External data

MURLs


def MURLs(
    args:VAR_POSITIONAL, kwargs:VAR_KEYWORD
):

A class with external medical dataset URLs.

IXI

source

download_ixi_data


def download_ixi_data(
    path:(<class 'str'>, <class 'pathlib.Path'>)='../data'
)->Path:

Download T1 scans and demographic information from the IXI dataset.

Args: path: Path to the directory where the data will be stored. Defaults to ‘../data’.

Returns: The path to the stored CSV file.

IXITiny

source

download_ixi_tiny


def download_ixi_tiny(
    path:(<class 'str'>, <class 'pathlib.Path'>)='../data'
)->Path:

Download the tiny version of the IXI dataset provided by TorchIO.

Args: path: The directory where the data will be stored. If not provided, defaults to ‘../data’.

Returns: The path to the directory where the data is stored.

Lower spine data

source

download_spine_test_data


def download_spine_test_data(
    path:(<class 'str'>, <class 'pathlib.Path'>)='../data'
)->DataFrame:

Downloads T2w scans from the study ’Fully Automatic Localization and Segmentation of 3D Vertebral Bodies from CT/MR Images via a Learning-Based Method’ by Chu et. al.

Args: path: Directory where the downloaded data will be stored and extracted. Defaults to ‘../data’.

Returns: Processed dataframe containing image paths, label paths, and subject IDs.

source

download_example_spine_data


def download_example_spine_data(
    path:(<class 'str'>, <class 'pathlib.Path'>)='../data'
)->Path:

Downloads example T2w scan and corresponding predicted mask.

Args: path: Directory where the downloaded data will be stored and extracted. Defaults to ‘../data’.

Returns: Path to the directory where the example data has been extracted.

MedMNIST3D

source

download_medmnist3d_dataset


def download_medmnist3d_dataset(
    study:str, path:(<class 'str'>, <class 'pathlib.Path'>)='../data', max_workers:int=1, skip_download:bool=True
):

Downloads and processes a particular MedMNIST3D dataset.

Args: study: MedMNIST dataset (‘OrganMNIST3D’, ‘NoduleMNIST3D’, ‘AdrenalMNIST3D’, ‘FractureMNIST3D’, ‘VesselMNIST3D’, ‘SynapseMNIST3D’) path: Directory to store and extract downloaded data. Defaults to ‘../data’. max_workers: Maximum number of worker processes for data processing. Defaults to 1. skip_download: Flag to indicate if the dataset should be re-downloaded if the dataset exists locally. Default set to False.

Returns: Two pandas DataFrames. The first DataFrame combines training and validation data, and the second DataFrame contains the testing data.

Endometrical cancer

source

download_example_endometrial_cancer_data


def download_example_endometrial_cancer_data(
    path:(<class 'str'>, <class 'pathlib.Path'>)='../data', multi_channel:bool=True
):

Download example data for endometrial cancer.

Args: path (str or Path): Path to save the downloaded data. multi_channel (bool): If True, download multi-channel data (Vibe, T2, and ADC). Otherwise, download only Vibe.