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Change: Only embed specs/namespaces for types that are included in NWB file on export #615

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Change: Only embed specs/namespaces for types that are included in NWB file on export #615

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42 changes: 40 additions & 2 deletions NwbFile.m
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,20 @@ function export(obj, filename)
typename,...
varargin{:});
end

function nwbTypeNames = listNwbTypes(obj)
% listNwbTypes - List all unique NWB types in file
objectMap = searchProperties(containers.Map, obj, '', '');

objects = objectMap.values();
objectClassNames = cellfun(@(c) string(class(c)), objects);
objectClassNames = unique(objectClassNames);

keep = startsWith(objectClassNames, "types.");
ignore = startsWith(objectClassNames, "types.untyped");

nwbTypeNames = objectClassNames(keep & ~ignore);
end
end

%% PRIVATE
Expand Down Expand Up @@ -131,7 +145,7 @@ function resolveReferences(obj, fid, references)
end
end

function embedSpecifications(~, fid)
function embedSpecifications(obj, fid)
try
attrId = H5A.open(fid, '/.specloc');
specLocation = H5R.get_name(fid, 'H5R_OBJECT', H5A.read(attrId));
Expand All @@ -144,6 +158,15 @@ function embedSpecifications(~, fid)
end

JsonData = schemes.exportJson();

% Only embed namespaces for types that are included in the file
includedNwbTypes = obj.listNwbTypes();
namespaceNames = getNamespacesOfTypes(includedNwbTypes);

allMatlabNamespaceNames = strrep({JsonData.name}, '-', '_');
[~, keepIdx] = intersect(allMatlabNamespaceNames, namespaceNames, 'stable');
JsonData = JsonData(keepIdx);

for iJson = 1:length(JsonData)
JsonDatum = JsonData(iJson);
schemaNamespaceLocation = strjoin({specLocation, JsonDatum.name}, '/');
Expand Down Expand Up @@ -244,4 +267,19 @@ function embedSpecifications(~, fid)
searchProperties(pathToObjectMap, propValue, fullPath, typename, varargin{:});
end
end
end
end

function namespaceNames = getNamespacesOfTypes(nwbTypeNames)
% getNamespacesOfTypes - Get namespace names for a list of nwb types
arguments
nwbTypeNames (1,:) string
end

namespaceNames = repmat("", size(nwbTypeNames));
pattern = '[types.]+\.(\w+)\.';

for i = 1:numel(nwbTypeNames)
namespaceNames(i) = regexp(nwbTypeNames(i), pattern, 'tokens', 'once');
end
namespaceNames = unique(namespaceNames);
end