nettracer3d 0.8.2__py3-none-any.whl → 0.8.3__py3-none-any.whl

nettracer3d/community_extractor.py

@@ -517,21 +517,90 @@ def rgb_to_color_name(rgb: Tuple[int, int, int]) -> str:
         distance = np.sqrt(np.sum((rgb_array - np.array(color_rgb)) ** 2))
         if distance < min_distance:
             min_distance = distance
-            closest_color = color_name + f" {str(rgb_array)}"
-            
+            #closest_color = color_name + f" {str(rgb_array)}" # <- if we want RGB names
+            closest_color = color_name
+
     return closest_color
 
-def convert_node_colors_to_names(node_to_color: Dict[int, Tuple[int, int, int]]) -> Dict[int, str]:
+def convert_node_colors_to_names(node_to_color: Dict[int, Tuple[int, int, int]], 
+                                show_legend: bool = True,
+                                figsize: Tuple[int, int] = (10, 8),
+                                save_path: str = None) -> Dict[int, str]:
     """
     Convert a dictionary of node-to-RGB mappings to node-to-color-name mappings.
+    Optionally displays a matplotlib legend showing the mappings.
     
     Args:
         node_to_color: Dictionary mapping node IDs to RGB tuples
+        show_legend: Whether to display the color legend plot
+        figsize: Figure size as (width, height) for the legend
+        save_path: Optional path to save the legend figure
         
     Returns:
         Dictionary mapping node IDs to color names
     """
-    return {node: rgb_to_color_name(color) for node, color in node_to_color.items()}
+    # Convert colors to names
+    node_to_names = {node: rgb_to_color_name(color) for node, color in node_to_color.items()}
+    
+    # Create legend if requested
+    if show_legend:
+        import matplotlib.pyplot as plt
+        from matplotlib.patches import Rectangle
+        
+        num_entries = len(node_to_color)
+        
+        # Calculate dynamic spacing based on number of entries
+        entry_height = 0.8
+        total_height = num_entries * entry_height + 1.5  # Extra space for title and margins
+        
+        # Create figure and axis with proper scaling
+        fig, ax = plt.subplots(figsize=figsize)
+        ax.set_xlim(0, 10)
+        ax.set_ylim(0, total_height)
+        ax.axis('off')
+        
+        # Title
+        ax.text(5, total_height - 0.5, 'Color Legend', 
+                fontsize=16, fontweight='bold', ha='center')
+        
+        # Sort nodes for consistent display
+        sorted_nodes = sorted(node_to_color.keys())
+        
+        # Create legend entries
+        for i, node in enumerate(sorted_nodes):
+            y_pos = total_height - (i + 1) * entry_height - 0.8
+            rgb = node_to_color[node]
+            color_name = node_to_names[node]
+            
+            # Normalize RGB values for matplotlib (0-1 range)
+            norm_rgb = tuple(c/255.0 for c in rgb)
+            
+            # Draw color swatch (using actual RGB values)
+            swatch = Rectangle((1.0, y_pos - 0.15), 0.8, 0.3, 
+                              facecolor=norm_rgb, edgecolor='black', linewidth=1)
+            ax.add_patch(swatch)
+            
+            # Node ID (exactly as it appears in dict keys)
+            ax.text(0.2, y_pos, str(node), fontsize=12, fontweight='bold', 
+                    va='center', ha='left')
+            
+            # Color name (mapped name, nicely formatted)
+            ax.text(2.2, y_pos, color_name.replace('_', ' ').title(), 
+                    fontsize=11, va='center', ha='left')
+        
+        # Add border around the legend
+        border = Rectangle((0.1, 0.1), 9.8, total_height - 0.2, 
+                          fill=False, edgecolor='gray', linewidth=2)
+        ax.add_patch(border)
+        
+        plt.tight_layout()
+        
+        if save_path:
+            plt.savefig(save_path, dpi=300, bbox_inches='tight')
+            
+        plt.show()
+    
+    return node_to_names
 
 def generate_distinct_colors(n_colors: int) -> List[Tuple[int, int, int]]:
     """
@@ -596,7 +665,7 @@ def assign_node_colors(node_list: List[int], labeled_array: np.ndarray) -> Tuple
     
     # Convert colors for naming
     node_to_color_rgb = {k: tuple(v[:3]) for k, v in node_to_color.items()}
-    node_to_color_names = convert_node_colors_to_names(node_to_color_rgb)
+    node_to_color_names = convert_node_colors_to_names(node_to_color_rgb, show_legend = False)
     
     return rgba_array, node_to_color_names
 

{nettracer3d-0.8.2.dist-info → nettracer3d-0.8.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.8.2
+Version: 0.8.3
 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/
@@ -107,11 +107,6 @@ 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 0.8.2 Updates -- 
+-- Version 0.8.3 Updates -- 
 
-	* Bug Fixes.
-	* Improved some of the image viewer window features.
-	* New option to zoom in on specific windows by clicking + dragging while in zoom mode.
-	* Added more features to UMAP/community neighborhood clustering (optional DBSCAN clustering, results more robust to node distribution)
-	* Made Napari and optional rather than core dependency.
-	* Added Cellpose as an optional dependency.
+	* Added better color legend display

{nettracer3d-0.8.2.dist-info → nettracer3d-0.8.3.dist-info}/RECORD

@@ -1,6 +1,6 @@
 nettracer3d/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nettracer3d/cellpose_manager.py,sha256=qZpTxSkmPb38Pru8TmjJ88xxcD_wM02EfJB5Mw9Xx4Y,6021
-nettracer3d/community_extractor.py,sha256=oa4e0bAwUALDgu_QdBiqNNn1XrmOW3drD5bjwey81BI,25313
+nettracer3d/community_extractor.py,sha256=08WWUO94ToZFglBU9X1L-T-WJuaIa-8t35-52kN4i6g,28167
 nettracer3d/excelotron.py,sha256=lS5vnpoOGZWp7fdqVpTPqeC-mUKrfwDrWHfx4PQ7Uzg,71384
 nettracer3d/modularity.py,sha256=O9OeKbjD3v6gSFz9K2GzP6LsxlpQaPfeJbM1pyIEigw,21788
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
@@ -16,9 +16,9 @@ nettracer3d/segmenter.py,sha256=VatOSpc41lxhPuYLTTejCxG1CcwP5hwiQ3ZFK9OBavA,6011
 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-0.8.2.dist-info/licenses/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
-nettracer3d-0.8.2.dist-info/METADATA,sha256=QlUhREQ7hy0wHfA8nKn6Qu_W-QONoGPSQY5yp9GEBYE,7112
-nettracer3d-0.8.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-0.8.2.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.8.2.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.8.2.dist-info/RECORD,,
+nettracer3d-0.8.3.dist-info/licenses/LICENSE,sha256=gM207DhJjWrxLuEWXl0Qz5ISbtWDmADfjHp3yC2XISs,888
+nettracer3d-0.8.3.dist-info/METADATA,sha256=yVQGa_obriAzfkWCzXCS0EYtxBRD8UmHL8OWmFIxFJ8,6750
+nettracer3d-0.8.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-0.8.3.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.8.3.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.8.3.dist-info/RECORD,,