def test_write_dataset_iterable_multidimensional_array(self):
a = np.arange(30).reshape(5, 2, 3)
aiter = iter(a)
daiter = DataChunkIterator.from_iterable(aiter, buffer_size=2)
self.io.write_dataset(self.f, DatasetBuilder('test_dataset', daiter, attributes={}))
dset = self.f['test_dataset']
self.assertListEqual(dset[:].tolist(), a.tolist())
def test_write_dataset_datachunkiterator(self):
a = np.arange(30).reshape(5, 2, 3)
aiter = iter(a)
daiter = DataChunkIterator.from_iterable(aiter, buffer_size=2)
ts = TimeSeries('ts_name', daiter, 'A', timestamps=np.arange(5))
self.nwbfile.add_acquisition(ts)
with NWBHDF5IO(self.path, 'w') as io:
io.write(self.nwbfile)
infile = File(self.path, 'r')
dset = infile['/acquisition/ts_name/data']
self.assertListEqual(dset[:].tolist(), a.tolist())
def test_write_dataset_iterable_multidimensional_array_compression(self):
a = np.arange(30).reshape(5, 2, 3)
aiter = iter(a)
daiter = DataChunkIterator.from_iterable(aiter, buffer_size=2)
wrapped_daiter = H5DataIO(data=daiter,
compression='gzip',
compression_opts=5,
shuffle=True,
fletcher32=True)
self.io.write_dataset(self.f, DatasetBuilder('test_dataset', wrapped_daiter, attributes={}))
dset = self.f['test_dataset']
self.assertEqual(dset.shape, a.shape)
self.assertListEqual(dset[:].tolist(), a.tolist())
self.assertEqual(dset.compression, 'gzip')
self.assertEqual(dset.compression_opts, 5)
self.assertEqual(dset.shuffle, True)
self.assertEqual(dset.fletcher32, True)
def test_write_dataset_datachunkiterator_with_compression(self):
a = np.arange(30).reshape(5, 2, 3)
aiter = iter(a)
daiter = DataChunkIterator.from_iterable(aiter, buffer_size=2)
wrapped_daiter = H5DataIO(data=daiter,
compression='gzip',
compression_opts=5,
shuffle=True,
fletcher32=True)
ts = TimeSeries('ts_name',
wrapped_daiter,
'A',
timestamps=np.arange(5))
self.nwbfile.add_acquisition(ts)
with NWBHDF5IO(self.path, 'w') as io:
io.write(self.nwbfile)
infile = File(self.path, 'r')
dset = infile['/acquisition/ts_name/data']
self.assertEqual(dset.shape, a.shape)
self.assertListEqual(dset[:].tolist(), a.tolist())
self.assertEqual(dset.compression, 'gzip')
self.assertEqual(dset.compression_opts, 5)
self.assertEqual(dset.shuffle, True)
self.assertEqual(dset.fletcher32, True)
def test_maxshape(self):
a = np.arange(30).reshape(5, 2, 3)
aiter = iter(a)
daiter = DataChunkIterator.from_iterable(aiter, buffer_size=2)
self.assertEqual(daiter.maxshape, (None, 2, 3))
def test_dtype(self):
a = np.arange(30, dtype='int32').reshape(5, 2, 3)
aiter = iter(a)
daiter = DataChunkIterator.from_iterable(aiter, buffer_size=2)
self.assertEqual(daiter.dtype, a.dtype)