Fix: Ensure DataStub size is updated when the underlying dataset is expanded via a DataPipe

+io/+space/getSize.m

@@ -0,0 +1,30 @@
+function [datasetSize, datasetMaxSize] = getSize(spaceId)
+% getSize - Retrieves the current and maximum sizes of a dataset.
+%
+% Syntax:
+%   [datasetSize, datasetMaxSize] = io.space.getSize(spaceId)
+%
+% Input Arguments:
+%   spaceId {H5ML.id} - Identifier for the dataspace from which 
+%   the dimensions are retrieved.
+%
+% Output Arguments:
+%   datasetSize - Current size of the dataset dimensions.
+%   datasetMaxSize - Maximum size of the dataset dimensions.
+%
+% Note:
+%   - Flips dimensions as the h5 function returns dimensions in C-style order
+%     whereas MATLAB represents data in F-style order
+%   - Replaces H5 constants with Inf for unlimited dimensions
+
+    arguments
+        spaceId {matnwb.common.compatibility.mustBeA(spaceId, "H5ML.id")}
+    end
+
+    [~, h5Dims, h5MaxDims] = H5S.get_simple_extent_dims(spaceId);
+    datasetSize = fliplr(h5Dims);
+    datasetMaxSize = fliplr(h5MaxDims);
+
+    h5Unlimited = H5ML.get_constant_value('H5S_UNLIMITED');
+    datasetMaxSize(datasetMaxSize == h5Unlimited) = Inf;
+end

+tests/+fixtures/ExtensionGenerationFixture.m

@@ -46,10 +46,13 @@ function clearGenerated(fixture)
             namespaceName = extractBefore(namespaceFilename, '.');
 
             generatedTypesDirectory = fullfile(fixture.TypesOutputFolder, "+types", "+"+namespaceName);
-            rmdir(generatedTypesDirectory, 's');
-
+            if isfolder(generatedTypesDirectory)
+                rmdir(generatedTypesDirectory, 's');
+            end
             cacheFile = fullfile(fixture.TypesOutputFolder, "namespaces", namespaceName+".mat");
-            delete(cacheFile)
+            if isfile(cacheFile)
+                delete(cacheFile)
+            end
         end
     end
 end

+tests/+unit/dataStubTest.m

@@ -1,5 +1,14 @@
 classdef dataStubTest < tests.abstract.NwbTestCase
 
+    methods (TestClassSetup)
+        function generateTestSchemas(testCase)
+            % Generate the rrs and cs test extensions for use in all tests
+            % of this test suite, using fixture for proper cleanup
+            testCase.applyTestSchemaFixture('rrs');
+            testCase.applyTestSchemaFixture('cs');
+        end
+    end
+
     methods (TestMethodSetup)
         function setupMethod(testCase)
             % Use a fixture to create a temporary working directory
@@ -70,9 +79,6 @@
 
         function testObjectCopy(testCase)
 
-            testCase.applyTestSchemaFixture('rrs');
-            testCase.applyTestSchemaFixture('cs');
-
             nwb = NwbFile(...
                 'identifier', 'DATASTUB',...
                 'session_description', 'test datastub object copy',...
@@ -91,10 +97,12 @@
             nwb.acquisition.set('rc', rc);
             nwb.analysis.set('rcRef', rcRef);
             nwbExport(nwb, 'original.nwb');
+
             nwbOriginalIn = nwbRead('original.nwb', 'ignorecache');
             tests.util.verifyContainerEqual(testCase, nwbOriginalIn, nwb);
 
             nwbExport(nwbOriginalIn, 'copy.nwb');
+
             nwbCopyIn = nwbRead('copy.nwb', 'ignorecache');
             tests.util.verifyContainerEqual(testCase, nwbCopyIn, nwb);
         end
@@ -138,11 +146,6 @@
         end
 
         function testResolveCompoundDataType(testCase)
-
-            % Generate the compound test schema using fixture
-            testCase.applyTestSchemaFixture('rrs');
-            testCase.applyTestSchemaFixture('cs');
-
             % Set up file with compound dataset
             nwb = tests.factory.NWBFile();
 
@@ -178,5 +181,34 @@
                 compoundRefInDirectRead.dims, ...
                 compoundRefIn.data.dims )
         end
+
+        function testNestedDataIndexing(testCase)
+            % Set up file with compound dataset
+
+            nwb = tests.factory.NWBFile();
+
+            ts = tests.factory.TimeSeriesWithTimestamps();
+            nwb.acquisition.set('timeseries', ts);
+
+            tsPath = '/acquisition/timeseries';
+            tsDataPath = [tsPath '/data'];
+
+            compoundRef = types.cs.CompoundRefData('data', table(...
+                rand(2, 1),...
+                rand(2, 1),...
+                [types.untyped.ObjectView(tsPath); types.untyped.ObjectView(tsPath)],...
+                [types.untyped.RegionView(tsDataPath, 1:2); types.untyped.RegionView(tsDataPath, 2:3)],...
+                'VariableNames', {'a', 'b', 'objref', 'regref'}));
+
+            nwb.analysis.set('compoundRef', compoundRef);
+            nwbExport(nwb, 'test.nwb');
+
+            % Read in data
+            nwbIn = nwbRead('test.nwb', 'ignorecache');
+            compoundRefIn = nwbIn.analysis.get('compoundRef');
+
+            testCase.verifyClass(compoundRefIn.data(1:2).a, 'double');
+            testCase.verifyLength(compoundRefIn.data(1:2).a, 2);
+        end
     end
 end

+types/+untyped/+datapipe/BoundPipe.m

@@ -4,7 +4,7 @@
     properties (SetAccess = private)
         config = types.untyped.datapipe.Configuration.empty;
         pipeProperties = {};
-        stub = types.untyped.DataStub.empty;
+        stub types.untyped.DataStub = types.untyped.DataStub.empty;
     end
 
     properties (SetAccess = private, Dependent)
@@ -24,14 +24,8 @@
 
             obj.stub = types.untyped.DataStub(filename, path);
 
-            sid = obj.stub.get_space();
-            [~, h5_dims, h5_maxdims] = H5S.get_simple_extent_dims(sid);
-            H5S.close(sid);
-
-            current_size = fliplr(h5_dims);
-            max_size = fliplr(h5_maxdims);
-            h5_unlimited = H5ML.get_constant_value('H5S_UNLIMITED');
-            max_size(max_size == h5_unlimited) = Inf;
+            current_size = obj.stub.dims;
+            max_size = obj.stub.maxDims;
 
             did = obj.getDataset();
 
@@ -224,6 +218,7 @@ function append(obj, data)
             H5F.close(fid);
 
             obj.config.offset = obj.config.offset + data_size(obj.config.axis);
+            obj.stub.updateSize()
         end
 
         function property = getPipeProperty(obj, type)

+types/+untyped/@DataStub/DataStub.m

@@ -13,9 +13,15 @@
         ndims;
         dataType;
     end
+
+    properties (Dependent, SetAccess = private, GetAccess = ?types.untyped.datapipe.BoundPipe)
+        maxDims
+    end
+
     properties (Access = private)
         dims_ double
-        dataType_  {mustBeA(dataType_, ["char", "string", "struct"])} = string.empty % Can be char (simple type) or struct (compound type descriptor)
+        dataType_  {matnwb.common.compatibility.mustBeA(dataType_, ["char", "string", "struct"])} = string.empty % Can be char (simple type) or struct (compound type descriptor)
+        maxDims_ double
     end
 
     methods
@@ -37,25 +43,21 @@
                 obj.dataType_ = dataType;  % Keep as struct for compound types
             end
         end
-
-        function sid = get_space(obj) % Todo: private method
-            fid = H5F.open(obj.filename);
-            did = H5D.open(fid, obj.path);
-            sid = H5D.get_space(did);
-            H5D.close(did);
-            H5F.close(fid);
-        end
-
+
         function dims = get.dims(obj)
             if isempty(obj.dims_)
-                sid = obj.get_space();
-                [~, h5_dims, ~] = H5S.get_simple_extent_dims(sid);
-                obj.dims_ = fliplr(h5_dims);
-                H5S.close(sid);
+                obj.updateSize()
             end
             dims = obj.dims_;
         end
-
+
+        function maxDims = get.maxDims(obj)
+            if isempty(obj.maxDims_)
+                obj.updateSize()
+            end
+            maxDims = obj.maxDims_;
+        end
+
         function nd = get.ndims(obj)
             nd = length(obj.dims);
         end
@@ -185,10 +187,10 @@
 
         refs = export(obj, fid, fullpath, refs);
 
-        function B = subsref(obj, S)
+        function varargout = subsref(obj, S)
             CurrentSubRef = S(1);
             if ~isscalar(obj) || strcmp(CurrentSubRef.type, '.')
-                B = builtin('subsref', obj, S);
+                [varargout{1:nargout}] = builtin('subsref', obj, S);
                 return;
             end
 
@@ -200,9 +202,9 @@
                 selectionRank, rank);
             data = obj.load_mat_style(CurrentSubRef.subs{:});
             if isscalar(S)
-                B = data;
+                varargout = {data};
             else
-                B = subsref(data, S(2:end));
+                [varargout{1:nargout}] = subsref(data, S(2:end));
             end
         end
 
@@ -225,4 +227,36 @@
             tf = isstruct(dt);
         end
     end
+
+    methods % Custom indexing
+        function n = numArgumentsFromSubscript(obj, subs, indexingContext)
+            if ~isscalar(subs) && strcmp(subs(1).type, '()')
+                % Typical indexing pattern into compound data type, i.e
+                % data(1:3).fieldName. Assume/expect one output.
+                n = 1;
+            else
+                n = builtin('numArgumentsFromSubscript', obj, subs, indexingContext);
+            end
+        end
+    end
+
+    methods (Access = {?types.untyped.DataStub, ?types.untyped.datapipe.BoundPipe})
+        function updateSize(obj)
+        % updateSize - Should be called to initialize values or when dataset 
+        % space is expanded
+            sid = get_space(obj);
+            [obj.dims_, obj.maxDims_] = io.space.getSize(sid);
+            H5S.close(sid);
+        end
+    end
+
+    methods (Access = private) 
+        function sid = get_space(obj)
+            fid = H5F.open(obj.filename);
+            did = H5D.open(fid, obj.path);
+            sid = H5D.get_space(did);
+            H5D.close(did);
+            H5F.close(fid);
+        end
+    end
 end