From 5fa576c10b2cef55383018fb9ee37a257abe93cb Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 16 Jun 2023 15:46:39 +0100
Subject: [PATCH] Remove avwutils unit tests - they have been added to the
fsl/avwutils project
---
unit_tests/avwutils/fix_orient/feedsRun | 166 -----------
unit_tests/avwutils/fslchpixdim/feedsRun | 58 ----
unit_tests/avwutils/fslcomplex/feedsRun | 132 ---------
unit_tests/avwutils/fslcreatehd/feedsRun | 265 ------------------
unit_tests/avwutils/fslcreatehd/mni2mm.xml | 44 ---
.../{avwutils => flirt}/avscale/feedsRun | 0
6 files changed, 665 deletions(-)
delete mode 100755 unit_tests/avwutils/fix_orient/feedsRun
delete mode 100755 unit_tests/avwutils/fslchpixdim/feedsRun
delete mode 100755 unit_tests/avwutils/fslcomplex/feedsRun
delete mode 100755 unit_tests/avwutils/fslcreatehd/feedsRun
delete mode 100644 unit_tests/avwutils/fslcreatehd/mni2mm.xml
rename unit_tests/{avwutils => flirt}/avscale/feedsRun (100%)
diff --git a/unit_tests/avwutils/fix_orient/feedsRun b/unit_tests/avwutils/fix_orient/feedsRun
deleted file mode 100755
index 0e0e575..0000000
--- a/unit_tests/avwutils/fix_orient/feedsRun
+++ /dev/null
@@ -1,166 +0,0 @@
-#!/usr/bin/env fslpython
-"""Test the standard recipe for fixing a broken orientation, from "The labels
-in FSLView are wrong or missing and no conversion to NIfTI can fix this", on
-this page:
-
-https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
-
- If this really cannot be fixed at the conversion stage, then it is
- possible to fix by the follow (only to be attempted after reading the
- following section on background information on NIfTI orientation):
- fslorient -deleteorient imagename ; fslswapdim imagename a b c imagename ;
- fslorient -setqformcode 1 imagename ; where a b c need to be chosen,
- usually by trial and error, so that the image after this is in the same
- orientation (as viewed in FSLView) as the MNI152 images. However, unless
- you have some way of telling left from right in the image (e.g. by a
- vitamin capsule or clearly known structural asymmetry) this method can
- easily result in an incorrect left-right labelling and so should not be
- attempted.
-
-The recipe involves:
-
- 1. resetting the image affines
-
- 2. transposing the data array until it is in a
- RAS orientation
-
- 3. Enabling the qform affine which, after step
- 1, should be a diagonal matrix with pixdims
- as scaling parameters.
-
-Specifically, the recipe is as follows:
-
- # 1. clear the sform/qform affines
- fslorient -deleteorient image
-
- # 2. rotate the data into RAS orientation (exact
- # command depends on original data orientation)
- fslswapdim image x z y image
-
- # 3. reset the qform code. The qform should be
- # a diagonal matrix, and the image data array
- # should be in RAS orientation, so after this
- # step the image should be labelled correctly.
- fslorient -setqformcode 1 image
-
-
-This recipe makes some key assumptions:
-
- - fslorient -deleteorient (step 1) deleting/
- clearing the affines - the qform must be
- reset to be a scaling matrix.
-
- - fslswapdim (step 2) not touching the affines
- when the s/qform codes are 0
-
-These are required so that, in step 3, the qform is a diagonal matrix with
-correct scaling paramaters.
-
-Some bugs were introduced in FSL 6.0.0 (fixed in FSL 6.0.6) which broke the
-above assumptions:
-
- - fslorient -deleteorient was not clearing the original
- affines
- - fslswapdim was applying the rotations/flips to both the
- data, and to the s/qforms, even if the s/qform codes were
- set to 0.
-"""
-
-import numpy as np
-import nibabel as nib
-import os
-import subprocess as sp
-import shlex
-import sys
-import traceback
-
-def sprun(cmd):
- sp.run(shlex.split(cmd), check=True)
-
-
-# Test the original recipe for fixing the
-# orientation of an image, as described above
-def test_fix_orient():
-
- data = np.random.random((10, 10, 10))
- orig_qform = np.array([[2, 0, 0, 10],
- [0, 2, 0, -20],
- [0, 0, 2, 50],
- [0, 0, 0, 1]])
- image = nib.Nifti1Image(data, np.eye(4))
- image.set_sform(np.eye(4), 0)
- image.set_qform(orig_qform, 1)
-
- image.to_filename('orig.nii.gz')
- sprun('imcp orig cleared')
- sprun('fslorient -deleteorient cleared')
- sprun('fslswapdim cleared x z y swapped')
- sprun('imcp swapped fixed')
- sprun('fslorient -setqformcode 1 fixed')
-
- fixed = nib.load('fixed.nii.gz')
-
- new_data = fixed.get_fdata()
- new_qform, qcode = fixed.get_qform(coded=True)
- _, scode = fixed.get_sform(coded=True)
-
- # new qform should be a scaling matrix (not
- # necessarily equivalent to the original
- assert qcode == 1
- assert scode == 0
- assert np.all(np.isclose(new_qform, np.diag([2, 2, 2, 1])))
- assert np.all(np.isclose(new_data, data.transpose((0, 2, 1))))
-
-
-# An alternate strategy which involves
-# explicitly clobbering the qform
-def test_fix_orient_alternate():
- # original qform
- data = np.random.random((10, 10, 10))
- orig_qform = np.array([[2, 0, 0, 10],
- [0, 2, 0, -20],
- [0, 0, 2, 50],
- [0, 0, 0, 1]])
- image = nib.Nifti1Image(data, np.eye(4))
- image.set_sform(np.eye(4), 0)
- image.set_qform(orig_qform, 1)
-
- image.to_filename('orig.nii.gz')
- sprun('imcp orig cleared')
- sprun('fslorient -deleteorient cleared')
- sprun('fslswapdim cleared x z y swapped')
- sprun('imcp swapped fixed1')
- sprun('fslorient -setqform 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 fixed1')
- sprun('imcp fixed1 fixed')
- sprun('fslorient -setqformcode 1 fixed')
-
- fixed = nib.load('fixed.nii.gz')
-
- new_data = fixed.get_fdata()
- new_qform, qcode = fixed.get_qform(coded=True)
- _, scode = fixed.get_sform(coded=True)
-
- # new qform should be a scaling matrix (not
- # necessarily equivalent to the original
- assert qcode == 1
- assert scode == 0
- assert np.all(np.isclose(new_qform, np.diag([2, 2, 2, 1])))
- assert np.all(np.isclose(new_data, data.transpose((0, 2, 1))))
-
-
-if __name__ == '__main__':
- tests = [test_fix_orient,
- test_fix_orient_alternate]
-
- result = 0
- for test in tests:
- try:
- os.chdir(sys.argv[1])
- test()
- print(f'\nTest {test.__name__} PASSED')
- except Exception as e:
- print(f'\nTest {test.__name__} FAILED')
- traceback.print_exc()
- result = 1
-
- sys.exit(result)
diff --git a/unit_tests/avwutils/fslchpixdim/feedsRun b/unit_tests/avwutils/fslchpixdim/feedsRun
deleted file mode 100755
index 56bcee4..0000000
--- a/unit_tests/avwutils/fslchpixdim/feedsRun
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env fslpython
-
-import os
-import sys
-import subprocess as sp
-
-import numpy as np
-import nibabel as nib
-
-
-def create_image(shape, pixdim):
- pixdim = list(pixdim)
- data = np.random.random(shape).astype(np.float32)
- hdr = nib.Nifti1Header()
-
- hdr.set_data_dtype(np.float32)
- hdr.set_data_shape(shape)
- hdr.set_zooms(pixdim[:len(shape)])
-
- return nib.Nifti1Image(data, np.eye(4), hdr)
-
-
-def check_image(origimg, changedimg, exppixdim):
-
- gotshape = changedimg.shape
- gotpixdim = list(changedimg.header.get_zooms())
- gotdata = changedimg.get_fdata()
-
- assert origimg.shape == gotshape
- assert gotpixdim == exppixdim
- assert np.all(origimg.get_fdata() == gotdata)
-
-
-def run_tests():
- # (image shape, command, exppixdims)
- tests = [
- ((5, 5, 5), '2 2 2', (2, 2, 2)),
- ((5, 5, 5), '2 2 2 2', (2, 2, 2)),
- ((5, 5, 5, 5), '2 2 2', (2, 2, 2, 1)),
- ((5, 5, 5, 5), '2 2 2 2', (2, 2, 2, 2)),
- ]
-
- for shape, cmd, exppixdim in tests:
-
- imgfile = 'image.nii.gz'
- img = create_image(shape, [1] * len(shape))
- img.to_filename(imgfile)
-
- try:
- sp.run(['fslchpixdim', imgfile] + list(cmd.split()))
- check_image(img, nib.load(imgfile), list(exppixdim))
-
- finally:
- os.remove(imgfile)
-
-
-if __name__ == '__main__':
- sys.exit(run_tests())
diff --git a/unit_tests/avwutils/fslcomplex/feedsRun b/unit_tests/avwutils/fslcomplex/feedsRun
deleted file mode 100755
index a84cc1d..0000000
--- a/unit_tests/avwutils/fslcomplex/feedsRun
+++ /dev/null
@@ -1,132 +0,0 @@
-#!/usr/bin/env fslpython
-"""Test that fslcomplex produces correct outputs. Specifically tests that the
-output files have orientation info that matches that of the input files.
-"""
-
-import numpy as np
-import nibabel as nib
-import subprocess as sp
-import os.path as op
-import shlex
-import sys
-import traceback
-
-from fsl.utils.tempdir import tempdir
-from fsl.data.image import addExt
-
-
-def sprun(cmd):
- print(f'RUN {cmd}')
- sp.run(shlex.split(cmd), check=True)
-
-
-def imtest(path):
- try:
- addExt(path)
- return True
- except Exception:
- return False
-
-
-# radio=[True|False] -> whether or not
-# to add a flip on the affine X axis
-def create_test_input_data(radio, seed=1):
-
- np.random.seed(seed)
-
- real = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
- imag = np.random.randint(0, 100, (10, 10, 10)).astype(np.float32)
- affine = np.diag([3, 3, 3, 1])
-
- if radio:
- affine[0, 0] *= -1
- affine[:3, 3] = [37, 20, 30]
- real = np.flip(real, 0)
- imag = np.flip(imag, 0)
- else:
- affine[:3, 3] = [10, 20, 30]
-
- comp = real + imag * 1j
- abso = np.abs(comp)
- phase = np.arctan2(comp.imag, comp.real)
- comp4d = np.concatenate((comp.reshape(10, 10, 10, 1),
- comp.reshape(10, 10, 10, 1)), 3)
-
- real = nib.Nifti1Image(real, affine)
- imag = nib.Nifti1Image(imag, affine)
- comp = nib.Nifti1Image(comp, affine)
- comp4d = nib.Nifti1Image(comp4d, affine)
- abso = nib.Nifti1Image(abso, affine)
- phase = nib.Nifti1Image(phase, affine)
-
- real .set_qform(*real .get_sform(coded=True))
- imag .set_qform(*comp .get_sform(coded=True))
- comp .set_qform(*comp .get_sform(coded=True))
- comp4d.set_qform(*comp4d.get_sform(coded=True))
- abso .set_qform(*abso .get_sform(coded=True))
- phase .set_qform(*phase .get_sform(coded=True))
-
- real .to_filename('real_in.nii.gz')
- imag .to_filename('imag_in.nii.gz')
- comp .to_filename('complex_in.nii.gz')
- comp4d.to_filename('complex4d_in.nii.gz')
- abso .to_filename('abs_in.nii.gz')
- phase .to_filename('phase_in.nii.gz')
-
-
-def compare_images(file1, file2):
- img1 = nib.load(addExt(file1))
- img2 = nib.load(addExt(file2))
- data1 = np.asanyarray(img1.dataobj)
- data2 = np.asanyarray(img2.dataobj)
- assert img1.header['sform_code'] == img2.header['sform_code']
- assert img1.header['qform_code'] == img2.header['qform_code']
- assert np.all(np.isclose(img1.get_sform(), img2.get_sform()))
- assert np.all(np.isclose(img1.get_qform(), img2.get_qform()))
- assert np.all(np.isclose(img1.header['pixdim'], img2.header['pixdim']))
- assert np.all(np.isclose(data1, data2))
-
-
-def test_fslcomplex_call(args, infiles, outfiles, radio):
- with tempdir():
- create_test_input_data(radio)
- sprun(f'fslcomplex {args} {infiles} {outfiles}')
- for outfile in outfiles.split(' '):
-
- if not imtest(outfile):
- continue
-
- prefix = outfile.split('_')[0]
- infile = f'{prefix}_in'
-
- print(f'Comparing {outfile} against {infile}')
-
- compare_images(infile, outfile)
-
-
-if __name__ == '__main__':
- tests = [
- ('-realabs', 'complex_in', 'abs_out'),
- ('-realphase', 'complex_in', 'phase_out'),
- ('-realpolar', 'complex_in', 'abs_out phase_out'),
- ('-realcartesian', 'complex_in', 'real_out imag_out'),
- ('-complex', 'real_in imag_in', 'complex_out'),
- ('-complexpolar', 'abs_in phase_in', 'complex_out'),
- ('-copyonly', 'complex_in', 'complex_out'),
- ('-complexsplit', 'complex4d_in', 'complex_out 0 0'),
- ('-complexsplit', 'complex4d_in', 'complex_out 1 1'),
- ('-complexmerge', 'complex_in complex_in', 'complex4d_out'),
- ]
-
- result = 0
- for radio in [True, False]:
- for args, infiles, outfiles in tests:
- try:
- test_fslcomplex_call(args, infiles, outfiles, radio)
- print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] PASSED')
- except Exception as e:
- print(f'\nTest fslcomplex {args} {infiles} {outfiles} [radio: {radio}] FAILED')
- traceback.print_exc()
- result = 1
-
- sys.exit(result)
diff --git a/unit_tests/avwutils/fslcreatehd/feedsRun b/unit_tests/avwutils/fslcreatehd/feedsRun
deleted file mode 100755
index 339553d..0000000
--- a/unit_tests/avwutils/fslcreatehd/feedsRun
+++ /dev/null
@@ -1,265 +0,0 @@
-#!/usr/bin/env fslpython
-
-import os
-import os.path as op
-import sys
-import subprocess as sp
-
-import numpy as np
-import nibabel as nib
-
-
-THISDIR = op.dirname(op.abspath(__file__))
-
-
-# 2=char, 4=short, 8=int, 16=float, 64=double
-DTYPE_MAPPING = {
- 2 : np.uint8,
- 4 : np.int16,
- 8 : np.int32,
- 16 : np.float32,
- 64 : np.float64
-}
-
-MNI152_2MM_AFFINE = np.array([[-2, 0, 0, 90],
- [ 0, 2, 0, -126],
- [ 0, 0, 2, -72],
- [ 0, 0, 0, 1]])
-
-
-def validate_result(imgfile, expshape, exppixdim, exporigin, expdtype):
-
- img = nib.load(imgfile)
- hdr = img.header
- expshape = list(expshape)
- exppixdim = list(exppixdim)
- exporigin = list(exporigin)
-
- if (len(expshape) == 3) or \
- expshape[3] in (0, 1):
- expndims = 3
- else:
- expndims = 4
-
- expaffine = np.diag(exppixdim[:3] + [1])
- expaffine[0, 0] *= -1
- expaffine[:3, 3] = exporigin
- expaffine[0, 3] *= exppixdim[0]
- expaffine[1, 3] *= -exppixdim[1]
- expaffine[2, 3] *= -exppixdim[2]
-
- assert len(img.shape) == expndims
- assert list(img.shape) == expshape[ :expndims]
- assert list(hdr.get_zooms()) == exppixdim[:expndims]
- assert img.get_data_dtype() == expdtype
- assert np.all(np.isclose(img.affine, expaffine))
-
-
-def create_image(shape, pixdim, origin, dtype):
- pixdim = list(pixdim)
- affine = np.diag(pixdim[:3] + [1])
- affine[:3, 3] = origin
- data = np.random.randint(1, 100, shape).astype(dtype)
- hdr = nib.Nifti1Header()
-
- hdr.set_data_dtype(dtype)
- hdr.set_data_shape(shape)
- hdr.set_zooms(pixdim[:len(shape)])
-
- return nib.Nifti1Image(data, affine, hdr)
-
-
-def test_new_file():
- tests = [
-
- # 4th dim of size 0 or 1 should
- # result in a 3D image (this
- # is coded in validate_result)
- ' 5 5 5 0 2 2 2 0 0 0 0 2',
- ' 5 5 5 0 2 2 2 1 0 0 0 2',
- ' 5 5 5 1 2 2 2 1 0 0 0 2',
- ' 5 5 5 1 2 2 2 1 0 0 0 4',
- ' 5 5 5 1 2 2 2 1 0 0 0 8',
- ' 5 5 5 1 2 2 2 1 0 0 0 16',
- ' 5 5 5 1 2 2 2 1 1 2 3 64',
- ' 5 5 5 1 0.5 1.5 1.25 1 0 0 0 2',
- ' 5 5 5 1 0.5 1.5 1.25 1.5 0 0 0 2',
- ' 5 5 5 1 0.5 1.5 1.25 0.5 0 0 0 2',
- '30 30 30 5 5 10 3 5 10 20 10 2',
- ]
-
- for test in tests:
- args = list(test.split())
- imgfile = 'image.nii.gz'
-
- try:
- os.remove(imgfile)
- except:
- pass
-
- print(['fslcreatehd'] + args + [imgfile])
-
- sp.run(['fslcreatehd'] + args + [imgfile])
-
- args = [float(a) for a in args]
- expshape = args[:4]
- exppixdim = args[4:8]
- exporigin = args[8:11]
- expdtype = DTYPE_MAPPING[args[11]]
-
- try:
- validate_result(
- imgfile, expshape, exppixdim, exporigin, expdtype)
- finally:
- os.remove(imgfile)
-
-
-def test_existing_file():
-
- # each test is a tuple containing:
- # - dtype_of_existing_image
- # - shape_of_existing_image
- # - exp_shape (set to None if image should not be overwritten)
- # - fslcreatehd_args
- tests = [
- # 4th dim of 0 or 1 should result in a 3D image
- (2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 2'),
- (2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 1 2 3 2'),
- (2, (5, 5, 5), None, '5 5 5 1 2 2 2 2 0 0 0 2'),
-
- # dtype arg should be ignored for existing images
- (2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 4'),
- (4, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 2'),
-
- # data should be overwritten if any
- # of the first 3 dims are different,
- # or if a 4th dim is specified
- (2, (5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 4'),
- (2, (5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 1 2 3 2'),
- (2, (5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 1 2 3 2'),
-
- # 4D - same rules apply
- (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 4'),
- (4, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 1 2 3 2'),
-
- # data overwritten if nelements
- # change
- (2, (5, 5, 5, 5), (5, 5, 5), '5 5 5 0 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), (5, 5, 5), '5 5 5 1 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 1 2 3 2'),
- (2, (5, 5, 5, 5), (5, 5, 5, 2), '5 5 5 2 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 0 0 0 2'),
- (2, (5, 5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 1 2 3 2'),
- ]
-
- for (dtype, shape, expshape, args) in tests:
- imgfile = 'image.nii.gz'
- dtype = DTYPE_MAPPING[dtype]
- args = list(args.split())
- img = create_image(shape, (1, 1, 1, 1), (0, 0, 0), dtype)
-
- img.to_filename(imgfile)
-
- sp.run(['fslcreatehd'] + args + [imgfile])
-
- checkdata = expshape is None
-
- if expshape is None:
- expshape = shape
-
- args = [float(a) for a in args]
- exppixdim = args[4:8]
- exporigin = args[8:11]
-
- try:
- validate_result(imgfile, expshape, exppixdim, exporigin, dtype)
-
- if checkdata:
- data = np.asanyarray(img.dataobj)
- datacopy = np.asanyarray(nib.load(imgfile).dataobj)
- assert np.all(data == datacopy)
-
- finally:
- os.remove(imgfile)
-
-
-def test_new_file_xml():
- xmlfile = op.join(THISDIR, 'mni2mm.xml')
- sp.run(['fslcreatehd', xmlfile, 'mni.nii.gz'])
- img = nib.load('mni.nii.gz')
-
- assert img.shape == (91, 109, 91)
- assert img.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
- assert img.header['intent_code'] == 10
- assert img.header['intent_p1'] == 20
- assert img.header['intent_p2'] == 30
- assert img.header['intent_p3'] == 40
-
-
-def test_existing_file_xml_same_shape():
- xmlfile = op.join(THISDIR, 'mni2mm.xml')
- img = create_image((91, 109, 91), (3, 3, 3), (5, 5, 5), np.float32)
- img.to_filename('image.nii.gz')
-
- sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
-
- result = nib.load('image.nii.gz')
-
- assert result.shape == (91, 109, 91)
- assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
-
- # bug in FSL<=6.0.4 caused intent codes to not be set
- assert result.header['intent_code'] == 10
- assert result.header['intent_p1'] == 20
- assert result.header['intent_p2'] == 30
- assert result.header['intent_p3'] == 40
- assert np.all(result.affine == MNI152_2MM_AFFINE)
-
- # data should be preserved
- assert np.all(result.get_fdata() == img.get_fdata())
-
-
-def test_existing_file_xml_different_shape():
-
- xmlfile = op.join(THISDIR, 'mni2mm.xml')
- img = create_image((20, 20, 20), (3, 3, 3), (5, 5, 5), np.float32)
-
- img.to_filename('image.nii.gz')
-
- sp.run(['fslcreatehd', xmlfile, 'image.nii.gz'])
-
- result = nib.load('image.nii.gz')
-
- assert result.shape == (91, 109, 91)
- assert result.header.get_zooms()[:3] == (2.0, 2.0, 2.0)
- assert result.header['intent_code'] == 10
- assert result.header['intent_p1'] == 20
- assert result.header['intent_p2'] == 30
- assert result.header['intent_p3'] == 40
- assert np.all(result.affine == MNI152_2MM_AFFINE)
-
- # data should be cleared
- assert np.all(result.get_fdata() == 0)
-
-
-def main():
- outdir = sys.argv[1]
- os.chdir(outdir)
-
- test_new_file()
- test_existing_file()
- test_new_file_xml()
- test_existing_file_xml_same_shape()
- test_existing_file_xml_different_shape()
-
-
-if __name__ == '__main__':
- sys.exit(main())
diff --git a/unit_tests/avwutils/fslcreatehd/mni2mm.xml b/unit_tests/avwutils/fslcreatehd/mni2mm.xml
deleted file mode 100644
index 06b8043..0000000
--- a/unit_tests/avwutils/fslcreatehd/mni2mm.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-<nifti_image
- image_offset = '352'
- ndim = '3'
- nx = '91'
- ny = '109'
- nz = '91'
- nt = '1'
- dx = '2'
- dy = '2'
- dz = '2'
- dt = '1'
- datatype = '4'
- nvox = '902629'
- nbyper = '2'
- scl_slope = '1'
- scl_inter = '0'
- intent_code = '10'
- intent_p1 = '20'
- intent_p2 = '30'
- intent_p3 = '40'
- intent_name = ''
- toffset = '0'
- xyz_units = '2'
- time_units = '8'
- freq_dim = '0'
- phase_dim = '0'
- slice_dim = '0'
- descrip = 'FSL5.0'
- aux_file = ''
- qform_code = '4'
- qfac = '-1'
- quatern_b = '0'
- quatern_c = '1'
- quatern_d = '0'
- qoffset_x = '90'
- qoffset_y = '-126'
- qoffset_z = '-72'
- sform_code = '4'
- sto_xyz_matrix = '-2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1'
- slice_code = '0'
- slice_start = '0'
- scl_end = '0'
- scl_duration = '0'
-/>
diff --git a/unit_tests/avwutils/avscale/feedsRun b/unit_tests/flirt/avscale/feedsRun
similarity index 100%
rename from unit_tests/avwutils/avscale/feedsRun
rename to unit_tests/flirt/avscale/feedsRun
--
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