nettracer3d 0.2.8__tar.gz → 0.3.0__tar.gz

{nettracer3d-0.2.8/src/nettracer3d.egg-info → nettracer3d-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.2.8
+Version: 0.3.0
 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

{nettracer3d-0.2.8 → nettracer3d-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.2.8"
+version = "0.3.0"
 authors = [
   { name="Liam McLaughlin", email="boom2449@gmail.com" },
 ]

{nettracer3d-0.2.8 → nettracer3d-0.3.0}/src/nettracer3d/nettracer.py

@@ -322,15 +322,25 @@ def create_and_save_dataframe(pairwise_connections, excel_filename = None):
         df = pd.concat([df, temp_df], axis=1)
 
     if excel_filename is not None:
-
-        try:
+        # Remove file extension if present to use as base path
+        base_path = excel_filename.rsplit('.', 1)[0]
         
-            # Save the DataFrame to an Excel file
-            df.to_excel(excel_filename, index=False)
-            print(f"Network file saved to {excel_filename}")
-
+        # First try to save as CSV
+        try:
+            csv_path = f"{base_path}.csv"
+            df.to_csv(csv_path, index=False)
+            print(f"Network file saved to {csv_path}")
+            return
         except Exception as e:
-            print(f"Unable to write network file to disk... please make sure that {excel_filename} is being saved to a valid directory and try again")
+            print(f"Could not save as CSV: {str(e)}")
+            
+            # If CSV fails, try to save as Excel
+            try:
+                xlsx_path = f"{base_path}.xlsx"
+                df.to_excel(xlsx_path, index=False)
+                print(f"Network file saved to {xlsx_path}")
+            except Exception as e:
+                print(f"Unable to write network file to disk... please make sure that {base_path}.xlsx is being saved to a valid directory and try again")
 
     else:
         return df
@@ -686,29 +696,35 @@ def fill_holes_3d(array):
 
     array = binarize(array)
     inv_array = invert_array(array)
+
     
     # Create arrays for all three planes
     array_xy = np.zeros_like(inv_array, dtype=np.uint8)
     array_xz = np.zeros_like(inv_array, dtype=np.uint8)
     array_yz = np.zeros_like(inv_array, dtype=np.uint8)
-    
+
+
     # Process XY plane
     for z in range(inv_array.shape[0]):
         array_xy[z] = process_slice(inv_array[z])
+
+    if array.shape[0] > 3: #only use these dimensions for sufficiently large zstacks
         
-    # Process XZ plane    
-    for y in range(inv_array.shape[1]):
-        slice_xz = inv_array[:, y, :]
-        array_xz[:, y, :] = process_slice(slice_xz)
+        # Process XZ plane    
+        for y in range(inv_array.shape[1]):
+            slice_xz = inv_array[:, y, :]
+            array_xz[:, y, :] = process_slice(slice_xz)
+            
+        # Process YZ plane
+        for x in range(inv_array.shape[2]):
+            slice_yz = inv_array[:, :, x]
+            array_yz[:, :, x] = process_slice(slice_yz)
         
-    # Process YZ plane
-    for x in range(inv_array.shape[2]):
-        slice_yz = inv_array[:, :, x]
-        array_yz[:, :, x] = process_slice(slice_yz)
-    
-    # Combine results from all three planes
-    filled = (array_xy | array_xz | array_yz) * 255
-    return array + filled
+        # Combine results from all three planes
+        filled = (array_xy | array_xz | array_yz) * 255
+        return array + filled
+    else:
+        return array_xy * 255
 
 
 
@@ -2425,7 +2441,7 @@ class Network_3D:
 
 
         if filename is None:
-            filename = "drawn_network.tif"
+            filename = "overlay_1.tif"
         elif not filename.endswith(('.tif', '.tiff')):
             filename += '.tif'
 
@@ -2441,7 +2457,7 @@ class Network_3D:
     def save_id_overlay(self, directory = None, filename = None):
 
         if filename is None:
-            filename = "labelled_node_indices.tif"
+            filename = "overlay_2.tif"
         if not filename.endswith(('.tif', '.tiff')):
             filename += '.tif'
 
@@ -2462,9 +2478,7 @@ class Network_3D:
         :param directory: (Optional - Val = None; String). The path to an intended directory to save the properties to.
         """
 
-
-        if directory is None:
-            directory = encapsulate(parent_dir = parent_dir, name = name)
+        directory = encapsulate(parent_dir = parent_dir, name = name)
 
         try:
             self.save_nodes(directory)
@@ -2725,7 +2739,7 @@ class Network_3D:
         items = directory_info(directory)
 
         for item in items:
-            if item == 'node_communities.xlsx':
+            if item == 'node_communities.xlsx' or item == 'node_communities.csv':
                 if directory is not None:
                     self._communities = network_analysis.read_excel_to_singval_dict(f'{directory}/{item}')
                     print("Succesfully loaded communities")
@@ -2777,7 +2791,7 @@ class Network_3D:
         items = directory_info(directory)
 
         for item in items:
-            if item == 'drawn_network.tif':
+            if item == 'overlay_1.tif':
                 if directory is not None:
                     self._network_overlay = tifffile.imread(f'{directory}/{item}')
                     print("Succesfully loaded network overlay")
@@ -2802,7 +2816,7 @@ class Network_3D:
         items = directory_info(directory)
 
         for item in items:
-            if item == 'labelled_node_indices.tif':
+            if item == 'overlay_2.tif':
                 if directory is not None:
                     self._id_overlay = tifffile.imread(f'{directory}/{item}')
                     print("Succesfully loaded id overlay")
@@ -2816,7 +2830,7 @@ class Network_3D:
         #print("Could not find id overlay. They must be in the specified directory and named 'labelled_node_indices.tif'")
 
 
-    def assemble(self, directory = None, node_path = None, edge_path = None, search_region_path = None, network_path = None, node_centroids_path = None, node_identities_path = None, edge_centroids_path = None, scaling_path = None, net_overlay_path = None, id_overlay_path = None):
+    def assemble(self, directory = None, node_path = None, edge_path = None, search_region_path = None, network_path = None, node_centroids_path = None, node_identities_path = None, edge_centroids_path = None, scaling_path = None, net_overlay_path = None, id_overlay_path = None, community_path = None ):
         """
         Can be called on a Network_3D object to load all properties simultaneously from a specified directory. It will look for files with the names specified in the property loading methods, in the active directory if none is specified.
         Alternatively, for each property a filepath to any file may be passed to look there to load. This method is intended to be used together with the dump method to easily save and load the Network_3D objects once they had been calculated. 
@@ -2840,6 +2854,7 @@ class Network_3D:
         self.load_node_identities(directory, node_identities_path)
         self.load_edge_centroids(directory, edge_centroids_path)
         self.load_scaling(directory, scaling_path)
+        self.load_communities(directory, community_path)
         self.load_network_overlay(directory, net_overlay_path)
         self.load_id_overlay(directory, id_overlay_path)
 
@@ -3132,8 +3147,7 @@ class Network_3D:
         """
 
 
-        if directory is None:
-            directory = encapsulate()
+        directory = encapsulate()
 
         self._xy_scale = xy_scale
         self._z_scale = z_scale

{nettracer3d-0.2.8 → nettracer3d-0.3.0}/src/nettracer3d/nettracer_gui.py

@@ -2402,6 +2402,13 @@ class ImageViewerWindow(QMainWindow):
                 except Exception as e:
                     print(f"Error loading node identity table: {e}")
 
+
+            if hasattr(my_network, 'communities') and my_network.communities is not None:
+                try:
+                    self.format_for_upperright_table(my_network.communities, 'NodeID', 'Community', 'Node Communities')
+                except Exception as e:
+                    print(f"Error loading node community table: {e}")
+
         except Exception as e:
             QMessageBox.critical(
                 self,
@@ -2456,6 +2463,57 @@ class ImageViewerWindow(QMainWindow):
             else:
                 btn.setStyleSheet("")
 
+    def reduce_rgb_dimension(self, array, method='first'):
+        """
+        Reduces a 4D array (Z, Y, X, C) to 3D (Z, Y, X) by dropping the color dimension
+        using the specified method.
+        
+        Parameters:
+        -----------
+        array : numpy.ndarray
+            4D array with shape (Z, Y, X, C) where C is the color channel dimension
+        method : str, optional
+            Method to use for reduction:
+            - 'first': takes the first color channel (default)
+            - 'mean': averages across color channels
+            - 'max': takes maximum value across color channels
+            - 'min': takes minimum value across color channels
+        
+        Returns:
+        --------
+        numpy.ndarray
+            3D array with shape (Z, Y, X)
+        
+        Raises:
+        -------
+        ValueError
+            If input array is not 4D or method is not recognized
+        """
+        if array.ndim != 4:
+            raise ValueError(f"Expected 4D array, got {array.ndim}D array")
+        
+        if method not in ['first', 'mean', 'max', 'min']:
+            raise ValueError(f"Unknown method: {method}")
+        
+        if method == 'first':
+            return array[..., 0]
+        elif method == 'mean':
+            return np.mean(array, axis=-1)
+        elif method == 'max':
+            return np.max(array, axis=-1)
+        else:  # min
+            return np.min(array, axis=-1)
+
+    def confirm_rgb_dialog(self):
+        """Shows a dialog asking user to confirm if image is 2D RGB"""
+        msg = QMessageBox()
+        msg.setIcon(QMessageBox.Icon.Question)
+        msg.setText("Image Format Detection")
+        msg.setInformativeText("Is this a 2D color (RGB/CMYK) image?")
+        msg.setWindowTitle("Confirm Image Format")
+        msg.setStandardButtons(QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No)
+        return msg.exec() == QMessageBox.StandardButton.Yes
+
     def load_channel(self, channel_index, channel_data=None, data=False, assign_shape = True):
         """Load a channel and enable active channel selection if needed."""
 
@@ -2469,14 +2527,22 @@ class ImageViewerWindow(QMainWindow):
                     "TIFF Files (*.tif *.tiff)"
                 )
                 self.channel_data[channel_index] = tifffile.imread(filename)
-                if len(self.channel_data[channel_index].shape) == 2:
-                    #self.channel_data[channel_index] = np.stack((self.channel_data[channel_index], self.channel_data[channel_index]), axis = 0) #currently handle 2d arrays by just making them 3d
+                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) == 3:  # potentially 2D RGB
+                if self.channel_data[channel_index].shape[-1] in (3, 4):  # last dim is 3 or 4
+                    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)
+                        
+            if len(self.channel_data[channel_index].shape) == 4 and (channel_index == 0 or channel_index == 1):
+                self.channel_data[channel_index] = self.reduce_rgb_dimension(self.channel_data[channel_index])
+
+
 
             if channel_index == 0:
                 my_network.nodes = self.channel_data[channel_index]

{nettracer3d-0.2.8 → nettracer3d-0.3.0}/src/nettracer3d/network_analysis.py

@@ -149,15 +149,14 @@ def read_excel_to_lists(file_path, sheet_name=0):
     for column_name, column_data in df.items():
         # Convert the column values to a list and append to the data_lists
         data_lists.append(column_data.tolist())
-
     master_list = [[], [], []]
     for i in range(0, len(data_lists), 3):
-        master_list[0].extend(data_lists[i])
-        master_list[1].extend(data_lists[i+1])
+        master_list[0].extend([int(x) for x in data_lists[i]])
+        master_list[1].extend([int(x) for x in data_lists[i+1]])
         try:
-            master_list[2].extend(data_lists[i+2])
+            master_list[2].extend([int(x) for x in data_lists[i+2]])
         except IndexError:
-            master_list[2].extend(0)
+            master_list[2].extend([0])  # Note: Changed to list with single int 0
             
     return master_list
 
@@ -576,34 +575,35 @@ def find_centroids(nodes, down_factor = None, network = None):
 
     return centroid_dict
 
-def _save_centroid_dictionary(centroid_dict, filepath = None, index = 'Node ID'):
+def _save_centroid_dictionary(centroid_dict, filepath=None, index='Node ID'):
     # Convert dictionary to DataFrame with keys as index and values as a column
-    #for item in centroid_dict:
-        #representative = centroid_dict[item]
-        #break
-
-    #if len(representative) == 3:
-        #df = pd.DataFrame.from_dict(centroid_dict, orient='index', columns=['Z', 'Y', 'X'])
-    #elif len(representative) == 2:
-        #df = pd.DataFrame.from_dict(centroid_dict, orient='index', columns=['Y', 'X'])
-
     df = pd.DataFrame.from_dict(centroid_dict, orient='index', columns=['Z', 'Y', 'X'])
-
-    # Rename the index to 'Node ID'
+    
+    # Rename the index to specified name
     df.index.name = index
-
+    
     if filepath is None:
-        try:
-            # Save DataFrame to Excel file
-            df.to_excel('centroids.xlsx', engine='openpyxl')
-        except Exception as e:
-            print("Could not save centroids to active directory")
+        base_path = 'centroids'
     else:
+        # Remove file extension if present to use as base path
+        base_path = filepath.rsplit('.', 1)[0]
+    
+    # First try to save as CSV
+    try:
+        csv_path = f"{base_path}.csv"
+        df.to_csv(csv_path)
+        print(f"Successfully saved centroids to {csv_path}")
+        return
+    except Exception as e:
+        print(f"Could not save centroids as CSV: {str(e)}")
+        
+        # If CSV fails, try to save as Excel
         try:
-            # Save DataFrame to Excel file
-            df.to_excel(filepath, engine='openpyxl')
+            xlsx_path = f"{base_path}.xlsx"
+            df.to_excel(xlsx_path, engine='openpyxl')
+            print(f"Successfully saved centroids to {xlsx_path}")
         except Exception as e:
-            print(f"Could not save centroids to {filepath}")
+            print(f"Could not save centroids as XLSX: {str(e)}")
 
 def _find_centroids_GPU(nodes, node_list=None, down_factor=None):
     """Internal use version to get centroids without saving"""
@@ -1229,15 +1229,31 @@ def edge_to_node(network, node_identities = None):
 
 
 def save_singval_dict(dict, index_name, valname, filename):
-
-    #index name goes on the left, valname on the right
+    # Convert dictionary to DataFrame
     df = pd.DataFrame.from_dict(dict, orient='index', columns=[valname])
-
-    # Rename the index to 'Node ID'
+    
+    # Rename the index
     df.index.name = index_name
-
-    # Save DataFrame to Excel file
-    df.to_excel(filename, engine='openpyxl')
+    
+    # Remove file extension if present to use as base path
+    base_path = filename.rsplit('.', 1)[0]
+    
+    # First try to save as CSV
+    try:
+        csv_path = f"{base_path}.csv"
+        df.to_csv(csv_path)
+        print(f"Successfully saved {valname} data to {csv_path}")
+        return
+    except Exception as e:
+        print(f"Could not save as CSV: {str(e)}")
+        
+        # If CSV fails, try to save as Excel
+        try:
+            xlsx_path = f"{base_path}.xlsx"
+            df.to_excel(xlsx_path, engine='openpyxl')
+            print(f"Successfully saved {valname} data to {xlsx_path}")
+        except Exception as e:
+            print(f"Could not save as XLSX: {str(e)}")
 
 
 def rand_net_weighted(num_rows, num_nodes, nodes):

{nettracer3d-0.2.8 → nettracer3d-0.3.0/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.2.8
+Version: 0.3.0
 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