nettracer3d 0.7.8__py3-none-any.whl → 0.8.0__py3-none-any.whl

nettracer3d/proximity.py

@@ -361,7 +361,7 @@ def convert_centroids_to_array(centroids_list, xy_scale = 1, z_scale = 1):
     """
     # Determine how many centroids we have
     n_points = len(centroids_list)
-    
+
     # Get dimensionality from the first centroid
     dim = len(list(centroids_list)[0])
     
@@ -404,7 +404,12 @@ def generate_r_values(points_array, step_size, bounds = None, dim = 2, max_propo
 
     
     # Calculate the longest dimension
-    dimensions = max_coords - min_coords
+    try:
+        dimensions = max_coords - min_coords
+    except: # Presume dimension mismatch
+        min_coords = np.array([0,0,0])
+        dimensions = max_coords - min_coords
+
     max_dimension = np.max(dimensions)
     
     # Calculate maximum r value (typically half the shortest side for 2D,
@@ -459,7 +464,10 @@ def optimized_ripleys_k(reference_points, subset_points, r_values, bounds=None,
     # Calculate volume of study area
     min_bounds, max_bounds = bounds
     sides = max_bounds - min_bounds
-    volume = np.prod(sides)
+    if dim == 2:
+        volume = sides[0] * sides[1]
+    else:
+        volume = np.prod(sides)
     
     # Point intensity (points per unit volume)
     intensity = n_ref / volume
@@ -618,7 +626,7 @@ def compute_ripleys_h(k_values, r_values, dimension=2):
     else:
         raise ValueError("Dimension must be 2 or 3")
 
-def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12, 5)):
+def plot_ripley_functions(r_values, k_values, h_values, dimension=2, rootiden = None, compiden = None, figsize=(12, 5)):
     """
     Plot Ripley's K and H functions with theoretical Poisson distribution references
     adjusted for edge effects.
@@ -651,7 +659,10 @@ def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12
     ax1.plot(r_values, theo_k, 'r--', label='Theoretical K(r) for CSR')
     ax1.set_xlabel('Distance (r)')
     ax1.set_ylabel('L(r)')
-    ax1.set_title("Ripley's K Function")
+    if rootiden is None or compiden is None:
+        ax1.set_title("Ripley's K Function")
+    else:
+        ax1.set_title(f"Ripley's K Function for {compiden} Clustering Around {rootiden}")
     ax1.legend()
     ax1.grid(True, alpha=0.3)
     
@@ -660,7 +671,10 @@ def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12
     ax2.plot(r_values, theo_h, 'r--', label='Theoretical H(r) for CSR')
     ax2.set_xlabel('Distance (r)')
     ax2.set_ylabel('L(r) Normalized')
-    ax2.set_title("Ripley's H Function")
+    if rootiden is None or compiden is None:
+        ax2.set_title("Ripley's H Function")
+    else:
+        ax2.set_title(f"Ripley's H Function for {compiden} Clustering Around {rootiden}")
     ax2.axhline(y=0, color='k', linestyle='-', alpha=0.3)
     ax2.legend()
     ax2.grid(True, alpha=0.3)

nettracer3d/segmenter.py

@@ -1412,7 +1412,7 @@ class InteractiveSegmenter:
                  use_two=self.use_two,
                  mem_lock=self.mem_lock)
 
-        print(f"Model data saved to {file_name}")
+        print(f"Model data saved to {file_name}. Please retrain current model prior to segmentation.")
 
 
     def load_model(self, file_name):

nettracer3d/segmenter_GPU.py

@@ -1221,7 +1221,7 @@ class InteractiveSegmenter:
                  use_two=self.use_two,
                  mem_lock=self.mem_lock)
 
-        print(f"Model data saved to {file_name}")
+        print(f"Model data saved to {file_name}. Please retrain current model prior to segmentation.")
 
 
     def load_model(self, file_name):

nettracer3d/simple_network.py

@@ -174,32 +174,50 @@ def show_identity_network(excel_file_path, node_identities, geometric=False, geo
     G = nx.Graph()
     G.add_edges_from(edges)
 
-    # Create a more sophisticated color palette using a combination of colormap sequences
+    # ENHANCED COLOR LOGIC - Generate bright, contrasting colors
     unique_categories = list(set(identity_dict.values()))
     num_categories = len(unique_categories)
     
-    # Create a color palette that combines multiple colormaps for more distinct colors
-    if num_categories <= 10:
-        colors = plt.cm.tab10(np.linspace(0, 1, num_categories))
-    elif num_categories <= 20:
-        colors1 = plt.cm.tab20(np.linspace(0, 1, min(num_categories, 20)))
-        colors = colors1[:num_categories]
-    else:
-        # For large number of categories, combine multiple distinct colormaps
-        colors1 = plt.cm.tab20(np.linspace(0, 1, 20))
-        colors2 = plt.cm.Set3(np.linspace(0, 1, 12))
-        colors3 = plt.cm.Pastel1(np.linspace(0, 1, 9))
-        colors4 = plt.cm.Paired(np.linspace(0, 1, 12))
-        
-        # Combine and take needed number of colors
-        all_colors = np.vstack([colors1, colors2, colors3, colors4])
-        # Shuffle the colors to ensure adjacent categories have distinct colors
-        np.random.seed(42)  # For consistency
-        np.random.shuffle(all_colors)
-        colors = all_colors[:num_categories]
-
-    color_map = {category: mcolors.to_hex(color[:3]) 
-                 for category, color in zip(unique_categories, colors)}
+    def generate_distinct_colors(n):
+        """Generate visually distinct, bright colors with maximum contrast"""
+        if n <= 12:
+            # Use carefully selected high-contrast colors for small sets
+            base_colors = [
+                '#FF0000',  # Bright Red
+                '#0066FF',  # Bright Blue
+                '#00CC00',  # Bright Green
+                '#FF8800',  # Bright Orange
+                '#8800FF',  # Bright Purple
+                '#FFFF00',  # Bright Yellow
+                '#FF0088',  # Bright Pink
+                '#00FFFF',  # Bright Cyan
+                '#88FF00',  # Bright Lime
+                '#FF4400',  # Red-Orange
+                '#0088FF',  # Sky Blue
+                '#CC00FF'   # Magenta
+            ]
+            return base_colors[:n]
+        else:
+            # For larger sets, use HSV color space for maximum separation
+            colors = []
+            import colorsys
+            for i in range(n):
+                hue = (i * 360 / n) % 360
+                # Alternate saturation and value to create more distinction
+                sat = 0.85 if i % 2 == 0 else 0.95
+                val = 0.95 if i % 3 != 0 else 0.85
+                
+                # Convert HSV to RGB
+                rgb = colorsys.hsv_to_rgb(hue/360, sat, val)
+                hex_color = '#{:02x}{:02x}{:02x}'.format(
+                    int(rgb[0]*255), int(rgb[1]*255), int(rgb[2]*255)
+                )
+                colors.append(hex_color)
+            return colors
+    
+    # Generate the enhanced color palette
+    colors = generate_distinct_colors(num_categories)
+    color_map = dict(zip(unique_categories, colors))
 
     # Node size handling
     node_dict = {node: 30 if identity_dict[node] == 'Edge' else 100 
@@ -225,11 +243,11 @@ def show_identity_network(excel_file_path, node_identities, geometric=False, geo
     # Create separate axes for the graph and legend
     graph_ax = plt.gca()
     
-    # Draw the network
+    # Draw the network with enhanced font styling
     node_colors = [color_map[identity_dict[node]] for node in G.nodes()]
     nx.draw(G, pos, ax=graph_ax, with_labels=True, font_color='black', 
             font_weight='bold', node_size=node_sizes_list, 
-            node_color=node_colors, alpha=0.8, font_size=12)
+            node_color=node_colors, alpha=0.8, font_size=11, font_family='sans-serif')
 
     # Create custom legend with multiple columns if needed
     legend_handles = [Patch(color=color, label=category) 

{nettracer3d-0.7.8.dist-info → nettracer3d-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.8
+Version: 0.8.0
 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/
@@ -73,14 +73,11 @@ 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 0.7.8 (and 0.7.7) Updates -- 
-
-	* Bug Fixes
-	* Added the excel helper loader for better automated loading from QuPath exports specifically
-	* Added the ability to cluster communities into broader neighborhoods (with KMeans) based on their compositions.
-	* Added heatmap and UMAP graph displays based on community compositions.
-	* Added the ability to show heatmaps of nodes based on their density within their communities
-	* Added the ability to cluster nodes into communities based on spatial grouping in arbitrarily-sized cells (rather than just using the network)
-	* Added function to crop the current image
-	* More options under 'Modify Network'
-	* 'Show 3D' method now can render a bounding box.
+-- Version 0.8.0 Updates -- 
+
+	* Added ability to threshold nodes by degree.
+	* Improved image viewer window performance.
+	* Bug fixes and a few optimizations.
+	* Added ability to 'merge node identities' which just uses the nodes image as a reference for collecting 'identity' information from a group of other images - ie can use with cell nuclei (DAPI) to see what markers from the same imaging session overlap.
+	* Added ability to search for specific nodes directly in the nodes image with 'shift + f' or right click.
+	

nettracer3d-0.8.0.dist-info/RECORD

@@ -0,0 +1,23 @@
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+nettracer3d/community_extractor.py,sha256=ZOz97Au4k7dHK8azarWQtxCPyvwzGmDHNL8kTIC9by8,22670
+nettracer3d/excelotron.py,sha256=lS5vnpoOGZWp7fdqVpTPqeC-mUKrfwDrWHfx4PQ7Uzg,71384
+nettracer3d/modularity.py,sha256=O9OeKbjD3v6gSFz9K2GzP6LsxlpQaPfeJbM1pyIEigw,21788
+nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
+nettracer3d/neighborhoods.py,sha256=kkKR8m6Gjw34cDd_mytAIwLxqvuNBtQb2hU4JuBY9pI,12301
+nettracer3d/nettracer.py,sha256=494nHDmdrdfecTAShbXc0eFE2tG6WKJtEqKvJyt4sh4,227141
+nettracer3d/nettracer_gui.py,sha256=Pc_t5pDk0P4gpyC1axx37JJX6EpMvXdj0UHbqjqENrQ,501757
+nettracer3d/network_analysis.py,sha256=h-5yzUWdE0hcWYy8wcBA5LV1bRhdqiMnKbQLrRzb1Sw,41443
+nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
+nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
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+nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
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+nettracer3d/segmenter_GPU.py,sha256=sFVmz_cYIVOQqnfFV3peK9hzb6IoIV5WDQHH9Lws96I,53915
+nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA,9947
+nettracer3d/smart_dilate.py,sha256=DOEOQq9ig6-AO4MpqAG0CqrGDFqw5_UBeqfSedqHk28,25933
+nettracer3d-0.8.0.dist-info/licenses/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
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+nettracer3d-0.8.0.dist-info/RECORD,,

nettracer3d-0.7.8.dist-info/RECORD

@@ -1,23 +0,0 @@
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-nettracer3d/community_extractor.py,sha256=BrONCLRLYUdMfLe_018AQi0k0J7xwVahc_lmsOO5Pwo,23086
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-nettracer3d/modularity.py,sha256=O9OeKbjD3v6gSFz9K2GzP6LsxlpQaPfeJbM1pyIEigw,21788
-nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
-nettracer3d/neighborhoods.py,sha256=kkKR8m6Gjw34cDd_mytAIwLxqvuNBtQb2hU4JuBY9pI,12301
-nettracer3d/nettracer.py,sha256=M1KFIPg7WCzm8BXQOreuEVhgjg0PpLKRg4Y88DyVuK8,225843
-nettracer3d/nettracer_gui.py,sha256=WTcN-tOk4vzDLhnVN4un5PEkC90GDp3sxZZhgLifMOM,468787
-nettracer3d/network_analysis.py,sha256=h-5yzUWdE0hcWYy8wcBA5LV1bRhdqiMnKbQLrRzb1Sw,41443
-nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
-nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
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