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Commit 19380e0b authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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RF: re-work applyxfm tests - no longer rely on external data. Use benchmark 

data for evaluation
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with 209 additions and 35 deletions
unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsRun deleted 100755 → 0
+ 0
− 35
View file @ 270f7f8e
#!/usr/bin/env fslpython
"""
test applyxfm4D matfile directory option with user prefix
"""
from subprocess import run, PIPE
from os.path import join
from tempfile import mkdtemp
import os
import sys
OUTDIR = sys.argv[1]
INDIR = sys.argv[2]
FSLDIR = os.environ.get('FSLDIR')
FSLBIN = join(FSLDIR, 'bin')
print(INDIR)
def test_applyxfm4D_userprefix():
# use trilinear interp for speed
cmd = [
join(FSLBIN, 'applyxfm4D'),
join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_in.nii.gz'),
join(INDIR, 'unit_tests', 'applyxfm4D', 'applyxfm4D_ref.nii.gz'),
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
join(INDIR, 'unit_tests', 'applyxfm4D', 'matfiles_user_prefix'),
'-interp',
'trilinear',
'-userprefix',
'myprefix_'
]
run_result = run(cmd, stdout=PIPE, check=True)
stdout_string = run_result.stdout.decode('utf-8')
# check that the files were written to disk
# the brain extracted input should exist
assert os.path.isfile(join(OUTDIR, 'applyxfm4D_out.nii.gz')) == True
test_applyxfm4D_userprefix()
unit_tests/applyxfm4D/feedsRun.fail 0 → 100755
+ 21
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D correct failure
"""
import sys
from subprocess import run, CalledProcessError
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'applyxfm4D_mat.mat']
try:
run(cmd, check=True)
assert False
except CalledProcessError as e:
print("test_applyxfm4D correctly failed. This is good!")
assert e.returncode != 0
unit_tests/applyxfm4D/feedsRun.fourdigit 0 → 100755
+ 19
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D matfile directory option with 4 digit numbers in filenames
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'matfiles_four_digit',
'-interp',
'trilinear',
'-fourdigit']
run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.nn 0 → 100755
+ 19
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D nn interp
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'applyxfm4D_mat.mat',
'-singlematrix',
'-interp',
'nn']
run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.sinc 0 → 100755
+ 19
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D sinc interp
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'applyxfm4D_mat.mat',
'-singlematrix',
'-interp',
'sinc']
run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.singlematrix 0 → 100755
+ 19
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D single matrix option
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'applyxfm4D_mat.mat',
'-singlematrix',
'-interp',
'nn']
run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.spline 0 → 100755
+ 19
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D spline interp
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'applyxfm4D_mat.mat',
'-singlematrix',
'-interp',
'spline']
run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.transdir 0 → 100755
+ 18
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D matfile directory option
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'matfiles_five_digit',
'-interp',
'trilinear']
run_result = run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.trilinear 0 → 100755
+ 19
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D trilinear interp
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'applyxfm4D_mat.mat',
'-singlematrix',
'-interp',
'trilinear']
run(cmd, check=True)
unit_tests/applyxfm4D/feedsRun.userprefix 0 → 100755
+ 20
− 0
View file @ 19380e0b
#!/usr/bin/env fslpython
"""
test applyxfm4D matfile directory option with user prefix
"""
import sys
from subprocess import run
from os.path import join
OUTDIR = sys.argv[1]
cmd = [
'applyxfm4D',
'applyxfm4D_in.nii.gz',
'applyxfm4D_ref.nii.gz',
join(OUTDIR, 'applyxfm4D_out.nii.gz'),
'matfiles_user_prefix',
'-interp',
'trilinear',
'-userprefix',
'myprefix_']
run_result = run(cmd, check=True)
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00000 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00001 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00002 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00003 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00004 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00005 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00006 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00007 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
unit_tests/applyxfm4D/matfiles_five_digit/MAT_00008 0 → 100644
+ 4
− 0
View file @ 19380e0b
1.0000000000 0.0000000000 0.0000000000 -0.3750000000
0.0000000000 1.0000000000 0.0000000000 0.8958333450
0.0000000000 0.0000000000 1.0000000000 2.0000000000
0.0000000000 0.0000000000 0.0000000000 1.0000000000
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