def get(self, bounding_box: BoundingBox) -> Data:
indexes = self._queryBoundingBox(bounding_box)
data = []
stack_volumes = [volume for i, volume in self.stack if i in indexes]
stack_disjoint = list(set(indexes) - set([i for i, v in self.stack]))
for volume in stack_volumes:
sub_bbox = bounding_box.intersect(volume.getBoundingBox())
data.append(volume.get(sub_bbox))
for index in stack_disjoint:
volume = self.volumes[index]
i = self._pushStack(index, volume)
sub_bbox = bounding_box.intersect(volume.getBoundingBox())
data.append(volume.get(sub_bbox))
shape = bounding_box.getNumpyDim()
array = Array(np.zeros(shape).astype(np.uint16),
bounding_box=bounding_box,
iteration_size=BoundingBox(Vector(0, 0, 0),
bounding_box.getSize()),
stride=bounding_box.getSize())
[array.set(item) for item in data]
return Data(array.getArray(), bounding_box)
def get(self, bounding_box: BoundingBox) -> Data:
"""
Requests a data sample from the volume. If the bounding box does
not exist, then the method raises a ValueError.
:param bounding_box: The bounding box of the request data sample
:return: The data sample requested
"""
if bounding_box.isDisjoint(self.getBoundingBox()):
error_string = ("Bounding box must be inside dataset " +
"dimensions instead bounding box is {} while " +
"the dataset dimensions are {}")
error_string = error_string.format(bounding_box,
self.getBoundingBox())
raise ValueError(error_string)
sub_bounding_box = bounding_box.intersect(self.getBoundingBox())
array = self.getArray(sub_bounding_box)
before_pad = bounding_box.getEdges()[0] - sub_bounding_box.getEdges(
)[0]
after_pad = bounding_box.getEdges()[1] - sub_bounding_box.getEdges()[1]
if before_pad != Vector(0, 0, 0) or after_pad != Vector(0, 0, 0):
pad_size = tuple(
zip(before_pad.getNumpyDim(), after_pad.getNumpyDim()))
array = np.pad(array, pad_width=pad_size, mode="constant")
return Data(array, bounding_box)