diff --git a/.gitignore b/.gitignore index b4c11ed..99fb2ca 100755 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,5 @@ ipython_config.py *.par data/IC5063_x3nl030/POLARIZATION_COMPARISON/POLARIZATION_COMPARISON-20220329T133819Z-001.zip src/IC5063_x_y_F_P_PA.txt +src/IC5063_x_y_F_Q_U_P_PA.txt +src/NGC1068_x_y_F_Q_U_P_PA.txt diff --git a/data/PictorA_x25d040/README.md b/data/PictorA_x25d040/README.md deleted file mode 100755 index 7393031..0000000 --- a/data/PictorA_x25d040/README.md +++ /dev/null @@ -1,5 +0,0 @@ -Observation data -Instrument : FOC -Proposal ID : 5156 -Target name : Pictor-A -Dataset : X25D040 diff --git a/plots/3C109_x3mc010/3C109_FOC.png b/plots/3C109_x3mc010/3C109_FOC.png deleted file mode 100755 index eca2ded..0000000 Binary files a/plots/3C109_x3mc010/3C109_FOC.png and /dev/null differ diff --git a/plots/3C109_x3mc010/3C109_FOC_IQU.png b/plots/3C109_x3mc010/3C109_FOC_IQU.png deleted file mode 100755 index d82e883..0000000 Binary files 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Binary files a/plots/PictorA_x25d040/PictorA_FOC_errors_background_flux.png and /dev/null differ diff --git a/plots/PictorA_x25d040/PictorA_FOC_errors_background_location.png b/plots/PictorA_x25d040/PictorA_FOC_errors_background_location.png deleted file mode 100755 index 0cd1ab3..0000000 Binary files a/plots/PictorA_x25d040/PictorA_FOC_errors_background_location.png and /dev/null differ diff --git a/src/FOC_reduction.py b/src/FOC_reduction.py index 993d08e..b47ec35 100755 --- a/src/FOC_reduction.py +++ b/src/FOC_reduction.py @@ -13,17 +13,18 @@ import lib.reduction as proj_red #Functions used in reduction pipeline import lib.plots as proj_plots #Functions for plotting data from lib.convex_hull import image_hull from lib.deconvolve import from_file_psf +import matplotlib.pyplot as plt def main(): ##### User inputs ## Input and output locations - globals()['data_folder'] = "../data/NGC1068_x274020/" - 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' - globals()['plots_folder'] = "../plots/NGC1068_x274020/" +# globals()['data_folder'] = "../data/NGC1068_x274020/" +# 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' +# globals()['plots_folder'] = "../plots/NGC1068_x274020/" # globals()['data_folder'] = "../data/NGC1068_x14w010/" # infiles = ['x14w0101t_c0f.fits','x14w0102t_c0f.fits','x14w0103t_c0f.fits', @@ -62,10 +63,10 @@ def main(): # 'x3995202r_c0f.fits','x3995206r_c0f.fits'] # globals()['plots_folder'] = "../plots/PG1630+377_x39510/" -# globals()['data_folder'] = "../data/IC5063_x3nl030/" -# infiles = ['x3nl0301r_c0f.fits','x3nl0302r_c0f.fits','x3nl0303r_c0f.fits'] -# psf_file = 'IC5063_f502m00.fits' -# globals()['plots_folder'] = "../plots/IC5063_x3nl030/" + globals()['data_folder'] = "../data/IC5063_x3nl030/" + infiles = ['x3nl0301r_c0f.fits','x3nl0302r_c0f.fits','x3nl0303r_c0f.fits'] + psf_file = 'IC5063_f502m00.fits' + globals()['plots_folder'] = "../plots/IC5063_x3nl030/" # globals()['data_folder'] = "../data/MKN3_x3nl010/" # infiles = ['x3nl0101r_c0f.fits','x3nl0102r_c0f.fits','x3nl0103r_c0f.fits'] @@ -118,7 +119,7 @@ def main(): # Final crop crop = False #Crop to desired ROI # Polarization map output - figname = 'NGC1068_FOC' #target/intrument name + figname = 'IC5063_FOC' #target/intrument name figtype = '_combine_FWHM020' #additionnal informations SNRp_cut = 10. #P measurments with SNR>3 SNRi_cut = 100. #I measurments with SNR>30, which implies an uncertainty in P of 4.7%. @@ -141,12 +142,12 @@ def main(): if rebin: data_array, error_array, headers, Dxy = proj_red.rebin_array(data_array, error_array, headers, pxsize=pxsize, scale=px_scale, operation=rebin_operation) # Align and rescale images with oversampling. - data_mask = np.zeros(data_array.shape[1:]).astype(bool) + data_mask = np.ones(data_array.shape[1:]).astype(bool) if px_scale.lower() not in ['full','integrate']: data_array, error_array, headers, data_mask = proj_red.align_data(data_array, headers, error_array, upsample_factor=int(Dxy.min()), ref_center=align_center, return_shifts=False) if px_scale.lower() not in ['full','integrate']: - vertex = image_hull((1.-data_mask),step=5,null_val=0.,inside=True) + vertex = image_hull(data_mask,step=5,null_val=0.,inside=True) else: vertex = np.array([0.,0.,data_array.shape[2],data_array.shape[2]]) shape = np.array([vertex[1]-vertex[0],vertex[3]-vertex[2]]) diff --git a/src/lib/convex_hull.py b/src/lib/convex_hull.py index 08cf5ea..fd6e3fc 100755 --- a/src/lib/convex_hull.py +++ b/src/lib/convex_hull.py @@ -7,6 +7,33 @@ from copy import deepcopy import numpy as np +def clean_ROI(image): + H,J = [],[] + + shape = np.array(image.shape) + row, col = np.indices(shape) + + for i in range(0,shape[0]): + r = row[i,:][image[i,:]>0.] + c = col[i,:][image[i,:]>0.] + if len(r)>1 and len(c)>1: + H.append((r[0],c[0])) + H.append((r[-1],c[-1])) + H = np.array(H) + for j in range(0,shape[1]): + r = row[:,j][image[:,j]>0.] + c = col[:,j][image[:,j]>0.] + if len(r)>1 and len(c)>1: + J.append((r[0],c[0])) + J.append((r[-1],c[-1])) + J = np.array(J) + xmin = np.min([H[:,1].min(),J[:,1].min()]) + xmax = np.max([H[:,1].max(),J[:,1].max()])+1 + ymin = np.min([H[:,0].min(),J[:,0].min()]) + ymax = np.max([H[:,0].max(),J[:,0].max()])+1 + return np.array([xmin,xmax,ymin,ymax]) + + # Define angle and vectors operations def vector(A, B): """ diff --git a/src/lib/fits.py b/src/lib/fits.py index 54b96a1..0d7eb5f 100755 --- a/src/lib/fits.py +++ b/src/lib/fits.py @@ -12,7 +12,7 @@ prototypes : import numpy as np from astropy.io import fits from astropy import wcs -from lib.convex_hull import image_hull +from lib.convex_hull import image_hull, clean_ROI def get_obs_data(infiles, data_folder="", compute_flux=False): @@ -78,33 +78,6 @@ def get_obs_data(infiles, data_folder="", compute_flux=False): return data_array, headers -def clean_ROI(image): - H,J = [],[] - - shape = np.array(image.shape) - row, col = np.indices(shape) - - for i in range(0,shape[0]): - r = row[i,:][image[i,:]>0.] - c = col[i,:][image[i,:]>0.] - if len(r)>1 and len(c)>1: - H.append((r[0],c[0])) - H.append((r[-1],c[-1])) - H = np.array(H) - for j in range(0,shape[1]): - r = row[:,j][image[:,j]>0.] - c = col[:,j][image[:,j]>0.] - if len(r)>1 and len(c)>1: - J.append((r[0],c[0])) - J.append((r[-1],c[-1])) - J = np.array(J) - xmin = np.min([H[:,1].min(),J[:,1].min()])-1 - xmax = np.max([H[:,1].max(),J[:,1].max()])+1 - ymin = np.min([H[:,0].min(),J[:,0].min()])-1 - ymax = np.max([H[:,0].max(),J[:,0].max()])+1 - return np.array([xmin,xmax,ymin,ymax]) - - def save_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, P, debiased_P, s_P, s_P_P, PA, s_PA, s_PA_P, headers, data_mask, filename, data_folder="", return_hdul=False): @@ -145,10 +118,10 @@ def save_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, P, debiased_P, s_P, exp_tot = np.array([header['exptime'] for header in headers]).sum() new_wcs = wcs.WCS(ref_header).deepcopy() - vertex = clean_ROI(1.-data_mask) + vertex = clean_ROI(data_mask) shape = vertex[1::2]-vertex[0::2] new_wcs.array_shape = shape - new_wcs.wcs.crpix -= vertex[0::2] + new_wcs.wcs.crpix = np.array(new_wcs.wcs.crpix) - vertex[0::-2] header = new_wcs.to_header() header['instrume'] = (ref_header['instrume'], 'Instrument from which data is reduced') @@ -179,7 +152,7 @@ def save_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, P, debiased_P, s_P, new_Stokes_cov = np.zeros((3,3,shape[0],shape[1])) for i in range(3): for j in range(3): - Stokes_cov[i,j][data_mask] = 0. + Stokes_cov[i,j][(1-data_mask).astype(bool)] = 0. new_Stokes_cov[i,j] = Stokes_cov[i,j][vertex[0]:vertex[1],vertex[2]:vertex[3]] Stokes_cov = new_Stokes_cov diff --git a/src/lib/plots.py b/src/lib/plots.py index db91ffe..c56fe44 100755 --- a/src/lib/plots.py +++ b/src/lib/plots.py @@ -13,7 +13,7 @@ from copy import deepcopy import numpy as np import matplotlib.pyplot as plt from matplotlib.patches import Rectangle -from matplotlib.widgets import RectangleSelector, Button +from matplotlib.widgets import RectangleSelector, Button, Slider from matplotlib.transforms import Bbox import matplotlib.font_manager as fm from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar, AnchoredDirectionArrows @@ -219,23 +219,19 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c stkQ = Stokes[np.argmax([Stokes[i].header['datatype']=='Q_stokes' for i in range(len(Stokes))])] stkU = Stokes[np.argmax([Stokes[i].header['datatype']=='U_stokes' for i in range(len(Stokes))])] stk_cov = Stokes[np.argmax([Stokes[i].header['datatype']=='IQU_cov_matrix' for i in range(len(Stokes))])] - #pol = Stokes[np.argmax([Stokes[i].header['datatype']=='Pol_deg' for i in range(len(Stokes))])] pol = Stokes[np.argmax([Stokes[i].header['datatype']=='Pol_deg_debiased' for i in range(len(Stokes))])] pol_err = Stokes[np.argmax([Stokes[i].header['datatype']=='Pol_deg_err' for i in range(len(Stokes))])] - #pol_err_Poisson = Stokes[np.argmax([Stokes[i].header['datatype']=='Pol_deg_err_Poisson_noise' for i in range(len(Stokes))])] pang = Stokes[np.argmax([Stokes[i].header['datatype']=='Pol_ang' for i in range(len(Stokes))])] - pang_err = Stokes[np.argmax([Stokes[i].header['datatype']=='Pol_ang_err' for i in range(len(Stokes))])] - if data_mask is None: - data_mask = Stokes[np.argmax([Stokes[i].header['datatype']=='Data_mask' for i in range(len(Stokes))])].data.astype(bool) + try: + if data_mask is None: + data_mask = Stokes[np.argmax([Stokes[i].header['datatype']=='Data_mask' for i in range(len(Stokes))])].data.astype(bool) + except KeyError: + data_mask = np.ones(stkI.shape).astype(bool) pivot_wav = Stokes[0].header['photplam'] convert_flux = Stokes[0].header['photflam'] wcs = WCS(Stokes[0]).deepcopy() - #Get image mask - if data_mask is None: - data_mask = np.zeros(stkI.shape).astype(bool) - #Plot Stokes parameters map if display is None or display.lower() == 'default': plot_Stokes(Stokes, savename=savename, plots_folder=plots_folder) @@ -252,7 +248,6 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c SNRi[maskI] = stkI.data[maskI]/np.sqrt(stk_cov.data[0,0][maskI]) pol.data[SNRi < SNRi_cut] = np.nan - data_mask = (1.-data_mask).astype(bool) mask = (SNRp > SNRp_cut) * (SNRi > SNRi_cut) # Look for pixel of max polarization @@ -339,13 +334,13 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c if step_vec == 0: pol.data[np.isfinite(pol.data)] = 1./2. step_vec = 1 - X, Y = np.meshgrid(np.linspace(0,stkI.data.shape[1],stkI.data.shape[1])-0.5, np.linspace(0,stkI.data.shape[0],stkI.data.shape[0])-0.5) + 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', fontproperties=fontprops) ax.add_artist(pol_sc) - north_dir = AnchoredDirectionArrows(ax.transAxes, "E", "N", length=-0.08, fontsize=0.03, loc=1, aspect_ratio=-1, sep_y=0.01, sep_x=0.01, angle=-Stokes[0].header['orientat'], color='w', arrow_props={'ec': 'w', 'fc': 'w', 'alpha': 1,'lw': 2}) + 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=-Stokes[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) # Display instrument FOV @@ -383,6 +378,7 @@ def polarization_map(Stokes, data_mask=None, rectangle=None, SNRp_cut=3., SNRi_c plt.show() return fig, ax + class align_maps(object): """ Class to interactively align maps with different WCS. @@ -430,7 +426,7 @@ class align_maps(object): self.ax1.add_artist(px_sc) try: - north_dir1 = AnchoredDirectionArrows(self.ax1.transAxes, "E", "N", length=-0.08, fontsize=0.03, loc=1, aspect_ratio=-1, sep_y=0.01, sep_x=0.01, angle=-self.map[0].header['orientat'], color='w', arrow_props={'ec': 'w', 'fc': 'w', 'alpha': 1,'lw': 2}) + 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) except KeyError: pass @@ -452,7 +448,7 @@ class align_maps(object): self.ax2.add_artist(px_sc) 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': 'w', 'fc': 'w', 'alpha': 1,'lw': 2}) + 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) except KeyError: pass @@ -527,6 +523,8 @@ class overplot_radio(align_maps): 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): + 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))])] @@ -568,7 +566,7 @@ class overplot_radio(align_maps): pol.data[np.isfinite(pol.data)] = 1./2. step_vec = 1 - X, Y = np.meshgrid(np.linspace(0,stkI.data.shape[0],stkI.data.shape[0]), np.linspace(0,stkI.data.shape[1],stkI.data.shape[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') self.ax.autoscale(False) @@ -584,7 +582,7 @@ class overplot_radio(align_maps): 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': 'w', 'fc': 'w', 'alpha': 1,'lw': 2}) + 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) @@ -599,6 +597,7 @@ 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_pol(align_maps): """ Class to overplot maps from different observations. @@ -646,7 +645,7 @@ class overplot_pol(align_maps): #Display full size polarization vectors pol.data[np.isfinite(pol.data)] = 1./2. step_vec = 1 - X, Y = np.meshgrid(np.linspace(0,stkI.data.shape[0],stkI.data.shape[0]), np.linspace(0,stkI.data.shape[1],stkI.data.shape[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') @@ -661,7 +660,7 @@ class overplot_pol(align_maps): px_size = self.wcs_other.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': 'w', 'fc': 'w', 'alpha': 1,'lw': 2}) + 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) @@ -750,7 +749,7 @@ class crop_map(object): self.wcs_crop = self.wcs.deepcopy() self.wcs_crop.array_shape = shape if self.crpix_in_RS(): - self.wcs_crop.wcs.crpix -= self.RSextent[::2] + self.wcs_crop.wcs.crpix = np.array(self.wcs_crop.wcs.crpix) - self.RSextent[::2] else: self.wcs_crop.wcs.crval = self.wcs.wcs_pix2world([self.RScenter],1)[0] self.wcs_crop.wcs.crpix = self.RScenter-self.RSextent[::2] @@ -793,6 +792,7 @@ class crop_map(object): def writeto(self, filename): self.hdul_crop.writeto(filename,overwrite=True) + class crop_Stokes(crop_map): """ Class to interactively crop a polarization map to desired Region of Interest. @@ -810,7 +810,7 @@ class crop_Stokes(crop_map): self.wcs_crop = self.wcs.deepcopy() self.wcs_crop.array_shape = shape if self.crpix_in_RS(): - self.wcs_crop.wcs.crpix -= self.RSextent[::2] + self.wcs_crop.wcs.crpix = np.array(self.wcs_crop.wcs.crpix) - self.RSextent[::2] else: self.wcs_crop.wcs.crval = self.wcs.wcs_pix2world([self.RScenter],1)[0] self.wcs_crop.wcs.crpix = self.RScenter-self.RSextent[::2] @@ -849,4 +849,151 @@ class crop_Stokes(crop_map): @property def data_mask(self): - return self.hdul_crop[-1].data \ No newline at end of file + return self.hdul_crop[-1].data + +class pol_map(object): + """ + Class to interactively study polarization maps. + """ + def __init__(self,Stokes, SNRp_cut=3., SNRi_cut=30.): + + self.Stokes = Stokes + self.wcs = deepcopy(WCS(Stokes[0].header)) + self.SNRp_cut = SNRp_cut + self.SNRi_cut = SNRi_cut + self.SNRi = deepcopy(self.SNRi_cut) + self.SNRp = deepcopy(self.SNRp_cut) + self.region = None + + #Get data + self.pivot_wav = self.Stokes[0].header['photplam'] + self.convert_flux = self.Stokes[0].header['photflam'] + self.I = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='I_stokes' for i in range(len(Stokes))])].data + self.Q = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='Q_stokes' for i in range(len(Stokes))])].data + self.U = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='U_stokes' for i in range(len(Stokes))])].data + self.IQU_cov = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='IQU_cov_matrix' for i in range(len(Stokes))])].data + self.P = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='Pol_deg_debiased' for i in range(len(Stokes))])].data + self.s_P = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='Pol_deg_err' for i in range(len(Stokes))])].data + self.PA = self.Stokes[np.argmax([self.Stokes[i].header['datatype']=='Pol_ang' for i in range(len(Stokes))])].data + + #Create figure + fontprops = fm.FontProperties(size=16) + self.fig = plt.figure(figsize=(15,15)) + self.fig.subplots_adjust(hspace=0, wspace=0, right=0.9) + self.ax = self.fig.add_subplot(111,projection=self.wcs) + self.ax.set_facecolor('black') + + self.ax.coords.grid(True, color='white', ls='dotted', alpha=0.5) + self.ax.coords[0].set_axislabel('Right Ascension (J2000)') + self.ax.coords[0].set_axislabel_position('t') + self.ax.coords[0].set_ticklabel_position('t') + self.ax.coords[1].set_axislabel('Declination (J2000)') + self.ax.coords[1].set_axislabel_position('l') + self.ax.coords[1].set_ticklabel_position('l') + self.ax.axis('equal') + + #Display total flux + im = self.ax.imshow(self.I*self.convert_flux, vmin=0., vmax=self.I[self.I > 0.].max()*self.convert_flux, aspect='auto', cmap='inferno') + cbar_ax = self.fig.add_axes([0.95, 0.12, 0.01, 0.75]) + cbar = plt.colorbar(im, cax=cbar_ax, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]") + #Display polarization vectors in SNR_cut + self.pol_vector() + + #Display scales and orientation + px_size = self.wcs.wcs.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='white', fontproperties=fontprops) + self.ax.add_artist(px_sc) + pol_sc = AnchoredSizeBar(self.ax.transData, 2., r"$P$= 100%", 4, pad=0.5, sep=5, borderpad=0.5, frameon=False, size_vertical=0.005, color='white', fontproperties=fontprops) + self.ax.add_artist(pol_sc) + north_dir = AnchoredDirectionArrows(self.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=-self.Stokes[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.ax.add_artist(north_dir) + + #Display integrated values in ROI + self.pol_int + + #Set axes for sliders (SNRp_cut, SNRi_cut) + ax_I_cut = self.fig.add_axes([0.125, 0.080, 0.35, 0.01]) + ax_P_cut = self.fig.add_axes([0.125, 0.055, 0.35, 0.01]) + ax_reset = self.fig.add_axes([0.125, 0.020, 0.05, 0.02]) + SNRi_max = np.max(self.I[self.IQU_cov[0,0]>0.]/np.sqrt(self.IQU_cov[0,0][self.IQU_cov[0,0]>0.])) + SNRp_max = np.max(self.P[self.s_P>0.]/self.s_P[self.s_P > 0.]) + s_I_cut = Slider(ax_I_cut,r"$SNR^{I}_{cut}$",1.,SNRi_max,valstep=1,valinit=self.SNRi_cut) + s_P_cut = Slider(ax_P_cut,r"$SNR^{P}_{cut}$",1.,SNRp_max,valstep=1,valinit=self.SNRp_cut) + b_reset = Button(ax_reset,"Reset") + + def update_snri(val): + self.SNRi = val + self.quiver.remove() + self.pol_vector() + self.fig.canvas.draw_idle() + + def update_snrp(val): + self.SNRp = val + self.quiver.remove() + self.pol_vector() + self.fig.canvas.draw_idle() + + def reset(event): + s_I_cut.reset() + s_P_cut.reset() + + s_I_cut.on_changed(update_snri) + s_P_cut.on_changed(update_snrp) + b_reset.on_clicked(reset) + + plt.show(block=True) + + @property + def cut(self): + s_I = np.sqrt(self.IQU_cov[0,0]) + SNRp_mask, SNRi_mask = np.zeros(self.P.shape).astype(bool), np.zeros(self.I.shape).astype(bool) + SNRp_mask[self.s_P > 0.] = self.P[self.s_P > 0.] / self.s_P[self.s_P > 0.] > self.SNRp + SNRi_mask[s_I > 0.] = self.I[s_I > 0.] / s_I[s_I > 0.] > self.SNRi + return np.logical_and(SNRi_mask,SNRp_mask) + + def pol_vector(self): + P_cut = np.ones(self.P.shape)*np.nan + P_cut[self.cut] = self.P[self.cut] + X, Y = np.meshgrid(np.arange(self.I.shape[1]),np.arange(self.I.shape[0])) + XY_U, XY_V = P_cut*np.cos(np.pi/2. + self.PA*np.pi/180.), P_cut*np.sin(np.pi/2. + self.PA*np.pi/180.) + + self.quiver = self.ax.quiver(X, Y, XY_U, XY_V, units='xy', scale=0.5, scale_units='xy', pivot='mid', headwidth=0., headlength=0., headaxislength=0., width=0.1, color='white') + return self.quiver + + @property + def pol_int(self): + if self.region is None: + n_pix = self.I.size + s_I = np.sqrt(self.IQU_cov[0,0]) + I_reg = self.I.sum() + I_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_I**2)) + P_reg = self.Stokes[0].header['P_int'] + P_reg_err = self.Stokes[0].header['P_int_err'] + PA_reg = self.Stokes[0].header['PA_int'] + PA_reg_err = self.Stokes[0].header['PA_int_err'] + else: + n_pix = self.I[self.region].size + s_I = np.sqrt(self.IQU_cov[0,0]) + s_Q = np.sqrt(self.IQU_cov[1,1]) + s_U = np.sqrt(self.IQU_cov[2,2]) + s_IQ = self.IQU_cov[0,1] + s_IU = self.IQU_cov[0,2] + s_QU = self.IQU_cov[1,2] + + I_reg = self.I[self.region].sum() + Q_reg = self.Q[self.region].sum() + U_reg = self.U[self.region].sum() + I_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_I[self.region]**2)) + Q_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_Q[self.region]**2)) + U_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_U[self.region]**2)) + IQ_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_IQ[self.region]**2)) + IU_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_IU[self.region]**2)) + QU_reg_err = np.sqrt(n_pix)*np.sqrt(np.sum(s_QU[self.region]**2)) + + P_reg = np.sqrt(Q_reg**2+U_reg**2)/I_reg + P_reg_err = np.sqrt((Q_reg**2*Q_reg_err**2 + U_reg**2*U_reg_err**2 + 2.*Q_reg*U_reg*QU_reg_err)/(Q_reg**2 + U_reg**2) + ((Q_reg/I_reg)**2 + (U_reg/I_reg)**2)*I_reg_err**2 - 2.*(Q_reg/I_reg)*IQ_reg_err - 2.*(U_reg/I_reg)*IU_reg_err)/I_reg + + PA_reg = princ_angle((90./np.pi)*np.arctan2(U_reg,Q_reg)) + PA_reg_err = (90./(np.pi*(Q_reg**2+U_reg**2)))*np.sqrt(U_reg**2*Q_reg_err**2 + Q_reg**2*U_reg_err**2 - 2.*Q_reg*U_reg*QU_reg_err) + + return self.ax.annotate(r"$F_{{\lambda}}^{{int}}$({0:.0f} $\AA$) = {1} $ergs \cdot cm^{{-2}} \cdot s^{{-1}} \cdot \AA^{{-1}}$".format(self.pivot_wav,sci_not(I_reg*self.convert_flux,I_reg_err*self.convert_flux,2))+"\n"+r"$P^{{int}}$ = {0:.1f} $\pm$ {1:.1f} %".format(P_reg*100.,P_reg_err*100.)+"\n"+r"$\theta_{{P}}^{{int}}$ = {0:.1f} $\pm$ {1:.1f} °".format(PA_reg,PA_reg_err), color='white', fontsize=12, xy=(0.01, 0.90), xycoords='axes fraction') \ No newline at end of file diff --git a/src/lib/reduction.py b/src/lib/reduction.py index 88c2adc..c1c0e33 100755 --- a/src/lib/reduction.py +++ b/src/lib/reduction.py @@ -50,7 +50,7 @@ from astropy import log log.setLevel('ERROR') import warnings from lib.deconvolve import deconvolve_im, gaussian_psf -from lib.convex_hull import image_hull +from lib.convex_hull import image_hull, clean_ROI from lib.plots import plot_obs from lib.cross_correlation import phase_cross_correlation @@ -723,8 +723,11 @@ def align_data(data_array, headers, error_array=None, upsample_factor=1., res_shape = int(np.ceil(np.sqrt(2.5)*np.max(shape[1:]))) rescaled_image = np.zeros((shape[0],res_shape,res_shape)) rescaled_error = np.ones((shape[0],res_shape,res_shape)) - rescaled_mask = np.ones((shape[0],res_shape,res_shape),dtype=bool) + rescaled_mask = np.zeros((shape[0],res_shape,res_shape),dtype=bool) res_center = (np.array(rescaled_image.shape[1:])/2).astype(int) + res_shift = res_center-ref_center + res_mask = np.zeros((res_shape,res_shape),dtype=bool) + res_mask[res_shift[0]:res_shift[0]+shape[1], res_shift[1]:res_shift[1]+shape[2]] = True shifts, errors = [], [] for i,image in enumerate(data_array): @@ -734,21 +737,19 @@ def align_data(data_array, headers, error_array=None, upsample_factor=1., shift, error, phase_diff = phase_cross_correlation(ref_data, image, upsample_factor=upsample_factor) # Rescale image to requested output - center = np.fix(ref_center-shift).astype(int) - res_shift = res_center-ref_center rescaled_image[i,res_shift[0]:res_shift[0]+shape[1], res_shift[1]:res_shift[1]+shape[2]] = deepcopy(image) rescaled_error[i,res_shift[0]:res_shift[0]+shape[1], res_shift[1]:res_shift[1]+shape[2]] = deepcopy(error_array[i]) - rescaled_mask[i,res_shift[0]:res_shift[0]+shape[1], - res_shift[1]:res_shift[1]+shape[2]] = False # Shift images to align rescaled_image[i] = sc_shift(rescaled_image[i], shift, cval=0.) rescaled_error[i] = sc_shift(rescaled_error[i], shift, cval=background[i]) - rescaled_mask[i] = sc_shift(rescaled_mask[i], shift, cval=True) + curr_mask = sc_shift(res_mask, shift, cval=False) + mask_vertex = clean_ROI(curr_mask) + rescaled_mask[i,mask_vertex[2]:mask_vertex[3],mask_vertex[0]:mask_vertex[1]] = True rescaled_image[i][rescaled_image[i] < 0.] = 0. - rescaled_image[i][1-rescaled_mask[i]] = 0. + rescaled_image[i][(1-rescaled_mask[i]).astype(bool)] = 0. # Uncertainties from shifting prec_shift = np.array([1.,1.])/upsample_factor @@ -840,13 +841,13 @@ def smooth_data(data_array, error_array, data_mask, headers, FWHM=1., for r in range(smoothed.shape[0]): for c in range(smoothed.shape[1]): # Compute distance from current pixel - dist_rc = np.where(data_mask, fmax, np.sqrt((r-xx)**2+(c-yy)**2)) + dist_rc = np.where(data_mask, np.sqrt((r-xx)**2+(c-yy)**2), fmax) # Catch expected "OverflowWarning" as we overflow values that are not in the image with warnings.catch_warnings(record=True) as w: g_rc = np.array([np.exp(-0.5*(dist_rc/stdev)**2),]*data_array.shape[0]) # Apply weighted combination - smoothed[r,c] = (1.-data_mask[r,c])*np.sum(data_array*weight*g_rc)/np.sum(weight*g_rc) - error[r,c] = (1.-data_mask[r,c])*np.sqrt(np.sum(weight*g_rc**2))/np.sum(weight*g_rc) + smoothed[r,c] = np.where(data_mask[r,c], np.sum(data_array*weight*g_rc)/np.sum(weight*g_rc), 0.) + error[r,c] = np.where(data_mask[r,c], np.sqrt(np.sum(weight*g_rc**2))/np.sum(weight*g_rc), 0.) # Nan handling error[np.isnan(smoothed)] = 0. @@ -861,12 +862,12 @@ def smooth_data(data_array, error_array, data_mask, headers, FWHM=1., xx, yy = np.indices(image.shape) for r in range(image.shape[0]): for c in range(image.shape[1]): - dist_rc = np.where(data_mask, fmax, np.sqrt((r-xx)**2+(c-yy)**2)) + dist_rc = np.where(data_mask, np.sqrt((r-xx)**2+(c-yy)**2), fmax) # Catch expected "OverflowWarning" as we overflow values that are not in the image with warnings.catch_warnings(record=True) as w: g_rc = np.exp(-0.5*(dist_rc/stdev)**2)/(2.*np.pi*stdev**2) - smoothed[i][r,c] = (1.-data_mask[r,c])*np.sum(image*g_rc) - error[i][r,c] = (1.-data_mask[r,c])*np.sqrt(np.sum(error_array[i]**2*g_rc**2)) + smoothed[i][r,c] = np.where(data_mask[r,c], np.sum(image*g_rc), 0.) + error[i][r,c] = np.where(data_mask[r,c], np.sqrt(np.sum(error_array[i]**2*g_rc**2)), 0.) # Nan handling error[i][np.isnan(smoothed[i])] = 0. @@ -1185,7 +1186,7 @@ def compute_Stokes(data_array, error_array, data_mask, headers, Stokes_cov[0,0], Stokes_cov[1,1], Stokes_cov[2,2] = Stokes_error**2 #Compute integrated values for P, PA before any rotation - mask = (1-data_mask).astype(bool) + mask = deepcopy(data_mask).astype(bool) n_pix = I_stokes[mask].size I_diluted = I_stokes[mask].sum() Q_diluted = Q_stokes[mask].sum() @@ -1383,7 +1384,9 @@ def rotate_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, data_mask, headers, new_I_stokes = sc_rotate(new_I_stokes, ang, order=5, reshape=False, cval=0.) new_Q_stokes = sc_rotate(new_Q_stokes, ang, order=5, reshape=False, cval=0.) new_U_stokes = sc_rotate(new_U_stokes, ang, order=5, reshape=False, cval=0.) - new_data_mask = (sc_rotate(data_mask.astype(float)*10., ang, order=5, reshape=False, cval=10.).astype(int)).astype(bool) + new_data_mask = sc_rotate(data_mask.astype(float)*10., ang, order=5, reshape=False, cval=0.) + new_data_mask[new_data_mask < 2] = 0. + new_data_mask = new_data_mask.astype(bool) for i in range(3): for j in range(3): new_Stokes_cov[i,j] = sc_rotate(new_Stokes_cov[i,j], ang, @@ -1435,7 +1438,7 @@ def rotate_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, data_mask, headers, new_Stokes_cov[np.isnan(new_Stokes_cov)] = fmax #Compute updated integrated values for P, PA - mask = (1-new_data_mask).astype(bool) + mask = deepcopy(new_data_mask).astype(bool) n_pix = new_I_stokes[mask].size I_diluted = new_I_stokes[mask].sum() Q_diluted = new_Q_stokes[mask].sum() @@ -1500,7 +1503,9 @@ def rotate_data(data_array, error_array, data_mask, headers, ang): new_error_array.append(sc_rotate(error_array[i], ang, order=5, reshape=False, cval=error_array.mean())) new_data_array = np.array(new_data_array) - new_data_mask = sc_rotate(data_mask, ang, order=5, reshape=False, cval=True) + new_data_mask = sc_rotate(data_mask*10., ang, order=5, reshape=False, cval=0.) + new_data_mask[new_data_mask < 2] = 0. + new_data_mask = new_data_mask.astype(bool) new_error_array = np.array(new_error_array) for i in range(new_data_array.shape[0]): diff --git a/src/lib/test_overplot.py b/src/lib/test_overplot.py index 0e23a0b..a409169 100755 --- a/src/lib/test_overplot.py +++ b/src/lib/test_overplot.py @@ -1,11 +1,15 @@ #!/usr/bin/python3 from astropy.io import fits import numpy as np +from copy import deepcopy from plots import overplot_radio -Stokes_UV = fits.open("../../data/IC5063_x3nl030/IC5063_FOC_combine_FWHM020_pol.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") levelsMorganti = np.array([1.,2.,3.,8.,16.,32.,64.,128.]) @@ -18,3 +22,15 @@ A.plot(levels=levels18GHz, SNRp_cut=10.0, SNRi_cut=100.0, savename='../../plots/ levels24GHz = levelsMorganti*0.46*1e-3 B = overplot_radio(Stokes_UV, Stokes_24GHz) B.plot(levels=levels24GHz, SNRp_cut=10.0, SNRi_cut=100.0, savename='../../plots/IC5063_x3nl030/24GHz_overplot_forced.png') + +levels103GHz = np.linspace(1,99,11)/100.*np.max(deepcopy(Stokes_103GHz[0].data[Stokes_103GHz[0].data > 0.])) +C = overplot_radio(Stokes_UV, Stokes_103GHz) +C.plot(levels=levels103GHz, SNRp_cut=10.0, SNRi_cut=100.0, savename='../../plots/IC5063_x3nl030/103GHz_overplot_forced.png') + +levels229GHz = np.linspace(1,99,11)/100.*np.max(deepcopy(Stokes_229GHz[0].data[Stokes_229GHz[0].data > 0.])) +D = overplot_radio(Stokes_UV, Stokes_229GHz) +D.plot(levels=levels229GHz, SNRp_cut=10.0, SNRi_cut=100.0, savename='../../plots/IC5063_x3nl030/229GHz_overplot_forced.png') + +levels357GHz = np.linspace(1,99,11)/100.*np.max(deepcopy(Stokes_357GHz[0].data[Stokes_357GHz[0].data > 0.])) +E = overplot_radio(Stokes_UV, Stokes_357GHz) +E.plot(levels=levels357GHz, SNRp_cut=10.0, SNRi_cut=100.0, savename='../../plots/IC5063_x3nl030/357GHz_overplot_forced.png')