Source code for

# Copyright 2020 - 2021 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

from typing import Any, Callable, Optional, Sequence, Union

import numpy as np
from import Dataset

from monai.config import DtypeLike
from import ImageReader
from monai.transforms import LoadImage, Randomizable, apply_transform
from monai.utils import MAX_SEED, get_seed

[docs]class ImageDataset(Dataset, Randomizable): """ Loads image/segmentation pairs of files from the given filename lists. Transformations can be specified for the image and segmentation arrays separately. The difference between this dataset and `ArrayDataset` is that this dataset can apply transform chain to images and segs and return both the images and metadata, and no need to specify transform to load images from files. For more information, please see the image_dataset demo in the MONAI tutorial repo, """ def __init__( self, image_files: Sequence[str], seg_files: Optional[Sequence[str]] = None, labels: Optional[Sequence[float]] = None, transform: Optional[Callable] = None, seg_transform: Optional[Callable] = None, image_only: bool = True, transform_with_metadata: bool = False, dtype: DtypeLike = np.float32, reader: Optional[Union[ImageReader, str]] = None, *args, **kwargs, ) -> None: """ Initializes the dataset with the image and segmentation filename lists. The transform `transform` is applied to the images and `seg_transform` to the segmentations. Args: image_files: list of image filenames seg_files: if in segmentation task, list of segmentation filenames labels: if in classification task, list of classification labels transform: transform to apply to image arrays seg_transform: transform to apply to segmentation arrays image_only: if True return only the image volume, otherwise, return image volume and the metadata transform_with_metadata: if True, the metadata will be passed to the transforms whenever possible. dtype: if not None convert the loaded image to this data type reader: register reader to load image file and meta data, if None, will use the default readers. If a string of reader name provided, will construct a reader object with the `*args` and `**kwargs` parameters, supported reader name: "NibabelReader", "PILReader", "ITKReader", "NumpyReader" args: additional parameters for reader if providing a reader name kwargs: additional parameters for reader if providing a reader name Raises: ValueError: When ``seg_files`` length differs from ``image_files`` """ if seg_files is not None and len(image_files) != len(seg_files): raise ValueError( "Must have same the number of segmentation as image files: " f"images={len(image_files)}, segmentations={len(seg_files)}." ) self.image_files = image_files self.seg_files = seg_files self.labels = labels self.transform = transform self.seg_transform = seg_transform if image_only and transform_with_metadata: raise ValueError("transform_with_metadata=True requires image_only=False.") self.image_only = image_only self.transform_with_metadata = transform_with_metadata self.loader = LoadImage(reader, image_only, dtype, *args, **kwargs) self.set_random_state(seed=get_seed()) self._seed = 0 # transform synchronization seed def __len__(self) -> int: return len(self.image_files)
[docs] def randomize(self, data: Optional[Any] = None) -> None: self._seed = self.R.randint(MAX_SEED, dtype="uint32")
def __getitem__(self, index: int): self.randomize() meta_data, seg_meta_data, seg, label = None, None, None, None # load data and optionally meta if self.image_only: img = self.loader(self.image_files[index]) if self.seg_files is not None: seg = self.loader(self.seg_files[index]) else: img, meta_data = self.loader(self.image_files[index]) if self.seg_files is not None: seg, seg_meta_data = self.loader(self.seg_files[index]) # apply the transforms if self.transform is not None: if isinstance(self.transform, Randomizable): self.transform.set_random_state(seed=self._seed) img = apply_transform( self.transform, (img, meta_data) if self.transform_with_metadata else img, map_items=False ) if self.transform_with_metadata: img, meta_data = img if self.seg_transform is not None: if isinstance(self.seg_transform, Randomizable): self.seg_transform.set_random_state(seed=self._seed) seg = apply_transform( self.seg_transform, (seg, seg_meta_data) if self.transform_with_metadata else seg, map_items=False ) if self.transform_with_metadata: seg, seg_meta_data = seg if self.labels is not None: label = self.labels[index] # construct outputs data = [img] if seg is not None: data.append(seg) if label is not None: data.append(label) if not self.image_only and meta_data is not None: data.append(meta_data) if not self.image_only and seg_meta_data is not None: data.append(seg_meta_data) if len(data) == 1: return data[0] # use tuple instead of list as the default collate_fn callback of MONAI DataLoader flattens nested lists return tuple(data)