // let data_traces: (Plotly.Data & { x: number, y: number })[] = [];
-    // for (let model of payload) {
-    //   for (let xs of model.data) {
-    //     theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
-    //     data_traces.push({ x: xs.Q, y: xs.R, mode: 'markers', name: xs.label + ' data' });
-    //   }
-    // }
 
     const layout: Partial<Plotly.Layout> = {
+      uirevision: reflectivity_type.value,
       xaxis: {
         title: {
           text: '$Q (Å^{-1})$'
         },
         type: 'linear',
-        // autorange: true
+        autorange: true,
       },
       yaxis: {
         title: { text: 'Reflectivity' },
         exponentformat: 'e',
         showexponent: 'all',
-        // type: (/^(Log|Q4)/.test(reflectivity_type.value)) ? 'log' : 'linear',
-        type: 'log',
-        // autorange: true
+        type: (/^(Log|Q4)/.test(reflectivity_type.value)) ? 'log' : 'linear',
+        autorange: true,
       },
     };
 
-    if (plot.value !== undefined) {
-      console.log('update');
-      const trace_updates = {
-        x: [...theory_traces.map((t) => t.x), ...data_traces.map((t) => t.x)],
-        y: [...theory_traces.map((t) => t.y), ...data_traces.map((t) => t.y)],
-      }
-      // if (["Log", "Linear"].includes(reflectivity_type.value)) {
-      //   trace_updates.error_y = [...theory_traces.map((t) => null), ...data_traces.map((t) => t.error_y.array)]
-      // }
-      await Plotly.update(plot_div.value, trace_updates, layout);
-    }
-    else {
-      plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
-    }
+    plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
+    
   });
 }
 
diff --git a/refl1d-web-gui/src/components/FileBrowser.vue b/refl1d-web-gui/src/components/FileBrowser.vue
index 58936ad5..690ebdb1 100644
--- a/refl1d-web-gui/src/components/FileBrowser.vue
+++ b/refl1d-web-gui/src/components/FileBrowser.vue
@@ -27,7 +27,6 @@ onMounted(() => {
   modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
   props.socket.on('local_file_path', () => {
     props.socket.emit('get_last_message', 'local_file_path', ({message: new_pathlist, timestamp}) => {
-      console.log(new_pathlist);
       pathlist.value = new_pathlist;
     });
   });

From 54ff8e9197e5b06ef6ac25155c31c831a3014303 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 11 Oct 2022 13:01:50 -0400
Subject: [PATCH 059/221] add REST GET endpoints for other clients, and
 refactor message bus

Store last message for all topics, and send to client on new connection.
---
 refl1d/webserver.py | 106 +++++++++++++++++++++-----------------------
 1 file changed, 50 insertions(+), 56 deletions(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index b9532412..b7ae4f22 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -1,6 +1,6 @@
 # from .main import setup_bumps
 
-from typing import Any, Dict, List
+from typing import Dict, List, Optional, Union
 from datetime import datetime
 from aiohttp import web
 import numpy as np
@@ -31,47 +31,31 @@
         "settings": dict(fitter.settings)
     }
 
-# set up mutable state of fitters:
-# fitter_settings = deepcopy(FITTER_DEFAULTS)
-# active_fitter = "amoeba"
 
+routes = web.RouteTableDef()
 # sio = socketio.AsyncServer(cors_allowed_origins="*", serializer='msgpack')
 sio = socketio.AsyncServer(cors_allowed_origins="*")
 app = web.Application()
 static_dir_path = Path(__file__).parent / 'webview'
 sio.attach(app)
 
-# class TopicManager:
-#     topics: Dict[str, Any] = {}
-
-#     def subscribe(self, sid: str, topic: str):
-#         sio.enter_room(sid, topic)
-
-#     def unsubscribe(self, sid: str, topic: str):
-#         sio.leave_room(sid, topic)
-
-#     def get(self, topic: str):
-#         return self.topics.get(topic, None)
-
-#     async def publish(self, topic: str, message):
-#         timestamp = datetime.now().timestamp()
-#         self.topics[topic] = {"message": message, "timestamp": timestamp}
-#         await sio.emit("message-available", timestamp, room=topic)
-
-# topicManager = TopicManager()
-
-# use context storage: within the aiohttp app, see 
-# class TopicData(TypedDict):
-#     message: Any
-#     timestamp: float
-
-# topic_buffers: Dict[str, TopicData] = {}
-
 topics: Dict[str, Dict] = {}
 app["topics"] = topics
 app["problem"] = {"fitProblem": None, "filepath": None}
 problem = None
 
+def rest_get(fn):
+    """
+    Add a REST (GET) route for the function, which can also be used for 
+    """
+    @routes.get(f"/{fn.__name__}")
+    async def handler(request: web.Request):
+        result = await fn(**request.query)
+        return web.json_response(result)
+    
+    # pass the function to the next decorator unchanged...
+    return fn
+
 async def index(request):
     """Serve the client-side application."""
     # redirect to static built site:
@@ -79,6 +63,9 @@ async def index(request):
     
 @sio.event
 async def connect(sid, environ, data=None):
+    # re-send last message for all topics
+    for topic, contents in topics.items():
+        await sio.emit(topic, contents, to=sid)
     print("connect ", sid)
 
 @sio.event
@@ -86,13 +73,14 @@ async def load_model_file(sid: str, pathlist: List[str], filename: str):
     from bumps.cli import load_model
     path = Path(*pathlist, filename)
     app["problem"]["fitProblem"] = load_model(str(path))
-    await sio.emit("update_model", True)
-    await sio.emit("update_parameters", True)
+    await publish("", "update_model", True)
+    await publish("", "update_parameters", True)
 
 def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
     fresnel_calculator = probe.fresnel(substrate, surface)
     Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
     Q, R = theory
+    output: Dict[str, Union[str, np.ndarray]]
     assert isinstance(FQ, np.ndarray)
     if len(Q) != len(probe.Q):
         # Saving interpolated data
@@ -115,7 +103,8 @@ def get_probe_data(theory, probe, substrate=None, surface=None):
         return [get_single_probe_data(theory, probe, substrate, surface)]
 
 @sio.event
-def get_plot_data(sid: str, view: str = 'linear'):
+@rest_get
+async def get_plot_data(sid: str="", view: str = 'linear'):
     # TODO: implement view-dependent return instead of doing this in JS
     # (calculate x,y,dy.dx for given view, excluding log)
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
@@ -139,18 +128,22 @@ def get_plot_data(sid: str, view: str = 'linear'):
     return to_dict(result)
 
 @sio.event
-async def get_model(sid: str):
+@rest_get
+async def get_model(sid: str=""):
     from bumps.serialize import to_dict
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     return to_dict(fitProblem)
 
 @sio.event
-async def get_profile_plot(sid: str):
+@rest_get
+async def get_profile_plot(sid: str=""):
     import mpld3
     import matplotlib.pyplot as plt
     import time
     print('queueing new profile plot...', time.time())
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if fitProblem is None:
+        return None
     fig = plt.figure()
     for model in iter(fitProblem.models):
         model.plot_profile()
@@ -160,7 +153,8 @@ async def get_profile_plot(sid: str):
     return dfig
 
 @sio.event
-def get_parameters(sid: str):
+@rest_get
+async def get_parameters(sid: str = ""):
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     if fitProblem is None:
         return []
@@ -190,37 +184,35 @@ async def set_parameter01(sid: str, parameter_name: str, parameter_value01: floa
     nice_new_value = nice(new_value, digits=VALUE_PRECISION)
     parameter.value = nice_new_value
     fitProblem.model_update()
-    await sio.emit("update_parameters", True)
+    await publish("", "update_parameters", True)
     return new_value
 
-@sio.event
-async def subscribe(sid: str, topic: str):
-    sio.enter_room(sid, topic)
-    last_timestamp = topics.get(topic, {}).get("timestamp", None)
-    if last_timestamp is not None:
-        await sio.emit(topic, last_timestamp, to=sid)
-
-@sio.event
-def unsubscribe(sid: str, topic: str):
-    sio.leave_room(sid, topic)
-
 @sio.event
 async def publish(sid: str, topic: str, message):
-    timestamp = datetime.now().timestamp()
-    topics[topic] = {"message": message, "timestamp": f"{timestamp:.6f}"}
-    await sio.emit(topic, timestamp, room=topic)
+    timestamp_str = f"{datetime.now().timestamp():.6f}"
+    contents = {"message": message, "timestamp": timestamp_str}
+    topics[topic] = contents
+    await sio.emit(topic, contents)
 
 @sio.event
-def get_last_message(sid: str, topic: str):
+@rest_get
+async def get_last_message(sid: str="", topic: str=""):
     # this is a GET request in disguise -
     # emitter must handle the response in a callback,
     # as no separate response event is emitted.  
     return topics.get(topic, {})
 
+@rest_get
+async def get_all_messages():
+    return topics
+
 @sio.event
-def get_dirlisting(sid: str, pathlist: List[str]):
+@rest_get
+async def get_dirlisting(sid: str="", pathlist: Optional[List[str]]=None):
     # GET request
     # TODO: use psutil to get disk listing as well?
+    if pathlist is None:
+        pathlist = []
     subfolders = []
     files = []
     for p in Path(*pathlist).iterdir():
@@ -231,9 +223,10 @@ def get_dirlisting(sid: str, pathlist: List[str]):
             files.append(p.name)
     return dict(subfolders=subfolders, files=files)
 
-app.on_startup.append(lambda App: publish('', 'fitter_defaults', FITTER_DEFAULTS))
-app.on_startup.append(lambda App: publish('', 'fitter_settings', deepcopy(FITTER_DEFAULTS)))
-app.on_startup.append(lambda App: publish('', 'fitter_active', 'amoeba'))
+@sio.event
+@rest_get
+async def get_fitter_defaults(sid: str=""):
+    return FITTER_DEFAULTS
 
 @sio.event
 def disconnect(sid):
@@ -259,4 +252,5 @@ def nice(v, digits=4):
 
 if __name__ == '__main__':
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
+    app.add_routes(routes)
     web.run_app(app)
\ No newline at end of file

From 53c7df5ac7f5ec51b5b89aaa1da3692e6b2d20ee Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 11 Oct 2022 13:02:29 -0400
Subject: [PATCH 060/221] use new topics bus (sending most messages directly
 instead of empty signal)

---
 refl1d-web-gui/src/components/FileBrowser.vue | 13 ++++----
 refl1d-web-gui/src/components/FitOptions.vue  | 32 ++++++++-----------
 refl1d-web-gui/src/components/ModelView.vue   | 23 ++++++-------
 refl1d-web-gui/src/components/SummaryView.vue |  5 +--
 4 files changed, 32 insertions(+), 41 deletions(-)

diff --git a/refl1d-web-gui/src/components/FileBrowser.vue b/refl1d-web-gui/src/components/FileBrowser.vue
index 690ebdb1..478f0f94 100644
--- a/refl1d-web-gui/src/components/FileBrowser.vue
+++ b/refl1d-web-gui/src/components/FileBrowser.vue
@@ -22,15 +22,13 @@ const subdirlist = shallowRef<string[]>([])
 const filelist = shallowRef<string[]>([])
 const chosenFile = ref("");
 
+props.socket.on('local_file_path', ({message: new_pathlist, timestamp}) => {
+  pathlist.value = new_pathlist;
+})
+
 let modal: Modal;
 onMounted(() => {
   modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
-  props.socket.on('local_file_path', () => {
-    props.socket.emit('get_last_message', 'local_file_path', ({message: new_pathlist, timestamp}) => {
-      pathlist.value = new_pathlist;
-    });
-  });
-  props.socket.emit('subscribe', 'local_file_path');
 });
 
 function close() {
@@ -105,7 +103,8 @@ defineExpose({
             <h3>Files:</h3>
             <div class="row row-cols-3">
               <div class="btn col overflow-hidden border" :class="{'btn-warning': filename === chosenFile}"
-                v-for="filename in filelist" :key="filename" @click="chosenFile = filename" @dblclick="chosenFile=filename;chooseFile()">
+                v-for="filename in filelist" :key="filename" @click="chosenFile = filename"
+                @dblclick="chosenFile=filename;chooseFile()">
                 {{filename}}
               </div>
             </div>
diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
index f7296865..60e5f8dc 100644
--- a/refl1d-web-gui/src/components/FitOptions.vue
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -39,25 +39,18 @@ const FIT_FIELDS = {
 // const active_settings = ref<{ name: string, settings: object}>({name: "", settings: {}});
 const active_settings = ref({});
 
-props.socket.on('fitter_settings', () => {
-  props.socket.emit('get_last_message', 'fitter_settings', (payload) => {
-    fitter_settings.value = payload?.message;
-  });
-});
-props.socket.on('fitter_defaults', () => {
-  props.socket.emit('get_last_message', 'fitter_defaults', (payload) => {
-    fitter_defaults.value = payload?.message;
-  });
-});
-props.socket.on('fitter_active', () => {
-  props.socket.emit('get_last_message', 'fitter_active', (payload) => {
-    fitter_active.value = payload?.message;
-  });
+props.socket.emit("get_fitter_defaults", (new_fitter_defaults) => {
+  fitter_defaults.value = new_fitter_defaults;
+  fitter_settings.value = structuredClone(new_fitter_defaults);
+})
+
+props.socket.on('fitter_settings', ({timestamp, message: new_fitter_settings}) => {
+    fitter_settings.value = new_fitter_settings
 });
 
-props.socket.emit('subscribe', 'fitter_settings');
-props.socket.emit('subscribe', 'fitter_defaults');
-props.socket.emit('subscribe', 'fitter_active');
+props.socket.on('fitter_active', ({timestamp, message: new_fitter_active}) => {
+    fitter_active.value = new_fitter_active
+});
 
 let modal: Modal;
 
@@ -102,6 +95,9 @@ function process_settings() {
 }
 
 function save() {
+  if (anyIsInvalid.value) {
+    return;
+  }
   const new_settings = structuredClone(fitter_settings.value);
   new_settings[fitter_active_local.value] = { settings: process_settings() };
   props.socket.emit("publish", "fitter_settings", new_settings);
@@ -180,7 +176,7 @@ defineExpose({
                   <input v-else-if="FIT_FIELDS[sname][1]==='boolean'" class="form-check-input m-2" type="checkbox"
                     v-model="active_settings[sname]" />
                   <input v-else :class="{'form-control': true, 'is-invalid': !validate(active_settings[sname], sname)}"
-                    type="text" v-model="active_settings[sname]" />
+                    type="text" v-model="active_settings[sname]" @keydown.enter="save" />
                 </div>
               </div>
             </div>
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index e71ecfd5..5e51dd0b 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -15,10 +15,8 @@ const props = defineProps<{
 }>();
 
 onMounted(() => {
-  props.socket.on('update_parameters', ({ message, timestamp }) => {
-    if (props.visible) {
-      draw_requested.value = true;
-    }
+  props.socket.on('update_parameters', () => {
+    draw_requested.value = true;
   });
   window.requestAnimationFrame(draw_if_needed);
 });
@@ -27,11 +25,8 @@ function fetch_and_draw() {
   props.socket.emit('get_profile_plot', (payload) => {
     if (props.visible) {
       let plotdata = { ...payload };
-      console.log(plotdata, plot_div.value);
       plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
       plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      // delete payload.width;
-      // delete payload.height;
       /* Data Parsing Functions */
       // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
       mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
@@ -40,19 +35,19 @@ function fetch_and_draw() {
 }
 
 function draw_if_needed(timestamp: number) {
-  if (draw_requested.value) {
+  if (draw_requested.value && props.visible) {
     fetch_and_draw();
     draw_requested.value = false;
   }
   window.requestAnimationFrame(draw_if_needed);
 }
 
-watch(() => props.visible, (value) => {
-  if (value) {
-    console.log('visible', value);
-    fetch_and_draw();
-  }
-});
+// watch(() => props.visible, (value) => {
+//   if (value) {
+//     console.log('visible', value);
+//     fetch_and_draw();
+//   }
+// });
 
 </script>
     
diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index 87261c80..cf3efa71 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -50,8 +50,9 @@ function fetch_and_draw() {
   });
 }
 
-function onMove(param_index) {
-  props.socket.volatile.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
+async function onMove(param_index) {
+  // props.socket.volatile.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
+  props.socket.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
 }
 
 async function onInactive(param) {

From b933046d061059f2799fc5efae601e29aea84e5b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 11 Oct 2022 13:21:52 -0400
Subject: [PATCH 061/221] implement model reload (and add to menu)

---
 refl1d-web-gui/src/App.vue | 15 ++++++++++++++-
 refl1d/webserver.py        |  1 +
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index fa3e67be..c7f98123 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
-import { onMounted, ref } from 'vue';
+import { onMounted, ref, shallowRef } from 'vue';
 import { io } from 'socket.io-client';
 import FitOptions from './components/FitOptions.vue';
 import DataView from './components/DataView.vue';
@@ -23,6 +23,7 @@ const menuToggle = ref<HTMLButtonElement>();
 const fitOptions = ref<typeof FitOptions>();
 const fileBrowser = ref<typeof FileBrowser>();
 const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
+const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
 
 // Create a SocketIO connection, to be passed to child components
 // so that they can do their own communications with the host.
@@ -42,6 +43,10 @@ socket.on('disconnect', (payload) => {
   // connected.value = false;
 })
 
+socket.on('model_loaded', ({message: {pathlist, filename}}) => {
+  model_loaded.value = {pathlist, filename};
+})
+
 function disconnect() {
   socket.disconnect();
   connected.value = false;
@@ -62,6 +67,13 @@ function selectOpenFile() {
   // file_picker.value?.click();
 }
 
+function reloadModel() {
+  if (model_loaded.value) {
+    const {pathlist, filename} = model_loaded.value;
+    socket.emit("load_model_file", pathlist, filename);
+  }
+}
+
 function openFitOptions() {
   fitOptions.value?.open();
 }
@@ -106,6 +118,7 @@ onMounted(() => {
               <ul class="dropdown-menu">
                 <li><a class="dropdown-item" href="#" @click="selectOpenFile">Open</a></li>
                 <li><a class="dropdown-item" href="#">Save</a></li>
+                <li><a class="dropdown-item" :class="{disabled: model_loaded === undefined}" href="#" @click="reloadModel">Reload</a></li>
                 <li>
                   <hr class="dropdown-divider">
                 </li>
diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index b7ae4f22..c63392a4 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -73,6 +73,7 @@ async def load_model_file(sid: str, pathlist: List[str], filename: str):
     from bumps.cli import load_model
     path = Path(*pathlist, filename)
     app["problem"]["fitProblem"] = load_model(str(path))
+    await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename})
     await publish("", "update_model", True)
     await publish("", "update_parameters", True)
 

From 8a939827cf219fb9254baf96a532040cab545d9f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 11 Oct 2022 13:56:12 -0400
Subject: [PATCH 062/221] add model selector for profile plot

---
 refl1d-web-gui/src/App.vue                  |  4 ++--
 refl1d-web-gui/src/components/ModelView.vue | 13 +++++++++++--
 refl1d/webserver.py                         | 20 ++++++++++++++------
 3 files changed, 27 insertions(+), 10 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index c7f98123..5c7417c5 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -55,7 +55,7 @@ function disconnect() {
 function selectOpenFile() {
   if (fileBrowser.value) {
     fileBrowserSelectCallback.value = (pathlist, filename) => {
-      socket.emit("load_model_file", pathlist, filename);
+      socket.emit("load_problem_file", pathlist, filename);
     }
     fileBrowser.value.open();
   }
@@ -70,7 +70,7 @@ function selectOpenFile() {
 function reloadModel() {
   if (model_loaded.value) {
     const {pathlist, filename} = model_loaded.value;
-    socket.emit("load_model_file", pathlist, filename);
+    socket.emit("load_problem_file", pathlist, filename);
   }
 }
 
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index 5e51dd0b..a9c09676 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -9,11 +9,17 @@ const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
 const draw_requested = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
+const model_names = ref<string[]>([]);
+const current_model = ref(0);
 const props = defineProps<{
   socket: Socket,
   visible: boolean
 }>();
 
+props.socket.on('model_loaded', ({message: {model_names: new_model_names}}) => {
+  model_names.value = new_model_names;
+});
+
 onMounted(() => {
   props.socket.on('update_parameters', () => {
     draw_requested.value = true;
@@ -22,7 +28,7 @@ onMounted(() => {
 });
 
 function fetch_and_draw() {
-  props.socket.emit('get_profile_plot', (payload) => {
+  props.socket.emit('get_profile_plot', current_model.value, (payload) => {
     if (props.visible) {
       let plotdata = { ...payload };
       plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
@@ -52,7 +58,10 @@ function draw_if_needed(timestamp: number) {
 </script>
     
 <template>
-  <div class="container d-flex flex-grow-1">
+  <div class="container d-flex flex-grow-1 flex-column">
+    <select v-model="current_model" @change="draw_requested=true">
+      <option v-for="(name, index) in model_names" :key="index" :value="index">{{index}}: {{name ?? ""}}</option>
+    </select>
     <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
     </div>
   </div>
diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index c63392a4..5f42187c 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -69,11 +69,16 @@ async def connect(sid, environ, data=None):
     print("connect ", sid)
 
 @sio.event
-async def load_model_file(sid: str, pathlist: List[str], filename: str):
+async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     from bumps.cli import load_model
     path = Path(*pathlist, filename)
-    app["problem"]["fitProblem"] = load_model(str(path))
-    await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename})
+    print('model loading: ', str(path))
+    problem = load_model(str(path))
+    app["problem"]["fitProblem"] = problem
+    print('model loaded: ', str(path))
+
+    model_names = [getattr(m, 'name', None) for m in list(problem.models)]
+    await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename, "model_names": model_names})
     await publish("", "update_model", True)
     await publish("", "update_parameters", True)
 
@@ -137,7 +142,7 @@ async def get_model(sid: str=""):
 
 @sio.event
 @rest_get
-async def get_profile_plot(sid: str=""):
+async def get_profile_plot(sid: str="", model_index: int=0):
     import mpld3
     import matplotlib.pyplot as plt
     import time
@@ -145,9 +150,12 @@ async def get_profile_plot(sid: str=""):
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     if fitProblem is None:
         return None
+    models = list(fitProblem.models)
+    if (model_index > len(models)):
+        return None
     fig = plt.figure()
-    for model in iter(fitProblem.models):
-        model.plot_profile()
+    model = models[model_index]
+    model.plot_profile()
     dfig = mpld3.fig_to_dict(plt.gcf())
     plt.close(fig)
     # await sio.emit("profile_plot", dfig, to=sid)

From 6bcac0f57be67dc82d197df1c1c56e27f08c7bac Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 11 Oct 2022 14:21:34 -0400
Subject: [PATCH 063/221] allow setting initially active tab in
 PanelTabContainer

---
 refl1d-web-gui/src/App.vue                          | 6 +++---
 refl1d-web-gui/src/components/PanelTabContainer.vue | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 5c7417c5..91774d08 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -40,7 +40,7 @@ socket.on('connect', () => {
 
 socket.on('disconnect', (payload) => {
   console.log("disconnected!", payload);
-  // connected.value = false;
+  connected.value = false;
 })
 
 socket.on('model_loaded', ({message: {pathlist, filename}}) => {
@@ -163,10 +163,10 @@ onMounted(() => {
     </nav>
     <div class="flex-grow-1 row">
       <div class="col d-flex flex-column">
-        <PanelTabContainer :panels="panels" :socket="socket" />
+        <PanelTabContainer :panels="panels" :socket="socket" :initially_active="0"/>
       </div>
       <div class="col d-flex flex-column">
-        <PanelTabContainer :panels="panels" :socket="socket" />
+        <PanelTabContainer :panels="panels" :socket="socket" :initially_active="1"/>
       </div>
     </div>
   </div>
diff --git a/refl1d-web-gui/src/components/PanelTabContainer.vue b/refl1d-web-gui/src/components/PanelTabContainer.vue
index 06563338..74069e51 100644
--- a/refl1d-web-gui/src/components/PanelTabContainer.vue
+++ b/refl1d-web-gui/src/components/PanelTabContainer.vue
@@ -13,6 +13,7 @@ const panelVisible = ref<boolean[]>([]);
 const props = defineProps<{
   socket: Socket,
   panels: {title: string, component: unknown}[],
+  initially_active?: number
 }>();
 
 let triggers: Tab[] = [];
@@ -37,7 +38,7 @@ onMounted(() => {
     triggers.push(tabTrigger);
   }
   if (triggers.length > 0) {
-    activateTab(0);
+    activateTab(props.initially_active ?? 0);
   }
 });
 </script>

From 5a894a256f212f017f260a47103b0d7fd993c5d1 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 11 Oct 2022 17:09:56 -0400
Subject: [PATCH 064/221] add function to initiate fit from client

---
 refl1d-web-gui/src/App.vue                   | 12 +++++++++++-
 refl1d-web-gui/src/components/FitOptions.vue |  4 +++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 91774d08..caf7b10d 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -78,6 +78,16 @@ function openFitOptions() {
   fitOptions.value?.open();
 }
 
+function startFit() {
+  const fitter_active = fitOptions.value?.fitter_active;
+  const fitter_settings = fitOptions.value?.fitter_settings;
+
+  if (fitter_active && fitter_settings) {
+    const fit_args = fitter_settings[fitter_active];
+    socket.emit("start_fit", fitter_active, fit_args);
+  }
+}
+
 onMounted(() => {
   const menuToggleButton = new Button(menuToggle.value);
 });
@@ -131,7 +141,7 @@ onMounted(() => {
                 Fitting
               </a>
               <ul class="dropdown-menu">
-                <li><a class="dropdown-item" href="#">Start</a></li>
+                <li><a class="dropdown-item" href="#" @click="startFit">Start</a></li>
                 <li><a class="dropdown-item" href="#">Stop</a></li>
                 <li>
                   <hr class="dropdown-divider">
diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d-web-gui/src/components/FitOptions.vue
index 60e5f8dc..a3b18f53 100644
--- a/refl1d-web-gui/src/components/FitOptions.vue
+++ b/refl1d-web-gui/src/components/FitOptions.vue
@@ -131,7 +131,9 @@ const anyIsInvalid = computed(() => {
 
 defineExpose({
   close,
-  open
+  open,
+  fitter_settings,
+  fitter_active
 })
 </script>
 

From 1d300c4cf36769b63646c7238f0f15011d0b4636 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 26 Oct 2022 11:05:47 -0400
Subject: [PATCH 065/221] add method to get profile data instead of plot, and
 start a fitter

---
 refl1d/webserver.py | 51 +++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 47 insertions(+), 4 deletions(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 5f42187c..49e251a6 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -19,11 +19,14 @@
 mimetypes.add_type("image/png", ".png")
 mimetypes.add_type("image/svg+xml", ".svg")
 
-from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit
+from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit
 from bumps.serialize import to_dict
+from bumps.mapper import MPMapper
 import refl1d.fitproblem, refl1d.probe
 
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
+FITTERS_BY_ID = dict([(fitter.id, fitter) for fitter in FITTERS])
+print(FITTERS_BY_ID)
 FITTER_DEFAULTS = {}
 for fitter in FITTERS:
     FITTER_DEFAULTS[fitter.id] = {
@@ -82,6 +85,18 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     await publish("", "update_model", True)
     await publish("", "update_parameters", True)
 
+@sio.event
+async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
+    kwargs = {} if kwargs is None else kwargs
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    mapper = MPMapper.start_mapper(fitProblem, None, cpus=0)
+    monitors = []
+    fitclass = FITTERS_BY_ID[fitter_id]
+    driver = FitDriver(fitclass=fitclass, mapper=mapper, problem=fitProblem, monitors=monitors, **kwargs)
+    x, fx = driver.fit()
+    driver.show()
+
+
 def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
     fresnel_calculator = probe.fresnel(substrate, surface)
     Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
@@ -144,6 +159,8 @@ async def get_model(sid: str=""):
 @rest_get
 async def get_profile_plot(sid: str="", model_index: int=0):
     import mpld3
+    import matplotlib
+    matplotlib.use("agg")
     import matplotlib.pyplot as plt
     import time
     print('queueing new profile plot...', time.time())
@@ -153,14 +170,40 @@ async def get_profile_plot(sid: str="", model_index: int=0):
     models = list(fitProblem.models)
     if (model_index > len(models)):
         return None
-    fig = plt.figure()
     model = models[model_index]
+    fig = plt.figure()
     model.plot_profile()
-    dfig = mpld3.fig_to_dict(plt.gcf())
+    dfig = mpld3.fig_to_dict(fig)
     plt.close(fig)
     # await sio.emit("profile_plot", dfig, to=sid)
     return dfig
 
+@sio.event
+@rest_get
+async def get_profile_data(sid: str="", model_index: int=0):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if fitProblem is None:
+        return None
+    models = list(fitProblem.models)
+    if (model_index > len(models)):
+        return None
+    model = models[model_index]
+    output = {}
+    output["ismagnetic"] = model.ismagnetic
+    if model.ismagnetic:
+        if not model.step_interfaces:
+            z, rho, irho, rhoM, thetaM = model.magnetic_step_profile()
+            output['step_profile'] = dict(z=z, rho=rho, irho=irho, rhoM=rhoM, thetaM=thetaM)
+        z, rho, irho, rhoM, thetaM = model.magnetic_smooth_profile()
+        output['smooth_profile'] = dict(z=z, rho=rho, irho=irho, rhoM=rhoM, thetaM=thetaM)
+    else:
+        if not model.step_interfaces:
+            z, rho, irho = model.step_profile()
+            output['step_profile'] = dict(z=z, rho=rho, irho=irho)
+        z, rho, irho = model.smooth_profile()
+        output['smooth_profile'] = dict(z=z, rho=rho, irho=irho)
+    return to_dict(output)
+
 @sio.event
 @rest_get
 async def get_parameters(sid: str = ""):
@@ -262,4 +305,4 @@ def nice(v, digits=4):
 if __name__ == '__main__':
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     app.add_routes(routes)
-    web.run_app(app)
\ No newline at end of file
+    web.run_app(app)

From 7aa044f57b037d5eb2f96c5970349a55f3e45258 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 26 Oct 2022 11:06:29 -0400
Subject: [PATCH 066/221] start without plotting because data won't be ready

---
 refl1d-web-gui/src/components/DataView.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index 82768ea5..2c5f2d53 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -6,7 +6,7 @@ import type { Socket } from 'socket.io-client';
 
 const title = "Reflectivity";
 const plot_div = ref<HTMLDivElement | null>(null);
-const draw_requested = ref(true);
+const draw_requested = ref(false);
 const plot = ref<Plotly.PlotlyHTMLElement>();
 
 const props = defineProps<{

From 84855656e3696e923caa3e8a922d9cf2577055ba Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 28 Oct 2022 14:41:11 -0400
Subject: [PATCH 067/221] add drawing busy flag

---
 refl1d-web-gui/src/components/ModelView.vue | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d-web-gui/src/components/ModelView.vue
index a9c09676..b9849345 100644
--- a/refl1d-web-gui/src/components/ModelView.vue
+++ b/refl1d-web-gui/src/components/ModelView.vue
@@ -8,6 +8,7 @@ import mpld3 from 'mpld3';
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
 const draw_requested = ref(false);
+const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const model_names = ref<string[]>([]);
 const current_model = ref(0);
@@ -37,13 +38,18 @@ function fetch_and_draw() {
       // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
       mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
     }
+    drawing_busy.value = false;
   });
 }
 
 function draw_if_needed(timestamp: number) {
-  if (draw_requested.value && props.visible) {
-    fetch_and_draw();
+  if (drawing_busy.value) {
+    console.log("busy!");
+  }
+  if (draw_requested.value && props.visible && !drawing_busy.value) {
+    drawing_busy.value = true;
     draw_requested.value = false;
+    fetch_and_draw();
   }
   window.requestAnimationFrame(draw_if_needed);
 }

From 7a9d509fdfced7939e9180355ff3bbbe78e87e6a Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 31 Oct 2022 14:27:06 -0400
Subject: [PATCH 068/221] update actions

---
 .github/workflows/test.yml     | 8 ++++----
 .github/workflows/unstable.yml | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index dada9105..4fe72062 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -19,10 +19,10 @@ jobs:
           # pure python wheels
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.config.py }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.config.py }}
 
@@ -66,7 +66,7 @@ jobs:
     # See the following for how to upload to a release
     #  https://eugene-babichenko.github.io/blog/2020/05/09/github-actions-cross-platform-auto-releases/
     - name: Archive artifacts
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: artifacts
         path: |
@@ -80,7 +80,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Retrieve all artifacts
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: artifacts
 
diff --git a/.github/workflows/unstable.yml b/.github/workflows/unstable.yml
index 5f8ad970..302d985f 100644
--- a/.github/workflows/unstable.yml
+++ b/.github/workflows/unstable.yml
@@ -20,10 +20,10 @@ jobs:
           # all using to stable abi
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.config.py }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.config.py }}
 
@@ -60,7 +60,7 @@ jobs:
     # See the following for how to upload to a release
     #  https://eugene-babichenko.github.io/blog/2020/05/09/github-actions-cross-platform-auto-releases/
     - name: Archive artifacts
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       with:
         name: artifacts
         path: |
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Retrieve all artifacts
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v3
       with:
         name: artifacts
 

From ffd92c63465b20c370387d48acc81bd54dc28b59 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 31 Oct 2022 14:29:00 -0400
Subject: [PATCH 069/221] add new model view based on profile xy instead of
 matplotlib

---
 refl1d-web-gui/src/App.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index caf7b10d..b54f23d4 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -9,13 +9,15 @@ import PanelTabContainer from './components/PanelTabContainer.vue';
 import FileBrowser from './components/FileBrowser.vue';
 import SummaryView from './components/SummaryView.vue';
 import ModelInspect from './components/ModelInspect.vue';
+import ModelViewPlotly from './components/ModelViewPlotly.vue';
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
 
 const panels = [
   {title: 'Reflectivity', component: DataView},
   {title: 'Parameters', component: SummaryView},
   {title: 'Profile', component: ModelView},
-  {title: 'Model', component: ModelInspect}
+  {title: 'Model', component: ModelInspect},
+  {title: 'Profile2', component: ModelViewPlotly}
 ];
 
 const connected = ref(false);

From 345529d2f1ecc19fe3582e8eed639e37be86a4a2 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 1 Nov 2022 16:42:41 -0400
Subject: [PATCH 070/221] make min, max and value editable in summary view (and
 add scroll interaction to slider)

---
 refl1d-web-gui/src/components/SummaryView.vue | 36 +++++++++++++++----
 refl1d/webserver.py                           | 30 ++++++++++++----
 2 files changed, 53 insertions(+), 13 deletions(-)

diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index cf3efa71..6ed1cc56 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -52,7 +52,27 @@ function fetch_and_draw() {
 
 async function onMove(param_index) {
   // props.socket.volatile.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
-  props.socket.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
+  props.socket.emit('set_parameter', parameters.value[param_index].name, "value01", parameters_local01.value[param_index]);
+}
+
+async function editItem(ev, item_name: "min" | "max" | "value", index: number) {
+  const new_value = ev.target.innerText;
+  if (validate_numeric(new_value)) {
+    props.socket.emit('set_parameter', parameters.value[index].name, item_name, new_value);
+  }
+}
+
+function validate_numeric(value: string, allow_inf: boolean = false) {
+  if (allow_inf && (value === "inf" || value === "-inf")) {
+    return true
+  }
+  return !Number.isNaN(Number(value))
+}
+
+async function scrollParam(ev, index) {
+  const sign = Math.sign(ev.deltaY);
+  parameters_local01.value[index] -= 0.01 * sign;
+  props.socket.emit('set_parameter', parameters.value[index].name, "value01", parameters_local01.value[index]);
 }
 
 async function onInactive(param) {
@@ -80,16 +100,20 @@ watch(() => props.visible, (value) => {
       </div>
     </div>
     <div class="row align-items-center px-1" v-for="(param, index) in parameters" :key="param.name">
-      <div class="col-2 border-bottom">{{param.name}}</div>
+      <div class="col-2 border-bottom">{{ param.name }}</div>
       <div class="col-5">
         <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="parameters_local01[index]"
-          @mousedown="param.active=true" @input="onMove(index)" @change="onInactive(param)" />
+          @mousedown="param.active = true" @input="onMove(index)" @change="onInactive(param)"
+          @wheel="scrollParam($event, index)" />
       </div>
       <div class="col-5">
         <div class="row">
-          <div class="col-4">{{parameters_localstr[index]}}</div>
-          <div class="col-4">{{param.min}}</div>
-          <div class="col-4">{{param.max}}</div>
+          <div class="col-4" contenteditable="true" @blur="editItem($event, 'value', index)"
+            @keydown.enter="$event?.target?.blur()">{{ parameters_localstr[index] }}</div>
+          <div class="col-4" contenteditable="true" @blur="editItem($event, 'min', index)"
+            @keydown.enter="$event?.target?.blur()">{{ param.min }}</div>
+          <div class="col-4" contenteditable="true" @blur="editItem($event, 'max', index)"
+            @keydown.enter="$event?.target?.blur()">{{ param.max }}</div>
         </div>
       </div>
     </div>
diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 49e251a6..7cfac015 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -1,6 +1,6 @@
 # from .main import setup_bumps
 
-from typing import Dict, List, Optional, Union
+from typing import Dict, List, Literal, Optional, Union
 from datetime import datetime
 from aiohttp import web
 import numpy as np
@@ -22,6 +22,7 @@
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit
 from bumps.serialize import to_dict
 from bumps.mapper import MPMapper
+from bumps.parameter import Parameter
 import refl1d.fitproblem, refl1d.probe
 
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
@@ -224,20 +225,35 @@ async def get_parameters(sid: str = ""):
     return to_dict(parameters)
 
 @sio.event
-async def set_parameter01(sid: str, parameter_name: str, parameter_value01: float):
+async def set_parameter(sid: str, parameter_name: str, property: Literal["value01", "value", "min", "max"], value: Union[float, str]):
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     if fitProblem is None:
         return
     parameter_matches = [p for p in fitProblem._parameters if p.name == parameter_name]
     if len(parameter_matches) < 1:
         return
-    parameter = parameter_matches[0]
-    new_value  = parameter.prior.put01(parameter_value01)
-    nice_new_value = nice(new_value, digits=VALUE_PRECISION)
-    parameter.value = nice_new_value
+    parameter: Parameter = parameter_matches[0]
+    if property == "value01":
+        new_value  = parameter.prior.put01(value)
+        nice_new_value = nice(new_value, digits=VALUE_PRECISION)
+        parameter.clip_set(nice_new_value)
+    elif property == "value":
+        new_value = float(value)
+        nice_new_value = nice(new_value, digits=VALUE_PRECISION)
+        parameter.clip_set(nice_new_value)
+    elif property == "min":
+        lo = float(value)
+        hi = parameter.prior.limits[1]
+        parameter.range(lo, hi)
+        parameter.add_prior()
+    elif property == "max":
+        lo = parameter.prior.limits[0]
+        hi = float(value)
+        parameter.range(lo, hi)
+        parameter.add_prior()
     fitProblem.model_update()
     await publish("", "update_parameters", True)
-    return new_value
+    return
 
 @sio.event
 async def publish(sid: str, topic: str, message):

From aa411192ed56f4de682c6f54b9f149aa99d3f16f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 2 Nov 2022 22:33:20 -0400
Subject: [PATCH 071/221] adding Parameter tab

---
 .../src/components/ParameterView.vue          | 122 ++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100644 refl1d-web-gui/src/components/ParameterView.vue

diff --git a/refl1d-web-gui/src/components/ParameterView.vue b/refl1d-web-gui/src/components/ParameterView.vue
new file mode 100644
index 00000000..da447cfa
--- /dev/null
+++ b/refl1d-web-gui/src/components/ParameterView.vue
@@ -0,0 +1,122 @@
+<script setup lang="ts">
+import { ref, onMounted, watch, onUpdated, computed, shallowRef, nextTick } from 'vue';
+import type { Socket } from 'socket.io-client';
+
+const title = "Parameters";
+const active_parameter = ref("");
+
+const props = defineProps<{
+  socket: Socket,
+  visible: Boolean
+}>();
+
+type parameter_info = {
+  name: string,
+  id: string,
+  fittable: boolean,
+  fixed: boolean,
+  path: string,
+  link: string,
+  value_str: string,
+  min_str: string,
+  max_str: string,
+  active?: boolean,
+}
+
+const parameters = ref<parameter_info[]>([]);
+const parameters_local = ref<parameter_info[]>([]);
+
+onMounted(() => {
+  props.socket.on('update_parameters', () => {
+    fetch_and_draw();
+  });
+});
+
+function fetch_and_draw() {
+  if (!props.visible) {
+    // do nothing if not visible
+    return
+  }
+  props.socket.emit('get_parameters', false, (payload: parameter_info[]) => {
+    // console.log(payload);
+    const pl = parameters_local.value;
+    payload.forEach((p, i) => {
+      if (!(pl[i]?.active)) {
+        pl.splice(i, 1, p);
+      }
+    });
+    pl.splice(payload.length);
+  });
+}
+
+async function editItem(ev, item_name: "min" | "max" | "value", index: number) {
+  const new_value = ev.target.innerText;
+  if (validate_numeric(new_value)) {
+    props.socket.emit('set_parameter', parameters_local.value[index].id, item_name, new_value);
+  }
+}
+
+function validate_numeric(value: string, allow_inf: boolean = false) {
+  if (allow_inf && (value === "inf" || value === "-inf")) {
+    return true
+  }
+  return !Number.isNaN(Number(value))
+}
+
+async function onInactive(param) {
+  param.active = false;
+  fetch_and_draw();
+}
+
+async function setFittable(ev, index) {
+  console.log(ev, ev.target, index, parameters_local.value[index].fixed);
+  const parameter = parameters_local.value[index];
+  props.socket.emit('set_parameter', parameter.id, "fixed", !parameter.fixed);
+}
+
+watch(() => props.visible, (value) => {
+  fetch_and_draw();
+});
+
+</script>
+        
+<template>
+  <table class="table">
+    <thead class="border-bottom py-1">
+      <tr>
+      <th scope="col">Fit?</th>
+      <th scope="col">Name</th>
+      <th scope="col">Value</th>
+      <th scope="col">Path</th>
+      <th scope="col">Linked</th>
+      </tr>
+    </thead>
+    <tbody>
+      <tr class="py-1" v-for="(param, index) in parameters_local" :key="param.id">
+        <td>
+          <input class="form-check-input" type="checkbox" :checked="!param.fixed"
+          :disabled="!param.fittable" @click.prevent="setFittable($event, index)" />
+        </td>
+        <td>{{ param.name }}</td>
+        <td contenteditable="true" spellcheck="false" @blur="editItem($event, 'value', index)" @keydown.enter="$event?.target?.blur()">{{ param.value_str }}
+        </td>
+      <td >{{ param.path }}</td>
+      <td :title="param.link">{{ (param.link) ? 'true' : '' }}</td>
+      </tr>
+    </tbody>
+  </table>
+</template>
+    
+<style scoped>
+span.value {
+  text-align: right;
+}
+
+div.param-name {
+  word-break: break-word;
+}
+
+.scroll-x {
+  overflow-x: auto;
+}
+</style>
\ No newline at end of file

From 178cd4128d029a7b91c41bf90715e879b0e04b5a Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 2 Nov 2022 22:34:10 -0400
Subject: [PATCH 072/221] refactor get_parameters to support summary and
 parameters view

---
 refl1d/webserver.py | 126 +++++++++++++++++++++++++++++++++++++-------
 1 file changed, 106 insertions(+), 20 deletions(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index 7cfac015..cb1a48ff 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -1,7 +1,8 @@
 # from .main import setup_bumps
 
-from typing import Dict, List, Literal, Optional, Union
+from typing import Dict, List, Literal, Optional, Union, TypedDict
 from datetime import datetime
+import warnings
 from aiohttp import web
 import numpy as np
 import asyncio
@@ -22,8 +23,10 @@
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit
 from bumps.serialize import to_dict
 from bumps.mapper import MPMapper
-from bumps.parameter import Parameter
+from bumps.parameter import Parameter, unique
+import bumps.fitproblem
 import refl1d.fitproblem, refl1d.probe
+from refl1d.experiment import Experiment
 
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
 FITTERS_BY_ID = dict([(fitter.id, fitter) for fitter in FITTERS])
@@ -132,6 +135,7 @@ async def get_plot_data(sid: str="", view: str = 'linear'):
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     result = []
     for model in fitProblem.models:
+        assert(isinstance(model, Experiment))
         theory = model.reflectivity()
         probe = model.probe
         result.append(get_probe_data(theory, probe, model._substrate, model._surface))
@@ -172,6 +176,7 @@ async def get_profile_plot(sid: str="", model_index: int=0):
     if (model_index > len(models)):
         return None
     model = models[model_index]
+    assert(isinstance(model, Experiment))
     fig = plt.figure()
     model.plot_profile()
     dfig = mpld3.fig_to_dict(fig)
@@ -189,6 +194,7 @@ async def get_profile_data(sid: str="", model_index: int=0):
     if (model_index > len(models)):
         return None
     model = models[model_index]
+    assert(isinstance(model, Experiment))
     output = {}
     output["ismagnetic"] = model.ismagnetic
     if model.ismagnetic:
@@ -207,32 +213,36 @@ async def get_profile_data(sid: str="", model_index: int=0):
 
 @sio.event
 @rest_get
-async def get_parameters(sid: str = ""):
+async def get_parameters(sid: str = "", only_fittable: bool = False):
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     if fitProblem is None:
         return []
-    raw_parameters = fitProblem._parameters
-    parameters = []
-    for rp in raw_parameters:
-        p = {}
-        low, high = (v for v in rp.prior.limits)
-        p['min'] = VALUE_FORMAT.format(nice(low))
-        p['max'] = VALUE_FORMAT.format(nice(high))
-        p['value_str'] = VALUE_FORMAT.format(nice(rp.value))
-        p['value01'] = rp.prior.get01(rp.value)
-        p['name'] = rp.name
-        parameters.append(p)
-    return to_dict(parameters)
+
+    all_parameters = fitProblem.model_parameters()
+    if only_fittable:
+        parameter_infos = params_to_list(unique(all_parameters))
+        # only include params with priors:
+        parameter_infos = [pi for pi in parameter_infos if pi['fittable'] and not pi['fixed']]
+    else:
+        parameter_infos = params_to_list(all_parameters)
+        
+    return to_dict(parameter_infos)
 
 @sio.event
-async def set_parameter(sid: str, parameter_name: str, property: Literal["value01", "value", "min", "max"], value: Union[float, str]):
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+async def set_parameter(sid: str, parameter_id: str, property: Literal["value01", "value", "min", "max"], value: Union[float, str, bool]):
+    fitProblem: bumps.fitproblem.FitProblem = app["problem"]["fitProblem"]
     if fitProblem is None:
         return
-    parameter_matches = [p for p in fitProblem._parameters if p.name == parameter_name]
-    if len(parameter_matches) < 1:
+
+    parameter = fitProblem._parameters_by_id.get(parameter_id, None)
+    if parameter is None:
+        warnings.warn(f"Attempting to update parameter that doesn't exist: {parameter_id}")
         return
-    parameter: Parameter = parameter_matches[0]
+
+    if parameter.prior is None:
+        warnings.warn(f"Attempting to set prior properties on parameter without priors: {parameter}")
+        return
+
     if property == "value01":
         new_value  = parameter.prior.put01(value)
         nice_new_value = nice(new_value, digits=VALUE_PRECISION)
@@ -251,6 +261,11 @@ async def set_parameter(sid: str, parameter_name: str, property: Literal["value0
         hi = float(value)
         parameter.range(lo, hi)
         parameter.add_prior()
+    elif property == "fixed":
+        if parameter.fittable:
+            parameter.fixed = bool(value)
+            fitProblem.model_reset()
+            print(f"setting parameter: {parameter}.fixed to {value}")
     fitProblem.model_update()
     await publish("", "update_parameters", True)
     return
@@ -318,6 +333,77 @@ def nice(v, digits=4):
         return sign*floor(abs(v)/scale+0.5)*scale
     
 
+class ParamInfo(TypedDict, total=False):
+    id: str
+    name: str
+    paths: List[str]
+    value_str: str
+    fittable: bool
+    fixed: bool
+    value01: Optional[float]
+    min_str: Optional[str]
+    max_str: Optional[str]
+
+
+def params_to_dict(params, output=None, pathlist=None, links=None) -> Dict[str, ParamInfo]:
+    output: Dict[str, ParamInfo] = {} if output is None else output
+    pathlist = [] if pathlist is None else pathlist
+    if isinstance(params,dict):
+        for k in sorted(params.keys()):
+            params_to_dict(params[k], output=output, pathlist=pathlist + [k])
+    elif isinstance(params, tuple) or isinstance(params, list):
+        for i, v in enumerate(params):
+            params_to_dict(v, output=output, pathlist=pathlist + [f"[{i:d}]"])
+    elif isinstance(params, Parameter):
+        path = ".".join(pathlist)
+        existing = output.get(params.id, None)
+        if existing is not None:
+            existing["paths"].append(".".join(pathlist))
+        else:
+            value_str = VALUE_FORMAT.format(nice(params.value))
+            has_prior = params.has_prior()
+            new_item: ParamInfo = { 
+                "id": params.id,
+                "name": str(params.name),
+                "paths": [path],
+                "value_str": value_str, "fittable": params.fittable, "fixed": params.fixed }
+            if has_prior:
+                assert(params.prior is not None)
+                lo, hi = params.prior.limits
+                new_item['value01'] = params.prior.get01(params.value)
+                new_item['min_str'] = VALUE_FORMAT.format(nice(lo))
+                new_item['max_str'] = VALUE_FORMAT.format(nice(hi))
+            output[params.id] = new_item
+    return output
+
+def params_to_list(params, output=None, pathlist=None, links=None) -> List[ParamInfo]:
+    output = [] if output is None else output
+    links = {} if links is None else links
+    pathlist = [] if pathlist is None else pathlist
+    if isinstance(params,dict):
+        for k in sorted(params.keys()):
+            params_to_list(params[k], output=output, pathlist=pathlist + [k], links=links)
+    elif isinstance(params, tuple) or isinstance(params, list):
+        for i, v in enumerate(params):
+            params_to_list(v, output=output, pathlist=pathlist + [f"[{i:d}]"], links=links)
+    elif isinstance(params, Parameter):
+        link_path = links.get(params.id, "")
+        if link_path == "":
+            links[params.id] = pathlist
+        value_str = VALUE_FORMAT.format(nice(params.value))
+        link = ".".join(link_path)
+        path = ".".join(pathlist)
+        has_prior = params.has_prior()
+        new_item = {"id": params.id, "name": params.name, "path": path, "link": link, "value_str": value_str, "fittable": params.fittable, "fixed": params.fixed, "has_prior": has_prior}
+        if has_prior:
+            assert(params.prior is not None)
+            lo, hi = params.prior.limits
+            new_item['value01'] = params.prior.get01(params.value)
+            new_item['min_str'] = VALUE_FORMAT.format(nice(lo))
+            new_item['max_str'] = VALUE_FORMAT.format(nice(hi))
+        output.append(new_item)
+    return output
+
 if __name__ == '__main__':
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     app.add_routes(routes)

From 7daefbc12d344bffbd9dd6481000bf3a7e566e0e Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 2 Nov 2022 22:34:35 -0400
Subject: [PATCH 073/221] add Parameter tab to app

---
 refl1d-web-gui/src/App.vue | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index b54f23d4..3d9f0b11 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -10,14 +10,16 @@ import FileBrowser from './components/FileBrowser.vue';
 import SummaryView from './components/SummaryView.vue';
 import ModelInspect from './components/ModelInspect.vue';
 import ModelViewPlotly from './components/ModelViewPlotly.vue';
+import ParameterView from './components/ParameterView.vue';
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
 
 const panels = [
   {title: 'Reflectivity', component: DataView},
-  {title: 'Parameters', component: SummaryView},
+  {title: 'Summary', component: SummaryView},
   {title: 'Profile', component: ModelView},
   {title: 'Model', component: ModelInspect},
-  {title: 'Profile2', component: ModelViewPlotly}
+  {title: 'Profile2', component: ModelViewPlotly},
+  {title: 'Parameters', component: ParameterView},
 ];
 
 const connected = ref(false);

From 712333808699aa366554e27fed92faf6ce4b4f45 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 2 Nov 2022 22:35:14 -0400
Subject: [PATCH 074/221] modify Summary tab to work with parameters by id

---
 refl1d-web-gui/src/components/SummaryView.vue | 25 ++++++++++---------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index 6ed1cc56..ecef364b 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -12,10 +12,11 @@ const props = defineProps<{
 
 type parameter_info = {
   name: string,
+  id: string,
   value01: number,
   value_str: string,
-  min: string,
-  max: string,
+  min_str: string,
+  max_str: string,
   active?: boolean,
 }
 
@@ -34,7 +35,7 @@ function fetch_and_draw() {
     // do nothing if not visible
     return
   }
-  props.socket.emit('get_parameters', (payload: parameter_info[]) => {
+  props.socket.emit('get_parameters', true, (payload: parameter_info[]) => {
     // console.log(payload);
     const pv = parameters.value;
     payload.forEach((p, i) => {
@@ -52,13 +53,13 @@ function fetch_and_draw() {
 
 async function onMove(param_index) {
   // props.socket.volatile.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
-  props.socket.emit('set_parameter', parameters.value[param_index].name, "value01", parameters_local01.value[param_index]);
+  props.socket.emit('set_parameter', parameters.value[param_index].id, "value01", parameters_local01.value[param_index]);
 }
 
 async function editItem(ev, item_name: "min" | "max" | "value", index: number) {
   const new_value = ev.target.innerText;
   if (validate_numeric(new_value)) {
-    props.socket.emit('set_parameter', parameters.value[index].name, item_name, new_value);
+    props.socket.emit('set_parameter', parameters.value[index].id, item_name, new_value);
   }
 }
 
@@ -72,7 +73,7 @@ function validate_numeric(value: string, allow_inf: boolean = false) {
 async function scrollParam(ev, index) {
   const sign = Math.sign(ev.deltaY);
   parameters_local01.value[index] -= 0.01 * sign;
-  props.socket.emit('set_parameter', parameters.value[index].name, "value01", parameters_local01.value[index]);
+  props.socket.emit('set_parameter', parameters.value[index].id, "value01", parameters_local01.value[index]);
 }
 
 async function onInactive(param) {
@@ -94,7 +95,7 @@ watch(() => props.visible, (value) => {
       <div class="col-5">
         <div class="row">
           <div class="col-4">Value</div>
-          <div class="col-4">Min.</div>
+          <div class="col-4">Min</div>
           <div class="col-4">Max</div>
         </div>
       </div>
@@ -108,12 +109,12 @@ watch(() => props.visible, (value) => {
       </div>
       <div class="col-5">
         <div class="row">
-          <div class="col-4" contenteditable="true" @blur="editItem($event, 'value', index)"
+          <div class="col-4" contenteditable="true" spellcheck="false" @blur="editItem($event, 'value', index)"
             @keydown.enter="$event?.target?.blur()">{{ parameters_localstr[index] }}</div>
-          <div class="col-4" contenteditable="true" @blur="editItem($event, 'min', index)"
-            @keydown.enter="$event?.target?.blur()">{{ param.min }}</div>
-          <div class="col-4" contenteditable="true" @blur="editItem($event, 'max', index)"
-            @keydown.enter="$event?.target?.blur()">{{ param.max }}</div>
+          <div class="col-4" contenteditable="true" spellcheck="false" @blur="editItem($event, 'min', index)"
+            @keydown.enter="$event?.target?.blur()">{{ param.min_str }}</div>
+          <div class="col-4" contenteditable="true" spellcheck="false" @blur="editItem($event, 'max', index)"
+            @keydown.enter="$event?.target?.blur()">{{ param.max_str }}</div>
         </div>
       </div>
     </div>

From 1c3ec79c042d320c5ad18fac741cadbf20111ef1 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 2 Nov 2022 22:43:15 -0400
Subject: [PATCH 075/221] adding profile plot tab that uses plotly instead of
 mpld3

---
 .../src/components/ModelViewPlotly.vue        | 117 ++++++++++++++++++
 1 file changed, 117 insertions(+)
 create mode 100644 refl1d-web-gui/src/components/ModelViewPlotly.vue

diff --git a/refl1d-web-gui/src/components/ModelViewPlotly.vue b/refl1d-web-gui/src/components/ModelViewPlotly.vue
new file mode 100644
index 00000000..87d23956
--- /dev/null
+++ b/refl1d-web-gui/src/components/ModelViewPlotly.vue
@@ -0,0 +1,117 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import * as Plotly from 'plotly.js/lib/core';
+
+const title = "Profile";
+const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
+const plot_div_id = ref(`div-${uuidv4()}`);
+const model_names = ref<string[]>([]);
+const current_model = ref(0);
+const props = defineProps<{
+  socket: Socket,
+  visible: boolean
+}>();
+
+props.socket.on('model_loaded', ({message: {model_names: new_model_names}}) => {
+  model_names.value = new_model_names;
+});
+
+onMounted(() => {
+  props.socket.on('update_parameters', () => {
+    draw_requested.value = true;
+  });
+  window.requestAnimationFrame(draw_if_needed);
+});
+
+function generate_new_traces(profile_data) {
+  let traces: (Plotly.Data & { x: number, y: number })[] = [];
+  const { step_profile, smooth_profile } = profile_data;
+
+  traces.push({ x: step_profile.z, y: step_profile.rho, mode: 'lines', name: 'rho', line: {width: 2}})
+  traces.push({ x: step_profile.z, y: step_profile.irho, mode: 'lines', name: 'irho', line: {width: 2}});
+  if (step_profile.rho_m) {
+    traces.push({ x: step_profile.z, y: step_profile.rho_m, mode: 'lines', name: 'rho_m', line: {width: 2}});
+  }
+
+  traces.push({ x: smooth_profile.z, y: smooth_profile.rho, mode: 'lines', name: 'rho', line: {width: 2}})
+  traces.push({ x: smooth_profile.z, y: smooth_profile.irho, mode: 'lines', name: 'irho', line: {width: 2}});
+  if (smooth_profile.rho_m) {
+    traces.push({ x: smooth_profile.z, y: smooth_profile.rho_m, mode: 'lines', name: 'rho_m', line: {width: 2}});
+  }
+
+  return traces;
+}
+
+
+
+function fetch_and_draw() {
+  if (!props.visible) {
+    return
+  }
+  props.socket.emit('get_profile_data', current_model.value, async (payload) => {
+    if (plot_div.value == null) {
+      return
+    }
+    console.log(payload);
+    const traces = generate_new_traces(payload);
+
+    const layout: Partial<Plotly.Layout> = {
+      uirevision: 1,
+      xaxis: {
+        title: {
+          text: 'z'
+        },
+        type: 'linear',
+        autorange: true,
+      },
+      yaxis: {
+        title: { text: 'SLD (10^6 / A^{-2})' },
+        exponentformat: 'e',
+        showexponent: 'all',
+        type: 'linear',
+        autorange: true,
+      },
+    };
+
+    await Plotly.react(plot_div.value, [...traces], layout);
+    
+  });
+}
+
+
+function draw_if_needed(timestamp: number) {
+  if (draw_requested.value && props.visible) {
+    fetch_and_draw();
+    draw_requested.value = false;
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+// watch(() => props.visible, (value) => {
+//   if (value) {
+//     console.log('visible', value);
+//     fetch_and_draw();
+//   }
+// });
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <select v-model="current_model" @change="draw_requested=true">
+      <option v-for="(name, index) in model_names" :key="index" :value="index">{{index}}: {{name ?? ""}}</option>
+    </select>
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file

From 46041a5efcf3778da8554fbf93d3ec9d7e4d21a7 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 11:00:21 -0400
Subject: [PATCH 076/221] fix margins for plots, and make them responsive to
 container size (\!)

---
 refl1d-web-gui/src/components/DataView.vue        | 11 ++++++++++-
 refl1d-web-gui/src/components/ModelViewPlotly.vue | 11 ++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d-web-gui/src/components/DataView.vue
index 2c5f2d53..7524a25f 100644
--- a/refl1d-web-gui/src/components/DataView.vue
+++ b/refl1d-web-gui/src/components/DataView.vue
@@ -105,9 +105,18 @@ function fetch_and_draw() {
         type: (/^(Log|Q4)/.test(reflectivity_type.value)) ? 'log' : 'linear',
         autorange: true,
       },
+      margin: {
+        l: 75,
+        r: 50,
+        t: 25,
+        b: 75,
+        pad: 4
+      }
     };
 
-    plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout);
+    const config = {responsive: true}
+
+    plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout, config);
     
   });
 }
diff --git a/refl1d-web-gui/src/components/ModelViewPlotly.vue b/refl1d-web-gui/src/components/ModelViewPlotly.vue
index 87d23956..800d8a42 100644
--- a/refl1d-web-gui/src/components/ModelViewPlotly.vue
+++ b/refl1d-web-gui/src/components/ModelViewPlotly.vue
@@ -75,9 +75,18 @@ function fetch_and_draw() {
         type: 'linear',
         autorange: true,
       },
+      margin: {
+        l: 75,
+        r: 50,
+        t: 25,
+        b: 75,
+        pad: 4
+      }
     };
 
-    await Plotly.react(plot_div.value, [...traces], layout);
+    const config = {responsive: true}
+
+    await Plotly.react(plot_div.value, [...traces], layout, config);
     
   });
 }

From 53c8e9cc6a4e3d43fb6281826ab420abb9cf59cd Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 11:03:05 -0400
Subject: [PATCH 077/221] convert summary to table, and add nowrap

---
 refl1d-web-gui/src/components/SummaryView.vue | 67 ++++++++++---------
 1 file changed, 36 insertions(+), 31 deletions(-)

diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d-web-gui/src/components/SummaryView.vue
index ecef364b..7a9cd4b7 100644
--- a/refl1d-web-gui/src/components/SummaryView.vue
+++ b/refl1d-web-gui/src/components/SummaryView.vue
@@ -88,41 +88,46 @@ watch(() => props.visible, (value) => {
 </script>
         
 <template>
-  <div class="">
-    <div class="row border-bottom py-1">
-      <div class="col-2">Fit Parameter</div>
-      <div class="col-5"></div>
-      <div class="col-5">
-        <div class="row">
-          <div class="col-4">Value</div>
-          <div class="col-4">Min</div>
-          <div class="col-4">Max</div>
-        </div>
-      </div>
-    </div>
-    <div class="row align-items-center px-1" v-for="(param, index) in parameters" :key="param.name">
-      <div class="col-2 border-bottom">{{ param.name }}</div>
-      <div class="col-5">
-        <input type="range" class="form-range" min="0" max="1.0" step="0.005" v-model.number="parameters_local01[index]"
-          @mousedown="param.active = true" @input="onMove(index)" @change="onInactive(param)"
-          @wheel="scrollParam($event, index)" />
-      </div>
-      <div class="col-5">
-        <div class="row">
-          <div class="col-4" contenteditable="true" spellcheck="false" @blur="editItem($event, 'value', index)"
-            @keydown.enter="$event?.target?.blur()">{{ parameters_localstr[index] }}</div>
-          <div class="col-4" contenteditable="true" spellcheck="false" @blur="editItem($event, 'min', index)"
-            @keydown.enter="$event?.target?.blur()">{{ param.min_str }}</div>
-          <div class="col-4" contenteditable="true" spellcheck="false" @blur="editItem($event, 'max', index)"
-            @keydown.enter="$event?.target?.blur()">{{ param.max_str }}</div>
-        </div>
-      </div>
-    </div>
-  </div>
+  <table class="table">
+    <thead class="border-bottom py-1">
+      <tr>
+        <th scope="col">Fit Parameter</th>
+        <th scope="col"></th>
+        <th scope="col">Value</th>
+        <th scope="col">Min</th>
+        <th scope="col">Max</th>
+      </tr>
+    </thead>
+    <tbody>
+      <tr class="py-1" v-for="(param, index) in parameters" :key="param.id">
+        <td>{{ param.name }}</td>
+        <td>
+          <input type="range" class="form-range" min="0" max="1.0" step="0.005"
+            v-model.number="parameters_local01[index]" @mousedown="param.active = true" @input="onMove(index)"
+            @change="onInactive(param)" @wheel="scrollParam($event, index)" />
+        </td>
+        <td class="editable" contenteditable="true" spellcheck="false" @blur="editItem($event, 'value', index)"
+          @keydown.enter="$event?.target?.blur()">{{ parameters_localstr[index] }}</td>
+        <td class="editable" contenteditable="true" spellcheck="false" @blur="editItem($event, 'min', index)"
+          @keydown.enter="$event?.target?.blur()">{{ param.min_str }}</td>
+        <td class="editable" contenteditable="true" spellcheck="false" @blur="editItem($event, 'max', index)"
+          @keydown.enter="$event?.target?.blur()">{{ param.max_str }}</td>
+      </tr>
+    </tbody>
+  </table>
 </template>
     
 <style scoped>
 svg {
   width: 100%;
+  white-space: nowrap;
+}
+
+td.editable {
+  min-width: 5em;
+}
+
+td > input {
+  min-width: 5em;
 }
 </style>
\ No newline at end of file

From 7d488bcbdff65809f52a0d1b5ac78e39e0b2a330 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 11:03:39 -0400
Subject: [PATCH 078/221] fix height and make panels scrollable

---
 refl1d-web-gui/src/App.vue | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 3d9f0b11..7d834bd5 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -99,7 +99,7 @@ onMounted(() => {
 </script>
 
 <template>
-  <div class="h-100 d-flex flex-column">
+  <div class="h-100 w-100 m-0 d-flex flex-column">
     <nav class="navbar navbar-expand-lg navbar-dark bg-dark">
       <div class="container-fluid">
         <div class="navbar-brand">
@@ -175,11 +175,11 @@ onMounted(() => {
         </div>
       </div>
     </nav>
-    <div class="flex-grow-1 row">
-      <div class="col d-flex flex-column">
+    <div class="flex-grow-1 row overflow-hidden">
+      <div class="col d-flex flex-column mh-100 overflow-auto">
         <PanelTabContainer :panels="panels" :socket="socket" :initially_active="0"/>
       </div>
-      <div class="col d-flex flex-column">
+      <div class="col d-flex flex-column mh-100 overflow-auto">
         <PanelTabContainer :panels="panels" :socket="socket" :initially_active="1"/>
       </div>
     </div>

From 4608d38f30f147eb22ccfc81f573b79f377b326e Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 11:04:11 -0400
Subject: [PATCH 079/221] update x,y labels on profile plot

---
 refl1d-web-gui/src/components/ModelViewPlotly.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelViewPlotly.vue b/refl1d-web-gui/src/components/ModelViewPlotly.vue
index 800d8a42..a3fb9aaa 100644
--- a/refl1d-web-gui/src/components/ModelViewPlotly.vue
+++ b/refl1d-web-gui/src/components/ModelViewPlotly.vue
@@ -63,13 +63,13 @@ function fetch_and_draw() {
       uirevision: 1,
       xaxis: {
         title: {
-          text: 'z'
+          text: 'z (Å)'
         },
         type: 'linear',
         autorange: true,
       },
       yaxis: {
-        title: { text: 'SLD (10^6 / A^{-2})' },
+        title: { text: '$\\text{SLD} (10^6 / Å^{-2})$' },
         exponentformat: 'e',
         showexponent: 'all',
         type: 'linear',

From b40a3beb47c48f6a93fdd6389ab1039ece8b3897 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 11:05:54 -0400
Subject: [PATCH 080/221] use combined paths list instead of path and link
 columns

---
 .../src/components/ParameterView.vue          | 33 ++++++++-----------
 1 file changed, 14 insertions(+), 19 deletions(-)

diff --git a/refl1d-web-gui/src/components/ParameterView.vue b/refl1d-web-gui/src/components/ParameterView.vue
index da447cfa..a90180ee 100644
--- a/refl1d-web-gui/src/components/ParameterView.vue
+++ b/refl1d-web-gui/src/components/ParameterView.vue
@@ -17,6 +17,7 @@ type parameter_info = {
   fixed: boolean,
   path: string,
   link: string,
+  writable: boolean,
   value_str: string,
   min_str: string,
   max_str: string,
@@ -84,39 +85,33 @@ watch(() => props.visible, (value) => {
   <table class="table">
     <thead class="border-bottom py-1">
       <tr>
-      <th scope="col">Fit?</th>
-      <th scope="col">Name</th>
-      <th scope="col">Value</th>
-      <th scope="col">Path</th>
-      <th scope="col">Linked</th>
+        <th scope="col">Fit?</th>
+        <th scope="col">Name</th>
+        <th scope="col">Value</th>
+        <th scope="col">Paths</th>
       </tr>
     </thead>
     <tbody>
       <tr class="py-1" v-for="(param, index) in parameters_local" :key="param.id">
         <td>
-          <input class="form-check-input" type="checkbox" :checked="!param.fixed"
-          :disabled="!param.fittable" @click.prevent="setFittable($event, index)" />
+          <input class="form-check-input" v-if="param.fittable" type="checkbox" :checked="!param.fixed"
+            @click.prevent="setFittable($event, index)" />
         </td>
         <td>{{ param.name }}</td>
-        <td contenteditable="true" spellcheck="false" @blur="editItem($event, 'value', index)" @keydown.enter="$event?.target?.blur()">{{ param.value_str }}
+        <td :contenteditable="param.writable" spellcheck="false" @blur="editItem($event, 'value', index)"
+          @keydown.enter="$event?.target?.blur()">{{ param.value_str }}
+        </td>
+        <td>
+          <p class="my-0" v-for="path in param.paths" :key="path">{{ path }}</p>
         </td>
-      <td >{{ param.path }}</td>
-      <td :title="param.link">{{ (param.link) ? 'true' : '' }}</td>
       </tr>
     </tbody>
   </table>
 </template>
     
 <style scoped>
-span.value {
-  text-align: right;
-}
-
-div.param-name {
-  word-break: break-word;
-}
 
-.scroll-x {
-  overflow-x: auto;
+table {
+  white-space: nowrap;
 }
 </style>
\ No newline at end of file

From 52981a00337961cc610c5048aa42491b8a4f428a Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 11:06:27 -0400
Subject: [PATCH 081/221] return parameters list with all paths for a single
 parameter, rather than one entry per path

---
 refl1d/webserver.py | 48 +++++++++++----------------------------------
 1 file changed, 11 insertions(+), 37 deletions(-)

diff --git a/refl1d/webserver.py b/refl1d/webserver.py
index cb1a48ff..edfa5529 100644
--- a/refl1d/webserver.py
+++ b/refl1d/webserver.py
@@ -23,7 +23,7 @@
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit
 from bumps.serialize import to_dict
 from bumps.mapper import MPMapper
-from bumps.parameter import Parameter, unique
+from bumps.parameter import Parameter, Variable, unique
 import bumps.fitproblem
 import refl1d.fitproblem, refl1d.probe
 from refl1d.experiment import Experiment
@@ -333,30 +333,31 @@ def nice(v, digits=4):
         return sign*floor(abs(v)/scale+0.5)*scale
     
 
-class ParamInfo(TypedDict, total=False):
+class ParamInfo(TypedDict):
     id: str
     name: str
     paths: List[str]
     value_str: str
     fittable: bool
     fixed: bool
+    writable: bool
     value01: Optional[float]
     min_str: Optional[str]
     max_str: Optional[str]
 
 
-def params_to_dict(params, output=None, pathlist=None, links=None) -> Dict[str, ParamInfo]:
-    output: Dict[str, ParamInfo] = {} if output is None else output
+def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[ParamInfo]:
+    lookup: Dict[str, ParamInfo] = {} if lookup is None else lookup
     pathlist = [] if pathlist is None else pathlist
     if isinstance(params,dict):
         for k in sorted(params.keys()):
-            params_to_dict(params[k], output=output, pathlist=pathlist + [k])
+            params_to_list(params[k], lookup=lookup, pathlist=pathlist + [k])
     elif isinstance(params, tuple) or isinstance(params, list):
         for i, v in enumerate(params):
-            params_to_dict(v, output=output, pathlist=pathlist + [f"[{i:d}]"])
+            params_to_list(v, lookup=lookup, pathlist=pathlist + [f"[{i:d}]"])
     elif isinstance(params, Parameter):
         path = ".".join(pathlist)
-        existing = output.get(params.id, None)
+        existing = lookup.get(params.id, None)
         if existing is not None:
             existing["paths"].append(".".join(pathlist))
         else:
@@ -366,6 +367,7 @@ def params_to_dict(params, output=None, pathlist=None, links=None) -> Dict[str,
                 "id": params.id,
                 "name": str(params.name),
                 "paths": [path],
+                "writable": type(params.slot) in [Variable, Parameter], 
                 "value_str": value_str, "fittable": params.fittable, "fixed": params.fixed }
             if has_prior:
                 assert(params.prior is not None)
@@ -373,36 +375,8 @@ def params_to_dict(params, output=None, pathlist=None, links=None) -> Dict[str,
                 new_item['value01'] = params.prior.get01(params.value)
                 new_item['min_str'] = VALUE_FORMAT.format(nice(lo))
                 new_item['max_str'] = VALUE_FORMAT.format(nice(hi))
-            output[params.id] = new_item
-    return output
-
-def params_to_list(params, output=None, pathlist=None, links=None) -> List[ParamInfo]:
-    output = [] if output is None else output
-    links = {} if links is None else links
-    pathlist = [] if pathlist is None else pathlist
-    if isinstance(params,dict):
-        for k in sorted(params.keys()):
-            params_to_list(params[k], output=output, pathlist=pathlist + [k], links=links)
-    elif isinstance(params, tuple) or isinstance(params, list):
-        for i, v in enumerate(params):
-            params_to_list(v, output=output, pathlist=pathlist + [f"[{i:d}]"], links=links)
-    elif isinstance(params, Parameter):
-        link_path = links.get(params.id, "")
-        if link_path == "":
-            links[params.id] = pathlist
-        value_str = VALUE_FORMAT.format(nice(params.value))
-        link = ".".join(link_path)
-        path = ".".join(pathlist)
-        has_prior = params.has_prior()
-        new_item = {"id": params.id, "name": params.name, "path": path, "link": link, "value_str": value_str, "fittable": params.fittable, "fixed": params.fixed, "has_prior": has_prior}
-        if has_prior:
-            assert(params.prior is not None)
-            lo, hi = params.prior.limits
-            new_item['value01'] = params.prior.get01(params.value)
-            new_item['min_str'] = VALUE_FORMAT.format(nice(lo))
-            new_item['max_str'] = VALUE_FORMAT.format(nice(hi))
-        output.append(new_item)
-    return output
+            lookup[params.id] = new_item
+    return list(lookup.values())
 
 if __name__ == '__main__':
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))

From cf7b15c25eb09023c47548efe5c53a4ee5136fad Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 16:42:36 -0400
Subject: [PATCH 082/221] use updated CDN for mathjax

---
 refl1d-web-gui/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d-web-gui/index.html b/refl1d-web-gui/index.html
index ddd28ef3..529eaf55 100644
--- a/refl1d-web-gui/index.html
+++ b/refl1d-web-gui/index.html
@@ -5,7 +5,7 @@
     <link rel="icon" href="./src/assets/refl1d-icon_48x48x32.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <script type="text/javascript" async
-      src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTML">
+      src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-svg.min.js">
     </script>
     <title>Refl1D</title>
   </head>

From 2fbafd93fe3e058b94b8e2b975ba93b78aba4815 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 16:42:50 -0400
Subject: [PATCH 083/221] make app full-width

---
 refl1d-web-gui/src/App.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index 7d834bd5..a221954e 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -193,6 +193,8 @@ html,
 body,
 #app {
   height: 100%;
+  width: 100%;
+  overflow-x: hidden;
 }
 
 div#connection_status {

From e5b8c2a3c144babd19ac75181936e5eba55cb657 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 16:43:30 -0400
Subject: [PATCH 084/221] add custom handler for legend, tying visibility of
 plots of smooth and step profile together

---
 .../src/components/ModelViewPlotly.vue        | 85 +++++++++++++++----
 1 file changed, 68 insertions(+), 17 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelViewPlotly.vue b/refl1d-web-gui/src/components/ModelViewPlotly.vue
index a3fb9aaa..9662ddbd 100644
--- a/refl1d-web-gui/src/components/ModelViewPlotly.vue
+++ b/refl1d-web-gui/src/components/ModelViewPlotly.vue
@@ -16,7 +16,7 @@ const props = defineProps<{
   visible: boolean
 }>();
 
-props.socket.on('model_loaded', ({message: {model_names: new_model_names}}) => {
+props.socket.on('model_loaded', ({ message: { model_names: new_model_names } }) => {
   model_names.value = new_model_names;
 });
 
@@ -28,19 +28,24 @@ onMounted(() => {
 });
 
 function generate_new_traces(profile_data) {
-  let traces: (Plotly.Data & { x: number, y: number })[] = [];
+  let traces: (Plotly.Data & { x: number[], y: number[] })[] = [];
   const { step_profile, smooth_profile } = profile_data;
+  console.log(profile_data);
 
-  traces.push({ x: step_profile.z, y: step_profile.rho, mode: 'lines', name: 'rho', line: {width: 2}})
-  traces.push({ x: step_profile.z, y: step_profile.irho, mode: 'lines', name: 'irho', line: {width: 2}});
-  if (step_profile.rho_m) {
-    traces.push({ x: step_profile.z, y: step_profile.rho_m, mode: 'lines', name: 'rho_m', line: {width: 2}});
+  traces.push({ x: step_profile.z, y: step_profile.rho, mode: 'lines', name: 'rho', line: { color: "green", width: 2, dash: "dot" }, showlegend: false });
+  traces.push({ x: smooth_profile.z, y: smooth_profile.rho, mode: 'lines', name: 'rho', line: { color: "green", width: 2 } });
+
+  traces.push({ x: step_profile.z, y: step_profile.irho, mode: 'lines', name: 'irho', line: { color: "blue", width: 2, dash: "dot" }, showlegend: false });
+  traces.push({ x: smooth_profile.z, y: smooth_profile.irho, mode: 'lines', name: 'irho', line: { color: "blue", width: 2 } });
+
+  if (step_profile.rhoM && smooth_profile.rhoM) {
+    traces.push({ x: step_profile.z, y: step_profile.rhoM, mode: 'lines', name: 'rhoM', line: { color: "red", width: 2, dash: "dot" }, showlegend: false });
+    traces.push({ x: smooth_profile.z, y: smooth_profile.rhoM, mode: 'lines', name: 'rhoM', line: { color: "red", width: 2 } });
   }
 
-  traces.push({ x: smooth_profile.z, y: smooth_profile.rho, mode: 'lines', name: 'rho', line: {width: 2}})
-  traces.push({ x: smooth_profile.z, y: smooth_profile.irho, mode: 'lines', name: 'irho', line: {width: 2}});
-  if (smooth_profile.rho_m) {
-    traces.push({ x: smooth_profile.z, y: smooth_profile.rho_m, mode: 'lines', name: 'rho_m', line: {width: 2}});
+  if (step_profile.thetaM && smooth_profile.thetaM) {
+    traces.push({ x: step_profile.z, y: step_profile.thetaM, mode: 'lines', name: 'thetaM', yaxis: "y2", line: { color: "gold", width: 2, dash: "dot" }, showlegend: false });
+    traces.push({ x: smooth_profile.z, y: smooth_profile.thetaM, mode: 'lines', name: 'thetaM', yaxis: "y2", line: { color: "gold", width: 2 } });
   }
 
   return traces;
@@ -63,18 +68,27 @@ function fetch_and_draw() {
       uirevision: 1,
       xaxis: {
         title: {
-          text: 'z (Å)'
+          text: 'depth (Å)'
         },
         type: 'linear',
         autorange: true,
       },
       yaxis: {
-        title: { text: '$\\text{SLD} (10^6 / Å^{-2})$' },
+        title: { text: '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$' },
         exponentformat: 'e',
         showexponent: 'all',
         type: 'linear',
         autorange: true,
       },
+      yaxis2: {
+        title: { text: '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$' },
+        type: 'linear',
+        autorange: false,
+        range: [0, 360],
+        anchor: 'x',
+        overlaying: 'y',
+        side: 'right'
+      },
       margin: {
         l: 75,
         r: 50,
@@ -84,10 +98,47 @@ function fetch_and_draw() {
       }
     };
 
-    const config = {responsive: true}
+    const config = { responsive: true }
+
+    const plot = await Plotly.react(plot_div.value, [...traces], layout, config);
+
+    let legend_click_timeout: number | undefined;
+
+    plot.removeAllListeners('plotly_legendclick');
+    plot.on('plotly_legendclick', (ev) => {
+      // match visibility of step and smooth profiles:
+      const dbl_clicked = (legend_click_timeout !== undefined);
+      if (dbl_clicked) {
+        clearTimeout(legend_click_timeout);
+        legend_click_timeout = undefined;
+      }
+      const { config, curveNumber, data } = ev;
+      const visibility = data.map((d) => d.visible ?? true);
+      const current_is_visible = (visibility[curveNumber] === true);
+      if (dbl_clicked) {
+        // algorithm is to make all visible if any are hidden, 
+        // or hide all but clicked if all are visible.
+        const some_hidden = visibility.some(v => (v !== true));
+        let visibility_update: (boolean | 'legendonly' | undefined)[];
+        if (!some_hidden) {
+          visibility_update = data.map((_, i) => ((i === curveNumber - 1) || (i === curveNumber)) ? true : 'legendonly');
+        }
+        else {
+          visibility_update = data.map((_, i) => true);
+        }
+        Plotly.restyle(plot, { visible: visibility_update });
+      }
+      else {
+        const new_visibility = current_is_visible ? 'legendonly' : true;
+        const visibility_update = [new_visibility, new_visibility];
+        legend_click_timeout = setTimeout(() => {
+          Plotly.restyle(plot, { visible: visibility_update }, [curveNumber - 1, curveNumber]);
+          legend_click_timeout = undefined;
+        }, config.doubleClickDelay);
+      }
+      return false;
+    });
 
-    await Plotly.react(plot_div.value, [...traces], layout, config);
-    
   });
 }
 
@@ -111,8 +162,8 @@ function draw_if_needed(timestamp: number) {
     
 <template>
   <div class="container d-flex flex-grow-1 flex-column">
-    <select v-model="current_model" @change="draw_requested=true">
-      <option v-for="(name, index) in model_names" :key="index" :value="index">{{index}}: {{name ?? ""}}</option>
+    <select v-model="current_model" @change="draw_requested = true">
+      <option v-for="(name, index) in model_names" :key="index" :value="index">{{ index }}: {{ name ?? "" }}</option>
     </select>
     <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
     </div>

From bae6a22fa1ef55f381f37e7e8b44cc8194e8bf6c Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 3 Nov 2022 16:52:07 -0400
Subject: [PATCH 085/221] turns out plotly can group traces together in the
 legend already.  Removing custom handler - use 'legendgroup' tag in traces
 instead

---
 .../src/components/ModelViewPlotly.vue        | 53 +++----------------
 1 file changed, 8 insertions(+), 45 deletions(-)

diff --git a/refl1d-web-gui/src/components/ModelViewPlotly.vue b/refl1d-web-gui/src/components/ModelViewPlotly.vue
index 9662ddbd..166b996d 100644
--- a/refl1d-web-gui/src/components/ModelViewPlotly.vue
+++ b/refl1d-web-gui/src/components/ModelViewPlotly.vue
@@ -32,20 +32,20 @@ function generate_new_traces(profile_data) {
   const { step_profile, smooth_profile } = profile_data;
   console.log(profile_data);
 
-  traces.push({ x: step_profile.z, y: step_profile.rho, mode: 'lines', name: 'rho', line: { color: "green", width: 2, dash: "dot" }, showlegend: false });
-  traces.push({ x: smooth_profile.z, y: smooth_profile.rho, mode: 'lines', name: 'rho', line: { color: "green", width: 2 } });
+  traces.push({ x: step_profile.z, y: step_profile.rho, mode: 'lines', name: 'rho', legendgroup: 'rho', line: { color: "green", width: 2, dash: "dot" }, showlegend: false });
+  traces.push({ x: smooth_profile.z, y: smooth_profile.rho, mode: 'lines', name: 'rho', legendgroup: 'rho', line: { color: "green", width: 2 } });
 
-  traces.push({ x: step_profile.z, y: step_profile.irho, mode: 'lines', name: 'irho', line: { color: "blue", width: 2, dash: "dot" }, showlegend: false });
-  traces.push({ x: smooth_profile.z, y: smooth_profile.irho, mode: 'lines', name: 'irho', line: { color: "blue", width: 2 } });
+  traces.push({ x: step_profile.z, y: step_profile.irho, mode: 'lines', name: 'irho', legendgroup: 'irho', line: { color: "blue", width: 2, dash: "dot" }, showlegend: false });
+  traces.push({ x: smooth_profile.z, y: smooth_profile.irho, mode: 'lines', name: 'irho', legendgroup: 'irho', line: { color: "blue", width: 2 } });
 
   if (step_profile.rhoM && smooth_profile.rhoM) {
-    traces.push({ x: step_profile.z, y: step_profile.rhoM, mode: 'lines', name: 'rhoM', line: { color: "red", width: 2, dash: "dot" }, showlegend: false });
-    traces.push({ x: smooth_profile.z, y: smooth_profile.rhoM, mode: 'lines', name: 'rhoM', line: { color: "red", width: 2 } });
+    traces.push({ x: step_profile.z, y: step_profile.rhoM, mode: 'lines', name: 'rhoM', legendgroup: 'rhoM', line: { color: "red", width: 2, dash: "dot" }, showlegend: false });
+    traces.push({ x: smooth_profile.z, y: smooth_profile.rhoM, mode: 'lines', name: 'rhoM', legendgroup: 'rhoM', line: { color: "red", width: 2 } });
   }
 
   if (step_profile.thetaM && smooth_profile.thetaM) {
-    traces.push({ x: step_profile.z, y: step_profile.thetaM, mode: 'lines', name: 'thetaM', yaxis: "y2", line: { color: "gold", width: 2, dash: "dot" }, showlegend: false });
-    traces.push({ x: smooth_profile.z, y: smooth_profile.thetaM, mode: 'lines', name: 'thetaM', yaxis: "y2", line: { color: "gold", width: 2 } });
+    traces.push({ x: step_profile.z, y: step_profile.thetaM, mode: 'lines', name: 'thetaM', legendgroup: 'thetaM', yaxis: "y2", line: { color: "gold", width: 2, dash: "dot" }, showlegend: false });
+    traces.push({ x: smooth_profile.z, y: smooth_profile.thetaM, mode: 'lines', name: 'thetaM', legendgroup: 'thetaM', yaxis: "y2", line: { color: "gold", width: 2 } });
   }
 
   return traces;
@@ -102,43 +102,6 @@ function fetch_and_draw() {
 
     const plot = await Plotly.react(plot_div.value, [...traces], layout, config);
 
-    let legend_click_timeout: number | undefined;
-
-    plot.removeAllListeners('plotly_legendclick');
-    plot.on('plotly_legendclick', (ev) => {
-      // match visibility of step and smooth profiles:
-      const dbl_clicked = (legend_click_timeout !== undefined);
-      if (dbl_clicked) {
-        clearTimeout(legend_click_timeout);
-        legend_click_timeout = undefined;
-      }
-      const { config, curveNumber, data } = ev;
-      const visibility = data.map((d) => d.visible ?? true);
-      const current_is_visible = (visibility[curveNumber] === true);
-      if (dbl_clicked) {
-        // algorithm is to make all visible if any are hidden, 
-        // or hide all but clicked if all are visible.
-        const some_hidden = visibility.some(v => (v !== true));
-        let visibility_update: (boolean | 'legendonly' | undefined)[];
-        if (!some_hidden) {
-          visibility_update = data.map((_, i) => ((i === curveNumber - 1) || (i === curveNumber)) ? true : 'legendonly');
-        }
-        else {
-          visibility_update = data.map((_, i) => true);
-        }
-        Plotly.restyle(plot, { visible: visibility_update });
-      }
-      else {
-        const new_visibility = current_is_visible ? 'legendonly' : true;
-        const visibility_update = [new_visibility, new_visibility];
-        legend_click_timeout = setTimeout(() => {
-          Plotly.restyle(plot, { visible: visibility_update }, [curveNumber - 1, curveNumber]);
-          legend_click_timeout = undefined;
-        }, config.doubleClickDelay);
-      }
-      return false;
-    });
-
   });
 }
 

From 99da3ef56d14d45bc97a4c88fc176484f228f93d Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 30 Nov 2022 09:20:33 -0500
Subject: [PATCH 086/221] adding Log view panel

---
 refl1d-web-gui/src/components/LogView.vue | 38 +++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 refl1d-web-gui/src/components/LogView.vue

diff --git a/refl1d-web-gui/src/components/LogView.vue b/refl1d-web-gui/src/components/LogView.vue
new file mode 100644
index 00000000..aca2d0ff
--- /dev/null
+++ b/refl1d-web-gui/src/components/LogView.vue
@@ -0,0 +1,38 @@
+<script setup lang="ts">
+import { ref, onMounted } from 'vue';
+import type { Socket } from 'socket.io-client';
+
+const title = "Log";
+
+const props = defineProps<{
+  socket: Socket,
+  visible: Boolean
+}>();
+
+const log_info = ref<string[]>([]);
+
+onMounted(() => {
+  props.socket.on('log', ({message}) => {
+    log_info.value.push(message);
+  });
+});
+
+</script>
+        
+<template>
+  <div class="log">
+    <pre class="message" v-for="(message, index) of log_info" :key="index">{{message}}</pre>
+  </div>
+</template>
+    
+<style scoped>
+
+div.log {
+  white-space: nowrap;
+}
+
+.message {
+  font-family: 'Courier New', Courier, monospace;
+  line-height: 1em;
+}
+</style>
\ No newline at end of file

From 9675a89ebfcfd957e5655de68086ff379e19938f Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 30 Nov 2022 09:20:44 -0500
Subject: [PATCH 087/221] use LogView panel

---
 refl1d-web-gui/src/App.vue | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/refl1d-web-gui/src/App.vue b/refl1d-web-gui/src/App.vue
index a221954e..0eb55b7e 100644
--- a/refl1d-web-gui/src/App.vue
+++ b/refl1d-web-gui/src/App.vue
@@ -11,11 +11,14 @@ import SummaryView from './components/SummaryView.vue';
 import ModelInspect from './components/ModelInspect.vue';
 import ModelViewPlotly from './components/ModelViewPlotly.vue';
 import ParameterView from './components/ParameterView.vue';
+import LogView from './components/LogView.vue';
+
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
 
 const panels = [
   {title: 'Reflectivity', component: DataView},
   {title: 'Summary', component: SummaryView},
+  {title: 'Log', component: LogView},
   {title: 'Profile', component: ModelView},
   {title: 'Model', component: ModelInspect},
   {title: 'Profile2', component: ModelViewPlotly},
@@ -88,10 +91,14 @@ function startFit() {
 
   if (fitter_active && fitter_settings) {
     const fit_args = fitter_settings[fitter_active];
-    socket.emit("start_fit", fitter_active, fit_args);
+    socket.emit("start_fit_thread", fitter_active, fit_args);
   }
 }
 
+function stopFit() {
+  socket.emit("stop_fit")
+}
+
 onMounted(() => {
   const menuToggleButton = new Button(menuToggle.value);
 });
@@ -146,7 +153,7 @@ onMounted(() => {
               </a>
               <ul class="dropdown-menu">
                 <li><a class="dropdown-item" href="#" @click="startFit">Start</a></li>
-                <li><a class="dropdown-item" href="#">Stop</a></li>
+                <li><a class="dropdown-item" href="#" @click="stopFit">Stop</a></li>
                 <li>
                   <hr class="dropdown-divider">
                 </li>

From c8c8b535ce0d9b8154db4645443ea67de5a94ed7 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 30 Nov 2022 09:39:54 -0500
Subject: [PATCH 088/221] adding main entrypoint for webview/server

---
 {refl1d-web-gui => refl1d/webview/client}/README.md |   0
 .../webview/client}/index.html                      |   0
 .../webview/client}/package.json                    |   0
 .../webview/client}/src/App.vue                     |   0
 .../client}/src/assets/refl1d-icon_256x256x32.png   | Bin
 .../client}/src/assets/refl1d-icon_48x48x32.png     | Bin
 .../webview/client}/src/components/DataView.vue     |   0
 .../webview/client}/src/components/FileBrowser.vue  |   0
 .../webview/client}/src/components/FitOptions.vue   |   0
 .../webview/client}/src/components/LogView.vue      |   0
 .../webview/client}/src/components/ModelInspect.vue |   0
 .../webview/client}/src/components/ModelView.vue    |   0
 .../client}/src/components/ModelViewPlotly.vue      |   0
 .../client}/src/components/PanelTabContainer.vue    |   0
 .../client}/src/components/ParameterView.vue        |   0
 .../webview/client}/src/components/SummaryView.vue  |   0
 .../webview/client}/src/fitter_defaults.ts          |   0
 .../webview/client}/src/main.js                     |   0
 .../webview/client}/src/style.css                   |   0
 .../webview/client}/vite.config.js                  |   0
 refl1d/webview/server/__main__.py                   |   3 +++
 refl1d/{ => webview/server}/webserver.py            |   0
 22 files changed, 3 insertions(+)
 rename {refl1d-web-gui => refl1d/webview/client}/README.md (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/index.html (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/package.json (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/App.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/assets/refl1d-icon_256x256x32.png (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/assets/refl1d-icon_48x48x32.png (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/DataView.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/FileBrowser.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/FitOptions.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/LogView.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/ModelInspect.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/ModelView.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/ModelViewPlotly.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/PanelTabContainer.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/ParameterView.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/components/SummaryView.vue (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/fitter_defaults.ts (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/main.js (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/src/style.css (100%)
 rename {refl1d-web-gui => refl1d/webview/client}/vite.config.js (100%)
 create mode 100644 refl1d/webview/server/__main__.py
 rename refl1d/{ => webview/server}/webserver.py (100%)

diff --git a/refl1d-web-gui/README.md b/refl1d/webview/client/README.md
similarity index 100%
rename from refl1d-web-gui/README.md
rename to refl1d/webview/client/README.md
diff --git a/refl1d-web-gui/index.html b/refl1d/webview/client/index.html
similarity index 100%
rename from refl1d-web-gui/index.html
rename to refl1d/webview/client/index.html
diff --git a/refl1d-web-gui/package.json b/refl1d/webview/client/package.json
similarity index 100%
rename from refl1d-web-gui/package.json
rename to refl1d/webview/client/package.json
diff --git a/refl1d-web-gui/src/App.vue b/refl1d/webview/client/src/App.vue
similarity index 100%
rename from refl1d-web-gui/src/App.vue
rename to refl1d/webview/client/src/App.vue
diff --git a/refl1d-web-gui/src/assets/refl1d-icon_256x256x32.png b/refl1d/webview/client/src/assets/refl1d-icon_256x256x32.png
similarity index 100%
rename from refl1d-web-gui/src/assets/refl1d-icon_256x256x32.png
rename to refl1d/webview/client/src/assets/refl1d-icon_256x256x32.png
diff --git a/refl1d-web-gui/src/assets/refl1d-icon_48x48x32.png b/refl1d/webview/client/src/assets/refl1d-icon_48x48x32.png
similarity index 100%
rename from refl1d-web-gui/src/assets/refl1d-icon_48x48x32.png
rename to refl1d/webview/client/src/assets/refl1d-icon_48x48x32.png
diff --git a/refl1d-web-gui/src/components/DataView.vue b/refl1d/webview/client/src/components/DataView.vue
similarity index 100%
rename from refl1d-web-gui/src/components/DataView.vue
rename to refl1d/webview/client/src/components/DataView.vue
diff --git a/refl1d-web-gui/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
similarity index 100%
rename from refl1d-web-gui/src/components/FileBrowser.vue
rename to refl1d/webview/client/src/components/FileBrowser.vue
diff --git a/refl1d-web-gui/src/components/FitOptions.vue b/refl1d/webview/client/src/components/FitOptions.vue
similarity index 100%
rename from refl1d-web-gui/src/components/FitOptions.vue
rename to refl1d/webview/client/src/components/FitOptions.vue
diff --git a/refl1d-web-gui/src/components/LogView.vue b/refl1d/webview/client/src/components/LogView.vue
similarity index 100%
rename from refl1d-web-gui/src/components/LogView.vue
rename to refl1d/webview/client/src/components/LogView.vue
diff --git a/refl1d-web-gui/src/components/ModelInspect.vue b/refl1d/webview/client/src/components/ModelInspect.vue
similarity index 100%
rename from refl1d-web-gui/src/components/ModelInspect.vue
rename to refl1d/webview/client/src/components/ModelInspect.vue
diff --git a/refl1d-web-gui/src/components/ModelView.vue b/refl1d/webview/client/src/components/ModelView.vue
similarity index 100%
rename from refl1d-web-gui/src/components/ModelView.vue
rename to refl1d/webview/client/src/components/ModelView.vue
diff --git a/refl1d-web-gui/src/components/ModelViewPlotly.vue b/refl1d/webview/client/src/components/ModelViewPlotly.vue
similarity index 100%
rename from refl1d-web-gui/src/components/ModelViewPlotly.vue
rename to refl1d/webview/client/src/components/ModelViewPlotly.vue
diff --git a/refl1d-web-gui/src/components/PanelTabContainer.vue b/refl1d/webview/client/src/components/PanelTabContainer.vue
similarity index 100%
rename from refl1d-web-gui/src/components/PanelTabContainer.vue
rename to refl1d/webview/client/src/components/PanelTabContainer.vue
diff --git a/refl1d-web-gui/src/components/ParameterView.vue b/refl1d/webview/client/src/components/ParameterView.vue
similarity index 100%
rename from refl1d-web-gui/src/components/ParameterView.vue
rename to refl1d/webview/client/src/components/ParameterView.vue
diff --git a/refl1d-web-gui/src/components/SummaryView.vue b/refl1d/webview/client/src/components/SummaryView.vue
similarity index 100%
rename from refl1d-web-gui/src/components/SummaryView.vue
rename to refl1d/webview/client/src/components/SummaryView.vue
diff --git a/refl1d-web-gui/src/fitter_defaults.ts b/refl1d/webview/client/src/fitter_defaults.ts
similarity index 100%
rename from refl1d-web-gui/src/fitter_defaults.ts
rename to refl1d/webview/client/src/fitter_defaults.ts
diff --git a/refl1d-web-gui/src/main.js b/refl1d/webview/client/src/main.js
similarity index 100%
rename from refl1d-web-gui/src/main.js
rename to refl1d/webview/client/src/main.js
diff --git a/refl1d-web-gui/src/style.css b/refl1d/webview/client/src/style.css
similarity index 100%
rename from refl1d-web-gui/src/style.css
rename to refl1d/webview/client/src/style.css
diff --git a/refl1d-web-gui/vite.config.js b/refl1d/webview/client/vite.config.js
similarity index 100%
rename from refl1d-web-gui/vite.config.js
rename to refl1d/webview/client/vite.config.js
diff --git a/refl1d/webview/server/__main__.py b/refl1d/webview/server/__main__.py
new file mode 100644
index 00000000..d764dfdc
--- /dev/null
+++ b/refl1d/webview/server/__main__.py
@@ -0,0 +1,3 @@
+from .webserver import main
+
+main()
\ No newline at end of file
diff --git a/refl1d/webserver.py b/refl1d/webview/server/webserver.py
similarity index 100%
rename from refl1d/webserver.py
rename to refl1d/webview/server/webserver.py

From f72e622f0337782431ba99e96c83f74062997c54 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 30 Nov 2022 09:41:46 -0500
Subject: [PATCH 089/221] working fit_thread

---
 refl1d/webview/server/webserver.py | 97 +++++++++++++++++++++++++++++-
 1 file changed, 95 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index edfa5529..0d261a65 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -3,6 +3,7 @@
 from typing import Dict, List, Literal, Optional, Union, TypedDict
 from datetime import datetime
 import warnings
+from queue import Queue
 from aiohttp import web
 import numpy as np
 import asyncio
@@ -10,6 +11,7 @@
 from pathlib import Path, PurePath
 import json
 from copy import deepcopy
+from blinker import Signal
 
 import mimetypes
 mimetypes.add_type("text/css", ".css")
@@ -28,6 +30,11 @@
 import refl1d.fitproblem, refl1d.probe
 from refl1d.experiment import Experiment
 
+from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
+
+# can get by name and not just by id
+EVT_LOG = Signal('log')
+
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
 FITTERS_BY_ID = dict([(fitter.id, fitter) for fitter in FITTERS])
 print(FITTERS_BY_ID)
@@ -43,14 +50,21 @@
 # sio = socketio.AsyncServer(cors_allowed_origins="*", serializer='msgpack')
 sio = socketio.AsyncServer(cors_allowed_origins="*")
 app = web.Application()
-static_dir_path = Path(__file__).parent / 'webview'
+static_dir_path = Path(__file__).parent.parent / 'client' / 'dist'
 sio.attach(app)
 
 topics: Dict[str, Dict] = {}
 app["topics"] = topics
 app["problem"] = {"fitProblem": None, "filepath": None}
+app["fitting"] = {
+    "fit_thread": None,
+    "abort": False,
+    "uncertainty_state": None,
+    "abort_queue": Queue(),
+}
 problem = None
 
+
 def rest_get(fn):
     """
     Add a REST (GET) route for the function, which can also be used for 
@@ -100,6 +114,81 @@ async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
     x, fx = driver.fit()
     driver.show()
 
+@sio.event
+async def stop_fit(sid: str):
+    abort_queue: Queue = app["fitting"]["abort_queue"]
+    abort_queue.put(True)
+
+@sio.event
+async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
+    options = {} if options is None else options
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    fitclass = FITTERS_BY_ID[fitter_id]
+    if app["problem"].get("fit_thread", None) is not None:
+        # warn that fit is alread running...
+        print("fit already running...")
+        return
+    
+    # TODO: better access to model parameters
+    if len(fitProblem.getp()) == 0:
+        raise ValueError("Problem has no fittable parameters")
+
+    # Start a new thread worker and give fit problem to the worker.
+    # Clear abort and uncertainty state
+    app["fitting"]["abort"] = False
+    app["fitting"]["uncertainty_state"] = None
+    abort_queue: Queue = app["fitting"]["abort_queue"]
+    for _ in range(abort_queue.qsize()):
+        abort_queue.get_nowait()
+        abort_queue.task_done()
+    fit_thread = FitThread(
+        abort_queue=abort_queue,
+        problem=fitProblem,
+        fitclass=fitclass,
+        options=options,
+        # Number of seconds between updates to the GUI, or 0 for no updates
+        convergence_update=5,
+        uncertainty_update=3600,
+        )
+    fit_thread.start()
+    await publish("", "fit_active", True)
+
+def fit_progress_handler(event):
+    print("event: ", event)
+    message = event.get("message", None)
+    if message == 'complete' or message == 'improvement':
+        fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+        fitProblem.setp(event["point"])
+        fitProblem.model_update()
+        asyncio.run_coroutine_threadsafe(publish("", "update_parameters", True), app.loop)
+    if message == 'complete':
+        asyncio.run_coroutine_threadsafe(publish("", "fit_active", False), app.loop)
+
+EVT_FIT_PROGRESS.connect(fit_progress_handler)
+
+def fit_complete_handler(event):
+    print("event: ", event)
+    message = event.get("message", None)
+    fit_thread = app["fitting"]["fit_thread"]
+    if fit_thread is not None:
+        fit_thread.join(1) # 1 second timeout on join
+        if fit_thread.is_alive():
+            EVT_LOG.send("fit thread failed to complete")
+    app["fitting"]["fit_thread"] = None
+    problem: refl1d.fitproblem.FitProblem = event["problem"]
+    chisq = nice(2*event["value"]/problem.dof)
+    problem.setp(event["point"])
+    problem.model_update()
+    asyncio.run_coroutine_threadsafe(publish("", "update_parameters", True), app.loop)
+    EVT_LOG.send("done with chisq %g"%chisq)
+    EVT_LOG.send(event["info"])
+
+EVT_FIT_COMPLETE.connect(fit_complete_handler)
+
+def log_handler(message):
+    asyncio.run_coroutine_threadsafe(publish("", "log", message), app.loop)
+
+EVT_LOG.connect(log_handler)
 
 def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
     fresnel_calculator = probe.fresnel(substrate, surface)
@@ -276,6 +365,7 @@ async def publish(sid: str, topic: str, message):
     contents = {"message": message, "timestamp": timestamp_str}
     topics[topic] = contents
     await sio.emit(topic, contents)
+    # print("emitted: ", topic, contents)
 
 @sio.event
 @rest_get
@@ -378,7 +468,10 @@ def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[Param
             lookup[params.id] = new_item
     return list(lookup.values())
 
-if __name__ == '__main__':
+def main():
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     app.add_routes(routes)
     web.run_app(app)
+
+if __name__ == '__main__':
+    main()

From 1dcfba0f5e43ea31311003b609843ca85a2db833 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 30 Nov 2022 09:42:00 -0500
Subject: [PATCH 090/221] adding fit_thread for webserver

---
 refl1d/webview/server/fit_thread.py | 229 ++++++++++++++++++++++++++++
 1 file changed, 229 insertions(+)
 create mode 100644 refl1d/webview/server/fit_thread.py

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
new file mode 100644
index 00000000..de71afef
--- /dev/null
+++ b/refl1d/webview/server/fit_thread.py
@@ -0,0 +1,229 @@
+
+from copy import deepcopy
+from threading import Thread
+from queue import Queue
+
+from blinker import Signal
+
+from bumps import monitor
+from bumps.fitters import FitDriver
+from bumps.mapper import MPMapper, SerialMapper, can_pickle
+from bumps.util import redirect_console
+
+#from .convergence_view import ConvergenceMonitor
+# ==============================================================================
+
+PROGRESS_DELAY = 5
+IMPROVEMENT_DELAY = 5
+
+EVT_FIT_PROGRESS = Signal()
+EVT_FIT_COMPLETE = Signal()
+
+# NOTE: GUI monitors are running in a separate thread.  They should not
+# touch the problem internals.
+
+
+class GUIProgressMonitor(monitor.TimedUpdate):
+    def __init__(self, problem, progress=None, improvement=None):
+        monitor.TimedUpdate.__init__(
+            self, progress=progress or PROGRESS_DELAY,
+            improvement=improvement or IMPROVEMENT_DELAY)
+        self.problem = problem
+
+    def show_progress(self, history):
+        evt = dict(
+            problem=self.problem,
+            message="progress",
+            step=history.step[0],
+            value=history.value[0],
+            point=history.point[0]+0)  # avoid race
+        EVT_FIT_PROGRESS.send(evt)
+
+    def show_improvement(self, history):
+        evt = dict(
+            problem=self.problem,
+            message="improvement",
+            step=history.step[0],
+            value=history.value[0],
+            point=history.point[0]+0)  # avoid race
+        EVT_FIT_PROGRESS.send(evt)
+
+
+class GUIMonitor(monitor.Monitor):
+    """
+    Generic GUI monitor for fitting.
+
+    Sends a fit progress event to the selected window every *rate*
+    seconds. The *monitor* is a bumps monitor which processes fit
+    history as it arrives. Instead of the usual *show_progress* method
+    to update the managing process it has a *progress* method which
+    returns a dictionary of progress attributes.  These attributes are
+    added to a *FitProgressEvent* along with *problem* and *message* which
+    is then posted to *win*.
+
+    *problem* should be the fit problem handed to the fit thread, and not
+    a copy. This is because it is used for direct comparison with the current
+    fit object in the progress panels so that stray messages don't cause
+    confusion when making graphs.
+
+    *message* is a dispatch string used by the OnFitProgress event processor
+    in the app to determine which progress panel should receive the event.
+
+    TODO: this is a pretty silly design, especially since GUI monitor is only
+    used for the convergence plot, and a separate monitor class was created
+    for DREAM progress updates.
+    """
+
+    def __init__(self, problem, message, monitor, rate=0):
+        self.time = 0
+        self.rate = rate  # rate=0 for no progress update, only final
+        self.problem = problem
+        self.message = message
+        self.monitor = monitor
+
+    def config_history(self, history):
+        self.monitor.config_history(history)
+        history.requires(time=1)
+
+    def __call__(self, history):
+        self.monitor(history)
+        if self.rate > 0 and history.time[0] >= self.time+self.rate:
+            evt = dict(
+                problem=self.problem,
+                message=self.message,
+                **self.monitor.progress())
+            EVT_FIT_PROGRESS.send(evt)
+            self.time = history.time[0]
+
+    def final(self):
+        """
+        Close out the monitor
+        """
+        evt = dict(
+            problem=self.problem,
+            message=self.message,
+            **self.monitor.progress())
+        EVT_FIT_PROGRESS.send(evt)
+
+# Horrible hacks:
+# (1) We are grabbing uncertainty_state from the history on monitor update
+# and holding onto it for the monitor final call. Need to restructure the
+# history/monitor interaction so that object lifetimes are better controlled.
+# (2) We set the uncertainty state directly in the GUI window. This is an
+# attempt to work around a memory leak which causes problems in the GUI when
+# it is updated too frequently. If the problem is that the event structure
+# is too large and wx isn't cleaning up properly then this should address it,
+# but if the problem lies within the DREAM plot functions or within matplotlib
+# then this change won't do anything and should be reverted.
+
+
+class DreamMonitor(monitor.Monitor):
+    def __init__(self, problem, message, fitter, rate=0):
+        self.time = 0
+        self.rate = rate  # rate=0 for no progress update, only final
+        self.problem = problem
+        self.fitter = fitter
+        self.message = message
+        self.uncertainty_state = None
+
+    def config_history(self, history):
+        history.requires(time=1)
+
+    def __call__(self, history):
+        self.uncertainty_state = getattr(history, 'uncertainty_state', None)
+        if (self.rate > 0 and history.time[0] >= self.time+self.rate
+                and self.uncertainty_state is not None):
+            # Note: win.uncertainty_state protected by win.fit_lock
+            self.time = history.time[0]
+            #self.win.uncertainty_state = self.uncertainty_state
+            evt = dict(
+                problem=self.problem,
+                message="uncertainty_update",
+                # uncertainty_state=deepcopy(self.uncertainty_state),
+            )
+            EVT_FIT_PROGRESS.send(evt)
+
+    def final(self):
+        """
+        Close out the monitor
+        """
+        if self.uncertainty_state is not None:
+            # Note: win.uncertainty_state protected by win.fit_lock
+            # self.win.uncertainty_state = self.uncertainty_state
+            evt = dict(
+                problem=self.problem,
+                message="uncertainty_final",
+                # uncertainty_state=deepcopy(self.uncertainty_state),
+            )
+            EVT_FIT_PROGRESS.send(evt)
+
+# ==============================================================================
+
+
+class FitThread(Thread):
+    """Run the fit in a separate thread from the GUI thread."""
+
+    def __init__(self, abort_queue=None, problem=None,
+                 fitclass=None, options=None, mapper=None,
+                 convergence_update=5, uncertainty_update=300):
+        # base class initialization
+        # Process.__init__(self)
+
+        Thread.__init__(self)
+        self.abort_queue: Queue = abort_queue
+        self.problem = problem
+        self.fitclass = fitclass
+        self.options = options if isinstance(options, dict) else dict()
+        self.mapper = mapper
+        self.convergence_update = convergence_update
+        self.uncertainty_update = uncertainty_update
+
+    def abort_test(self):
+        return not self.abort_queue.empty()
+
+    def run(self):
+        # TODO: we have no interlocks on changes in problem state.  What
+        # happens when the user changes the problem while a fit is being run?
+        # May want to keep a history of changes to the problem definition,
+        # along with a function to reverse them so we can handle undo.
+
+        # NOTE: Problem must be the original problem (not a copy) when used
+        # inside the GUI monitor otherwise AppPanel will not be able to
+        # recognize that it is the same problem when updating views.
+        monitors = [GUIProgressMonitor(self.problem),
+                    # GUIMonitor(self.problem,
+                    #            message="convergence_update",
+                    #            monitor=ConvergenceMonitor(),
+                    #            rate=self.convergence_update),
+                    DreamMonitor(self.problem,
+                                 fitter=self.fitclass,
+                                 message="uncertainty_update",
+                                 rate=self.uncertainty_update),
+                    ]
+        # Only use parallel if the problem can be pickled
+        mapper = MPMapper if can_pickle(self.problem) else SerialMapper
+
+        # Be safe and send a private copy of the problem to the fitting engine
+        # print "fitclass",self.fitclass
+        problem = deepcopy(self.problem)
+        # print "fitclass id",id(self.fitclass),self.fitclass,threading.current_thread()
+        driver = FitDriver(
+            self.fitclass, problem=problem,
+            monitors=monitors, abort_test=self.abort_test,
+            mapper=mapper.start_mapper(problem, []),
+            **self.options)
+
+        x, fx = driver.fit()
+        # Give final state message from monitors
+        for M in monitors:
+            if hasattr(M, 'final'):
+                M.final()
+
+        with redirect_console() as fid:
+            driver.show()
+            captured_output = fid.getvalue()
+
+        evt = dict(message="complete", problem=self.problem,
+                   point=x, value=fx, info=captured_output)
+        EVT_FIT_COMPLETE.send(evt)
+        self.result = evt

From 03e63df9bbac4e589d7d481191cc3111f1ac8ce4 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 30 Nov 2022 09:50:33 -0500
Subject: [PATCH 091/221] build in local dist dir now

---
 refl1d/webview/client/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index b71bb585..7a56978e 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -3,7 +3,7 @@
   "version": "0.0.0",
   "scripts": {
     "dev": "vite",
-    "build": "vite build --outDir ../refl1d/webview --emptyOutDir",
+    "build": "vite build --outDir dist --emptyOutDir",
     "preview": "vite preview --port 4173"
   },
   "dependencies": {

From 9919b84b7ff983975708293feb1f075557b75fb7 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 15:51:54 -0500
Subject: [PATCH 092/221] allow passing fig object to show_errors (for GUI)

---
 refl1d/errors.py | 109 +++++++++++++++++++++++++++--------------------
 1 file changed, 62 insertions(+), 47 deletions(-)

diff --git a/refl1d/errors.py b/refl1d/errors.py
index 431125cc..59fbe6d2 100644
--- a/refl1d/errors.py
+++ b/refl1d/errors.py
@@ -229,7 +229,7 @@ def align_profiles(profiles, slabs, align):
                 for m in profiles.keys())
 
 def show_errors(errors, contours=CONTOURS, npoints=200,
-                align='auto', plots=1, save=None):
+                align='auto', plots=1, save=None, fig=None):
     """
     Plot the aligned profiles and the distribution of the residuals for
     profiles and residuals returned from calc_errors.
@@ -259,15 +259,20 @@ def show_errors(errors, contours=CONTOURS, npoints=200,
     """
     import matplotlib.pyplot as plt
 
+    if fig is not None and plots != 1:
+        raise ValueError("can only pass in a figure object if exactly 1 plot is requested")
+
     if plots == 0: # Don't create plots, just save the data
         _save_profile_data(errors, contours=contours, npoints=npoints,
                            align=align, save=save)
         _save_residual_data(errors, contours=contours, save=save)
     elif plots == 1: # Subplots for profiles/residuals
-        plt.subplot(211)
-        show_profiles(errors, contours=contours, npoints=npoints, align=align)
-        plt.subplot(212)
-        show_residuals(errors, contours=contours)
+        if fig is None:
+            fig = plt.gcf()
+        ax_profiles = fig.add_subplot(211)
+        show_profiles(errors, contours=contours, npoints=npoints, align=align, axes=ax_profiles)
+        ax_residuals = fig.add_subplot(212)
+        show_residuals(errors, contours=contours, axes=ax_residuals)
         if save:
             plt.savefig(save+"-err.png")
     elif plots == 2:  # Separate plots for profiles/residuals
@@ -296,24 +301,24 @@ def show_errors(errors, contours=CONTOURS, npoints=200,
                 plt.savefig(save+"-err%d.png"%fignum)
             fignum += 1
 
-def show_profiles(errors, align, contours, npoints):
+def show_profiles(errors, align, contours, npoints, axes=None):
     profiles, slabs, _, _ = errors
     if align is not None:
         profiles = align_profiles(profiles, slabs, align)
 
     if contours:
-        _profiles_contour(profiles, contours, npoints)
+        _profiles_contour(profiles, contours, npoints, axes=axes)
     else:
-        _profiles_overplot(profiles)
+        _profiles_overplot(profiles, axes=axes)
 
 
-def show_residuals(errors, contours):
+def show_residuals(errors, contours, axes=None):
     _, _, Q, residuals = errors
 
     if False and contours:
         _residuals_contour(Q, residuals, contours=contours)
     else:
-        _residuals_overplot(Q, residuals)
+        _residuals_overplot(Q, residuals, axes=axes)
 
 
 def _save_profile_data(errors, align, contours, npoints, save):
@@ -376,34 +381,36 @@ def _write_file(path, data, title, columns):
 def dark(color):
     return dhsv(color, dv=-0.2)
 
-def _profiles_overplot(profiles):
+def _profiles_overplot(profiles, axes=None):
     for model, group in profiles.items():
         name = model.name
         absorbing = any((L[2] != 1e-4).any() for L in group)
         magnetic = (len(group[0]) > 3)
         # Note: Use 3 colours per dataset for consistency
-        _draw_overplot(group, 1, name + ' rho')
+        _draw_overplot(group, 1, name + ' rho', axes=axes)
         if absorbing:
-            _draw_overplot(group, 2, name + ' irho')
+            _draw_overplot(group, 2, name + ' irho', axes=axes)
         else:
-            next_color()
+            next_color(axes=axes)
         if magnetic:
-            _draw_overplot(group, 3, name + ' rhoM')
+            _draw_overplot(group, 3, name + ' rhoM', axes=axes)
         else:
-            next_color()
-    _profile_labels()
+            next_color(axes=axes)
+    _profile_labels(axes=axes)
 
-def _draw_overplot(group, index, label):
+def _draw_overplot(group, index, label, axes=None):
     import matplotlib.pyplot as plt
+    if axes is None:
+        axes = plt.gca()
     alpha = 0.1
-    color = next_color()
+    color = next_color(axes=axes)
     for L in group[1:]:
-        plt.plot(L[0], L[index], '-', color=color, alpha=alpha)
+        axes.plot(L[0], L[index], '-', color=color, alpha=alpha)
     # Plot best
     L = group[0]
-    plt.plot(L[0], L[index], '-', label=label, color=dark(color))
+    axes.plot(L[0], L[index], '-', label=label, color=dark(color))
 
-def _profiles_contour(profiles, contours=CONTOURS, npoints=200):
+def _profiles_contour(profiles, contours=CONTOURS, npoints=200, axes=None):
     for model, group in profiles.items():
         name = model.name if model.name is not None else 'model'
         absorbing = any((L[2] > 1e-4).any() for L in group)
@@ -412,46 +419,52 @@ def _profiles_contour(profiles, contours=CONTOURS, npoints=200):
         z = np.hstack([line[0] for line in group])
         zp = np.linspace(np.min(z), np.max(z), npoints)
         # Note: Use 3 colours per dataset for consistency
-        _draw_contours(group, 1, name + ' rho', zp, contours)
+        _draw_contours(group, 1, name + ' rho', zp, contours, axes=axes)
         if absorbing:
-            _draw_contours(group, 2, name + ' irho', zp, contours)
+            _draw_contours(group, 2, name + ' irho', zp, contours, axes=axes)
         else:
-            next_color()
+            next_color(axes=axes)
         if magnetic:
-            _draw_contours(group, 3, name + ' rhoM', zp, contours)
+            _draw_contours(group, 3, name + ' rhoM', zp, contours, axes=axes)
         else:
-            next_color()
-    _profile_labels()
+            next_color(axes=axes)
+    _profile_labels(axes=axes)
 
-def _draw_contours(group, index, label, zp, contours):
+def _draw_contours(group, index, label, zp, contours, axes=None):
     import matplotlib.pyplot as plt
-    color = next_color()
+    if axes is None:
+        axes = plt.gca()
+    color = next_color(axes=axes)
     # Interpolate on common z
     fp = np.vstack([np.interp(zp, L[0], L[index]) for L in group])
     # Plot the quantiles
-    plot_quantiles(zp, fp, contours, color)
+    plot_quantiles(zp, fp, contours, color, axes=axes)
     # Plot the best
-    plt.plot(zp, fp[0], '-', label=label, color=dark(color))
+    axes.plot(zp, fp[0], '-', label=label, color=dark(color))
 
-def _profile_labels():
+def _profile_labels(axes=None):
     import matplotlib.pyplot as plt
-    plt.legend()
-    plt.xlabel(u'z (Å)')
-    plt.ylabel(u'SLD (10⁻⁶/Ų)')
+    if axes is None:
+        axes = plt.gca()
+    axes.legend()
+    axes.set_xlabel(u'z (Å)')
+    axes.set_ylabel(u'SLD (10⁻⁶/Ų)')
 
-def _residuals_overplot(Q, residuals):
+def _residuals_overplot(Q, residuals, axes=None):
     import matplotlib.pyplot as plt
+    if axes is None:
+        axes = plt.gca()
     alpha = 0.4
     shift = 0
     for m, r in residuals.items():
-        color = next_color()
-        plt.plot(Q[m], shift+r[:, 1:], '.', markersize=1, color=color, alpha=alpha)
-        plt.plot(Q[m], shift+r[:, 0], '.', label=m.name, markersize=1, color=dark(color))
+        color = next_color(axes=axes)
+        axes.plot(Q[m], shift+r[:, 1:], '.', markersize=1, color=color, alpha=alpha)
+        axes.plot(Q[m], shift+r[:, 0], '.', label=m.name, markersize=1, color=dark(color))
         # Use 3 colours from cycle so reflectivity matches rho for each dataset
-        next_color()
-        next_color()
+        next_color(axes=axes)
+        next_color(axes=axes)
         shift += 5
-    _residuals_labels()
+    _residuals_labels(axes=axes)
 
 def _residuals_contour(Q, residuals, contours=CONTOURS):
     import matplotlib.pyplot as plt
@@ -466,11 +479,13 @@ def _residuals_contour(Q, residuals, contours=CONTOURS):
         shift += 5
     _residuals_labels()
 
-def _residuals_labels():
+def _residuals_labels(axes=None):
     import matplotlib.pyplot as plt
-    plt.legend()
-    plt.xlabel(u'Q (1/Å)')
-    plt.ylabel(u'Residuals')
+    if axes is None:
+        axes = plt.gca()
+    axes.legend()
+    axes.set_xlabel(u'Q (1/Å)')
+    axes.set_ylabel(u'Residuals')
 
 # ==== Helper functions =====
 

From 8ae8b17b1439120135fafb233ad080033faa90db Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 15:53:40 -0500
Subject: [PATCH 093/221] adding new panels to webview client

---
 .../client/src/components/ConvergenceView.vue | 64 +++++++++++++++++++
 .../client/src/components/CorrelationView.vue | 64 +++++++++++++++++++
 .../src/components/ModelUncertaintyView.vue   | 64 +++++++++++++++++++
 .../src/components/ParameterTraceView.vue     | 64 +++++++++++++++++++
 .../client/src/components/UncertaintyView.vue | 64 +++++++++++++++++++
 5 files changed, 320 insertions(+)
 create mode 100644 refl1d/webview/client/src/components/ConvergenceView.vue
 create mode 100644 refl1d/webview/client/src/components/CorrelationView.vue
 create mode 100644 refl1d/webview/client/src/components/ModelUncertaintyView.vue
 create mode 100644 refl1d/webview/client/src/components/ParameterTraceView.vue
 create mode 100644 refl1d/webview/client/src/components/UncertaintyView.vue

diff --git a/refl1d/webview/client/src/components/ConvergenceView.vue b/refl1d/webview/client/src/components/ConvergenceView.vue
new file mode 100644
index 00000000..e30cf9fa
--- /dev/null
+++ b/refl1d/webview/client/src/components/ConvergenceView.vue
@@ -0,0 +1,64 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import mpld3 from 'mpld3';
+
+const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
+const drawing_busy = ref(false);
+const plot_div_id = ref(`div-${uuidv4()}`);
+const props = defineProps<{
+  socket: Socket,
+  visible: boolean
+}>();
+
+onMounted(() => {
+  props.socket.on('convergence_update', () => {
+    draw_requested.value = true;
+  });
+  window.requestAnimationFrame(draw_if_needed);
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_convergence_plot', (payload) => {
+    if (props.visible) {
+      let plotdata = { ...payload };
+      // console.log({plotdata});
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+      /* Data Parsing Functions */
+      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+    }
+    drawing_busy.value = false;
+  });
+}
+
+function draw_if_needed(timestamp: number) {
+  if (drawing_busy.value) {
+    console.log("busy!");
+  }
+  if (draw_requested.value && props.visible && !drawing_busy.value) {
+    drawing_busy.value = true;
+    draw_requested.value = false;
+    fetch_and_draw();
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/CorrelationView.vue b/refl1d/webview/client/src/components/CorrelationView.vue
new file mode 100644
index 00000000..3b43290e
--- /dev/null
+++ b/refl1d/webview/client/src/components/CorrelationView.vue
@@ -0,0 +1,64 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import mpld3 from 'mpld3';
+
+const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
+const drawing_busy = ref(false);
+const plot_div_id = ref(`div-${uuidv4()}`);
+const props = defineProps<{
+  socket: Socket,
+  visible: boolean
+}>();
+
+onMounted(() => {
+  props.socket.on('uncertainty_update', () => {
+    draw_requested.value = true;
+  });
+  window.requestAnimationFrame(draw_if_needed);
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_correlation_plot', (payload) => {
+    if (props.visible) {
+      let plotdata = { ...payload };
+      console.log({plotdata});
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+      /* Data Parsing Functions */
+      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+    }
+    drawing_busy.value = false;
+  });
+}
+
+function draw_if_needed(timestamp: number) {
+  if (drawing_busy.value) {
+    console.log("busy!");
+  }
+  if (draw_requested.value && props.visible && !drawing_busy.value) {
+    drawing_busy.value = true;
+    draw_requested.value = false;
+    fetch_and_draw();
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/ModelUncertaintyView.vue b/refl1d/webview/client/src/components/ModelUncertaintyView.vue
new file mode 100644
index 00000000..73cbab6e
--- /dev/null
+++ b/refl1d/webview/client/src/components/ModelUncertaintyView.vue
@@ -0,0 +1,64 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import mpld3 from 'mpld3';
+
+const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
+const drawing_busy = ref(false);
+const plot_div_id = ref(`div-${uuidv4()}`);
+const props = defineProps<{
+  socket: Socket,
+  visible: boolean
+}>();
+
+onMounted(() => {
+  props.socket.on('uncertainty_update', () => {
+    draw_requested.value = true;
+  });
+  window.requestAnimationFrame(draw_if_needed);
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_model_uncertainty_plot', (payload) => {
+    if (props.visible) {
+      let plotdata = { ...payload };
+      console.log({plotdata});
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+      /* Data Parsing Functions */
+      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+    }
+    drawing_busy.value = false;
+  });
+}
+
+function draw_if_needed(timestamp: number) {
+  if (drawing_busy.value) {
+    console.log("busy!");
+  }
+  if (draw_requested.value && props.visible && !drawing_busy.value) {
+    drawing_busy.value = true;
+    draw_requested.value = false;
+    fetch_and_draw();
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/ParameterTraceView.vue b/refl1d/webview/client/src/components/ParameterTraceView.vue
new file mode 100644
index 00000000..d912cd4d
--- /dev/null
+++ b/refl1d/webview/client/src/components/ParameterTraceView.vue
@@ -0,0 +1,64 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import mpld3 from 'mpld3';
+
+const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
+const drawing_busy = ref(false);
+const plot_div_id = ref(`div-${uuidv4()}`);
+const props = defineProps<{
+  socket: Socket,
+  visible: boolean
+}>();
+
+onMounted(() => {
+  props.socket.on('uncertainty_update', () => {
+    draw_requested.value = true;
+  });
+  window.requestAnimationFrame(draw_if_needed);
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_parameter_trace_plot', (payload) => {
+    if (props.visible) {
+      let plotdata = { ...payload };
+      console.log({plotdata});
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+      /* Data Parsing Functions */
+      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+    }
+    drawing_busy.value = false;
+  });
+}
+
+function draw_if_needed(timestamp: number) {
+  if (drawing_busy.value) {
+    console.log("busy!");
+  }
+  if (draw_requested.value && props.visible && !drawing_busy.value) {
+    drawing_busy.value = true;
+    draw_requested.value = false;
+    fetch_and_draw();
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/UncertaintyView.vue b/refl1d/webview/client/src/components/UncertaintyView.vue
new file mode 100644
index 00000000..d01f6197
--- /dev/null
+++ b/refl1d/webview/client/src/components/UncertaintyView.vue
@@ -0,0 +1,64 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import mpld3 from 'mpld3';
+
+const plot_div = ref<HTMLDivElement>();
+const draw_requested = ref(false);
+const drawing_busy = ref(false);
+const plot_div_id = ref(`div-${uuidv4()}`);
+const props = defineProps<{
+  socket: Socket,
+  visible: boolean
+}>();
+
+onMounted(() => {
+  props.socket.on('uncertainty_update', () => {
+    draw_requested.value = true;
+  });
+  window.requestAnimationFrame(draw_if_needed);
+});
+
+function fetch_and_draw() {
+  props.socket.emit('get_uncertainty_plot', (payload) => {
+    if (props.visible) {
+      let plotdata = { ...payload };
+      console.log({plotdata});
+      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+      /* Data Parsing Functions */
+      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
+      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+    }
+    drawing_busy.value = false;
+  });
+}
+
+function draw_if_needed(timestamp: number) {
+  if (drawing_busy.value) {
+    console.log("busy!");
+  }
+  if (draw_requested.value && props.visible && !drawing_busy.value) {
+    drawing_busy.value = true;
+    draw_requested.value = false;
+    fetch_and_draw();
+  }
+  window.requestAnimationFrame(draw_if_needed);
+}
+
+</script>
+    
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file

From ef73d3e61f2c8439dfcbd7ada006c99b610e5dda Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 15:54:48 -0500
Subject: [PATCH 094/221] send the correct options to the fitter (wasn't
 working before)

---
 refl1d/webview/client/src/App.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 0eb55b7e..3fd5e88a 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -91,7 +91,7 @@ function startFit() {
 
   if (fitter_active && fitter_settings) {
     const fit_args = fitter_settings[fitter_active];
-    socket.emit("start_fit_thread", fitter_active, fit_args);
+    socket.emit("start_fit_thread", fitter_active, fit_args.settings);
   }
 }
 

From f97cfbc42df6262219fd9c44e8b3337ede08cd6b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 15:55:08 -0500
Subject: [PATCH 095/221] use new fit results view panels in GUI

---
 refl1d/webview/client/src/App.vue | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 3fd5e88a..c65d7ceb 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -12,6 +12,11 @@ import ModelInspect from './components/ModelInspect.vue';
 import ModelViewPlotly from './components/ModelViewPlotly.vue';
 import ParameterView from './components/ParameterView.vue';
 import LogView from './components/LogView.vue';
+import ConvergenceView from './components/ConvergenceView.vue';
+import CorrelationView from './components/CorrelationView.vue';
+import ParameterTraceView from './components/ParameterTraceView.vue';
+import ModelUncertaintyView from './components/ModelUncertaintyView.vue';
+import UncertaintyView from './components/UncertaintyView.vue';
 
 // import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
 
@@ -19,10 +24,15 @@ const panels = [
   {title: 'Reflectivity', component: DataView},
   {title: 'Summary', component: SummaryView},
   {title: 'Log', component: LogView},
+  {title: 'Convergence', component: ConvergenceView},
   {title: 'Profile', component: ModelView},
   {title: 'Model', component: ModelInspect},
   {title: 'Profile2', component: ModelViewPlotly},
   {title: 'Parameters', component: ParameterView},
+  {title: 'Correlations', component: CorrelationView},
+  {title: 'Trace', component: ParameterTraceView},
+  {title: 'Model Uncertainty', component: ModelUncertaintyView},
+  {title: 'Uncertainty', component: UncertaintyView},
 ];
 
 const connected = ref(false);

From bae215f106e36ba8ecf4f1afa2a424eb71a53f21 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 15:56:41 -0500
Subject: [PATCH 096/221] working ConvergenceMonitor, composed of old
 GUIProgressMonitor mashed together with old ConvergenceMonitor

---
 refl1d/webview/server/fit_thread.py | 51 +++++++++++++++++------------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
index de71afef..8d7d51bf 100644
--- a/refl1d/webview/server/fit_thread.py
+++ b/refl1d/webview/server/fit_thread.py
@@ -5,10 +5,12 @@
 
 from blinker import Signal
 
+import numpy as np
 from bumps import monitor
 from bumps.fitters import FitDriver
 from bumps.mapper import MPMapper, SerialMapper, can_pickle
 from bumps.util import redirect_console
+from bumps.history import History
 
 #from .convergence_view import ConvergenceMonitor
 # ==============================================================================
@@ -49,17 +51,13 @@ def show_improvement(self, history):
         EVT_FIT_PROGRESS.send(evt)
 
 
-class GUIMonitor(monitor.Monitor):
+class ConvergenceMonitor(monitor.Monitor):
     """
     Generic GUI monitor for fitting.
 
-    Sends a fit progress event to the selected window every *rate*
-    seconds. The *monitor* is a bumps monitor which processes fit
-    history as it arrives. Instead of the usual *show_progress* method
-    to update the managing process it has a *progress* method which
-    returns a dictionary of progress attributes.  These attributes are
-    added to a *FitProgressEvent* along with *problem* and *message* which
-    is then posted to *win*.
+    Sends a convergence_update event every *rate*
+    seconds.  Gathers statistics about the best, worst, median and +/- 1 interquartile
+    range.  This will be the input for the convergence plot.
 
     *problem* should be the fit problem handed to the fit thread, and not
     a copy. This is because it is used for direct comparison with the current
@@ -68,33 +66,42 @@ class GUIMonitor(monitor.Monitor):
 
     *message* is a dispatch string used by the OnFitProgress event processor
     in the app to determine which progress panel should receive the event.
-
-    TODO: this is a pretty silly design, especially since GUI monitor is only
-    used for the convergence plot, and a separate monitor class was created
-    for DREAM progress updates.
     """
 
-    def __init__(self, problem, message, monitor, rate=0):
+    def __init__(self, problem, message="convergence_update", rate=0):
         self.time = 0
         self.rate = rate  # rate=0 for no progress update, only final
         self.problem = problem
         self.message = message
-        self.monitor = monitor
+        self.pop = []
+
 
     def config_history(self, history):
-        self.monitor.config_history(history)
-        history.requires(time=1)
+        history.requires(time=1, population_values=1, value=1)
 
     def __call__(self, history):
-        self.monitor(history)
+        # from old ConvergenceMonitor:
+        best = history.value[0]
+        try:
+            pop = history.population_values[0]
+            n = len(pop)
+            p = np.sort(pop)
+            QI,Qmid, = int(0.2*n),int(0.5*n)
+            self.pop.append((best, p[0],p[QI],p[Qmid],p[-1-QI],p[-1]))
+        except AttributeError:
+            self.pop.append((best, ))
+
         if self.rate > 0 and history.time[0] >= self.time+self.rate:
             evt = dict(
                 problem=self.problem,
                 message=self.message,
-                **self.monitor.progress())
+                pop=self.progress())
             EVT_FIT_PROGRESS.send(evt)
             self.time = history.time[0]
 
+    def progress(self):
+        return np.empty((0,1),'d') if not self.pop else np.array(self.pop)
+
     def final(self):
         """
         Close out the monitor
@@ -102,7 +109,7 @@ def final(self):
         evt = dict(
             problem=self.problem,
             message=self.message,
-            **self.monitor.progress())
+            pop=self.progress())
         EVT_FIT_PROGRESS.send(evt)
 
 # Horrible hacks:
@@ -139,7 +146,7 @@ def __call__(self, history):
             evt = dict(
                 problem=self.problem,
                 message="uncertainty_update",
-                # uncertainty_state=deepcopy(self.uncertainty_state),
+                uncertainty_state=deepcopy(self.uncertainty_state),
             )
             EVT_FIT_PROGRESS.send(evt)
 
@@ -153,7 +160,7 @@ def final(self):
             evt = dict(
                 problem=self.problem,
                 message="uncertainty_final",
-                # uncertainty_state=deepcopy(self.uncertainty_state),
+                uncertainty_state=deepcopy(self.uncertainty_state),
             )
             EVT_FIT_PROGRESS.send(evt)
 
@@ -191,6 +198,8 @@ def run(self):
         # inside the GUI monitor otherwise AppPanel will not be able to
         # recognize that it is the same problem when updating views.
         monitors = [GUIProgressMonitor(self.problem),
+                    ConvergenceMonitor(self.problem, 
+                                       rate=self.convergence_update),
                     # GUIMonitor(self.problem,
                     #            message="convergence_update",
                     #            monitor=ConvergenceMonitor(),

From 760be0b3d61fed73e2a08b4c9d67adf08bf8d735 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 15:58:16 -0500
Subject: [PATCH 097/221] add new plot renderers (mpld3) for DREAM output
 interpretation, e.g. Uncertainty, Model Uncertainty, Parameter Trace, etc

---
 refl1d/webview/server/webserver.py | 176 +++++++++++++++++++++++++++++
 1 file changed, 176 insertions(+)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 0d261a65..b1dbac9e 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -300,6 +300,182 @@ async def get_profile_data(sid: str="", model_index: int=0):
         output['smooth_profile'] = dict(z=z, rho=rho, irho=irho)
     return to_dict(output)
 
+@sio.event
+@rest_get
+async def get_convergence_plot(sid: str=""):
+    # NOTE: this is slow.  Creating the figure takes around 0.15 seconds, 
+    # and converting to mpld3 can take as much as 0.5 seconds.
+    # Might want to replace with plotting on the client side (normalizing population takes around 1 ms)
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    population = app["fitting"]["population"]
+    if population is not None and fitProblem is not None:
+        import mpld3
+        import matplotlib
+        matplotlib.use("agg")
+        import matplotlib.pyplot as plt
+        import time
+        start_time = time.time()
+        print('queueing new convergence plot...', start_time)
+
+        normalized_pop = 2*population/fitProblem.dof
+        best, pop = normalized_pop[:, 0], normalized_pop[:, 1:]
+        print("time to normalize population: ", time.time() - start_time)
+        fig = plt.figure()
+        axes = fig.add_subplot(111)
+
+        ni,npop = pop.shape
+        iternum = np.arange(1,ni+1)
+        tail = int(0.25*ni)
+        c = bumps.plotutil.coordinated_colors(base=(0.4,0.8,0.2))
+        if npop==5:
+            axes.fill_between(iternum[tail:], pop[tail:,1], pop[tail:,3],
+                                color=c['light'], label='_nolegend_')
+            axes.plot(iternum[tail:],pop[tail:,2],
+                        label="80% range", color=c['base'])
+            axes.plot(iternum[tail:],pop[tail:,0],
+                        label="_nolegend_", color=c['base'])
+        axes.plot(iternum[tail:], best[tail:], label="best",
+                    color=c['dark'])
+        axes.set_xlabel('iteration number')
+        axes.set_ylabel('chisq')
+        axes.legend()
+        #plt.gca().set_yscale('log')
+        # fig.draw()
+        print("time to render but not serialize...", time.time() - start_time)
+        dfig = mpld3.fig_to_dict(fig)
+        plt.close(fig)
+        # await sio.emit("profile_plot", dfig, to=sid)
+        end_time = time.time()
+        print("time to draw convergence plot:", end_time - start_time)
+        return dfig
+    else:
+        return None
+
+@sio.event
+@rest_get
+async def get_correlation_plot(sid: str = ""):
+    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    if uncertainty_state is not None:
+        import mpld3
+        import matplotlib
+        matplotlib.use("agg")
+        import matplotlib.pyplot as plt
+        import time
+        start_time = time.time()
+        print('queueing new correlation plot...', start_time)
+
+        fig = plt.figure()
+        axes = fig.add_subplot(111)
+        bumps.dream.views.plot_corrmatrix(uncertainty_state.draw(), fig=fig)
+        print("time to render but not serialize...", time.time() - start_time)
+        fig.canvas.draw()
+        dfig = mpld3.fig_to_dict(fig)
+        plt.close(fig)
+        # await sio.emit("profile_plot", dfig, to=sid)
+        end_time = time.time()
+        print("time to draw correlation plot:", end_time - start_time)
+        return dfig
+    else:
+        return None
+
+@sio.event
+@rest_get
+async def get_uncertainty_plot(sid: str = ""):
+    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    if uncertainty_state is not None:
+        import mpld3
+        import matplotlib
+        matplotlib.use("agg")
+        import matplotlib.pyplot as plt
+        import time
+        start_time = time.time()
+        print('queueing new correlation plot...', start_time)
+
+        fig = plt.figure()
+        draw = uncertainty_state.draw()
+        stats = bumps.dream.stats.var_stats(draw)
+        bumps.dream.varplot.plot_vars(draw, stats, fig=fig)
+        print("time to render but not serialize...", time.time() - start_time)
+        fig.canvas.draw()
+        dfig = mpld3.fig_to_dict(fig)
+        plt.close(fig)
+        # await sio.emit("profile_plot", dfig, to=sid)
+        end_time = time.time()
+        print("time to draw correlation plot:", end_time - start_time)
+        return dfig
+    else:
+        return None
+
+@sio.event
+@rest_get
+async def get_model_uncertainty_plot(sid: str = ""):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    if uncertainty_state is not None:
+        import mpld3
+        import matplotlib
+        matplotlib.use("agg")
+        import matplotlib.pyplot as plt
+        import time
+        start_time = time.time()
+        print('queueing new model uncertainty plot...', start_time)
+
+        fig = plt.figure()
+        errs = bumps.errplot.calc_errors_from_state(fitProblem, uncertainty_state)
+        print('errors calculated: ', time.time() - start_time)
+        bumps.errplot.show_errors(errs, fig=fig)
+        print("time to render but not serialize...", time.time() - start_time)
+        fig.canvas.draw()
+        dfig = mpld3.fig_to_dict(fig)
+        plt.close(fig)
+        # await sio.emit("profile_plot", dfig, to=sid)
+        end_time = time.time()
+        print("time to draw model uncertainty plot:", end_time - start_time)
+        return dfig
+    else:
+        return None
+
+@sio.event
+@rest_get
+async def get_parameter_trace_plot(sid: str=""):
+    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    if uncertainty_state is not None:
+        import mpld3
+        import matplotlib
+        matplotlib.use("agg")
+        import matplotlib.pyplot as plt
+        import time
+
+        start_time = time.time()
+        print('queueing new parameter_trace plot...', start_time)
+
+        fig = plt.figure()
+        axes = fig.add_subplot(111)
+
+        # begin plotting:
+        var = 0
+        portion = None
+        draw, points, _ = uncertainty_state.chains()
+        label = uncertainty_state.labels[var]
+        start = int((1-portion)*len(draw)) if portion else 0
+        genid = np.arange(uncertainty_state.generation-len(draw)+start, uncertainty_state.generation)+1
+        axes.plot(genid*uncertainty_state.thinning,
+             np.squeeze(points[start:, uncertainty_state._good_chains, var]))
+        axes.set_xlabel('Generation number')
+        axes.set_ylabel(label)
+        fig.canvas.draw()
+
+        print("time to render but not serialize...", time.time() - start_time)
+        dfig = mpld3.fig_to_dict(fig)
+        plt.close(fig)
+        # await sio.emit("profile_plot", dfig, to=sid)
+        end_time = time.time()
+        print("time to draw parameter_trace plot:", end_time - start_time)
+        return dfig
+    else:
+        return None
+    
+
 @sio.event
 @rest_get
 async def get_parameters(sid: str = "", only_fittable: bool = False):

From ef9e3abb953bd1afead457a8c7311d4278b97d9f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 16:01:23 -0500
Subject: [PATCH 098/221] update fit_progress_handler to recognize more types
 of message, and use new publish_sync function to trigger a publish in the
 asyncio loop from an event

---
 refl1d/webview/server/webserver.py | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index b1dbac9e..2df05798 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -153,22 +153,25 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
     fit_thread.start()
     await publish("", "fit_active", True)
 
-def fit_progress_handler(event):
-    print("event: ", event)
+def fit_progress_handler(event: Dict):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     message = event.get("message", None)
     if message == 'complete' or message == 'improvement':
-        fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
         fitProblem.setp(event["point"])
         fitProblem.model_update()
-        asyncio.run_coroutine_threadsafe(publish("", "update_parameters", True), app.loop)
-    if message == 'complete':
-        asyncio.run_coroutine_threadsafe(publish("", "fit_active", False), app.loop)
+        publish_sync("", "update_parameters")
+        if message == 'complete':
+            publish_sync("", "fit_active", False)
+    elif message == 'convergence_update':
+        app["fitting"]["population"] = event["pop"]
+        publish_sync("", "convergence_update")
+    elif message == 'uncertainty_update' or message == 'uncertainty_final':
+        app["fitting"]["uncertainty_state"] = event["uncertainty_state"]
+        publish_sync("", "uncertainty_update")
 
 EVT_FIT_PROGRESS.connect(fit_progress_handler)
 
 def fit_complete_handler(event):
-    print("event: ", event)
-    message = event.get("message", None)
     fit_thread = app["fitting"]["fit_thread"]
     if fit_thread is not None:
         fit_thread.join(1) # 1 second timeout on join
@@ -179,14 +182,14 @@ def fit_complete_handler(event):
     chisq = nice(2*event["value"]/problem.dof)
     problem.setp(event["point"])
     problem.model_update()
-    asyncio.run_coroutine_threadsafe(publish("", "update_parameters", True), app.loop)
+    publish_sync("", "update_parameters", True)
     EVT_LOG.send("done with chisq %g"%chisq)
     EVT_LOG.send(event["info"])
 
 EVT_FIT_COMPLETE.connect(fit_complete_handler)
 
 def log_handler(message):
-    asyncio.run_coroutine_threadsafe(publish("", "log", message), app.loop)
+    publish_sync("", "log", message)
 
 EVT_LOG.connect(log_handler)
 
@@ -536,13 +539,16 @@ async def set_parameter(sid: str, parameter_id: str, property: Literal["value01"
     return
 
 @sio.event
-async def publish(sid: str, topic: str, message):
+async def publish(sid: str, topic: str, message=None):
     timestamp_str = f"{datetime.now().timestamp():.6f}"
     contents = {"message": message, "timestamp": timestamp_str}
     topics[topic] = contents
     await sio.emit(topic, contents)
     # print("emitted: ", topic, contents)
 
+def publish_sync(sid: str, topic: str, message=None):
+    return asyncio.run_coroutine_threadsafe(publish(sid, topic, message), app.loop)
+
 @sio.event
 @rest_get
 async def get_last_message(sid: str="", topic: str=""):

From 382ebbc0420054cfcee55a132b4c59f4581f5e6b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 2 Dec 2022 16:02:30 -0500
Subject: [PATCH 099/221] update imports

---
 refl1d/webview/server/webserver.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 2df05798..7942d876 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -27,9 +27,18 @@
 from bumps.mapper import MPMapper
 from bumps.parameter import Parameter, Variable, unique
 import bumps.fitproblem
+import bumps.plotutil
+import bumps.dream.views, bumps.dream.varplot, bumps.dream.stats
+import bumps.errplot
+import refl1d.errors
 import refl1d.fitproblem, refl1d.probe
 from refl1d.experiment import Experiment
 
+# Register the refl1d model loader
+import refl1d.fitplugin
+import bumps.cli
+bumps.cli.install_plugin(refl1d.fitplugin)
+
 from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
 
 # can get by name and not just by id
@@ -60,6 +69,7 @@
     "fit_thread": None,
     "abort": False,
     "uncertainty_state": None,
+    "population": None,
     "abort_queue": Queue(),
 }
 problem = None
@@ -154,6 +164,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
     await publish("", "fit_active", True)
 
 def fit_progress_handler(event: Dict):
+    print("progress event message: ", event.get("message", ""))
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     message = event.get("message", None)
     if message == 'complete' or message == 'improvement':
@@ -172,6 +183,8 @@ def fit_progress_handler(event: Dict):
 EVT_FIT_PROGRESS.connect(fit_progress_handler)
 
 def fit_complete_handler(event):
+    print("complete event: ", event.get("message", ""))
+    message = event.get("message", None)
     fit_thread = app["fitting"]["fit_thread"]
     if fit_thread is not None:
         fit_thread.join(1) # 1 second timeout on join

From b5391712f79f55294f452fe2300aa34157f8dd72 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 7 Dec 2022 11:18:37 -0500
Subject: [PATCH 100/221] enable connecting to socket.io even when behind a
 proxy

---
 refl1d/webview/client/src/App.vue | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index c65d7ceb..a9ab43c7 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -44,10 +44,12 @@ const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
 
 // Create a SocketIO connection, to be passed to child components
 // so that they can do their own communications with the host.
+const base_path = window.location.pathname;
 
 const socket = io('', {
-  // this is mostly here to test what happens on server fail:
-  reconnectionAttempts: 10
+   // this is mostly here to test what happens on server fail:
+   path: `${base_path}socket.io`,
+   reconnectionAttempts: 10
 });
 
 socket.on('connect', () => {

From e785ac57eee2fc100b29b821deda0a7533862c4f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 7 Dec 2022 11:19:33 -0500
Subject: [PATCH 101/221] don't navigate page to href=# with menu links or in
 filebrowser

---
 refl1d/webview/client/src/App.vue             | 40 +++++++++----------
 .../client/src/components/FileBrowser.vue     |  4 +-
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index a9ab43c7..4932ce1d 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -133,54 +133,54 @@ onMounted(() => {
         <div class="collapse navbar-collapse" id="navbarSupportedContent">
           <ul class="navbar-nav me-auto mb-2 mb-lg-0">
             <!-- <li class="nav-item dropdown">
-              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+              <div class="nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 Session
-              </a>
+              </div>
               <ul class="dropdown-menu">
-                <li><a class="dropdown-item" href="#" @click="connect">New</a></li>
-                <li><a class="dropdown-item" href="#" @click="disconnect">Disconnect</a></li>
-                <li><a class="dropdown-item" href="#" @click="reconnect">Existing</a></li>
+                <li><button class="btn btn-link dropdown-item"  @click="connect">New</div></li>
+                <li><button class="btn btn-link dropdown-item"  @click="disconnect">Disconnect</div></li>
+                <li><button class="btn btn-link dropdown-item"  @click="reconnect">Existing</div></li>
               </ul>
             </li> -->
             <li class="nav-item dropdown">
-              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+              <button class="btn btn-link nav-link dropdown-toggle" role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 File
-              </a>
+              </button>
               <ul class="dropdown-menu">
-                <li><a class="dropdown-item" href="#" @click="selectOpenFile">Open</a></li>
-                <li><a class="dropdown-item" href="#">Save</a></li>
-                <li><a class="dropdown-item" :class="{disabled: model_loaded === undefined}" href="#" @click="reloadModel">Reload</a></li>
+                <li><button class="btn btn-link dropdown-item" @click="selectOpenFile">Open</button></li>
+                <li><button class="btn btn-link dropdown-item" >Save</button></li>
+                <li><button class="btn btn-link dropdown-item" :class="{disabled: model_loaded === undefined}"  @click="reloadModel">Reload</button></li>
                 <li>
                   <hr class="dropdown-divider">
                 </li>
-                <li><a class="dropdown-item" href="#">Quit</a></li>
+                <li><button class="btn btn-link dropdown-item" >Quit</button></li>
               </ul>
             </li>
             <li class="nav-item dropdown">
-              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+              <button class="btn btn-link nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 Fitting
-              </a>
+              </button>
               <ul class="dropdown-menu">
-                <li><a class="dropdown-item" href="#" @click="startFit">Start</a></li>
-                <li><a class="dropdown-item" href="#" @click="stopFit">Stop</a></li>
+                <li><button class="btn btn-link dropdown-item"  @click="startFit">Start</button></li>
+                <li><button class="btn btn-link dropdown-item"  @click="stopFit">Stop</button></li>
                 <li>
                   <hr class="dropdown-divider">
                 </li>
-                <li><a class="dropdown-item" href="#" @click="openFitOptions">Options...</a></li>
+                <li><button class="btn btn-link dropdown-item"  @click="openFitOptions">Options...</button></li>
               </ul>
             </li>
             <!-- <li class="nav-item dropdown">
-              <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown"
+              <div class="nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 Reflectivity
-              </a>
+              </div>
               <ul class="dropdown-menu">
                 <li v-for="plot_type in REFLECTIVITY_PLOTS" :key="plot_type">
-                  <a :class="{'dropdown-item': true, active: (plot_type === reflectivity_type)}" href="#"
-                    @click="set_reflectivity(plot_type)">{{plot_type}}</a>
+                  <div :class="{'dropdown-item': true, active: (plot_type === reflectivity_type)}" 
+                    @click="set_reflectivity(plot_type)">{{plot_type}}</div>
                 </li>
               </ul>
             </li> -->
diff --git a/refl1d/webview/client/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
index 478f0f94..16fc27b5 100644
--- a/refl1d/webview/client/src/components/FileBrowser.vue
+++ b/refl1d/webview/client/src/components/FileBrowser.vue
@@ -86,7 +86,7 @@ defineExpose({
             <nav aria-label="breadcrumb">
               <ol class="breadcrumb">
                 <li v-for="(pathitem, index) in pathlist" :key="index" class="breadcrumb-item">
-                  <a href="#" @click="setPath(pathlist.slice(0, index+1))">{{pathitem}}</a>
+                  <a href="#" @click.prevent="setPath(pathlist.slice(0, index+1))">{{pathitem}}</a>
                 </li>
               </ol>
             </nav>
@@ -95,7 +95,7 @@ defineExpose({
             <h3>Subdirectories:</h3>
             <div class="row row-cols-3">
               <div class="col overflow-hidden" v-for="subdir in subdirlist" :key="subdir">
-                <a href="#" @click="subdirClick(subdir)" :title="subdir">{{subdir}}</a>
+                <a href="#" @click.prevent="subdirClick(subdir)" :title="subdir">{{subdir}}</a>
               </div>
             </div>
           </div>

From 0891f43ccc2e9d38e4fa46be26428270f2739b3b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 7 Dec 2022 11:22:09 -0500
Subject: [PATCH 102/221] add command line options to pass port to server

---
 refl1d/webview/server/webserver.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 7942d876..264c0289 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -663,10 +663,21 @@ def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[Param
             lookup[params.id] = new_item
     return list(lookup.values())
 
+import argparse
+
 def main():
+    parser = argparse.ArgumentParser()
+    # parser.add_argument('-d', '--debug', action='store_true', help='autoload modules on change')
+    # parser.add_argument('-x', '--headless', action='store_true', help='do not automatically load client in browser')
+    parser.add_argument('--external', action='store_true', help='listen on all interfaces, including external (local connections only if not set)')
+    parser.add_argument('-p', '--port', default=None, type=int, help='port on which to start the server')
+    # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
+    args = parser.parse_args()
+
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     app.add_routes(routes)
-    web.run_app(app)
+    hostname = 'localhost' if not args.external else '0.0.0.0'
+    web.run_app(app, host=hostname, port=args.port)
 
 if __name__ == '__main__':
     main()

From 4209effe4051a3b82410735bb8f8577184be1db9 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 7 Dec 2022 11:22:32 -0500
Subject: [PATCH 103/221] serve index.html directly from / route

---
 refl1d/webview/server/webserver.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 264c0289..afae7314 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -59,7 +59,9 @@
 # sio = socketio.AsyncServer(cors_allowed_origins="*", serializer='msgpack')
 sio = socketio.AsyncServer(cors_allowed_origins="*")
 app = web.Application()
-static_dir_path = Path(__file__).parent.parent / 'client' / 'dist'
+index_path = Path(__file__).parent.parent / 'client' / 'dist'
+static_assets_path = index_path / 'assets'
+
 sio.attach(app)
 
 topics: Dict[str, Dict] = {}
@@ -90,7 +92,7 @@ async def handler(request: web.Request):
 async def index(request):
     """Serve the client-side application."""
     # redirect to static built site:
-    return web.HTTPFound('/static/index.html')
+    return web.FileResponse(index_path / 'index.html')
     
 @sio.event
 async def connect(sid, environ, data=None):
@@ -546,7 +548,7 @@ async def set_parameter(sid: str, parameter_id: str, property: Literal["value01"
         if parameter.fittable:
             parameter.fixed = bool(value)
             fitProblem.model_reset()
-            print(f"setting parameter: {parameter}.fixed to {value}")
+            # print(f"setting parameter: {parameter}.fixed to {value}")
     fitProblem.model_update()
     await publish("", "update_parameters", True)
     return
@@ -600,7 +602,7 @@ async def get_fitter_defaults(sid: str=""):
 def disconnect(sid):
     print('disconnect ', sid)
 
-app.router.add_static('/static', static_dir_path)
+app.router.add_static('/assets', static_assets_path)
 app.router.add_get('/', index)
 
 VALUE_PRECISION = 6

From b661db710327cfa7f37f843975b7790a9a1ea413 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 7 Dec 2022 18:14:25 -0500
Subject: [PATCH 104/221] add webview to packages in setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 9853a98b..1c23260a 100755
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@
 from setuptools import setup, Extension
 from setuptools.command.build_ext import build_ext
 
-packages = ['refl1d', 'refl1d.view', 'refl1d.lib_numba']
+packages = ['refl1d', 'refl1d.view', 'refl1d.lib_numba', 'refl1d.webview']
 
 version = None
 for line in open(os.path.join("refl1d", "__init__.py")):

From 958d79c6989c563f36c12cced9cfba0abdb3c1a6 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Wed, 7 Dec 2022 21:50:31 -0500
Subject: [PATCH 105/221] add client files to MANIFEST.in

---
 MANIFEST.in | 1 +
 setup.py    | 1 +
 2 files changed, 2 insertions(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 2b910976..a4378380 100755
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -14,6 +14,7 @@ include master_builder.py
 include refl1d.iss
 include setup_py2exe.py
 include refl1d/lib/*.h refl1d/lib/erf.c
+recursive-include refl1d/webview/client/dist *.html *.js *.css *.svg *.png
 
 # Delete files
 #prune this that
diff --git a/setup.py b/setup.py
index 1c23260a..684c50da 100755
--- a/setup.py
+++ b/setup.py
@@ -49,6 +49,7 @@
         ],
     packages=packages,
     #package_data=gui_resources.package_data(),
+    include_package_data=True,
     scripts=['bin/refl1d_cli.py', 'bin/refl1d_gui.py'],
     entry_points={
         'console_scripts': ['refl1d=refl1d.main:cli'],

From 86f1e320ff8416aeb378839b884ac597058182a8 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 8 Dec 2022 13:44:26 -0500
Subject: [PATCH 106/221] include all source files needed for building the
 webview client

---
 MANIFEST.in | 5 ++++-
 setup.py    | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index a4378380..93b1d93e 100755
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -15,6 +15,9 @@ include refl1d.iss
 include setup_py2exe.py
 include refl1d/lib/*.h refl1d/lib/erf.c
 recursive-include refl1d/webview/client/dist *.html *.js *.css *.svg *.png
-
+recursive-include refl1d/webview/client/src *.html *.js *.css *.svg *.png *.vue
+include refl1d/webview/client/*.html
+include refl1d/webview/client/*.js
+include refl1d/webview/client/*.json
 # Delete files
 #prune this that
diff --git a/setup.py b/setup.py
index 684c50da..1c0ac626 100755
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@
 from setuptools import setup, Extension
 from setuptools.command.build_ext import build_ext
 
-packages = ['refl1d', 'refl1d.view', 'refl1d.lib_numba', 'refl1d.webview']
+packages = ['refl1d', 'refl1d.view', 'refl1d.lib_numba', 'refl1d.webview.server']
 
 version = None
 for line in open(os.path.join("refl1d", "__init__.py")):

From 9da99dce7b8f24ecf6ee46970a5213475e715a7e Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 9 Dec 2022 12:56:29 -0500
Subject: [PATCH 107/221] adding npmignore, needed for building npm packages
 cleanly

---
 refl1d/webview/client/.npmignore | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 refl1d/webview/client/.npmignore

diff --git a/refl1d/webview/client/.npmignore b/refl1d/webview/client/.npmignore
new file mode 100644
index 00000000..e2d91bfc
--- /dev/null
+++ b/refl1d/webview/client/.npmignore
@@ -0,0 +1 @@
+refl1d-webview-client*.tgz

From d33bd1775dde47437fd1477c1944a51f48770745 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 9 Dec 2022 12:56:56 -0500
Subject: [PATCH 108/221] ignore packed webview clients

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 7ff75743..ee7d3aae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@
 *.swp
 *.so
 *.bak
+refl1d-webview-client*.tgz
 /build/
 /dist/
 /refl1d.egg-info/

From 3cf0b182e956b8eb6e15ffe81c394af8f50f4786 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 9 Dec 2022 12:58:01 -0500
Subject: [PATCH 109/221] add build_prod script, creates unmangled paths for
 builds to be published on npmjs.org

---
 refl1d/webview/client/package.json | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index 7a56978e..bbb54acf 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -1,16 +1,17 @@
 {
-  "name": "refl1d-web-gui",
-  "version": "0.0.0",
+  "name": "refl1d-webview-client",
+  "version": "0.0.1",
   "scripts": {
     "dev": "vite",
-    "build": "vite build --outDir dist --emptyOutDir",
+    "build": "vite build --emptyOutDir -m development && echo -n $npm_package_version > dist/VERSION",
+    "build_prod": "vite build --emptyOutDir -m production && echo -n $npm_package_version > dist/VERSION",
     "preview": "vite preview --port 4173"
   },
   "dependencies": {
     "bootstrap": "^5.2.1",
     "json-difference": "^1.8.2",
     "mpld3": "^0.5.8",
-    "plotly.js": "^2.14.0",
+    "plotly.js": "^2.16.4",
     "socket.io-client": "^4.5.2",
     "uuid": "^9.0.0",
     "vue": "^3.2.38",
@@ -20,6 +21,6 @@
     "@types/plotly.js": "^2.12.5",
     "@types/uuid": "^8.3.4",
     "@vitejs/plugin-vue": "^3.0.3",
-    "vite": "^3.0.9"
+    "vite": "^3.2.5"
   }
 }

From 9ac83614f1eb3ffe0495591d6642e35414c70661 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 9 Dec 2022 12:58:48 -0500
Subject: [PATCH 110/221] write unhashed filenames for production mode

---
 refl1d/webview/client/vite.config.js | 40 +++++++++++++++++++---------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/refl1d/webview/client/vite.config.js b/refl1d/webview/client/vite.config.js
index 1502e210..c86d400c 100644
--- a/refl1d/webview/client/vite.config.js
+++ b/refl1d/webview/client/vite.config.js
@@ -4,17 +4,31 @@ import { defineConfig } from 'vite'
 import vue from '@vitejs/plugin-vue'
 
 // https://vitejs.dev/config/
-export default defineConfig({
-  plugins: [vue()],
-  base: '',
-  resolve: {
-    alias: {
-      '@': fileURLToPath(new URL('./src', import.meta.url))
+export default ({mode}) => {
+  return defineConfig({
+    plugins: [vue()],
+    base: '',
+    resolve: {
+      alias: {
+        '@': fileURLToPath(new URL('./src', import.meta.url))
+      }
+    },
+    define: {
+      // By default, Vite doesn't include shims for NodeJS/
+      // necessary for segment analytics lib to work
+      global: {},
+    },
+    build: {
+      rollupOptions: {
+        output: {
+          // Default
+          // dir: 'dist',
+          entryFileNames: (mode == 'production') ? 'assets/[name].js' : 'assets/[name].[hash].js',
+          assetFileNames: (mode == 'production') ? 'assets/[name][extname]' : undefined,
+          // chunkFileNames: "chunk-[name].js",
+          // manualChunks: undefined,
+        }
+      }
     }
-  },
-  define: {
-    // By default, Vite doesn't include shims for NodeJS/
-    // necessary for segment analytics lib to work
-    global: {},
-  }
-})
+  })
+}

From 997a175774ba2208d017b334f78c4a71bb855cc6 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 9 Dec 2022 12:59:38 -0500
Subject: [PATCH 111/221] check version of locally-built client, and use it if
 there's a match, fall back to CDN

---
 refl1d/webview/server/webserver.py | 24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index afae7314..2a8583ef 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -59,7 +59,8 @@
 # sio = socketio.AsyncServer(cors_allowed_origins="*", serializer='msgpack')
 sio = socketio.AsyncServer(cors_allowed_origins="*")
 app = web.Application()
-index_path = Path(__file__).parent.parent / 'client' / 'dist'
+client_path = Path(__file__).parent.parent / 'client'
+index_path = client_path / 'dist'
 static_assets_path = index_path / 'assets'
 
 sio.attach(app)
@@ -91,8 +92,22 @@ async def handler(request: web.Request):
 
 async def index(request):
     """Serve the client-side application."""
-    # redirect to static built site:
-    return web.FileResponse(index_path / 'index.html')
+    # check if the locally-build site has the correct version:
+    with open(client_path / 'package.json', 'r') as package_json:
+        client_version = json.load(package_json)['version'].strip()
+
+    try:
+        local_version = open(index_path / 'VERSION', 'rt').read().strip()
+    except FileNotFoundError:
+        local_version = None
+
+    if client_version == local_version:
+        return web.FileResponse(index_path / 'index.html')
+    else:
+        CDN = f"https://cdn.jsdelivr.net/npm/refl1d-webview-client@{client_version}/dist"
+        with open(client_path / 'index_template.txt', 'r') as index_template:
+            index_html = index_template.read().format(cdn=CDN)
+        return web.Response(body=index_html, content_type="text/html")
     
 @sio.event
 async def connect(sid, environ, data=None):
@@ -602,7 +617,8 @@ async def get_fitter_defaults(sid: str=""):
 def disconnect(sid):
     print('disconnect ', sid)
 
-app.router.add_static('/assets', static_assets_path)
+if Path.exists(static_assets_path):
+    app.router.add_static('/assets', static_assets_path)
 app.router.add_get('/', index)
 
 VALUE_PRECISION = 6

From ba0b8d892f04f673bd52fac8be5b941dcd013dd9 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Sun, 11 Dec 2022 23:46:19 -0500
Subject: [PATCH 112/221] add template for fallback CDN client

---
 refl1d/webview/client/index_template.txt | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 refl1d/webview/client/index_template.txt

diff --git a/refl1d/webview/client/index_template.txt b/refl1d/webview/client/index_template.txt
new file mode 100644
index 00000000..3f054cda
--- /dev/null
+++ b/refl1d/webview/client/index_template.txt
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <link rel="icon" href="{cdn}/assets/refl1d-icon_48x48x32.png" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <script type="text/javascript" async
+      src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-svg.min.js">
+    </script>
+    <title>Refl1D</title>
+    <script type="module" crossorigin src="{cdn}/assets/index.js"></script>
+    <link rel="stylesheet" href="{cdn}/assets/index.css">
+  </head>
+  <body>
+    <div id="app"></div>
+  </body>
+</html>

From 7ea1bbf8fc9da584bbb218c84698c90f27a32267 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Sun, 11 Dec 2022 23:51:24 -0500
Subject: [PATCH 113/221] include index template in manifest

---
 MANIFEST.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 93b1d93e..163692c4 100755
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -19,5 +19,6 @@ recursive-include refl1d/webview/client/src *.html *.js *.css *.svg *.png *.vue
 include refl1d/webview/client/*.html
 include refl1d/webview/client/*.js
 include refl1d/webview/client/*.json
+include refl1d/webview/client/*.txt
 # Delete files
 #prune this that

From 3f60f5e6482db7e7e9d8c147599f41fe77511f4a Mon Sep 17 00:00:00 2001
From: acaruana2009 <55897898+acaruana2009@users.noreply.github.com>
Date: Wed, 4 Jan 2023 16:38:04 +0000
Subject: [PATCH 114/221] Update .gitignore

added all `__pycache__` folders to `.gitignore`
---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index ee7d3aae..d305bcc0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@
 .idea
 *.pyd
 *.pyc
+**/__pycache__/
 *.swp
 *.so
 *.bak

From cef1f3a80eebcb88c1c0484963c8ead3c2f73287 Mon Sep 17 00:00:00 2001
From: acaruana2009 <55897898+acaruana2009@users.noreply.github.com>
Date: Wed, 4 Jan 2023 16:47:49 +0000
Subject: [PATCH 115/221] FIX: add probe labels to plotly refl plot

Legend on reflectivity plot now shows the probe labels in the legend.
---
 refl1d/webview/server/webserver.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 2a8583ef..3c9113b9 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -236,7 +236,7 @@ def get_single_probe_data(theory, probe, substrate=None, surface=None, label='')
         output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, theory = R, fresnel = FQ, background=probe.background.value, intensity=probe.intensity.value)
     else:
         output = dict(Q = probe.Q, dQ = probe.dQ, theory = R, fresnel = FQ)
-    output['label'] = label
+    output['label'] = f"{probe.label()} {label}"
     return output
 
 def get_probe_data(theory, probe, substrate=None, surface=None):

From e13619cc84dd4e88640dc49c9d5a7115bf579bfb Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Thu, 5 Jan 2023 09:25:07 -0500
Subject: [PATCH 116/221] use node to put package version in VERSION file

---
 refl1d/webview/client/package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index bbb54acf..6966175a 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -3,8 +3,8 @@
   "version": "0.0.1",
   "scripts": {
     "dev": "vite",
-    "build": "vite build --emptyOutDir -m development && echo -n $npm_package_version > dist/VERSION",
-    "build_prod": "vite build --emptyOutDir -m production && echo -n $npm_package_version > dist/VERSION",
+    "build": "vite build --emptyOutDir -m development && node -p process.env.npm_package_version > dist/VERSION",
+    "build_prod": "vite build --emptyOutDir -m production && node -p process.env.npm_package_version > dist/VERSION",
     "preview": "vite preview --port 4173"
   },
   "dependencies": {

From 25be800349d0cb95114370c9135db5aee5f9910d Mon Sep 17 00:00:00 2001
From: acaruana2009 <55897898+acaruana2009@users.noreply.github.com>
Date: Thu, 5 Jan 2023 15:12:10 +0000
Subject: [PATCH 117/221] DEV: New plotly SLD profile plot

Recreating the SLD profile plot from the wxpython GUI in plotly. For development purposes, this is using the profile tab (this used to show a matplotlib version of the SLD profile).
---
 .gitignore                                    |   2 +
 .../client/src/components/ModelView.vue       |  35 +-
 refl1d/webview/server/profile_plot.py         | 337 ++++++++++++++++++
 refl1d/webview/server/webserver.py            |  33 +-
 4 files changed, 374 insertions(+), 33 deletions(-)
 create mode 100644 refl1d/webview/server/profile_plot.py

diff --git a/.gitignore b/.gitignore
index d305bcc0..292f3f53 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,8 @@
 *.pyd
 *.pyc
 **/__pycache__/
+**/node_modules/
+/refl1d/webview/client/dist/
 *.swp
 *.so
 *.bak
diff --git a/refl1d/webview/client/src/components/ModelView.vue b/refl1d/webview/client/src/components/ModelView.vue
index b9849345..8b339e7b 100644
--- a/refl1d/webview/client/src/components/ModelView.vue
+++ b/refl1d/webview/client/src/components/ModelView.vue
@@ -3,12 +3,11 @@
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
-import mpld3 from 'mpld3';
+import * as Plotly from 'plotly.js/lib/core';
 
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
 const draw_requested = ref(false);
-const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const model_names = ref<string[]>([]);
 const current_model = ref(0);
@@ -17,7 +16,7 @@ const props = defineProps<{
   visible: boolean
 }>();
 
-props.socket.on('model_loaded', ({message: {model_names: new_model_names}}) => {
+props.socket.on('model_loaded', ({ message: { model_names: new_model_names } }) => {
   model_names.value = new_model_names;
 });
 
@@ -29,27 +28,25 @@ onMounted(() => {
 });
 
 function fetch_and_draw() {
-  props.socket.emit('get_profile_plot', current_model.value, (payload) => {
+  props.socket.emit('get_profile_plot', current_model.value, async (payload) => {
+    console.log(payload);
+    if (plot_div.value == null) {
+      return
+    }
     if (props.visible) {
       let plotdata = { ...payload };
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      /* Data Parsing Functions */
-      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+      console.log(plotdata);
+      const { data, layout } = plotdata;
+      const config = { responsive: true }
+      const plot = await Plotly.react(plot_div_id.value, [...data], layout, config);
     }
-    drawing_busy.value = false;
   });
 }
 
 function draw_if_needed(timestamp: number) {
-  if (drawing_busy.value) {
-    console.log("busy!");
-  }
-  if (draw_requested.value && props.visible && !drawing_busy.value) {
-    drawing_busy.value = true;
-    draw_requested.value = false;
+  if (draw_requested.value && props.visible) {
     fetch_and_draw();
+    draw_requested.value = false;
   }
   window.requestAnimationFrame(draw_if_needed);
 }
@@ -62,11 +59,11 @@ function draw_if_needed(timestamp: number) {
 // });
 
 </script>
-    
+
 <template>
   <div class="container d-flex flex-grow-1 flex-column">
-    <select v-model="current_model" @change="draw_requested=true">
-      <option v-for="(name, index) in model_names" :key="index" :value="index">{{index}}: {{name ?? ""}}</option>
+    <select v-model="current_model" @change="draw_requested = true">
+      <option v-for="(name, index) in model_names" :key="index" :value="index">{{ index }}: {{ name ?? "" }}</option>
     </select>
     <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
     </div>
diff --git a/refl1d/webview/server/profile_plot.py b/refl1d/webview/server/profile_plot.py
new file mode 100644
index 00000000..b10e9e6b
--- /dev/null
+++ b/refl1d/webview/server/profile_plot.py
@@ -0,0 +1,337 @@
+# Below taken from the GUI profile plot methods in Refl1d - modified to be stand alone
+# This is to allow for the layer labels to be easily added to the SLD plots
+
+# Originally written for use in a jupyter notebook
+# Adapted to act as a prototype for the profile plotting in the new GUI for refl1d
+
+from refl1d.view.config import thickness_color, pick_radius
+from numpy import inf
+from matplotlib import transforms
+import matplotlib.pyplot as plt
+import numpy as np
+import plotly.graph_objs as go
+blend_xy = transforms.blended_transform_factory
+
+
+# === Sample information ===
+class FindLayers:
+    def __init__(self, experiment, axes=None, x_offset=0):
+
+        self.experiment = experiment
+        self.axes = axes
+        self.x_offset = x_offset
+        if (axes is not None) and isinstance(axes, plt.Axes):
+            self.xcoords = blend_xy(axes.transData, axes.transAxes)
+        self._show_labels = True
+        self._show_boundaries = True
+
+        self._find_layer_boundaries()
+
+    def find(self, z):
+        return self.experiment.sample.find(z - self.x_offset)
+
+    def _find_layer_boundaries(self):
+        offset = self.x_offset
+        boundary = [-inf, offset]
+        if hasattr(self.experiment, 'sample'):
+            for L in self.experiment.sample[1:-1]:
+                dx = L.thickness.value
+                offset += dx
+                boundary.append(offset)
+        boundary.append(inf)
+        self.boundary = np.asarray(boundary)
+
+    def sample_labels(self):
+        return [L.name for L in self.experiment.sample]
+
+    def sample_layer(self, n):
+        return self.experiment.sample[n]
+
+    def label_offsets(self):
+        z = self.boundary[1:-1]
+        left = -20
+        middle = [(a + b) / 2. for a, b in zip(z[:-1], z[1:])]
+        right = z[-1] + 150
+        return [left] + middle + [right]
+
+    def reset_markers_mpl(self):
+        """
+        Reset all markers, for matplotlib plots
+        """
+        # self.clear_markers()
+        if not isinstance(self.axes, plt.Axes):
+            raise ValueError("reset_markers_mpl can only be used with type: axes=matplotlib.axes.Axes")
+
+        ax = self.axes
+
+        # Add bars
+        style = dict(linewidth=1, linestyle='-',
+                     color=thickness_color, alpha=0.75,
+                     pickradius=pick_radius,
+                     visible=self._show_boundaries,
+                     )
+        self.markers = [ax.axvline(x=z, **style)
+                        for z in self.boundary[1:-1]]
+
+        # fittable = [self.profile.sample_layer(idx).thickness.fittable
+        #             for idx,_ in enumerate(self.markers)]
+        # fittable[0] = False # First interface is not fittable
+        # for f,m in zip(fittable,self.markers):
+        #     if not f: m.set(linestyle='--', linewidth=1.25)
+        # self.connect_markers(m for f,m in zip(fittable,self.markers) if f)
+
+        # Add labels
+        offsets = self.label_offsets()
+        labels = self.sample_labels()
+        style = dict(transform=self.axes.get_xaxis_transform(),
+                     ha='left', va='bottom',
+                     rotation=45, fontsize=16,  # 'medium',
+                     visible=self._show_labels,
+                     )
+        self.textmark = [ax.text(z, 1, s, **style)
+                         for z, s in zip(offsets, labels)]
+
+    def reset_markers_plotly(self):
+        """
+        Reset all markers, for plotly plots
+        """
+        # self.clear_markers()
+        if not isinstance(self.axes, go.Figure):
+            raise ValueError("reset_markers_plotly can only be used with type: axes=plotly.graph_objs.Figure")
+
+        fig = self.axes
+
+        # Add bars
+        fittable = [self.experiment.sample[idx].thickness.fittable
+                    for idx, _ in enumerate(self.boundary[1:-1])]
+        fittable[0] = False  # First interface is not fittable
+
+        for f, z_pos in zip(fittable, self.boundary[1:-1]):
+            if not f:
+                line_dict = dict(dash="dash")
+            else:
+                line_dict = dict(dash="solid")
+
+            fig.add_vline(x=z_pos, opacity=0.75,
+                          line=line_dict,
+                          )
+
+        # for f,m in zip(fittable,self.markers):
+        #     if not f: m.set(linestyle='--', linewidth=1.25)
+        # self.connect_markers(m for f,m in zip(fittable,self.markers) if f)
+
+        # Add labels
+        offsets = self.label_offsets()
+        labels = self.sample_labels()
+        for label_pos, label in zip(offsets, labels):
+            fig.add_annotation(text=label,
+                               textangle=-30,
+                               x=label_pos,
+                               yref="paper",
+                               y=1.05,
+                               showarrow=False
+                               )
+
+
+def determine_problem_fitness(problem, active_model):
+    if hasattr(problem, 'active_model'):
+        problem_fitness = problem.set_active_model(active_model)
+        problem_fitness = problem.active_model.fitness
+    else:
+        problem_fitness = problem.fitness
+
+    return problem_fitness
+
+
+def generate_best_profile(model):
+    if hasattr(model, "active_model"):
+        model = model.active_model
+
+    if model.ismagnetic:
+        best = model.magnetic_smooth_profile()
+    else:
+        best = model.smooth_profile()
+    return best
+# ============================================================================= #
+# Plotting script below
+# ============================================================================= #
+
+
+def plot_sld_profile(model):
+    """
+    Basic plot script to plot up SLD profiles using Paul's layer finding code
+    """
+    fig, ax = plt.subplots(1, 1, figsize=(8, 6))
+
+    theta_axis = ax.twinx()
+    # ax.legend(fontsize=16, framealpha=0.5, ncol=3)
+
+    if model.ismagnetic:
+        z_best, rho_best, irho_best, rhoM_best, thetaM_best = generate_best_profile(model)
+        ax.plot(z_best, rhoM_best, label=r"$\rho_{M}$ mSLD", color="b")
+        ax.plot(z_best, thetaM_best, label=r"Magnetic Angle $\theta_{M} \circ$", color="orange")
+        ax.set_ylabel(r"$\rho, \rho_{i}, \rho_{M} \left(10^{-6}\AA^{-2}\right)$", fontsize=18)
+    else:
+        z_best, rho_best, irho_best = generate_best_profile(model)
+        ax.set_ylabel(r"$\rho, \rho_{i} \left(10^{-6}\AA^{-2}\right)$", fontsize=18)
+
+    ax.plot(z_best, rho_best, label=r"$\rho$ SLD", color="k")
+    ax.plot(z_best, irho_best, label=r"$\rho_{i}$ Im SLD", color="g")
+
+    ax.legend(fontsize=16, framealpha=0.5, ncol=3)
+    ax.grid(True)
+    ax.set_xlabel(r"z $\left(\AA\right)$", fontsize=18)
+    ax.tick_params(axis='y', labelsize=16)
+    ax.tick_params(axis='x', labelsize=16)
+
+    layer_markers = FindLayers(model, axes=ax)
+    layer_markers.reset_markers_mpl()
+
+    return fig, ax
+
+
+def plot_sld_profile_plotly(model):
+    fig = go.Figure()
+    if model.ismagnetic:
+        z_best, rho_best, irho_best, rhoM_best, thetaM_best = generate_best_profile(model)
+        fig.add_scattergl(x=z_best, y=rhoM_best, name="$\\rho_{M}$")
+        yaxis_title = '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$'
+
+        fig.add_scattergl(x=z_best, y=thetaM_best, name="$\\theta_{M}$", yaxis="y2")
+        # TODO: need to make axis scaling for thetaM dependent on if thetaM exceeds 0-360
+        fig.update_layout(yaxis2={
+            'title': {'text': '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$'},
+            'type': 'linear',
+            'autorange': False,
+            'range': [0, 360],
+            'anchor': 'x',
+            'overlaying': 'y',
+            'side': 'right',
+            'ticks': "inside",
+            # 'ticklen': 20,
+        })
+    else:
+        z_best, rho_best, irho_best = generate_best_profile(model)
+        yaxis_title = '$\\text{SLD: } \\rho, \\rho_i / 10^{-6} \\text{Å}^{-2}$'
+
+    fig.add_scattergl(x=z_best, y=rho_best, name="$\\rho$", hovertext="SLD")
+    fig.add_scattergl(x=z_best, y=irho_best, name="$\\rho_{i}$")
+
+    fig.update_layout(uirevision=1, plot_bgcolor="white")
+
+    fig.update_layout(xaxis={
+        'title': {'text': 'depth (Å)'},
+        'type': 'linear',
+        'autorange': True,
+        # 'gridcolor': "Grey",
+        'ticks': "inside",
+        # 'ticklen': 20,
+        'showline': True,
+        'linewidth': 1,
+        'linecolor': 'black',
+        'mirror': "ticks",
+        'side': 'bottom'
+    })
+
+    fig.update_layout(yaxis={
+        'title': {'text': yaxis_title},
+        'exponentformat': 'e',
+        'showexponent': 'all',
+        'type': 'linear',
+        'autorange': True,
+        # 'gridcolor': "Grey",
+        'ticks': "inside",
+        # 'ticklen': 20,
+        'showline': True,
+        'linewidth': 1,
+        'linecolor': 'black',
+        'mirror': True
+    })
+
+    fig.update_layout(margin={
+        "l": 75,
+        "r": 50,
+        "t": 25,
+        "b": 75,
+        "pad": 4
+    })
+
+    marker_positions = FindLayers(model, axes=fig)
+    marker_positions.reset_markers_plotly()
+
+    # fig.show(renderer='firefox')
+    return fig
+
+# def plot_contours(model, title, savepath=None, nsamples=1000, show_contours=True, show_mag=True, savetitle=None,
+#                   store=None, ultranest=False, dream=False, align=0):
+#     if show_contours:
+#         # data, columns = generate_contour_data(model)
+#         if ultranest:
+#             points_array = model.post_samples
+#             sub_array = points_array[np.sort(np.random.randint(points_array.shape[0], size=nsamples)), :]
+#             errors = calc_errors(model.problem, sub_array)
+#             data, columns = generate_profile_data(errors)
+#         # if this comment is removed the above code will not overwrite the previous reference to the errors object
+#         # and it will act as a bad memory leak - using more ram everytime the function is called
+#         if dream:
+#             state, points = load_dream_state_notebook(problem=model.problem, store=store)
+#             errors = calc_errors(model.problem, points[-nsamples:-1])
+#             data, columns = generate_profile_data(errors, align)
+#
+#     # get best profile manually as we are not using DREAM state
+#     if show_mag:
+#         z_best, rho_best, irho_best, rhoM_best, thetaM_best = generate_best_profile(model)
+#     else:
+#         z_best, rho_best, irho_best = generate_best_profile(model)
+#
+#     fig, ax = plt.subplots(1, 1, figsize=(8, 6))
+#
+#     # rho
+#     if show_contours:
+#         z, best, sig2lo, sig2hi, siglo, sighi = data[0]
+#         ax.plot(z, best, label=r"$\rho$ SLD", color="orange")
+#         ax.fill_between(z, siglo, sighi, alpha=0.5, color="orange", label=r"$\rho$ SLD $1\sigma$")
+#         ax.fill_between(z, sig2lo, sig2hi, alpha=0.25, color="orange", label=r"$\rho$ SLD $2\sigma$")
+#     else:
+#         ax.plot(z_best, rho_best, label=r"$\rho$ SLD", color="orange")
+#
+#     # irho
+#     # ax.plot(z_best, irho_best, label=r"$\rho_{i}$ Im SLD")
+#     # if show_contours:
+#     #     z, best, sig2lo, sig2hi, siglo, sighi = data[1]
+#     #     ax.fill_between(z, siglo, sighi, alpha=0.5)
+#     #     ax.fill_between(z, sig2lo, sig2hi, alpha=0.25)
+#     if show_mag:
+#         if show_contours:
+#             z, best, sig2lo, sig2hi, siglo, sighi = data[2]
+#             ax.plot(z, best, label=r"$\rho_{M}$ mSLD", color="b")
+#             ax.fill_between(z, siglo, sighi, alpha=0.5, color="b", label=r"$\rho_{M}$ mSLD $1\sigma$")
+#             ax.fill_between(z, sig2lo, sig2hi, alpha=0.25, color="b", label=r"$\rho_{M}$ mSLD $2\sigma$")
+#         else:
+#             ax.plot(z_best, rhoM_best, label=r"$\rho_{M}$ mSLD", color="b")
+#
+#     # ax.legend(fontsize=14, loc='upper right', framealpha=0.5, ncol=2)
+#     ax.legend(fontsize=16, framealpha=0.5, ncol=3)
+#
+#     ax.grid(True)
+#     ax.set_xlabel(r"z $\left(\AA\right)$", fontsize=18)
+#     ax.set_ylabel(r"$\rho, \rho_{i} \left(10^{-6}\AA^{-2}\right)$", fontsize=18)
+#     if show_mag:
+#         ax.set_ylabel(r"$\rho, \rho_{M} \left(10^{-6}\AA^{-2}\right)$", fontsize=18)
+#     ax.tick_params(axis='y', labelsize=16)
+#     ax.tick_params(axis='x', labelsize=16)
+#
+#     experiment = model.determine_problem_fitness()
+#
+#     layer_markers = FindLayers(experiment, axes=ax)
+#     layer_markers.reset_markers()
+#     fig.suptitle(title)
+#     # if np.max(rho_best) > 75:
+#     #     top = np.max(rho_best)*1.15
+#     # else:
+#     #     top =75
+#     # ax.set_ylim(top=top)
+#     if savepath:
+#         if savetitle:
+#             title = savetitle
+#         plt.savefig(f"{savepath}/{title}.png")
diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 3c9113b9..01d30b45 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -40,6 +40,7 @@
 bumps.cli.install_plugin(refl1d.fitplugin)
 
 from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
+from .profile_plot import plot_sld_profile_plotly
 
 # can get by name and not just by id
 EVT_LOG = Signal('log')
@@ -101,6 +102,7 @@ async def index(request):
     except FileNotFoundError:
         local_version = None
 
+    print(index_path, local_version, client_version, local_version == client_version)
     if client_version == local_version:
         return web.FileResponse(index_path / 'index.html')
     else:
@@ -285,26 +287,29 @@ async def get_model(sid: str=""):
 @sio.event
 @rest_get
 async def get_profile_plot(sid: str="", model_index: int=0):
-    import mpld3
-    import matplotlib
-    matplotlib.use("agg")
-    import matplotlib.pyplot as plt
-    import time
-    print('queueing new profile plot...', time.time())
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     if fitProblem is None:
         return None
     models = list(fitProblem.models)
-    if (model_index > len(models)):
+    if model_index > len(models):
         return None
     model = models[model_index]
-    assert(isinstance(model, Experiment))
-    fig = plt.figure()
-    model.plot_profile()
-    dfig = mpld3.fig_to_dict(fig)
-    plt.close(fig)
-    # await sio.emit("profile_plot", dfig, to=sid)
-    return dfig
+    assert (isinstance(model, Experiment))
+
+    # data = np.random.random((100,200))
+    # x = np.arange(0, 10, 0.1)
+    # y = np.random.random(x.shape) + x
+    # import plotly.express as px
+    # fig = px.imshow(data)
+    # fig.update_yaxes(exponentformat='e',
+    #                  title={'text': r"$\frac{I}{I_0}$"})
+    # fig = px.line(x=x, y=y)
+
+    fig = plot_sld_profile_plotly(model)
+
+    # print(to_dict(fig.to_dict()))
+
+    return to_dict(fig.to_dict())
 
 @sio.event
 @rest_get

From 9bef1337e8d3301c27e5ff7073a584dd7752d0f8 Mon Sep 17 00:00:00 2001
From: acaruana2009 <55897898+acaruana2009@users.noreply.github.com>
Date: Thu, 5 Jan 2023 21:45:04 +0000
Subject: [PATCH 118/221] Update plotly SLD profile style

---
 refl1d/webview/server/profile_plot.py | 40 ++++++++++++++++++++++-----
 1 file changed, 33 insertions(+), 7 deletions(-)

diff --git a/refl1d/webview/server/profile_plot.py b/refl1d/webview/server/profile_plot.py
index b10e9e6b..f0595652 100644
--- a/refl1d/webview/server/profile_plot.py
+++ b/refl1d/webview/server/profile_plot.py
@@ -128,7 +128,8 @@ def reset_markers_plotly(self):
                                textangle=-30,
                                x=label_pos,
                                yref="paper",
-                               y=1.05,
+                               y=1.0,
+                               yanchor="bottom",
                                showarrow=False
                                )
 
@@ -194,10 +195,13 @@ def plot_sld_profile_plotly(model):
     fig = go.Figure()
     if model.ismagnetic:
         z_best, rho_best, irho_best, rhoM_best, thetaM_best = generate_best_profile(model)
-        fig.add_scattergl(x=z_best, y=rhoM_best, name="$\\rho_{M}$")
-        yaxis_title = '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$'
 
-        fig.add_scattergl(x=z_best, y=thetaM_best, name="$\\theta_{M}$", yaxis="y2")
+        fig.add_scattergl(x=z_best, y=thetaM_best,
+                          name="$\\theta_{M}$", yaxis="y2",
+                          hovertemplate='(%{x}, %{y})<br>'
+                                        'Theta M'
+                                        '<extra></extra>',
+                          line={"color": "gold"})
         # TODO: need to make axis scaling for thetaM dependent on if thetaM exceeds 0-360
         fig.update_layout(yaxis2={
             'title': {'text': '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$'},
@@ -210,12 +214,28 @@ def plot_sld_profile_plotly(model):
             'ticks': "inside",
             # 'ticklen': 20,
         })
+
+        fig.add_scattergl(x=z_best, y=rhoM_best, name="$\\rho_{M}$",
+                          hovertemplate='(%{x}, %{y})<br>'
+                                        'M SLD'
+                                        '<extra></extra>',
+                          line={"color": "blue"})
+        yaxis_title = '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$'
+
     else:
         z_best, rho_best, irho_best = generate_best_profile(model)
         yaxis_title = '$\\text{SLD: } \\rho, \\rho_i / 10^{-6} \\text{Å}^{-2}$'
 
-    fig.add_scattergl(x=z_best, y=rho_best, name="$\\rho$", hovertext="SLD")
-    fig.add_scattergl(x=z_best, y=irho_best, name="$\\rho_{i}$")
+    fig.add_scattergl(x=z_best, y=irho_best, name="$\\rho_{i}$",
+                      hovertemplate='(%{x}, %{y})<br>'
+                                    'Im SLD'
+                                    '<extra></extra>',
+                      line={"color": "green"})
+    fig.add_scattergl(x=z_best, y=rho_best, name="$\\rho$",
+                      hovertemplate='(%{x}, %{y})<br>'
+                                    'SLD'
+                                    '<extra></extra>',
+                      line={"color": "black"})
 
     fig.update_layout(uirevision=1, plot_bgcolor="white")
 
@@ -251,11 +271,17 @@ def plot_sld_profile_plotly(model):
     fig.update_layout(margin={
         "l": 75,
         "r": 50,
-        "t": 25,
+        "t": 50,
         "b": 75,
         "pad": 4
     })
 
+    fig.update_layout(legend={
+        "x": -0.1,
+        "bgcolor": "rgba(255,215,0,0.15)",
+        "traceorder": "reversed"
+    })
+
     marker_positions = FindLayers(model, axes=fig)
     marker_positions.reset_markers_plotly()
 

From 754d5455dd861f2d7d8dc8891e5ec05d098cc5b9 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 9 Jan 2023 15:57:59 -0500
Subject: [PATCH 119/221] plotly version of varplot

---
 refl1d/webview/server/varplot.py | 255 +++++++++++++++++++++++++++++++
 1 file changed, 255 insertions(+)
 create mode 100644 refl1d/webview/server/varplot.py

diff --git a/refl1d/webview/server/varplot.py b/refl1d/webview/server/varplot.py
new file mode 100644
index 00000000..305e4f84
--- /dev/null
+++ b/refl1d/webview/server/varplot.py
@@ -0,0 +1,255 @@
+"""
+Build layout for histogram plots
+"""
+
+__all__ = ['var_plot_size', 'plot_vars', 'plot_var']
+
+from math import ceil, sqrt
+from typing import Dict
+
+import numpy as np
+
+# Set space between plots in horiz and vert.
+H_SPACE = 0.2
+V_SPACE = 0.2
+
+# Set top, bottom, left margins.
+T_MARGIN = 0.2
+B_MARGIN = 0.2
+L_MARGIN = 0.2
+R_MARGIN = 0.4
+
+# Set desired plot sizes.
+TILE_W = 3.0
+TILE_H = 2.0
+CBAR_WIDTH = 0.75
+CBAR_COLORS = 64
+
+LINE_COLOR = "red"
+ANNOTATION_COLOR = "blue"
+HISTOGRAM_COLORMAP = "Greens_r"
+
+
+def tile_axes_square(n):
+    """
+    Determine number of columns by finding the
+    next greatest square, then determine number
+    of rows needed.
+    """
+    cols = int(ceil(sqrt(n)))
+    rows = int(ceil(n/float(cols)))
+    return cols, rows
+
+
+def plot_vars(draw, all_vstats, **kw):
+    from plotly.subplots import make_subplots
+
+    n = len(all_vstats)
+    ncol, nrow = tile_axes_square(n)
+
+    snllf = np.sort(-draw.logp)
+    vmin, vmax = snllf[0], snllf[int(0.98*(len(snllf)-1))]  # robust range
+    cbar_edges = np.linspace(vmin, vmax, CBAR_COLORS)
+    titles = [vstats.label for vstats in all_vstats]
+
+    # fig = make_subplots(rows=nrow, cols=ncol, subplot_titles=titles)
+    fig = make_subplots(rows=nrow, cols=ncol)
+    fig.update_yaxes(secondary_y = True)
+
+    for k, vstats in enumerate(all_vstats):
+        row = (k // ncol) + 1
+        col = (k % ncol) + 1
+        plot_var(fig, draw, vstats, k, cbar_edges=cbar_edges, row=row, col=col, **kw)
+    
+    fig.update_xaxes(dict(exponentformat='e'), overwrite=True)
+    fig.update_yaxes(dict(showticklabels=False))
+    fig.update_layout(height=600, width=800, coloraxis_colorbar_title="-logP")
+    fig.update_layout(coloraxis = {'colorscale': HISTOGRAM_COLORMAP, "cmin": vmin, "cmax": vmax})
+    
+    return fig
+
+
+def plot_var(fig, draw, vstats, var, cbar_edges, nbins=30, row=None, col=None):
+    import plotly.graph_objects as go
+    assert isinstance(fig, go.Figure)
+    values = draw.points[:, var].flatten()
+    bin_range = vstats.p95_range
+    #bin_range = np.min(values), np.max(values)
+    showscale = (row == 0 and col == 0)
+    showscale = True
+    traces = _make_logp_histogram(values, draw.logp, nbins, bin_range,
+                         draw.weights, cbar_edges=cbar_edges, showscale=showscale)
+
+    fig.add_traces(traces, rows=row, cols=col)
+    _decorate_histogram(vstats, fig, row=row, col=col)
+
+
+def _decorate_histogram(vstats, fig, col=None, row=None):
+    import plotly.graph_objects as go
+
+    l95, h95 = vstats.p95_range
+    l68, h68 = vstats.p68_range
+    # Shade things inside 1-sigma
+    assert isinstance(fig, go.Figure)
+    fig.add_vrect(x0=l68, x1=h68, fillcolor='gold', opacity=0.5, layer='below', line={"width": 0}, col=col, row=row)
+
+    def marker(symbol, position, info_template):
+        if position < l95:
+            symbol, position, ha = '<'+symbol, l95, 'left'
+        elif position > h95:
+            symbol, position, ha = '>'+symbol, h95, 'right'
+        else:
+            symbol, position, ha = symbol, position, 'center'
+        fig.add_annotation(
+            xref="x",
+            yref="y domain",
+            x=position,
+            y=0.95,
+            text=symbol,
+            showarrow=False,
+            font=dict(color=ANNOTATION_COLOR),
+            col=col,
+            row=row,
+            hovertext=info_template.format(position=position)
+        )
+
+        #pylab.axvline(v)
+
+    marker('|', vstats.median, "median: {position}")
+    marker('E', vstats.mean, "mean: {position}")
+    marker('*', vstats.best, "best: {position}")
+    
+    fig.add_annotation(
+        xref="x domain",
+        yref="y domain",
+        x = 0.0,
+        y = 1.1,
+        text = vstats.label,
+        col=col,
+        row=row,
+        showarrow=False
+    )
+
+def _make_logp_histogram(values, logp, nbins, ci, weights, cbar_edges, showscale=False):
+    from numpy import (ones_like, searchsorted, linspace, cumsum, diff,
+                       unique, argsort, array, hstack, exp)
+    import plotly.graph_objects as go
+
+    if weights is None:
+        weights = ones_like(logp)
+    # TODO: values are being sorted to collect stats and again to plot
+    idx = argsort(values)
+    values, weights, logp = values[idx], weights[idx], logp[idx]
+    #open('/tmp/out','a').write("ci=%s, range=%s\n"
+    #                           % (ci,(min(values),max(values))))
+    edges = linspace(ci[0], ci[1], nbins+1)
+    bin_index = range(nbins)
+    idx = searchsorted(values[1:-1], edges)
+
+
+    bins = []  # marginalized maximum likelihood
+
+    # H, xedges, yedges = np.histogram2d(values, -logp, bins=(edges, cbar_edges), weights=weights)
+    # ybins = len(yedges) - 1
+    # x = (xedges[:-1] + xedges[1:]) / 2.0
+    # cbar_values = ((cbar_edges[:-1] + cbar_edges[1:]) / 2.0)[::-1]
+    # x = x.repeat(ybins) # match length of y array
+    # y = H.flatten(order="C")
+    # color = np.tile(cbar_values, nbins)
+
+    # # filter out empty y values (speeds up drawing, omitting empty rectangles):
+    # y_nonzero = (y > 0)
+    # # print(f"y_zeros: {y_nonzero}, {len([z for z in y_nonzero if z])} out of {len(y)}")
+    # x = x[y_nonzero]
+    # color = color[y_nonzero]
+    # y = y[y_nonzero]
+    # traces.append(go.Bar(x=x, y=y, showlegend=False, marker=dict(color=color, coloraxis='coloraxis', line=dict(width=0))))
+    # # traces.append(go.Bar(x=x, y=y, showlegend=False, hoverinfo='skip', marker=dict(color=color, coloraxis='coloraxis', line=dict(width=0))))
+
+    xscatt = []
+    yscatt = []
+    zscatt = []
+
+    for i, s, e, xlo, xhi \
+            in zip(bin_index, idx[:-1], idx[1:], edges[:-1], edges[1:]):
+        if s == e:
+            continue
+
+        pv = -logp[s:e]
+        # weights for samples within interval
+        pw = weights[s:e]
+        # vertical colorbar top edges is the cumulative sum of the weights
+        bin_height = pw.sum()
+
+         # parameter interval endpoints
+        x = array([xlo, xhi], 'd')
+        xav = (xlo + xhi)/2
+        # -logp values within interval, with sort index from low to high
+        pv = -logp[s:e]
+        pidx = argsort(pv)
+        pv = pv[pidx]
+        # weights for samples within interval, sorted
+        pw = weights[s:e][pidx]
+        # vertical colorbar top edges is the cumulative sum of the weights
+        y_top = cumsum(pw)
+        bin_height = y_top[-1]
+
+        change_point = searchsorted(pv[1:-1], cbar_edges)
+        tops = unique(hstack((change_point, len(pv)-1)))
+        # For plotly Bar plot, y values should be [size along y] (stacked)
+        yy = np.diff(hstack((0, y_top[tops])))
+        zz = pv[tops][:, None].flatten()
+        xx = np.ones(tops.shape, dtype=float) * xav
+        
+        xscatt.extend(xx.tolist())
+        yscatt.extend(yy.tolist())
+        zscatt.extend(zz.tolist())
+        
+        # centerpoint, histogram height, maximum likelihood for each bin
+        bin_max_likelihood = exp(cbar_edges[0] - pv[0])
+        bins.append(((xlo+xhi)/2, bin_height, bin_max_likelihood))
+
+    bar_trace = go.Bar(x=xscatt, y=yscatt, showlegend=False, hoverinfo='skip', marker=dict(color=zscatt, coloraxis='coloraxis', line=dict(width=0)))
+    # Check for broken distribution
+    if not bins:
+        return
+    centers, height, maxlikelihood = array(bins).T
+    # Normalize maximum likelihood plot so it contains the same area as the
+    # histogram, unless it is really spikey, in which case make sure it has
+    # about the same height as the histogram.
+    maxlikelihood *= np.sum(height)/np.sum(maxlikelihood)
+    hist_peak = np.max(height)
+    ml_peak = np.max(maxlikelihood)
+    if ml_peak > hist_peak*1.3:
+        maxlikelihood *= hist_peak*1.3/ml_peak
+    
+    scatter_trace = go.Scatter(x=centers, y=maxlikelihood, hoverinfo='skip', showlegend=False, line={"color": LINE_COLOR})
+    # return dict(bar_trace=bar_trace, scatter_trace=scatter_trace)
+    return [bar_trace, scatter_trace]
+
+    ## plot marginal gaussian approximation along with histogram
+    #def G(x, mean, std):
+    #    return np.exp(-((x-mean)/std)**2/2)/np.sqrt(2*np.pi*std**2)
+    ## TODO: use weighted average for standard deviation
+    #mean, std = np.average(values, weights=weights), np.std(values, ddof=1)
+    #pdf = G(centers, mean, std)
+    #pylab.plot(centers, pdf*np.sum(height)/np.sum(pdf), '-b')
+
+
+def test():
+    import pickle
+    test_data = pickle.loads(open("./varplot.pickle", 'rb').read())
+    draw = test_data['draw']
+    stats = test_data['stats']
+    import time
+    start_time = time.time()
+    fig = plot_vars(draw, stats)
+    print(f"generating plot took: {time.time() - start_time} seconds")
+    # print(fig)
+    # print(test_data.keys())
+    fig.write_json(open("varplot.json", "w"))
+    fig.write_html(open("varplot.html", "w"))
+    fig.show()
+
+if __name__ == '__main__':
+    test()
\ No newline at end of file

From 4797ee412ab59a3dbfe8a90c4abe6ef398bd3d2e Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 9 Jan 2023 15:58:34 -0500
Subject: [PATCH 120/221] use new plotly varplot for uncertainty plot

---
 refl1d/webview/server/webserver.py | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 01d30b45..5b7b3715 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -41,6 +41,7 @@
 
 from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
 from .profile_plot import plot_sld_profile_plotly
+from .varplot import plot_vars
 
 # can get by name and not just by id
 EVT_LOG = Signal('log')
@@ -421,26 +422,13 @@ async def get_correlation_plot(sid: str = ""):
 async def get_uncertainty_plot(sid: str = ""):
     uncertainty_state = app["fitting"].get("uncertainty_state", None)
     if uncertainty_state is not None:
-        import mpld3
-        import matplotlib
-        matplotlib.use("agg")
-        import matplotlib.pyplot as plt
         import time
         start_time = time.time()
-        print('queueing new correlation plot...', start_time)
-
-        fig = plt.figure()
+        print('queueing new uncertainty plot...', start_time)
         draw = uncertainty_state.draw()
         stats = bumps.dream.stats.var_stats(draw)
-        bumps.dream.varplot.plot_vars(draw, stats, fig=fig)
-        print("time to render but not serialize...", time.time() - start_time)
-        fig.canvas.draw()
-        dfig = mpld3.fig_to_dict(fig)
-        plt.close(fig)
-        # await sio.emit("profile_plot", dfig, to=sid)
-        end_time = time.time()
-        print("time to draw correlation plot:", end_time - start_time)
-        return dfig
+        fig = plot_vars(draw, stats)
+        return to_dict(fig.to_dict())
     else:
         return None
 

From b685bb2ab90b8f8070158ff21eb1cebe5319ceaa Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 9 Jan 2023 15:58:49 -0500
Subject: [PATCH 121/221] use new plotly uncertainty plot

---
 .../client/src/components/UncertaintyView.vue | 25 +++++++++++++------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/refl1d/webview/client/src/components/UncertaintyView.vue b/refl1d/webview/client/src/components/UncertaintyView.vue
index d01f6197..bef8e71e 100644
--- a/refl1d/webview/client/src/components/UncertaintyView.vue
+++ b/refl1d/webview/client/src/components/UncertaintyView.vue
@@ -3,7 +3,12 @@
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
-import mpld3 from 'mpld3';
+import * as Plotly from 'plotly.js/lib/core';
+import Bar from 'plotly.js/lib/bar';
+
+Plotly.register([
+  Bar,
+])
 
 const plot_div = ref<HTMLDivElement>();
 const draw_requested = ref(false);
@@ -21,16 +26,20 @@ onMounted(() => {
   window.requestAnimationFrame(draw_if_needed);
 });
 
+
 function fetch_and_draw() {
-  props.socket.emit('get_uncertainty_plot', (payload) => {
+  props.socket.emit('get_uncertainty_plot', async (payload) => {
+    if (plot_div.value == null) {
+      return
+    }
     if (props.visible) {
       let plotdata = { ...payload };
-      console.log({plotdata});
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      /* Data Parsing Functions */
-      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
+      const { data, layout } = plotdata;
+      delete layout.width;
+      delete layout.height;
+      delete layout.heighth;
+      const config = { responsive: true }
+      const plot = await Plotly.react(plot_div_id.value, [...data], layout, config);
     }
     drawing_busy.value = false;
   });

From 735e43c5c5e0feef0c2251c539653fd3399e9a13 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Tue, 14 Dec 2021 11:40:19 -0500
Subject: [PATCH 122/221] automatically filter data points that contain nan in
 any column

---
 refl1d/probe.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/refl1d/probe.py b/refl1d/probe.py
index 17581ef8..7900d2df 100644
--- a/refl1d/probe.py
+++ b/refl1d/probe.py
@@ -250,6 +250,17 @@ def _set_TLR(self, T, dT, L, dL, R, dR, dQ):
         # Make sure that we are dealing with vectors
         T, dT, L, dL = [np.ones_like(Q)*v for v in (T, dT, L, dL)]
 
+        # remove nan
+        nan_indices = set()
+        for column in [T, dT, L, dL, R, dR, Q, dQ]:
+            if column is not None:
+                indices = np.argwhere(np.isnan(column)).flatten()
+                nan_indices.update(indices)
+
+        nan_indices = list(nan_indices)
+        T, dT, L, dL, R, dR, Q, dQ = (
+            np.delete(c, nan_indices) if c is not None else None for c in [T, dT, L, dL, R, dR, Q, dQ])
+
         # Probe stores sorted values for convenience of resolution calculator
         idx = np.argsort(Q)
         self.T, self.dT = T[idx], dT[idx]

From 68242d83d1637451db90406702e69a74fd5c7099 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Tue, 10 Jan 2023 13:41:24 -0500
Subject: [PATCH 123/221] density should not be in Material class schema, it is
 a derived parameter

---
 refl1d/material.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/material.py b/refl1d/material.py
index 3389a2d5..92434be6 100644
--- a/refl1d/material.py
+++ b/refl1d/material.py
@@ -217,7 +217,7 @@ class Material(Scatterer):
     formula: str # Formula
     formula_density: float
     formula_natural_density: Union[float, Literal[None]]
-    density: Parameter
+    # density: Parameter
     value: Parameter
     fitby: Literal['bulk_density', 'number_density', 'natural_density', 'relative_density', 'cell_volume'] = 'bulk_density'
     use_incoherent: bool = False

From 38f79393850060341eddd91883c07d4ec39b9a97 Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Tue, 10 Jan 2023 13:02:04 -0500
Subject: [PATCH 124/221] convert dQ to regular property, create ProbeSchema

---
 refl1d/probe.py | 48 +++++++++++++++++++++++++-----------------------
 1 file changed, 25 insertions(+), 23 deletions(-)

diff --git a/refl1d/probe.py b/refl1d/probe.py
index 7900d2df..ea98ce91 100644
--- a/refl1d/probe.py
+++ b/refl1d/probe.py
@@ -80,9 +80,28 @@ def make_probe(**kw):
     else:
         return XrayProbe(**kw)
 
+@schema(classname="Probe", init=False, eq=False)
+class ProbeSchema:
+    name: Optional[str] = None
+    filename: Optional[str] = None
+    radiation: Literal["neutron", "xray"] = "xray"
+    intensity: Parameter = 1.0
+    background: Parameter = 0
+    back_absorption: Parameter = 0
+    theta_offset: Parameter = 0
+    sample_broadening: Parameter = 0
+    back_reflectivity: bool = False
+    R: Optional[Any] = None
+    dR: Optional[Any] = 0
+    T: List[float] = field_desc("List of theta values (incident angle)")
+    dT: Optional[Any] = 0
+    L: List[float] = field_desc("List of lambda values (wavelength, in Angstroms)")
+    dL: Optional[Any] = 0
+    dQ: Optional[Any] = None
+    resolution: Literal["normal", "uniform"] = "uniform"
 
 @schema()
-class Probe:
+class Probe(ProbeSchema):
     r"""
     Defines the incident beam used to study the material.
 
@@ -156,23 +175,6 @@ class Probe:
     large isotropic incoherent scattering cross section.
 
     """
-    name: Optional[str] = None
-    filename: Optional[str] = None
-    radiation: Literal["neutron", "xray"] = "xray"
-    intensity: Parameter = 1.0
-    background: Parameter = 0
-    back_absorption: Parameter = 0
-    theta_offset: Parameter = 0
-    sample_broadening: Parameter = 0
-    back_reflectivity: bool = False
-    R: Optional[Any] = None
-    dR: Optional[Any] = 0
-    T: List[float] = field_desc("List of theta values (incident angle)")
-    dT: Optional[Any] = 0
-    L: List[float] = field_desc("List of lambda values (wavelength, in Angstroms)")
-    dL: Optional[Any] = 0
-    dQ: Optional[Any] = None
-    resolution: Literal["normal", "uniform"] = "uniform"
 
     polarized = False
     Aguide = BASE_GUIDE_ANGLE  # default guide field for unpolarized measurements
@@ -229,7 +231,6 @@ def __init__(self, T=None, dT=0, L=None, dL=0, data=None,
         self.name = name
         self.filename = filename
         self.resolution = resolution
-        self.__class__.dQ = property(self._get_dQ, self._set_dQ)
 
     def _set_TLR(self, T, dT, L, dL, R, dR, dQ):
         #if L is None:
@@ -425,8 +426,9 @@ def Q(self, Q):
             del self.T, self.L
         self.Qo = Q
 
-    @staticmethod
-    def _get_dQ(self):
+    @property
+    def dQ(self):
+        print('getting dQ')
         if self.sample_broadening.value == 0:
             dQ = self.dQo
         else:
@@ -434,8 +436,8 @@ def _get_dQ(self):
                                width=self.sample_broadening.value)
         return dQ
         
-    @staticmethod
-    def _set_dQ(self, dQ):
+    @dQ.setter
+    def dQ(self, dQ):
         self.dQo = dQ
 
     @property

From 3b39192c6e01e8d086d79bdb04c5399f103fd2bc Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Tue, 10 Jan 2023 13:46:04 -0500
Subject: [PATCH 125/221] remove debug message

---
 refl1d/probe.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/refl1d/probe.py b/refl1d/probe.py
index ea98ce91..f70d1a64 100644
--- a/refl1d/probe.py
+++ b/refl1d/probe.py
@@ -428,7 +428,6 @@ def Q(self, Q):
 
     @property
     def dQ(self):
-        print('getting dQ')
         if self.sample_broadening.value == 0:
             dQ = self.dQo
         else:

From 35d88fe694926c24288cbd0c0b410930769cc61c Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 10 Jan 2023 15:43:25 -0500
Subject: [PATCH 126/221] add Save functionality to webview (saves json)

---
 refl1d/webview/client/src/App.vue  | 19 +++++++++++++-
 refl1d/webview/server/webserver.py | 42 +++++++++++++++++++++++++++---
 2 files changed, 56 insertions(+), 5 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 4932ce1d..8cfdff74 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -86,6 +86,23 @@ function selectOpenFile() {
   // file_picker.value?.click();
 }
 
+async function saveFile(ev: Event) {
+  if (model_loaded.value === undefined) {
+    alert('no file to save');
+    return;
+  }
+  const {pathlist, filename} = model_loaded.value;
+  console.log('saving:', {pathlist, filename});
+  socket.emit("save_problem_file", pathlist, filename, false, async(confirm_overwrite: boolean) => {
+    if (confirm_overwrite) {
+      const overwrite = await confirm(`File ${filename} exists: overwrite?`);
+      if (overwrite) {
+        socket.emit("save_problem_file", {pathlist, filename, overwrite: true});
+      }
+    }
+  });
+}
+
 function reloadModel() {
   if (model_loaded.value) {
     const {pathlist, filename} = model_loaded.value;
@@ -150,7 +167,7 @@ onMounted(() => {
               </button>
               <ul class="dropdown-menu">
                 <li><button class="btn btn-link dropdown-item" @click="selectOpenFile">Open</button></li>
-                <li><button class="btn btn-link dropdown-item" >Save</button></li>
+                <li><button class="btn btn-link dropdown-item" :disabled="!model_loaded" @click="saveFile">Save</button></li>
                 <li><button class="btn btn-link dropdown-item" :class="{disabled: model_loaded === undefined}"  @click="reloadModel">Reload</button></li>
                 <li>
                   <hr class="dropdown-divider">
diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 5b7b3715..f9cba21c 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -23,7 +23,7 @@
 mimetypes.add_type("image/svg+xml", ".svg")
 
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit
-from bumps.serialize import to_dict
+from bumps.serialize import to_dict, from_dict
 from bumps.mapper import MPMapper
 from bumps.parameter import Parameter, Variable, unique
 import bumps.fitproblem
@@ -45,6 +45,7 @@
 
 # can get by name and not just by id
 EVT_LOG = Signal('log')
+MODEL_EXT = '.json'
 
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
 FITTERS_BY_ID = dict([(fitter.id, fitter) for fitter in FITTERS])
@@ -69,7 +70,7 @@
 
 topics: Dict[str, Dict] = {}
 app["topics"] = topics
-app["problem"] = {"fitProblem": None, "filepath": None}
+app["problem"] = {"fitProblem": None, "pathlist": None, "filename": None}
 app["fitting"] = {
     "fit_thread": None,
     "abort": False,
@@ -121,11 +122,18 @@ async def connect(sid, environ, data=None):
 
 @sio.event
 async def load_problem_file(sid: str, pathlist: List[str], filename: str):
-    from bumps.cli import load_model
     path = Path(*pathlist, filename)
     print('model loading: ', str(path))
-    problem = load_model(str(path))
+    if filename.endswith(".json"):
+        with open(path, "rt") as input_file:
+            serialized = json.loads(input_file.read())
+        problem = from_dict(serialized)
+    else:
+        from bumps.cli import load_model
+        problem = load_model(str(path))
     app["problem"]["fitProblem"] = problem
+    app["problem"]["pathlist"] = pathlist
+    app["problem"]["filename"] = filename
     print('model loaded: ', str(path))
 
     model_names = [getattr(m, 'name', None) for m in list(problem.models)]
@@ -133,6 +141,32 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     await publish("", "update_model", True)
     await publish("", "update_parameters", True)
 
+@sio.event
+async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, filename: Optional[str] = None, overwrite: bool = False):
+    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if fitProblem is None:
+        print("Save failed: no problem loaded.")
+        return
+    if pathlist is None:
+        pathlist = app["problem"]["pathlist"]
+    if filename is None:
+        filename = app["problem"]["filename"]
+
+    if pathlist is None or filename is None:
+        print("no filename and path provided to save")
+        return
+
+    path = Path(*pathlist)
+    save_filename = Path(filename).stem + MODEL_EXT
+    print({"path": path, "filename": save_filename})
+    if not overwrite and Path.exists(path / save_filename):
+        #confirmation needed:
+        return True
+
+    serialized = to_dict(fitProblem)
+    with open(Path(path, save_filename), "wt") as output_file:
+        output_file.write(json.dumps(serialized))
+
 @sio.event
 async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
     kwargs = {} if kwargs is None else kwargs

From 9d35a90bba44425d6531a5af6d0b168e623ad7ed Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 10 Jan 2023 15:43:41 -0500
Subject: [PATCH 127/221] add full filename as tooltip

---
 refl1d/webview/client/src/components/FileBrowser.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
index 16fc27b5..87332ba9 100644
--- a/refl1d/webview/client/src/components/FileBrowser.vue
+++ b/refl1d/webview/client/src/components/FileBrowser.vue
@@ -103,7 +103,7 @@ defineExpose({
             <h3>Files:</h3>
             <div class="row row-cols-3">
               <div class="btn col overflow-hidden border" :class="{'btn-warning': filename === chosenFile}"
-                v-for="filename in filelist" :key="filename" @click="chosenFile = filename"
+                v-for="filename in filelist" :key="filename" @click="chosenFile = filename" :title="filename"
                 @dblclick="chosenFile=filename;chooseFile()">
                 {{filename}}
               </div>

From eeb27f665ab7306b6baa1767310e4904f6a50f27 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 13 Jan 2023 13:40:09 -0500
Subject: [PATCH 128/221] use random available port for server if not specified
 with -p, and start browser

---
 refl1d/webview/server/webserver.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index f9cba21c..f999e8e0 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -713,16 +713,24 @@ def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[Param
 def main():
     parser = argparse.ArgumentParser()
     # parser.add_argument('-d', '--debug', action='store_true', help='autoload modules on change')
-    # parser.add_argument('-x', '--headless', action='store_true', help='do not automatically load client in browser')
+    parser.add_argument('-x', '--headless', action='store_true', help='do not automatically load client in browser')
     parser.add_argument('--external', action='store_true', help='listen on all interfaces, including external (local connections only if not set)')
-    parser.add_argument('-p', '--port', default=None, type=int, help='port on which to start the server')
+    parser.add_argument('-p', '--port', default=0, type=int, help='port on which to start the server')
     # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
     args = parser.parse_args()
 
     app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     app.add_routes(routes)
     hostname = 'localhost' if not args.external else '0.0.0.0'
-    web.run_app(app, host=hostname, port=args.port)
+
+    import socket
+    sock = socket.socket()
+    sock.bind((hostname, args.port))
+    _, port = sock.getsockname()
+    if not args.headless:
+        import webbrowser
+        webbrowser.open_new_tab(f"http://{hostname}:{port}/")
+    web.run_app(app, sock=sock)
 
 if __name__ == '__main__':
     main()

From 4d6631ae0828b6635099bbb3554a6df67449fdb2 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 13 Jan 2023 14:37:40 -0500
Subject: [PATCH 129/221] fix scrolling within panels (don't scrol nav tabs at
 top)

---
 refl1d/webview/client/src/App.vue                          | 4 ++--
 refl1d/webview/client/src/components/PanelTabContainer.vue | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 8cfdff74..c1db4db4 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -212,10 +212,10 @@ onMounted(() => {
       </div>
     </nav>
     <div class="flex-grow-1 row overflow-hidden">
-      <div class="col d-flex flex-column mh-100 overflow-auto">
+      <div class="col d-flex flex-column mh-100">
         <PanelTabContainer :panels="panels" :socket="socket" :initially_active="0"/>
       </div>
-      <div class="col d-flex flex-column mh-100 overflow-auto">
+      <div class="col d-flex flex-column mh-100">
         <PanelTabContainer :panels="panels" :socket="socket" :initially_active="1"/>
       </div>
     </div>
diff --git a/refl1d/webview/client/src/components/PanelTabContainer.vue b/refl1d/webview/client/src/components/PanelTabContainer.vue
index 74069e51..9a6bce3e 100644
--- a/refl1d/webview/client/src/components/PanelTabContainer.vue
+++ b/refl1d/webview/client/src/components/PanelTabContainer.vue
@@ -49,7 +49,7 @@ onMounted(() => {
       <a ref="tabTriggers" class="nav-link" href="#" @click="activateTab(index)">{{panels[index]?.title}}</a>
     </li>
   </ul>
-  <div class="tab-content d-flex flex-column flex-grow-1">
+  <div class="tab-content d-flex flex-column flex-grow-1 overflow-auto">
     <div ref="panelContainers" class="tab-pane flex-column flex-grow-1" v-for="(panel, index) in props.panels"
       :key="index">
       <component :is="panel.component" :socket="props.socket" :visible="panelVisible[index]"></component>

From 6884ee3ec296e951d7ffd4e3c83342d47127a384 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 18 Jan 2023 09:47:14 -0500
Subject: [PATCH 130/221] don't need MML MathJax

---
 refl1d/webview/client/index.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/index.html b/refl1d/webview/client/index.html
index 529eaf55..c55b2ea8 100644
--- a/refl1d/webview/client/index.html
+++ b/refl1d/webview/client/index.html
@@ -5,7 +5,7 @@
     <link rel="icon" href="./src/assets/refl1d-icon_48x48x32.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <script type="text/javascript" async
-      src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-svg.min.js">
+      src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-svg.min.js">
     </script>
     <title>Refl1D</title>
   </head>

From 1421ad4c1b01db4b1b74d55b8732604c70de15bb Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 18 Jan 2023 19:05:45 -0500
Subject: [PATCH 131/221] use unicode axis labels instead of latex, for speed

---
 refl1d/webview/client/src/components/DataView.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/src/components/DataView.vue b/refl1d/webview/client/src/components/DataView.vue
index 7524a25f..33d5ce34 100644
--- a/refl1d/webview/client/src/components/DataView.vue
+++ b/refl1d/webview/client/src/components/DataView.vue
@@ -93,7 +93,7 @@ function fetch_and_draw() {
       uirevision: reflectivity_type.value,
       xaxis: {
         title: {
-          text: '$Q (Å^{-1})$'
+          text: 'Q (Å<sup>-1</sup>)'
         },
         type: 'linear',
         autorange: true,

From 972fae45d5453519eda3431b5e3629358e5b15a5 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 18 Jan 2023 19:12:52 -0500
Subject: [PATCH 132/221] use Vue to show/hide panels instead of Tab function
 from Bootstrap

---
 .../src/components/PanelTabContainer.vue      | 34 +++----------------
 1 file changed, 4 insertions(+), 30 deletions(-)

diff --git a/refl1d/webview/client/src/components/PanelTabContainer.vue b/refl1d/webview/client/src/components/PanelTabContainer.vue
index 9a6bce3e..76868653 100644
--- a/refl1d/webview/client/src/components/PanelTabContainer.vue
+++ b/refl1d/webview/client/src/components/PanelTabContainer.vue
@@ -2,13 +2,12 @@
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import type { DefineComponent, Component } from 'vue';
 import type { Socket } from 'socket.io-client';
-import { Tab } from 'bootstrap/dist/js/bootstrap.esm';
 
 // type PanelComponent = DefineComponent<{socket: Socket, visible: boolean}, any>;
 
 const tabTriggers = ref<HTMLAnchorElement[]>([]);
 const panelContainers = ref<HTMLDivElement[]>([]);
-const panelVisible = ref<boolean[]>([]);
+const activePanel = ref(0);
 
 const props = defineProps<{
   socket: Socket,
@@ -16,44 +15,19 @@ const props = defineProps<{
   initially_active?: number
 }>();
 
-let triggers: Tab[] = [];
-
-function activateTab(index) {
-  triggers?.[index].show();
-  panelContainers.value.forEach((el, i) => {
-    if (i === index) {
-      el.classList.add('active');
-      panelVisible.value[i] = true;
-    }
-    else {
-      el.classList.remove('active');
-      panelVisible.value[i] = false;
-    }
-  });
-}
-
 onMounted(() => {
-  for (let triggerEl of tabTriggers.value) {
-    let tabTrigger = new Tab(triggerEl);
-    triggers.push(tabTrigger);
-  }
-  if (triggers.length > 0) {
-    activateTab(props.initially_active ?? 0);
-  }
+  activePanel.value = props.initially_active ?? 0;
 });
 </script>
 
 <template>
   <ul class="nav nav-tabs">
     <li class="nav-item" v-for="(panel, index) in props.panels" :key="index">
-      <a ref="tabTriggers" class="nav-link" href="#" @click="activateTab(index)">{{panels[index]?.title}}</a>
+      <a ref="tabTriggers" :class="{'nav-link': true, active: index == activePanel}" href="#" @click="activePanel = index">{{panels[index]?.title}}</a>
     </li>
   </ul>
   <div class="tab-content d-flex flex-column flex-grow-1 overflow-auto">
-    <div ref="panelContainers" class="tab-pane flex-column flex-grow-1" v-for="(panel, index) in props.panels"
-      :key="index">
-      <component :is="panel.component" :socket="props.socket" :visible="panelVisible[index]"></component>
-    </div>
+      <component :is="panels[activePanel].component" :socket="props.socket" :visible="true"></component>
   </div>
 </template>
 

From 419e39de048b882569cb785068b3046c1784e5fd Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 18 Jan 2023 19:13:59 -0500
Subject: [PATCH 133/221] use getter function instead of message event to
 populate current file path on open

---
 refl1d/webview/client/src/components/FileBrowser.vue | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/refl1d/webview/client/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
index 87332ba9..8dc9d8c7 100644
--- a/refl1d/webview/client/src/components/FileBrowser.vue
+++ b/refl1d/webview/client/src/components/FileBrowser.vue
@@ -2,7 +2,6 @@
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import { Modal } from 'bootstrap/dist/js/bootstrap.esm';
 import { Socket } from 'socket.io-client';
-import { emitValidationErrors } from 'mapbox-gl/dist/mapbox-gl-unminified';
 
 const props = defineProps<{
   socket: Socket,
@@ -22,10 +21,6 @@ const subdirlist = shallowRef<string[]>([])
 const filelist = shallowRef<string[]>([])
 const chosenFile = ref("");
 
-props.socket.on('local_file_path', ({message: new_pathlist, timestamp}) => {
-  pathlist.value = new_pathlist;
-})
-
 let modal: Modal;
 onMounted(() => {
   modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
@@ -37,9 +32,11 @@ function close() {
 }
 
 function open() {
+  props.socket.emit('get_current_pathlist', (new_pathlist) => {
+    setPath(new_pathlist);
+  })
   modal?.show();
   isOpen.value = true;
-  setPath();
 }
 
 function subdirClick(subdir: string) {

From cdc67b40367bfb2759f3e5fd832c873671b8f38b Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 13:28:43 -0500
Subject: [PATCH 134/221] patch socketio to add asyncEmit method, can await
 results

---
 refl1d/webview/client/src/asyncSocket.ts | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 refl1d/webview/client/src/asyncSocket.ts

diff --git a/refl1d/webview/client/src/asyncSocket.ts b/refl1d/webview/client/src/asyncSocket.ts
new file mode 100644
index 00000000..a343d904
--- /dev/null
+++ b/refl1d/webview/client/src/asyncSocket.ts
@@ -0,0 +1,13 @@
+import { Socket } from 'socket.io-client';
+
+declare module 'socket.io-client' {
+  class Socket {
+    public asyncEmit(ev: string, ...args: any[]): Promise<any>;
+  }
+}
+
+Socket.prototype.asyncEmit = async function asyncEmit(ev: string, ...args: any[]) {
+  return new Promise((resolve, reject) => {
+    this.emit(ev, ...args, resolve);
+  })
+};
\ No newline at end of file

From c50f18d67f2e576c50eb6af1af805b5454c43a62 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 13:29:05 -0500
Subject: [PATCH 135/221] apply asyncEmit socketio patch

---
 refl1d/webview/client/src/App.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index c1db4db4..e23f56af 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -2,6 +2,7 @@
 import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
 import { onMounted, ref, shallowRef } from 'vue';
 import { io } from 'socket.io-client';
+import './asyncSocket';
 import FitOptions from './components/FitOptions.vue';
 import DataView from './components/DataView.vue';
 import ModelView from './components/ModelView.vue';

From f4f461d9ae5a8fdb740d16d2d806944804fd575d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 13:29:54 -0500
Subject: [PATCH 136/221] add standardized method for setting up the drawing
 loop in the client components

---
 refl1d/webview/client/src/setupDrawLoop.ts | 51 ++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 refl1d/webview/client/src/setupDrawLoop.ts

diff --git a/refl1d/webview/client/src/setupDrawLoop.ts b/refl1d/webview/client/src/setupDrawLoop.ts
new file mode 100644
index 00000000..7ba91079
--- /dev/null
+++ b/refl1d/webview/client/src/setupDrawLoop.ts
@@ -0,0 +1,51 @@
+import { ref, onMounted, onBeforeUnmount } from 'vue';
+import type { Socket } from 'socket.io-client';
+import './asyncSocket';
+
+export function setupDrawLoop(topic: string, socket: Socket, draw: Function, name: string = '') {
+  const mounted = ref(false);
+  const drawing_busy = ref(false);
+  const draw_requested = ref(false);
+  const latest_timestamp = ref<string>();
+
+  const topic_callback = function() {
+    draw_requested.value = true;
+  }
+
+  const draw_if_needed = async function() {
+    if (!mounted.value) {
+      return;
+    }
+    if (drawing_busy.value) {
+      console.log(`drawing ${name} busy!`);
+    }
+    else if (draw_requested.value) {
+      drawing_busy.value = true;
+      draw_requested.value = false;
+      await draw(latest_timestamp.value);
+      drawing_busy.value = false;
+    }
+    window.requestAnimationFrame(draw_if_needed);
+  }
+
+  onMounted(async () => {
+    mounted.value = true;
+    socket.on(topic, topic_callback);
+
+    const messages = await socket.asyncEmit('get_topic_messages', topic);
+    // console.log(topic, messages);
+    const last_message = messages.pop();
+    if (last_message) {
+      draw_requested.value = true;
+      latest_timestamp.value = last_message.timestamp;
+    }
+    window.requestAnimationFrame(draw_if_needed);
+  });
+
+  onBeforeUnmount(() => { 
+    mounted.value = false;
+    socket.off(topic, topic_callback);
+  });
+
+  return { mounted, drawing_busy, draw_requested };
+}

From c86ae91a263ce511526006fa297c9b700a1e9c97 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 16:11:11 -0500
Subject: [PATCH 137/221] use new setupDrawLoop function in panels

---
 .../client/src/components/ConvergenceView.vue |  46 ++-----
 .../client/src/components/CorrelationView.vue |  50 +++-----
 .../client/src/components/DataView.vue        |  96 +++++---------
 .../client/src/components/ModelInspect.vue    |  56 +++++----
 .../src/components/ModelUncertaintyView.vue   |  50 +++-----
 .../client/src/components/ModelView.vue       |  54 +++-----
 .../client/src/components/ModelViewPlotly.vue | 118 +++++++-----------
 .../src/components/ParameterTraceView.vue     |  45 ++-----
 .../client/src/components/ParameterView.vue   |  40 ++----
 .../client/src/components/SummaryView.vue     |  53 ++++----
 .../client/src/components/UncertaintyView.vue |  55 +++-----
 11 files changed, 229 insertions(+), 434 deletions(-)

diff --git a/refl1d/webview/client/src/components/ConvergenceView.vue b/refl1d/webview/client/src/components/ConvergenceView.vue
index e30cf9fa..05a10ce2 100644
--- a/refl1d/webview/client/src/components/ConvergenceView.vue
+++ b/refl1d/webview/client/src/components/ConvergenceView.vue
@@ -1,51 +1,27 @@
 <script setup lang="ts">
 /// <reference types="@types/uuid"/>
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
 import mpld3 from 'mpld3';
 
+const title = "Convergence";
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
-const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
-onMounted(() => {
-  props.socket.on('convergence_update', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
-});
+setupDrawLoop('convergence_update', props.socket, fetch_and_draw, title);
 
-function fetch_and_draw() {
-  props.socket.emit('get_convergence_plot', (payload) => {
-    if (props.visible) {
-      let plotdata = { ...payload };
-      // console.log({plotdata});
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      /* Data Parsing Functions */
-      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-    }
-    drawing_busy.value = false;
-  });
-}
-
-function draw_if_needed(timestamp: number) {
-  if (drawing_busy.value) {
-    console.log("busy!");
-  }
-  if (draw_requested.value && props.visible && !drawing_busy.value) {
-    drawing_busy.value = true;
-    draw_requested.value = false;
-    fetch_and_draw();
-  }
-  window.requestAnimationFrame(draw_if_needed);
+async function fetch_and_draw() {
+  const payload = await props.socket.asyncEmit('get_convergence_plot');
+  let plotdata = { ...payload };
+  // console.log({plotdata});
+  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
 }
 
 </script>
diff --git a/refl1d/webview/client/src/components/CorrelationView.vue b/refl1d/webview/client/src/components/CorrelationView.vue
index 3b43290e..576f1873 100644
--- a/refl1d/webview/client/src/components/CorrelationView.vue
+++ b/refl1d/webview/client/src/components/CorrelationView.vue
@@ -1,51 +1,33 @@
 <script setup lang="ts">
 /// <reference types="@types/uuid"/>
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
+import { cache } from '../plotcache';
 import mpld3 from 'mpld3';
 
+const title = "Correlations"
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
-const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
+
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
-onMounted(() => {
-  props.socket.on('uncertainty_update', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
-});
-
-function fetch_and_draw() {
-  props.socket.emit('get_correlation_plot', (payload) => {
-    if (props.visible) {
-      let plotdata = { ...payload };
-      console.log({plotdata});
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      /* Data Parsing Functions */
-      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-    }
-    drawing_busy.value = false;
-  });
-}
+setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
 
-function draw_if_needed(timestamp: number) {
-  if (drawing_busy.value) {
-    console.log("busy!");
-  }
-  if (draw_requested.value && props.visible && !drawing_busy.value) {
-    drawing_busy.value = true;
-    draw_requested.value = false;
-    fetch_and_draw();
+async function fetch_and_draw(latest_timestamp: string) {
+  let { timestamp, plotdata } = cache[title] ?? {};
+  if (timestamp !== latest_timestamp) {
+    console.log("fetching new correlation plot", timestamp, latest_timestamp);
+    const payload = await props.socket.asyncEmit('get_correlation_plot');
+    plotdata = { ...payload };
+    cache[title] = {timestamp: latest_timestamp, plotdata};
   }
-  window.requestAnimationFrame(draw_if_needed);
+  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
 }
 
 </script>
diff --git a/refl1d/webview/client/src/components/DataView.vue b/refl1d/webview/client/src/components/DataView.vue
index 33d5ce34..9fb91f19 100644
--- a/refl1d/webview/client/src/components/DataView.vue
+++ b/refl1d/webview/client/src/components/DataView.vue
@@ -3,17 +3,17 @@
 import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import * as Plotly from 'plotly.js/lib/core';
 import type { Socket } from 'socket.io-client';
+import { setupDrawLoop } from '../setupDrawLoop';
 
 const title = "Reflectivity";
 const plot_div = ref<HTMLDivElement | null>(null);
-const draw_requested = ref(false);
-const plot = ref<Plotly.PlotlyHTMLElement>();
 
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
+setupDrawLoop('update_parameters', props.socket, fetch_and_draw);
+
 const REFLECTIVITY_PLOTS = [
   "Fresnel",
   "Log Fresnel",
@@ -26,14 +26,6 @@ type ReflectivityPlotEnum = typeof REFLECTIVITY_PLOTS;
 type ReflectivityPlot = ReflectivityPlotEnum[number];
 const reflectivity_type = ref<ReflectivityPlot>("Log");
 
-
-onMounted(() => {
-  props.socket.on('update_parameters', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
-});
-
 function generate_new_traces(model_data, view: ReflectivityPlot) {
   let theory_traces: (Plotly.Data & { x: number, y: number })[] = [];
   let data_traces: (Plotly.Data & { x: number, y: number })[] = [];
@@ -78,63 +70,39 @@ function generate_new_traces(model_data, view: ReflectivityPlot) {
   return {theory_traces, data_traces};
 }
 
-function fetch_and_draw() {
-  if (!props.visible) {
-    return
-  }
-  props.socket.emit('get_plot_data', 'linear', async (payload) => {
-    if (plot_div.value === null) {
-      return
-    }
-    // console.log(payload);
-    const { theory_traces, data_traces } = generate_new_traces(payload, reflectivity_type.value)
-
-    const layout: Partial<Plotly.Layout> = {
-      uirevision: reflectivity_type.value,
-      xaxis: {
-        title: {
-          text: 'Q (Å<sup>-1</sup>)'
-        },
-        type: 'linear',
-        autorange: true,
-      },
-      yaxis: {
-        title: { text: 'Reflectivity' },
-        exponentformat: 'e',
-        showexponent: 'all',
-        type: (/^(Log|Q4)/.test(reflectivity_type.value)) ? 'log' : 'linear',
-        autorange: true,
+async function fetch_and_draw() {
+  const payload = await props.socket.asyncEmit('get_plot_data', 'linear');
+  // console.log(payload);
+  const { theory_traces, data_traces } = generate_new_traces(payload, reflectivity_type.value)
+  const layout: Partial<Plotly.Layout> = {
+    uirevision: reflectivity_type.value,
+    xaxis: {
+      title: {
+        text: 'Q (Å<sup>-1</sup>)'
       },
-      margin: {
-        l: 75,
-        r: 50,
-        t: 25,
-        b: 75,
-        pad: 4
-      }
-    };
-
-    const config = {responsive: true}
-
-    plot.value = await Plotly.react(plot_div.value, [...theory_traces, ...data_traces], layout, config);
-    
-  });
-}
+      type: 'linear',
+      autorange: true,
+    },
+    yaxis: {
+      title: { text: 'Reflectivity' },
+      exponentformat: 'e',
+      showexponent: 'all',
+      type: (/^(Log|Q4)/.test(reflectivity_type.value)) ? 'log' : 'linear',
+      autorange: true,
+    },
+    margin: {
+      l: 75,
+      r: 50,
+      t: 25,
+      b: 75,
+      pad: 4
+    }
+  };
 
-function draw_if_needed(timestamp: number) {
-  if (draw_requested.value && props.visible) {
-    fetch_and_draw();
-    draw_requested.value = false;
-  }
-  window.requestAnimationFrame(draw_if_needed);
+  const config = {responsive: true}
+  await Plotly.react(plot_div.value as HTMLDivElement, [...theory_traces, ...data_traces], layout, config);
 }
 
-// watch(() => props.visible, (value) => {
-//   if (value) {
-//     fetch_and_draw();
-//   }
-// });
-
 </script>
 
 <template>
diff --git a/refl1d/webview/client/src/components/ModelInspect.vue b/refl1d/webview/client/src/components/ModelInspect.vue
index 524ab44f..0b72ae6f 100644
--- a/refl1d/webview/client/src/components/ModelInspect.vue
+++ b/refl1d/webview/client/src/components/ModelInspect.vue
@@ -1,5 +1,6 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef, nextTick } from 'vue';
+import { ref, onMounted } from 'vue';
+import { setupDrawLoop } from '../setupDrawLoop';
 import JsonViewer from 'vue-json-viewer';
 import { getDiff } from 'json-difference';
 import type { Socket } from 'socket.io-client';
@@ -15,43 +16,44 @@ type json =
 
 const title = "Model";
 const active_parameter = ref("");
+const modelJson = ref<json>({});
 
 const props = defineProps<{
   socket: Socket,
-  visible: Boolean
 }>();
 
-const modelJson = ref<json>();
+setupDrawLoop('update_parameters', props.socket, fetch_and_draw);
 
-props.socket.on('update_parameters', fetch_and_draw);
+props.socket.on('model_loaded', () => { fetch_and_draw(true) });
 
-function fetch_and_draw() {
-  if (props.visible) {
-    props.socket.emit('get_model', (payload: json) => {
-      const old_model: json = modelJson.value as Record<string, any>;
-      const new_model: json = payload as Record<string, any>;
-      const diff = getDiff(old_model, new_model);
-      for (let [path, oldval, newval] of diff.edited) {
-        const { target, parent, key } = resolve_diffpath(old_model, path);
-        // trigger reactive update;
-        if (typeof (key) === 'number' && Array.isArray(parent)) {
-          parent.splice(key, 1, newval);
-        }
-        else {
-          parent[key] = newval;
-        }
+async function fetch_and_draw(reset: boolean = false) {
+  const payload: json = await props.socket.asyncEmit('get_model');
+  if (reset) {
+    modelJson.value = payload;
+  }
+  else {
+    // do update of existing model:
+    const old_model: json = modelJson.value as Record<string, any>;
+    const new_model: json = payload as Record<string, any>;
+    const diff = getDiff(old_model, new_model);
+    for (let [path, oldval, newval] of diff.edited) {
+      const { target, parent, key } = resolve_diffpath(old_model, path);
+      // trigger reactive update;
+      if (typeof (key) === 'number' && Array.isArray(parent)) {
+        parent.splice(key, 1, newval);
+      }
+      else {
+        parent[key] = newval;
       }
-    });
+    }
   }
 }
 
-watch(() => props.visible, (value) => {
-  if (value) {
-    props.socket.emit('get_model', (payload: json) => {
-      modelJson.value = payload;
-    });
-  }
-});
+onMounted(() => {
+  props.socket.emit('get_model', (payload: json) => {
+    modelJson.value = payload;
+  });
+})
 
 // function* traverse(o: object, path: string[]=[]) {
 //     for (var i of Object.keys(o)) {
diff --git a/refl1d/webview/client/src/components/ModelUncertaintyView.vue b/refl1d/webview/client/src/components/ModelUncertaintyView.vue
index 73cbab6e..9636811c 100644
--- a/refl1d/webview/client/src/components/ModelUncertaintyView.vue
+++ b/refl1d/webview/client/src/components/ModelUncertaintyView.vue
@@ -1,51 +1,33 @@
 <script setup lang="ts">
 /// <reference types="@types/uuid"/>
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
+import { cache } from '../plotcache';
 import mpld3 from 'mpld3';
 
+const title = "Model Uncertainty"
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
-const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
+
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
-onMounted(() => {
-  props.socket.on('uncertainty_update', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
-});
-
-function fetch_and_draw() {
-  props.socket.emit('get_model_uncertainty_plot', (payload) => {
-    if (props.visible) {
-      let plotdata = { ...payload };
-      console.log({plotdata});
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      /* Data Parsing Functions */
-      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-    }
-    drawing_busy.value = false;
-  });
-}
+setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
 
-function draw_if_needed(timestamp: number) {
-  if (drawing_busy.value) {
-    console.log("busy!");
-  }
-  if (draw_requested.value && props.visible && !drawing_busy.value) {
-    drawing_busy.value = true;
-    draw_requested.value = false;
-    fetch_and_draw();
+async function fetch_and_draw(latest_timestamp: string) {
+  let { timestamp, plotdata } = cache[title] ?? {};
+  if (timestamp !== latest_timestamp) {
+    console.log("fetching new model uncertainty plot", timestamp, latest_timestamp);
+    const payload = await props.socket.asyncEmit('get_model_uncertainty_plot');
+    plotdata = { ...payload };
+    cache[title] = {timestamp: latest_timestamp, plotdata};
   }
-  window.requestAnimationFrame(draw_if_needed);
+  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
 }
 
 </script>
diff --git a/refl1d/webview/client/src/components/ModelView.vue b/refl1d/webview/client/src/components/ModelView.vue
index 8b339e7b..1f0797c6 100644
--- a/refl1d/webview/client/src/components/ModelView.vue
+++ b/refl1d/webview/client/src/components/ModelView.vue
@@ -1,63 +1,43 @@
 <script setup lang="ts">
 /// <reference types="@types/uuid"/>
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref, onMounted, onBeforeUnmount, watch, onUpdated, computed, shallowRef } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
 import * as Plotly from 'plotly.js/lib/core';
 
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const model_names = ref<string[]>([]);
 const current_model = ref(0);
+
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
+const { draw_requested } = setupDrawLoop('update_parameters', props.socket, fetch_and_draw, title);
+
 props.socket.on('model_loaded', ({ message: { model_names: new_model_names } }) => {
   model_names.value = new_model_names;
 });
 
-onMounted(() => {
-  props.socket.on('update_parameters', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
+onMounted(async () => {
+  const messages = await props.socket.asyncEmit('get_topic_messages', 'model_loaded');
+  const new_model_names = messages?.[0]?.message?.model_names;
+  if (new_model_names != null) {
+    model_names.value = new_model_names;
+  }
 });
 
-function fetch_and_draw() {
-  props.socket.emit('get_profile_plot', current_model.value, async (payload) => {
-    console.log(payload);
-    if (plot_div.value == null) {
-      return
-    }
-    if (props.visible) {
-      let plotdata = { ...payload };
-      console.log(plotdata);
-      const { data, layout } = plotdata;
-      const config = { responsive: true }
-      const plot = await Plotly.react(plot_div_id.value, [...data], layout, config);
-    }
-  });
+async function fetch_and_draw() {
+  const payload = await props.socket.asyncEmit('get_profile_plot', current_model.value);
+  let plotdata = { ...payload };
+  const { data, layout } = plotdata;
+  const config = { responsive: true }
+  await Plotly.react(plot_div_id.value, [...data], layout, config);
 }
 
-function draw_if_needed(timestamp: number) {
-  if (draw_requested.value && props.visible) {
-    fetch_and_draw();
-    draw_requested.value = false;
-  }
-  window.requestAnimationFrame(draw_if_needed);
-}
-
-// watch(() => props.visible, (value) => {
-//   if (value) {
-//     console.log('visible', value);
-//     fetch_and_draw();
-//   }
-// });
-
 </script>
 
 <template>
diff --git a/refl1d/webview/client/src/components/ModelViewPlotly.vue b/refl1d/webview/client/src/components/ModelViewPlotly.vue
index 166b996d..81060f43 100644
--- a/refl1d/webview/client/src/components/ModelViewPlotly.vue
+++ b/refl1d/webview/client/src/components/ModelViewPlotly.vue
@@ -4,27 +4,31 @@ import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
 import * as Plotly from 'plotly.js/lib/core';
+import { setupDrawLoop } from '../setupDrawLoop';
 
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const model_names = ref<string[]>([]);
 const current_model = ref(0);
+
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
+const { draw_requested, drawing_busy, mounted } = setupDrawLoop('update_parameters', props.socket, fetch_and_draw);
+
 props.socket.on('model_loaded', ({ message: { model_names: new_model_names } }) => {
   model_names.value = new_model_names;
 });
 
 onMounted(() => {
-  props.socket.on('update_parameters', () => {
-    draw_requested.value = true;
+  props.socket.emit('get_topic_messages', 'model_loaded', (messages) => {
+    const new_model_names = messages?.[0]?.message?.model_names;
+    if (new_model_names != null) {
+      model_names.value = new_model_names;
+    }
   });
-  window.requestAnimationFrame(draw_if_needed);
 });
 
 function generate_new_traces(profile_data) {
@@ -51,76 +55,48 @@ function generate_new_traces(profile_data) {
   return traces;
 }
 
-
-
-function fetch_and_draw() {
-  if (!props.visible) {
-    return
-  }
-  props.socket.emit('get_profile_data', current_model.value, async (payload) => {
-    if (plot_div.value == null) {
-      return
-    }
-    console.log(payload);
-    const traces = generate_new_traces(payload);
-
-    const layout: Partial<Plotly.Layout> = {
-      uirevision: 1,
-      xaxis: {
-        title: {
-          text: 'depth (Å)'
-        },
-        type: 'linear',
-        autorange: true,
-      },
-      yaxis: {
-        title: { text: '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$' },
-        exponentformat: 'e',
-        showexponent: 'all',
-        type: 'linear',
-        autorange: true,
-      },
-      yaxis2: {
-        title: { text: '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$' },
-        type: 'linear',
-        autorange: false,
-        range: [0, 360],
-        anchor: 'x',
-        overlaying: 'y',
-        side: 'right'
+async function fetch_and_draw() {
+  const payload = await props.socket.asyncEmit('get_profile_data', current_model.value);
+  const traces = generate_new_traces(payload);
+  const layout: Partial<Plotly.Layout> = {
+    uirevision: 1,
+    xaxis: {
+      title: {
+        text: 'depth (Å)'
       },
-      margin: {
-        l: 75,
-        r: 50,
-        t: 25,
-        b: 75,
-        pad: 4
-      }
-    };
-
-    const config = { responsive: true }
-
-    const plot = await Plotly.react(plot_div.value, [...traces], layout, config);
-
-  });
-}
-
+      type: 'linear',
+      autorange: true,
+    },
+    yaxis: {
+      title: { text: '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$' },
+      exponentformat: 'e',
+      showexponent: 'all',
+      type: 'linear',
+      autorange: true,
+    },
+    yaxis2: {
+      title: { text: '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$' },
+      type: 'linear',
+      autorange: false,
+      range: [0, 360],
+      anchor: 'x',
+      overlaying: 'y',
+      side: 'right'
+    },
+    margin: {
+      l: 75,
+      r: 50,
+      t: 25,
+      b: 75,
+      pad: 4
+    }
+  };
 
-function draw_if_needed(timestamp: number) {
-  if (draw_requested.value && props.visible) {
-    fetch_and_draw();
-    draw_requested.value = false;
-  }
-  window.requestAnimationFrame(draw_if_needed);
+  const config = { responsive: true }
+  // this function is only called when mounted, so plot_div.value exists:
+  await Plotly.react(plot_div.value as HTMLDivElement, [...traces], layout, config);
 }
 
-// watch(() => props.visible, (value) => {
-//   if (value) {
-//     console.log('visible', value);
-//     fetch_and_draw();
-//   }
-// });
-
 </script>
     
 <template>
diff --git a/refl1d/webview/client/src/components/ParameterTraceView.vue b/refl1d/webview/client/src/components/ParameterTraceView.vue
index d912cd4d..3b51bb57 100644
--- a/refl1d/webview/client/src/components/ParameterTraceView.vue
+++ b/refl1d/webview/client/src/components/ParameterTraceView.vue
@@ -1,51 +1,26 @@
 <script setup lang="ts">
 /// <reference types="@types/uuid"/>
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
 import mpld3 from 'mpld3';
 
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
-const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
-onMounted(() => {
-  props.socket.on('uncertainty_update', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
-});
+setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw);
 
-function fetch_and_draw() {
-  props.socket.emit('get_parameter_trace_plot', (payload) => {
-    if (props.visible) {
-      let plotdata = { ...payload };
-      console.log({plotdata});
-      plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-      plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-      /* Data Parsing Functions */
-      // mpld3.draw_figure = function(figid, spec, process, clearElem) {}
-      mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-    }
-    drawing_busy.value = false;
-  });
-}
-
-function draw_if_needed(timestamp: number) {
-  if (drawing_busy.value) {
-    console.log("busy!");
-  }
-  if (draw_requested.value && props.visible && !drawing_busy.value) {
-    drawing_busy.value = true;
-    draw_requested.value = false;
-    fetch_and_draw();
-  }
-  window.requestAnimationFrame(draw_if_needed);
+async function fetch_and_draw() {
+  const payload = await props.socket.asyncEmit('get_parameter_trace_plot');
+  let plotdata = { ...payload };
+  console.log({plotdata});
+  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
+  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
+  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
 }
 
 </script>
diff --git a/refl1d/webview/client/src/components/ParameterView.vue b/refl1d/webview/client/src/components/ParameterView.vue
index a90180ee..7bbc6be9 100644
--- a/refl1d/webview/client/src/components/ParameterView.vue
+++ b/refl1d/webview/client/src/components/ParameterView.vue
@@ -1,21 +1,23 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef, nextTick } from 'vue';
+import { ref } from 'vue';
 import type { Socket } from 'socket.io-client';
+import { setupDrawLoop } from '../setupDrawLoop';
 
 const title = "Parameters";
 const active_parameter = ref("");
 
 const props = defineProps<{
   socket: Socket,
-  visible: Boolean
 }>();
 
+setupDrawLoop('update_parameters', props.socket, fetch_and_draw);
+
 type parameter_info = {
   name: string,
   id: string,
   fittable: boolean,
   fixed: boolean,
-  path: string,
+  paths: string[],
   link: string,
   writable: boolean,
   value_str: string,
@@ -27,27 +29,15 @@ type parameter_info = {
 const parameters = ref<parameter_info[]>([]);
 const parameters_local = ref<parameter_info[]>([]);
 
-onMounted(() => {
-  props.socket.on('update_parameters', () => {
-    fetch_and_draw();
-  });
-});
-
-function fetch_and_draw() {
-  if (!props.visible) {
-    // do nothing if not visible
-    return
-  }
-  props.socket.emit('get_parameters', false, (payload: parameter_info[]) => {
-    // console.log(payload);
-    const pl = parameters_local.value;
-    payload.forEach((p, i) => {
-      if (!(pl[i]?.active)) {
-        pl.splice(i, 1, p);
-      }
-    });
-    pl.splice(payload.length);
+async function fetch_and_draw() {
+  const payload = await props.socket.asyncEmit('get_parameters', false);
+  const pl = parameters_local.value;
+  payload.forEach((p, i) => {
+    if (!(pl[i]?.active)) {
+      pl.splice(i, 1, p);
+    }
   });
+  pl.splice(payload.length);
 }
 
 async function editItem(ev, item_name: "min" | "max" | "value", index: number) {
@@ -75,10 +65,6 @@ async function setFittable(ev, index) {
   props.socket.emit('set_parameter', parameter.id, "fixed", !parameter.fixed);
 }
 
-watch(() => props.visible, (value) => {
-  fetch_and_draw();
-});
-
 </script>
         
 <template>
diff --git a/refl1d/webview/client/src/components/SummaryView.vue b/refl1d/webview/client/src/components/SummaryView.vue
index 7a9cd4b7..65096618 100644
--- a/refl1d/webview/client/src/components/SummaryView.vue
+++ b/refl1d/webview/client/src/components/SummaryView.vue
@@ -1,15 +1,16 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef, nextTick } from 'vue';
+import { ref } from 'vue';
 import type { Socket } from 'socket.io-client';
+import { setupDrawLoop} from '../setupDrawLoop';
 
 const title = "Summary";
-const active_parameter = ref("");
 
 const props = defineProps<{
   socket: Socket,
-  visible: Boolean
 }>();
 
+setupDrawLoop('update_parameters', props.socket, fetch_and_draw, title);
+
 type parameter_info = {
   name: string,
   id: string,
@@ -24,31 +25,19 @@ const parameters = ref<parameter_info[]>([]);
 const parameters_local01 = ref<number[]>([]);
 const parameters_localstr = ref<string[]>([]);
 
-onMounted(() => {
-  props.socket.on('update_parameters', () => {
-    fetch_and_draw();
-  });
-});
-
-function fetch_and_draw() {
-  if (!props.visible) {
-    // do nothing if not visible
-    return
-  }
-  props.socket.emit('get_parameters', true, (payload: parameter_info[]) => {
-    // console.log(payload);
-    const pv = parameters.value;
-    payload.forEach((p, i) => {
-      parameters_localstr.value[i] = p.value_str;
-      if (!(pv[i]?.active)) {
-        pv.splice(i, 1, p);
-        parameters_local01.value[i] = p.value01;
-      }
-    });
-    pv.splice(payload.length);
-    parameters_local01.value.splice(payload.length);
-    parameters_localstr.value.splice(payload.length);
+async function fetch_and_draw() {
+  const payload: parameter_info[] = await props.socket.asyncEmit('get_parameters', true)
+  const pv = parameters.value;
+  payload.forEach((p, i) => {
+    parameters_localstr.value[i] = p.value_str;
+    if (!(pv[i]?.active)) {
+      pv.splice(i, 1, p);
+      parameters_local01.value[i] = p.value01;
+    }
   });
+  pv.splice(payload.length);
+  parameters_local01.value.splice(payload.length);
+  parameters_localstr.value.splice(payload.length);
 }
 
 async function onMove(param_index) {
@@ -81,14 +70,10 @@ async function onInactive(param) {
   fetch_and_draw();
 }
 
-watch(() => props.visible, (value) => {
-  fetch_and_draw();
-});
-
 </script>
         
 <template>
-  <table class="table">
+  <table class="table table-sm">
     <thead class="border-bottom py-1">
       <tr>
         <th scope="col">Fit Parameter</th>
@@ -127,6 +112,10 @@ td.editable {
   min-width: 5em;
 }
 
+td {
+
+}
+
 td > input {
   min-width: 5em;
 }
diff --git a/refl1d/webview/client/src/components/UncertaintyView.vue b/refl1d/webview/client/src/components/UncertaintyView.vue
index bef8e71e..820ae409 100644
--- a/refl1d/webview/client/src/components/UncertaintyView.vue
+++ b/refl1d/webview/client/src/components/UncertaintyView.vue
@@ -1,8 +1,10 @@
 <script setup lang="ts">
 /// <reference types="@types/uuid"/>
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref } from 'vue';
 import { Socket } from 'socket.io-client';
 import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
+import { cache } from '../plotcache';
 import * as Plotly from 'plotly.js/lib/core';
 import Bar from 'plotly.js/lib/bar';
 
@@ -10,51 +12,28 @@ Plotly.register([
   Bar,
 ])
 
+const title = "Uncertainty";
 const plot_div = ref<HTMLDivElement>();
-const draw_requested = ref(false);
-const drawing_busy = ref(false);
 const plot_div_id = ref(`div-${uuidv4()}`);
 const props = defineProps<{
   socket: Socket,
-  visible: boolean
 }>();
 
-onMounted(() => {
-  props.socket.on('uncertainty_update', () => {
-    draw_requested.value = true;
-  });
-  window.requestAnimationFrame(draw_if_needed);
-});
+setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
 
-
-function fetch_and_draw() {
-  props.socket.emit('get_uncertainty_plot', async (payload) => {
-    if (plot_div.value == null) {
-      return
-    }
-    if (props.visible) {
-      let plotdata = { ...payload };
-      const { data, layout } = plotdata;
-      delete layout.width;
-      delete layout.height;
-      delete layout.heighth;
-      const config = { responsive: true }
-      const plot = await Plotly.react(plot_div_id.value, [...data], layout, config);
-    }
-    drawing_busy.value = false;
-  });
-}
-
-function draw_if_needed(timestamp: number) {
-  if (drawing_busy.value) {
-    console.log("busy!");
-  }
-  if (draw_requested.value && props.visible && !drawing_busy.value) {
-    drawing_busy.value = true;
-    draw_requested.value = false;
-    fetch_and_draw();
+async function fetch_and_draw(latest_timestamp: string) {
+  let { timestamp, plotdata } = cache[title] ?? {};
+  if (timestamp !== latest_timestamp) {
+    console.log("fetching new uncertainty plot", timestamp, latest_timestamp);
+    const payload = await props.socket.asyncEmit('get_uncertainty_plot');
+    plotdata = { ...payload };
+    cache[title] = {timestamp: latest_timestamp, plotdata};
   }
-  window.requestAnimationFrame(draw_if_needed);
+  const { data, layout } = plotdata;
+  delete layout.width;
+  delete layout.height;
+  const config = { responsive: true }
+  await Plotly.react(plot_div_id.value, [...data], layout, config);
 }
 
 </script>

From 431fa6186be22a8e1b7035261b96e9ca6bb6fe97 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 16:11:47 -0500
Subject: [PATCH 138/221] minor Logging refactor - get log messages on
 instantiation

---
 refl1d/webview/client/src/components/LogView.vue | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/refl1d/webview/client/src/components/LogView.vue b/refl1d/webview/client/src/components/LogView.vue
index aca2d0ff..89f3e963 100644
--- a/refl1d/webview/client/src/components/LogView.vue
+++ b/refl1d/webview/client/src/components/LogView.vue
@@ -6,15 +6,15 @@ const title = "Log";
 
 const props = defineProps<{
   socket: Socket,
-  visible: Boolean
 }>();
 
 const log_info = ref<string[]>([]);
 
-onMounted(() => {
-  props.socket.on('log', ({message}) => {
-    log_info.value.push(message);
-  });
+props.socket.on('log', ({message, timestamp}) => {
+  log_info.value.push(message);
+});
+props.socket.emit('get_topic_messages', 'log', (messages) => {
+  log_info.value = [...log_info.value, ...(messages.map((m) => m.message))];
 });
 
 </script>

From 78705d36638e39249e9e2a3af1375ae0cd2d3483 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 16:17:59 -0500
Subject: [PATCH 139/221] convert topics in webserver to deque objects (ring
 buffer)

---
 refl1d/webview/server/webserver.py | 60 ++++++++++++++++++++++++------
 1 file changed, 49 insertions(+), 11 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index f999e8e0..e455fc26 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -1,9 +1,11 @@
 # from .main import setup_bumps
 
+import itertools
 from typing import Dict, List, Literal, Optional, Union, TypedDict
 from datetime import datetime
 import warnings
 from queue import Queue
+from collections import deque
 from aiohttp import web
 import numpy as np
 import asyncio
@@ -68,7 +70,28 @@
 
 sio.attach(app)
 
-topics: Dict[str, Dict] = {}
+TopicName = Literal[
+    "log",
+    "update_parameters",
+    "update_model",
+    "model_loaded",
+    "fit_active",
+    "uncertainty_update",
+    "convergence_update",
+    "fitter_settings",
+    "fitter_active",
+]
+topics: Dict[TopicName, "deque[Dict]"] = {
+    "log": deque([]),
+    "update_parameters": deque([], maxlen=1),
+    "update_model": deque([], maxlen=1),
+    "model_loaded": deque([], maxlen=1),
+    "fit_active": deque([], maxlen=1),
+    "convergence_update": deque([], maxlen=1),
+    "uncertainty_update": deque([], maxlen=1),
+    "fitter_settings": deque([], maxlen=1),
+    "fitter_active": deque([], maxlen=1),
+}
 app["topics"] = topics
 app["problem"] = {"fitProblem": None, "pathlist": None, "filename": None}
 app["fitting"] = {
@@ -116,8 +139,12 @@ async def index(request):
 @sio.event
 async def connect(sid, environ, data=None):
     # re-send last message for all topics
+    # now that panels are retrieving topics when they load, is this still
+    # needed or useful?
     for topic, contents in topics.items():
-        await sio.emit(topic, contents, to=sid)
+        message = contents[-1] if len(contents) > 0 else None
+        if message is not None:
+            await sio.emit(topic, message, to=sid)
     print("connect ", sid)
 
 @sio.event
@@ -599,7 +626,7 @@ async def set_parameter(sid: str, parameter_id: str, property: Literal["value01"
 async def publish(sid: str, topic: str, message=None):
     timestamp_str = f"{datetime.now().timestamp():.6f}"
     contents = {"message": message, "timestamp": timestamp_str}
-    topics[topic] = contents
+    topics[topic].append(contents)
     await sio.emit(topic, contents)
     # print("emitted: ", topic, contents)
 
@@ -608,15 +635,19 @@ def publish_sync(sid: str, topic: str, message=None):
 
 @sio.event
 @rest_get
-async def get_last_message(sid: str="", topic: str=""):
+async def get_topic_messages(sid: str="", topic: str="", max_num=None) -> List[Dict]:
     # this is a GET request in disguise -
     # emitter must handle the response in a callback,
-    # as no separate response event is emitted.  
-    return topics.get(topic, {})
-
-@rest_get
-async def get_all_messages():
-    return topics
+    # as no separate response event is emitted.
+    q = topics.get(topic, None)
+    if q is None:
+        raise ValueError(f"Topic: {topic} not defined")
+    elif max_num is None:
+        return list(q)
+    else:
+        q_length = len(q)
+        start = max(q_length - max_num, 0)
+        return list(itertools.islice(q, start, q_length))
 
 @sio.event
 @rest_get
@@ -635,6 +666,11 @@ async def get_dirlisting(sid: str="", pathlist: Optional[List[str]]=None):
             files.append(p.name)
     return dict(subfolders=subfolders, files=files)
 
+@sio.event
+@rest_get
+async def get_current_pathlist(sid: str="") -> List[str]:
+    return list(app['problem']['pathlist'])
+
 @sio.event
 @rest_get
 async def get_fitter_defaults(sid: str=""):
@@ -719,7 +755,9 @@ def main():
     # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
     args = parser.parse_args()
 
-    app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
+    # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
+    # set initial path to cwd:
+    app['problem']['pathlist'] = Path().absolute().parts
     app.add_routes(routes)
     hostname = 'localhost' if not args.external else '0.0.0.0'
 

From 22c727501993e12aa2d81f79ef2488fbd9467e22 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 16:18:30 -0500
Subject: [PATCH 140/221] adding plotcache

---
 refl1d/webview/client/src/plotcache.ts | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 refl1d/webview/client/src/plotcache.ts

diff --git a/refl1d/webview/client/src/plotcache.ts b/refl1d/webview/client/src/plotcache.ts
new file mode 100644
index 00000000..44b47920
--- /dev/null
+++ b/refl1d/webview/client/src/plotcache.ts
@@ -0,0 +1,2 @@
+// TODO: move cache to server?  Send timestamp code to server to retrieve plottables...
+export const cache: {[plot_type: string]: {timestamp: string, plotdata: object}} = {};
\ No newline at end of file

From 130f777337fee217ed535d20d1292318066dc8a5 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 17:47:02 -0500
Subject: [PATCH 141/221] convert profile plot labels from latex to unicode
 (until can figure out how to make MathJax go faster)

---
 refl1d/webview/server/profile_plot.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/refl1d/webview/server/profile_plot.py b/refl1d/webview/server/profile_plot.py
index f0595652..6ca113fc 100644
--- a/refl1d/webview/server/profile_plot.py
+++ b/refl1d/webview/server/profile_plot.py
@@ -196,15 +196,15 @@ def plot_sld_profile_plotly(model):
     if model.ismagnetic:
         z_best, rho_best, irho_best, rhoM_best, thetaM_best = generate_best_profile(model)
 
-        fig.add_scattergl(x=z_best, y=thetaM_best,
-                          name="$\\theta_{M}$", yaxis="y2",
+        fig.add_scatter(x=z_best, y=thetaM_best,
+                          name="θ<sub>M</sub>", yaxis="y2",
                           hovertemplate='(%{x}, %{y})<br>'
                                         'Theta M'
                                         '<extra></extra>',
                           line={"color": "gold"})
         # TODO: need to make axis scaling for thetaM dependent on if thetaM exceeds 0-360
         fig.update_layout(yaxis2={
-            'title': {'text': '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$'},
+            'title': {'text': 'Magnetic Angle θ<sub>M</sub> / °'},
             'type': 'linear',
             'autorange': False,
             'range': [0, 360],
@@ -215,23 +215,23 @@ def plot_sld_profile_plotly(model):
             # 'ticklen': 20,
         })
 
-        fig.add_scattergl(x=z_best, y=rhoM_best, name="$\\rho_{M}$",
+        fig.add_scatter(x=z_best, y=rhoM_best, name="ρ<sub>M</sub>",
                           hovertemplate='(%{x}, %{y})<br>'
                                         'M SLD'
                                         '<extra></extra>',
                           line={"color": "blue"})
-        yaxis_title = '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$'
+        yaxis_title = 'SLD: ρ, ρ<sub>i</sub>, ρ<sub>M</sub> / 10<sup>-6</sup> Å<sup>-2</sup>'
 
     else:
         z_best, rho_best, irho_best = generate_best_profile(model)
-        yaxis_title = '$\\text{SLD: } \\rho, \\rho_i / 10^{-6} \\text{Å}^{-2}$'
+        yaxis_title = 'SLD: ρ, ρ<sub>i</sub> / 10<sup>-6</sup> Å<sup>-2</sup>'
 
-    fig.add_scattergl(x=z_best, y=irho_best, name="$\\rho_{i}$",
+    fig.add_scatter(x=z_best, y=irho_best, name="ρ<sub>i</sub>",
                       hovertemplate='(%{x}, %{y})<br>'
                                     'Im SLD'
                                     '<extra></extra>',
                       line={"color": "green"})
-    fig.add_scattergl(x=z_best, y=rho_best, name="$\\rho$",
+    fig.add_scatter(x=z_best, y=rho_best, name="ρ",
                       hovertemplate='(%{x}, %{y})<br>'
                                     'SLD'
                                     '<extra></extra>',

From 59fba44f8e6c14ab23f225e5a05794d385995b00 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 17:48:08 -0500
Subject: [PATCH 142/221] remove matplotlib plotting routines from plotly
 implementation

---
 refl1d/webview/server/profile_plot.py | 94 +--------------------------
 1 file changed, 3 insertions(+), 91 deletions(-)

diff --git a/refl1d/webview/server/profile_plot.py b/refl1d/webview/server/profile_plot.py
index 6ca113fc..8bb8acfe 100644
--- a/refl1d/webview/server/profile_plot.py
+++ b/refl1d/webview/server/profile_plot.py
@@ -4,13 +4,10 @@
 # Originally written for use in a jupyter notebook
 # Adapted to act as a prototype for the profile plotting in the new GUI for refl1d
 
-from refl1d.view.config import thickness_color, pick_radius
+from refl1d.experiment import Experiment
 from numpy import inf
-from matplotlib import transforms
-import matplotlib.pyplot as plt
 import numpy as np
 import plotly.graph_objs as go
-blend_xy = transforms.blended_transform_factory
 
 
 # === Sample information ===
@@ -20,8 +17,6 @@ def __init__(self, experiment, axes=None, x_offset=0):
         self.experiment = experiment
         self.axes = axes
         self.x_offset = x_offset
-        if (axes is not None) and isinstance(axes, plt.Axes):
-            self.xcoords = blend_xy(axes.transData, axes.transAxes)
         self._show_labels = True
         self._show_boundaries = True
 
@@ -54,43 +49,6 @@ def label_offsets(self):
         right = z[-1] + 150
         return [left] + middle + [right]
 
-    def reset_markers_mpl(self):
-        """
-        Reset all markers, for matplotlib plots
-        """
-        # self.clear_markers()
-        if not isinstance(self.axes, plt.Axes):
-            raise ValueError("reset_markers_mpl can only be used with type: axes=matplotlib.axes.Axes")
-
-        ax = self.axes
-
-        # Add bars
-        style = dict(linewidth=1, linestyle='-',
-                     color=thickness_color, alpha=0.75,
-                     pickradius=pick_radius,
-                     visible=self._show_boundaries,
-                     )
-        self.markers = [ax.axvline(x=z, **style)
-                        for z in self.boundary[1:-1]]
-
-        # fittable = [self.profile.sample_layer(idx).thickness.fittable
-        #             for idx,_ in enumerate(self.markers)]
-        # fittable[0] = False # First interface is not fittable
-        # for f,m in zip(fittable,self.markers):
-        #     if not f: m.set(linestyle='--', linewidth=1.25)
-        # self.connect_markers(m for f,m in zip(fittable,self.markers) if f)
-
-        # Add labels
-        offsets = self.label_offsets()
-        labels = self.sample_labels()
-        style = dict(transform=self.axes.get_xaxis_transform(),
-                     ha='left', va='bottom',
-                     rotation=45, fontsize=16,  # 'medium',
-                     visible=self._show_labels,
-                     )
-        self.textmark = [ax.text(z, 1, s, **style)
-                         for z, s in zip(offsets, labels)]
-
     def reset_markers_plotly(self):
         """
         Reset all markers, for plotly plots
@@ -134,63 +92,17 @@ def reset_markers_plotly(self):
                                )
 
 
-def determine_problem_fitness(problem, active_model):
-    if hasattr(problem, 'active_model'):
-        problem_fitness = problem.set_active_model(active_model)
-        problem_fitness = problem.active_model.fitness
-    else:
-        problem_fitness = problem.fitness
-
-    return problem_fitness
-
-
-def generate_best_profile(model):
-    if hasattr(model, "active_model"):
-        model = model.active_model
-
+def generate_best_profile(model: Experiment):
     if model.ismagnetic:
         best = model.magnetic_smooth_profile()
     else:
         best = model.smooth_profile()
     return best
+
 # ============================================================================= #
 # Plotting script below
 # ============================================================================= #
 
-
-def plot_sld_profile(model):
-    """
-    Basic plot script to plot up SLD profiles using Paul's layer finding code
-    """
-    fig, ax = plt.subplots(1, 1, figsize=(8, 6))
-
-    theta_axis = ax.twinx()
-    # ax.legend(fontsize=16, framealpha=0.5, ncol=3)
-
-    if model.ismagnetic:
-        z_best, rho_best, irho_best, rhoM_best, thetaM_best = generate_best_profile(model)
-        ax.plot(z_best, rhoM_best, label=r"$\rho_{M}$ mSLD", color="b")
-        ax.plot(z_best, thetaM_best, label=r"Magnetic Angle $\theta_{M} \circ$", color="orange")
-        ax.set_ylabel(r"$\rho, \rho_{i}, \rho_{M} \left(10^{-6}\AA^{-2}\right)$", fontsize=18)
-    else:
-        z_best, rho_best, irho_best = generate_best_profile(model)
-        ax.set_ylabel(r"$\rho, \rho_{i} \left(10^{-6}\AA^{-2}\right)$", fontsize=18)
-
-    ax.plot(z_best, rho_best, label=r"$\rho$ SLD", color="k")
-    ax.plot(z_best, irho_best, label=r"$\rho_{i}$ Im SLD", color="g")
-
-    ax.legend(fontsize=16, framealpha=0.5, ncol=3)
-    ax.grid(True)
-    ax.set_xlabel(r"z $\left(\AA\right)$", fontsize=18)
-    ax.tick_params(axis='y', labelsize=16)
-    ax.tick_params(axis='x', labelsize=16)
-
-    layer_markers = FindLayers(model, axes=ax)
-    layer_markers.reset_markers_mpl()
-
-    return fig, ax
-
-
 def plot_sld_profile_plotly(model):
     fig = go.Figure()
     if model.ismagnetic:

From 4f05dc9f2d60228dcee01a39856b1bd4ccc8849d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 17:48:56 -0500
Subject: [PATCH 143/221] convert labels on ModelViewPlotly to UTF as well

---
 refl1d/webview/client/src/components/ModelViewPlotly.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/client/src/components/ModelViewPlotly.vue b/refl1d/webview/client/src/components/ModelViewPlotly.vue
index 81060f43..2512d42c 100644
--- a/refl1d/webview/client/src/components/ModelViewPlotly.vue
+++ b/refl1d/webview/client/src/components/ModelViewPlotly.vue
@@ -68,14 +68,14 @@ async function fetch_and_draw() {
       autorange: true,
     },
     yaxis: {
-      title: { text: '$\\text{SLD: } \\rho, \\rho_i, \\rho_M / 10^{-6} \\text{Å}^{-2}$' },
+      title: { text: 'SLD: ρ, ρ<sub>i</sub>, ρ<sub>M</sub> / 10<sup>-6</sup> Å<sup>-2</sup>' },
       exponentformat: 'e',
       showexponent: 'all',
       type: 'linear',
       autorange: true,
     },
     yaxis2: {
-      title: { text: '$\\text{Magnetic Angle } \\theta_M / {}^{\\circ}$' },
+      title: { text: 'Magnetic Angle θ<sub>M</sub> / °' },
       type: 'linear',
       autorange: false,
       range: [0, 360],

From 3df01b3c8cb5bdc79d9de06e1d025fa8019b82b3 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 19 Jan 2023 17:49:44 -0500
Subject: [PATCH 144/221] add layout options, including left-right, top-bottom
 and full

---
 refl1d/webview/client/src/App.vue             | 35 +++++++++++++++++--
 .../src/components/PanelTabContainer.vue      | 28 +++++++++------
 2 files changed, 49 insertions(+), 14 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index e23f56af..d3f9af72 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -36,12 +36,15 @@ const panels = [
   {title: 'Uncertainty', component: UncertaintyView},
 ];
 
+const LAYOUTS = ["left-right", "top-bottom", "full"];
 const connected = ref(false);
 const menuToggle = ref<HTMLButtonElement>();
 const fitOptions = ref<typeof FitOptions>();
 const fileBrowser = ref<typeof FileBrowser>();
 const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
 const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
+const active_layout = ref("left-right");
+const active_panel = ref([0,1]);
 
 // Create a SocketIO connection, to be passed to child components
 // so that they can do their own communications with the host.
@@ -190,6 +193,18 @@ onMounted(() => {
                 <li><button class="btn btn-link dropdown-item"  @click="openFitOptions">Options...</button></li>
               </ul>
             </li>
+            <li class="nav-item dropdown">
+              <button class="btn btn-link nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
+                aria-expanded="false">
+                Layout
+              </button>
+              <ul class="dropdown-menu">
+                <li v-for="layout in LAYOUTS" :key="layout" :class="{layout: true, active: active_layout === layout}">
+                  <button class="btn btn-link dropdown-item" :class="{layout: true, active: active_layout === layout}" @click="active_layout = layout">{{ layout }}</button>
+                </li>
+              </ul>
+            </li>
+
             <!-- <li class="nav-item dropdown">
               <div class="nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
@@ -212,14 +227,28 @@ onMounted(() => {
         </div>
       </div>
     </nav>
-    <div class="flex-grow-1 row overflow-hidden">
+    <div class="flex-grow-1 row overflow-hidden" v-if="active_layout === 'left-right'">
+      <div class="col d-flex flex-column mh-100 border-end border-success border-3">
+        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[0]" @panel_changed="(n) => { active_panel[0] = n }"/>
+      </div>
       <div class="col d-flex flex-column mh-100">
-        <PanelTabContainer :panels="panels" :socket="socket" :initially_active="0"/>
+        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[1]" @panel_changed="(n) => { active_panel[1] = n }"/>
+      </div>
+    </div>
+    <div class="flex-grow-1 d-flex flex-column" v-if="active_layout === 'top-bottom'">
+      <div class="d-flex flex-column flex-grow-1" style="overflow-y:scroll;">
+        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[0]" @panel_changed="(n) => { active_panel[0] = n }"/>
       </div>
+      <div class="d-flex flex-column flex-grow-1">
+        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[1]" @panel_changed="(n) => { active_panel[1] = n }"/>
+      </div>
+    </div>
+    <div class="flex-grow-1 row overflow-hidden" v-if="active_layout === 'full'">
       <div class="col d-flex flex-column mh-100">
-        <PanelTabContainer :panels="panels" :socket="socket" :initially_active="1"/>
+        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[0]" @panel_changed="(n) => { active_panel[0] = n }"/>
       </div>
     </div>
+
   </div>
   <FitOptions ref="fitOptions" :socket="socket" />
   <FileBrowser ref="fileBrowser" :socket="socket" title="Load Model File" :callback="fileBrowserSelectCallback" />
diff --git a/refl1d/webview/client/src/components/PanelTabContainer.vue b/refl1d/webview/client/src/components/PanelTabContainer.vue
index 76868653..690fa95d 100644
--- a/refl1d/webview/client/src/components/PanelTabContainer.vue
+++ b/refl1d/webview/client/src/components/PanelTabContainer.vue
@@ -1,33 +1,36 @@
 <script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
-import type { DefineComponent, Component } from 'vue';
+import { ref, onMounted } from 'vue';
 import type { Socket } from 'socket.io-client';
 
 // type PanelComponent = DefineComponent<{socket: Socket, visible: boolean}, any>;
 
 const tabTriggers = ref<HTMLAnchorElement[]>([]);
-const panelContainers = ref<HTMLDivElement[]>([]);
-const activePanel = ref(0);
 
 const props = defineProps<{
   socket: Socket,
   panels: {title: string, component: unknown}[],
-  initially_active?: number
+  active_panel: number
 }>();
 
-onMounted(() => {
-  activePanel.value = props.initially_active ?? 0;
-});
+const emit = defineEmits<{
+  (e: 'panel_changed', active_panel: number): void
+}>();
+
+
+function setActive(index: number) {
+  emit("panel_changed", index);
+}
+
 </script>
 
 <template>
   <ul class="nav nav-tabs">
     <li class="nav-item" v-for="(panel, index) in props.panels" :key="index">
-      <a ref="tabTriggers" :class="{'nav-link': true, active: index == activePanel}" href="#" @click="activePanel = index">{{panels[index]?.title}}</a>
+      <a ref="tabTriggers" :class="{'nav-link': true, active: index == active_panel}" href="#" @click="setActive(index)">{{panels[index]?.title}}</a>
     </li>
   </ul>
   <div class="tab-content d-flex flex-column flex-grow-1 overflow-auto">
-      <component :is="panels[activePanel].component" :socket="props.socket" :visible="true"></component>
+      <component :is="panels[active_panel].component" :socket="props.socket" :visible="true"></component>
   </div>
 </template>
 
@@ -36,7 +39,10 @@ onMounted(() => {
   display: none;
 }
 
-.tab-content>.tab-pane.active {
+.tab-content {
   display: flex !important;
+  flex-grow: 1;
+  flex-shrink: 0;
+  flex-basis: 200px;
 }
 </style>
\ No newline at end of file

From 07219f142b99e8b458f6be4967e697b7fe3db13d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 26 Jan 2023 14:50:25 -0500
Subject: [PATCH 145/221] add summary structure in log viewer for messages with
 title defined

---
 refl1d/webview/client/src/components/LogView.vue | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/client/src/components/LogView.vue b/refl1d/webview/client/src/components/LogView.vue
index 89f3e963..0f7e5034 100644
--- a/refl1d/webview/client/src/components/LogView.vue
+++ b/refl1d/webview/client/src/components/LogView.vue
@@ -8,10 +8,10 @@ const props = defineProps<{
   socket: Socket,
 }>();
 
-const log_info = ref<string[]>([]);
+const log_info = ref<{message: string, title?: string}[]>([]);
 
-props.socket.on('log', ({message, timestamp}) => {
-  log_info.value.push(message);
+props.socket.on('log', ({message: {message, title}}) => {
+    log_info.value.push({message, title});
 });
 props.socket.emit('get_topic_messages', 'log', (messages) => {
   log_info.value = [...log_info.value, ...(messages.map((m) => m.message))];
@@ -21,7 +21,13 @@ props.socket.emit('get_topic_messages', 'log', (messages) => {
         
 <template>
   <div class="log">
-    <pre class="message" v-for="(message, index) of log_info" :key="index">{{message}}</pre>
+    <div class="message" v-for="({message, title}, index) of log_info" :key="index">
+      <details v-if="title != null">
+        <summary>{{ title }}</summary>
+        <pre>{{ message }}</pre>
+      </details>
+      <span v-else>{{ message }}</span>
+    </div>
   </div>
 </template>
     

From 51aebdc529c09a16fb4b65d456447066ce96633d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 26 Jan 2023 14:50:42 -0500
Subject: [PATCH 146/221] send structured log messages (with optional title)

---
 refl1d/webview/server/webserver.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index e455fc26..3e072a1e 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -150,7 +150,8 @@ async def connect(sid, environ, data=None):
 @sio.event
 async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     path = Path(*pathlist, filename)
-    print('model loading: ', str(path))
+    print(f'model loading: {path}')
+    log_handler({"message": f'model_loading: {path}'})
     if filename.endswith(".json"):
         with open(path, "rt") as input_file:
             serialized = json.loads(input_file.read())
@@ -161,7 +162,9 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     app["problem"]["fitProblem"] = problem
     app["problem"]["pathlist"] = pathlist
     app["problem"]["filename"] = filename
-    print('model loaded: ', str(path))
+    print(f'model loaded: {path}')
+    log_handler({"message": f'model loaded: {path}'})
+
 
     model_names = [getattr(m, 'name', None) for m in list(problem.models)]
     await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename, "model_names": model_names})
@@ -194,6 +197,8 @@ async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, file
     with open(Path(path, save_filename), "wt") as output_file:
         output_file.write(json.dumps(serialized))
 
+    log_handler({"message": f'Saved: {filename} at path: {path}'})
+
 @sio.event
 async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
     kwargs = {} if kwargs is None else kwargs
@@ -242,7 +247,8 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
         uncertainty_update=3600,
         )
     fit_thread.start()
-    await publish("", "fit_active", True)
+    await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
+    log_handler({"message": json.dumps(to_dict(options), indent=2), "title": f"starting fitter {fitter_id}"})
 
 def fit_progress_handler(event: Dict):
     print("progress event message: ", event.get("message", ""))
@@ -270,15 +276,14 @@ def fit_complete_handler(event):
     if fit_thread is not None:
         fit_thread.join(1) # 1 second timeout on join
         if fit_thread.is_alive():
-            EVT_LOG.send("fit thread failed to complete")
+            EVT_LOG.send({"message": "fit thread failed to complete"})
     app["fitting"]["fit_thread"] = None
     problem: refl1d.fitproblem.FitProblem = event["problem"]
     chisq = nice(2*event["value"]/problem.dof)
     problem.setp(event["point"])
     problem.model_update()
     publish_sync("", "update_parameters", True)
-    EVT_LOG.send("done with chisq %g"%chisq)
-    EVT_LOG.send(event["info"])
+    EVT_LOG.send({"message": event["info"], "title": f"done with chisq {chisq}"})
 
 EVT_FIT_COMPLETE.connect(fit_complete_handler)
 

From f6bc631aeda549753960696f0c57ce6d69d3c89f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 1 Feb 2023 11:49:05 -0500
Subject: [PATCH 147/221] give _HashableModel a name based on index if one is
 not provided

---
 refl1d/errors.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/refl1d/errors.py b/refl1d/errors.py
index 59fbe6d2..c0d03d78 100644
--- a/refl1d/errors.py
+++ b/refl1d/errors.py
@@ -161,7 +161,7 @@ def calc_errors(problem, points):
     # TODO: return sane datastructure
     # Make a hashable version of model which just contains the name
     # attribute, which is all that the rest of this code accesses.
-    models = [_HashableModel(m) for m in _experiments(problem)]
+    models = [_HashableModel(m, i) for i, m in enumerate(_experiments(problem))]
 
     profiles = {h: [v[k] for v in profiles] for k, h in enumerate(models)}
     slabs = {h: [v[k] for v in slabs] for k, h in enumerate(models)}
@@ -179,8 +179,8 @@ def calc_errors(problem, points):
 
 class _HashableModel:
     name: str
-    def __init__(self, model):
-        self.name = model.name
+    def __init__(self, model, index):
+        self.name = model.name if model.name is not None else f"M{index}"
     def __str__(self):
         return f"model {self.name}"
 

From f538432a33f729d326202dbf5e9f64b664890ebe Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 1 Feb 2023 11:51:07 -0500
Subject: [PATCH 148/221] trigger server quit on Quit in client

---
 refl1d/webview/client/src/App.vue | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index d3f9af72..ee711ed2 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -132,6 +132,10 @@ function stopFit() {
   socket.emit("stop_fit")
 }
 
+function quit() {
+  socket.emit("shutdown");
+}
+
 onMounted(() => {
   const menuToggleButton = new Button(menuToggle.value);
 });
@@ -176,7 +180,7 @@ onMounted(() => {
                 <li>
                   <hr class="dropdown-divider">
                 </li>
-                <li><button class="btn btn-link dropdown-item" >Quit</button></li>
+                <li><button class="btn btn-link dropdown-item" @click="quit">Quit</button></li>
               </ul>
             </li>
             <li class="nav-item dropdown">

From 7cfc3a199c5aa87e9569d8dc9732c651bce00194 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 1 Feb 2023 11:54:10 -0500
Subject: [PATCH 149/221] make abort_queue required argument to FitThread

---
 refl1d/webview/server/fit_thread.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
index 8d7d51bf..e18490ad 100644
--- a/refl1d/webview/server/fit_thread.py
+++ b/refl1d/webview/server/fit_thread.py
@@ -170,14 +170,14 @@ def final(self):
 class FitThread(Thread):
     """Run the fit in a separate thread from the GUI thread."""
 
-    def __init__(self, abort_queue=None, problem=None,
+    def __init__(self, abort_queue: Queue, problem=None,
                  fitclass=None, options=None, mapper=None,
                  convergence_update=5, uncertainty_update=300):
         # base class initialization
         # Process.__init__(self)
 
         Thread.__init__(self)
-        self.abort_queue: Queue = abort_queue
+        self.abort_queue = abort_queue
         self.problem = problem
         self.fitclass = fitclass
         self.options = options if isinstance(options, dict) else dict()

From 465635a9044034856b8958bad4d920d6a6f39113 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 1 Feb 2023 17:34:13 -0500
Subject: [PATCH 150/221] set reuseaddr flag on socket, so we can reuse the
 port on quick restarts

---
 refl1d/webview/server/webserver.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 3e072a1e..a295075c 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -767,7 +767,8 @@ def main():
     hostname = 'localhost' if not args.external else '0.0.0.0'
 
     import socket
-    sock = socket.socket()
+    sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+    sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
     sock.bind((hostname, args.port))
     _, port = sock.getsockname()
     if not args.headless:

From fd971d189477c4d0532408a0b6ef46d73f001bd2 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 1 Feb 2023 17:35:56 -0500
Subject: [PATCH 151/221] add shutdown method to API for server

---
 refl1d/webview/server/webserver.py | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index a295075c..a2a27ed8 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -211,7 +211,7 @@ async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
     driver.show()
 
 @sio.event
-async def stop_fit(sid: str):
+async def stop_fit(sid: str = ""):
     abort_queue: Queue = app["fitting"]["abort_queue"]
     abort_queue.put(True)
 
@@ -685,6 +685,22 @@ async def get_fitter_defaults(sid: str=""):
 def disconnect(sid):
     print('disconnect ', sid)
 
+ 
+@sio.event
+async def shutdown(sid: str=""):
+    await stop_fit()
+    # disconnect all clients:
+    clients = list(sio.manager.rooms.get('/', {None: {}}).get(None).keys())
+    for client in clients:
+        await sio.disconnect(client)
+    import signal
+    import sys
+    # signal.raise_signal(signal.SIGINT)
+    await app.shutdown()
+    await app.cleanup()
+    print("killing...")
+    signal.raise_signal(signal.SIGKILL)
+
 if Path.exists(static_assets_path):
     app.router.add_static('/assets', static_assets_path)
 app.router.add_get('/', index)

From 983bc8b4b366fdda9fa836e1515fbb1a54db1309 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Tue, 7 Feb 2023 11:51:43 -0500
Subject: [PATCH 152/221] fix callbacks from fit events to be async/threadsafe

---
 refl1d/webview/server/webserver.py | 47 ++++++++++++++++--------------
 1 file changed, 25 insertions(+), 22 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index a2a27ed8..91d8b7ae 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -1,6 +1,7 @@
 # from .main import setup_bumps
 
 import itertools
+import threading
 from typing import Dict, List, Literal, Optional, Union, TypedDict
 from datetime import datetime
 import warnings
@@ -46,7 +47,6 @@
 from .varplot import plot_vars
 
 # can get by name and not just by id
-EVT_LOG = Signal('log')
 MODEL_EXT = '.json'
 
 FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
@@ -151,7 +151,7 @@ async def connect(sid, environ, data=None):
 async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     path = Path(*pathlist, filename)
     print(f'model loading: {path}')
-    log_handler({"message": f'model_loading: {path}'})
+    await log(f'model_loading: {path}')
     if filename.endswith(".json"):
         with open(path, "rt") as input_file:
             serialized = json.loads(input_file.read())
@@ -163,7 +163,7 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     app["problem"]["pathlist"] = pathlist
     app["problem"]["filename"] = filename
     print(f'model loaded: {path}')
-    log_handler({"message": f'model loaded: {path}'})
+    await log(f'model loaded: {path}')
 
 
     model_names = [getattr(m, 'name', None) for m in list(problem.models)]
@@ -197,7 +197,7 @@ async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, file
     with open(Path(path, save_filename), "wt") as output_file:
         output_file.write(json.dumps(serialized))
 
-    log_handler({"message": f'Saved: {filename} at path: {path}'})
+    await log(f'Saved: {filename} at path: {path}')
 
 @sio.event
 async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
@@ -247,50 +247,55 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
         uncertainty_update=3600,
         )
     fit_thread.start()
+    app["fitting"]["fit_thread"] = fit_thread
     await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
-    log_handler({"message": json.dumps(to_dict(options), indent=2), "title": f"starting fitter {fitter_id}"})
+    await log(json.dumps(to_dict(options), indent=2), title=f"starting fitter {fitter_id}")
 
-def fit_progress_handler(event: Dict):
+async def _fit_progress_handler(event: Dict):
     print("progress event message: ", event.get("message", ""))
     fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
     message = event.get("message", None)
     if message == 'complete' or message == 'improvement':
         fitProblem.setp(event["point"])
         fitProblem.model_update()
-        publish_sync("", "update_parameters")
+        await publish("", "update_parameters", True)
         if message == 'complete':
-            publish_sync("", "fit_active", False)
+            await publish("", "fit_active", False)
     elif message == 'convergence_update':
         app["fitting"]["population"] = event["pop"]
-        publish_sync("", "convergence_update")
+        await publish("", "convergence_update", True)
     elif message == 'uncertainty_update' or message == 'uncertainty_final':
         app["fitting"]["uncertainty_state"] = event["uncertainty_state"]
-        publish_sync("", "uncertainty_update")
+        await publish("", "uncertainty_update", True)
+
+def fit_progress_handler(event: Dict):
+    asyncio.run_coroutine_threadsafe(_fit_progress_handler(event), app.loop)
 
 EVT_FIT_PROGRESS.connect(fit_progress_handler)
 
-def fit_complete_handler(event):
+async def _fit_complete_handler(event):
     print("complete event: ", event.get("message", ""))
     message = event.get("message", None)
-    fit_thread = app["fitting"]["fit_thread"]
+    fit_thread: threading.Thread = app["fitting"]["fit_thread"]
     if fit_thread is not None:
         fit_thread.join(1) # 1 second timeout on join
         if fit_thread.is_alive():
-            EVT_LOG.send({"message": "fit thread failed to complete"})
+            await log("fit thread failed to complete")
     app["fitting"]["fit_thread"] = None
     problem: refl1d.fitproblem.FitProblem = event["problem"]
     chisq = nice(2*event["value"]/problem.dof)
     problem.setp(event["point"])
     problem.model_update()
-    publish_sync("", "update_parameters", True)
-    EVT_LOG.send({"message": event["info"], "title": f"done with chisq {chisq}"})
+    await publish("", "update_parameters", True)
+    await log(event["info"], title=f"done with chisq {chisq}")
 
-EVT_FIT_COMPLETE.connect(fit_complete_handler)
+def fit_complete_handler(event: Dict):
+    asyncio.run_coroutine_threadsafe(_fit_complete_handler(event), app.loop)
 
-def log_handler(message):
-    publish_sync("", "log", message)
+EVT_FIT_COMPLETE.connect(fit_complete_handler)
 
-EVT_LOG.connect(log_handler)
+async def log(message: str, title: Optional[str] = None):
+    await publish("", "log", {"message": message, "title": title})
 
 def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
     fresnel_calculator = probe.fresnel(substrate, surface)
@@ -635,8 +640,6 @@ async def publish(sid: str, topic: str, message=None):
     await sio.emit(topic, contents)
     # print("emitted: ", topic, contents)
 
-def publish_sync(sid: str, topic: str, message=None):
-    return asyncio.run_coroutine_threadsafe(publish(sid, topic, message), app.loop)
 
 @sio.event
 @rest_get
@@ -699,7 +702,7 @@ async def shutdown(sid: str=""):
     await app.shutdown()
     await app.cleanup()
     print("killing...")
-    signal.raise_signal(signal.SIGKILL)
+    signal.raise_signal(signal.SIGTERM)
 
 if Path.exists(static_assets_path):
     app.router.add_static('/assets', static_assets_path)

From 5deb33eac469cb9d80c53353669df63a93e96fae Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 7 Feb 2023 12:17:51 -0500
Subject: [PATCH 153/221] send update_model signal when model parameters list
 changes

---
 refl1d/webview/server/webserver.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 91d8b7ae..74b46882 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -628,6 +628,8 @@ async def set_parameter(sid: str, parameter_id: str, property: Literal["value01"
             parameter.fixed = bool(value)
             fitProblem.model_reset()
             # print(f"setting parameter: {parameter}.fixed to {value}")
+            # model has been changed: setp and getp will return different values!
+            await publish("", "update_model", True)
     fitProblem.model_update()
     await publish("", "update_parameters", True)
     return

From 3223c4f88805284293c29c29b9f70ee6225296f9 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 7 Feb 2023 15:24:50 -0500
Subject: [PATCH 154/221] adding class-based state for webserver

---
 refl1d/webview/server/webserver.py | 301 ++++++++++++++++++-----------
 1 file changed, 187 insertions(+), 114 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 74b46882..6f176297 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -1,5 +1,6 @@
 # from .main import setup_bumps
 
+from dataclasses import dataclass
 import itertools
 import threading
 from typing import Dict, List, Literal, Optional, Union, TypedDict
@@ -7,7 +8,7 @@
 import warnings
 from queue import Queue
 from collections import deque
-from aiohttp import web
+from aiohttp import web, ClientSession
 import numpy as np
 import asyncio
 import socketio
@@ -15,6 +16,7 @@
 import json
 from copy import deepcopy
 from blinker import Signal
+from uuid import uuid4
 
 import mimetypes
 mimetypes.add_type("text/css", ".css")
@@ -31,7 +33,7 @@
 from bumps.parameter import Parameter, Variable, unique
 import bumps.fitproblem
 import bumps.plotutil
-import bumps.dream.views, bumps.dream.varplot, bumps.dream.stats
+import bumps.dream.views, bumps.dream.varplot, bumps.dream.stats, bumps.dream.state
 import bumps.errplot
 import refl1d.errors
 import refl1d.fitproblem, refl1d.probe
@@ -70,7 +72,7 @@
 
 sio.attach(app)
 
-TopicName = Literal[
+TopicNameType = Literal[
     "log",
     "update_parameters",
     "update_model",
@@ -81,28 +83,58 @@
     "fitter_settings",
     "fitter_active",
 ]
-topics: Dict[TopicName, "deque[Dict]"] = {
-    "log": deque([]),
-    "update_parameters": deque([], maxlen=1),
-    "update_model": deque([], maxlen=1),
-    "model_loaded": deque([], maxlen=1),
-    "fit_active": deque([], maxlen=1),
-    "convergence_update": deque([], maxlen=1),
-    "uncertainty_update": deque([], maxlen=1),
-    "fitter_settings": deque([], maxlen=1),
-    "fitter_active": deque([], maxlen=1),
-}
-app["topics"] = topics
-app["problem"] = {"fitProblem": None, "pathlist": None, "filename": None}
-app["fitting"] = {
-    "fit_thread": None,
-    "abort": False,
-    "uncertainty_state": None,
-    "population": None,
-    "abort_queue": Queue(),
-}
-problem = None
 
+@dataclass
+class ProblemState:
+    fitProblem: Optional[bumps.fitproblem.FitProblem] = None
+    pathlist: Optional[List[str]] = None
+    filename: Optional[str] = None
+
+    def to_dict(self):
+        return {
+            "fitProblem": to_dict(self.fitProblem),
+            "pathlist": to_dict(self.pathlist),
+            "filename": to_dict(self.filename)
+        }
+    
+    def from_dict(self, serialized):
+        self.fitProblem = from_dict(serialized["fitProblem"])
+        self.pathlist = from_dict(serialized["pathlist"])
+        self.filename = from_dict(serialized["filename"])
+
+
+@dataclass
+class FittingState:
+    abort: bool = False
+    abort_queue: Queue = Queue()
+    population: Optional[List] = None
+    uncertainty_state: Optional[bumps.dream.state.MCMCDraw] = None
+    thread: Optional[FitThread] = None
+
+
+class State:
+    hostname: str
+    port: int
+    problem: Optional[ProblemState]
+    fitting: FittingState
+    topics: Dict[TopicNameType, "deque[Dict]"]
+
+    def __init__(self, problem: Optional[ProblemState] = None, fitting: Optional[FittingState] = None):
+        self.problem = problem
+        self.fitting = FittingState()
+        self.topics = {
+            "log": deque([]),
+            "update_parameters": deque([], maxlen=1),
+            "update_model": deque([], maxlen=1),
+            "model_loaded": deque([], maxlen=1),
+            "fit_active": deque([], maxlen=1),
+            "convergence_update": deque([], maxlen=1),
+            "uncertainty_update": deque([], maxlen=1),
+            "fitter_settings": deque([], maxlen=1),
+            "fitter_active": deque([], maxlen=1),
+        }
+
+state = State()
 
 def rest_get(fn):
     """
@@ -141,14 +173,14 @@ async def connect(sid, environ, data=None):
     # re-send last message for all topics
     # now that panels are retrieving topics when they load, is this still
     # needed or useful?
-    for topic, contents in topics.items():
+    for topic, contents in state.topics.items():
         message = contents[-1] if len(contents) > 0 else None
         if message is not None:
             await sio.emit(topic, message, to=sid)
     print("connect ", sid)
 
 @sio.event
-async def load_problem_file(sid: str, pathlist: List[str], filename: str):
+async def load_problem_file(sid: str, pathlist: List[str], filename: str):    
     path = Path(*pathlist, filename)
     print(f'model loading: {path}')
     await log(f'model_loading: {path}')
@@ -159,9 +191,9 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     else:
         from bumps.cli import load_model
         problem = load_model(str(path))
-    app["problem"]["fitProblem"] = problem
-    app["problem"]["pathlist"] = pathlist
-    app["problem"]["filename"] = filename
+    assert isinstance(problem, bumps.fitproblem.FitProblem)
+    problem_state = ProblemState(problem, pathlist, filename)
+    state.problem = problem_state
     print(f'model loaded: {path}')
     await log(f'model loaded: {path}')
 
@@ -173,14 +205,14 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
 
 @sio.event
 async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, filename: Optional[str] = None, overwrite: bool = False):
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    if fitProblem is None:
+    problem_state = state.problem
+    if problem_state is None:
         print("Save failed: no problem loaded.")
         return
     if pathlist is None:
-        pathlist = app["problem"]["pathlist"]
+        pathlist = problem_state.pathlist
     if filename is None:
-        filename = app["problem"]["filename"]
+        filename = problem_state.filename
 
     if pathlist is None or filename is None:
         print("no filename and path provided to save")
@@ -193,7 +225,7 @@ async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, file
         #confirmation needed:
         return True
 
-    serialized = to_dict(fitProblem)
+    serialized = to_dict(problem_state.fitProblem)
     with open(Path(path, save_filename), "wt") as output_file:
         output_file.write(json.dumps(serialized))
 
@@ -202,58 +234,72 @@ async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, file
 @sio.event
 async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
     kwargs = {} if kwargs is None else kwargs
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    mapper = MPMapper.start_mapper(fitProblem, None, cpus=0)
-    monitors = []
-    fitclass = FITTERS_BY_ID[fitter_id]
-    driver = FitDriver(fitclass=fitclass, mapper=mapper, problem=fitProblem, monitors=monitors, **kwargs)
-    x, fx = driver.fit()
-    driver.show()
+    problem_state = state.problem
+    if problem_state is None:
+        await log("Error: Can't start fit if no problem loaded")
+    else:
+        fitProblem = problem_state.fitProblem
+        mapper = MPMapper.start_mapper(fitProblem, None, cpus=0)
+        monitors = []
+        fitclass = FITTERS_BY_ID[fitter_id]
+        driver = FitDriver(fitclass=fitclass, mapper=mapper, problem=fitProblem, monitors=monitors, **kwargs)
+        x, fx = driver.fit()
+        driver.show()
 
 @sio.event
 async def stop_fit(sid: str = ""):
-    abort_queue: Queue = app["fitting"]["abort_queue"]
+    abort_queue = state.fitting.abort_queue
     abort_queue.put(True)
 
 @sio.event
 async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
-    options = {} if options is None else options
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    fitclass = FITTERS_BY_ID[fitter_id]
-    if app["problem"].get("fit_thread", None) is not None:
-        # warn that fit is alread running...
-        print("fit already running...")
-        return
-    
-    # TODO: better access to model parameters
-    if len(fitProblem.getp()) == 0:
-        raise ValueError("Problem has no fittable parameters")
-
-    # Start a new thread worker and give fit problem to the worker.
-    # Clear abort and uncertainty state
-    app["fitting"]["abort"] = False
-    app["fitting"]["uncertainty_state"] = None
-    abort_queue: Queue = app["fitting"]["abort_queue"]
-    for _ in range(abort_queue.qsize()):
-        abort_queue.get_nowait()
-        abort_queue.task_done()
-    fit_thread = FitThread(
-        abort_queue=abort_queue,
-        problem=fitProblem,
-        fitclass=fitclass,
-        options=options,
-        # Number of seconds between updates to the GUI, or 0 for no updates
-        convergence_update=5,
-        uncertainty_update=3600,
-        )
-    fit_thread.start()
-    app["fitting"]["fit_thread"] = fit_thread
-    await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
-    await log(json.dumps(to_dict(options), indent=2), title=f"starting fitter {fitter_id}")
+    options = {} if options is None else options    # session_id: str = app["active_session"]
+    fitProblem = state.problem.fitProblem if state.problem is not None else None
+    if fitProblem is None:
+        await log("Error: Can't start fit if no problem loaded")
+    else:
+        fit_state = state.fitting
+        fitclass = FITTERS_BY_ID[fitter_id]
+        if fit_state.thread is not None:
+            # warn that fit is alread running...
+            print("fit already running...")
+            await log("Can't start fit, a fit is already running...")
+            return
+        
+        # TODO: better access to model parameters
+        if len(fitProblem.getp()) == 0:
+            raise ValueError("Problem has no fittable parameters")
+
+        # Start a new thread worker and give fit problem to the worker.
+        # Clear abort and uncertainty state
+        fit_state.abort = False
+        fit_state.uncertainty_state = None
+        abort_queue: Queue = fit_state.abort_queue
+        for _ in range(abort_queue.qsize()):
+            abort_queue.get_nowait()
+            abort_queue.task_done()
+
+        fit_thread = FitThread(
+            abort_queue=abort_queue,
+            problem=fitProblem,
+            fitclass=fitclass,
+            options=options,
+            # session_id=session_id,
+            # Number of seconds between updates to the GUI, or 0 for no updates
+            convergence_update=5,
+            uncertainty_update=3600,
+            )
+        fit_thread.start()
+        fit_state.thread = fit_thread
+        await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
+        await log(json.dumps(to_dict(options), indent=2), title = f"starting fitter {fitter_id}")
 
 async def _fit_progress_handler(event: Dict):
-    print("progress event message: ", event.get("message", ""))
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    # session_id = event["session_id"]
+    problem_state = state.problem
+    fitProblem = problem_state.fitProblem if problem_state is not None else None
+    if fitProblem is None:
+        raise ValueError("should never happen: fit progress reported for session in which fitProblem is undefined")
     message = event.get("message", None)
     if message == 'complete' or message == 'improvement':
         fitProblem.setp(event["point"])
@@ -262,10 +308,10 @@ async def _fit_progress_handler(event: Dict):
         if message == 'complete':
             await publish("", "fit_active", False)
     elif message == 'convergence_update':
-        app["fitting"]["population"] = event["pop"]
+        state.fitting.population = event["pop"]
         await publish("", "convergence_update", True)
     elif message == 'uncertainty_update' or message == 'uncertainty_final':
-        app["fitting"]["uncertainty_state"] = event["uncertainty_state"]
+        state.fitting.uncertainty_state = event["uncertainty_state"]
         await publish("", "uncertainty_update", True)
 
 def fit_progress_handler(event: Dict):
@@ -276,12 +322,13 @@ def fit_progress_handler(event: Dict):
 async def _fit_complete_handler(event):
     print("complete event: ", event.get("message", ""))
     message = event.get("message", None)
-    fit_thread: threading.Thread = app["fitting"]["fit_thread"]
+    fit_thread = state.fitting.thread
     if fit_thread is not None:
+        # print(fit_thread)
         fit_thread.join(1) # 1 second timeout on join
         if fit_thread.is_alive():
             await log("fit thread failed to complete")
-    app["fitting"]["fit_thread"] = None
+    state.fitting.thread = None
     problem: refl1d.fitproblem.FitProblem = event["problem"]
     chisq = nice(2*event["value"]/problem.dof)
     problem.setp(event["point"])
@@ -328,7 +375,9 @@ def get_probe_data(theory, probe, substrate=None, surface=None):
 async def get_plot_data(sid: str="", view: str = 'linear'):
     # TODO: implement view-dependent return instead of doing this in JS
     # (calculate x,y,dy.dx for given view, excluding log)
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if state.problem is None or state.problem.fitProblem is None:
+        return None
+    fitProblem = state.problem.fitProblem
     result = []
     for model in fitProblem.models:
         assert(isinstance(model, Experiment))
@@ -353,15 +402,17 @@ async def get_plot_data(sid: str="", view: str = 'linear'):
 @rest_get
 async def get_model(sid: str=""):
     from bumps.serialize import to_dict
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
+    if state.problem is None or state.problem.fitProblem is None:
+        return None
+    fitProblem = state.problem.fitProblem
     return to_dict(fitProblem)
 
 @sio.event
 @rest_get
 async def get_profile_plot(sid: str="", model_index: int=0):
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    if fitProblem is None:
+    if state.problem is None or state.problem.fitProblem is None:
         return None
+    fitProblem = state.problem.fitProblem
     models = list(fitProblem.models)
     if model_index > len(models):
         return None
@@ -386,9 +437,9 @@ async def get_profile_plot(sid: str="", model_index: int=0):
 @sio.event
 @rest_get
 async def get_profile_data(sid: str="", model_index: int=0):
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    if fitProblem is None:
+    if state.problem is None or state.problem.fitProblem is None:
         return None
+    fitProblem = state.problem.fitProblem
     models = list(fitProblem.models)
     if (model_index > len(models)):
         return None
@@ -416,9 +467,11 @@ async def get_convergence_plot(sid: str=""):
     # NOTE: this is slow.  Creating the figure takes around 0.15 seconds, 
     # and converting to mpld3 can take as much as 0.5 seconds.
     # Might want to replace with plotting on the client side (normalizing population takes around 1 ms)
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    population = app["fitting"]["population"]
-    if population is not None and fitProblem is not None:
+    if state.problem is None or state.problem.fitProblem is None:
+        return None
+    fitProblem = state.problem.fitProblem
+    population = state.fitting.population
+    if population is not None:
         import mpld3
         import matplotlib
         matplotlib.use("agg")
@@ -464,7 +517,7 @@ async def get_convergence_plot(sid: str=""):
 @sio.event
 @rest_get
 async def get_correlation_plot(sid: str = ""):
-    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    uncertainty_state = state.fitting.uncertainty_state
     if uncertainty_state is not None:
         import mpld3
         import matplotlib
@@ -491,7 +544,7 @@ async def get_correlation_plot(sid: str = ""):
 @sio.event
 @rest_get
 async def get_uncertainty_plot(sid: str = ""):
-    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    uncertainty_state = state.fitting.uncertainty_state
     if uncertainty_state is not None:
         import time
         start_time = time.time()
@@ -506,8 +559,10 @@ async def get_uncertainty_plot(sid: str = ""):
 @sio.event
 @rest_get
 async def get_model_uncertainty_plot(sid: str = ""):
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    if state.problem is None or state.problem.fitProblem is None:
+        return None
+    fitProblem = state.problem.fitProblem
+    uncertainty_state = state.fitting.uncertainty_state
     if uncertainty_state is not None:
         import mpld3
         import matplotlib
@@ -535,7 +590,7 @@ async def get_model_uncertainty_plot(sid: str = ""):
 @sio.event
 @rest_get
 async def get_parameter_trace_plot(sid: str=""):
-    uncertainty_state = app["fitting"].get("uncertainty_state", None)
+    uncertainty_state = state.fitting.uncertainty_state
     if uncertainty_state is not None:
         import mpld3
         import matplotlib
@@ -576,9 +631,9 @@ async def get_parameter_trace_plot(sid: str=""):
 @sio.event
 @rest_get
 async def get_parameters(sid: str = "", only_fittable: bool = False):
-    fitProblem: refl1d.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    if fitProblem is None:
+    if state.problem is None or state.problem.fitProblem is None:
         return []
+    fitProblem = state.problem.fitProblem
 
     all_parameters = fitProblem.model_parameters()
     if only_fittable:
@@ -592,9 +647,9 @@ async def get_parameters(sid: str = "", only_fittable: bool = False):
 
 @sio.event
 async def set_parameter(sid: str, parameter_id: str, property: Literal["value01", "value", "min", "max"], value: Union[float, str, bool]):
-    fitProblem: bumps.fitproblem.FitProblem = app["problem"]["fitProblem"]
-    if fitProblem is None:
-        return
+    if state.problem is None or state.problem.fitProblem is None:
+        return None
+    fitProblem = state.problem.fitProblem
 
     parameter = fitProblem._parameters_by_id.get(parameter_id, None)
     if parameter is None:
@@ -635,20 +690,26 @@ async def set_parameter(sid: str, parameter_id: str, property: Literal["value01"
     return
 
 @sio.event
-async def publish(sid: str, topic: str, message=None):
+async def publish(sid: str, topic: TopicNameType, message=None):
     timestamp_str = f"{datetime.now().timestamp():.6f}"
     contents = {"message": message, "timestamp": timestamp_str}
-    topics[topic].append(contents)
+    # session = get_session(session_id)    
+    state.topics[topic].append(contents)
+    # if session_id == app["active_session"]:
+    #     await sio.emit(topic, contents)
     await sio.emit(topic, contents)
     # print("emitted: ", topic, contents)
 
 
 @sio.event
 @rest_get
-async def get_topic_messages(sid: str="", topic: str="", max_num=None) -> List[Dict]:
+async def get_topic_messages(sid: str="", topic: Optional[TopicNameType] = None, max_num=None) -> List[Dict]:
     # this is a GET request in disguise -
     # emitter must handle the response in a callback,
     # as no separate response event is emitted.
+    if topic is None:
+        return []    
+    topics = state.topics
     q = topics.get(topic, None)
     if q is None:
         raise ValueError(f"Topic: {topic} not defined")
@@ -678,8 +739,10 @@ async def get_dirlisting(sid: str="", pathlist: Optional[List[str]]=None):
 
 @sio.event
 @rest_get
-async def get_current_pathlist(sid: str="") -> List[str]:
-    return list(app['problem']['pathlist'])
+async def get_current_pathlist(sid: str="") -> Optional[List[str]]:
+    problem_state = state.problem
+    pathlist = problem_state.pathlist if problem_state is not None else None
+    return pathlist
 
 @sio.event
 @rest_get
@@ -690,7 +753,6 @@ async def get_fitter_defaults(sid: str=""):
 def disconnect(sid):
     print('disconnect ', sid)
 
- 
 @sio.event
 async def shutdown(sid: str=""):
     await stop_fit()
@@ -699,7 +761,6 @@ async def shutdown(sid: str=""):
     for client in clients:
         await sio.disconnect(client)
     import signal
-    import sys
     # signal.raise_signal(signal.SIGINT)
     await app.shutdown()
     await app.cleanup()
@@ -725,7 +786,7 @@ def nice(v, digits=4):
         return sign*floor(abs(v)/scale+0.5)*scale
     
 
-class ParamInfo(TypedDict):
+class ParamInfo(TypedDict, total=False):
     id: str
     name: str
     paths: List[str]
@@ -733,9 +794,9 @@ class ParamInfo(TypedDict):
     fittable: bool
     fixed: bool
     writable: bool
-    value01: Optional[float]
-    min_str: Optional[str]
-    max_str: Optional[str]
+    value01: float
+    min_str: str
+    max_str: str
 
 
 def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[ParamInfo]:
@@ -778,23 +839,35 @@ def main():
     parser.add_argument('-x', '--headless', action='store_true', help='do not automatically load client in browser')
     parser.add_argument('--external', action='store_true', help='listen on all interfaces, including external (local connections only if not set)')
     parser.add_argument('-p', '--port', default=0, type=int, help='port on which to start the server')
+    parser.add_argument('--hub', default=None, type=str, help='api address of parent hub (only used when called as subprocess)')
     # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
     args = parser.parse_args()
 
     # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     # set initial path to cwd:
-    app['problem']['pathlist'] = Path().absolute().parts
+    state.problem = ProblemState(pathlist=list(Path().absolute().parts))
     app.add_routes(routes)
     hostname = 'localhost' if not args.external else '0.0.0.0'
 
+    print(sio.manager.rooms)
+
     import socket
     sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
     sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
     sock.bind((hostname, args.port))
-    _, port = sock.getsockname()
+    host, port = sock.getsockname()
+    state.hostname = host
+    state.port = port
+    if args.hub is not None:
+        async def register_instance(application: web.Application):
+            async with ClientSession() as client_session:
+                await client_session.post(args.hub, json={"host": hostname, "port": port})
+        app.on_startup.append(register_instance)
     if not args.headless:
         import webbrowser
-        webbrowser.open_new_tab(f"http://{hostname}:{port}/")
+        async def open_browser(app: web.Application):
+            app.loop.call_later(0.25, lambda: webbrowser.open_new_tab(f"http://{hostname}:{port}/"))
+        app.on_startup.append(open_browser)
     web.run_app(app, sock=sock)
 
 if __name__ == '__main__':

From 693a1033fb6c155f5ae41c757df413fa7cb97580 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 7 Feb 2023 16:46:38 -0500
Subject: [PATCH 155/221] add save as... functionality to file browser in
 client

---
 refl1d/webview/client/src/App.vue             | 28 +++++++++++++++----
 .../client/src/components/FileBrowser.vue     | 21 +++++++++++---
 refl1d/webview/server/webserver.py            |  3 +-
 3 files changed, 41 insertions(+), 11 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index ee711ed2..aaf7588a 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -42,6 +42,8 @@ const menuToggle = ref<HTMLButtonElement>();
 const fitOptions = ref<typeof FitOptions>();
 const fileBrowser = ref<typeof FileBrowser>();
 const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
+const fileBrowserSaveFilename = ref<string>();
+const fileBrowserTitle = ref("Load Model File");
 const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
 const active_layout = ref("left-right");
 const active_panel = ref([0,1]);
@@ -77,9 +79,11 @@ function disconnect() {
 
 function selectOpenFile() {
   if (fileBrowser.value) {
+    fileBrowserTitle.value = "Load Model File";
     fileBrowserSelectCallback.value = (pathlist, filename) => {
       socket.emit("load_problem_file", pathlist, filename);
     }
+    fileBrowserSaveFilename.value = undefined;
     fileBrowser.value.open();
   }
   // const path = prompt("full path to file:");
@@ -90,16 +94,27 @@ function selectOpenFile() {
   // file_picker.value?.click();
 }
 
-async function saveFile(ev: Event) {
+async function saveFileAs(ev: Event) {
+  if (fileBrowser.value) {
+    fileBrowserTitle.value = "Save Problem"
+    fileBrowserSelectCallback.value = (pathlist, filename) => {
+      saveFile(ev, {pathlist, filename});
+    }
+    fileBrowserSaveFilename.value = model_loaded.value?.filename ?? "model.json";
+    fileBrowser.value.open();
+  }
+}
+
+async function saveFile(ev: Event, override?: {pathlist: string[], filename: string}) {
   if (model_loaded.value === undefined) {
     alert('no file to save');
     return;
   }
-  const {pathlist, filename} = model_loaded.value;
+  const {pathlist, filename} = override ?? model_loaded.value;
   console.log('saving:', {pathlist, filename});
-  socket.emit("save_problem_file", pathlist, filename, false, async(confirm_overwrite: boolean) => {
-    if (confirm_overwrite) {
-      const overwrite = await confirm(`File ${filename} exists: overwrite?`);
+  socket.emit("save_problem_file", pathlist, filename, false, async(confirm_overwrite: string | false) => {
+    if (confirm_overwrite !== false) {
+      const overwrite = await confirm(`File ${confirm_overwrite} exists: overwrite?`);
       if (overwrite) {
         socket.emit("save_problem_file", {pathlist, filename, overwrite: true});
       }
@@ -176,6 +191,7 @@ onMounted(() => {
               <ul class="dropdown-menu">
                 <li><button class="btn btn-link dropdown-item" @click="selectOpenFile">Open</button></li>
                 <li><button class="btn btn-link dropdown-item" :disabled="!model_loaded" @click="saveFile">Save</button></li>
+                <li><button class="btn btn-link dropdown-item" :disabled="!model_loaded" @click="saveFileAs">Save As</button></li>
                 <li><button class="btn btn-link dropdown-item" :class="{disabled: model_loaded === undefined}"  @click="reloadModel">Reload</button></li>
                 <li>
                   <hr class="dropdown-divider">
@@ -255,7 +271,7 @@ onMounted(() => {
 
   </div>
   <FitOptions ref="fitOptions" :socket="socket" />
-  <FileBrowser ref="fileBrowser" :socket="socket" title="Load Model File" :callback="fileBrowserSelectCallback" />
+  <FileBrowser ref="fileBrowser" :socket="socket" :title="fileBrowserTitle" :chosenfile_in="model_loaded?.filename" :savefilename="fileBrowserSaveFilename" :callback="fileBrowserSelectCallback" />
 </template>
 
 <style>
diff --git a/refl1d/webview/client/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
index 8dc9d8c7..9605a4be 100644
--- a/refl1d/webview/client/src/components/FileBrowser.vue
+++ b/refl1d/webview/client/src/components/FileBrowser.vue
@@ -6,6 +6,8 @@ import { Socket } from 'socket.io-client';
 const props = defineProps<{
   socket: Socket,
   title: string,
+  savefilename?: string,
+  chosenfile_in?: string,
   callback: (pathlist: string[], filename: string) => void
 }>();
 
@@ -35,6 +37,7 @@ function open() {
   props.socket.emit('get_current_pathlist', (new_pathlist) => {
     setPath(new_pathlist);
   })
+  chosenFile.value = props.chosenfile_in ?? "";
   modal?.show();
   isOpen.value = true;
 }
@@ -50,7 +53,7 @@ function subdirClick(subdir: string) {
 function setPath(new_pathlist?: string[]) {
   if (new_pathlist !== undefined) {
     pathlist.value = new_pathlist;
-    chosenFile.value = "";
+    // chosenFile.value = "";
   }
   props.socket.emit("get_dirlisting", pathlist.value, ({ files, subfolders }) => {
     subdirlist.value = subfolders.sort();
@@ -79,6 +82,16 @@ defineExpose({
           <button type="button" class="btn-close" @click="close" aria-label="Close"></button>
         </div>
         <div class="modal-body">
+          <div v-if="savefilename" class="container border-bottom">
+            <div class="row align-items-center mb-1">
+              <div class="col-auto">
+                <label for="userfilename" class="col-form-label">Filename:</label>
+              </div>
+              <div class="col">
+                <input type="text" id="userfilename" class="form-control" v-model="chosenFile">
+              </div>
+            </div>
+          </div>
           <div class="container border-bottom">
             <nav aria-label="breadcrumb">
               <ol class="breadcrumb">
@@ -99,8 +112,8 @@ defineExpose({
           <div class="container border-bottom">
             <h3>Files:</h3>
             <div class="row row-cols-3">
-              <div class="btn col overflow-hidden border" :class="{'btn-warning': filename === chosenFile}"
-                v-for="filename in filelist" :key="filename" @click="chosenFile = filename" :title="filename"
+              <div class="btn col overflow-hidden border" :class="{'btn-warning': filename == chosenFile}"
+                v-for="filename in filelist" :key="filename + chosenFile" @click="chosenFile = filename" :title="filename"
                 @dblclick="chosenFile=filename;chooseFile()">
                 {{filename}}
               </div>
@@ -108,7 +121,7 @@ defineExpose({
           </div>
           <div class="modal-footer">
             <button type="button" class="btn btn-secondary" @click="close">Cancel</button>
-            <button type="button" class="btn btn-primary" :class="{disabled: chosenFile==''}"
+            <button type="button" class="btn btn-primary" :class="{disabled: !(filelist.includes(chosenFile))}"
               @click="chooseFile">OK</button>
           </div>
         </div>
diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 6f176297..d011f614 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -223,13 +223,14 @@ async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, file
     print({"path": path, "filename": save_filename})
     if not overwrite and Path.exists(path / save_filename):
         #confirmation needed:
-        return True
+        return save_filename
 
     serialized = to_dict(problem_state.fitProblem)
     with open(Path(path, save_filename), "wt") as output_file:
         output_file.write(json.dumps(serialized))
 
     await log(f'Saved: {filename} at path: {path}')
+    return False
 
 @sio.event
 async def start_fit(sid: str="", fitter_id: str="", kwargs=None):

From e050b344ca4d6bb22cec99ec4f49425849cce663 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 9 Feb 2023 09:35:21 -0500
Subject: [PATCH 156/221] fix filebrowser ok button logic, and fix overwrite
 logic in app

---
 refl1d/webview/client/src/App.vue                    | 2 +-
 refl1d/webview/client/src/components/FileBrowser.vue | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index aaf7588a..72d57c90 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -116,7 +116,7 @@ async function saveFile(ev: Event, override?: {pathlist: string[], filename: str
     if (confirm_overwrite !== false) {
       const overwrite = await confirm(`File ${confirm_overwrite} exists: overwrite?`);
       if (overwrite) {
-        socket.emit("save_problem_file", {pathlist, filename, overwrite: true});
+        socket.emit("save_problem_file", pathlist, filename, overwrite);
       }
     }
   });
diff --git a/refl1d/webview/client/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
index 9605a4be..b7575db9 100644
--- a/refl1d/webview/client/src/components/FileBrowser.vue
+++ b/refl1d/webview/client/src/components/FileBrowser.vue
@@ -121,7 +121,7 @@ defineExpose({
           </div>
           <div class="modal-footer">
             <button type="button" class="btn btn-secondary" @click="close">Cancel</button>
-            <button type="button" class="btn btn-primary" :class="{disabled: !(filelist.includes(chosenFile))}"
+            <button type="button" class="btn btn-primary" :class="{disabled: chosenFile == ''}"
               @click="chooseFile">OK</button>
           </div>
         </div>

From 6ebd7c9292acace1399439eb5dc434f8a262b294 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 12:02:10 -0500
Subject: [PATCH 157/221] clean up shutdown tasks

---
 refl1d/webview/server/webserver.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index d011f614..ad39f71a 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -754,17 +754,14 @@ async def get_fitter_defaults(sid: str=""):
 def disconnect(sid):
     print('disconnect ', sid)
 
-@sio.event
-async def shutdown(sid: str=""):
-    await stop_fit()
+async def disconnect_all_clients():
     # disconnect all clients:
     clients = list(sio.manager.rooms.get('/', {None: {}}).get(None).keys())
     for client in clients:
         await sio.disconnect(client)
-    import signal
-    # signal.raise_signal(signal.SIGINT)
-    await app.shutdown()
-    await app.cleanup()
+
+@sio.event
+async def shutdown(sid: str=""):
     print("killing...")
     signal.raise_signal(signal.SIGTERM)
 
@@ -845,6 +842,12 @@ def main():
     args = parser.parse_args()
 
     # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
+    async def notice(message: str):
+        print(message)
+    app.on_cleanup.append(lambda App: notice("cleanup task"))
+    app.on_shutdown.append(lambda App: notice("shutdown task"))
+    app.on_shutdown.append(lambda App: stop_fit())
+    app.on_shutdown.append(lambda App: disconnect_all_clients())
     # set initial path to cwd:
     state.problem = ProblemState(pathlist=list(Path().absolute().parts))
     app.add_routes(routes)

From 4194ac7ffa9b1c9be76e307bce7c00e6b2c037a5 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 12:28:34 -0500
Subject: [PATCH 158/221] move state classes to separate module (to enable
 other implementations)

---
 refl1d/webview/server/webserver.py | 88 +++++++-----------------------
 1 file changed, 19 insertions(+), 69 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index ad39f71a..5582e9c7 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -3,7 +3,8 @@
 from dataclasses import dataclass
 import itertools
 import threading
-from typing import Dict, List, Literal, Optional, Union, TypedDict
+import signal
+from typing import Dict, List, Literal, Optional, Union, TypedDict, cast
 from datetime import datetime
 import warnings
 from queue import Queue
@@ -47,6 +48,8 @@
 from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
 from .profile_plot import plot_sld_profile_plotly
 from .varplot import plot_vars
+# from .state_hdf5_backed import State
+from .state import State
 
 # can get by name and not just by id
 MODEL_EXT = '.json'
@@ -84,55 +87,6 @@
     "fitter_active",
 ]
 
-@dataclass
-class ProblemState:
-    fitProblem: Optional[bumps.fitproblem.FitProblem] = None
-    pathlist: Optional[List[str]] = None
-    filename: Optional[str] = None
-
-    def to_dict(self):
-        return {
-            "fitProblem": to_dict(self.fitProblem),
-            "pathlist": to_dict(self.pathlist),
-            "filename": to_dict(self.filename)
-        }
-    
-    def from_dict(self, serialized):
-        self.fitProblem = from_dict(serialized["fitProblem"])
-        self.pathlist = from_dict(serialized["pathlist"])
-        self.filename = from_dict(serialized["filename"])
-
-
-@dataclass
-class FittingState:
-    abort: bool = False
-    abort_queue: Queue = Queue()
-    population: Optional[List] = None
-    uncertainty_state: Optional[bumps.dream.state.MCMCDraw] = None
-    thread: Optional[FitThread] = None
-
-
-class State:
-    hostname: str
-    port: int
-    problem: Optional[ProblemState]
-    fitting: FittingState
-    topics: Dict[TopicNameType, "deque[Dict]"]
-
-    def __init__(self, problem: Optional[ProblemState] = None, fitting: Optional[FittingState] = None):
-        self.problem = problem
-        self.fitting = FittingState()
-        self.topics = {
-            "log": deque([]),
-            "update_parameters": deque([], maxlen=1),
-            "update_model": deque([], maxlen=1),
-            "model_loaded": deque([], maxlen=1),
-            "fit_active": deque([], maxlen=1),
-            "convergence_update": deque([], maxlen=1),
-            "uncertainty_update": deque([], maxlen=1),
-            "fitter_settings": deque([], maxlen=1),
-            "fitter_active": deque([], maxlen=1),
-        }
 
 state = State()
 
@@ -192,8 +146,10 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
         from bumps.cli import load_model
         problem = load_model(str(path))
     assert isinstance(problem, bumps.fitproblem.FitProblem)
-    problem_state = ProblemState(problem, pathlist, filename)
-    state.problem = problem_state
+    # problem_state = ProblemState(problem, pathlist, filename)
+    state.problem.filename = filename
+    state.problem.pathlist = pathlist
+    state.problem.fitProblem = problem
     print(f'model loaded: {path}')
     await log(f'model loaded: {path}')
 
@@ -249,8 +205,8 @@ async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
 
 @sio.event
 async def stop_fit(sid: str = ""):
-    abort_queue = state.fitting.abort_queue
-    abort_queue.put(True)
+    abort_queue = state.abort_queue
+    abort_queue.put_nowait(True)
 
 @sio.event
 async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
@@ -261,7 +217,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
     else:
         fit_state = state.fitting
         fitclass = FITTERS_BY_ID[fitter_id]
-        if fit_state.thread is not None:
+        if state.fit_thread is not None:
             # warn that fit is alread running...
             print("fit already running...")
             await log("Can't start fit, a fit is already running...")
@@ -273,13 +229,9 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
 
         # Start a new thread worker and give fit problem to the worker.
         # Clear abort and uncertainty state
-        fit_state.abort = False
-        fit_state.uncertainty_state = None
-        abort_queue: Queue = fit_state.abort_queue
-        for _ in range(abort_queue.qsize()):
-            abort_queue.get_nowait()
-            abort_queue.task_done()
-
+        # state.abort = False
+        # state.fitting.uncertainty_state = None
+        state.abort_queue = abort_queue = Queue()
         fit_thread = FitThread(
             abort_queue=abort_queue,
             problem=fitProblem,
@@ -291,7 +243,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
             uncertainty_update=3600,
             )
         fit_thread.start()
-        fit_state.thread = fit_thread
+        state.fit_thread = fit_thread
         await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
         await log(json.dumps(to_dict(options), indent=2), title = f"starting fitter {fitter_id}")
 
@@ -312,7 +264,7 @@ async def _fit_progress_handler(event: Dict):
         state.fitting.population = event["pop"]
         await publish("", "convergence_update", True)
     elif message == 'uncertainty_update' or message == 'uncertainty_final':
-        state.fitting.uncertainty_state = event["uncertainty_state"]
+        state.fitting.uncertainty_state = cast(bumps.dream.state.MCMCDraw, event["uncertainty_state"])
         await publish("", "uncertainty_update", True)
 
 def fit_progress_handler(event: Dict):
@@ -323,13 +275,13 @@ def fit_progress_handler(event: Dict):
 async def _fit_complete_handler(event):
     print("complete event: ", event.get("message", ""))
     message = event.get("message", None)
-    fit_thread = state.fitting.thread
+    fit_thread = state.fit_thread
     if fit_thread is not None:
         # print(fit_thread)
         fit_thread.join(1) # 1 second timeout on join
         if fit_thread.is_alive():
             await log("fit thread failed to complete")
-    state.fitting.thread = None
+    state.fit_thread = None
     problem: refl1d.fitproblem.FitProblem = event["problem"]
     chisq = nice(2*event["value"]/problem.dof)
     problem.setp(event["point"])
@@ -849,12 +801,10 @@ async def notice(message: str):
     app.on_shutdown.append(lambda App: stop_fit())
     app.on_shutdown.append(lambda App: disconnect_all_clients())
     # set initial path to cwd:
-    state.problem = ProblemState(pathlist=list(Path().absolute().parts))
+    state.problem.pathlist = list(Path().absolute().parts)
     app.add_routes(routes)
     hostname = 'localhost' if not args.external else '0.0.0.0'
 
-    print(sio.manager.rooms)
-
     import socket
     sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
     sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)

From a838bde29c5d6434abdbc1a686eef7038e018161 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 12:29:04 -0500
Subject: [PATCH 159/221] add plain server state implementation

---
 refl1d/webview/server/state.py | 47 ++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 refl1d/webview/server/state.py

diff --git a/refl1d/webview/server/state.py b/refl1d/webview/server/state.py
new file mode 100644
index 00000000..5d53b03a
--- /dev/null
+++ b/refl1d/webview/server/state.py
@@ -0,0 +1,47 @@
+from collections import deque
+from queue import Queue
+from typing import Dict, List, Optional, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import bumps, bumps.fitproblem, bumps.dream.state
+    from .webserver import TopicNameType
+    from .fit_thread import FitThread
+
+class ProblemState:
+    fitProblem: Optional['bumps.fitproblem.FitProblem'] = None
+    pathlist: Optional[List[str]] = None
+    filename: Optional[str] = None
+
+class FittingState:
+    abort: bool = False
+    population: Optional[List] = None
+    uncertainty_state: Optional['bumps.dream.state.MCMCDraw']
+
+
+class State:
+    # These attributes are ephemeral, not to be serialized/stored:
+    hostname: str
+    port: int
+    abort_queue: Queue
+    fit_thread: Optional['FitThread'] = None
+
+    # State to be stored:
+    problem: ProblemState
+    fitting: FittingState
+    topics: Dict['TopicNameType', 'deque[Dict]']
+
+    def __init__(self, problem: Optional[ProblemState] = None, fitting: Optional[FittingState] = None):
+        self.problem = problem if problem is not None else ProblemState()
+        self.fitting = FittingState()
+        self.abort_queue = Queue()
+        self.topics = {
+            "log": deque([]),
+            "update_parameters": deque([], maxlen=1),
+            "update_model": deque([], maxlen=1),
+            "model_loaded": deque([], maxlen=1),
+            "fit_active": deque([], maxlen=1),
+            "convergence_update": deque([], maxlen=1),
+            "uncertainty_update": deque([], maxlen=1),
+            "fitter_settings": deque([], maxlen=1),
+            "fitter_active": deque([], maxlen=1),
+        }

From 4ea98e368d46b706ac4dafd46b7c2c0862c48612 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 12:51:50 -0500
Subject: [PATCH 160/221] add cleanup stub to State, needed for other
 implementations

---
 refl1d/webview/server/state.py     | 3 +++
 refl1d/webview/server/webserver.py | 1 +
 2 files changed, 4 insertions(+)

diff --git a/refl1d/webview/server/state.py b/refl1d/webview/server/state.py
index 5d53b03a..48d779f1 100644
--- a/refl1d/webview/server/state.py
+++ b/refl1d/webview/server/state.py
@@ -45,3 +45,6 @@ def __init__(self, problem: Optional[ProblemState] = None, fitting: Optional[Fit
             "fitter_settings": deque([], maxlen=1),
             "fitter_active": deque([], maxlen=1),
         }
+
+    async def cleanup(self):
+        pass
\ No newline at end of file
diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 5582e9c7..e9c96b88 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -800,6 +800,7 @@ async def notice(message: str):
     app.on_shutdown.append(lambda App: notice("shutdown task"))
     app.on_shutdown.append(lambda App: stop_fit())
     app.on_shutdown.append(lambda App: disconnect_all_clients())
+    app.on_shutdown.append(lambda App: state.cleanup())
     # set initial path to cwd:
     state.problem.pathlist = list(Path().absolute().parts)
     app.add_routes(routes)

From ff9673b9851e05e05790a12b1a075ef837b19833 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 12:59:02 -0500
Subject: [PATCH 161/221] use hdf-backed state

---
 refl1d/webview/server/webserver.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index e9c96b88..62a1018d 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -48,8 +48,8 @@
 from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
 from .profile_plot import plot_sld_profile_plotly
 from .varplot import plot_vars
-# from .state_hdf5_backed import State
-from .state import State
+from .state_hdf5_backed import State
+# from .state import State
 
 # can get by name and not just by id
 MODEL_EXT = '.json'

From 0f6ed2faecf77222c9722adaf69177fbacc439e5 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 12:59:20 -0500
Subject: [PATCH 162/221] state backed by hdf5 file

---
 refl1d/webview/server/state_hdf5_backed.py | 304 +++++++++++++++++++++
 1 file changed, 304 insertions(+)
 create mode 100644 refl1d/webview/server/state_hdf5_backed.py

diff --git a/refl1d/webview/server/state_hdf5_backed.py b/refl1d/webview/server/state_hdf5_backed.py
new file mode 100644
index 00000000..ae90867a
--- /dev/null
+++ b/refl1d/webview/server/state_hdf5_backed.py
@@ -0,0 +1,304 @@
+from typing import TYPE_CHECKING, Optional, Dict, List, Any, Literal, cast
+import json
+from queue import Queue
+from bumps.serialize import from_dict, to_dict
+import h5py
+import numpy as np
+
+import refl1d.fitproblem
+from bumps.dream.state import MCMCDraw
+
+
+if TYPE_CHECKING:
+    from .webserver import TopicNameType
+    from h5py import Group, Dataset
+    from .fit_thread import FitThread
+
+# slow, small:
+COMPRESSION = 9
+MAX_TOPIC_MESSAGE = 1024*100 # 100k
+MAX_PROBLEM_SIZE = 10*1024*1024 # 10 MB problem max size
+SESSION_FILE_NAME = "session.h5"
+
+def to_hdf5_group(state: 'State', group: 'Group'):
+    import h5py
+    fitting_grp = group.create_group("fitting")
+    topics_grp = group.create_group("topics")
+    problem_grp = group.create_group("problem")
+
+    if state.fitting.population is not None:
+        pop_shape = state.fitting.population.shape
+        fitting_grp.create_dataset("population", shape=pop_shape, maxshape=(None, pop_shape[1]), compression = COMPRESSION)
+    if state.fitting.uncertainty_state is not None:
+        write_uncertainty_state(state.fitting.uncertainty_state, fitting_grp)
+
+    for topic, contents in state.topics.items():
+        num_entries = len(contents)
+        maxlen = contents.maxlen
+        topic_dataset = topics_grp.create_dataset(topic, shape=(num_entries,), maxshape=(contents.maxlen), dtype=f"|S{MAX_TOPIC_MESSAGE}", compression=COMPRESSION)
+        for idx, message in enumerate(contents):
+            topic_dataset[idx] = json.dumps(message)
+
+    if state.problem is not None:
+        if state.problem.fitProblem is not None:
+            problem_json = json.dumps(to_dict(state.problem.fitProblem))
+            problem_grp['fitProblem'] = problem_json
+            problem_grp['fitProblem'].attrs["Content-Type"] = "application/json"
+        if state.problem.filename is not None:
+            problem_grp['filename'] = state.problem.filename
+        if state.problem.pathlist is not None:
+            pathlist_json = json.dumps(state.problem.pathlist)
+            problem_grp['pathlist'] = pathlist_json
+            problem_grp['pathlist'].attrs["Content-Type"] = "application/json"
+
+CACHE_MISS = object()
+
+class ProblemState:
+    _group: h5py.Group
+    _filename: Optional[str]
+    _pathlist: Optional[List[str]]
+    _fitProblem: Optional[refl1d.fitproblem.FitProblem]
+
+    def __init__(self, group: h5py.Group):
+        self._group = group
+
+    @property
+    def filename(self) -> Optional[str]:
+        # check cache:
+        cached_val = getattr(self, '_filename', CACHE_MISS)
+        if cached_val is CACHE_MISS:
+            backing_val = self._group['filename'][()] if 'filename' in self._group else None
+            setattr(self, '_filename', backing_val)
+            cached_val = backing_val
+        return cached_val
+    
+    @filename.setter
+    def filename(self, value: str):
+        dset = self._group.require_dataset('filename', (), h5py.vlen_dtype(str))
+        dset[()] = value
+        self._filename = value
+
+    @property
+    def pathlist(self) -> Optional[List[str]]:
+        cached_val = getattr(self, '_pathlist', CACHE_MISS)
+        if cached_val is CACHE_MISS:
+            backing_val = json.loads(self._group['pathlist'][()]) if 'pathlist' in self._group else None
+            setattr(self, '_pathlist', backing_val)
+            cached_val = backing_val
+        return cached_val
+    
+    @pathlist.setter
+    def pathlist(self, value: List[str]):
+        dset = self._group.require_dataset('pathlist', (), h5py.vlen_dtype(str))
+        dset[()] = json.dumps(value)
+        self._pathlist = value
+
+    @property
+    def fitProblem(self) -> Optional[refl1d.fitproblem.FitProblem]:
+        cached_val = getattr(self, '_fitProblem', CACHE_MISS)
+        if cached_val is CACHE_MISS:
+            backing_val = from_dict(json.loads(self._group['fitProblem'][()])) if 'fitProblem' in self._group else None
+            setattr(self, '_fitProblem', backing_val)
+            cached_val = backing_val
+        return cached_val
+    
+    @fitProblem.setter
+    def fitProblem(self, value: refl1d.fitproblem.FitProblem):
+        dset = self._group.require_dataset('fitProblem', (), h5py.vlen_dtype(str))
+        dset[()] = json.dumps(to_dict(value))
+        self._fitProblem = value
+
+class FittingState:
+    _group: h5py.Group
+    # cache items:
+    _population: np.ndarray
+    _uncertainty_state: 'MCMCDraw'
+
+    def __init__(self, group: h5py.Group):
+        self._group = group
+
+    @property
+    def population(self) -> Optional[np.ndarray]:
+        cached_val = getattr(self, '_population', CACHE_MISS)
+        if cached_val is CACHE_MISS:
+            backing_val = self._group['population'][()] if 'population' in self._group else None
+            if backing_val is not None:
+                setattr(self, '_population', backing_val)
+            cached_val = backing_val
+        return cached_val
+    
+    @population.setter
+    def population(self, value: np.ndarray):
+        pop_shape = value.shape
+        if not 'population' in self._group:
+            self._group.create_dataset("population", shape=pop_shape, data=value, maxshape=(None, None), compression = COMPRESSION)
+        else:
+            dset = cast(h5py.Dataset, self._group["population"])
+            if dset.shape != pop_shape:
+                dset.resize(pop_shape)        
+            dset[()] = value
+        self._population = value
+
+    @property
+    def uncertainty_state(self):
+        cached_val = getattr(self, '_uncertainty_state', CACHE_MISS)
+        if cached_val is CACHE_MISS:
+            backing_val = read_uncertainty_state(self._group) if 'gen_draws' in self._group else None
+            if backing_val is not None:
+                setattr(self, '_uncertainty_state', backing_val)
+            cached_val = backing_val
+        return cached_val
+
+    @uncertainty_state.setter
+    def uncertainty_state(self, value: 'MCMCDraw'):
+        print("writing uncertainty state: ", value)
+        write_uncertainty_state(value, self._group)
+        self._uncertainty_state = value
+        print("done writing uncertainty state.")
+
+class Topic:
+    dataset: h5py.Dataset
+    maxlen: Optional[int] = 1
+
+    def __init__(self, dataset: h5py.Dataset, maxlen: Optional[int] = 1):
+        self.dataset = dataset
+        self.maxlen = maxlen
+
+    def __getitem__(self, index: int):
+        return json.loads(self.dataset[index])
+    
+    def __setitem__(self, index: int, value: Dict):
+        self.dataset[index] = json.dumps(value)
+        self.dataset.flush()
+
+    def __len__(self):
+        return len(self.dataset)
+
+    def append(self, value: Dict):
+        current_len: int = self.dataset.size
+        if self.maxlen is None or current_len < self.maxlen:
+            self.dataset.resize((current_len+1,))
+            self[current_len] = value
+        else:
+            # not a true ring buffer: just overwrite last element when full
+            # (only works for length-1 buffers, but that's all we have)
+            self[current_len - 1] = value
+        self.dataset.flush()
+
+class TopicsDict:
+    group: 'Group'
+
+    def __init__(self, group: 'Group'):
+        self.group = group
+        for topic_name, maxlen in (
+            ("log", None),
+            ("update_parameters", 1),
+            ("update_model", 1),
+            ("model_loaded", 1),
+            ("fit_active", 1),
+            ("convergence_update", 1),
+            ("uncertainty_update", 1),
+            ("fitter_settings", 1),
+            ("fitter_active", 1)
+        ):
+            if topic_name in group:
+                topic_dataset = group[topic_name]
+            else:
+                topic_dataset = group.create_dataset(topic_name, shape=(0,), maxshape=(maxlen,), dtype=f"|S{MAX_TOPIC_MESSAGE}", compression=COMPRESSION)
+    
+    def __getitem__(self, key: 'TopicNameType') -> Topic:
+        topic_dataset = cast(h5py.Dataset, self.group[key])
+        return Topic(topic_dataset, maxlen=topic_dataset.maxshape[0])
+    
+    def get(self, key: 'TopicNameType', default: Any) -> Topic | Any:
+        return self[key] if key in self.group else default
+
+    def items(self):
+        return [(topic_name, self[topic_name]) for topic_name in self.group.keys()]
+
+class State:
+    hostname: str
+    port: int
+    problem: ProblemState
+    dream: FittingState
+    topics: TopicsDict
+    fit_thread: Optional['FitThread'] = None
+    abort_queue: Queue
+
+    def __init__(self, session_file_name: str = SESSION_FILE_NAME):
+        # self.problem = problem
+        # self.fitting = fitting if fitting is not None else FittingState()
+        self.abort_queue = Queue()
+        import h5py
+        self.session_file = session_file = h5py.File(session_file_name, "a", libver='latest')
+        topics_group = session_file.require_group("topics")
+        problem_group = session_file.require_group("problem")
+        fitting_group = session_file.require_group("fitting")
+        self.topics = TopicsDict(topics_group)
+        self.problem = ProblemState(problem_group)
+        self.fitting = FittingState(fitting_group)
+        session_file.swmr_mode = True
+
+    async def cleanup(self):
+        self.session_file.close()
+
+def write_uncertainty_state(state: 'MCMCDraw', group: 'Group', compression=COMPRESSION):
+        to_save = {}
+        # Build 2-D data structures
+        to_save["gen_draws"], to_save["gen_logp"] = state.logp(full=True)
+        _, to_save["AR"] = state.acceptance_rate()
+
+        to_save["thin_draws"], to_save["thin_point"], to_save["thin_logp"] = state.chains()
+        to_save["update_draws"], to_save["update_CR_weight"] = state.CR_weight()
+
+        #TODO: missing _outliers from save_state
+        for field_name, data in to_save.items():
+            if field_name in group:
+                dataset = cast(h5py.Dataset, group[field_name])
+                if dataset.shape != data.shape:
+                    dataset.resize(data.shape)
+                dataset[()] = data
+            else:
+                maxshape = tuple([None for dim in data.shape])
+                dataset = group.create_dataset(field_name, data=data, maxshape=maxshape, compression=compression)
+
+
+def read_uncertainty_state(group: 'Group', skip=0, report=0, derived_vars=0):
+
+    loaded: Dict[str, np.ndarray] = dict(group.items())
+    
+    # Guess dimensions
+    Ngen = loaded["gen_draws"].shape[0]
+    thinning = 1
+    Nthin, Npop, Nvar = loaded["thin_point"].shape
+    Nupdate, Ncr = loaded["update_CR_weight"].shape
+    Nthin -= skip
+
+    # Create empty draw and fill it with loaded data
+    state = MCMCDraw(0, 0, 0, 0, 0, 0, thinning)
+    #print("gen, var, pop", Ngen, Nvar, Npop)
+    state.draws = Ngen * Npop
+    state.generation = Ngen
+    state._gen_index = 0
+    state._gen_draws = loaded["gen_draws"][()]
+    state._gen_acceptance_rate = loaded["AR"][()]
+    state._gen_logp = loaded["gen_logp"][()]
+    state.thinning = thinning
+    state._thin_count = Ngen//thinning
+    state._thin_index = 0
+    state._thin_draws = loaded["thin_draws"][()]
+    state._thin_logp = loaded["thin_logp"][()]
+    state._thin_point = loaded["thin_point"][()]
+    state._gen_current = state._thin_point[-1].copy()
+    state._update_count = Nupdate
+    state._update_index = 0
+    state._update_draws = loaded["update_draws"][()]
+    state._update_CR_weight = loaded["update_CR_weight"][()]
+    state._outliers = []
+
+    bestidx = np.unravel_index(np.argmax(loaded["thin_logp"]), loaded["thin_logp"].shape)
+    state._best_logp = loaded["thin_logp"][bestidx]
+    state._best_x = loaded["thin_point"][bestidx]
+    state._best_gen = 0
+
+    return state
\ No newline at end of file

From c6e1e57a54f126eec51f8e31a1213e6103e426f3 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 15:22:03 -0500
Subject: [PATCH 163/221] add command line options to load a file, start a fit,
 and autoexit on completion, and specify store file

---
 refl1d/webview/server/webserver.py | 51 ++++++++++++++++++++++++++++--
 1 file changed, 48 insertions(+), 3 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 62a1018d..82fe1fee 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -88,7 +88,7 @@
 ]
 
 
-state = State()
+state: State # to be filled in later...
 
 def rest_get(fn):
     """
@@ -209,7 +209,7 @@ async def stop_fit(sid: str = ""):
     abort_queue.put_nowait(True)
 
 @sio.event
-async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
+async def start_fit_thread(sid: str="", fitter_id: str="", options=None, terminate_on_finish=False):
     options = {} if options is None else options    # session_id: str = app["active_session"]
     fitProblem = state.problem.fitProblem if state.problem is not None else None
     if fitProblem is None:
@@ -241,6 +241,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
             # Number of seconds between updates to the GUI, or 0 for no updates
             convergence_update=5,
             uncertainty_update=3600,
+            terminate_on_finish=terminate_on_finish,
             )
         fit_thread.start()
         state.fit_thread = fit_thread
@@ -276,8 +277,10 @@ async def _fit_complete_handler(event):
     print("complete event: ", event.get("message", ""))
     message = event.get("message", None)
     fit_thread = state.fit_thread
+    terminate = False
     if fit_thread is not None:
-        # print(fit_thread)
+        print(fit_thread)
+        terminate = fit_thread.terminate_on_finish
         fit_thread.join(1) # 1 second timeout on join
         if fit_thread.is_alive():
             await log("fit thread failed to complete")
@@ -288,6 +291,8 @@ async def _fit_complete_handler(event):
     problem.model_update()
     await publish("", "update_parameters", True)
     await log(event["info"], title=f"done with chisq {chisq}")
+    if terminate:
+        await shutdown()
 
 def fit_complete_handler(event: Dict):
     asyncio.run_coroutine_threadsafe(_fit_complete_handler(event), app.loop)
@@ -785,14 +790,54 @@ def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[Param
 
 def main():
     parser = argparse.ArgumentParser()
+    parser.add_argument('filename', nargs='?', help='problem file to load, .py or .json (serialized) fitproblem')
     # parser.add_argument('-d', '--debug', action='store_true', help='autoload modules on change')
     parser.add_argument('-x', '--headless', action='store_true', help='do not automatically load client in browser')
     parser.add_argument('--external', action='store_true', help='listen on all interfaces, including external (local connections only if not set)')
     parser.add_argument('-p', '--port', default=0, type=int, help='port on which to start the server')
     parser.add_argument('--hub', default=None, type=str, help='api address of parent hub (only used when called as subprocess)')
+    parser.add_argument('--fit', default=None, type=str, choices=list(FITTERS_BY_ID.keys()), help='fitting engine to use; see manual for details')
+    parser.add_argument('--start', action='store_true', help='start fit when problem loaded')
+    parser.add_argument('--store', default=None, type=str, help='backing file for state')
+    parser.add_argument('--exit', action='store_true', help='end process when fit complete (fit results lost unless store is specified)')
     # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
     args = parser.parse_args()
 
+    global state
+    if args.store is None:
+        state = State("in-memory.h5", in_memory=True)
+    else:
+        state = State(args.store)
+
+    # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
+    if args.fit is not None:
+        app.on_startup.append(lambda App: publish('', 'fitter_active', args.fit))
+
+    fitter_id = args.fit
+    if fitter_id is None:
+        fitter_id = state.topics.get("fitter_active", {"message": None})["message"]
+    if fitter_id is None:
+        fitter_id = 'amoeba'
+    fitter_settings = FITTER_DEFAULTS[fitter_id]
+
+    # if args.steps is not None:
+    #     fitter_settings["steps"] = args.steps
+
+    if args.filename is not None:
+        filepath = Path(args.filename)
+        pathlist = list(filepath.parent.parts)
+        filename = filepath.name
+        start = args.start
+        print(f"fitter for filename {filename} is {fitter_id}")
+        async def startup_task(App=None):
+            await load_problem_file("", pathlist, filename)
+            if start:
+                await start_fit_thread("", fitter_id, fitter_settings, args.exit)
+        
+        app.on_startup.append(startup_task)
+
+        # app.on_startup.append()
+
     # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
     async def notice(message: str):
         print(message)

From 6acf9e5da250a9fd109c65964230d20329b57bbc Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 15:22:33 -0500
Subject: [PATCH 164/221] allow in-memory use of hdf5 core driver

---
 refl1d/webview/server/state_hdf5_backed.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/state_hdf5_backed.py b/refl1d/webview/server/state_hdf5_backed.py
index ae90867a..71f2845d 100644
--- a/refl1d/webview/server/state_hdf5_backed.py
+++ b/refl1d/webview/server/state_hdf5_backed.py
@@ -225,12 +225,13 @@ class State:
     fit_thread: Optional['FitThread'] = None
     abort_queue: Queue
 
-    def __init__(self, session_file_name: str = SESSION_FILE_NAME):
+    def __init__(self, session_file_name: str = SESSION_FILE_NAME, in_memory: bool = False, backing_store: bool = False ):
         # self.problem = problem
         # self.fitting = fitting if fitting is not None else FittingState()
         self.abort_queue = Queue()
         import h5py
-        self.session_file = session_file = h5py.File(session_file_name, "a", libver='latest')
+        hdf_kw = dict(driver="core", backing_store=backing_store) if in_memory else dict()
+        self.session_file = session_file = h5py.File(session_file_name, "a", libver='latest', **hdf_kw)
         topics_group = session_file.require_group("topics")
         problem_group = session_file.require_group("problem")
         fitting_group = session_file.require_group("fitting")

From 4773e89de91469760323bcaeb83d27c7b5d396dc Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Fri, 10 Feb 2023 15:23:07 -0500
Subject: [PATCH 165/221] store flag for autoterminate in fit thread, to be
 applied on fit completion

---
 refl1d/webview/server/fit_thread.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
index e18490ad..2889766e 100644
--- a/refl1d/webview/server/fit_thread.py
+++ b/refl1d/webview/server/fit_thread.py
@@ -172,7 +172,8 @@ class FitThread(Thread):
 
     def __init__(self, abort_queue: Queue, problem=None,
                  fitclass=None, options=None, mapper=None,
-                 convergence_update=5, uncertainty_update=300):
+                 convergence_update=5, uncertainty_update=300,
+                 terminate_on_finish=False):
         # base class initialization
         # Process.__init__(self)
 
@@ -184,6 +185,7 @@ def __init__(self, abort_queue: Queue, problem=None,
         self.mapper = mapper
         self.convergence_update = convergence_update
         self.uncertainty_update = uncertainty_update
+        self.terminate_on_finish = terminate_on_finish
 
     def abort_test(self):
         return not self.abort_queue.empty()

From 9ed729d8c84eb7c7c4f16aa463953691edb3ce8d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 10:01:02 -0500
Subject: [PATCH 166/221] send chisq with progress updates

---
 refl1d/webview/server/fit_thread.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
index e18490ad..feee837a 100644
--- a/refl1d/webview/server/fit_thread.py
+++ b/refl1d/webview/server/fit_thread.py
@@ -7,7 +7,7 @@
 
 import numpy as np
 from bumps import monitor
-from bumps.fitters import FitDriver
+from bumps.fitters import FitDriver, nllf_scale, format_uncertainty
 from bumps.mapper import MPMapper, SerialMapper, can_pickle
 from bumps.util import redirect_console
 from bumps.history import History
@@ -33,11 +33,14 @@ def __init__(self, problem, progress=None, improvement=None):
         self.problem = problem
 
     def show_progress(self, history):
+        scale, err = nllf_scale(self.problem)
+        chisq = format_uncertainty(scale*history.value[0], err)
         evt = dict(
             problem=self.problem,
             message="progress",
             step=history.step[0],
             value=history.value[0],
+            chisq=chisq,
             point=history.point[0]+0)  # avoid race
         EVT_FIT_PROGRESS.send(evt)
 

From ef9da02e15e51584ff226ddf04b475a79b3a7a5b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 10:02:41 -0500
Subject: [PATCH 167/221] fix retrieving active fitter from topics

---
 refl1d/webview/server/webserver.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 82fe1fee..a56b24f8 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -250,6 +250,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None, termina
 
 async def _fit_progress_handler(event: Dict):
     # session_id = event["session_id"]
+    print("progress: ", event)
     problem_state = state.problem
     fitProblem = problem_state.fitProblem if problem_state is not None else None
     if fitProblem is None:
@@ -258,9 +259,12 @@ async def _fit_progress_handler(event: Dict):
     if message == 'complete' or message == 'improvement':
         fitProblem.setp(event["point"])
         fitProblem.model_update()
+        chisq_str = fitProblem.chisq_str()
         await publish("", "update_parameters", True)
         if message == 'complete':
             await publish("", "fit_active", False)
+        else:
+            await publish("", "fit_active", {"chisq": chisq_str})
     elif message == 'convergence_update':
         state.fitting.population = event["pop"]
         await publish("", "convergence_update", True)
@@ -815,7 +819,7 @@ def main():
 
     fitter_id = args.fit
     if fitter_id is None:
-        fitter_id = state.topics.get("fitter_active", {"message": None})["message"]
+        fitter_id = state.topics.get("fitter_active", [{"message": None}])[-1]["message"]
     if fitter_id is None:
         fitter_id = 'amoeba'
     fitter_settings = FITTER_DEFAULTS[fitter_id]

From 74b5185323e0c58cc7d80c97d5914f164d385b00 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 22:17:40 -0500
Subject: [PATCH 168/221] add fit progress events

---
 refl1d/webview/server/webserver.py | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index e9c96b88..a959cbc2 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -28,7 +28,7 @@
 mimetypes.add_type("image/png", ".png")
 mimetypes.add_type("image/svg+xml", ".svg")
 
-from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit
+from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit, nllf_scale, format_uncertainty
 from bumps.serialize import to_dict, from_dict
 from bumps.mapper import MPMapper
 from bumps.parameter import Parameter, Variable, unique
@@ -208,6 +208,12 @@ async def stop_fit(sid: str = ""):
     abort_queue = state.abort_queue
     abort_queue.put_nowait(True)
 
+def get_chisq(problem: refl1d.fitproblem.FitProblem, nllf=None):
+    nllf = problem.nllf() if nllf is None else nllf
+    scale, err = nllf_scale(problem)
+    chisq = format_uncertainty(scale*nllf, err)
+    return chisq
+
 @sio.event
 async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
     options = {} if options is None else options    # session_id: str = app["active_session"]
@@ -244,6 +250,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
             )
         fit_thread.start()
         state.fit_thread = fit_thread
+        await sio.emit("fit_progress", {}) # clear progress
         await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
         await log(json.dumps(to_dict(options), indent=2), title = f"starting fitter {fitter_id}")
 
@@ -259,10 +266,12 @@ async def _fit_progress_handler(event: Dict):
         fitProblem.model_update()
         await publish("", "update_parameters", True)
         if message == 'complete':
-            await publish("", "fit_active", False)
+            await publish("", "fit_active", {})
     elif message == 'convergence_update':
         state.fitting.population = event["pop"]
         await publish("", "convergence_update", True)
+    elif message == 'progress':
+        await sio.emit("fit_progress", to_dict(event))
     elif message == 'uncertainty_update' or message == 'uncertainty_final':
         state.fitting.uncertainty_state = cast(bumps.dream.state.MCMCDraw, event["uncertainty_state"])
         await publish("", "uncertainty_update", True)
@@ -286,6 +295,7 @@ async def _fit_complete_handler(event):
     chisq = nice(2*event["value"]/problem.dof)
     problem.setp(event["point"])
     problem.model_update()
+    await publish("", "fit_active", {})
     await publish("", "update_parameters", True)
     await log(event["info"], title=f"done with chisq {chisq}")
 
@@ -331,12 +341,14 @@ async def get_plot_data(sid: str="", view: str = 'linear'):
     if state.problem is None or state.problem.fitProblem is None:
         return None
     fitProblem = state.problem.fitProblem
-    result = []
+    chisq = get_chisq(fitProblem)
+    plotdata = []
+    result = {"chisq": chisq, "plotdata": plotdata}
     for model in fitProblem.models:
         assert(isinstance(model, Experiment))
         theory = model.reflectivity()
         probe = model.probe
-        result.append(get_probe_data(theory, probe, model._substrate, model._surface))
+        plotdata.append(get_probe_data(theory, probe, model._substrate, model._surface))
         # fresnel_calculator = probe.fresnel(model._substrate, model._surface)
         # Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
         # Q, R = theory

From 8552a3a933a2cc456f27f9f0cf6607817fc9c73a Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 22:18:05 -0500
Subject: [PATCH 169/221] history requires requires two steps?

---
 refl1d/webview/server/fit_thread.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
index feee837a..2d2b381f 100644
--- a/refl1d/webview/server/fit_thread.py
+++ b/refl1d/webview/server/fit_thread.py
@@ -36,7 +36,7 @@ def show_progress(self, history):
         scale, err = nllf_scale(self.problem)
         chisq = format_uncertainty(scale*history.value[0], err)
         evt = dict(
-            problem=self.problem,
+            # problem=self.problem,
             message="progress",
             step=history.step[0],
             value=history.value[0],
@@ -80,7 +80,9 @@ def __init__(self, problem, message="convergence_update", rate=0):
 
 
     def config_history(self, history):
-        history.requires(time=1, population_values=1, value=1)
+        history.requires(population_values=1, value=1)
+        history.requires(time=1)
+        # history.requires(time=1, population_values=1, value=1)
 
     def __call__(self, history):
         # from old ConvergenceMonitor:

From 1061fe3c0fce50d1d21a030a064afb65d69e70f2 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 22:18:22 -0500
Subject: [PATCH 170/221] adding chisq to data plot

---
 refl1d/webview/client/src/App.vue             | 27 ++++++++++++++++++-
 .../client/src/components/DataView.vue        | 17 ++++++++++--
 2 files changed, 41 insertions(+), 3 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 72d57c90..e3d52973 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -46,7 +46,9 @@ const fileBrowserSaveFilename = ref<string>();
 const fileBrowserTitle = ref("Load Model File");
 const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
 const active_layout = ref("left-right");
-const active_panel = ref([0,1]);
+const active_panel = ref([0, 1]);
+const fit_active = ref<{ fitter_id?: string, options?: {} }>({});
+const fit_progress = ref<{ chisq?: string, step?: number, value?: number }>({});
 
 // Create a SocketIO connection, to be passed to child components
 // so that they can do their own communications with the host.
@@ -72,6 +74,14 @@ socket.on('model_loaded', ({message: {pathlist, filename}}) => {
   model_loaded.value = {pathlist, filename};
 })
 
+socket.on('fit_active', ({ message: { fitter_id, options } }) => {
+  fit_active.value = { fitter_id, options };
+});
+
+socket.on('fit_progress', (event) => {
+  fit_progress.value = event;
+});
+
 function disconnect() {
   socket.disconnect();
   connected.value = false;
@@ -238,6 +248,21 @@ onMounted(() => {
               </ul>
             </li> -->
           </ul>
+          <div class="px-4 m-0">
+            <h4 class="m-0">
+              <!-- <div class="rounded p-2 bg-primary">Fitting: </div> -->
+              <div v-if="fit_active.fitter_id !== undefined" class="badge bg-secondary p-2 align-middle">
+                <span class="">Fitting</span>
+                <span class="align-middle px-1">Fitting: {{ fit_active.fitter_id }} step {{ fit_progress?.step }} of
+                  {{ fit_active?.options?.steps }}, chisq={{ fit_progress.chisq }}</span>
+                <button class="btn btn-danger btn-sm" @click="stopFit">Stop</button>
+              </div>
+              <div v-else class="badge bg-secondary p-2">
+                <span class="align-middle px-1">Not fitting</span>
+                <button class="btn btn-success btn-sm" @click="startFit">Start</button>
+              </div>
+            </h4>
+          </div>
           <div class="d-flex">
             <div id="connection_status"
               :class="{'btn': true, 'btn-outline-success': connected, 'btn-outline-danger': !connected}">
diff --git a/refl1d/webview/client/src/components/DataView.vue b/refl1d/webview/client/src/components/DataView.vue
index 9fb91f19..c1be000a 100644
--- a/refl1d/webview/client/src/components/DataView.vue
+++ b/refl1d/webview/client/src/components/DataView.vue
@@ -73,7 +73,7 @@ function generate_new_traces(model_data, view: ReflectivityPlot) {
 async function fetch_and_draw() {
   const payload = await props.socket.asyncEmit('get_plot_data', 'linear');
   // console.log(payload);
-  const { theory_traces, data_traces } = generate_new_traces(payload, reflectivity_type.value)
+  const { theory_traces, data_traces } = generate_new_traces(payload.plotdata, reflectivity_type.value)
   const layout: Partial<Plotly.Layout> = {
     uirevision: reflectivity_type.value,
     xaxis: {
@@ -96,7 +96,20 @@ async function fetch_and_draw() {
       t: 25,
       b: 75,
       pad: 4
-    }
+    },
+    annotations: [
+      {
+        xref: 'paper',
+        yref: 'paper',
+        xanchor: 'left',
+        x: 0.8,
+        yanchor: 'top',
+        y: -0.05,
+        text: `chisq = ${payload.chisq}`,
+        showarrow: false,
+        font: {size: 16}, 
+      }
+    ]
   };
 
   const config = {responsive: true}

From 92af059b2153aa02431618b89af4fc64d33ffd0f Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 22:19:46 -0500
Subject: [PATCH 171/221] adding 'save and start' button to fit options

---
 .../client/src/components/FitOptions.vue      | 21 ++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/refl1d/webview/client/src/components/FitOptions.vue b/refl1d/webview/client/src/components/FitOptions.vue
index a3b18f53..1b694e1a 100644
--- a/refl1d/webview/client/src/components/FitOptions.vue
+++ b/refl1d/webview/client/src/components/FitOptions.vue
@@ -94,14 +94,19 @@ function process_settings() {
   }))
 }
 
-function save() {
-  if (anyIsInvalid.value) {
-    return;
-  }
-  const new_settings = structuredClone(fitter_settings.value);
+function save(start: boolean = false) {
+   if (anyIsInvalid.value) {
+     return;
+   }
+   const new_settings = structuredClone(fitter_settings.value);
   new_settings[fitter_active_local.value] = { settings: process_settings() };
+  const fitter_settings_local = process_settings();
+  new_settings[fitter_active_local.value] = { settings: fitter_settings_local };
   props.socket.emit("publish", "fitter_settings", new_settings);
   props.socket.emit("publish", "fitter_active", fitter_active_local.value);
+  if (start) {
+    props.socket.emit("start_fit_thread", fitter_active_local.value, fitter_settings_local);
+  }
   close();
 }
 
@@ -186,8 +191,10 @@ defineExpose({
         </div>
         <div class="modal-footer">
           <button type="button" class="btn btn-secondary" @click="reset">Reset Defaults</button>
-          <button type="button" class="btn btn-primary" :class="{disabled: anyIsInvalid}" @click="save">Save
-            Changes</button>
+          <button type="button" class="btn btn-success" :class="{disabled: anyIsInvalid}" @click="save(true)">Save and Start</button>
+          <button type="button" class="btn btn-primary" :class="{disabled: anyIsInvalid}" @click="save(false)">
+            Save Changes</button>
+
         </div>
       </div>
     </div>

From 0a6ed36cdb2e560be37ac2c07c97dc959785987f Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Mon, 13 Feb 2023 22:22:24 -0500
Subject: [PATCH 172/221] get rid of extraneous 'Fitting'

---
 refl1d/webview/client/src/App.vue | 1 -
 1 file changed, 1 deletion(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index e3d52973..49ea5e66 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -252,7 +252,6 @@ onMounted(() => {
             <h4 class="m-0">
               <!-- <div class="rounded p-2 bg-primary">Fitting: </div> -->
               <div v-if="fit_active.fitter_id !== undefined" class="badge bg-secondary p-2 align-middle">
-                <span class="">Fitting</span>
                 <span class="align-middle px-1">Fitting: {{ fit_active.fitter_id }} step {{ fit_progress?.step }} of
                   {{ fit_active?.options?.steps }}, chisq={{ fit_progress.chisq }}</span>
                 <button class="btn btn-danger btn-sm" @click="stopFit">Stop</button>

From 7336102bf9834a626fe73b5abb4c451575296b31 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 14 Feb 2023 13:42:14 -0500
Subject: [PATCH 173/221] add help text to DREAM options for calculating steps
 from samples

---
 refl1d/webview/client/src/components/FitOptions.vue | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/refl1d/webview/client/src/components/FitOptions.vue b/refl1d/webview/client/src/components/FitOptions.vue
index 1b694e1a..cc9baedd 100644
--- a/refl1d/webview/client/src/components/FitOptions.vue
+++ b/refl1d/webview/client/src/components/FitOptions.vue
@@ -35,6 +35,10 @@ const FIT_FIELDS = {
   'outliers': ['Outliers', ["none", "iqr", "grubbs", "mahal"]]
 }
 
+const OPTIONS_HELP = {
+  'dream': 'if Steps == 0, Steps will be calculated as (Burn-in steps) + (Samples / (Population * Num. Fitted Params))'
+}
+
 // make another working copy for editing:
 // const active_settings = ref<{ name: string, settings: object}>({name: "", settings: {}});
 const active_settings = ref({});
@@ -174,6 +178,9 @@ defineExpose({
               </div>
             </div>
             <div class="row p-2">
+              <div class="row p-1 text-secondary" v-if="fitter_active_local in OPTIONS_HELP">
+                <span><em>{{ OPTIONS_HELP[fitter_active_local] }}</em></span>
+              </div>
               <div class="row p-1" v-for="(value, sname, index) in active_settings" :key="sname">
                 <label class="col-sm-4 col-form-label" :for="'setting_' + index">{{FIT_FIELDS[sname][0]}}</label>
                 <div class="col-sm-8">

From 87e70e9066d520db122c847f6181df0a0ad7401b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 14 Feb 2023 13:42:59 -0500
Subject: [PATCH 174/221] add method to calculate dream steps

---
 refl1d/webview/server/webserver.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index a959cbc2..2b51e2d9 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -214,6 +214,20 @@ def get_chisq(problem: refl1d.fitproblem.FitProblem, nllf=None):
     chisq = format_uncertainty(scale*nllf, err)
     return chisq
 
+def get_num_steps(fitter_id: str, num_fitparams: int, options: Optional[Dict] = None):
+    options = FITTER_DEFAULTS[fitter_id] if options is None else options
+    steps = options['steps']
+    if fitter_id == 'dream' and steps == 0:
+        print('dream: ', options)
+        total_pop = options['pop'] * num_fitparams
+        print('total_pop: ', total_pop)
+        sample_steps = int(options['samples'] / total_pop)
+        print('sample_steps: ', sample_steps)
+        print('steps: ', options['burn'] + sample_steps)
+        return options['burn'] + sample_steps
+    else:
+        return steps
+
 @sio.event
 async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
     options = {} if options is None else options    # session_id: str = app["active_session"]
@@ -230,13 +244,15 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
             return
         
         # TODO: better access to model parameters
-        if len(fitProblem.getp()) == 0:
+        num_params = len(fitProblem.getp())
+        if num_params == 0:
             raise ValueError("Problem has no fittable parameters")
 
         # Start a new thread worker and give fit problem to the worker.
         # Clear abort and uncertainty state
         # state.abort = False
         # state.fitting.uncertainty_state = None
+        num_steps = get_num_steps(fitter_id, num_params, options)
         state.abort_queue = abort_queue = Queue()
         fit_thread = FitThread(
             abort_queue=abort_queue,
@@ -251,7 +267,7 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
         fit_thread.start()
         state.fit_thread = fit_thread
         await sio.emit("fit_progress", {}) # clear progress
-        await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options)))
+        await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options, num_steps=num_steps)))
         await log(json.dumps(to_dict(options), indent=2), title = f"starting fitter {fitter_id}")
 
 async def _fit_progress_handler(event: Dict):

From f530e44cefcbd7c444c56317717e44feb6e93052 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 14 Feb 2023 13:43:19 -0500
Subject: [PATCH 175/221] add progress bar to fit status

---
 refl1d/webview/client/src/App.vue | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 49ea5e66..654d59fc 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -47,7 +47,7 @@ const fileBrowserTitle = ref("Load Model File");
 const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
 const active_layout = ref("left-right");
 const active_panel = ref([0, 1]);
-const fit_active = ref<{ fitter_id?: string, options?: {} }>({});
+const fit_active = ref<{ fitter_id?: string, options?: {}, num_steps?: number }>({});
 const fit_progress = ref<{ chisq?: string, step?: number, value?: number }>({});
 
 // Create a SocketIO connection, to be passed to child components
@@ -74,8 +74,8 @@ socket.on('model_loaded', ({message: {pathlist, filename}}) => {
   model_loaded.value = {pathlist, filename};
 })
 
-socket.on('fit_active', ({ message: { fitter_id, options } }) => {
-  fit_active.value = { fitter_id, options };
+socket.on('fit_active', ({ message: { fitter_id, options, num_steps } }) => {
+  fit_active.value = { fitter_id, options, num_steps };
 });
 
 socket.on('fit_progress', (event) => {
@@ -248,17 +248,25 @@ onMounted(() => {
               </ul>
             </li> -->
           </ul>
-          <div class="px-4 m-0">
+          <div class="flex-grow-1 px-4 m-0">
             <h4 class="m-0">
               <!-- <div class="rounded p-2 bg-primary">Fitting: </div> -->
               <div v-if="fit_active.fitter_id !== undefined" class="badge bg-secondary p-2 align-middle">
-                <span class="align-middle px-1">Fitting: {{ fit_active.fitter_id }} step {{ fit_progress?.step }} of
-                  {{ fit_active?.options?.steps }}, chisq={{ fit_progress.chisq }}</span>
+                <div class="align-middle pt-2 pb-1 px-1 d-inline-block">
+                  <span>Fitting: {{ fit_active.fitter_id }} step {{ fit_progress?.step }} of
+                  {{ fit_active?.num_steps }}, chisq={{ fit_progress.chisq }}</span>
+                  <div class="progress mt-1" style="height:3px;">
+                    <div class="progress-bar" role="progressbar" :aria-valuenow="fit_progress?.step" 
+                      aria-valuemin="0" :aria-valuemax="fit_active?.num_steps ?? 100" :style="{width: ((fit_progress.step ?? 0) * 100 / (fit_active.num_steps ?? 1)).toFixed(1) + '%'}"></div>
+                  </div>
+                </div>
                 <button class="btn btn-danger btn-sm" @click="stopFit">Stop</button>
               </div>
-              <div v-else class="badge bg-secondary p-2">
-                <span class="align-middle px-1">Not fitting</span>
-                <button class="btn btn-success btn-sm" @click="startFit">Start</button>
+              <div v-else class="badge bg-secondary p-1">
+                <div class="align-middle p-2 d-inline-block">
+                  <span>Not fitting</span>
+                </div>
+                <button class="btn btn-success btn-sm" @click="startFit">Start {{ fitOptions?.fitter_active ?? "" }}</button>
               </div>
             </h4>
           </div>

From b0aa3318a3aa94deba139cbfc7252afa07a672ac Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 15 Feb 2023 12:48:33 -0500
Subject: [PATCH 176/221] move fitting options to labeled button with gear icon

---
 refl1d/webview/client/src/App.vue                 | 15 +++++++++++----
 .../webview/client/src/components/FitOptions.vue  |  6 ++++--
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 654d59fc..1e177406 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -209,7 +209,7 @@ onMounted(() => {
                 <li><button class="btn btn-link dropdown-item" @click="quit">Quit</button></li>
               </ul>
             </li>
-            <li class="nav-item dropdown">
+            <!-- <li class="nav-item dropdown">
               <button class="btn btn-link nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
                 Fitting
@@ -222,7 +222,7 @@ onMounted(() => {
                 </li>
                 <li><button class="btn btn-link dropdown-item"  @click="openFitOptions">Options...</button></li>
               </ul>
-            </li>
+            </li> -->
             <li class="nav-item dropdown">
               <button class="btn btn-link nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
                 aria-expanded="false">
@@ -264,9 +264,16 @@ onMounted(() => {
               </div>
               <div v-else class="badge bg-secondary p-1">
                 <div class="align-middle p-2 d-inline-block">
-                  <span>Not fitting</span>
+                  <span>Fitting: </span>
                 </div>
-                <button class="btn btn-success btn-sm" @click="startFit">Start {{ fitOptions?.fitter_active ?? "" }}</button>
+                <button class="btn btn-light btn-sm me-2" @click="openFitOptions">
+                  {{ fitOptions?.fitter_active ?? "" }}
+                  <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-gear" viewBox="0 0 16 16">
+                    <path d="M8 4.754a3.246 3.246 0 1 0 0 6.492 3.246 3.246 0 0 0 0-6.492zM5.754 8a2.246 2.246 0 1 1 4.492 0 2.246 2.246 0 0 1-4.492 0z"/>
+                    <path d="M9.796 1.343c-.527-1.79-3.065-1.79-3.592 0l-.094.319a.873.873 0 0 1-1.255.52l-.292-.16c-1.64-.892-3.433.902-2.54 2.541l.159.292a.873.873 0 0 1-.52 1.255l-.319.094c-1.79.527-1.79 3.065 0 3.592l.319.094a.873.873 0 0 1 .52 1.255l-.16.292c-.892 1.64.901 3.434 2.541 2.54l.292-.159a.873.873 0 0 1 1.255.52l.094.319c.527 1.79 3.065 1.79 3.592 0l.094-.319a.873.873 0 0 1 1.255-.52l.292.16c1.64.893 3.434-.902 2.54-2.541l-.159-.292a.873.873 0 0 1 .52-1.255l.319-.094c1.79-.527 1.79-3.065 0-3.592l-.319-.094a.873.873 0 0 1-.52-1.255l.16-.292c.893-1.64-.902-3.433-2.541-2.54l-.292.159a.873.873 0 0 1-1.255-.52l-.094-.319zm-2.633.283c.246-.835 1.428-.835 1.674 0l.094.319a1.873 1.873 0 0 0 2.693 1.115l.291-.16c.764-.415 1.6.42 1.184 1.185l-.159.292a1.873 1.873 0 0 0 1.116 2.692l.318.094c.835.246.835 1.428 0 1.674l-.319.094a1.873 1.873 0 0 0-1.115 2.693l.16.291c.415.764-.42 1.6-1.185 1.184l-.291-.159a1.873 1.873 0 0 0-2.693 1.116l-.094.318c-.246.835-1.428.835-1.674 0l-.094-.319a1.873 1.873 0 0 0-2.692-1.115l-.292.16c-.764.415-1.6-.42-1.184-1.185l.159-.291A1.873 1.873 0 0 0 1.945 8.93l-.319-.094c-.835-.246-.835-1.428 0-1.674l.319-.094A1.873 1.873 0 0 0 3.06 4.377l-.16-.292c-.415-.764.42-1.6 1.185-1.184l.292.159a1.873 1.873 0 0 0 2.692-1.115l.094-.319z"/>
+                  </svg>
+                </button>
+                <button class="btn btn-success btn-sm" @click="startFit">Start</button>
               </div>
             </h4>
           </div>
diff --git a/refl1d/webview/client/src/components/FitOptions.vue b/refl1d/webview/client/src/components/FitOptions.vue
index cc9baedd..aefed075 100644
--- a/refl1d/webview/client/src/components/FitOptions.vue
+++ b/refl1d/webview/client/src/components/FitOptions.vue
@@ -36,7 +36,7 @@ const FIT_FIELDS = {
 }
 
 const OPTIONS_HELP = {
-  'dream': 'if Steps == 0, Steps will be calculated as (Burn-in steps) + (Samples / (Population * Num. Fitted Params))'
+  'dream': 'if Steps=0, Steps will be calculated as (Burn-in steps) + (Samples / (Population * Num. Fit Params))'
 }
 
 // make another working copy for editing:
@@ -149,7 +149,7 @@ defineExpose({
 <template>
   <div ref="dialog" class="modal fade" id="fitOptionsModal" tabindex="-1" aria-labelledby="fitOptionsLabel"
     :aria-hidden="isOpen">
-    <div class="modal-dialog">
+    <div class="modal-dialog modal-lg">
       <div class="modal-content">
         <div class="modal-header">
           <h5 class="modal-title" id="fitOptionsLabel">Fit Options</h5>
@@ -164,6 +164,7 @@ defineExpose({
                     :id="fname" :value="fname" @change="changeActiveFitter">
                   <label class="form-check-label" :for="fname">
                     {{fitter_defaults[fname].name}}
+                    <span v-if="fname !== 'scipy.leastsq'">({{ fname }})</span>
                   </label>
                 </div>
               </div>
@@ -173,6 +174,7 @@ defineExpose({
                     :id="fname" :value="fname" @change="changeActiveFitter">
                   <label class="form-check-label" :for="fname">
                     {{fitter_defaults[fname].name}}
+                    <span v-if="fname !== 'scipy.leastsq'">({{ fname }})</span>
                   </label>
                 </div>
               </div>

From d8e7df172a1af9bec90749bfe0b5a4309b9a9597 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Sun, 26 Feb 2023 07:37:39 -0500
Subject: [PATCH 177/221] make_probe should use new dQo init parameter for
 Probe

---
 refl1d/probe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/probe.py b/refl1d/probe.py
index 645fd0b9..a293f0f2 100644
--- a/refl1d/probe.py
+++ b/refl1d/probe.py
@@ -1573,7 +1573,7 @@ def fetch_key(key, override):
             T=data_T, dT=data_dT,
             L=data_L, dL=data_dL,
             data=(data_R, data_dR),
-            dQ=data_dQ,
+            dQo=data_dQ,
             **probe_args)
     else:
         # QProbe doesn't accept theta_offset or sample_broadening

From 302c1dd91fb220fc1c1c8694f3ccb2f1f9bd1a0c Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 27 Feb 2023 15:13:32 -0500
Subject: [PATCH 178/221] fix breakpoint so navbar doesn't collapse to burger
 menu too early, and remove old profile panel

---
 refl1d/webview/client/src/App.vue | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index 1e177406..d623ae42 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -10,7 +10,7 @@ import PanelTabContainer from './components/PanelTabContainer.vue';
 import FileBrowser from './components/FileBrowser.vue';
 import SummaryView from './components/SummaryView.vue';
 import ModelInspect from './components/ModelInspect.vue';
-import ModelViewPlotly from './components/ModelViewPlotly.vue';
+// import ModelViewPlotly from './components/ModelViewPlotly.vue';
 import ParameterView from './components/ParameterView.vue';
 import LogView from './components/LogView.vue';
 import ConvergenceView from './components/ConvergenceView.vue';
@@ -28,7 +28,7 @@ const panels = [
   {title: 'Convergence', component: ConvergenceView},
   {title: 'Profile', component: ModelView},
   {title: 'Model', component: ModelInspect},
-  {title: 'Profile2', component: ModelViewPlotly},
+  // {title: 'Profile2', component: ModelViewPlotly},
   {title: 'Parameters', component: ParameterView},
   {title: 'Correlations', component: CorrelationView},
   {title: 'Trace', component: ParameterTraceView},
@@ -169,7 +169,7 @@ onMounted(() => {
 
 <template>
   <div class="h-100 w-100 m-0 d-flex flex-column">
-    <nav class="navbar navbar-expand-lg navbar-dark bg-dark">
+    <nav class="navbar navbar-expand-sm navbar-dark bg-dark">
       <div class="container-fluid">
         <div class="navbar-brand">
           <img src="./assets/refl1d-icon_256x256x32.png" alt="" height="24" class="d-inline-block align-text-middle">

From 59f5ae38b30d8196d9d5eccd6dc05e6faf3b4073 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 27 Feb 2023 16:51:23 -0500
Subject: [PATCH 179/221] add requirements file for running webview server

---
 webview-requirements | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 webview-requirements

diff --git a/webview-requirements b/webview-requirements
new file mode 100644
index 00000000..f9ce2a9a
--- /dev/null
+++ b/webview-requirements
@@ -0,0 +1,7 @@
+aiohttp
+blinker
+python-socketio
+plotly
+mpld3
+matplotlib
+nodejs

From c4e86b722641790d3f247775b00be44eb4f160ac Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:45:52 -0500
Subject: [PATCH 180/221] allow opening store file in read_only mode

---
 refl1d/webview/server/state_hdf5_backed.py | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/server/state_hdf5_backed.py b/refl1d/webview/server/state_hdf5_backed.py
index 71f2845d..d17ee56a 100644
--- a/refl1d/webview/server/state_hdf5_backed.py
+++ b/refl1d/webview/server/state_hdf5_backed.py
@@ -225,20 +225,27 @@ class State:
     fit_thread: Optional['FitThread'] = None
     abort_queue: Queue
 
-    def __init__(self, session_file_name: str = SESSION_FILE_NAME, in_memory: bool = False, backing_store: bool = False ):
+    def __init__(self, session_file_name: str = SESSION_FILE_NAME, in_memory: bool = False, backing_store: bool = False, read_only: bool = False ):
         # self.problem = problem
         # self.fitting = fitting if fitting is not None else FittingState()
         self.abort_queue = Queue()
         import h5py
-        hdf_kw = dict(driver="core", backing_store=backing_store) if in_memory else dict()
-        self.session_file = session_file = h5py.File(session_file_name, "a", libver='latest', **hdf_kw)
+        hdf_kw = dict(libver="latest")
+        if in_memory:
+            hdf_kw.update(dict(driver="core", backing_store=backing_store))
+        if read_only:
+            hdf_kw["swmr"] = True
+        mode = "r" if read_only else "a"
+        self.session_file = session_file = h5py.File(session_file_name, mode, **hdf_kw)
         topics_group = session_file.require_group("topics")
         problem_group = session_file.require_group("problem")
         fitting_group = session_file.require_group("fitting")
         self.topics = TopicsDict(topics_group)
         self.problem = ProblemState(problem_group)
         self.fitting = FittingState(fitting_group)
-        session_file.swmr_mode = True
+        if not read_only:
+            session_file.swmr_mode = True
+
 
     async def cleanup(self):
         self.session_file.close()
@@ -251,9 +258,11 @@ def write_uncertainty_state(state: 'MCMCDraw', group: 'Group', compression=COMPR
 
         to_save["thin_draws"], to_save["thin_point"], to_save["thin_logp"] = state.chains()
         to_save["update_draws"], to_save["update_CR_weight"] = state.CR_weight()
+        to_save["labels"] = np.array(state.labels, dtype=h5py.string_dtype())
 
         #TODO: missing _outliers from save_state
         for field_name, data in to_save.items():
+            print(field_name, field_name in group)
             if field_name in group:
                 dataset = cast(h5py.Dataset, group[field_name])
                 if dataset.shape != data.shape:

From 32a06c017c5db8d6378e9869761ef9367c98434b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:46:58 -0500
Subject: [PATCH 181/221] fix retrieving last message from fitter_active topic

---
 refl1d/webview/server/webserver.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index a56b24f8..0fd5bef3 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -819,7 +819,9 @@ def main():
 
     fitter_id = args.fit
     if fitter_id is None:
-        fitter_id = state.topics.get("fitter_active", [{"message": None}])[-1]["message"]
+        fitter_active_topic = state.topics["fitter_active"]
+        if len(fitter_active_topic) > 0:
+            fitter_id = fitter_active_topic[-1]["message"]
     if fitter_id is None:
         fitter_id = 'amoeba'
     fitter_settings = FITTER_DEFAULTS[fitter_id]

From 79aa34a7209ea85dec3355c919f6cb2095c3d41e Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:50:31 -0500
Subject: [PATCH 182/221] cleanup docs, one less TODO

---
 refl1d/webview/server/fit_thread.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
index 2d2b381f..61109b9d 100644
--- a/refl1d/webview/server/fit_thread.py
+++ b/refl1d/webview/server/fit_thread.py
@@ -121,12 +121,6 @@ def final(self):
 # (1) We are grabbing uncertainty_state from the history on monitor update
 # and holding onto it for the monitor final call. Need to restructure the
 # history/monitor interaction so that object lifetimes are better controlled.
-# (2) We set the uncertainty state directly in the GUI window. This is an
-# attempt to work around a memory leak which causes problems in the GUI when
-# it is updated too frequently. If the problem is that the event structure
-# is too large and wx isn't cleaning up properly then this should address it,
-# but if the problem lies within the DREAM plot functions or within matplotlib
-# then this change won't do anything and should be reverted.
 
 
 class DreamMonitor(monitor.Monitor):

From 910c378092952d73209898f7454fc4fa59128c7d Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:51:13 -0500
Subject: [PATCH 183/221] adding client panel for new plotly correlations view

---
 .../src/components/CorrelationViewPlotly.vue  | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 refl1d/webview/client/src/components/CorrelationViewPlotly.vue

diff --git a/refl1d/webview/client/src/components/CorrelationViewPlotly.vue b/refl1d/webview/client/src/components/CorrelationViewPlotly.vue
new file mode 100644
index 00000000..4d249aee
--- /dev/null
+++ b/refl1d/webview/client/src/components/CorrelationViewPlotly.vue
@@ -0,0 +1,51 @@
+<script setup lang="ts">
+/// <reference types="@types/uuid"/>
+import { ref } from 'vue';
+import { Socket } from 'socket.io-client';
+import { v4 as uuidv4 } from 'uuid';
+import { setupDrawLoop } from '../setupDrawLoop';
+import { cache } from '../plotcache';
+import * as Plotly from 'plotly.js/lib/core';
+import Heatmap from 'plotly.js/lib/heatmap';
+
+Plotly.register([
+  Heatmap,
+])
+
+const title = "Correlations";
+const plot_div = ref<HTMLDivElement>();
+const plot_div_id = ref(`div-${uuidv4()}`);
+
+const props = defineProps<{
+  socket: Socket,
+}>();
+
+setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
+
+
+async function fetch_and_draw(latest_timestamp: string) {
+  let { timestamp, plotdata } = cache[title] ?? {};
+  if (timestamp !== latest_timestamp) {
+    const payload = await props.socket.asyncEmit('get_correlation_plot');
+    plotdata = { ...payload };
+    cache[title] = {timestamp: latest_timestamp, plotdata};
+  }
+  const { data, layout } = plotdata;
+  const config = { responsive: true, scrollZoom: true }
+  await Plotly.react(plot_div_id.value, [...data], layout, config);
+}
+
+</script>
+
+<template>
+  <div class="container d-flex flex-grow-1 flex-column">
+    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
+    </div>
+  </div>
+</template>
+
+<style scoped>
+svg {
+  width: 100%;
+}
+</style>
\ No newline at end of file

From a6a75ae2352c1b075b7ddd1986fb0c2610a416ec Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:51:44 -0500
Subject: [PATCH 184/221] use new plotly correlation panel

---
 refl1d/webview/client/src/App.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index d623ae42..c125ec91 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -14,7 +14,8 @@ import ModelInspect from './components/ModelInspect.vue';
 import ParameterView from './components/ParameterView.vue';
 import LogView from './components/LogView.vue';
 import ConvergenceView from './components/ConvergenceView.vue';
-import CorrelationView from './components/CorrelationView.vue';
+// import CorrelationView from './components/CorrelationView.vue';
+import CorrelationView from './components/CorrelationViewPlotly.vue';
 import ParameterTraceView from './components/ParameterTraceView.vue';
 import ModelUncertaintyView from './components/ModelUncertaintyView.vue';
 import UncertaintyView from './components/UncertaintyView.vue';

From 63bd80ceac2ba946055e4f26a40472440e0366ba Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:51:59 -0500
Subject: [PATCH 185/221] new plotly correlation plotter (python)

---
 refl1d/webview/server/corrplot.py | 161 ++++++++++++++++++++++++++++++
 1 file changed, 161 insertions(+)
 create mode 100644 refl1d/webview/server/corrplot.py

diff --git a/refl1d/webview/server/corrplot.py b/refl1d/webview/server/corrplot.py
new file mode 100644
index 00000000..75c0730a
--- /dev/null
+++ b/refl1d/webview/server/corrplot.py
@@ -0,0 +1,161 @@
+# This program is public domain
+# Authors Paul Kienzle, Brian Maranville
+"""
+2-D correlation histograms
+
+Generate 2-D correlation histograms and display them in a figure.
+
+Uses false color plots of density.
+"""
+__all__ = ['Corr2d']
+
+import numpy as np
+from numpy import inf
+
+import plotly.graph_objects as go
+from plotly.subplots import make_subplots
+
+class Corr2d(object):
+    """
+    Generate and manage 2D correlation histograms.
+    """
+    def __init__(self, data, labels=None, **kw):
+        if labels is None:
+            labels = ["P"+str(i+1) for i, _ in enumerate(data)]
+        self.N = len(data)
+        self.labels = labels
+        self.data = data
+        self.hists = _hists(data, **kw)
+        self.fig = None
+        #for k, v in self.hists.items():
+        #    print k, (v[1][0], v[1][-1]), (v[2][0], v[2][-1])
+
+    def R(self):
+        return np.corrcoef(self.data)
+
+    def __getitem__(self, i, j):
+        """
+        Retrieve correlation histogram for data[i] X data[j].
+
+        Returns bin i edges, bin j edges, and histogram
+        """
+        return self.hists[i, j]
+
+    def plot(self, title=None):
+        """
+        Plot the correlation histograms on the specified figure
+        """
+
+        fig = make_subplots(
+            rows=self.N-1,
+            cols=self.N-1,
+            horizontal_spacing=0,
+            vertical_spacing=0,
+            shared_yaxes=True,
+            shared_xaxes=True
+        )
+
+        # if title is not None:
+        #     fig.text(0.5, 0.95, title,
+        #              horizontalalignment='center',
+        #              fontproperties=FontProperties(size=16))
+        return _plot(fig, self.hists, self.labels, self.N)
+
+
+def _hists(data, ranges=None, **kw):
+    """
+    Generate pair-wise correlation histograms
+    """
+    n = len(data)
+    if ranges is None:
+        low, high = np.min(data, axis=1), np.max(data, axis=1)
+        ranges = [(l, h) for l, h in zip(low, high)]
+    return dict(((i, j), np.histogram2d(data[i], data[j],
+                                        range=[ranges[i], ranges[j]], **kw))
+                for i in range(0, n)
+                for j in range(i+1, n))
+
+
+def _plot(fig, hists, labels, n, show_ticks=None):
+    """
+    Plot pair-wise correlation histograms
+    """
+    # if n <= 1:
+    #     fig.text(0.5, 0.5, "No correlation plots when only one variable",
+    #              ha="center", va="center")
+    #     return
+    
+    vmin, vmax = float('inf'), float('-inf')
+    for data, _, _ in hists.values():
+        positive = data[data > 0]
+        if len(positive) > 0:
+            vmin = min(vmin, np.amin(positive))
+            vmax = max(vmax, np.amax(positive))
+    
+    fig = make_subplots(rows=n-1, cols=n-1, horizontal_spacing=0, vertical_spacing=0, shared_yaxes=True, shared_xaxes=True)
+    COLORSCALE = ["white", "yellow", "green", "blue", "red"]
+
+    for i in range(0, n-1):
+        fig.add_annotation(
+            xref="x domain",
+            yref="y domain",
+            xanchor="right",
+            x=-0.1,
+            y=0.1,
+            showarrow=False,
+            col=i+1,
+            row=n-i-1,
+            text=labels[i],
+            textangle=-90
+        )
+        for j in range(i+1, n):
+            data, x, y = hists[(i, j)]
+            data = np.clip(data, vmin, vmax)
+            trace = go.Heatmap(z=np.log10(data), coloraxis='coloraxis', hoverinfo='skip')
+            fig.add_traces([trace], rows=n-i-1, cols=j)
+    
+    log_cbar = dict(
+        tickvals=np.arange(int(np.log10(vmax)) + 1),
+        ticktext=10 ** np.arange(int(np.log10(vmax)) + 1),
+    )
+    fig.update_layout(coloraxis={'colorscale': COLORSCALE, "cmin": np.log10(vmin), "cmax": np.log10(vmax), 'colorbar': log_cbar})
+    fig.update_layout(plot_bgcolor='rgba(0, 0, 0, 0)')
+    # fig.update_layout(height=600, width=800)
+    fig.update_xaxes(visible=False)
+    fig.update_yaxes(visible=False)
+    return fig
+
+### NOT USED AT THE MOMENT: all below
+###
+def zoom(event, step):
+    ax = event.inaxes
+    if not hasattr(ax, 'zoomable'):
+        return
+
+    # TODO: test logscale
+    step *= 3
+
+    if ax.zoomable is not True and 'mapper' in ax.zoomable:
+        mapper = ax.zoomable['mapper']
+        if event.ydata is not None:
+            lo, hi = mapper.get_clim()
+            pt = event.ydata*(hi-lo)+lo
+            lo, hi = _rescale(lo, hi, pt, step)
+            mapper.set_clim((lo, hi))
+    if ax.zoomable is True and event.xdata is not None:
+        lo, hi = ax.get_xlim()
+        lo, hi = _rescale(lo, hi, event.xdata, step)
+        ax.set_xlim((lo, hi))
+    if ax.zoomable is True and event.ydata is not None:
+        lo, hi = ax.get_ylim()
+        lo, hi = _rescale(lo, hi, event.ydata, step)
+        ax.set_ylim((lo, hi))
+    ax.figure.canvas.draw_idle()
+
+
+def _rescale(lo, hi, pt, step):
+    scale = float(hi-lo)*step/(100 if step > 0 else 100-step)
+    bal = float(pt-lo)/(hi-lo)
+    new_lo = lo - bal*scale
+    new_hi = hi + (1-bal)*scale
+    return new_lo, new_hi

From c479f52656e2037037823fb5523f946311fa08db Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Thu, 2 Mar 2023 14:52:18 -0500
Subject: [PATCH 186/221] use new plotly correlation plotter

---
 refl1d/webview/server/webserver.py | 24 +++++++++---------------
 1 file changed, 9 insertions(+), 15 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 2b51e2d9..7c7b0560 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -497,28 +497,22 @@ async def get_convergence_plot(sid: str=""):
 
 @sio.event
 @rest_get
-async def get_correlation_plot(sid: str = ""):
+async def get_correlation_plot(sid: str = "", nbins: int=50):
+    from .corrplot import Corr2d
     uncertainty_state = state.fitting.uncertainty_state
-    if uncertainty_state is not None:
-        import mpld3
-        import matplotlib
-        matplotlib.use("agg")
-        import matplotlib.pyplot as plt
+
+    if isinstance(uncertainty_state, bumps.dream.state.MCMCDraw):
         import time
         start_time = time.time()
         print('queueing new correlation plot...', start_time)
-
-        fig = plt.figure()
-        axes = fig.add_subplot(111)
-        bumps.dream.views.plot_corrmatrix(uncertainty_state.draw(), fig=fig)
+        draw = uncertainty_state.draw()
+        c = Corr2d(draw.points.T, bins=nbins, labels=draw.labels)
+        fig = c.plot()
         print("time to render but not serialize...", time.time() - start_time)
-        fig.canvas.draw()
-        dfig = mpld3.fig_to_dict(fig)
-        plt.close(fig)
-        # await sio.emit("profile_plot", dfig, to=sid)
+        serialized = to_dict(fig.to_dict())
         end_time = time.time()
         print("time to draw correlation plot:", end_time - start_time)
-        return dfig
+        return serialized
     else:
         return None
 

From de523fcd83f2353469efe7a13ccc73af5f833360 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 6 Mar 2023 13:06:05 -0500
Subject: [PATCH 187/221] use vite plugin to generate VERSION file

---
 refl1d/webview/client/package.json   |  7 ++++---
 refl1d/webview/client/vite.config.js | 10 +++++++++-
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index 6966175a..b3dcb116 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -3,8 +3,8 @@
   "version": "0.0.1",
   "scripts": {
     "dev": "vite",
-    "build": "vite build --emptyOutDir -m development && node -p process.env.npm_package_version > dist/VERSION",
-    "build_prod": "vite build --emptyOutDir -m production && node -p process.env.npm_package_version > dist/VERSION",
+    "build": "vite build --emptyOutDir -m development",
+    "build_prod": "vite build --emptyOutDir -m production",
     "preview": "vite preview --port 4173"
   },
   "dependencies": {
@@ -21,6 +21,7 @@
     "@types/plotly.js": "^2.12.5",
     "@types/uuid": "^8.3.4",
     "@vitejs/plugin-vue": "^3.0.3",
-    "vite": "^3.2.5"
+    "vite": "^3.2.5",
+    "vite-plugin-generate-file": "^0.0.4"
   }
 }
diff --git a/refl1d/webview/client/vite.config.js b/refl1d/webview/client/vite.config.js
index c86d400c..b8c0dcef 100644
--- a/refl1d/webview/client/vite.config.js
+++ b/refl1d/webview/client/vite.config.js
@@ -2,11 +2,19 @@ import { fileURLToPath, URL } from 'node:url'
 
 import { defineConfig } from 'vite'
 import vue from '@vitejs/plugin-vue'
+import generateFile from 'vite-plugin-generate-file'
 
 // https://vitejs.dev/config/
 export default ({mode}) => {
   return defineConfig({
-    plugins: [vue()],
+    plugins: [
+      vue(),
+      generateFile([{
+        type: 'yaml',
+        output: 'VERSION',
+        data: process.env.npm_package_version.toString(),
+      }])
+    ],
     base: '',
     resolve: {
       alias: {

From a1d7331daaca9cfcaf831dacf650b671d377fc2b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 6 Mar 2023 13:06:33 -0500
Subject: [PATCH 188/221] allow override of backend server URL in client url
 search params

---
 refl1d/webview/client/src/App.vue | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
index c125ec91..5f8c76be 100644
--- a/refl1d/webview/client/src/App.vue
+++ b/refl1d/webview/client/src/App.vue
@@ -53,11 +53,15 @@ const fit_progress = ref<{ chisq?: string, step?: number, value?: number }>({});
 
 // Create a SocketIO connection, to be passed to child components
 // so that they can do their own communications with the host.
-const base_path = window.location.pathname;
+const queryString = window.location.search;
+const urlParams = new URLSearchParams(queryString);
 
-const socket = io('', {
-   // this is mostly here to test what happens on server fail:
-   path: `${base_path}socket.io`,
+const sio_base_path = urlParams.get('base_path') ?? window.location.pathname;
+const sio_server = urlParams.get('server') ?? '';
+
+const socket = io(sio_server, {
+    // this is mostly here to test what happens on server fail:
+   path: `${sio_base_path}socket.io`,
    reconnectionAttempts: 10
 });
 

From 5ff1421da5ec1ca33d9ab0b56737e3a443fd44a4 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 6 Mar 2023 13:08:21 -0500
Subject: [PATCH 189/221] version bump on webview client

---
 refl1d/webview/client/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index b3dcb116..230574f2 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -1,6 +1,6 @@
 {
   "name": "refl1d-webview-client",
-  "version": "0.0.1",
+  "version": "0.0.2",
   "scripts": {
     "dev": "vite",
     "build": "vite build --emptyOutDir -m development",

From 0e3f7f2a52caf7c114c57f5f0c6a24f2f8218b9b Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 6 Mar 2023 13:22:40 -0500
Subject: [PATCH 190/221] include inline 48x48 icon for refl1d in template

---
 refl1d/webview/client/index_template.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/index_template.txt b/refl1d/webview/client/index_template.txt
index 3f054cda..2e1710e1 100644
--- a/refl1d/webview/client/index_template.txt
+++ b/refl1d/webview/client/index_template.txt
@@ -2,7 +2,7 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
-    <link rel="icon" href="{cdn}/assets/refl1d-icon_48x48x32.png" />
+    <link rel="icon" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAADAAAAAwCAYAAABXAvmHAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAOwwAADsMBx2+oZAAADxBJREFUaN7NmluMXld5hp9vrX3455SxHceHEMdghSRKIOFUylEtJUAF4qL0hihtEVVbLrijVdWLthdtBZUoaitExRVthVS1Qq2oRKEhhwIhlAYoOD5ijw/j2B7H9pzn//dhrfV9vdj790wSoDgkwJaWNDP6Z+33fb/3/dbaa/+en+El4hyAExABQwQRuZ45/M8MvPOZmaZtu17ysjse+Pjnp/ff8+5q/n8fj6EdIuIA+7klIM5npinuue3e19/1oc88sjy57+64fe/ds3v3vnPt2OPfUNV1IP44JH7qBMbgZ/e/8s0v/8CnH7zauBur5dOxHi6kZnb73lLa/aOn5p5A3AZY/LkiMAa/68CrXn/gA5/60tUqzDbDhRR0I4u25uuwrLb3JbfnF0+vtOurRxEZAfrDJxT5qREYg7/lnre9+9b7//oLK3V7Qzta0Dat+xDXSFajNrImDzKxbXpfc+zoQRO5BNQ/BLwDfjoExGW5aYp7X/2u991y/yc+f3VtJW9Gly3EdRfSGokhyWqiVNJqrbpt2/bJ5ZXYLF49iMgqkJ6F3WOmk7M37nnRCXTgY7jpnvvev+d9f/HPS6uLEuorFtKqC7pKYkSyitbVRJ/w2jXTwdTM7vbYkSMG54HRMyppmmb3vPTltz/wt196UQmI87lpCrte854P3vzrH/3s+tqihfqKtGnNJV0nWUXShlYaoouIGYWKZE3SfGrbjF9ZapuVpScRWQbi2IZTN9/+2v2/8cmHh5M7X/piEZDxzV72y7/1+ze+508/tb66mEJ91YW0JlFXO8tYQ5CaJC0C+AS5GkWCXL1MTU7v2pg7csjgnPgsmKYwffMdr9v/wCe/PIKbmo359GIQEHHem6Z44O0f/MOd7/mjj69cvZBifcWFtCpBhySriNYQqYguIEAejUKhTFAkkbJVKydmp9urC+vtxupRTM9vv+WO1936wN98eSRuR1tdSjFV/oUlICLiMm+a4l2/+rt/PHPfRz56ZeFMDO2SD2lNQm+baA2tVAQXcAZZMsoEuXajTIJXKMhlZnJm1+LZo4/tvOMNr9x3/1/9y1DdjnZ4MQWtfLQNrmvf8f+BB3Fimu583x98YuYXf+8jly6fiKlZ9CGu98oPSdbSuoboWpxCkToCgwheIVMokpAp5MmT101qm7XH8rd++HUr1XA6jS5r0DUXbEigfmEIiIgYIs5U733/n3zaveqBD125fDqm9mrWxlWCbaCpJtIQXDe8GXmEIjqKZJ3iCTIVCgWnkFcjpvbcQ3vgLVxeuajWLEvQoUQb0lITrSZ7AcA7AxHT9Or7/+wz+qr7P3j10pFgYTVv4xopraNUJCLRNUQX8GoUsQebxsAhT5CpI1Mlj8rMbb/Exq57WFw+ryksStJaog1paIg0JN/+ZARERMzMBoMBdz/wl/+QXv7eDywtHAkpruVtXCPqOomKZC2NazFa8gjeHJkaeYI8GZl2ZPK+CznzuME0F449DurRXFyMG0QqAjXJWpKrUWl/kr2QCJgVg4n83vve/4/N4Kbf3EhtaNNansIynUdHRALRtZ3yZmSxU7zslc8V8iTkCoUKPiqDiW08feY7zD/+OcLTxxnc/koarQhU/ZrRoi7i1H6izZwHbN+9b/nU1YVTv33+0c8G6su5f9krCM0irdQka4iuJkno7LEFeGbjsHaez1NHIFeHyz1PPfkoqi312mVcqrDbbqdtVkk+YBJwamTxeRLoN4Fp14E735wk/d3aU8dSNpjIqnMnyKdL0kv2EZtVoo8EacgMsiTXlM+3dJtybB91FMlTktPEERfnvkUU8BNTxEvnKHfvodkxQ9IRzoQydK3XPR8CZkaWeSa27/zw8Kl5nHpSTFAWbHzzQdi4SFMmzJoupEEoUud531umTEJmm78X2lWjpKBOFUFbsizHmwfxhG8/xgQtLhl51K6i5q6fgHTPrGl6566b4mjlV+rRGgoOVUQcYbiGfutrlKWDlMiSkCejjJttMtNx1+lA5+bI1HX2QQjNKt3jcQYorihJly7hjp9gMp+haI2yr+jzqYADKCam3rH29MXd4iSZmagZpt3N6mNHmLh0idKV5GEzpPlWCyXIVSjUkaun0AyvEDXSNEMMEEAQnAlSDEgHDzNV1XjJyAxKk+snYGaICK4o3hmqEU6cmW15aBLBYkv7xLeZcBllNEqFPI4Vp2+Xne9z8+QqOFNCqKnjiBgDTnwHXhwewXuPrS4jx44yU87gU5er51MB9VnOcHX1bo0RM5xtefQWS1hZ0Jw9TXFhgSzP8UnxJnjrlM/UUVgHPksep0ZMNXWq2LAKDW23FojD4RADUcPnBcNjxyjWN8jJya+XgPTHHVPbd+wrvL/LktJXevwJDIfgiZqojnyPKQqy4PsVVzZtkzxF8mQGMbXUoWIYhjSxQqPie/XHkxtGckI1XGH94HeYzAb42PtZcE4ky8T1Q7xHrh0ybd0vCcDM7Lbbta0nDacmz95PCVin1ujCWbKVZcqs6DtHbxvNyDXDJ2hCzSjWbMSaKlbUMUDSTn0DZ+ANTJUUEy7LWDxzmGJ1yMANcN7nuaFqFqNpPywlzKw3PLjMi8syXJYDWLI7m9EI50WffXRjgCEgOaFtWDr2PSbcgCz6zu/mKZPDq1GnmioOqcI6dRxRhxoNCReVrcolM1SVpBHBEZuaxRNPMlVMkb3rvd89PowXL2yMTp0ejebPbayfPV2vnz41Wr94PtQrq221sYzFNIbpRMjz8kAIoSuQPRu8IXR/9/mAladOsv+2N+LdJD4pOYIzOvBhRKV193PbEGIijzk+0c9hWDKiJTQphqEohS9ZOHuE/QdeSzYxe9eBYuLuA9sn3vHWVEAsIXmobdgE1jaG6/PzzfLcqbC+cKlevrjglo5/Q4YLr9AUybJcrE+w9fbZPBM0xGW09ZDFs4c4cOfbiOsbOIEmVp3yaUQda4axIibDYonogCwmMIiaMFNUFUMR7eviHaEdMX/062RtphoF06gEj6UoRO+8TkyVcWKqLG7ee2ORveE1OCMlYdYZcx97o1lKkBe+k11AbEsd5BqNLB9w8dxRDrz0F8hwbMQRbRxRx4o61oxCgybwcUAMnjxmtCiYgRlqhpliBuNIJzN85jl/4ShZKryLpZEKTyoNzUFLiKVacoI2ZtaoWVJTV1BXT7vh0iXnvAPrYYr1U3ddCMb5N8R5qtEKF84fst1776Fq1iSkhjo2jGJNiIKkAgk5LmRYU9KEQFJFRLoYmu/s1IfCqaEYSCKLpZFKiEU3NIdUCppJXzERVMAJLgNWn6Zdu4r4nM3+L1uUl03/AoqSFwM7cfxrJ6yY2C2D6W1VqKlDS4jgQ4kmD6GEmBHE02qNSkRMUDWcOQRB0Y4QASFhOJyWkMbAC9CBoBlon0/rVVYFy6BaOkdoh+ActiXBhnQUpLOTbclFis2pGOrDi1fmvtuqMgqVhQTSq+baAYQccZPEwhFi21VXBTGHiWKiiAKmmJiJKE4sZKGAUBqWC1p24NO4f6liuLEd8cBw+TQR8OKAtMU6wvjVhF2zFmioT5rGE8CTq5fPHs937r9Xo9/hQ2mEQlwosJQTfY4VJeqFFBOqDi+dSGraV9YQzExEzCTEpj7iYiGkQjr/9+C74PTAbFNdgGrxLNrZvjeO6/r++LN2LcoxtdUR03gc+A7Io009/Ldmeelhl2Yg5EoP3jKPDQrCICPmDkvdHU0URbsmYYqhJg4RS1Vo2yfN7GQX4IGRMrkGnp6AmlyzEWJYgnZxvnsKMgHbEtjOcmYChkUN1TEzPQF8E/gP4BAQq8X5v3fqkDZ3pJyUl6RyQCpK4sQkJjlEEDxqW81phpiYpVFsm0OYfR94zKUSzLlngAeHGv1iTBdFSVi7Rlhe6JUXnvFKq1sQBLOYQn3MTOd68F8EjoCtA9TDpx/JQ/MENimW5RqLgphPEgYTaJZDVJSEiSCmiHUmcmIiFkehrQ6Z2SngK8CDzjLZvH8PfnNx6qCatSBKGq4QVpcQn13rONb16n7PYSl1yo/BPwh8n+50WUF8ShqWrx78BGVJKApiOSBMFKTMYS6CdYuXXVvX1cSZmMWNGOpDdOC/CjwKnHWKEc06S4yV7/0MitGiFjDfwvoSsVpDnO882t2mOxYybVKoDprpSeC/e/An6F5QjJOREHHra2c+NwrzX4yT210q8xRyh0nAnKI+YBp7MXvwGlZCWx00sxPAfwGPAE8BwZkyBtL9z7UgKkkb1FrMahBoqmU0bmAu7+zVfVTMUq2xPmxmc8DXgP8ETj4T/LU1QwAL1Zl/0ulJUiYIESSgYpgMwQKCXQMf2/pQP9/DPfhzQADMdfu+sfKbG7KkDUjA6A6kBCUOL2MxdPml37WZ1hrqQ71tHuuVPwlUzwUPmCaAevHov7pm/huWld4kqhlIlkGssdSYuwa+OQTMAQ/16p8H2vHcrvP4lgqgqNY9+DGBgNEQ1i6htF0zEMRM6xTrQ4ad7pV/CDgDND8Q/GYRvBm1zj/ysaKIXeZchhQOC+vmiKIalsIm+If7+Rd65a9dLqkmw8z1S3SyGiSChX4kLAXMQk/ADOcETVXqQjUG/zBwdqs6P/QyS4jzw6tzX5DL3/2sTM06802QXIzqsqjp1RDaQ32GHurnv8Sz3pUBOF96H8VJbcYwthZCqzFUllJlarWZ1qZUiLXEtYsmIKpxPYX6STrPf7UHP/9jgd8koQD1qUf/vIhXLsSZ7XlZ5KLLZ69E4wjYHPDlZ4F/ztz+zW9403v3DJrJHVMMtk0PZHp6IMWgFJ9n0qLSWCNNbLDUWvXEv0t9+dSKmR6m8/xX+nZ27rrAb1rJaWwXWZ2fm9z3ineVV44ur5984jDIHNhDwOPAZbq39j94CifsmBwUvzY9e+PbJ7fvumnb7v2zU7v3z07edOvMxO4DU8zsnGgHN2RuIpMnPvo7q5e//z+HRNwZM32kV+dC78vrA78JwQO58+5Npvo2Myvo1pBvAld+FHgAQdwUpnuBW4BZYBqYAWa9k22DzG+74cbd22/YsWvbmbljbdvUC8DXe+s8J1TPj4N4zGZAbgXzdJ1miR/g+ecS6DYzmSCZiOSI5MDAYMI0TWI21ZMaj0Xg8AsGfvNybH71IfGjvmKw5fo/APdXVpd2Y2AAAAAidEVYdENvbW1lbnQAQ3JlYXRlZCB3aXRoIEdJTVAgb24gYSBNYWOHqHdDAAAAAElFTkSuQmCC" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <script type="text/javascript" async
       src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/3.2.2/es5/tex-mml-svg.min.js">

From cc0e339b61334cdc7b7ed1ac90027762b54087ac Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 6 Mar 2023 13:23:09 -0500
Subject: [PATCH 191/221] remind myself how to publish updates to the client

---
 refl1d/webview/client/README.md | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/refl1d/webview/client/README.md b/refl1d/webview/client/README.md
index e8949d5e..df525e22 100644
--- a/refl1d/webview/client/README.md
+++ b/refl1d/webview/client/README.md
@@ -27,3 +27,17 @@ npm run dev
 ```sh
 npm run build
 ```
+
+# Publishing new client versions:
+(...after checking to make sure there aren't extraneous files in this folder)
+```sh
+npm version patch
+npm publish
+```
+
+and then
+```sh
+git commit package.json -m "webview client version bump"
+git pull
+git push
+```
\ No newline at end of file

From 2988e3a291212b646fb6bcac7405db9d180bfd1c Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 7 Mar 2023 11:52:14 -0500
Subject: [PATCH 192/221] adding script to build conda-packed environment
 (linux, osx)

---
 extra/build_conda_packed.sh | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100755 extra/build_conda_packed.sh

diff --git a/extra/build_conda_packed.sh b/extra/build_conda_packed.sh
new file mode 100755
index 00000000..9db40b40
--- /dev/null
+++ b/extra/build_conda_packed.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+ENV_NAME="refl1d-webview-packed"
+PYTHON_VERSION="3.10"
+DIRNAME="refl1d"
+
+eval "$(conda shell.bash hook)"
+conda activate base || { echo 'failed: conda not installed'; exit 1; }
+
+conda install -y conda-pack
+conda create -n "$ENV_NAME" -y "python=$PYTHON_VERSION"
+conda-pack -n "$ENV_NAME" -f -o "$ENV_NAME.tar.gz"
+
+# unpack the new environment, that contains only python + pip
+tmpdir=$(mktemp -d)
+destdir="$tmpdir/$DIRNAME"
+mkdir "$destdir"
+tar -xzf "$ENV_NAME.tar.gz" -C "$destdir"
+
+# activate the unpacked environment and install pip packages
+WORKING_DIRECTORY=$(pwd)
+cd "$tmpdir"
+source "$DIRNAME/bin/activate"
+pip install numba
+pip install git+https://github.com/bumps/bumps@dataclass_overlay
+pip install git+https://github.com/reflectometry/refl1d@webview
+pip install -r https://raw.githubusercontent.com/reflectometry/refl1d/webview/webview-requirements
+
+# zip it back up
+zip -y -r "$WORKING_DIRECTORY/refl1d-webview-$(uname -s)-$(uname -m).zip" "$DIRNAME"
+
+
+

From f028c3c17a3039348a27a09d6f3db935fdd915ff Mon Sep 17 00:00:00 2001
From: Brian Benjamin Maranville <brian.maranville@nist.gov>
Date: Tue, 7 Mar 2023 12:50:36 -0500
Subject: [PATCH 193/221] fix conda packed build, need to preserve symlinks so
 use tar instead of zip to distribute

---
 extra/build_conda_packed.sh | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/extra/build_conda_packed.sh b/extra/build_conda_packed.sh
index 9db40b40..28e2b7ef 100755
--- a/extra/build_conda_packed.sh
+++ b/extra/build_conda_packed.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-ENV_NAME="refl1d-webview-packed"
+ENV_NAME="isolated-base"
 PYTHON_VERSION="3.10"
 DIRNAME="refl1d"
 
@@ -18,16 +18,15 @@ mkdir "$destdir"
 tar -xzf "$ENV_NAME.tar.gz" -C "$destdir"
 
 # activate the unpacked environment and install pip packages
+conda deactivate
 WORKING_DIRECTORY=$(pwd)
 cd "$tmpdir"
 source "$DIRNAME/bin/activate"
-pip install numba
-pip install git+https://github.com/bumps/bumps@dataclass_overlay
-pip install git+https://github.com/reflectometry/refl1d@webview
+pip install --no-input numba
+pip install --no-input git+https://github.com/bumps/bumps@dataclass_overlay
+pip install --no-input git+https://github.com/reflectometry/refl1d@webview
 pip install -r https://raw.githubusercontent.com/reflectometry/refl1d/webview/webview-requirements
+source "$DIRNAME/bin/deactivate"
 
 # zip it back up
-zip -y -r "$WORKING_DIRECTORY/refl1d-webview-$(uname -s)-$(uname -m).zip" "$DIRNAME"
-
-
-
+tar -czf "$WORKING_DIRECTORY/refl1d-webview-$(uname -s)-$(uname -m).tar.gz" "$DIRNAME"

From 7da099ef99c19e5d3f380cfdf9c12a53e75c303e Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 10 Mar 2023 14:58:38 -0500
Subject: [PATCH 194/221] use simple to_json_compatible_dict locally, instead
 of model serializer, for sending results to client

---
 refl1d/webview/server/webserver.py | 62 +++++++++++++++++-------------
 1 file changed, 35 insertions(+), 27 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 7c7b0560..2fb00ec1 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -4,6 +4,7 @@
 import itertools
 import threading
 import signal
+from types import GeneratorType
 from typing import Dict, List, Literal, Optional, Union, TypedDict, cast
 from datetime import datetime
 import warnings
@@ -29,7 +30,7 @@
 mimetypes.add_type("image/svg+xml", ".svg")
 
 from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit, nllf_scale, format_uncertainty
-from bumps.serialize import to_dict, from_dict
+from bumps.serialize import to_dict as serialize, from_dict as deserialize
 from bumps.mapper import MPMapper
 from bumps.parameter import Parameter, Variable, unique
 import bumps.fitproblem
@@ -141,7 +142,7 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     if filename.endswith(".json"):
         with open(path, "rt") as input_file:
             serialized = json.loads(input_file.read())
-        problem = from_dict(serialized)
+        problem = deserialize(serialized)
     else:
         from bumps.cli import load_model
         problem = load_model(str(path))
@@ -181,7 +182,7 @@ async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, file
         #confirmation needed:
         return save_filename
 
-    serialized = to_dict(problem_state.fitProblem)
+    serialized = serialize(problem_state.fitProblem)
     with open(Path(path, save_filename), "wt") as output_file:
         output_file.write(json.dumps(serialized))
 
@@ -267,8 +268,8 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None):
         fit_thread.start()
         state.fit_thread = fit_thread
         await sio.emit("fit_progress", {}) # clear progress
-        await publish("", "fit_active", to_dict(dict(fitter_id=fitter_id, options=options, num_steps=num_steps)))
-        await log(json.dumps(to_dict(options), indent=2), title = f"starting fitter {fitter_id}")
+        await publish("", "fit_active", to_json_compatible_dict(dict(fitter_id=fitter_id, options=options, num_steps=num_steps)))
+        await log(json.dumps(to_json_compatible_dict(options), indent=2), title = f"starting fitter {fitter_id}")
 
 async def _fit_progress_handler(event: Dict):
     # session_id = event["session_id"]
@@ -287,7 +288,7 @@ async def _fit_progress_handler(event: Dict):
         state.fitting.population = event["pop"]
         await publish("", "convergence_update", True)
     elif message == 'progress':
-        await sio.emit("fit_progress", to_dict(event))
+        await sio.emit("fit_progress", to_json_compatible_dict(event))
     elif message == 'uncertainty_update' or message == 'uncertainty_final':
         state.fitting.uncertainty_state = cast(bumps.dream.state.MCMCDraw, event["uncertainty_state"])
         await publish("", "uncertainty_update", True)
@@ -377,16 +378,15 @@ async def get_plot_data(sid: str="", view: str = 'linear'):
         # else:
         #     output = dict(Q = probe.Q, dQ = probe.dQ, R = R, fresnel = FQ)
         # result.append(output)
-    return to_dict(result)
+    return to_json_compatible_dict(result)
 
 @sio.event
 @rest_get
 async def get_model(sid: str=""):
-    from bumps.serialize import to_dict
     if state.problem is None or state.problem.fitProblem is None:
         return None
     fitProblem = state.problem.fitProblem
-    return to_dict(fitProblem)
+    return serialize(fitProblem)
 
 @sio.event
 @rest_get
@@ -400,20 +400,8 @@ async def get_profile_plot(sid: str="", model_index: int=0):
     model = models[model_index]
     assert (isinstance(model, Experiment))
 
-    # data = np.random.random((100,200))
-    # x = np.arange(0, 10, 0.1)
-    # y = np.random.random(x.shape) + x
-    # import plotly.express as px
-    # fig = px.imshow(data)
-    # fig.update_yaxes(exponentformat='e',
-    #                  title={'text': r"$\frac{I}{I_0}$"})
-    # fig = px.line(x=x, y=y)
-
     fig = plot_sld_profile_plotly(model)
-
-    # print(to_dict(fig.to_dict()))
-
-    return to_dict(fig.to_dict())
+    return to_json_compatible_dict(fig.to_dict())
 
 @sio.event
 @rest_get
@@ -440,7 +428,7 @@ async def get_profile_data(sid: str="", model_index: int=0):
             output['step_profile'] = dict(z=z, rho=rho, irho=irho)
         z, rho, irho = model.smooth_profile()
         output['smooth_profile'] = dict(z=z, rho=rho, irho=irho)
-    return to_dict(output)
+    return to_json_compatible_dict(output)
 
 @sio.event
 @rest_get
@@ -509,7 +497,7 @@ async def get_correlation_plot(sid: str = "", nbins: int=50):
         c = Corr2d(draw.points.T, bins=nbins, labels=draw.labels)
         fig = c.plot()
         print("time to render but not serialize...", time.time() - start_time)
-        serialized = to_dict(fig.to_dict())
+        serialized = to_json_compatible_dict(fig.to_dict())
         end_time = time.time()
         print("time to draw correlation plot:", end_time - start_time)
         return serialized
@@ -527,7 +515,7 @@ async def get_uncertainty_plot(sid: str = ""):
         draw = uncertainty_state.draw()
         stats = bumps.dream.stats.var_stats(draw)
         fig = plot_vars(draw, stats)
-        return to_dict(fig.to_dict())
+        return to_json_compatible_dict(fig.to_dict())
     else:
         return None
 
@@ -618,7 +606,7 @@ async def get_parameters(sid: str = "", only_fittable: bool = False):
     else:
         parameter_infos = params_to_list(all_parameters)
         
-    return to_dict(parameter_infos)
+    return to_json_compatible_dict(parameter_infos)
 
 @sio.event
 async def set_parameter(sid: str, parameter_id: str, property: Literal["value01", "value", "min", "max"], value: Union[float, str, bool]):
@@ -756,7 +744,27 @@ def nice(v, digits=4):
         place = floor(log10(abs(v)))
         scale = 10**(place-(digits-1))
         return sign*floor(abs(v)/scale+0.5)*scale
-    
+
+
+def to_json_compatible_dict(obj):
+    if isinstance(obj, (list, tuple)):
+        return type(obj)(to_json_compatible_dict(v) for v in obj)
+    elif isinstance(obj, GeneratorType):
+        return list(to_json_compatible_dict(v) for v in obj)
+    elif isinstance(obj, dict):
+        return type(obj)((to_json_compatible_dict(k), to_json_compatible_dict(v))
+                        for k, v in obj.items())
+    elif isinstance(obj, np.ndarray) and obj.dtype.kind in ['f', 'i']:
+        return obj.tolist()
+    elif isinstance(obj, np.ndarray) and obj.dtype.kind == 'O':
+        return to_json_compatible_dict(obj.tolist())
+    elif isinstance(obj, float):
+        return str(obj) if np.isinf(obj) else obj
+    elif isinstance(obj, int) or isinstance(obj, str) or obj is None:
+        return obj
+    else:
+        raise ValueError("obj %s is not serializable" % str(obj))
+
 
 class ParamInfo(TypedDict, total=False):
     id: str

From 4a9fd95dd46c793c23ce9bde95b654fea956a8ef Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 10 Mar 2023 15:16:21 -0500
Subject: [PATCH 195/221] need to allow MixedExperiment and Experiment classes,
 so check for ExperimentBase class instead

---
 refl1d/webview/server/webserver.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 2fb00ec1..c1852edb 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -39,7 +39,7 @@
 import bumps.errplot
 import refl1d.errors
 import refl1d.fitproblem, refl1d.probe
-from refl1d.experiment import Experiment
+from refl1d.experiment import Experiment, ExperimentBase
 
 # Register the refl1d model loader
 import refl1d.fitplugin
@@ -362,7 +362,7 @@ async def get_plot_data(sid: str="", view: str = 'linear'):
     plotdata = []
     result = {"chisq": chisq, "plotdata": plotdata}
     for model in fitProblem.models:
-        assert(isinstance(model, Experiment))
+        assert(isinstance(model, ExperimentBase))
         theory = model.reflectivity()
         probe = model.probe
         plotdata.append(get_probe_data(theory, probe, model._substrate, model._surface))
@@ -398,7 +398,7 @@ async def get_profile_plot(sid: str="", model_index: int=0):
     if model_index > len(models):
         return None
     model = models[model_index]
-    assert (isinstance(model, Experiment))
+    assert (isinstance(model, ExperimentBase))
 
     fig = plot_sld_profile_plotly(model)
     return to_json_compatible_dict(fig.to_dict())
@@ -413,7 +413,7 @@ async def get_profile_data(sid: str="", model_index: int=0):
     if (model_index > len(models)):
         return None
     model = models[model_index]
-    assert(isinstance(model, Experiment))
+    assert(isinstance(model, ExperimentBase))
     output = {}
     output["ismagnetic"] = model.ismagnetic
     if model.ismagnetic:

From 77a5c186032621aaf6243b79219e8caaa6ce7c82 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Fri, 10 Mar 2023 15:16:46 -0500
Subject: [PATCH 196/221] add some typings and cleanup varplot (to be moved to
 bumps)

---
 refl1d/webview/server/varplot.py | 50 +++++++++++++++++---------------
 1 file changed, 27 insertions(+), 23 deletions(-)

diff --git a/refl1d/webview/server/varplot.py b/refl1d/webview/server/varplot.py
index 305e4f84..4006e03a 100644
--- a/refl1d/webview/server/varplot.py
+++ b/refl1d/webview/server/varplot.py
@@ -1,30 +1,36 @@
 """
-Build layout for histogram plots
+Build layout for histogram plots (plotly)
 """
 
 __all__ = ['var_plot_size', 'plot_vars', 'plot_var']
 
 from math import ceil, sqrt
-from typing import Dict
-
 import numpy as np
 
-# Set space between plots in horiz and vert.
-H_SPACE = 0.2
-V_SPACE = 0.2
+import typing
+if typing.TYPE_CHECKING:
+    from bumps.dream.state import Draw
+    from bumps.dream.stats import VarStats
+    import plotly.graph_objects as go
+
+# TODO: improve type hinting on VarStats (dataclass with optional fields?)
 
-# Set top, bottom, left margins.
-T_MARGIN = 0.2
-B_MARGIN = 0.2
-L_MARGIN = 0.2
-R_MARGIN = 0.4
+# # Set space between plots in horiz and vert.
+# H_SPACE = 0.2
+# V_SPACE = 0.2
 
-# Set desired plot sizes.
-TILE_W = 3.0
-TILE_H = 2.0
-CBAR_WIDTH = 0.75
-CBAR_COLORS = 64
+# # Set top, bottom, left margins.
+# T_MARGIN = 0.2
+# B_MARGIN = 0.2
+# L_MARGIN = 0.2
+# R_MARGIN = 0.4
 
+# # Set desired plot sizes.
+# TILE_W = 3.0
+# TILE_H = 2.0
+# CBAR_WIDTH = 0.75
+
+CBAR_COLORS = 64
 LINE_COLOR = "red"
 ANNOTATION_COLOR = "blue"
 HISTOGRAM_COLORMAP = "Greens_r"
@@ -41,7 +47,7 @@ def tile_axes_square(n):
     return cols, rows
 
 
-def plot_vars(draw, all_vstats, **kw):
+def plot_vars(draw: 'Draw', all_vstats, **kw):
     from plotly.subplots import make_subplots
 
     n = len(all_vstats)
@@ -50,7 +56,7 @@ def plot_vars(draw, all_vstats, **kw):
     snllf = np.sort(-draw.logp)
     vmin, vmax = snllf[0], snllf[int(0.98*(len(snllf)-1))]  # robust range
     cbar_edges = np.linspace(vmin, vmax, CBAR_COLORS)
-    titles = [vstats.label for vstats in all_vstats]
+    # titles = [vstats.label for vstats in all_vstats]
 
     # fig = make_subplots(rows=nrow, cols=ncol, subplot_titles=titles)
     fig = make_subplots(rows=nrow, cols=ncol)
@@ -65,13 +71,12 @@ def plot_vars(draw, all_vstats, **kw):
     fig.update_yaxes(dict(showticklabels=False))
     fig.update_layout(height=600, width=800, coloraxis_colorbar_title="-logP")
     fig.update_layout(coloraxis = {'colorscale': HISTOGRAM_COLORMAP, "cmin": vmin, "cmax": vmax})
-    
+
     return fig
 
 
-def plot_var(fig, draw, vstats, var, cbar_edges, nbins=30, row=None, col=None):
+def plot_var(fig: 'go.Figure', draw: 'Draw', vstats: 'VarStats', var: int, cbar_edges: np.ndarray, nbins=30, row=None, col=None):
     import plotly.graph_objects as go
-    assert isinstance(fig, go.Figure)
     values = draw.points[:, var].flatten()
     bin_range = vstats.p95_range
     #bin_range = np.min(values), np.max(values)
@@ -84,13 +89,12 @@ def plot_var(fig, draw, vstats, var, cbar_edges, nbins=30, row=None, col=None):
     _decorate_histogram(vstats, fig, row=row, col=col)
 
 
-def _decorate_histogram(vstats, fig, col=None, row=None):
+def _decorate_histogram(vstats: 'VarStats', fig: 'go.Figure', col: typing.Optional[int]=None, row: typing.Optional[int]=None):
     import plotly.graph_objects as go
 
     l95, h95 = vstats.p95_range
     l68, h68 = vstats.p68_range
     # Shade things inside 1-sigma
-    assert isinstance(fig, go.Figure)
     fig.add_vrect(x0=l68, x1=h68, fillcolor='gold', opacity=0.5, layer='below', line={"width": 0}, col=col, row=row)
 
     def marker(symbol, position, info_template):

From fe326a08ea347ed46d1176c4b502c74ea580c67f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 13 Mar 2023 12:25:30 -0400
Subject: [PATCH 197/221] don't show R if it is not defined in data view

---
 .../webview/client/src/components/DataView.vue   | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/refl1d/webview/client/src/components/DataView.vue b/refl1d/webview/client/src/components/DataView.vue
index c1be000a..eabb3db6 100644
--- a/refl1d/webview/client/src/components/DataView.vue
+++ b/refl1d/webview/client/src/components/DataView.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 /// <reference types="@types/plotly.js" />
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
+import { ref, onMounted, watch, onUpdated, computed, shallowRef, ssrContextKey } from 'vue';
 import * as Plotly from 'plotly.js/lib/core';
 import type { Socket } from 'socket.io-client';
 import { setupDrawLoop } from '../setupDrawLoop';
@@ -35,7 +35,13 @@ function generate_new_traces(model_data, view: ReflectivityPlot) {
       for (let model of model_data) {
         for (let xs of model) {
           theory_traces.push({ x: xs.Q, y: xs.theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
-          data_traces.push({ x: xs.Q, y: xs.R, error_y: {type: 'data', array: xs.dR, visible: true}, mode: 'markers', name: xs.label + ' data' });
+          if (xs.R !== undefined) {
+            const data_trace = { x: xs.Q, y: xs.R, mode: 'markers', name: xs.label + ' data' };
+            if (xs.dR !== undefined) {
+              data_trace.error_y = {type: 'data', array: xs.dR, visible: true};
+            }
+            data_traces.push(data_trace);
+          }
         }
       }
       break;
@@ -45,9 +51,11 @@ function generate_new_traces(model_data, view: ReflectivityPlot) {
       for (let model of model_data) {
         for (let xs of model) {
           const theory = xs.theory.map((y, i) => (y / (xs.fresnel[i])));
-          const R = xs.R.map((y, i) => (y / (xs.fresnel[i])));
           theory_traces.push({ x: xs.Q, y: theory, mode: 'lines', name: xs.label + ' theory', line: { width: 2 } });
-          data_traces.push({ x: xs.Q, y: R, mode: 'markers', name: xs.label + ' data' });
+          if (xs.R !== undefined) {
+            const R = xs.R.map((y, i) => (y / (xs.fresnel[i])));
+            data_traces.push({ x: xs.Q, y: R, mode: 'markers', name: xs.label + ' data' });
+          }
         }
       }
       break;

From 8a1d0f182e7b9b450f964b9306197b28a2d92664 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 13 Mar 2023 13:31:16 -0400
Subject: [PATCH 198/221] pass sample names to MixedExperiment parts

---
 refl1d/experiment.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/experiment.py b/refl1d/experiment.py
index a2944f50..c1f0e687 100644
--- a/refl1d/experiment.py
+++ b/refl1d/experiment.py
@@ -677,7 +677,7 @@ def __init__(self, samples=None, ratio=None, probe=None,
         self.probe = probe
         self.ratio = [Parameter.default(r, name="ratio %d"%i)
                       for i, r in enumerate(ratio)]
-        self.parts = [Experiment(s, probe, **kw) for s in samples]
+        self.parts = [Experiment(s, probe, name=s.name, **kw) for s in samples]
         self.coherent = coherent
         self.interpolation = interpolation
         self._substrate = self.samples[0][0].material

From b2bd144728f0947e4a0d4f138ecbeb63fa86568f Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 13 Mar 2023 13:31:59 -0400
Subject: [PATCH 199/221] refactor profile plots, and get_model_names, to
 support MixedExperiment

---
 .../client/src/components/ModelView.vue       | 24 +++++++--------
 refl1d/webview/server/webserver.py            | 30 +++++++++++++------
 2 files changed, 33 insertions(+), 21 deletions(-)

diff --git a/refl1d/webview/client/src/components/ModelView.vue b/refl1d/webview/client/src/components/ModelView.vue
index 1f0797c6..de1740f8 100644
--- a/refl1d/webview/client/src/components/ModelView.vue
+++ b/refl1d/webview/client/src/components/ModelView.vue
@@ -9,8 +9,8 @@ import * as Plotly from 'plotly.js/lib/core';
 const title = "Profile";
 const plot_div = ref<HTMLDivElement>();
 const plot_div_id = ref(`div-${uuidv4()}`);
-const model_names = ref<string[]>([]);
-const current_model = ref(0);
+const model_names = ref<{name: string, part_name: string, model_index: number, part_index: number}[]>([]);
+const current_model = ref<[number, number]>([0, 0]);
 
 const props = defineProps<{
   socket: Socket,
@@ -18,20 +18,19 @@ const props = defineProps<{
 
 const { draw_requested } = setupDrawLoop('update_parameters', props.socket, fetch_and_draw, title);
 
-props.socket.on('model_loaded', ({ message: { model_names: new_model_names } }) => {
-  model_names.value = new_model_names;
-});
+async function get_model_names() {
+  model_names.value = await props.socket.asyncEmit("get_model_names");
+}
+
+props.socket.on('model_loaded', get_model_names);
 
 onMounted(async () => {
-  const messages = await props.socket.asyncEmit('get_topic_messages', 'model_loaded');
-  const new_model_names = messages?.[0]?.message?.model_names;
-  if (new_model_names != null) {
-    model_names.value = new_model_names;
-  }
+  await get_model_names();
 });
 
 async function fetch_and_draw() {
-  const payload = await props.socket.asyncEmit('get_profile_plot', current_model.value);
+  const [model_index, sample_index] = current_model.value;
+  const payload = await props.socket.asyncEmit('get_profile_plot', model_index, sample_index);
   let plotdata = { ...payload };
   const { data, layout } = plotdata;
   const config = { responsive: true }
@@ -43,7 +42,8 @@ async function fetch_and_draw() {
 <template>
   <div class="container d-flex flex-grow-1 flex-column">
     <select v-model="current_model" @change="draw_requested = true">
-      <option v-for="(name, index) in model_names" :key="index" :value="index">{{ index }}: {{ name ?? "" }}</option>
+      <option v-for="{name, part_name, model_index, part_index} in model_names" :key="`${model_index}:${part_index}`" :value="[model_index, part_index]">
+        {{ model_index }}:{{ part_index }} --- {{ name ?? "" }}:{{ part_name ?? "" }}</option>
     </select>
     <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
     </div>
diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index c1852edb..467bfb39 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -5,7 +5,7 @@
 import threading
 import signal
 from types import GeneratorType
-from typing import Dict, List, Literal, Optional, Union, TypedDict, cast
+from typing import Dict, List, Literal, Optional, Union, Tuple, TypedDict, cast
 from datetime import datetime
 import warnings
 from queue import Queue
@@ -39,7 +39,7 @@
 import bumps.errplot
 import refl1d.errors
 import refl1d.fitproblem, refl1d.probe
-from refl1d.experiment import Experiment, ExperimentBase
+from refl1d.experiment import Experiment, MixedExperiment, ExperimentBase
 
 # Register the refl1d model loader
 import refl1d.fitplugin
@@ -153,13 +153,24 @@ async def load_problem_file(sid: str, pathlist: List[str], filename: str):
     state.problem.fitProblem = problem
     print(f'model loaded: {path}')
     await log(f'model loaded: {path}')
-
-
-    model_names = [getattr(m, 'name', None) for m in list(problem.models)]
-    await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename, "model_names": model_names})
+    await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename})
     await publish("", "update_model", True)
     await publish("", "update_parameters", True)
 
+@sio.event
+async def get_model_names(sid: str=""):
+    problem = state.problem.fitProblem
+    if problem is None:
+        return None
+    output: List[Dict] = []
+    for model_index, model in enumerate(problem.models):
+        if isinstance(model, Experiment):
+            output.append(dict(name=model.name, part_name=None, model_index=model_index, part_index=0))
+        elif isinstance(model, MixedExperiment):
+            for part_index, part in enumerate(model.parts):
+                output.append(dict(name=model.name, part_name=part.name, model_index=model_index, part_index=part_index))
+    return output
+
 @sio.event
 async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, filename: Optional[str] = None, overwrite: bool = False):
     problem_state = state.problem
@@ -390,7 +401,7 @@ async def get_model(sid: str=""):
 
 @sio.event
 @rest_get
-async def get_profile_plot(sid: str="", model_index: int=0):
+async def get_profile_plot(sid: str="", model_index: int=0, sample_index: int=0):
     if state.problem is None or state.problem.fitProblem is None:
         return None
     fitProblem = state.problem.fitProblem
@@ -398,8 +409,9 @@ async def get_profile_plot(sid: str="", model_index: int=0):
     if model_index > len(models):
         return None
     model = models[model_index]
-    assert (isinstance(model, ExperimentBase))
-
+    assert (isinstance(model, Union[Experiment, MixedExperiment]))
+    if isinstance(model, MixedExperiment):
+        model = model.parts[sample_index]
     fig = plot_sld_profile_plotly(model)
     return to_json_compatible_dict(fig.to_dict())
 

From 2dbb04f2441f4e28fd9f00779d44d0b4cf1691ac Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 13 Mar 2023 13:33:27 -0400
Subject: [PATCH 200/221] version bump: change to plot_profile interface

---
 refl1d/webview/client/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index 230574f2..ee63777b 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -1,6 +1,6 @@
 {
   "name": "refl1d-webview-client",
-  "version": "0.0.2",
+  "version": "0.0.3",
   "scripts": {
     "dev": "vite",
     "build": "vite build --emptyOutDir -m development",

From f71b87f899eb9eac04d217a2cea294c65fcc6157 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 13 Mar 2023 16:25:31 -0400
Subject: [PATCH 201/221] add monkey patch for plotly, to address issue
 https://github.com/plotly/plotly.py/issues/4100

---
 refl1d/webview/server/webserver.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 467bfb39..7475bc96 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -47,6 +47,18 @@
 bumps.cli.install_plugin(refl1d.fitplugin)
 
 from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
+
+### BEGIN PATCH
+# patch the plotly library to disable levenshtein lookup for missing strings
+# which is taking a ridiculous amount of time in make_subplots
+# See: https://github.com/plotly/plotly.py/issues/4100
+def disable_find_closest_string(string, strings):
+    raise ValueError()
+
+import _plotly_utils.utils
+_plotly_utils.utils.find_closest_string = disable_find_closest_string
+### END PATCH
+
 from .profile_plot import plot_sld_profile_plotly
 from .varplot import plot_vars
 # from .state_hdf5_backed import State

From a839265c5866bcd6efc83c009d08a5b036c349a7 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 14 Mar 2023 12:46:01 -0400
Subject: [PATCH 202/221] merging in hdf5-backed state changes to webserver

---
 refl1d/webview/server/webserver.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 3e9050f5..62d0ca06 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -297,7 +297,6 @@ async def start_fit_thread(sid: str="", fitter_id: str="", options=None, termina
 
 async def _fit_progress_handler(event: Dict):
     # session_id = event["session_id"]
-    print("progress: ", event)
     problem_state = state.problem
     fitProblem = problem_state.fitProblem if problem_state is not None else None
     if fitProblem is None:

From 3071725849f5e88056908e5b50a064d9fcad0548 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 14 Mar 2023 14:45:29 -0400
Subject: [PATCH 203/221] add type hints for command-line arguments

---
 refl1d/webview/server/webserver.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 62d0ca06..43bc79a2 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -842,6 +842,20 @@ def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[Param
 
 import argparse
 
+
+class Namespace(argparse.Namespace):
+    """ provide type hints for arguments """
+    filename: Optional[str]
+    headless: bool
+    external: bool
+    port: int
+    hub: Optional[str]
+    fit: Optional[str]
+    start: bool
+    store: Optional[str]
+    exit: bool
+
+
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('filename', nargs='?', help='problem file to load, .py or .json (serialized) fitproblem')
@@ -855,7 +869,7 @@ def main():
     parser.add_argument('--store', default=None, type=str, help='backing file for state')
     parser.add_argument('--exit', action='store_true', help='end process when fit complete (fit results lost unless store is specified)')
     # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
-    args = parser.parse_args()
+    args = parser.parse_args(namespace=Namespace())
 
     global state
     if args.store is None:

From 343edef5f0c88046a06c6ee411a65393d6462e15 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 15 Mar 2023 15:30:47 -0400
Subject: [PATCH 204/221] adding panels module to define which panels to show
 in webview

---
 refl1d/webview/client/src/panels.mjs | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 refl1d/webview/client/src/panels.mjs

diff --git a/refl1d/webview/client/src/panels.mjs b/refl1d/webview/client/src/panels.mjs
new file mode 100644
index 00000000..d144dc91
--- /dev/null
+++ b/refl1d/webview/client/src/panels.mjs
@@ -0,0 +1,10 @@
+import { panels as bumps_panels } from 'bumps-webview-client/src/panels';
+import DataView from './components/DataView.vue';
+import ModelView from './components/ModelView.vue';
+
+export const panels = [...bumps_panels];
+
+// replace the bumps data view with the refl1d one.
+panels.find(p => p.title === 'Data').component = DataView;
+// insert the profile panel at position 3
+panels.splice(2, 0, {title: 'Profile', component: ModelView});

From 750af678f1996b412b83a8312047846e84779629 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 15 Mar 2023 15:34:56 -0400
Subject: [PATCH 205/221] get main app from bumps-webview-client

---
 refl1d/webview/client/package.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index ee63777b..f8340a4a 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -9,6 +9,7 @@
   },
   "dependencies": {
     "bootstrap": "^5.2.1",
+    "bumps-webview-client": "^0.0.3",
     "json-difference": "^1.8.2",
     "mpld3": "^0.5.8",
     "plotly.js": "^2.16.4",

From d0bad675e45c9c855faf36543bd664f69051f3ef Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 15 Mar 2023 15:35:25 -0400
Subject: [PATCH 206/221] use imported App from bumps-webview-client

---
 refl1d/webview/client/src/main.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/client/src/main.js b/refl1d/webview/client/src/main.js
index acc9741a..8416b183 100644
--- a/refl1d/webview/client/src/main.js
+++ b/refl1d/webview/client/src/main.js
@@ -1,6 +1,7 @@
 import { createApp } from 'vue'
 import 'bootstrap/dist/css/bootstrap.min.css';
 import './style.css'
-import App from './App.vue'
+import App from 'bumps-webview-client/src/App.vue';
+import { panels } from './panels.mjs';
 
-createApp(App).mount('#app')
+createApp(App, {panels}).mount('#app');
\ No newline at end of file

From 4325c4b934f5852e609ddb2f09851d610c14242a Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Wed, 15 Mar 2023 15:35:45 -0400
Subject: [PATCH 207/221] remove components that were moved to base app in
 bumps-webview-client

---
 refl1d/webview/client/src/App.vue             | 333 ------------------
 .../client/src/components/ConvergenceView.vue |  40 ---
 .../client/src/components/CorrelationView.vue |  46 ---
 .../src/components/CorrelationViewPlotly.vue  |  51 ---
 .../client/src/components/FileBrowser.vue     | 137 -------
 .../client/src/components/FitOptions.vue      | 217 ------------
 .../webview/client/src/components/LogView.vue |  44 ---
 .../client/src/components/ModelInspect.vue    |  96 -----
 .../src/components/ModelUncertaintyView.vue   |  46 ---
 .../src/components/PanelTabContainer.vue      |  48 ---
 .../src/components/ParameterTraceView.vue     |  39 --
 .../client/src/components/ParameterView.vue   | 103 ------
 .../client/src/components/SummaryView.vue     | 122 -------
 .../client/src/components/UncertaintyView.vue |  52 ---
 14 files changed, 1374 deletions(-)
 delete mode 100644 refl1d/webview/client/src/App.vue
 delete mode 100644 refl1d/webview/client/src/components/ConvergenceView.vue
 delete mode 100644 refl1d/webview/client/src/components/CorrelationView.vue
 delete mode 100644 refl1d/webview/client/src/components/CorrelationViewPlotly.vue
 delete mode 100644 refl1d/webview/client/src/components/FileBrowser.vue
 delete mode 100644 refl1d/webview/client/src/components/FitOptions.vue
 delete mode 100644 refl1d/webview/client/src/components/LogView.vue
 delete mode 100644 refl1d/webview/client/src/components/ModelInspect.vue
 delete mode 100644 refl1d/webview/client/src/components/ModelUncertaintyView.vue
 delete mode 100644 refl1d/webview/client/src/components/PanelTabContainer.vue
 delete mode 100644 refl1d/webview/client/src/components/ParameterTraceView.vue
 delete mode 100644 refl1d/webview/client/src/components/ParameterView.vue
 delete mode 100644 refl1d/webview/client/src/components/SummaryView.vue
 delete mode 100644 refl1d/webview/client/src/components/UncertaintyView.vue

diff --git a/refl1d/webview/client/src/App.vue b/refl1d/webview/client/src/App.vue
deleted file mode 100644
index 5f8c76be..00000000
--- a/refl1d/webview/client/src/App.vue
+++ /dev/null
@@ -1,333 +0,0 @@
-<script setup lang="ts">
-import { Button } from 'bootstrap/dist/js/bootstrap.esm.js';
-import { onMounted, ref, shallowRef } from 'vue';
-import { io } from 'socket.io-client';
-import './asyncSocket';
-import FitOptions from './components/FitOptions.vue';
-import DataView from './components/DataView.vue';
-import ModelView from './components/ModelView.vue';
-import PanelTabContainer from './components/PanelTabContainer.vue';
-import FileBrowser from './components/FileBrowser.vue';
-import SummaryView from './components/SummaryView.vue';
-import ModelInspect from './components/ModelInspect.vue';
-// import ModelViewPlotly from './components/ModelViewPlotly.vue';
-import ParameterView from './components/ParameterView.vue';
-import LogView from './components/LogView.vue';
-import ConvergenceView from './components/ConvergenceView.vue';
-// import CorrelationView from './components/CorrelationView.vue';
-import CorrelationView from './components/CorrelationViewPlotly.vue';
-import ParameterTraceView from './components/ParameterTraceView.vue';
-import ModelUncertaintyView from './components/ModelUncertaintyView.vue';
-import UncertaintyView from './components/UncertaintyView.vue';
-
-// import { FITTERS as FITTER_DEFAULTS } from './fitter_defaults';
-
-const panels = [
-  {title: 'Reflectivity', component: DataView},
-  {title: 'Summary', component: SummaryView},
-  {title: 'Log', component: LogView},
-  {title: 'Convergence', component: ConvergenceView},
-  {title: 'Profile', component: ModelView},
-  {title: 'Model', component: ModelInspect},
-  // {title: 'Profile2', component: ModelViewPlotly},
-  {title: 'Parameters', component: ParameterView},
-  {title: 'Correlations', component: CorrelationView},
-  {title: 'Trace', component: ParameterTraceView},
-  {title: 'Model Uncertainty', component: ModelUncertaintyView},
-  {title: 'Uncertainty', component: UncertaintyView},
-];
-
-const LAYOUTS = ["left-right", "top-bottom", "full"];
-const connected = ref(false);
-const menuToggle = ref<HTMLButtonElement>();
-const fitOptions = ref<typeof FitOptions>();
-const fileBrowser = ref<typeof FileBrowser>();
-const fileBrowserSelectCallback = ref((pathlist: string[], filename: string) => { });
-const fileBrowserSaveFilename = ref<string>();
-const fileBrowserTitle = ref("Load Model File");
-const model_loaded = shallowRef<{pathlist: string[], filename: string}>();
-const active_layout = ref("left-right");
-const active_panel = ref([0, 1]);
-const fit_active = ref<{ fitter_id?: string, options?: {}, num_steps?: number }>({});
-const fit_progress = ref<{ chisq?: string, step?: number, value?: number }>({});
-
-// Create a SocketIO connection, to be passed to child components
-// so that they can do their own communications with the host.
-const queryString = window.location.search;
-const urlParams = new URLSearchParams(queryString);
-
-const sio_base_path = urlParams.get('base_path') ?? window.location.pathname;
-const sio_server = urlParams.get('server') ?? '';
-
-const socket = io(sio_server, {
-    // this is mostly here to test what happens on server fail:
-   path: `${sio_base_path}socket.io`,
-   reconnectionAttempts: 10
-});
-
-socket.on('connect', () => {
-  console.log(socket.id);
-  connected.value = true;
-});
-
-socket.on('disconnect', (payload) => {
-  console.log("disconnected!", payload);
-  connected.value = false;
-})
-
-socket.on('model_loaded', ({message: {pathlist, filename}}) => {
-  model_loaded.value = {pathlist, filename};
-})
-
-socket.on('fit_active', ({ message: { fitter_id, options, num_steps } }) => {
-  fit_active.value = { fitter_id, options, num_steps };
-});
-
-socket.on('fit_progress', (event) => {
-  fit_progress.value = event;
-});
-
-function disconnect() {
-  socket.disconnect();
-  connected.value = false;
-}
-
-function selectOpenFile() {
-  if (fileBrowser.value) {
-    fileBrowserTitle.value = "Load Model File";
-    fileBrowserSelectCallback.value = (pathlist, filename) => {
-      socket.emit("load_problem_file", pathlist, filename);
-    }
-    fileBrowserSaveFilename.value = undefined;
-    fileBrowser.value.open();
-  }
-  // const path = prompt("full path to file:");
-  // if (path != null) {
-  //   let defaulted_path = (path == '') ? '/home/bbm/dev/refl1d-modelbuilder/ISIS_GGG/GGG_GdIG_MultiFit.py' : path;
-  //   socket.emit("load_model_file", defaulted_path);
-  // }
-  // file_picker.value?.click();
-}
-
-async function saveFileAs(ev: Event) {
-  if (fileBrowser.value) {
-    fileBrowserTitle.value = "Save Problem"
-    fileBrowserSelectCallback.value = (pathlist, filename) => {
-      saveFile(ev, {pathlist, filename});
-    }
-    fileBrowserSaveFilename.value = model_loaded.value?.filename ?? "model.json";
-    fileBrowser.value.open();
-  }
-}
-
-async function saveFile(ev: Event, override?: {pathlist: string[], filename: string}) {
-  if (model_loaded.value === undefined) {
-    alert('no file to save');
-    return;
-  }
-  const {pathlist, filename} = override ?? model_loaded.value;
-  console.log('saving:', {pathlist, filename});
-  socket.emit("save_problem_file", pathlist, filename, false, async(confirm_overwrite: string | false) => {
-    if (confirm_overwrite !== false) {
-      const overwrite = await confirm(`File ${confirm_overwrite} exists: overwrite?`);
-      if (overwrite) {
-        socket.emit("save_problem_file", pathlist, filename, overwrite);
-      }
-    }
-  });
-}
-
-function reloadModel() {
-  if (model_loaded.value) {
-    const {pathlist, filename} = model_loaded.value;
-    socket.emit("load_problem_file", pathlist, filename);
-  }
-}
-
-function openFitOptions() {
-  fitOptions.value?.open();
-}
-
-function startFit() {
-  const fitter_active = fitOptions.value?.fitter_active;
-  const fitter_settings = fitOptions.value?.fitter_settings;
-
-  if (fitter_active && fitter_settings) {
-    const fit_args = fitter_settings[fitter_active];
-    socket.emit("start_fit_thread", fitter_active, fit_args.settings);
-  }
-}
-
-function stopFit() {
-  socket.emit("stop_fit")
-}
-
-function quit() {
-  socket.emit("shutdown");
-}
-
-onMounted(() => {
-  const menuToggleButton = new Button(menuToggle.value);
-});
-
-</script>
-
-<template>
-  <div class="h-100 w-100 m-0 d-flex flex-column">
-    <nav class="navbar navbar-expand-sm navbar-dark bg-dark">
-      <div class="container-fluid">
-        <div class="navbar-brand">
-          <img src="./assets/refl1d-icon_256x256x32.png" alt="" height="24" class="d-inline-block align-text-middle">
-          Refl1D
-        </div>
-        <button ref="menuToggle" class="navbar-toggler" type="button" data-bs-toggle="collapse"
-          data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false"
-          aria-label="Toggle navigation">
-          <span class="navbar-toggler-icon"></span>
-        </button>
-        <div class="collapse navbar-collapse" id="navbarSupportedContent">
-          <ul class="navbar-nav me-auto mb-2 mb-lg-0">
-            <!-- <li class="nav-item dropdown">
-              <div class="nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
-                aria-expanded="false">
-                Session
-              </div>
-              <ul class="dropdown-menu">
-                <li><button class="btn btn-link dropdown-item"  @click="connect">New</div></li>
-                <li><button class="btn btn-link dropdown-item"  @click="disconnect">Disconnect</div></li>
-                <li><button class="btn btn-link dropdown-item"  @click="reconnect">Existing</div></li>
-              </ul>
-            </li> -->
-            <li class="nav-item dropdown">
-              <button class="btn btn-link nav-link dropdown-toggle" role="button" data-bs-toggle="dropdown"
-                aria-expanded="false">
-                File
-              </button>
-              <ul class="dropdown-menu">
-                <li><button class="btn btn-link dropdown-item" @click="selectOpenFile">Open</button></li>
-                <li><button class="btn btn-link dropdown-item" :disabled="!model_loaded" @click="saveFile">Save</button></li>
-                <li><button class="btn btn-link dropdown-item" :disabled="!model_loaded" @click="saveFileAs">Save As</button></li>
-                <li><button class="btn btn-link dropdown-item" :class="{disabled: model_loaded === undefined}"  @click="reloadModel">Reload</button></li>
-                <li>
-                  <hr class="dropdown-divider">
-                </li>
-                <li><button class="btn btn-link dropdown-item" @click="quit">Quit</button></li>
-              </ul>
-            </li>
-            <!-- <li class="nav-item dropdown">
-              <button class="btn btn-link nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
-                aria-expanded="false">
-                Fitting
-              </button>
-              <ul class="dropdown-menu">
-                <li><button class="btn btn-link dropdown-item"  @click="startFit">Start</button></li>
-                <li><button class="btn btn-link dropdown-item"  @click="stopFit">Stop</button></li>
-                <li>
-                  <hr class="dropdown-divider">
-                </li>
-                <li><button class="btn btn-link dropdown-item"  @click="openFitOptions">Options...</button></li>
-              </ul>
-            </li> -->
-            <li class="nav-item dropdown">
-              <button class="btn btn-link nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
-                aria-expanded="false">
-                Layout
-              </button>
-              <ul class="dropdown-menu">
-                <li v-for="layout in LAYOUTS" :key="layout" :class="{layout: true, active: active_layout === layout}">
-                  <button class="btn btn-link dropdown-item" :class="{layout: true, active: active_layout === layout}" @click="active_layout = layout">{{ layout }}</button>
-                </li>
-              </ul>
-            </li>
-
-            <!-- <li class="nav-item dropdown">
-              <div class="nav-link dropdown-toggle"  role="button" data-bs-toggle="dropdown"
-                aria-expanded="false">
-                Reflectivity
-              </div>
-              <ul class="dropdown-menu">
-                <li v-for="plot_type in REFLECTIVITY_PLOTS" :key="plot_type">
-                  <div :class="{'dropdown-item': true, active: (plot_type === reflectivity_type)}" 
-                    @click="set_reflectivity(plot_type)">{{plot_type}}</div>
-                </li>
-              </ul>
-            </li> -->
-          </ul>
-          <div class="flex-grow-1 px-4 m-0">
-            <h4 class="m-0">
-              <!-- <div class="rounded p-2 bg-primary">Fitting: </div> -->
-              <div v-if="fit_active.fitter_id !== undefined" class="badge bg-secondary p-2 align-middle">
-                <div class="align-middle pt-2 pb-1 px-1 d-inline-block">
-                  <span>Fitting: {{ fit_active.fitter_id }} step {{ fit_progress?.step }} of
-                  {{ fit_active?.num_steps }}, chisq={{ fit_progress.chisq }}</span>
-                  <div class="progress mt-1" style="height:3px;">
-                    <div class="progress-bar" role="progressbar" :aria-valuenow="fit_progress?.step" 
-                      aria-valuemin="0" :aria-valuemax="fit_active?.num_steps ?? 100" :style="{width: ((fit_progress.step ?? 0) * 100 / (fit_active.num_steps ?? 1)).toFixed(1) + '%'}"></div>
-                  </div>
-                </div>
-                <button class="btn btn-danger btn-sm" @click="stopFit">Stop</button>
-              </div>
-              <div v-else class="badge bg-secondary p-1">
-                <div class="align-middle p-2 d-inline-block">
-                  <span>Fitting: </span>
-                </div>
-                <button class="btn btn-light btn-sm me-2" @click="openFitOptions">
-                  {{ fitOptions?.fitter_active ?? "" }}
-                  <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-gear" viewBox="0 0 16 16">
-                    <path d="M8 4.754a3.246 3.246 0 1 0 0 6.492 3.246 3.246 0 0 0 0-6.492zM5.754 8a2.246 2.246 0 1 1 4.492 0 2.246 2.246 0 0 1-4.492 0z"/>
-                    <path d="M9.796 1.343c-.527-1.79-3.065-1.79-3.592 0l-.094.319a.873.873 0 0 1-1.255.52l-.292-.16c-1.64-.892-3.433.902-2.54 2.541l.159.292a.873.873 0 0 1-.52 1.255l-.319.094c-1.79.527-1.79 3.065 0 3.592l.319.094a.873.873 0 0 1 .52 1.255l-.16.292c-.892 1.64.901 3.434 2.541 2.54l.292-.159a.873.873 0 0 1 1.255.52l.094.319c.527 1.79 3.065 1.79 3.592 0l.094-.319a.873.873 0 0 1 1.255-.52l.292.16c1.64.893 3.434-.902 2.54-2.541l-.159-.292a.873.873 0 0 1 .52-1.255l.319-.094c1.79-.527 1.79-3.065 0-3.592l-.319-.094a.873.873 0 0 1-.52-1.255l.16-.292c.893-1.64-.902-3.433-2.541-2.54l-.292.159a.873.873 0 0 1-1.255-.52l-.094-.319zm-2.633.283c.246-.835 1.428-.835 1.674 0l.094.319a1.873 1.873 0 0 0 2.693 1.115l.291-.16c.764-.415 1.6.42 1.184 1.185l-.159.292a1.873 1.873 0 0 0 1.116 2.692l.318.094c.835.246.835 1.428 0 1.674l-.319.094a1.873 1.873 0 0 0-1.115 2.693l.16.291c.415.764-.42 1.6-1.185 1.184l-.291-.159a1.873 1.873 0 0 0-2.693 1.116l-.094.318c-.246.835-1.428.835-1.674 0l-.094-.319a1.873 1.873 0 0 0-2.692-1.115l-.292.16c-.764.415-1.6-.42-1.184-1.185l.159-.291A1.873 1.873 0 0 0 1.945 8.93l-.319-.094c-.835-.246-.835-1.428 0-1.674l.319-.094A1.873 1.873 0 0 0 3.06 4.377l-.16-.292c-.415-.764.42-1.6 1.185-1.184l.292.159a1.873 1.873 0 0 0 2.692-1.115l.094-.319z"/>
-                  </svg>
-                </button>
-                <button class="btn btn-success btn-sm" @click="startFit">Start</button>
-              </div>
-            </h4>
-          </div>
-          <div class="d-flex">
-            <div id="connection_status"
-              :class="{'btn': true, 'btn-outline-success': connected, 'btn-outline-danger': !connected}">
-              {{(connected) ? 'connected' : 'disconnected'}}</div>
-
-          </div>
-        </div>
-      </div>
-    </nav>
-    <div class="flex-grow-1 row overflow-hidden" v-if="active_layout === 'left-right'">
-      <div class="col d-flex flex-column mh-100 border-end border-success border-3">
-        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[0]" @panel_changed="(n) => { active_panel[0] = n }"/>
-      </div>
-      <div class="col d-flex flex-column mh-100">
-        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[1]" @panel_changed="(n) => { active_panel[1] = n }"/>
-      </div>
-    </div>
-    <div class="flex-grow-1 d-flex flex-column" v-if="active_layout === 'top-bottom'">
-      <div class="d-flex flex-column flex-grow-1" style="overflow-y:scroll;">
-        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[0]" @panel_changed="(n) => { active_panel[0] = n }"/>
-      </div>
-      <div class="d-flex flex-column flex-grow-1">
-        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[1]" @panel_changed="(n) => { active_panel[1] = n }"/>
-      </div>
-    </div>
-    <div class="flex-grow-1 row overflow-hidden" v-if="active_layout === 'full'">
-      <div class="col d-flex flex-column mh-100">
-        <PanelTabContainer :panels="panels" :socket="socket" :active_panel="active_panel[0]" @panel_changed="(n) => { active_panel[0] = n }"/>
-      </div>
-    </div>
-
-  </div>
-  <FitOptions ref="fitOptions" :socket="socket" />
-  <FileBrowser ref="fileBrowser" :socket="socket" :title="fileBrowserTitle" :chosenfile_in="model_loaded?.filename" :savefilename="fileBrowserSaveFilename" :callback="fileBrowserSelectCallback" />
-</template>
-
-<style>
-html,
-body,
-#app {
-  height: 100%;
-  width: 100%;
-  overflow-x: hidden;
-}
-
-div#connection_status {
-  pointer-events: none;
-}
-</style>
diff --git a/refl1d/webview/client/src/components/ConvergenceView.vue b/refl1d/webview/client/src/components/ConvergenceView.vue
deleted file mode 100644
index 05a10ce2..00000000
--- a/refl1d/webview/client/src/components/ConvergenceView.vue
+++ /dev/null
@@ -1,40 +0,0 @@
-<script setup lang="ts">
-/// <reference types="@types/uuid"/>
-import { ref } from 'vue';
-import { Socket } from 'socket.io-client';
-import { v4 as uuidv4 } from 'uuid';
-import { setupDrawLoop } from '../setupDrawLoop';
-import mpld3 from 'mpld3';
-
-const title = "Convergence";
-const plot_div = ref<HTMLDivElement>();
-const plot_div_id = ref(`div-${uuidv4()}`);
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('convergence_update', props.socket, fetch_and_draw, title);
-
-async function fetch_and_draw() {
-  const payload = await props.socket.asyncEmit('get_convergence_plot');
-  let plotdata = { ...payload };
-  // console.log({plotdata});
-  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-}
-
-</script>
-    
-<template>
-  <div class="container d-flex flex-grow-1 flex-column">
-    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
-    </div>
-  </div>
-</template>
-
-<style scoped>
-svg {
-  width: 100%;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/CorrelationView.vue b/refl1d/webview/client/src/components/CorrelationView.vue
deleted file mode 100644
index 576f1873..00000000
--- a/refl1d/webview/client/src/components/CorrelationView.vue
+++ /dev/null
@@ -1,46 +0,0 @@
-<script setup lang="ts">
-/// <reference types="@types/uuid"/>
-import { ref } from 'vue';
-import { Socket } from 'socket.io-client';
-import { v4 as uuidv4 } from 'uuid';
-import { setupDrawLoop } from '../setupDrawLoop';
-import { cache } from '../plotcache';
-import mpld3 from 'mpld3';
-
-const title = "Correlations"
-const plot_div = ref<HTMLDivElement>();
-const plot_div_id = ref(`div-${uuidv4()}`);
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
-
-async function fetch_and_draw(latest_timestamp: string) {
-  let { timestamp, plotdata } = cache[title] ?? {};
-  if (timestamp !== latest_timestamp) {
-    console.log("fetching new correlation plot", timestamp, latest_timestamp);
-    const payload = await props.socket.asyncEmit('get_correlation_plot');
-    plotdata = { ...payload };
-    cache[title] = {timestamp: latest_timestamp, plotdata};
-  }
-  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-}
-
-</script>
-    
-<template>
-  <div class="container d-flex flex-grow-1 flex-column">
-    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
-    </div>
-  </div>
-</template>
-
-<style scoped>
-svg {
-  width: 100%;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/CorrelationViewPlotly.vue b/refl1d/webview/client/src/components/CorrelationViewPlotly.vue
deleted file mode 100644
index 4d249aee..00000000
--- a/refl1d/webview/client/src/components/CorrelationViewPlotly.vue
+++ /dev/null
@@ -1,51 +0,0 @@
-<script setup lang="ts">
-/// <reference types="@types/uuid"/>
-import { ref } from 'vue';
-import { Socket } from 'socket.io-client';
-import { v4 as uuidv4 } from 'uuid';
-import { setupDrawLoop } from '../setupDrawLoop';
-import { cache } from '../plotcache';
-import * as Plotly from 'plotly.js/lib/core';
-import Heatmap from 'plotly.js/lib/heatmap';
-
-Plotly.register([
-  Heatmap,
-])
-
-const title = "Correlations";
-const plot_div = ref<HTMLDivElement>();
-const plot_div_id = ref(`div-${uuidv4()}`);
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
-
-
-async function fetch_and_draw(latest_timestamp: string) {
-  let { timestamp, plotdata } = cache[title] ?? {};
-  if (timestamp !== latest_timestamp) {
-    const payload = await props.socket.asyncEmit('get_correlation_plot');
-    plotdata = { ...payload };
-    cache[title] = {timestamp: latest_timestamp, plotdata};
-  }
-  const { data, layout } = plotdata;
-  const config = { responsive: true, scrollZoom: true }
-  await Plotly.react(plot_div_id.value, [...data], layout, config);
-}
-
-</script>
-
-<template>
-  <div class="container d-flex flex-grow-1 flex-column">
-    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
-    </div>
-  </div>
-</template>
-
-<style scoped>
-svg {
-  width: 100%;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/FileBrowser.vue b/refl1d/webview/client/src/components/FileBrowser.vue
deleted file mode 100644
index b7575db9..00000000
--- a/refl1d/webview/client/src/components/FileBrowser.vue
+++ /dev/null
@@ -1,137 +0,0 @@
-<script setup lang="ts">
-import { ref, onMounted, watch, onUpdated, computed, shallowRef } from 'vue';
-import { Modal } from 'bootstrap/dist/js/bootstrap.esm';
-import { Socket } from 'socket.io-client';
-
-const props = defineProps<{
-  socket: Socket,
-  title: string,
-  savefilename?: string,
-  chosenfile_in?: string,
-  callback: (pathlist: string[], filename: string) => void
-}>();
-
-const emit = defineEmits<{
-  (e: 'selected', pathlist: string[], filename: string): void
-}>();
-
-const dialog = ref<HTMLDivElement>();
-const isOpen = ref(false);
-const pathlist = ref(["/"]);
-// const pathlist = ref(["/", "Users", "bbm", "dev", "refl1d-modelbuilder"]);
-const subdirlist = shallowRef<string[]>([])
-const filelist = shallowRef<string[]>([])
-const chosenFile = ref("");
-
-let modal: Modal;
-onMounted(() => {
-  modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
-});
-
-function close() {
-  modal?.hide();
-  isOpen.value = false;
-}
-
-function open() {
-  props.socket.emit('get_current_pathlist', (new_pathlist) => {
-    setPath(new_pathlist);
-  })
-  chosenFile.value = props.chosenfile_in ?? "";
-  modal?.show();
-  isOpen.value = true;
-}
-
-function subdirClick(subdir: string) {
-  pathlist.value.push(subdir);
-  setPath();
-  props.socket.emit("get_dirlisting", pathlist.value, ({ files, subfolders }) => {
-
-  })
-}
-
-function setPath(new_pathlist?: string[]) {
-  if (new_pathlist !== undefined) {
-    pathlist.value = new_pathlist;
-    // chosenFile.value = "";
-  }
-  props.socket.emit("get_dirlisting", pathlist.value, ({ files, subfolders }) => {
-    subdirlist.value = subfolders.sort();
-    filelist.value = files.sort();
-  })
-}
-
-function chooseFile() {
-  props.callback(pathlist.value, chosenFile.value);
-  close();
-}
-
-defineExpose({
-  close,
-  open
-})
-</script>
-
-<template>
-  <div ref="dialog" class="modal fade" id="fileBrowserModal" tabindex="-1" aria-labelledby="fileBrowserLabel"
-    :aria-hidden="isOpen">
-    <div class="modal-dialog modal-lg">
-      <div class="modal-content">
-        <div class="modal-header">
-          <h5 class="modal-title" id="fileBrowserLabel">{{title}}</h5>
-          <button type="button" class="btn-close" @click="close" aria-label="Close"></button>
-        </div>
-        <div class="modal-body">
-          <div v-if="savefilename" class="container border-bottom">
-            <div class="row align-items-center mb-1">
-              <div class="col-auto">
-                <label for="userfilename" class="col-form-label">Filename:</label>
-              </div>
-              <div class="col">
-                <input type="text" id="userfilename" class="form-control" v-model="chosenFile">
-              </div>
-            </div>
-          </div>
-          <div class="container border-bottom">
-            <nav aria-label="breadcrumb">
-              <ol class="breadcrumb">
-                <li v-for="(pathitem, index) in pathlist" :key="index" class="breadcrumb-item">
-                  <a href="#" @click.prevent="setPath(pathlist.slice(0, index+1))">{{pathitem}}</a>
-                </li>
-              </ol>
-            </nav>
-          </div>
-          <div class="container border-bottom">
-            <h3>Subdirectories:</h3>
-            <div class="row row-cols-3">
-              <div class="col overflow-hidden" v-for="subdir in subdirlist" :key="subdir">
-                <a href="#" @click.prevent="subdirClick(subdir)" :title="subdir">{{subdir}}</a>
-              </div>
-            </div>
-          </div>
-          <div class="container border-bottom">
-            <h3>Files:</h3>
-            <div class="row row-cols-3">
-              <div class="btn col overflow-hidden border" :class="{'btn-warning': filename == chosenFile}"
-                v-for="filename in filelist" :key="filename + chosenFile" @click="chosenFile = filename" :title="filename"
-                @dblclick="chosenFile=filename;chooseFile()">
-                {{filename}}
-              </div>
-            </div>
-          </div>
-          <div class="modal-footer">
-            <button type="button" class="btn btn-secondary" @click="close">Cancel</button>
-            <button type="button" class="btn btn-primary" :class="{disabled: chosenFile == ''}"
-              @click="chooseFile">OK</button>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</template>
-
-<style scoped>
-.active {
-  background-color: light
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/FitOptions.vue b/refl1d/webview/client/src/components/FitOptions.vue
deleted file mode 100644
index aefed075..00000000
--- a/refl1d/webview/client/src/components/FitOptions.vue
+++ /dev/null
@@ -1,217 +0,0 @@
-<script setup lang="ts">
-import { ref, onMounted, computed, shallowRef } from 'vue';
-import { Modal } from 'bootstrap/dist/js/bootstrap.esm';
-import type { Socket } from 'socket.io-client';
-
-const props = defineProps<{socket: Socket}>();
-
-type FitSetting = { name: string, settings: object };
-const dialog = ref<HTMLDivElement>();
-const isOpen = ref(false);
-const fitter_defaults = shallowRef<{ [fit_name: string]: FitSetting }>({});
-const fitter_settings = shallowRef<{ [fit_name: string]: FitSetting }>({});
-const fitter_active = ref<string>("amoeba");
-const fitter_active_local = ref("amoeba");
-
-const FIT_FIELDS = {
-  'starts': ['Starts', 'integer'],
-  'steps': ['Steps', 'integer'],
-  'samples': ['Samples', 'integer'],
-  'xtol': ['x tolerance', 'float'],
-  'ftol': ['f(x) tolerance', 'float'],
-  'alpha': ['Convergence', 'float'],
-  'stop': ['Stopping criteria', 'string'],
-  'thin': ['Thinning', 'integer'],
-  'burn': ['Burn-in steps', 'integer'],
-  'pop': ['Population', 'float'],
-  'init': ['Initializer', ["eps", "lhs", "cov", "random"]],
-  'CR': ['Crossover ratio', 'float'],
-  'F': ['Scale', 'float'],
-  'nT': ['# Temperatures', 'integer'],
-  'Tmin': ['Min temperature', 'float'],
-  'Tmax': ['Max temperature', 'float'],
-  'radius': ['Simplex radius', 'float'],
-  'trim': ['Burn-in trim', 'boolean'],
-  'outliers': ['Outliers', ["none", "iqr", "grubbs", "mahal"]]
-}
-
-const OPTIONS_HELP = {
-  'dream': 'if Steps=0, Steps will be calculated as (Burn-in steps) + (Samples / (Population * Num. Fit Params))'
-}
-
-// make another working copy for editing:
-// const active_settings = ref<{ name: string, settings: object}>({name: "", settings: {}});
-const active_settings = ref({});
-
-props.socket.emit("get_fitter_defaults", (new_fitter_defaults) => {
-  fitter_defaults.value = new_fitter_defaults;
-  fitter_settings.value = structuredClone(new_fitter_defaults);
-})
-
-props.socket.on('fitter_settings', ({timestamp, message: new_fitter_settings}) => {
-    fitter_settings.value = new_fitter_settings
-});
-
-props.socket.on('fitter_active', ({timestamp, message: new_fitter_active}) => {
-    fitter_active.value = new_fitter_active
-});
-
-let modal: Modal;
-
-onMounted(() => {
-  modal = new Modal(dialog.value, { backdrop: 'static', keyboard: false });
-
-});
-
-function close() {
-  modal?.hide();
-}
-
-function open() {
-  // copy the  fitter_active_local from the server state:
-  fitter_active_local.value = fitter_active.value;
-  changeActiveFitter();
-  modal?.show();
-}
-
-const fit_names = computed(() => Object.keys(fitter_defaults?.value));
-
-function changeActiveFitter() {
-  active_settings.value = structuredClone(fitter_settings.value[fitter_active_local.value]?.settings) ?? {};
-}
-
-function process_settings() {
-  return Object.fromEntries(Object.entries(active_settings.value).map(([sname, value]) => {
-    const field_type = FIT_FIELDS[sname][1];
-    let processed_value: any = value;
-    if (field_type === 'integer') {
-      processed_value = Math.round(Number(value));
-    }
-    else if (field_type === 'float') {
-      processed_value = Number(value);
-    }
-    else if (field_type === 'boolean') {
-      // probably unnecessary if it is bound to a checkbox
-      processed_value = Boolean(value);
-    }
-    return [sname, processed_value];
-  }))
-}
-
-function save(start: boolean = false) {
-   if (anyIsInvalid.value) {
-     return;
-   }
-   const new_settings = structuredClone(fitter_settings.value);
-  new_settings[fitter_active_local.value] = { settings: process_settings() };
-  const fitter_settings_local = process_settings();
-  new_settings[fitter_active_local.value] = { settings: fitter_settings_local };
-  props.socket.emit("publish", "fitter_settings", new_settings);
-  props.socket.emit("publish", "fitter_active", fitter_active_local.value);
-  if (start) {
-    props.socket.emit("start_fit_thread", fitter_active_local.value, fitter_settings_local);
-  }
-  close();
-}
-
-function reset() {
-  active_settings.value = structuredClone(fitter_defaults.value[fitter_active_local.value].settings) ?? {};
-}
-
-function validate(value, field_name) {
-  const field_type = FIT_FIELDS[field_name][1];
-  if (Array.isArray(field_type) || field_type === 'boolean') {
-    // there's no way to get an incorrect option.
-    return true;
-  }
-  const float_value = Number(value);
-  if (isNaN(float_value)) {
-    return false;
-  }
-  if (field_type === 'integer' && parseInt(value, 10) != float_value) {
-    return false;
-  }
-  return true;
-}
-
-const anyIsInvalid = computed(() => {
-  return Object.entries(active_settings.value).some(([sname, value]) => !validate(value, sname));
-})
-
-defineExpose({
-  close,
-  open,
-  fitter_settings,
-  fitter_active
-})
-</script>
-
-<template>
-  <div ref="dialog" class="modal fade" id="fitOptionsModal" tabindex="-1" aria-labelledby="fitOptionsLabel"
-    :aria-hidden="isOpen">
-    <div class="modal-dialog modal-lg">
-      <div class="modal-content">
-        <div class="modal-header">
-          <h5 class="modal-title" id="fitOptionsLabel">Fit Options</h5>
-          <button type="button" class="btn-close" @click="close" aria-label="Close"></button>
-        </div>
-        <div class="modal-body">
-          <div class="container">
-            <div class="row border-bottom">
-              <div class="col">
-                <div class="form-check" v-for="fname in fit_names.slice(0,3)" :key="fname">
-                  <input class="form-check-input" v-model="fitter_active_local" type="radio" name="flexRadio"
-                    :id="fname" :value="fname" @change="changeActiveFitter">
-                  <label class="form-check-label" :for="fname">
-                    {{fitter_defaults[fname].name}}
-                    <span v-if="fname !== 'scipy.leastsq'">({{ fname }})</span>
-                  </label>
-                </div>
-              </div>
-              <div class="col">
-                <div class="form-check" v-for="fname in fit_names.slice(3)" :key="fname">
-                  <input class="form-check-input" v-model="fitter_active_local" type="radio" name="flexRadio"
-                    :id="fname" :value="fname" @change="changeActiveFitter">
-                  <label class="form-check-label" :for="fname">
-                    {{fitter_defaults[fname].name}}
-                    <span v-if="fname !== 'scipy.leastsq'">({{ fname }})</span>
-                  </label>
-                </div>
-              </div>
-            </div>
-            <div class="row p-2">
-              <div class="row p-1 text-secondary" v-if="fitter_active_local in OPTIONS_HELP">
-                <span><em>{{ OPTIONS_HELP[fitter_active_local] }}</em></span>
-              </div>
-              <div class="row p-1" v-for="(value, sname, index) in active_settings" :key="sname">
-                <label class="col-sm-4 col-form-label" :for="'setting_' + index">{{FIT_FIELDS[sname][0]}}</label>
-                <div class="col-sm-8">
-                  <select v-if="Array.isArray(FIT_FIELDS[sname][1])" v-model="active_settings[sname]" class="form-select">
-                    <option v-for="opt in FIT_FIELDS[sname][1]">{{opt}}</option>
-                  </select>
-                  <input v-else-if="FIT_FIELDS[sname][1]==='boolean'" class="form-check-input m-2" type="checkbox"
-                    v-model="active_settings[sname]" />
-                  <input v-else :class="{'form-control': true, 'is-invalid': !validate(active_settings[sname], sname)}"
-                    type="text" v-model="active_settings[sname]" @keydown.enter="save" />
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-        <div class="modal-footer">
-          <button type="button" class="btn btn-secondary" @click="reset">Reset Defaults</button>
-          <button type="button" class="btn btn-success" :class="{disabled: anyIsInvalid}" @click="save(true)">Save and Start</button>
-          <button type="button" class="btn btn-primary" :class="{disabled: anyIsInvalid}" @click="save(false)">
-            Save Changes</button>
-
-        </div>
-      </div>
-    </div>
-  </div>
-</template>
-
-<style scoped>
-.form-check label {
-  user-select: none;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/LogView.vue b/refl1d/webview/client/src/components/LogView.vue
deleted file mode 100644
index 0f7e5034..00000000
--- a/refl1d/webview/client/src/components/LogView.vue
+++ /dev/null
@@ -1,44 +0,0 @@
-<script setup lang="ts">
-import { ref, onMounted } from 'vue';
-import type { Socket } from 'socket.io-client';
-
-const title = "Log";
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-const log_info = ref<{message: string, title?: string}[]>([]);
-
-props.socket.on('log', ({message: {message, title}}) => {
-    log_info.value.push({message, title});
-});
-props.socket.emit('get_topic_messages', 'log', (messages) => {
-  log_info.value = [...log_info.value, ...(messages.map((m) => m.message))];
-});
-
-</script>
-        
-<template>
-  <div class="log">
-    <div class="message" v-for="({message, title}, index) of log_info" :key="index">
-      <details v-if="title != null">
-        <summary>{{ title }}</summary>
-        <pre>{{ message }}</pre>
-      </details>
-      <span v-else>{{ message }}</span>
-    </div>
-  </div>
-</template>
-    
-<style scoped>
-
-div.log {
-  white-space: nowrap;
-}
-
-.message {
-  font-family: 'Courier New', Courier, monospace;
-  line-height: 1em;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/ModelInspect.vue b/refl1d/webview/client/src/components/ModelInspect.vue
deleted file mode 100644
index 0b72ae6f..00000000
--- a/refl1d/webview/client/src/components/ModelInspect.vue
+++ /dev/null
@@ -1,96 +0,0 @@
-<script setup lang="ts">
-import { ref, onMounted } from 'vue';
-import { setupDrawLoop } from '../setupDrawLoop';
-import JsonViewer from 'vue-json-viewer';
-import { getDiff } from 'json-difference';
-import type { Socket } from 'socket.io-client';
-
-// from https://github.com/microsoft/TypeScript/issues/1897#issuecomment-1228063688
-type json =
-  | string
-  | number
-  | boolean
-  | null
-  | json[]
-  | { [key: string]: json };
-
-const title = "Model";
-const active_parameter = ref("");
-const modelJson = ref<json>({});
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('update_parameters', props.socket, fetch_and_draw);
-
-props.socket.on('model_loaded', () => { fetch_and_draw(true) });
-
-async function fetch_and_draw(reset: boolean = false) {
-  const payload: json = await props.socket.asyncEmit('get_model');
-  if (reset) {
-    modelJson.value = payload;
-  }
-  else {
-    // do update of existing model:
-    const old_model: json = modelJson.value as Record<string, any>;
-    const new_model: json = payload as Record<string, any>;
-    const diff = getDiff(old_model, new_model);
-    for (let [path, oldval, newval] of diff.edited) {
-      const { target, parent, key } = resolve_diffpath(old_model, path);
-      // trigger reactive update;
-      if (typeof (key) === 'number' && Array.isArray(parent)) {
-        parent.splice(key, 1, newval);
-      }
-      else {
-        parent[key] = newval;
-      }
-    }
-  }
-}
-
-onMounted(() => {
-  props.socket.emit('get_model', (payload: json) => {
-    modelJson.value = payload;
-  });
-})
-
-// function* traverse(o: object, path: string[]=[]) {
-//     for (var i of Object.keys(o)) {
-//         const itemPath = path.concat(i);
-//         yield [i,o[i],itemPath,o];
-//         if (o[i] !== null && typeof(o[i])=="object") {
-//             //going one step down in the object tree!!
-//             yield* traverse(o[i],itemPath);
-//         }
-//     }
-// }
-
-// function resolve(o: object, path: string[] = []) {
-//   let target = o;
-//   for (let pfrag of path) {
-//     target = target[pfrag];
-//   }
-//   return target;
-// }
-
-const ARRAY_PATH_RE = /^([0-9]+)\[\]$/;
-function resolve_diffpath(o: object, diffpath: string) {
-  const pathitems = diffpath.split('/');
-  let target = o;
-  let parent: object = o;
-  let key: number | string = "";
-  for (let pathitem of pathitems) {
-    const array_path = pathitem.match(ARRAY_PATH_RE);
-    parent = target;
-    key = (array_path) ? Number(array_path[1]) : pathitem;
-    target = target[key];
-  }
-  return { target, parent, key };
-}
-
-</script>
-
-<template>
-  <JsonViewer :value="modelJson" />
-</template>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/ModelUncertaintyView.vue b/refl1d/webview/client/src/components/ModelUncertaintyView.vue
deleted file mode 100644
index 9636811c..00000000
--- a/refl1d/webview/client/src/components/ModelUncertaintyView.vue
+++ /dev/null
@@ -1,46 +0,0 @@
-<script setup lang="ts">
-/// <reference types="@types/uuid"/>
-import { ref } from 'vue';
-import { Socket } from 'socket.io-client';
-import { v4 as uuidv4 } from 'uuid';
-import { setupDrawLoop } from '../setupDrawLoop';
-import { cache } from '../plotcache';
-import mpld3 from 'mpld3';
-
-const title = "Model Uncertainty"
-const plot_div = ref<HTMLDivElement>();
-const plot_div_id = ref(`div-${uuidv4()}`);
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
-
-async function fetch_and_draw(latest_timestamp: string) {
-  let { timestamp, plotdata } = cache[title] ?? {};
-  if (timestamp !== latest_timestamp) {
-    console.log("fetching new model uncertainty plot", timestamp, latest_timestamp);
-    const payload = await props.socket.asyncEmit('get_model_uncertainty_plot');
-    plotdata = { ...payload };
-    cache[title] = {timestamp: latest_timestamp, plotdata};
-  }
-  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-}
-
-</script>
-    
-<template>
-  <div class="container d-flex flex-grow-1 flex-column">
-    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
-    </div>
-  </div>
-</template>
-
-<style scoped>
-svg {
-  width: 100%;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/PanelTabContainer.vue b/refl1d/webview/client/src/components/PanelTabContainer.vue
deleted file mode 100644
index 690fa95d..00000000
--- a/refl1d/webview/client/src/components/PanelTabContainer.vue
+++ /dev/null
@@ -1,48 +0,0 @@
-<script setup lang="ts">
-import { ref, onMounted } from 'vue';
-import type { Socket } from 'socket.io-client';
-
-// type PanelComponent = DefineComponent<{socket: Socket, visible: boolean}, any>;
-
-const tabTriggers = ref<HTMLAnchorElement[]>([]);
-
-const props = defineProps<{
-  socket: Socket,
-  panels: {title: string, component: unknown}[],
-  active_panel: number
-}>();
-
-const emit = defineEmits<{
-  (e: 'panel_changed', active_panel: number): void
-}>();
-
-
-function setActive(index: number) {
-  emit("panel_changed", index);
-}
-
-</script>
-
-<template>
-  <ul class="nav nav-tabs">
-    <li class="nav-item" v-for="(panel, index) in props.panels" :key="index">
-      <a ref="tabTriggers" :class="{'nav-link': true, active: index == active_panel}" href="#" @click="setActive(index)">{{panels[index]?.title}}</a>
-    </li>
-  </ul>
-  <div class="tab-content d-flex flex-column flex-grow-1 overflow-auto">
-      <component :is="panels[active_panel].component" :socket="props.socket" :visible="true"></component>
-  </div>
-</template>
-
-<style scoped>
-.tab-content>.tab-pane {
-  display: none;
-}
-
-.tab-content {
-  display: flex !important;
-  flex-grow: 1;
-  flex-shrink: 0;
-  flex-basis: 200px;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/ParameterTraceView.vue b/refl1d/webview/client/src/components/ParameterTraceView.vue
deleted file mode 100644
index 3b51bb57..00000000
--- a/refl1d/webview/client/src/components/ParameterTraceView.vue
+++ /dev/null
@@ -1,39 +0,0 @@
-<script setup lang="ts">
-/// <reference types="@types/uuid"/>
-import { ref } from 'vue';
-import { Socket } from 'socket.io-client';
-import { v4 as uuidv4 } from 'uuid';
-import { setupDrawLoop } from '../setupDrawLoop';
-import mpld3 from 'mpld3';
-
-const plot_div = ref<HTMLDivElement>();
-const plot_div_id = ref(`div-${uuidv4()}`);
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw);
-
-async function fetch_and_draw() {
-  const payload = await props.socket.asyncEmit('get_parameter_trace_plot');
-  let plotdata = { ...payload };
-  console.log({plotdata});
-  plotdata.width = Math.round(plot_div.value?.clientWidth ?? 640) - 16;
-  plotdata.height = Math.round(plot_div.value?.clientHeight ?? 480) - 16;
-  mpld3.draw_figure(plot_div_id.value, plotdata, false, true);
-}
-
-</script>
-    
-<template>
-  <div class="container d-flex flex-grow-1 flex-column">
-    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
-    </div>
-  </div>
-</template>
-
-<style scoped>
-svg {
-  width: 100%;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/ParameterView.vue b/refl1d/webview/client/src/components/ParameterView.vue
deleted file mode 100644
index 7bbc6be9..00000000
--- a/refl1d/webview/client/src/components/ParameterView.vue
+++ /dev/null
@@ -1,103 +0,0 @@
-<script setup lang="ts">
-import { ref } from 'vue';
-import type { Socket } from 'socket.io-client';
-import { setupDrawLoop } from '../setupDrawLoop';
-
-const title = "Parameters";
-const active_parameter = ref("");
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('update_parameters', props.socket, fetch_and_draw);
-
-type parameter_info = {
-  name: string,
-  id: string,
-  fittable: boolean,
-  fixed: boolean,
-  paths: string[],
-  link: string,
-  writable: boolean,
-  value_str: string,
-  min_str: string,
-  max_str: string,
-  active?: boolean,
-}
-
-const parameters = ref<parameter_info[]>([]);
-const parameters_local = ref<parameter_info[]>([]);
-
-async function fetch_and_draw() {
-  const payload = await props.socket.asyncEmit('get_parameters', false);
-  const pl = parameters_local.value;
-  payload.forEach((p, i) => {
-    if (!(pl[i]?.active)) {
-      pl.splice(i, 1, p);
-    }
-  });
-  pl.splice(payload.length);
-}
-
-async function editItem(ev, item_name: "min" | "max" | "value", index: number) {
-  const new_value = ev.target.innerText;
-  if (validate_numeric(new_value)) {
-    props.socket.emit('set_parameter', parameters_local.value[index].id, item_name, new_value);
-  }
-}
-
-function validate_numeric(value: string, allow_inf: boolean = false) {
-  if (allow_inf && (value === "inf" || value === "-inf")) {
-    return true
-  }
-  return !Number.isNaN(Number(value))
-}
-
-async function onInactive(param) {
-  param.active = false;
-  fetch_and_draw();
-}
-
-async function setFittable(ev, index) {
-  console.log(ev, ev.target, index, parameters_local.value[index].fixed);
-  const parameter = parameters_local.value[index];
-  props.socket.emit('set_parameter', parameter.id, "fixed", !parameter.fixed);
-}
-
-</script>
-        
-<template>
-  <table class="table">
-    <thead class="border-bottom py-1">
-      <tr>
-        <th scope="col">Fit?</th>
-        <th scope="col">Name</th>
-        <th scope="col">Value</th>
-        <th scope="col">Paths</th>
-      </tr>
-    </thead>
-    <tbody>
-      <tr class="py-1" v-for="(param, index) in parameters_local" :key="param.id">
-        <td>
-          <input class="form-check-input" v-if="param.fittable" type="checkbox" :checked="!param.fixed"
-            @click.prevent="setFittable($event, index)" />
-        </td>
-        <td>{{ param.name }}</td>
-        <td :contenteditable="param.writable" spellcheck="false" @blur="editItem($event, 'value', index)"
-          @keydown.enter="$event?.target?.blur()">{{ param.value_str }}
-        </td>
-        <td>
-          <p class="my-0" v-for="path in param.paths" :key="path">{{ path }}</p>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-</template>
-    
-<style scoped>
-
-table {
-  white-space: nowrap;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/SummaryView.vue b/refl1d/webview/client/src/components/SummaryView.vue
deleted file mode 100644
index 65096618..00000000
--- a/refl1d/webview/client/src/components/SummaryView.vue
+++ /dev/null
@@ -1,122 +0,0 @@
-<script setup lang="ts">
-import { ref } from 'vue';
-import type { Socket } from 'socket.io-client';
-import { setupDrawLoop} from '../setupDrawLoop';
-
-const title = "Summary";
-
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('update_parameters', props.socket, fetch_and_draw, title);
-
-type parameter_info = {
-  name: string,
-  id: string,
-  value01: number,
-  value_str: string,
-  min_str: string,
-  max_str: string,
-  active?: boolean,
-}
-
-const parameters = ref<parameter_info[]>([]);
-const parameters_local01 = ref<number[]>([]);
-const parameters_localstr = ref<string[]>([]);
-
-async function fetch_and_draw() {
-  const payload: parameter_info[] = await props.socket.asyncEmit('get_parameters', true)
-  const pv = parameters.value;
-  payload.forEach((p, i) => {
-    parameters_localstr.value[i] = p.value_str;
-    if (!(pv[i]?.active)) {
-      pv.splice(i, 1, p);
-      parameters_local01.value[i] = p.value01;
-    }
-  });
-  pv.splice(payload.length);
-  parameters_local01.value.splice(payload.length);
-  parameters_localstr.value.splice(payload.length);
-}
-
-async function onMove(param_index) {
-  // props.socket.volatile.emit('set_parameter01', parameters.value[param_index].name, parameters_local01.value[param_index]);
-  props.socket.emit('set_parameter', parameters.value[param_index].id, "value01", parameters_local01.value[param_index]);
-}
-
-async function editItem(ev, item_name: "min" | "max" | "value", index: number) {
-  const new_value = ev.target.innerText;
-  if (validate_numeric(new_value)) {
-    props.socket.emit('set_parameter', parameters.value[index].id, item_name, new_value);
-  }
-}
-
-function validate_numeric(value: string, allow_inf: boolean = false) {
-  if (allow_inf && (value === "inf" || value === "-inf")) {
-    return true
-  }
-  return !Number.isNaN(Number(value))
-}
-
-async function scrollParam(ev, index) {
-  const sign = Math.sign(ev.deltaY);
-  parameters_local01.value[index] -= 0.01 * sign;
-  props.socket.emit('set_parameter', parameters.value[index].id, "value01", parameters_local01.value[index]);
-}
-
-async function onInactive(param) {
-  param.active = false;
-  fetch_and_draw();
-}
-
-</script>
-        
-<template>
-  <table class="table table-sm">
-    <thead class="border-bottom py-1">
-      <tr>
-        <th scope="col">Fit Parameter</th>
-        <th scope="col"></th>
-        <th scope="col">Value</th>
-        <th scope="col">Min</th>
-        <th scope="col">Max</th>
-      </tr>
-    </thead>
-    <tbody>
-      <tr class="py-1" v-for="(param, index) in parameters" :key="param.id">
-        <td>{{ param.name }}</td>
-        <td>
-          <input type="range" class="form-range" min="0" max="1.0" step="0.005"
-            v-model.number="parameters_local01[index]" @mousedown="param.active = true" @input="onMove(index)"
-            @change="onInactive(param)" @wheel="scrollParam($event, index)" />
-        </td>
-        <td class="editable" contenteditable="true" spellcheck="false" @blur="editItem($event, 'value', index)"
-          @keydown.enter="$event?.target?.blur()">{{ parameters_localstr[index] }}</td>
-        <td class="editable" contenteditable="true" spellcheck="false" @blur="editItem($event, 'min', index)"
-          @keydown.enter="$event?.target?.blur()">{{ param.min_str }}</td>
-        <td class="editable" contenteditable="true" spellcheck="false" @blur="editItem($event, 'max', index)"
-          @keydown.enter="$event?.target?.blur()">{{ param.max_str }}</td>
-      </tr>
-    </tbody>
-  </table>
-</template>
-    
-<style scoped>
-svg {
-  width: 100%;
-  white-space: nowrap;
-}
-
-td.editable {
-  min-width: 5em;
-}
-
-td {
-
-}
-
-td > input {
-  min-width: 5em;
-}
-</style>
\ No newline at end of file
diff --git a/refl1d/webview/client/src/components/UncertaintyView.vue b/refl1d/webview/client/src/components/UncertaintyView.vue
deleted file mode 100644
index 820ae409..00000000
--- a/refl1d/webview/client/src/components/UncertaintyView.vue
+++ /dev/null
@@ -1,52 +0,0 @@
-<script setup lang="ts">
-/// <reference types="@types/uuid"/>
-import { ref } from 'vue';
-import { Socket } from 'socket.io-client';
-import { v4 as uuidv4 } from 'uuid';
-import { setupDrawLoop } from '../setupDrawLoop';
-import { cache } from '../plotcache';
-import * as Plotly from 'plotly.js/lib/core';
-import Bar from 'plotly.js/lib/bar';
-
-Plotly.register([
-  Bar,
-])
-
-const title = "Uncertainty";
-const plot_div = ref<HTMLDivElement>();
-const plot_div_id = ref(`div-${uuidv4()}`);
-const props = defineProps<{
-  socket: Socket,
-}>();
-
-setupDrawLoop('uncertainty_update', props.socket, fetch_and_draw, title);
-
-async function fetch_and_draw(latest_timestamp: string) {
-  let { timestamp, plotdata } = cache[title] ?? {};
-  if (timestamp !== latest_timestamp) {
-    console.log("fetching new uncertainty plot", timestamp, latest_timestamp);
-    const payload = await props.socket.asyncEmit('get_uncertainty_plot');
-    plotdata = { ...payload };
-    cache[title] = {timestamp: latest_timestamp, plotdata};
-  }
-  const { data, layout } = plotdata;
-  delete layout.width;
-  delete layout.height;
-  const config = { responsive: true }
-  await Plotly.react(plot_div_id.value, [...data], layout, config);
-}
-
-</script>
-    
-<template>
-  <div class="container d-flex flex-grow-1 flex-column">
-    <div class="flex-grow-1" ref="plot_div" :id="plot_div_id">
-    </div>
-  </div>
-</template>
-
-<style scoped>
-svg {
-  width: 100%;
-}
-</style>
\ No newline at end of file

From b755fd65cd32af33200bbdeb1d459dd74473f53d Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 16 Mar 2023 12:33:19 -0400
Subject: [PATCH 208/221] import almost all functions from bumps webview,
 leaving only refl1d-specific functions

---
 refl1d/webview/server/webserver.py | 892 +----------------------------
 1 file changed, 31 insertions(+), 861 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 43bc79a2..48ad4a66 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -1,120 +1,20 @@
-# from .main import setup_bumps
-
-from dataclasses import dataclass
-import itertools
-import threading
-import signal
-from types import GeneratorType
-from typing import Dict, List, Literal, Optional, Union, Tuple, TypedDict, cast
-from datetime import datetime
-import warnings
-from queue import Queue
-from collections import deque
-from aiohttp import web, ClientSession
-import numpy as np
-import asyncio
-import socketio
-from pathlib import Path, PurePath
+from aiohttp import web
 import json
-from copy import deepcopy
-from blinker import Signal
-from uuid import uuid4
-
-import mimetypes
-mimetypes.add_type("text/css", ".css")
-mimetypes.add_type("text/html", ".html")
-mimetypes.add_type("application/json", ".json")
-mimetypes.add_type("text/javascript", ".js")
-mimetypes.add_type("text/javascript", ".mjs")
-mimetypes.add_type("image/png", ".png")
-mimetypes.add_type("image/svg+xml", ".svg")
-
-from bumps.fitters import DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit, FitDriver, fit, nllf_scale, format_uncertainty
-from bumps.serialize import to_dict as serialize, from_dict as deserialize
-from bumps.mapper import MPMapper
-from bumps.parameter import Parameter, Variable, unique
-import bumps.fitproblem
-import bumps.plotutil
-import bumps.dream.views, bumps.dream.varplot, bumps.dream.stats, bumps.dream.state
-import bumps.errplot
-import refl1d.errors
-import refl1d.fitproblem, refl1d.probe
-from refl1d.experiment import Experiment, MixedExperiment, ExperimentBase
-
-# Register the refl1d model loader
-import refl1d.fitplugin
-import bumps.cli
-bumps.cli.install_plugin(refl1d.fitplugin)
-
-from .fit_thread import FitThread, EVT_FIT_COMPLETE, EVT_FIT_PROGRESS
-
-### BEGIN PATCH
-# patch the plotly library to disable levenshtein lookup for missing strings
-# which is taking a ridiculous amount of time in make_subplots
-# See: https://github.com/plotly/plotly.py/issues/4100
-def disable_find_closest_string(string, strings):
-    raise ValueError()
+from pathlib import Path
+from typing import Union, Dict
 
-import _plotly_utils.utils
-_plotly_utils.utils.find_closest_string = disable_find_closest_string
-### END PATCH
+import numpy as np
+import bumps.webview.server.webserver as server
+from bumps.webview.server.webserver import app, main, sio, rest_get, state, get_chisq, to_json_compatible_dict
+from refl1d.experiment import Experiment, ExperimentBase, MixedExperiment
+import refl1d.probe
 
 from .profile_plot import plot_sld_profile_plotly
-from .varplot import plot_vars
-from .state_hdf5_backed import State
-# from .state import State
-
-# can get by name and not just by id
-MODEL_EXT = '.json'
-
-FITTERS = (DreamFit, LevenbergMarquardtFit, SimplexFit, DEFit, MPFit, BFGSFit)
-FITTERS_BY_ID = dict([(fitter.id, fitter) for fitter in FITTERS])
-print(FITTERS_BY_ID)
-FITTER_DEFAULTS = {}
-for fitter in FITTERS:
-    FITTER_DEFAULTS[fitter.id] = {
-        "name": fitter.name,
-        "settings": dict(fitter.settings)
-    }
 
-
-routes = web.RouteTableDef()
-# sio = socketio.AsyncServer(cors_allowed_origins="*", serializer='msgpack')
-sio = socketio.AsyncServer(cors_allowed_origins="*")
-app = web.Application()
 client_path = Path(__file__).parent.parent / 'client'
 index_path = client_path / 'dist'
 static_assets_path = index_path / 'assets'
 
-sio.attach(app)
-
-TopicNameType = Literal[
-    "log",
-    "update_parameters",
-    "update_model",
-    "model_loaded",
-    "fit_active",
-    "uncertainty_update",
-    "convergence_update",
-    "fitter_settings",
-    "fitter_active",
-]
-
-
-state: State # to be filled in later...
-
-def rest_get(fn):
-    """
-    Add a REST (GET) route for the function, which can also be used for 
-    """
-    @routes.get(f"/{fn.__name__}")
-    async def handler(request: web.Request):
-        result = await fn(**request.query)
-        return web.json_response(result)
-    
-    # pass the function to the next decorator unchanged...
-    return fn
-
 async def index(request):
     """Serve the client-side application."""
     # check if the locally-build site has the correct version:
@@ -135,248 +35,6 @@ async def index(request):
             index_html = index_template.read().format(cdn=CDN)
         return web.Response(body=index_html, content_type="text/html")
     
-@sio.event
-async def connect(sid, environ, data=None):
-    # re-send last message for all topics
-    # now that panels are retrieving topics when they load, is this still
-    # needed or useful?
-    for topic, contents in state.topics.items():
-        message = contents[-1] if len(contents) > 0 else None
-        if message is not None:
-            await sio.emit(topic, message, to=sid)
-    print("connect ", sid)
-
-@sio.event
-async def load_problem_file(sid: str, pathlist: List[str], filename: str):    
-    path = Path(*pathlist, filename)
-    print(f'model loading: {path}')
-    await log(f'model_loading: {path}')
-    if filename.endswith(".json"):
-        with open(path, "rt") as input_file:
-            serialized = json.loads(input_file.read())
-        problem = deserialize(serialized)
-    else:
-        from bumps.cli import load_model
-        problem = load_model(str(path))
-    assert isinstance(problem, bumps.fitproblem.FitProblem)
-    # problem_state = ProblemState(problem, pathlist, filename)
-    state.problem.filename = filename
-    state.problem.pathlist = pathlist
-    state.problem.fitProblem = problem
-    print(f'model loaded: {path}')
-    await log(f'model loaded: {path}')
-    await publish("", "model_loaded", {"pathlist": pathlist, "filename": filename})
-    await publish("", "update_model", True)
-    await publish("", "update_parameters", True)
-
-@sio.event
-async def get_model_names(sid: str=""):
-    problem = state.problem.fitProblem
-    if problem is None:
-        return None
-    output: List[Dict] = []
-    for model_index, model in enumerate(problem.models):
-        if isinstance(model, Experiment):
-            output.append(dict(name=model.name, part_name=None, model_index=model_index, part_index=0))
-        elif isinstance(model, MixedExperiment):
-            for part_index, part in enumerate(model.parts):
-                output.append(dict(name=model.name, part_name=part.name, model_index=model_index, part_index=part_index))
-    return output
-
-@sio.event
-async def save_problem_file(sid: str, pathlist: Optional[List[str]] = None, filename: Optional[str] = None, overwrite: bool = False):
-    problem_state = state.problem
-    if problem_state is None:
-        print("Save failed: no problem loaded.")
-        return
-    if pathlist is None:
-        pathlist = problem_state.pathlist
-    if filename is None:
-        filename = problem_state.filename
-
-    if pathlist is None or filename is None:
-        print("no filename and path provided to save")
-        return
-
-    path = Path(*pathlist)
-    save_filename = Path(filename).stem + MODEL_EXT
-    print({"path": path, "filename": save_filename})
-    if not overwrite and Path.exists(path / save_filename):
-        #confirmation needed:
-        return save_filename
-
-    serialized = serialize(problem_state.fitProblem)
-    with open(Path(path, save_filename), "wt") as output_file:
-        output_file.write(json.dumps(serialized))
-
-    await log(f'Saved: {filename} at path: {path}')
-    return False
-
-@sio.event
-async def start_fit(sid: str="", fitter_id: str="", kwargs=None):
-    kwargs = {} if kwargs is None else kwargs
-    problem_state = state.problem
-    if problem_state is None:
-        await log("Error: Can't start fit if no problem loaded")
-    else:
-        fitProblem = problem_state.fitProblem
-        mapper = MPMapper.start_mapper(fitProblem, None, cpus=0)
-        monitors = []
-        fitclass = FITTERS_BY_ID[fitter_id]
-        driver = FitDriver(fitclass=fitclass, mapper=mapper, problem=fitProblem, monitors=monitors, **kwargs)
-        x, fx = driver.fit()
-        driver.show()
-
-@sio.event
-async def stop_fit(sid: str = ""):
-    abort_queue = state.abort_queue
-    abort_queue.put_nowait(True)
-
-def get_chisq(problem: refl1d.fitproblem.FitProblem, nllf=None):
-    nllf = problem.nllf() if nllf is None else nllf
-    scale, err = nllf_scale(problem)
-    chisq = format_uncertainty(scale*nllf, err)
-    return chisq
-
-def get_num_steps(fitter_id: str, num_fitparams: int, options: Optional[Dict] = None):
-    options = FITTER_DEFAULTS[fitter_id] if options is None else options
-    steps = options['steps']
-    if fitter_id == 'dream' and steps == 0:
-        print('dream: ', options)
-        total_pop = options['pop'] * num_fitparams
-        print('total_pop: ', total_pop)
-        sample_steps = int(options['samples'] / total_pop)
-        print('sample_steps: ', sample_steps)
-        print('steps: ', options['burn'] + sample_steps)
-        return options['burn'] + sample_steps
-    else:
-        return steps
-
-@sio.event
-async def start_fit_thread(sid: str="", fitter_id: str="", options=None, terminate_on_finish=False):
-    options = {} if options is None else options    # session_id: str = app["active_session"]
-    fitProblem = state.problem.fitProblem if state.problem is not None else None
-    if fitProblem is None:
-        await log("Error: Can't start fit if no problem loaded")
-    else:
-        fit_state = state.fitting
-        fitclass = FITTERS_BY_ID[fitter_id]
-        if state.fit_thread is not None:
-            # warn that fit is alread running...
-            print("fit already running...")
-            await log("Can't start fit, a fit is already running...")
-            return
-        
-        # TODO: better access to model parameters
-        num_params = len(fitProblem.getp())
-        if num_params == 0:
-            raise ValueError("Problem has no fittable parameters")
-
-        # Start a new thread worker and give fit problem to the worker.
-        # Clear abort and uncertainty state
-        # state.abort = False
-        # state.fitting.uncertainty_state = None
-        num_steps = get_num_steps(fitter_id, num_params, options)
-        state.abort_queue = abort_queue = Queue()
-        fit_thread = FitThread(
-            abort_queue=abort_queue,
-            problem=fitProblem,
-            fitclass=fitclass,
-            options=options,
-            # session_id=session_id,
-            # Number of seconds between updates to the GUI, or 0 for no updates
-            convergence_update=5,
-            uncertainty_update=3600,
-            terminate_on_finish=terminate_on_finish,
-            )
-        fit_thread.start()
-        state.fit_thread = fit_thread
-        await sio.emit("fit_progress", {}) # clear progress
-        await publish("", "fit_active", to_json_compatible_dict(dict(fitter_id=fitter_id, options=options, num_steps=num_steps)))
-        await log(json.dumps(to_json_compatible_dict(options), indent=2), title = f"starting fitter {fitter_id}")
-
-async def _fit_progress_handler(event: Dict):
-    # session_id = event["session_id"]
-    problem_state = state.problem
-    fitProblem = problem_state.fitProblem if problem_state is not None else None
-    if fitProblem is None:
-        raise ValueError("should never happen: fit progress reported for session in which fitProblem is undefined")
-    message = event.get("message", None)
-    if message == 'complete' or message == 'improvement':
-        fitProblem.setp(event["point"])
-        fitProblem.model_update()
-        await publish("", "update_parameters", True)
-        if message == 'complete':
-            await publish("", "fit_active", {})
-    elif message == 'convergence_update':
-        state.fitting.population = event["pop"]
-        await publish("", "convergence_update", True)
-    elif message == 'progress':
-        await sio.emit("fit_progress", to_json_compatible_dict(event))
-    elif message == 'uncertainty_update' or message == 'uncertainty_final':
-        state.fitting.uncertainty_state = cast(bumps.dream.state.MCMCDraw, event["uncertainty_state"])
-        await publish("", "uncertainty_update", True)
-
-def fit_progress_handler(event: Dict):
-    asyncio.run_coroutine_threadsafe(_fit_progress_handler(event), app.loop)
-
-EVT_FIT_PROGRESS.connect(fit_progress_handler)
-
-async def _fit_complete_handler(event):
-    print("complete event: ", event.get("message", ""))
-    message = event.get("message", None)
-    fit_thread = state.fit_thread
-    terminate = False
-    if fit_thread is not None:
-        print(fit_thread)
-        terminate = fit_thread.terminate_on_finish
-        fit_thread.join(1) # 1 second timeout on join
-        if fit_thread.is_alive():
-            await log("fit thread failed to complete")
-    state.fit_thread = None
-    problem: refl1d.fitproblem.FitProblem = event["problem"]
-    chisq = nice(2*event["value"]/problem.dof)
-    problem.setp(event["point"])
-    problem.model_update()
-    await publish("", "fit_active", {})
-    await publish("", "update_parameters", True)
-    await log(event["info"], title=f"done with chisq {chisq}")
-    if terminate:
-        await shutdown()
-
-def fit_complete_handler(event: Dict):
-    asyncio.run_coroutine_threadsafe(_fit_complete_handler(event), app.loop)
-
-EVT_FIT_COMPLETE.connect(fit_complete_handler)
-
-async def log(message: str, title: Optional[str] = None):
-    await publish("", "log", {"message": message, "title": title})
-
-def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
-    fresnel_calculator = probe.fresnel(substrate, surface)
-    Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
-    Q, R = theory
-    output: Dict[str, Union[str, np.ndarray]]
-    assert isinstance(FQ, np.ndarray)
-    if len(Q) != len(probe.Q):
-        # Saving interpolated data
-        output = dict(Q = Q, theory = R, fresnel=np.interp(Q, probe.Q, FQ))
-    elif getattr(probe, 'R', None) is not None:
-        output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, theory = R, fresnel = FQ, background=probe.background.value, intensity=probe.intensity.value)
-    else:
-        output = dict(Q = probe.Q, dQ = probe.dQ, theory = R, fresnel = FQ)
-    output['label'] = f"{probe.label()} {label}"
-    return output
-
-def get_probe_data(theory, probe, substrate=None, surface=None):
-    if isinstance(probe, refl1d.probe.PolarizedNeutronProbe):
-        output = []
-        for xsi, xsi_th, suffix in zip(probe.xs, theory, ('--', '-+', '+-', '++')):
-            if xsi is not None:
-                output.append(get_single_probe_data(xsi_th, xsi, substrate, surface, suffix))
-        return output
-    else:
-        return [get_single_probe_data(theory, probe, substrate, surface)]
 
 @sio.event
 @rest_get
@@ -408,14 +66,6 @@ async def get_plot_data(sid: str="", view: str = 'linear'):
         # result.append(output)
     return to_json_compatible_dict(result)
 
-@sio.event
-@rest_get
-async def get_model(sid: str=""):
-    if state.problem is None or state.problem.fitProblem is None:
-        return None
-    fitProblem = state.problem.fitProblem
-    return serialize(fitProblem)
-
 @sio.event
 @rest_get
 async def get_profile_plot(sid: str="", model_index: int=0, sample_index: int=0):
@@ -432,513 +82,33 @@ async def get_profile_plot(sid: str="", model_index: int=0, sample_index: int=0)
     fig = plot_sld_profile_plotly(model)
     return to_json_compatible_dict(fig.to_dict())
 
-@sio.event
-@rest_get
-async def get_profile_data(sid: str="", model_index: int=0):
-    if state.problem is None or state.problem.fitProblem is None:
-        return None
-    fitProblem = state.problem.fitProblem
-    models = list(fitProblem.models)
-    if (model_index > len(models)):
-        return None
-    model = models[model_index]
-    assert(isinstance(model, ExperimentBase))
-    output = {}
-    output["ismagnetic"] = model.ismagnetic
-    if model.ismagnetic:
-        if not model.step_interfaces:
-            z, rho, irho, rhoM, thetaM = model.magnetic_step_profile()
-            output['step_profile'] = dict(z=z, rho=rho, irho=irho, rhoM=rhoM, thetaM=thetaM)
-        z, rho, irho, rhoM, thetaM = model.magnetic_smooth_profile()
-        output['smooth_profile'] = dict(z=z, rho=rho, irho=irho, rhoM=rhoM, thetaM=thetaM)
-    else:
-        if not model.step_interfaces:
-            z, rho, irho = model.step_profile()
-            output['step_profile'] = dict(z=z, rho=rho, irho=irho)
-        z, rho, irho = model.smooth_profile()
-        output['smooth_profile'] = dict(z=z, rho=rho, irho=irho)
-    return to_json_compatible_dict(output)
-
-@sio.event
-@rest_get
-async def get_convergence_plot(sid: str=""):
-    # NOTE: this is slow.  Creating the figure takes around 0.15 seconds, 
-    # and converting to mpld3 can take as much as 0.5 seconds.
-    # Might want to replace with plotting on the client side (normalizing population takes around 1 ms)
-    if state.problem is None or state.problem.fitProblem is None:
-        return None
-    fitProblem = state.problem.fitProblem
-    population = state.fitting.population
-    if population is not None:
-        import mpld3
-        import matplotlib
-        matplotlib.use("agg")
-        import matplotlib.pyplot as plt
-        import time
-        start_time = time.time()
-        print('queueing new convergence plot...', start_time)
-
-        normalized_pop = 2*population/fitProblem.dof
-        best, pop = normalized_pop[:, 0], normalized_pop[:, 1:]
-        print("time to normalize population: ", time.time() - start_time)
-        fig = plt.figure()
-        axes = fig.add_subplot(111)
-
-        ni,npop = pop.shape
-        iternum = np.arange(1,ni+1)
-        tail = int(0.25*ni)
-        c = bumps.plotutil.coordinated_colors(base=(0.4,0.8,0.2))
-        if npop==5:
-            axes.fill_between(iternum[tail:], pop[tail:,1], pop[tail:,3],
-                                color=c['light'], label='_nolegend_')
-            axes.plot(iternum[tail:],pop[tail:,2],
-                        label="80% range", color=c['base'])
-            axes.plot(iternum[tail:],pop[tail:,0],
-                        label="_nolegend_", color=c['base'])
-        axes.plot(iternum[tail:], best[tail:], label="best",
-                    color=c['dark'])
-        axes.set_xlabel('iteration number')
-        axes.set_ylabel('chisq')
-        axes.legend()
-        #plt.gca().set_yscale('log')
-        # fig.draw()
-        print("time to render but not serialize...", time.time() - start_time)
-        dfig = mpld3.fig_to_dict(fig)
-        plt.close(fig)
-        # await sio.emit("profile_plot", dfig, to=sid)
-        end_time = time.time()
-        print("time to draw convergence plot:", end_time - start_time)
-        return dfig
-    else:
-        return None
-
-@sio.event
-@rest_get
-async def get_correlation_plot(sid: str = "", nbins: int=50):
-    from .corrplot import Corr2d
-    uncertainty_state = state.fitting.uncertainty_state
-
-    if isinstance(uncertainty_state, bumps.dream.state.MCMCDraw):
-        import time
-        start_time = time.time()
-        print('queueing new correlation plot...', start_time)
-        draw = uncertainty_state.draw()
-        c = Corr2d(draw.points.T, bins=nbins, labels=draw.labels)
-        fig = c.plot()
-        print("time to render but not serialize...", time.time() - start_time)
-        serialized = to_json_compatible_dict(fig.to_dict())
-        end_time = time.time()
-        print("time to draw correlation plot:", end_time - start_time)
-        return serialized
-    else:
-        return None
-
-@sio.event
-@rest_get
-async def get_uncertainty_plot(sid: str = ""):
-    uncertainty_state = state.fitting.uncertainty_state
-    if uncertainty_state is not None:
-        import time
-        start_time = time.time()
-        print('queueing new uncertainty plot...', start_time)
-        draw = uncertainty_state.draw()
-        stats = bumps.dream.stats.var_stats(draw)
-        fig = plot_vars(draw, stats)
-        return to_json_compatible_dict(fig.to_dict())
-    else:
-        return None
-
-@sio.event
-@rest_get
-async def get_model_uncertainty_plot(sid: str = ""):
-    if state.problem is None or state.problem.fitProblem is None:
-        return None
-    fitProblem = state.problem.fitProblem
-    uncertainty_state = state.fitting.uncertainty_state
-    if uncertainty_state is not None:
-        import mpld3
-        import matplotlib
-        matplotlib.use("agg")
-        import matplotlib.pyplot as plt
-        import time
-        start_time = time.time()
-        print('queueing new model uncertainty plot...', start_time)
-
-        fig = plt.figure()
-        errs = bumps.errplot.calc_errors_from_state(fitProblem, uncertainty_state)
-        print('errors calculated: ', time.time() - start_time)
-        bumps.errplot.show_errors(errs, fig=fig)
-        print("time to render but not serialize...", time.time() - start_time)
-        fig.canvas.draw()
-        dfig = mpld3.fig_to_dict(fig)
-        plt.close(fig)
-        # await sio.emit("profile_plot", dfig, to=sid)
-        end_time = time.time()
-        print("time to draw model uncertainty plot:", end_time - start_time)
-        return dfig
-    else:
-        return None
-
-@sio.event
-@rest_get
-async def get_parameter_trace_plot(sid: str=""):
-    uncertainty_state = state.fitting.uncertainty_state
-    if uncertainty_state is not None:
-        import mpld3
-        import matplotlib
-        matplotlib.use("agg")
-        import matplotlib.pyplot as plt
-        import time
-
-        start_time = time.time()
-        print('queueing new parameter_trace plot...', start_time)
-
-        fig = plt.figure()
-        axes = fig.add_subplot(111)
-
-        # begin plotting:
-        var = 0
-        portion = None
-        draw, points, _ = uncertainty_state.chains()
-        label = uncertainty_state.labels[var]
-        start = int((1-portion)*len(draw)) if portion else 0
-        genid = np.arange(uncertainty_state.generation-len(draw)+start, uncertainty_state.generation)+1
-        axes.plot(genid*uncertainty_state.thinning,
-             np.squeeze(points[start:, uncertainty_state._good_chains, var]))
-        axes.set_xlabel('Generation number')
-        axes.set_ylabel(label)
-        fig.canvas.draw()
-
-        print("time to render but not serialize...", time.time() - start_time)
-        dfig = mpld3.fig_to_dict(fig)
-        plt.close(fig)
-        # await sio.emit("profile_plot", dfig, to=sid)
-        end_time = time.time()
-        print("time to draw parameter_trace plot:", end_time - start_time)
-        return dfig
-    else:
-        return None
-    
-
-@sio.event
-@rest_get
-async def get_parameters(sid: str = "", only_fittable: bool = False):
-    if state.problem is None or state.problem.fitProblem is None:
-        return []
-    fitProblem = state.problem.fitProblem
-
-    all_parameters = fitProblem.model_parameters()
-    if only_fittable:
-        parameter_infos = params_to_list(unique(all_parameters))
-        # only include params with priors:
-        parameter_infos = [pi for pi in parameter_infos if pi['fittable'] and not pi['fixed']]
-    else:
-        parameter_infos = params_to_list(all_parameters)
-        
-    return to_json_compatible_dict(parameter_infos)
-
-@sio.event
-async def set_parameter(sid: str, parameter_id: str, property: Literal["value01", "value", "min", "max"], value: Union[float, str, bool]):
-    if state.problem is None or state.problem.fitProblem is None:
-        return None
-    fitProblem = state.problem.fitProblem
-
-    parameter = fitProblem._parameters_by_id.get(parameter_id, None)
-    if parameter is None:
-        warnings.warn(f"Attempting to update parameter that doesn't exist: {parameter_id}")
-        return
-
-    if parameter.prior is None:
-        warnings.warn(f"Attempting to set prior properties on parameter without priors: {parameter}")
-        return
-
-    if property == "value01":
-        new_value  = parameter.prior.put01(value)
-        nice_new_value = nice(new_value, digits=VALUE_PRECISION)
-        parameter.clip_set(nice_new_value)
-    elif property == "value":
-        new_value = float(value)
-        nice_new_value = nice(new_value, digits=VALUE_PRECISION)
-        parameter.clip_set(nice_new_value)
-    elif property == "min":
-        lo = float(value)
-        hi = parameter.prior.limits[1]
-        parameter.range(lo, hi)
-        parameter.add_prior()
-    elif property == "max":
-        lo = parameter.prior.limits[0]
-        hi = float(value)
-        parameter.range(lo, hi)
-        parameter.add_prior()
-    elif property == "fixed":
-        if parameter.fittable:
-            parameter.fixed = bool(value)
-            fitProblem.model_reset()
-            # print(f"setting parameter: {parameter}.fixed to {value}")
-            # model has been changed: setp and getp will return different values!
-            await publish("", "update_model", True)
-    fitProblem.model_update()
-    await publish("", "update_parameters", True)
-    return
-
-@sio.event
-async def publish(sid: str, topic: TopicNameType, message=None):
-    timestamp_str = f"{datetime.now().timestamp():.6f}"
-    contents = {"message": message, "timestamp": timestamp_str}
-    # session = get_session(session_id)    
-    state.topics[topic].append(contents)
-    # if session_id == app["active_session"]:
-    #     await sio.emit(topic, contents)
-    await sio.emit(topic, contents)
-    # print("emitted: ", topic, contents)
-
-
-@sio.event
-@rest_get
-async def get_topic_messages(sid: str="", topic: Optional[TopicNameType] = None, max_num=None) -> List[Dict]:
-    # this is a GET request in disguise -
-    # emitter must handle the response in a callback,
-    # as no separate response event is emitted.
-    if topic is None:
-        return []    
-    topics = state.topics
-    q = topics.get(topic, None)
-    if q is None:
-        raise ValueError(f"Topic: {topic} not defined")
-    elif max_num is None:
-        return list(q)
-    else:
-        q_length = len(q)
-        start = max(q_length - max_num, 0)
-        return list(itertools.islice(q, start, q_length))
-
-@sio.event
-@rest_get
-async def get_dirlisting(sid: str="", pathlist: Optional[List[str]]=None):
-    # GET request
-    # TODO: use psutil to get disk listing as well?
-    if pathlist is None:
-        pathlist = []
-    subfolders = []
-    files = []
-    for p in Path(*pathlist).iterdir():
-        if p.is_dir():
-            subfolders.append(p.name)
-        else:
-            # files.append(p.resolve().name)
-            files.append(p.name)
-    return dict(subfolders=subfolders, files=files)
-
-@sio.event
-@rest_get
-async def get_current_pathlist(sid: str="") -> Optional[List[str]]:
-    problem_state = state.problem
-    pathlist = problem_state.pathlist if problem_state is not None else None
-    return pathlist
-
-@sio.event
-@rest_get
-async def get_fitter_defaults(sid: str=""):
-    return FITTER_DEFAULTS
-
-@sio.event
-def disconnect(sid):
-    print('disconnect ', sid)
-
-async def disconnect_all_clients():
-    # disconnect all clients:
-    clients = list(sio.manager.rooms.get('/', {None: {}}).get(None).keys())
-    for client in clients:
-        await sio.disconnect(client)
-
-@sio.event
-async def shutdown(sid: str=""):
-    print("killing...")
-    signal.raise_signal(signal.SIGTERM)
-
-if Path.exists(static_assets_path):
-    app.router.add_static('/assets', static_assets_path)
-app.router.add_get('/', index)
-
-VALUE_PRECISION = 6
-VALUE_FORMAT = "{{:.{:d}g}}".format(VALUE_PRECISION)
 
-def nice(v, digits=4):
-    """Fix v to a value with a given number of digits of precision"""
-    from math import log10, floor
-    if v == 0. or not np.isfinite(v):
-        return v
-    else:
-        sign = v/abs(v)
-        place = floor(log10(abs(v)))
-        scale = 10**(place-(digits-1))
-        return sign*floor(abs(v)/scale+0.5)*scale
-
-
-def to_json_compatible_dict(obj):
-    if isinstance(obj, (list, tuple)):
-        return type(obj)(to_json_compatible_dict(v) for v in obj)
-    elif isinstance(obj, GeneratorType):
-        return list(to_json_compatible_dict(v) for v in obj)
-    elif isinstance(obj, dict):
-        return type(obj)((to_json_compatible_dict(k), to_json_compatible_dict(v))
-                        for k, v in obj.items())
-    elif isinstance(obj, np.ndarray) and obj.dtype.kind in ['f', 'i']:
-        return obj.tolist()
-    elif isinstance(obj, np.ndarray) and obj.dtype.kind == 'O':
-        return to_json_compatible_dict(obj.tolist())
-    elif isinstance(obj, float):
-        return str(obj) if np.isinf(obj) else obj
-    elif isinstance(obj, int) or isinstance(obj, str) or obj is None:
-        return obj
+def get_single_probe_data(theory, probe, substrate=None, surface=None, label=''):
+    fresnel_calculator = probe.fresnel(substrate, surface)
+    Q, FQ = probe.apply_beam(probe.calc_Q, fresnel_calculator(probe.calc_Q))
+    Q, R = theory
+    output: Dict[str, Union[str, np.ndarray]]
+    assert isinstance(FQ, np.ndarray)
+    if len(Q) != len(probe.Q):
+        # Saving interpolated data
+        output = dict(Q = Q, theory = R, fresnel=np.interp(Q, probe.Q, FQ))
+    elif getattr(probe, 'R', None) is not None:
+        output = dict(Q = probe.Q, dQ = probe.dQ, R = probe.R, dR = probe.dR, theory = R, fresnel = FQ, background=probe.background.value, intensity=probe.intensity.value)
     else:
-        raise ValueError("obj %s is not serializable" % str(obj))
-
-
-class ParamInfo(TypedDict, total=False):
-    id: str
-    name: str
-    paths: List[str]
-    value_str: str
-    fittable: bool
-    fixed: bool
-    writable: bool
-    value01: float
-    min_str: str
-    max_str: str
-
-
-def params_to_list(params, lookup=None, pathlist=None, links=None) -> List[ParamInfo]:
-    lookup: Dict[str, ParamInfo] = {} if lookup is None else lookup
-    pathlist = [] if pathlist is None else pathlist
-    if isinstance(params,dict):
-        for k in sorted(params.keys()):
-            params_to_list(params[k], lookup=lookup, pathlist=pathlist + [k])
-    elif isinstance(params, tuple) or isinstance(params, list):
-        for i, v in enumerate(params):
-            params_to_list(v, lookup=lookup, pathlist=pathlist + [f"[{i:d}]"])
-    elif isinstance(params, Parameter):
-        path = ".".join(pathlist)
-        existing = lookup.get(params.id, None)
-        if existing is not None:
-            existing["paths"].append(".".join(pathlist))
-        else:
-            value_str = VALUE_FORMAT.format(nice(params.value))
-            has_prior = params.has_prior()
-            new_item: ParamInfo = { 
-                "id": params.id,
-                "name": str(params.name),
-                "paths": [path],
-                "writable": type(params.slot) in [Variable, Parameter], 
-                "value_str": value_str, "fittable": params.fittable, "fixed": params.fixed }
-            if has_prior:
-                assert(params.prior is not None)
-                lo, hi = params.prior.limits
-                new_item['value01'] = params.prior.get01(params.value)
-                new_item['min_str'] = VALUE_FORMAT.format(nice(lo))
-                new_item['max_str'] = VALUE_FORMAT.format(nice(hi))
-            lookup[params.id] = new_item
-    return list(lookup.values())
-
-import argparse
-
-
-class Namespace(argparse.Namespace):
-    """ provide type hints for arguments """
-    filename: Optional[str]
-    headless: bool
-    external: bool
-    port: int
-    hub: Optional[str]
-    fit: Optional[str]
-    start: bool
-    store: Optional[str]
-    exit: bool
-
-
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('filename', nargs='?', help='problem file to load, .py or .json (serialized) fitproblem')
-    # parser.add_argument('-d', '--debug', action='store_true', help='autoload modules on change')
-    parser.add_argument('-x', '--headless', action='store_true', help='do not automatically load client in browser')
-    parser.add_argument('--external', action='store_true', help='listen on all interfaces, including external (local connections only if not set)')
-    parser.add_argument('-p', '--port', default=0, type=int, help='port on which to start the server')
-    parser.add_argument('--hub', default=None, type=str, help='api address of parent hub (only used when called as subprocess)')
-    parser.add_argument('--fit', default=None, type=str, choices=list(FITTERS_BY_ID.keys()), help='fitting engine to use; see manual for details')
-    parser.add_argument('--start', action='store_true', help='start fit when problem loaded')
-    parser.add_argument('--store', default=None, type=str, help='backing file for state')
-    parser.add_argument('--exit', action='store_true', help='end process when fit complete (fit results lost unless store is specified)')
-    # parser.add_argument('-c', '--config-file', type=str, help='path to JSON configuration to load')
-    args = parser.parse_args(namespace=Namespace())
+        output = dict(Q = probe.Q, dQ = probe.dQ, theory = R, fresnel = FQ)
+    output['label'] = f"{probe.label()} {label}"
+    return output
 
-    global state
-    if args.store is None:
-        state = State("in-memory.h5", in_memory=True)
+def get_probe_data(theory, probe, substrate=None, surface=None):
+    if isinstance(probe, refl1d.probe.PolarizedNeutronProbe):
+        output = []
+        for xsi, xsi_th, suffix in zip(probe.xs, theory, ('--', '-+', '+-', '++')):
+            if xsi is not None:
+                output.append(get_single_probe_data(xsi_th, xsi, substrate, surface, suffix))
+        return output
     else:
-        state = State(args.store)
-
-    # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
-    if args.fit is not None:
-        app.on_startup.append(lambda App: publish('', 'fitter_active', args.fit))
-
-    fitter_id = args.fit
-    if fitter_id is None:
-        fitter_active_topic = state.topics["fitter_active"]
-        if len(fitter_active_topic) > 0:
-            fitter_id = fitter_active_topic[-1]["message"]
-    if fitter_id is None:
-        fitter_id = 'amoeba'
-    fitter_settings = FITTER_DEFAULTS[fitter_id]
-
-    # if args.steps is not None:
-    #     fitter_settings["steps"] = args.steps
-
-    if args.filename is not None:
-        filepath = Path(args.filename)
-        pathlist = list(filepath.parent.parts)
-        filename = filepath.name
-        start = args.start
-        print(f"fitter for filename {filename} is {fitter_id}")
-        async def startup_task(App=None):
-            await load_problem_file("", pathlist, filename)
-            if start:
-                await start_fit_thread("", fitter_id, fitter_settings, args.exit)
-        
-        app.on_startup.append(startup_task)
-
-        # app.on_startup.append()
+        return [get_single_probe_data(theory, probe, substrate, surface)]
 
-    # app.on_startup.append(lambda App: publish('', 'local_file_path', Path().absolute().parts))
-    async def notice(message: str):
-        print(message)
-    app.on_cleanup.append(lambda App: notice("cleanup task"))
-    app.on_shutdown.append(lambda App: notice("shutdown task"))
-    app.on_shutdown.append(lambda App: stop_fit())
-    app.on_shutdown.append(lambda App: disconnect_all_clients())
-    app.on_shutdown.append(lambda App: state.cleanup())
-    # set initial path to cwd:
-    state.problem.pathlist = list(Path().absolute().parts)
-    app.add_routes(routes)
-    hostname = 'localhost' if not args.external else '0.0.0.0'
 
-    import socket
-    sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-    sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
-    sock.bind((hostname, args.port))
-    host, port = sock.getsockname()
-    state.hostname = host
-    state.port = port
-    if args.hub is not None:
-        async def register_instance(application: web.Application):
-            async with ClientSession() as client_session:
-                await client_session.post(args.hub, json={"host": hostname, "port": port})
-        app.on_startup.append(register_instance)
-    if not args.headless:
-        import webbrowser
-        async def open_browser(app: web.Application):
-            app.loop.call_later(0.25, lambda: webbrowser.open_new_tab(f"http://{hostname}:{port}/"))
-        app.on_startup.append(open_browser)
-    web.run_app(app, sock=sock)
 
-if __name__ == '__main__':
-    main()
+main(index=index, static_assets_path=static_assets_path, arg_defaults={"serializer": "dataclass"})
\ No newline at end of file

From 4c33d97581c3cee61e0c9dba604068250fed8552 Mon Sep 17 00:00:00 2001
From: Brian Ben Maranville <brian.maranville@nist.gov>
Date: Thu, 16 Mar 2023 12:34:12 -0400
Subject: [PATCH 209/221] removing componnents that were moved to
 bumps.webview.server

---
 refl1d/webview/server/corrplot.py          | 161 -----------
 refl1d/webview/server/fit_thread.py        | 239 ----------------
 refl1d/webview/server/state.py             |  50 ----
 refl1d/webview/server/state_hdf5_backed.py | 314 ---------------------
 refl1d/webview/server/varplot.py           | 259 -----------------
 5 files changed, 1023 deletions(-)
 delete mode 100644 refl1d/webview/server/corrplot.py
 delete mode 100644 refl1d/webview/server/fit_thread.py
 delete mode 100644 refl1d/webview/server/state.py
 delete mode 100644 refl1d/webview/server/state_hdf5_backed.py
 delete mode 100644 refl1d/webview/server/varplot.py

diff --git a/refl1d/webview/server/corrplot.py b/refl1d/webview/server/corrplot.py
deleted file mode 100644
index 75c0730a..00000000
--- a/refl1d/webview/server/corrplot.py
+++ /dev/null
@@ -1,161 +0,0 @@
-# This program is public domain
-# Authors Paul Kienzle, Brian Maranville
-"""
-2-D correlation histograms
-
-Generate 2-D correlation histograms and display them in a figure.
-
-Uses false color plots of density.
-"""
-__all__ = ['Corr2d']
-
-import numpy as np
-from numpy import inf
-
-import plotly.graph_objects as go
-from plotly.subplots import make_subplots
-
-class Corr2d(object):
-    """
-    Generate and manage 2D correlation histograms.
-    """
-    def __init__(self, data, labels=None, **kw):
-        if labels is None:
-            labels = ["P"+str(i+1) for i, _ in enumerate(data)]
-        self.N = len(data)
-        self.labels = labels
-        self.data = data
-        self.hists = _hists(data, **kw)
-        self.fig = None
-        #for k, v in self.hists.items():
-        #    print k, (v[1][0], v[1][-1]), (v[2][0], v[2][-1])
-
-    def R(self):
-        return np.corrcoef(self.data)
-
-    def __getitem__(self, i, j):
-        """
-        Retrieve correlation histogram for data[i] X data[j].
-
-        Returns bin i edges, bin j edges, and histogram
-        """
-        return self.hists[i, j]
-
-    def plot(self, title=None):
-        """
-        Plot the correlation histograms on the specified figure
-        """
-
-        fig = make_subplots(
-            rows=self.N-1,
-            cols=self.N-1,
-            horizontal_spacing=0,
-            vertical_spacing=0,
-            shared_yaxes=True,
-            shared_xaxes=True
-        )
-
-        # if title is not None:
-        #     fig.text(0.5, 0.95, title,
-        #              horizontalalignment='center',
-        #              fontproperties=FontProperties(size=16))
-        return _plot(fig, self.hists, self.labels, self.N)
-
-
-def _hists(data, ranges=None, **kw):
-    """
-    Generate pair-wise correlation histograms
-    """
-    n = len(data)
-    if ranges is None:
-        low, high = np.min(data, axis=1), np.max(data, axis=1)
-        ranges = [(l, h) for l, h in zip(low, high)]
-    return dict(((i, j), np.histogram2d(data[i], data[j],
-                                        range=[ranges[i], ranges[j]], **kw))
-                for i in range(0, n)
-                for j in range(i+1, n))
-
-
-def _plot(fig, hists, labels, n, show_ticks=None):
-    """
-    Plot pair-wise correlation histograms
-    """
-    # if n <= 1:
-    #     fig.text(0.5, 0.5, "No correlation plots when only one variable",
-    #              ha="center", va="center")
-    #     return
-    
-    vmin, vmax = float('inf'), float('-inf')
-    for data, _, _ in hists.values():
-        positive = data[data > 0]
-        if len(positive) > 0:
-            vmin = min(vmin, np.amin(positive))
-            vmax = max(vmax, np.amax(positive))
-    
-    fig = make_subplots(rows=n-1, cols=n-1, horizontal_spacing=0, vertical_spacing=0, shared_yaxes=True, shared_xaxes=True)
-    COLORSCALE = ["white", "yellow", "green", "blue", "red"]
-
-    for i in range(0, n-1):
-        fig.add_annotation(
-            xref="x domain",
-            yref="y domain",
-            xanchor="right",
-            x=-0.1,
-            y=0.1,
-            showarrow=False,
-            col=i+1,
-            row=n-i-1,
-            text=labels[i],
-            textangle=-90
-        )
-        for j in range(i+1, n):
-            data, x, y = hists[(i, j)]
-            data = np.clip(data, vmin, vmax)
-            trace = go.Heatmap(z=np.log10(data), coloraxis='coloraxis', hoverinfo='skip')
-            fig.add_traces([trace], rows=n-i-1, cols=j)
-    
-    log_cbar = dict(
-        tickvals=np.arange(int(np.log10(vmax)) + 1),
-        ticktext=10 ** np.arange(int(np.log10(vmax)) + 1),
-    )
-    fig.update_layout(coloraxis={'colorscale': COLORSCALE, "cmin": np.log10(vmin), "cmax": np.log10(vmax), 'colorbar': log_cbar})
-    fig.update_layout(plot_bgcolor='rgba(0, 0, 0, 0)')
-    # fig.update_layout(height=600, width=800)
-    fig.update_xaxes(visible=False)
-    fig.update_yaxes(visible=False)
-    return fig
-
-### NOT USED AT THE MOMENT: all below
-###
-def zoom(event, step):
-    ax = event.inaxes
-    if not hasattr(ax, 'zoomable'):
-        return
-
-    # TODO: test logscale
-    step *= 3
-
-    if ax.zoomable is not True and 'mapper' in ax.zoomable:
-        mapper = ax.zoomable['mapper']
-        if event.ydata is not None:
-            lo, hi = mapper.get_clim()
-            pt = event.ydata*(hi-lo)+lo
-            lo, hi = _rescale(lo, hi, pt, step)
-            mapper.set_clim((lo, hi))
-    if ax.zoomable is True and event.xdata is not None:
-        lo, hi = ax.get_xlim()
-        lo, hi = _rescale(lo, hi, event.xdata, step)
-        ax.set_xlim((lo, hi))
-    if ax.zoomable is True and event.ydata is not None:
-        lo, hi = ax.get_ylim()
-        lo, hi = _rescale(lo, hi, event.ydata, step)
-        ax.set_ylim((lo, hi))
-    ax.figure.canvas.draw_idle()
-
-
-def _rescale(lo, hi, pt, step):
-    scale = float(hi-lo)*step/(100 if step > 0 else 100-step)
-    bal = float(pt-lo)/(hi-lo)
-    new_lo = lo - bal*scale
-    new_hi = hi + (1-bal)*scale
-    return new_lo, new_hi
diff --git a/refl1d/webview/server/fit_thread.py b/refl1d/webview/server/fit_thread.py
deleted file mode 100644
index 7440122d..00000000
--- a/refl1d/webview/server/fit_thread.py
+++ /dev/null
@@ -1,239 +0,0 @@
-
-from copy import deepcopy
-from threading import Thread
-from queue import Queue
-
-from blinker import Signal
-
-import numpy as np
-from bumps import monitor
-from bumps.fitters import FitDriver, nllf_scale, format_uncertainty
-from bumps.mapper import MPMapper, SerialMapper, can_pickle
-from bumps.util import redirect_console
-from bumps.history import History
-
-#from .convergence_view import ConvergenceMonitor
-# ==============================================================================
-
-PROGRESS_DELAY = 5
-IMPROVEMENT_DELAY = 5
-
-EVT_FIT_PROGRESS = Signal()
-EVT_FIT_COMPLETE = Signal()
-
-# NOTE: GUI monitors are running in a separate thread.  They should not
-# touch the problem internals.
-
-
-class GUIProgressMonitor(monitor.TimedUpdate):
-    def __init__(self, problem, progress=None, improvement=None):
-        monitor.TimedUpdate.__init__(
-            self, progress=progress or PROGRESS_DELAY,
-            improvement=improvement or IMPROVEMENT_DELAY)
-        self.problem = problem
-
-    def show_progress(self, history):
-        scale, err = nllf_scale(self.problem)
-        chisq = format_uncertainty(scale*history.value[0], err)
-        evt = dict(
-            # problem=self.problem,
-            message="progress",
-            step=history.step[0],
-            value=history.value[0],
-            chisq=chisq,
-            point=history.point[0]+0)  # avoid race
-        EVT_FIT_PROGRESS.send(evt)
-
-    def show_improvement(self, history):
-        evt = dict(
-            problem=self.problem,
-            message="improvement",
-            step=history.step[0],
-            value=history.value[0],
-            point=history.point[0]+0)  # avoid race
-        EVT_FIT_PROGRESS.send(evt)
-
-
-class ConvergenceMonitor(monitor.Monitor):
-    """
-    Generic GUI monitor for fitting.
-
-    Sends a convergence_update event every *rate*
-    seconds.  Gathers statistics about the best, worst, median and +/- 1 interquartile
-    range.  This will be the input for the convergence plot.
-
-    *problem* should be the fit problem handed to the fit thread, and not
-    a copy. This is because it is used for direct comparison with the current
-    fit object in the progress panels so that stray messages don't cause
-    confusion when making graphs.
-
-    *message* is a dispatch string used by the OnFitProgress event processor
-    in the app to determine which progress panel should receive the event.
-    """
-
-    def __init__(self, problem, message="convergence_update", rate=0):
-        self.time = 0
-        self.rate = rate  # rate=0 for no progress update, only final
-        self.problem = problem
-        self.message = message
-        self.pop = []
-
-
-    def config_history(self, history):
-        history.requires(population_values=1, value=1)
-        history.requires(time=1)
-        # history.requires(time=1, population_values=1, value=1)
-
-    def __call__(self, history):
-        # from old ConvergenceMonitor:
-        best = history.value[0]
-        try:
-            pop = history.population_values[0]
-            n = len(pop)
-            p = np.sort(pop)
-            QI,Qmid, = int(0.2*n),int(0.5*n)
-            self.pop.append((best, p[0],p[QI],p[Qmid],p[-1-QI],p[-1]))
-        except AttributeError:
-            self.pop.append((best, ))
-
-        if self.rate > 0 and history.time[0] >= self.time+self.rate:
-            evt = dict(
-                problem=self.problem,
-                message=self.message,
-                pop=self.progress())
-            EVT_FIT_PROGRESS.send(evt)
-            self.time = history.time[0]
-
-    def progress(self):
-        return np.empty((0,1),'d') if not self.pop else np.array(self.pop)
-
-    def final(self):
-        """
-        Close out the monitor
-        """
-        evt = dict(
-            problem=self.problem,
-            message=self.message,
-            pop=self.progress())
-        EVT_FIT_PROGRESS.send(evt)
-
-# Horrible hacks:
-# (1) We are grabbing uncertainty_state from the history on monitor update
-# and holding onto it for the monitor final call. Need to restructure the
-# history/monitor interaction so that object lifetimes are better controlled.
-
-
-class DreamMonitor(monitor.Monitor):
-    def __init__(self, problem, message, fitter, rate=0):
-        self.time = 0
-        self.rate = rate  # rate=0 for no progress update, only final
-        self.problem = problem
-        self.fitter = fitter
-        self.message = message
-        self.uncertainty_state = None
-
-    def config_history(self, history):
-        history.requires(time=1)
-
-    def __call__(self, history):
-        self.uncertainty_state = getattr(history, 'uncertainty_state', None)
-        if (self.rate > 0 and history.time[0] >= self.time+self.rate
-                and self.uncertainty_state is not None):
-            # Note: win.uncertainty_state protected by win.fit_lock
-            self.time = history.time[0]
-            #self.win.uncertainty_state = self.uncertainty_state
-            evt = dict(
-                problem=self.problem,
-                message="uncertainty_update",
-                uncertainty_state=deepcopy(self.uncertainty_state),
-            )
-            EVT_FIT_PROGRESS.send(evt)
-
-    def final(self):
-        """
-        Close out the monitor
-        """
-        if self.uncertainty_state is not None:
-            # Note: win.uncertainty_state protected by win.fit_lock
-            # self.win.uncertainty_state = self.uncertainty_state
-            evt = dict(
-                problem=self.problem,
-                message="uncertainty_final",
-                uncertainty_state=deepcopy(self.uncertainty_state),
-            )
-            EVT_FIT_PROGRESS.send(evt)
-
-# ==============================================================================
-
-
-class FitThread(Thread):
-    """Run the fit in a separate thread from the GUI thread."""
-
-    def __init__(self, abort_queue: Queue, problem=None,
-                 fitclass=None, options=None, mapper=None,
-                 convergence_update=5, uncertainty_update=300,
-                 terminate_on_finish=False):
-        # base class initialization
-        # Process.__init__(self)
-
-        Thread.__init__(self)
-        self.abort_queue = abort_queue
-        self.problem = problem
-        self.fitclass = fitclass
-        self.options = options if isinstance(options, dict) else dict()
-        self.mapper = mapper
-        self.convergence_update = convergence_update
-        self.uncertainty_update = uncertainty_update
-        self.terminate_on_finish = terminate_on_finish
-
-    def abort_test(self):
-        return not self.abort_queue.empty()
-
-    def run(self):
-        # TODO: we have no interlocks on changes in problem state.  What
-        # happens when the user changes the problem while a fit is being run?
-        # May want to keep a history of changes to the problem definition,
-        # along with a function to reverse them so we can handle undo.
-
-        # NOTE: Problem must be the original problem (not a copy) when used
-        # inside the GUI monitor otherwise AppPanel will not be able to
-        # recognize that it is the same problem when updating views.
-        monitors = [GUIProgressMonitor(self.problem),
-                    ConvergenceMonitor(self.problem, 
-                                       rate=self.convergence_update),
-                    # GUIMonitor(self.problem,
-                    #            message="convergence_update",
-                    #            monitor=ConvergenceMonitor(),
-                    #            rate=self.convergence_update),
-                    DreamMonitor(self.problem,
-                                 fitter=self.fitclass,
-                                 message="uncertainty_update",
-                                 rate=self.uncertainty_update),
-                    ]
-        # Only use parallel if the problem can be pickled
-        mapper = MPMapper if can_pickle(self.problem) else SerialMapper
-
-        # Be safe and send a private copy of the problem to the fitting engine
-        # print "fitclass",self.fitclass
-        problem = deepcopy(self.problem)
-        # print "fitclass id",id(self.fitclass),self.fitclass,threading.current_thread()
-        driver = FitDriver(
-            self.fitclass, problem=problem,
-            monitors=monitors, abort_test=self.abort_test,
-            mapper=mapper.start_mapper(problem, []),
-            **self.options)
-
-        x, fx = driver.fit()
-        # Give final state message from monitors
-        for M in monitors:
-            if hasattr(M, 'final'):
-                M.final()
-
-        with redirect_console() as fid:
-            driver.show()
-            captured_output = fid.getvalue()
-
-        evt = dict(message="complete", problem=self.problem,
-                   point=x, value=fx, info=captured_output)
-        EVT_FIT_COMPLETE.send(evt)
-        self.result = evt
diff --git a/refl1d/webview/server/state.py b/refl1d/webview/server/state.py
deleted file mode 100644
index 48d779f1..00000000
--- a/refl1d/webview/server/state.py
+++ /dev/null
@@ -1,50 +0,0 @@
-from collections import deque
-from queue import Queue
-from typing import Dict, List, Optional, TYPE_CHECKING
-
-if TYPE_CHECKING:
-    import bumps, bumps.fitproblem, bumps.dream.state
-    from .webserver import TopicNameType
-    from .fit_thread import FitThread
-
-class ProblemState:
-    fitProblem: Optional['bumps.fitproblem.FitProblem'] = None
-    pathlist: Optional[List[str]] = None
-    filename: Optional[str] = None
-
-class FittingState:
-    abort: bool = False
-    population: Optional[List] = None
-    uncertainty_state: Optional['bumps.dream.state.MCMCDraw']
-
-
-class State:
-    # These attributes are ephemeral, not to be serialized/stored:
-    hostname: str
-    port: int
-    abort_queue: Queue
-    fit_thread: Optional['FitThread'] = None
-
-    # State to be stored:
-    problem: ProblemState
-    fitting: FittingState
-    topics: Dict['TopicNameType', 'deque[Dict]']
-
-    def __init__(self, problem: Optional[ProblemState] = None, fitting: Optional[FittingState] = None):
-        self.problem = problem if problem is not None else ProblemState()
-        self.fitting = FittingState()
-        self.abort_queue = Queue()
-        self.topics = {
-            "log": deque([]),
-            "update_parameters": deque([], maxlen=1),
-            "update_model": deque([], maxlen=1),
-            "model_loaded": deque([], maxlen=1),
-            "fit_active": deque([], maxlen=1),
-            "convergence_update": deque([], maxlen=1),
-            "uncertainty_update": deque([], maxlen=1),
-            "fitter_settings": deque([], maxlen=1),
-            "fitter_active": deque([], maxlen=1),
-        }
-
-    async def cleanup(self):
-        pass
\ No newline at end of file
diff --git a/refl1d/webview/server/state_hdf5_backed.py b/refl1d/webview/server/state_hdf5_backed.py
deleted file mode 100644
index d17ee56a..00000000
--- a/refl1d/webview/server/state_hdf5_backed.py
+++ /dev/null
@@ -1,314 +0,0 @@
-from typing import TYPE_CHECKING, Optional, Dict, List, Any, Literal, cast
-import json
-from queue import Queue
-from bumps.serialize import from_dict, to_dict
-import h5py
-import numpy as np
-
-import refl1d.fitproblem
-from bumps.dream.state import MCMCDraw
-
-
-if TYPE_CHECKING:
-    from .webserver import TopicNameType
-    from h5py import Group, Dataset
-    from .fit_thread import FitThread
-
-# slow, small:
-COMPRESSION = 9
-MAX_TOPIC_MESSAGE = 1024*100 # 100k
-MAX_PROBLEM_SIZE = 10*1024*1024 # 10 MB problem max size
-SESSION_FILE_NAME = "session.h5"
-
-def to_hdf5_group(state: 'State', group: 'Group'):
-    import h5py
-    fitting_grp = group.create_group("fitting")
-    topics_grp = group.create_group("topics")
-    problem_grp = group.create_group("problem")
-
-    if state.fitting.population is not None:
-        pop_shape = state.fitting.population.shape
-        fitting_grp.create_dataset("population", shape=pop_shape, maxshape=(None, pop_shape[1]), compression = COMPRESSION)
-    if state.fitting.uncertainty_state is not None:
-        write_uncertainty_state(state.fitting.uncertainty_state, fitting_grp)
-
-    for topic, contents in state.topics.items():
-        num_entries = len(contents)
-        maxlen = contents.maxlen
-        topic_dataset = topics_grp.create_dataset(topic, shape=(num_entries,), maxshape=(contents.maxlen), dtype=f"|S{MAX_TOPIC_MESSAGE}", compression=COMPRESSION)
-        for idx, message in enumerate(contents):
-            topic_dataset[idx] = json.dumps(message)
-
-    if state.problem is not None:
-        if state.problem.fitProblem is not None:
-            problem_json = json.dumps(to_dict(state.problem.fitProblem))
-            problem_grp['fitProblem'] = problem_json
-            problem_grp['fitProblem'].attrs["Content-Type"] = "application/json"
-        if state.problem.filename is not None:
-            problem_grp['filename'] = state.problem.filename
-        if state.problem.pathlist is not None:
-            pathlist_json = json.dumps(state.problem.pathlist)
-            problem_grp['pathlist'] = pathlist_json
-            problem_grp['pathlist'].attrs["Content-Type"] = "application/json"
-
-CACHE_MISS = object()
-
-class ProblemState:
-    _group: h5py.Group
-    _filename: Optional[str]
-    _pathlist: Optional[List[str]]
-    _fitProblem: Optional[refl1d.fitproblem.FitProblem]
-
-    def __init__(self, group: h5py.Group):
-        self._group = group
-
-    @property
-    def filename(self) -> Optional[str]:
-        # check cache:
-        cached_val = getattr(self, '_filename', CACHE_MISS)
-        if cached_val is CACHE_MISS:
-            backing_val = self._group['filename'][()] if 'filename' in self._group else None
-            setattr(self, '_filename', backing_val)
-            cached_val = backing_val
-        return cached_val
-    
-    @filename.setter
-    def filename(self, value: str):
-        dset = self._group.require_dataset('filename', (), h5py.vlen_dtype(str))
-        dset[()] = value
-        self._filename = value
-
-    @property
-    def pathlist(self) -> Optional[List[str]]:
-        cached_val = getattr(self, '_pathlist', CACHE_MISS)
-        if cached_val is CACHE_MISS:
-            backing_val = json.loads(self._group['pathlist'][()]) if 'pathlist' in self._group else None
-            setattr(self, '_pathlist', backing_val)
-            cached_val = backing_val
-        return cached_val
-    
-    @pathlist.setter
-    def pathlist(self, value: List[str]):
-        dset = self._group.require_dataset('pathlist', (), h5py.vlen_dtype(str))
-        dset[()] = json.dumps(value)
-        self._pathlist = value
-
-    @property
-    def fitProblem(self) -> Optional[refl1d.fitproblem.FitProblem]:
-        cached_val = getattr(self, '_fitProblem', CACHE_MISS)
-        if cached_val is CACHE_MISS:
-            backing_val = from_dict(json.loads(self._group['fitProblem'][()])) if 'fitProblem' in self._group else None
-            setattr(self, '_fitProblem', backing_val)
-            cached_val = backing_val
-        return cached_val
-    
-    @fitProblem.setter
-    def fitProblem(self, value: refl1d.fitproblem.FitProblem):
-        dset = self._group.require_dataset('fitProblem', (), h5py.vlen_dtype(str))
-        dset[()] = json.dumps(to_dict(value))
-        self._fitProblem = value
-
-class FittingState:
-    _group: h5py.Group
-    # cache items:
-    _population: np.ndarray
-    _uncertainty_state: 'MCMCDraw'
-
-    def __init__(self, group: h5py.Group):
-        self._group = group
-
-    @property
-    def population(self) -> Optional[np.ndarray]:
-        cached_val = getattr(self, '_population', CACHE_MISS)
-        if cached_val is CACHE_MISS:
-            backing_val = self._group['population'][()] if 'population' in self._group else None
-            if backing_val is not None:
-                setattr(self, '_population', backing_val)
-            cached_val = backing_val
-        return cached_val
-    
-    @population.setter
-    def population(self, value: np.ndarray):
-        pop_shape = value.shape
-        if not 'population' in self._group:
-            self._group.create_dataset("population", shape=pop_shape, data=value, maxshape=(None, None), compression = COMPRESSION)
-        else:
-            dset = cast(h5py.Dataset, self._group["population"])
-            if dset.shape != pop_shape:
-                dset.resize(pop_shape)        
-            dset[()] = value
-        self._population = value
-
-    @property
-    def uncertainty_state(self):
-        cached_val = getattr(self, '_uncertainty_state', CACHE_MISS)
-        if cached_val is CACHE_MISS:
-            backing_val = read_uncertainty_state(self._group) if 'gen_draws' in self._group else None
-            if backing_val is not None:
-                setattr(self, '_uncertainty_state', backing_val)
-            cached_val = backing_val
-        return cached_val
-
-    @uncertainty_state.setter
-    def uncertainty_state(self, value: 'MCMCDraw'):
-        print("writing uncertainty state: ", value)
-        write_uncertainty_state(value, self._group)
-        self._uncertainty_state = value
-        print("done writing uncertainty state.")
-
-class Topic:
-    dataset: h5py.Dataset
-    maxlen: Optional[int] = 1
-
-    def __init__(self, dataset: h5py.Dataset, maxlen: Optional[int] = 1):
-        self.dataset = dataset
-        self.maxlen = maxlen
-
-    def __getitem__(self, index: int):
-        return json.loads(self.dataset[index])
-    
-    def __setitem__(self, index: int, value: Dict):
-        self.dataset[index] = json.dumps(value)
-        self.dataset.flush()
-
-    def __len__(self):
-        return len(self.dataset)
-
-    def append(self, value: Dict):
-        current_len: int = self.dataset.size
-        if self.maxlen is None or current_len < self.maxlen:
-            self.dataset.resize((current_len+1,))
-            self[current_len] = value
-        else:
-            # not a true ring buffer: just overwrite last element when full
-            # (only works for length-1 buffers, but that's all we have)
-            self[current_len - 1] = value
-        self.dataset.flush()
-
-class TopicsDict:
-    group: 'Group'
-
-    def __init__(self, group: 'Group'):
-        self.group = group
-        for topic_name, maxlen in (
-            ("log", None),
-            ("update_parameters", 1),
-            ("update_model", 1),
-            ("model_loaded", 1),
-            ("fit_active", 1),
-            ("convergence_update", 1),
-            ("uncertainty_update", 1),
-            ("fitter_settings", 1),
-            ("fitter_active", 1)
-        ):
-            if topic_name in group:
-                topic_dataset = group[topic_name]
-            else:
-                topic_dataset = group.create_dataset(topic_name, shape=(0,), maxshape=(maxlen,), dtype=f"|S{MAX_TOPIC_MESSAGE}", compression=COMPRESSION)
-    
-    def __getitem__(self, key: 'TopicNameType') -> Topic:
-        topic_dataset = cast(h5py.Dataset, self.group[key])
-        return Topic(topic_dataset, maxlen=topic_dataset.maxshape[0])
-    
-    def get(self, key: 'TopicNameType', default: Any) -> Topic | Any:
-        return self[key] if key in self.group else default
-
-    def items(self):
-        return [(topic_name, self[topic_name]) for topic_name in self.group.keys()]
-
-class State:
-    hostname: str
-    port: int
-    problem: ProblemState
-    dream: FittingState
-    topics: TopicsDict
-    fit_thread: Optional['FitThread'] = None
-    abort_queue: Queue
-
-    def __init__(self, session_file_name: str = SESSION_FILE_NAME, in_memory: bool = False, backing_store: bool = False, read_only: bool = False ):
-        # self.problem = problem
-        # self.fitting = fitting if fitting is not None else FittingState()
-        self.abort_queue = Queue()
-        import h5py
-        hdf_kw = dict(libver="latest")
-        if in_memory:
-            hdf_kw.update(dict(driver="core", backing_store=backing_store))
-        if read_only:
-            hdf_kw["swmr"] = True
-        mode = "r" if read_only else "a"
-        self.session_file = session_file = h5py.File(session_file_name, mode, **hdf_kw)
-        topics_group = session_file.require_group("topics")
-        problem_group = session_file.require_group("problem")
-        fitting_group = session_file.require_group("fitting")
-        self.topics = TopicsDict(topics_group)
-        self.problem = ProblemState(problem_group)
-        self.fitting = FittingState(fitting_group)
-        if not read_only:
-            session_file.swmr_mode = True
-
-
-    async def cleanup(self):
-        self.session_file.close()
-
-def write_uncertainty_state(state: 'MCMCDraw', group: 'Group', compression=COMPRESSION):
-        to_save = {}
-        # Build 2-D data structures
-        to_save["gen_draws"], to_save["gen_logp"] = state.logp(full=True)
-        _, to_save["AR"] = state.acceptance_rate()
-
-        to_save["thin_draws"], to_save["thin_point"], to_save["thin_logp"] = state.chains()
-        to_save["update_draws"], to_save["update_CR_weight"] = state.CR_weight()
-        to_save["labels"] = np.array(state.labels, dtype=h5py.string_dtype())
-
-        #TODO: missing _outliers from save_state
-        for field_name, data in to_save.items():
-            print(field_name, field_name in group)
-            if field_name in group:
-                dataset = cast(h5py.Dataset, group[field_name])
-                if dataset.shape != data.shape:
-                    dataset.resize(data.shape)
-                dataset[()] = data
-            else:
-                maxshape = tuple([None for dim in data.shape])
-                dataset = group.create_dataset(field_name, data=data, maxshape=maxshape, compression=compression)
-
-
-def read_uncertainty_state(group: 'Group', skip=0, report=0, derived_vars=0):
-
-    loaded: Dict[str, np.ndarray] = dict(group.items())
-    
-    # Guess dimensions
-    Ngen = loaded["gen_draws"].shape[0]
-    thinning = 1
-    Nthin, Npop, Nvar = loaded["thin_point"].shape
-    Nupdate, Ncr = loaded["update_CR_weight"].shape
-    Nthin -= skip
-
-    # Create empty draw and fill it with loaded data
-    state = MCMCDraw(0, 0, 0, 0, 0, 0, thinning)
-    #print("gen, var, pop", Ngen, Nvar, Npop)
-    state.draws = Ngen * Npop
-    state.generation = Ngen
-    state._gen_index = 0
-    state._gen_draws = loaded["gen_draws"][()]
-    state._gen_acceptance_rate = loaded["AR"][()]
-    state._gen_logp = loaded["gen_logp"][()]
-    state.thinning = thinning
-    state._thin_count = Ngen//thinning
-    state._thin_index = 0
-    state._thin_draws = loaded["thin_draws"][()]
-    state._thin_logp = loaded["thin_logp"][()]
-    state._thin_point = loaded["thin_point"][()]
-    state._gen_current = state._thin_point[-1].copy()
-    state._update_count = Nupdate
-    state._update_index = 0
-    state._update_draws = loaded["update_draws"][()]
-    state._update_CR_weight = loaded["update_CR_weight"][()]
-    state._outliers = []
-
-    bestidx = np.unravel_index(np.argmax(loaded["thin_logp"]), loaded["thin_logp"].shape)
-    state._best_logp = loaded["thin_logp"][bestidx]
-    state._best_x = loaded["thin_point"][bestidx]
-    state._best_gen = 0
-
-    return state
\ No newline at end of file
diff --git a/refl1d/webview/server/varplot.py b/refl1d/webview/server/varplot.py
deleted file mode 100644
index 4006e03a..00000000
--- a/refl1d/webview/server/varplot.py
+++ /dev/null
@@ -1,259 +0,0 @@
-"""
-Build layout for histogram plots (plotly)
-"""
-
-__all__ = ['var_plot_size', 'plot_vars', 'plot_var']
-
-from math import ceil, sqrt
-import numpy as np
-
-import typing
-if typing.TYPE_CHECKING:
-    from bumps.dream.state import Draw
-    from bumps.dream.stats import VarStats
-    import plotly.graph_objects as go
-
-# TODO: improve type hinting on VarStats (dataclass with optional fields?)
-
-# # Set space between plots in horiz and vert.
-# H_SPACE = 0.2
-# V_SPACE = 0.2
-
-# # Set top, bottom, left margins.
-# T_MARGIN = 0.2
-# B_MARGIN = 0.2
-# L_MARGIN = 0.2
-# R_MARGIN = 0.4
-
-# # Set desired plot sizes.
-# TILE_W = 3.0
-# TILE_H = 2.0
-# CBAR_WIDTH = 0.75
-
-CBAR_COLORS = 64
-LINE_COLOR = "red"
-ANNOTATION_COLOR = "blue"
-HISTOGRAM_COLORMAP = "Greens_r"
-
-
-def tile_axes_square(n):
-    """
-    Determine number of columns by finding the
-    next greatest square, then determine number
-    of rows needed.
-    """
-    cols = int(ceil(sqrt(n)))
-    rows = int(ceil(n/float(cols)))
-    return cols, rows
-
-
-def plot_vars(draw: 'Draw', all_vstats, **kw):
-    from plotly.subplots import make_subplots
-
-    n = len(all_vstats)
-    ncol, nrow = tile_axes_square(n)
-
-    snllf = np.sort(-draw.logp)
-    vmin, vmax = snllf[0], snllf[int(0.98*(len(snllf)-1))]  # robust range
-    cbar_edges = np.linspace(vmin, vmax, CBAR_COLORS)
-    # titles = [vstats.label for vstats in all_vstats]
-
-    # fig = make_subplots(rows=nrow, cols=ncol, subplot_titles=titles)
-    fig = make_subplots(rows=nrow, cols=ncol)
-    fig.update_yaxes(secondary_y = True)
-
-    for k, vstats in enumerate(all_vstats):
-        row = (k // ncol) + 1
-        col = (k % ncol) + 1
-        plot_var(fig, draw, vstats, k, cbar_edges=cbar_edges, row=row, col=col, **kw)
-    
-    fig.update_xaxes(dict(exponentformat='e'), overwrite=True)
-    fig.update_yaxes(dict(showticklabels=False))
-    fig.update_layout(height=600, width=800, coloraxis_colorbar_title="-logP")
-    fig.update_layout(coloraxis = {'colorscale': HISTOGRAM_COLORMAP, "cmin": vmin, "cmax": vmax})
-
-    return fig
-
-
-def plot_var(fig: 'go.Figure', draw: 'Draw', vstats: 'VarStats', var: int, cbar_edges: np.ndarray, nbins=30, row=None, col=None):
-    import plotly.graph_objects as go
-    values = draw.points[:, var].flatten()
-    bin_range = vstats.p95_range
-    #bin_range = np.min(values), np.max(values)
-    showscale = (row == 0 and col == 0)
-    showscale = True
-    traces = _make_logp_histogram(values, draw.logp, nbins, bin_range,
-                         draw.weights, cbar_edges=cbar_edges, showscale=showscale)
-
-    fig.add_traces(traces, rows=row, cols=col)
-    _decorate_histogram(vstats, fig, row=row, col=col)
-
-
-def _decorate_histogram(vstats: 'VarStats', fig: 'go.Figure', col: typing.Optional[int]=None, row: typing.Optional[int]=None):
-    import plotly.graph_objects as go
-
-    l95, h95 = vstats.p95_range
-    l68, h68 = vstats.p68_range
-    # Shade things inside 1-sigma
-    fig.add_vrect(x0=l68, x1=h68, fillcolor='gold', opacity=0.5, layer='below', line={"width": 0}, col=col, row=row)
-
-    def marker(symbol, position, info_template):
-        if position < l95:
-            symbol, position, ha = '<'+symbol, l95, 'left'
-        elif position > h95:
-            symbol, position, ha = '>'+symbol, h95, 'right'
-        else:
-            symbol, position, ha = symbol, position, 'center'
-        fig.add_annotation(
-            xref="x",
-            yref="y domain",
-            x=position,
-            y=0.95,
-            text=symbol,
-            showarrow=False,
-            font=dict(color=ANNOTATION_COLOR),
-            col=col,
-            row=row,
-            hovertext=info_template.format(position=position)
-        )
-
-        #pylab.axvline(v)
-
-    marker('|', vstats.median, "median: {position}")
-    marker('E', vstats.mean, "mean: {position}")
-    marker('*', vstats.best, "best: {position}")
-    
-    fig.add_annotation(
-        xref="x domain",
-        yref="y domain",
-        x = 0.0,
-        y = 1.1,
-        text = vstats.label,
-        col=col,
-        row=row,
-        showarrow=False
-    )
-
-def _make_logp_histogram(values, logp, nbins, ci, weights, cbar_edges, showscale=False):
-    from numpy import (ones_like, searchsorted, linspace, cumsum, diff,
-                       unique, argsort, array, hstack, exp)
-    import plotly.graph_objects as go
-
-    if weights is None:
-        weights = ones_like(logp)
-    # TODO: values are being sorted to collect stats and again to plot
-    idx = argsort(values)
-    values, weights, logp = values[idx], weights[idx], logp[idx]
-    #open('/tmp/out','a').write("ci=%s, range=%s\n"
-    #                           % (ci,(min(values),max(values))))
-    edges = linspace(ci[0], ci[1], nbins+1)
-    bin_index = range(nbins)
-    idx = searchsorted(values[1:-1], edges)
-
-
-    bins = []  # marginalized maximum likelihood
-
-    # H, xedges, yedges = np.histogram2d(values, -logp, bins=(edges, cbar_edges), weights=weights)
-    # ybins = len(yedges) - 1
-    # x = (xedges[:-1] + xedges[1:]) / 2.0
-    # cbar_values = ((cbar_edges[:-1] + cbar_edges[1:]) / 2.0)[::-1]
-    # x = x.repeat(ybins) # match length of y array
-    # y = H.flatten(order="C")
-    # color = np.tile(cbar_values, nbins)
-
-    # # filter out empty y values (speeds up drawing, omitting empty rectangles):
-    # y_nonzero = (y > 0)
-    # # print(f"y_zeros: {y_nonzero}, {len([z for z in y_nonzero if z])} out of {len(y)}")
-    # x = x[y_nonzero]
-    # color = color[y_nonzero]
-    # y = y[y_nonzero]
-    # traces.append(go.Bar(x=x, y=y, showlegend=False, marker=dict(color=color, coloraxis='coloraxis', line=dict(width=0))))
-    # # traces.append(go.Bar(x=x, y=y, showlegend=False, hoverinfo='skip', marker=dict(color=color, coloraxis='coloraxis', line=dict(width=0))))
-
-    xscatt = []
-    yscatt = []
-    zscatt = []
-
-    for i, s, e, xlo, xhi \
-            in zip(bin_index, idx[:-1], idx[1:], edges[:-1], edges[1:]):
-        if s == e:
-            continue
-
-        pv = -logp[s:e]
-        # weights for samples within interval
-        pw = weights[s:e]
-        # vertical colorbar top edges is the cumulative sum of the weights
-        bin_height = pw.sum()
-
-         # parameter interval endpoints
-        x = array([xlo, xhi], 'd')
-        xav = (xlo + xhi)/2
-        # -logp values within interval, with sort index from low to high
-        pv = -logp[s:e]
-        pidx = argsort(pv)
-        pv = pv[pidx]
-        # weights for samples within interval, sorted
-        pw = weights[s:e][pidx]
-        # vertical colorbar top edges is the cumulative sum of the weights
-        y_top = cumsum(pw)
-        bin_height = y_top[-1]
-
-        change_point = searchsorted(pv[1:-1], cbar_edges)
-        tops = unique(hstack((change_point, len(pv)-1)))
-        # For plotly Bar plot, y values should be [size along y] (stacked)
-        yy = np.diff(hstack((0, y_top[tops])))
-        zz = pv[tops][:, None].flatten()
-        xx = np.ones(tops.shape, dtype=float) * xav
-        
-        xscatt.extend(xx.tolist())
-        yscatt.extend(yy.tolist())
-        zscatt.extend(zz.tolist())
-        
-        # centerpoint, histogram height, maximum likelihood for each bin
-        bin_max_likelihood = exp(cbar_edges[0] - pv[0])
-        bins.append(((xlo+xhi)/2, bin_height, bin_max_likelihood))
-
-    bar_trace = go.Bar(x=xscatt, y=yscatt, showlegend=False, hoverinfo='skip', marker=dict(color=zscatt, coloraxis='coloraxis', line=dict(width=0)))
-    # Check for broken distribution
-    if not bins:
-        return
-    centers, height, maxlikelihood = array(bins).T
-    # Normalize maximum likelihood plot so it contains the same area as the
-    # histogram, unless it is really spikey, in which case make sure it has
-    # about the same height as the histogram.
-    maxlikelihood *= np.sum(height)/np.sum(maxlikelihood)
-    hist_peak = np.max(height)
-    ml_peak = np.max(maxlikelihood)
-    if ml_peak > hist_peak*1.3:
-        maxlikelihood *= hist_peak*1.3/ml_peak
-    
-    scatter_trace = go.Scatter(x=centers, y=maxlikelihood, hoverinfo='skip', showlegend=False, line={"color": LINE_COLOR})
-    # return dict(bar_trace=bar_trace, scatter_trace=scatter_trace)
-    return [bar_trace, scatter_trace]
-
-    ## plot marginal gaussian approximation along with histogram
-    #def G(x, mean, std):
-    #    return np.exp(-((x-mean)/std)**2/2)/np.sqrt(2*np.pi*std**2)
-    ## TODO: use weighted average for standard deviation
-    #mean, std = np.average(values, weights=weights), np.std(values, ddof=1)
-    #pdf = G(centers, mean, std)
-    #pylab.plot(centers, pdf*np.sum(height)/np.sum(pdf), '-b')
-
-
-def test():
-    import pickle
-    test_data = pickle.loads(open("./varplot.pickle", 'rb').read())
-    draw = test_data['draw']
-    stats = test_data['stats']
-    import time
-    start_time = time.time()
-    fig = plot_vars(draw, stats)
-    print(f"generating plot took: {time.time() - start_time} seconds")
-    # print(fig)
-    # print(test_data.keys())
-    fig.write_json(open("varplot.json", "w"))
-    fig.write_html(open("varplot.html", "w"))
-    fig.show()
-
-if __name__ == '__main__':
-    test()
\ No newline at end of file

From b6e98940feef71f3a67a2a2768a691112bfed48c Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 20 Mar 2023 09:44:13 -0400
Subject: [PATCH 210/221] put back in the get_model_names method, which is
 needed!

---
 refl1d/webview/server/webserver.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 48ad4a66..31022dff 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -1,7 +1,7 @@
 from aiohttp import web
 import json
 from pathlib import Path
-from typing import Union, Dict
+from typing import Union, Dict, List
 
 import numpy as np
 import bumps.webview.server.webserver as server
@@ -109,6 +109,18 @@ def get_probe_data(theory, probe, substrate=None, surface=None):
     else:
         return [get_single_probe_data(theory, probe, substrate, surface)]
 
-
+@sio.event
+async def get_model_names(sid: str=""):
+    problem = state.problem.fitProblem
+    if problem is None:
+        return None
+    output: List[Dict] = []
+    for model_index, model in enumerate(problem.models):
+        if isinstance(model, Experiment):
+            output.append(dict(name=model.name, part_name=None, model_index=model_index, part_index=0))
+        elif isinstance(model, MixedExperiment):
+            for part_index, part in enumerate(model.parts):
+                output.append(dict(name=model.name, part_name=part.name, model_index=model_index, part_index=part_index))
+    return output
 
 main(index=index, static_assets_path=static_assets_path, arg_defaults={"serializer": "dataclass"})
\ No newline at end of file

From 58a659fcc1fc629ecb84a320817673e25de5621d Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 20 Mar 2023 13:11:40 -0400
Subject: [PATCH 211/221] fix import of bumps main

---
 refl1d/webview/server/webserver.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index 31022dff..a126f7dc 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -4,8 +4,7 @@
 from typing import Union, Dict, List
 
 import numpy as np
-import bumps.webview.server.webserver as server
-from bumps.webview.server.webserver import app, main, sio, rest_get, state, get_chisq, to_json_compatible_dict
+from bumps.webview.server.webserver import app, main as bumps_main, sio, rest_get, state, get_chisq, to_json_compatible_dict
 from refl1d.experiment import Experiment, ExperimentBase, MixedExperiment
 import refl1d.probe
 
@@ -123,4 +122,9 @@ async def get_model_names(sid: str=""):
                 output.append(dict(name=model.name, part_name=part.name, model_index=model_index, part_index=part_index))
     return output
 
-main(index=index, static_assets_path=static_assets_path, arg_defaults={"serializer": "dataclass"})
\ No newline at end of file
+
+def main():
+    bumps_main(index=index, static_assets_path=static_assets_path, arg_defaults={"serializer": "dataclass"})
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 20f20889efd0f6f162835df624fbf9a107079512 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Mon, 20 Mar 2023 13:13:30 -0400
Subject: [PATCH 212/221] rename data panel to reflectivity

---
 refl1d/webview/client/src/panels.mjs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/src/panels.mjs b/refl1d/webview/client/src/panels.mjs
index d144dc91..9dc9a51c 100644
--- a/refl1d/webview/client/src/panels.mjs
+++ b/refl1d/webview/client/src/panels.mjs
@@ -5,6 +5,6 @@ import ModelView from './components/ModelView.vue';
 export const panels = [...bumps_panels];
 
 // replace the bumps data view with the refl1d one.
-panels.find(p => p.title === 'Data').component = DataView;
+panels.splice(0, 1, {title: 'Reflectivity', component: DataView});
 // insert the profile panel at position 3
 panels.splice(2, 0, {title: 'Profile', component: ModelView});

From 8b71c17fa2bf85aa3d2c9d78b5b03e03e7f266c1 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 22 Mar 2023 09:45:20 -0400
Subject: [PATCH 213/221] update plotly

---
 refl1d/webview/client/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index f8340a4a..1e408161 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -12,7 +12,7 @@
     "bumps-webview-client": "^0.0.3",
     "json-difference": "^1.8.2",
     "mpld3": "^0.5.8",
-    "plotly.js": "^2.16.4",
+    "plotly.js": "^2.20.0",
     "socket.io-client": "^4.5.2",
     "uuid": "^9.0.0",
     "vue": "^3.2.38",

From 2f4db58d96c870ddb9603c05e26f41332bd5a290 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 22 Mar 2023 12:47:32 -0400
Subject: [PATCH 214/221] register bumps plugin so model_uncertainty plot will
 work

---
 refl1d/webview/server/webserver.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/refl1d/webview/server/webserver.py b/refl1d/webview/server/webserver.py
index a126f7dc..5acacbce 100644
--- a/refl1d/webview/server/webserver.py
+++ b/refl1d/webview/server/webserver.py
@@ -8,6 +8,11 @@
 from refl1d.experiment import Experiment, ExperimentBase, MixedExperiment
 import refl1d.probe
 
+# Register the refl1d model loader
+import refl1d.fitplugin
+import bumps.cli
+bumps.cli.install_plugin(refl1d.fitplugin)
+
 from .profile_plot import plot_sld_profile_plotly
 
 client_path = Path(__file__).parent.parent / 'client'

From 5e5b4e673938fcdd3b2ff098dc83aeff5702b2fd Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 22 Mar 2023 15:08:58 -0400
Subject: [PATCH 215/221] version bump to pull in latest bumps client version

---
 refl1d/webview/client/package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/refl1d/webview/client/package.json b/refl1d/webview/client/package.json
index 1e408161..4d1e269c 100644
--- a/refl1d/webview/client/package.json
+++ b/refl1d/webview/client/package.json
@@ -1,6 +1,6 @@
 {
   "name": "refl1d-webview-client",
-  "version": "0.0.3",
+  "version": "0.0.4",
   "scripts": {
     "dev": "vite",
     "build": "vite build --emptyOutDir -m development",
@@ -9,7 +9,7 @@
   },
   "dependencies": {
     "bootstrap": "^5.2.1",
-    "bumps-webview-client": "^0.0.3",
+    "bumps-webview-client": "^0.0.4",
     "json-difference": "^1.8.2",
     "mpld3": "^0.5.8",
     "plotly.js": "^2.20.0",

From 8ee21077d570b6455415f61011c68772ae5826f1 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 22 Mar 2023 15:44:01 -0400
Subject: [PATCH 216/221] adding __init__.py for registering packages

---
 refl1d/webview/__init__.py        | 0
 refl1d/webview/server/__init__.py | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 refl1d/webview/__init__.py
 create mode 100644 refl1d/webview/server/__init__.py

diff --git a/refl1d/webview/__init__.py b/refl1d/webview/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/refl1d/webview/server/__init__.py b/refl1d/webview/server/__init__.py
new file mode 100644
index 00000000..e69de29b

From 148f9f854616eb6346d1021d710fbc8359329273 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Tue, 28 Mar 2023 17:05:31 -0400
Subject: [PATCH 217/221] need h5py for file-backed state in webview

---
 webview-requirements | 1 +
 1 file changed, 1 insertion(+)

diff --git a/webview-requirements b/webview-requirements
index f9ce2a9a..8ddca1e5 100644
--- a/webview-requirements
+++ b/webview-requirements
@@ -5,3 +5,4 @@ plotly
 mpld3
 matplotlib
 nodejs
+h5py

From 7347aec16f12574f774bdaf28fc99c933070b74d Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 29 Mar 2023 11:12:13 -0400
Subject: [PATCH 218/221] rework material classes, eliminate fitby

---
 refl1d/material.py | 269 ++++++++++++++++++++++-----------------------
 1 file changed, 129 insertions(+), 140 deletions(-)

diff --git a/refl1d/material.py b/refl1d/material.py
index 92434be6..c900ffd1 100644
--- a/refl1d/material.py
+++ b/refl1d/material.py
@@ -168,178 +168,167 @@ def sld(self, probe):
 # still have to convert Element to/from string repr
 # ELEMENTS = Enum('elements', [(e.name, e.symbol) for e in periodictable.elements._element.values()])
 
-@schema()
-class Material(Scatterer):
+schema()
+class BaseMaterial(Scatterer):
     """
     Description of a solid block of material.
 
     :Parameters:
+        *name* : string
+
         *formula* : Formula
 
             Composition can be initialized from either a string or a chemical
             formula.  Valid values are defined in periodictable.formula.
 
-        *density* : float | |g/cm^3|
-
-            If specified, set the bulk density for the material.
+        *use_incoherent* = False : boolean
 
-        *natural_density* : float | |g/cm^3|
+            True if incoherent scattering should be interpreted as absorption.
+ 
+    """
+    name: str
+    formula: str # Formula
+    use_incoherent: bool = False
+    density: Union[Parameter, Expression] # to be filled in by inheriting classes
 
-            If specified, set the natural bulk density for the material.
+    # not in the schema:
+    _formula: BaseFormula
 
-        *use_incoherent* = False : boolean
+    def __init__(self, formula: Union[str, BaseFormula], name=None, use_incoherent=False):
+        # coerce formula to string repr:
+        self.formula = str(formula)
+        self.name = name if name is not None else str(self._formula)
+        self.use_incoherent = use_incoherent
 
-            True if incoherent scattering should be interpreted as absorption.
+    def sld(self, probe):
+        rho, irho, incoh = probe.scattering_factors(
+            self._formula, density=self.density.value)
+        if self.use_incoherent:
+            raise NotImplementedError("incoherent scattering not supported")
+            #irho += incoh
+        return rho, irho
+    def __str__(self):
+        return self.name
+    def __repr__(self):
+        return "Material(%s)"%self.name
 
-        *fitby* = 'bulk_density' : string
+@schema()
+class Material(BaseMaterial):
+    """
+    A solid block of material, described by its bulk density
 
-            Which density parameter is the fitting parameter.  The choices
-            are *bulk_density*, *natural_density*, *relative_density* or
-            *cell_volume*.  See :meth:`fitby` for details.
+    :Parameters:
+        *density* : float | |g/cm^3|
+            the bulk density for the material.
+    """
+    def __init__(self, formula: Union[str, BaseFormula], density: Union[float, Parameter], name=None, use_incoherent=False):
+        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
+        self._formula = periodictable.formula(formula, density=density)
+        self.density = Parameter.default(density, name=self.name+" density", limits=(0, inf))
+        self.bulk_density = self.density
 
-        *value* : Parameter or float | units depends on fitby type
 
-            Initial value for the fitted density parameter.  If None, the
-            value will be initialized from the material density.
+@schema()
+class NaturalDensityMaterial(BaseMaterial):
+    """
+    A solid block of material, described by its natural density
 
-    For example, to fit Pd by cell volume use::
+    :Parameters:
+        *natural_density* : float | |g/cm^3|
+            the natural bulk density for the material.
+    """
+    def __init__(self, formula: Union[str, BaseFormula], natural_density: Union[float, Parameter], name=None, use_incoherent=False):
+        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
+        self._formula: BaseFormula = periodictable.formula(formula, natural_density=natural_density)
+        self.natural_density = Parameter.default(natural_density, name=self.name+" nat. density", limits=(0, inf))
+        self.density = self.natural_density / self._formula.natural_mass_ratio()
 
-        >>> m = Material('Pd', fitby='cell_volume')
-        >>> m.cell_volume.range(1, 10)
-        Parameter(Pd cell volume)
-        >>> print("%.2f %.2f"%(m.density.value, m.cell_volume.value))
-        12.02 14.70
 
-    You can change density representation by calling *material.fitby(type)*.
+@schema()
+class NumberDensityMaterial(BaseMaterial):
+    """
+    A solid block of material, described by its number density
 
+    :Parameters:
+        *natural_density* : float | |g/cm^3|
+            the natural bulk density for the material.
     """
-    name: str
-    formula: str # Formula
-    formula_density: float
-    formula_natural_density: Union[float, Literal[None]]
-    # density: Parameter
-    value: Parameter
-    fitby: Literal['bulk_density', 'number_density', 'natural_density', 'relative_density', 'cell_volume'] = 'bulk_density'
-    use_incoherent: bool = False
+    def __init__(self, formula: Union[str, BaseFormula], number_density: Union[float, Parameter], name=None, use_incoherent=False):
+        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
+        self._formula: BaseFormula = periodictable.formula(formula)
+        self.number_density = Parameter.default(number_density, name=self.name+" number density", limits=(0, inf))
+        self.density = self.number_density / avogadro_number * self._formula.mass
+        self._formula.density = float(self.density)
 
-    def __init__(self, formula=None, name=None, use_incoherent=False,
-                 formula_density=None, formula_natural_density=None,
-                 fitby='bulk_density', value=None):
-        self._formula = periodictable.formula(formula, density=formula_density,
-                                             natural_density=formula_natural_density)
-        self.formula_density = formula_density
-        self.formula_natural_density = formula_natural_density
-        self.formula = formula
-        self.name = name if name is not None else str(self._formula)
-        self.density = Parameter(name=self.name + " density")
 
-        self.use_incoherent = use_incoherent
-        self._fitby(type=fitby, value=value)
+@schema()
+class RelativeDensityMaterial(BaseMaterial):
+    """
+    A solid block of material, described by its relative density
 
-    def _fitby(self, type='bulk_density', value=None):
-        """
-        Specify the fitting parameter to use for material density.
-
-        :Parameters:
-            *type* : string
-                Density representation
-            *value* : Parameter
-                Initial value, or associated parameter.
-
-        Density type can be one of the following:
-
-            *bulk_density* : |g/cm^3| or kg/L
-                Density is *bulk_density*
-            *natural_density* : |g/cm^3| or kg/L
-                Density is *natural_density* / (natural mass/isotope mass)
-            *relative_density* : unitless
-                Density is *relative_density* * formula density
-            *cell_volume* : |Ang^3|
-                Density is mass / *cell_volume*
-            *number_density*: [atoms/cm^3]
-                Density is *number_density* * molar mass / avogadro constant
+    :Parameters:
+        *relative_density* : unitless
+            Density is *relative_density* * formula density
 
-        The resulting material will have a *density* attribute with the
-        computed material density in addition to the *fitby*
-        attribute specified.
+        *density* : float | |g/cm^3|
+            if specified, the bulk density for the material.
 
-        .. Note::
+        *natural_density* : float | |g/cm^3|
+            if specified, the natural bulk density for the material.
+    """
+    def __init__(self, 
+                 formula: Union[str, BaseFormula],
+                 relative_density: Union[float, Parameter],
+                 density: Optional[float]=None,
+                 natural_density: Optional[float]=None,
+                 name=None,
+                 use_incoherent=False):
+        if density is None and natural_density is None:
+            raise ValueError("must specify one of density or natural_density")
+        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
+        self._formula: BaseFormula = periodictable.formula(formula, density=density, natural_density=natural_density)
+        self.relative_density = Parameter.default(relative_density, name=self.name+" rel. density", limits=(0, inf))
+        self.density = self._formula.density*self.relative_density
 
-            Calling *fitby* replaces the *density* parameter in the
-            material, so be sure to do so before using *density* in a
-            parameter expression.  Using *bumps.parameter.WrappedParameter*
-            for *density* is another alternative.
-        """
 
-        if type == 'bulk_density':
-            if value is None:
-                value = self._formula.density
-            self.value =  Parameter.default(
-                value, name=self.name+" density", limits=(0, None))
-            self.density.equals(self.value)
-        elif type == "number_density":
-            if value is None:
-                value = avogadro_number / self._formula.mass * self._formula.density
-            self.value = Parameter.default(
-                value, name=self.name+" number density", limits=(0, None))
-            self.density.equals(self.value / avogadro_number * self._formula.mass)
-        elif type == 'natural_density':
-            if value is None:
-                value = self._formula.natural_density
-            self.value = Parameter.default(
-                value, name=self.name+" nat. density", limits=(0, None))
-            self.density.equals(self.value / self._formula.natural_mass_ratio())
-        elif type == 'relative_density':
-            if value is None:
-                value = 1
-            self.value = Parameter.default(
-                value, name=self.name+" rel. density", limits=(0, None))
-            self.density.equals(self._formula.density*self.value)
-        ## packing factor code should be correct, but radii are unreliable
-        #elif type is 'packing_factor':
-        #    max_density = self.formula.mass/self.formula.volume(packing_factor=1)
-        #    if value is None:
-        #        value = self.formula.density/max_density
-        #    self.packing_factor = Parameter.default(
-        #        value, name=self.name+" packing factor")
-        #    self.density = self.packing_factor * max_density
-        elif type == 'cell_volume':
-            # Density is in grams/cm^3.
-            # Mass is in grams.
-            # Volume is in A^3 = 1e24*cm^3.
-            if value is None:
-                value = (1e24*self._formula.molecular_mass)/self._formula.density
-            self.value = Parameter.default(
-                value, name=self.name+" cell volume", limits=(0, None))
-            self.density.equals((1e24*self._formula.molecular_mass)/self.value)
-        else:
-            raise ValueError("Unknown density calculation type '%s'"%type)
-        self.fitby = type
+@schema()
+class CellVolumeMaterial(BaseMaterial):
+    """
+    A solid block of material, described by the volume of one unit cell
 
-    def parameters(self):
-        return {'density': self.density, "value": self.value}
+    :Parameters:
+        *cell_volume* : |Ang^3|
+                Density is mass / *cell_volume*
 
-    def to_dict(self):
-        return to_dict({
-            'type': type(self).__name__,
-            'name': self.name,
-            'formula': self.formula,
-            'density': self.density,
-            'use_incoherent': self.use_incoherent,
-            # TODO: what about fitby, natural_density and cell_volume?
-        })
+        *density* : float | |g/cm^3|
+            if specified, the bulk density for the material.
+
+        *natural_density* : float | |g/cm^3|
+            if specified, the natural bulk density for the material.
+            
+    
+    For example, to fit Pd by cell volume use::
+        >>> m = Material('Pd', fitby='cell_volume')
+        >>> m.cell_volume.range(1, 10)
+        Parameter(Pd cell volume)
+        >>> print("%.2f %.2f"%(m.density.value, m.cell_volume.value))
+        12.02 14.70
+    
+    """
+    def __init__(self, 
+                 formula: Union[str, BaseFormula],
+                 cell_volume: Union[float, Parameter],
+                 density: Optional[float]=None,
+                 natural_density: Optional[float]=None,
+                 name=None,
+                 use_incoherent=False):
+        if density is None and natural_density is None:
+            raise ValueError("must specify one of density or natural_density")
+        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
+        self._formula: BaseFormula = periodictable.formula(formula, density=density, natural_density=natural_density)
+        self.cell_volume = Parameter.default(cell_volume, name=self.name+" cell volume", limits=(0, inf))
+        self.density = (1e24*self._formula.molecular_mass)/self.cell_volume
 
-    def sld(self, probe):
-        rho, irho, incoh = probe.scattering_factors(
-            self._formula, density=self.density.value)
-        if self.use_incoherent:
-            raise NotImplementedError("incoherent scattering not supported")
-            #irho += incoh
-        return rho, irho
-    def __str__(self):
-        return self.name
-    def __repr__(self):
-        return "Material(%s)"%self.name
 
 class Compound(Scatterer):
     """

From 2f235baa8b57795ae09b7f484ec2378f608435ec Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 29 Mar 2023 12:11:04 -0400
Subject: [PATCH 219/221] add class factory function to match old usage

---
 refl1d/material.py | 119 ++++++++++++++++++++++++++++++++++++---------
 1 file changed, 96 insertions(+), 23 deletions(-)

diff --git a/refl1d/material.py b/refl1d/material.py
index c900ffd1..5a7cbaeb 100644
--- a/refl1d/material.py
+++ b/refl1d/material.py
@@ -168,7 +168,7 @@ def sld(self, probe):
 # still have to convert Element to/from string repr
 # ELEMENTS = Enum('elements', [(e.name, e.symbol) for e in periodictable.elements._element.values()])
 
-schema()
+@schema()
 class BaseMaterial(Scatterer):
     """
     Description of a solid block of material.
@@ -194,9 +194,10 @@ class BaseMaterial(Scatterer):
     # not in the schema:
     _formula: BaseFormula
 
-    def __init__(self, formula: Union[str, BaseFormula], name=None, use_incoherent=False):
+    def __init__(self, formula: Union[str, BaseFormula], density=None, natural_density=None, name=None, use_incoherent=False):
         # coerce formula to string repr:
         self.formula = str(formula)
+        self._formula: BaseFormula = periodictable.formula(formula, density=density, natural_density=natural_density)
         self.name = name if name is not None else str(self._formula)
         self.use_incoherent = use_incoherent
 
@@ -212,8 +213,33 @@ def __str__(self):
     def __repr__(self):
         return "Material(%s)"%self.name
 
+
+FitByChoices = Literal["bulk_density", "natural_density", "relative_density", "number_density", "cell_volume"]
+
+def Material(
+        formula: Union[str, BaseFormula],
+        density: Optional[float]=None,
+        natural_density: Optional[float]=None,
+        name: Optional[str]=None,
+        use_incoherent: bool=False,
+        fitby: FitByChoices="bulk_density", 
+        **kw):
+    if fitby == "bulk_density":
+        return BulkDensityMaterial(formula, density=density, name=name, use_incoherent=use_incoherent)
+    elif fitby == "natural_density":
+        return NaturalDensityMaterial(formula, natural_density=natural_density, name=name, use_incoherent=use_incoherent)
+    elif fitby == "relative_density":
+        return RelativeDensityMaterial(formula, density=density, natural_density=natural_density, name=name, use_incoherent=use_incoherent, **kw)
+    elif fitby == "number_density":
+        return NumberDensityMaterial(formula, density=density, natural_density=natural_density, name=name, use_incoherent=use_incoherent, **kw)
+    elif fitby == "cell_volume":
+        return CellVolumeMaterial(formula, density=density, natural_density=natural_density, name=name, use_incoherent=use_incoherent, **kw)
+    else:
+        raise ValueError(f'unknown value "{fitby}" of fitby: should be one of ["bulk_density", "natural_density", "relative_density", "number_density", "cell_volume"]')
+
+
 @schema()
-class Material(BaseMaterial):
+class BulkDensityMaterial(BaseMaterial):
     """
     A solid block of material, described by its bulk density
 
@@ -221,9 +247,20 @@ class Material(BaseMaterial):
         *density* : float | |g/cm^3|
             the bulk density for the material.
     """
-    def __init__(self, formula: Union[str, BaseFormula], density: Union[float, Parameter], name=None, use_incoherent=False):
-        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
-        self._formula = periodictable.formula(formula, density=density)
+    bulk_density: Parameter
+    density: Parameter
+
+    def __init__(self,
+                 formula: Union[str, BaseFormula],
+                 density: Optional[Union[float, Parameter]]=None,
+                 name=None,
+                 use_incoherent=False):
+        BaseMaterial.__init__(self, formula, density=density, name=name, use_incoherent=use_incoherent)
+        if density is None:
+            if self._formula.density is not None:
+                density = self._formula.density
+            else:
+                raise ValueError(f"material {self._formula} does not have known density: please provide it in arguments")
         self.density = Parameter.default(density, name=self.name+" density", limits=(0, inf))
         self.bulk_density = self.density
 
@@ -237,9 +274,20 @@ class NaturalDensityMaterial(BaseMaterial):
         *natural_density* : float | |g/cm^3|
             the natural bulk density for the material.
     """
-    def __init__(self, formula: Union[str, BaseFormula], natural_density: Union[float, Parameter], name=None, use_incoherent=False):
-        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
-        self._formula: BaseFormula = periodictable.formula(formula, natural_density=natural_density)
+    natural_density: Parameter
+    density: Expression
+
+    def __init__(self,
+                 formula: Union[str, BaseFormula],
+                 natural_density: Optional[Union[float, Parameter]]=None,
+                 name=None,
+                 use_incoherent=False):
+        BaseMaterial.__init__(self, formula, natural_density=natural_density, name=name, use_incoherent=use_incoherent)
+        if natural_density is None:
+            if self._formula.density is not None:
+                natural_density = self._formula.density
+            else:
+                raise ValueError(f"material {self._formula} does not have known natural_density: please provide it in arguments")
         self.natural_density = Parameter.default(natural_density, name=self.name+" nat. density", limits=(0, inf))
         self.density = self.natural_density / self._formula.natural_mass_ratio()
 
@@ -250,12 +298,31 @@ class NumberDensityMaterial(BaseMaterial):
     A solid block of material, described by its number density
 
     :Parameters:
+        *number_density*: [atoms/cm^3]
+                Density is *number_density* * molar mass / avogadro constant
+
+        *density* : float | |g/cm^3|
+            if specified, the bulk density for the material.
+
         *natural_density* : float | |g/cm^3|
-            the natural bulk density for the material.
+            if specified, the natural bulk density for the material.
     """
-    def __init__(self, formula: Union[str, BaseFormula], number_density: Union[float, Parameter], name=None, use_incoherent=False):
-        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
-        self._formula: BaseFormula = periodictable.formula(formula)
+    number_density: Parameter
+    density: Expression
+
+    def __init__(self,
+                 formula: Union[str, BaseFormula],
+                 number_density: Optional[Union[float, Parameter]]=None,
+                 density: Optional[float]=None,
+                 natural_density: Optional[float]=None,
+                 name=None,
+                 use_incoherent=False):
+        BaseMaterial.__init__(self, formula, density=density, natural_density=natural_density, name=name, use_incoherent=use_incoherent)
+        if number_density is None:
+            if self._formula.density is not None:
+                number_density = avogadro_number / self._formula.mass * self._formula.density
+            else:
+                raise ValueError(f"material {self._formula} does not have known density: please provide density or natural_density argument")
         self.number_density = Parameter.default(number_density, name=self.name+" number density", limits=(0, inf))
         self.density = self.number_density / avogadro_number * self._formula.mass
         self._formula.density = float(self.density)
@@ -276,17 +343,20 @@ class RelativeDensityMaterial(BaseMaterial):
         *natural_density* : float | |g/cm^3|
             if specified, the natural bulk density for the material.
     """
+    relative_density: Parameter
+
     def __init__(self, 
                  formula: Union[str, BaseFormula],
-                 relative_density: Union[float, Parameter],
+                 relative_density: Optional[Union[float, Parameter]]=None,
                  density: Optional[float]=None,
                  natural_density: Optional[float]=None,
                  name=None,
                  use_incoherent=False):
-        if density is None and natural_density is None:
-            raise ValueError("must specify one of density or natural_density")
-        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
-        self._formula: BaseFormula = periodictable.formula(formula, density=density, natural_density=natural_density)
+        BaseMaterial.__init__(self, formula, density=density, natural_density=natural_density, name=name, use_incoherent=use_incoherent)
+        if self._formula.density is None and density is None and natural_density is None:
+            raise ValueError(f"material {self._formula} does not have known density: please provide density or natural_density argument")
+        if relative_density is None:
+            relative_density = 1
         self.relative_density = Parameter.default(relative_density, name=self.name+" rel. density", limits=(0, inf))
         self.density = self._formula.density*self.relative_density
 
@@ -315,17 +385,20 @@ class CellVolumeMaterial(BaseMaterial):
         12.02 14.70
     
     """
+    cell_volume: Parameter
+
     def __init__(self, 
                  formula: Union[str, BaseFormula],
-                 cell_volume: Union[float, Parameter],
+                 cell_volume: Optional[Union[float, Parameter]]=None,
                  density: Optional[float]=None,
                  natural_density: Optional[float]=None,
                  name=None,
                  use_incoherent=False):
-        if density is None and natural_density is None:
-            raise ValueError("must specify one of density or natural_density")
-        BaseMaterial.__init__(self, formula, name=name, use_incoherent=use_incoherent)
-        self._formula: BaseFormula = periodictable.formula(formula, density=density, natural_density=natural_density)
+        BaseMaterial.__init__(self, formula, density=density, natural_density=natural_density, name=name, use_incoherent=use_incoherent)
+        if self._formula.density is None and density is None and natural_density is None:
+            raise ValueError(f"material {self._formula} does not have known density: please provide density or natural_density argument")
+        if cell_volume is None:
+            cell_volume = (1e24*self._formula.molecular_mass)/self._formula.density
         self.cell_volume = Parameter.default(cell_volume, name=self.name+" cell volume", limits=(0, inf))
         self.density = (1e24*self._formula.molecular_mass)/self.cell_volume
 

From 29e4d9a8a1986e5a4ae9041276f33481ff8f623a Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 29 Mar 2023 14:05:37 -0400
Subject: [PATCH 220/221] revert to 'density' keyword for Material

---
 refl1d/materialdb.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/refl1d/materialdb.py b/refl1d/materialdb.py
index 465c15ed..60bdffec 100644
--- a/refl1d/materialdb.py
+++ b/refl1d/materialdb.py
@@ -32,10 +32,10 @@
 rho_DHO = periodictable.formula('DHO').mass/periodictable.formula('H2O').mass
 
 air = Vacuum()
-water = H2O = Material('H2O', formula_density=1, name='water')
-heavywater = D2O = Material('D2O', formula_density=rho_D2O)
-lightheavywater = DHO = Material('DHO', formula_density=rho_DHO)
+water = H2O = Material('H2O', density=1, name='water')
+heavywater = D2O = Material('D2O', density=rho_D2O)
+lightheavywater = DHO = Material('DHO', density=rho_DHO)
 silicon = Si = Material('Si')
-sapphire = Al2O3 = Material('Al2O3', formula_density=3.965, name='sapphire')
+sapphire = Al2O3 = Material('Al2O3', density=3.965, name='sapphire')
 gold = Au = Material('Au', name='gold')
-permalloy = Ni8Fe2 = Material('Ni8Fe2', formula_density=8.692, name='permalloy')
+permalloy = Ni8Fe2 = Material('Ni8Fe2', density=8.692, name='permalloy')

From fe3f68011edf2e2214ed62f96181485b7674e0d0 Mon Sep 17 00:00:00 2001
From: bbm <brian.maranville@nist.gov>
Date: Wed, 29 Mar 2023 14:13:10 -0400
Subject: [PATCH 221/221] add parameters() aggregator for new Material classes

---
 refl1d/material.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/refl1d/material.py b/refl1d/material.py
index 5a7cbaeb..02188dd4 100644
--- a/refl1d/material.py
+++ b/refl1d/material.py
@@ -264,6 +264,9 @@ def __init__(self,
         self.density = Parameter.default(density, name=self.name+" density", limits=(0, inf))
         self.bulk_density = self.density
 
+    def parameters(self):
+        return dict(density=self.density)
+
 
 @schema()
 class NaturalDensityMaterial(BaseMaterial):
@@ -291,6 +294,9 @@ def __init__(self,
         self.natural_density = Parameter.default(natural_density, name=self.name+" nat. density", limits=(0, inf))
         self.density = self.natural_density / self._formula.natural_mass_ratio()
 
+    def parameters(self):
+        return dict(density=self.density, natural_density=self.natural_density)
+
 
 @schema()
 class NumberDensityMaterial(BaseMaterial):
@@ -327,6 +333,9 @@ def __init__(self,
         self.density = self.number_density / avogadro_number * self._formula.mass
         self._formula.density = float(self.density)
 
+    def parameters(self):
+        return dict(density=self.density, number_density=self.number_density)
+
 
 @schema()
 class RelativeDensityMaterial(BaseMaterial):
@@ -360,6 +369,9 @@ def __init__(self,
         self.relative_density = Parameter.default(relative_density, name=self.name+" rel. density", limits=(0, inf))
         self.density = self._formula.density*self.relative_density
 
+    def parameters(self):
+        return dict(density=self.density, relative_density=self.relative_density)
+
 
 @schema()
 class CellVolumeMaterial(BaseMaterial):
@@ -402,6 +414,9 @@ def __init__(self,
         self.cell_volume = Parameter.default(cell_volume, name=self.name+" cell volume", limits=(0, inf))
         self.density = (1e24*self._formula.molecular_mass)/self.cell_volume
 
+    def parameters(self):
+        return dict(density=self.density, cell_volume=self.cell_volume)
+
 
 class Compound(Scatterer):
     """