move napari viewer parameter to end (backwards compatibility breaking…

…) and return pandas DataFrames
Cryaaa · May 8, 2022 · 246099c · 246099c
1 parent e312dd8
commit 246099c
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Showing 4 changed files with 66 additions and 60 deletions.
diff --git a/demo/handle_timelapse_data.ipynb b/demo/handle_timelapse_data.ipynb
diff --git a/demo/tables.ipynb b/demo/tables.ipynb
diff --git a/napari_skimage_regionprops/_regionprops.py b/napari_skimage_regionprops/_regionprops.py
@@ -1,22 +1,23 @@
 import warnings
 
 import numpy as np
+import pandas
 from napari import Viewer
 from napari_tools_menu import register_function
 import napari
 import math
 from ._all_frames import analyze_all_frames
 
-def regionprops(image_layer : napari.layers.Layer, labels_layer: napari.layers.Labels, napari_viewer : Viewer, size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False):
+def regionprops(image_layer : napari.layers.Layer, labels_layer: napari.layers.Labels, size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False, napari_viewer : Viewer = None):
     warnings.warn("napari_skimage_regionprops.regionprops is deprecated. Use regionprops_table instead.")
     image_data = None
     if image_layer is not None:
         image_data = image_layer.data
 
     regionprops_table(image_data, labels_layer.data, napari_viewer, size, intensity, perimeter, shape, position, moments)
 
-@register_function(menu="Measurement > Regionprops (nsr)")
-def regionprops_table(image : napari.types.ImageData, labels: napari.types.LabelsData, napari_viewer : Viewer = None, size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False):
+@register_function(menu="Measurement > Regionprops (scikit-image, nsr)")
+def regionprops_table(image : napari.types.ImageData, labels: napari.types.LabelsData, size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False, napari_viewer : Viewer = None) -> "pandas.DataFrame":
     """
     Adds a table widget to a given napari viewer with quantitative analysis results derived from an image-label pair.
     """
@@ -71,9 +72,11 @@ def standard_deviation_intensity(region, intensities):
         properties = properties + ['solidity', 'extent', 'feret_diameter_max', 'local_centroid']
         if len(labels.shape) == 2:
             properties = properties + ['major_axis_length', 'minor_axis_length', 'orientation', 'eccentricity']
+            # we need these two to compute some shape descriptors
             if not size:
-                # we need these two to compute some shape descriptors
-                properties = properties + ['area', 'perimeter']
+                properties = properties + ['area']
+            if not perimeter:
+                properties = properties + ['perimeter']
         else:
             properties = properties + ['moments_central']
         # euler_number,
@@ -148,7 +151,8 @@ def standard_deviation_intensity(region, intensities):
         from ._table import add_table
         add_table(labels_layer, napari_viewer)
     else:
-        return table
+        import pandas
+        return pandas.DataFrame(table)
 
 def ellipsoid_axis_lengths(table):
     """Compute ellipsoid major, intermediate and minor axis length.

diff --git a/napari_skimage_regionprops/_tests/test_function.py b/napari_skimage_regionprops/_tests/test_function.py
@@ -149,7 +149,7 @@ def test_regionprops_without_moments(make_napari_viewer):
 
     # analyze everything we can
     from napari_skimage_regionprops import regionprops
-    regionprops(image_layer, labels_layer, viewer, True, True, True, True, True, False)
+    regionprops(image_layer, labels_layer, size=True, intensity=True, perimeter=True, shape=True, position=True, moments=False, napari_viewer=viewer)
 
 def test_3d_2d(make_napari_viewer):
 
@@ -180,7 +180,8 @@ def test_3d_2d(make_napari_viewer):
 
     # analyze everything we can
     from napari_skimage_regionprops import regionprops
-    regionprops(image_layer, labels_layer, viewer, True, True, True, True, True, True)
+    regionprops(image_layer, labels_layer, size=True, intensity=True, perimeter=True, shape=True, position=True,
+                moments=True, napari_viewer=viewer)
 
     # there is now a table in the viewer
     assert len(viewer.window._dock_widgets) == num_dw + 1
@@ -222,7 +223,8 @@ def test_3d(make_napari_viewer):
 
     # analyze everything we can
     from napari_skimage_regionprops import regionprops
-    regionprops(image_layer, labels_layer, viewer, True, True, True, True, True, True)
+    regionprops(image_layer, labels_layer, size=True, intensity=True, perimeter=True, shape=True, position=True,
+                moments=True, napari_viewer=viewer)
 
     # there is now a table in the viewer
     assert len(viewer.window._dock_widgets) == num_dw + 1
@@ -265,7 +267,8 @@ def test_3d_dask(make_napari_viewer):
 
     # analyze everything we can
     from napari_skimage_regionprops import regionprops
-    regionprops(image_layer, labels_layer, viewer, True, True, True, True, True, True)
+    regionprops(image_layer, labels_layer, size=True, intensity=True, perimeter=True, shape=True, position=True,
+                moments=True, napari_viewer=viewer)
 
     # there is now a table in the viewer
     assert len(viewer.window._dock_widgets) == num_dw + 1
@@ -312,7 +315,8 @@ def test_4d_3d(make_napari_viewer):
 
     # analyze everything we can
     from napari_skimage_regionprops import regionprops
-    regionprops(image_layer, labels_layer, viewer, True, True, True, True, True, True)
+    regionprops(image_layer, labels_layer, size=True, intensity=True, perimeter=True, shape=True, position=True,
+                moments=True, napari_viewer=viewer)
 
     # there is now a table in the viewer
     assert len(viewer.window._dock_widgets) == num_dw + 1