def test_check_atlases():
atlases = atlasreader.check_atlases('all')
assert len(atlases) == len(atlasreader._ATLASES)
atlases = atlasreader.check_atlases('default')
assert len(atlases) == len(atlasreader._DEFAULT)
atlases = atlasreader.check_atlases(['aal', 'destrieux'])
assert atlasreader.check_atlases(atlases) == atlases
assert atlasreader.check_atlases(atlases[0]) == atlases[0]
def main():
"""
The primary entrypoint for calling atlas reader via the command line
All parameters are read via argparse, so this should only be called from
the command line!
"""
opts = _get_parser()
create_output(opts.filename,
atlas=check_atlases(opts.atlas),
voxel_thresh=opts.voxel_thresh,
cluster_extent=opts.cluster_extent,
prob_thresh=opts.prob_thresh,
outdir=opts.outdir)
def queryatlas_main():
"""
The primary entrypoint for querying atlases via the command line
All parameters are read via argparse, so this should only be called from
the command line!
"""
opts = _queryatlas_parser()
print('{0:<25} {1:<25}\n{2:<25} {2:<25}'.format('Atlas', 'Label',
'=' * 10))
for atlas in check_atlases(opts.atlas):
label = read_atlas_peak(atlas, opts.coordinate, opts.prob_thresh)
if isinstance(label, list):
label = '\n{}'.format(' ' * 26).join(
['{:>2}% {}'.format(*e) for e in label])
print('{:<25} {}'.format(atlas.atlas, label))