nettracer3d 1.0.4__py3-none-any.whl → 1.0.6__py3-none-any.whl

nettracer3d/nettracer.py

@@ -5294,32 +5294,35 @@ class Network_3D:
                             new_list.append(centroid)
 
             else:
-
                 if mode == 1:
-
                     legal = self.edges != 0
-
                 elif mode == 2:
-
                     legal = self.network_overlay != 0
-
                 elif mode == 3:
-
                     legal = self.id_overlay != 0
-
                 if self.nodes is None:
-
                     temp_array = proximity.populate_array(self.node_centroids, shape = legal.shape)
                 else:
                     temp_array = self.nodes
-
                 if dim == 2:
                     volume = np.count_nonzero(legal) * self.xy_scale**2
+                    # Pad in x and y dimensions (assuming shape is [y, x])
+                    legal = np.pad(legal, pad_width=1, mode='constant', constant_values=0)
                 else:
                     volume = np.count_nonzero(legal) * self.z_scale * self.xy_scale**2
+                    # Pad in x, y, and z dimensions (assuming shape is [z, y, x])
+                    legal = np.pad(legal, pad_width=1, mode='constant', constant_values=0)
+                
                 print(f"Using {volume} for the volume measurement (Volume of provided mask as scaled by xy and z scaling)")
-
-                legal = smart_dilate.compute_distance_transform_distance(legal, sampling = [self.z_scale, self.xy_scale, self.xy_scale]) # Get true distances
+                
+                # Compute distance transform on padded array
+                legal = smart_dilate.compute_distance_transform_distance(legal, sampling = [self.z_scale, self.xy_scale, self.xy_scale])
+                
+                # Remove padding after distance transform
+                if dim == 2:
+                    legal = legal[1:-1, 1:-1]  # Remove padding from x and y dimensions
+                else:
+                    legal = legal[1:-1, 1:-1, 1:-1]  # Remove padding from x, y, and z dimensions
                 
                 max_avail = np.max(legal) # Most internal point
                 min_legal = factor * max_avail # Values of stuff 25% within the tissue

nettracer3d/nettracer_gui.py

@@ -2009,7 +2009,7 @@ class ImageViewerWindow(QMainWindow):
                                 self.parent().toggle_channel(1)
                             # Navigate to the Z-slice
                             self.parent().slice_slider.setValue(int(centroid[0]))
-                            print(f"Found edge {value} at Z-slice {centroid[0]}")
+                            print(f"Found edge {value} at [Z,Y,X] -> {centroid}")
 
                         else:
                             print(f"Edge {value} not found in centroids dictionary")
@@ -2045,9 +2045,9 @@ class ImageViewerWindow(QMainWindow):
                             # Navigate to the Z-slice
                             self.parent().slice_slider.setValue(int(centroid[0]))
                             if mode == 0:
-                                print(f"Found node {value} at Z-slice {centroid[0]}")
+                                print(f"Found node {value} at [Z,Y,X] -> {centroid}")
                             elif mode == 2:
-                                print(f"Found node {value} from community {com} at Z-slice {centroid[0]}")
+                                print(f"Found node {value} from community {com} at [Z,Y,X] -> {centroid}")
 
                             
                         else:
@@ -2332,7 +2332,7 @@ class ImageViewerWindow(QMainWindow):
         unique_labels = np.unique(input_array[binary_mask])
         print(f"Processing {len(unique_labels)} unique labels")
         
-        # Get all bounding boxes at once - this is very fast
+        # Get all bounding boxes at once
         bounding_boxes = ndimage.find_objects(input_array)
         
         # Prepare work items - just check if bounding box exists for each label
@@ -2348,7 +2348,7 @@ class ImageViewerWindow(QMainWindow):
                 bbox = bounding_boxes[bbox_index]
                 work_items.append((orig_label, bbox))
         
-        print(f"Created {len(work_items)} work items")
+        #print(f"Created {len(work_items)} work items")
         
         # If we have work items, process them
         if len(work_items) == 0:
@@ -2368,7 +2368,7 @@ class ImageViewerWindow(QMainWindow):
                 return orig_label, bbox, labeled_sub, num_cc
                 
             except Exception as e:
-                print(f"Error processing label {orig_label}: {e}")
+                #print(f"Error processing label {orig_label}: {e}")
                 return orig_label, bbox, None, 0
         
         # Execute in parallel
@@ -2384,7 +2384,7 @@ class ImageViewerWindow(QMainWindow):
         
         for orig_label, bbox, labeled_sub, num_cc in results:
             if num_cc > 0 and labeled_sub is not None:
-                print(f"Label {orig_label}: {num_cc} components")
+                #print(f"Label {orig_label}: {num_cc} components")
                 # Remap labels and place in output
                 for cc_id in range(1, num_cc + 1):
                     mask = labeled_sub == cc_id
@@ -2397,7 +2397,7 @@ class ImageViewerWindow(QMainWindow):
 
     def handle_seperate(self):
         """
-        Fixed version with proper mask handling and debugging
+        Seperate objects in an array that share a label but do not touch
         """
         try:
             # Handle nodes
@@ -2406,7 +2406,6 @@ class ImageViewerWindow(QMainWindow):
                 # Create highlight overlay (this should preserve original label values)
                 self.create_highlight_overlay(node_indices=self.clicked_values['nodes'])
                                 
-                # DON'T convert to boolean yet - we need the original labels!
                 # Create a boolean mask for where we have highlighted values
                 highlight_mask = self.highlight_overlay != 0
                 
@@ -2416,7 +2415,7 @@ class ImageViewerWindow(QMainWindow):
                 # Get non-highlighted part of the array
                 non_highlighted = np.where(highlight_mask, 0, my_network.nodes)
                 
-                # Calculate max_val properly
+                # Calculate max_val
                 max_val = np.max(non_highlighted) if np.any(non_highlighted) else 0
                                 
                 # Process highlighted part
@@ -10087,7 +10086,7 @@ class ViolinDialog(QDialog):
         # Convert all remaining columns to float type (batch conversion)
         df_copy = df_copy.astype(float)
         
-        # First, calculate the centerpoint for each column by finding the median across all identity groups
+        # First, calculate the centerpoint for each column by finding the min across all identity groups
         column_centerpoints = {}
         
         for column in df_copy.columns:
@@ -10098,7 +10097,7 @@ class ViolinDialog(QDialog):
                 valid_nodes = [node for node in node_list if node in df_copy.index]
                 if valid_nodes and ((str(identity) == str(column)) or str(identity) == f'{str(column)}+'):
                     # Get the median value for this identity in this column
-                    identity_min = df_copy.loc[valid_nodes, column].median()
+                    identity_min = df_copy.loc[valid_nodes, column].min()
                     centerpoint = identity_min
                     break  # Found the match, no need to continue
             
@@ -10107,6 +10106,7 @@ class ViolinDialog(QDialog):
                 column_centerpoints[column] = centerpoint
             else:
                 # Fallback: if no matching identity, use column median
+                print(f"Could not find {str(column)} in node identities. As a fallback, using the median of all values in this channel rather than the minimum of user-designated valid values.")
                 column_centerpoints[column] = df_copy[column].median()
         
         # Now normalize each column using Z-score-like calculation with identity centerpoint
@@ -10191,38 +10191,44 @@ class ViolinDialog(QDialog):
 
         from . import neighborhoods
 
-        if self.idens.currentIndex() != 0:
+        try:
 
-            iden = self.idens.currentText()
-            iden_list = []
-            import ast
+            if self.idens.currentIndex() != 0:
 
-            for item in my_network.node_identities:
+                iden = self.idens.currentText()
+                iden_list = []
+                import ast
 
-                try:
-                    parse = ast.literal_eval(my_network.node_identities[item])
-                    if iden in parse:
-                        iden_list.append(item)
-                except:
-                    if (iden == my_network.node_identities[item]):
-                        iden_list.append(item)
+                for item in my_network.node_identities:
 
-            violin_dict = df_to_dict_by_rows(self.df, iden_list, f"Z-Score-like Channel Intensities of Identity {iden}, {len(iden_list)} Nodes")
+                    try:
+                        parse = ast.literal_eval(my_network.node_identities[item])
+                        if iden in parse:
+                            iden_list.append(item)
+                    except:
+                        if (iden == my_network.node_identities[item]):
+                            iden_list.append(item)
 
-            neighborhoods.create_violin_plots(violin_dict, graph_title=f"Z-Score-like Channel Intensities of Identity {iden}, {len(iden_list)} Nodes")
+                violin_dict = df_to_dict_by_rows(self.df, iden_list, f"Z-Score-like Channel Intensities of Identity {iden}, {len(iden_list)} Nodes")
 
+                neighborhoods.create_violin_plots(violin_dict, graph_title=f"Z-Score-like Channel Intensities of Identity {iden}, {len(iden_list)} Nodes")
+        except:
+            pass
 
-        if self.coms.currentIndex() != 0:
+        try:
+            if self.coms.currentIndex() != 0:
 
-            com = self.coms.currentText()
+                com = self.coms.currentText()
 
-            com_dict = n3d.invert_dict(my_network.communities)
+                com_dict = n3d.invert_dict(my_network.communities)
 
-            com_list = com_dict[int(com)]
+                com_list = com_dict[int(com)]
 
-            violin_dict = df_to_dict_by_rows(self.df, com_list, f"Z-Score-like Channel Intensities of Community/Neighborhood {com}, {len(com_list)} Nodes")
+                violin_dict = df_to_dict_by_rows(self.df, com_list, f"Z-Score-like Channel Intensities of Community/Neighborhood {com}, {len(com_list)} Nodes")
 
-            neighborhoods.create_violin_plots(violin_dict, graph_title=f"Z-Score-like Channel Intensities of Community/Neighborhood {com}, {len(com_list)} Nodes")
+                neighborhoods.create_violin_plots(violin_dict, graph_title=f"Z-Score-like Channel Intensities of Community/Neighborhood {com}, {len(com_list)} Nodes")
+        except:
+            pass
 
 
     def run2(self):

{nettracer3d-1.0.4.dist-info → nettracer3d-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.4
+Version: 1.0.6
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <liamm@wustl.edu>
 Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
@@ -110,7 +110,6 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.0.4 Updates --
+-- Version 1.0.5 Updates --
 
-	* Some small bug fixes and adjustments
-	* Heatmap theoretical distances can now be calculated based on an area constrained within a binary mask.
+	* Bug fix

{nettracer3d-1.0.4.dist-info → nettracer3d-1.0.6.dist-info}/RECORD

@@ -5,8 +5,8 @@ nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,750
 nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
 nettracer3d/neighborhoods.py,sha256=lh4_zuTwgTq-u8VHy72buBfZf58FEJo9sH3IIBuZr68,52735
-nettracer3d/nettracer.py,sha256=6r5aGtmiHxGkfCh5lJuREAoloZ3WKvcaRAD7kmWXedk,273957
-nettracer3d/nettracer_gui.py,sha256=0QzoDa6o2z-iVZzM3v4tePFV-tvw-lkD_24tQ0fZ1sU,666134
+nettracer3d/nettracer.py,sha256=rgQvMtojoA5UqXbDjeMRcz2BpaebwKLF5CPAlR_xZwY,274675
+nettracer3d/nettracer_gui.py,sha256=5aqo5fWVfzcTVjCa1HlFflnrCFQoZvaPZYjM-QT94_E,666407
 nettracer3d/network_analysis.py,sha256=kBzsVaq4dZkMe0k-VGvQIUvM-tK0ZZ8bvb-wtsugZRQ,46150
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=kZcR1PekLg0riioNeGcALIXQyZ5PtHA_9MT6z7Zovdk,10401
@@ -17,9 +17,9 @@ nettracer3d/segmenter.py,sha256=aOO3PwZ2UeizEIFX7N8midwzTzbEDzgM2jQ7WTdbrUg,7067
 nettracer3d/segmenter_GPU.py,sha256=OUekQljLKPiC4d4hNZmqrRa9HSVQ6HcCnILiAfHE5Hg,78051
 nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA,9947
 nettracer3d/smart_dilate.py,sha256=TvRUh6B4q4zIdCO1BWH-xgTdND5OUNmo99eyxG9oIAU,27145
-nettracer3d-1.0.4.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
-nettracer3d-1.0.4.dist-info/METADATA,sha256=VMs_Lcaa3xnnLTrror42GmRUJBdzIcyGk0sMtJZZ9Eo,7120
-nettracer3d-1.0.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-1.0.4.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-1.0.4.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-1.0.4.dist-info/RECORD,,
+nettracer3d-1.0.6.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
+nettracer3d-1.0.6.dist-info/METADATA,sha256=euIZXznP4dHg1VtnfCPyP2c7qK9xC1ovv8OfIUNSXRY,6984
+nettracer3d-1.0.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-1.0.6.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-1.0.6.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-1.0.6.dist-info/RECORD,,