nettracer3d 0.3.8__py3-none-any.whl → 0.4.0__py3-none-any.whl

nettracer3d/nettracer.py

@@ -22,9 +22,7 @@ except:
     pass
 from . import node_draw
 from . import network_draw
-from skimage.morphology import skeletonize_3d
-#from skimage.segmentation import watershed
-from skimage.feature import peak_local_max
+from skimage import morphology as mpg
 from concurrent.futures import ThreadPoolExecutor, as_completed
 from . import smart_dilate
 from . import modularity
@@ -864,6 +862,11 @@ def dilate_3D(tiff_array, dilated_x, dilated_y, dilated_z):
     """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 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.
 
@@ -1500,7 +1503,7 @@ def skeletonize(arrayimage, directory = None):
     else:
         image = None
 
-    arrayimage = (skeletonize_3d(arrayimage))
+    arrayimage = (mpg.skeletonize(arrayimage))
 
     if type(image) == str:
         if directory is None:
@@ -4182,6 +4185,51 @@ class Network_3D:
 
         return array
 
+    def community_id_info(self):
+        def invert_dict(d):
+            inverted = {}
+            for key, value in d.items():
+                inverted.setdefault(value, []).append(key)
+            return inverted
+
+        community_dict = invert_dict(self.communities)
+        summation = 0
+        id_set = set(self.node_identities.values())
+        output = {sort: 0 for sort in id_set}
+        template = copy.deepcopy(output)
+
+        for community in community_dict:
+            counter = copy.deepcopy(template)
+            nodes = community_dict[community]
+            size = len(nodes)
+            summation += size
+            
+            # Count identities in this community
+            for node in nodes:
+                counter[self.node_identities[node]] += 1
+            
+            # Convert to proportions within this community and weight by size
+            for sort in counter:
+                if size > 0:  # Avoid division by zero
+                    counter[sort] = (counter[sort]) * size  # proportion * size
+                    
+            # Add to running totals
+            for sort, weighted_count in counter.items():
+                output[sort] = output.get(sort, 0) + weighted_count
+
+        # Normalize by total size
+        dictsum = 0
+        for sort in output:
+            output[sort] = output[sort]/summation
+            dictsum += output[sort]
+
+        for sort in output:
+            output[sort] = output[sort]/dictsum
+
+        return output
+
+
+
 
     def kd_network(self, distance = 100, targets = None):
 

nettracer3d/nettracer_gui.py

@@ -1784,8 +1784,10 @@ class ImageViewerWindow(QMainWindow):
         network_menu = analysis_menu.addMenu("Network")
         netshow_action = network_menu.addAction("Show Network")
         netshow_action.triggered.connect(self.show_netshow_dialog)
-        partition_action = network_menu.addAction("Community Partition + Community Stats")
+        partition_action = network_menu.addAction("Community Partition +Generic Community Stats")
         partition_action.triggered.connect(self.show_partition_dialog)
+        com_identity_action = network_menu.addAction("Identity Makeup of Network Communities (Weighted avg by community size)")
+        com_identity_action.triggered.connect(self.handle_com_id)
         stats_menu = analysis_menu.addMenu("Stats")
         allstats_action = stats_menu.addAction("Calculate Generic Network Stats")
         allstats_action.triggered.connect(self.stats)
@@ -2996,6 +2998,21 @@ class ImageViewerWindow(QMainWindow):
         dialog = PartitionDialog(self)
         dialog.exec()
 
+    def handle_com_id(self):
+        if my_network.node_identities is None:
+            print("Node identities must be set")
+
+        if my_network.communities is None:
+            self.show_partition_dialog()
+
+            if my_network.communities is None:
+                return
+
+        info = my_network.community_id_info()
+
+        self.format_for_upperright_table(info, 'Node Identity Type', 'Weighted Proportion in Communities', 'Weighted Average of Community Makeup')
+
+
     def show_radial_dialog(self):
         dialog = RadialDialog(self)
         dialog.exec()
@@ -4368,6 +4385,8 @@ class PartitionDialog(QDialog):
         except Exception as e:
             print(f"Error creating communities: {e}")
 
+
+
 class RadialDialog(QDialog):
 
     def __init__(self, parent=None):

{nettracer3d-0.3.8.dist-info → nettracer3d-0.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.3.8
+Version: 0.4.0
 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-0.3.8.dist-info → nettracer3d-0.4.0.dist-info}/RECORD

@@ -3,16 +3,16 @@ 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=wv7v06YUcn5lMyefcc_znQlXF5iDxvUdoc0fXOKlGTw,12982
-nettracer3d/nettracer.py,sha256=CfAdS3SnigL4TkfqwHRIg0WeBtwJ1nGysNq5pfSSwVU,201682
-nettracer3d/nettracer_gui.py,sha256=VJJE03DebIgK_A1Pga7tfUxiQOUXZ0fTYG5ZwThd35M,289339
+nettracer3d/nettracer.py,sha256=sFwHz-Ghoft3nNS3H691EcMTpoeLKT3I_X-6m6vXpyg,203264
+nettracer3d/nettracer_gui.py,sha256=GSTICp2V0MAwMpw6RcUrR0kdF721bpBOGMHnOK2LHLM,290039
 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=KYs4QUbt1U79RLzTvt8BmrxeGVaeKOQ2brtzTjjA78c,11011
 nettracer3d/simple_network.py,sha256=fP1gkDdtQcHruEZpUdasKdZeVacoLOxKhR3bY0L1CAQ,15426
 nettracer3d/smart_dilate.py,sha256=howfO6Lw5PxNjkaOBSCjkmf7fyau_-_8iTct2mAuTAQ,22083
-nettracer3d-0.3.8.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.3.8.dist-info/METADATA,sha256=FS6GRDErGwT93g0XvCatJ36Z4s8olwVrgTrJER-ldks,2894
-nettracer3d-0.3.8.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nettracer3d-0.3.8.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.3.8.dist-info/RECORD,,
+nettracer3d-0.4.0.dist-info/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.4.0.dist-info/METADATA,sha256=lu39yZioerqbPHonV_S5P04-KeJlncq5MqitDJffkWw,2894
+nettracer3d-0.4.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nettracer3d-0.4.0.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.4.0.dist-info/RECORD,,