Merge pull request #3346 from ericpre/add_example_converting_color_image

Add example converting color image and fix navigator event disconnection

.gitignore

@@ -31,6 +31,7 @@ setup/windows/requires/*
 setup/windows/reccomends/*
 doc/auto_examples
 examples/io/*.msa
+examples/io/rgb*.jpg
 doc/gh-pages
 doc/log.txt
 *Thumbs.db

examples/io/convert_color_image.py

@@ -0,0 +1,81 @@
+"""
+Adjust contrast and save RGB images
+===================================
+
+This example shows how to adjust the contrast and intensities using
+scikit-image and save it as an RGB image.
+
+When saving an RGB image to ``jpg``, only 8 bits are supported and the image
+intensity needs to be rescaled to 0-255 before converting to 8 bits,
+otherwise, the intensities will be cropped at the value of 255.
+
+"""
+
+import hyperspy.api as hs
+import numpy as np
+import skimage as ski
+
+#%%
+#
+# Adjust contrast
+# ###############
+#
+# In hyperspy, color images are defined as Signal1D with the signal dimension
+# corresponding to the color channel (red, green and blue)
+
+# The dtype can be changed to a custom dtype, which is convenient to visualise
+# the color image
+s = hs.signals.Signal1D(ski.data.astronaut())
+s.change_dtype("rgb8")
+print(s)
+
+#%%
+# Display the color image
+s.plot()
+
+#%%
+# Processing is usually performed on standard dtype (e.g. ``uint8``, ``uint16``), because
+# most functions from scikit-image, numpy, scipy, etc. only support standard ``dtype``.
+# Convert from RGB to unsigned integer 16 bits
+s.change_dtype("uint8")
+print(s)
+
+#%%
+# Adjust contrast (gamma correction)
+s.data = ski.exposure.adjust_gamma(s.data, gamma=0.2)
+
+#%%
+#
+# Save to ``jpg``
+# ###############
+#
+# Change dtype back to custom dtype ``rgb8``
+s.change_dtype("rgb8")
+
+#%%
+# Save as jpg
+s.save("rgb8_image.jpg", overwrite=True)
+
+
+#%%
+#
+# Save ``rgb16`` image to ``jpg``
+# ###############################
+#
+# The last part of this example shows how to save ``rgb16`` to a ``jpg`` file
+#
+# Create a signal with ``rgb16`` dtype
+s2 = hs.signals.Signal1D(ski.data.astronaut().astype("uint16") * 100)
+
+#%%
+# To save a color image to ``jpg``, the signal needs to be converted to ``rgb8`` because
+# ``jpg`` only support 8-bit RGB
+# Rescale intensity to fit the unsigned integer 8 bits (2**8 = 256 intensity level)
+s2.data = ski.exposure.rescale_intensity(s2.data, out_range=(0, 255))
+
+#%%
+# Now that the values have been rescaled to the 0-255 range, we can convert the data type
+# to unsigned integer 8 bit and then ``rgb8`` to be able to save the RGB image in ``jpg`` format
+s2.change_dtype("uint8")
+s2.change_dtype("rgb8")
+s2.save("rgb16_image_saved_as_jpg.jpg", overwrite=True)

hyperspy/signal.py

@@ -3075,6 +3075,10 @@ def get_dynamic_explorer_wrapper(*args, **kwargs):
             else:
                 return navigator(as_numpy=True)
 
+        # function to disconnect when closing the navigator
+        function_to_disconnect = None
+        connected_event_copy = self.events.data_changed.connected.copy()
+
         if not isinstance(navigator, BaseSignal) and navigator == "auto":
             if self.navigator is not None:
                 navigator = self.navigator
@@ -3100,6 +3104,11 @@ def get_dynamic_explorer_wrapper(*args, **kwargs):
                         s=self,
                         axis=self.axes_manager.signal_axes,
                     )
+                    # Sets are not ordered, to retrieve the function to disconnect
+                    # take the difference with the previous copy
+                    function_to_disconnect = list(
+                        self.events.data_changed.connected - connected_event_copy
+                    )[0]
                 if navigator.axes_manager.navigation_dimension == 1:
                     navigator = interactive(
                         f=navigator.as_signal1D,
@@ -3178,6 +3187,7 @@ def is_shape_compatible(navigation_shape, shape):
         self._plot.plot(**kwargs)
         self.events.data_changed.connect(self.update_plot, [])
 
+        # Disconnect event when closing signal
         p = (
             self._plot.signal_plot
             if self._plot.signal_plot
@@ -3186,6 +3196,17 @@ def is_shape_compatible(navigation_shape, shape):
         p.events.closed.connect(
             lambda: self.events.data_changed.disconnect(self.update_plot), []
         )
+        # Disconnect events to the navigator when closing navigator
+        if function_to_disconnect is not None:
+            self._plot.navigator_plot.events.closed.connect(
+                lambda: self.events.data_changed.disconnect(function_to_disconnect), []
+            )
+            self._plot.navigator_plot.events.closed.connect(
+                lambda: self.axes_manager.events.any_axis_changed.disconnect(
+                    function_to_disconnect
+                ),
+                [],
+            )
 
         if plot_markers:
             if self.metadata.has_item("Markers"):
@@ -5677,10 +5698,16 @@ def change_dtype(self, dtype, rechunk=False):
                         "Only signals with dtype uint16 can be converted to "
                         "rgb16 images"
                     )
+                replot = self._plot is not None and self._plot.is_active
+                if replot:
+                    # Close the figure to avoid error with events
+                    self._plot.close()
                 self.data = rgb_tools.regular_array2rgbx(self.data)
                 self.axes_manager.remove(-1)
                 self.axes_manager._set_signal_dimension(2)
                 self._assign_subclass()
+                if replot:
+                    self.plot()
                 return
             else:
                 dtype = np.dtype(dtype)
@@ -5689,6 +5716,10 @@ def change_dtype(self, dtype, rechunk=False):
 
             if ddtype != dtype:
                 raise ValueError("It is only possibile to change to %s." % ddtype)
+            replot = self._plot is not None and self._plot.is_active
+            if replot:
+                # Close the figure to avoid error with events
+                self._plot.close()
             self.data = rgb_tools.rgbx2regular_array(self.data)
             self.axes_manager._append_axis(
                 size=self.data.shape[-1],
@@ -5699,6 +5730,8 @@ def change_dtype(self, dtype, rechunk=False):
             )
             self.axes_manager._set_signal_dimension(1)
             self._assign_subclass()
+            if replot:
+                self.plot()
             return
         else:
             self.data = self.data.astype(dtype)

hyperspy/tests/drawing/test_plot_signal.py

@@ -136,6 +136,24 @@ def test_plot_data_changed_event(sdim):
     return plt.gcf()
 
 
+@pytest.mark.parametrize("ndim", [0, 1, 2])
+@pytest.mark.parametrize("sdim", [1, 2])
+def test_plot_event_close(sdim, ndim):
+    # check that the events are correctly disconnected after closing
+    dim = sdim + ndim
+    nav_event = 1 if sdim + ndim >= 3 else 0
+    data = np.arange(5**dim).reshape((5,) * dim)
+    s = hs.signals.Signal1D(data) if sdim == 1 else hs.signals.Signal2D(data)
+    assert len(s.events.data_changed.connected) == 0
+    assert len(s.axes_manager.events.any_axis_changed.connected) == 0
+    s.plot()
+    assert len(s.events.data_changed.connected) == 1 + nav_event
+    assert len(s.axes_manager.events.any_axis_changed.connected) == nav_event
+    s._plot.close()
+    assert len(s.events.data_changed.connected) == 0
+    assert len(s.axes_manager.events.any_axis_changed.connected) == 0
+
+
 def _get_figure(test_plot, data_type, plot_type):
     if plot_type == "sig":
         plot = "signal_plot"

hyperspy/tests/signals/test_rgb.py

@@ -56,6 +56,17 @@ def test_wrong_rgb(self):
         with pytest.raises(AttributeError):
             self.im.change_dtype("rgb8")
 
+    def test_change_dtype_with_plot(self):
+        # Check that changing dtype with a plot open
+        # doesn't raise any error
+        s = self.s
+        s.plot()
+        assert s._plot.navigator_plot is not None
+        s.change_dtype("rgba8")
+        assert s._plot.navigator_plot is None
+        s.change_dtype("uint8")
+        assert s._plot.navigator_plot is not None
+
 
 class TestRGBA16:
     def setup_method(self, method):

upcoming_changes/3346.bugfix.rst

@@ -0,0 +1 @@
+Fix navigator event disconnection and fix plot when changing dtype from/to rbgx.

upcoming_changes/3346.enhancements.rst

@@ -0,0 +1 @@
+Add example showing how to handle RGB images.