Merge pull request #598 from NeurodataWithoutBorders/597-nwb-to-table…

…-bug

Fix: bug in nwbToTable (Issue #597 )

+tests/+unit/dynamicTableTest.m

@@ -0,0 +1,72 @@
+function tests = dynamicTableTest()
+    tests = functiontests(localfunctions);
+end
+
+function setupOnce(testCase)
+    rootPath = fullfile(fileparts(mfilename('fullpath')), '..', '..');
+    testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath));
+    testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);
+    generateCore('savedir', '.');
+    rehash();
+end
+
+function setup(testCase) %#ok<INUSD>
+    % pass
+end
+
+function testNwbToTableWithReferencedTablesAsRowIndices(testCase)
+    % The default mode for the toTable() method is to return the row indices
+    % for dynamic table regions. This test verifies that the data type of
+    % the converted table columns is int64, the default type for indices.
+    dtr_table = createDynamicTableWithTableRegionReferences();
+    convertedTable = dtr_table.toTable();
+
+    testCase.verifyClass(convertedTable.dtr_col_a(1), 'int64')
+    testCase.verifyClass(convertedTable.dtr_col_b(1), 'int64')
+end
+
+function testNwbToTableWithReferencedTablesAsTableRows(testCase)
+    % An alternative mode for the toTable() method is to return the referenced
+    % table rows for dynamic table regions as subtables. This test verifies that 
+    % the data type of the converted table columns is table.
+    dtr_table = createDynamicTableWithTableRegionReferences();
+    convertedTable = dtr_table.toTable(false); % Return 
+
+    row1colA = convertedTable.dtr_col_a(1);
+    row1colB = convertedTable.dtr_col_b(1);
+    if iscell(row1colA); row1colA = row1colA{1}; end
+    if iscell(row1colB); row1colB = row1colB{1}; end
+
+    testCase.verifyClass(row1colA, 'table')
+    testCase.verifyClass(row1colB, 'table')
+end
+
+% Non-test functions
+function dtr_table = createDynamicTableWithTableRegionReferences()
+    % Create a dynamic table with two columns, where the data of each column is 
+    % a dynamic table region referencing another dynamic table.
+    T = table([1;2;3], {'a';'b';'c'}, 'VariableNames', {'col1', 'col2'});
+    T.Properties.VariableDescriptions = {'column #1', 'column #2'};
+
+    T = util.table2nwb(T);
+
+    dtr_col_a = types.hdmf_common.DynamicTableRegion( ...
+        'description', 'references multiple rows of earlier table', ...
+        'data', [0; 1; 1; 0], ...  # 0-indexed
+        'table',types.untyped.ObjectView(T) ...  % object view of target table
+    );
+
+    dtr_col_b = types.hdmf_common.DynamicTableRegion( ...
+        'description', 'references multiple rows of earlier table', ...
+        'data', [1; 2; 2; 1], ...  # 0-indexed
+        'table',types.untyped.ObjectView(T) ...  % object view of target table
+    );
+
+    dtr_table = types.hdmf_common.DynamicTable( ...
+        'description', 'test table with DynamicTableRegion', ...
+        'colnames', {'dtr_col_a', 'dtr_col_b'}, ...
+        'dtr_col_a', dtr_col_a, ...
+        'dtr_col_b', dtr_col_b, ...
+        'id',types.hdmf_common.ElementIdentifiers('data', [0; 1; 2; 3]) ...
+    );
+end

+types/+util/+dynamictable/nwbToTable.m

@@ -2,7 +2,7 @@
 %NWBTOTABLE converts from a NWB DynamicTable to a MATLAB table 
 %
 %   MATLABTABLE = NWBTOTABLE(T) converts object T of class types.core.DynamicTable
-%   into a MATLAB Tale
+%   into a MATLAB Table
 %   
 %   MATLABTABLE = NWBTOTABLE(T, INDEX) If INDEX is FALSE, includes rows referenced by a
 %   DynamicTableRegion as nested subtables
@@ -50,10 +50,10 @@
 );
 
 % deal with DynamicTableRegion columns when index is false
-columns = DynamicTable.colnames;
-i = 1;
-while i < length(columns)
-    cn = DynamicTable.colnames{i};
+[columns, remainingColumns] = deal(DynamicTable.colnames);
+
+for i = 1:length(columns)
+    cn = columns{i};
     if isprop(DynamicTable, cn)
         cv = DynamicTable.(cn);
     elseif isprop(DynamicTable, 'vectorindex') && DynamicTable.vectorindex.isKey(cn) % Schema version < 2.3.0
@@ -71,15 +71,17 @@
             cv{r,1} = ref_table.getRow(row_idxs(r)+1);
         end
         matlabTable.(cn) = cv;
-        columns(i) = [];
+        remainingColumns = setdiff(remainingColumns, cn, 'stable');
     else
-        i = i+1;
+        % pass
     end
 end
 % append remaining columns to table
 % making the assumption that length of ids reflects table height
 matlabTable = [matlabTable DynamicTable.getRow( ...
     1:length(ids), ...
-    'columns', columns ...
+    'columns', remainingColumns ...
 )];
 
+% Update the columns order to be the same as the original 
+matlabTable = matlabTable(:, [{'id'}, columns]);