nettracer3d 0.5.9__tar.gz → 0.6.1__tar.gz

{nettracer3d-0.5.9/src/nettracer3d.egg-info → nettracer3d-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.5.9
+Version: 0.6.1
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <mclaughlinliam99@gmail.com>
 Project-URL: User_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
@@ -44,6 +44,10 @@ NetTracer3D is free to use/fork for academic/nonprofit use so long as citation i
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.5.9 updates --
+-- Version 0.6.1 updates --
 
-1. Bug fixes
+1. New feature for the machine learning segmenter. Now has a RAM lock mode which will always limit it to computing 1 chunk at a time, in both the interactive segmenter and the gross-segmenter. Feature map calculation within the chunk is made parallel to compensate which should allow this to function more optimally with RAM without really sacrificing performance. This should prevent the segmenter from majorly leaking memory in large arrays.
+2. New function - 'Image' -> 'Select Objects'. Essentially just arbitrary selects/deselects lists of nodes or edges from the user in case there are some they are interested in but can't conveniently find. Allows imports from spreadsheets in case the user preorganizes some set of objects they want to select/deselect.
+3. Brightness/Contrast now shades out of 65,535 instead of 255 which should allow better brightening options to images above 8bit depth.
+4. Select all function updated to use the mini highlight overlay in larger images. Also reports the number of nodes/edges in the array in the cmd window when used.
+5. Deleted the now unused 'hub_getter.py' script from the package.

{nettracer3d-0.5.9 → nettracer3d-0.6.1}/README.md

@@ -8,6 +8,10 @@ NetTracer3D is free to use/fork for academic/nonprofit use so long as citation i
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.5.9 updates --
+-- Version 0.6.1 updates --
 
-1. Bug fixes
+1. New feature for the machine learning segmenter. Now has a RAM lock mode which will always limit it to computing 1 chunk at a time, in both the interactive segmenter and the gross-segmenter. Feature map calculation within the chunk is made parallel to compensate which should allow this to function more optimally with RAM without really sacrificing performance. This should prevent the segmenter from majorly leaking memory in large arrays.
+2. New function - 'Image' -> 'Select Objects'. Essentially just arbitrary selects/deselects lists of nodes or edges from the user in case there are some they are interested in but can't conveniently find. Allows imports from spreadsheets in case the user preorganizes some set of objects they want to select/deselect.
+3. Brightness/Contrast now shades out of 65,535 instead of 255 which should allow better brightening options to images above 8bit depth.
+4. Select all function updated to use the mini highlight overlay in larger images. Also reports the number of nodes/edges in the array in the cmd window when used.
+5. Deleted the now unused 'hub_getter.py' script from the package.

{nettracer3d-0.5.9 → nettracer3d-0.6.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.5.9"
+version = "0.6.1"
 authors = [
   { name="Liam McLaughlin", email="mclaughlinliam99@gmail.com" },
 ]

{nettracer3d-0.5.9 → nettracer3d-0.6.1}/src/nettracer3d/nettracer.py

@@ -27,7 +27,6 @@ from skimage import morphology as mpg
 from . import smart_dilate
 from . import modularity
 from . import simple_network
-from . import hub_getter
 from . import community_extractor
 from . import network_analysis
 from . import morphology
@@ -3934,28 +3933,6 @@ class Network_3D:
 
         return degrees, nodes
 
-    def get_hubs(self, proportion = None, down_factor = 1, directory = None):
-        """
-        Method to isolate hub regions of a network (Removing all nodes below some proportion of highest degrees), also generating overlays that relate this information to the 3D structure.
-        Overlays include a grayscale image where nodes are assigned a grayscale value corresponding to their degree, and a numerical index where numbers are drawn at nodes corresponding to their degree.
-        These will be saved to the active directory if none is specified. Note calculations will be done with node_centroids unless a down_factor is passed. Note that a down_factor must be passed if there are no node_centroids.
-        :param proportion: (Optional - Val = None; Float). A float of 0 to 1 that details what proportion of highest node degrees to include in the output. Note that this value will be set to 0.1 by default.
-        :param down_factor: (Optional - Val = 1; int). A factor to downsample nodes by while calculating centroids, assuming no node_centroids property was set.
-        :param directory: (Optional - Val = None; string). A path to a directory to save outputs.
-        :returns: A dictionary of degree values for each node above the desired proportion of highest degree nodes.
-        """
-        if down_factor > 1:
-            centroids = self._node_centroids.copy()
-            for item in self._node_centroids:
-                centroids[item] = np.round((self._node_centroids[item]) / down_factor)
-            nodes = downsample(self._nodes, down_factor)
-            hubs = hub_getter.get_hubs(nodes, self._network, proportion, directory = directory, centroids = centroids)
-
-        else:
-            hubs = hub_getter.get_hubs(self._nodes, self._network, proportion, directory = directory, centroids = self._node_centroids)
-
-        return hubs 
-
 
     def isolate_connected_component(self, key = None, directory = None, full_edges = None, gen_images = True):
         """