fix package calling and clean scripts

package/src/emission_center.py

@@ -0,0 +1,77 @@
+#!/usr/bin/python
+# -*- coding:utf-8 -*-
+from pathlib import Path
+from sys import path as syspath
+
+syspath.append(str(Path(__file__).parent.parent))
+
+
+def main(infile, target=None, output_dir=None):
+    from os.path import join as pathjoin
+
+    import numpy as np
+    from astropy.io.fits import open as fits_open
+    from astropy.wcs import WCS
+    from lib.plots import polarization_map
+    from lib.utils import CenterConf, PCconf
+    from matplotlib.patches import Rectangle
+    from matplotlib.pyplot import show
+
+    output = []
+    levelssnr = np.array([3.0, 4.0])
+    levelsconf = np.array([0.99])
+
+    Stokes = fits_open(infile)
+    stkI = Stokes["I_STOKES"].data
+    QN, UN, QN_ERR, UN_ERR = np.full((4, stkI.shape[0], stkI.shape[1]), np.nan)
+    for sflux, nflux in zip(
+        [Stokes["Q_STOKES"].data, Stokes["U_STOKES"].data, np.sqrt(Stokes["IQU_COV_MATRIX"].data[1, 1]), np.sqrt(Stokes["IQU_COV_MATRIX"].data[2, 2])],
+        [QN, UN, QN_ERR, UN_ERR],
+    ):
+        nflux[stkI > 0.0] = sflux[stkI > 0.0] / stkI[stkI > 0.0]
+    Stokesconf = PCconf(QN, UN, QN_ERR, UN_ERR)
+    Stokesmask = Stokes["DATA_MASK"].data.astype(bool)
+    Stokessnr = np.zeros(Stokesmask.shape)
+    Stokessnr[Stokes["POL_DEG_ERR"].data > 0.0] = (
+        Stokes["POL_DEG_DEBIASED"].data[Stokes["POL_DEG_ERR"].data > 0.0] / Stokes["POL_DEG_ERR"].data[Stokes["POL_DEG_ERR"].data > 0.0]
+    )
+
+    Stokescentconf, Stokescenter = CenterConf(Stokesconf > 0.99, Stokes["POL_ANG"].data, Stokes["POL_ANG_ERR"].data)
+    Stokespos = WCS(Stokes[0].header).pixel_to_world(*Stokescenter)
+
+    if target is None:
+        target = Stokes[0].header["TARGNAME"]
+
+    fig, ax = polarization_map(Stokes, P_cut=0.99, step_vec=2, scale_vec=5, display="i")
+
+    snrcont = ax.contour(Stokessnr, levelssnr, colors="b")
+    confcont = ax.contour(Stokesconf, levelsconf, colors="r")
+    confcenter = ax.plot(*Stokescenter, marker="+", color="gray", label="Best confidence for center: {0}".format(Stokespos.to_string("hmsdms")))
+    confcentcont = ax.contour(Stokescentconf, [0.01], colors="gray")
+    handles, labels = ax.get_legend_handles_labels()
+    labels.append(r"$SNR_P \geq$ 3 and 4  contours")
+    handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=snrcont.get_edgecolor()[0]))
+    labels.append(r"Polarization $Conf_{99\%}$ contour")
+    handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcont.get_edgecolor()[0]))
+    labels.append(r"Center $Conf_{99\%}$ contour")
+    handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcentcont.get_edgecolor()[0]))
+    ax.legend(handles=handles, labels=labels, bbox_to_anchor=(0.0, -0.12, 1.0, 0.102), loc="lower left", mode="expand", borderaxespad=0.0)
+    show()
+
+    if output_dir is not None:
+        filename = pathjoin(output_dir, "%s_center.pdf" % target)
+        fig.savefig(filename, dpi=150, facecolor="None")
+        output.append(filename)
+    return output
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Look for the center of emission for a given reduced observation")
+    parser.add_argument("-t", "--target", metavar="targetname", required=False, help="the name of the target", type=str, default=None)
+    parser.add_argument("-f", "--file", metavar="path", required=False, help="The full or relative path to the data product", type=str, default=None)
+    parser.add_argument("-o", "--output_dir", metavar="directory_path", required=False, help="output directory path for the plots", type=str, default="./data")
+    args = parser.parse_args()
+    exitcode = main(infile=args.file, target=args.target, output_dir=args.output_dir)
+    print("Written to: ", exitcode)