def test_read_zarr(self):
from z5py.dataset import Dataset
dtypes = list(Dataset._dtype_dict.keys())
zarr_compressors = {'blosc': numcodecs.Blosc(),
'zlib': numcodecs.Zlib(),
'raw': None,
'bzip2': numcodecs.BZ2()}
# conda-forge version of numcodecs is not up-to-data
# for python 3.5 and GZip is missing
# thats why we need to check explicitly here to not fail the test
if hasattr(numcodecs, 'GZip'):
zarr_compressors.update({'gzip': numcodecs.GZip()})
zarr.open(self.path)
for dtype in dtypes:
for compression in zarr_compressors:
data = np.random.randint(0, 127, size=self.shape).astype(dtype)
# write the data with zarr
key = 'test_%s_%s' % (dtype, compression)
ar = zarr.open(os.path.join(self.path, key), mode='w',
shape=self.shape, chunks=self.chunks,
dtype=dtype, compressor=zarr_compressors[compression])
ar[:] = data
# read with z5py
out = z5py.File(self.path)[key][:]
self.assertEqual(data.shape, out.shape)
self.assertTrue(np.allclose(data, out))
def test_read_zarr(self):
import numcodecs
from z5py.dataset import Dataset
dtypes = list(Dataset._zarr_dtype_dict.values())
compressions = Dataset.compressors_zarr
zarr_compressors = {
'blosc': numcodecs.Blosc(),
'zlib': numcodecs.Zlib(),
'raw': None,
'bzip2': numcodecs.BZ2()
}
for dtype in dtypes:
for compression in compressions:
data = np.random.randint(0, 127, size=self.shape).astype(dtype)
# write the data with zarr
key = 'test_%s_%s' % (dtype, compression)
ar = zarr.open(os.path.join(self.path, key),
mode='w',
shape=self.shape,
chunks=self.chunks,
dtype=dtype,
compressor=zarr_compressors[compression])
ar[:] = data
# read with z5py
out = z5py.File(self.path)[key][:]
self.assertEqual(data.shape, out.shape)
self.assertTrue(np.allclose(data, out))
def make_test_data(bucket_name=None):
""" Make zarr test data in an s3 bucket.
The bucket `bucket_name` must already exist and
access credentials must be stored in a way that can be accessed by
s3fs.
"""
import s3fs
import zarr
import numcodecs
if bucket_name is None:
bucket_name = TestS3.bucket_name
# access the s3 filesysyem
fs = s3fs.S3FileSystem(anon=False)
store = s3fs.S3Map(root=bucket_name, s3=fs)
# test data image
data = TestS3.data
# write remote zarr data
f = zarr.group(store)
f.attrs['Q'] = 42
# create dataset
ds = f.create_dataset('data', shape=data.shape, chunks=(256, 256, 3), dtype=data.dtype,
compressor=numcodecs.Zlib())
ds[:] = data
ds.attrs['x'] = 'y'
# create a and dataset group
g = f.create_group('group')
ds = g.create_dataset('data', shape=data.shape, chunks=(256, 256, 3), dtype=data.dtype,
compressor=numcodecs.Zlib())
ds[:] = data
ds.attrs['x'] = 'y'
def _translator(self, name: str, h5obj: Union[h5py.Dataset, h5py.Group]):
"""Produce Zarr metadata for all groups and datasets in the HDF5 file.
"""
refs = {}
if isinstance(h5obj, h5py.Dataset):
lggr.debug(f'HDF5 dataset: {h5obj.name}')
if h5obj.id.get_create_plist().get_layout() == h5py.h5d.COMPACT:
RuntimeError(
f'Compact HDF5 datasets not yet supported: <{h5obj.name} '
f'{h5obj.shape} {h5obj.dtype} {h5obj.nbytes} bytes>')
return
#
# check for unsupported HDF encoding/filters
#
if h5obj.scaleoffset:
raise RuntimeError(
f'{h5obj.name} uses HDF5 scaleoffset filter - not supported by reference-maker'
)
if h5obj.compression in ('szip', 'lzf'):
raise RuntimeError(
f'{h5obj.name} uses szip or lzf compression - not supported by reference-maker'
)
if h5obj.compression == 'gzip':
compression = numcodecs.Zlib(level=h5obj.compression_opts)
else:
compression = None
# Add filter for shuffle
filters = []
if h5obj.shuffle:
filters.append(
numcodecs.Shuffle(elementsize=h5obj.dtype.itemsize))
# Get storage info of this HDF5 dataset...
cinfo = self._storage_info(h5obj)
if h5py.h5ds.is_scale(h5obj.id) and not cinfo:
return
# Create a Zarr array equivalent to this HDF5 dataset...
za = self._zroot.create_dataset(h5obj.name,
shape=h5obj.shape,
dtype=h5obj.dtype,
chunks=h5obj.chunks or False,
fill_value=h5obj.fillvalue,
compression=compression,
filters=filters,
overwrite=True)
lggr.debug(f'Created Zarr array: {za}')
self._transfer_attrs(h5obj, za)
adims = self._get_array_dims(h5obj)
za.attrs['_ARRAY_DIMENSIONS'] = adims
lggr.debug(f'_ARRAY_DIMENSIONS = {adims}')
# Store chunk location metadata...
if cinfo:
for k, v in cinfo.items():
if h5obj.fletcher32:
logging.info("Discarding fletcher32 checksum")
v['size'] -= 4
self.store[za._chunk_key(k)] = [
self._uri, v['offset'], v['size']
]
elif isinstance(h5obj, h5py.Group):
lggr.debug(f'HDF5 group: {h5obj.name}')
zgrp = self._zroot.create_group(h5obj.name)
self._transfer_attrs(h5obj, zgrp)
import zarr
import numcodecs
from skimage.data import astronaut
# choose chunks s.t. we do have overhanging edge-chunks
CHUNKS = (100, 100, 1)
STR_TO_COMPRESSOR = {
'gzip': numcodecs.GZip(),
'blosc': numcodecs.Blosc(),
'zlib': numcodecs.Zlib()
}
def generate_zarr_format(compressors=['gzip', 'blosc', 'zlib', None]):
path = '../data/zarr.zr'
im = astronaut()
f = zarr.open(path)
for compressor in compressors:
name = compressor if compressor is not None else 'raw'
compressor_impl = STR_TO_COMPRESSOR[
compressor] if compressor is not None else None
f.create_dataset(name,
data=im,
chunks=CHUNKS,
compressor=compressor_impl)
# this needs PR https://github.com/zarr-developers/zarr/pull/309
def generate_n5_format(compressors=['gzip', None]):
path = '../data/zarr.n5'