nettracer3d 0.7.9__tar.gz → 0.8.0__tar.gz

{nettracer3d-0.7.9/src/nettracer3d.egg-info → nettracer3d-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.9
+Version: 0.8.0
 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/
@@ -73,6 +73,11 @@ 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 0.7.9 Updates -- 
+-- Version 0.8.0 Updates -- 
 
-	* The GPU segmenter was being imported regardless of GPU status, causing the program to fail without cupy (which should be optional), fixed that.
+	* Added ability to threshold nodes by degree.
+	* Improved image viewer window performance.
+	* Bug fixes and a few optimizations.
+	* Added ability to 'merge node identities' which just uses the nodes image as a reference for collecting 'identity' information from a group of other images - ie can use with cell nuclei (DAPI) to see what markers from the same imaging session overlap.
+	* Added ability to search for specific nodes directly in the nodes image with 'shift + f' or right click.
+	

{nettracer3d-0.7.9 → nettracer3d-0.8.0}/README.md

@@ -34,6 +34,11 @@ 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 0.7.9 Updates -- 
-
-	* The GPU segmenter was being imported regardless of GPU status, causing the program to fail without cupy (which should be optional), fixed that.
+-- Version 0.8.0 Updates -- 
+
+	* Added ability to threshold nodes by degree.
+	* Improved image viewer window performance.
+	* Bug fixes and a few optimizations.
+	* Added ability to 'merge node identities' which just uses the nodes image as a reference for collecting 'identity' information from a group of other images - ie can use with cell nuclei (DAPI) to see what markers from the same imaging session overlap.
+	* Added ability to search for specific nodes directly in the nodes image with 'shift + f' or right click.
+	

{nettracer3d-0.7.9 → nettracer3d-0.8.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.7.9"
+version = "0.8.0"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-0.7.9 → nettracer3d-0.8.0}/src/nettracer3d/community_extractor.py

@@ -492,48 +492,39 @@ def generate_distinct_colors(n_colors: int) -> List[Tuple[int, int, int]]:
     return colors
 
 def assign_node_colors(node_list: List[int], labeled_array: np.ndarray) -> Tuple[np.ndarray, Dict[int, str]]:
-    """
-    Assign distinct colors to nodes and create an RGBA image.
-    
-    Args:
-        node_list: List of node IDs
-        labeled_array: 3D numpy array with labels corresponding to node IDs
+    """fast version using lookup table approach."""
     
-    Returns:
-        Tuple of (RGBA-coded numpy array (H, W, D, 4), dictionary mapping nodes to color names)
-    """
-    
-    # Sort communities by size (descending)
-    sorted_nodes= sorted(node_list, reverse=True)
+    # Sort nodes by size (descending)
+    sorted_nodes = sorted(node_list, reverse=True)
     
     # Generate distinct colors
     colors = generate_distinct_colors(len(node_list))
-    random.shuffle(colors) #Randomly sorted to make adjacent structures likely stand out
+    random.shuffle(colors)  # Randomly sorted to make adjacent structures likely stand out
     
     # Convert RGB colors to RGBA by adding alpha channel
-    colors_rgba = [(r, g, b, 255) for r, g, b in colors]  # Full opacity for colored regions
+    colors_rgba = np.array([(r, g, b, 255) for r, g, b in colors], dtype=np.uint8)
     
-    # Create mapping from community to color
+    # Create mapping from node to color
     node_to_color = {node: colors_rgba[i] for i, node in enumerate(sorted_nodes)}
     
-    # Create RGBA array (initialize with transparent background)
-    rgba_array = np.zeros((*labeled_array.shape, 4), dtype=np.uint8)
+    # Create lookup table
+    max_label = max(max(labeled_array.flat), max(node_list) if node_list else 0)
+    color_lut = np.zeros((max_label + 1, 4), dtype=np.uint8)  # Transparent by default
     
-    # Assign colors to each voxel based on its label
-    for label in np.unique(labeled_array):
-        if label in node_to_color:  # Skip background (usually label 0)
-            mask = labeled_array == label
-            for i in range(4):  # RGBA channels
-                rgba_array[mask, i] = node_to_color[label][i]
-
-    # Convert the RGB portion of community_to_color back to RGB for color naming
+    for node_id, color in node_to_color.items():
+        color_lut[node_id] = color
+    
+    # Single vectorized operation - eliminates all loops!
+    rgba_array = color_lut[labeled_array]
+    
+    # Convert colors for naming
     node_to_color_rgb = {k: tuple(v[:3]) for k, v in node_to_color.items()}
     node_to_color_names = convert_node_colors_to_names(node_to_color_rgb)
     
     return rgba_array, node_to_color_names
 
 def assign_community_colors(community_dict: Dict[int, int], labeled_array: np.ndarray) -> Tuple[np.ndarray, Dict[int, str]]:
-    """Ultra-fast version using lookup table approach."""
+    """fast version using lookup table approach."""
     
     # Same setup as before
     communities = set(community_dict.values())

{nettracer3d-0.7.9 → nettracer3d-0.8.0}/src/nettracer3d/nettracer.py

@@ -548,6 +548,7 @@ def remove_branches(skeleton, length):
     return image_copy
 
 
+
 def estimate_object_radii(labeled_array, gpu=False, n_jobs=None, xy_scale = 1, z_scale = 1):
     """
     Estimate the radii of labeled objects in a 3D numpy array.
@@ -1485,21 +1486,21 @@ def remove_zeros(input_list):
 
 
 def combine_edges(edge_labels_1, edge_labels_2):
-    """Internal method to combine the edges and 'inner edges' into a single array while preserving their IDs. Prioritizes 'edge_labels_1' when overlapped"""
-
-    edge_labels_1 = edge_labels_1.astype(np.uint32)
-    edge_labels_2 = edge_labels_2.astype(np.uint32)
-
-    max_val = np.max(edge_labels_1) 
-    edge_bools_1 = edge_labels_1 == 0 #Get boolean mask where edges do not exist.
-    edge_bools_2 = edge_labels_2 > 0 #Get boolean mask where inner edges exist.
-    edge_labels_2 = edge_labels_2 + max_val #Add the maximum edge ID to all inner edges so the two can be merged without overriding eachother
-    edge_labels_2 = edge_labels_2 * edge_bools_2 #Eliminate any indices that should be 0 from inner edges.
-    edge_labels_2 = edge_labels_2 * edge_bools_1 #Eliminate any indices where outer edges overlap inner edges (Outer edges are giving overlap priority)
-    edge_labels = edge_labels_1 + edge_labels_2 #Combine the outer edges with the inner edges modified via the above steps
-
-    return edge_labels
-
+    """
+    let NumPy handle promotion automatically
+    """
+    # Early exit if no combination needed
+    mask = (edge_labels_1 == 0) & (edge_labels_2 > 0)
+    if not np.any(mask):
+        return edge_labels_1.copy()
+    
+    max_val = np.max(edge_labels_1)
+    
+    # Let NumPy handle dtype promotion automatically
+    # This will promote to the smallest type that can handle the operation
+    offset_labels = edge_labels_2 + max_val
+    
+    return np.where(mask, offset_labels, edge_labels_1)
 
 def combine_nodes(root_nodes, other_nodes, other_ID, identity_dict, root_ID = None):
 
@@ -1507,15 +1508,10 @@ def combine_nodes(root_nodes, other_nodes, other_ID, identity_dict, root_ID = No
 
     print("Combining node arrays")
 
-    root_nodes = root_nodes.astype(np.uint32)
-    other_nodes = other_nodes.astype(np.uint32)
-
-    max_val = np.max(root_nodes) 
-    root_bools = root_nodes == 0 #Get boolean mask where root nodes do not exist.
-    other_bools = other_nodes > 0 #Get boolean mask where other nodes exist.
-    other_nodes = other_nodes + max_val #Add the maximum root node labels to other nodes so the two can be merged without overriding eachother
-    other_nodes = other_nodes * other_bools #Eliminate any indices that should be 0 from other_nodes.
-    other_nodes = other_nodes * root_bools #Eliminate any indices where other nodes overlap root nodes (root node are giving overlap priority)
+    mask = (root_nodes == 0) & (other_nodes > 0)
+    if np.any(mask):
+        max_val = np.max(root_nodes)
+        other_nodes[:] = np.where(mask, other_nodes + max_val, 0)
 
     if root_ID is not None:
         rootIDs = list(np.unique(root_nodes)) #Sets up adding these vals to the identitiy dictionary. Gets skipped if this has already been done.
@@ -1530,6 +1526,11 @@ def combine_nodes(root_nodes, other_nodes, other_ID, identity_dict, root_ID = No
 
     if root_ID is not None: #Adds the root vals to the dictionary if it hasn't already
 
+        if other_ID.endswith('.tiff'):
+            other_ID = other_ID[:-5]
+        elif other_ID.endswith('.tif'):
+            other_ID = other_ID[:-4]
+
         for item in rootIDs:
             identity_dict[item] = root_ID
 
@@ -1538,6 +1539,11 @@ def combine_nodes(root_nodes, other_nodes, other_ID, identity_dict, root_ID = No
             other_ID = os.path.basename(other_ID)
         except:
             pass
+        if other_ID.endswith('.tiff'):
+            other_ID = other_ID[:-5]
+        elif other_ID.endswith('.tif'):
+            other_ID = other_ID[:-4]
+
         identity_dict[item] = other_ID
 
     nodes = root_nodes + other_nodes #Combine the outer edges with the inner edges modified via the above steps
@@ -1609,6 +1615,17 @@ def downsample(data, factor, directory=None, order=0):
     
     return data
 
+
+def otsu_binarize(image_array):
+
+    """Automated binarize method for seperating the foreground"""
+
+    from skimage.filters import threshold_otsu
+
+    threshold = threshold_otsu(image_array)
+    binary_mask = image_array > threshold
+    return binary_mask
+
 def binarize(arrayimage, directory = None):
     """
     Can be used to binarize an image. Binary output will be saved to the active directory if none is specified.
@@ -3428,7 +3445,7 @@ class Network_3D:
         """
         self._nodes, num_nodes = label_objects(nodes, structure_3d)
 
-    def merge_nodes(self, addn_nodes_name, label_nodes = True):
+    def merge_nodes(self, addn_nodes_name, label_nodes = True, root_id = "Root_Nodes"):
         """
         Merges the self._nodes attribute with alternate labelled node images. The alternate nodes can be inputted as a string for a filepath to a tif,
         or as a directory address containing only tif images, which will merge the _nodes attribute with all tifs in the folder. The _node_identities attribute
@@ -3439,8 +3456,13 @@ class Network_3D:
         :param label_nodes: (Optional - Val = True; Boolean). Will label all discrete objects in each node file being merged if True. If False, will not label.
         """
 
-        nodes_name = 'Root_Nodes'
+        nodes_name = root_id
 
+        try:
+            nodes_name = os.path.splitext(os.path.basename(nodes_name))[0]
+        except:
+            pass
+            
         identity_dict = {} #A dictionary to deliniate the node identities
 
         try: #Try presumes the input is a tif
@@ -3462,7 +3484,10 @@ class Network_3D:
             for i, addn_nodes in enumerate(addn_nodes_list):
                 try:
                     addn_nodes_ID = addn_nodes
-                    addn_nodes = tifffile.imread(f'{addn_nodes_name}/{addn_nodes}')
+                    try:
+                        addn_nodes = tifffile.imread(f'{addn_nodes_name}/{addn_nodes}')
+                    except:
+                        continue
 
                     if label_nodes is True:
                         addn_nodes, num_nodes2 = label_objects(addn_nodes)  # Label the node objects. Note this presumes no overlap between node masks.
@@ -4649,11 +4674,15 @@ class Network_3D:
             else:
                 min_coords, max_coords = bounds
 
-            dim_list = max_coords - min_coords
+            try:
+                dim_list = max_coords - min_coords
+            except:
+                min_coords = np.array([0,0,0])
+                bounds = (min_coords, max_coords)
+                dim_list = max_coords - min_coords
 
             new_list = []
 
-
             if dim == 3:
                 for centroid in roots:
 
@@ -4688,7 +4717,7 @@ class Network_3D:
 
         h_vals = proximity.compute_ripleys_h(k_vals, r_vals, dim)
 
-        proximity.plot_ripley_functions(r_vals, k_vals, h_vals, dim)
+        proximity.plot_ripley_functions(r_vals, k_vals, h_vals, dim, root, targ)
 
         return r_vals, k_vals, h_vals
 
@@ -5082,6 +5111,58 @@ class Network_3D:
 
         return heat_dict
 
+    def merge_node_ids(self, path, data):
+
+        if self.node_identities is None: # Prepare modular dict
+
+            self.node_identities = {}
+
+            nodes = list(np.unique(data))
+            if 0 in nodes:
+                del nodes[0]
+
+            for node in nodes:
+                self.node_identities[node] = ''
+
+        img_list = directory_info(path)
+
+        for i, img in enumerate(img_list):
+            mask = tifffile.imread(f'{path}/{img}')
+
+            if len(np.unique(mask)) != 2:
+
+                mask = otsu_binarize(mask)
+
+            nodes = data * mask
+            nodes = list(np.unique(nodes))
+            if 0 in nodes:
+                del nodes[0]
+
+            if img.endswith('.tiff'):
+                base_name = img[:-5]
+            elif img.endswith('.tif'):
+                base_name = img[:-4]
+            else:
+                base_name = img
+
+            for node in self.node_identities.keys():
+
+                try:
+
+                    if node in nodes:
+
+                        self.node_identities[node] += f" {base_name}+"
+
+                    else:
+
+                        self.node_identities[node] += f" {base_name}-"
+
+                except:
+                    pass
+
+
+
+
 
 
 if __name__ == "__main__":