nettracer3d 0.4.4__py3-none-any.whl → 0.4.5__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-0.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.4.4
+Version: 0.4.5
 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
@@ -25,12 +25,26 @@ 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"
+Requires-Dist: torch==2.2.0+cu118; extra == "cuda11"
+Requires-Dist: torchvision==0.17.0+cu118; extra == "cuda11"
+Requires-Dist: torchaudio==2.2.0+cu118; extra == "cuda11"
 Provides-Extra: cuda12
 Requires-Dist: cupy-cuda12x; extra == "cuda12"
+Requires-Dist: torch==2.2.0+cu121; extra == "cuda12"
+Requires-Dist: torchvision==0.17.0+cu121; extra == "cuda12"
+Requires-Dist: torchaudio==2.2.0+cu121; extra == "cuda12"
 Provides-Extra: cupy
 Requires-Dist: cupy; extra == "cupy"
+Requires-Dist: torch; extra == "cupy"
+Requires-Dist: torchvision; extra == "cupy"
+Requires-Dist: torchaudio; extra == "cupy"
+Provides-Extra: gpu
+Requires-Dist: cupy-cuda11x; (platform_system == "Linux" and platform_machine == "x86_64") and extra == "gpu"
+Requires-Dist: cupy-cuda12x; platform_system == "Windows" and extra == "gpu"
+Requires-Dist: cupy; platform_system == "Darwin" and extra == "gpu"
 
 NetTracer3D is a python package developed for both 2D and 3D analysis of microscopic images in the .tif file format. It supports generation of 3D networks showing the relationships between objects (or nodes) in three dimensional space, either based on their own proximity or connectivity via connecting objects such as nerves or blood vessels. In addition to these functionalities are several advanced 3D data processing algorithms, such as labeling of branched structures or abstraction of branched structures into networks. Note that nettracer3d uses segmented data, which can be segmented from other softwares such as ImageJ and imported into NetTracer3D, although it does offer its own segmentation via intensity and volumetric thresholding, or random forest machine learning segmentation. NetTracer3D currently has a fully functional GUI. To use the GUI, after installing the nettracer3d package via pip, enter the command 'nettracer3d' in your command prompt:
 

{nettracer3d-0.4.4.dist-info → nettracer3d-0.4.5.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-0.4.5.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.4.5.dist-info/METADATA,sha256=heriQfrxj6N0iPIgLTqKaVMnC81iUmjFI44dQ4BeyW4,3676
+nettracer3d-0.4.5.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nettracer3d-0.4.5.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.4.5.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.4.5.dist-info/RECORD,,