nettracer3d 0.7.1__tar.gz → 0.7.3__tar.gz

{nettracer3d-0.7.1/src/nettracer3d.egg-info → nettracer3d-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.1
+Version: 0.7.3
 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/
@@ -73,14 +73,9 @@ 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 0.7.0 Updates -- 
+-- Version 0.7.2 Updates -- 
 
-1. Added new function in 'Analyze -> Stats -> Cluster Analysis'
-    * This function allows the user to create a ripley's K or H function to compare the relative clustering of two types of nodes, or of one type of node vs itself.
-
-2. Added new function in 'Analyze -> Randomize -> Scramble Nodes'
-    * This function randomly rearranges the node (centroids) for comparison with other centroid-using methods, as a possible way to demonstrate non-random behavior.
-    * The randomize menu is likewise new and the 'Generate Equivalent Random Network' method was moved there.
-
-3. Bug fixes.
-    * Importantly fixed a bug with dt-based dilation not working in 2D, which I had accidentally introduced recently.
+    * Added new option to the modify network qualities menu to remove node centroids with unassigned id values.
+    * Bug fixes, mainly:
+        * Had to fix a bug with the ripley's function that was making it always evaluate nodes of one id against themselves even when a seperate id was specified.
+        * Fixed some bugs when processing 2D images.

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/README.md

@@ -34,14 +34,9 @@ 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 0.7.0 Updates -- 
+-- Version 0.7.2 Updates -- 
 
-1. Added new function in 'Analyze -> Stats -> Cluster Analysis'
-    * This function allows the user to create a ripley's K or H function to compare the relative clustering of two types of nodes, or of one type of node vs itself.
-
-2. Added new function in 'Analyze -> Randomize -> Scramble Nodes'
-    * This function randomly rearranges the node (centroids) for comparison with other centroid-using methods, as a possible way to demonstrate non-random behavior.
-    * The randomize menu is likewise new and the 'Generate Equivalent Random Network' method was moved there.
-
-3. Bug fixes.
-    * Importantly fixed a bug with dt-based dilation not working in 2D, which I had accidentally introduced recently.
+    * Added new option to the modify network qualities menu to remove node centroids with unassigned id values.
+    * Bug fixes, mainly:
+        * Had to fix a bug with the ripley's function that was making it always evaluate nodes of one id against themselves even when a seperate id was specified.
+        * Fixed some bugs when processing 2D images.

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.7.1"
+version = "0.7.3"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/src/nettracer3d/morphology.py

@@ -518,7 +518,7 @@ def compute_distance_transform_distance_GPU(nodes, sampling = [1,1,1]):
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = cp.squeeze(nodes)  # Convert to 2D for processing
-        del sampling[0]
+        sampling = [sampling[1], sampling[2]]
     
     # Compute the distance transform on the GPU
     distance = cpx.distance_transform_edt(nodes, sampling = sampling)
@@ -534,7 +534,7 @@ def compute_distance_transform_distance(nodes, sampling = [1,1,1]):
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
-        del sampling[0]
+        sampling = [sampling[1], sampling[2]]
 
     # Fallback to CPU if there's an issue with GPU computation
     distance = ndimage.distance_transform_edt(nodes, sampling = sampling)

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/src/nettracer3d/nettracer.py

@@ -3948,6 +3948,19 @@ class Network_3D:
         except:
             print("Could not update voxel scaling")
 
+
+
+    def remove_ids(self):
+
+        new_centroids = {}
+
+        for node in self.node_identities.keys():
+            new_centroids[node] = self.node_centroids[node]
+
+        self.node_centroids = new_centroids
+
+
+
     def remove_trunk_post(self):
         """
         Removes the 'edge' trunk from a network. In this case, the trunk is the edge that creates the most node-node connections. There may be times when many nodes are connected by a single, expansive edge that obfuscates the rest of the edges. Removing the trunk to a node can better reveal these edges.
@@ -4444,11 +4457,11 @@ class Network_3D:
             for node, nodeid in self.node_identities.items(): #Otherwise we need to pull out this info
                 if nodeid == root:
                     roots.append(self._node_centroids[node])
-                elif nodeid == targ:
+                if nodeid == targ:
                     targs.append(self._node_centroids[node])
-        
+
         rooties = proximity.convert_centroids_to_array(roots, xy_scale = self.xy_scale, z_scale = self.z_scale)
-        targs = proximity.convert_centroids_to_array(roots, xy_scale = self.xy_scale, z_scale = self.z_scale)
+        targs = proximity.convert_centroids_to_array(targs, xy_scale = self.xy_scale, z_scale = self.z_scale)
         points_array = np.vstack((rooties, targs))
         del rooties
 

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/src/nettracer3d/nettracer_gui.py

@@ -2384,7 +2384,10 @@ class ImageViewerWindow(QMainWindow):
 
 
             if self.selection_rect is not None:
-                self.selection_rect.remove()
+                try:
+                    self.selection_rect.remove()
+                except:
+                    pass
                 self.selection_rect = None
                 self.canvas.draw()
 
@@ -2793,6 +2796,21 @@ class ImageViewerWindow(QMainWindow):
         show3d_action = image_menu.addAction("Show 3D (Napari)")
         show3d_action.triggered.connect(self.show3d_dialog)
 
+        # Help
+
+        help_button = menubar.addAction("Help")
+        help_button.triggered.connect(self.help_me)
+
+    def help_me(self):
+
+        import webbrowser
+        try:
+            webbrowser.open('https://nettracer3d.readthedocs.io/en/latest/')
+            return True
+        except Exception as e:
+            print(f"Error opening URL: {e}")
+            return False
+
 
     def stats(self):
         """Method to get and display the network stats"""
@@ -3526,13 +3544,12 @@ class ImageViewerWindow(QMainWindow):
                 except Exception as e:
                     QMessageBox.critical(self, "Error", f"Error loading image: {str(e)}")
 
-
-                if len(self.channel_data[channel_index].shape) == 2:  # handle 2d data
-                    self.channel_data[channel_index] = np.expand_dims(self.channel_data[channel_index], axis=0)
-
             else:
                 self.channel_data[channel_index] = channel_data
 
+            if len(self.channel_data[channel_index].shape) == 2:  # handle 2d data
+                self.channel_data[channel_index] = np.expand_dims(self.channel_data[channel_index], axis=0)
+
             try:
                 if len(self.channel_data[channel_index].shape) == 3:  # potentially 2D RGB
                     if self.channel_data[channel_index].shape[-1] in (3, 4):  # last dim is 3 or 4
@@ -3673,8 +3690,8 @@ class ImageViewerWindow(QMainWindow):
             # Update corresponding network property
             if channel_index == 0:
                 my_network.nodes = None
-                my_network.node_centroids = None
-                my_network.node_identities = None
+                #my_network.node_centroids = None
+                #my_network.node_identities = None
             elif channel_index == 1:
                 my_network.edges = None
                 my_network.edge_centroids = None
@@ -6181,7 +6198,6 @@ class RandNodeDialog(QDialog):
             if mode == 0 and not (my_network.nodes is None and my_network.edges is None and my_network.network_overlay is None and my_network.id_overlay is None):
                 pass
             elif mode == 1 or (my_network.nodes is None and my_network.edges is None and my_network.network_overlay is None and my_network.id_overlay is None):
-                print("HELLO")
                 # Convert string labels to integers if necessary
                 if any(isinstance(k, str) for k in my_network.node_centroids.keys()):
                     label_map = {label: idx for idx, label in enumerate(my_network.node_centroids.keys())}
@@ -9528,6 +9544,11 @@ class ModifyDialog(QDialog):
         self.setWindowTitle("Modify Network Qualities")
         self.setModal(True)
         layout = QFormLayout(self)
+
+        self.revid = QPushButton("Remove Unassigned")
+        self.revid.setCheckable(True)
+        self.revid.setChecked(False)
+        layout.addRow("Remove Unassigned IDs from Centroid List?:", self.revid)
         
         # trunk checkbox (default false)
         self.trunk = QPushButton("Remove Trunk")
@@ -9595,6 +9616,7 @@ class ModifyDialog(QDialog):
 
         try:
 
+            revid = self.revid.isChecked()
             trunk = self.trunk.isChecked()
             if not trunk:
                 trunknode = self.trunknode.isChecked()
@@ -9610,6 +9632,15 @@ class ModifyDialog(QDialog):
             if isolate and my_network.node_identities is not None:
                 self.show_isolate_dialog()
 
+            if revid:
+                try:
+                    my_network.remove_ids()
+                    self.parent().format_for_upperright_table(my_network.node_centroids, 'NodeID', ['Z', 'Y', 'X'], 'Node Centroids')
+                except:
+                    pass
+
+
+
             if edgeweight:
                 my_network.remove_edge_weights()
             if prune and my_network.node_identities is not None:

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/src/nettracer3d/proximity.py

@@ -428,7 +428,7 @@ def optimized_ripleys_k(reference_points, subset_points, r_values, bounds=None,
     """
     n_ref = len(reference_points)
     n_subset = len(subset_points)
-    
+
     # Determine bounds if not provided
     if bounds is None:
         min_coords = np.min(reference_points, axis=0)

{nettracer3d-0.7.1 → nettracer3d-0.7.3}/src/nettracer3d/smart_dilate.py

@@ -165,7 +165,7 @@ def dilate_3D_old(tiff_array, dilated_x=3, dilated_y=3, dilated_z=3):
     # Handle special case for 2D arrays
     if tiff_array.shape[0] == 1:
         # Call 2D dilation function if needed
-        return dilate_2D(tiff_array, 1)  # For a 3x3 kernel, radius is 1
+        return nettracer.dilate_2D(tiff_array, 1)  # For a 3x3 kernel, radius is 1
     
     # Create a simple 3x3x3 cubic kernel (all ones)
     kernel = np.ones((3, 3, 3), dtype=bool)
@@ -471,7 +471,7 @@ def compute_distance_transform_GPU(nodes, return_dists = False, sampling = [1, 1
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
-        del sampling[0]
+        sampling = [sampling[1], sampling[2]]
     
     # Convert numpy array to CuPy array
     nodes_cp = cp.asarray(nodes)
@@ -504,7 +504,7 @@ def compute_distance_transform(nodes, return_dists = False, sampling = [1, 1, 1]
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
-        del sampling[0]
+        sampling = [sampling[1], sampling[2]]
 
     dists, nearest_label_indices = distance_transform_edt(nodes, return_indices=True, sampling = sampling)
 
@@ -531,7 +531,7 @@ def compute_distance_transform_distance_GPU(nodes, sampling = [1, 1, 1]):
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
-        del sampling[0]
+        sampling = [sampling[1], sampling[2]]
 
     # Convert numpy array to CuPy array
     nodes_cp = cp.asarray(nodes)
@@ -553,7 +553,7 @@ def compute_distance_transform_distance(nodes, sampling = [1, 1, 1]):
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
-        del sampling[0]
+        sampling = [sampling[1], sampling[2]]
 
     # Fallback to CPU if there's an issue with GPU computation
     distance = distance_transform_edt(nodes, sampling = sampling)

{nettracer3d-0.7.1 → nettracer3d-0.7.3/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.1
+Version: 0.7.3
 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/
@@ -73,14 +73,9 @@ 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 0.7.0 Updates -- 
+-- Version 0.7.2 Updates -- 
 
-1. Added new function in 'Analyze -> Stats -> Cluster Analysis'
-    * This function allows the user to create a ripley's K or H function to compare the relative clustering of two types of nodes, or of one type of node vs itself.
-
-2. Added new function in 'Analyze -> Randomize -> Scramble Nodes'
-    * This function randomly rearranges the node (centroids) for comparison with other centroid-using methods, as a possible way to demonstrate non-random behavior.
-    * The randomize menu is likewise new and the 'Generate Equivalent Random Network' method was moved there.
-
-3. Bug fixes.
-    * Importantly fixed a bug with dt-based dilation not working in 2D, which I had accidentally introduced recently.
+    * Added new option to the modify network qualities menu to remove node centroids with unassigned id values.
+    * Bug fixes, mainly:
+        * Had to fix a bug with the ripley's function that was making it always evaluate nodes of one id against themselves even when a seperate id was specified.
+        * Fixed some bugs when processing 2D images.