nettracer3d 0.3.7__tar.gz → 0.3.9__tar.gz

{nettracer3d-0.3.7/src/nettracer3d.egg-info → nettracer3d-0.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.3.7
+Version: 0.3.9
 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-0.3.7 → nettracer3d-0.3.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.3.7"
+version = "0.3.9"
 authors = [
   { name="Liam McLaughlin", email="boom2449@gmail.com" },
 ]

{nettracer3d-0.3.7 → nettracer3d-0.3.9}/src/nettracer3d/nettracer.py

@@ -23,8 +23,6 @@ except:
 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 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.
 
@@ -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-0.3.7 → nettracer3d-0.3.9}/src/nettracer3d/nettracer_gui.py

@@ -167,6 +167,7 @@ class ImageViewerWindow(QMainWindow):
         self.zoom_button.setFixedSize(40, 40)
         self.zoom_button.clicked.connect(self.toggle_zoom_mode)
         control_layout.addWidget(self.zoom_button)
+        self.resizing = False
 
         self.pan_button = QPushButton("✋")
         self.pan_button.setCheckable(True)
@@ -1783,8 +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)
@@ -2797,8 +2800,12 @@ class ImageViewerWindow(QMainWindow):
     def update_slice(self):
         """Queue a slice update when slider moves."""
         # Store current view settings
-        current_xlim = self.ax.get_xlim() if hasattr(self, 'ax') and self.ax.get_xlim() != (0, 1) else None
-        current_ylim = self.ax.get_ylim() if hasattr(self, 'ax') and self.ax.get_ylim() != (0, 1) else None
+        if not self.resizing:
+            current_xlim = self.ax.get_xlim() if hasattr(self, 'ax') and self.ax.get_xlim() != (0, 1) else None
+            current_ylim = self.ax.get_ylim() if hasattr(self, 'ax') and self.ax.get_ylim() != (0, 1) else None
+        else:
+            current_xlim = None
+            current_ylim = None
         
         # Store the pending slice and view settings
         self.pending_slice = (self.slice_slider.value(), (current_xlim, current_ylim))
@@ -2855,11 +2862,8 @@ class ImageViewerWindow(QMainWindow):
         self.ax = self.figure.add_subplot(111)
         
         # Store current zoom limits if they exist and weren't provided
-        if preserve_zoom is None and hasattr(self, 'ax'):
-            current_xlim = self.ax.get_xlim() if self.ax.get_xlim() != (0, 1) else None
-            current_ylim = self.ax.get_ylim() if self.ax.get_ylim() != (0, 1) else None
-        else:
-            current_xlim, current_ylim = preserve_zoom if preserve_zoom else (None, None)
+ 
+        current_xlim, current_ylim = preserve_zoom if preserve_zoom else (None, None)
         
         # Define base colors for each channel with increased intensity
         base_colors = self.base_colors
@@ -2934,10 +2938,7 @@ class ImageViewerWindow(QMainWindow):
                          cmap=highlight_cmap,
                          alpha=0.5)
 
-        # Restore zoom limits if they existed
-        if current_xlim is not None and current_ylim is not None:
-            self.ax.set_xlim(current_xlim)
-            self.ax.set_ylim(current_ylim)
+
         
         # Style the axes
         self.ax.set_xlabel('X')
@@ -2978,8 +2979,17 @@ class ImageViewerWindow(QMainWindow):
         if active_channels:
             self.ax.set_xlim(-0.5, min_width - 0.5)
             self.ax.set_ylim(min_height - 0.5, -0.5)
+
+        if self.resizing:
+            self.original_xlim = self.ax.get_xlim()
+            self.original_ylim = self.ax.get_ylim()
+        # Restore zoom limits if they existed
+        if current_xlim is not None and current_ylim is not None:
+            self.ax.set_xlim(current_xlim)
+            self.ax.set_ylim(current_ylim)
         
         self.canvas.draw()
+
     def show_netshow_dialog(self):
         dialog = NetShowDialog(self)
         dialog.exec()
@@ -2988,6 +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()
@@ -4360,6 +4385,8 @@ class PartitionDialog(QDialog):
         except Exception as e:
             print(f"Error creating communities: {e}")
 
+
+
 class RadialDialog(QDialog):
 
     def __init__(self, parent=None):
@@ -4956,6 +4983,7 @@ class ResizeDialog(QDialog):
 
     def run_resize(self, undo = False):
         try:
+            self.parent().resizing = True
             # Get parameters
             try:
                 resize = float(self.resize.text()) if self.resize.text() else None
@@ -5104,6 +5132,7 @@ class ResizeDialog(QDialog):
                     
             self.parent().update_display()
             self.reset_fields()
+            self.parent().resizing = False
             self.accept()
             
         except Exception as e:
@@ -6034,6 +6063,7 @@ class GenNodesDialog(QDialog):
             )
 
             if down_factor > 0 and not self.called:
+                self.parent().resizing = True
 
                 my_network.edges = n3d.downsample(my_network.edges, down_factor, order = order)
                 my_network.xy_scale = my_network.xy_scale * down_factor
@@ -6061,6 +6091,7 @@ class GenNodesDialog(QDialog):
 
 
             self.parent().update_display()
+            self.parent().resizing = False
             self.accept()
             
         except Exception as e:

{nettracer3d-0.3.7 → nettracer3d-0.3.9/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.3.7
+Version: 0.3.9
 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