nettracer3d 1.2.3__py3-none-any.whl → 1.2.4__py3-none-any.whl

nettracer3d/filaments.py

@@ -93,16 +93,24 @@ class VesselDenoiser:
         # A voxel contributes to surface area if any neighbor is different
         for axis in range(3):
             for direction in [-1, 1]:
-                # Shift array to compare with neighbors
-                shifted = np.roll(labeled, direction, axis=axis)
+                # Pad with zeros only on the axis we're checking
+                pad_width = [(1, 1) if i == axis else (0, 0) for i in range(3)]
+                padded = np.pad(labeled, pad_width, mode='constant', constant_values=0)
                 
-                # Find faces exposed to different label (including background)
-                exposed_faces = (labeled != shifted) & (labeled > 0)
+                # Roll the padded array
+                shifted = np.roll(padded, direction, axis=axis)
+                
+                # Extract the center region (original size) from shifted
+                slices = [slice(1, -1) if i == axis else slice(None) for i in range(3)]
+                shifted_cropped = shifted[tuple(slices)]
+                
+                # Find exposed faces
+                exposed_faces = (labeled != shifted_cropped) & (labeled > 0)
                 
-                # Count exposed faces per label
                 face_counts = np.bincount(labeled[exposed_faces], 
                                          minlength=num_features + 1)
                 surface_areas += face_counts
+        del padded
         
         # Calculate sphericity for each component
         # Sphericity = (surface area of sphere with same volume) / (actual surface area)

nettracer3d/nettracer.py

@@ -750,35 +750,37 @@ def estimate_object_radii(labeled_array, gpu=False, n_jobs=None, xy_scale = 1, z
 
 def get_surface_areas(labeled, xy_scale=1, z_scale=1):
     labels = np.unique(labeled)
-    labels = labels[labels > 0]  # Remove background label
+    labels = labels[labels > 0]
     max_label = int(np.max(labeled))
     
-    # Size array to accommodate highest label value
     surface_areas = np.zeros(max_label + 1, dtype=np.float64)
     
-    # Check each of 6 face directions (±x, ±y, ±z)
     for axis in range(3):
-        # Determine face area based on axis (anisotropic scaling)
-        if axis == 2:  # z-axis: face is in xy plane
+        if axis == 2:
             face_area = xy_scale * xy_scale
-        else:  # x or y axis: face is perpendicular to xy plane
+        else:
             face_area = xy_scale * z_scale
         
         for direction in [-1, 1]:
-            # Shift array to compare with neighbors
-            shifted = np.roll(labeled, direction, axis=axis)
+            # Pad with zeros only on the axis we're checking
+            pad_width = [(1, 1) if i == axis else (0, 0) for i in range(3)]
+            padded = np.pad(labeled, pad_width, mode='constant', constant_values=0)
+            
+            # Roll the padded array
+            shifted = np.roll(padded, direction, axis=axis)
             
-            # Find faces exposed to different label (including background)
-            exposed_faces = (labeled != shifted) & (labeled > 0)
+            # Extract the center region (original size) from shifted
+            slices = [slice(1, -1) if i == axis else slice(None) for i in range(3)]
+            shifted_cropped = shifted[tuple(slices)]
+            
+            # Find exposed faces
+            exposed_faces = (labeled != shifted_cropped) & (labeled > 0)
             
-            # Count exposed faces per label
             face_counts = np.bincount(labeled[exposed_faces], 
                                      minlength=max_label + 1)
             surface_areas += face_counts * face_area
     
-    # Create dictionary mapping label to surface area
     result = {int(label): float(surface_areas[label]) for label in labels}
-        
     return result
 
 def break_and_label_skeleton(skeleton, peaks = 1, branch_removal = 0, comp_dil = 0, max_vol = 0, directory = None, return_skele = False, nodes = None, compute = True, unify = False, xy_scale = 1, z_scale = 1):
@@ -5560,14 +5562,14 @@ class Network_3D:
                 except:
                     pass
 
-            title1 = f'Neighborhood Distribution of Nodes in Network from Nodes: {root}'
-            title2 = f'Neighborhood Distribution of Nodes in Network from Nodes {root} as a proportion of total nodes of that ID'
+            title1 = f'Neighborhood Distribution of Nodes in Network from Node Type: {root}'
+            title2 = f'Neighborhood Distribution of Nodes in Network from Node Type {root} as a Proportion (# neighbors with ID x / Total # ID x)'
 
 
         elif mode == 1: #Search neighborhoods morphologically, obtain densities
             neighborhood_dict, total_dict, densities = morphology.search_neighbor_ids(self._nodes, targets, node_identities, neighborhood_dict, total_dict, search, self._xy_scale, self._z_scale, root, fastdil = fastdil)
-            title1 = f'Volumetric Neighborhood Distribution of Nodes in image that are {search} from nodes: {root}'
-            title2 = f'Density Distribution of Nodes in image that are {search} from Nodes {root} as a proportion of total node volume of that ID'
+            title1 = f'Volumetric Neighborhood Distribution of Nodes in image that are {search} from Node Type: {root}'
+            title2 = f'Density Distribution of Nodes in image that are {search} from Node Type {root} as a proportion (Vol neighors with ID x / Total vol ID x)'
 
 
         for identity in neighborhood_dict:
@@ -5578,7 +5580,7 @@ class Network_3D:
         network_analysis.create_bar_graph(proportion_dict, title2, "Node Identity", "Proportion", directory=directory)
 
         try:
-            network_analysis.create_bar_graph(densities, f'Relative Density of Node Identities with {search} from nodes {root}', "Node Identity", "Density Search/Density Total", directory=directory)
+            network_analysis.create_bar_graph(densities, f'Relative Density of Node Identities with {search} from Node Type {root}', "Node Identity", "Density within search region/Density within entire image", directory=directory)
         except:
             densities = None
 
@@ -6233,14 +6235,14 @@ class Network_3D:
         if proportional:
 
             identities2, id_set2 = self.community_id_info_per_com(proportional = True)
-            output = neighborhoods.plot_dict_heatmap(identities2, id_set2, title = "Neighborhood Heatmap by Proportional Composition of Nodes in Neighborhood vs All Nodes")
+            output = neighborhoods.plot_dict_heatmap(identities2, id_set2, title = "Neighborhood Heatmap by Proportional Composition of Nodes in Neighborhood vs All Nodes in Image")
             matrixes.append(output)
 
             identities3 = {}
             for iden in identities2:
                 identities3[iden] = identities2[iden]/len_dict[iden][1]
 
-            output = neighborhoods.plot_dict_heatmap(identities3, id_set2, title = "Neighborhood Heatmap by Proportional Composition of Nodes in Neighborhood vs All Nodes Divided by Neighborhood Total Proportion of All Nodes (val < 1 = underrepresented, val > 1 = overrepresented)", center_at_one = True)
+            output = neighborhoods.plot_dict_heatmap(identities3, id_set2, title = "Over/Underrepresentation of Node Identities per Neighborhood (val < 1 = underrepresented, val > 1 = overrepresented)", center_at_one = True)
             matrixes.append(output)
 
         return len_dict, matrixes, id_set

nettracer3d/nettracer_gui.py

@@ -10090,7 +10090,7 @@ class NeighborIdentityDialog(QDialog):
             self.root = None
 
         self.mode = QComboBox()
-        self.mode.addItems(["From Network - Based on Absolute Connectivity", "Use Labeled Nodes - Based on Morphological Neighborhood Densities"])
+        self.mode.addItems(["From Network - Quantifies Neighbors Based on Adjacent Network Connections", "Use Labeled Nodes - Quantifies Neighbors Volume of Neighbor Within Search Region"])
         self.mode.setCurrentIndex(0)
         layout.addRow("Mode", self.mode)
 

{nettracer3d-1.2.3.dist-info → nettracer3d-1.2.4.dist-info}/METADATA

@@ -1,10 +1,9 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.2.3
+Version: 1.2.4
 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/
-Project-URL: Video_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
 Project-URL: Reference_Citation_For_Use, https://doi.org/10.1101/2024.07.29.605633
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: Other/Proprietary License
@@ -101,8 +100,6 @@ While not related to NetTracer3D, if you want to use Cellpose3 (for which GPU-us
 This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays.
 
 
-For a (slightly outdated) video tutorial on using the GUI: https://www.youtube.com/watch?v=cRatn5VTWDY
-
 NetTracer3D is free to use/fork for academic/nonprofit use so long as citation is provided, and is available for commercial use at a fee (see license file for information).
 The current citation is here: 
 
@@ -110,8 +107,9 @@ 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 1.2.3 Updates --
+-- Version 1.2.4 Updates --
 
-	* Tweaked the 'branch unification params' - now hard rejects any sharp forks in the branches so branches will mostly be straight.
+	* Fixed bug for calculating surface area when the surface was on the edge of the image.
+	* Removed video tutorial from youtube for being outdated. May add new one later.
 	
 	

{nettracer3d-1.2.3.dist-info → nettracer3d-1.2.4.dist-info}/RECORD

@@ -3,12 +3,12 @@ nettracer3d/branch_stitcher.py,sha256=gyDVPUnApS2jmlIglJoRVEVY8WXLqwpr0_8rNdvy9u
 nettracer3d/cellpose_manager.py,sha256=NfRqW6Zl7yRU4qHCS_KjmR0R6QANSSgCO0_dr-eivxg,6694
 nettracer3d/community_extractor.py,sha256=rPXXWwMX05mfD_ogULEouLy8CST-aOaoSw45NhloKVg,31754
 nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,75072
-nettracer3d/filaments.py,sha256=-gUoiXg4n5qTHhGvzh1gkLeDjStECRGbaGpau_NGVRM,43280
+nettracer3d/filaments.py,sha256=ks3-ThdHRKu5hPk04R_YHAmVpwCqXraR0LWW0VRlAts,43693
 nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=QlBPsJAswBoinjZuouNwEfGEGwclvenlZ1Vmo288QLo,23287
 nettracer3d/neighborhoods.py,sha256=Bje77gWzXRIYyXkDlnFQnbUALnIt8dheLXHVFQsAKuc,53156
-nettracer3d/nettracer.py,sha256=JaoNXP67vLzaw6HUQ6mtB7qye1U92wZDJYI3vEpsDS4,294237
-nettracer3d/nettracer_gui.py,sha256=AKXT_4M-wuuijPzj6XfMV6fYKQ0WJYW0A_YdcO7kfYc,741978
+nettracer3d/nettracer.py,sha256=9iQ51fvYUNsHA90lZd4cEVz_4AZZToTy22SjJoZNPHY,294254
+nettracer3d/nettracer_gui.py,sha256=oStQZCqzi_nDFq8NKjMA1n0cuMv77gKekOd6XQFO5H4,742021
 nettracer3d/network_analysis.py,sha256=kBzsVaq4dZkMe0k-VGvQIUvM-tK0ZZ8bvb-wtsugZRQ,46150
 nettracer3d/network_draw.py,sha256=Uw0w1MoFiYMirkdM_XDAfy_m5_MoVaZkkGpoYzN9_-c,14259
 nettracer3d/node_draw.py,sha256=LeSftKJiNGkC7cpBJuf8Y9JeTUaUjcD6I2byclmZCb4,10484
@@ -21,9 +21,9 @@ nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA
 nettracer3d/smart_dilate.py,sha256=gtL7hxzae93PJQsGLnUrwQ6Wb0evnHHREh0rHyUh_48,28644
 nettracer3d/stats.py,sha256=0YwrVLeEvll3PlbL5-0_9dstldr48PvxJrQm-PiC8jY,36607
 nettracer3d/tutorial.py,sha256=cUxiBf5RaBTtr9uJ2qoxZjRkcAY8mrvS9_LEqiwoxLc,153564
-nettracer3d-1.2.3.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
-nettracer3d-1.2.3.dist-info/METADATA,sha256=rVv3ho6njj9VWX6XrKz0ri1mHYBwo_zO8Mb7d7XHBaM,7110
-nettracer3d-1.2.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-1.2.3.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-1.2.3.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-1.2.3.dist-info/RECORD,,
+nettracer3d-1.2.4.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
+nettracer3d-1.2.4.dist-info/METADATA,sha256=snQxa9urY2-QGfYTHg0cpeUfNuCa2qhfRum9aMD1otk,6971
+nettracer3d-1.2.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-1.2.4.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-1.2.4.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-1.2.4.dist-info/RECORD,,