def __init__(
self,
*,
stack_axis: str,
datasources: Iterable[DataSource],
):
self.stack_axis = stack_axis
self.datasources = sorted(datasources,
key=lambda ds: ds.location[stack_axis])
tile_shapes = {ds.tile_shape for ds in self.datasources}
if len(tile_shapes) != 1:
raise ValueError(
f"All datasources must have the same tile shape. Tile shapes: {tile_shapes}"
)
tile_shape = tile_shapes.pop()
if any(ds.shape[stack_axis] % tile_shape[stack_axis] != 0
for ds in self.datasources):
raise ValueError(
f"Stacking over axis that are not multiple of the tile size is not supported"
)
self.stack_levels = [
ds.location[stack_axis] for ds in self.datasources
]
interval = Interval5D.enclosing(ds.interval for ds in self.datasources)
super().__init__(dtype=self.datasources[0].dtype,
interval=interval,
axiskeys=stack_axis +
Point5D.LABELS.replace(stack_axis, ""),
tile_shape=tile_shape)
def label_at(self, point: Point5D) -> int:
point_roi = Interval5D.enclosing([point])
if not self.interval.contains(point_roi):
raise ValueError(f"Point {point} is not inside the labels at {self.interval}")
label = self.cut(point_roi).raw("x")[0]
if label == 0:
raise ValueError(f"Point {point} is not on top of an object")
return label
def show(self):
data = self.data_tile.retrieve().cut(copy=True)
for axis in "xyz":
increment = Point5D.zero(**{axis: 1})
for pos in (self.position + increment, self.position - increment):
if data.interval.contains(Interval5D.enclosing([pos])):
data.paint_point(pos, 0)
data.paint_point(self.position, 255)
data.show_images()
def merge(annotations: Sequence["Annotation"],
color_map: Optional[Dict[Color, np.uint8]] = None) -> Array5D:
out_roi = Interval5D.enclosing(annot.interval for annot in annotations)
out = Array5D.allocate(interval=out_roi,
value=0,
dtype=np.dtype('uint8'))
color_map = color_map or Color.create_color_map(
annot.color for annot in annotations)
for annot in annotations:
out.set(annot.colored(color_map[annot.color]), mask_value=0)
return out
def __init__(
self,
*,
position: Point5D, # an anchor point within datasource
klass: int,
datasource: DataSource, # an object label is tied to the datasource
components_extractor:
ConnectedComponentsExtractor, # and also to the method used to extract the objects
):
position_roi = DataRoi(datasource,
**Interval5D.enclosing([position]).to_dict())
self.data_tile = position_roi.get_tiles(
datasource.tile_shape,
clamp=False).__next__().clamped(datasource.shape)
self.position = position
self.klass = klass
self.datasource = datasource
self.components_extractor = components_extractor
# compute connected components in constructor to prevent creation of bad annotation
self.label = components_extractor.compute(
self.data_tile).label_at(position)