Renamed plotting commands to *_plot()

pyramid/dataset.py

@@ -274,8 +274,8 @@ class DataSet(object):
             mlab.axes(plot)
             return plot
 
-    def display_phase(self, mag_data=None, title='Phase Map',
-                      cmap='RdBu', limit=None, norm=None):
+    def phase_plots(self, mag_data=None, title='Phase Map',
+                    cmap='RdBu', limit=None, norm=None):
         """Display all phasemaps saved in the :class:`~.DataSet` as a colormesh.
 
         Parameters
@@ -301,17 +301,17 @@ class DataSet(object):
         None
 
         """
-        self._log.debug('Calling display_phase')
+        self._log.debug('Calling phase_plots')
         if mag_data is not None:
             phase_maps = self.create_phase_maps(mag_data)
         else:
             phase_maps = self.phase_maps
-        [phase_map.display_phase('{} ({})'.format(title, self.projectors[i].get_info()),
-                                 cmap=cmap, limit=limit, norm=norm)
+        [phase_map.phase_plot('{} ({})'.format(title, self.projectors[i].get_info()),
+                              cmap=cmap, limit=limit, norm=norm)
          for (i, phase_map) in enumerate(phase_maps)]
 
-    def display_combined(self, mag_data=None, title='Combined Plot', cmap='RdBu', limit=None,
-                         norm=None, gain='auto', interpolation='none', grad_encode='bright'):
+    def combined_plots(self, mag_data=None, title='Combined Plot', cmap='RdBu', limit=None,
+                       norm=None, gain='auto', interpolation='none', grad_encode='bright'):
         """Display all phasemaps and the resulting color coded holography images.
 
         Parameters
@@ -347,12 +347,12 @@ class DataSet(object):
         None
 
         """
-        self._log.debug('Calling display_combined')
+        self._log.debug('Calling combined_plots')
         if mag_data is not None:
             phase_maps = self.create_phase_maps(mag_data)
         else:
             phase_maps = self.phase_maps
         for (i, phase_map) in enumerate(phase_maps):
-            phase_map.display_combined('{} ({})'.format(title, self.projectors[i].get_info()),
-                                       cmap, limit, norm, gain, interpolation, grad_encode)
+            phase_map.combined_plot('{} ({})'.format(title, self.projectors[i].get_info()),
+                                    cmap, limit, norm, gain, interpolation, grad_encode)
         plt.show()

pyramid/phasemap.py

@@ -40,7 +40,7 @@ class PhaseMap(object):
     corresponding holographic contour map are provided. Holographic contour maps are created by
     taking the cosine of the (optionally amplified) phase and encoding the direction of the
     2-dimensional gradient via color. The directional encoding can be seen by using the
-    :func:`~.make_color_wheel` function. Use the :func:`~.display_combined` function to plot the
+    :func:`~.make_color_wheel` function. Use the :func:`~.combined_plot` function to plot the
     phase map and the holographic contour map next to each other.
 
     Attributes
@@ -591,8 +591,8 @@ class PhaseMap(object):
             phase = np.loadtxt(filename, delimiter='\t', skiprows=2)
         return cls(a, phase)
 
-    def display_phase(self, title='Phase Map', cbar_title=None, cmap='RdBu', limit=None,
-                      norm=None, axis=None, cbar=True, show_mask=True, show_conf=True):
+    def phase_plot(self, title='Phase Map', cbar_title=None, cmap='RdBu', limit=None,
+                   norm=None, axis=None, cbar=True, show_mask=True, show_conf=True):
         """Display the phasemap as a colormesh.
 
         Parameters
@@ -624,7 +624,7 @@ class PhaseMap(object):
             The axis on which the graph is plotted and the colorbar.
 
         """
-        self._log.debug('Calling display_phase')
+        self._log.debug('Calling phase_plot')
         # Take units into consideration:
         phase = self.phase * self.UNITDICT[self.unit]
         if limit is None:
@@ -671,8 +671,8 @@ class PhaseMap(object):
         # Return plotting axis:
         return axis
 
-    def display_phase3d(self, title='Phase Map', cmap='RdBu'):
-        """Display the phasemap as a 3-D surface with contourplots.
+    def phase3d_plot(self, title='Phase Map', cmap='RdBu'):
+        """Display the phasemap as a 3D surface with contourplots.
 
         Parameters
         ----------
@@ -688,7 +688,7 @@ class PhaseMap(object):
             The axis on which the graph is plotted.
 
         """
-        self._log.debug('Calling display_phase3d')
+        self._log.debug('Calling phase3d_plot')
         # Take units into consideration:
         phase = self.phase * self.UNITDICT[self.unit]
         # Create figure and axis:
@@ -707,8 +707,8 @@ class PhaseMap(object):
         # Return plotting axis:
         return axis
 
-    def display_holo(self, title=None, gain='auto', axis=None, grad_encode='bright',
-                     interpolation='none'):
+    def holo_plot(self, title=None, gain='auto', axis=None, grad_encode='bright',
+                  interpolation='none'):
         """Display the color coded holography image.
 
         Parameters
@@ -734,7 +734,7 @@ class PhaseMap(object):
             The axis on which the graph is plotted.
 
         """
-        self._log.debug('Calling display_holo')
+        self._log.debug('Calling holo_plot')
         # Calculate gain if 'auto' is selected:
         if gain == 'auto':
             gain = 4 * 2 * np.pi / (np.abs(self.phase).max() + 1E-30)
@@ -789,10 +789,10 @@ class PhaseMap(object):
         # Return plotting axis:
         return axis
 
-    def display_combined(self, sup_title='Combined Plot', phase_title='Phase Map', holo_title=None,
-                         cbar_title=None, cmap='RdBu', limit=None, norm=None, gain='auto',
-                         interpolation='none', grad_encode='bright', cbar=True, show_mask=True,
-                         show_conf=True):
+    def combined_plot(self, sup_title='Combined Plot', phase_title='Phase Map', holo_title=None,
+                      cbar_title=None, cmap='RdBu', limit=None, norm=None, gain='auto',
+                      interpolation='none', grad_encode='bright', cbar=True, show_mask=True,
+                      show_conf=True):
         """Display the phase map and the resulting color coded holography image in one plot.
 
         Parameters
@@ -838,19 +838,19 @@ class PhaseMap(object):
             The axes on which the graphs are plotted.
 
         """
-        self._log.debug('Calling display_combined')
+        self._log.debug('Calling combined_plot')
         # Create combined plot and set title:
         fig = plt.figure(figsize=(15, 7))
         fig.suptitle(sup_title, fontsize=20)
         # Plot holography image:
         holo_axis = fig.add_subplot(1, 2, 1, aspect='equal')
-        self.display_holo(title=holo_title, gain=gain, axis=holo_axis, interpolation=interpolation,
-                          grad_encode=grad_encode)
+        self.holo_plot(title=holo_title, gain=gain, axis=holo_axis, interpolation=interpolation,
+                       grad_encode=grad_encode)
         # Plot phase map:
         phase_axis = fig.add_subplot(1, 2, 2, aspect='equal')
         fig.subplots_adjust(right=0.85)
-        self.display_phase(title=phase_title, cbar_title=cbar_title, cmap=cmap, limit=limit,
-                           norm=norm, axis=phase_axis, cbar=cbar, show_mask=show_mask,
-                           show_conf=show_conf)
+        self.phase_plot(title=phase_title, cbar_title=cbar_title, cmap=cmap, limit=limit,
+                        norm=norm, axis=phase_axis, cbar=cbar, show_mask=show_mask,
+                        show_conf=show_conf)
         # Return the plotting axes:
         return phase_axis, holo_axis

pyramid/utils/mag_slicer.py

@@ -99,14 +99,14 @@ class Main(QMainWindow, UI_MainWindow):
             self.phase_mapper = PhaseMapperRDFC(kernel)
             self.phase_map = self.phase_mapper(self.projector(self.mag_data))
             self.canvasPhase.figure.axes[0].clear()
-            self.phase_map.display_phase(axis=self.canvasPhase.figure.axes[0], cbar=False)
+            self.phase_map.phase_plot(axis=self.canvasPhase.figure.axes[0], cbar=False)
             if self.checkBoxSmooth.isChecked():
                 interpolation = 'bilinear'
             else:
                 interpolation = 'none'
             self.canvasHolo.figure.axes[0].clear()
-            self.phase_map.display_holo(axis=self.canvasHolo.figure.axes[0], gain=gain,
-                                        interpolation=interpolation)
+            self.phase_map.holo_plot(axis=self.canvasHolo.figure.axes[0], gain=gain,
+                                     interpolation=interpolation)
             self.canvasPhase.draw()
             self.canvasHolo.draw()
 

pyramid/utils/phasemap_creator.py

@@ -77,8 +77,8 @@ class Main(QMainWindow, UI_MainWindow):
             show_conf = self.checkBox_conf.isChecked()
             self.canvas.figure.axes[0].clear()
             self.canvas.figure.axes[0].hold(True)
-            self.phase_map.display_phase('PhaseMap', axis=self.canvas.figure.axes[0],
-                                         show_mask=show_mask, show_conf=show_conf, cbar=False)
+            self.phase_map.phase_plot('PhaseMap', axis=self.canvas.figure.axes[0],
+                                      show_mask=show_mask, show_conf=show_conf, cbar=False)
             self.canvas.draw()
 
     def update_mask(self):

pyramid/utils/reconstruction_2d_from_phasemap.py

@@ -43,9 +43,9 @@ def reconstruction_2d_from_phasemap(filename, b_0=1, lam=1E-3, max_iter=100, ram
         if ar_dens is None:
             ar_dens = np.max(dim) // 128
         mag_data_rec.quiver_plot('Reconstructed Distribution', ar_dens=ar_dens)
-        phase_map.display_combined('Input Phase')
+        phase_map.combined_plot('Input Phase')
         phase_map -= fwd_model.ramp(index=0)
-        phase_map.display_combined('Input Phase (ramp corrected)')
+        phase_map.combined_plot('Input Phase (ramp corrected)')
         phase_map_rec = pm(mag_data_rec)
         title = 'Reconstructed Phase'
         if ramp_order >= 0:
@@ -54,10 +54,10 @@ def reconstruction_2d_from_phasemap(filename, b_0=1, lam=1E-3, max_iter=100, ram
         if ramp_order >= 1:
             print('ramp:', ramp)
             title += ', (Fitted Ramp: (u:{:.2g}, v:{:.2g}) [rad/nm]'.format(*ramp)
-        phase_map_rec.display_combined(title)
+        phase_map_rec.combined_plot(title)
         difference = (phase_map_rec.phase - phase_map.phase).mean()
-        (phase_map_rec - phase_map).display_phase('Difference (mean: {:.2g})'.format(difference))
+        (phase_map_rec - phase_map).phase_plot('Difference (mean: {:.2g})'.format(difference))
         if ramp_order is not None:
-            fwd_model.ramp(0).display_combined('Fitted Ramp')
+            fwd_model.ramp(0).combined_plot('Fitted Ramp')
     # Return reconstructed magnetisation distribution and cost function:
     return mag_data_rec, cost

pyramid/utils/reconstruction_3d_from_magdata.py

@@ -71,7 +71,7 @@ def reconstruction_3d_from_magdata(filename, b_0=1, lam=1E-3, max_iter=100, ramp
     fwd_model.finalize()
     # Plot input:
     if plot_input:
-        data.display_phase()
+        data.phase_plots()
     # Plot results:
     if plot_results:
         data.display_mask(ar_dens=ar_dens)

scripts/magdata/magdata_from_dat.py

@@ -28,5 +28,5 @@ mag_data = py.VectorData(a, magnitude)
 mag_data.save_to_hdf5('magdata_dat_{}'.format(filename.replace('.dat', '.hdf5')), overwrite=True)
 mag_data.quiver_plot3d(ar_dens=4, coloring='amplitude')
 mag_data.quiver_plot3d(ar_dens=4, coloring='angle')
-py.pm(mag_data).display_combined(interpolation='bilinear')
+py.pm(mag_data).combined_plot(interpolation='bilinear')
 plt.show()

scripts/magdata/magdata_from_vtk.py

@@ -124,5 +124,5 @@ a *= 10
 mag_data = pr.VectorData(a, magnitude)
 mag_data.save_to_hdf5('magdata_vtk_{}'.format(filename.replace('.vtk', '.hdf5')), overwrite=True)
 # Plot stuff:
-pr.pm(mag_data).display_combined()
+pr.pm(mag_data).combined_plot()
 plt.show()

scripts/phasemap/phasemap_from_dm3.py

@@ -55,5 +55,5 @@ confidence = np.where(np.asarray(im_conf) >= threshold, 1, 0)
 # Create and save PhaseMap object:
 phase_map = pr.PhaseMap(a, phase, mask, confidence, unit='rad')
 phase_map.save_to_hdf5(filename, overwrite=True)
-phase_map.display_combined()
+phase_map.combined_plot()
 plt.show()

scripts/phasemap/phasemap_from_image.py

@@ -41,5 +41,5 @@ if path_mask is not None:
 # Create and save PhaseMap object:
 phase_map = py.PhaseMap(a, phase, mask, confidence=None, unit='rad')
 phase_map.save_to_hdf5(filename, overwrite=True)
-phase_map.display_combined()
+phase_map.combined_plot()
 plt.show()

scripts/phasemap/phasemap_from_raw.py

@@ -37,5 +37,5 @@ mask = np.where(np.asarray(im_mask) >= threshold, True, False)
 # Create and save PhaseMap object:
 phase_map = pr.PhaseMap(a, phase, mask, confidence=None, unit='rad')
 phase_map.save_to_hdf5(filename, overwrite=True)
-phase_map.display_combined()
+phase_map.combined_plot()
 plt.show()