def read_binary_mask(self, tf: tarfile.TarFile) -> bm.BinaryMaskCollection:
log: Optional[Log] = None
masks: MutableSequence[bm.MaskData] = []
pixel_ticks: Optional[Mapping[Axes, ArrayLike[int]]] = None
physical_ticks: Optional[Mapping[Coordinates,
ArrayLike[Number]]] = None
while True:
tarinfo: Optional[tarfile.TarInfo] = tf.next()
if tarinfo is None:
break
# wrap it in a BytesIO object to ensure we never seek backwards.
extracted_fh = tf.extractfile(tarinfo)
if extracted_fh is None:
raise ValueError(f"Unable to extract file {tarinfo.name}")
byte_stream = io.BytesIO(extracted_fh.read())
if tarinfo.name == v0_0.LOG_FILENAME:
string_stream = codecs.getreader("utf-8")(byte_stream)
log = Log.decode(string_stream.read())
elif tarinfo.name == v0_0.PIXEL_TICKS_FILE:
pixel_ticks = pickle.load(byte_stream)
elif tarinfo.name == v0_0.PHYSICAL_TICKS_FILE:
physical_ticks = pickle.load(byte_stream)
elif tarinfo.name.startswith(v0_0.MASK_PREFIX):
mask_on_disk: v0_0.MaskOnDisk = pickle.load(byte_stream)
if not isinstance(mask_on_disk, v0_0.MaskOnDisk):
raise TypeError(
f"mask does not conform to expected mask structure")
masks.append(
bm.MaskData(mask_on_disk.binary_mask, mask_on_disk.offsets,
None))
else:
warnings.warn(
f"Unexpected file in binary mask collection {tarinfo.name}",
DataFormatWarning)
if pixel_ticks is None:
raise ValueError("pixel coordinates not found")
if physical_ticks is None:
raise ValueError("physical coordinates not found")
return bm.BinaryMaskCollection(pixel_ticks, physical_ticks, masks, log)
def log(self) -> Log:
"""Returns a copy of the provenance data. Modifications to this copy will not affect the
log stored on this label image."""
return Log.decode(self.label_image.attrs[AttrKeys.LOG])