def test_parse_cmdline_5():
# no rigid transform matrix outside feat mode
args = [
'-i',
join("refin", "filtered_func_data.nii.gz"), '-o',
join("out"), '-p',
join("refin", "mc", "prefiltered_func_data_mcf.par"), '-w',
join("refin", "reg", "highres2standard_warp.nii.gz"), '-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_6():
# no non-linear warp defined outside feat mode
args = [
'-i',
join("ABSENT", "filtered_func_data.nii.gz"), '-o',
join("out"), '-p',
join("refin", "mc", "prefiltered_func_data_mcf.par"), '-a',
join("refin", "reg", "example_func2highres.mat"), '-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_3():
# no output dir outside feat mode
args = [
'-i',
join("refin", "filtered_func_data.nii.gz"), '-p',
join("refin", "mc", "prefiltered_func_data_mcf.par"), '-a',
join("refin", "reg", "example_func2highres.mat"), '-w',
join("refin", "reg", "highres2standard_warp.nii.gz"), '-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_4():
# no motion parameters file outside feat mode
args = [
'-i',
join("refin", "filtered_func_data.nii.gz"), '-o',
join("out"), '-a',
join("refin", "reg", "example_func2highres.mat"), '-w',
join("refin", "reg", "highres2standard_warp.nii.gz"), '-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_6():
# no non-linear warp defined outside feat mode
args = [
'-i', join("ABSENT", "filtered_func_data.nii.gz"),
'-o', join("out"),
'-p', join("refin", "mc", "prefiltered_func_data_mcf.par"),
'-a', join("refin", "reg", "example_func2highres.mat"),
'-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_5():
# no rigid transform matrix outside feat mode
args = [
'-i', join("refin", "filtered_func_data.nii.gz"),
'-o', join("out"),
'-p', join("refin", "mc", "prefiltered_func_data_mcf.par"),
'-w', join("refin", "reg", "highres2standard_warp.nii.gz"),
'-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_4():
# no motion parameters file outside feat mode
args = [
'-i', join("refin", "filtered_func_data.nii.gz"),
'-o', join("out"),
'-a', join("refin", "reg", "example_func2highres.mat"),
'-w', join("refin", "reg", "highres2standard_warp.nii.gz"),
'-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_3():
# no output dir outside feat mode
args = [
'-i', join("refin", "filtered_func_data.nii.gz"),
'-p', join("refin", "mc", "prefiltered_func_data_mcf.par"),
'-a', join("refin", "reg", "example_func2highres.mat"),
'-w', join("refin", "reg", "highres2standard_warp.nii.gz"),
'-s', "31415926"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_7():
# illegal T1 value
args = [
'-i',
join("refin", "filtered_func_data.nii.gz"), '-o',
join("out"), '-p',
join("refin", "mc", "prefiltered_func_data_mcf.par"), '-a',
join("refin", "reg", "example_func2highres.mat"), '-w',
join("refin", "reg", "highres2standard_warp.nii.gz"), '-s', "31415926",
'--tr', "0.2"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_7():
# illegal T1 value
args = [
'-i', join("refin", "filtered_func_data.nii.gz"),
'-o', join("out"),
'-p', join("refin", "mc", "prefiltered_func_data_mcf.par"),
'-a', join("refin", "reg", "example_func2highres.mat"),
'-w', join("refin", "reg", "highres2standard_warp.nii.gz"),
'-s', "31415926",
'--tr', "0.2"
]
with assert_raises(SystemExit) as context:
aroma.parse_cmdline(args)
assert context.exception.code == 2
def test_parse_cmdline_1():
args = [
'-i',
join("refin", "filtered_func_data.nii.gz"), '-o',
join("out"), '-p',
join("refin", "mc", "prefiltered_func_data_mcf.par"), '-a',
join("refin", "reg", "example_func2highres.mat"), '-w',
join("refin", "reg", "highres2standard_warp.nii.gz"), '-s', "31415926"
]
parsed_args = aroma.parse_cmdline(args)
assert parsed_args.infile == join(os.getcwd(),
'refin/filtered_func_data.nii.gz')
assert parsed_args.outdir == join(os.getcwd(), 'out')
assert parsed_args.mc == join(os.getcwd(),
'refin/mc/prefiltered_func_data_mcf.par')
assert parsed_args.affmat == join(os.getcwd(),
'refin/reg/example_func2highres.mat')
assert parsed_args.warp == join(os.getcwd(),
'refin/reg/highres2standard_warp.nii.gz')
assert parsed_args.seed == 31415926
assert parsed_args.TR is None
assert parsed_args.denoise_type == 'nonaggr'
assert parsed_args.dim == 0
assert parsed_args.featdir is None
assert parsed_args.loglevel == 'INFO'
assert parsed_args.existing_mask is None
assert parsed_args.melodic_dir is None
def test_parse_cmdline_1():
args = [
'-i', join("refin", "filtered_func_data.nii.gz"),
'-o', join("out"),
'-p', join("refin", "mc", "prefiltered_func_data_mcf.par"),
'-a', join("refin", "reg", "example_func2highres.mat"),
'-w', join("refin", "reg", "highres2standard_warp.nii.gz"),
'-s', "31415926"
]
parsed_args = aroma.parse_cmdline(args)
assert parsed_args.infile == join(os.getcwd(), 'refin/filtered_func_data.nii.gz')
assert parsed_args.outdir == join(os.getcwd(), 'out')
assert parsed_args.mc == join(os.getcwd(), 'refin/mc/prefiltered_func_data_mcf.par')
assert parsed_args.affmat == join(os.getcwd(), 'refin/reg/example_func2highres.mat')
assert parsed_args.warp == join(os.getcwd(), 'refin/reg/highres2standard_warp.nii.gz')
assert parsed_args.seed == 31415926
assert parsed_args.TR is None
assert parsed_args.denoise_type == 'nonaggr'
assert parsed_args.dim == 0
assert parsed_args.featdir is None
assert parsed_args.loglevel == 'INFO'
assert parsed_args.existing_mask is None
assert parsed_args.melodic_dir is None