nettracer3d 1.0.5__tar.gz → 1.0.7__tar.gz

{nettracer3d-1.0.5/src/nettracer3d.egg-info → nettracer3d-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.5
+Version: 1.0.7
 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 +110,7 @@ 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 1.0.7 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
+	* Added handling if the user tries to load in a multichannel 3dimensional image (note this will not detect if you have a multi-channel image of 2d planes, it will think those are 3d. For now those can be split up with other software, or you can use the crop function to just isolate the channel you want as if it were a z-plane).

{nettracer3d-1.0.5 → nettracer3d-1.0.7}/README.md

@@ -65,7 +65,7 @@ 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 1.0.7 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
+	* Added handling if the user tries to load in a multichannel 3dimensional image (note this will not detect if you have a multi-channel image of 2d planes, it will think those are 3d. For now those can be split up with other software, or you can use the crop function to just isolate the channel you want as if it were a z-plane).

{nettracer3d-1.0.5 → nettracer3d-1.0.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.0.5"
+version = "1.0.7"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-1.0.5 → nettracer3d-1.0.7}/src/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-1.0.5 → nettracer3d-1.0.7}/src/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
@@ -5061,6 +5060,10 @@ class ImageViewerWindow(QMainWindow):
             dialog = MergeNodeIdDialog(self)
             dialog.exec()
 
+    def show_multichan_dialog(self, data):
+        dialog = MultiChanDialog(self, data)
+        dialog.show()
+
     def show_gray_water_dialog(self):
         """Show the gray watershed parameter dialog."""
         dialog = GrayWaterDialog(self)
@@ -5163,7 +5166,7 @@ class ImageViewerWindow(QMainWindow):
 
             my_network.edges = (my_network.nodes == 0) * my_network.edges
 
-            my_network.calculate_all(my_network.nodes, my_network.edges, xy_scale = my_network.xy_scale, z_scale = my_network.z_scale, search = None, diledge = None, inners = False, hash_inners = False, remove_trunk = 0, ignore_search_region = True, other_nodes = None, label_nodes = True, directory = None, GPU = False, fast_dil = False, skeletonize = False, GPU_downsample = None)
+            my_network.calculate_all(my_network.nodes, my_network.edges, xy_scale = my_network.xy_scale, z_scale = my_network.z_scale, search = None, diledge = None, inners = False, remove_trunk = 0, ignore_search_region = True, other_nodes = None, label_nodes = True, directory = None, GPU = False, fast_dil = False, skeletonize = False, GPU_downsample = None)
 
             self.load_channel(1, my_network.edges, data = True)
             self.load_channel(0, my_network.nodes, data = True)
@@ -5917,6 +5920,16 @@ class ImageViewerWindow(QMainWindow):
         msg.setStandardButtons(QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
         return msg.exec() == QMessageBox.StandardButton.Yes
 
+    def confirm_multichan_dialog(self):
+        """Shows a dialog asking user to confirm if image is multichan"""
+        msg = QMessageBox()
+        msg.setIcon(QMessageBox.Icon.Question)
+        msg.setText("Image Format Alert")
+        msg.setInformativeText("Is this a Multi-Channel (4D) image?")
+        msg.setWindowTitle("Confirm Image Format")
+        msg.setStandardButtons(QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
+        return msg.exec() == QMessageBox.StandardButton.Yes
+
     def confirm_resize_dialog(self):
         """Shows a dialog asking user to resize image"""
         msg = QMessageBox()
@@ -6000,7 +6013,7 @@ class ImageViewerWindow(QMainWindow):
             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
-                        if not data and self.shape is None:
+                        if not data:
                             if self.confirm_rgb_dialog():
                                 # User confirmed it's 2D RGB, expand to 4D
                                 self.channel_data[channel_index] = np.expand_dims(self.channel_data[channel_index], axis=0)
@@ -6010,12 +6023,18 @@ class ImageViewerWindow(QMainWindow):
             except:
                 pass
 
-            if not color:
-                try:
-                    if len(self.channel_data[channel_index].shape) == 4 and (channel_index == 0 or channel_index == 1):
+            if len(self.channel_data[channel_index].shape) == 4:
+                if not self.channel_data[channel_index].shape[-1] in (3, 4):
+                    if self.confirm_multichan_dialog(): # User is trying to load 4D channel stack:
+                        my_data = copy.deepcopy(self.channel_data[channel_index])
+                        self.channel_data[channel_index] = None 
+                        self.show_multichan_dialog(data = my_data)
+                        return
+                elif not color and (channel_index == 0 or channel_index == 1):
+                    try:
                         self.channel_data[channel_index] = self.reduce_rgb_dimension(self.channel_data[channel_index], 'weight')
-                except:
-                    pass
+                    except:
+                        pass
 
             reset_resize = False
 
@@ -8432,6 +8451,89 @@ class MergeNodeIdDialog(QDialog):
             print(traceback.format_exc())
             #print(f"Error: {e}")
 
+class MultiChanDialog(QDialog):
+
+    def __init__(self, parent=None, data = None):
+
+        super().__init__(parent)
+        self.setWindowTitle("Channel Loading")
+        self.setModal(False)
+        
+        layout = QFormLayout(self)
+
+        self.data = data
+
+        self.nodes = QComboBox()
+        self.edges = QComboBox()
+        self.overlay1 = QComboBox()
+        self.overlay2 = QComboBox()
+        options = ["None"]
+        for i in range(self.data.shape[0]):
+            options.append(str(i))
+        self.nodes.addItems(options)
+        self.edges.addItems(options)
+        self.overlay1.addItems(options)
+        self.overlay2.addItems(options)
+        self.nodes.setCurrentIndex(0)
+        self.edges.setCurrentIndex(0)
+        self.overlay1.setCurrentIndex(0)
+        self.overlay2.setCurrentIndex(0)
+        layout.addRow("Load this channel into nodes?", self.nodes)
+        layout.addRow("Load this channel into edges?", self.edges)
+        layout.addRow("Load this channel into overlay1?", self.overlay1)
+        layout.addRow("Load this channel into overlay2?", self.overlay2)
+
+        run_button = QPushButton("Load Channels")
+        run_button.clicked.connect(self.run)
+        layout.addWidget(run_button)
+
+        run_button2 = QPushButton("Save Channels to Directory")
+        run_button2.clicked.connect(self.run2)
+        layout.addWidget(run_button2)
+
+
+    def run(self):
+
+        try:
+            node_chan = int(self.nodes.currentText())
+            self.parent().load_channel(0, self.data[node_chan, :, :, :], data = True)
+        except:
+            pass
+        try:
+            edge_chan = int(self.edges.currentText())
+            self.parent().load_channel(1, self.data[edge_chan, :, :, :], data = True)
+        except:
+            pass
+        try:
+            overlay1_chan = int(self.overlay1.currentText())
+            self.parent().load_channel(2, self.data[overlay1_chan, :, :, :], data = True)
+        except:
+            pass
+        try:
+            overlay2_chan = int(self.overlay2.currentText())
+            self.parent().load_channel(3, self.data[overlay2_chan, :, :, :], data = True)
+        except:
+            pass
+
+    def run2(self):
+
+        try:
+            # First let user select parent directory
+            parent_dir = QFileDialog.getExistingDirectory(
+                self,
+                "Select Location to Save Channels",
+                "",
+                QFileDialog.Option.ShowDirsOnly
+            )
+
+            for i in range(self.data.shape[0]):
+                try:
+                    tifffile.imwrite(f'{parent_dir}/C{i}.tif', self.data[i, :, :, :])
+                except:
+                    continue
+        except:
+            pass
+
 
 class Show3dDialog(QDialog):
     def __init__(self, parent=None):
@@ -10192,38 +10294,44 @@ 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-1.0.5 → nettracer3d-1.0.7/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.5
+Version: 1.0.7
 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 +110,7 @@ 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 1.0.7 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
+	* Added handling if the user tries to load in a multichannel 3dimensional image (note this will not detect if you have a multi-channel image of 2d planes, it will think those are 3d. For now those can be split up with other software, or you can use the crop function to just isolate the channel you want as if it were a z-plane).