Merge pull request #3192 from pietsjoh/pcolormesh

Use pcolormesh for image plots involving non-uniform axes

hyperspy/drawing/image.py

@@ -377,7 +377,8 @@ def plot(self, data_function_kwargs={}, **kwargs):
     def _add_colorbar(self):
         # Bug extend='min' or extend='both' and power law norm
         # Use it when it is fixed in matplotlib
-        self._colorbar = plt.colorbar(self.ax.images[0], ax=self.ax)
+        ims = self.ax.images if len(self.ax.images) else self.ax.collections
+        self._colorbar = plt.colorbar(ims[0], ax=self.ax)
         self.set_quantity_label()
         self._colorbar.set_label(
             self.quantity_label, rotation=-90, va='bottom')
@@ -432,7 +433,8 @@ def update(self, data_changed=True, auto_contrast=None, vmin=None,
             data = rgb_tools.rgbx2regular_array(data, plot_friendly=True)
             data = self._current_data = data
             self._is_rgb = True
-        ims = self.ax.images
+
+        ims = self.ax.images if len(self.ax.images) else self.ax.collections
 
         # Turn on centre_colormap if a diverging colormap is used.
         if not self._is_rgb and self.centre_colormap == "auto":
@@ -532,8 +534,11 @@ def format_coord(x, y):
         if self.no_nans:
             data = np.nan_to_num(data)
 
-        if ims:  # the images has already been drawn previously
-            ims[0].set_data(data)
+        if ims:  # the images have already been drawn previously
+            if len(self.ax.images): # imshow
+                ims[0].set_data(data)
+            else: # pcolormesh
+                ims[0].set_array(data.ravel())
             # update extent:
             if 'x' in self.autoscale:
                 self._extent[0] = self.xaxis.axis[0] - self.xaxis.scale / 2
@@ -563,19 +568,24 @@ def format_coord(x, y):
                 ims[0].changed()
             self.render_figure()
         else:  # no signal have been drawn yet
-            new_args = {'extent': self._extent,
-                        'aspect': self._aspect,
-                        'animated': self.figure.canvas.supports_blit,
-                        }
+            new_args = {"animated": self.figure.canvas.supports_blit}
             if not self._is_rgb:
                 if norm is None:
                     new_args.update({'vmin': vmin, 'vmax':vmax})
                 else:
                     new_args['norm'] = norm
             new_args.update(kwargs)
-            self.ax.imshow(data, **new_args)
-
-        if self.axes_ticks == 'off':
+            if self.xaxis.is_uniform and self.yaxis.is_uniform:
+                # pcolormesh doesn't have extent and aspect as arguments
+                # aspect is set earlier via self.ax.set_aspect() anyways
+                new_args.update({"extent": self._extent, "aspect": self._aspect})
+                self.ax.imshow(data, **new_args)
+            else:
+                self.ax.pcolormesh(
+                    self.xaxis.axis, self.yaxis.axis, data, **new_args
+                )
+                self.ax.invert_yaxis()
+        if self.axes_ticks == "off":
             self.ax.set_axis_off()
 
     def _update(self):

hyperspy/signal.py

@@ -2852,11 +2852,7 @@ def get_dynamic_explorer_wrapper(*args, **kwargs):
                 navigator = "slider"
             elif (self.axes_manager.navigation_dimension == 1 and
                     self.axes_manager.signal_dimension == 1):
-                if (self.axes_manager.navigation_axes[0].is_uniform and
-                        self.axes_manager.signal_axes[0].is_uniform):
-                    navigator = "data"
-                else:
-                    navigator = "spectrum"
+                navigator = "data"
             elif self.axes_manager.navigation_dimension > 0:
                 if self.axes_manager.signal_dimension == 0:
                     navigator = self.deepcopy()

hyperspy/tests/drawing/test_plot_signal1d.py

@@ -211,7 +211,7 @@ def test_plot_spectra_auto_update(self):
         return ax.get_figure()
 
 
-class TestPlotNonLinearAxis:
+class TestPlotNonUniformAxis:
 
     def setup_method(self, method):
         dict0 = {'size': 10, 'name': 'Axis0', 'units': 'A', 'scale': 0.2,
@@ -229,6 +229,34 @@ def test_plot_non_uniform_sig(self):
         self.s.plot()
         return self.s._plot.signal_plot.figure
 
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_non_uniform_sig_update(self):
+        s2 = self.s
+        s2.plot()
+        s2.axes_manager[0].index += 1
+        return s2._plot.signal_plot.figure
+
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_uniform_nav(self):
+        self.s.plot()
+        return self.s._plot.navigator_plot.figure
+
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_uniform_nav_update(self):
+        s2 = self.s
+        s2.plot()
+        s2.axes_manager[0].index += 1
+        return self.s._plot.navigator_plot.figure
+
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_uniform_sig(self):
+        self.s.plot()
+        return self.s._plot.signal_plot.figure
+
     @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
                                    tolerance=default_tol, style=style_pytest_mpl)
     def test_plot_non_uniform_nav(self):

hyperspy/tests/drawing/test_plot_signal2d.py

@@ -259,6 +259,28 @@ def test_plot_non_uniform_nav(self):
         self.s.plot()
         return self.s._plot.navigator_plot.figure
 
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_non_uniform_2s1n_sig(self):
+        self.s.plot()
+        return self.s._plot.signal_plot.figure
+
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_non_uniform_2s1n_update_sig(self):
+        s2 = self.s
+        s2.axes_manager[0].index += 1
+        s2.plot()
+        return s2._plot.signal_plot.figure
+
+    @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
+                                   tolerance=default_tol, style=style_pytest_mpl)
+    def test_plot_non_uniform_2s1n_update_nav(self):
+        s2 = self.s
+        s2.axes_manager[0].index += 1
+        s2.plot()
+        return s2._plot.navigator_plot.figure
+
     @pytest.mark.mpl_image_compare(baseline_dir=baseline_dir,
                                    tolerance=default_tol, style=style_pytest_mpl)
     def test_plot_non_uniform_sig(self):

upcoming_changes/3192.new.rst

@@ -0,0 +1,3 @@
+Switch to pcolormesh for image plots involving non-uniform axes.
+The following cases are covered: 2D-signal with arbitrary navigation-dimension, 1D-navigation and 1D-signal (linescan).
+Not covered are 2D-navigation images (still uses sliders).