Tibeuleu/FOC_Reduction
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replace src/analysis with execution from src/lib/plots and move unused scripts to utils

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This commit is contained in:
Thibault Barnouin
2024-05-21 17:11:09 +02:00
parent a515182b2c
commit d3915b3706
4 changed files with 82 additions and 16 deletions
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37
src/lib/plots.py
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@@ -1,3 +1,4 @@
#!/usr/bin/python
"""
Library functions for displaying informations using matplotlib
@@ -54,7 +55,7 @@ from astropy.wcs import WCS
from astropy.io import fits
from astropy.coordinates import SkyCoord
from scipy.ndimage import zoom as sc_zoom
from lib.utils import rot2D, princ_angle, sci_not
from utils import rot2D, princ_angle, sci_not
def plot_obs(data_array, headers, rectangle=None, savename=None, plots_folder="", **kwargs):
@@ -423,7 +424,7 @@ def polarisation_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c
X, Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0]))
U, V = poldata*np.cos(np.pi/2.+pangdata*np.pi/180.), poldata*np.sin(np.pi/2.+pangdata*np.pi/180.)
ax.quiver(X[::step_vec, ::step_vec], Y[::step_vec, ::step_vec], U[::step_vec, ::step_vec], V[::step_vec, ::step_vec], units='xy', angles='uv',
scale=1./vec_scale, scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.2, linewidth=0.3, color='w', edgecolor='k')
scale=1./vec_scale, scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='w', edgecolor='k')
pol_sc = AnchoredSizeBar(ax.transData, vec_scale, r"$P$= 100 %", 4, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='w')
ax.add_artist(pol_sc)
@@ -734,7 +735,7 @@ class overplot_radio(align_maps):
self.X, self.Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0]))
self.U, self.V = pol*np.cos(np.pi/2.+pang*np.pi/180.), pol*np.sin(np.pi/2.+pang*np.pi/180.)
self.Q = self.ax_overplot.quiver(self.X[::step_vec, ::step_vec], self.Y[::step_vec, ::step_vec], self.U[::step_vec, ::step_vec], self.V[::step_vec, ::step_vec], units='xy', angles='uv', scale=1./self.vec_scale,
scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.1, linewidth=0.5, color='white', edgecolor='black', label="{0:s} polarisation map".format(self.map_observer))
scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='white', edgecolor='black', label="{0:s} polarisation map".format(self.map_observer))
self.ax_overplot.autoscale(False)
# Display other map as contours
@@ -853,7 +854,7 @@ class overplot_chandra(align_maps):
self.X, self.Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0]))
self.U, self.V = pol*np.cos(np.pi/2.+pang*np.pi/180.), pol*np.sin(np.pi/2.+pang*np.pi/180.)
self.Q = self.ax_overplot.quiver(self.X[::step_vec, ::step_vec], self.Y[::step_vec, ::step_vec], self.U[::step_vec, ::step_vec], self.V[::step_vec, ::step_vec], units='xy', angles='uv', scale=1./self.vec_scale,
scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.1, linewidth=0.5, color='white', edgecolor='black', label="{0:s} polarisation map".format(self.map_observer))
scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='white', edgecolor='black', label="{0:s} polarisation map".format(self.map_observer))
self.ax_overplot.autoscale(False)
# Display other map as contours
@@ -971,8 +972,8 @@ class overplot_pol(align_maps):
px_scale = self.other_wcs.wcs.get_cdelt()[0]/self.wcs_UV.wcs.get_cdelt()[0]
self.X, self.Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0]))
self.U, self.V = pol*np.cos(np.pi/2.+pang*np.pi/180.), pol*np.sin(np.pi/2.+pang*np.pi/180.)
self.Q = self.ax_overplot.quiver(self.X[::step_vec, ::step_vec], self.Y[::step_vec, ::step_vec], self.U[::step_vec, ::step_vec], self.V[::step_vec, ::step_vec], units='xy', angles='uv', scale=px_scale/self.vec_scale, scale_units='xy', pivot='mid',
headwidth=0., headlength=0., headaxislength=0., width=0.1/px_scale, linewidth=0.5, color='white', edgecolor='black', transform=self.ax_overplot.get_transform(self.wcs_UV), label="{0:s} polarisation map".format(self.map_observer))
self.Q = self.ax_overplot.quiver(self.X[::step_vec, ::step_vec], self.Y[::step_vec, ::step_vec], self.U[::step_vec, ::step_vec], self.V[::step_vec, ::step_vec], units='xy', angles='uv', scale=1./self.vec_scale, scale_units='xy', pivot='mid',
headwidth=0., headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='white', edgecolor='black', transform=self.ax_overplot.get_transform(self.wcs_UV), label="{0:s} polarisation map".format(self.map_observer))
# Display Stokes I as contours
if levels is None:
@@ -1128,7 +1129,7 @@ class align_pol(object):
X, Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0]))
U, V = pol*np.cos(np.pi/2.+pang*np.pi/180.), pol*np.sin(np.pi/2.+pang*np.pi/180.)
ax.quiver(X[::step_vec, ::step_vec], Y[::step_vec, ::step_vec], U[::step_vec, ::step_vec], V[::step_vec, ::step_vec], units='xy',
angles='uv', scale=0.5, scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.1, color='w')
angles='uv', scale=0.5, scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='w')
pol_sc = AnchoredSizeBar(ax.transData, 2., r"$P$= 100 %", 4, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='w')
ax.add_artist(pol_sc)
@@ -2349,12 +2350,12 @@ class pol_map(object):
if hasattr(self, 'quiver'):
self.quiver.remove()
self.quiver = ax.quiver(X, Y, XY_U, XY_V, units='xy', scale=1./self.vec_scale, scale_units='xy', pivot='mid', headwidth=0.,
headlength=0., headaxislength=0., width=0.2, linewidth=0.3, color='white', edgecolor='black')
headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='white', edgecolor='black')
fig.canvas.draw_idle()
return self.quiver
else:
ax.quiver(X, Y, XY_U, XY_V, units='xy', scale=1./self.vec_scale, scale_units='xy', pivot='mid', headwidth=0.,
headlength=0., headaxislength=0., width=0.2, linewidth=0.3, color='white', edgecolor='black')
headlength=0., headaxislength=0., width=0.5, linewidth=0.8, color='white', edgecolor='black')
fig.canvas.draw_idle()
def pol_int(self, fig=None, ax=None):
@@ -2463,3 +2464,21 @@ class pol_map(object):
if self.region is not None:
ax.contour(self.region.astype(float), levels=[0.5], colors='white', linewidths=0.8)
fig.canvas.draw_idle()
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Interactively plot the pipeline products')
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('-p', '--snrp', metavar='snrp_cut', required=False, help='the cut in signal-to-noise for the polarisation degree', type=float, default=3.)
parser.add_argument('-i', '--snri', metavar='snri_cut', required=False, help='the cut in signal-to-noise for the intensity', type=float, default=3.)
parser.add_argument('-l', '--lim', metavar='flux_lim', nargs=2, required=False, help='limits for the intensity map', default=None)
args = parser.parse_args()
if args.file is not None:
Stokes_UV = fits.open(args.file, mode='readonly')
p = pol_map(Stokes_UV, SNRp_cut=args.snrp, SNRi_cut=args.snri, flux_lim=args.lim)
else:
print("python3 plots.py -f <path_to_reduced_fits> -p <SNRp_cut> -i <SNRi_cut> -l <flux_lim>")

4
src/analysis.py → utils/analysis.py
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@@ -1,4 +1,4 @@
#!/usr/bin/python3
#!/usr/bin/python
from getopt import getopt, error as get_error
from sys import argv
@@ -30,7 +30,7 @@ except get_error as err:
if fits_path is not None:
from astropy.io import fits
from lib.plots import pol_map
from src.lib.plots import pol_map
Stokes_UV = fits.open(fits_path)
p = pol_map(Stokes_UV, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, flux_lim=flux_lim)

10
src/comparison_Kishimoto.py → utils/comparison_Kishimoto.py
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@@ -1,8 +1,8 @@
# !/usr/bin/env python
from lib.background import gauss, bin_centers
from lib.deconvolve import zeropad
from lib.reduction import align_data
from lib.plots import princ_angle
#!/usr/bin/python
from src.lib.background import gauss, bin_centers
from src.lib.deconvolve import zeropad
from src.lib.reduction import align_data
from src.lib.plots import princ_angle
from matplotlib.colors import LogNorm
from os.path import join as path_join
from astropy.io import fits

47
utils/get_cdelt.py Executable file
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@@ -0,0 +1,47 @@
#!/usr/bin/python
def main(infiles=None):
"""
Retrieve native spatial resolution from given observation.
"""
from os.path import join as path_join
from warnings import catch_warnings, filterwarnings
from astropy.io.fits import getheader
from astropy.wcs import WCS, FITSFixedWarning
from numpy.linalg import eig
if infiles is None:
print("Usage: \"python get_cdelt.py -f infiles\"")
return 1
prod = [["/".join(filepath.split('/')[:-1]), filepath.split('/')[-1]] for filepath in infiles]
data_folder = prod[0][0]
infiles = [p[1] for p in prod]
cdelt = {}
size = {}
for currfile in infiles:
with catch_warnings():
filterwarnings('ignore', message="'datfix' made the change", category=FITSFixedWarning)
wcs = WCS(getheader(path_join(data_folder, currfile))).celestial
key = currfile[:-5]
size[key] = wcs.array_shape
if wcs.wcs.has_cd():
cdelt[key] = eig(wcs.wcs.cd)[0]*3600.
else:
cdelt[key] = wcs.wcs.cdelt*3600.
print("Image name, native resolution in arcsec and shape")
for currfile in infiles:
key = currfile[:-5]
print(key, cdelt[key], size[key])
return 0
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description='Query MAST for target products')
parser.add_argument('-f', '--files', metavar='path', required=False, nargs='*', help='the full or relative path to the data products', default=None)
args = parser.parse_args()
exitcode = main(infiles=args.files)