adjustements to pdf static output

2024-09-25 17:36:05 +02:00
parent 8df2fcce63
commit f84898a9b4
3 changed files with 148 additions and 129 deletions
--- a/package/lib/plots.py
+++ b/package/lib/plots.py
@@ -60,7 +60,10 @@ from mpl_toolkits.axes_grid1.anchored_artists import (
 )
 from scipy.ndimage import zoom as sc_zoom

-from .utils import PCconf, princ_angle, rot2D, sci_not
+try:
+    from .utils import PCconf, princ_angle, rot2D, sci_not
+except ImportError:
+    from utils import PCconf, princ_angle, rot2D, sci_not


 def plot_obs(data_array, headers, rectangle=None, savename=None, plots_folder="", **kwargs):
@@ -205,7 +208,6 @@ def plot_Stokes(Stokes, savename=None, plots_folder=""):
        else:
            savename = savename[:-4] + "_IQU" + savename[-4:]
        fig.savefig(path_join(plots_folder, savename), bbox_inches="tight", dpi=150, facecolor="None")
-    plt.show()
    return 0


@@ -562,7 +564,7 @@ def polarization_map(
    if savename is not None:
        if savename[-4:] not in [".png", ".jpg", ".pdf"]:
            savename += ".pdf"
-        fig.savefig(path_join(plots_folder, savename), bbox_inches="tight", dpi=150, facecolor="None")
+        fig.savefig(path_join(plots_folder, savename), bbox_inches="tight", dpi=300, facecolor="None")

    return fig, ax

@@ -3353,132 +3355,149 @@ if __name__ == "__main__":
    parser.add_argument(
        "-pdf", "--static-pdf", metavar="static_pdf", required=False, help="Whether the analysis tool or the static pdfs should be outputed", default=None
    )
+    parser.add_argument(
+        "-t", "--type", metavar="type", required=False, help="Type of plot to be be outputed", default=None
+    )
    args = parser.parse_args()

    if args.file is not None:
        Stokes_UV = fits.open(args.file, mode="readonly")
        if args.static_pdf is not None:
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"]]),
-                plots_folder=args.static_pdf,
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "I"]),
-                plots_folder=args.static_pdf,
-                display="Intensity",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "P_flux"]),
-                plots_folder=args.static_pdf,
-                display="Pol_Flux",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "P"]),
-                plots_folder=args.static_pdf,
-                display="Pol_deg",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "PA"]),
-                plots_folder=args.static_pdf,
-                display="Pol_ang",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "I_err"]),
-                plots_folder=args.static_pdf,
-                display="I_err",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "P_err"]),
-                plots_folder=args.static_pdf,
-                display="Pol_deg_err",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRi"]),
-                plots_folder=args.static_pdf,
-                display="SNRi",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut if args.p_cut >= 1.0 else 3.0,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRp"]),
-                plots_folder=args.static_pdf,
-                display="SNRp",
-            )
-            polarization_map(
-                Stokes_UV,
-                Stokes_UV["DATA_MASK"].data.astype(bool),
-                P_cut=args.p_cut if args.p_cut < 1.0 else 0.99,
-                SNRi_cut=args.snri,
-                flux_lim=args.lim,
-                step_vec=args.step_vec,
-                scale_vec=args.scale_vec,
-                savename="_".join([Stokes_UV[0].header["FILENAME"], "confP"]),
-                plots_folder=args.static_pdf,
-                display="confp",
-            )
+            if args.type is not None:
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], args.type]),
+                    plots_folder=args.static_pdf,
+                    display=args.type,
+                )
+            else:
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"]]),
+                    plots_folder=args.static_pdf,
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "I"]),
+                    plots_folder=args.static_pdf,
+                    display="Intensity",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "P_flux"]),
+                    plots_folder=args.static_pdf,
+                    display="Pol_Flux",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "P"]),
+                    plots_folder=args.static_pdf,
+                    display="Pol_deg",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "PA"]),
+                    plots_folder=args.static_pdf,
+                    display="Pol_ang",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "I_err"]),
+                    plots_folder=args.static_pdf,
+                    display="I_err",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "P_err"]),
+                    plots_folder=args.static_pdf,
+                    display="Pol_deg_err",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRi"]),
+                    plots_folder=args.static_pdf,
+                    display="SNRi",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut if args.pcut >= 1.0 else 3.0,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRp"]),
+                    plots_folder=args.static_pdf,
+                    display="SNRp",
+                )
+                polarization_map(
+                    Stokes_UV,
+                    Stokes_UV["DATA_MASK"].data.astype(bool),
+                    P_cut=args.pcut if args.pcut < 1.0 else 0.99,
+                    SNRi_cut=args.snri,
+                    flux_lim=args.lim,
+                    step_vec=args.step_vec,
+                    scale_vec=args.scale_vec,
+                    savename="_".join([Stokes_UV[0].header["FILENAME"], "confP"]),
+                    plots_folder=args.static_pdf,
+                    display="confp",
+                )
        else:
-            pol_map(Stokes_UV, P_cut=args.p_cut, SNRi_cut=args.snri, step_vec=args.step_vec, scale_vec=args.scale_vec, flux_lim=args.lim, pa_err=args.pang_err)
+            pol_map(Stokes_UV, P_cut=args.pcut, SNRi_cut=args.snri, step_vec=args.step_vec, scale_vec=args.scale_vec, flux_lim=args.lim, pa_err=args.pang_err, selection=args.type)
    else:
        print(
            "python3 plots.py -f <path_to_reduced_fits> -p <P_cut> -i <SNRi_cut> -st <step_vec> -sc <scale_vec> -l <flux_lim> -pa <pa_err> --pdf <static_pdf>"
--- a/package/src/emission_center.py
+++ b/package/src/emission_center.py
@@ -40,16 +40,16 @@ def main(infile, target=None, output_dir=None):
    if target is None:
        target = Stokes[0].header["TARGNAME"]

-    fig = figure(figsize=(8,9),layout="constrained")
+    fig = figure(figsize=(8,8),layout="constrained")
    fig, ax = polarization_map(Stokes, P_cut=0.99, step_vec=2, scale_vec=5, display="i", fig=fig)

    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")
-    confcont = ax.contour(Stokesconf, [0.99], colors="r")
+    confcentcont = ax.contour(Stokescentconf, [0.001], colors="gray")
+    confcont = ax.contour(Stokesconf, [0.9905], colors="r")
    snr3cont = ax.contour(Stokessnr, [3.0], colors="b", linestyles="dashed")
    snr4cont = ax.contour(Stokessnr, [4.0], colors="b")
    handles, labels = ax.get_legend_handles_labels()
-    labels.append(r"Center $Conf_{99\%}$ contour")
+    labels.append(r"Center $Conf_{99.9\%}$ contour")
    handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcentcont.get_edgecolor()[0]))
    labels.append(r"Polarization $Conf_{99\%}$ contour")
    handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcont.get_edgecolor()[0]))
@@ -61,7 +61,7 @@ def main(infile, target=None, output_dir=None):

    if output_dir is not None:
        filename = pathjoin(output_dir, "%s_center.pdf" % target)
-        fig.savefig(filename, dpi=150, facecolor="None")
+        fig.savefig(filename, dpi=300, facecolor="None")
        output.append(filename)
    show()
    return output
--- a/package/src/overplot_MRK463E.py
+++ b/package/src/overplot_MRK463E.py
@@ -10,7 +10,7 @@ from astropy.io import fits
 from lib.plots import overplot_chandra, overplot_pol
 from matplotlib.colors import LogNorm

-Stokes_UV = fits.open("./data/MRK463E/5960/MRK463E_FOC_b0.05arcsec_c0.07arcsec.fits")
+Stokes_UV = fits.open("./data/MRK463E/5960/MRK463E_FOC_b0.05arcsec_c0.10arcsec.fits")
 Stokes_IR = fits.open("./data/MRK463E/WFPC2/IR_rot_crop.fits")
 Stokes_Xr = fits.open("./data/MRK463E/Chandra/X_ray_crop.fits")