Electrodes table schema change

+file/fillClass.m

@@ -55,10 +55,22 @@
     depnm = ['types.' strrep(ParentNamespace.name, '-', '_') '.' parentName]; %WRITE
 end
 
+rawClass = namespace.getClass(name);
+switch rawClass('class_type')
+    case 'groups'
+        h5TypeName = 'types.untyped.IsGroup';
+    case 'datasets'
+        h5TypeName = 'types.untyped.IsDataset';
+    otherwise
+        error('NWB:File:FillClass:InvalidClassType',...
+            '`class_type` must be of `groups` or `datasets`');
+end
+
 %% return classfile string
 classDef = [...
-    'classdef ' name ' < ' depnm newline... %header, dependencies
-    '% ' upper(name) ' ' class.doc]; %name, docstr
+    sprintf('classdef %s < %s & %s\n', name, depnm, h5TypeName)... % header, dependencies
+    sprintf('%% %s %s', upper(name), class.doc)]; % name, docstr
+
 propgroups = {...
     @()file.fillProps(classprops, readonly, 'SetAccess=protected')...
     @()file.fillProps(classprops, setdiff([required optional], readonly))...

+types/+untyped/IsDataset.m

@@ -0,0 +1,5 @@
+classdef IsDataset < handle
+    %ISDATASET Stub defining this class as a Dataset object
+
+end
+

+types/+untyped/IsGroup.m

@@ -0,0 +1,5 @@
+classdef IsGroup < handle
+    %ISGROUP Stub class stating that this class is a H5 Group object.
+
+end
+

+types/+untyped/MetaClass.m

@@ -29,9 +29,9 @@
             end
 
 
-            if isa(obj, 'types.core.NWBContainer')
+            if isa(obj, 'types.untyped.IsGroup')
                 io.writeGroup(fid, fullpath);
-            elseif isa(obj, 'types.core.NWBData') || isa(obj, 'types.core.SpecFile')
+            elseif isa(obj, 'types.untyped.IsDataset')
                 try
                     if isa(obj.data, 'types.untyped.DataStub')
                         refs = obj.data.export(fid, fullpath, refs);

nwb-schema/core/nwb.file.yaml

@@ -309,6 +309,7 @@ groups:
         doc: Physical group of electrodes.
         quantity: '*'
       - name: electrodes
+        neurodata_type_def: Electrodes
         neurodata_type_inc: DynamicTable
         doc: A table of all electrodes (i.e. channels) used for recording.
         quantity: '?'
@@ -331,7 +332,7 @@ groups:
           doc: Impedance of the channel.
         - name: location
           neurodata_type_inc: VectorData
-          dtype: text
+          dtype: ascii
           doc: Location of the electrode (channel). Specify the area, layer, comments
             on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
             standard atlas names for anatomical regions when possible.
@@ -347,7 +348,7 @@ groups:
           doc: Reference to the ElectrodeGroup this electrode is a part of.
         - name: group_name
           neurodata_type_inc: VectorData
-          dtype: text
+          dtype: ascii
           doc: Name of the ElectrodeGroup this electrode is a part of.
         - name: rel_x
           neurodata_type_inc: VectorData

nwb-schema/core/nwb.misc.yaml

@@ -127,6 +127,7 @@ groups:
     doc: The metric used, e.g. phase, amplitude, power.
   groups:
   - name: bands
+    neurodata_type_def: FrequencyBands
     neurodata_type_inc: DynamicTable
     doc: Table for describing the bands that this series was generated from. There
       should be one row in this table for each band.

tutorials/ecephys.m

@@ -49,8 +49,10 @@
 device_name = 'implant';
 nwb.general_devices.set(device_name, types.core.Device());
 device_link = types.untyped.SoftLink(['/general/devices/' device_name]);
+group_data = [];
+group_name_data = {};
 for ishank = 1:length(shank_channels)
-    nelecs = shank_channels(ishank);
+    nelecs_in_shank = shank_channels(ishank);
     group_name = ['shank' num2str(ishank)];
     nwb.general_extracellular_ephys.set(group_name, ...
         types.core.ElectrodeGroup( ...
@@ -59,22 +61,43 @@
         'device', device_link));
     group_object_view = types.untyped.ObjectView( ...
         ['/general/extracellular_ephys/' group_name]);
-    for ielec = 1:length(nelecs)
-        if ishank == 1 && ielec == 1
-            tbl = table(NaN, NaN, NaN, NaN, {'unknown'}, {'unknown'}, ...
-                group_object_view, {[group_name 'elec' num2str(ielec)]}, ...
-                'VariableNames', variables);
-        else
-            tbl = [tbl; {NaN, NaN, NaN, NaN, 'unknown', 'unknown', ...
-                group_object_view, [group_name 'elec' num2str(ielec)]}];
-        end
-    end        
+    group_data = [group_data, repmat(group_object_view, 1, nelecs_in_shank)];
+    group_name_vec = cell(1, nelecs_in_shank);
+    group_name_vec(:) = {group_name};
+    group_name_data = [group_name_data, group_name_vec];
 end
 
+nelecs = sum(shank_channels);
+
+filtering_data = cell(1, nelecs);
+filtering_data(:) = {'n/a'};
+location_data = filtering_data;
+
+electrode_table = types.core.Electrodes( ...
+    'colnames', {'x', 'y', 'z', 'imp', 'location', 'filtering', 'group', 'label'}, ...
+    'description', 'description', ...
+    'id', types.hdmf_common.ElementIdentifiers('data', 0:(nelecs-1)), ...
+    'x', types.hdmf_common.VectorData('data', NaN(1,nelecs), ...
+        'description', 'x'), ...
+    'y', types.hdmf_common.VectorData('data', NaN(1,nelecs), ...
+        'description', 'y'), ...
+    'z', types.hdmf_common.VectorData('data', NaN(1,nelecs), ...
+        'description', 'z'), ...
+    'imp', types.hdmf_common.VectorData('data', NaN(1,nelecs), ...
+        'description', 'imp'), ...
+    'filtering', types.hdmf_common.VectorData('data', filtering_data, ...
+        'description', 'filtering'), ...
+    'location', types.hdmf_common.VectorData('data', location_data, ...
+        'description', 'location'), ...
+    'group', types.hdmf_common.VectorData('data', group_data, ...
+        'description', 'electrode group'), ...
+    'group_name', types.hdmf_common.VectorData('data', group_name_data, ...
+        'description', 'group name'));
+
+
 % add the |DynamicTable| object to the NWB file in
 % /general/extracellular_ephys/electrodes
 
-electrode_table = util.table2nwb(tbl, 'all electrodes');
 nwb.general_extracellular_ephys_electrodes = electrode_table;
 
 %% Multielectrode recording
@@ -91,7 +114,7 @@
 electrode_table_region = types.hdmf_common.DynamicTableRegion( ...
     'table', electrodes_object_view, ...
     'description', 'all electrodes', ...
-    'data', [0 height(tbl)-1]');
+    'data', [0 nelecs-1]');
 
 %%
 % once you have the |ElectrodeTableRegion| object, you can create an