""" Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine License: GNU GPL 2.0 """ import reprlib from pathlib import Path import dask.distributed from loguru import logger class SlideDataset: """ Container for a dataset of WSIs Args: slides: list of SlideData objects """ def __init__(self, slides): self.slides = slides self._tile_dataset = None def __getitem__(self, ix): return self.slides[ix] def __len__(self): return len(self.slides) def __repr__(self): out = [] out.append(f"SlideDataset object with {len(self)} slides") out.append(f"names: {reprlib.repr([s.name for s in self.slides])}") out.append(f"shapes: {reprlib.repr([s.shape for s in self.slides])}") out = ",\n\t".join(out) out += ")" return out def run(self, pipeline, client=None, distributed=True, **kwargs): """ Runs a preprocessing pipeline on all slides in the dataset Args: pipeline (pathml.preprocessing.pipeline.Pipeline): Preprocessing pipeline. client: dask.distributed client distributed (bool): Whether to distribute model using client. Defaults to True. kwargs (dict): keyword arguments passed to :meth:`~pathml.core.slide_data.SlideData.run` for each slide """ shutdown_after = False # run preprocessing if client is None and distributed: client = dask.distributed.Client() shutdown_after = True logger.info( f"creating a default distributed.Client(): {client.scheduler_info()}" ) for slide in self.slides: slide.run( pipeline=pipeline, client=client, distributed=distributed, **kwargs ) if shutdown_after: client.shutdown() def write(self, dir, filenames=None): """ Write all SlideData objects to the specified directory. Calls .write() method for each slide in the dataset. Optionally pass a list of filenames to use, otherwise filenames will be created from ``.name`` attributes of each slide. Args: dir (Union[str, bytes, os.PathLike]): Path to directory where slides are to be saved filenames (List[str], optional): list of filenames to be used. """ d = Path(dir) if filenames: if len(filenames) != self.__len__(): # pragma: no cover raise ValueError( f"input list of filenames has {len(filenames)} elements but must be same length as number of slides in dataset ({self.__len__()})" ) for i, slide in enumerate(self.slides): if filenames: slide_path = d / (filenames[i] + ".h5path") elif slide.name: slide_path = d / (slide.name + ".h5path") else: # pragma: no cover raise ValueError( "slide does not have a .name attribute. Must supply a 'filenames' argument." ) slide.write(slide_path)