Source code for nidata.atlas.msdl_atlas

# *- encoding: utf-8 -*-
# Author: Alexandre Abraham, Philippe Gervais
# License: simplified BSD

import os.path as op


from ...core.datasets import HttpDataset


class MSDLDataset(HttpDataset):
    """Download and load the MSDL brain atlas.

    Parameters
    ----------
    data_dir: string, optional
        Path of the data directory. Used to force data storage in a specified
        location. Default: None

    url: string, optional
        Override download URL. Used for test only (or if you setup a mirror of
        the data).

    Returns
    -------
    data: dict
        Dictionary-like object, the interest attributes are :
        - 'labels': str. Path to csv file containing labels.
        - 'maps': str. path to nifti file containing regions definition.

    References
    ----------
    :Download:
        https://team.inria.fr/parietal/files/2015/01/MSDL_rois.zip

    :Paper to cite:
        `Multi-subject dictionary learning to segment an atlas of brain
        spontaneous activity <http://hal.inria.fr/inria-00588898/en>`_
        Gaël Varoquaux, Alexandre Gramfort, Fabian Pedregosa, Vincent Michel,
        Bertrand Thirion. Information Processing in Medical Imaging, 2011,
        pp. 562-573, Lecture Notes in Computer Science.

    :Other references:
        `Learning and comparing functional connectomes across subjects
        <http://hal.inria.fr/hal-00812911/en>`_.
        Gaël Varoquaux, R.C. Craddock NeuroImage, 2013.

    """
    def fetch(self, url=None, resume=True, verbose=1):
        url = 'https://team.inria.fr/parietal/files/2015/01/MSDL_rois.zip'
        opts = {'uncompress': True}

        files = [(op.join('MSDL_rois', 'msdl_rois_labels.csv'), url, opts),
                 (op.join('MSDL_rois', 'msdl_rois.nii'), url, opts)]
        files = self.fetcher.fetch(files, force=not resume, verbose=verbose)
        return dict(labels=files[0], maps=files[1])


def fetch_msdl_atlas(data_dir=None, url=None, resume=True, verbose=1):
    return MSDLDataset(data_dir=data_dir) \
        .fetch(url=url, resume=resume, verbose=verbose)