def test_prepare_searchlight_mvpa_data():
processed_data, labels = io.prepare_searchlight_mvpa_data(dir, extension, epoch_file)
expected_searchlight_processed_data = np.load(
os.path.join(os.path.dirname(__file__), "data/expected_searchlight_processed_data.npy")
)
for idx in range(len(processed_data)):
assert np.allclose(
processed_data[idx], expected_searchlight_processed_data[idx]
), "raw data do not match in test_prepare_searchlight_mvpa_data"
assert np.array_equal(labels, expected_labels), "the labels do not match in test_prepare_searchlight_mvpa_data"
data_dir = sys.argv[1]
extension = sys.argv[2]
mask_file = sys.argv[3]
epoch_file = sys.argv[4]
# all MPI processes read the mask; the mask file is small
mask_img = nib.load(mask_file)
mask = mask_img.get_data().astype(np.bool)
data = None
labels = None
if MPI.COMM_WORLD.Get_rank()==0:
logger.info(
'mask size: %d' %
np.sum(mask)
)
data, labels = io.prepare_searchlight_mvpa_data(data_dir, extension, epoch_file)
# the following line is an example to leaving a subject out
#epoch_info = [x for x in epoch_info if x[1] != 0]
num_subjs = int(sys.argv[5])
# create a Searchlight object
sl = Searchlight(sl_rad=1)
mvs = MVPAVoxelSelector(data, mask, labels, num_subjs, sl)
clf = svm.SVC(kernel='linear', shrinking=False, C=1)
# only rank 0 has meaningful return values
score_volume, results = mvs.run(clf)
# this output is just for result checking
if MPI.COMM_WORLD.Get_rank()==0:
score_volume = np.nan_to_num(score_volume.astype(np.float))
io.write_nifti_file(score_volume, mask_img.affine, 'result_score.nii.gz')
seq_volume = np.zeros(mask.shape, dtype=np.int)
seq = np.zeros(len(results), dtype=np.int)