do some reduction over M87 POS1 & POS3 observations from 95 to 99

src/FOC_reduction.py

@@ -90,22 +90,22 @@ from astropy.wcs import WCS
 #globals()['plots_folder'] = "../plots/3C273_x0u20/"
 
 #BEWARE: 5 observations separated by 1 year each (1995, 1996, 1997, 1998, 1999)
-#globals()['data_folder'] = "../data/M87/POS1/"
+globals()['data_folder'] = "../data/M87/POS1/"
 #globals()['infiles'] = ['x2py010ct_c0f.fits','x2py010dt_c0f.fits','x2py010et_c0f.fits','x2py010ft_c0f.fits'] #1995
 #globals()['infiles'] = ['x3be010ct_c0f.fits','x3be010dt_c0f.fits','x3be010et_c0f.fits','x3be010ft_c0f.fits'] #1996
 #globals()['infiles'] = ['x43r010km_c0f.fits','x43r010mm_c0f.fits','x43r010om_c0f.fits','x43r010rm_c0f.fits'] #1997
 #globals()['infiles'] = ['x43r110kr_c0f.fits','x43r110mr_c0f.fits','x43r110or_c0f.fits','x43r110rr_c0f.fits'] #1998
-#globals()['infiles'] = ['x43r210kr_c0f.fits','x43r210mr_c0f.fits','x43r210or_c0f.fits','x43r210rr_c0f.fits'] #1999
-#globals()['plots_folder'] = "../plots/M87/POS1/"
+globals()['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)
-globals()['data_folder'] = "../data/M87/POS3/"
-globals()['infiles'] = ['x2py030at_c0f.fits','x2py030bt_c0f.fits','x2py030ct_c0f.fits','x2py0309t_c0f.fits'] #1995
+#globals()['data_folder'] = "../data/M87/POS3/"
+#globals()['infiles'] = ['x2py030at_c0f.fits','x2py030bt_c0f.fits','x2py030ct_c0f.fits','x2py0309t_c0f.fits'] #1995
 #globals()['infiles'] = ['x3be030at_c0f.fits','x3be030bt_c0f.fits','x3be030ct_c0f.fits','x3be0309t_c0f.fits'] #1996
 #globals()['infiles'] = ['x43r030em_c0f.fits','x43r030gm_c0f.fits','x43r030im_c0f.fits','x43r030lm_c0f.fits'] #1997
 #globals()['infiles'] = ['x43r130er_c0f.fits','x43r130fr_c0f.fits','x43r130ir_c0f.fits','x43r130lr_c0f.fits'] #1998
 #globals()['infiles'] = ['x43r230er_c0f.fits','x43r230fr_c0f.fits','x43r230ir_c0f.fits','x43r230lr_c0f.fits'] #1999
-globals()['plots_folder'] = "../plots/M87/POS3/"
+#globals()['plots_folder'] = "../plots/M87/POS3/"
 
 
 def main():
@@ -136,7 +136,7 @@ def main():
     display_data = False
     # Smoothing
     smoothing_function = 'combine'  #gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine
-    smoothing_FWHM = 0.07           #If None, no smoothing is done
+    smoothing_FWHM = 0.10           #If None, no smoothing is done
     smoothing_scale = 'arcsec'      #pixel or arcsec
     # Rotation
     rotate_stokes = True            #rotation to North convention can give erroneous results
@@ -145,8 +145,8 @@ def main():
     crop = False                    #Crop to desired ROI
     final_display = True
     # Polarization map output
-    figname = 'M87_POS3_1995_FOC'         #target/intrument name
-    figtype = '_combine_FWHM005'    #additionnal informations
+    figname = 'M87_POS1_1999_FOC'         #target/intrument name
+    figtype = '_combine_FWHM010'    #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

src/lib/plots.py

@@ -526,6 +526,11 @@ class align_maps(object):
         self.axreset = self.fig.add_axes([0.60, 0.01, 0.1, 0.04])
         self.breset = Button(self.axreset, 'Leave as is')
         self.breset.label.set_fontsize(8)
+        self.enter = self.fig.canvas.mpl_connect('key_press_event', self.on_key)
+
+    def on_key(self, event):
+        if event.key.lower() == "enter":
+            self.on_close_align(event)
 
     def get_aligned_wcs(self):
         return self.wcs_map, self.wcs_other
@@ -556,10 +561,16 @@ class align_maps(object):
 
         self.aligned = True
 
-    def apply_align(self, event):
-        self.wcs_map.wcs.crpix = np.array(self.cr_map.get_data())
+    def apply_align(self, event=None):
+        if np.array(self.cr_map.get_data()).shape == (2,1):
+            self.wcs_map.wcs.crpix = np.array(self.cr_map.get_data())[:,0]
+        else:
+            self.wcs_map.wcs.crpix = np.array(self.cr_map.get_data())
+        if np.array(self.cr_other.get_data()).shape == (2,1):
+            self.wcs_other.wcs.crpix = np.array(self.cr_other.get_data())[:,0]
+        else:
+            self.wcs_other.wcs.crpix = np.array(self.cr_other.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()
 
@@ -569,8 +580,9 @@ class align_maps(object):
         self.aligned = True
 
     def on_close_align(self, event):
-        self.aligned = True
-        #print(self.get_aligned_wcs())
+        if not self.aligned:
+            self.aligned = True
+            self.apply_align()
 
     def align(self):
         self.fig.canvas.draw()
@@ -808,8 +820,6 @@ class align_pol(object):
         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]
-            print(x_lim[0], y_lim[0], wcs.pixel_to_world(x_lim[0], y_lim[0]))
-            print(x_lim[1], y_lim[1], wcs.pixel_to_world(x_lim[1], y_lim[1]))
             ax.set(xlim=x_lim,ylim=y_lim)
 
         if v_lim is None:
@@ -820,6 +830,8 @@ class align_pol(object):
         for key, value in [["cmap",[["cmap","inferno"]]], ["norm",[["vmin",vmin],["vmax",vmax]]]]:
             try:
                 test = kwargs[key]
+                if str(type(test)) == "<class 'matplotlib.colors.LogNorm'>":
+                    kwargs[key] = LogNorm(vmin, vmax)
             except KeyError:
                 for key_i, val_i in value:
                     kwargs[key_i] = val_i
@@ -856,17 +868,16 @@ class align_pol(object):
     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.])])
+        eps = 1e-35
+        vmin = np.min([np.min(curr_map[0].data[curr_map[0].data > SNRi_cut*np.max([eps*np.ones(curr_map[0].data.shape),np.sqrt(curr_map[3].data[0,0])],axis=0)]) for curr_map in self.other_maps])/2.5
+        vmax = np.max([np.max(curr_map[0].data[curr_map[0].data > SNRi_cut*np.max([eps*np.ones(curr_map[0].data.shape),np.sqrt(curr_map[3].data[0,0])],axis=0)]) for curr_map in self.other_maps])
+        vmin = np.min([vmin, np.min(self.ref_map[0].data[self.ref_map[0].data > SNRi_cut*np.max([eps*np.ones(self.ref_map[0].data.shape),np.sqrt(self.ref_map[3].data[0,0])],axis=0)])])/2.5
+        vmax = np.max([vmax, np.max(self.ref_map[0].data[self.ref_map[0].data > SNRi_cut*np.max([eps*np.ones(self.ref_map[0].data.shape),np.sqrt(self.ref_map[3].data[0,0])],axis=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+'_0', **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))])
-        print(x_lim[0], y_lim[0], ax_lim[0])
-        print(x_lim[1], y_lim[1], ax_lim[1])
         
         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)

src/lib/reduction.py

@@ -1503,7 +1503,6 @@ def rotate_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, data_mask, headers,
         new_wcs = WCS(header).deepcopy()
 
         new_wcs.wcs.pc = np.dot(mrot, new_wcs.wcs.pc)
-        print(new_wcs.wcs.pc)
         new_wcs.wcs.crpix = np.dot(mrot, new_wcs.wcs.crpix - old_center[::-1]) + new_center[::-1]
         new_wcs.wcs.set()
         for key, val in new_wcs.to_header().items():

src/overplot.py

@@ -45,28 +45,28 @@ from matplotlib.colors import LogNorm
 #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_folder1 = "../data/M87/POS1/"
-#plots_folder1 = "../plots/M87/POS1/"
-#basename1 = "test"
-#M87_1_95 = fits.open(data_folder1+"M87_POS1_1995_FOC_combine_FWHM005.fits")
-#M87_1_96 = fits.open(data_folder1+"M87_POS1_1996_FOC_combine_FWHM005.fits")
-#M87_1_97 = fits.open(data_folder1+"M87_POS1_1997_FOC_combine_FWHM005.fits")
-#M87_1_98 = fits.open(data_folder1+"M87_POS1_1998_FOC_combine_FWHM005.fits")
-#M87_1_99 = fits.open(data_folder1+"M87_POS1_1999_FOC_combine_FWHM005.fits")
+data_folder1 = "../data/M87/POS1/"
+plots_folder1 = "../plots/M87/POS1/"
+basename1 = "M87_015_log_core"
+M87_1_95 = fits.open(data_folder1+"M87_POS1_1995_FOC_combine_FWHM010.fits")
+M87_1_96 = fits.open(data_folder1+"M87_POS1_1996_FOC_combine_FWHM010.fits")
+M87_1_97 = fits.open(data_folder1+"M87_POS1_1997_FOC_combine_FWHM010.fits")
+M87_1_98 = fits.open(data_folder1+"M87_POS1_1998_FOC_combine_FWHM010.fits")
+M87_1_99 = fits.open(data_folder1+"M87_POS1_1999_FOC_combine_FWHM010.fits")
+
+H = align_pol(np.array([M87_1_95,M87_1_96,M87_1_97,M87_1_98,M87_1_99]), norm=LogNorm())
+H.plot(SNRp_cut=3.0, SNRi_cut=30.0, savename=plots_folder1+'animated_loop/'+basename1, norm=LogNorm())
+command("convert -delay 50 -loop 0 {0:s}animated_loop/{1:s}*.png {0:s}animated_loop/{1:s}.gif".format(plots_folder1, basename1))
+
+#data_folder3 = "../data/M87/POS3/"
+#plots_folder3 = "../plots/M87/POS3/"
+#basename3 = "M87_005_log_star"
+#M87_3_95 = fits.open(data_folder3+"M87_POS3_1995_FOC_combine_FWHM005.fits")
+#M87_3_96 = fits.open(data_folder3+"M87_POS3_1996_FOC_combine_FWHM005.fits")
+#M87_3_97 = fits.open(data_folder3+"M87_POS3_1997_FOC_combine_FWHM005.fits")
+#M87_3_98 = fits.open(data_folder3+"M87_POS3_1998_FOC_combine_FWHM005.fits")
+#M87_3_99 = fits.open(data_folder3+"M87_POS3_1999_FOC_combine_FWHM005.fits")
 #
-#H = align_pol(np.array([M87_1_95,M87_1_96,M87_1_97,M87_1_98,M87_1_99]))#, norm=LogNorm())
-#H.plot(SNRp_cut=3.0, SNRi_cut=30.0, savename=plots_folder1+'animated_loop/'+basename1, 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_folder1, basename1))
-
-data_folder3 = "../data/M87/POS3/"
-plots_folder3 = "../plots/M87/POS3/"
-basename3 = "test"
-M87_3_95 = fits.open(data_folder3+"M87_POS3_1995_FOC_combine_FWHM005.fits")
-M87_3_96 = fits.open(data_folder3+"M87_POS3_1996_FOC_combine_FWHM005.fits")
-M87_3_97 = fits.open(data_folder3+"M87_POS3_1997_FOC_combine_FWHM005.fits")
-M87_3_98 = fits.open(data_folder3+"M87_POS3_1998_FOC_combine_FWHM005.fits")
-M87_3_99 = fits.open(data_folder3+"M87_POS3_1999_FOC_combine_FWHM005.fits")
-
-I = align_pol(np.array([M87_3_95,M87_3_96,M87_3_97,M87_3_98,M87_3_99]))#, norm=LogNorm())
-I.plot(SNRp_cut=3.0, SNRi_cut=30.0, savename=plots_folder3+'animated_loop/'+basename3, 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_folder3, basename3))
+#I = align_pol(np.array([M87_3_95,M87_3_96,M87_3_97,M87_3_98,M87_3_99]), norm=LogNorm())
+#I.plot(SNRp_cut=3.0, SNRi_cut=30.0, savename=plots_folder3+'animated_loop/'+basename3, norm=LogNorm())
+#command("convert -delay 20 -loop 0 {0:s}animated_loop/{1:s}*.png {0:s}animated_loop/{1:s}.gif".format(plots_folder3, basename3))