def _build_manifest(self, image: Image, segment_slugs: dict) -> dict:
manifest = {
"image": {
"precision_bytes":
image.get_image_data().dtype.itemsize,
"size":
list(image.get_image_data().shape
), # the image volume byte sequence does not contain this
"voxel_size":
list(image.get_voxel_size())
if image.get_voxel_size() else None,
"voxel_spacing":
list(image.get_voxel_spacing())
if image.get_voxel_spacing() else None,
},
"meta_data":
image.get_meta_data(),
"slices": [
self._build_image_slice_manifest(image_slice)
for image_slice in image.get_slices()
],
"segments": [
self._build_image_segment_manifest(
image_segment,
segment_slugs[image_segment.get_identifier()])
for image_segment in image.get_segments()
],
}
# make sure the result will actually be readable
self._validate_manifest(manifest)
return manifest
def _generate_segment_slugs(self, image: Image) -> dict:
result = {}
for num, segment in enumerate(image.get_segments()):
while True:
slug = generate_random_string()
if slug not in result:
break
result[segment.get_identifier()] = slug
return result
def write(self,
image: Image,
path: str,
*,
override_if_existing: bool = False) -> None:
self._logger.debug("Writing image to gmh file under: {}".format(path))
if os.path.exists(path) and not override_if_existing:
raise ValueError(f"Path does already exist: {path}")
temporary_file_path = f"{path}.tmp"
assert not os.path.exists(temporary_file_path)
with tarfile.open(temporary_file_path, "w") as tar_file_handle:
def add_file(name: str, content) -> None:
if isinstance(content, str):
content = content.encode()
member = tarfile.TarInfo(name)
member.size = len(content)
tar_file_handle.addfile(member, io.BytesIO(content))
segment_slugs = self._generate_segment_slugs(image)
add_file("manifest.json",
self._build_manifest_document(image, segment_slugs))
add_file("image_data.npy", image.get_image_data().tobytes())
for image_segment in image.get_segments():
if image_segment.is_empty():
continue
segment_slug = segment_slugs[image_segment.get_identifier()]
add_file(
IMAGE_SEGMENT_MASK_MEMBER_NAME_FORMAT.format(segment_slug),
image_segment.get_mask_in_bounding_box().tobytes())
# swap written file into target path
if os.path.exists(path):
os.remove(path)
os.rename(temporary_file_path, path)