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b/plots/NGC1068_x274020/NGC1068_FOC_combine_FWHM010_SNRi.png differ diff --git a/plots/NGC1068_x274020/NGC1068_FOC_combine_FWHM010_SNRp.png b/plots/NGC1068_x274020/NGC1068_FOC_combine_FWHM010_SNRp.png new file mode 100644 index 0000000..aeb40c7 Binary files /dev/null and b/plots/NGC1068_x274020/NGC1068_FOC_combine_FWHM010_SNRp.png differ diff --git a/src/FOC_reduction.py b/src/FOC_reduction.py index 4fb80a4..681b236 100755 --- a/src/FOC_reduction.py +++ b/src/FOC_reduction.py @@ -24,7 +24,7 @@ def main(): # infiles = ['x274020at_c0f.fits','x274020bt_c0f.fits','x274020ct_c0f.fits', # 'x274020dt_c0f.fits','x274020et_c0f.fits','x274020ft_c0f.fits', # 'x274020gt_c0f.fits','x274020ht_c0f.fits','x274020it_c0f.fits'] -# psf_file = 'NGC1068_f253m00.fits' +## psf_file = 'NGC1068_f253m00.fits' # globals()['plots_folder'] = "../plots/NGC1068_x274020/" # globals()['data_folder'] = "../data/IC5063_x3nl030/" @@ -88,11 +88,11 @@ def main(): #BEWARE: 5 observations separated by 1 year each (1995, 1996, 1997, 1998, 1999) globals()['data_folder'] = "../data/M87/POS1/" - infiles = ['x2py010ct_c0f.fits','x2py010dt_c0f.fits','x2py010et_c0f.fits','x2py010ft_c0f.fits'] #1995 +# infiles = ['x2py010ct_c0f.fits','x2py010dt_c0f.fits','x2py010et_c0f.fits','x2py010ft_c0f.fits'] #1995 # infiles = ['x3be010ct_c0f.fits','x3be010dt_c0f.fits','x3be010et_c0f.fits','x3be010ft_c0f.fits'] #1996 # infiles = ['x43r010km_c0f.fits','x43r010mm_c0f.fits','x43r010om_c0f.fits','x43r010rm_c0f.fits'] #1997 # infiles = ['x43r110kr_c0f.fits','x43r110mr_c0f.fits','x43r110or_c0f.fits','x43r110rr_c0f.fits'] #1998 -# infiles = ['x43r210kr_c0f.fits','x43r210mr_c0f.fits','x43r210or_c0f.fits','x43r210rr_c0f.fits'] #1999 + infiles = ['x43r210kr_c0f.fits','x43r210mr_c0f.fits','x43r210or_c0f.fits','x43r210rr_c0f.fits'] #1999 globals()['plots_folder'] = "../plots/M87/POS1/" #BEWARE: 5 observations separated by 1 year each (1995, 1996, 1997, 1998, 1999) @@ -123,7 +123,7 @@ def main(): # Data binning rebin = True if rebin: - pxsize = 0.1 + pxsize = 0.20 px_scale = 'arcsec' #pixel, arcsec or full rebin_operation = 'sum' #sum or average # Alignement @@ -131,7 +131,7 @@ def main(): display_data = False # Smoothing smoothing_function = 'combine' #gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine - smoothing_FWHM = 0.10 #If None, no smoothing is done + smoothing_FWHM = 0.20 #If None, no smoothing is done smoothing_scale = 'arcsec' #pixel or arcsec # Rotation rotate_stokes = True #rotation to North convention can give erroneous results @@ -140,8 +140,8 @@ def main(): crop = False #Crop to desired ROI final_display = True # Polarization map output - figname = 'M87_POS1_1995_FOC' #target/intrument name - figtype = '_combine_FWHM01' #additionnal informations + figname = 'M87_POS1_1999_FOC' #target/intrument name + figtype = '_combine_FWHM020' #additionnal informations SNRp_cut = 3. #P measurments with SNR>3 SNRi_cut = 30. #I measurments with SNR>30, which implies an uncertainty in P of 4.7%. step_vec = 0 #plot all vectors in the array. if step_vec = 2, then every other vector will be plotted diff --git a/src/lib/plots.py b/src/lib/plots.py index db0dc20..86501db 100755 --- a/src/lib/plots.py +++ b/src/lib/plots.py @@ -43,7 +43,6 @@ from matplotlib.patches import Rectangle, Circle from matplotlib.path import Path from matplotlib.widgets import RectangleSelector, LassoSelector, Button, Slider, TextBox from matplotlib.colors import LogNorm -from matplotlib.ticker import LogFormatter import matplotlib.font_manager as fm from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar, AnchoredDirectionArrows from astropy.wcs import WCS @@ -327,7 +326,7 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c elif display.lower() in ['s_p','pol_err','pol_deg_err']: # Display polarization degree error map display='s_p' - vmin, vmax = 0., 10. + vmin, vmax = 0., np.max(pol_err.data[SNRp > SNRp_cut])*100. p_err = deepcopy(pol_err.data) p_err[p_err > vmax/100.] = np.nan im = ax.imshow(p_err*100., vmin=vmin, vmax=vmax, aspect='equal', cmap='inferno', alpha=1.) @@ -470,11 +469,16 @@ class align_maps(object): self.ax1.set_facecolor('k') vmin, vmax = 0., np.max(data[data > 0.]*convert_flux) - im1 = self.ax1.imshow(data*convert_flux, vmin=vmin, vmax=vmax, aspect='equal', cmap='inferno', alpha=1.) + 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) - fontprops = fm.FontProperties(size=16) 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', fontproperties=fontprops) + 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: @@ -552,6 +556,7 @@ class align_maps(object): def apply_align(self, event): self.wcs_map.wcs.crpix = np.array(self.cr_map.get_data()) + self.wcs_map.wcs.crval = np.array(self.wcs_map.pixel_to_world_values(*self.wcs_map.wcs.crpix)) self.wcs_other.wcs.crpix = np.array(self.cr_other.get_data()) self.wcs_other.wcs.crval = self.wcs_map.wcs.crval self.fig.canvas.draw_idle() @@ -650,10 +655,10 @@ class overplot_radio(align_maps): self.fig2.canvas.draw() def plot(self, levels, SNRp_cut=3., SNRi_cut=30., savename=None) -> None: - self.align() - if self.aligned: - self.overplot(other_levels=levels, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename) - plt.show(block=True) + while not self.aligned: + self.align() + self.overplot(other_levels=levels, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename) + plt.show(block=True) class overplot_pol(align_maps): @@ -738,10 +743,125 @@ class overplot_pol(align_maps): self.fig2.canvas.draw() def plot(self, SNRp_cut=3., SNRi_cut=30., savename=None, **kwargs) -> None: - self.align() - if self.aligned: - self.overplot(SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename, **kwargs) - plt.show(block=True) + while not self.aligned(): + self.align() + self.overplot(SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename, **kwargs) + plt.show(block=True) + + +class align_pol(object): + def __init__(self, maps, **kwargs): + maps = np.array(maps) + self.ref_map, self.other_maps = maps[0], maps[1:] + + self.wcs = WCS(self.ref_map[0].header) + self.wcs_other = np.array([WCS(map[0].header) for map in self.other_maps]) + + self.aligned = np.zeros(self.other_maps.shape[0], dtype=bool) + + self.kwargs = kwargs + + def single_plot(self, curr_map, wcs, v_lim=None, ax_lim=None, SNRp_cut=3., SNRi_cut=30., savename=None, **kwargs): + #Get data + stkI = curr_map[np.argmax([curr_map[i].header['datatype']=='I_stokes' for i in range(len(curr_map))])] + stkQ = curr_map[np.argmax([curr_map[i].header['datatype']=='Q_stokes' for i in range(len(curr_map))])] + stkU = curr_map[np.argmax([curr_map[i].header['datatype']=='U_stokes' for i in range(len(curr_map))])] + stk_cov = curr_map[np.argmax([curr_map[i].header['datatype']=='IQU_cov_matrix' for i in range(len(curr_map))])] + pol = curr_map[np.argmax([curr_map[i].header['datatype']=='Pol_deg_debiased' for i in range(len(curr_map))])] + pol_err = curr_map[np.argmax([curr_map[i].header['datatype']=='Pol_deg_err' for i in range(len(curr_map))])] + pang = curr_map[np.argmax([curr_map[i].header['datatype']=='Pol_ang' for i in range(len(curr_map))])] + try: + data_mask = curr_map[np.argmax([curr_map[i].header['datatype']=='Data_mask' for i in range(len(curr_map))])].data.astype(bool) + except KeyError: + data_mask = np.ones(stkI.shape).astype(bool) + + pivot_wav = curr_map[0].header['photplam'] + convert_flux = curr_map[0].header['photflam'] + + #Compute SNR and apply cuts + pol.data[pol.data == 0.] = np.nan + pol_err.data[pol_err.data == 0.] = np.nan + SNRp = pol.data/pol_err.data + SNRp[np.isnan(SNRp)] = 0. + pol.data[SNRp < SNRp_cut] = np.nan + + maskI = stk_cov.data[0,0] > 0 + SNRi = np.zeros(stkI.data.shape) + SNRi[maskI] = stkI.data[maskI]/np.sqrt(stk_cov.data[0,0][maskI]) + pol.data[SNRi < SNRi_cut] = np.nan + + mask = (SNRp > SNRp_cut) * (SNRi > SNRi_cut) + + #Plot the map + plt.rcParams.update({'font.size': 10}) + plt.rcdefaults() + fig = plt.figure(figsize=(10,10)) + ax = fig.add_subplot(111, projection=wcs) + ax.set(xlabel="Right Ascension (J2000)", ylabel="Declination (J2000)", facecolor='k') + fig.subplots_adjust(hspace=0, wspace=0, right=0.9) + cbar_ax = fig.add_axes([0.95, 0.12, 0.01, 0.75]) + + if not ax_lim is None: + lim = np.concatenate([wcs.world_to_pixel(ax_lim[i]) for i in range(len(ax_lim))]) + x_lim, y_lim = lim[0::2], lim[1::2] + ax.set(xlim=x_lim,ylim=y_lim) + + if v_lim is None: + vmin, vmax = 0., np.max(stkI.data[stkI.data > 0.]*convert_flux) + else: + vmin, vmax = v_lim*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 + + im = ax.imshow(stkI.data*convert_flux, aspect='equal', **kwargs) + cbar = plt.colorbar(im, cax=cbar_ax, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]") + + px_size = wcs.wcs.get_cdelt()[0]*3600. + px_sc = AnchoredSizeBar(ax.transData, 1./px_size, '1 arcsec', 3, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='w') + ax.add_artist(px_sc) + + north_dir = AnchoredDirectionArrows(ax.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=curr_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}) + ax.add_artist(north_dir) + + 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 = 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') + 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) + + if not savename is None: + fig.savefig(savename+".png",bbox_inches='tight',dpi=300) + + plt.show(block=True) + return fig, ax + + def align(self): + for i, curr_map in enumerate(self.other_maps): + curr_align = align_maps(self.ref_map, curr_map, **self.kwargs) + self.wcs, self.wcs_other[i] = curr_align.align() + self.aligned[i] = curr_align.aligned + + def plot(self, SNRp_cut=3., SNRi_cut=30., savename=None, **kwargs): + while not self.aligned.all(): + self.align() + + vmin = np.min([np.min(curr_map[0].data[curr_map[0].data > 0.]) for curr_map in self.other_maps]) + vmax = np.max([np.max(curr_map[0].data[curr_map[0].data > 0.]) for curr_map in self.other_maps]) + vmin, vmax = np.min([vmin, np.min(self.ref_map[0].data[self.ref_map[0].data > 0.])]), np.max([vmax, np.max(self.ref_map[0].data[self.ref_map[0].data > 0.])]) + v_lim = np.array([vmin, vmax]) + + fig, ax = self.single_plot(self.ref_map, self.wcs, v_lim = v_lim, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename, **kwargs) + x_lim, y_lim = ax.get_xlim(), ax.get_ylim() + ax_lim = np.array([self.wcs.pixel_to_world(x_lim[i], y_lim[i]) for i in range(len(x_lim))]) + + for i, curr_map in enumerate(self.other_maps): + self.single_plot(curr_map, self.wcs_other[i], v_lim=v_lim, ax_lim=ax_lim, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=savename+'_'+str(i+1), **kwargs) class crop_map(object): diff --git a/src/overplot.py b/src/overplot.py index 11488ce..1c0f0a9 100755 --- a/src/overplot.py +++ b/src/overplot.py @@ -1,20 +1,21 @@ #!/usr/bin/python3 +from os import system as command from astropy.io import fits import numpy as np from copy import deepcopy -from lib.plots import overplot_radio, overplot_pol +from lib.plots import overplot_radio, overplot_pol, align_pol from matplotlib.colors import LogNorm -Stokes_UV = fits.open("../data/IC5063_x3nl030/IC5063_FOC_combine_FWHM020.fits") -Stokes_18GHz = fits.open("../data/IC5063_x3nl030/radio/IC5063.18GHz.fits") -Stokes_24GHz = fits.open("../data/IC5063_x3nl030/radio/IC5063.24GHz.fits") -Stokes_103GHz = fits.open("../data/IC5063_x3nl030/radio/I5063_103GHz.fits") -Stokes_229GHz = fits.open("../data/IC5063_x3nl030/radio/I5063_229GHz.fits") -Stokes_357GHz = fits.open("../data/IC5063_x3nl030/radio/I5063_357GHz.fits") -Stokes_S2 = fits.open("../data/IC5063_x3nl030/POLARIZATION_COMPARISON/S2_rot_crop.fits") -Stokes_IR = fits.open("../data/IC5063_x3nl030/IR/u2e65g01t_c0f_rot.fits") +#Stokes_UV = fits.open("../data/IC5063_x3nl030/IC5063_FOC_combine_FWHM020.fits") +#Stokes_18GHz = fits.open("../data/IC5063_x3nl030/radio/IC5063.18GHz.fits") +#Stokes_24GHz = fits.open("../data/IC5063_x3nl030/radio/IC5063.24GHz.fits") +#Stokes_103GHz = fits.open("../data/IC5063_x3nl030/radio/I5063_103GHz.fits") +#Stokes_229GHz = fits.open("../data/IC5063_x3nl030/radio/I5063_229GHz.fits") +#Stokes_357GHz = fits.open("../data/IC5063_x3nl030/radio/I5063_357GHz.fits") +#Stokes_S2 = fits.open("../data/IC5063_x3nl030/POLARIZATION_COMPARISON/S2_rot_crop.fits") +#Stokes_IR = fits.open("../data/IC5063_x3nl030/IR/u2e65g01t_c0f_rot.fits") -levelsMorganti = np.array([1.,2.,3.,8.,16.,32.,64.,128.]) +#levelsMorganti = np.array([1.,2.,3.,8.,16.,32.,64.,128.]) ##levels18GHz = np.array([0.6, 1.5, 3, 6, 12, 24, 48, 96])/100.*Stokes_18GHz[0].data.max() #levels18GHz = levelsMorganti*0.28*1e-3 @@ -41,5 +42,18 @@ levelsMorganti = np.array([1.,2.,3.,8.,16.,32.,64.,128.]) #F = overplot_pol(Stokes_UV, Stokes_S2) #F.plot(SNRp_cut=3.0, SNRi_cut=80.0, savename='../plots/IC5063_x3nl030/S2_overplot_forced.png', norm=LogNorm(vmin=5e-20,vmax=5e-18)) -G = overplot_pol(Stokes_UV, Stokes_IR, norm=LogNorm(vmin=1e-17,vmax=5e-15), cmap='inferno_r') -G.plot(SNRp_cut=3.0, SNRi_cut=60.0, savename='../plots/IC5063_x3nl030/IR_overplot_forced.png', norm=LogNorm(vmin=1e-17,vmax=5e-15), cmap='inferno_r') +#G = overplot_pol(Stokes_UV, Stokes_IR, norm=LogNorm(vmin=1e-17,vmax=5e-15), cmap='inferno_r') +#G.plot(SNRp_cut=3.0, SNRi_cut=60.0, savename='../plots/IC5063_x3nl030/IR_overplot_forced.png', norm=LogNorm(vmin=1e-17,vmax=5e-15), cmap='inferno_r') + +data_folder = "../data/M87/POS1/" +plots_folder = "../plots/M87/POS1/" +basename = "M87_005_log_core" +M87_95 = fits.open(data_folder+"M87_POS1_1995_FOC_combine_FWHM005.fits") +M87_96 = fits.open(data_folder+"M87_POS1_1996_FOC_combine_FWHM005.fits") +M87_97 = fits.open(data_folder+"M87_POS1_1997_FOC_combine_FWHM005.fits") +M87_98 = fits.open(data_folder+"M87_POS1_1998_FOC_combine_FWHM005.fits") +M87_99 = fits.open(data_folder+"M87_POS1_1999_FOC_combine_FWHM005.fits") + +H = align_pol(np.array([M87_95,M87_96,M87_97,M87_98,M87_99]), norm=LogNorm()) +H.plot(SNRp_cut=3.0, SNRi_cut=30.0, savename=plots_folder+'animated_loop/'+basename, norm=LogNorm()) +command("convert -delay 20 -loop 0 {0:s}animated_loop/{1:s}*.png {0:s}animated_loop/{1:s}.gif && rm {0:s}animated_loop/{1:s}*.png".format(plots_folder, basename))