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add overplot_chandra and capabilities to overplot classes

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This commit is contained in:
Thibault Barnouin
2023-12-06 16:31:29 +01:00
parent b75d159c39
commit 824c63d0bc
2 changed files with 136 additions and 29 deletions
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161
src/lib/plots.py
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@@ -17,6 +17,9 @@ prototypes :
class overplot_radio(align_maps)
Class inherited from align_maps to overplot radio data as contours.
class overplot_chandra(align_maps)
Class inherited from align_maps to overplot chandra data as contours.
class overplot_pol(align_maps)
Class inherited from align_maps to overplot UV polarization vectors on other maps.
@@ -49,6 +52,7 @@ import matplotlib.patheffects as pe
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar, AnchoredDirectionArrows
from astropy.wcs import WCS
from astropy.io import fits
from scipy.ndimage import zoom as sc_zoom
def princ_angle(ang):
@@ -503,22 +507,30 @@ class align_maps(object):
if len(self.map[0].data.shape) == 4:
self.map[0].data = self.map[0].data[0,0]
elif len(self.map[0].data.shape) == 3:
self.map[0].data = self.map[0].data[1]
self.map[0].data = self.map[0].data[0]
self.wcs_other = deepcopy(WCS(self.other_map[0])).celestial
if len(self.other_map[0].data.shape) == 4:
self.other_map[0].data = self.other_map[0].data[0,0]
elif len(self.other_map[0].data.shape) == 3:
self.other_map[0].data = self.other_map[0].data[1]
self.other_map[0].data = self.other_map[0].data[0]
try:
convert_flux = self.map[0].header['photflam']
self.convert_flux = self.map[0].header['photflam']
except KeyError:
convert_flux = 1.
self.convert_flux = 1.
try:
other_convert = self.other_map[0].header['photflam']
self.pivot_wav = self.map[0].header['photplam']
except KeyError:
other_convert = 1.
pass
try:
self.other_convert = self.other_map[0].header['photflam']
except KeyError:
self.other_convert = 1.
try:
self.other_pivot_wav = self.other_map[0].header['photplam']
except KeyError:
pass
#Get data
data = self.map[0].data
@@ -530,19 +542,24 @@ class align_maps(object):
self.ax1 = self.fig.add_subplot(121, projection=self.wcs_map)
self.ax1.set_facecolor('k')
vmin, vmax = 0., np.max(data[data > 0.]*convert_flux)
old_kwargs = deepcopy(kwargs)
vmin, vmax = np.min(data[data > 0.])*self.convert_flux, np.max(data[data > 0.])*self.convert_flux
for key, value in [["cmap",[["cmap","inferno"]]], ["norm",[["vmin",vmin],["vmax",vmax]]]]:
try:
test = kwargs[key]
except KeyError:
for key_i, val_i in value:
kwargs[key_i] = val_i
im1 = self.ax1.imshow(data*convert_flux, aspect='equal', **kwargs)
im1 = self.ax1.imshow(data*self.convert_flux, aspect='equal', **kwargs)
px_size = self.wcs_map.wcs.get_cdelt()[0]*3600.
px_sc = AnchoredSizeBar(self.ax1.transData, 1./px_size, '1 arcsec', 3, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='w')
self.ax1.add_artist(px_sc)
try:
annote1 = self.ax1.annotate(r"$\lambda$ = {0:.0f} $\AA$".format(self.pivot_wav), color='white', fontsize=12, xy=(0.01, 0.93), xycoords='axes fraction',path_effects=[pe.withStroke(linewidth=0.5,foreground='k')])
except AttributeError:
pass
try:
north_dir1 = AnchoredDirectionArrows(self.ax1.transAxes, "E", "N", length=-0.08, fontsize=0.025, loc=1, aspect_ratio=-1, sep_y=0.01, sep_x=0.01, back_length=0., head_length=10., head_width=10., angle=-self.map[0].header['orientat'], color='white', text_props={'ec': None, 'fc': 'w', 'alpha': 1, 'lw': 0.4}, arrow_props={'ec': None,'fc':'w','alpha': 1,'lw': 1})
self.ax1.add_artist(north_dir1)
@@ -557,20 +574,25 @@ class align_maps(object):
self.ax2 = self.fig.add_subplot(122, projection=self.wcs_other)
self.ax2.set_facecolor('k')
vmin, vmax = 0., np.max(other_data[other_data > 0.]*other_convert)
kwargs = old_kwargs
vmin, vmax = np.min(other_data[other_data > 0.])*self.other_convert, np.max(other_data[other_data > 0.])*self.other_convert
for key, value in [["cmap",[["cmap","inferno"]]], ["norm",[["vmin",vmin],["vmax",vmax]]]]:
try:
test = kwargs[key]
except KeyError:
for key_i, val_i in value:
kwargs[key_i] = val_i
im2 = self.ax2.imshow(other_data*other_convert, aspect='equal', **kwargs)
im2 = self.ax2.imshow(other_data*self.other_convert, aspect='equal', **kwargs)
fontprops = fm.FontProperties(size=16)
px_size = self.wcs_other.wcs.get_cdelt()[0]*3600.
px_sc = AnchoredSizeBar(self.ax2.transData, 1./px_size, '1 arcsec', 3, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='w', fontproperties=fontprops)
self.ax2.add_artist(px_sc)
try:
annote2 = self.ax2.annotate(r"$\lambda$ = {0:.0f} $\AA$".format(self.other_pivot_wav), color='white', fontsize=12, xy=(0.01, 0.93), xycoords='axes fraction',path_effects=[pe.withStroke(linewidth=0.5,foreground='k')])
except AttributeError:
pass
try:
north_dir2 = AnchoredDirectionArrows(self.ax2.transAxes, "E", "N", length=-0.08, fontsize=0.03, loc=1, aspect_ratio=-1, sep_y=0.01, sep_x=0.01, angle=-self.other_map[0].header['orientat'], color='w', arrow_props={'ec': None, 'fc': 'w', 'alpha': 1,'lw': 2})
self.ax2.add_artist(north_dir2)
@@ -661,7 +683,7 @@ class overplot_radio(align_maps):
Class to overplot maps from different observations.
Inherit from class align_maps in order to get the same WCS on both maps.
"""
def overplot(self, other_levels, SNRp_cut=3., SNRi_cut=30., savename=None):
def overplot(self, other_levels, SNRp_cut=3., SNRi_cut=30., vec_scale=2, savename=None):
self.Stokes_UV = self.map
self.wcs_UV = self.wcs_map
#Get Data
@@ -673,14 +695,14 @@ class overplot_radio(align_maps):
pang = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='Pol_ang' for i in range(len(self.Stokes_UV))])]
other_data = self.other_map[0].data
other_convert = 1.
self.other_convert = 1.
other_unit = self.other_map[0].header['bunit']
if other_unit.lower() == 'jy/beam':
other_unit = r"mJy/Beam"
other_convert = 1e3
self.other_convert = 1e3
other_freq = self.other_map[0].header['crval3']
convert_flux = self.Stokes_UV[0].header['photflam']
self.convert_flux = self.Stokes_UV[0].header['photflam']
#Compute SNR and apply cuts
pol.data[pol.data == 0.] = np.nan
@@ -698,8 +720,8 @@ class overplot_radio(align_maps):
self.fig2.subplots_adjust(hspace=0, wspace=0, right=0.9)
#Display UV intensity map with polarization vectors
vmin, vmax = 0., np.max(stkI.data[stkI.data > 0.]*convert_flux)
im = self.ax.imshow(stkI.data*convert_flux, vmin=vmin, vmax=vmax, aspect='equal', cmap='inferno', alpha=1.)
vmin, vmax = 0., np.max(stkI.data[stkI.data > 0.]*self.convert_flux)
im = self.ax.imshow(stkI.data*self.convert_flux, vmin=vmin, vmax=vmax, aspect='equal', cmap='inferno', alpha=1.)
cbar_ax = self.fig2.add_axes([0.95, 0.12, 0.01, 0.75])
cbar = plt.colorbar(im, cax=cbar_ax, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
@@ -707,11 +729,11 @@ class overplot_radio(align_maps):
step_vec = 1
X, Y = np.meshgrid(np.arange(stkI.data.shape[1]), np.arange(stkI.data.shape[0]))
U, V = pol.data*np.cos(np.pi/2.+pang.data*np.pi/180.), pol.data*np.sin(np.pi/2.+pang.data*np.pi/180.)
Q = self.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')
Q = self.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=0.1,color='w')
self.ax.autoscale(False)
#Display other map as contours
other_cont = self.ax.contour(other_data*other_convert, transform=self.ax.get_transform(self.wcs_other), levels=other_levels*other_convert, colors='grey')
other_cont = self.ax.contour(other_data*self.other_convert, transform=self.ax.get_transform(self.wcs_other), levels=other_levels*self.other_convert, colors='grey')
self.ax.clabel(other_cont, inline=True, fontsize=8)
self.ax.set(xlabel="Right Ascension (J2000)", ylabel="Declination (J2000)", title="HST/FOC UV polarization map of {0:s} overplotted with {1:.2f}GHz map in {2:s}.".format(obj, other_freq*1e-9, other_unit))
@@ -741,6 +763,90 @@ class overplot_radio(align_maps):
self.overplot(other_levels=levels, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename)
plt.show(block=True)
class overplot_chandra(align_maps):
"""
Class to overplot maps from different observations.
Inherit from class align_maps in order to get the same WCS on both maps.
"""
def overplot(self, other_levels, SNRp_cut=3., SNRi_cut=30., vec_scale=2, zoom=1, savename=None):
self.Stokes_UV = self.map
self.wcs_UV = self.wcs_map
#Get Data
obj = self.Stokes_UV[0].header['targname']
stkI = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='I_stokes' for i in range(len(self.Stokes_UV))])]
stk_cov = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='IQU_cov_matrix' for i in range(len(self.Stokes_UV))])]
pol = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='Pol_deg_debiased' for i in range(len(self.Stokes_UV))])]
pol_err = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='Pol_deg_err' for i in range(len(self.Stokes_UV))])]
pang = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='Pol_ang' for i in range(len(self.Stokes_UV))])]
other_data = sc_zoom(self.other_map[0].data,zoom)
self.wcs_other.wcs.crpix *= zoom
self.wcs_other.wcs.cdelt /= zoom
other_unit = 'counts'
if (other_levels < 100.).all() and (other_levels > 0.).all():
other_levels *= other_data.max()/100.
self.convert_flux = self.Stokes_UV[0].header['photflam']
#Compute SNR and apply cuts
pol.data[pol.data == 0.] = np.nan
SNRp = pol.data/pol_err.data
SNRp[np.isnan(SNRp)] = 0.
pol.data[SNRp < SNRp_cut] = np.nan
SNRi = stkI.data/np.sqrt(stk_cov.data[0,0])
SNRi[np.isnan(SNRi)] = 0.
pol.data[SNRi < SNRi_cut] = np.nan
plt.rcParams.update({'font.size': 16})
self.fig2 = plt.figure(figsize=(15,15))
self.ax = self.fig2.add_subplot(111, projection=self.wcs_UV)
self.ax.set_facecolor('k')
self.fig2.subplots_adjust(hspace=0, wspace=0, right=0.9)
#Display UV intensity map with polarization vectors
vmin, vmax = 0., np.max(stkI.data[stkI.data > 0.]*self.convert_flux)
im = self.ax.imshow(stkI.data*self.convert_flux, vmin=vmin, vmax=vmax, aspect='equal', cmap='inferno', alpha=1.)
cbar_ax = self.fig2.add_axes([0.95, 0.12, 0.01, 0.75])
cbar = plt.colorbar(im, cax=cbar_ax, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
pol.data[np.isfinite(pol.data)] = 1./2.
step_vec = 1
X, Y = np.meshgrid(np.arange(stkI.data.shape[1]), np.arange(stkI.data.shape[0]))
U, V = pol.data*np.cos(np.pi/2.+pang.data*np.pi/180.), pol.data*np.sin(np.pi/2.+pang.data*np.pi/180.)
Q = self.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=0.1,color='w')
self.ax.autoscale(False)
#Display other map as contours
other_cont = self.ax.contour(other_data, transform=self.ax.get_transform(self.wcs_other), levels=other_levels, colors='grey')
self.ax.clabel(other_cont, inline=True, fontsize=8)
self.ax.set(xlabel="Right Ascension (J2000)", ylabel="Declination (J2000)", title="HST/FOC UV polarization map of {0:s} overplotted with Chandra map in counts.".format(obj))
#Display pixel scale and North direction
fontprops = fm.FontProperties(size=16)
px_size = self.wcs_UV.wcs.get_cdelt()[0]*3600.
px_sc = AnchoredSizeBar(self.ax.transData, 1./px_size, '1 arcsec', 3, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='w', fontproperties=fontprops)
self.ax.add_artist(px_sc)
north_dir = AnchoredDirectionArrows(self.ax.transAxes, "E", "N", length=-0.08, fontsize=0.03, loc=1, aspect_ratio=-1, sep_y=0.01, sep_x=0.01, angle=-self.Stokes_UV[0].header['orientat'], color='w', arrow_props={'ec': None, 'fc': 'w', 'alpha': 1,'lw': 2})
self.ax.add_artist(north_dir)
self.cr_map, = self.ax.plot(*self.wcs_map.wcs.crpix, 'r+')
crpix_other = self.wcs_map.world_to_pixel(self.wcs_other.pixel_to_world(*self.wcs_other.wcs.crpix))
self.cr_other, = self.ax.plot(*crpix_other, 'g+')
if not(savename is None):
if not savename[-4:] in ['.png', '.jpg', '.pdf']:
savename += '.pdf'
self.fig2.savefig(savename,bbox_inches='tight',dpi=200)
self.fig2.canvas.draw()
def plot(self, levels, SNRp_cut=3., SNRi_cut=30., zoom=1, savename=None) -> None:
while not self.aligned:
self.align()
self.overplot(other_levels=levels, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, zoom=zoom, savename=savename)
plt.show(block=True)
class overplot_pol(align_maps):
"""
@@ -758,13 +864,9 @@ class overplot_pol(align_maps):
pol_err = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='Pol_deg_err' for i in range(len(self.Stokes_UV))])]
pang = self.Stokes_UV[np.argmax([self.Stokes_UV[i].header['datatype']=='Pol_ang' for i in range(len(self.Stokes_UV))])]
convert_flux = self.Stokes_UV[0].header['photflam']
self.convert_flux = self.Stokes_UV[0].header['photflam']
other_data = self.other_map[0].data
try:
other_convert = self.other_map[0].header['photflam']
except KeyError:
other_convert = 1.
#Compute SNR and apply cuts
pol.data[pol.data == 0.] = np.nan
@@ -782,8 +884,8 @@ class overplot_pol(align_maps):
self.fig2.subplots_adjust(hspace=0, wspace=0, right=0.9)
#Display Stokes I as contours
levels_stkI = np.rint(np.linspace(10,99,10))/100.*np.max(stkI.data[stkI.data > 0.]*convert_flux)
cont_stkI = self.ax.contour(stkI.data*convert_flux, transform=self.ax.get_transform(self.wcs_UV), levels=levels_stkI, colors='grey', alpha=0.5)
levels_stkI = np.rint(np.linspace(10,99,10))/100.*np.max(stkI.data[stkI.data > 0.]*self.convert_flux)
cont_stkI = self.ax.contour(stkI.data*self.convert_flux, transform=self.ax.get_transform(self.wcs_UV), levels=levels_stkI, colors='grey', alpha=0.5)
#self.ax.clabel(cont_stkI, inline=True, fontsize=8)
self.ax.autoscale(False)
@@ -796,14 +898,14 @@ class overplot_pol(align_maps):
Q = self.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=0.1,linewidth=0.5,color='white',edgecolor='black')
#Display "other" intensity map
vmin, vmax = 0., np.max(other_data[other_data > 0.]*other_convert)
vmin, vmax = np.min(other_data[other_data > 0.]*self.other_convert), np.max(other_data[other_data > 0.]*self.other_convert)
for key, value in [["cmap",[["cmap","inferno"]]], ["norm",[["vmin",vmin],["vmax",vmax]]]]:
try:
test = kwargs[key]
except KeyError:
for key_i, val_i in value:
kwargs[key_i] = val_i
im = self.ax.imshow(other_data*other_convert, transform=self.ax.get_transform(self.wcs_other), alpha=1., **kwargs)
im = self.ax.imshow(other_data*self.other_convert, transform=self.ax.get_transform(self.wcs_other), alpha=1., **kwargs)
cbar_ax = self.fig2.add_axes([0.95, 0.12, 0.01, 0.75])
cbar = plt.colorbar(im, cax=cbar_ax, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
@@ -820,6 +922,11 @@ class overplot_pol(align_maps):
self.cr_map, = self.ax.plot(*self.wcs_map.wcs.crpix, 'r+')
crpix_other = self.wcs_map.world_to_pixel(self.wcs_other.pixel_to_world(*self.wcs_other.wcs.crpix))
self.cr_other, = self.ax.plot(*crpix_other, 'g+')
try:
annote2 = self.ax.annotate(r"$\lambda$ = {0:.0f} $\AA$".format(self.other_pivot_wav), color='white', fontsize=15, xy=(0.01, 0.98), xycoords='axes fraction',path_effects=[pe.withStroke(linewidth=0.5,foreground='k')])
except AttributeError:
pass
if not(savename is None):
if not savename[-4:] in ['.png', '.jpg', '.pdf']: