Merge pull request #1968 from AEljarrat/bug_iterate_signal_with_markers

Bug iterate signal with markers

hyperspy/signal.py

@@ -4146,12 +4146,35 @@ def get_current_signal(self, auto_title=True, auto_filename=True):
         <Signal2D, title:  (2, 1), dimensions: (32, 32)>
 
         """
+
+        metadata = self.metadata.deepcopy()
+
+        # Check if marker update
+        if metadata.has_item('Markers'):
+            marker_name_list = metadata.Markers.keys()
+            markers_dict = metadata.Markers.__dict__
+            for marker_name in marker_name_list:
+                marker = markers_dict[marker_name]['_dtb_value_']
+                if marker.auto_update:
+                    marker.axes_manager = self.axes_manager
+                    key_dict = {}
+                    for key in marker.data.dtype.names:
+                        key_dict[key] = marker.get_data_position(key)
+                    marker.set_data(**key_dict)
+
         cs = self.__class__(
             self(),
             axes=self.axes_manager._get_signal_axes_dicts(),
-            metadata=self.metadata.as_dictionary(),
+            metadata=metadata.as_dictionary(),
             attributes={'_lazy': False})
 
+        if cs.metadata.has_item('Markers'):
+            temp_marker_dict = cs.metadata.Markers.as_dictionary()
+            markers_dict = markers_metadata_dict_to_markers(
+                temp_marker_dict,
+                cs.axes_manager)
+            cs.metadata.Markers = markers_dict
+
         if auto_filename is True and self.tmp_parameters.has_item('filename'):
             cs.tmp_parameters.filename = (self.tmp_parameters.filename +
                                           '_' +

hyperspy/tests/drawing/test_plot_markers.py

@@ -19,7 +19,7 @@
 import pytest
 
 from hyperspy.misc.test_utils import update_close_figure, sanitize_dict
-from hyperspy.signals import Signal2D, Signal1D
+from hyperspy.signals import Signal2D, Signal1D, BaseSignal
 from hyperspy.utils import markers, stack
 from hyperspy.drawing.marker import dict2marker
 from hyperspy.datasets.example_signals import EDS_TEM_Spectrum
@@ -474,6 +474,42 @@ def test_plot_eds_lines():
     s.axes_manager.navigation_axes[0].index = 1
     return s._plot.signal_plot.figure
 
+def test_iterate_markers():
+    from skimage.feature import peak_local_max
+    import scipy.misc
+    ims = BaseSignal(scipy.misc.face()).as_signal2D([1,2])
+    index = np.array([peak_local_max(im.data, min_distance=100,
+                             num_peaks=4) for im in ims])
+    # Add multiple markers
+    for i in range(4):
+        xs = index[:, i, 1]
+        ys = index[:, i, 0]
+        m = markers.point(x=xs, y=ys, color='red')
+        ims.add_marker(m, plot_marker=True, permanent=True)
+        m = markers.text(x=10+xs, y=10+ys, text=str(i), color='k')
+        ims.add_marker(m, plot_marker=True, permanent=True)
+    xs = index[:, :, 1]
+    ys = index[:, :, 0]
+    m = markers.rectangle(np.min(xs, 1),
+                          np.min(ys, 1),
+                          np.max(xs, 1),
+                          np.max(ys, 1),
+                          color='green')
+    ims.add_marker(m, plot_marker=True, permanent=True)
+
+    for im in ims:
+        m_original = ims.metadata.Markers
+        m_iterated = im.metadata.Markers
+        for key in m_original.keys():
+            mo = m_original[key]
+            mi = m_iterated[key]
+            assert mo.__class__.__name__         == mi.__class__.__name__
+            assert mo.name                       == mi.name
+            assert mo.get_data_position('x1')    == mi.get_data_position('x1')
+            assert mo.get_data_position('y1')    == mi.get_data_position('y1')
+            assert mo.get_data_position('text')  == mi.get_data_position('text')
+            assert mo.marker_properties['color'] == \
+                                                   mi.marker_properties['color']
 
 @update_close_figure
 def test_plot_eds_markers_close():