def __init__(self, path: Path, *, location: Point5D = Point5D.zero(), filesystem: FS):
try:
raw_data = skimage.io.imread(filesystem.openbin(path.as_posix()))
except ValueError:
raise UnsupportedUrlException(path)
axiskeys = "yxc"[: len(raw_data.shape)]
super().__init__(url=filesystem.desc(path.as_posix()), data=raw_data, axiskeys=axiskeys, location=location)
def __init__(self,
path: Path,
*,
location: Point5D = Point5D.zero(),
filesystem: FS):
self._dataset: Optional[h5py.Dataset] = None
try:
self._dataset, outer_path, inner_path = self.openDataset(
path, filesystem=filesystem)
axiskeys = self.getAxisKeys(self._dataset)
tile_shape = Shape5D.create(raw_shape=self._dataset.chunks
or self._dataset.shape,
axiskeys=axiskeys)
super().__init__(
url=filesystem.desc(outer_path.as_posix()) + "/" +
inner_path.as_posix(),
tile_shape=tile_shape,
shape=Shape5D.create(raw_shape=self._dataset.shape,
axiskeys=axiskeys),
dtype=self._dataset.dtype,
name=self._dataset.file.filename.split("/")[-1] +
self._dataset.name,
location=location,
axiskeys=axiskeys,
)
except Exception as e:
if self._dataset:
self._dataset.file.close()
raise e
def __init__(self,
path: Path,
*,
location: Point5D = Point5D.zero(),
chunk_size: Optional[Shape5D] = None,
filesystem: FS):
"""A DataSource that handles Neurogancer's precomputed chunks
path: a path all the pay down to the scale, i.e., if some scale has
"key": "my_scale"
then your path should end in "my_scale"
chunk_size: a valid chunk_size for the scale selected by 'path'
"""
self.filesystem = filesystem.opendir(path.parent.as_posix())
self.info = PrecomputedChunksInfo.load(path=Path("info"),
filesystem=self.filesystem)
self.scale = self.info.get_scale(key=path.name)
super().__init__(
url="precomputed://" + filesystem.desc(path.as_posix()),
tile_shape=self.scale.get_tile_shape_5d(
self.info.num_channels, tile_shape_hint=chunk_size),
shape=self.scale.get_shape_5d(self.info.num_channels),
dtype=self.info.data_type,
name=path.name,
location=location,
axiskeys=self.scale.
axiskeys[::
-1], # externally reported axiskeys are always c-ordered
)
encoding_type = self.scale.encoding
if encoding_type == "raw":
noop = lambda data: data
self.decompressor = noop
self.compressor = noop
else:
raise NotImplementedError(
f"Don't know how to decompress {compression_type}")
def install_from_fs(self,
name: str,
source_fs: FS,
path: str = ".",
output_name: str = None):
"""
Copy a module directory from where it is located to the installation directory.
:param name: Name of the module
:param source_fs: FS object pointing to the source location
:param path: Path to the module directory from the source location root
:param output_name: Name to give to the module's directory at installation
"""
path_to_module = join(path, name)
if name not in source_fs.listdir(path):
raise InvalidModuleError(
name,
"Module directory not found - Given path should be the parent directory"
)
if "__manifest__.py" not in source_fs.listdir(path_to_module):
raise InvalidModuleError(
name,
"Manifest not found - Given path should be the parent directory"
)
self.pretty_print(output_name,
"Copying from {}".format(
source_fs.desc(path_to_module)),
level=VERBOSE_FULL)
copy_dir(source_fs, path_to_module, self.install_dir, output_name
or name)
self.pretty_print(output_name,
"Installed and up to date.",
status=LOG_STATUS_OK,
level=VERBOSE_NORMAL)