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 interpolate_from_points(cls, color: Color, voxels: Sequence[Point5D],
raw_data: DataSource):
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)
anchor = voxels[0]
for voxel in voxels:
for interp_voxel in anchor.interpolate_until(voxel):
scribblings.paint_point(point=interp_voxel, value=True)
anchor = voxel
return cls(scribblings._data,
axiskeys=scribblings.axiskeys,
color=color,
raw_data=raw_data,
location=start)