Jonas cutthrough timeseries script

scripts/cutthrough_timeseries.py

@@ -0,0 +1,172 @@
+import sys, os
+import numpy as np
+from scipy.ndimage import uniform_filter1d
+import pytools as pt
+import matplotlib.pyplot as plt
+import argparse
+
+r_e = 6.371e6
+
+"""
+    Script for plotting a cut-through timeseries, aka keogram, aka time-elongation map, etc. for a given variable, a given set of coordinates, and a range of times.
+
+    This script takes 12 parameters, example usage:
+
+    python cutthrough_timeseries.py -var <var> -fnr <fnr0> <fnr1> -pointfile <pointfile> -bulkpath <bulkpath> -bulkprefix <bulkprefix> -outputname <outputname> -outputdir <outputdir> -intpol <intpol> -filt <filt> -op <op> -cmap <cmap>
+
+
+    Parameter descriptions:
+        var: Variable to plot (e.g. "proton/vg_rho", "vg_b_vol")
+        fnr0: First file number to plot
+        fnr1: Last file number to plot
+        pointfile: Path to text file containing coordinates. Each row should correspond to one point, having 3 columns containing coordinates (X,Y,Z), in units of RE
+        bulkpath: Path to directory containing bulk files
+        bulkprefix: Starting string of bulk file name (e.g. bulk, bulk1, bulk5)
+        outputname: Name of output file
+        outputdir: Path to output directory
+        intpol: Interpolate to cut-through sample points? (True/False), default=False
+        filt: Filter out slowly changing signal? (<=0: no filtering, >0: filter with specified window size), default=-1
+        op: Variable operator, default="pass"
+        cmap: Colormap, default="viridis"
+"""
+
+
+def jplots(
+    var,
+    fnr0,
+    fnr1,
+    bulkpath,
+    bulkprefix,
+    outputname,
+    outputdir,
+    intpol=False,
+    filt=-1,
+    op="pass",
+    cmap="viridis",
+    pointfile=None,
+):
+
+    fnr_arr = np.arange(fnr0, fnr1 + 0.1, 1, dtype=int)
+    t_arr = np.zeros_like(fnr_arr).astype(float)
+
+    if bulkpath[-1] != "/":
+        bulkpath += "/"
+
+    coords = np.loadtxt(pointfile) * r_e
+    point_list = np.arange(len(coords))
+    if not intpol:
+        fobj = pt.vlsvfile.VlsvReader(
+            bulkpath + bulkprefix + ".{}.vlsv".format(str(fnr0).zfill(7))
+        )
+        cellids = [int(fobj.get_cellid(coord)) for coord in coords]
+
+    data_arr = np.zeros((fnr_arr.size, point_list.size), dtype=float)
+
+    for idx in range(fnr_arr.size):
+        fnr = fnr_arr[idx]
+        vlsvobj = pt.vlsvfile.VlsvReader(
+            bulkpath + bulkprefix + ".{}.vlsv".format(str(fnr).zfill(7))
+        )
+        t_arr[idx] = vlsvobj.read_parameter("time")
+        if intpol:
+            data_arr[idx, :] = [
+                vlsvobj.read_interpolated_variable(var, coord, operator=op)
+                for coord in coords
+            ]
+        else:
+            data_arr[idx, :] = vlsvobj.read_variable(var, operator=op, cellids=cellids)
+
+    if filt > 0:
+        data_arr = data_arr - uniform_filter1d(data_arr, size=filt, axis=0)
+
+    XmeshXY, YmeshXY = np.meshgrid(point_list, t_arr)
+
+    fig, ax = plt.subplots(1, 1, figsize=(8, 12), constrained_layout=True)
+
+    im = ax.pcolormesh(
+        XmeshXY,
+        YmeshXY,
+        data_arr,
+        shading="gouraud",
+        cmap=cmap,
+        rasterized=True,
+    )
+
+    ax.set_xlim(point_list[0], point_list[-1])
+    ax.set_ylim(t_arr[0], t_arr[-1])
+    ax.set_xlabel("Point along cut", labelpad=10, fontsize=16)
+    ax.set_ylabel("Time [s]", labelpad=10, fontsize=16)
+    ax.set_title(var, pad=10, fontsize=16)
+
+    cb = fig.colorbar(im, ax=ax)
+
+    if not os.path.exists(outputdir):
+        try:
+            os.makedirs(outputdir)
+        except OSError:
+            pass
+
+    if outputdir[-1] != "/":
+        outputdir += "/"
+
+    fig.savefig(outputdir + outputname, dpi=300)
+    plt.close(fig)
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    "-var", help="Variable to plot (e.g. proton/vg_rho)", type=str, required=True
+)
+parser.add_argument("-op", help="Operator for variable", type=str, default="pass")
+parser.add_argument(
+    "-fnr", nargs=2, help="First and last file number to plot", type=int, required=True
+)
+parser.add_argument(
+    "-pointfile",
+    help="A file with coordinates defining the curve to plot along",
+    type=str,
+)
+parser.add_argument(
+    "-bulkpath", help="Path to directory with bulk files", type=str, required=True
+)
+parser.add_argument(
+    "-bulkprefix",
+    help="Starting string of bulk file name (e.g. bulk, bulk1,bulk5)",
+    type=str,
+    required=True,
+)
+parser.add_argument("-outputdir", help="Output file directory", type=str)
+parser.add_argument("-outputname", help="Output file name", type=str)
+parser.add_argument(
+    "-intpol",
+    help="Interpolate to cut-through sample points? (True/False)",
+    type=bool,
+    default=False,
+)
+parser.add_argument(
+    "-filt",
+    help="Filter out slowly changing signal? (<=0: no filtering, >0: filter with specified window size)",
+    type=int,
+    default=-1,
+)
+parser.add_argument(
+    "-cmap", help="Colormap to use for plot", type=str, default="viridis"
+)
+args = parser.parse_args()
+
+if __name__ == "__main__":
+
+    jplots(
+        var=args.var,
+        fnr0=args.fnr[0],
+        fnr1=args.fnr[1],
+        bulkpath=args.bulkpath,
+        bulkprefix=args.bulkprefix,
+        outputdir=args.outputdir,
+        outputname=args.outputname,
+        intpol=args.intpol,
+        filt=args.filt,
+        op=args.op,
+        cmap=args.cmap,
+        pointfile=args.pointfile,
+    )