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TEST: Allow SVD columns to flip sign #3405

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Merged
merged 2 commits into from
Nov 6, 2021
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TEST: Allow SVD columns to flip sign #3405

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921c583
TEST: Simplify CompCor expected results test
effigies Nov 6, 2021
de0d541
TEST: Allow SVD columns to flip sign, validate comparator
effigies Nov 6, 2021
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108 changes: 68 additions & 40 deletions nipype/algorithms/tests/test_CompCor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,41 @@
from ..confounds import CompCor, TCompCor, ACompCor


def close_up_to_column_sign(a, b, rtol=1e-05, atol=1e-08, equal_nan=False):
"""SVD can produce sign flips on a per-column basis."""
kwargs = dict(rtol=rtol, atol=atol, equal_nan=equal_nan)
if np.allclose(a, b, **kwargs):
return True

ret = True
for acol, bcol in zip(a.T, b.T):
ret &= np.allclose(acol, bcol, **kwargs) or np.allclose(acol, -bcol, **kwargs)
if not ret:
break

return ret


@pytest.mark.parametrize(
"a, b, close",
[
([[0.1, 0.2], [0.3, 0.4]], [[-0.1, 0.2], [-0.3, 0.4]], True),
([[0.1, 0.2], [0.3, 0.4]], [[-0.1, 0.2], [0.3, -0.4]], False),
],
)
def test_close_up_to_column_sign(a, b, close):
a = np.asanyarray(a)
b = np.asanyarray(b)
assert close_up_to_column_sign(a, b) == close
# Sign flips of all columns never changes result
assert close_up_to_column_sign(a, -b) == close
assert close_up_to_column_sign(-a, b) == close
assert close_up_to_column_sign(-a, -b) == close
# Trivial case
assert close_up_to_column_sign(a, a)
assert close_up_to_column_sign(b, b)


class TestCompCor:
"""Note: Tests currently do a poor job of testing functionality"""

Expand Down Expand Up @@ -42,11 +77,11 @@ def setup_class(self, tmpdir):

def test_compcor(self):
expected_components = [
["-0.1989607212", "-0.5753813646"],
["0.5692369697", "0.5674945949"],
["-0.6662573243", "0.4675843432"],
["0.4206466244", "-0.3361270124"],
["-0.1246655485", "-0.1235705610"],
[-0.1989607212, -0.5753813646],
[0.5692369697, 0.5674945949],
[-0.6662573243, 0.4675843432],
[0.4206466244, -0.3361270124],
[-0.1246655485, -0.1235705610],
]

self.run_cc(
Expand All @@ -73,11 +108,11 @@ def test_compcor(self):

def test_compcor_variance_threshold_and_metadata(self):
expected_components = [
["-0.2027150345", "-0.4954813834"],
["0.2565929051", "0.7866217875"],
["-0.3550986008", "-0.0089784905"],
["0.7512786244", "-0.3599828482"],
["-0.4500578942", "0.0778209345"],
[-0.2027150345, -0.4954813834],
[0.2565929051, 0.7866217875],
[-0.3550986008, -0.0089784905],
[0.7512786244, -0.3599828482],
[-0.4500578942, 0.0778209345],
]
expected_metadata = {
"component": "CompCor00",
Expand Down Expand Up @@ -111,11 +146,11 @@ def test_tcompcor(self):
self.run_cc(
ccinterface,
[
["-0.1114536190", "-0.4632908609"],
["0.4566907310", "0.6983205193"],
["-0.7132557407", "0.1340170559"],
["0.5022537643", "-0.5098322262"],
["-0.1342351356", "0.1407855119"],
[-0.1114536190, -0.4632908609],
[0.4566907310, 0.6983205193],
[-0.7132557407, 0.1340170559],
[0.5022537643, -0.5098322262],
[-0.1342351356, 0.1407855119],
],
"tCompCor",
)
Expand All @@ -138,11 +173,11 @@ def test_compcor_no_regress_poly(self):
pre_filter=False,
),
[
["0.4451946442", "-0.7683311482"],
["-0.4285129505", "-0.0926034137"],
["0.5721540256", "0.5608764842"],
["-0.5367548139", "0.0059943226"],
["-0.0520809054", "0.2940637551"],
[0.4451946442, -0.7683311482],
[-0.4285129505, -0.0926034137],
[0.5721540256, 0.5608764842],
[-0.5367548139, 0.0059943226],
[-0.0520809054, 0.2940637551],
],
)

Expand Down Expand Up @@ -225,27 +260,20 @@ def run_cc(
assert os.path.getsize(expected_file) > 0

with open(ccresult.outputs.components_file, "r") as components_file:
if expected_n_components is None:
expected_n_components = min(
ccinterface.inputs.num_components, self.fake_data.shape[3]
)
header = components_file.readline().rstrip().split("\t")
components_data = np.loadtxt(components_file, delimiter="\t")

if expected_n_components is None:
expected_n_components = min(
ccinterface.inputs.num_components, self.fake_data.shape[3]
)

assert header == [
f"{expected_header}{i:02d}" for i in range(expected_n_components)
]

components_data = [line.rstrip().split("\t") for line in components_file]

# the first item will be '#', we can throw it out
header = components_data.pop(0)
expected_header = [
expected_header + "{:02d}".format(i)
for i in range(expected_n_components)
]
for i, heading in enumerate(header):
assert expected_header[i] in heading

num_got_timepoints = len(components_data)
assert num_got_timepoints == self.fake_data.shape[3]
for index, timepoint in enumerate(components_data):
assert len(timepoint) == expected_n_components
assert timepoint[:2] == expected_components[index]
assert components_data.shape == (self.fake_data.shape[3], expected_n_components)
assert close_up_to_column_sign(components_data[:, :2], expected_components)

if ccinterface.inputs.save_metadata:
expected_metadata_file = ccinterface._list_outputs()["metadata_file"]
Expand Down