diff --git a/tests/test_image_resample.py b/tests/test_image_resample.py index 8fb488760ed74a14a0714c92d7815ac2a87f43f6..6961e7aa71c63a09d21f93ca5e128d8622b678a9 100644 --- a/tests/test_image_resample.py +++ b/tests/test_image_resample.py @@ -9,13 +9,13 @@ import pytest import scipy.ndimage as ndimage import fsl.data.image as fslimage -import fsl.utils.transform as transform +import fsl.transform.affine as affine import fsl.utils.image.resample as resample from . import make_random_image def random_affine(): - return transform.compose( + return affine.compose( 0.25 + 4.75 * np.random.random(3), -50 + 100 * np.random.random(3), -np.pi + 2 * np.pi * np.random.random(3)) @@ -61,9 +61,9 @@ def test_resample(seed): resx, resy, resz = restestcoords.T resvals = resampled[resx, resy, resz] - res2orig = transform.concat(img.worldToVoxMat, xf) + res2orig = affine.concat(img.worldToVoxMat, xf) - origtestcoords = transform.transform(restestcoords, res2orig) + origtestcoords = affine.transform(restestcoords, res2orig) # remove any coordinates which are out of # bounds in the original image space, or @@ -130,8 +130,8 @@ def test_resample_origin(seed): shape = np.random.randint(5, 50, 3) res = resample.resample(img, shape, origin='corner') res = fslimage.Image(res[0], xform=res[1]) - imgb = transform.axisBounds(img.shape, img.voxToWorldMat) - resb = transform.axisBounds(res.shape, res.voxToWorldMat) + imgb = affine.axisBounds(img.shape, img.voxToWorldMat) + resb = affine.axisBounds(res.shape, res.voxToWorldMat) assert np.all(np.isclose(imgb, resb, rtol=1e-5, atol=1e-5)) # with origin='centre' image @@ -142,8 +142,8 @@ def test_resample_origin(seed): res = resample.resample(img, shape, origin='centre') res = fslimage.Image(res[0], xform=res[1]) off = (np.array(img.shape) / np.array(res.shape) - 1) / 2 - imgb = np.array(transform.axisBounds(img.shape, img.voxToWorldMat)) - resb = np.array(transform.axisBounds(res.shape, res.voxToWorldMat)) + imgb = np.array(affine.axisBounds(img.shape, img.voxToWorldMat)) + resb = np.array(affine.axisBounds(res.shape, res.voxToWorldMat)) assert np.all(np.isclose(imgb, resb + off, rtol=1e-5, atol=1e-5)) # with origin='corner', using @@ -165,7 +165,7 @@ def test_resample_origin(seed): def test_resampleToPixdims(): img = fslimage.Image(make_random_image(dims=(10, 10, 10))) - imglo, imghi = transform.axisBounds(img.shape, img.voxToWorldMat) + imglo, imghi = affine.axisBounds(img.shape, img.voxToWorldMat) oldpix = np.array(img.pixdim, dtype=np.float) oldshape = np.array(img.shape, dtype=np.float) @@ -177,7 +177,7 @@ def test_resampleToPixdims(): res = resample.resampleToPixdims(img, newpix, origin=origin) res = fslimage.Image(res[0], xform=res[1]) - reslo, reshi = transform.axisBounds(res.shape, res.voxToWorldMat) + reslo, reshi = affine.axisBounds(res.shape, res.voxToWorldMat) resfov = reshi - reslo expfov = newpix * res.shape @@ -219,7 +219,7 @@ def test_resampleToReference2(): img[1, 1, 1] = 1 img = fslimage.Image(img) - refv2w = transform.scaleOffsetXform([1, 1, 1], [-1, -1, -1]) + refv2w = affine.scaleOffsetXform([1, 1, 1], [-1, -1, -1]) ref = np.zeros((5, 5, 5), dtype=np.float) ref = fslimage.Image(ref, xform=refv2w) res = resample.resampleToReference(img, ref, order=0) @@ -235,7 +235,7 @@ def test_resampleToReference3(): # Test resampling image to ref # with mismatched dimensions imgdata = np.random.randint(0, 65536, (5, 5, 5)) - img = fslimage.Image(imgdata, xform=transform.scaleOffsetXform( + img = fslimage.Image(imgdata, xform=affine.scaleOffsetXform( (2, 2, 2), (0.5, 0.5, 0.5))) # reference/expected data when @@ -270,7 +270,7 @@ def test_resampleToReference4(): # the image and ref are out of # alignment, but this affine # will bring them into alignment - img2ref = transform.scaleOffsetXform([2, 2, 2], [10, 10, 10]) + img2ref = affine.scaleOffsetXform([2, 2, 2], [10, 10, 10]) imgdata = np.random.randint(0, 65536, (5, 5, 5)) refdata = np.zeros((5, 5, 5))