DLC2Action project GUI

.gitignore

@@ -139,4 +139,4 @@ dmypy.json
 
 #data
 last_action_choice.pickle
-/config.yaml
+dlc2action_annotation/config.yaml

dev-tools/update_license_headers.py

@@ -6,11 +6,12 @@
 Thanks @stes - https://github.com/DeepLabCut/DeepLabCut/blob/master/tools/update_license_headers.py
 """
 
-import tempfile
-import glob
-import yaml
 import fnmatch
+import glob
 import subprocess
+import tempfile
+
+import yaml
 
 
 def load_config(filename):

annotator.py → dlc2action_annotation/annotator.py

@@ -10,7 +10,7 @@
 from typing import Optional
 
 import click
-from PyQt5.QtCore import pyqtSignal
+from PyQt5.QtCore import pyqtSignal, Qt
 from PyQt5.QtGui import QIcon
 from PyQt5.QtWidgets import (
     QAction,
@@ -22,11 +22,16 @@
     QStatusBar,
 )
 
-from utils import get_settings, read_settings, read_video
-from widgets.core.backup import BackupManager
-from widgets.dialog import Form
-from widgets.settings import SettingsWindow
-from widgets.viewer import Viewer as Viewer
+from dlc2action_annotation.utils import (
+    get_library_path,
+    get_settings,
+    read_settings,
+    read_video,
+)
+from dlc2action_annotation.widgets.core.backup import BackupManager
+from dlc2action_annotation.widgets.dialog import Form
+from dlc2action_annotation.widgets.settings import SettingsWindow
+from dlc2action_annotation.widgets.viewer import Viewer as Viewer
 
 
 class MainWindow(QMainWindow):
@@ -39,7 +44,7 @@ def __init__(
         dev=False,
         active_learning=False,
         show_settings=False,
-        config_file="config.yaml",
+        config_file=None,
         al_points_dictionary=None,
         clustering_parameters=None,
         skeleton_files=None,
@@ -50,6 +55,8 @@ def __init__(
         backup_interval: int = 30,
     ):
         super(MainWindow, self).__init__()
+        if config_file is None:
+            config_file = os.path.join(get_library_path(), "config.yaml")
         self.toolbar = None
         self.menubar = None
         self.viewer: Optional[Viewer] = None
@@ -256,7 +263,9 @@ def run_viewer(
 
         if self.backup_dir is None:
             default_video_path = Path(self.videos[0])
-            backup_path = default_video_path.with_name(default_video_path.stem + "_backups")
+            backup_path = default_video_path.with_name(
+                default_video_path.stem + "_backups"
+            )
         else:
             backup_path = Path(self.backup_dir)
         self.backup_manager = BackupManager(
@@ -335,39 +344,40 @@ def load_data(self, type):
 
     def _createActions(self):
         # File actions
+        icons_path = os.path.join(get_library_path(), "img")
         self.play_action = QAction(self)
         self.play_action.setText("Play / Stop")
-        self.play_action.setIcon(QIcon("icons/pause-button.png"))
+        self.play_action.setIcon(QIcon(os.path.join(icons_path, "pause-button.png")))
         self.play_action.triggered.connect(lambda: self.viewer.on_play())
         self.move_action = QAction(self, checkable=True)
         self.move_action.setChecked(True)
         self.move_action.setText("Move")
         self.move_action.setShortcut("Ctrl+M")
-        self.move_action.setIcon(QIcon("icons/hand.png"))
+        self.move_action.setIcon(QIcon(os.path.join(icons_path, "hand.png")))
         self.move_action.triggered.connect(self.viewer.set_move_mode)
         self.remove_action = QAction(self, checkable=True)
         self.remove_action.setText("Remove")
-        self.remove_action.setIcon(QIcon("icons/trash.png"))
+        self.remove_action.setIcon(QIcon(os.path.join(icons_path, "trash.png")))
         self.remove_action.triggered.connect(self.viewer.set_remove_mode)
         self.remove_action.setShortcut("Ctrl+R")
         self.new_action = QAction(self, checkable=True)
         self.new_action.setText("New")
         self.new_action.triggered.connect(self.viewer.set_new_mode)
         self.new_action.setShortcut("Ctrl+N")
-        self.new_action.setIcon(QIcon("icons/plus.png"))
+        self.new_action.setIcon(QIcon(os.path.join(icons_path, "plus.png")))
         self.cut_action = QAction(self, checkable=True)
         self.cut_action.setText("Cut")
-        self.cut_action.setIcon(QIcon("icons/scissors.png"))
+        self.cut_action.setIcon(QIcon(os.path.join(icons_path, "scissors.png")))
         self.cut_action.triggered.connect(self.viewer.set_cut_mode)
         self.cut_action.setShortcut("Ctrl+C")
         self.ass_action = QAction(self, checkable=True)
         self.ass_action.setText("Assign")
-        self.ass_action.setIcon(QIcon("icons/pantone.png"))
+        self.ass_action.setIcon(QIcon(os.path.join(icons_path, "pantone.png")))
         self.ass_action.triggered.connect(self.viewer.set_ass_mode)
         self.ass_action.setShortcut("Ctrl+A")
         self.amb_action = QAction(self, checkable=True)
         self.amb_action.setText("Ambiguous")
-        self.amb_action.setIcon(QIcon("icons/transparency.png"))
+        self.amb_action.setIcon(QIcon(os.path.join(icons_path, "transparency.png")))
         self.amb_action.triggered.connect(self.viewer.set_amb_mode)
         self.amb_action.setShortcut("Ctrl+B")
 
@@ -580,11 +590,28 @@ def set_settings(self, event):
 )
 @click.option("--active_learning", "-a", is_flag=True, help="Active learning mode")
 @click.option("--open-settings", "-s", is_flag=True, help="Open settings window")
-@click.option("--config_file", "-c", default="config.yaml", help="The config file path")
-@click.option("--backup-dir", "-b", default=None, help="The directory where backups are saved")
-@click.option("--backup-interval", default=30, type=int, help="The interval between backups, in minutes")
-def main(video, multiview, dev, active_learning, open_settings, config_file, backup_dir, backup_interval):
+@click.option("--config_file", "-c", default=None, help="The config file path")
+@click.option(
+    "--backup-dir", "-b", default=None, help="The directory where backups are saved"
+)
+@click.option(
+    "--backup-interval",
+    default=30,
+    type=int,
+    help="The interval between backups, in minutes",
+)
+def main(
+    video,
+    multiview,
+    dev,
+    active_learning,
+    open_settings,
+    config_file,
+    backup_dir,
+    backup_interval,
+):
     app = QApplication(sys.argv)
+    app.setAttribute(Qt.AA_UseHighDpiPixmaps)
 
     window = MainWindow(
         videos=video,

cluster.py → dlc2action_annotation/cluster.py

@@ -11,6 +11,7 @@
 from itertools import groupby
 from typing import Iterable
 
+import annotator
 import click
 import numpy as np
 import pyqtgraph as pg
@@ -36,16 +37,21 @@
 )
 from sklearn import datasets, decomposition, manifold
 from vispy.scene import SceneCanvas
-
-import annotator
-from utils import get_color, get_settings, read_skeleton, read_stack, read_video
 from widgets.dialog import (
     EpisodeParamsSelector,
     EpisodeSelector,
     SuggestionParamsSelector,
 )
 from widgets.viewbox import VideoViewBox
 
+from dlc2action_annotation.utils import (
+    get_color,
+    get_settings,
+    read_skeleton,
+    read_stack,
+    read_video,
+)
+
 
 class Annotation:
     def __init__(self, filename):

file_utils/draw_histogram.py → dlc2action_annotation/file_utils/draw_histogram.py

@@ -5,8 +5,9 @@
 #
 import os
 import pickle
-import click
 from collections import defaultdict
+
+import click
 from matplotlib import pyplot as plt
 
 

file_utils/extract_DLC_errors.py → dlc2action_annotation/file_utils/extract_DLC_errors.py

@@ -3,15 +3,16 @@
 #
 # This project and all its files are licensed under GNU AGPLv3 or later version. A copy is included in https://github.com/AlexEMG/DLC2action/LICENSE.AGPL.
 #
-from PIL import Image
-import numpy as np
 import pickle
+from collections import defaultdict
+
+import click
 import dask.array as da
+import numpy as np
 from dask import delayed
-from pims import PyAVReaderIndexed
-import click
-from collections import defaultdict
 from matplotlib import pyplot as plt
+from PIL import Image
+from pims import PyAVReaderIndexed
 
 
 def load_labels(labels_file):

file_utils/file_transformer.py → dlc2action_annotation/file_utils/file_transformer.py

@@ -3,12 +3,13 @@
 #
 # This project and all its files are licensed under GNU AGPLv3 or later version. A copy is included in https://github.com/AlexEMG/DLC2action/LICENSE.AGPL.
 #
+import os
 import pickle
-import pandas as pd
+
+import click
 import numpy as np
-import os
+import pandas as pd
 from tqdm import tqdm
-import click
 
 
 class FileTransformer:

file_utils/split.py → dlc2action_annotation/file_utils/split.py

@@ -3,19 +3,20 @@
 #
 # This project and all its files are licensed under GNU AGPLv3 or later version. A copy is included in https://github.com/AlexEMG/DLC2action/LICENSE.AGPL.
 #
-import re
 import math
-import pandas as pd
+import re
 from optparse import OptionParser
 
+import pandas as pd
+
 """This script can be used to split and downsample larger videos into smaller files that 
 are loaded faster"""
 
 length_regexp = "Duration: (\d{2}):(\d{2}):(\d{2})\.\d+,"
 re_length = re.compile(length_regexp)
 
-from subprocess import check_call, PIPE, Popen
 import shlex
+from subprocess import PIPE, Popen, check_call
 
 
 def main():
@@ -130,7 +131,6 @@ def parse_options():
         options.skeleton_file = None
 
     if options.filename and options.split_size and options.ds and options.fps:
-
         return (
             options.filename,
             options.split_size,