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Allow return of labelids in find_parcel_centroids #113

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Allow return of labelids in find_parcel_centroids #113

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18 changes: 15 additions & 3 deletions netneurotools/freesurfer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,8 @@ def _decode_list(vals):


def find_parcel_centroids(*, lhannot, rhannot, method='surface',
version='fsaverage', surf='sphere', drop=None):
version='fsaverage', surf='sphere', drop=None,
get_labelids=False):
"""
Returns vertex coords corresponding to centroids of parcels in annotations

Expand Down Expand Up @@ -144,6 +145,8 @@ def find_parcel_centroids(*, lhannot, rhannot, method='surface',
Specifies regions in {lh,rh}annot for which the parcel centroid should
not be calculated. If not specified, centroids for parcels defined in
`netneurotools.freesurfer.FSIGNORE` are not calculated. Default: None
get_labelids: boolean, optional
If True, return a list of label ids corresponding to each centroid

Returns
-------
Expand All @@ -153,6 +156,9 @@ def find_parcel_centroids(*, lhannot, rhannot, method='surface',
hemiid : (N,) numpy.ndarray
Array denoting hemisphere designation of coordinates in `centroids`,
where `hemiid=0` denotes the left and `hemiid=1` the right hemisphere
labelid : (N,) numpy.ndarray
Only returned if get_labelids == True. Array denoting label of coordinates in
`centroids`

Notes
-----
Expand Down Expand Up @@ -189,7 +195,7 @@ def find_parcel_centroids(*, lhannot, rhannot, method='surface',

surfaces = fetch_fsaverage(version)[surf]

centroids, hemiid = [], []
centroids, hemiid, labelid = [], [], []
for n, (annot, surf) in enumerate(zip([lhannot, rhannot], surfaces)):
vertices, faces = read_geometry(surf)
labels, ctab, names = read_annot(annot)
Expand All @@ -207,8 +213,14 @@ def find_parcel_centroids(*, lhannot, rhannot, method='surface',
roi = _geodesic_parcel_centroid(vertices, faces, inds)
centroids.append(roi)
hemiid.append(n)
if get_labelids:
labelid.append(lab)

return np.row_stack(centroids), np.asarray(hemiid)
main = np.row_stack(centroids), np.asarray(hemiid),
if get_labelids:
return *main, np.asarray(labelid)

return main


def _geodesic_parcel_centroid(vertices, faces, inds):
Expand Down