nettracer3d 0.4.4__py3-none-any.whl → 0.4.6__py3-none-any.whl

nettracer3d/smart_dilate.py

@@ -19,9 +19,16 @@ except:
 
 
 def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
-    """Internal method to dilate an array in 3D.
+    """Internal method to dilate an array in 3D. Dilation this way is much faster than using a distance transform although the latter is theoretically more accurate.
     Arguments are an array,  and the desired pixel dilation amounts in X, Y, Z."""
 
+    if tiff_array.shape[0] == 1:
+        return dilate_2D(tiff_array, ((dilated_x - 1) / 2))
+
+    if dilated_x == 3 and dilated_y == 3  and dilated_z == 3:
+
+        return dilate_3D_old(tiff_array, dilated_x, dilated_y, dilated_z)
+
     def create_circular_kernel(diameter):
         """Create a 2D circular kernel with a given radius.
 
@@ -85,9 +92,17 @@ def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
         dilated_slice = cv2.dilate(tiff_slice, kernel, iterations=1)
         return y, dilated_slice
 
+    """
+    def process_slice_third(x):
+        tiff_slice = tiff_array[:, :, x].astype(np.uint8)
+        dilated_slice = cv2.dilate(tiff_slice, kernel, iterations=1)
+        return x, dilated_slice
+    """
+
     # Create empty arrays to store the dilated results for the XY and XZ planes
     dilated_xy = np.zeros_like(tiff_array, dtype=np.uint8)
     dilated_xz = np.zeros_like(tiff_array, dtype=np.uint8)
+    #dilated_yz = np.zeros_like(tiff_array, dtype=np.uint8)
 
     kernel_x = int(dilated_x)
     kernel = create_circular_kernel(kernel_x)
@@ -104,7 +119,10 @@ def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
     kernel_x = int(dilated_x)
     kernel_z = int(dilated_z)
 
-    kernel = create_ellipsoidal_kernel(kernel_x, kernel_z)
+    if kernel_x == kernel_z:
+        kernel = create_circular_kernel(kernel_z)
+    else:
+        kernel = create_ellipsoidal_kernel(kernel_x, kernel_z)
 
     with ThreadPoolExecutor(max_workers=num_cores) as executor:
         futures = {executor.submit(process_slice_other, y): y for y in range(tiff_array.shape[1])}
@@ -113,8 +131,18 @@ def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
             y, dilated_slice = future.result()
             dilated_xz[:, y, :] = dilated_slice
 
+    """
+    with ThreadPoolExecutor(max_workers=num_cores) as executor:
+        futures = {executor.submit(process_slice_other, x): x for x in range(tiff_array.shape[2])}
+        
+        for future in as_completed(futures):
+            x, dilated_slice = future.result()
+            dilated_yz[:, :, x] = dilated_slice
+    """
+
+
     # Overlay the results
-    final_result = dilated_xy | dilated_xz
+    final_result = (dilated_xy | dilated_xz)
 
     return final_result
 

{nettracer3d-0.4.4.dist-info → nettracer3d-0.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.4.4
+Version: 0.4.6
 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
@@ -11,7 +11,7 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: numpy==1.26.4
 Requires-Dist: scipy
 Requires-Dist: scikit-image
 Requires-Dist: Pillow
@@ -25,6 +25,7 @@ Requires-Dist: python-louvain
 Requires-Dist: tifffile
 Requires-Dist: qtrangeslider
 Requires-Dist: PyQt6
+Requires-Dist: scikit-learn
 Provides-Extra: cuda11
 Requires-Dist: cupy-cuda11x; extra == "cuda11"
 Provides-Extra: cuda12

{nettracer3d-0.4.4.dist-info → nettracer3d-0.4.6.dist-info}/RECORD

@@ -3,19 +3,19 @@ nettracer3d/community_extractor.py,sha256=8bRDJOfZhOFLtpkJVaDQrQ4O8wUywyr-EfVvW5
 nettracer3d/hub_getter.py,sha256=KiNtxdajLkwB1ftslvrh1FE1Ch9ZCFEmHSEEotwR-To,8298
 nettracer3d/modularity.py,sha256=V1f3s_vGd8EuVz27mzq6ycIGr0BWIpH7c7NU4QjgAHU,30247
 nettracer3d/morphology.py,sha256=CsRWB0DY-vBBlKdF9IQwgfYYZswuE7n1Iu_Osxgmxnw,13042
-nettracer3d/nettracer.py,sha256=x-4xjEJNWzTy5gKvpGAmRzlWD3Wx-lomH_ItqRNv9v8,207727
-nettracer3d/nettracer_gui.py,sha256=1b5sFTCe3Jinc200vRTknGsY_Xm2rj-BG2CDyo-gHGU,324790
+nettracer3d/nettracer.py,sha256=hDccGy6RybSJFvY6dsN1l5eM3wKZW93CizlTvgEeyNs,209690
+nettracer3d/nettracer_gui.py,sha256=eljw6WT8lcKHRD8RPQZ3uwtovrN4YbCKqPWLMifxuVI,333511
 nettracer3d/network_analysis.py,sha256=MJBBjslA1k_R8ymid77U-qGSgzxFVfzGVQhE0IdhnbE,48046
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=BMiD_FrlOHeGD4AQZ_Emd152PfxFuMgGf2x4S0TOTnw,9752
 nettracer3d/proximity.py,sha256=B1pmFegx5Wb0JKI5rvpILv2VRU09f6M2iljAQAqBja0,11059
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
-nettracer3d/segmenter.py,sha256=Inp3m6ajgR03zh_JyJt3Qntb-ZXmxuxVDBbmQnhb3pM,11619
+nettracer3d/segmenter.py,sha256=7CqPKxvc6dqu3RoOxUNWFL48CcuV7RwmIzkekqpW6uE,28733
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
-nettracer3d/smart_dilate.py,sha256=JALeAZ7LLU2psTuI5wlCZobtDx8I0CfihdoEblwfhOY,23520
-nettracer3d-0.4.4.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.4.4.dist-info/METADATA,sha256=4os3ofWdAzCFAfKt0LvFlUE4atoVKO26s0OKUq1NO7s,2884
-nettracer3d-0.4.4.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nettracer3d-0.4.4.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.4.4.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.4.4.dist-info/RECORD,,
+nettracer3d/smart_dilate.py,sha256=dvbG2UhWzMQrtDqSj281rixNRgwUHOFGlJZ9RSl6rKs,24590
+nettracer3d-0.4.6.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.4.6.dist-info/METADATA,sha256=VPVlkgxFID3-nvAGcwTbuoOhw_tV8xEeu4mtdu3KJ_s,2921
+nettracer3d-0.4.6.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nettracer3d-0.4.6.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.4.6.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.4.6.dist-info/RECORD,,