def test_n5_to_h5(self):
from z5py.converter import convert_to_h5
n5_file = os.path.join(self.tmp_dir, 'tmp.n5')
h5_file = os.path.join(self.tmp_dir, 'tmp.h5')
f = z5py.File(n5_file, use_zarr_format=False)
# test conversion for 4 different compression pairs
for pair in self.compressor_pairs:
key = 'data_%s_%s' % pair
compression_a, compression_b = pair
ds = f.create_dataset(key,
dtype='float32',
compression=compression_a,
shape=self.shape,
chunks=self.chunks)
data = np.arange(ds.size).reshape(ds.shape).astype(ds.dtype)
ds[:] = data
compression_b = None if compression_b == 'raw' else compression_b
convert_to_h5(n5_file,
h5_file,
key,
key,
chunks=self.chunks,
n_threads=1,
compression=compression_b)
with h5py.File(h5_file, 'r') as fh5:
data_h5 = fh5[key][:]
self.assertTrue(np.allclose(data, data_h5))
def test_n5_to_h5_with_roi(self):
from z5py.converter import convert_to_h5
h5_file = os.path.join(self.tmp_dir, 'tmp.h5')
n5_file = os.path.join(self.tmp_dir, 'tmp.n5')
n5_key = 'data'
with z5py.File(n5_file, 'w') as f:
ds = f.create_dataset(n5_key,
shape=self.shape,
chunks=self.chunks,
dtype='float64')
data = np.arange(ds.size).reshape(ds.shape).astype(ds.dtype)
ds[:] = data
# define roi
roi = np.s_[5:45, 9:83, 10:60]
out_of_roi_mask = np.ones(self.shape, dtype='bool')
out_of_roi_mask[roi] = False
roi_shape = tuple(rr.stop - rr.start for rr in roi)
# convert dataset with roi
h5_key = 'data_roi'
convert_to_h5(n5_file,
h5_file,
n5_key,
h5_key,
n_threads=8,
roi=roi,
fit_to_roi=False)
with h5py.File(h5_file, 'r') as f:
data_h5 = f[h5_key][:]
self.assertEqual(data.shape, data_h5.shape)
self.assertTrue(np.allclose(data[roi], data_h5[roi]))
self.assertTrue(np.allclose(data_h5[out_of_roi_mask], 0))
# convert dataset with roi and fit_to_roi
h5_key = 'data_roi_fit'
convert_to_h5(n5_file,
h5_file,
n5_key,
h5_key,
n_threads=8,
roi=roi,
fit_to_roi=True)
with h5py.File(h5_file, 'r') as f:
data_h5 = f[h5_key][:]
self.assertEqual(roi_shape, data_h5.shape)
self.assertTrue(np.allclose(data[roi], data_h5))
import argparse
from z5py.converter import convert_to_h5
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("n5_in_path")
parser.add_argument("h5_out_path")
parser.add_argument("in_path_in_file")
parser.add_argument("out_path_in_file")
parser.add_argument("--n_threads", type=int, default=16)
args = parser.parse_args()
convert_to_h5(args.n5_in_path,
args.h5_out_path,
args.in_path_in_file,
args.out_path_in_file,
n_threads=args.n_threads)
"""
/scratch/beuttenm/hylfm/cache/b01highc_2_ls_reg_8743bf3e67c30c171928d3cc30e75a895047dae013848c7585034fa0.n5 /g/kreshuk/LF_computed/zenodo_upload/small_2.h5 ls_reg ls_reg
"""