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Merge pull request #509 from NeurodataWithoutBorders/508-remove-inter…
…national-datestring-parsing Remove international datestring parsing for version checks
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,85 +1,85 @@ | ||
| function parsed = parseDataset(filename, info, fullpath, Blacklist) | ||
| %typed and untyped being container maps containing type and untyped datasets | ||
| % the maps store information regarding information and stored data | ||
| % NOTE, dataset name is in path format so we need to parse that out. | ||
| name = info.Name; | ||
| %typed and untyped being container maps containing type and untyped datasets | ||
| % the maps store information regarding information and stored data | ||
| % NOTE, dataset name is in path format so we need to parse that out. | ||
| name = info.Name; | ||
|
|
||
| %check if typed and parse attributes | ||
| [attrargs, Type] = io.parseAttributes(filename, info.Attributes, fullpath, Blacklist); | ||
| %check if typed and parse attributes | ||
| [attrargs, Type] = io.parseAttributes(filename, info.Attributes, fullpath, Blacklist); | ||
|
|
||
| fid = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT'); | ||
| did = H5D.open(fid, fullpath); | ||
| props = attrargs; | ||
| datatype = info.Datatype; | ||
| dataspace = info.Dataspace; | ||
| fid = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT'); | ||
| did = H5D.open(fid, fullpath); | ||
| props = attrargs; | ||
| datatype = info.Datatype; | ||
| dataspace = info.Dataspace; | ||
|
|
||
| parsed = containers.Map; | ||
| afields = keys(attrargs); | ||
| if ~isempty(afields) | ||
| anames = strcat(name, '_', afields); | ||
| parsed = [parsed; containers.Map(anames, attrargs.values(afields))]; | ||
| end | ||
| parsed = containers.Map; | ||
| afields = keys(attrargs); | ||
| if ~isempty(afields) | ||
| anames = strcat(name, '_', afields); | ||
| parsed = [parsed; containers.Map(anames, attrargs.values(afields))]; | ||
| end | ||
|
|
||
| % loading h5t references are required | ||
| % unfortunately also a bottleneck | ||
| if strcmp(datatype.Class, 'H5T_REFERENCE') | ||
| tid = H5D.get_type(did); | ||
| data = io.parseReference(did, tid, H5D.read(did)); | ||
| H5T.close(tid); | ||
| elseif ~strcmp(dataspace.Type, 'simple') | ||
| data = H5D.read(did); | ||
| % loading h5t references are required | ||
| % unfortunately also a bottleneck | ||
| if strcmp(datatype.Class, 'H5T_REFERENCE') | ||
| tid = H5D.get_type(did); | ||
| data = io.parseReference(did, tid, H5D.read(did)); | ||
| H5T.close(tid); | ||
| elseif ~strcmp(dataspace.Type, 'simple') | ||
| data = H5D.read(did); | ||
|
|
||
| switch datatype.Class | ||
| case 'H5T_STRING' | ||
| if datetime(version('-date')) < datetime('25-Feb-2020') | ||
| % MATLAB 2020a fixed string support for HDF5, making | ||
| % reading strings "consistent" with regular use. | ||
| data = data .'; | ||
| end | ||
| datadim = size(data); | ||
| if datadim(1) > 1 | ||
| %multidimensional strings should become cellstr | ||
| data = strtrim(mat2cell(data, ones(datadim(1), 1), datadim(2))); | ||
| end | ||
| case 'H5T_ENUM' | ||
| if io.isBool(datatype.Type) | ||
| data = strcmp('TRUE', data); | ||
| else | ||
| warning('NWB:Dataset:UnknownEnum', ... | ||
| ['Encountered unknown enum under field `%s` with %d members. ' ... | ||
| 'Will be saved as cell array of characters.'], ... | ||
| info.Name, length(datatype.Type.Member)); | ||
| end | ||
| end | ||
| else | ||
| sid = H5D.get_space(did); | ||
| pid = H5D.get_create_plist(did); | ||
| isChunked = H5P.get_layout(pid) == H5ML.get_constant_value('H5D_CHUNKED'); | ||
|
|
||
| tid = H5D.get_type(did); | ||
| class_id = H5T.get_class(tid); | ||
| isNumeric = class_id == H5ML.get_constant_value('H5T_INTEGER')... | ||
| || class_id == H5ML.get_constant_value('H5T_FLOAT'); | ||
| if isChunked && isNumeric | ||
| data = types.untyped.DataPipe('filename', filename, 'path', fullpath); | ||
| elseif any(dataspace.Size == 0) | ||
| data = []; | ||
| switch datatype.Class | ||
| case 'H5T_STRING' | ||
| if verLessThan('MATLAB', '9.8') | ||
| % MATLAB 2020a fixed string support for HDF5, making | ||
| % reading strings "consistent" with regular use. | ||
| data = data .'; | ||
| end | ||
| datadim = size(data); | ||
| if datadim(1) > 1 | ||
| %multidimensional strings should become cellstr | ||
| data = strtrim(mat2cell(data, ones(datadim(1), 1), datadim(2))); | ||
| end | ||
| case 'H5T_ENUM' | ||
| if io.isBool(datatype.Type) | ||
| data = strcmp('TRUE', data); | ||
| else | ||
| warning('NWB:Dataset:UnknownEnum', ... | ||
| ['Encountered unknown enum under field `%s` with %d members. ' ... | ||
| 'Will be saved as cell array of characters.'], ... | ||
| info.Name, length(datatype.Type.Member)); | ||
| end | ||
| end | ||
| else | ||
| data = types.untyped.DataStub(filename, fullpath); | ||
| sid = H5D.get_space(did); | ||
| pid = H5D.get_create_plist(did); | ||
| isChunked = H5P.get_layout(pid) == H5ML.get_constant_value('H5D_CHUNKED'); | ||
|
|
||
| tid = H5D.get_type(did); | ||
| class_id = H5T.get_class(tid); | ||
| isNumeric = class_id == H5ML.get_constant_value('H5T_INTEGER')... | ||
| || class_id == H5ML.get_constant_value('H5T_FLOAT'); | ||
| if isChunked && isNumeric | ||
| data = types.untyped.DataPipe('filename', filename, 'path', fullpath); | ||
| elseif any(dataspace.Size == 0) | ||
| data = []; | ||
| else | ||
| data = types.untyped.DataStub(filename, fullpath); | ||
| end | ||
| H5T.close(tid); | ||
| H5P.close(pid); | ||
| H5S.close(sid); | ||
| end | ||
| H5T.close(tid); | ||
| H5P.close(pid); | ||
| H5S.close(sid); | ||
| end | ||
|
|
||
| if isempty(Type.typename) | ||
| %untyped group | ||
| parsed(name) = data; | ||
| else | ||
| props('data') = data; | ||
| kwargs = io.map2kwargs(props); | ||
| parsed = eval([Type.typename '(kwargs{:})']); | ||
| end | ||
| H5D.close(did); | ||
| H5F.close(fid); | ||
| if isempty(Type.typename) | ||
| %untyped group | ||
| parsed(name) = data; | ||
| else | ||
| props('data') = data; | ||
| kwargs = io.map2kwargs(props); | ||
| parsed = eval([Type.typename '(kwargs{:})']); | ||
| end | ||
| H5D.close(did); | ||
| H5F.close(fid); | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,35 +1,35 @@ | ||
| function tests = boolTest() | ||
| tests = functiontests(localfunctions); | ||
| tests = functiontests(localfunctions); | ||
| end | ||
|
|
||
| function setupOnce(testCase) | ||
| rootPath = fullfile(fileparts(mfilename('fullpath')), '..', '..'); | ||
| testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath)); | ||
| rootPath = fullfile(fileparts(mfilename('fullpath')), '..', '..'); | ||
| testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath)); | ||
| end | ||
|
|
||
| function setup(testCase) | ||
| testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture); | ||
| generateCore('savedir', '.'); | ||
| schemaPath = fullfile(misc.getMatnwbDir(),... | ||
| '+tests', '+unit', 'boolSchema', 'bool.namespace.yaml'); | ||
| generateExtension(schemaPath, 'savedir', '.'); | ||
| rehash(); | ||
| testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture); | ||
| generateCore('savedir', '.'); | ||
| schemaPath = fullfile(misc.getMatnwbDir(),... | ||
| '+tests', '+unit', 'boolSchema', 'bool.namespace.yaml'); | ||
| generateExtension(schemaPath, 'savedir', '.'); | ||
| rehash(); | ||
| end | ||
|
|
||
| function testIo(testCase) | ||
| nwb = NwbFile(... | ||
| 'identifier', 'BOOL',... | ||
| 'session_description', 'test bool',... | ||
| 'session_start_time', datetime()); | ||
| boolContainer = types.bool.BoolContainer(... | ||
| 'data', logical(randi([0,1], 100, 1)), ... | ||
| 'attribute', false); | ||
| scalarBoolContainer = types.bool.BoolContainer(... | ||
| 'data', false, ... | ||
| 'attribute', true); | ||
| nwb.acquisition.set('bool', boolContainer); | ||
| nwb.acquisition.set('scalarbool', scalarBoolContainer); | ||
| nwb.export('test.nwb'); | ||
| nwbActual = nwbRead('test.nwb', 'ignorecache'); | ||
| tests.util.verifyContainerEqual(testCase, nwbActual, nwb); | ||
| nwb = NwbFile(... | ||
| 'identifier', 'BOOL',... | ||
| 'session_description', 'test bool',... | ||
| 'session_start_time', datetime()); | ||
| boolContainer = types.bool.BoolContainer(... | ||
| 'data', logical(randi([0,1], 100, 1)), ... | ||
| 'attribute', false); | ||
| scalarBoolContainer = types.bool.BoolContainer(... | ||
| 'data', false, ... | ||
| 'attribute', true); | ||
| nwb.acquisition.set('bool', boolContainer); | ||
| nwb.acquisition.set('scalarbool', scalarBoolContainer); | ||
| nwb.export('test.nwb'); | ||
| nwbActual = nwbRead('test.nwb', 'ignorecache'); | ||
| tests.util.verifyContainerEqual(testCase, nwbActual, nwb); | ||
| end |