diff --git a/tests/test_transform/test_affine.py b/tests/test_transform/test_affine.py index 90901c6bae8b04f22e2c3f219944aa36b453ba19..73ec93c4c246eb4e7ab4b7734eaa6cb53ff7443f 100644 --- a/tests/test_transform/test_affine.py +++ b/tests/test_transform/test_affine.py @@ -22,7 +22,7 @@ import pytest import fsl.transform as transform -datadir = op.join(op.dirname(__file__), '..', 'testdata') +datadir = op.join(op.dirname(__file__), 'testdata') def readlines(filename): diff --git a/tests/test_transform/test_flirt.py b/tests/test_transform/test_flirt.py index 98ebc08a21c64dc6b6a8e0c57cc27487c69b6a7d..c301fc75cf1739f94940f046625cf713276d9ac2 100644 --- a/tests/test_transform/test_flirt.py +++ b/tests/test_transform/test_flirt.py @@ -16,7 +16,7 @@ import fsl.utils.tempdir as tempdir from .test_affine import readlines -datadir = op.join(op.dirname(__file__), '..', 'testdata') +datadir = op.join(op.dirname(__file__), 'testdata') def test_read_write(): diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py index 2017bb55cef47f38e4e62d8dc5d67577b03ef330..59a6d7d634d73c354bfcc08c2f7a09481640c5e6 100644 --- a/tests/test_transform/test_nonlinear.py +++ b/tests/test_transform/test_nonlinear.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import itertools as it +import os.path as op import numpy as np import nibabel as nib @@ -8,6 +9,10 @@ import nibabel as nib import fsl.data.image as fslimage import fsl.transform as transform import fsl.transform.nonlinear as nonlinear +import fsl.transform.fnirt as fnirt + + +datadir = op.join(op.dirname(__file__), 'testdata') def _random_image(): @@ -191,3 +196,25 @@ def test_DisplacementField_transform(): got = absfield.transform(rcoords) assert np.all(np.isnan(got[0, :])) assert np.all(np.isclose(got[1, :], scoords[1, :])) + +def test_coefficientFieldToDisplacementField(): + + nldir = op.join(datadir, 'nonlinear') + src = op.join(nldir, 'src.nii.gz') + ref = op.join(nldir, 'ref.nii.gz') + cf = op.join(nldir, 'coefficientfield.nii.gz') + df = op.join(nldir, 'displacementfield.nii.gz') + + src = fslimage.Image(src) + ref = fslimage.Image(ref) + cf = fnirt.readFnirt(cf, src, ref) + rdf = fnirt.readFnirt(df, src, ref) + adf = nonlinear.convertDisplacementType(rdf) + + tol = dict(atol=1e-5, rtol=1e-5) + + rcnv = nonlinear.coefficientFieldToDisplacementField(cf) + acnv = nonlinear.coefficientFieldToDisplacementField(cf, dispType='absolute') + + assert np.all(np.isclose(rcnv.data, rdf.data, **tol)) + assert np.all(np.isclose(acnv.data, adf.data, **tol)) diff --git a/tests/testdata/test_transform_test_axisBounds.txt b/tests/test_transform/testdata/test_transform_test_axisBounds.txt similarity index 100% rename from tests/testdata/test_transform_test_axisBounds.txt rename to tests/test_transform/testdata/test_transform_test_axisBounds.txt diff --git a/tests/testdata/test_transform_test_compose.txt b/tests/test_transform/testdata/test_transform_test_compose.txt similarity index 100% rename from tests/testdata/test_transform_test_compose.txt rename to tests/test_transform/testdata/test_transform_test_compose.txt diff --git a/tests/testdata/test_transform_test_concat.txt b/tests/test_transform/testdata/test_transform_test_concat.txt similarity index 100% rename from tests/testdata/test_transform_test_concat.txt rename to tests/test_transform/testdata/test_transform_test_concat.txt diff --git a/tests/testdata/test_transform_test_flirtMatrixToSform.txt b/tests/test_transform/testdata/test_transform_test_flirtMatrixToSform.txt similarity index 100% rename from tests/testdata/test_transform_test_flirtMatrixToSform.txt rename to tests/test_transform/testdata/test_transform_test_flirtMatrixToSform.txt diff --git a/tests/testdata/test_transform_test_invert.txt b/tests/test_transform/testdata/test_transform_test_invert.txt similarity index 100% rename from tests/testdata/test_transform_test_invert.txt rename to tests/test_transform/testdata/test_transform_test_invert.txt diff --git a/tests/testdata/test_transform_test_scaleoffsetxform.txt b/tests/test_transform/testdata/test_transform_test_scaleoffsetxform.txt similarity index 100% rename from tests/testdata/test_transform_test_scaleoffsetxform.txt rename to tests/test_transform/testdata/test_transform_test_scaleoffsetxform.txt diff --git a/tests/testdata/test_transform_test_transform_00.txt b/tests/test_transform/testdata/test_transform_test_transform_00.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_00.txt rename to tests/test_transform/testdata/test_transform_test_transform_00.txt diff --git a/tests/testdata/test_transform_test_transform_01.txt b/tests/test_transform/testdata/test_transform_test_transform_01.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_01.txt rename to tests/test_transform/testdata/test_transform_test_transform_01.txt diff --git a/tests/testdata/test_transform_test_transform_02.txt b/tests/test_transform/testdata/test_transform_test_transform_02.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_02.txt rename to tests/test_transform/testdata/test_transform_test_transform_02.txt diff --git a/tests/testdata/test_transform_test_transform_03.txt b/tests/test_transform/testdata/test_transform_test_transform_03.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_03.txt rename to tests/test_transform/testdata/test_transform_test_transform_03.txt diff --git a/tests/testdata/test_transform_test_transform_04.txt b/tests/test_transform/testdata/test_transform_test_transform_04.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_04.txt rename to tests/test_transform/testdata/test_transform_test_transform_04.txt diff --git a/tests/testdata/test_transform_test_transform_05.txt b/tests/test_transform/testdata/test_transform_test_transform_05.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_05.txt rename to tests/test_transform/testdata/test_transform_test_transform_05.txt diff --git a/tests/testdata/test_transform_test_transform_06.txt b/tests/test_transform/testdata/test_transform_test_transform_06.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_06.txt rename to tests/test_transform/testdata/test_transform_test_transform_06.txt diff --git a/tests/testdata/test_transform_test_transform_07.txt b/tests/test_transform/testdata/test_transform_test_transform_07.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_07.txt rename to tests/test_transform/testdata/test_transform_test_transform_07.txt diff --git a/tests/testdata/test_transform_test_transform_08.txt b/tests/test_transform/testdata/test_transform_test_transform_08.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_08.txt rename to tests/test_transform/testdata/test_transform_test_transform_08.txt diff --git a/tests/testdata/test_transform_test_transform_09.txt b/tests/test_transform/testdata/test_transform_test_transform_09.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_09.txt rename to tests/test_transform/testdata/test_transform_test_transform_09.txt diff --git a/tests/testdata/test_transform_test_transform_10.txt b/tests/test_transform/testdata/test_transform_test_transform_10.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_10.txt rename to tests/test_transform/testdata/test_transform_test_transform_10.txt diff --git a/tests/testdata/test_transform_test_transform_11.txt b/tests/test_transform/testdata/test_transform_test_transform_11.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_11.txt rename to tests/test_transform/testdata/test_transform_test_transform_11.txt diff --git a/tests/testdata/test_transform_test_transform_12.txt b/tests/test_transform/testdata/test_transform_test_transform_12.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_12.txt rename to tests/test_transform/testdata/test_transform_test_transform_12.txt diff --git a/tests/testdata/test_transform_test_transform_13.txt b/tests/test_transform/testdata/test_transform_test_transform_13.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_13.txt rename to tests/test_transform/testdata/test_transform_test_transform_13.txt diff --git a/tests/testdata/test_transform_test_transform_14.txt b/tests/test_transform/testdata/test_transform_test_transform_14.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_14.txt rename to tests/test_transform/testdata/test_transform_test_transform_14.txt diff --git a/tests/testdata/test_transform_test_transform_15.txt b/tests/test_transform/testdata/test_transform_test_transform_15.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_15.txt rename to tests/test_transform/testdata/test_transform_test_transform_15.txt diff --git a/tests/testdata/test_transform_test_transform_16.txt b/tests/test_transform/testdata/test_transform_test_transform_16.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_16.txt rename to tests/test_transform/testdata/test_transform_test_transform_16.txt diff --git a/tests/testdata/test_transform_test_transform_17.txt b/tests/test_transform/testdata/test_transform_test_transform_17.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_17.txt rename to tests/test_transform/testdata/test_transform_test_transform_17.txt diff --git a/tests/testdata/test_transform_test_transform_18.txt b/tests/test_transform/testdata/test_transform_test_transform_18.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_18.txt rename to tests/test_transform/testdata/test_transform_test_transform_18.txt diff --git a/tests/testdata/test_transform_test_transform_19.txt b/tests/test_transform/testdata/test_transform_test_transform_19.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_19.txt rename to tests/test_transform/testdata/test_transform_test_transform_19.txt diff --git a/tests/testdata/test_transform_test_transform_20.txt b/tests/test_transform/testdata/test_transform_test_transform_20.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_20.txt rename to tests/test_transform/testdata/test_transform_test_transform_20.txt diff --git a/tests/testdata/test_transform_test_transform_coords.txt b/tests/test_transform/testdata/test_transform_test_transform_coords.txt similarity index 100% rename from tests/testdata/test_transform_test_transform_coords.txt rename to tests/test_transform/testdata/test_transform_test_transform_coords.txt