fusion-tools 2.2.2__tar.gz → 2.2.3__tar.gz

{fusion_tools-2.2.2 → fusion_tools-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.2.2
+Version: 2.2.3
 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-2.2.3}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="fusion-tools",
-    version="2.2.2",
+    version="2.2.3",
     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-2.2.3}/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

{fusion_tools-2.2.2 → fusion_tools-2.2.3}/src/fusion_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.2.2
+Version: 2.2.3
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border