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adjustements to pdf static output

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This commit is contained in:
Thibault Barnouin
2024-09-25 17:36:05 +02:00
parent 8df2fcce63
commit f84898a9b4
3 changed files with 148 additions and 129 deletions
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265
package/lib/plots.py
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@@ -60,7 +60,10 @@ from mpl_toolkits.axes_grid1.anchored_artists import (
) )
from scipy.ndimage import zoom as sc_zoom 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): 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: else:
savename = savename[:-4] + "_IQU" + savename[-4:] savename = savename[:-4] + "_IQU" + savename[-4:]
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=150, facecolor="None")
plt.show()
return 0 return 0
@@ -562,7 +564,7 @@ def polarization_map(
if savename is not None: if savename is not None:
if savename[-4:] not in [".png", ".jpg", ".pdf"]: if savename[-4:] not in [".png", ".jpg", ".pdf"]:
savename += ".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 return fig, ax
@@ -3353,132 +3355,149 @@ if __name__ == "__main__":
parser.add_argument( 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 "-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() args = parser.parse_args()
if args.file is not None: if args.file is not None:
Stokes_UV = fits.open(args.file, mode="readonly") Stokes_UV = fits.open(args.file, mode="readonly")
if args.static_pdf is not None: if args.static_pdf is not None:
polarization_map( if args.type is not None:
Stokes_UV, polarization_map(
Stokes_UV["DATA_MASK"].data.astype(bool), Stokes_UV,
P_cut=args.p_cut, Stokes_UV["DATA_MASK"].data.astype(bool),
SNRi_cut=args.snri, P_cut=args.pcut,
flux_lim=args.lim, SNRi_cut=args.snri,
step_vec=args.step_vec, flux_lim=args.lim,
scale_vec=args.scale_vec, step_vec=args.step_vec,
savename="_".join([Stokes_UV[0].header["FILENAME"]]), scale_vec=args.scale_vec,
plots_folder=args.static_pdf, savename="_".join([Stokes_UV[0].header["FILENAME"], args.type]),
) plots_folder=args.static_pdf,
polarization_map( display=args.type,
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), else:
P_cut=args.p_cut, polarization_map(
SNRi_cut=args.snri, Stokes_UV,
flux_lim=args.lim, Stokes_UV["DATA_MASK"].data.astype(bool),
step_vec=args.step_vec, P_cut=args.pcut,
scale_vec=args.scale_vec, SNRi_cut=args.snri,
savename="_".join([Stokes_UV[0].header["FILENAME"], "I"]), flux_lim=args.lim,
plots_folder=args.static_pdf, step_vec=args.step_vec,
display="Intensity", scale_vec=args.scale_vec,
) savename="_".join([Stokes_UV[0].header["FILENAME"]]),
polarization_map( plots_folder=args.static_pdf,
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "P_flux"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="Pol_Flux", savename="_".join([Stokes_UV[0].header["FILENAME"], "I"]),
) plots_folder=args.static_pdf,
polarization_map( display="Intensity",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "P"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="Pol_deg", savename="_".join([Stokes_UV[0].header["FILENAME"], "P_flux"]),
) plots_folder=args.static_pdf,
polarization_map( display="Pol_Flux",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "PA"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="Pol_ang", savename="_".join([Stokes_UV[0].header["FILENAME"], "P"]),
) plots_folder=args.static_pdf,
polarization_map( display="Pol_deg",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "I_err"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="I_err", savename="_".join([Stokes_UV[0].header["FILENAME"], "PA"]),
) plots_folder=args.static_pdf,
polarization_map( display="Pol_ang",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "P_err"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="Pol_deg_err", savename="_".join([Stokes_UV[0].header["FILENAME"], "I_err"]),
) plots_folder=args.static_pdf,
polarization_map( display="I_err",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRi"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="SNRi", savename="_".join([Stokes_UV[0].header["FILENAME"], "P_err"]),
) plots_folder=args.static_pdf,
polarization_map( display="Pol_deg_err",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut if args.p_cut >= 1.0 else 3.0, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRp"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="SNRp", savename="_".join([Stokes_UV[0].header["FILENAME"], "SNRi"]),
) plots_folder=args.static_pdf,
polarization_map( display="SNRi",
Stokes_UV, )
Stokes_UV["DATA_MASK"].data.astype(bool), polarization_map(
P_cut=args.p_cut if args.p_cut < 1.0 else 0.99, Stokes_UV,
SNRi_cut=args.snri, Stokes_UV["DATA_MASK"].data.astype(bool),
flux_lim=args.lim, P_cut=args.pcut if args.pcut >= 1.0 else 3.0,
step_vec=args.step_vec, SNRi_cut=args.snri,
scale_vec=args.scale_vec, flux_lim=args.lim,
savename="_".join([Stokes_UV[0].header["FILENAME"], "confP"]), step_vec=args.step_vec,
plots_folder=args.static_pdf, scale_vec=args.scale_vec,
display="confp", 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: 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: else:
print( 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>" "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>"

10
package/src/emission_center.py
View File

@@ -40,16 +40,16 @@ def main(infile, target=None, output_dir=None):
if target is None: if target is None:
target = Stokes[0].header["TARGNAME"] 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) 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"))) 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") confcentcont = ax.contour(Stokescentconf, [0.001], colors="gray")
confcont = ax.contour(Stokesconf, [0.99], colors="r") confcont = ax.contour(Stokesconf, [0.9905], colors="r")
snr3cont = ax.contour(Stokessnr, [3.0], colors="b", linestyles="dashed") snr3cont = ax.contour(Stokessnr, [3.0], colors="b", linestyles="dashed")
snr4cont = ax.contour(Stokessnr, [4.0], colors="b") snr4cont = ax.contour(Stokessnr, [4.0], colors="b")
handles, labels = ax.get_legend_handles_labels() 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])) handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcentcont.get_edgecolor()[0]))
labels.append(r"Polarization $Conf_{99\%}$ contour") labels.append(r"Polarization $Conf_{99\%}$ contour")
handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcont.get_edgecolor()[0])) 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: if output_dir is not None:
filename = pathjoin(output_dir, "%s_center.pdf" % target) 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) output.append(filename)
show() show()
return output return output

2
package/src/overplot_MRK463E.py
View File

@@ -10,7 +10,7 @@ from astropy.io import fits
from lib.plots import overplot_chandra, overplot_pol from lib.plots import overplot_chandra, overplot_pol
from matplotlib.colors import LogNorm 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_IR = fits.open("./data/MRK463E/WFPC2/IR_rot_crop.fits")
Stokes_Xr = fits.open("./data/MRK463E/Chandra/X_ray_crop.fits") Stokes_Xr = fits.open("./data/MRK463E/Chandra/X_ray_crop.fits")