import datasets from typing import List import pandas as pd import numpy as np from pathlib import Path import os _DESCRIPTION = "Prostate dataset." class Prostate158Dataset(datasets.GeneratorBasedBuilder): VERSION = datasets.Version("1.1.0") BUILDER_CONFIGS = [ datasets.BuilderConfig( name="2d", version=VERSION, description="Return all the dataset in a 2d image format", ), # datasets.BuilderConfig( # name="2d_array", # version=VERSION, # description="Return all the dataset in a 2d array format", # ), # datasets.BuilderConfig( # name="3d_array", # version=VERSION, # description="Return all the dataset in a 2d array format", # ), datasets.BuilderConfig( name="3d_path", version=VERSION, description="Return all the dataset in a 3d path format", ), ] DEFAULT_CONFIG_NAME = "3d_path" def _info(self): if self.config.name == "2d": features = datasets.Features( { "t2": datasets.Image(), "adc": datasets.Image(), "dwi": datasets.Image(), "t2_anatomy_reader1": datasets.Image(), "adc_tumor_reader1": datasets.Image(), } ) # elif self.config.name == "2d_array": # features = datasets.Features( # { # "t2": datasets.Array2D(shape=(200,200), dtype="int"), # "adc": datasets.Array2D(shape=(200,200), dtype="int"), # "dwi": datasets.Array2D(shape=(200,200), dtype="int"), # "t2_anatomy_reader1": datasets.Array2D(shape=(200,200), dtype="int"), # "adc_tumor_reader1": datasets.Array2D(shape=(200,200), dtype="int"), # } # ) elif self.config.name == "3d_path": features = datasets.Features( { "t2_path": datasets.Value(dtype="string"), "adc_path": datasets.Value(dtype="string"), "dwi_path": datasets.Value(dtype="string"), "t2_anatomy_reader1_path": datasets.Value(dtype="string"), "adc_tumor_reader1_path": datasets.Value(dtype="string"), } ) # elif self.config.name == "3d_array": # features = datasets.Features( # { # "t2": datasets.Array3D(shape=(200,200,20), dtype="int"), # "adc": datasets.Array3D(shape=(200,200,20), dtype="int"), # "dwi": datasets.Array3D(shape=(200,200,20), dtype="int"), # "t2_anatomy_reader1": datasets.Array3D(shape=(200,200,20), dtype="int"), # "adc_tumor_reader1": datasets.Array3D(shape=(200,200,20), dtype="int"), # } # ) return datasets.DatasetInfo( description=_DESCRIPTION, features=features, ) def _split_generators( self, dl_manager: datasets.DownloadManager ) -> List[datasets.SplitGenerator]: downloaded_files = dl_manager.download_and_extract("data.zip") return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={ "split": "train", "downloaded_files": Path(downloaded_files), }, ), datasets.SplitGenerator( name=datasets.Split.VALIDATION, gen_kwargs={ "split": "valid", "downloaded_files": Path(downloaded_files), }, ), datasets.SplitGenerator( name=datasets.Split.TEST, gen_kwargs={ "split": "test", "downloaded_files": Path(downloaded_files), }, ), ] def _generate_examples(self, split, downloaded_files): images_list = ["t2", "adc", "dwi", "t2_anatomy_reader1", "adc_tumor_reader1"] df = pd.read_csv(downloaded_files / f"{split}.csv") if self.config.name == "2d": import nibabel as nib from PIL import Image # moving imports here to not require unnecessary packages to other users yield_index = -1 for row in df.to_dict(orient="records"): images_data = {image_name: nib.load(downloaded_files / row[image_name]).get_fdata() for image_name in images_list} for i in range(images_data["t2"].shape[2]): yield_index += 1 yield yield_index, {image_name: Image.fromarray(image[:, :, i]) for image_name, image in images_data.items()} # elif self.config.name == "2d_array": # import nibabel as nib # yield_index = -1 # for row in df.to_dict(orient="records"): # images_data = {image_name: nib.load(downloaded_files / row[image_name]).get_fdata() for image_name in images_list} # for i in range(images_data["t2"].shape[2]): # yield_index += 1 # yield yield_index, {image_name: image[:, :, i] for image_name, image in images_data.items()} elif self.config.name == "3d_path": for idx, row in enumerate(df.to_dict(orient="records")): yield idx, {image_name+"_path": downloaded_files / row[image_name] for image_name in images_list} # elif self.config.name == "3d_array": # import nibabel as nib # for idx, row in enumerate(df.to_dict(orient="records")): # yield idx, {image_name: nib.load(downloaded_files / row[image_name]).get_fdata() for image_name in images_list}