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ENH Brain.add_label(): find labels in subfolder #85

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Merged
merged 3 commits into from
Jan 26, 2014
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ENH Brain.add_label(): find labels in subfolder #85

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3137e98
ENH Brain.add_label(): find labels in subfolder
christianbrodbeck Jan 21, 2014
9301b87
ENH: specify relative label location using `subdir` argument
christianbrodbeck Jan 24, 2014
ffa0325
FIX add_label & DOC
christianbrodbeck Jan 26, 2014
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21 changes: 15 additions & 6 deletions surfer/viz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -991,8 +991,8 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
self.annot_list = al
self._toggle_render(True, views)

def add_label(self, label, color="crimson", alpha=1,
scalar_thresh=None, borders=False, hemi=None):
def add_label(self, label, color="crimson", alpha=1, scalar_thresh=None,
borders=False, hemi=None, subdir=None):
"""Add an ROI label to the image.

Parameters
Expand All @@ -1015,6 +1015,12 @@ def add_label(self, label, color="crimson", alpha=1,
If None, it is assumed to belong to the hemipshere being
shown. If two hemispheres are being shown, an error will
be thrown.
subdir : None | str
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Might make it a bit clearer that this is only relevant when the label is in the Freesurfer SUBJECTS_DIR tree.

If a label is specified as name, subdir can be used to indicate
that the label file is in a sub-directory of the subject's
label directory rather than in the label directory itself (e.g.
for ``$SUBJECTS_DIR/$SUBJECT/label/aparc/lh.cuneus.label``
``brain.add_label('cuneus', subdir='aparc')``).

Notes
-----
Expand All @@ -1027,10 +1033,13 @@ def add_label(self, label, color="crimson", alpha=1,
label_name = os.path.basename(filepath).split('.')[1]
else:
label_name = label
filepath = pjoin(self.subjects_dir,
self.subject_id,
'label',
".".join([hemi, label_name, 'label']))
label_fname = ".".join([hemi, label_name, 'label'])
if subdir is None:
filepath = pjoin(self.subjects_dir, self.subject_id,
'label', label_fname)
else:
filepath = pjoin(self.subjects_dir, self.subject_id,
'label', subdir, label_fname)
if not os.path.exists(filepath):
raise ValueError('Label file %s does not exist'
% filepath)
Expand Down