Change: Only embed specs/namespaces for types that are included in NWB file on export

+schemes/+utility/listNwbTypeHierarchy.m

@@ -0,0 +1,21 @@
+function parentTypeNames = listNwbTypeHierarchy(nwbTypeName)
+% listNwbTypeHierarchy - List the NWB type hierarchy for an NWB type
+    arguments
+        nwbTypeName (1,1) string
+    end
+
+    parentTypeNames = string.empty;  % Initialize an empty cell array
+    currentType = nwbTypeName; % Start with the specific type
+
+    while ~strcmp(currentType, 'types.untyped.MetaClass')
+        parentTypeNames(end+1) = currentType; %#ok<AGROW>
+
+        % Use MetaClass information to get the parent type
+        metaClass = meta.class.fromName(currentType);
+        if isempty(metaClass.SuperclassList)
+            break; % Reached the base type
+        end
+        % NWB parent type should always be the first superclass in the list
+        currentType = metaClass.SuperclassList(1).Name;
+    end
+end

NwbFile.m

@@ -74,8 +74,7 @@ function export(obj, filename, mode)
             end
 
             try
-                jsonSpecs = schemes.exportJson();
-                io.spec.writeEmbeddedSpecifications(output_file_id, jsonSpecs);
+                obj.embedSpecifications(output_file_id)
                 refs = [email protected](obj, output_file_id, '/', {});
                 obj.resolveReferences(output_file_id, refs);
                 H5F.close(output_file_id);
@@ -118,10 +117,49 @@ function export(obj, filename, mode)
                 typename,...
                 varargin{:});
         end
+
+        function nwbTypeNames = listNwbTypes(obj)
+        % listNwbTypes - List all unique NWB types in file
+            objectMap = searchProperties(containers.Map, obj, '', '');
+
+            objects = objectMap.values();
+            objectClassNames = cellfun(@(c) string(class(c)), objects);
+            objectClassNames = unique(objectClassNames);
+
+            keep = startsWith(objectClassNames, "types.");
+            ignore = startsWith(objectClassNames, "types.untyped");
+
+            nwbTypeNames = objectClassNames(keep & ~ignore);
+        end
     end
 
     %% PRIVATE
     methods(Access=private)
+        function embedSpecifications(obj, output_file_id)
+            jsonSpecs = schemes.exportJson();
+
+            % Resolve the name of all types and parent types that are
+            % included in this file, in order to only include the specs for
+            % namespaces of types that are included in the file.
+            includedNwbTypes = obj.listNwbTypes();
+            includedNwbTypesWithParents = string.empty;
+            for i = 1:numel(includedNwbTypes)
+                typeHierarchy = schemes.utility.listNwbTypeHierarchy(includedNwbTypes{i});
+                includedNwbTypesWithParents = [includedNwbTypesWithParents, typeHierarchy]; %#ok<AGROW>
+            end
+
+            % Get the namespace names
+            namespaceNames = getNamespacesOfTypes(includedNwbTypesWithParents);
+
+            % In the specs, the hyphen (-) is used as a word separator, while in
+            % matnwb the underscore (_) is used. Translate names here:
+            allMatlabNamespaceNames = strrep({jsonSpecs.name}, '-', '_');
+            [~, keepIdx] = intersect(allMatlabNamespaceNames, namespaceNames, 'stable');
+            jsonSpecs = jsonSpecs(keepIdx);
+
+            io.spec.writeEmbeddedSpecifications(output_file_id, jsonSpecs);
+        end
+
         function resolveReferences(obj, fid, references)
             while ~isempty(references)
                 resolved = false(size(references));
@@ -215,4 +253,19 @@ function resolveReferences(obj, fid, references)
             searchProperties(pathToObjectMap, propValue, fullPath, typename, varargin{:});
         end
     end
-end
+end
+
+function namespaceNames = getNamespacesOfTypes(nwbTypeNames)
+% getNamespacesOfTypes - Get namespace names for a list of nwb types
+    arguments
+        nwbTypeNames (1,:) string
+    end
+
+    namespaceNames = repmat("", size(nwbTypeNames));
+    pattern = '[types.]+\.(\w+)\.';
+
+    for i = 1:numel(nwbTypeNames)
+        namespaceNames(i) = regexp(nwbTypeNames(i), pattern, 'tokens', 'once');
+    end
+    namespaceNames = unique(namespaceNames);
+end