update utils and tutorials

* create_indexed_column no longer needs the path
* update ecephys tutorial to use objects instead of paths
    * generate new html
* update ophys tutorial to use objects instead of paths
    * generate new html

+util/createElectrodeTable.m

@@ -1,24 +1,24 @@
 function table = createElectrodeTable()
 table = types.hdmf_common.DynamicTable(...
+    'description', 'A table of all electrodes (i.e. channels) used for recording.', ...
     'colnames', {'x', 'y', 'z', 'imp', 'location', 'filtering', 'group', 'group_name'},...
     'id', types.hdmf_common.ElementIdentifiers('data', []),...
     'x', types.hdmf_common.VectorData('data', [],...
-    'description', 'the x coordinate of the channel location'),...
+        'description', 'the x coordinate of the channel location'),...
     'y', types.hdmf_common.VectorData('data', [],...
-    'description', 'the y coordinate of the channel location'),...
+        'description', 'the y coordinate of the channel location'),...
     'z', types.hdmf_common.VectorData('data', [],...
-    'description', 'the z coordinate of the channel location'),...
+        'description', 'the z coordinate of the channel location'),...
     'imp', types.hdmf_common.VectorData('data', [],...
-    'description', 'the impedance of the channel'),...
+        'description', 'the impedance of the channel'),...
     'location', types.hdmf_common.VectorData('data', {},...
-    'description', 'the location of channel within the subject e.g. brain region'),...
+        'description', 'the location of channel within the subject e.g. brain region'),...
     'filtering', types.hdmf_common.VectorData('data', [],...
-    'description', 'description of hardware filtering'),...
+        'description', 'description of hardware filtering'),...
     'group', types.hdmf_common.VectorData('data', types.untyped.ObjectView.empty,...
-    'description', 'a reference to the ElectrodeGroup this electrodes is a part of'),...
+        'description', 'a reference to the ElectrodeGroup this electrodes is a part of'),...
     'group_name', types.hdmf_common.VectorData('data', {},...
-    'description', 'name of the ElectrodeGroup this electrode is a part of'),...
-    'description', 'A table of all electrodes (i.e. channels) used for recording.'...
-    );
+        'description', 'name of the ElectrodeGroup this electrode is a part of')...
+);
 end
 

+util/create_indexed_column.m

@@ -1,20 +1,16 @@
-function [data_vector, data_index] = create_indexed_column(data, path, ids, description, table)
+function [data_vector, data_index] = create_indexed_column(data, description, table)
 %CREATE_INDEXED_COLUMN creates the index and vector NWB objects for storing
 %a vector column in an NWB DynamicTable
 %
-%   [DATA_VECTOR, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA, PATH)
+%   [DATA_VECTOR, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA)
 %   expects DATA as a cell array where each cell is all of the data
 %   for a row and PATH is the path to the indexed data in the NWB file
-%   EXAMPLE: [data_vector, data_index] = util.create_indexed_colum({[1,2,3], [1,2,3,4]}, '/units/spike_times')
-%
-%   [DATA_VECTOR, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA, PATH, IDS)
-%   expects DATA as a single array 1D of doubles and IDS as a single 1D array of ints.
-%   EXAMPLE: [data_vector, data_index] = util.create_indexed_colum([1,2,3,1,2,3,4], '/units/spike_times', [0,0,0,1,1,1,1])
+%   EXAMPLE: [data_vector, data_index] = util.create_indexed_colum({[1,2,3], [1,2,3,4]})
 %   
-%   [DATA_VECTOR, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA, PATH, IDS, DESCRIPTION)
+%   [DATA_VECTOR, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA, DESCRIPTION)
 %   adds the string DESCRIPTION in the description field of the data vector
 %   
-%   [DYNAMICTABLEREGION, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA, PATH, IDS, DESCRIPTION, TABLE)
+%   [DYNAMICTABLEREGION, DATA_INDEX] = CREATE_INDEXED_COLUMN(DATA, DESCRIPTION, TABLE)
 %   If TABLE is supplied as on ObjectView of an NWB DynamicTable, a
 %   DynamicTableRegion is instead output which references this table.
 %   DynamicTableRegions can be indexed just like DataVectors
@@ -23,27 +19,32 @@
     description = 'no description';
 end
 
-if ~exist('ids', 'var') || isempty(ids)
-    bounds = NaN(length(data),1);
-    for i = 1:length(data)
-        bounds(i) = length(data{i});
-    end
-    bounds = int64(cumsum(bounds));
-    data = cell2mat(data)';
-else
-    [sorted_ids, order] = sort(ids);
-    data = data(order);
-    bounds = int64([find(diff(sorted_ids)), length(ids)]);
+bounds = NaN(length(data), 1);
+for i = 1:length(data)
+    bounds(i) = length(data{i});
 end
+bounds = int64(cumsum(bounds));
+
+data = cell2mat(data)';
 
 if exist('table', 'var')
-    data_vector = types.hdmf_common.DynamicTableRegion('table', table, ...
-        'description', description, 'data', data);
+    data_vector = types.hdmf_common.DynamicTableRegion( ...
+        'table', table, ...
+        'description', description, ...
+        'data', data ...
+    );
 else
-    data_vector = types.hdmf_common.VectorData('data', data, 'description', description);
+    data_vector = types.hdmf_common.VectorData( ...
+        'data', data, ...
+        'description', description ...
+    );
 end
 
-ov = types.untyped.ObjectView(path);
-data_index = types.hdmf_common.VectorIndex('data', bounds, 'target', ov);
+ov = types.untyped.ObjectView(data_vector);
+data_index = types.hdmf_common.VectorIndex( ...
+    'data', bounds, ...
+    'target', ov, ...
+    'description', 'indexes data' ...
+);
 
 

+util/read_indexed_column.m

@@ -1,7 +1,7 @@
 function data = read_indexed_column(vector_index, vector_data, row)
 %READ_INDEXED_COLUMN returns the data for a specific row of an indexed vector
 %
-%   DATA = READ_INDEXED_COLUMN(VECTOR_INDEX, ROW) takes a VectorIndex from a
+%   DATA = READ_INDEXED_COLUMN(VECTOR_INDEX, VECTRO_DATA, ROW) takes a VectorIndex from a
 %   DynamicTable and a ROW number and outputs the DATA for that row (1-indexed).
 
 try
@@ -18,12 +18,8 @@
         lower_bound = vector_index.data(row - 1) + 1;
     end
 end
-%%
-% Then select the corresponding spike_times_index element
-if isa(vector_data.data,'types.untyped.DataStub')
-    data = vector_data.data.load(lower_bound,upper_bound);
-else
-    data = vector_data.data(lower_bound:upper_bound);
+
+data = vector_data.data(lower_bound:upper_bound);
 end
 
 

+util/table2nwb.m

@@ -30,6 +30,6 @@
     if ~strcmp(col.Properties.VariableNames{1},'id')
         nwbtable.vectordata.set(col.Properties.VariableNames{1}, ...
             types.hdmf_common.VectorData('data', col.Variables',...
-            'description','my description'));
+            'description', 'my description'));
     end
 end