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[ENH]: Allow BOLDWarper to warp between MNI spaces #302

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merged 10 commits into from
Feb 21, 2024
Merged

[ENH]: Allow BOLDWarper to warp between MNI spaces #302

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8545670
update: add support for multi MNI transformations in BOLDWarper
synchon Feb 7, 2024
783c686
update: improve tests for BOLDWarper
synchon Feb 7, 2024
9fd6e44
fix: change interpolation method for BOLDWarper to LanczosWindowedSinc
synchon Feb 8, 2024
bf3bb87
fix: correct parametrized parameters for BOLDWarper test
synchon Feb 8, 2024
1bbe60b
chore: add changelog 302.enh
synchon Feb 8, 2024
31037f7
update: improve tests for BOLDWarper preprocess to multi MNI
synchon Feb 13, 2024
8952035
chore: raise error if BOLDWarper is not needed for warping
synchon Feb 16, 2024
6db58fe
update: remove space restriction in BOLDWarper
synchon Feb 16, 2024
5a4bf8c
update: improve test in test_bold_warper.py
synchon Feb 21, 2024
37a68eb
chore: skip multi MNI warping via BOLDWarper test
synchon Feb 21, 2024
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update: improve test in test_bold_warper.py
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@synchon
synchon committed Feb 21, 2024
commit 5a4bf8c397181f8fbe083ff5f37c346c9542e3c9
16 changes: 4 additions & 12 deletions junifer/preprocess/tests/test_bold_warper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
from typing import TYPE_CHECKING, List, Tuple

import pytest
from numpy.testing import assert_array_equal, assert_raises

from junifer.datagrabber import DataladHCP1200, DMCC13Benchmark
from junifer.datareader import DefaultDataReader
Expand Down Expand Up @@ -135,18 +136,6 @@ def test_BOLDWarper_preprocess_to_native(
("f9057kp", "wave1bas", "Rest", "AP", "1"),
"MNI152NLin6Asym",
],
[
DMCC13Benchmark(
types=["BOLD"],
sessions=["wave1bas"],
tasks=["Rest"],
phase_encodings=["AP"],
runs=["1"],
native_t1w=False,
),
("f9057kp", "wave1bas", "Rest", "AP", "1"),
"MNI152NLin2009cAsym",
],
],
)
@pytest.mark.skipif(
Expand All @@ -170,6 +159,7 @@ def test_BOLDWarper_preprocess_to_multi_mni(
with datagrabber as dg:
# Read data
element_data = DefaultDataReader().fit_transform(dg[element])
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pre_xfm_data = element_data["BOLD"]["data"].get_fdata().copy()
# Preprocess data
data_type, data = BOLDWarper(reference=space).preprocess(
input=element_data["BOLD"],
Expand All @@ -178,3 +168,5 @@ def test_BOLDWarper_preprocess_to_multi_mni(
assert data_type == "BOLD"
assert isinstance(data, dict)
assert data["space"] == space
with assert_raises(AssertionError):
assert_array_equal(pre_xfm_data, data["data"])
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