Merge pull request #100 from rmarkello/fetch_mmp

[ENH] Add fetcher for MMP atlas

Author: rmarkello

netneurotools/data/osf.json

@@ -352,6 +352,15 @@
             "md5": "d8378f33107ed5d98c27e8070ebb5aa2"
         }
     },
+    "atl-mmpall": {
+        "fslr32k": {
+            "url": [
+                "mb37e",
+                "6047bac259e910009b83114f"
+            ],
+            "md5": "fd641742685a239d9c3f60e19a280ca2"
+        }
+    },
     "atl-voneconomo_koskinas": {
         "url": [
             "mb37e",

netneurotools/datasets/__init__.py

@@ -6,12 +6,12 @@
     'fetch_cammoun2012', 'fetch_pauli2018', 'fetch_fsaverage', 'fetch_conte69',
     'fetch_connectome', 'available_connectomes', 'fetch_vazquez_rodriguez2019',
     'fetch_mirchi2018', 'make_correlated_xy', 'fetch_schaefer2018',
-    'fetch_hcp_standards', 'fetch_voneconomo'
+    'fetch_hcp_standards', 'fetch_voneconomo', 'fetch_mmpall'
 ]
 
 from .fetchers import (fetch_cammoun2012, fetch_pauli2018, fetch_fsaverage,
                        fetch_conte69, fetch_connectome, available_connectomes,
                        fetch_vazquez_rodriguez2019, fetch_schaefer2018,
-                       fetch_hcp_standards, fetch_voneconomo)
+                       fetch_hcp_standards, fetch_voneconomo, fetch_mmpall)
 from .generators import (make_correlated_xy)
 from .mirchi import (fetch_mirchi2018)

netneurotools/datasets/fetchers.py

@@ -610,6 +610,77 @@ def fetch_hcp_standards(data_dir=None, url=None, resume=True, verbose=1):
     return op.join(data_dir, dataset_name)
 
 
+def fetch_mmpall(version='fslr32k', data_dir=None, url=None, resume=True,
+                 verbose=1):
+    """
+    Downloads .label.gii files for Glasser et al., 2016 MMPAll atlas
+
+    Parameters
+    ----------
+    version : {'fslr32k'}
+        Specifies which surface annotation files should be matched to. Default:
+        'fslr32k'
+    data_dir : str, optional
+        Path to use as data directory. If not specified, will check for
+        environmental variable 'NNT_DATA'; if that is not set, will use
+        `~/nnt-data` instead. Default: None
+    url : str, optional
+        URL from which to download data. Default: None
+    resume : bool, optional
+        Whether to attempt to resume partial download, if possible. Default:
+        True
+    verbose : int, optional
+        Modifies verbosity of download, where higher numbers mean more updates.
+        Default: 1
+
+    Returns
+    -------
+    filenames : :class:`sklearn.utils.Bunch`
+        Namedtuple with fields ('lh', 'rh') corresponding to filepaths to
+        left/right hemisphere parcellation files
+
+    References
+    ----------
+    Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D., Harwell,
+    J., Yacoub, E., ... & Van Essen, D. C. (2016). A multi-modal parcellation
+    of human cerebral cortex. Nature, 536(7615), 171-178.
+
+    Notes
+    -----
+    License: https://www.humanconnectome.org/study/hcp-young-adult/document/
+    wu-minn-hcp-consortium-open-access-data-use-terms
+    """
+
+    versions = ['fslr32k']
+    if version not in versions:
+        raise ValueError('The version of Glasser et al., 2016 parcellation '
+                         'requested "{}" does not exist. Must be one of {}'
+                         .format(version, versions))
+
+    dataset_name = 'atl-mmpall'
+
+    data_dir = _get_data_dir(data_dir=data_dir)
+    info = _get_dataset_info(dataset_name)[version]
+    if url is None:
+        url = info['url']
+    opts = {
+        'uncompress': True,
+        'md5sum': info['md5'],
+        'move': '{}.tar.gz'.format(dataset_name)
+    }
+
+    hemispheres = ['L', 'R']
+    filenames = [
+        'atl-MMPAll_space-{}_hemi-{}_deterministic.label.gii'
+        .format(version, hemi) for hemi in hemispheres
+    ]
+
+    files = [(op.join(dataset_name, version, f), url, opts) for f in filenames]
+    data = _fetch_files(data_dir, files=files, resume=resume, verbose=verbose)
+
+    return ANNOT(*data)
+
+
 def fetch_voneconomo(data_dir=None, url=None, resume=True, verbose=1):
     """
     Fetches von-Economo Koskinas probabilistic FreeSurfer atlas
@@ -632,8 +703,7 @@ def fetch_voneconomo(data_dir=None, url=None, resume=True, verbose=1):
     Returns
     -------
     filenames : :class:`sklearn.utils.Bunch`
-        Dictionary-like object with keys of format '{}Parcels{}Networks' where
-        corresponding values are the left/right hemisphere annotation files
+        Dictionary-like object with keys ['gcs', 'ctab', 'info']
 
     References
     ----------

netneurotools/tests/test_datasets.py

@@ -148,6 +148,13 @@ def test_fetch_hcp_standards(tmpdir):
     assert os.path.isdir(hcp)
 
 
+def test_fetch_mmpall(tmpdir):
+    mmp = datasets.fetch_mmpall(data_dir=tmpdir, verbose=0)
+    assert len(mmp) == 2
+    assert all(os.path.isfile(hemi) for hemi in mmp)
+    assert all(hasattr(mmp, attr) for attr in ('lh', 'rh'))
+
+
 def test_fetch_voneconomo(tmpdir):
     vek = datasets.fetch_voneconomo(data_dir=tmpdir, verbose=0)
     assert all(hasattr(vek, k) and len(vek[k]) == 2 for k in ['gcs', 'ctab'])