From 552f07d7163e250be3bbb9e49e5d14fafc188090 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 2 May 2019 23:12:47 +0100
Subject: [PATCH] TEST: Resample tests separated out into separate module. Add
to transform.decompose test
---
tests/test_image.py | 167 ------------------------------
tests/test_image_resample.py | 190 +++++++++++++++++++++++++++++++++++
tests/test_transform.py | 11 ++
3 files changed, 201 insertions(+), 167 deletions(-)
create mode 100644 tests/test_image_resample.py
diff --git a/tests/test_image.py b/tests/test_image.py
index c97afa047..85dde7c66 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -1065,173 +1065,6 @@ def _test_Image_save(imgtype):
img2 = None
-def test_image_resample(seed):
-
- with tempdir() as td:
-
- fname = op.join(td, 'test.nii')
-
- # Random base image shapes
- for i in range(25):
-
- shape = np.random.randint(5, 50, 3)
- make_random_image(fname, shape)
- img = fslimage.Image(fname, mmap=False)
-
- # bad shape
- with pytest.raises(ValueError):
- img.resample((10, 10))
- with pytest.raises(ValueError):
- img.resample((10, 10, 10, 10))
-
- # resampling to the same shape should be a no-op
- samei, samex = img.resample(shape)
- assert np.all(samei == img[:])
- assert np.all(samex == img.voxToWorldMat)
-
- # Random resampled image shapes
- for j in range(10):
-
- rshape = np.random.randint(5, 50, 3)
- resampled, xf = img.resample(rshape, order=0)
-
- img.save('base.nii.gz')
- fslimage.Image(resampled, xform=xf,
- mmap=False).save('res.nii.gz')
-
- assert tuple(resampled.shape) == tuple(rshape)
-
- # 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
-
- resx, resy, resz = restestcoords.T
- resvals = resampled[resx, resy, resz]
-
- res2orig = transform.concat(img.worldToVoxMat, xf)
-
- origtestcoords = transform.transform(restestcoords, res2orig)
-
- # 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)
-
- origtestcoords = np.array(origtestcoords.round(), dtype=np.int)
-
- origtestcoords = origtestcoords[~out, :]
- restestcoords = restestcoords[ ~out, :]
-
- resx, resy, resz = restestcoords.T
- origx, origy, origz = origtestcoords.T
-
- origvals = img[:][origx, origy, origz]
- resvals = resampled[resx, resy, resz]
-
- assert np.all(np.isclose(resvals, origvals))
-
- del img
- img = None
-
-
-def test_image_resample_4d(seed):
-
- fname = 'test.nii.gz'
-
- with tempdir():
-
- make_random_image(fname, (10, 10, 10, 10))
-
- # resample one volume
- img = fslimage.Image(fname)
- slc = (slice(None), slice(None), slice(None), 3)
- resampled = img.resample(img.shape[:3], slc)[0]
- assert np.all(resampled == img[..., 3])
-
- # resample up
- resampled = img.resample((15, 15, 15), slc)[0]
- assert tuple(resampled.shape) == (15, 15, 15)
-
- # resample down
- resampled = img.resample((5, 5, 5), slc)[0]
- assert tuple(resampled.shape) == (5, 5, 5)
-
- # resample the entire image
- resampled = img.resample((15, 15, 15, 10), None)[0]
- assert tuple(resampled.shape) == (15, 15, 15, 10)
-
- resampled = img.resample((5, 5, 5, 10), None)[0]
- assert tuple(resampled.shape) == (5, 5, 5, 10)
-
- # resample along the fourth dim
- resampled = img.resample((15, 15, 15, 15), None)[0]
- assert tuple(resampled.shape) == (15, 15, 15, 15)
-
- resampled = img.resample((5, 5, 5, 15), None)[0]
- assert tuple(resampled.shape) == (5, 5, 5, 15)
-
- del img
- del resampled
- img = None
- resampled = None
-
-
-def test_Image_resample_offset(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 = img.resample(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 = img.resample(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 = img.resample((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())
-
-
def test_Image_init_xform_nifti1(): _test_Image_init_xform(1)
def test_Image_init_xform_nifti2(): _test_Image_init_xform(2)
def _test_Image_init_xform(imgtype):
diff --git a/tests/test_image_resample.py b/tests/test_image_resample.py
new file mode 100644
index 000000000..6adecb3bf
--- /dev/null
+++ b/tests/test_image_resample.py
@@ -0,0 +1,190 @@
+#!/usr/bin/env python
+
+
+import itertools as it
+import os.path as op
+import numpy as np
+
+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:
+
+ fname = op.join(td, 'test.nii')
+
+ # Random base image shapes
+ for i in range(25):
+
+ shape = np.random.randint(5, 50, 3)
+ make_random_image(fname, shape)
+ img = fslimage.Image(fname, mmap=False)
+
+ # bad shape
+ with pytest.raises(ValueError):
+ resample.resample(img, (10, 10))
+ with pytest.raises(ValueError):
+ resample.resample(img, (10, 10, 10, 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)
+
+ # Random resampled image shapes
+ for j in range(10):
+
+ rshape = np.random.randint(5, 50, 3)
+ resampled, xf = resample.resample(img, rshape, order=0)
+
+ img.save('base.nii.gz')
+ fslimage.Image(resampled, xform=xf,
+ mmap=False).save('res.nii.gz')
+
+ assert tuple(resampled.shape) == tuple(rshape)
+
+ # 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
+
+ resx, resy, resz = restestcoords.T
+ resvals = resampled[resx, resy, resz]
+
+ res2orig = transform.concat(img.worldToVoxMat, xf)
+
+ origtestcoords = transform.transform(restestcoords, res2orig)
+
+ # 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)
+
+ origtestcoords = np.array(origtestcoords.round(), dtype=np.int)
+
+ origtestcoords = origtestcoords[~out, :]
+ restestcoords = restestcoords[ ~out, :]
+
+ resx, resy, resz = restestcoords.T
+ origx, origy, origz = origtestcoords.T
+
+ origvals = img[:][origx, origy, origz]
+ resvals = resampled[resx, resy, resz]
+
+ assert np.all(np.isclose(resvals, origvals))
+
+ del img
+ img = None
+
+
+def test_resample_4d(seed):
+
+ fname = 'test.nii.gz'
+
+ with tempdir():
+
+ make_random_image(fname, (10, 10, 10, 10))
+
+ # 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)
+
+ # resample down
+ resampled = resample.resample(img, (5, 5, 5), slc)[0]
+ assert tuple(resampled.shape) == (5, 5, 5)
+
+ # 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)
+
+ # resample along the fourth dim
+ resampled = resample.resample(img, (15, 15, 15, 15), None)[0]
+ assert tuple(resampled.shape) == (15, 15, 15, 15)
+
+ resampled = resample.resample(img, (5, 5, 5, 15), None)[0]
+ assert tuple(resampled.shape) == (5, 5, 5, 15)
+
+ del img
+ del resampled
+ img = None
+ resampled = None
+
+
+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())
+
+
+def test_resampleToPixdims():
+ pass
+
+
+def test_resampleToReference():
+ pass
diff --git a/tests/test_transform.py b/tests/test_transform.py
index a6688b85f..70b86019a 100644
--- a/tests/test_transform.py
+++ b/tests/test_transform.py
@@ -268,6 +268,17 @@ def test_compose_and_decompose():
assert np.all(np.isclose(rotat, rots))
assert np.all(np.isclose(rotaf, rmat))
+ # decompose should accept a 3x3
+ # affine, and return translations of 0
+ transform.decompose(xform[:3, :3])
+ sc, of, rot = transform.decompose(xform[:3, :3])
+ sc, of, rot = np.array(sc), np.array(of), np.array(rot)
+ assert np.all(np.isclose(sc, [1, 1, 1]))
+ assert np.all(np.isclose(of, [0, 0, 0]))
+ assert np.all(np.isclose(rot, rots))
+
+
+
def test_rotMatToAxisAngles(seed):
--
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