Source code for eisen.datasets.camelyon

import h5py
import os
import numpy as np

from import Dataset

[docs]class PatchCamelyon(Dataset): """ This object implements the capability of reading PatchCamelyon data. Further information about this dataset can be found on the official website Through this module, users are able to make use of the challenge data by simply specifying the directory where the data is locally stored. Therefore it is necessary to first download the data, store or unpack it in a specific directory and then instantiate an object of type PatchCamelyon which will make use of the data in the directory as well as the h5 files that are part of the dataset and make it available to Eisen. .. note:: This dataset will generate data entries with keys: 'image', 'label' and optionally 'mask'. The generated image and label are tensors. .. code-block:: python from eisen.datasets import PatchCamelyon dset = PatchCamelyon( '/data/root/path', 'camelyon_patch_level_2_split_train_x.h5', 'camelyon_patch_level_2_split_train_y.h5', 'camelyon_patch_level_2_split_train_mask.h5' ) """
[docs] def __init__(self, data_dir, x_h5_file, y_h5_file, mask_h5_file=None, transform=None): """ :param data_dir: the base directory where the data is located :type data_dir: str :param x_h5_file: the relative path of the H5 file containing x (the images) :type x_h5_file: str :param y_h5_file: the relative path of the H5 file containing y (the labels) :type y_h5_file: str :param mask_h5_file: the relative path of the H5 file containing masks :type mask_h5_file: str :param transform: a transform object (can be the result of a composition of transforms) :type transform: callable .. code-block:: python from eisen.datasets import PatchCamelyon dset = PatchCamelyon( data_dir='/data/root/path', x_h5_file='camelyon_patch_level_2_split_train_x.h5', y_h5_file='camelyon_patch_level_2_split_train_y.h5', mask_h5_file='camelyon_patch_level_2_split_train_mask.h5', transform=transform ) <json> [ {"name": "x_h5_file", "type": "string", "value": ""}, {"name": "y_h5_file", "type": "string", "value": ""}, {"name": "mask_h5_file", "type": "string", "value": ""} ] </json> """ self.x = h5py.File(os.path.join(data_dir, x_h5_file), "r")["x"] self.y = h5py.File(os.path.join(data_dir, y_h5_file), "r")["y"] assert len(self.x) == len(self.y) if mask_h5_file: self.mask = h5py.File(os.path.join(data_dir, mask_h5_file), "r")["mask"] assert len(self.x) == len(self.mask) else: self.mask = None self.transform = transform
def __len__(self): return len(self.x) def __getitem__(self, idx): item = { "image": self.x[idx].transpose([2, 0, 1]).astype(np.float32), "label": np.squeeze(self.y[idx].astype(np.float32))[np.newaxis], } if self.mask: item["mask"] = self.mask[idx] if self.transform: item = self.transform(item) return item


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