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Merge pull request #164 from NeurodataWithoutBorders/todo/file-amend
Allow Amending NWB Files
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,40 @@ | ||
| function writeDataset(fid, fullpath, data, varargin) | ||
| assert(isempty(varargin) || iscellstr(varargin),... | ||
| 'options should be character arrays.'); | ||
| [tid, sid, data] = io.mapData2H5(fid, data, varargin{:}); | ||
| did = H5D.create(fid, fullpath, tid, sid, 'H5P_DEFAULT'); | ||
| [~, dims, ~] = H5S.get_simple_extent_dims(sid); | ||
| try | ||
| dcpl = H5P.create('H5P_DATASET_CREATE'); | ||
| if any(strcmp('forceChunking', varargin)) | ||
| H5P.set_chunk(dcpl, dims) | ||
| end | ||
| did = H5D.create(fid, fullpath, tid, sid, dcpl); | ||
| H5P.close(dcpl); | ||
| 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 == dims); | ||
| if ~is_same_dims && is_chunked | ||
| H5D.set_extent(did, dims); | ||
| elseif ~is_same_dims | ||
| warning('Attempted to change size of continuous dataset `%s`. Skipping.',... | ||
| fullpath); | ||
| 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); | ||
| if isa(tid, 'H5ML.id') | ||
| H5T.close(tid); | ||
| end | ||
| H5S.close(sid); | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| classdef AmendTest < tests.system.NwbTestInterface | ||
| methods (Test) | ||
| function testAmend(testCase) | ||
| filename = ['MatNWB.' testCase.className() '.testRoundTrip.nwb']; | ||
| nwbExport(testCase.file, filename); | ||
| testCase.appendContainer(testCase.file); | ||
| nwbExport(testCase.file, filename); | ||
|
|
||
| writeContainer = testCase.getContainer(testCase.file); | ||
| readFile = nwbRead(filename); | ||
| readContainer = testCase.getContainer(readFile); | ||
| testCase.verifyContainerEqual(readContainer, writeContainer); | ||
| end | ||
| end | ||
|
|
||
| methods (Abstract) | ||
| appendContainer(testCase, file); | ||
| end | ||
| end | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,26 @@ | ||
| classdef NWBFileIOTest < tests.system.PyNWBIOTest | ||
| methods | ||
| function addContainer(testCase, file) %#ok<INUSL> | ||
| ts = types.core.TimeSeries(... | ||
| 'data', int32(100:10:190) .', ... | ||
| 'data_unit', 'SIunit', ... | ||
| 'timestamps', (0:9) .', ... | ||
| 'data_resolution', 0.1); | ||
| file.acquisition.set('test_timeseries', ts); | ||
| clust = types.core.Clustering( ... | ||
| 'description', 'A fake Clustering interface', ... | ||
| 'num', [0, 1, 2, 0, 1, 2] .', ... | ||
| 'peak_over_rms', [100, 101, 102] .', ... | ||
| 'times', (10:10:60) .'); | ||
| mod = types.core.ProcessingModule( ... | ||
| 'description', 'a test module', ... | ||
| 'Clustering', clust); | ||
| file.processing.set('test_module', mod); | ||
| methods | ||
| function addContainer(testCase, file) %#ok<INUSL> | ||
| ts = types.core.TimeSeries(... | ||
| 'data', int32(100:10:190) .', ... | ||
| 'data_unit', 'SIunit', ... | ||
| 'timestamps', (0:9) .', ... | ||
| 'data_resolution', 0.1); | ||
| file.acquisition.set('test_timeseries', ts); | ||
| clust = types.core.Clustering( ... | ||
| 'description', 'A fake Clustering interface', ... | ||
| 'num', [0, 1, 2, 0, 1, 2] .', ... | ||
| 'peak_over_rms', [100, 101, 102] .', ... | ||
| 'times', (10:10:60) .'); | ||
| mod = types.core.ProcessingModule( ... | ||
| 'description', 'a test module', ... | ||
| 'Clustering', clust); | ||
| file.processing.set('test_module', mod); | ||
| end | ||
|
|
||
| function c = getContainer(testCase, file) %#ok<INUSL> | ||
| c = file; | ||
| end | ||
| end | ||
|
|
||
| function c = getContainer(testCase, file) %#ok<INUSL> | ||
| c = file; | ||
| end | ||
| end | ||
| end | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| classdef NwbTestInterface < matlab.unittest.TestCase | ||
| properties | ||
| % registry | ||
| file | ||
| root; | ||
| end | ||
|
|
||
| methods (TestClassSetup) | ||
| function setupClass(testCase) | ||
| rootPath = fullfile(fileparts(mfilename('fullpath')), '..', '..'); | ||
| testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath)); | ||
| testCase.root = rootPath; | ||
| end | ||
| end | ||
|
|
||
| methods (TestMethodSetup) | ||
| function setupMethod(testCase) | ||
| testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture); | ||
| generateCore(fullfile(testCase.root, ... | ||
| 'schema', 'core', 'nwb.namespace.yaml')); | ||
| testCase.file = NwbFile( ... | ||
| 'session_description', 'a test NWB File', ... | ||
| 'identifier', 'TEST123', ... | ||
| 'session_start_time', '2018-12-02T12:57:27.371444-08:00', ... | ||
| 'file_create_date', datestr([2017, 4, 15, 12, 0, 0], 'yyyy-mm-dd HH:MM:SS'),... | ||
| 'timestamps_reference_time', '2018-12-02T12:57:27.371444-08:00'); | ||
| testCase.addContainer(testCase.file); | ||
| end | ||
| end | ||
|
|
||
| methods | ||
| function n = className(testCase) | ||
| classSplit = strsplit(class(testCase), '.'); | ||
| n = classSplit{end}; | ||
| end | ||
|
|
||
| function verifyContainerEqual(testCase, actual, expected) | ||
| testCase.verifyEqual(class(actual), class(expected)); | ||
| props = properties(actual); | ||
| for i = 1:numel(props) | ||
| prop = props{i}; | ||
| if strcmp(prop, 'file_create_date') | ||
| continue; | ||
| end | ||
| val1 = actual.(prop); | ||
| val2 = expected.(prop); | ||
| failmsg = ['Values for property ''' prop ''' are not equal']; | ||
| if startsWith(class(val1), 'types.core.') | ||
| verifyContainerEqual(testCase, val1, val2); | ||
| elseif isa(val1, 'types.untyped.Set') | ||
| verifySetEqual(testCase, val1, val2, failmsg); | ||
| elseif isdatetime(val1) | ||
| testCase.verifyEqual(char(val1), char(val2)); | ||
| else | ||
| if isa(val1, 'types.untyped.DataStub') | ||
| trueval = val1.load(); | ||
| else | ||
| trueval = val1; | ||
| end | ||
|
|
||
| if isvector(val2) && isvector(trueval) && numel(val2) == numel(trueval) | ||
| trueval = reshape(trueval, size(val2)); | ||
| end | ||
| testCase.verifyEqual(trueval, val2, failmsg); | ||
| end | ||
| end | ||
| end | ||
|
|
||
| function verifySetEqual(testCase, actual, expected, failmsg) | ||
| testCase.verifyEqual(class(actual), class(expected)); | ||
| ak = actual.keys(); | ||
| ek = expected.keys(); | ||
| verifyTrue(testCase, isempty(setxor(ak, ek)), failmsg); | ||
| for i=1:numel(ak) | ||
| key = ak{i}; | ||
| verifyContainerEqual(testCase, actual.get(key), ... | ||
| expected.get(key)); | ||
| end | ||
| end | ||
|
|
||
| function verifyUntypedEqual(testCase, actual, expected) | ||
| testCase.verifyEqual(class(actual), class(expected)); | ||
| props = properties(actual); | ||
| for i = 1:numel(props) | ||
| prop = props{i}; | ||
| val1 = actual.(prop); | ||
| val2 = expected.(prop); | ||
| if isa(val1, 'types.core.NWBContainer') || isa(val1, 'types.core.NWBData') | ||
| verifyContainerEqual(testCase, val1, val2); | ||
| else | ||
| testCase.verifyEqual(val1, val2, ... | ||
| ['Values for property ''' prop ''' are not equal']); | ||
| end | ||
| end | ||
| end | ||
|
|
||
| end | ||
|
|
||
| methods(Abstract) | ||
| addContainer(testCase, file); | ||
| c = getContainer(testCase, file); | ||
| end | ||
| end | ||
|
|
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