def from_json_value(cls, data: JsonValue) -> "Annotation":
data_dict = ensureJsonObject(data)
raw_voxels = ensureJsonArray(data_dict.get("voxels"))
voxels: Sequence[Point5D] = [
Point5D.from_json_value(raw_voxel) for raw_voxel in raw_voxels
]
color = Color.from_json_data(data_dict.get("color"))
raw_data = DataSource.from_json_value(data_dict.get("raw_data"))
start = Point5D.min_coords(voxels)
stop = Point5D.max_coords(
voxels
) + 1 # +1 because slice.stop is exclusive, but max_point isinclusive
scribbling_roi = Interval5D.create_from_start_stop(start=start,
stop=stop)
if scribbling_roi.shape.c != 1:
raise ValueError(
f"Annotations must not span multiple channels: {voxels}")
scribblings = Array5D.allocate(scribbling_roi,
dtype=np.dtype(bool),
value=False)
for voxel in voxels:
scribblings.paint_point(point=voxel, value=True)
return cls(scribblings._data,
axiskeys=scribblings.axiskeys,
color=color,
raw_data=raw_data,
location=start)
def from_json_value(cls, value: JsonValue) -> "N5DataSource":
value_obj = ensureJsonObject(value)
raw_location = value_obj.get("location")
return N5DataSource(
path=Path(ensureJsonString(value_obj.get("path"))),
filesystem=JsonableFilesystem.from_json_value(value_obj.get("filesystem")),
location=raw_location if raw_location is None else Point5D.from_json_value(raw_location),
)
def from_json_value(cls, value: JsonValue) -> "SkimageDataSource":
value_obj = ensureJsonObject(value)
raw_location = value_obj.get("location")
raw_tile_shape = value_obj.get("tile_shape")
return SkimageDataSource(
path=Path(ensureJsonString(value_obj.get("path"))),
location=Point5D.zero()
if raw_location is None else Point5D.from_json_value(raw_location),
filesystem=JsonableFilesystem.from_json_value(
value_obj.get("filesystem")),
tile_shape=None if raw_tile_shape is None else
Shape5D.from_json_value(raw_tile_shape))
def from_json_value(cls, value: JsonValue) -> "H5DataSource":
value_obj = ensureJsonObject(value)
raw_location = value_obj.get("location")
return H5DataSource(
outer_path=Path(ensureJsonString(value_obj.get("outer_path"))),
inner_path=PurePosixPath(
ensureJsonString(value_obj.get("inner_path"))),
filesystem=JsonableFilesystem.from_json_value(
value_obj.get("filesystem")),
location=Point5D.zero()
if raw_location is None else Point5D.from_json_value(raw_location),
)
def from_json_value(cls,
value: JsonValue) -> "PrecomputedChunksDataSource":
value_obj = ensureJsonObject(value)
raw_location = value_obj.get("location")
raw_chunk_size = value_obj.get("chunk_size")
return PrecomputedChunksDataSource(
path=Path(ensureJsonString(value_obj.get("path"))),
resolution=ensureJsonIntTripplet(
value_obj.get("spatial_resolution")
), # FIXME? change to just resolution?
location=None
if raw_location is None else Point5D.from_json_value(raw_location),
chunk_size=None if raw_chunk_size is None else
Shape5D.from_json_value(raw_chunk_size),
filesystem=JsonableFilesystem.from_json_value(
value_obj.get("filesystem")),
)
