def get_image(
self,
item: str,
aligned_group: int = 0,
x_slice: Optional[Union[int, slice]] = None,
y_slice: Optional[Union[int, slice]] = None,
) -> ImageStack:
"""
Parameters
----------
item: str
The name of the tileset ex. 'primary' or 'nuclei'
aligned_group: int
The aligned subgroup, default 0
x_slice: int or slice
The cropping parameters for the x axis
y_slice:
The cropping parameters for the y axis
Returns
-------
The instantiated ImageStack
"""
crop_params = copy.copy(
(self.aligned_coordinate_groups[item][aligned_group]))
crop_params._x_slice = x_slice
crop_params._y_slice = y_slice
return ImageStack.from_tileset(self._images[item],
crop_parameters=crop_params)
def setup_imagestack() -> ImageStack:
"""Build an imagestack with labeled indices (i.e., indices that do not start at 0 or are not
sequential non-negative integers).
"""
collection = build_image(
range(1),
ROUND_LABELS,
CH_LABELS,
ZPLANE_LABELS,
tile_fetcher_factory(UniqueTiles, True),
)
tileset = list(collection.all_tilesets())[0][1]
return ImageStack.from_tileset(tileset)
def get_image(
self,
item: str,
crop_parameters: Optional[CropParameters] = None) -> ImageStack:
return ImageStack.from_tileset(self._images[item], crop_parameters)
def __getitem__(self, item) -> ImageStack:
if isinstance(self._images[item], TileSet):
self._images[item] = ImageStack.from_tileset(self._images[item])
return self._images[item]
