def write_multiscale(pyramid: List, group: zarr.Group) -> None:
"""Write a pyramid with multiscale metadata to disk."""
paths = []
for path, dataset in enumerate(pyramid):
group.create_dataset(str(path), data=pyramid[path])
paths.append({"path": str(path)})
multiscales = [{"version": "0.1", "datasets": paths}]
group.attrs["multiscales"] = multiscales
def write_array(self, group: zarr.Group, name: str,
array: np.ndarray) -> None:
if array.dtype.kind == 'V':
self.write_dataframe(group, name, array)
else:
dtype = str if array.dtype.kind == 'O' else array.dtype
group.create_dataset(name,
data=array,
shape=array.shape,
chunks=calc_chunk(array.shape),
dtype=dtype,
compressor=COMPRESSOR,
overwrite=True)
def write_multiscale(
pyramid: List,
group: zarr.Group,
chunks: Union[Tuple[Any, ...], int] = None,
) -> None:
"""Write a pyramid with multiscale metadata to disk."""
paths = []
for path, dataset in enumerate(pyramid):
# TODO: chunks here could be different per layer
group.create_dataset(str(path), data=dataset, chunks=chunks)
paths.append({"path": str(path)})
multiscales = [{"version": "0.2", "datasets": paths}]
group.attrs["multiscales"] = multiscales
def create_zarr_obj_array(g: zarr.Group,
name: str,
data,
dtype: Union[str, Any] = None,
overwrite: bool = True) -> zarr.hierarchy:
"""
Creates and returns a Zarr object array.
A Zarr object array can contain any type of object.
https://zarr.readthedocs.io/en/stable/tutorial.html#object-arrays
Args:
g (zarr.hierarchy):
name (str):
data ():
dtype (Union[str, Any]):
overwrite (bool):
Returns:
A Zarr object Array.
"""
data = np.array(data)
if dtype is None or dtype == object:
dtype = 'U' + str(max([len(str(x)) for x in data]))
if np.issubdtype(data.dtype, np.dtype('S')):
data = data.astype('U')
dtype = data.dtype
return g.create_dataset(name,
data=data,
chunks=(100000, ),
shape=len(data),
dtype=dtype,
overwrite=overwrite)
def create_zarr_dataset(g: zarr.Group,
name: str,
chunks: tuple,
dtype: Any,
shape: Tuple,
overwrite: bool = True) -> zarr.hierarchy:
"""
Creates and returns a Zarr array.
Args:
g (zarr.hierarchy):
name (str):
chunks (tuple):
dtype (Any):
shape (Tuple):
overwrite (bool):
Returns:
A Zarr Array.
"""
from numcodecs import Blosc
compressor = Blosc(cname='lz4', clevel=5, shuffle=Blosc.BITSHUFFLE)
return g.create_dataset(name,
chunks=chunks,
dtype=dtype,
shape=shape,
compressor=compressor,
overwrite=overwrite)
def write_series(self, group: zarr.Group, name: str, array: np.ndarray,
data_type: str) -> None:
if data_type == 'data_frame':
if not is_categorical_dtype(
array) and name != '_index' and is_string_dtype(array):
keywords = set(array)
if len(keywords
) <= array.size / 10.0: # at least 10x reduction
array = pd.Categorical(array,
categories=natsorted(keywords))
if is_categorical_dtype(array):
# write category keys
categories = group.require_group('_categories')
values = array.categories.values
if isinstance(values[0], bytes):
values = np.array([x.decode() for x in values],
dtype=object)
dtype = str if values.dtype.kind == 'O' else values.dtype
categories.create_dataset(name,
data=values,
shape=values.shape,
chunks=calc_chunk(values.shape),
dtype=dtype,
compressor=COMPRESSOR,
overwrite=True)
# write codes
codes_arr = group.create_dataset(name,
data=array.codes,
shape=array.codes.shape,
chunks=calc_chunk(
array.codes.shape),
dtype=array.codes.dtype,
compressor=COMPRESSOR,
overwrite=True)
codes_arr.attrs['ordered'] = array.ordered
return None
dtype = str if array.dtype.kind == 'O' else array.dtype
group.create_dataset(name,
data=array,
shape=array.shape,
chunks=calc_chunk(array.shape),
dtype=dtype,
compressor=COMPRESSOR,
overwrite=True)
def write_multiscale(
pyramid: List,
group: zarr.Group,
chunks: Union[Tuple[Any, ...], int] = None,
fmt: Format = CurrentFormat(),
axes: Union[str, List[str]] = None,
) -> None:
"""
Write a pyramid with multiscale metadata to disk.
Parameters
----------
pyramid: List of np.ndarray
the image data to save. Largest level first
All image arrays MUST be up to 5-dimensional with dimensions
ordered (t, c, z, y, x)
group: zarr.Group
the group within the zarr store to store the data in
chunks: int or tuple of ints,
size of the saved chunks to store the image
fmt: Format
The format of the ome_zarr data which should be used.
Defaults to the most current.
axes: str or list of str
the names of the axes. e.g. "tczyx". Not needed for v0.1 or v0.2
or for v0.3 if 2D or 5D. Otherwise this must be provided
"""
dims = len(pyramid[0].shape)
axes = _validate_axes_names(dims, axes, fmt)
paths = []
for path, dataset in enumerate(pyramid):
# TODO: chunks here could be different per layer
group.create_dataset(str(path), data=dataset, chunks=chunks)
paths.append(str(path))
write_multiscales_metadata(group, paths, fmt, axes)
def create_zarr_obj_array(
g: zarr.Group,
name: str,
data,
dtype: Union[str, Any] = None,
overwrite: bool = True,
chunk_size: int = 100000,
) -> zarr.hierarchy:
"""
Creates and returns a Zarr object array.
A Zarr object array can contain any type of object.
https://zarr.readthedocs.io/en/stable/tutorial.html#object-arrays
Args:
g (zarr.hierarchy):
name (str):
data ():
dtype (Union[str, Any]):
overwrite (bool):
chunk_size (int):
Returns:
A Zarr object Array.
"""
from numcodecs import Blosc
compressor = Blosc(cname="lz4", clevel=5, shuffle=Blosc.BITSHUFFLE)
data = np.array(data)
if dtype is None or dtype == object:
dtype = "U" + str(max([len(str(x)) for x in data]))
if np.issubdtype(data.dtype, np.dtype("S")):
data = data.astype("U")
dtype = data.dtype
if chunk_size is None or chunk_size is False:
chunks = False
else:
chunks = (chunk_size, )
return g.create_dataset(
name,
data=data,
chunks=chunks,
shape=len(data),
dtype=dtype,
overwrite=overwrite,
compressor=compressor,
)
