nettracer3d 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

nettracer3d/nettracer_gui.py

@@ -1069,24 +1069,29 @@ class ImageViewerWindow(QMainWindow):
 
             neighbors = set()  # Use a set from the start to avoid duplicates
             nodes += self.clicked_values['nodes']
+
+            try:
             
-            # Get the existing DataFrame from the model
-            original_df = self.network_table.model()._data
-            
-            # Create mask for pairs that have nodes of the ID in question
-            mask = (
-                (original_df.iloc[:, 0].isin(nodes)) | (original_df.iloc[:, 1].isin(nodes))
-            )
-            
-            # Filter the DataFrame to only include direct connections
-            filtered_df = original_df[mask].copy()
-            
-            # Create new model with filtered DataFrame and update selection table
-            new_model = PandasModel(filtered_df)
-            self.selection_table.setModel(new_model)
-            
-            # Switch to selection table
-            self.selection_button.click()
+                # Get the existing DataFrame from the model
+                original_df = self.network_table.model()._data
+                
+                # Create mask for pairs that have nodes of the ID in question
+                mask = (
+                    (original_df.iloc[:, 0].isin(nodes)) | (original_df.iloc[:, 1].isin(nodes))
+                )
+
+                
+                # Filter the DataFrame to only include direct connections
+                filtered_df = original_df[mask].copy()
+                
+                # Create new model with filtered DataFrame and update selection table
+                new_model = PandasModel(filtered_df)
+                self.selection_table.setModel(new_model)
+                
+                # Switch to selection table
+                self.selection_button.click()
+            except:
+                pass
 
             print(f"Found {len(filtered_df)} direct connections between nodes of ID {sort} and their neighbors (of any ID)")
 
@@ -2065,18 +2070,19 @@ class ImageViewerWindow(QMainWindow):
                     x_idx = int(round(event.xdata))
                     y_idx = int(round(event.ydata))
                     # Check if Ctrl key is pressed (using matplotlib's key_press system)
-                    ctrl_pressed = 'ctrl' in event.modifiers  
-                    if self.channel_data[self.active_channel][self.current_slice, y_idx, x_idx] != 0:
-                        clicked_value = self.channel_data[self.active_channel][self.current_slice, y_idx, x_idx]
-                    else:
-                        if not ctrl_pressed:
-                            self.clicked_values = {
-                                'nodes': [],
-                                'edges': []
-                            }
-                            self.create_highlight_overlay()
-                        return
-                    
+                    ctrl_pressed = 'ctrl' in event.modifiers
+                    if len(self.channel_data[self.active_channel].shape) != 4:  
+                        if self.channel_data[self.active_channel][self.current_slice, y_idx, x_idx] != 0:
+                            clicked_value = self.channel_data[self.active_channel][self.current_slice, y_idx, x_idx]
+                        else:
+                            if not ctrl_pressed:
+                                self.clicked_values = {
+                                    'nodes': [],
+                                    'edges': []
+                                }
+                                self.create_highlight_overlay()
+                            return
+                        
 
                     starting_vals = copy.deepcopy(self.clicked_values)
                     
@@ -5834,8 +5840,12 @@ class MachineWindow(QMainWindow):
 
         if self.parent().active_channel == 0:
             if self.parent().channel_data[0] is not None:
-                active_data = self.parent().channel_data[0]
-                act_channel = 0
+                try:
+                    active_data = self.parent().channel_data[0]
+                    act_channel = 0
+                except:
+                    active_data = self.parent().channel_data[1]
+                    act_channel = 1
             else:
                 active_data = self.parent().channel_data[1]
                 act_channel = 1

nettracer3d/node_draw.py

@@ -175,7 +175,11 @@ def degree_draw(degree_dict, centroid_dict, nodes):
 
     for node in centroid_dict:
 
-        degree = degree_dict[node]
+        try:
+            degree = degree_dict[node]
+        except:
+            continue
+            
         z, y, x = centroid_dict[node].astype(int)
 
         try:

nettracer3d/segmenter.py

@@ -2,8 +2,14 @@ from sklearn.ensemble import RandomForestClassifier
 import numpy as np
 try:
     import torch
+except:
+    pass
+try:
     import cupy as cp
     import cupyx.scipy.ndimage as cpx
+except:
+    pass
+try:
     from cuml.ensemble import RandomForestClassifier as cuRandomForestClassifier
 except:
     pass
@@ -19,9 +25,15 @@ class InteractiveSegmenter:
         self.image_3d = image_3d
         self.patterns = []
 
-        self.use_gpu = use_gpu and cp.cuda.is_available()
+        try:
+            self.use_gpu = use_gpu and cp.cuda.is_available()
+        except:
+            self.use_gpu = False
         if self.use_gpu:
-            print(f"Using GPU: {torch.cuda.get_device_name()}")
+            try:
+                print(f"Using GPU: {torch.cuda.get_device_name()}")
+            except:
+                pass
             self.image_gpu = cp.asarray(image_3d)
             try:
                 self.model = cuRandomForestClassifier(

nettracer3d/smart_dilate.py

@@ -23,7 +23,7 @@ def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
     Arguments are an array,  and the desired pixel dilation amounts in X, Y, Z."""
 
     if tiff_array.shape[0] == 1:
-        return dilate_2D(tiff_array, ((dilated_x - 1) / 2))
+        return nettracer.dilate_2D(tiff_array, ((dilated_x - 1) / 2))
 
     if dilated_x == 3 and dilated_y == 3  and dilated_z == 3:
 

{nettracer3d-0.5.0.dist-info → nettracer3d-0.5.2.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.5.0
+Version: 0.5.2
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
-Author-email: Liam McLaughlin <boom2449@gmail.com>
-Project-URL: User_Manual, https://drive.google.com/drive/folders/1fTkz3n4LN9_VxKRKC8lVQSlrz_wq0bVn?usp=drive_link
+Author-email: Liam McLaughlin <mclaughlinliam99@gmail.com>
+Project-URL: User_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
 Project-URL: Reference_Citation_For_Use, https://doi.org/10.1101/2024.07.29.605633
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: Other/Proprietary License
@@ -36,8 +36,8 @@ Requires-Dist: cupy; extra == "cupy"
 NetTracer3D is a python package developed for both 2D and 3D analysis of microscopic images in the .tif file format. It supports generation of 3D networks showing the relationships between objects (or nodes) in three dimensional space, either based on their own proximity or connectivity via connecting objects such as nerves or blood vessels. In addition to these functionalities are several advanced 3D data processing algorithms, such as labeling of branched structures or abstraction of branched structures into networks. Note that nettracer3d uses segmented data, which can be segmented from other softwares such as ImageJ and imported into NetTracer3D, although it does offer its own segmentation via intensity and volumetric thresholding, or random forest machine learning segmentation. NetTracer3D currently has a fully functional GUI. To use the GUI, after installing the nettracer3d package via pip, enter the command 'nettracer3d' in your command prompt:
 
 
-This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays. More advanced documentation (especially for the GUI) is coming down the line, but for now please see: https://drive.google.com/drive/folders/1fTkz3n4LN9_VxKRKC8lVQSlrz_wq0bVn?usp=drive_link
-for a user manual that provides older documentation.
+This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays. More advanced documentation is coming down the line, but for now please see: https://www.youtube.com/watch?v=cRatn5VTWDY
+for a video tutorial on using the GUI.
 
 NetTracer3D is free to use/fork for academic/nonprofit use so long as citation is provided, and is available for commercial use at a fee (see license file for information).
 

{nettracer3d-0.5.0.dist-info → nettracer3d-0.5.2.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=CsRWB0DY-vBBlKdF9IQwgfYYZswuE7n1Iu_Osxgmxnw,13042
 nettracer3d/nettracer.py,sha256=hDccGy6RybSJFvY6dsN1l5eM3wKZW93CizlTvgEeyNs,209690
-nettracer3d/nettracer_gui.py,sha256=Owg9ZmRqP8fZRvZpAd5T0VpwYyYc40RfVRtRiN9XnKI,339971
+nettracer3d/nettracer_gui.py,sha256=dQUhNeeVQCkuXrvtdUmqSs184Gr8Y-neoWPWcXhGaAo,340385
 nettracer3d/network_analysis.py,sha256=MJBBjslA1k_R8ymid77U-qGSgzxFVfzGVQhE0IdhnbE,48046
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
-nettracer3d/node_draw.py,sha256=BMiD_FrlOHeGD4AQZ_Emd152PfxFuMgGf2x4S0TOTnw,9752
+nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
 nettracer3d/proximity.py,sha256=B1pmFegx5Wb0JKI5rvpILv2VRU09f6M2iljAQAqBja0,11059
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
-nettracer3d/segmenter.py,sha256=EUH7KEiYhET_D6j0T-wKqZaohcvIGYYIEwUU2Dzl51Q,29502
+nettracer3d/segmenter.py,sha256=Rr5MUUWgGHYzzTy4hzbO3zzJhNIKsyjV1Qxg99Pb8QY,29686
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
-nettracer3d/smart_dilate.py,sha256=dvbG2UhWzMQrtDqSj281rixNRgwUHOFGlJZ9RSl6rKs,24590
-nettracer3d-0.5.0.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.5.0.dist-info/METADATA,sha256=UoZAyKclOEgiSTlefWVpC8WVD1YMsm6Zjt7R9bdLufw,3029
-nettracer3d-0.5.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nettracer3d-0.5.0.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.5.0.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.5.0.dist-info/RECORD,,
+nettracer3d/smart_dilate.py,sha256=Kekm6YIVlJniMvJMG6_AwwNmCqK2l4Qtvg9VzzqPKMw,24600
+nettracer3d-0.5.2.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.5.2.dist-info/METADATA,sha256=M7khbzBNHwsNJ2KqmNKwnP1rvk1v37E6BI7dD9mQU58,2912
+nettracer3d-0.5.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nettracer3d-0.5.2.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.5.2.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.5.2.dist-info/RECORD,,