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[FIX] get_clusters_table: ensure input is 3D and accept filenames #2701

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merged 3 commits into from Feb 18, 2021
Merged

[FIX] get_clusters_table: ensure input is 3D and accept filenames #2701

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44cc9ba
ensure input is 3d and accept filenames
jdkent Feb 17, 2021
536e594
add extra dimension to data
jdkent Feb 17, 2021
e2d92e1
fix style
jdkent Feb 17, 2021
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3 changes: 3 additions & 0 deletions nilearn/reporting/_get_clusters_table.py
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Expand Up @@ -14,6 +14,7 @@

from nilearn.image import get_data
from nilearn.image.resampling import coord_transform
from nilearn._utils import check_niimg_3d

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def _local_max(data, affine, min_distance):
Expand Down Expand Up @@ -159,6 +160,8 @@ def get_clusters_table(stat_img, stat_threshold, cluster_threshold=None,
"""
cols = ['Cluster ID', 'X', 'Y', 'Z', 'Peak Stat', 'Cluster Size (mm3)']

# check that stat_img is niimg-like object and 3D
stat_img = check_niimg_3d(stat_img)
# If cluster threshold is used, there is chance that stat_map will be
# modified, therefore copy is needed
if cluster_threshold is None:
Expand Down
14 changes: 13 additions & 1 deletion nilearn/reporting/tests/test_reporting.py
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Expand Up @@ -69,7 +69,7 @@ def test_local_max():
assert np.all(np.isnan(vals))


def test_get_clusters_table():
def test_get_clusters_table(tmp_path):
shape = (9, 10, 11)
data = np.zeros(shape)
data[2:4, 5:7, 6:8] = 5.
Expand All @@ -87,6 +87,18 @@ def test_get_clusters_table():
cluster_table = get_clusters_table(stat_img, 4, 9)
assert len(cluster_table) == 0

# test with filename
fname = str(tmp_path / "stat_img.nii.gz")
stat_img.to_filename(fname)
cluster_table = get_clusters_table(fname, 4, 0)
assert len(cluster_table) == 1

# test with extra dimension
data_extra_dim = data[..., np.newaxis]
stat_img_extra_dim = nib.Nifti1Image(data_extra_dim, np.eye(4))
cluster_table = get_clusters_table(stat_img_extra_dim, 4, 0)
assert len(cluster_table) == 1


def test_get_clusters_table_not_modifying_stat_image():
shape = (9, 10, 11)
Expand Down