Merge in changes for functional modelling maps.

README.rst

@@ -113,8 +113,8 @@ Command line help
                     [--authoring] [--debug]
                     [--only-networks] [--save-drawml] [--save-geojson] [--tippecanoe]
                     [--initial-zoom N] [--max-zoom N]
-                    [--export-features EXPORT_FILE] [--export-neurons EXPORT_FILE] [--export-svg EXPORT_FILE]
-                    [--single-file {celldl,svg}]
+                    [--export-bondgraphs] [--export-features EXPORT_FILE] [--export-neurons EXPORT_FILE]
+                    [--export-svg EXPORT_FILE] [--single-file {celldl,svg}]
                     --output OUTPUT --source SOURCE
 
     Generate a flatmap from its source manifest.
@@ -163,6 +163,8 @@ Command line help
       --max-zoom N          Maximum zoom level (defaults to 10)
 
     Miscellaneous:
+      --export-bondgraphs
+                            Export functional modelling components as CellDL bondgraphs
       --export-features EXPORT_FILE
                             Export identifiers and anatomical terms of labelled features as JSON
       --export-neurons EXPORT_FILE

mapmaker/__init__.py

@@ -31,6 +31,9 @@
 MIN_ZOOM  =  2   #: Default minimum zoom level for generated flatmaps
 MAX_ZOOM  = 10   #: Default maximum zoom level for generated flatmaps
 
+# For showing rasterised image of detailed map on its base map before the details show
+ZOOM_OFFSET_FROM_BASE = 2
+
 #===============================================================================
 
 from .maker import MapMaker

mapmaker/__main__.py

@@ -34,7 +34,7 @@ def arg_parser():
 
     log_options = parser.add_argument_group('Logging')
     log_options.add_argument('--log', dest='logFile', metavar='LOG_FILE',
-                        help="Append messages to a log file")
+                        help="Append messages to a log file as JSON")
     log_options.add_argument('--silent', action='store_true',
                         help='Suppress all messages to screen')
     log_options.add_argument('--verbose', action='store_true',
@@ -93,6 +93,8 @@ def arg_parser():
     misc_options = parser.add_argument_group('Miscellaneous')
     misc_options.add_argument('--commit', metavar='GIT_COMMIT',
                         help='The branch/tag/commit to use when the source is a Git repository')
+    misc_options.add_argument('--export-bondgraphs', dest='exportBondgraphs', action='store_true',
+                        help='Export functional modelling components as CellDL bondgraphs')
     misc_options.add_argument('--export-features', dest='exportFeatures', metavar='EXPORT_FILE',
                         help='Export identifiers and anatomical terms of labelled features as JSON')
     misc_options.add_argument('--export-neurons', dest='exportNeurons', metavar='EXPORT_FILE',

mapmaker/annotation/__init__.py

@@ -26,7 +26,7 @@
 from mapmaker.knowledgebase.celldl import FC_CLASS
 from mapmaker.knowledgebase.sckan import PATH_TYPE
 from mapmaker.shapes import Shape
-from mapmaker.sources.fc_powerpoint.components import is_connector
+from mapmaker.shapes.types import is_connector
 from mapmaker.utils import log
 
 from .json_annotations import JsonAnnotations

mapmaker/flatmap/__init__.py

@@ -18,7 +18,7 @@
 #
 #===============================================================================
 
-from collections import OrderedDict
+from collections import defaultdict, OrderedDict
 from datetime import datetime, timezone
 import os
 from typing import Optional, TYPE_CHECKING
@@ -45,7 +45,7 @@
 from .layers import FEATURES_TILE_LAYER, MapLayer
 
 # Exports
-from .manifest import Manifest, SourceManifest
+from .manifest import Manifest, SourceBackground, SourceManifest
 
 if TYPE_CHECKING:
     from mapmaker.annotation import Annotator
@@ -63,9 +63,7 @@ def __init__(self, manifest: Manifest, maker: 'MapMaker', annotator: Optional['A
         self.__id = maker.id
         self.__uuid = maker.uuid
         self.__map_dir = maker.map_dir
-        self.__map_kind = (MAP_KIND.FUNCTIONAL if manifest.kind == 'functional'
-                      else MAP_KIND.CENTRELINE if manifest.kind == 'centreline'
-                      else MAP_KIND.ANATOMICAL)
+        self.__map_kind = manifest.map_kind
         self.__manifest = manifest
         self.__local_id = manifest.id
         self.__models = manifest.models
@@ -195,6 +193,13 @@ def initialise(self):
             knowledge = get_knowledge(self.__models)
             if 'label' in knowledge:
                 self.__metadata['describes'] = knowledge['label']
+        if self.map_kind == MAP_KIND.FUNCTIONAL:
+            self.__metadata['style'] = 'functional'
+        elif self.map_kind == MAP_KIND.CENTRELINE:
+            self.__metadata['style'] = 'centreline'
+        else:
+            self.__metadata['style'] = 'anatomical'
+        self.__metadata['map-kinds'] = self.__manifest.map_kinds
 
         self.__entities = set()
 
@@ -211,6 +216,7 @@ def initialise(self):
         self.__features_with_name: dict[str, Feature] = {}
         self.__last_geojson_id = 0
         self.__features_by_geojson_id: dict[int, Feature] = {}
+        self.__associated_layers: defaultdict[str, list[int]] = defaultdict(list)
 
         # Used to find annotated features containing a region
         self.__feature_search = None
@@ -272,11 +278,11 @@ def has_feature(self, feature_id: str) -> bool:
 
     def get_feature(self, feature_id: str) -> Optional[Feature]:
     #===========================================================
-        return self.__features_with_id.get(feature_id)
-
-    def get_feature_by_name(self, full_name: str) -> Optional[Feature]:
-    #==================================================================
-        return self.__features_with_name.get(full_name.replace(" ", "_"))
+        if self.map_kind == MAP_KIND.FUNCTIONAL:
+            return self.__features_with_name.get(feature_id.replace(" ", "_"),
+                self.__features_with_id.get(feature_id))
+        else:
+            return self.__features_with_id.get(feature_id)
 
     def get_feature_by_geojson_id(self, geojson_id: int) -> Optional[Feature]:
     #=========================================================================
@@ -285,17 +291,21 @@ def get_feature_by_geojson_id(self, geojson_id: int) -> Optional[Feature]:
     def new_feature(self, layer_id: str, geometry, properties, is_group=False) -> Feature:
     #=====================================================================================
         self.__last_geojson_id += 1
+        properties['layer'] = layer_id
         self.properties_store.update_properties(properties)   # Update from JSON properties file
         feature = Feature(self.__last_geojson_id, geometry, properties, is_group=is_group)
-        feature.set_property('layer', layer_id)
-        if (name := properties.get('name', properties.get('label', ''))) != '':
-            self.__features_with_name[f'{layer_id}/{name.replace(" ", "_")}'] = feature
         self.__features_by_geojson_id[feature.geojson_id] = feature
         if feature.id:
             if feature.id in self.__features_with_id:
                 pass
             else:
                 self.__features_with_id[feature.id] = feature
+        if self.map_kind == MAP_KIND.FUNCTIONAL:
+            if (name := properties.get('name', '')) != '':
+                self.__features_with_name[f'{layer_id}/{name.replace(" ", "_")}'] = feature
+        if (associated_layers := properties.get('associated-details')) is not None:
+            for layer in associated_layers:
+                self.__associated_layers[layer].append(feature.geojson_id)
         return feature
 
     def network_feature(self, feature: Feature) -> bool:
@@ -364,7 +374,7 @@ def add_source_layers(self, layer_number: int, source: 'MapSource'):
         for layer in source.layers:
             self.add_layer(layer)
             if layer.exported:
-                layer.add_raster_layer(layer.id, source.extent, source)
+                layer.add_raster_layers(source.extent, source)
         # The first layer is used as the base map
         if layer_number == 0:
             if source.kind == 'details':
@@ -377,6 +387,38 @@ def add_source_layers(self, layer_number: int, source: 'MapSource'):
           and source.kind not in SOURCE_DETAIL_KINDS):
             raise ValueError('Can only have a single base map')
 
+    """
+    The ``feature`` has details that appear when zoomed.
+    """
+    def add_details_layer(self, feature: Feature, details_layer: str, description: Optional[str]=None) -> Optional[int]:
+    #===================================================================================================================
+        if feature.layer is not None:
+            feature.set_property('details-layer', details_layer)
+            zoom_point = self.add_zoom_point(feature, description)
+            if zoom_point is not None:
+                zoom_point.set_property('details-layer', details_layer)
+            # Set the ``associated-details`` property for connections to features associated with the details layer
+            for geojson_id in self.__associated_layers.get(details_layer, []):
+                if (associated_feature := self.get_feature_by_geojson_id(geojson_id)) is not None:
+                    for connection_id in associated_feature.get_property('connections', []):
+                        if (connection := self.get_feature(connection_id)) is not None:
+                            connection.append_property('associated-details', details_layer)
+            return zoom_point.geojson_id if zoom_point else None
+
+    def add_zoom_point(self, feature: Feature, description: Optional[str]=None) -> Optional[Feature]:
+    #================================================================================================
+        if feature.layer is not None:
+            zoom_point = self.new_feature(feature.properties['layer'], feature.geometry.centroid, {
+                'kind': 'zoom-point',
+                'tile-layer': feature.properties['tile-layer']
+            })
+            if description is not None:
+                zoom_point.set_property('label', description)
+            if (models := feature.models) is not None:
+                zoom_point.set_property('models', models)
+            feature.layer.add_feature(zoom_point)
+            return zoom_point
+
     def layer_metadata(self):
     #========================
         metadata = []
@@ -390,7 +432,9 @@ def layer_metadata(self):
                         {   'id': raster_layer.id,
                             'options': {
                                 'max-zoom': raster_layer.max_zoom,
-                                'min-zoom': raster_layer.min_zoom
+                                'min-zoom': raster_layer.min_zoom,
+                                'background': raster_layer.background_layer,
+                                'detail-layer': layer.detail_layer
                             }
                         } for raster_layer in layer.raster_layers
                     ]
@@ -399,6 +443,10 @@ def layer_metadata(self):
                     map_layer['min-zoom'] = layer.min_zoom
                 if layer.max_zoom is not None:
                     map_layer['max-zoom'] = layer.max_zoom
+                if layer.parent_layer is not None:
+                    map_layer['extent'] = layer.extent
+                    map_layer['parent-layer'] = layer.parent_layer
+                    map_layer['zoom-point'] = layer.zoom_point_id
                 metadata.append(map_layer)
         return metadata
 
@@ -482,11 +530,11 @@ def __add_detail_features(self, layer, detail_layer, lowres_features):
             else:                             # nerve
                 feature.pop_property('maxzoom')
 
-            if hires_layer.source.raster_source is not None:
+            if len(hires_layer.source.raster_sources):
                 extent = transform.transform_extent(hires_layer.source.extent)
-                layer.add_raster_layer('{}_{}'.format(detail_layer.id, hires_layer.id),
-                                        extent, hires_layer.source, minzoom,
-                                        local_world_to_base=transform)
+                layer.add_raster_layers(extent, hires_layer.source,
+                                        id=f'{detail_layer.id}_{hires_layer.id}',
+                                        min_zoom=minzoom, local_world_to_base=transform)
 
             # The detail layer gets a scaled copy of each high-resolution feature
             for hires_feature in hires_layer.features: