From 5f67d58c5679b64a9971793647563223374eb181 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 3 May 2019 13:40:48 +0100
Subject: [PATCH] TEST: Expand resample tests
---
tests/test_image_resample.py | 301 +++++++++++++++++++----------------
1 file changed, 168 insertions(+), 133 deletions(-)
diff --git a/tests/test_image_resample.py b/tests/test_image_resample.py
index 6adecb3bf..8802ded1e 100644
--- a/tests/test_image_resample.py
+++ b/tests/test_image_resample.py
@@ -2,7 +2,6 @@
import itertools as it
-import os.path as op
import numpy as np
import pytest
@@ -10,181 +9,217 @@ import pytest
import fsl.data.image as fslimage
import fsl.utils.transform as transform
import fsl.utils.image.resample as resample
-from fsl.utils.tempdir import tempdir
-
from . import make_random_image
def test_resample(seed):
- with tempdir() as td:
+ # Random base image shapes
+ for i in range(25):
- fname = op.join(td, 'test.nii')
+ shape = np.random.randint(5, 50, 3)
+ img = fslimage.Image(make_random_image(dims=shape))
- # Random base image shapes
- for i in range(25):
+ # bad shape
+ with pytest.raises(ValueError):
+ resample.resample(img, (10, 10))
+ with pytest.raises(ValueError):
+ resample.resample(img, (10, 10, 10, 10))
- shape = np.random.randint(5, 50, 3)
- make_random_image(fname, shape)
- img = fslimage.Image(fname, mmap=False)
+ # resampling to the same shape should be a no-op
+ samei, samex = resample.resample(img, shape)
+ assert np.all(samei == img[:])
+ assert np.all(samex == img.voxToWorldMat)
- # bad shape
- with pytest.raises(ValueError):
- resample.resample(img, (10, 10))
- with pytest.raises(ValueError):
- resample.resample(img, (10, 10, 10, 10))
+ # Random resampled image shapes
+ for j in range(10):
- # resampling to the same shape should be a no-op
- samei, samex = resample.resample(img, shape)
- assert np.all(samei == img[:])
- assert np.all(samex == img.voxToWorldMat)
+ rshape = np.random.randint(5, 50, 3)
+ resampled, xf = resample.resample(img, rshape, order=0)
- # Random resampled image shapes
- for j in range(10):
+ assert tuple(resampled.shape) == tuple(rshape)
- rshape = np.random.randint(5, 50, 3)
- resampled, xf = resample.resample(img, rshape, order=0)
+ # We used nearest neighbour interp, so the
+ # values in the resampled image should match
+ # corresponding values in the original. Let's
+ # check some whynot.
+ restestcoords = np.array([
+ np.random.randint(0, rshape[0], 100),
+ np.random.randint(0, rshape[1], 100),
+ np.random.randint(0, rshape[2], 100)]).T
- img.save('base.nii.gz')
- fslimage.Image(resampled, xform=xf,
- mmap=False).save('res.nii.gz')
+ resx, resy, resz = restestcoords.T
+ resvals = resampled[resx, resy, resz]
- assert tuple(resampled.shape) == tuple(rshape)
+ res2orig = transform.concat(img.worldToVoxMat, xf)
- # We used nearest neighbour interp, so the
- # values in the resampled image should match
- # corresponding values in the original. Let's
- # check some whynot.
- restestcoords = np.array([
- np.random.randint(0, rshape[0], 100),
- np.random.randint(0, rshape[1], 100),
- np.random.randint(0, rshape[2], 100)]).T
+ origtestcoords = transform.transform(restestcoords, res2orig)
- resx, resy, resz = restestcoords.T
- resvals = resampled[resx, resy, resz]
+ # remove any coordinates which are out of
+ # bounds in the original image space, or
+ # are right on a voxel boundary (where the
+ # nn interp could have gone either way), or
+ # have value == 0 in the resampled space.
+ out = ((origtestcoords < 0) |
+ (origtestcoords >= shape - 0.5) |
+ (np.isclose(np.modf(origtestcoords)[0], 0.5)))
+ out = np.any(out, axis=1) | (resvals == 0)
- res2orig = transform.concat(img.worldToVoxMat, xf)
+ origtestcoords = np.array(origtestcoords.round(), dtype=np.int)
- origtestcoords = transform.transform(restestcoords, res2orig)
+ origtestcoords = origtestcoords[~out, :]
+ restestcoords = restestcoords[ ~out, :]
- # remove any coordinates which are out of
- # bounds in the original image space, or
- # are right on a voxel boundary (where the
- # nn interp could have gone either way), or
- # have value == 0 in the resampled space.
- out = ((origtestcoords < 0) |
- (origtestcoords >= shape - 0.5) |
- (np.isclose(np.modf(origtestcoords)[0], 0.5)))
- out = np.any(out, axis=1) | (resvals == 0)
+ resx, resy, resz = restestcoords.T
+ origx, origy, origz = origtestcoords.T
- origtestcoords = np.array(origtestcoords.round(), dtype=np.int)
+ origvals = img[:][origx, origy, origz]
+ resvals = resampled[resx, resy, resz]
- origtestcoords = origtestcoords[~out, :]
- restestcoords = restestcoords[ ~out, :]
+ assert np.all(np.isclose(resvals, origvals))
- resx, resy, resz = restestcoords.T
- origx, origy, origz = origtestcoords.T
- origvals = img[:][origx, origy, origz]
- resvals = resampled[resx, resy, resz]
+def test_resample_4d(seed):
- assert np.all(np.isclose(resvals, origvals))
+ # resample one volume
+ img = fslimage.Image(make_random_image(dims=(10, 10, 10, 10)))
+ slc = (slice(None), slice(None), slice(None), 3)
+ resampled = resample.resample(img, img.shape[:3], slc)[0]
+ assert np.all(resampled == img[..., 3])
- del img
- img = None
+ # resample up
+ resampled = resample.resample(img, (15, 15, 15), slc)[0]
+ assert tuple(resampled.shape) == (15, 15, 15)
+ # resample down
+ resampled = resample.resample(img, (5, 5, 5), slc)[0]
+ assert tuple(resampled.shape) == (5, 5, 5)
-def test_resample_4d(seed):
+ # resample the entire image
+ resampled = resample.resample(img, (15, 15, 15, 10), None)[0]
+ assert tuple(resampled.shape) == (15, 15, 15, 10)
- fname = 'test.nii.gz'
+ resampled = resample.resample(img, (5, 5, 5, 10), None)[0]
+ assert tuple(resampled.shape) == (5, 5, 5, 10)
- with tempdir():
+ # resample along the fourth dim
+ resampled = resample.resample(img, (15, 15, 15, 15), None)[0]
+ assert tuple(resampled.shape) == (15, 15, 15, 15)
- make_random_image(fname, (10, 10, 10, 10))
+ resampled = resample.resample(img, (5, 5, 5, 15), None)[0]
+ assert tuple(resampled.shape) == (5, 5, 5, 15)
- # resample one volume
- img = fslimage.Image(fname)
- slc = (slice(None), slice(None), slice(None), 3)
- resampled = resample.resample(img, img.shape[:3], slc)[0]
- assert np.all(resampled == img[..., 3])
- # resample up
- resampled = resample.resample(img, (15, 15, 15), slc)[0]
- assert tuple(resampled.shape) == (15, 15, 15)
+def test_resample_origin(seed):
- # resample down
- resampled = resample.resample(img, (5, 5, 5), slc)[0]
- assert tuple(resampled.shape) == (5, 5, 5)
+ img = fslimage.Image(make_random_image(dims=(10, 10, 10)))
+
+ # with origin='corner', image
+ # bounding boxes should match
+ for i in range(25):
+ 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)
+ assert np.all(np.isclose(imgb, resb, rtol=1e-5, atol=1e-5))
+
+ # with origin='centre' image
+ # bounding boxes should be offset
+ # by (size_resampled - size_orig) / 2
+ for i in range(25):
+ shape = np.random.randint(5, 50, 3)
+ 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))
+ assert np.all(np.isclose(imgb, resb + off, rtol=1e-5, atol=1e-5))
+
+ # with origin='corner', using
+ # linear interp, when we down-
+ # sample an image to a shape
+ # that divides evenly into the
+ # original shape, a downsampled
+ # voxel should equal the average
+ # of the original voxels inside
+ # it.
+ res = resample.resample(img, (5, 5, 5), smooth=False, origin='corner')[0]
+ for x, y, z in it.product(range(5), range(5), range(5)):
+ block = img[x * 2: x * 2 + 2,
+ y * 2: y * 2 + 2,
+ z * 2: z * 2 + 2]
+ assert np.isclose(res[x, y, z], block.mean())
- # resample the entire image
- resampled = resample.resample(img, (15, 15, 15, 10), None)[0]
- assert tuple(resampled.shape) == (15, 15, 15, 10)
- resampled = resample.resample(img, (5, 5, 5, 10), None)[0]
- assert tuple(resampled.shape) == (5, 5, 5, 10)
+def test_resampleToPixdims():
- # resample along the fourth dim
- resampled = resample.resample(img, (15, 15, 15, 15), None)[0]
- assert tuple(resampled.shape) == (15, 15, 15, 15)
+ img = fslimage.Image(make_random_image(dims=(10, 10, 10)))
+ imglo, imghi = transform.axisBounds(img.shape, img.voxToWorldMat)
+ oldpix = np.array(img.pixdim, dtype=np.float)
+ oldshape = np.array(img.shape, dtype=np.float)
- resampled = resample.resample(img, (5, 5, 5, 15), None)[0]
- assert tuple(resampled.shape) == (5, 5, 5, 15)
+ for i, origin in it.product(range(25), ('centre', 'corner')):
- del img
- del resampled
- img = None
- resampled = None
+ # random pixdims in the range 0.1 - 5.0
+ newpix = 0.1 + 4.9 * np.random.random(3)
+ expshape = np.round(oldshape * (oldpix / newpix))
+ res = resample.resampleToPixdims(img, newpix, origin=origin)
+ res = fslimage.Image(res[0], xform=res[1])
+ reslo, reshi = transform.axisBounds(res.shape, res.voxToWorldMat)
+ resfov = reshi - reslo
+ expfov = newpix * res.shape
-def test_resample_origin(seed):
- with tempdir() as td:
- fname = op.join(td, 'test.nii')
-
- make_random_image(fname, (10, 10, 10))
- img = fslimage.Image(fname)
-
- # with origin='corner', image
- # bounding boxes should match
- for i in range(25):
- 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)
- assert np.all(np.isclose(imgb, resb, rtol=1e-5, atol=1e-5))
-
- # with origin='centre' image
- # bounding boxes should be offset
- # by (size_resampled - size_orig) / 2
- for i in range(25):
- shape = np.random.randint(5, 50, 3)
- 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))
- assert np.all(np.isclose(imgb, resb + off, rtol=1e-5, atol=1e-5))
-
- # with origin='corner', using
- # linear interp, when we down-
- # sample an image to a shape
- # that divides evenly into the
- # original shape, a downsampled
- # voxel should equal the average
- # of the original voxels inside
- # it.
- res = resample.resample(img, (5, 5, 5), smooth=False, origin='corner')[0]
- for x, y, z in it.product(range(5), range(5), range(5)):
- block = img[x * 2: x * 2 + 2,
- y * 2: y * 2 + 2,
- z * 2: z * 2 + 2]
- assert np.isclose(res[x, y, z], block.mean())
+ assert np.all(np.isclose(res.shape, expshape))
+ assert np.all(np.isclose(res.pixdim, newpix))
+ assert np.all(np.isclose(resfov, expfov, rtol=1e-2, atol=1e-2))
+ if origin == 'corner':
+ assert np.all(np.isclose(imglo, reslo))
+ assert np.all(np.isclose(reshi, reslo + expfov,
+ rtol=1e-2, atol=1e-2))
-def test_resampleToPixdims():
- pass
def test_resampleToReference():
- pass
+
+ def random_v2w():
+ return transform.compose(
+ 0.25 + 4.75 * np.random.random(3),
+ -50 + 100 * np.random.random(3),
+ -np.pi + 2 * np.pi * np.random.random(3))
+
+ # Basic test - output has same
+ # dimensions/space as reference
+ for i in range(25):
+
+ ishape = np.random.randint(5, 50, 3)
+ rshape = np.random.randint(5, 50, 3)
+ iv2w = random_v2w()
+ rv2w = random_v2w()
+ img = fslimage.Image(make_random_image(dims=ishape, xform=iv2w))
+ ref = fslimage.Image(make_random_image(dims=rshape, xform=rv2w))
+ res = resample.resampleToReference(img, ref)
+ res = fslimage.Image(res[0], header=ref.header)
+
+ assert res.sameSpace(ref)
+
+ # More specific test - output
+ # data gets transformed correctly
+ # into reference space
+
+ img = np.zeros((5, 5, 5), dtype=np.float)
+ img[1, 1, 1] = 1
+ img = fslimage.Image(img)
+
+ refv2w = transform.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)
+
+ exp = np.zeros((5, 5, 5), dtype=np.float)
+ exp[2, 2, 2] = 1
+
+ assert np.all(np.isclose(res[0], exp))
--
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