fusion-tools 2.2.2__tar.gz → 2.2.4__tar.gz

{fusion_tools-2.2.2 → fusion_tools-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.2.2
+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-2.2.2 → fusion_tools-2.2.4}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="fusion-tools",
-    version="2.2.2",
+    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-2.2.2 → 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-2.2.2 → fusion_tools-2.2.4}/src/fusion_tools/components/segmentation.py

@@ -1258,7 +1258,8 @@ class BulkLabels(Tool):
                 State({'type': 'bulk-labels-include-structures','index': ALL},'value'),
                 State({'type': 'bulk-labels-add-property-div','index': ALL},'children'),
                 State({'type':'bulk-labels-spatial-query-div','index': ALL},'children'),
-                State({'type': 'map-annotations-store','index': ALL},'data')
+                State({'type': 'map-annotations-store','index': ALL},'data'),
+                State({'type': 'map-slide-information','index': ALL},'data')
             ]
         )(self.update_label_structures)
 
@@ -1316,7 +1317,8 @@ class BulkLabels(Tool):
                 State({'type': 'bulk-labels-label-rationale','index': ALL},'value'),
                 State({'type': 'bulk-labels-label-source','index': ALL},'children'),
                 State({'type': 'bulk-labels-label-method','index': ALL},'value'),
-                State({'type': 'map-annotations-store','index': ALL},'data')
+                State({'type': 'map-annotations-store','index': ALL},'data'),
+                State({'type':'map-slide-information','index':ALL},'data')
             ]
         )(self.apply_labels)
 
@@ -1592,7 +1594,7 @@ class BulkLabels(Tool):
 
         return processed_filters
 
-    def parse_spatial_divs(self, spatial_query_parent: list)->list:
+    def parse_spatial_divs(self, spatial_query_parent: list, slide_information:dict)->list:
         """Parsing through parent div containing all spatial queries and returning them in list form
 
         :param spatial_query_parent: Div containing spatial query child divs
@@ -1601,6 +1603,7 @@ class BulkLabels(Tool):
         :rtype: list
         """
         processed_queries = []
+        x_scale = slide_information['x_scale']
         if not spatial_query_parent is None:
             for div in spatial_query_parent:
                 div_children = div['props']['children'][0]['props']['children']
@@ -1622,12 +1625,12 @@ class BulkLabels(Tool):
                             processed_queries.append({
                                 'type': query_type,
                                 'structure': query_structure,
-                                'distance': query_distance*self.x_scale
+                                'distance': query_distance*x_scale
                             })
 
         return processed_queries
 
-    def update_label_structures(self, update_structures_click:list, include_structures:list, filter_properties:list, spatial_queries:list, current_features:list):
+    def update_label_structures(self, update_structures_click:list, include_structures:list, filter_properties:list, spatial_queries:list, current_features:list, slide_information:list):
         """Go through current structures and return all those that pass spatial and property filters.
 
         :param update_structures_click: Button clicked
@@ -1650,11 +1653,13 @@ class BulkLabels(Tool):
         include_structures = get_pattern_matching_value(include_structures)
         current_features = json.loads(get_pattern_matching_value(current_features))
 
+        slide_information = json.loads(get_pattern_matching_value(slide_information))
+
         include_properties = get_pattern_matching_value(filter_properties)
         spatial_queries = get_pattern_matching_value(spatial_queries)
 
         processed_filters = self.parse_filter_divs(include_properties)
-        processed_spatial_queries = self.parse_spatial_divs(spatial_queries)
+        processed_spatial_queries = self.parse_spatial_divs(spatial_queries, slide_information)
 
         filtered_geojson, filtered_ref_list = process_filters_queries(processed_filters, processed_spatial_queries, include_structures, current_features)
 
@@ -1823,7 +1828,7 @@ class BulkLabels(Tool):
 
         return values_selector
 
-    def parse_marker_div(self, parent_marker_div):
+    def parse_marker_div(self, parent_marker_div,slide_information):
         """Parse div containing markers, extracting position and data from each
 
         :param parent_marker_div: Div containing all current Markers
@@ -1839,7 +1844,7 @@ class BulkLabels(Tool):
             data = json.loads(p['props']['children'][-1]['props']['children'])
             
             marker_coords.append(
-                [coords[1]/self.x_scale,coords[0]/self.y_scale]
+                [coords[1]/slide_information['x_scale'],coords[0]/slide_information['y_scale']]
             )
             marker_data.append(data)
             
@@ -1914,7 +1919,7 @@ class BulkLabels(Tool):
 
         return current_labels
 
-    def apply_labels(self, button_click, current_markers, current_data, label_type, label_text, label_rationale, label_source, label_method, current_annotations):
+    def apply_labels(self, button_click, current_markers, current_data, label_type, label_text, label_rationale, label_source, label_method, current_annotations,slide_information):
         """Applying current label to marked structures
 
         :param button_click: Button clicked
@@ -1954,8 +1959,9 @@ class BulkLabels(Tool):
         current_data = json.loads(get_pattern_matching_value(current_data))
         current_annotations = json.loads(get_pattern_matching_value(current_annotations))
         current_markers = get_pattern_matching_value(current_markers)
+        slide_information = json.loads(get_pattern_matching_value(slide_information))
 
-        marker_positions, marker_data = self.parse_marker_div(current_markers)
+        marker_positions, marker_data = self.parse_marker_div(current_markers,slide_information)
         labeled_items = self.search_labels(marker_positions, current_data, label_type, label_text, label_method)
 
         #TODO: Applying property to structures
@@ -2091,9 +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-2.2.2 → 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-2.2.2 → fusion_tools-2.2.4}/src/fusion_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.2.2
+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