def test_run_interface():
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_raises(ValueError, mc.run) # script is mandatory
mc.inputs.script = 'a=1;'
yield assert_raises(IOError, mc.run) # foo_m is not an executable
cwd = os.getcwd()
basedir = mkdtemp()
os.chdir(basedir)
res = mlab.MatlabCommand(script='foo', paths=[basedir], mfile=True).run() # bypasses ubuntu dash issue
yield assert_equal(res.runtime.returncode, 1)
res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run() # bypasses ubuntu dash issue
yield assert_equal(res.runtime.returncode, 0)
os.chdir(cwd)
rmtree(basedir)
def test_reslice():
moving = example_data(infile="functional.nii")
space_defining = example_data(infile="T1.nii")
reslice = spmu.Reslice(matlab_cmd="mymatlab_version")
assert_equal(reslice.inputs.matlab_cmd, "mymatlab_version")
reslice.inputs.in_file = moving
reslice.inputs.space_defining = space_defining
assert_equal(reslice.inputs.interp, 0)
assert_raises(TraitError, reslice.inputs.trait_set, interp="nearest")
assert_raises(TraitError, reslice.inputs.trait_set, interp=10)
reslice.inputs.interp = 1
script = reslice._make_matlab_command(None)
outfile = fname_presuffix(moving, prefix="r")
assert_equal(reslice.inputs.out_file, outfile)
expected = "\nflags.mean=0;\nflags.which=1;\nflags.mask=0;"
assert_equal(expected in script.replace(" ", ""), True)
expected_interp = "flags.interp = 1;\n"
assert_equal(expected_interp in script, True)
assert_equal("spm_reslice(invols, flags);" in script, True)
def test_reslice():
moving = example_data(infile='functional.nii')
space_defining = example_data(infile='T1.nii')
reslice = spmu.Reslice(matlab_cmd='mymatlab_version')
assert_equal(reslice.inputs.matlab_cmd, 'mymatlab_version')
reslice.inputs.in_file = moving
reslice.inputs.space_defining = space_defining
assert_equal(reslice.inputs.interp, 0)
assert_raises(TraitError, reslice.inputs.trait_set, interp='nearest')
assert_raises(TraitError, reslice.inputs.trait_set, interp=10)
reslice.inputs.interp = 1
script = reslice._make_matlab_command(None)
outfile = fname_presuffix(moving, prefix='r')
assert_equal(reslice.inputs.out_file, outfile)
expected = '\nflags.mean=0;\nflags.which=1;\nflags.mask=0;'
assert_equal(expected in script.replace(' ', ''), True)
expected_interp = 'flags.interp = 1;\n'
assert_equal(expected_interp in script, True)
assert_equal('spm_reslice(invols, flags);' in script, True)
def test_reslice():
moving = example_data(infile='functional.nii')
space_defining = example_data(infile='T1.nii')
reslice = spmu.Reslice(matlab_cmd='mymatlab_version')
assert_equal(reslice.inputs.matlab_cmd, 'mymatlab_version')
reslice.inputs.in_file = moving
reslice.inputs.space_defining = space_defining
assert_equal(reslice.inputs.interp, 0)
assert_raises(TraitError, reslice.inputs.trait_set, interp='nearest')
assert_raises(TraitError, reslice.inputs.trait_set, interp=10)
reslice.inputs.interp = 1
script = reslice._make_matlab_command(None)
outfile = fname_presuffix(moving, prefix='r')
assert_equal(reslice.inputs.out_file, outfile)
expected = '\nflags.mean=0;\nflags.which=1;\nflags.mask=0;'
assert_equal(expected in script.replace(' ', ''), True)
expected_interp = 'flags.interp = 1;\n'
assert_equal(expected_interp in script, True)
assert_equal('spm_reslice(invols, flags);' in script, True)
def test_dicom_import():
dicom = example_data(infile="dicomdir/123456-1-1.dcm")
di = spmu.DicomImport(matlab_cmd="mymatlab")
assert_equal(di.inputs.matlab_cmd, "mymatlab")
assert_equal(di.inputs.output_dir_struct, "flat")
assert_equal(di.inputs.output_dir, "./converted_dicom")
assert_equal(di.inputs.format, "nii")
assert_equal(di.inputs.icedims, False)
assert_raises(TraitError, di.inputs.trait_set, output_dir_struct="wrong")
assert_raises(TraitError, di.inputs.trait_set, format="FAT")
assert_raises(TraitError, di.inputs.trait_set, in_files=["does_sfd_not_32fn_exist.dcm"])
di.inputs.in_files = [dicom]
assert_equal(di.inputs.in_files, [dicom])
def test_dicom_import():
dicom = example_data(infile='dicomdir/123456-1-1.dcm')
di = spmu.DicomImport(matlab_cmd='mymatlab')
assert_equal(di.inputs.matlab_cmd, 'mymatlab')
assert_equal(di.inputs.output_dir_struct, 'flat')
assert_equal(di.inputs.output_dir, './converted_dicom')
assert_equal(di.inputs.format, 'nii')
assert_equal(di.inputs.icedims, False)
assert_raises(TraitError, di.inputs.trait_set, output_dir_struct='wrong')
assert_raises(TraitError, di.inputs.trait_set, format='FAT')
assert_raises(TraitError, di.inputs.trait_set, in_files=['does_sfd_not_32fn_exist.dcm'])
di.inputs.in_files = [dicom]
assert_equal(di.inputs.in_files, [dicom])
def test_dicom_import():
dicom = example_data(infile='dicomdir/123456-1-1.dcm')
di = spmu.DicomImport(matlab_cmd='mymatlab')
assert_equal(di.inputs.matlab_cmd, 'mymatlab')
assert_equal(di.inputs.output_dir_struct, 'flat')
assert_equal(di.inputs.output_dir, './converted_dicom')
assert_equal(di.inputs.format, 'nii')
assert_equal(di.inputs.icedims, False)
assert_raises(TraitError, di.inputs.trait_set, output_dir_struct='wrong')
assert_raises(TraitError, di.inputs.trait_set, format='FAT')
assert_raises(TraitError, di.inputs.trait_set, in_files=['does_sfd_not_32fn_exist.dcm'])
di.inputs.in_files = [dicom]
assert_equal(di.inputs.in_files, [dicom])
def test_bet():
tmp_infile, tp_dir = setup_infile()
better = fsl.BET()
yield assert_equal(better.cmd, 'bet')
# Test raising error with mandatory args absent
yield assert_raises(ValueError, better.run)
# Test generated outfile name
better.inputs.in_file = tmp_infile
outfile = fsl_name(better, 'foo_brain')
outpath = os.path.join(os.getcwd(), outfile)
realcmd = 'bet %s %s' % (tmp_infile, outpath)
yield assert_equal(better.cmdline, realcmd)
# Test specified outfile name
outfile = fsl_name(better, '/newdata/bar')
better.inputs.out_file = outfile
realcmd = 'bet %s %s' % (tmp_infile, outfile)
yield assert_equal(better.cmdline, realcmd)
# infile foo.nii doesn't exist
def func():
better.run(in_file='foo2.nii', out_file='bar.nii')
yield assert_raises(TraitError, func)
# .run() based parameter setting
better = fsl.BET()
better.inputs.frac = 0.40
outfile = fsl_name(better, 'outfile')
betted = better.run(in_file=tmp_infile, out_file=outfile)
yield assert_equal(betted.interface.inputs.in_file, tmp_infile)
yield assert_equal(betted.interface.inputs.out_file, outfile)
realcmd = 'bet %s %s -f 0.40' % (tmp_infile, outfile)
yield assert_equal(betted.runtime.cmdline, realcmd)
# Our options and some test values for them
# Should parallel the opt_map structure in the class for clarity
opt_map = {
'outline': ('-o', True),
'mask': ('-m', True),
'skull': ('-s', True),
'no_output': ('-n', True),
'frac': ('-f 0.40', 0.4),
'vertical_gradient': ('-g 0.75', 0.75),
'radius': ('-r 20', 20),
'center': ('-c 54 75 80', [54, 75, 80]),
'threshold': ('-t', True),
'mesh': ('-e', True),
#'verbose': ('-v', True),
#'flags': ('--i-made-this-up', '--i-made-this-up'),
}
# Currently we don't test -R, -S, -B, -Z, -F, -A or -A2
# test each of our arguments
better = fsl.BET()
outfile = fsl_name(better, 'foo_brain')
outpath = os.path.join(os.getcwd(), outfile)
for name, settings in opt_map.items():
better = fsl.BET(**{name: settings[1]})
# Add mandatory input
better.inputs.in_file = tmp_infile
realcmd = ' '.join([better.cmd, tmp_infile, outpath, settings[0]])
yield assert_equal(better.cmdline, realcmd)
teardown_infile(tmp_dir)
def test_flirt():
# setup
tmpdir, infile, reffile = setup_flirt()
flirter = fsl.FLIRT()
yield assert_equal(flirter.cmd, 'flirt')
flirter.inputs.bins = 256
flirter.inputs.cost = 'mutualinfo'
flirted = flirter.run(in_file=infile, reference=reffile,
out_file='outfile', out_matrix_file='outmat.mat')
flirt_est = flirter.run(in_file=infile, reference=reffile,
out_matrix_file='outmat.mat')
yield assert_not_equal(flirter, flirted)
yield assert_not_equal(flirted, flirt_est)
yield assert_equal(flirter.inputs.bins, flirted.interface.inputs.bins)
yield assert_equal(flirter.inputs.cost, flirt_est.interface.inputs.cost)
realcmd = 'flirt -in %s -ref %s -out outfile -omat outmat.mat ' \
'-bins 256 -cost mutualinfo' % (infile, reffile)
yield assert_equal(flirted.runtime.cmdline, realcmd)
flirter = fsl.FLIRT()
# infile not specified
yield assert_raises(ValueError, flirter.run)
flirter.inputs.in_file = infile
# reference not specified
yield assert_raises(ValueError, flirter.run)
flirter.inputs.reference = reffile
res = flirter.run()
# Generate outfile and outmatrix
pth, fname, ext = split_filename(infile)
outfile = os.path.join(os.getcwd(),
fsl_name(flirter, '%s_flirt' %fname))
outmat = '%s_flirt.mat' % fname
outmat = os.path.join(os.getcwd(), outmat)
realcmd = 'flirt -in %s -ref %s -out %s -omat %s' % (infile, reffile,
outfile, outmat)
yield assert_equal(res.interface.cmdline, realcmd)
_, tmpfile = tempfile.mkstemp(suffix = '.nii', dir = tmpdir)
# Loop over all inputs, set a reasonable value and make sure the
# cmdline is updated correctly.
for key, trait_spec in sorted(fsl.FLIRT.input_spec().traits().items()):
# Skip mandatory inputs and the trait methods
if key in ('trait_added', 'trait_modified', 'in_file', 'reference',
'environ', 'output_type', 'out_file', 'out_matrix_file',
'in_matrix_file'):
continue
param = None
value = None
if key == 'args':
param = '-v'
value = '-v'
elif isinstance(trait_spec.trait_type, File):
value = tmpfile
param = trait_spec.argstr % value
elif trait_spec.default is False:
param = trait_spec.argstr
value = True
elif key in ('searchr_x', 'searchr_y', 'searchr_z'):
value = [-45, 45]
param = trait_spec.argstr % ' '.join(str(elt) for elt in value)
else:
value = trait_spec.default
param = trait_spec.argstr % value
cmdline = 'flirt -in %s -ref %s' % (infile, reffile)
# Handle autogeneration of outfile
pth, fname, ext = split_filename(infile)
outfile = os.path.join(os.getcwd(),
fsl_name(fsl.FLIRT(),'%s_flirt' % fname))
outfile = ' '.join(['-out', outfile])
# Handle autogeneration of outmatrix
outmatrix = '%s_flirt.mat' % fname
outmatrix = os.path.join(os.getcwd(), outmatrix)
outmatrix = ' '.join(['-omat', outmatrix])
# Build command line
cmdline = ' '.join([cmdline, outfile, outmatrix, param])
flirter = fsl.FLIRT(in_file = infile, reference = reffile)
setattr(flirter.inputs, key, value)
yield assert_equal(flirter.cmdline, cmdline)
# Test OutputSpec
flirter = fsl.FLIRT(in_file = infile, reference = reffile)
pth, fname, ext = split_filename(infile)
flirter.inputs.out_file = ''.join(['foo', ext])
flirter.inputs.out_matrix_file = ''.join(['bar', ext])
outs = flirter._list_outputs()
yield assert_equal(outs['out_file'], flirter.inputs.out_file)
yield assert_equal(outs['out_matrix_file'], flirter.inputs.out_matrix_file)
teardown_flirt(tmpdir)
origdir = os.getcwd()
os.chdir(tempdir)
node = pe.Node(utility.Function(input_names=["size"],
output_names=["random_array"],
function=make_random_array),
name="should_fail")
try:
node.inputs.size = 10
node.run()
finally:
os.chdir(origdir)
shutil.rmtree(tempdir)
assert_raises(NameError, should_fail)
def test_function_with_imports():
tempdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(tempdir)
node = pe.Node(utility.Function(input_names=["size"],
output_names=["random_array"],
function=make_random_array,
imports=["import numpy as np"]),
name="should_not_fail")
print(node.inputs.function_str)
try:
origdir = os.getcwd()
os.chdir(tempdir)
node = pe.Node(utility.Function(input_names=["size"],
output_names=["random_array"],
function=make_random_array),
name="should_fail")
try:
node.inputs.size = 10
node.run()
finally:
os.chdir(origdir)
shutil.rmtree(tempdir)
assert_raises(NameError, should_fail)
def test_function_with_imports():
tempdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(tempdir)
node = pe.Node(utility.Function(input_names=["size"],
output_names=["random_array"],
function=make_random_array,
imports=["import numpy as np"]),
name="should_not_fail")
print node.inputs.function_str
try:
def test_init():
yield assert_raises(Exception, pe.Workflow)
pipe = pe.Workflow(name='pipe')
yield assert_equal(type(pipe._graph), nx.DiGraph)
yield assert_equal(pipe._execgraph, None)