nettracer3d 0.7.5__py3-none-any.whl → 0.7.7__py3-none-any.whl

nettracer3d/proximity.py

@@ -9,6 +9,7 @@ import multiprocessing as mp
 import pandas as pd
 import matplotlib.pyplot as plt
 from typing import Dict, Union, Tuple, List, Optional
+from collections import defaultdict
 
 
 # Related to morphological border searching:
@@ -142,15 +143,17 @@ def find_shared_value_pairs(input_dict):
 
 #Related to kdtree centroid searching:
 
-def populate_array(centroids):
+def populate_array(centroids, clip=False):
     """
     Create a 3D array from centroid coordinates.
     
     Args:
         centroids: Dictionary where keys are object IDs and values are [z,y,x] coordinates
+        clip: Boolean, if True, transpose all centroids so minimum values become 0
     
     Returns:
-        3D numpy array where values are object IDs at their centroid locations
+        If clip=False: 3D numpy array where values are object IDs at their centroid locations
+        If clip=True: Tuple of (3D numpy array, dictionary with clipped centroids)
     """
     # Input validation
     if not centroids:
@@ -163,21 +166,39 @@ def populate_array(centroids):
     min_coords = coords.min(axis=0)
     max_coords = coords.max(axis=0)
     
-    # Check for negative coordinates
-    if np.any(min_coords < 0):
+    # Check for negative coordinates only if not clipping
+    if not clip and np.any(min_coords < 0):
         raise ValueError("Negative coordinates found in centroids")
     
+    # Apply clipping if requested
+    clipped_centroids = {}
+    if clip:
+        # Transpose all coordinates so minimum becomes 0
+        coords = coords - min_coords
+        max_coords = max_coords - min_coords
+        min_coords = np.zeros_like(min_coords)
+        
+        # Create dictionary with clipped centroids
+        for i, obj_id in enumerate(centroids.keys()):
+            clipped_centroids[obj_id] = coords[i].tolist()
+    
     # Create array
     array = np.zeros((max_coords[0] + 1, 
                      max_coords[1] + 1, 
                      max_coords[2] + 1), dtype=int)
     
-    # Populate array with rounded coordinates
-    for obj_id, coord in centroids.items():
-        z, y, x = np.round([coord[0], coord[1], coord[2]]).astype(int)
+    # Populate array with (possibly clipped) rounded coordinates
+    for i, (obj_id, coord) in enumerate(centroids.items()):
+        if clip:
+            z, y, x = coords[i]  # Use pre-computed clipped coordinates
+        else:
+            z, y, x = np.round([coord[0], coord[1], coord[2]]).astype(int)
         array[z, y, x] = obj_id
         
-    return array
+    if clip:
+        return array, clipped_centroids
+    else:
+        return array
 
 def find_neighbors_kdtree(radius, centroids=None, array=None, targets=None):
     # Get coordinates of nonzero points
@@ -646,4 +667,63 @@ def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12
     
     plt.tight_layout()
     plt.show()
-    #plt.clf()
+    #plt.clf()
+
+
+
+
+def partition_objects_into_cells(object_centroids, cell_size):
+    """
+    Partition objects into 3D grid cells based on their centroids.
+    
+    Args:
+        object_centroids (dict): Dictionary with object labels as keys and [z,y,x] coordinates as values
+        cell_size (tuple or int): Size of each cell. If int, creates cubic cells. If tuple, (z_size, y_size, x_size)
+    
+    Returns:
+        dict: Dictionary with cell numbers as keys and lists of object labels as values
+    """
+    
+    if not object_centroids:
+        return {}
+    
+    # Handle cell_size input
+    if isinstance(cell_size, (int, float)):
+        cell_size = (cell_size, cell_size, cell_size)
+    elif len(cell_size) == 1:
+        cell_size = (cell_size[0], cell_size[0], cell_size[0])
+    
+    # Extract centroids and find bounds
+    centroids = np.array(list(object_centroids.values()))
+    labels = list(object_centroids.keys())
+    
+    # Find the bounding box of all centroids
+    min_coords = np.min(centroids, axis=0)  # [min_z, min_y, min_x]
+    max_coords = np.max(centroids, axis=0)  # [max_z, max_y, max_x]
+    
+    # Calculate number of cells in each dimension
+    dimensions = max_coords - min_coords
+    num_cells = np.ceil(dimensions / np.array(cell_size)).astype(int)
+    
+    # Initialize result dictionary
+    cell_assignments = defaultdict(list)
+    
+    # Assign each object to a cell
+    for i, (label, centroid) in enumerate(object_centroids.items()):
+        # Calculate which cell this centroid belongs to
+        relative_pos = np.array(centroid) - min_coords
+        cell_indices = np.floor(relative_pos / np.array(cell_size)).astype(int)
+        
+        # Ensure indices don't exceed bounds (handles edge cases)
+        cell_indices = np.minimum(cell_indices, num_cells - 1)
+        cell_indices = np.maximum(cell_indices, 0)
+        
+        # Convert 3D cell indices to a single cell number
+        cell_number = (cell_indices[0] * num_cells[1] * num_cells[2] + 
+                      cell_indices[1] * num_cells[2] + 
+                      cell_indices[2])
+        
+        cell_assignments[int(cell_number)].append(label)
+    
+    # Convert defaultdict to regular dict and sort keys
+    return dict(sorted(cell_assignments.items()))

nettracer3d/smart_dilate.py

@@ -108,6 +108,8 @@ def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
 
     num_cores = mp.cpu_count()
 
+
+
     with ThreadPoolExecutor(max_workers=num_cores) as executor:
         futures = {executor.submit(process_slice, z): z for z in range(tiff_array.shape[0])}
 
@@ -246,14 +248,14 @@ def invert_array(array):
     return np.logical_not(array).astype(np.uint8)
 
 def process_chunk(start_idx, end_idx, nodes, ring_mask, nearest_label_indices):
-    nodes_chunk = nodes[start_idx:end_idx]
-    ring_mask_chunk = ring_mask[start_idx:end_idx]
+    nodes_chunk = nodes[:, start_idx:end_idx, :]
+    ring_mask_chunk = ring_mask[:, start_idx:end_idx, :]
     dilated_nodes_with_labels_chunk = np.copy(nodes_chunk)
     ring_indices = np.argwhere(ring_mask_chunk)
 
     for index in ring_indices:
         z, y, x = index
-        nearest_z, nearest_y, nearest_x = nearest_label_indices[:, z + start_idx, y, x]
+        nearest_z, nearest_y, nearest_x = nearest_label_indices[:, z, y + start_idx, x]
         try: #There was an index error here once on the highest val of the second axis. I could not understand why because it usually doesnt hence the try block.
             dilated_nodes_with_labels_chunk[z, y, x] = nodes[nearest_z, nearest_y, nearest_x]
         except:
@@ -332,10 +334,10 @@ def smart_dilate(nodes, dilate_xy, dilate_z, directory = None, GPU = True, fast_
 
     # Step 5: Process in parallel chunks using ThreadPoolExecutor
     num_cores = mp.cpu_count()  # Use all available CPU cores
-    chunk_size = nodes.shape[0] // num_cores  # Divide the array into chunks along the z-axis
+    chunk_size = nodes.shape[1] // num_cores  # Divide the array into chunks along the y-axis
 
     with ThreadPoolExecutor(max_workers=num_cores) as executor:
-        args_list = [(i * chunk_size, (i + 1) * chunk_size if i != num_cores - 1 else nodes.shape[0], nodes, ring_mask, nearest_label_indices) for i in range(num_cores)]
+        args_list = [(i * chunk_size, (i + 1) * chunk_size if i != num_cores - 1 else nodes.shape[1], nodes, ring_mask, nearest_label_indices) for i in range(num_cores)]
         results = list(executor.map(lambda args: process_chunk(*args), args_list))
 
     del ring_mask
@@ -343,7 +345,7 @@ def smart_dilate(nodes, dilate_xy, dilate_z, directory = None, GPU = True, fast_
     del nearest_label_indices
 
     # Combine results from chunks
-    dilated_nodes_with_labels = np.concatenate(results, axis=0)
+    dilated_nodes_with_labels = np.concatenate(results, axis=1)
 
 
     if (dilated_nodes_with_labels.shape[1] < original_shape[1]) and fast_dil: #If downsample was used, upsample output
@@ -368,7 +370,7 @@ def round_to_odd(number):
             rounded -= 1
     return rounded
 
-def smart_label(binary_array, label_array, directory = None, GPU = True, predownsample = None):
+def smart_label(binary_array, label_array, directory = None, GPU = True, predownsample = None, remove_template = False):
 
     original_shape = binary_array.shape
 
@@ -419,12 +421,11 @@ def smart_label(binary_array, label_array, directory = None, GPU = True, predown
                         break
                     except cp.cuda.memory.OutOfMemoryError:
                         down_factor += 1
-                binary_mask = binary_array #Need this for later to stamp out the correct output
                 binary_core = binarize(small_array)
                 label_array = small_array
-                binary_array = nettracer.downsample(binary_array, downsample_needed)
-                binary_array = nettracer.dilate_3D_old(binary_array)
-                ring_mask = binary_array & invert_array(binary_core)
+                binary_small = nettracer.downsample(binary_array, downsample_needed)
+                binary_small = nettracer.dilate_3D_old(binary_small)
+                ring_mask = binary_small & invert_array(binary_core)
 
         else:
             goto_except = 1/0
@@ -440,18 +441,21 @@ def smart_label(binary_array, label_array, directory = None, GPU = True, predown
 
     # Step 5: Process in parallel chunks using ThreadPoolExecutor
     num_cores = mp.cpu_count()  # Use all available CPU cores
-    chunk_size = label_array.shape[0] // num_cores  # Divide the array into chunks along the z-axis
+    chunk_size = label_array.shape[1] // num_cores  # Divide the array into chunks along the z-axis
+
 
     with ThreadPoolExecutor(max_workers=num_cores) as executor:
-        args_list = [(i * chunk_size, (i + 1) * chunk_size if i != num_cores - 1 else label_array.shape[0], label_array, ring_mask, nearest_label_indices) for i in range(num_cores)]
+        args_list = [(i * chunk_size, (i + 1) * chunk_size if i != num_cores - 1 else label_array.shape[1], label_array, ring_mask, nearest_label_indices) for i in range(num_cores)]
         results = list(executor.map(lambda args: process_chunk(*args), args_list))
 
     # Combine results from chunks
-    dilated_nodes_with_labels = np.concatenate(results, axis=0)
+    dilated_nodes_with_labels = np.concatenate(results, axis=1)
 
     if label_array.shape[1] < original_shape[1]: #If downsample was used, upsample output
         dilated_nodes_with_labels = nettracer.upsample_with_padding(dilated_nodes_with_labels, downsample_needed, original_shape)
-        dilated_nodes_with_labels = dilated_nodes_with_labels * binary_mask
+        dilated_nodes_with_labels = dilated_nodes_with_labels * binary_array
+    elif remove_template:
+        dilated_nodes_with_labels = dilated_nodes_with_labels * binary_array
 
     if string_bool:
         if directory is not None:
@@ -465,6 +469,7 @@ def smart_label(binary_array, label_array, directory = None, GPU = True, predown
             except Exception as e:
                 print(f"Could not save search region file to active directory")
 
+
     return dilated_nodes_with_labels
 
 def compute_distance_transform_GPU(nodes, return_dists = False, sampling = [1, 1, 1]):

{nettracer3d-0.7.5.dist-info → nettracer3d-0.7.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.5
+Version: 0.7.7
 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/
@@ -28,6 +28,7 @@ Requires-Dist: PyQt6
 Requires-Dist: scikit-learn
 Requires-Dist: nibabel
 Requires-Dist: setuptools
+Requires-Dist: umap-learn
 Provides-Extra: cuda11
 Requires-Dist: cupy-cuda11x; extra == "cuda11"
 Provides-Extra: cuda12
@@ -72,11 +73,6 @@ 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 0.7.5 Updates -- 
+-- Version 0.7.7 Updates -- 
 
-	* Bug fixes
-	* The segmenter GPU option has been updated to include 2D segmentation and to also be able to load/save models.
-	* A new function (Analyze -> Stats -> Calculate Generic Network Histograms has been added (gives a few histograms about the network and their corresponding tables. Previously stats mostly gave averages).
-	* The function 'Analyze -> Data/Overlays -> Get Hub Information' now looks for the upper hubs unique to each separate network component. It will also ignore smaller components that have too few nodes to be reasonably considered having hubs relative to the threshold the user sets.
-	* The function to split non-connected nodes has been improved a bit (its faster albeit still slowish - its a tough operation)
-	* Removed python-louvain dependence, now uses networkx for Louvain partitioning. (On top of this, now the user can set the random seed they desire for partitioning for reproducibility purposes).
+	* See documentation once updated

nettracer3d-0.7.7.dist-info/RECORD

@@ -0,0 +1,23 @@
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+nettracer3d/community_extractor.py,sha256=BrONCLRLYUdMfLe_018AQi0k0J7xwVahc_lmsOO5Pwo,23086
+nettracer3d/excelotron.py,sha256=jTAwMKIvyLgQBhDSHAhlTH02c9rQAKMck4ic5lE2KM4,68224
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+nettracer3d/neighborhoods.py,sha256=oCnvfGSjWdpPUdzUn_WhQVSIptGIYSVI0rmzWP_CfE0,7795
+nettracer3d/nettracer.py,sha256=RR3UFReS86AHQXHBZkzwQfhtA8pFtDK9K41pvxY5lbg,223147
+nettracer3d/nettracer_gui.py,sha256=8ZaReS5KbY4hgIWn65FHkBlTyrWwwowbsr09DATq3g4,454229
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+nettracer3d-0.7.7.dist-info/RECORD,,

{nettracer3d-0.7.5.dist-info → nettracer3d-0.7.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

nettracer3d-0.7.5.dist-info/RECORD

@@ -1,21 +0,0 @@
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-nettracer3d/community_extractor.py,sha256=vzckLJfubplcQUAIr4UNgezxUJIdeFmH6CTWk8jYjOw,23739
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-nettracer3d-0.7.5.dist-info/licenses/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
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