Merge pull request #113 from napakalas/issue-#112

Issue #112

Author: dbrnz

mapmaker/flatmap/__init__.py

@@ -247,7 +247,13 @@ def save_feature_for_node_lookup(self, feature: Feature):
     def features_for_anatomical_node(self, anatomical_node: AnatomicalNode, warn: bool=True) -> Optional[tuple[AnatomicalNode, set[Feature]]]:
     #=========================================================================================================================================
         if self.__feature_node_map is not None:
-            return self.__feature_node_map.features_for_anatomical_node(anatomical_node, warn=warn)
+            if len((features:=self.__feature_node_map.features_for_anatomical_node(anatomical_node, warn=warn))[1]) > 0:
+                return features
+            if len(fts:=set(feature for feature in self.__features_with_id.values()
+                            if feature.models in [features[0][0]]+list(features[0][1])
+                            and feature.get_property('kind')=='proxy')) > 0:
+                return (anatomical_node, fts)
+            return features
 
     def duplicate_feature_id(self, feature_ids: str) -> bool:
     #========================================================
@@ -299,6 +305,7 @@ def __add_proxied_features(self):
         if self.__bottom_exported_layer is None:
             log.warning('No exported layer on which to add proxy features', type='proxy')
             return
+        proxy_seqs = {}
         for proxy_definition in self.__properties_store.proxies:
             feature_model = proxy_definition['feature']
             if self.__feature_node_map.has_model(feature_model):
@@ -308,16 +315,17 @@ def __add_proxied_features(self):
                     if not self.__feature_node_map.has_model(proxy_model):
                         log.warning('Proxy missing from map', type='proxy', models=feature_model, proxy=proxy_model)
                     for feature in self.__feature_node_map.get_features(proxy_model):
-                        self.__add_proxy_feature(feature, feature_model)
+                        proxy_seqs[feature.id] = proxy_seqs.get(feature.id, -1) + 1
+                        self.__add_proxy_feature(feature, feature_model, proxy_seqs[feature.id])
 
-    def __add_proxy_feature(self, feature: Feature, feature_model: str):
-    #===================================================================
+    def __add_proxy_feature(self, feature: Feature, feature_model: str, proxy_seq: int):
+    #================================================================================
         if 'Polygon' not in feature.geometry.geom_type:
             log.warning('Proxy feature must have a polygon shape', type='proxy', models=feature_model, feature=feature)
         elif self.__bottom_exported_layer is not None:
             self.__bottom_exported_layer.add_feature(
-                self.new_feature(self.__bottom_exported_layer.id, proxy_dot(feature.geometry), {   # type: ignore
-                    'id': f'proxy_on_{feature.id}',
+                self.new_feature(self.__bottom_exported_layer.id, proxy_dot(feature.geometry, proxy_seq), {   # type: ignore
+                    'id': f'proxy_{proxy_seq}_on_{feature.id}',
                     'tile-layer': FEATURES_TILE_LAYER,
                     'models': feature_model,
                     'kind': 'proxy'

mapmaker/flatmap/feature.py

@@ -130,7 +130,7 @@ def __init__(self, terms_alias_file: Optional[str]=None):
                 for alias in equivalence.get('aliases', []):
                     alias = (alias[0], tuple(alias[1])) if isinstance(alias, list) else alias
                     if alias in self.__anatomical_aliases:
-                        self.__log.error('Alias cannot map to both terms, alias=alias, terms=[self.__anatomical_aliases[alias], term]')
+                        self.__log.error(f'Alias cannot map to both terms, alias=alias, terms={[self.__anatomical_aliases[alias], term]}')
                     else:
                         self.__anatomical_aliases[alias] = term
         self.__model_to_features: dict[str|tuple, set[Feature]] = defaultdict(set)

mapmaker/geometry/proxy_dot.py

@@ -23,7 +23,7 @@
 
 #===============================================================================
 
-def proxy_dot(poly: MultiPolygon|Polygon) -> Polygon:
+def proxy_dot(poly: MultiPolygon|Polygon, proxy_seq: int) -> Polygon:
     envelope_coords = shapely.oriented_envelope(poly).boundary.coords
     edge_coords = list(zip(envelope_coords, envelope_coords[1:]))
     edges = [LineString(coords) for coords in edge_coords]
@@ -35,8 +35,9 @@ def proxy_dot(poly: MultiPolygon|Polygon) -> Polygon:
         median_line = LineString([p0, p1])
     else:
         median_line = LineString([p1, p0])
-    proxy_point = shapely.line_interpolate_point(median_line, 0.8, normalized=True)
-
-    return proxy_point.buffer(median_line.length/16)
+    distance = 0.8 - proxy_seq * 0.15
+    proxy_point = shapely.line_interpolate_point(median_line, distance, normalized=True)
+    median_distance = median_line.length/16 if median_line.length/16 < 1000 else 1000
+    return proxy_point.buffer(median_distance)
 
 #===============================================================================

mapmaker/properties/pathways.py

@@ -673,9 +673,18 @@ def __route_network_connectivity(self, network: Network):
                 path = paths_by_id[path_id]
                 path_geojson_ids = []
                 path_taxons = None
+                added_properties = {
+                    key: value for key, value in [
+                        ('missing-nodes', path.connectivity.graph.get('missing_nodes')),
+                        ('alert', path.connectivity.graph.get('alert')),
+                        ('biological-sex', path.connectivity.graph.get('biological-sex')),
+                        ('completeness', path.connectivity.graph.get('completeness')),
+                    ] if value is not None
+                }
+                
                 for geometric_shape in geometric_shapes:
                     if geometric_shape.properties.get('type') not in ['arrow', 'junction']:
-                        properties = DEFAULT_PATH_PROPERTIES.copy()
+                        properties = DEFAULT_PATH_PROPERTIES.copy() | added_properties
                         if routed_path.centrelines is not None:
                             # The list of nerve models that the path is associated with
                             properties['nerves'] = routed_path.centrelines_model
@@ -700,7 +709,7 @@ def __route_network_connectivity(self, network: Network):
                             path_taxons = feature.get_property('taxons')
 
                 for geometric_shape in geometric_shapes:
-                    properties = DEFAULT_PATH_PROPERTIES.copy()
+                    properties = DEFAULT_PATH_PROPERTIES.copy() | added_properties
                     properties.update(geometric_shape.properties)
                     if properties.get('type') in ['arrow', 'junction']:
                         properties['kind'] = path.path_type.viewer_kind