Merge branch 'master' of https://github.com/haesleinhuepf/napari-skim…

…age-regionprops
haesleinhuepf · Mar 14, 2023 · cdd258a · cdd258a
2 parents 7b0855c + c60dc4b
commit cdd258a
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Showing 10 changed files with 2,085 additions and 2,066 deletions.
diff --git a/demo/intersection_over_target_area_explained.ipynb b/demo/intersection_over_target_area_explained.ipynb
diff --git a/demo/measure_relationship_to_other_channels_functions.ipynb b/demo/measure_relationship_to_other_channels_functions.ipynb
diff --git a/demo/measure_relationship_to_other_channels_plugin.ipynb b/demo/measure_relationship_to_other_channels_plugin.ipynb
diff --git a/demo/measure_things_inside_things_functions.ipynb b/demo/measure_things_inside_things_functions.ipynb
diff --git a/demo/measure_things_inside_things_plugin.ipynb b/demo/measure_things_inside_things_plugin.ipynb
diff --git a/napari_skimage_regionprops/__init__.py b/napari_skimage_regionprops/__init__.py
@@ -2,7 +2,7 @@
 from ._regionprops import regionprops, regionprops_table, regionprops_table_all_frames
 from ._multichannel import link_two_label_images, measure_labels, measure_labels_with_intensity
 from ._multichannel import measure_labels_in_labels_with_intensity, measure_labels_in_labels
-from ._multichannel import regionprops_measure_things_inside_things
+from ._multichannel import regionprops_measure_relationship_to_other_channels
 from ._process_tables import merge_measurements_to_reference, make_summary_table
 from ._parametric_images import visualize_measurement_on_labels, relabel, map_measurements_on_labels
 from ._measure_points import measure_points

diff --git a/napari_skimage_regionprops/_multichannel.py b/napari_skimage_regionprops/_multichannel.py
diff --git a/napari_skimage_regionprops/_process_tables.py b/napari_skimage_regionprops/_process_tables.py
@@ -1,11 +1,10 @@
-import pandas
 from typing import List
 
 
 def merge_measurements_to_reference(
         table_reference_labels_properties: "pandas.DataFrame",
         table_linking_labels: List["pandas.DataFrame"],
-        table_labels_to_measure_properties: List["pandas.DataFrame"],
+        table_other_channel_labels_properties: List["pandas.DataFrame"],
         suffixes=None) -> List["pandas.DataFrame"]:
     """
     Merge measurements from target to reference table through a linking table.
@@ -19,7 +18,7 @@ def merge_measurements_to_reference(
         a list of tables. Each table should contain 2 columns, a
         label_reference' and a 'label_target'. Each table row associates a
         target label to a reference label.
-    table_labels_to_measure_properties : List["pandas.DataFrame"]
+    table_other_channel_labels_properties : List["pandas.DataFrame"]
         a list of tables to be used as targets with a column 'label' and other
         columns with features.
     suffixes : List[str], optional
@@ -40,20 +39,20 @@ def merge_measurements_to_reference(
         list_table_linking_labels = [table_linking_labels]
     else:
         list_table_linking_labels = table_linking_labels
-    if not isinstance(table_labels_to_measure_properties, list):
-        list_table_labels_to_measure_properties = [
-            table_labels_to_measure_properties]
+    if not isinstance(table_other_channel_labels_properties, list):
+        list_table_other_channel_labels_properties = [
+            table_other_channel_labels_properties]
     else:
-        list_table_labels_to_measure_properties = \
-            table_labels_to_measure_properties
+        list_table_other_channel_labels_properties = \
+            table_other_channel_labels_properties
     # Build custom suffixes or check if provided suffixes match data size
-    n_measurement_tables = len(list_table_labels_to_measure_properties)
+    n_measurement_tables = len(list_table_other_channel_labels_properties)
     if suffixes is None:
         n_leading_zeros = n_measurement_tables // 10
         suffixes = ['_reference'] + ['_' + str(i+1).zfill(1+n_leading_zeros)
                                      for i in range(n_measurement_tables)]
     else:
-        if len(suffixes) != len(table_labels_to_measure_properties) + 1:
+        if len(suffixes) != len(table_other_channel_labels_properties) + 1:
             print(('Error: List of suffixes must have the same length as the'
                   'number of tables containing measurements'))
             return
@@ -70,19 +69,19 @@ def merge_measurements_to_reference(
                          'label_target': 'label' + suffixes[i+1]},
                 inplace=True)
     # Rename columns of tables with properties from other channels
-    for i, table_labels_to_measure_properties in enumerate(
-            list_table_labels_to_measure_properties):
-        table_labels_to_measure_properties.columns = [
+    for i, table_other_channel_labels_properties in enumerate(
+            list_table_other_channel_labels_properties):
+        table_other_channel_labels_properties.columns = [
             props + suffixes[i+1]
-            for props in table_labels_to_measure_properties.columns]
+            for props in table_other_channel_labels_properties.columns]
 
     output_table_list = []
     # Consecutively merge linking_labels tables and properties from other 
     # channels tables to the reference table
-    for i, table_linking_labels, table_labels_to_measure_properties in zip(
+    for i, table_linking_labels, table_other_channel_labels_properties in zip(
             range(n_measurement_tables),
             list_table_linking_labels,
-            list_table_labels_to_measure_properties):
+            list_table_other_channel_labels_properties):
         # Merge other labels to label_reference
         output_table = pd.merge(table_reference_labels_properties,
                                 table_linking_labels,
@@ -93,12 +92,13 @@ def merge_measurements_to_reference(
             'label' + suffixes[i+1]].fillna(0)
         # Merge other properties to output table based on new labels column
         output_table = pd.merge(output_table,
-                                table_labels_to_measure_properties,
+                                table_other_channel_labels_properties,
                                 how='outer', on='label' + suffixes[i+1])
         # Ensure label columns type to be integer
         for column in output_table.columns:
             if column.startswith('label'):
                 output_table[column] = output_table[column].astype(int)
+        output_table = output_table.sort_values(by='label' + suffixes[0])
         # Append output table to list (each table may have different shapes)
         output_table_list.append(output_table)
     return output_table_list
@@ -157,7 +157,7 @@ def make_summary_table(table: List["pandas.DataFrame"],
                 print(('Could not infer suffixes from column names. Please '
                        'provide a list of suffixes identifying different '
                        'channels'))
-    if isinstance(table, pandas.DataFrame):
+    if isinstance(table, pd.DataFrame):
         table = [table]
 
     if 'count' in statistics_list:

diff --git a/...props/_tests/test_things_inside_things.py → ...e_regionprops/_tests/test_multichannel.py b/...props/_tests/test_things_inside_things.py → ...e_regionprops/_tests/test_multichannel.py
@@ -1,7 +1,7 @@
 
 def test_napari_regionprops_map_2channels_2D(make_napari_viewer):
     import numpy as np
-    from napari_skimage_regionprops import regionprops_measure_things_inside_things
+    from napari_skimage_regionprops import regionprops_measure_relationship_to_other_channels
 
     viewer = make_napari_viewer()
 
@@ -25,16 +25,16 @@ def test_napari_regionprops_map_2channels_2D(make_napari_viewer):
     viewer.add_labels(ref_labels, name='ref_labels')
     viewer.add_labels(target_labels, name='target_labels')
 
-    widget = regionprops_measure_things_inside_things()
-    regionprops_measure_things_inside_things_function = widget._function
+    widget = regionprops_measure_relationship_to_other_channels()
+    regionprops_measure_relationship_to_other_channels_function = widget._function
     # Measure everything we can
-    table = regionprops_measure_things_inside_things_function(
+    table = regionprops_measure_relationship_to_other_channels_function(
         ref_labels,
         multichannel_image[..., 0],
         [target_labels],
         [multichannel_image[..., 1]],
         intensity = True,
-        things_inside_things = True,
+        relate_to_other_channels = True,
         size = True,
         perimeter = True,
         shape = True,
@@ -63,7 +63,7 @@ def test_napari_regionprops_map_2channels_2D(make_napari_viewer):
 
 def test_napari_regionprops_map_3channels_2D(make_napari_viewer):
     import numpy as np
-    from napari_skimage_regionprops import regionprops_measure_things_inside_things
+    from napari_skimage_regionprops import regionprops_measure_relationship_to_other_channels
 
     viewer = make_napari_viewer()
 
@@ -91,17 +91,17 @@ def test_napari_regionprops_map_3channels_2D(make_napari_viewer):
     viewer.add_labels(target_labels, name='target_labels')
     viewer.add_labels(target_labels_B, name='target_labels_B')
 
-    widget = regionprops_measure_things_inside_things()
-    regionprops_measure_things_inside_things_function = widget._function
+    widget = regionprops_measure_relationship_to_other_channels()
+    regionprops_measure_relationship_to_other_channels_function = widget._function
 
     # Measure everything we can
-    table = regionprops_measure_things_inside_things_function(
+    table = regionprops_measure_relationship_to_other_channels_function(
         ref_labels,
         multichannel_image[..., 0],
         [target_labels, target_labels_B],
         [multichannel_image[..., 1], multichannel_image[..., 2]],
         intensity = True,
-        things_inside_things = True,
+        relate_to_other_channels = True,
         size = True,
         perimeter = True,
         shape = True,
@@ -134,7 +134,7 @@ def test_napari_regionprops_map_3channels_2D(make_napari_viewer):
 
 def test_napari_regionprops_map_2channels_3D(make_napari_viewer):
     import numpy as np
-    from napari_skimage_regionprops import regionprops_measure_things_inside_things
+    from napari_skimage_regionprops import regionprops_measure_relationship_to_other_channels
 
     viewer = make_napari_viewer()
 
@@ -170,17 +170,17 @@ def test_napari_regionprops_map_2channels_3D(make_napari_viewer):
     viewer.add_labels(ref_labels_3D, name='ref_labels_3D')
     viewer.add_labels(target_labels_3D, name='target_labels_3D')
 
-    widget = regionprops_measure_things_inside_things()
-    regionprops_measure_things_inside_things_function = widget._function
+    widget = regionprops_measure_relationship_to_other_channels()
+    regionprops_measure_relationship_to_other_channels_function = widget._function
 
     # Measure everything we can
-    table = regionprops_measure_things_inside_things_function(
+    table = regionprops_measure_relationship_to_other_channels_function(
         ref_labels_3D,
         multichannel_image[0],
         [target_labels_3D],
         [multichannel_image[1]],
         intensity = True,
-        things_inside_things = True,
+        relate_to_other_channels = True,
         size = True,
         perimeter = True,
         shape = True,

diff --git a/requirements.txt b/requirements.txt
@@ -6,3 +6,4 @@ pandas
 napari-tools-menu>=0.1.19
 napari-workflows
 imageio!=2.22.1
+Deprecated