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]