def test_hdf5_read_from_non_chunked(self):
import nifty.hdf5 as nhdf5
fpath = os.path.join(self.tempFolder, '_nifty_test_array_.h5')
shape = (101, 102, 103)
data = numpy.ones(shape=shape, dtype='uint64')
with h5py.File(fpath, 'a') as f:
f.create_dataset("data", shape, dtype='uint64', data=data)
hidT = nhdf5.openFile(fpath)
array = nhdf5.Hdf5ArrayUInt64(hidT, "data")
ashape = array.shape
self.assertEqual(array.ndim, 3)
self.assertEqual(len(ashape), 3)
self.assertEqual(shape, tuple(ashape))
self.assertFalse(array.isChunked)
chunkShape = array.chunkShape
self.assertEqual(len(chunkShape), 3)
self.assertEqual(tuple(chunkShape), shape)
subarray = array[0:10, 0:10, 0:10]
expected = data[0:10, 0:10, 0:10]
self.assertEqual(subarray.shape, expected.shape)
self.assertTrue(numpy.allclose(subarray, expected))
def test_create_zipped_array(self):
import nifty.hdf5 as nhdf5
fpath = os.path.join(self.tempFolder, '_nifty_test_array_.h5')
shape = [101,102,103]
chunks = [11,12,13]
hidT = nhdf5.createFile(fpath)
array = nhdf5.Hdf5ArrayUInt64(
groupHandle=hidT,
datasetName="data",
shape=shape,
chunkShape=chunks,
compression=9
)
ashape = array.shape
self.assertEqual(array.ndim, 3)
self.assertEqual(shape, ashape)
chunkShape = array.chunkShape
self.assertEqual(chunkShape, chunks)
ends = [10,11,12]
toWrite = numpy.arange(ends[0]*ends[1]*ends[2]).reshape(ends)
array[0:ends[0], 0:ends[1], 0:ends[2]] = toWrite
subarray = array[0:ends[0], 0:ends[1], 0:ends[2]]
self.assertTrue(numpy.array_equal(toWrite, subarray))