bugfix: parametric images didn't work with timelapse data

Cryaaa · May 5, 2022 · 9350db8 · 9350db8
1 parent 648ce9c
commit 9350db8
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Showing 2 changed files with 14 additions and 4 deletions.
diff --git a/napari_skimage_regionprops/_parametric_images.py b/napari_skimage_regionprops/_parametric_images.py
@@ -2,17 +2,27 @@
 import numpy
 
 @register_function(menu="Visualization > Measurements on labels (nsr)")
-def visualize_measurement_on_labels(labels_layer:"napari.layers.Labels", column:str = "label") -> "napari.types.ImageData":
+def visualize_measurement_on_labels(labels_layer:"napari.layers.Labels", column:str = "label", viewer:"napari.Viewer" = None) -> "napari.types.ImageData":
+    import pandas as pd
 
     labels = labels_layer.data
-    table = labels_layer.properties
+    table = pd.DataFrame(labels_layer.properties)
+
+    if len(labels.shape) == 4:
+        current_timepoint = viewer.dims.current_step[0]
+        labels = labels[current_timepoint]
+
+        if "frame" in table.keys():
+            table = table[table['frame'] == current_timepoint]
+
     measurements = table[column]
 
     if isinstance(measurements, numpy.ndarray):
         measurements = measurements.tolist()
 
     try:
-        import pyclesperanto_prototype as cle; return cle.pull(cle.replace_intensities(labels, numpy.asarray([0] + measurements)))
+        import pyclesperanto_prototype as cle
+        return cle.pull(cle.replace_intensities(labels, numpy.asarray([0] + measurements)))
     except ImportError:
         return relabel_numpy(labels, measurements)
 

diff --git a/napari_skimage_regionprops/_table.py b/napari_skimage_regionprops/_table.py
@@ -68,7 +68,7 @@ def _double_clicked_table(self):
             print("Selected column", selected_column)
             if selected_column is not None:
                 from ._parametric_images import visualize_measurement_on_labels
-                new_layer = self._viewer.add_image(visualize_measurement_on_labels(self._layer, selected_column),
+                new_layer = self._viewer.add_image(visualize_measurement_on_labels(self._layer, selected_column, self._viewer),
                                        name=selected_column + " in " + self._layer.name)
                 new_layer.contrast_limits = [np.min(self._table[selected_column]), np.max(self._table[selected_column])]
                 new_layer.colormap = "jet"