nettracer3d 0.9.5__py3-none-any.whl → 0.9.7__py3-none-any.whl

nettracer3d/proximity.py

@@ -966,4 +966,94 @@ def partition_objects_into_cells(object_centroids, cell_size):
         cell_assignments[int(cell_number)].append(int(label))
     
     # Convert defaultdict to regular dict and sort keys
-    return dict(sorted(cell_assignments.items()))
+    return dict(sorted(cell_assignments.items()))
+
+
+
+# To use with the merge node identities manual calculation: 
+
+def get_reslice_indices_for_id(slice_obj, array_shape):
+    """Convert slice object to padded indices accounting for dilation and boundaries"""
+    if slice_obj is None:
+        return None, None, None
+        
+    z_slice, y_slice, x_slice = slice_obj
+    
+    # Extract min/max from slices
+    z_min, z_max = z_slice.start, z_slice.stop - 1
+    y_min, y_max = y_slice.start, y_slice.stop - 1
+    x_min, x_max = x_slice.start, x_slice.stop - 1
+
+    # Boundary checks
+    y_max = min(y_max, array_shape[1] - 1)
+    x_max = min(x_max, array_shape[2] - 1)
+    z_max = min(z_max, array_shape[0] - 1)
+    y_min = max(y_min, 0)
+    x_min = max(x_min, 0)
+    z_min = max(z_min, 0)
+
+    return [z_min, z_max], [y_min, y_max], [x_min, x_max]
+
+
+def _get_node_edge_dict_id(label_array, edge_array, label):
+    """Internal method used for the secondary algorithm to find which nodes interact with which edges."""
+    
+    # Create compound condition: label matches AND edge value > 0
+    valid_mask = (label_array == label) & (edge_array > 0)
+    valid_edges = edge_array[valid_mask]
+    
+    if len(valid_edges) > 0:
+        edge_val = np.mean(valid_edges)
+    else:
+        edge_val = 0  
+    
+    return edge_val
+    
+def process_label_id(args):
+    """Modified to use pre-computed bounding boxes instead of argwhere"""
+    nodes, edges, label, array_shape, bounding_boxes = args
+    
+    # Get the pre-computed bounding box for this label
+    slice_obj = bounding_boxes[int(label)-1]  # -1 because label numbers start at 1
+    if slice_obj is None:
+        return None, None, None
+        
+    z_vals, y_vals, x_vals = get_reslice_indices_for_id(slice_obj, array_shape)
+    if z_vals is None:
+        return None, None, None
+        
+    sub_nodes = reslice_3d_array((nodes, z_vals, y_vals, x_vals))
+    sub_edges = reslice_3d_array((edges, z_vals, y_vals, x_vals))
+    return label, sub_nodes, sub_edges
+
+
+def create_node_dictionary_id(nodes, edges, num_nodes):
+    """Modified to pre-compute all bounding boxes using find_objects"""
+    node_dict = {}
+    array_shape = nodes.shape
+    
+    # Get all bounding boxes at once
+    bounding_boxes = ndimage.find_objects(nodes)
+    
+    # Use ThreadPoolExecutor for parallel execution
+    with ThreadPoolExecutor(max_workers=mp.cpu_count()) as executor:
+        # Create args list with bounding_boxes included
+        args_list = [(nodes, edges, i, array_shape, bounding_boxes) 
+                    for i in range(1, int(num_nodes) + 1)]
+
+        # Execute parallel tasks to process labels
+        results = executor.map(process_label_id, args_list)
+
+        # Process results in parallel
+        for label, sub_nodes, sub_edges in results:
+            executor.submit(create_dict_entry_id, node_dict, label, sub_nodes, sub_edges)
+
+    return node_dict
+
+def create_dict_entry_id(node_dict, label, sub_nodes, sub_edges):
+    """Internal method used for the secondary algorithm to pass around args in parallel."""
+
+    if label is None:
+        pass
+    else:
+        node_dict[label] = _get_node_edge_dict_id(sub_nodes, sub_edges, label)

nettracer3d/segmenter.py

@@ -192,10 +192,10 @@ class InteractiveSegmenter:
         if image_2d is None:
             image_2d = self.image_3d[z, :, :]
 
-        if image_2d.ndim == 3 and image_2d.shape[-1] == 3:
+        if image_2d.ndim == 3 and (image_2d.shape[-1] == 3 or image_2d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_2d.shape[-1]):
                 channel_features = self.compute_deep_feature_maps_cpu_2d(image_2d = image_2d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -308,10 +308,10 @@ class InteractiveSegmenter:
         if image_2d is None:
             image_2d = self.image_3d[z, :, :]
 
-        if image_2d.ndim == 3 and image_2d.shape[-1] == 3:
+        if image_2d.ndim == 3 and (image_2d.shape[-1] == 3 or image_2d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_2d.shape[-1]):
                 channel_features = self.compute_feature_maps_cpu_2d(image_2d = image_2d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -361,10 +361,10 @@ class InteractiveSegmenter:
         if image_3d is None:
             image_3d = self.image_3d
 
-        if image_3d.ndim == 4 and image_3d.shape[-1] == 3:
+        if image_3d.ndim == 4 and (image_3d.shape[-1] == 3 or image_3d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_3d.shape[-1]):
                 channel_features = self.compute_deep_feature_maps_cpu(image_3d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -483,127 +483,15 @@ class InteractiveSegmenter:
         
         return features
 
-    def compute_deep_feature_maps_cpu_smaller(self, image_3d=None): #smaller
-        """Optimized version using determinant instead of full eigenvalue computation. Currently not in use anywhere"""
-        if image_3d is None:
-            image_3d = self.image_3d
-        
-        # Calculate total number of features (using determinant instead of 3 eigenvalues)
-        num_basic_features = 1 + len(self.sigmas) + len(self.dogs)
-        num_gradient_features = len(self.sigmas)
-        num_laplacian_features = len(self.sigmas)
-        num_hessian_features = len(self.sigmas) * 3  # determinant + trace + frobenius norm
-        
-        total_features = num_basic_features + num_gradient_features + num_laplacian_features + num_hessian_features
-        
-        # Pre-allocate result array
-        features = np.empty(image_3d.shape + (total_features,), dtype=image_3d.dtype)
-        features[..., 0] = image_3d
-        
-        feature_idx = 1
-        
-        # Cache for Gaussian filters
-        gaussian_cache = {}
-        all_sigmas = set(self.sigmas)
-        for s1, s2 in self.dogs:
-            all_sigmas.add(s1)
-            all_sigmas.add(s2)
-        
-        # Pre-compute all Gaussian filters
-        for sigma in all_sigmas:
-            gaussian_cache[sigma] = ndimage.gaussian_filter(image_3d, sigma)
-        
-        # Gaussian smoothing
-        for sigma in self.sigmas:
-            features[..., feature_idx] = gaussian_cache[sigma]
-            feature_idx += 1
-        
-        # Difference of Gaussians
-        for s1, s2 in self.dogs:
-            features[..., feature_idx] = gaussian_cache[s1] - gaussian_cache[s2]
-            feature_idx += 1
-        
-        # Gaussian gradient magnitudes
-        for sigma in self.sigmas:
-            gaussian_img = gaussian_cache[sigma]
-            gx = ndimage.sobel(gaussian_img, axis=2, mode='reflect')
-            gy = ndimage.sobel(gaussian_img, axis=1, mode='reflect')
-            gz = ndimage.sobel(gaussian_img, axis=0, mode='reflect')
-            features[..., feature_idx] = np.sqrt(gx**2 + gy**2 + gz**2)
-            feature_idx += 1
-        
-        # Laplacian of Gaussian
-        for sigma in self.sigmas:
-            gaussian_img = gaussian_cache[sigma]
-            features[..., feature_idx] = ndimage.laplace(gaussian_img, mode='reflect')
-            feature_idx += 1
-        
-        # Hessian-based features (much faster than full eigenvalue computation)
-        for sigma in self.sigmas:
-            gaussian_img = gaussian_cache[sigma]
-            
-            # Compute second derivatives
-            hxx = ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 0, 2], mode='reflect')
-            hyy = ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 2, 0], mode='reflect')
-            hzz = ndimage.gaussian_filter(gaussian_img, sigma=0, order=[2, 0, 0], mode='reflect')
-            hxy = ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 1, 1], mode='reflect')
-            hxz = ndimage.gaussian_filter(gaussian_img, sigma=0, order=[1, 0, 1], mode='reflect')
-            hyz = ndimage.gaussian_filter(gaussian_img, sigma=0, order=[1, 1, 0], mode='reflect')
-            
-            # Hessian determinant (captures overall curvature)
-            determinant = (hxx * (hyy * hzz - hyz**2) - 
-                          hxy * (hxy * hzz - hxz * hyz) + 
-                          hxz * (hxy * hyz - hyy * hxz))
-            features[..., feature_idx] = determinant
-            feature_idx += 1
-            
-            # Hessian trace (sum of eigenvalues)
-            trace = hxx + hyy + hzz
-            features[..., feature_idx] = trace
-            feature_idx += 1
-            
-            # Frobenius norm (overall curvature magnitude)
-            frobenius_norm = np.sqrt(hxx**2 + hyy**2 + hzz**2 + 2*(hxy**2 + hxz**2 + hyz**2))
-            features[..., feature_idx] = frobenius_norm
-            feature_idx += 1
-
-        """
-        # Normalize features: zero-mean, unit variance per feature band
-        # Compute mean and std across spatial dimensions (0,1,2), keeping feature dimension
-        feature_means = np.mean(features, axis=(0, 1, 2), keepdims=True)
-        feature_stds = np.std(features, axis=(0, 1, 2), keepdims=True)
-        
-        # Avoid division by zero for constant features
-        feature_stds = np.where(feature_stds == 0, 1, feature_stds)
-        
-        # Normalize in-place for memory efficiency
-        features = (features - feature_means) / feature_stds
-        """
-        # Normalize only morphological features, keep intensity features raw
-        intensity_features = features[..., :num_basic_features]  # original + gaussians + DoGs
-        morphology_features = features[..., num_basic_features:]  # gradients + laplacians + eigenvalues
-
-        # Normalize only morphological features
-        morph_means = np.mean(morphology_features, axis=(0,1,2), keepdims=True)
-        morph_stds = np.std(morphology_features, axis=(0,1,2), keepdims=True)
-        morph_stds = np.where(morph_stds == 0, 1, morph_stds)
-        morphology_features = (morphology_features - morph_means) / morph_stds
-
-        # Recombine
-        features = np.concatenate([intensity_features, morphology_features], axis=-1)
-
-        return features
-
-
     def compute_feature_maps_cpu(self, image_3d=None): #lil
         """Optimized version that caches Gaussian filters to avoid redundant computation"""
         if image_3d is None:
             image_3d = self.image_3d
 
-        if image_3d.ndim == 4 and image_3d.shape[-1] == 3:
+        if image_3d.ndim == 4 and (image_3d.shape[-1] == 3 or image_3d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_3d.shape[-1]):
                 channel_features = self.compute_feature_maps_cpu(image_3d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -1420,7 +1308,10 @@ class InteractiveSegmenter:
                 chunk_size = max(16, min(chunk_size, min(self.image_3d.shape) // 2))
                 chunk_size = ((chunk_size + 7) // 16) * 16
         
-        depth, height, width = self.image_3d.shape
+        try:
+            depth, height, width = self.image_3d.shape
+        except:
+            depth, height, width, rgb = self.image_3d.shape
         
         # Calculate chunk grid dimensions
         z_chunks = (depth + chunk_size - 1) // chunk_size

nettracer3d/segmenter_GPU.py

@@ -320,10 +320,10 @@ class InteractiveSegmenter:
         if image_3d is None:
             image_3d = self.image_3d  # Assuming this is already a cupy array
 
-        if image_3d.ndim == 4 and image_3d.shape[-1] == 3:
+        if image_3d.ndim == 4 and (image_3d.shape[-1] == 3 or image_3d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_3d.shape[-1]):
                 channel_features = self.compute_feature_maps_gpu(image_3d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -376,10 +376,10 @@ class InteractiveSegmenter:
         if image_3d is None:
             image_3d = self.image_3d  # Assuming this is already a cupy array
 
-        if image_3d.ndim == 4 and image_3d.shape[-1] == 3:
+        if image_3d.ndim == 4 and (image_3d.shape[-1] == 3 or image_3d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_3d.shape[-1]):
                 channel_features = self.compute_deep_feature_maps_gpu(image_3d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -507,10 +507,10 @@ class InteractiveSegmenter:
         if image_2d is None:
             image_2d = cp.asarray(self.image_3d[z, :, :])
 
-        if image_2d.ndim == 3 and image_2d.shape[-1] == 3:
+        if image_2d.ndim == 3 and (image_2d.shape[-1] == 3 or image_2d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_2d.shape[-1]):
                 channel_features = self.compute_feature_maps_gpu_2d(image_2d = image_2d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -567,10 +567,10 @@ class InteractiveSegmenter:
         if image_2d is None:
             image_2d = cp.asarray(self.image_3d[z, :, :])
 
-        if image_2d.ndim == 3 and image_2d.shape[-1] == 3:
+        if image_2d.ndim == 3 and (image_2d.shape[-1] == 3 or image_2d.shape[-1] == 4):
             # RGB case - process each channel
             features_per_channel = []
-            for channel in range(3):
+            for channel in range(image_2d.shape[-1]):
                 channel_features = self.compute_deep_feature_maps_gpu_2d(image_2d = image_2d[..., channel])
                 features_per_channel.append(channel_features)
             
@@ -1082,7 +1082,10 @@ class InteractiveSegmenter:
                 chunk_size = max(16, min(chunk_size, min(self.image_3d.shape) // 2))
                 chunk_size = ((chunk_size + 7) // 16) * 16
         
-        depth, height, width = self.image_3d.shape
+        try:
+            depth, height, width = self.image_3d.shape
+        except:
+            depth, height, width, rgb = self.image_3d.shape
         
         # Calculate chunk grid dimensions
         z_chunks = (depth + chunk_size - 1) // chunk_size

{nettracer3d-0.9.5.dist-info → nettracer3d-0.9.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.9.5
+Version: 0.9.7
 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/
@@ -110,8 +110,7 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.9.5 Updates --
+-- Version 0.9.7 Updates --
 
-	* Adjusted how pan mode works a little bit.
-	* Bug Fixes
-	* Erode can now optionally preserve object labels.
+	* Fixed a bug with the segmenter and color images.
+	* The overlay 2 is now cyan by default.

{nettracer3d-0.9.5.dist-info → nettracer3d-0.9.7.dist-info}/RECORD

@@ -4,22 +4,22 @@ nettracer3d/community_extractor.py,sha256=yFHwygfeK-p0bjUMaIpeq_v6LbsKZiVAvPD6nh
 nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,75072
 nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
-nettracer3d/neighborhoods.py,sha256=2QzGKkQCSUerxigkcHF4iN7ys8kv-KHTbkD_9_2Krgo,58365
-nettracer3d/nettracer.py,sha256=Yse2gTI_WaITRJmJxUttqAgsxUzUq5wcvFdGPOw-7r4,266988
-nettracer3d/nettracer_gui.py,sha256=J3vVucTa3HIzfdspHJRQ2cJTD4xTOmxEqbapvMPCy8U,617103
+nettracer3d/neighborhoods.py,sha256=iIaHU1COIdRtzRpAuIQKfLGLNKYFK3dL8Vb_EeJIlEA,46459
+nettracer3d/nettracer.py,sha256=d9Mhz-pHox5OfGGUSTrkTBJzCWCrbQvClTu2ANt-jUE,267943
+nettracer3d/nettracer_gui.py,sha256=VsZep2sgES10ZePVJDoUoFGgsg3wGRW-rAp1NMgQQwQ,628409
 nettracer3d/network_analysis.py,sha256=kBzsVaq4dZkMe0k-VGvQIUvM-tK0ZZ8bvb-wtsugZRQ,46150
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=kZcR1PekLg0riioNeGcALIXQyZ5PtHA_9MT6z7Zovdk,10401
 nettracer3d/painting.py,sha256=K_dwngivw80r-Yyg4btKMsWGn566ZE9PnrQl986uxJE,23497
-nettracer3d/proximity.py,sha256=ZCfthYpQbDBwXBcVioxyzgO9PZACu6mQ8pSXdldP1TM,38592
+nettracer3d/proximity.py,sha256=WaHPwE6ypeInFO_LnMT0zaVE53jX3TJx6h7nmtYtr8U,41824
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
-nettracer3d/segmenter.py,sha256=-Llkhp3TlAIBXZNhcfMFQRdg0vec1xtlOm0c4_bSU9U,75761
-nettracer3d/segmenter_GPU.py,sha256=optCZ_zLIfe99rgqmyKWUZlWW5TF5jEC_C3keu1m7VQ,77771
+nettracer3d/segmenter.py,sha256=aOO3PwZ2UeizEIFX7N8midwzTzbEDzgM2jQ7WTdbrUg,70671
+nettracer3d/segmenter_GPU.py,sha256=OUekQljLKPiC4d4hNZmqrRa9HSVQ6HcCnILiAfHE5Hg,78051
 nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA,9947
 nettracer3d/smart_dilate.py,sha256=TvRUh6B4q4zIdCO1BWH-xgTdND5OUNmo99eyxG9oIAU,27145
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-nettracer3d-0.9.5.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.9.5.dist-info/RECORD,,
+nettracer3d-0.9.7.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
+nettracer3d-0.9.7.dist-info/METADATA,sha256=oJJZS4YPNc21NZd5sFUY6doxe5vpgzZwdEObUGIwswg,7067
+nettracer3d-0.9.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-0.9.7.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.9.7.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.9.7.dist-info/RECORD,,