nettracer3d 0.2.9__tar.gz → 0.3.0__tar.gz

{nettracer3d-0.2.9/src/nettracer3d.egg-info → nettracer3d-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.2.9
+Version: 0.3.0
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <boom2449@gmail.com>
 Project-URL: User_Manual, https://drive.google.com/drive/folders/1fTkz3n4LN9_VxKRKC8lVQSlrz_wq0bVn?usp=drive_link

{nettracer3d-0.2.9 → nettracer3d-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.2.9"
+version = "0.3.0"
 authors = [
   { name="Liam McLaughlin", email="boom2449@gmail.com" },
 ]

{nettracer3d-0.2.9 → nettracer3d-0.3.0}/src/nettracer3d/nettracer.py

@@ -696,29 +696,35 @@ def fill_holes_3d(array):
 
     array = binarize(array)
     inv_array = invert_array(array)
+
     
     # Create arrays for all three planes
     array_xy = np.zeros_like(inv_array, dtype=np.uint8)
     array_xz = np.zeros_like(inv_array, dtype=np.uint8)
     array_yz = np.zeros_like(inv_array, dtype=np.uint8)
-    
+
+
     # Process XY plane
     for z in range(inv_array.shape[0]):
         array_xy[z] = process_slice(inv_array[z])
+
+    if array.shape[0] > 3: #only use these dimensions for sufficiently large zstacks
         
-    # Process XZ plane    
-    for y in range(inv_array.shape[1]):
-        slice_xz = inv_array[:, y, :]
-        array_xz[:, y, :] = process_slice(slice_xz)
+        # Process XZ plane    
+        for y in range(inv_array.shape[1]):
+            slice_xz = inv_array[:, y, :]
+            array_xz[:, y, :] = process_slice(slice_xz)
+            
+        # Process YZ plane
+        for x in range(inv_array.shape[2]):
+            slice_yz = inv_array[:, :, x]
+            array_yz[:, :, x] = process_slice(slice_yz)
         
-    # Process YZ plane
-    for x in range(inv_array.shape[2]):
-        slice_yz = inv_array[:, :, x]
-        array_yz[:, :, x] = process_slice(slice_yz)
-    
-    # Combine results from all three planes
-    filled = (array_xy | array_xz | array_yz) * 255
-    return array + filled
+        # Combine results from all three planes
+        filled = (array_xy | array_xz | array_yz) * 255
+        return array + filled
+    else:
+        return array_xy * 255
 
 
 

{nettracer3d-0.2.9 → nettracer3d-0.3.0}/src/nettracer3d/network_analysis.py

@@ -157,7 +157,6 @@ def read_excel_to_lists(file_path, sheet_name=0):
             master_list[2].extend([int(x) for x in data_lists[i+2]])
         except IndexError:
             master_list[2].extend([0])  # Note: Changed to list with single int 0
-    print(master_list)
             
     return master_list
 

{nettracer3d-0.2.9 → nettracer3d-0.3.0/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.2.9
+Version: 0.3.0
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <boom2449@gmail.com>
 Project-URL: User_Manual, https://drive.google.com/drive/folders/1fTkz3n4LN9_VxKRKC8lVQSlrz_wq0bVn?usp=drive_link