nettracer3d 1.2.8__tar.gz → 1.2.9__tar.gz

{nettracer3d-1.2.8/src/nettracer3d.egg-info → nettracer3d-1.2.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.2.8
+Version: 1.2.9
 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/
@@ -70,35 +70,27 @@ Please see: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTW
 
 	* pip install nettracer3d
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 3. **For 3D Displays**: Or if you also want Napari for 3D displays:
 
 	* pip install nettracer3d[viz]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 4. **Optional Performance Boost**: If you are trying to process large images, you may also want to include the 'edt' module in your package. This will allow parallelized CPU calculations for several of the search functions which can increase their speed by an order of magnitude or more depending on how many cores your CPU has. This can be a major benefit if you have a strong CPU and sufficient RAM. It requires an extra pre-installation step, thus is not included by default. You will also have to install the C++ build tools from windows. Please head to this link, then download and run the installer: https://visualstudio.microsoft.com/visual-cpp-build-tools/. In the menu of the installer, select the 'Desktop Development with C++' option, then proceed to download/install it using the installation menu. You will likely want to be using the Python distributed from the actual Python website and not the windows store (or elsewhere) or the edt module may not work properly. To bundle with edt use:
 
 	* pip install nettracer3d[edt]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 
 5. **Recommended full package**: Or if you want to just get both edt and napari at once:
 	
 	* pip install nettracer3d[rec]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 
 6. Likewise, if you already installed the default version, you can add napari and/or edt with just:
 
 	* pip install edt
 	* pip install napari
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
    
 --- Installing as a Python package in Anaconda---
 
@@ -162,8 +154,7 @@ NetTracer3D is freely available for academic and nonprofit use and can obtained
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.2.8 Updates --
+-- Version 1.2.9 Updates --
 
-	* Made edt an optional dependency.
-	* Updated readme
+	* Some minor adjustments.
 	

{nettracer3d-1.2.8 → nettracer3d-1.2.9}/README.md

@@ -20,35 +20,27 @@ Please see: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTW
 
 	* pip install nettracer3d
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 3. **For 3D Displays**: Or if you also want Napari for 3D displays:
 
 	* pip install nettracer3d[viz]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 4. **Optional Performance Boost**: If you are trying to process large images, you may also want to include the 'edt' module in your package. This will allow parallelized CPU calculations for several of the search functions which can increase their speed by an order of magnitude or more depending on how many cores your CPU has. This can be a major benefit if you have a strong CPU and sufficient RAM. It requires an extra pre-installation step, thus is not included by default. You will also have to install the C++ build tools from windows. Please head to this link, then download and run the installer: https://visualstudio.microsoft.com/visual-cpp-build-tools/. In the menu of the installer, select the 'Desktop Development with C++' option, then proceed to download/install it using the installation menu. You will likely want to be using the Python distributed from the actual Python website and not the windows store (or elsewhere) or the edt module may not work properly. To bundle with edt use:
 
 	* pip install nettracer3d[edt]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 
 5. **Recommended full package**: Or if you want to just get both edt and napari at once:
 	
 	* pip install nettracer3d[rec]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 
 6. Likewise, if you already installed the default version, you can add napari and/or edt with just:
 
 	* pip install edt
 	* pip install napari
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
    
 --- Installing as a Python package in Anaconda---
 
@@ -112,8 +104,7 @@ NetTracer3D is freely available for academic and nonprofit use and can obtained
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.2.8 Updates --
+-- Version 1.2.9 Updates --
 
-	* Made edt an optional dependency.
-	* Updated readme
+	* Some minor adjustments.
 	

{nettracer3d-1.2.8 → nettracer3d-1.2.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.2.8"
+version = "1.2.9"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-1.2.8 → nettracer3d-1.2.9}/src/nettracer3d/nettracer.py

@@ -5608,7 +5608,7 @@ class Network_3D:
                 print(f"Using {volume} for the volume measurement (Volume of provided mask as scaled by xy and z scaling)")
                 
                 # Compute distance transform on padded array
-                legal = smart_dilate.compute_distance_transform_distance(legal, sampling = [self.z_scale, self.xy_scale, self.xy_scale])
+                legal = smart_dilate.compute_distance_transform_distance(legal, sampling = [self.z_scale, self.xy_scale, self.xy_scale], fast_dil = True)
                 
                 # Remove padding after distance transform
                 if dim == 2:

{nettracer3d-1.2.8 → nettracer3d-1.2.9}/src/nettracer3d/smart_dilate.py

@@ -11,7 +11,7 @@ try:
     import edt
     print("Parallel search functions enabled")
 except:
-    print("Parallel search functions disabled (requires edt package), will fall back to single-threaded")
+    print("Some parallel search functions disabled (requires edt package), will fall back to single-threaded")
 import math
 import re
 from . import nettracer
@@ -297,9 +297,13 @@ def process_chunk(start_idx, end_idx, nodes, ring_mask, nearest_label_indices):
 def smart_dilate(nodes, dilate_xy = 0, dilate_z = 0, directory = None, GPU = True, fast_dil = True, predownsample = None, use_dt_dil_amount = None, xy_scale = 1, z_scale = 1):
 
     if fast_dil:
-        dilated = nettracer.dilate_3D_dt(nodes, use_dt_dil_amount, xy_scale, z_scale, fast_dil = True)
-        return smart_label_watershed(dilated, nodes, directory = None, remove_template = False)
-
+        try:
+            import edt
+            dilated = nettracer.dilate_3D_dt(nodes, use_dt_dil_amount, xy_scale, z_scale, fast_dil = True)
+            return smart_label_watershed(dilated, nodes, directory = None, remove_template = False)
+        except:
+            print("edt package not found. Please use 'pip install edt' if you would like to enable parallel searching.")
+            return smart_dilate_short(nodes, use_dt_dil_amount, directory, xy_scale, z_scale)
     else:
         return smart_dilate_short(nodes, use_dt_dil_amount, directory, xy_scale, z_scale)
 
@@ -703,7 +707,7 @@ def compute_distance_transform_distance(nodes, sampling=[1, 1, 1], fast_dil=Fals
                         str(nodes.dtype),
                         tuple(sampling)
                     )
-                    result_shape, result_dtype = future.result(timeout=300)  # Add timeout
+                    result_shape, result_dtype = future.result()
                 
                 distance = np.ndarray(result_shape, dtype=result_dtype, buffer=output_shm.buf).copy()
                 

{nettracer3d-1.2.8 → nettracer3d-1.2.9/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.2.8
+Version: 1.2.9
 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/
@@ -70,35 +70,27 @@ Please see: https://www.youtube.com/watch?v=_4uDy0mzG94&list=PLsrhxiimzKJMZ3_gTW
 
 	* pip install nettracer3d
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 3. **For 3D Displays**: Or if you also want Napari for 3D displays:
 
 	* pip install nettracer3d[viz]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 4. **Optional Performance Boost**: If you are trying to process large images, you may also want to include the 'edt' module in your package. This will allow parallelized CPU calculations for several of the search functions which can increase their speed by an order of magnitude or more depending on how many cores your CPU has. This can be a major benefit if you have a strong CPU and sufficient RAM. It requires an extra pre-installation step, thus is not included by default. You will also have to install the C++ build tools from windows. Please head to this link, then download and run the installer: https://visualstudio.microsoft.com/visual-cpp-build-tools/. In the menu of the installer, select the 'Desktop Development with C++' option, then proceed to download/install it using the installation menu. You will likely want to be using the Python distributed from the actual Python website and not the windows store (or elsewhere) or the edt module may not work properly. To bundle with edt use:
 
 	* pip install nettracer3d[edt]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 
 5. **Recommended full package**: Or if you want to just get both edt and napari at once:
 	
 	* pip install nettracer3d[rec]
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 
 6. Likewise, if you already installed the default version, you can add napari and/or edt with just:
 
 	* pip install edt
 	* pip install napari
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
    
 --- Installing as a Python package in Anaconda---
 
@@ -162,8 +154,7 @@ NetTracer3D is freely available for academic and nonprofit use and can obtained
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.2.8 Updates --
+-- Version 1.2.9 Updates --
 
-	* Made edt an optional dependency.
-	* Updated readme
+	* Some minor adjustments.