Fix issue where, when running 2d feature extraction with node analysi…

…s, problems arise when trying to calculate min/max of velocity aggregate stats from voxels in the node
aelefebv · Oct 31, 2024 · c57b0e1 · c57b0e1
1 parent a1df7a1
commit c57b0e1
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/nellie/feature_extraction/hierarchical.py b/nellie/feature_extraction/hierarchical.py
@@ -1105,6 +1105,9 @@ def aggregate_stats_for_class(child_class, t, list_of_idxs):
 
         # populate the idxs_array with the values from the stat_array at the indices in idxs_array
         stat_values = stat_array[idxs_array.astype(int)]
+        # if the shape has a second dimension of length 0, reshape it to have a second dimension of length 1, where all values are nan
+        if stat_values.shape[1] == 0:
+            stat_values = np.full((stat_values.shape[0], 1), np.nan)
 
         # calculate various statistics for the subset
         mean = np.nanmean(stat_values, axis=1)

diff --git a/nellie/run.py b/nellie/run.py
@@ -28,7 +28,7 @@ def run(file_info, remove_edges=False, otsu_thresh_intensity=False, threshold=No
     vox_reassign = VoxelReassigner(im_info)
     vox_reassign.run()
 
-    hierarchy = Hierarchy(im_info)
+    hierarchy = Hierarchy(im_info, skip_nodes=False)
     hierarchy.run()
 
     return im_info
@@ -63,7 +63,8 @@ def run(file_info, remove_edges=False, otsu_thresh_intensity=False, threshold=No
     #             continue
     #         im_info = run(tif_file, remove_edges=False, ch=ch, num_t=num_t)
 
-    test_file = '/Users/austin/test_files/nellie_all_tests/yeast_3d_mitochondria.ome.tif'
+    # test_file = '/Users/austin/test_files/nellie_all_tests/yeast_3d_mitochondria.ome.tif'
+    test_file = '/Users/austin/Downloads/26598942-Pos213-t_008-y_1744-x_0329.ome.tif'
     # test_file = all_paths[1]
     file_info = FileInfo(test_file)
     file_info.find_metadata()