fusion-tools 2.2.3__tar.gz → 2.2.4__tar.gz

{fusion_tools-2.2.3 → fusion_tools-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.2.3
+Version: 2.2.4
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border

{fusion_tools-2.2.3 → fusion_tools-2.2.4}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="fusion-tools",
-    version="2.2.3",
+    version="2.2.4",
     author="Sam Border",
     author_email="sam.border2256@gmail.com",
     description="Modular visualization and analysis dashboard creation for high-resolution microscopy images",

{fusion_tools-2.2.3 → fusion_tools-2.2.4}/src/fusion_tools/components/maps.py

@@ -1346,8 +1346,6 @@ class MultiFrameSlideMap(SlideMap):
                 else:
                     frame_names = [f'Frame {i}' for i in range(len(image_metadata['frames']))]
 
-                print(frame_names)
-                print(len(image_metadata['frames']))
                 # This is a multi-frame image
                 if len(image_metadata['frames'])==3:
                     # Treat this as an RGB image by default

{fusion_tools-2.2.3 → fusion_tools-2.2.4}/src/fusion_tools/components/segmentation.py

@@ -2097,9 +2097,10 @@ class BulkLabels(Tool):
         n_marked = len(get_pattern_matching_value(current_markers))
 
         patched_list = Patch()
-        values_to_remove = np.where(clear_click)[0].tolist()
-        for v in values_to_remove:
-            del patched_list[v]
+        for v_idx,v in enumerate(clear_click):
+            if v:
+                del patched_list[v_idx]
+                break
         
         new_structures_div = [
             dbc.Alert(

{fusion_tools-2.2.3 → fusion_tools-2.2.4}/src/fusion_tools/utils/shapes.py

@@ -67,33 +67,30 @@ def load_geojson(geojson_path: str, name:Union[str,None]=None) -> dict:
     with open(geojson_path,'r') as f:
         geojson_anns = json.load(f)
         f.close()
-    
-    print(type(geojson_anns))
-    print(len(geojson_anns))
 
     if type(geojson_anns)==list:
         for g in geojson_anns:
             if not 'properties' in g:
                 g['properties'] = {}
+            else:
+                if 'name' in g['properties'] and name is None:
+                    name = g['properties']['name']
 
             geo_id = uuid.uuid4().hex[:24] if not '_id' in g['properties'] else g['properties']['_id']
             g['properties'] = g['properties'] | {'name': name if not name is None else geo_id, '_id': geo_id}
 
-            
             for f_idx, f in enumerate(g['features']):
                 f['properties'] = f['properties'] | {'name': name if not name is None else geo_id, '_id': uuid.uuid4().hex[:24], '_index': f_idx}
 
     elif type(geojson_anns)==dict:
         if not 'properties' in geojson_anns:
             geojson_anns['properties'] = {}
-            geo_id = uuid.uuid4().hex[:24] if not '_id' in g['properties'] else geojson_anns['properties']['_id']
-            geojson_anns['properties'] = geojson_anns['properties'] | {'name': name if not name is None else geo_id, '_id': geo_id}
-
-            
-            for f_idx, f in enumerate(geojson_anns['features']):
-                f['properties'] = f['properties'] | {'name': name if not name is None else geo_id, '_id': uuid.uuid4().hex[:24], '_index': f_idx}
 
+        geo_id = uuid.uuid4().hex[:24] if not '_id' in g['properties'] else geojson_anns['properties']['_id']
+        geojson_anns['properties'] = geojson_anns['properties'] | {'name': name if not name is None else geo_id, '_id': geo_id}
 
+        for f_idx, f in enumerate(geojson_anns['features']):
+            f['properties'] = f['properties'] | {'name': name if not name is None else geo_id, '_id': uuid.uuid4().hex[:24], '_index': f_idx}
 
     return geojson_anns
 
@@ -1016,8 +1013,6 @@ def process_filters_queries(filter_list:list, spatial_list:list, structures:list
         structure_filtered = [gpd.GeoDataFrame.from_features(i['features']) for i in all_geo_list]
         name_order = [i['properties']['name'] for i in all_geo_list]
 
-    #all_names = [i['properties']['name'] for i in all_geo_list]
-
     # Now going through spatial queries
     filter_reference_list = {
         n: {}
@@ -1048,6 +1043,8 @@ def process_filters_queries(filter_list:list, spatial_list:list, structures:list
                     )
 
                 intermediate_gdf = intermediate_gdf.drop([i for i in ['index_left','index_right'] if i in intermediate_gdf], axis = 1)
+                intermediate_gdf = intermediate_gdf.drop([i for i in intermediate_gdf if '_right' in i],axis=1)
+                intermediate_gdf.columns = [i.replace('_left','') if '_left' in i else i for i in intermediate_gdf ]
 
             remainder_structures.append(intermediate_gdf)
     else:
@@ -1060,21 +1057,11 @@ def process_filters_queries(filter_list:list, spatial_list:list, structures:list
     }
     for g,name in zip(remainder_structures,name_order):
         g_json = g.to_geo_dict(show_bbox=True)
-        #feature_geos = [i['geometry'] for i in g_json['features']]
-
-
         filter_reference_list[name] = {
             i+len(combined_geojson['features']):j['properties']['_index']
             for i,j in enumerate(g_json['features'])
         }
         combined_geojson['features'].extend(g_json['features'])
-        """
-        if len(g_json['features'])>0:
-            for idx, i in enumerate(all_geo_list[all_names.index(name)]['features']):
-                if i['geometry'] in feature_geos:
-                    filter_reference_list[name][len(combined_geojson['features'])] = idx
-                    combined_geojson['features'].append(g_json['features'][feature_geos.index(i['geometry'])])
-        """
 
     # Going through property filters:
     if len(filter_list)>0:

{fusion_tools-2.2.3 → fusion_tools-2.2.4}/src/fusion_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.2.3
+Version: 2.2.4
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border