From 7f98bf93d364db0d6d74f82fd33728ddb90a0acd Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 12:02:41 -0400
Subject: [PATCH 01/17] Minor refactoring

- renamed variables to for clarity
- retabbed function files to include one scope for base/private functions.
---
 +io/writeCompound.m         | 196 ++++++++++++++++++------------------
 +types/+untyped/MetaClass.m |   6 +-
 NwbFile.m                   | 152 ++++++++++++++--------------
 3 files changed, 177 insertions(+), 177 deletions(-)

diff --git a/+io/writeCompound.m b/+io/writeCompound.m
index c7db74b1..503b03b2 100644
--- a/+io/writeCompound.m
+++ b/+io/writeCompound.m
@@ -1,119 +1,119 @@
 function writeCompound(fid, fullpath, data, varargin)
-%convert to a struct
-if istable(data)
-    data = table2struct(data);
-elseif isa(data, 'containers.Map')
-    names = keys(data);
-    vals = values(data, names);
+    %convert to a struct
+    if istable(data)
+        data = table2struct(data);
+    elseif isa(data, 'containers.Map')
+        names = keys(data);
+        vals = values(data, names);
 
-    s = struct();
-    for i=1:length(names)
-        s.(misc.str2validName(names{i})) = vals{i};
+        s = struct();
+        for i=1:length(names)
+            s.(misc.str2validName(names{i})) = vals{i};
+        end
+        data = s;
     end
-    data = s;
-end
 
-%convert to scalar struct
-names = fieldnames(data);
-if isempty(names)
-    numrows = 0;
-elseif isscalar(data)
-    if ischar(data.(names{1}))
-        numrows = 1;
+    %convert to scalar struct
+    names = fieldnames(data);
+    if isempty(names)
+        numrows = 0;
+    elseif isscalar(data)
+        if ischar(data.(names{1}))
+            numrows = 1;
+        else
+            numrows = length(data.(names{1}));
+        end
     else
-        numrows = length(data.(names{1}));
+        numrows = length(data);
+        s = struct();
+        for i=1:length(names)
+            s.(names{i}) = {data.(names{i})};
+        end
+        data = s;
     end
-else
-    numrows = length(data);
-    s = struct();
+
+    %check for references and construct tid.
+    classes = cell(length(names), 1);
+    tids = cell(size(classes));
+    sizes = zeros(size(classes));
     for i=1:length(names)
-        s.(names{i}) = {data.(names{i})};
-    end
-    data = s;
-end
+        val = data.(names{i});
+        if iscell(val) && ~iscellstr(val)
+            data.(names{i}) = [val{:}];
+            val = val{1};
+        end
 
-%check for references and construct tid.
-classes = cell(length(names), 1);
-tids = cell(size(classes));
-sizes = zeros(size(classes));
-for i=1:length(names)
-    val = data.(names{i});
-    if iscell(val) && ~iscellstr(val)
-        data.(names{i}) = [val{:}];
-        val = val{1};
+        classes{i} = class(val);
+        tids{i} = io.getBaseType(classes{i});
+        sizes(i) = H5T.get_size(tids{i});
     end
 
-    classes{i} = class(val);
-    tids{i} = io.getBaseType(classes{i});
-    sizes(i) = H5T.get_size(tids{i});
-end
-
-tid = H5T.create('H5T_COMPOUND', sum(sizes));
-for i=1:length(names)
-    %insert columns into compound type
-    H5T.insert(tid, names{i}, sum(sizes(1:i-1)), tids{i});
-end
-%close custom type ids (errors if char base type)
-isH5ml = tids(cellfun('isclass', tids, 'H5ML.id'));
-for i=1:length(isH5ml)
-    H5T.close(isH5ml{i});
-end
-%optimizes for type size
-H5T.pack(tid);
+    tid = H5T.create('H5T_COMPOUND', sum(sizes));
+    for i=1:length(names)
+        %insert columns into compound type
+        H5T.insert(tid, names{i}, sum(sizes(1:i-1)), tids{i});
+    end
+    %close custom type ids (errors if char base type)
+    isH5ml = tids(cellfun('isclass', tids, 'H5ML.id'));
+    for i=1:length(isH5ml)
+        H5T.close(isH5ml{i});
+    end
+    %optimizes for type size
+    H5T.pack(tid);
 
-ref_i = strcmp(classes, 'types.untyped.ObjectView') |...
-    strcmp(classes, 'types.untyped.RegionView');
+    isReferenceClass = strcmp(classes, 'types.untyped.ObjectView') |...
+        strcmp(classes, 'types.untyped.RegionView');
 
-% convert logical values
-boolNames = names(strcmp(classes, 'logical'));
-for iField = 1:length(boolNames)
-    data.(boolNames{iField}) = strcmp('TRUE', data.(boolNames{iField}));
-end
+    % convert logical values
+    boolNames = names(strcmp(classes, 'logical'));
+    for iField = 1:length(boolNames)
+        data.(boolNames{iField}) = strcmp('TRUE', data.(boolNames{iField}));
+    end
 
-%transpose numeric column arrays to row arrays
-% reference and str arrays are handled below
-transposeNames = names(~ref_i);
-for i=1:length(transposeNames)
-    nm = transposeNames{i};
-    if iscolumn(data.(nm))
-        data.(nm) = data.(nm) .';
+    %transpose numeric column arrays to row arrays
+    % reference and str arrays are handled below
+    transposeNames = names(~isReferenceClass);
+    for i=1:length(transposeNames)
+        nm = transposeNames{i};
+        if iscolumn(data.(nm))
+            data.(nm) = data.(nm) .';
+        end
     end
-end
 
-%attempt to convert raw reference information
-refNames = names(ref_i);
-for i=1:length(refNames)
-    data.(refNames{i}) = io.getRefData(fid, data.(refNames{i}));
-end
+    %attempt to convert raw reference information
+    referenceNames = names(isReferenceClass);
+    for i=1:length(referenceNames)
+        data.(referenceNames{i}) = io.getRefData(fid, data.(referenceNames{i}));
+    end
 
-try
-    sid = H5S.create_simple(1, numrows, []);
-    did = H5D.create(fid, fullpath, tid, sid, 'H5P_DEFAULT');
-catch ME
-    if contains(ME.message, 'name already exists')
-        did = H5D.open(fid, fullpath);
-        create_plist = H5D.get_create_plist(did);
-        edit_sid = H5D.get_space(did);
-        [~, edit_dims, ~] = H5S.get_simple_extent_dims(edit_sid);
-        layout = H5P.get_layout(create_plist);
-        is_chunked = layout == H5ML.get_constant_value('H5D_CHUNKED');
-        is_same_dims = all(edit_dims == numrows);
+    try
+        sid = H5S.create_simple(1, numrows, []);
+        did = H5D.create(fid, fullpath, tid, sid, 'H5P_DEFAULT');
+    catch ME
+        if contains(ME.message, 'name already exists')
+            did = H5D.open(fid, fullpath);
+            create_plist = H5D.get_create_plist(did);
+            edit_sid = H5D.get_space(did);
+            [~, edit_dims, ~] = H5S.get_simple_extent_dims(edit_sid);
+            layout = H5P.get_layout(create_plist);
+            is_chunked = layout == H5ML.get_constant_value('H5D_CHUNKED');
+            is_same_dims = all(edit_dims == numrows);
 
-        if ~is_same_dims
-            if is_chunked
-                H5D.set_extent(did, dims);
-            else
-                warning('Attempted to change size of continuous compound `%s`.  Skipping.',...
-                    fullpath);
+            if ~is_same_dims
+                if is_chunked
+                    H5D.set_extent(did, dims);
+                else
+                    warning('Attempted to change size of continuous compound `%s`.  Skipping.',...
+                        fullpath);
+                end
             end
+            H5P.close(create_plist);
+            H5S.close(edit_sid);
+        else
+            rethrow(ME);
         end
-        H5P.close(create_plist);
-        H5S.close(edit_sid);
-    else
-        rethrow(ME);
     end
-end
-H5D.write(did, tid, sid, sid, 'H5P_DEFAULT', data);
-H5D.close(did);
-H5S.close(sid);
+    H5D.write(did, tid, sid, sid, 'H5P_DEFAULT', data);
+    H5D.close(did);
+    H5S.close(sid);
 end
\ No newline at end of file
diff --git a/+types/+untyped/MetaClass.m b/+types/+untyped/MetaClass.m
index 11ed19b7..6d7840a9 100644
--- a/+types/+untyped/MetaClass.m
+++ b/+types/+untyped/MetaClass.m
@@ -26,11 +26,11 @@
                     io.writeDataset(fid, fullpath, obj.data, 'forceArray');
                 end
             catch ME
-                refs = obj.capture_ref_errors(ME, fullpath, refs);
+                refs = obj.captureReferenceErrors(ME, fullpath, refs);
             end
         end
         
-        function refs = capture_ref_errors(~, ME, fullpath, refs)
+        function refs = captureReferenceErrors(~, ME, fullpath, refs)
             if any(strcmp(ME.identifier, {...
                     'NWB:getRefData:InvalidPath',...
                     'NWB:ObjectView:MissingPath'}))
@@ -58,7 +58,7 @@
                 try
                     io.getRefData(fid, props{i});
                 catch ME
-                    refs = obj.capture_ref_errors(ME, fullpath, refs);
+                    refs = obj.captureReferenceErrors(ME, fullpath, refs);
                 end
             end
             
diff --git a/NwbFile.m b/NwbFile.m
index 76c3c288..24e5dc6f 100644
--- a/NwbFile.m
+++ b/NwbFile.m
@@ -10,7 +10,7 @@
     %    nwbExport(nwb, 'epoch.nwb');
     %
     % See also NWBREAD, GENERATECORE, GENERATEEXTENSION
-    
+
     methods
         function obj = NwbFile(varargin)
             obj = obj@types.core.NWBFile(varargin{:});
@@ -18,14 +18,14 @@
                 types.util.checkUnset(obj, unique(varargin(1:2:end)));
             end
         end
-        
+
         function export(obj, filename)
             %add to file create date
             current_time = datetime('now', 'TimeZone', 'local');
             if isa(obj.file_create_date, 'types.untyped.DataStub')
                 obj.file_create_date = obj.file_create_date.load();
             end
-            
+
             if isempty(obj.file_create_date)
                 obj.file_create_date = current_time;
             elseif iscell(obj.file_create_date)
@@ -33,12 +33,12 @@ function export(obj, filename)
             else
                 obj.file_create_date = {obj.file_create_date current_time};
             end
-            
+
             %equate reference time to session_start_time if empty
             if isempty(obj.timestamps_reference_time)
                 obj.timestamps_reference_time = obj.session_start_time;
             end
-            
+
             try
                 output_file_id = H5F.create(filename);
                 isEditingFile = false;
@@ -49,14 +49,14 @@ function export(obj, filename)
                 else
                     isEditingFile = strcmp(ME.identifier, 'MATLAB:imagesci:hdf5io:resourceAlreadyExists');
                 end
-                
+
                 if isEditingFile
                     output_file_id = H5F.open(filename, 'H5F_ACC_RDWR', 'H5P_DEFAULT');
                 else
                     rethrow(ME);
                 end
             end
-            
+
             try
                 obj.embedSpecifications(output_file_id);
                 refs = export@types.core.NWBFile(obj, output_file_id, '/', {});
@@ -71,7 +71,7 @@ function export(obj, filename)
                 rethrow(ME);
             end
         end
-        
+
         function o = resolve(obj, path)
             if ischar(path)
                 path = {path};
@@ -84,7 +84,7 @@ function export(obj, filename)
                 o = o{1};
             end
         end
-        
+
         function objectMap = searchFor(obj, typename, varargin)
             % Searches this NwbFile object for a given typename
             % Including the full namespace is optional.
@@ -98,7 +98,7 @@ function export(obj, filename)
                 varargin{:});
         end
     end
-    
+
     %% PRIVATE
     methods(Access=private)
         function resolveReferences(obj, fid, references)
@@ -111,10 +111,8 @@ function resolveReferences(obj, fid, references)
                     exportSuccess = isempty(unresolvedRefs);
                     resolved(iRef) = exportSuccess;
                 end
-                
-                if any(resolved)
-                    references(resolved) = [];
-                else
+
+                if ~any(resolved)
                     errorFormat = ['object(s) could not be created:\n%s\n\nThe '...
                         'listed object(s) above contain an ObjectView, '...
                         'RegionView , or SoftLink object that has failed to resolve itself. '...
@@ -124,9 +122,11 @@ function resolveReferences(obj, fid, references)
                     error('NWB:NwbFile:UnresolvedReferences',...
                         errorFormat, file.addSpaces(unresolvedRefs, 4));
                 end
+
+                references(resolved) = [];
             end
         end
-        
+
         function embedSpecifications(~, fid)
             try
                 attrId = H5A.open(fid, '/.specloc');
@@ -138,7 +138,7 @@ function embedSpecifications(~, fid)
                 specView = types.untyped.ObjectView(specLocation);
                 io.writeAttribute(fid, '/.specloc', specView);
             end
-            
+
             JsonData = schemes.exportJson();
             for iJson = 1:length(JsonData)
                 JsonDatum = JsonData(iJson);
@@ -164,80 +164,80 @@ function embedSpecifications(~, fid)
                     io.writeDataset(fid, path, Json(name));
                 end
             end
-            
-            function versionNames = getVersionNames(namespaceGroupId)
-                [~, ~, versionNames] = H5L.iterate(namespaceGroupId,...
-                    'H5_INDEX_NAME', 'H5_ITER_NATIVE',...
-                    0, @removeGroups, {});
-                function [status, versionNames] = removeGroups(~, name, versionNames)
-                    versionNames{end+1} = name;
-                    status = 0;
-                end
-            end
         end
     end
 end
 
-function tf = metaHasType(mc, typeSuffix)
-assert(isa(mc, 'meta.class'));
-tf = false;
-if contains(mc.Name, typeSuffix, 'IgnoreCase', true)
-    tf = true;
-    return;
+function versionNames = getVersionNames(namespaceGroupId)
+    [~, ~, versionNames] = H5L.iterate(namespaceGroupId,...
+        'H5_INDEX_NAME', 'H5_ITER_NATIVE',...
+        0, @removeGroups, {});
+    function [status, versionNames] = removeGroups(~, name, versionNames)
+        versionNames{end+1} = name;
+        status = 0;
+    end
 end
 
-for i = 1:length(mc.SuperclassList)
-    sc = mc.SuperclassList(i);
-    if metaHasType(sc, typeSuffix)
+function tf = metaHasType(mc, typeSuffix)
+    assert(isa(mc, 'meta.class'));
+    tf = false;
+    if contains(mc.Name, typeSuffix, 'IgnoreCase', true)
         tf = true;
         return;
     end
-end
+
+    for i = 1:length(mc.SuperclassList)
+        sc = mc.SuperclassList(i);
+        if metaHasType(sc, typeSuffix)
+            tf = true;
+            return;
+        end
+    end
 end
 
 function pathToObjectMap = searchProperties(...
-    pathToObjectMap,...
-    obj,...
-    basePath,...
-    typename,...
-    varargin)
-assert(all(iscellstr(varargin)),...
-    'NWB:NwbFile:SearchProperties:InvalidVariableArguments',...
-    'Optional keywords for searchFor must be char arrays.');
-shouldSearchSuperClasses = any(strcmpi(varargin, 'includeSubClasses'));
-
-if isa(obj, 'types.untyped.MetaClass')
-    propertyNames = properties(obj);
-    getProperty = @(x, prop) x.(prop);
-elseif isa(obj, 'types.untyped.Set')
-    propertyNames = obj.keys();
-    getProperty = @(x, prop) x.get(prop);
-elseif isa(obj, 'types.untyped.Anon')
-    propertyNames = {obj.name};
-    getProperty = @(x, prop) x.value;
-else
-    error('NWB:NwbFile:SearchProperties:InvalidType',...
-        'Invalid object type passed %s', class(obj));
-end
+        pathToObjectMap,...
+        obj,...
+        basePath,...
+        typename,...
+        varargin)
+    assert(all(iscellstr(varargin)),...
+        'NWB:NwbFile:SearchProperties:InvalidVariableArguments',...
+        'Optional keywords for searchFor must be char arrays.');
+    shouldSearchSuperClasses = any(strcmpi(varargin, 'includeSubClasses'));
 
-searchTypename = @(obj, typename) contains(class(obj), typename, 'IgnoreCase', true);
-if shouldSearchSuperClasses
-    searchTypename = @(obj, typename) metaHasType(metaclass(obj), typename);
-end
+    if isa(obj, 'types.untyped.MetaClass')
+        propertyNames = properties(obj);
+        getProperty = @(x, prop) x.(prop);
+    elseif isa(obj, 'types.untyped.Set')
+        propertyNames = obj.keys();
+        getProperty = @(x, prop) x.get(prop);
+    elseif isa(obj, 'types.untyped.Anon')
+        propertyNames = {obj.name};
+        getProperty = @(x, prop) x.value;
+    else
+        error('NWB:NwbFile:SearchProperties:InvalidType',...
+            'Invalid object type passed %s', class(obj));
+    end
 
-for i = 1:length(propertyNames)
-    propName = propertyNames{i};
-    propValue = getProperty(obj, propName);
-    fullPath = [basePath '/' propName];
-    if searchTypename(propValue, typename)
-        pathToObjectMap(fullPath) = propValue;
+    searchTypename = @(obj, typename) contains(class(obj), typename, 'IgnoreCase', true);
+    if shouldSearchSuperClasses
+        searchTypename = @(obj, typename) metaHasType(metaclass(obj), typename);
     end
-    
-    if isa(propValue, 'types.untyped.GroupClass')...
-            || isa(propValue, 'types.untyped.Set')...
-            || isa(propValue, 'types.untyped.Anon')
-        % recursible (even if there is a match!)
-        searchProperties(pathToObjectMap, propValue, fullPath, typename, varargin{:});
+
+    for i = 1:length(propertyNames)
+        propName = propertyNames{i};
+        propValue = getProperty(obj, propName);
+        fullPath = [basePath '/' propName];
+        if searchTypename(propValue, typename)
+            pathToObjectMap(fullPath) = propValue;
+        end
+
+        if isa(propValue, 'types.untyped.GroupClass')...
+                || isa(propValue, 'types.untyped.Set')...
+                || isa(propValue, 'types.untyped.Anon')
+            % recursible (even if there is a match!)
+            searchProperties(pathToObjectMap, propValue, fullPath, typename, varargin{:});
+        end
     end
-end
 end
\ No newline at end of file

From 3c34bed7c6490bf7b66edeb20c56d5a2f6249e0b Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 12:03:51 -0400
Subject: [PATCH 02/17] Add workarounds for VectorData unit class

---
 +file/fillExport.m   | 372 ++++++++++++++++++++++---------------------
 +file/processClass.m |  19 +++
 2 files changed, 213 insertions(+), 178 deletions(-)

diff --git a/+file/fillExport.m b/+file/fillExport.m
index 1f590e5b..c9d7ae81 100644
--- a/+file/fillExport.m
+++ b/+file/fillExport.m
@@ -1,206 +1,222 @@
-function festr = fillExport(propnames, raw, parentName)
-hdrstr = 'function refs = export(obj, fid, fullpath, refs)';
-if isa(raw, 'file.Dataset')
-    propnames = propnames(~strcmp(propnames, 'data'));
-end
+function festr = fillExport(propertyNames, RawClass, parentName)
+    exportHeader = 'function refs = export(obj, fid, fullpath, refs)';
+    if isa(RawClass, 'file.Dataset')
+        propertyNames = propertyNames(~strcmp(propertyNames, 'data'));
+    end
 
-bodystr = {strjoin({...
-    ['refs = export@' parentName '(obj, fid, fullpath, refs);']...
-    'if any(strcmp(refs, fullpath))'...
-    '    return;'...
-    'end'...
-    }, newline)};
-
-if isa(raw, 'file.Group') && strcmp(raw.type, 'NWBFile')
-    %NWBFile is technically the root `group`, which in HDF5 is a single `/`
-    % this messes with property creation so we reassign the path here to
-    % empty string so concatenation looks right
-    bodystr = [bodystr {'fullpath = '''';'}];
-end
+    exportBody = {strjoin({...
+        ['refs = export@' parentName '(obj, fid, fullpath, refs);']...
+        'if any(strcmp(refs, fullpath))'...
+        '    return;'...
+        'end'...
+        }, newline)};
 
-for i = 1:length(propnames)
-    pnm = propnames{i};
-    pathProps = traverseRaw(pnm, raw);
-    if isempty(pathProps)
-        keyboard;
-%         bodystr{end+1} = fillDataExport(pnm, 
+    if isa(RawClass, 'file.Group') && strcmp(RawClass.type, 'NWBFile')
+        %NWBFile is technically the root `group`, which in HDF5 is a single `/`
+        % this messes with property creation so we reassign the path here to
+        % empty string so concatenation looks right
+        exportBody = [exportBody {'fullpath = '''';'}];
     end
-    prop = pathProps{end};
-    elideProps = pathProps(1:end-1);
-    elisions = cell(length(elideProps),1);
-    %Construct elisions
-    for j = 1:length(elideProps)
-        elisions{j} = elideProps{j}.name;
-    end
-    
-    elisions = strjoin(elisions, '/');
-    if ~isempty(elideProps) && all(cellfun('isclass', elideProps, 'file.Group'))
-        bodystr{end+1} = ['io.writeGroup(fid, [fullpath ''/' elisions ''']);'];
-    end
-    bodystr{end+1} = fillDataExport(pnm, prop, elisions);
-end
 
-festr = strjoin({hdrstr...
-    file.addSpaces(strjoin(bodystr, newline), 4)...
-    'end'}, newline);
-end
-
-function path = traverseRaw(propname, raw)
-path = {};
-switch class(raw)
-    case 'file.Group'
-        %get names of both subgroups and datasets
-        gnames = {};
-        dsnames = {};
-        lnknames = {};
-        anames = {};
-        
-        if ~isempty(raw.attributes)
-            anames = {raw.attributes.name};
+    for i = 1:length(propertyNames)
+        propertyName = propertyNames{i};
+        pathProps = traverseRaw(propertyName, RawClass);
+        if isempty(pathProps)
+            keyboard;
         end
-        
-        if ~isempty(raw.subgroups)
-            gnames = {raw.subgroups.name};
-            lowerGroupTypes = lower({raw.subgroups.type});
-            useLower = [raw.subgroups.isConstrainedSet] | cellfun('isempty', gnames);
-            gnames(useLower) = lowerGroupTypes(useLower);
+        prop = pathProps{end};
+        elideProps = pathProps(1:end-1);
+        elisions = cell(length(elideProps),1);
+        % Construct elisions
+        for j = 1:length(elideProps)
+            elisions{j} = elideProps{j}.name;
         end
-        
-        if ~isempty(raw.datasets)
-            dsnames = {raw.datasets.name};
-            lowerDsTypes = lower({raw.datasets.type});
-            useLower = [raw.datasets.isConstrainedSet] | cellfun('isempty', dsnames);
-            dsnames(useLower) = lowerDsTypes(useLower);
+
+        elisions = strjoin(elisions, '/');
+        if ~isempty(elideProps) && all(cellfun('isclass', elideProps, 'file.Group'))
+            exportBody{end+1} = ['io.writeGroup(fid, [fullpath ''/' elisions ''']);'];
         end
-        
-        if ~isempty(raw.links)
-            lnknames = {raw.links.name};
+        if strcmp(propertyName, 'unit') && strcmp(RawClass.type, 'VectorData')
+            exportBody{end+1} = fillVectorDataUnitConditional();
+        else
+            exportBody{end+1} = fillDataExport(propertyName, prop, elisions);
         end
-        
-        if any(strcmp([anames gnames dsnames lnknames], propname))
-            amatch = strcmp(anames, propname);
-            gmatch = strcmp(gnames, propname);
-            dsmatch = strcmp(dsnames, propname);
-            lnkmatch = strcmp(lnknames, propname);
-            if any(amatch)
-                path = {raw.attributes(amatch)};
-            elseif any(gmatch)
-                path = {raw.subgroups(gmatch)};
-            elseif any(dsmatch)
-                path = {raw.datasets(dsmatch)};
-            elseif any(lnkmatch)
-                path = {raw.links(lnkmatch)};
-            end
+    end
+
+    festr = strjoin({exportHeader...
+        file.addSpaces(strjoin(exportBody, newline), 4)...
+        'end'}, newline);
+end
+
+function exportBody = fillVectorDataUnitConditional()
+    exportBody = strjoin({...
+          'validUnitPaths = strcat(''units/'', {''waveform_mean'', ''waveform_sd'', ''waveforms''});' ...
+        , 'if ~isempty(obj.unit) && any(endsWith(fullpath, validUnitPaths))' ...
+        , '    io.writeAttribute(fid, [fullpath ''/unit''], obj.unit);' ...
+        , 'end'}, newline);
+end
+
+function path = traverseRaw(propertyName, RawClass)
+    % returns a cell array of named tokens which may or may not indicate an identifier.
+    % these tokens are relative to the Raw class
+    path = {}; 
+
+    if isa(RawClass, 'file.Dataset')
+        if isempty(RawClass.attributes)
             return;
         end
-        
-        %find true path for elided property
-        if startsWith(propname, dsnames) || startsWith(propname, gnames)
-            for i=1:length(gnames)
-                nm = gnames{i};
-                suffix = propname(length(nm)+2:end);
-                if startsWith(propname, nm)
-                    res = traverseRaw(suffix, raw.subgroups(i));
-                    if ~isempty(res)
-                        path = [{raw.subgroups(i)} res];
-                        return;
-                    end
+        matchesAttribute = strcmp({RawClass.attributes.name}, propertyName);
+        path = {RawClass.attributes(matchesAttribute)};
+        return;
+    end
+
+    % probably a file.Group
+
+    % get names of both subgroups and datasets
+    subgroupNames = {};
+    datasetNames = {};
+    linkNames = {};
+    attributeNames = {};
+
+    if ~isempty(RawClass.attributes)
+        attributeNames = {RawClass.attributes.name};
+    end
+
+    if ~isempty(RawClass.subgroups)
+        subgroupNames = {RawClass.subgroups.name};
+        lowerGroupTypes = lower({RawClass.subgroups.type});
+        useLower = [RawClass.subgroups.isConstrainedSet] | cellfun('isempty', subgroupNames);
+        subgroupNames(useLower) = lowerGroupTypes(useLower);
+    end
+
+    if ~isempty(RawClass.datasets)
+        datasetNames = {RawClass.datasets.name};
+        lowerDsTypes = lower({RawClass.datasets.type});
+        useLower = [RawClass.datasets.isConstrainedSet] | cellfun('isempty', datasetNames);
+        datasetNames(useLower) = lowerDsTypes(useLower);
+    end
+
+    if ~isempty(RawClass.links)
+        linkNames = {RawClass.links.name};
+    end
+
+    if any(strcmp([attributeNames subgroupNames datasetNames linkNames], propertyName))
+        isAttribute = strcmp(attributeNames, propertyName);
+        isGroup = strcmp(subgroupNames, propertyName);
+        isDataset = strcmp(datasetNames, propertyName);
+        isLink = strcmp(linkNames, propertyName);
+        if any(isAttribute)
+            path = {RawClass.attributes(isAttribute)};
+        elseif any(isGroup)
+            path = {RawClass.subgroups(isGroup)};
+        elseif any(isDataset)
+            path = {RawClass.datasets(isDataset)};
+        elseif any(isLink)
+            path = {RawClass.links(isLink)};
+        end
+        return;
+    end
+
+    % find true path for elided property
+    if startsWith(propertyName, datasetNames) || startsWith(propertyName, subgroupNames)
+        for i=1:length(subgroupNames)
+            name = subgroupNames{i};
+            suffix = propertyName(length(name)+2:end);
+            if startsWith(propertyName, name)
+                res = traverseRaw(suffix, RawClass.subgroups(i));
+                if ~isempty(res)
+                    path = [{RawClass.subgroups(i)} res];
+                    return;
                 end
             end
-            for i=1:length(dsnames)
-                nm = dsnames{i};
-                suffix = propname(length(nm)+2:end);
-                if startsWith(propname, nm)
-                    res = traverseRaw(suffix, raw.datasets(i));
-                    if ~isempty(res)
-                        path = [{raw.datasets(i)} res];
-                        return;
-                    end
+        end
+        for i=1:length(datasetNames)
+            name = datasetNames{i};
+            suffix = propertyName(length(name)+2:end);
+            if startsWith(propertyName, name)
+                res = traverseRaw(suffix, RawClass.datasets(i));
+                if ~isempty(res)
+                    path = [{RawClass.datasets(i)} res];
+                    return;
                 end
             end
         end
-    case 'file.Dataset'
-        if isempty(raw.attributes)
-            return;
-        end
-        attrmatch = strcmp({raw.attributes.name}, propname);
-        path = {raw.attributes(attrmatch)};
-end
+    end
 end
 
 function fde = fillDataExport(name, prop, elisions)
-if isempty(elisions)
-    fullpath = ['[fullpath ''/' prop.name ''']'];
-    elisionpath = 'fullpath';
-else
-    fullpath = ['[fullpath ''/' elisions '/' prop.name ''']'];
-    elisionpath = ['[fullpath ''/' elisions ''']'];
-end
-
-if (isa(prop, 'file.Group') || isa(prop, 'file.Dataset')) && prop.isConstrainedSet
-    fde = ['refs = obj.' name '.export(fid, ' elisionpath ', refs);'];
-elseif isa(prop, 'file.Link') || isa(prop, 'file.Group') ||...
-        (isa(prop, 'file.Dataset') && ~isempty(prop.type))
-    % obj, loc_id, path, refs
-    fde = ['refs = obj.' name '.export(fid, ' fullpath ', refs);'];
-elseif isa(prop, 'file.Dataset') %untyped dataset
-    options = {};
-    
-    % special case due to unique behavior of file_create_date
-    if strcmp(name, 'file_create_date')
-        options = [options {'''forceChunking''', '''forceArray'''}];
-    elseif ~prop.scalar
-        options = [options {'''forceArray'''}];
-    end
-        
-    
-    % untyped compound
-    if isstruct(prop.dtype)
-        writerStr = 'io.writeCompound';
+    if isempty(elisions)
+        fullpath = ['[fullpath ''/' prop.name ''']'];
+        elisionpath = 'fullpath';
     else
-        writerStr = 'io.writeDataset';
+        fullpath = ['[fullpath ''/' elisions '/' prop.name ''']'];
+        elisionpath = ['[fullpath ''/' elisions ''']'];
     end
-    
-    % just to guarantee optional arguments are correct syntax
-    nameProp = sprintf('obj.%s', name);
-    nameArgs = [{nameProp} options];
-    nameArgs = strjoin(nameArgs, ', ');
-    fde = strjoin({...
-        ['if startsWith(class(obj.' name '), ''types.untyped.'')']...
-        ['    refs = obj.' name '.export(fid, ' fullpath ', refs);']...
-        ['elseif ~isempty(obj.' name ')']...
-        [sprintf('    %s(fid, %s, %s);', writerStr, fullpath, nameArgs)]...
-        'end'...
-        }, newline);
-else
-    if prop.scalar
-        forceArrayFlag = '';
+
+    if (isa(prop, 'file.Group') || isa(prop, 'file.Dataset')) && prop.isConstrainedSet
+        % is a sub-object (with an export function)
+        fde = ['refs = obj.' name '.export(fid, ' elisionpath ', refs);'];
+    elseif isa(prop, 'file.Link') || isa(prop, 'file.Group') ||...
+            (isa(prop, 'file.Dataset') && ~isempty(prop.type))
+        % obj, loc_id, path, refs
+        fde = ['refs = obj.' name '.export(fid, ' fullpath ', refs);'];
+    elseif isa(prop, 'file.Dataset') %untyped dataset
+        options = {};
+
+        % special case due to unique behavior of file_create_date
+        if strcmp(name, 'file_create_date')
+            options = [options {'''forceChunking''', '''forceArray'''}];
+        elseif ~prop.scalar
+            options = [options {'''forceArray'''}];
+        end
+
+        % untyped compound
+        if isstruct(prop.dtype)
+            writerStr = 'io.writeCompound';
+        else
+            writerStr = 'io.writeDataset';
+        end
+
+        % just to guarantee optional arguments are correct syntax
+        nameProp = sprintf('obj.%s', name);
+        nameArgs = [{nameProp} options];
+        nameArgs = strjoin(nameArgs, ', ');
+        fde = strjoin({...
+            ['if startsWith(class(obj.' name '), ''types.untyped.'')']...
+            ['    refs = obj.' name '.export(fid, ' fullpath ', refs);']...
+            ['elseif ~isempty(obj.' name ')']...
+            [sprintf('    %s(fid, %s, %s);', writerStr, fullpath, nameArgs)]...
+            'end'...
+            }, newline);
     else
-        forceArrayFlag = ', ''forceArray''';
+        if prop.scalar
+            forceArrayFlag = '';
+        else
+            forceArrayFlag = ', ''forceArray''';
+        end
+        fde = sprintf('io.writeAttribute(fid, %1$s, obj.%2$s%3$s);',...
+            fullpath, name, forceArrayFlag);
     end
-    fde = sprintf('io.writeAttribute(fid, %1$s, obj.%2$s%3$s);',...
-        fullpath, name, forceArrayFlag);
-end
 
-propertyChecks = {};
+    propertyChecks = {};
 
-if isa(prop, 'file.Attribute') && ~isempty(prop.dependent)
-    %if attribute is dependent, check before writing
-    if isempty(elisions) || strcmp(elisions, prop.dependent)
-        depPropname = prop.dependent;
-    else
-        flattened = strfind(elisions, '/');
-        flattened = strrep(elisions(1:flattened(end)), '/', '_');
-        depPropname = [flattened prop.dependent];
+    if isa(prop, 'file.Attribute') && ~isempty(prop.dependent)
+        %if attribute is dependent, check before writing
+        if isempty(elisions) || strcmp(elisions, prop.dependent)
+            depPropname = prop.dependent;
+        else
+            flattened = strfind(elisions, '/');
+            flattened = strrep(elisions(1:flattened(end)), '/', '_');
+            depPropname = [flattened prop.dependent];
+        end
+        propertyChecks{end+1} = ['~isempty(obj.' depPropname ')'];
     end
-    propertyChecks{end+1} = ['~isempty(obj.' depPropname ')'];
-end
 
-if ~prop.required
-    propertyChecks{end+1} = ['~isempty(obj.' name ')'];
-end
+    if ~prop.required
+        propertyChecks{end+1} = ['~isempty(obj.' name ')'];
+    end
 
-if ~isempty(propertyChecks)
-    fde = ['if ' strjoin(propertyChecks, ' && ') newline file.addSpaces(fde, 4) newline 'end'];
-end
+    if ~isempty(propertyChecks)
+        fde = ['if ' strjoin(propertyChecks, ' && ') newline file.addSpaces(fde, 4) newline 'end'];
+    end
 end
\ No newline at end of file
diff --git a/+file/processClass.m b/+file/processClass.m
index 6f288a0a..f1ad17a2 100644
--- a/+file/processClass.m
+++ b/+file/processClass.m
@@ -23,7 +23,11 @@
                 error('NWB:FileGen:InvalidClassType',...
                     'Class type %s is invalid', node('class_type'));
         end
+        if strcmp(nodename, 'VectorData') && strcmp(namespace.name, 'hdmf_common')
+            class = patchVectorData(class);
+        end
         props = class.getProps();
+
         pregen(nodename) = struct('class', class, 'props', props);
     end
     try
@@ -39,4 +43,19 @@
     parentPropNames = keys(pregen(pname).props);
     inherited = union(inherited, intersect(names, parentPropNames));
 end
+end
+
+function class = patchVectorData(class)
+    % adds an optional "units" attribute added by the Units table.
+    % derived from schema 2.6.0
+    source = containers.Map();
+    source('name') = 'unit';
+    source('doc') = ['NOTE: this is a special value for compatibility with the Units table and is ' ...
+        'only written to file when detected to be in that specific HDF5 Group. ' ...
+        'The value must be ''volts'''];
+    source('dtype') = 'text';
+    source('value') = 'volts';
+    source('required') = false;
+    
+    class.attributes(end+1) = file.Attribute(source);
 end
\ No newline at end of file

From e032c75567a35c64c0545866198f6402d6d3f146 Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 12:04:21 -0400
Subject: [PATCH 03/17] Fix special duplicate H5D case

If the object's data is not a reference but has region/object references in its attributes, then
this error may occur because all reference corrections require calling `export` again.

Since we want to limit the possibility of object reference cycles, it's better to write any dataset
given that it's not reference data and just check for duplicates before doing so.
---
 +types/+untyped/MetaClass.m | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/+types/+untyped/MetaClass.m b/+types/+untyped/MetaClass.m
index 6d7840a9..74ddebd2 100644
--- a/+types/+untyped/MetaClass.m
+++ b/+types/+untyped/MetaClass.m
@@ -14,6 +14,11 @@
                 io.writeGroup(fid, fullpath);
                 return;
             end
+
+            if H5L.exists(fid, fullpath, 'H5P_DEFAULT')
+                % skip if already written.
+                return;
+            end
             
             try
                 if isa(obj.data, 'types.untyped.DataStub')...

From 586935b0acf8bb6efb941bdd639c0003bbbae691 Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 13:21:39 -0400
Subject: [PATCH 04/17] Fix fillProps case when groups are empty

Used to error, now short-circuits the output.
---
 +file/fillProps.m | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/+file/fillProps.m b/+file/fillProps.m
index 97b0fdfc..a68aa15f 100644
--- a/+file/fillProps.m
+++ b/+file/fillProps.m
@@ -1,6 +1,12 @@
 function s = fillProps(props, names, varargin)
-    validateattributes(props, {'containers.Map'}, {}, mfilename, 'props', 1);
-    validateattributes(names, {'cell'}, {'vector'}, mfilename, 'names', 2);
+    % Fills the property list in the classdef
+    assert(isa(props, 'containers.Map'));
+    assert(iscellstr(names) || isstring(names));
+    s = '';
+    if isempty(names)
+        return;
+    end
+
     p = inputParser;
     p.addParameter('PropertyAttributes', '', ...
         @(x)validateattributes(x, {'char'}, {'scalartext'}, mfilename, 'Attribute'));
@@ -26,14 +32,10 @@
         options = ['(' p.Results.PropertyAttributes ')'];
     end
 
-    if isempty(proplines)
-        s = '';
-    else
-        s = strjoin({...
-            ['properties' options]...
-            file.addSpaces(strjoin(proplines, newline), 4)...
-            'end'}, newline);
-    end
+    s = strjoin({...
+        ['properties' options]...
+        file.addSpaces(strjoin(proplines, newline), 4)...
+        'end'}, newline);
 end
 
 function propStr = getPropStr(prop, propName)

From 1093dde421fc9ebcfccfd304976e5c8919f1384a Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 13:22:51 -0400
Subject: [PATCH 05/17] Fix excessive warnings in generated files

Removed the data-class setter format and use the correct handle-class one (without returning self).
---
 +file/fillSetters.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/+file/fillSetters.m b/+file/fillSetters.m
index 9e945898..941e60eb 100644
--- a/+file/fillSetters.m
+++ b/+file/fillSetters.m
@@ -3,7 +3,7 @@
 for i=1:length(propnames)
     nm = propnames{i};
     fsstr{i} = strjoin({...
-        ['function obj = set.' nm '(obj, val)']...
+        ['function set.' nm '(obj, val)']...
         ['    obj.' nm ' = obj.validate_' nm '(val);']...
         'end'}, newline);
 end

From ae59c3a04b3e7e04af986aabe55d679ee478417e Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 13:24:22 -0400
Subject: [PATCH 06/17] Add special hidden properties to fillClass

For hard-coding VectorData.unit.
Also retabbed to maintain consistent scope for functions.
---
 +file/fillClass.m | 223 +++++++++++++++++++++++++---------------------
 1 file changed, 122 insertions(+), 101 deletions(-)

diff --git a/+file/fillClass.m b/+file/fillClass.m
index 79f3acb5..5f024fc0 100644
--- a/+file/fillClass.m
+++ b/+file/fillClass.m
@@ -1,119 +1,140 @@
 function template = fillClass(name, namespace, processed, classprops, inherited)
-%name is the name of the scheme
-%namespace is the namespace context for this class
+    %name is the name of the scheme
+    %namespace is the namespace context for this class
 
-%% PROCESSING
-class = processed(1);
+    %% PROCESSING
+    class = processed(1);
 
-allprops = keys(classprops);
-required = {};
-optional = {};
-readonly = {};
-defaults = {};
-dependent = {};
-%separate into readonly, required, and optional properties
-for i=1:length(allprops)
-    pnm = allprops{i};
-    prop = classprops(pnm);
+    allProperties = keys(classprops);
+    required = {};
+    optional = {};
+    readonly = {};
+    defaults = {};
+    dependent = {};
+    hidden = {}; % special hidden properties for hard-coded workarounds
+    %separate into readonly, required, and optional properties
+    for iGroup = 1:length(allProperties)
+        propertyName = allProperties{iGroup};
+        prop = classprops(propertyName);
 
-    isRequired = ischar(prop) || isa(prop, 'containers.Map') || isstruct(prop);
-    iIsPropertyRequired = false;
-    if isa(prop, 'file.interface.HasProps')
-        iIsPropertyRequired = false(size(prop));
-        for iProp = 1:length(prop)
-            p = prop(iProp);
-            iIsPropertyRequired(iProp) = p.required;
-        end
-    end
-    
-    if isRequired || all(iIsPropertyRequired)
-        required = [required {pnm}];
-    else
-        optional = [optional {pnm}];
-    end
-    
-    if isa(prop, 'file.Attribute')
-        if prop.readonly
-            readonly = [readonly {pnm}];
+        isRequired = ischar(prop) || isa(prop, 'containers.Map') || isstruct(prop);
+        isPropertyRequired = false;
+        if isa(prop, 'file.interface.HasProps')
+            isPropertyRequired = false(size(prop));
+            for iProp = 1:length(prop)
+                p = prop(iProp);
+                isPropertyRequired(iProp) = p.required;
+            end
         end
-        
-        if ~isempty(prop.value)
-            defaults = [defaults {pnm}];
+
+        if isRequired || all(isPropertyRequired)
+            required = [required {propertyName}];
+        else
+            optional = [optional {propertyName}];
         end
-       
-        if ~isempty(prop.dependent)
-            %extract prefix
-            parentName = strrep(pnm, ['_' prop.name], '');
-            parent = classprops(parentName);
-            if ~parent.required
-                dependent = [dependent {pnm}];
+
+        if isa(prop, 'file.Attribute')
+            if prop.readonly
+                readonly = [readonly {propertyName}];
+            end
+
+            if ~isempty(prop.value)
+                defaults = [defaults {propertyName}];
+            end
+
+            if ~isempty(prop.dependent)
+                %extract prefix
+                parentName = strrep(propertyName, ['_' prop.name], '');
+                parent = classprops(parentName);
+                if ~parent.required
+                    dependent = [dependent {propertyName}];
+                end
+            end
+
+            if strcmp(namespace.name, 'hdmf_common') ...
+                && strcmp(name, 'VectorData') ...
+                && strcmp(prop.name, 'unit')
+                hidden{end+1} = propertyName;
             end
         end
     end
-end
-nonInherited = setdiff(allprops, inherited);
-readonly = intersect(readonly, nonInherited);
-required = intersect(required, nonInherited);
-optional = intersect(optional, nonInherited);
+    nonInherited = setdiff(allProperties, inherited);
+    readonly = intersect(readonly, nonInherited);
+    required = setdiff(intersect(required, nonInherited), readonly);
+    optional = setdiff(intersect(optional, nonInherited), readonly);
 
-%% CLASSDEF
-if length(processed) <= 1
-    depnm = 'types.untyped.MetaClass'; %WRITE
-else
-    parentName = processed(2).type; %WRITE
-    depnm = namespace.getFullClassName(parentName);
-end
+    %% CLASSDEF
+    if length(processed) <= 1
+        depnm = 'types.untyped.MetaClass'; %WRITE
+    else
+        parentName = processed(2).type; %WRITE
+        depnm = namespace.getFullClassName(parentName);
+    end
 
-if isa(processed, 'file.Group')
-    classTag = 'types.untyped.GroupClass';
-else
-    classTag = 'types.untyped.DatasetClass';
-end
+    if isa(processed, 'file.Group')
+        classTag = 'types.untyped.GroupClass';
+    else
+        classTag = 'types.untyped.DatasetClass';
+    end
 
-%% return classfile string
-classDef = [...
-    'classdef ' name ' < ' depnm ' & ' classTag newline... %header, dependencies
-    '% ' upper(name) ' ' class.doc]; %name, docstr
-propgroups = {...
-    @()file.fillProps(classprops, readonly, 'PropertyAttributes', 'SetAccess=protected')...
-    @()file.fillProps(classprops, setdiff(required, readonly), 'IsRequired', true)...
-    @()file.fillProps(classprops, setdiff(optional, readonly))...
-    };
-docsep = {...
-    '% READONLY PROPERTIES'...
-    '% REQUIRED PROPERTIES'...
-    '% OPTIONAL PROPERTIES'...
-    };
-propsDef = '';
-for i=1:length(propgroups)
-    pg = propgroups{i};
-    pdef = pg();
-    if ~isempty(pdef)
-        propsDef = strjoin({propsDef docsep{i} pdef}, newline);
+    %% return classfile string
+    classDefinitionHeader = [...
+        'classdef ' name ' < ' depnm ' & ' classTag newline... %header, dependencies
+        '% ' upper(name) ' ' class.doc]; %name, docstr
+    hiddenAndReadonly = intersect(hidden, readonly);
+    hidden = setdiff(hidden, hiddenAndReadonly);
+    readonly = setdiff(readonly, hiddenAndReadonly);
+    PropertyGroups = struct(...
+        'Function', {...
+        @()file.fillProps(classprops, hiddenAndReadonly, 'PropertyAttributes', 'Hidden, SetAccess = protected') ...
+        , @()file.fillProps(classprops, hidden, 'PropertyAttributes', 'Hidden') ...
+        , @()file.fillProps(classprops, readonly, 'PropertyAttributes', 'SetAccess = protected') ...
+        , @()file.fillProps(classprops, required, 'IsRequired', true) ...
+        , @()file.fillProps(classprops, optional)...
+        } ...
+        , 'Separator', { ...
+        '% HIDDEN READONLY PROPERTIES' ...
+        , '% HIDDEN PROPERTIES' ...
+        , '% READONLY PROPERTIES' ...
+        , '% REQUIRED PROPERTIES' ...
+        , '% OPTIONAL PROPERTIES' ...
+        } ...
+        );
+    fullPropertyDefinition = '';
+    for iGroup = 1:length(PropertyGroups)
+        Group = PropertyGroups(iGroup);
+        propertyDefinitionBody = Group.Function();
+        if isempty(propertyDefinitionBody)
+            continue;
+        end
+        fullPropertyDefinition = strjoin({...
+            fullPropertyDefinition ...
+            , Group.Separator ...
+            , propertyDefinitionBody ...
+            }, newline);
     end
-end
 
-constructorBody = file.fillConstructor(...
-    name,...
-    depnm,...
-    defaults,... %all defaults, regardless of inheritance
-    classprops,...
-    namespace);
-setterFcns = file.fillSetters(setdiff(nonInherited, readonly));
-validatorFcns = file.fillValidators(allprops, classprops, namespace);
-exporterFcns = file.fillExport(nonInherited, class, depnm);
-methodBody = strjoin({constructorBody...
-    '%% SETTERS' setterFcns...
-    '%% VALIDATORS' validatorFcns...
-    '%% EXPORT' exporterFcns}, newline);
+    constructorBody = file.fillConstructor(...
+        name,...
+        depnm,...
+        defaults,... %all defaults, regardless of inheritance
+        classprops,...
+        namespace);
+    setterFcns = file.fillSetters(setdiff(nonInherited, union(readonly, hiddenAndReadonly)));
+    validatorFcns = file.fillValidators(allProperties, classprops, namespace);
+    exporterFcns = file.fillExport(nonInherited, class, depnm);
+    methodBody = strjoin({constructorBody...
+        '%% SETTERS' setterFcns...
+        '%% VALIDATORS' validatorFcns...
+        '%% EXPORT' exporterFcns}, newline);
 
-if strcmp(name, 'DynamicTable')
-    methodBody = strjoin({methodBody, '%% TABLE METHODS', file.fillDynamicTableMethods()}, newline);
-end
+    if strcmp(name, 'DynamicTable')
+        methodBody = strjoin({methodBody, '%% TABLE METHODS', file.fillDynamicTableMethods()}, newline);
+    end
 
-fullMethodBody = strjoin({'methods' ...
-    file.addSpaces(methodBody, 4) 'end'}, newline);
-template = strjoin({classDef propsDef fullMethodBody 'end'}, ...
-    [newline newline]);
+    fullMethodBody = strjoin({'methods' ...
+        file.addSpaces(methodBody, 4) 'end'}, newline);
+    template = strjoin({classDefinitionHeader fullPropertyDefinition fullMethodBody 'end'}, ...
+        [newline newline]);
 end
 

From 17442535a8cf1926feafa03687ab820f3091016d Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 13:25:28 -0400
Subject: [PATCH 07/17] Add Hidden property checks to checkUnset

Now that we have hidden properties in our generated classes.
---
 +types/+util/checkUnset.m | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/+types/+util/checkUnset.m b/+types/+util/checkUnset.m
index ee90d6fd..7e702e6d 100644
--- a/+types/+util/checkUnset.m
+++ b/+types/+util/checkUnset.m
@@ -1,18 +1,22 @@
 function checkUnset(obj, argin)
-props = properties(obj);
-anonNames = {};
-for i = 1:length(props)
-    p = obj.(props{i});
-    if isa(p, 'types.untyped.Anon')
-        anonNames = [anonNames;{p.name}];
-    elseif isa(p, 'types.untyped.Set')
-        anonNames = [anonNames;keys(p) .'];
+    publicProperties = properties(obj);
+    objMetaClass = metaclass(obj);
+    isHiddenProperty = logical([objMetaClass.PropertyList.Hidden]);
+    hiddenProperties = {objMetaClass.PropertyList(isHiddenProperty).Name};
+    allProperties = union(publicProperties, hiddenProperties);
+    anonNames = {};
+    for i = 1:length(allProperties)
+        p = obj.(allProperties{i});
+        if isa(p, 'types.untyped.Anon')
+            anonNames = [anonNames;{p.name}];
+        elseif isa(p, 'types.untyped.Set')
+            anonNames = [anonNames;keys(p) .'];
+        end
     end
-end
-dropped = setdiff(argin, [props;anonNames]);
-assert(isempty(dropped),...
-    'NWB:CheckUnset:InvalidProperties',...
-    ['Unexpected properties {%s}.  '...
+    dropped = setdiff(argin, [allProperties;anonNames]);
+    assert(isempty(dropped),...
+        'NWB:CheckUnset:InvalidProperties',...
+        ['Unexpected properties {%s}.  '...
         '\n\nYour schema version may be incompatible with the file.  '...
         'Consider checking the schema version of the file with '...
         '`util.getSchemaVersion(filename)` '...

From 6d05afb2eff30f8f9a11ae753fd496d2194c8ddf Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 14:03:28 -0400
Subject: [PATCH 08/17] fix concatentation dimensions

---
 +types/+util/checkUnset.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/+types/+util/checkUnset.m b/+types/+util/checkUnset.m
index 7e702e6d..8e27ddb8 100644
--- a/+types/+util/checkUnset.m
+++ b/+types/+util/checkUnset.m
@@ -13,7 +13,7 @@ function checkUnset(obj, argin)
             anonNames = [anonNames;keys(p) .'];
         end
     end
-    dropped = setdiff(argin, [allProperties;anonNames]);
+    dropped = setdiff(argin, union(allProperties, anonNames));
     assert(isempty(dropped),...
         'NWB:CheckUnset:InvalidProperties',...
         ['Unexpected properties {%s}.  '...

From 07db7026aa771ecc1e50706c1140485280f2840d Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 14:05:29 -0400
Subject: [PATCH 09/17] add sampling_rate, and resolution hidden attributes for
 vectordata

---
 +file/fillClass.m    |   2 +-
 +file/fillExport.m   |  28 +++++++++--
 +file/processClass.m | 111 +++++++++++++++++++++++++++----------------
 3 files changed, 96 insertions(+), 45 deletions(-)

diff --git a/+file/fillClass.m b/+file/fillClass.m
index 5f024fc0..eabb3bc6 100644
--- a/+file/fillClass.m
+++ b/+file/fillClass.m
@@ -53,7 +53,7 @@
 
             if strcmp(namespace.name, 'hdmf_common') ...
                 && strcmp(name, 'VectorData') ...
-                && strcmp(prop.name, 'unit')
+                && any(strcmp(prop.name, {'unit', 'sampling_rate', 'resolution'}))
                 hidden{end+1} = propertyName;
             end
         end
diff --git a/+file/fillExport.m b/+file/fillExport.m
index c9d7ae81..1fb5a1c2 100644
--- a/+file/fillExport.m
+++ b/+file/fillExport.m
@@ -36,16 +36,30 @@
         if ~isempty(elideProps) && all(cellfun('isclass', elideProps, 'file.Group'))
             exportBody{end+1} = ['io.writeGroup(fid, [fullpath ''/' elisions ''']);'];
         end
+
         if strcmp(propertyName, 'unit') && strcmp(RawClass.type, 'VectorData')
             exportBody{end+1} = fillVectorDataUnitConditional();
+        elseif strcmp(propertyName, 'sampling_rate') && strcmp(RawClass.type, 'VectorData')
+            exportBody{end+1} = fillVectorDataSamplingRateConditional();
+        elseif strcmp(propertyName, 'resolution') && strcmp(RawClass.type, 'VectorData')
+            exportBody{end+1} = fillVectorDataResolutionConditional();
         else
             exportBody{end+1} = fillDataExport(propertyName, prop, elisions);
         end
     end
 
-    festr = strjoin({exportHeader...
-        file.addSpaces(strjoin(exportBody, newline), 4)...
-        'end'}, newline);
+    festr = strjoin({ ...
+        exportHeader ...
+        , file.addSpaces(strjoin(exportBody, newline), 4) ...
+        , 'end' ...
+        }, newline);
+end
+
+function exportBody = fillVectorDataResolutionConditional()
+    exportBody = strjoin({...
+        'if ~isempty(obj.resolution) && any(endsWith(fullpath, ''units/spike_times''))' ...
+        , '    io.writeAttribute(fid, [fullpath ''/resolution''], obj.resolution);' ...
+        , 'end'}, newline);
 end
 
 function exportBody = fillVectorDataUnitConditional()
@@ -56,6 +70,14 @@
         , 'end'}, newline);
 end
 
+function exportBody = fillVectorDataSamplingRateConditional()
+    exportBody = strjoin({...
+          'validDataSamplingPaths = strcat(''units/'', {''waveform_mean'', ''waveform_sd'', ''waveforms''});' ...
+        , 'if ~isempty(obj.sampling_rate) && any(endsWith(fullpath, validDataSamplingPaths))' ...
+        , '    io.writeAttribute(fid, [fullpath ''/sampling_rate''], obj.sampling_rate);' ...
+        , 'end'}, newline);
+end
+
 function path = traverseRaw(propertyName, RawClass)
     % returns a cell array of named tokens which may or may not indicate an identifier.
     % these tokens are relative to the Raw class
diff --git a/+file/processClass.m b/+file/processClass.m
index f1ad17a2..1ccfc21e 100644
--- a/+file/processClass.m
+++ b/+file/processClass.m
@@ -1,52 +1,52 @@
 function [Processed, classprops, inherited] = processClass(name, namespace, pregen)
-inherited = {};
-branch = [{namespace.getClass(name)} namespace.getRootBranch(name)];
-branchNames = cell(size(branch));
-TYPEDEF_KEYS = {'neurodata_type_def', 'data_type_def'};
-for i = 1:length(branch)
-    hasTypeDefs = isKey(branch{i}, TYPEDEF_KEYS);
-    branchNames{i} = branch{i}(TYPEDEF_KEYS{hasTypeDefs});
-end
+    inherited = {};
+    branch = [{namespace.getClass(name)} namespace.getRootBranch(name)];
+    branchNames = cell(size(branch));
+    TYPEDEF_KEYS = {'neurodata_type_def', 'data_type_def'};
+    for i = 1:length(branch)
+        hasTypeDefs = isKey(branch{i}, TYPEDEF_KEYS);
+        branchNames{i} = branch{i}(TYPEDEF_KEYS{hasTypeDefs});
+    end
+
+    for iAncestor = 1:length(branch)
+        node = branch{iAncestor};
+        hasTypeDefs = isKey(node, TYPEDEF_KEYS);
+        nodename = node(TYPEDEF_KEYS{hasTypeDefs});
 
-for iAncestor = 1:length(branch)
-    node = branch{iAncestor};
-    hasTypeDefs = isKey(node, TYPEDEF_KEYS);
-    nodename = node(TYPEDEF_KEYS{hasTypeDefs});
-    
-    if ~isKey(pregen, nodename)
-        switch node('class_type')
-            case 'groups'
-                class = file.Group(node);
-            case 'datasets'
-                class = file.Dataset(node);
-            otherwise
-                error('NWB:FileGen:InvalidClassType',...
-                    'Class type %s is invalid', node('class_type'));
+        if ~isKey(pregen, nodename)
+            switch node('class_type')
+                case 'groups'
+                    class = file.Group(node);
+                case 'datasets'
+                    class = file.Dataset(node);
+                otherwise
+                    error('NWB:FileGen:InvalidClassType',...
+                        'Class type %s is invalid', node('class_type'));
+            end
+            if strcmp(nodename, 'VectorData') && strcmp(namespace.name, 'hdmf_common')
+                class = patchVectorData(class);
+            end
+            props = class.getProps();
+
+            pregen(nodename) = struct('class', class, 'props', props);
         end
-        if strcmp(nodename, 'VectorData') && strcmp(namespace.name, 'hdmf_common')
-            class = patchVectorData(class);
+        try
+            Processed(iAncestor) = pregen(nodename).class;
+        catch
+            keyboard;
         end
-        props = class.getProps();
-
-        pregen(nodename) = struct('class', class, 'props', props);
     end
-    try
-        Processed(iAncestor) = pregen(nodename).class;
-    catch
-        keyboard;
+    classprops = pregen(name).props;
+    names = keys(classprops);
+    for iAncestor = 2:length(Processed)
+        pname = Processed(iAncestor).type;
+        parentPropNames = keys(pregen(pname).props);
+        inherited = union(inherited, intersect(names, parentPropNames));
     end
 end
-classprops = pregen(name).props;
-names = keys(classprops);
-for iAncestor=2:length(Processed)
-    pname = Processed(iAncestor).type;
-    parentPropNames = keys(pregen(pname).props);
-    inherited = union(inherited, intersect(names, parentPropNames));
-end
-end
 
 function class = patchVectorData(class)
-    % adds an optional "units" attribute added by the Units table.
+    %% Unit Attribute
     % derived from schema 2.6.0
     source = containers.Map();
     source('name') = 'unit';
@@ -56,6 +56,35 @@
     source('dtype') = 'text';
     source('value') = 'volts';
     source('required') = false;
-    
+    class.attributes(end+1) = file.Attribute(source);
+
+    %% Sampling Rate Attribute
+    % derived from schema 2.6.0
+
+    source = containers.Map();
+    source('name') = 'sampling_rate';
+    source('doc') = ['NOTE: this is a special value for compatibility with the Units table and is ' ...
+        'only written to file when detected to be in that specific HDF5 Group. ' ...
+        'Must be Hertz'];
+    source('dtype') = 'float32';
+    source('required') = false;
+
+    class.attributes(end+1) = file.Attribute(source);
+    %% Resolution Attribute
+    % derived from schema 2.6.0
+
+    source = containers.Map();
+    source('name') = 'resolution';
+    source('doc') = ['NOTE: this is a special value for compatibility with the Units table and is ' ...
+        'only written to file when detected to be in that specific HDF5 Group. ' ...
+        'The smallest possible difference between two spike times. ' ...
+        'Usually 1 divided by the acquisition sampling rate from which spike times were extracted, ' ...
+        'but could be larger if the acquisition time series was downsampled or smaller if the ' ...
+        'acquisition time series was smoothed/interpolated ' ...
+        'and it is possible for the spike time to be between samples.' ...
+        ];
+    source('dtype') = 'float64';
+    source('required') = false;
+
     class.attributes(end+1) = file.Attribute(source);
 end
\ No newline at end of file

From 97c7e33b7b9d4edfa2fae234d6295159e1681fcf Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 14:08:48 -0400
Subject: [PATCH 10/17] fix duplicate property list

---
 +file/fillClass.m | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/+file/fillClass.m b/+file/fillClass.m
index eabb3bc6..21a10f95 100644
--- a/+file/fillClass.m
+++ b/+file/fillClass.m
@@ -60,8 +60,9 @@
     end
     nonInherited = setdiff(allProperties, inherited);
     readonly = intersect(readonly, nonInherited);
-    required = setdiff(intersect(required, nonInherited), readonly);
-    optional = setdiff(intersect(optional, nonInherited), readonly);
+    exclusivePropertyGroups = union(readonly, hidden);
+    required = setdiff(intersect(required, nonInherited), exclusivePropertyGroups);
+    optional = setdiff(intersect(optional, nonInherited), exclusivePropertyGroups);
 
     %% CLASSDEF
     if length(processed) <= 1

From 3b2e26045cc44cddd273ae906fdbfa3ab8a63bdf Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 14:30:46 -0400
Subject: [PATCH 11/17] Move H5O dup fix specific to datastub calls

Originally applied to all export calls. This may cause issues for datapipes and simply rewriting
data so the check is now applied to datastubs instead.
---
 +types/+untyped/DataStub.m  | 4 ++--
 +types/+untyped/MetaClass.m | 5 -----
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/+types/+untyped/DataStub.m b/+types/+untyped/DataStub.m
index 54bf4b0b..49deb779 100644
--- a/+types/+untyped/DataStub.m
+++ b/+types/+untyped/DataStub.m
@@ -349,8 +349,8 @@
                 end
                 
                 io.writeCompound(fid, fullpath, data);
-            else
-                %copy data over and return destination
+            elseif ~H5L.exists(fid, fullpath)
+                % copy data over and return destination.
                 ocpl = H5P.create('H5P_OBJECT_COPY');
                 lcpl = H5P.create('H5P_LINK_CREATE');
                 H5O.copy(src_fid, obj.path, fid, fullpath, ocpl, lcpl);
diff --git a/+types/+untyped/MetaClass.m b/+types/+untyped/MetaClass.m
index 74ddebd2..6d7840a9 100644
--- a/+types/+untyped/MetaClass.m
+++ b/+types/+untyped/MetaClass.m
@@ -14,11 +14,6 @@
                 io.writeGroup(fid, fullpath);
                 return;
             end
-
-            if H5L.exists(fid, fullpath, 'H5P_DEFAULT')
-                % skip if already written.
-                return;
-            end
             
             try
                 if isa(obj.data, 'types.untyped.DataStub')...

From 7d1371ed187aacb1016112b9edbb810b42d6e63a Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 17 May 2023 14:37:19 -0400
Subject: [PATCH 12/17] fix invalid H5L call

---
 +types/+untyped/DataStub.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/+types/+untyped/DataStub.m b/+types/+untyped/DataStub.m
index 49deb779..6e82f53e 100644
--- a/+types/+untyped/DataStub.m
+++ b/+types/+untyped/DataStub.m
@@ -349,7 +349,7 @@
                 end
                 
                 io.writeCompound(fid, fullpath, data);
-            elseif ~H5L.exists(fid, fullpath)
+            elseif ~H5L.exists(fid, fullpath, 'H5P_DEFAULT')
                 % copy data over and return destination.
                 ocpl = H5P.create('H5P_OBJECT_COPY');
                 lcpl = H5P.create('H5P_LINK_CREATE');

From 384099d8ab8a36930736838d171ae2fe8bc74877 Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Tue, 23 May 2023 15:00:56 -0400
Subject: [PATCH 13/17] Add draft interop tests for Units

Currently throws a strange error when testing out to pynwb
---
 +tests/+system/PyNWBIOTest.py    | 10 ++++++++++
 +tests/+system/UnitTimesIOTest.m | 24 +++++++++++++++++++-----
 2 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/+tests/+system/PyNWBIOTest.py b/+tests/+system/PyNWBIOTest.py
index ac614dec..8eed0065 100644
--- a/+tests/+system/PyNWBIOTest.py
+++ b/+tests/+system/PyNWBIOTest.py
@@ -9,6 +9,7 @@
 from pynwb import get_manager, NWBFile, TimeSeries
 from pynwb.ecephys import ElectricalSeries, Clustering
 from pynwb.ophys import OpticalChannel, TwoPhotonSeries
+from pynwb.misc import Units
 from hdmf.backends.hdf5 import HDF5IO
 from hdmf.container import Container, Data
 
@@ -200,3 +201,12 @@ def addContainer(self, file):
 
     def getContainer(self, file):
         return file
+
+
+class UnitTimesIOTest(PyNWBIOTest):
+    def addContainer(self, file):
+        self.file.units = Units('units', waveform_rate=1., resolution=3.)
+        self.file.units.add_unit(waveform_mean=[5], waveform_sd=[7], waveforms=np.full((1, 1), 9),
+                                 spike_times=[11])
+    def getContainer(self, file):
+        return file
diff --git a/+tests/+system/UnitTimesIOTest.m b/+tests/+system/UnitTimesIOTest.m
index 79509fd0..36d8ab6c 100644
--- a/+tests/+system/UnitTimesIOTest.m
+++ b/+tests/+system/UnitTimesIOTest.m
@@ -1,12 +1,26 @@
-classdef UnitTimesIOTest < tests.system.RoundTripTest
+classdef UnitTimesIOTest < tests.system.PyNWBIOTest
     methods
         function addContainer(~, file)
             file.units = types.core.Units( ...
-                'colnames', {'spike_times', 'waveforms'}, 'description', 'test Units');
+                'colnames', {'spike_times', 'waveforms', 'waveform_sd', 'waveform_mean'} ...
+                , 'description', 'test Units' ...
+                );
             
-            file.units.addRow('spike_times', rand(), 'waveforms', rand());
-            file.units.addRow('spike_times', rand(3,1), 'waveforms', rand(3,1));
-            file.units.addRow('spike_times', rand(5,1), 'waveforms', {rand(5,1);rand(7,1)});
+            file.units.addRow( ...
+                'spike_times', 11 ...
+                , 'waveforms', 9 ...
+                , 'waveform_sd', 7 ...
+                , 'waveform_mean', 5 ...
+                );
+            file.units.spike_times.description = 'the spike times for each unit';
+
+            % set optional hidden vector data attributes
+            file.units.spike_times.resolution = 3;
+            Units = file.units;
+            [Units.waveform_mean.sampling_rate ...
+                , Units.waveform_sd.sampling_rate ...
+                , Units.waveforms.sampling_rate ... 
+                ] = deal(1);
         end
         
         function c = getContainer(~, file)

From 2cac7e1e1c7f72f36cc682505bed2a93f4a15a4a Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 24 May 2023 12:59:24 -0400
Subject: [PATCH 14/17] fix python validation errors

---
 +tests/+system/PyNWBIOTest.py    | 6 +++++-
 +tests/+system/UnitTimesIOTest.m | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/+tests/+system/PyNWBIOTest.py b/+tests/+system/PyNWBIOTest.py
index 8eed0065..486b817c 100644
--- a/+tests/+system/PyNWBIOTest.py
+++ b/+tests/+system/PyNWBIOTest.py
@@ -58,7 +58,11 @@ def assertContainerEqual(self, container1, container2):           # noqa: C901
         type1 = type(container1)
         type2 = type(container2)
         self.assertEqual(type1, type2)
-        for nwbfield in container1.__nwbfields__:
+        try:
+            container_fields = container1.__nwbfields__
+        except AttributeError:
+            container_fields = container1.__fields__
+        for nwbfield in container_fields:
             with self.subTest(nwbfield=nwbfield, container_type=type1.__name__):
                 f1 = getattr(container1, nwbfield)
                 f2 = getattr(container2, nwbfield)
diff --git a/+tests/+system/UnitTimesIOTest.m b/+tests/+system/UnitTimesIOTest.m
index 36d8ab6c..85e8cac3 100644
--- a/+tests/+system/UnitTimesIOTest.m
+++ b/+tests/+system/UnitTimesIOTest.m
@@ -3,7 +3,7 @@
         function addContainer(~, file)
             file.units = types.core.Units( ...
                 'colnames', {'spike_times', 'waveforms', 'waveform_sd', 'waveform_mean'} ...
-                , 'description', 'test Units' ...
+                , 'description', 'data on spiking units' ...
                 );
             
             file.units.addRow( ...

From 5019db6ece0a4cf6b1ec8c3a3faa8498ce12ff39 Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 24 May 2023 13:27:14 -0400
Subject: [PATCH 15/17] fix tests to better accommodate default values

Mostly description and default columns were missing. These have been filled in.

The getContainer() function was also changed so as to test the entire Units table and not just
one column.
---
 +tests/+system/PyNWBIOTest.py    |  2 +-
 +tests/+system/UnitTimesIOTest.m | 36 +++++++++++++++++++++++++++-----
 2 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/+tests/+system/PyNWBIOTest.py b/+tests/+system/PyNWBIOTest.py
index 486b817c..2962409d 100644
--- a/+tests/+system/PyNWBIOTest.py
+++ b/+tests/+system/PyNWBIOTest.py
@@ -213,4 +213,4 @@ def addContainer(self, file):
         self.file.units.add_unit(waveform_mean=[5], waveform_sd=[7], waveforms=np.full((1, 1), 9),
                                  spike_times=[11])
     def getContainer(self, file):
-        return file
+        return file.units
diff --git a/+tests/+system/UnitTimesIOTest.m b/+tests/+system/UnitTimesIOTest.m
index 85e8cac3..d199ad5a 100644
--- a/+tests/+system/UnitTimesIOTest.m
+++ b/+tests/+system/UnitTimesIOTest.m
@@ -2,17 +2,43 @@
     methods
         function addContainer(~, file)
             file.units = types.core.Units( ...
-                'colnames', {'spike_times', 'waveforms', 'waveform_sd', 'waveform_mean'} ...
+                'colnames', {'spike_times'; 'waveform_mean'; 'waveform_sd'; 'waveforms'} ...
                 , 'description', 'data on spiking units' ...
                 );
             
             file.units.addRow( ...
                 'spike_times', 11 ...
-                , 'waveforms', 9 ...
-                , 'waveform_sd', 7 ...
-                , 'waveform_mean', 5 ...
+                , 'waveforms', int32(9) ...
+                , 'waveform_sd', single(7) ...
+                , 'waveform_mean', single(5) ...
                 );
+            % the following is solely for a2a comparison with files.
             file.units.spike_times.description = 'the spike times for each unit';
+            file.units.waveforms.description = ['Individual waveforms for each spike. ' ...
+                'If the dataset is three-dimensional, the third dimension shows the response ' ...
+                'from different electrodes that all observe this unit simultaneously. ' ...
+                'In this case, the `electrodes` column of this Units table should be used to ' ...
+                'indicate which electrodes are associated with this unit, ' ...
+                'and the electrodes dimension here should be in the same order as the ' ...
+                'electrodes referenced in the `electrodes` column of this table.'];
+            file.units.waveform_sd.description = ['the spike waveform standard deviation for each ' ...
+                'spike unit'];
+            file.units.waveform_mean.description = 'the spike waveform mean for each spike unit';
+            file.units.spike_times_index = types.hdmf_common.VectorIndex( ...
+                'target', types.untyped.ObjectView(file.units.spike_times) ...
+                , 'description', 'Index for VectorData ''spike_times''' ...
+                , 'data', 1 ...
+                );
+            file.units.waveforms_index = types.hdmf_common.VectorIndex( ...
+                'target', types.untyped.ObjectView(file.units.waveforms) ...
+                , 'description', 'Index for VectorData ''waveforms''' ...
+                , 'data', 1 ...
+                );
+            file.units.waveforms_index_index = types.hdmf_common.VectorIndex( ...
+                'target', types.untyped.ObjectView(file.units.waveforms_index) ...
+                , 'description', 'Index for VectorData ''waveforms_index''' ...
+                , 'data', 1 ...
+                );
 
             % set optional hidden vector data attributes
             file.units.spike_times.resolution = 3;
@@ -24,7 +50,7 @@ function addContainer(~, file)
         end
         
         function c = getContainer(~, file)
-            c = file.units.spike_times;
+            c = file.units;
         end
     end
 end
\ No newline at end of file

From 890d077afd6585d7ff88084b7d57ec7e37ec1889 Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 24 May 2023 13:28:34 -0400
Subject: [PATCH 16/17] remove integral minimum type validation from tests

---
 +tests/+util/verifyContainerEqual.m | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/+tests/+util/verifyContainerEqual.m b/+tests/+util/verifyContainerEqual.m
index f51084c1..1bf3179f 100644
--- a/+tests/+util/verifyContainerEqual.m
+++ b/+tests/+util/verifyContainerEqual.m
@@ -53,18 +53,10 @@ function verifyContainerEqual(testCase, actual, expected, ignoreList)
             testCase.verifyGreaterThanOrEqual(actualNtfs, expectedNtfs - 10, failmsg);
             testCase.verifyLessThanOrEqual(actualNtfs, expectedNtfs + 10, failmsg);
         end
-    elseif startsWith(class(expectedVal), 'int') || startsWith(class(expectedVal), 'uint')
-        actualTypeSize = regexp(class(actualVal), 'int(\d+)', 'once', 'tokens');
-        expectedTypeSize = regexp(class(expectedVal), 'int(\d+)', 'once', 'tokens');
-        testCase.verifyGreaterThanOrEqual(...
-            str2double(actualTypeSize{1}),...
-            str2double(expectedTypeSize{1}));
-        
-        if startsWith(class(expectedVal), 'int')
-            testCase.verifyEqual(int64(actualVal), int64(expectedVal), failmsg);
-        else
-            testCase.verifyEqual(uint64(actualVal), uint64(expectedVal), failmsg);
-        end
+    elseif startsWith(class(expectedVal), 'int')
+        testCase.verifyEqual(int64(actualVal), int64(expectedVal), failmsg);
+    elseif startsWith(class(expectedVal), 'uint')
+        testCase.verifyEqual(uint64(actualVal), uint64(expectedVal), failmsg);
     else
         testCase.verifyEqual(actualVal, expectedVal, failmsg);
     end

From 235c16fbb87680de14e9e6e3e2896b1113a046b1 Mon Sep 17 00:00:00 2001
From: Lawrence Niu <lawrence@mbfbioscience.com>
Date: Wed, 24 May 2023 13:39:22 -0400
Subject: [PATCH 17/17] revert type diff

---
 +tests/+system/UnitTimesIOTest.m | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/+tests/+system/UnitTimesIOTest.m b/+tests/+system/UnitTimesIOTest.m
index d199ad5a..47671e27 100644
--- a/+tests/+system/UnitTimesIOTest.m
+++ b/+tests/+system/UnitTimesIOTest.m
@@ -9,8 +9,8 @@ function addContainer(~, file)
             file.units.addRow( ...
                 'spike_times', 11 ...
                 , 'waveforms', int32(9) ...
-                , 'waveform_sd', single(7) ...
-                , 'waveform_mean', single(5) ...
+                , 'waveform_sd', 7 ...
+                , 'waveform_mean', 5 ...
                 );
             % the following is solely for a2a comparison with files.
             file.units.spike_times.description = 'the spike times for each unit';