""" Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine License: GNU GPL 2.0 """ import pickle import pathml.core.tile from pathml.preprocessing.transforms import Transform class Pipeline(Transform): """ Compose a sequence of Transforms Args: transform_sequence (list): sequence of transforms to be consecutively applied. List of `pathml.core.Transform` objects """ def __init__(self, transform_sequence=None): assert transform_sequence is None or all( [isinstance(t, Transform) for t in transform_sequence] ), "All elements in input list must be of type pathml.core.Transform" self.transforms = transform_sequence def __len__(self): return len(self.transforms) def __repr__(self): if self.transforms is None: return "Pipeline()" else: out = "Pipeline([\n" for t in self.transforms: out += f"\t{repr(t)},\n" out += "])" return out def apply(self, tile): # this function has side effects # modifies the tile in place, but also returns the modified tile # need to do this for dask distributed assert isinstance( tile, pathml.core.tile.Tile ), f"argument of type {type(tile)} must be a pathml.core.Tile object." if self.transforms: for t in self.transforms: t.apply(tile) return tile def save(self, filename): """ save pipeline to disk Args: filename (str): save path on disk """ pickle.dump(self, open(filename, "wb"))