def test_staple():
# Create a node object
staple = LabelFusion()
# Check if the command is properly defined
assert staple.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
staple.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
staple.inputs.in_file = in_file
staple.inputs.kernel_size = 2.0
staple.inputs.file_to_seg = file_to_seg
staple.inputs.template_file = template_file
staple.inputs.template_num = 2
staple.inputs.classifier_type = 'STAPLE'
cmd_tmp = '{cmd} -in {in_file} -STAPLE -ALL -out {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('seg_LabFusion'),
in_file=in_file,
file_to_seg=file_to_seg,
template_file=template_file,
out_file=os.path.join(
os.getcwd(), 'im1_staple.nii'))
assert staple.cmdline == expected_cmd
def test_mv():
# Create a node object
mv = LabelFusion()
# Check if the command is properly defined
assert mv.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
mv.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
mv.inputs.in_file = in_file
mv.inputs.file_to_seg = file_to_seg
mv.inputs.template_file = template_file
mv.inputs.template_num = 2
mv.inputs.classifier_type = 'MV'
mv.inputs.sm_ranking = 'ROINCC'
mv.inputs.dilation_roi = 2
cmd_tmp = '{cmd} -in {in_file} -MV -ROINCC 2 2 {file_to_seg} \
{template_file} -out {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('seg_LabFusion'),
in_file=in_file,
file_to_seg=file_to_seg,
template_file=template_file,
out_file=os.path.join(
os.getcwd(), 'im1_mv.nii'))
assert mv.cmdline == expected_cmd
def test_reg_jacobian_jac_l():
# Create a reg_jacobian object
nr = RegJacobian()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_jacobian')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr.inputs.ref_file = ref_file
nr.inputs.trans_file = trans_file
nr.inputs.type = 'jacL'
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jacL {jac}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_jacobian'),
ref=ref_file,
trans=trans_file,
jac=os.path.join(os.getcwd(), 'warpfield_jacL.nii.gz'))
assert nr.cmdline == expected_cmd
def test_normalize_tpms(tmpdir):
in_mask = example_data("tpms_msk.nii.gz")
mskdata = np.asanyarray(nb.load(in_mask).dataobj)
mskdata[mskdata > 0.0] = 1.0
mapdata = []
in_files = []
out_files = []
for i in range(3):
mapname = example_data("tpm_%02d.nii.gz" % i)
filename = tmpdir.join("modtpm_%02d.nii.gz" % i).strpath
out_files.append(tmpdir.join("normtpm_%02d.nii.gz" % i).strpath)
im = nb.load(mapname)
data = im.get_fdata()
mapdata.append(data)
nb.Nifti1Image(2.0 * (data * mskdata), im.affine,
im.header).to_filename(filename)
in_files.append(filename)
normalize_tpms(in_files, in_mask, out_files=out_files)
sumdata = np.zeros_like(mskdata)
for i, tstfname in enumerate(out_files):
normdata = nb.load(tstfname).get_fdata()
sumdata += normdata
assert np.all(normdata[mskdata == 0] == 0)
assert np.allclose(normdata, mapdata[i])
assert np.allclose(sumdata[sumdata > 0.0], 1.0)
def test_reg_average_avg_lts():
# Create a reg_average object
nr = RegAverage()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_average')
# Assign some input data
one_file = example_data('TransformParameters.0.txt')
two_file = example_data('ants_Affine.txt')
three_file = example_data('elastix.txt')
nr.inputs.avg_lts_files = [one_file, two_file, three_file]
nr.cmdline
# Read the reg_average_cmd
reg_average_cmd = os.path.join(os.getcwd(), 'reg_average_cmd')
with open(reg_average_cmd, 'rb') as f:
argv = f.read()
os.remove(reg_average_cmd)
expected_argv = ('%s %s -avg_lts %s %s %s' %
(get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.txt'), one_file,
two_file, three_file))
assert argv == expected_argv
expected_cmd = ('%s --cmd_file %s' %
(get_custom_path('reg_average'), reg_average_cmd))
assert nr.cmdline == expected_cmd
def test_reg_transform_comp_nii():
# Create a reg_transform object
nr = RegTransform()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_transform')
# Assign some input data
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
trans2_file = example_data('anatomical.nii')
nr.inputs.ref1_file = ref_file
nr.inputs.comp_input2 = trans2_file
nr.inputs.comp_input = trans_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -ref {ref_file} -omp 4 -comp {trans1} {trans2} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
ref_file=ref_file,
trans1=trans_file,
trans2=trans2_file,
out_file=os.path.join(
os.getcwd(), 'warpfield_trans.nii.gz'))
assert nr.cmdline == expected_cmd
def test_reg_f3d():
# Create a reg_f3d object
nr = RegF3D()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_f3d')
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
rmask_file = example_data('mask.nii')
nr.inputs.ref_file = ref_file
nr.inputs.flo_file = flo_file
nr.inputs.rmask_file = rmask_file
nr.inputs.omp_core_val = 4
nr.inputs.vel_flag = True
nr.inputs.be_val = 0.1
nr.inputs.le_val = 0.1
expected_cmd = get_custom_path('reg_f3d') + ' ' + '-be 0.100000 ' +\
'-cpp ' + os.getcwd() + os.sep + 'im2_cpp.nii.gz ' +'-flo ' + flo_file + ' ' +\
'-le 0.100000 ' + '-omp 4 ' + '-ref ' + ref_file + ' ' +\
'-res ' + os.getcwd() + os.sep + 'im2_res.nii.gz ' + '-rmask ' + rmask_file + ' ' + '-vel'
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_average_avg_lts():
# Create a reg_average object
nr = RegAverage()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_average')
# Assign some input data
one_file = example_data('TransformParameters.0.txt')
two_file = example_data('ants_Affine.txt')
three_file = example_data('elastix.txt')
nr.inputs.avg_lts_files = [one_file, two_file, three_file]
nr.cmdline
# Read the reg_average_cmd
reg_average_cmd = os.path.join(os.getcwd(), 'reg_average_cmd')
with open(reg_average_cmd, 'rb') as f:
argv = f.read()
os.remove(reg_average_cmd)
expected_argv = ('%s %s -avg_lts %s %s %s'
% (get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.txt'),
one_file, two_file, three_file))
yield assert_equal, argv, expected_argv
expected_cmd = ('%s --cmd_file %s'
% (get_custom_path('reg_average'), reg_average_cmd))
yield assert_equal, nr.cmdline, expected_cmd
def test_overlap(tmpdir):
from nipype.algorithms.metrics import Overlap
def check_close(val1, val2):
import numpy.testing as npt
return npt.assert_almost_equal(val1, val2, decimal=3)
in1 = example_data("segmentation0.nii.gz")
in2 = example_data("segmentation1.nii.gz")
tmpdir.chdir()
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in1
res = overlap.run()
check_close(res.outputs.jaccard, 1.0)
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
res = overlap.run()
check_close(res.outputs.jaccard, 0.99705)
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
overlap.inputs.vol_units = "mm"
res = overlap.run()
check_close(res.outputs.jaccard, 0.99705)
check_close(res.outputs.roi_voldiff, np.array([0.0063086, -0.0025506,
0.0]))
def test_dvars(tmpdir):
ground_truth = np.loadtxt(example_data('ds003_sub-01_mc.DVARS'))
dvars = ComputeDVARS(
in_file=example_data('ds003_sub-01_mc.nii.gz'),
in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'),
save_all=True,
intensity_normalization=0)
os.chdir(str(tmpdir))
res = dvars.run()
dv1 = np.loadtxt(res.outputs.out_all, skiprows=1)
assert (np.abs(dv1[:, 0] - ground_truth[:, 0]).sum() / len(dv1)) < 0.05
assert (np.abs(dv1[:, 1] - ground_truth[:, 1]).sum() / len(dv1)) < 0.05
assert (np.abs(dv1[:, 2] - ground_truth[:, 2]).sum() / len(dv1)) < 0.05
dvars = ComputeDVARS(
in_file=example_data('ds003_sub-01_mc.nii.gz'),
in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'),
save_all=True)
res = dvars.run()
dv1 = np.loadtxt(res.outputs.out_all, skiprows=1)
assert (np.abs(dv1[:, 0] - ground_truth[:, 0]).sum() / len(dv1)) < 0.05
assert (np.abs(dv1[:, 1] - ground_truth[:, 1]).sum() / len(dv1)) > 0.05
assert (np.abs(dv1[:, 2] - ground_truth[:, 2]).sum() / len(dv1)) < 0.05
def test_bedpostx2():
filelist, outdir, cwd = create_files_in_directory()
bpx = fsl.BEDPOSTX()
# make sure command gets called
yield assert_equal, bpx.cmd, 'bedpostx'
# test raising error with mandatory args absent
yield assert_raises, ValueError, bpx.run
# .inputs based parameters setting
bpx2 = fsl.BEDPOSTX()
bpx2.inputs.mask = example_data('mask.nii')
bpx2.inputs.dwi = example_data('diffusion.nii')
bpx2.inputs.bvals = example_data('bvals')
bpx2.inputs.bvecs = example_data('bvecs')
bpx2.inputs.fibres = 2
bpx2.inputs.weight = 0.3
bpx2.inputs.burn_period = 200
bpx2.inputs.jumps = 500
bpx2.inputs.sampling = 20
actualCmdline = sorted(bpx2.cmdline.split())
cmd = 'bedpostx bedpostx -b 200 -n 2 -j 500 -s 20 -w 0.30'
desiredCmdline = sorted(cmd.split())
yield assert_equal, actualCmdline, desiredCmdline
def test_reg_aladin():
# Create a reg_aladin object
nr = RegAladin()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_aladin')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
rmask_file = example_data('mask.nii')
nr.inputs.ref_file = ref_file
nr.inputs.flo_file = flo_file
nr.inputs.rmask_file = rmask_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -aff {aff} -flo {flo} -omp 4 -ref {ref} -res {res} \
-rmask {rmask}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_aladin'),
aff=os.path.join(os.getcwd(), 'im2_aff.txt'),
flo=flo_file,
ref=ref_file,
res=os.path.join(os.getcwd(), 'im2_res.nii.gz'),
rmask=rmask_file)
assert nr.cmdline == expected_cmd
def test_reg_jacobian_jac_l():
# Create a reg_jacobian object
nr = RegJacobian()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_jacobian')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr.inputs.ref_file = ref_file
nr.inputs.trans_file = trans_file
nr.inputs.type = 'jacL'
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jacL {jac}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_jacobian'),
ref=ref_file,
trans=trans_file,
jac=os.path.join(os.getcwd(),
'warpfield_jacL.nii.gz'))
assert nr.cmdline == expected_cmd
def test_seg_filllesions():
# Create a node object
seg_fill = FillLesions()
# Check if the command is properly defined
assert seg_fill.cmd == get_custom_path('seg_FillLesions')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
seg_fill.run()
# Assign some input data
in_file = example_data('im1.nii')
lesion_mask = example_data('im2.nii')
seg_fill.inputs.in_file = in_file
seg_fill.inputs.lesion_mask = lesion_mask
expected_cmd = '{cmd} -i {in_file} -l {lesion_mask} -o {out_file}'.format(
cmd=get_custom_path('seg_FillLesions'),
in_file=in_file,
lesion_mask=lesion_mask,
out_file=os.path.join(os.getcwd(), 'im1_lesions_filled.nii'))
assert seg_fill.cmdline == expected_cmd
def test_reg_f3d():
""" tests for reg_f3d interface"""
# Create a reg_f3d object
nr_f3d = RegF3D()
# Check if the command is properly defined
assert nr_f3d.cmd == get_custom_path('reg_f3d')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_f3d.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
rmask_file = example_data('mask.nii')
nr_f3d.inputs.ref_file = ref_file
nr_f3d.inputs.flo_file = flo_file
nr_f3d.inputs.rmask_file = rmask_file
nr_f3d.inputs.omp_core_val = 4
nr_f3d.inputs.vel_flag = True
nr_f3d.inputs.be_val = 0.1
nr_f3d.inputs.le_val = 0.1
cmd_tmp = '{cmd} -be 0.100000 -cpp {cpp} -flo {flo} -le 0.100000 -omp 4 \
-ref {ref} -res {res} -rmask {rmask} -vel'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_f3d'),
cpp=os.path.join(os.getcwd(), 'im2_cpp.nii.gz'),
flo=flo_file,
ref=ref_file,
res=os.path.join(os.getcwd(), 'im2_res.nii.gz'),
rmask=rmask_file)
assert nr_f3d.cmdline == expected_cmd
def test_staple():
# Create a node object
staple = LabelFusion()
# Check if the command is properly defined
assert staple.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
staple.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
staple.inputs.in_file = in_file
staple.inputs.kernel_size = 2.0
staple.inputs.file_to_seg = file_to_seg
staple.inputs.template_file = template_file
staple.inputs.template_num = 2
staple.inputs.classifier_type = 'STAPLE'
cmd_tmp = '{cmd} -in {in_file} -STAPLE -ALL -out {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_LabFusion'),
in_file=in_file,
file_to_seg=file_to_seg,
template_file=template_file,
out_file=os.path.join(os.getcwd(), 'im1_staple.nii'))
assert staple.cmdline == expected_cmd
def test_mv():
# Create a node object
mv = LabelFusion()
# Check if the command is properly defined
assert mv.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
mv.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
mv.inputs.in_file = in_file
mv.inputs.file_to_seg = file_to_seg
mv.inputs.template_file = template_file
mv.inputs.template_num = 2
mv.inputs.classifier_type = 'MV'
mv.inputs.sm_ranking = 'ROINCC'
mv.inputs.dilation_roi = 2
cmd_tmp = '{cmd} -in {in_file} -MV -ROINCC 2 2 {file_to_seg} \
{template_file} -out {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_LabFusion'),
in_file=in_file,
file_to_seg=file_to_seg,
template_file=template_file,
out_file=os.path.join(os.getcwd(), 'im1_mv.nii'))
assert mv.cmdline == expected_cmd
def test_reg_average_avg_nii():
# Create a reg_average object
nr = RegAverage()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_average')
# Assign some input data
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
nr.inputs.avg_files = [one_file, two_file, three_file]
nr.cmdline
# Read the reg_average_cmd
reg_average_cmd = os.path.join(os.getcwd(), 'reg_average_cmd')
with open(reg_average_cmd, 'rb') as f:
argv = f.read()
os.remove(reg_average_cmd)
expected_argv = '%s %s -avg %s %s %s' % (get_custom_path(
'reg_average'), os.path.join(
os.getcwd(), 'avg_out.nii.gz'), one_file, two_file, three_file)
assert argv == expected_argv
expected_cmd = ('%s --cmd_file %s' %
(get_custom_path('reg_average'), reg_average_cmd))
assert nr.cmdline == expected_cmd
def test_reg_measure():
""" tests for reg_measure interface """
# Create a reg_measure object
nr_measure = RegMeasure()
# Check if the command is properly defined
assert nr_measure.cmd == get_custom_path('reg_measure')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_measure.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
nr_measure.inputs.ref_file = ref_file
nr_measure.inputs.flo_file = flo_file
nr_measure.inputs.measure_type = 'lncc'
nr_measure.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -flo {flo} -lncc -omp 4 -out {out} -ref {ref}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_measure'),
flo=flo_file,
out='im2_lncc.txt',
ref=ref_file)
assert nr_measure.cmdline == expected_cmd
def test_dvars(tmpdir):
ground_truth = np.loadtxt(example_data('ds003_sub-01_mc.DVARS'))
dvars = ComputeDVARS(in_file=example_data('ds003_sub-01_mc.nii.gz'),
in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'),
save_all=True,
intensity_normalization=0)
os.chdir(str(tmpdir))
res = dvars.run()
dv1 = np.loadtxt(res.outputs.out_all, skiprows=1)
assert (np.abs(dv1[:, 0] - ground_truth[:, 0]).sum()/ len(dv1)) < 0.05
assert (np.abs(dv1[:, 1] - ground_truth[:, 1]).sum() / len(dv1)) < 0.05
assert (np.abs(dv1[:, 2] - ground_truth[:, 2]).sum() / len(dv1)) < 0.05
dvars = ComputeDVARS(in_file=example_data('ds003_sub-01_mc.nii.gz'),
in_mask=example_data(
'ds003_sub-01_mc_brainmask.nii.gz'),
save_all=True)
res = dvars.run()
dv1 = np.loadtxt(res.outputs.out_all, skiprows=1)
assert (np.abs(dv1[:, 0] - ground_truth[:, 0]).sum() / len(dv1)) < 0.05
assert (np.abs(dv1[:, 1] - ground_truth[:, 1]).sum() / len(dv1)) > 0.05
assert (np.abs(dv1[:, 2] - ground_truth[:, 2]).sum() / len(dv1)) < 0.05
def test_merge():
# Create a node object
merge = Merge()
# Check if the command is properly defined
assert merge.cmd == get_custom_path('seg_maths')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
merge.run()
# Assign some input data
in_file = example_data('im1.nii')
file1 = example_data('im2.nii')
file2 = example_data('im3.nii')
merge.inputs.in_file = in_file
merge.inputs.merge_files = [file1, file2]
merge.inputs.dimension = 2
merge.inputs.output_datatype = 'float'
cmd_tmp = '{cmd} {in_file} -merge 2 2 {f1} {f2} -odt float {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_maths'),
in_file=in_file,
f1=file1,
f2=file2,
out_file=os.path.join(os.getcwd(), 'im1_merged.nii'))
assert merge.cmdline == expected_cmd
def test_tuple_maths():
# Create a node object
tuplem = TupleMaths()
# Check if the command is properly defined
assert tuplem.cmd == get_custom_path('seg_maths')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
tuplem.run()
# Assign some input data
in_file = example_data('im1.nii')
op_file = example_data('im2.nii')
tuplem.inputs.in_file = in_file
tuplem.inputs.operation = 'lncc'
tuplem.inputs.operand_file1 = op_file
tuplem.inputs.operand_value2 = 2.0
tuplem.inputs.output_datatype = 'float'
cmd_tmp = '{cmd} {in_file} -lncc {op} 2.00000000 -odt float {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_maths'),
in_file=in_file,
op=op_file,
out_file=os.path.join(os.getcwd(), 'im1_lncc.nii'))
assert tuplem.cmdline == expected_cmd
def test_seg_em():
# Create a reg_aladin object
test_node = FitDwi()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_dwi')
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
test_node.inputs.source_file = in_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_file
cmd_tmp = '{cmd} -bval {bval} -bvec {bvec} -famap dwifit__famap -mcmap \
dwifit__mcmap -mdmap dwifit__mdmap -res dwifit__resmap -rgbmap dwifit__rgbmap \
-source {in_file} -syn dwifit__syn -tenmap2 dwifit__tenmap2 -v1map \
dwifit__v1map'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_dwi'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file)
yield assert_equal, test_node.cmdline, expected_cmd
def test_JointFusion_cmd():
at = JointFusion()
at.inputs.dimension = 3
at.inputs.modalities = 1
at.inputs.method = 'Joint[0.1,2]'
at.inputs.output_label_image = 'fusion_labelimage_output.nii'
warped_intensity_images = [example_data('im1.nii'),
example_data('im2.nii')]
at.inputs.warped_intensity_images = warped_intensity_images
segmentation_images = [example_data('segmentation0.nii.gz'),
example_data('segmentation1.nii.gz')]
at.inputs.warped_label_images = segmentation_images
T1_image = example_data('T1.nii')
at.inputs.target_image = T1_image
at.inputs.patch_radius = [3,2,1]
at.inputs.search_radius = [1,2,3]
expected_command = ('jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3'
' -tg %s -g %s -g %s -l %s -l %s'
' fusion_labelimage_output.nii') % (T1_image,
warped_intensity_images[0],
warped_intensity_images[1],
segmentation_images[0],
segmentation_images[1])
yield assert_equal, at.cmdline, expected_command
# setting intensity or labels with unequal lengths raises error
yield assert_raises, AssertionError, at._format_arg, 'warped_intensity_images', InputMultiPath, warped_intensity_images + [example_data('im3.nii')]
def test_normalize_tpms(tmpdir):
tempdir = str(tmpdir)
in_mask = example_data('tpms_msk.nii.gz')
mskdata = nb.load(in_mask, mmap=NUMPY_MMAP).get_data()
mskdata[mskdata > 0.0] = 1.0
mapdata = []
in_files = []
out_files = []
for i in range(3):
mapname = example_data('tpm_%02d.nii.gz' % i)
filename = os.path.join(tempdir, 'modtpm_%02d.nii.gz' % i)
out_files.append(os.path.join(tempdir, 'normtpm_%02d.nii.gz' % i))
im = nb.load(mapname, mmap=NUMPY_MMAP)
data = im.get_data()
mapdata.append(data.copy())
nb.Nifti1Image(2.0 * (data * mskdata), im.affine,
im.header).to_filename(filename)
in_files.append(filename)
normalize_tpms(in_files, in_mask, out_files=out_files)
sumdata = np.zeros_like(mskdata)
for i, tstfname in enumerate(out_files):
normdata = nb.load(tstfname, mmap=NUMPY_MMAP).get_data()
sumdata += normdata
assert np.all(normdata[mskdata == 0] == 0)
assert np.allclose(normdata, mapdata[i])
assert np.allclose(sumdata[sumdata > 0.0], 1.0)
def test_reg_average_avg_nii():
# Create a reg_average object
nr = RegAverage()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_average')
# Assign some input data
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
nr.inputs.avg_files = [one_file, two_file, three_file]
nr.cmdline
# Read the reg_average_cmd
reg_average_cmd = os.path.join(os.getcwd(), 'reg_average_cmd')
with open(reg_average_cmd, 'rb') as f:
argv = f.read()
os.remove(reg_average_cmd)
expected_argv = '%s %s -avg %s %s %s' % (get_custom_path('reg_average'),
os.path.join(os.getcwd(),
'avg_out.nii.gz'),
one_file, two_file, three_file)
yield assert_equal, argv, expected_argv
expected_cmd = ('%s --cmd_file %s'
% (get_custom_path('reg_average'), reg_average_cmd))
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_resample_blank():
# Create a reg_resample object
nr = RegResample()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_resample')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
trans_file = example_data('warpfield.nii')
nr.inputs.ref_file = ref_file
nr.inputs.flo_file = flo_file
nr.inputs.trans_file = trans_file
nr.inputs.type = 'blank'
nr.inputs.inter_val = 'LIN'
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -flo {flo} -inter 1 -omp 4 -ref {ref} -trans {trans} \
-blank {blank}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_resample'),
flo=flo_file,
ref=ref_file,
trans=trans_file,
blank=os.path.join(os.getcwd(),
'im2_blank.nii.gz'))
assert nr.cmdline == expected_cmd
def test_overlap():
from nipype.algorithms.metrics import Overlap
def check_close(val1, val2):
import numpy.testing as npt
return npt.assert_almost_equal(val1, val2, decimal=3)
tempdir = mkdtemp()
in1 = example_data('segmentation0.nii.gz')
in2 = example_data('segmentation1.nii.gz')
os.chdir(tempdir)
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in1
res = overlap.run()
yield check_close, res.outputs.jaccard, 1.0
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
res = overlap.run()
yield check_close, res.outputs.jaccard, 0.99705
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
overlap.inputs.vol_units = 'mm'
res = overlap.run()
yield check_close, res.outputs.jaccard, 0.99705
yield (check_close, res.outputs.roi_voldiff,
np.array([0.0063086, -0.0025506, 0.0]))
rmtree(tempdir)
def test_merge():
# Create a node object
merge = Merge()
# Check if the command is properly defined
assert merge.cmd == get_custom_path('seg_maths')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
merge.run()
# Assign some input data
in_file = example_data('im1.nii')
file1 = example_data('im2.nii')
file2 = example_data('im3.nii')
merge.inputs.in_file = in_file
merge.inputs.merge_files = [file1, file2]
merge.inputs.dimension = 2
merge.inputs.output_datatype = 'float'
cmd_tmp = '{cmd} {in_file} -merge 2 2 {f1} {f2} -odt float {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('seg_maths'),
in_file=in_file,
f1=file1,
f2=file2,
out_file=os.path.join(
os.getcwd(), 'im1_merged.nii'))
print merge.cmdline
print '\n'
print expected_cmd
assert merge.cmdline == expected_cmd
def test_reg_resample_blank():
# Create a reg_resample object
nr = RegResample()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_resample')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
trans_file = example_data('warpfield.nii')
nr.inputs.ref_file = ref_file
nr.inputs.flo_file = flo_file
nr.inputs.trans_file = trans_file
nr.inputs.type = 'blank'
nr.inputs.inter_val = 'LIN'
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -flo {flo} -inter 1 -omp 4 -ref {ref} -trans {trans} \
-blank {blank}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_resample'),
flo=flo_file,
ref=ref_file,
trans=trans_file,
blank=os.path.join(os.getcwd(), 'im2_blank.nii.gz'))
assert nr.cmdline == expected_cmd
def test_tuple_maths():
# Create a node object
tuplem = TupleMaths()
# Check if the command is properly defined
assert tuplem.cmd == get_custom_path('seg_maths')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
tuplem.run()
# Assign some input data
in_file = example_data('im1.nii')
op_file = example_data('im2.nii')
tuplem.inputs.in_file = in_file
tuplem.inputs.operation = 'lncc'
tuplem.inputs.operand_file1 = op_file
tuplem.inputs.operand_value2 = 2.0
tuplem.inputs.output_datatype = 'float'
cmd_tmp = '{cmd} {in_file} -lncc {op} 2.00000000 -odt float {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('seg_maths'),
in_file=in_file,
op=op_file,
out_file=os.path.join(
os.getcwd(), 'im1_lncc.nii'))
assert tuplem.cmdline == expected_cmd
def test_seg_patchmatch():
# Create a node object
seg_patchmatch = PatchMatch()
# Check if the command is properly defined
cmd = get_custom_path('seg_PatchMatch', env_dir='NIFTYSEGDIR')
assert seg_patchmatch.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
seg_patchmatch.run()
# Assign some input data
in_file = example_data('im1.nii')
mask_file = example_data('im2.nii')
db_file = example_data('db.xml')
seg_patchmatch.inputs.in_file = in_file
seg_patchmatch.inputs.mask_file = mask_file
seg_patchmatch.inputs.database_file = db_file
cmd_tmp = '{cmd} -i {in_file} -m {mask_file} -db {db} -o {out_file}'
expected_cmd = cmd_tmp.format(
cmd=cmd,
in_file=in_file,
mask_file=mask_file,
db=db_file,
out_file='im1_pm.nii.gz',
)
assert seg_patchmatch.cmdline == expected_cmd
def test_JointFusion_cmd():
at = JointFusion()
at.inputs.dimension = 3
at.inputs.modalities = 1
at.inputs.method = 'Joint[0.1,2]'
at.inputs.output_label_image = 'fusion_labelimage_output.nii'
warped_intensity_images = [example_data('im1.nii'),
example_data('im2.nii')]
at.inputs.warped_intensity_images = warped_intensity_images
segmentation_images = [example_data('segmentation0.nii.gz'),
example_data('segmentation1.nii.gz')]
at.inputs.warped_label_images = segmentation_images
T1_image = example_data('T1.nii')
at.inputs.target_image = T1_image
at.inputs.patch_radius = [3,2,1]
at.inputs.search_radius = [1,2,3]
expected_command = ('jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3'
' -tg %s -g %s -g %s -l %s -l %s'
' fusion_labelimage_output.nii') % (T1_image,
warped_intensity_images[0],
warped_intensity_images[1],
segmentation_images[0],
segmentation_images[1])
yield assert_equal, at.cmdline, expected_command
# setting intensity or labels with unequal lengths raises error
yield assert_raises, AssertionError, at._format_arg, 'warped_intensity_images', InputMultiPath, warped_intensity_images + [example_data('im3.nii')]
def test_reg_measure():
""" tests for reg_measure interface """
# Create a reg_measure object
nr_measure = RegMeasure()
# Check if the command is properly defined
assert nr_measure.cmd == get_custom_path('reg_measure')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_measure.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
nr_measure.inputs.ref_file = ref_file
nr_measure.inputs.flo_file = flo_file
nr_measure.inputs.measure_type = 'lncc'
nr_measure.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -flo {flo} -lncc -omp 4 -out {out} -ref {ref}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_measure'),
flo=flo_file,
out=os.path.join(os.getcwd(),
'im2_lncc.txt'),
ref=ref_file)
assert nr_measure.cmdline == expected_cmd
def test_bedpostx2():
filelist, outdir, cwd = create_files_in_directory()
bpx = fsl.BEDPOSTX()
# make sure command gets called
yield assert_equal, bpx.cmd, 'bedpostx'
# test raising error with mandatory args absent
yield assert_raises, ValueError, bpx.run
# .inputs based parameters setting
bpx2 = fsl.BEDPOSTX()
bpx2.inputs.mask = example_data('mask.nii')
bpx2.inputs.dwi = example_data('diffusion.nii')
bpx2.inputs.bvals = example_data('bvals')
bpx2.inputs.bvecs = example_data('bvecs')
bpx2.inputs.fibres = 2
bpx2.inputs.weight = 0.3
bpx2.inputs.burn_period = 200
bpx2.inputs.jumps = 500
bpx2.inputs.sampling = 20
actualCmdline = sorted(bpx2.cmdline.split())
cmd = 'bedpostx bedpostx -b 200 -n 2 -j 500 -s 20 -w 0.30'
desiredCmdline = sorted(cmd.split())
yield assert_equal, actualCmdline, desiredCmdline
def test_seg_calctopncc():
""" Test interfaces for seg_CalctoNCC"""
# Create a node object
calctopncc = CalcTopNCC()
# Check if the command is properly defined
assert calctopncc.cmd == get_custom_path('seg_CalcTopNCC')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
calctopncc.run()
# Assign some input data
in_file = example_data('im1.nii')
file1 = example_data('im2.nii')
file2 = example_data('im3.nii')
calctopncc.inputs.in_file = in_file
calctopncc.inputs.num_templates = 2
calctopncc.inputs.in_templates = [file1, file2]
calctopncc.inputs.top_templates = 1
cmd_tmp = '{cmd} -target {in_file} -templates 2 {file1} {file2} -n 1'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('seg_CalcTopNCC'),
in_file=in_file,
file1=file1,
file2=file2)
assert calctopncc.cmdline == expected_cmd
def test_overlap(tmpdir):
from nipype.algorithms.metrics import Overlap
def check_close(val1, val2):
import numpy.testing as npt
return npt.assert_almost_equal(val1, val2, decimal=3)
in1 = example_data("segmentation0.nii.gz")
in2 = example_data("segmentation1.nii.gz")
os.chdir(str(tmpdir))
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in1
res = overlap.run()
check_close(res.outputs.jaccard, 1.0)
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
res = overlap.run()
check_close(res.outputs.jaccard, 0.99705)
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
overlap.inputs.vol_units = "mm"
res = overlap.run()
check_close(res.outputs.jaccard, 0.99705)
check_close(res.outputs.roi_voldiff, np.array([0.0063086, -0.0025506, 0.0]))
def test_overlap():
from nipype.algorithms.metrics import Overlap
def check_close(val1, val2):
import numpy.testing as npt
return npt.assert_almost_equal(val1, val2, decimal=3)
tempdir = mkdtemp()
in1 = example_data('segmentation0.nii.gz')
in2 = example_data('segmentation1.nii.gz')
os.chdir(tempdir)
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in1
res = overlap.run()
yield check_close, res.outputs.jaccard, 1.0
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
res = overlap.run()
yield check_close, res.outputs.jaccard, 0.99705
overlap = Overlap()
overlap.inputs.volume1 = in1
overlap.inputs.volume2 = in2
overlap.inputs.vol_units = 'mm'
res = overlap.run()
yield check_close, res.outputs.jaccard, 0.99705
yield (check_close, res.outputs.roi_voldiff,
np.array([0.0063086, -0.0025506, 0.0]))
rmtree(tempdir)
def test_reg_aladin():
""" tests for reg_aladin interface"""
# Create a reg_aladin object
nr_aladin = RegAladin()
# Check if the command is properly defined
assert nr_aladin.cmd == get_custom_path('reg_aladin')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_aladin.run()
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
rmask_file = example_data('mask.nii')
nr_aladin.inputs.ref_file = ref_file
nr_aladin.inputs.flo_file = flo_file
nr_aladin.inputs.rmask_file = rmask_file
nr_aladin.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -aff {aff} -flo {flo} -omp 4 -ref {ref} -res {res} \
-rmask {rmask}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_aladin'),
aff='im2_aff.txt',
flo=flo_file,
ref=ref_file,
res='im2_res.nii.gz',
rmask=rmask_file,
)
assert nr_aladin.cmdline == expected_cmd
def test_seg_calctopncc():
""" Test interfaces for seg_CalctoNCC"""
# Create a node object
calctopncc = CalcTopNCC()
# Check if the command is properly defined
assert calctopncc.cmd == get_custom_path('seg_CalcTopNCC')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
calctopncc.run()
# Assign some input data
in_file = example_data('im1.nii')
file1 = example_data('im2.nii')
file2 = example_data('im3.nii')
calctopncc.inputs.in_file = in_file
calctopncc.inputs.num_templates = 2
calctopncc.inputs.in_templates = [file1, file2]
calctopncc.inputs.top_templates = 1
cmd_tmp = '{cmd} -target {in_file} -templates 2 {file1} {file2} -n 1'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_CalcTopNCC'),
in_file=in_file,
file1=file1,
file2=file2
)
assert calctopncc.cmdline == expected_cmd
def test_reg_transform_comp_nii():
# Create a reg_transform object
nr = RegTransform()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_transform')
# Assign some input data
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
trans2_file = example_data('anatomical.nii')
nr.inputs.ref1_file = ref_file
nr.inputs.comp_input2 = trans2_file
nr.inputs.comp_input = trans_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -ref {ref_file} -omp 4 -comp {trans1} {trans2} {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_transform'),
ref_file=ref_file,
trans1=trans_file,
trans2=trans2_file,
out_file=os.path.join(os.getcwd(), 'warpfield_trans.nii.gz'))
assert nr.cmdline == expected_cmd
def test_fd():
tempdir = mkdtemp()
ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt'))
fd = FramewiseDisplacement(in_plots=example_data('fsl_mcflirt_movpar.txt'),
out_file=tempdir + '/fd.txt')
res = fd.run()
yield assert_equal, np.allclose(ground_truth, np.loadtxt(res.outputs.out_file)), True
yield assert_equal, np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-4, True
rmtree(tempdir)
def setUp(self):
self.accuracy = 10
self.path_to_fixed = example_data("segmentation0.nii.gz")
self.path_to_moving = example_data("segmentation1.nii.gz")
self.fixed_sitk = sitk.ReadImage(self.path_to_fixed)
self.moving_sitk = sitk.ReadImage(self.path_to_moving)
def test_BaseInterface_load_save_inputs():
tmp_dir = tempfile.mkdtemp()
tmp_json = os.path.join(tmp_dir, 'settings.json')
class InputSpec(nib.TraitedSpec):
input1 = nib.traits.Int()
input2 = nib.traits.Float()
input3 = nib.traits.Bool()
input4 = nib.traits.Str()
class DerivedInterface(nib.BaseInterface):
input_spec = InputSpec
def __init__(self, **inputs):
super(DerivedInterface, self).__init__(**inputs)
inputs_dict = {'input1': 12, 'input3': True, 'input4': 'some string'}
bif = DerivedInterface(**inputs_dict)
bif.save_inputs_to_json(tmp_json)
bif2 = DerivedInterface()
bif2.load_inputs_from_json(tmp_json)
yield assert_equal, bif2.inputs.get_traitsfree(), inputs_dict
bif3 = DerivedInterface(from_file=tmp_json)
yield assert_equal, bif3.inputs.get_traitsfree(), inputs_dict
inputs_dict2 = inputs_dict.copy()
inputs_dict2.update({'input4': 'some other string'})
bif4 = DerivedInterface(from_file=tmp_json, input4=inputs_dict2['input4'])
yield assert_equal, bif4.inputs.get_traitsfree(), inputs_dict2
bif5 = DerivedInterface(input4=inputs_dict2['input4'])
bif5.load_inputs_from_json(tmp_json, overwrite=False)
yield assert_equal, bif5.inputs.get_traitsfree(), inputs_dict2
bif6 = DerivedInterface(input4=inputs_dict2['input4'])
bif6.load_inputs_from_json(tmp_json)
yield assert_equal, bif6.inputs.get_traitsfree(), inputs_dict
# test get hashval in a complex interface
from nipype.interfaces.ants import Registration
settings = example_data(
example_data('smri_ants_registration_settings.json'))
with open(settings) as setf:
data_dict = json.load(setf)
tsthash = Registration()
tsthash.load_inputs_from_json(settings)
yield assert_equal, {}, check_dict(data_dict,
tsthash.inputs.get_traitsfree())
tsthash2 = Registration(from_file=settings)
yield assert_equal, {}, check_dict(data_dict,
tsthash2.inputs.get_traitsfree())
_, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp')
yield assert_equal, 'ec5755e07287e04a4b409e03b77a517c', hashvalue
def setUp(self):
self.accuracy = 10
self.path_to_fixed = example_data("segmentation0.nii.gz")
self.path_to_moving = example_data("segmentation1.nii.gz")
self.fixed = st.Stack.from_filename(self.path_to_fixed)
self.moving = st.Stack.from_filename(self.path_to_moving)
def test_dvars(tmpdir):
ground_truth = np.loadtxt(example_data('ds003_sub-01_mc.DVARS'))
dvars = ComputeDVARS(in_file=example_data('ds003_sub-01_mc.nii.gz'),
in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'),
save_all=True)
os.chdir(str(tmpdir))
res = dvars.run()
dv1 = np.loadtxt(res.outputs.out_std)
assert (np.abs(dv1 - ground_truth).sum()/ len(dv1)) < 0.05
def test_BaseInterface_load_save_inputs():
tmp_dir = tempfile.mkdtemp()
tmp_json = os.path.join(tmp_dir, 'settings.json')
class InputSpec(nib.TraitedSpec):
input1 = nib.traits.Int()
input2 = nib.traits.Float()
input3 = nib.traits.Bool()
input4 = nib.traits.Str()
class DerivedInterface(nib.BaseInterface):
input_spec = InputSpec
def __init__(self, **inputs):
super(DerivedInterface, self).__init__(**inputs)
inputs_dict = {'input1': 12, 'input3': True,
'input4': 'some string'}
bif = DerivedInterface(**inputs_dict)
bif.save_inputs_to_json(tmp_json)
bif2 = DerivedInterface()
bif2.load_inputs_from_json(tmp_json)
yield assert_equal, bif2.inputs.get_traitsfree(), inputs_dict
bif3 = DerivedInterface(from_file=tmp_json)
yield assert_equal, bif3.inputs.get_traitsfree(), inputs_dict
inputs_dict2 = inputs_dict.copy()
inputs_dict2.update({'input4': 'some other string'})
bif4 = DerivedInterface(from_file=tmp_json, input4=inputs_dict2['input4'])
yield assert_equal, bif4.inputs.get_traitsfree(), inputs_dict2
bif5 = DerivedInterface(input4=inputs_dict2['input4'])
bif5.load_inputs_from_json(tmp_json, overwrite=False)
yield assert_equal, bif5.inputs.get_traitsfree(), inputs_dict2
bif6 = DerivedInterface(input4=inputs_dict2['input4'])
bif6.load_inputs_from_json(tmp_json)
yield assert_equal, bif6.inputs.get_traitsfree(), inputs_dict
# test get hashval in a complex interface
from nipype.interfaces.ants import Registration
settings = example_data(example_data('smri_ants_registration_settings.json'))
with open(settings) as setf:
data_dict = json.load(setf)
tsthash = Registration()
tsthash.load_inputs_from_json(settings)
yield assert_equal, {}, check_dict(data_dict, tsthash.inputs.get_traitsfree())
tsthash2 = Registration(from_file=settings)
yield assert_equal, {}, check_dict(data_dict, tsthash2.inputs.get_traitsfree())
_, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp')
yield assert_equal, 'ec5755e07287e04a4b409e03b77a517c', hashvalue
def test_dvars(tmpdir):
ground_truth = np.loadtxt(example_data('ds003_sub-01_mc.DVARS'))
dvars = ComputeDVARS(
in_file=example_data('ds003_sub-01_mc.nii.gz'),
in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'),
save_all=True)
os.chdir(str(tmpdir))
res = dvars.run()
dv1 = np.loadtxt(res.outputs.out_std)
assert (np.abs(dv1 - ground_truth).sum() / len(dv1)) < 0.05
def test_apply_transform():
moving = example_data(infile="functional.nii")
mat = example_data(infile="trans.mat")
applymat = spmu.ApplyTransform(matlab_cmd="mymatlab")
assert applymat.inputs.matlab_cmd == "mymatlab"
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = "[p n e v] = spm_fileparts(V.fname);"
assert expected in scrpt
expected = "V.mat = transform.M * V.mat;"
assert expected in scrpt
def test_apply_transform():
moving = example_data(infile='functional.nii')
mat = example_data(infile='trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd='mymatlab')
assert_equal(applymat.inputs.matlab_cmd, 'mymatlab')
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = 'img_space = spm_get_space(infile);'
assert_equal(expected in scrpt, True)
expected = 'spm_get_space(infile, transform.M * img_space);'
assert_equal(expected in scrpt, True)
def test_apply_transform():
moving = example_data(infile='functional.nii')
mat = example_data(infile='trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd='mymatlab')
assert_equal(applymat.inputs.matlab_cmd, 'mymatlab')
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = '[p n e v] = spm_fileparts(V.fname);'
assert_equal(expected in scrpt, True)
expected = 'V.mat = transform.M * V.mat;'
assert_equal(expected in scrpt, True)
def test_fit_asl():
""" Testing FitAsl interface."""
# Create the test node
fit_asl = FitAsl()
# Check if the command is properly defined
cmd = get_custom_path('fit_asl', env_dir='NIFTYFIT_DIR')
assert fit_asl.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_asl.run()
# Tests on the interface:
# Runs cbf fitting assuming all tissue is GM!
in_file = example_data('asl.nii.gz')
fit_asl.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} -syn {syn}'
expected_cmd = cmd_tmp.format(
cmd=cmd,
in_file=in_file,
cbf='asl_cbf.nii.gz',
error='asl_error.nii.gz',
syn='asl_syn.nii.gz',
)
assert fit_asl.cmdline == expected_cmd
# Runs cbf fitting using IR/SR T1 data to estimate the local T1 and uses
# the segmentation data to fit tissue specific blood flow parameters
# (lambda,transit times,T1)
fit_asl2 = FitAsl(sig=True)
in_file = example_data('asl.nii.gz')
t1map = example_data('T1map.nii.gz')
seg = example_data('segmentation0.nii.gz')
fit_asl2.inputs.source_file = in_file
fit_asl2.inputs.t1map = t1map
fit_asl2.inputs.seg = seg
cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} \
-seg {seg} -sig -syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=cmd,
in_file=in_file,
t1map=t1map,
seg=seg,
cbf='asl_cbf.nii.gz',
error='asl_error.nii.gz',
syn='asl_syn.nii.gz',
)
assert fit_asl2.cmdline == expected_cmd
def test_apply_transform():
moving = example_data(infile="functional.nii")
mat = example_data(infile="trans.mat")
applymat = spmu.ApplyTransform(matlab_cmd="mymatlab")
assert_equal(applymat.inputs.matlab_cmd, "mymatlab")
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = "img_space = spm_get_space(infile);"
assert_equal(expected in scrpt, True)
expected = "spm_get_space(infile, M * img_space);"
assert_equal(expected in scrpt, True)
def test_apply_transform():
moving = example_data(infile='functional.nii')
mat = example_data(infile='trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd='mymatlab')
assert_equal(applymat.inputs.matlab_cmd, 'mymatlab')
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = '[p n e v] = spm_fileparts(V.fname);'
assert_equal(expected in scrpt, True)
expected = 'V.mat = transform.M * V.mat;'
assert_equal(expected in scrpt, True)
def test_read_csv():
"""Test that reading the data from csv file gives you back a reasonable
time-series object """
CA = nitime.CoherenceAnalyzer()
CA.inputs.TR = 1.89 # bogus value just to pass traits test
CA.inputs.in_file = example_data('fmri_timeseries_nolabels.csv')
yield assert_raises, ValueError, CA._read_csv
CA.inputs.in_file = example_data('fmri_timeseries.csv')
data, roi_names = CA._read_csv()
yield assert_equal, data[0][0], 10125.9
yield assert_equal, roi_names[0], 'WM'
def test_read_csv():
"""Test that reading the data from csv file gives you back a reasonable
time-series object """
CA = nitime.CoherenceAnalyzer()
CA.inputs.TR = 1.89 # bogus value just to pass traits test
CA.inputs.in_file = example_data('fmri_timeseries_nolabels.csv')
yield assert_raises, ValueError, CA._read_csv
CA.inputs.in_file = example_data('fmri_timeseries.csv')
data, roi_names = CA._read_csv()
yield assert_equal, data[0][0], 10125.9
yield assert_equal, roi_names[0], 'WM'