nettracer3d 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

nettracer3d/smart_dilate.py

@@ -447,11 +447,11 @@ def compute_distance_transform(nodes):
 
     if is_pseudo_3d:
         # For 2D input, we get (2, H, W) but need (3, 1, H, W)
-        H, W = nearest_label_indices_np[0].shape
-        indices_4d = np.zeros((3, 1, H, W), dtype=nearest_label_indices_np.dtype)
-        indices_4d[1:, 0] = nearest_label_indices_np  # Copy Y and X coordinates
+        H, W = nearest_label_indices[0].shape
+        indices_4d = np.zeros((3, 1, H, W), dtype=nearest_label_indices.dtype)
+        indices_4d[1:, 0] = nearest_label_indices  # Copy Y and X coordinates
         # indices_4d[0] stays 0 for all Z coordinates
-        nearest_label_indices_np = indices_4d
+        nearest_label_indices = indices_4d
 
     return nearest_label_indices
 

{nettracer3d-0.6.0.dist-info → nettracer3d-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.6.0
+Version: 0.6.2
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <mclaughlinliam99@gmail.com>
 Project-URL: User_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
@@ -44,6 +44,8 @@ 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 0.6.0 updates --
+-- Version 0.6.2 updates --
 
-1. Bug fixes
+1. Fixed bug with performing 2D distance transforms on CPU
+
+2. Updated ram_lock mode in the segmenter to use smaller chunks and garbage collect better.

{nettracer3d-0.6.0.dist-info → nettracer3d-0.6.2.dist-info}/RECORD

@@ -1,21 +1,20 @@
 nettracer3d/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nettracer3d/community_extractor.py,sha256=Zq8ZM595CTzeR6zLEZ4I6KvhkNfCPUReWvAKxTlaVfk,33495
-nettracer3d/hub_getter.py,sha256=KiNtxdajLkwB1ftslvrh1FE1Ch9ZCFEmHSEEotwR-To,8298
 nettracer3d/modularity.py,sha256=V1f3s_vGd8EuVz27mzq6ycIGr0BWIpH7c7NU4QjgAHU,30247
 nettracer3d/morphology.py,sha256=yQ0GuieMVXOQpaohZlPnkEXEuCUjf8Fg352axyK8nbM,10755
-nettracer3d/nettracer.py,sha256=OE95IH1TfAZvT-htv1LEhw1EpnnEpkA83R5EcGMQDQg,209828
-nettracer3d/nettracer_gui.py,sha256=P4ErQwOkk8XaByrXJ6sngoitllex_s03gBx1OsrsI_Y,369311
+nettracer3d/nettracer.py,sha256=AS3r7Wg3MWv-FARApRCrzyuzb0l0_h944EfXFI75lng,207912
+nettracer3d/nettracer_gui.py,sha256=MSV0nod7qP_OP6PThRXdi4NB_dZFEo2-QZUqBBvpVmw,377440
 nettracer3d/network_analysis.py,sha256=MJBBjslA1k_R8ymid77U-qGSgzxFVfzGVQhE0IdhnbE,48046
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
 nettracer3d/proximity.py,sha256=FnIiI_AzfXd22HwCIFIyQRZxKYJ8YscIDdPnIv-wsO4,10560
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
-nettracer3d/segmenter.py,sha256=PgKGDTkuQPntTHBuLvSCplOPkGIqd2EQce4l9rhes9I,51938
+nettracer3d/segmenter.py,sha256=ixx6rPprP5hMwObcwJDMJ-wVVpgUn6eTKiIJohg9KE4,83313
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
-nettracer3d/smart_dilate.py,sha256=Kekm6YIVlJniMvJMG6_AwwNmCqK2l4Qtvg9VzzqPKMw,24600
-nettracer3d-0.6.0.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.6.0.dist-info/METADATA,sha256=5PXzQKPbZ92NCWcxv4WbtpK8VcG4rGaXMJ2O-A3F26c,2990
-nettracer3d-0.6.0.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-nettracer3d-0.6.0.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.6.0.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.6.0.dist-info/RECORD,,
+nettracer3d/smart_dilate.py,sha256=6m03KHtRMv0zfJ2aHc1Om4Fhh2abPy-IqDzRCmIEHCY,24588
+nettracer3d-0.6.2.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.6.2.dist-info/METADATA,sha256=LxWDK4jsNYNErRWDsPUf_lY1rWt8y-83aB0R1cXqoOQ,3131
+nettracer3d-0.6.2.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+nettracer3d-0.6.2.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.6.2.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.6.2.dist-info/RECORD,,

{nettracer3d-0.6.0.dist-info → nettracer3d-0.6.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.2)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

nettracer3d/hub_getter.py

@@ -1,248 +0,0 @@
-import networkx as nx
-import pandas as pd
-import numpy as np
-import tifffile
-from scipy import ndimage
-from . import network_analysis
-from . import node_draw
-
-def upsample_with_padding(data, factor, original_shape):
-    # Upsample the input binary array while adding padding to match the original shape
-
-    # Get the dimensions of the original and upsampled arrays
-    original_shape = np.array(original_shape)
-    binary_array = zoom(data, factor, order=0)
-    upsampled_shape = np.array(binary_array.shape)
-
-    # Calculate the positive differences in dimensions
-    difference_dims = original_shape - upsampled_shape
-
-    # Calculate the padding amounts for each dimension
-    padding_dims = np.maximum(difference_dims, 0)
-    padding_before = padding_dims // 2
-    padding_after = padding_dims - padding_before
-
-    # Pad the binary array along each dimension
-    padded_array = np.pad(binary_array, [(padding_before[0], padding_after[0]),
-                                         (padding_before[1], padding_after[1]),
-                                         (padding_before[2], padding_after[2])], mode='constant', constant_values=0)
-
-    # Calculate the subtraction amounts for each dimension
-    sub_dims = np.maximum(-difference_dims, 0)
-    sub_before = sub_dims // 2
-    sub_after = sub_dims - sub_before
-
-    # Remove planes from the beginning and end
-    if sub_dims[0] == 0:
-        trimmed_planes = padded_array
-    else:
-        trimmed_planes = padded_array[sub_before[0]:-sub_after[0], :, :]
-
-    # Remove rows from the beginning and end
-    if sub_dims[1] == 0:
-        trimmed_rows = trimmed_planes
-    else:
-        trimmed_rows = trimmed_planes[:, sub_before[1]:-sub_after[1], :]
-
-    # Remove columns from the beginning and end
-    if sub_dims[2] == 0:
-        trimmed_array = trimmed_rows
-    else:
-        trimmed_array = trimmed_rows[:, :, sub_before[2]:-sub_after[2]]
-
-    return trimmed_array
-
-
-def weighted_network(excel_file_path):
-    """creates a network where the edges have weights proportional to the number of connections they make between the same structure"""
-    # Read the Excel file into a pandas DataFrame
-    master_list = read_excel_to_lists(excel_file_path)
-
-    # Create a graph
-    G = nx.Graph()
-
-    # Create a dictionary to store edge weights based on node pairs
-    edge_weights = {}
-
-    nodes_a = master_list[0]
-    nodes_b = master_list[1]
-
-    # Iterate over the DataFrame rows and update edge weights
-    for i in range(len(nodes_a)):
-        node1, node2 = nodes_a[i], nodes_b[i]
-        edge = (node1, node2) if node1 < node2 else (node2, node1)  # Ensure consistent order
-        edge_weights[edge] = edge_weights.get(edge, 0) + 1
-
-    # Add edges to the graph with weights
-    for edge, weight in edge_weights.items():
-        G.add_edge(edge[0], edge[1], weight=weight)
-
-    return G, edge_weights
-
-def read_excel_to_lists(file_path, sheet_name=0):
-    """Convert a pd dataframe to lists"""
-    # Read the Excel file into a DataFrame without headers
-    df = pd.read_excel(file_path, header=None, sheet_name=sheet_name)
-
-    df = df.drop(0)
-
-    # Initialize an empty list to store the lists of values
-    data_lists = []
-
-    # Iterate over each column in the DataFrame
-    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])
-
-        try:
-            master_list[2].extend(data_lists[i+2])
-        except IndexError:
-            pass
-
-    return master_list
-
-def labels_to_boolean(label_array, labels_list):
-    # Use np.isin to create a boolean array with a single operation
-    boolean_array = np.isin(label_array, labels_list)
-    
-    return boolean_array
-
-def get_hubs(nodepath, network, proportion = None, directory = None, centroids = None, gen_more_images = False):
-
-    if type(nodepath) == str:
-        nodepath = tifffile.imread(nodepath)
-
-        if len(np.unique(nodepath)) < 3:
-        
-            structure_3d = np.ones((3, 3, 3), dtype=int)
-            nodepath, num_nodes = ndimage.label(nodepath, structure=structure_3d)
-
-    if type(network) == str:
-        G, weights = weighted_network(network)
-    else:
-        G = network
-
-    if proportion is None:
-        proportion = 0.10
-        print("Isolating top 0.10 high degree nodes by default. Specify 'proportion = 0.x' for custom node isolation.")
-    else:
-        print(f"Isolating top {proportion} high degree nodes")
-
-
-    node_list = list(G.nodes)
-    node_dict = {}
-
-    for node in node_list:
-        node_dict[node] = (G.degree(node))
-
-    # Calculate the number of top proportion% entries
-    num_items = len(node_dict)
-    num_top_10_percent = max(1, int(num_items * proportion))  # Ensure at least one item
-
-    # Sort the dictionary by values in descending order and get the top 10%
-    sorted_items = sorted(node_dict.items(), key=lambda item: item[1], reverse=True)
-    top_10_percent_items = sorted_items[:num_top_10_percent]
-
-    # Extract the keys from the top proportion% items
-    top_10_percent_keys = [key for key, value in top_10_percent_items]
-
-    masks = labels_to_boolean(nodepath, top_10_percent_keys)
-
-    masks = masks * nodepath #Makes it save with labels
-
-    # Convert boolean values to 0 and 255
-    #masks = masks.astype(np.uint8) * 255
-
-    if directory is None:
-
-        tifffile.imwrite("isolated_hubs.tif", masks)
-        print(f"Isolated hubs saved to isolated_hubs.tif")
-
-
-    else:
-
-        tifffile.imwrite(f"{directory}/isolated_hubs.tif", masks)
-        print(f"Isolated hubs saved to {directory}/isolated_hubs.tif")
-
-    if centroids is None:
-        for item in nodepath.shape:
-            if item < 5:
-                down_factor = 1
-                break
-            else:
-                down_factor = 5
-
-        centroids = network_analysis._find_centroids(masks, top_10_percent_keys, down_factor = down_factor)
-
-    degree_dict = {}
-
-    for node in top_10_percent_keys:
-        degree_dict[node] = G.degree(node)
-
-    labels = node_draw.degree_draw(degree_dict, centroids, masks)
-
-    if directory is None:
-
-        tifffile.imwrite("hub_degree_labels.tif", labels)
-        print("Node hub labels saved to hub_degree_labels.tif")
-
-    else:
-        tifffile.imwrite(f"{directory}/hub_degree_labels.tif", labels)
-        print(f"Node hub labels saved to {directory}/hub_degree_labels.tif")
-
-    masks = node_draw.degree_infect(degree_dict, masks)
-
-    if directory is None:
-
-        tifffile.imwrite("hub_degree_labels_grayscale.tif", masks)
-        print(f"Node hub grayscale labels saved to hub_degree_labels_grayscale.tif")
-
-
-    else:
-        tifffile.imwrite(f"{directory}/hub_degree_labels_grayscale.tif", masks)
-        print(f"Node hub grayscale labels saved to {directory}/hub_degree_labels_grayscale.tif")
-
-    return top_10_percent_keys
-
-
-
-if __name__ == "__main__":
-
-    masks = input("Labelled nodes?: ")
-    outer_net = input('outer edges?: ')
-
-    masks = tifffile.imread(masks)
-    outer_G, weights = weighted_network(outer_net)
-
-
-    node_list = list(outer_G.nodes)
-    node_dict = {}
-
-    for node in node_list:
-        node_dict[node] = (outer_G.degree(node))
-
-    # Calculate the number of top 10% entries
-    num_items = len(node_dict)
-    num_top_10_percent = max(1, int(num_items * 0.10))  # Ensure at least one item
-
-    # Sort the dictionary by values in descending order and get the top 10%
-    sorted_items = sorted(node_dict.items(), key=lambda item: item[1], reverse=True)
-    top_10_percent_items = sorted_items[:num_top_10_percent]
-
-    # Extract the keys from the top 10% items
-    top_10_percent_keys = [key for key, value in top_10_percent_items]
-
-    mask2 = labels_to_boolean(masks, top_10_percent_keys)
-
-    # Convert boolean values to 0 and 255
-    mask2 = mask2.astype(np.uint8) * 255
-
-    tifffile.imwrite("isolated_vertices.tif", mask2)