nettracer3d 0.5.5__py3-none-any.whl → 0.5.7__py3-none-any.whl

nettracer3d/nettracer_gui.py

@@ -3980,10 +3980,17 @@ class CustomTableView(QTableView):
                 save_menu = context_menu.addMenu("Save As")
                 save_csv = save_menu.addAction("CSV")
                 save_excel = save_menu.addAction("Excel")
+                save_gephi = save_menu.addAction("Gephi")
+                save_graphml = save_menu.addAction("GraphML")
+                save_pajek = save_menu.addAction("Pajek")
                 
                 # Connect the actions - ensure we're saving the active table
                 save_csv.triggered.connect(lambda: self.parent.active_table.save_table_as('csv'))
                 save_excel.triggered.connect(lambda: self.parent.active_table.save_table_as('xlsx'))
+                save_gephi.triggered.connect(lambda: self.parent.active_table.save_table_as('gexf'))
+                save_graphml.triggered.connect(lambda: self.parent.active_table.save_table_as('graphml'))
+                save_pajek.triggered.connect(lambda: self.parent.active_table.save_table_as('net'))
+
 
                 if self == self.parent.selection_table:
                     set_action = context_menu.addAction("Swap with network table (also sets internal network properties - may affect related functions)")
@@ -4061,14 +4068,19 @@ class CustomTableView(QTableView):
             table_name = "Selection"
         
         # Get save file name
-        file_filter = "CSV Files (*.csv)" if file_type == 'csv' else "Excel Files (*.xlsx)"
+        file_filter = ("CSV Files (*.csv)" if file_type == 'csv' else 
+                      "Excel Files (*.xlsx)" if file_type == 'excel' else 
+                      "Gephi Graph (*.gexf)" if file_type == 'gexf' else
+                      "GraphML (*.graphml)" if file_type == 'graphml' else
+                      "Pajek Network (*.net)")
+
         filename, _ = QFileDialog.getSaveFileName(
             self,
             f"Save {table_name} Table As",
             "",
             file_filter
         )
-        
+
         if filename:
             try:
                 if file_type == 'csv':
@@ -4076,11 +4088,28 @@ class CustomTableView(QTableView):
                     if not filename.endswith('.csv'):
                         filename += '.csv'
                     df.to_csv(filename, index=False)
-                else:
+                elif file_type == 'xlsx':
                     # If user didn't type extension, add .xlsx
                     if not filename.endswith('.xlsx'):
                         filename += '.xlsx'
                     df.to_excel(filename, index=False)
+                elif file_type == 'gexf':
+                    # If user didn't type extension, add .gexf
+                    if not filename.endswith('.gexf'):
+                        filename += '.gexf'
+                    #for node in my_network.network.nodes():
+                        #my_network.network.nodes[node]['label'] = str(node)
+                    nx.write_gexf(my_network.network, filename, encoding='utf-8', prettyprint=True)
+                elif file_type == 'graphml':
+                    # If user didn't type extension, add .graphml
+                    if not filename.endswith('.graphml'):
+                        filename += '.graphml'
+                    nx.write_graphml(my_network.network, filename)
+                elif file_type == 'net':
+                    # If user didn't type extension, add .net
+                    if not filename.endswith('.net'):
+                        filename += '.net'
+                    nx.write_pajek(my_network.network, filename)
                     
                 QMessageBox.information(
                     self,
@@ -6569,8 +6598,12 @@ class MachineWindow(QMainWindow):
             # Clean up when done
             self.segmenter.cleanup()
 
-        for z,y,x in foreground_coords:
-            self.parent().highlight_overlay[z,y,x] = 255
+        fg_array = np.array(list(foreground_coords))
+        if len(fg_array) > 0:  # Check if we have any foreground coordinates
+            # Unpack into separate coordinate arrays
+            z_coords, y_coords, x_coords = fg_array[:, 0], fg_array[:, 1], fg_array[:, 2]
+            # Assign values in a single vectorized operation
+            self.parent().highlight_overlay[z_coords, y_coords, x_coords] = 255
 
         self.parent().load_channel(3, self.parent().highlight_overlay, True)
 

nettracer3d/segmenter.py

@@ -764,26 +764,30 @@ class InteractiveSegmenter:
             Returns:
                 List of chunks, where each chunk contains the coordinates for one z-slice
             """
+            # Pre-calculate the number of coordinates per z-slice
+            coords_per_slice = self.image_3d.shape[1] * self.image_3d.shape[2]
+
+            # Create all coordinates at once
             chunks = []
-            
-            # Process one z-slice at a time
             for z in range(self.image_3d.shape[0]):
-                # For each z-slice, gather all y,x coordinates
+                # Create y, x meshgrid once
                 y_coords, x_coords = np.meshgrid(
                     np.arange(self.image_3d.shape[1]),
                     np.arange(self.image_3d.shape[2]),
                     indexing='ij'
                 )
                 
-                # Create the z-slice coordinates
-                z_array = np.full_like(y_coords, z)
-                coords = np.stack([z_array, y_coords, x_coords]).reshape(3, -1).T
+                # Create the slice coordinates more efficiently
+                slice_coords = np.column_stack((
+                    np.full(coords_per_slice, z),
+                    y_coords.ravel(),
+                    x_coords.ravel()
+                ))
                 
-                # Convert to list of tuples and add as a chunk
-                chunks.append(list(map(tuple, coords)))
-            
-            return chunks
+                # Convert to list of tuples
+                chunks.append(list(map(tuple, slice_coords)))
 
+            return chunks
         try:
             from cuml.ensemble import RandomForestClassifier as cuRandomForestClassifier
         except:
@@ -853,7 +857,7 @@ class InteractiveSegmenter:
         print("Segmenting chunks...")
 
         
-        with ThreadPoolExecutor() as executor:
+        with ThreadPoolExecutor(max_workers=multiprocessing.cpu_count()) as executor:
             if gpu:
                 try:
                     futures = [executor.submit(self.process_chunk_GPU, chunk) for chunk in chunks]

{nettracer3d-0.5.5.dist-info → nettracer3d-0.5.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.5.5
+Version: 0.5.7
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <mclaughlinliam99@gmail.com>
 Project-URL: User_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
@@ -44,10 +44,6 @@ NetTracer3D is free to use/fork for academic/nonprofit use so long as citation i
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.5.5 updates --
+-- Version 0.5.7 updates --
 
-1. When the highlight overlay is being used in big overlays (and therefore defaulting to the mini overlay), updated system to just make one 2d overlay that regenerates on slice movement. Decided this was better than having it sit in a bigger 3d array when said array wasn't being used for anything and had to be rebuilt on slice movement or 3d operations anyway.
-
-2. For the random forrest segmenter, added the option to segment by 2D slice instead of 3D. In short, the 3D version was very greedy with its RAM usage and essentially computes a set of feature maps for the target array that are equivalent dims. By default it makes 7 of these, so a 1 GB array is going to demand 7GB of RAM to store its feature maps. The 2D slice version segments by 2D slice instead, meaning it stores only feature maps for slices with actual slices on them for training the model, and then for predicting voxel foreground/background, it computes the feature maps for the current slice (admittedly in the threadpool so this is amplified by core amount in the CPU but generally speaking this will save a lot of RAM). The reason I made this segmenter is to give NetTracer3D all the bells and whistles to let a user do everything in one program, but admittedly there are more efficient ML segmenters out there, such as through FIJI's big data viewer which is a lot better at handling big arrays in memory. I considered a way to compute 3D feature maps one at a time, save them in chunks to hard mem, and then open them while doing the chunked total segmentation but frankly this would likely be too slow to want to use so I will just suggest using 2D slice segmenter if RAM runs low.
-
-I do not anticipate any major updates for this project for the foreseeable future beyond bug fixes. 
+1. Minor change - Can now export network as .gexf (Gephi), .GraphML, or .net (Pajek) for other network analysis softwares to use.

{nettracer3d-0.5.5.dist-info → nettracer3d-0.5.7.dist-info}/RECORD

@@ -4,18 +4,18 @@ nettracer3d/hub_getter.py,sha256=KiNtxdajLkwB1ftslvrh1FE1Ch9ZCFEmHSEEotwR-To,829
 nettracer3d/modularity.py,sha256=V1f3s_vGd8EuVz27mzq6ycIGr0BWIpH7c7NU4QjgAHU,30247
 nettracer3d/morphology.py,sha256=yQ0GuieMVXOQpaohZlPnkEXEuCUjf8Fg352axyK8nbM,10755
 nettracer3d/nettracer.py,sha256=OE95IH1TfAZvT-htv1LEhw1EpnnEpkA83R5EcGMQDQg,209828
-nettracer3d/nettracer_gui.py,sha256=lKNl6T9998fMIYKrWdOhoAQlOLGeCiSaAP2chXCIDdQ,365336
+nettracer3d/nettracer_gui.py,sha256=TGxxDRfZzSQsurtn_XC1dlt8NLQCPZN0W5LZSbxTAZE,367424
 nettracer3d/network_analysis.py,sha256=MJBBjslA1k_R8ymid77U-qGSgzxFVfzGVQhE0IdhnbE,48046
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
 nettracer3d/proximity.py,sha256=FnIiI_AzfXd22HwCIFIyQRZxKYJ8YscIDdPnIv-wsO4,10560
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
-nettracer3d/segmenter.py,sha256=hqe7VLRkil65d_KYyUwWbU7SbM7v-krVSeZfLUlHlfY,49587
+nettracer3d/segmenter.py,sha256=zFWv9chXZ1rgw24KYKvIaQqkptUHy03vMKjmPgwv0-M,49793
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
 nettracer3d/smart_dilate.py,sha256=Kekm6YIVlJniMvJMG6_AwwNmCqK2l4Qtvg9VzzqPKMw,24600
-nettracer3d-0.5.5.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.5.5.dist-info/METADATA,sha256=8t96LyM9LOlvtwllVY0XrFszSZ5pj1J8t6wjPdVQ7Us,4746
-nettracer3d-0.5.5.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-nettracer3d-0.5.5.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.5.5.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.5.5.dist-info/RECORD,,
+nettracer3d-0.5.7.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.5.7.dist-info/METADATA,sha256=WR2-IsGW-YlgJhNNutjAQfGPcE-Fl_MS1-itY3nT0FQ,3107
+nettracer3d-0.5.7.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+nettracer3d-0.5.7.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.5.7.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.5.7.dist-info/RECORD,,