nettracer3d 0.7.4__py3-none-any.whl → 0.7.6__py3-none-any.whl

nettracer3d/network_analysis.py

@@ -4,7 +4,6 @@ import json
 import tifffile
 import numpy as np
 from networkx.algorithms import community
-from community import community_louvain
 from scipy.ndimage import zoom
 from scipy import ndimage
 from . import node_draw
@@ -239,183 +238,6 @@ def weighted_network(excel_file_path):
 
     return G, edge_weights
 
-def community_partition_simple(nodes, network, centroids = None, down_factor = None, color_code = False, directory = None):
-
-    G = network
-
-    communities = list(nx.community.label_propagation_communities(G))
-    partition = {}
-    for i, community in enumerate(communities):
-        for node in community:
-            partition[node] = i + 1
-    print(partition)
-
-
-    print("Generating excel notebook containing community of each node...")
-    if type(nodes) == str:
-        nodes = tifffile.imread(nodes)
-
-        if len(np.unique(nodes)) < 3:
-        
-            structure_3d = np.ones((3, 3, 3), dtype=int)
-            nodes, num_nodes = ndimage.label(nodes, structure=structure_3d)
-
-    # Convert dictionary to DataFrame with keys as index and values as a column
-    df = pd.DataFrame.from_dict(partition, orient='index', columns=['CommunityID'])
-
-    # Rename the index to 'Node ID'
-    df.index.name = 'Node ID'
-
-    if directory is None:
-
-        # Save DataFrame to Excel file
-        df.to_excel('communities.xlsx', engine='openpyxl')
-        print("Community info saved to communities.xls")
-    else:
-        df.to_excel(f'{directory}/communities.xlsx', engine='openpyxl')
-        print(f"Community info saved to {directory}/communities.xls")
-
-
-    print("Drawing overlay containing community labels for each node...")
-
-    if centroids is None:
-        centroids = _find_centroids(nodes, down_factor = down_factor)
-
-    labels = node_draw.degree_draw(partition, centroids, nodes)
-
-    if directory is None:
-        tifffile.imwrite("community_labels.tif", labels)
-        print("Community labels saved to community_labels.tif")
-    else:
-        tifffile.imwrite(f"{directory}/community_labels.tif", labels)
-        print(f"Community labels saved to {directory}/community_labels.tif")
-
-    print("Drawing overlay containing grayscale community labels for each node...")
-
-    masks = node_draw.degree_infect(partition, nodes)
-
-    if color_code:
-        print("And drawing color coded community labels...")
-        colored_masks = _color_code(masks)
-
-        if directory is None:
-
-            tifffile.imwrite("community_labels_colorcoded.tif", colored_masks)
-            print("Color coded communities saved to community_labels_colorcoded.tif")
-
-        else:
-            tifffile.imwrite(f"{directory}/community_labels_colorcoded.tif", colored_masks)
-            print(f"Color coded communities saved to {directory}/community_labels_colorcoded.tif")
-
-
-    if directory is None:
-
-        tifffile.imwrite("community_labels_grayscale.tif", masks)
-        print("Grayscale labeled communities saved to community_labels_grayscale.tif")
-
-    else:
-        tifffile.imwrite(f"{directory}/community_labels_grayscale.tif", masks)
-        print(f"Grayscale labeled communities saved to {directory}/community_labels_grayscale.tif")
-
-    return partition 
-
-
-def community_partition(nodes, network, centroids = None, down_factor = None, color_code = False, directory = None):
-
-    G, edge_weights = weighted_network(network)
-
-    G = nx.Graph()
-
-    # Find the maximum and minimum edge weights
-    max_weight = max(weight for edge, weight in edge_weights.items())
-    min_weight = min(weight for edge, weight in edge_weights.items())
-
-    if max_weight > 1:
-        # Normalize edge weights to the range [0.1, 1.0]
-        normalized_weights = {edge: 0.1 + 0.9 * ((weight - min_weight) / (max_weight - min_weight)) for edge, weight in edge_weights.items()}
-    else:
-        normalized_weights = {edge: 0.1 for edge, weight in edge_weights.items()}
-
-    # Add edges to the graph with normalized weights
-    for edge, normalized_weight in normalized_weights.items():
-        G.add_edge(edge[0], edge[1], weight=normalized_weight)
-
-    # Perform Louvain community detection
-    partition = community_louvain.best_partition(G)
-
-    for key in partition.keys():
-       partition[key] = partition[key] + 1 
-
-
-    print("Generating excel notebook containing community of each node...")
-    if type(nodes) == str:
-        nodes = tifffile.imread(nodes)
-
-        if len(np.unique(nodes)) < 3:
-        
-            structure_3d = np.ones((3, 3, 3), dtype=int)
-            nodes, num_nodes = ndimage.label(nodes, structure=structure_3d)
-
-    # Convert dictionary to DataFrame with keys as index and values as a column
-    df = pd.DataFrame.from_dict(partition, orient='index', columns=['CommunityID'])
-
-    # Rename the index to 'Node ID'
-    df.index.name = 'Node ID'
-
-    if directory is None:
-
-        # Save DataFrame to Excel file
-        df.to_excel('communities.xlsx', engine='openpyxl')
-        print("Community info saved to communities.xls")
-    else:
-        df.to_excel(f'{directory}/communities.xlsx', engine='openpyxl')
-        print(f"Community info saved to {directory}/communities.xls")
-
-
-    print("Drawing overlay containing community labels for each node...")
-
-    if centroids is None:
-        centroids = _find_centroids(nodes, down_factor = down_factor)
-
-    labels = node_draw.degree_draw(partition, centroids, nodes)
-
-    if directory is None:
-        tifffile.imwrite("community_labels.tif", labels)
-        print("Community labels saved to community_labels.tif")
-    else:
-        tifffile.imwrite(f"{directory}/community_labels.tif", labels)
-        print(f"Community labels saved to {directory}/community_labels.tif")
-
-    print("Drawing overlay containing grayscale community labels for each node...")
-
-    masks = node_draw.degree_infect(partition, nodes)
-
-    if color_code:
-        print("And drawing color coded community labels...")
-        colored_masks = _color_code(masks)
-
-        if directory is None:
-
-            tifffile.imwrite("community_labels_colorcoded.tif", colored_masks)
-            print("Color coded communities saved to community_labels_colorcoded.tif")
-
-        else:
-            tifffile.imwrite(f"{directory}/community_labels_colorcoded.tif", colored_masks)
-            print(f"Color coded communities saved to {directory}/community_labels_colorcoded.tif")
-
-
-    if directory is None:
-
-        tifffile.imwrite("community_labels_grayscale.tif", masks)
-        print("Grayscale labeled communities saved to community_labels_grayscale.tif")
-
-    else:
-        tifffile.imwrite(f"{directory}/community_labels_grayscale.tif", masks)
-        print(f"Grayscale labeled communities saved to {directory}/community_labels_grayscale.tif")
-
-    return partition
-
-
 
 def _color_code(grayscale_image):
     """Color code a grayscale array. Currently expects linearly ascending grayscale labels, will crash if there are gaps. (Main use case is grayscale anyway)"""

nettracer3d/segmenter.py

@@ -1188,24 +1188,12 @@ class InteractiveSegmenter:
 
         if self.current_speed != speed:
             self.feature_cache = None
-            if use_gpu:
-                try:
-                    self.model = cuRandomForestClassifier(
-                        n_estimators=100,
-                        max_depth=None
-                    )
-                except:
-                    self.model = RandomForestClassifier(
-                        n_estimators=100,
-                        n_jobs=-1,
-                        max_depth=None
-                    )
-            else:
-                self.model = RandomForestClassifier(
-                    n_estimators=100,
-                    n_jobs=-1,
-                    max_depth=None
-                )
+
+            self.model = RandomForestClassifier(
+                n_estimators=100,
+                n_jobs=-1,
+                max_depth=None
+            )
 
 
         if use_two:
@@ -1272,7 +1260,7 @@ class InteractiveSegmenter:
                         background_features.append(feature_vector)
 
 
-        elif mem_lock: #Forces ram efficiency
+        else: #Forces ram efficiency
 
             box_size = self.master_chunk
 
@@ -1348,32 +1336,6 @@ class InteractiveSegmenter:
                 for local_z, local_y, local_x in local_back_coords:
                     feature = subarray_features[local_z, local_y, local_x]
                     background_features.append(feature)
-
-        else:
-
-            self.two_slices = []
-
-            if self.use_two: #Clarifies if we need to redo feature cache for 3D
-
-                self.feature_cache = None
-                self.use_two = False
-
-            if self.feature_cache is None:
-                with self.lock:
-                    if self.feature_cache is None and speed:
-                        if use_gpu:
-                            self.feature_cache = self.compute_feature_maps()
-                        else:
-                            self.feature_cache = self.compute_feature_maps_cpu()
-
-                    elif self.feature_cache is None and not speed:
-                        if use_gpu:
-
-                            self.feature_cache = self.compute_deep_feature_maps()
-                        else:
-                            self.feature_cache = self.compute_deep_feature_maps_cpu()
-
-
             try:
                 # Get foreground coordinates and features
                 z_fore, y_fore, x_fore = np.where(foreground_array == 1)
@@ -1485,20 +1447,11 @@ class InteractiveSegmenter:
         if self._currently_segmenting is not None:
             return
 
-        #with self.lock <- cant remember why this was here
         if speed:
-
-            if self.mem_lock:
-                output = self.compute_feature_maps_cpu_2d_parallel(z = z)
-            else:
-                output = self.compute_feature_maps_cpu_2d(z = z)
+            output = self.compute_feature_maps_cpu_2d_parallel(z = z)
 
         elif not speed:
-
-            if self.mem_lock:
-                output = self.compute_deep_feature_maps_cpu_2d_parallel(z = z)
-            else:
-                output = self.compute_deep_feature_maps_cpu_2d(z = z)
+            output = self.compute_deep_feature_maps_cpu_2d_parallel(z = z)
 
         return output