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Commit 39d2c4e0 authored by Taylor Hanayik's avatar Taylor Hanayik Committed by Paul McCarthy
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added Applyxfm4d tests

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unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs 0 → 100644
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unit_tests/applyxfm4D
unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D correct failure
"""
from subprocess import run, PIPE, CalledProcessError
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')
# applyxfm4D fmri.nii.gz brain.nii.gz applyxfm4D_out f2b.mat -singlematrix -interp nn
def test_applyxfm4D_fail():
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', 'applyxfm4D_mat.mat')
]
try:
run_result = run(cmd, stdout=PIPE, check=True)
stdout_string = run_result.stdout.decode('utf-8')
assert False
except CalledProcessError as e:
print("test_applyxfm4D correctly failed. This is good!")
assert e.returncode != 0
print("running test_applyxfm4D_fail()")
test_applyxfm4D_fail()
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#!/usr/bin/env fslpython
"""
test applyxfm4D matfile directory option with 4 digit numbers in filenames
"""
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_fourdigit():
# 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_four_digit'),
'-interp',
'trilinear',
'-fourdigit'
]
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_fourdigit()
unit_tests/applyxfm4D/applyxfm4D_nn/feedsInputs 0 → 100644
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unit_tests/applyxfm4D
unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D nn interp
"""
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_nn():
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', 'applyxfm4D_mat.mat'),
'-singlematrix',
'-interp',
'nn'
]
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_nn()
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unit_tests/applyxfm4D
unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D sinc interp
"""
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_sinc():
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', 'applyxfm4D_mat.mat'),
'-singlematrix',
'-interp',
'sinc'
]
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_sinc()
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unit_tests/applyxfm4D
unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D single matrix option
"""
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_singlematrix():
# use nearestneighbour 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', 'applyxfm4D_mat.mat'),
'-singlematrix',
'-interp',
'nn'
]
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_singlematrix()
unit_tests/applyxfm4D/applyxfm4D_spline/feedsInputs 0 → 100644
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unit_tests/applyxfm4D
unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D spline interp
"""
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_spline():
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', 'applyxfm4D_mat.mat'),
'-singlematrix',
'-interp',
'spline'
]
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_spline()
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unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D matfile directory option
"""
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_transdir():
# 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_five_digit'),
'-interp',
'trilinear'
]
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_transdir()
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unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun 0 → 100755
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#!/usr/bin/env fslpython
"""
test applyxfm4D trilinear interp
"""
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_trilinear():
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', 'applyxfm4D_mat.mat'),
'-singlematrix',
'-interp',
'trilinear'
]
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_trilinear()
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#!/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()
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