RF: re-work applyxfm tests - no longer rely on external data. Use benchmark

data for evaluation

unit_tests/applyxfm4D/applyxfm4D_fail/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_fail/feedsRun

-#!/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()

unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_fourdigit/feedsRun

-#!/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_mat.mat

+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/applyxfm4D_nn/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_nn/feedsRun

-#!/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()

unit_tests/applyxfm4D/applyxfm4D_sinc/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_sinc/feedsRun

-#!/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()

unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_singlematrix/feedsRun

-#!/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

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_spline/feedsRun

-#!/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()

unit_tests/applyxfm4D/applyxfm4D_transdir/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_transdir/feedsRun

-#!/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()

unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsInputs

-unit_tests/applyxfm4D

unit_tests/applyxfm4D/applyxfm4D_trilinear/feedsRun

-#!/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()

unit_tests/applyxfm4D/applyxfm4D_userprefix/feedsInputs

-unit_tests/applyxfm4D