add Data dump to analysis tool, replot NGC1068

src/FOC_reduction.py

@@ -104,14 +104,14 @@ def main():
     rebin = True
     if rebin:
         pxsize = 0.10
-        px_scale = 'full'         #pixel, arcsec or full
+        px_scale = 'arcsec'         #pixel, arcsec or full
         rebin_operation = 'sum'     #sum or average
     # Alignement
     align_center = 'image'        #If None will align image to image center
     display_data = False
     # Smoothing
     smoothing_function = 'combine'  #gaussian_after, gaussian or combine
-    smoothing_FWHM = None           #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
@@ -120,7 +120,7 @@ def main():
     crop = False        #Crop to desired ROI
     # Polarization map output
     figname = 'NGC1068_FOC'         #target/intrument name
-    figtype = '_full'    #additionnal informations
+    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%.
     step_vec = 1    #plot all vectors in the array. if step_vec = 2, then every other vector will be plotted

src/lib/plots.py

@@ -1137,17 +1137,18 @@ class pol_map(object):
         ax_save = self.fig.add_axes([0.850, 0.070, 0.05, 0.02])
         b_save = Button(ax_save, "Save")
         ax_text_save = self.fig.add_axes([0.3, 0.020, 0.5, 0.025],visible=False)
-        text_box = TextBox(ax_text_save, "Save to:", initial='')
+        text_save = TextBox(ax_text_save, "Save to:", initial='')
 
         def saveplot(event):
             ax_text_save.set(visible=True)
             ax_snr_reset.set(visible=False)
             ax_save.set(visible=False)
+            ax_dump.set(visible=False)
             self.fig.canvas.draw_idle()
 
         b_save.on_clicked(saveplot)
 
-        def submit(expression):
+        def submit_save(expression):
             ax_text_save.set(visible=False)
             if expression != '':
                 save_fig = plt.figure(figsize=(15,15))
@@ -1161,12 +1162,57 @@ class pol_map(object):
                     expression += '.png'
                 save_fig.savefig(expression, bbox_inches='tight', dpi=200)
                 plt.close(save_fig)
-                text_box.set_val('')
+                text_save.set_val('')
             ax_snr_reset.set(visible=True)
             ax_save.set(visible=True)
+            ax_dump.set(visible=True)
             self.fig.canvas.draw_idle()
 
-        text_box.on_submit(submit)
+        text_save.on_submit(submit_save)
+
+        #Set axe for data dump
+        ax_dump = self.fig.add_axes([0.850, 0.045, 0.05, 0.02])
+        b_dump = Button(ax_dump, "Dump")
+        ax_text_dump = self.fig.add_axes([0.3, 0.020, 0.5, 0.025],visible=False)
+        text_dump = TextBox(ax_text_dump, "Dump to:", initial='')
+
+        def dump(event):
+            ax_text_dump.set(visible=True)
+            ax_snr_reset.set(visible=False)
+            ax_save.set(visible=False)
+            ax_dump.set(visible=False)
+            self.fig.canvas.draw_idle()
+
+            shape = np.array(self.I.shape)
+            center = (shape/2).astype(int)
+            cdelt_arcsec = self.wcs.wcs.cdelt*3600
+            xx, yy = np.indices(shape)
+            x, y = (xx-center[0])*cdelt_arcsec[0], (yy-center[1])*cdelt_arcsec[1]
+
+            P, PA = np.zeros(shape), np.zeros(shape)
+            P[self.cut] = self.P[self.cut]
+            PA[self.cut] = self.PA[self.cut]
+            dump_list = []
+            for i in range(shape[0]):
+                for j in range(shape[1]):
+                    dump_list.append([x[i,j], y[i,j], self.I[i,j]*self.convert_flux, self.Q[i,j]*self.convert_flux, self.U[i,j]*self.convert_flux, P[i,j], PA[i,j]])
+            self.data_dump = np.array(dump_list)
+
+        b_dump.on_clicked(dump)
+
+        def submit_dump(expression):
+            ax_text_dump.set(visible=False)
+            if expression != '':
+                if not expression[-4:] in ['.txt', '.dat']:
+                    expression += '.txt'
+                np.savetxt(expression, self.data_dump)
+                text_dump.set_val('')
+            ax_snr_reset.set(visible=True)
+            ax_save.set(visible=True)
+            ax_dump.set(visible=True)
+            self.fig.canvas.draw_idle()
+
+        text_dump.on_submit(submit_dump)
 
         #Set axes for display buttons
         ax_tf = self.fig.add_axes([0.925, 0.085, 0.05, 0.02])

src/lib/reduction.py

@@ -500,17 +500,41 @@ def get_error(data_array, headers, sub_shape=(15,15), display=False,
         ax.set_title("Background flux and error computed for each image")
         plt.legend()
 
+        fig2, ax2 = plt.subplots(figsize=(10,10))
+        data0 = data[0]*convert_flux
+        instr = headers[0]['instrume']
+        rootname = headers[0]['rootname']
+        exptime = headers[0]['exptime']
+        filt = headers[0]['filtnam1']
+        #plots
+        im = ax2.imshow(data0, vmin=data0.min(), vmax=data0.max(), origin='lower', cmap='gray')
+        x, y, width, height, angle, color = rectangle[0]
+        ax2.add_patch(Rectangle((x, y),width,height,edgecolor=color,fill=False))
+        ax2.annotate(instr+":"+rootname, color='white', fontsize=5,
+                xy=(0.02, 0.95), xycoords='axes fraction')
+        ax2.annotate(filt, color='white', fontsize=10, xy=(0.02, 0.02),
+                xycoords='axes fraction')
+        ax2.annotate(exptime, color='white', fontsize=5, xy=(0.80, 0.02),
+                xycoords='axes fraction')
+        ax2.set(title="Location of background computation.",
+                xlabel='pixel offset',
+                ylabel='pixel offset')
+
+        fig2.subplots_adjust(hspace=0, wspace=0, right=0.85)
+        cbar_ax = fig2.add_axes([0.9, 0.12, 0.02, 0.75])
+        fig2.colorbar(im, cax=cbar_ax, label=r"Flux [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
+
         if not(savename is None):
-            #fig.suptitle(savename+"_background_flux")
             fig.savefig(plots_folder+savename+"_background_flux.png",
                     bbox_inches='tight')
+            fig2.savefig(plots_folder+savename+'_'+filt+'_background_location.png',
+                    bbox_inches='tight')
             vmin = np.min(np.log10(data[data > 0.]))
             vmax = np.max(np.log10(data[data > 0.]))
             plot_obs(data, headers, vmin=data.min(), vmax=data.max(),
                     rectangle=rectangle,
                     savename=savename+"_background_location",
                     plots_folder=plots_folder)
-
         else:
             vmin = np.min(np.log10(data[data > 0.]))
             vmax = np.max(np.log10(data[data > 0.]))
@@ -1186,7 +1210,7 @@ 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 = deepcopy(data_mask).astype(bool)
+        mask = np.logical_and(data_mask.astype(bool), (I_stokes > 0.))
         n_pix = I_stokes[mask].size
         I_diluted = I_stokes[mask].sum()
         Q_diluted = Q_stokes[mask].sum()