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_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_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_tools_iso():
# Create a reg_tools object
nr = RegTools()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_tools')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
in_file = example_data('im1.nii')
nr.inputs.in_file = in_file
nr.inputs.iso_flag = True
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -in {in_file} -iso -omp 4 -out {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_tools'),
in_file=in_file,
out_file=os.path.join(
os.getcwd(), 'im1_tools.nii.gz'))
assert nr.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_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_tools_iso():
# Create a reg_tools object
nr = RegTools()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_tools')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr.run()
# Assign some input data
in_file = example_data('im1.nii')
nr.inputs.in_file = in_file
nr.inputs.iso_flag = True
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -in {in_file} -iso -omp 4 -out {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_tools'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_tools.nii.gz'))
assert 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_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_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_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_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_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_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_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_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_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_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_reg_jacobian_jac():
""" Test interface for RegJacobian """
# Create a reg_jacobian object
nr_jacobian = RegJacobian()
# Check if the command is properly defined
assert nr_jacobian.cmd == get_custom_path('reg_jacobian')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_jacobian.run()
# Test Reg Jacobian: jac
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_jacobian.inputs.ref_file = ref_file
nr_jacobian.inputs.trans_file = trans_file
nr_jacobian.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jac {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_jac.nii.gz'))
assert nr_jacobian.cmdline == expected_cmd
# Test Reg Jacobian: jac m
nr_jacobian_2 = RegJacobian(type='jacM', omp_core_val=4)
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_jacobian_2.inputs.ref_file = ref_file
nr_jacobian_2.inputs.trans_file = trans_file
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jacM {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_jacM.nii.gz'))
assert nr_jacobian_2.cmdline == expected_cmd
# Test Reg Jacobian: jac l
nr_jacobian_3 = RegJacobian(type='jacL', omp_core_val=4)
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_jacobian_3.inputs.ref_file = ref_file
nr_jacobian_3.inputs.trans_file = trans_file
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_jacobian_3.cmdline == expected_cmd
def test_reg_jacobian_jac():
""" Test interface for RegJacobian """
# Create a reg_jacobian object
nr_jacobian = RegJacobian()
# Check if the command is properly defined
assert nr_jacobian.cmd == get_custom_path('reg_jacobian')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_jacobian.run()
# Test Reg Jacobian: jac
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_jacobian.inputs.ref_file = ref_file
nr_jacobian.inputs.trans_file = trans_file
nr_jacobian.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jac {jac}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_jacobian'),
ref=ref_file,
trans=trans_file,
jac='warpfield_jac.nii.gz')
assert nr_jacobian.cmdline == expected_cmd
# Test Reg Jacobian: jac m
nr_jacobian_2 = RegJacobian(type='jacM', omp_core_val=4)
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_jacobian_2.inputs.ref_file = ref_file
nr_jacobian_2.inputs.trans_file = trans_file
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jacM {jac}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_jacobian'),
ref=ref_file,
trans=trans_file,
jac='warpfield_jacM.nii.gz')
assert nr_jacobian_2.cmdline == expected_cmd
# Test Reg Jacobian: jac l
nr_jacobian_3 = RegJacobian(type='jacL', omp_core_val=4)
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_jacobian_3.inputs.ref_file = ref_file
nr_jacobian_3.inputs.trans_file = trans_file
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='warpfield_jacL.nii.gz')
assert nr_jacobian_3.cmdline == expected_cmd
def test_reg_resample_res():
""" tests for reg_resample interface """
# Create a reg_resample object
nr_resample = RegResample()
# Check if the command is properly defined
assert nr_resample.cmd == get_custom_path('reg_resample')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_resample.run()
# Resample res
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
trans_file = example_data('warpfield.nii')
nr_resample.inputs.ref_file = ref_file
nr_resample.inputs.flo_file = flo_file
nr_resample.inputs.trans_file = trans_file
nr_resample.inputs.inter_val = 'LIN'
nr_resample.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -flo {flo} -inter 1 -omp 4 -ref {ref} -trans {trans} \
-res {res}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_resample'),
flo=flo_file,
ref=ref_file,
trans=trans_file,
res='im2_res.nii.gz')
assert nr_resample.cmdline == expected_cmd
# test_reg_resample_blank()
nr_resample_2 = RegResample(type='blank', inter_val='LIN', omp_core_val=4)
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
trans_file = example_data('warpfield.nii')
nr_resample_2.inputs.ref_file = ref_file
nr_resample_2.inputs.flo_file = flo_file
nr_resample_2.inputs.trans_file = trans_file
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='im2_blank.nii.gz')
assert nr_resample_2.cmdline == expected_cmd
def test_reg_resample_res():
""" tests for reg_resample interface """
# Create a reg_resample object
nr_resample = RegResample()
# Check if the command is properly defined
assert nr_resample.cmd == get_custom_path('reg_resample')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_resample.run()
# Resample res
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
trans_file = example_data('warpfield.nii')
nr_resample.inputs.ref_file = ref_file
nr_resample.inputs.flo_file = flo_file
nr_resample.inputs.trans_file = trans_file
nr_resample.inputs.inter_val = 'LIN'
nr_resample.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -flo {flo} -inter 1 -omp 4 -ref {ref} -trans {trans} \
-res {res}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_resample'),
flo=flo_file,
ref=ref_file,
trans=trans_file,
res='im2_res.nii.gz')
assert nr_resample.cmdline == expected_cmd
# test_reg_resample_blank()
nr_resample_2 = RegResample(type='blank', inter_val='LIN', omp_core_val=4)
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
trans_file = example_data('warpfield.nii')
nr_resample_2.inputs.ref_file = ref_file
nr_resample_2.inputs.flo_file = flo_file
nr_resample_2.inputs.trans_file = trans_file
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='im2_blank.nii.gz')
assert nr_resample_2.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_seg_calctopncc():
""" Test interfaces for seg_CalctoNCC"""
# Create a node object
calctopncc = CalcTopNCC()
# Check if the command is properly defined
cmd = get_custom_path('seg_CalcTopNCC', env_dir='NIFTYSEGDIR')
assert calctopncc.cmd == cmd
# 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=cmd,
in_file=in_file,
file1=file1,
file2=file2,
)
assert calctopncc.cmdline == expected_cmd
def test_seg_em():
# Create a node object
seg_em = EM()
# Check if the command is properly defined
cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')
assert seg_em.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
seg_em.run()
# Assign some input data
in_file = example_data('im1.nii')
seg_em.inputs.in_file = in_file
seg_em.inputs.no_prior = 4
cmd_tmp = '{cmd} -in {in_file} -nopriors 4 -bc_out {bc_out} -out \
{out_file} -out_outlier {out_outlier}'
expected_cmd = cmd_tmp.format(
cmd=cmd,
in_file=in_file,
out_file='im1_em.nii.gz',
bc_out='im1_bc_em.nii.gz',
out_outlier='im1_outlier_em.nii.gz',
)
assert seg_em.cmdline == expected_cmd
def test_merge():
# Create a node object
merge = Merge()
# Check if the command is properly defined
cmd = get_custom_path('seg_maths', env_dir='NIFTYSEGDIR')
assert merge.cmd == cmd
# 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=cmd,
in_file=in_file,
f1=file1,
f2=file2,
out_file='im1_merged.nii')
assert merge.cmdline == expected_cmd
def test_binary_maths():
# Create a node object
binarym = BinaryMaths()
# Check if the command is properly defined
cmd = get_custom_path('seg_maths', env_dir='NIFTYSEGDIR')
assert binarym.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
binarym.run()
# Assign some input data
in_file = example_data('im1.nii')
binarym.inputs.in_file = in_file
binarym.inputs.operand_value = 2.0
binarym.inputs.operation = 'sub'
binarym.inputs.output_datatype = 'float'
cmd_tmp = '{cmd} {in_file} -sub 2.00000000 -odt float {out_file}'
expected_cmd = cmd_tmp.format(cmd=cmd,
in_file=in_file,
out_file='im1_sub.nii')
assert binarym.cmdline == expected_cmd
def test_seg_filllesions():
# Create a node object
seg_fill = FillLesions()
# Check if the command is properly defined
cmd = get_custom_path('seg_FillLesions', env_dir='NIFTYSEGDIR')
assert seg_fill.cmd == cmd
# 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=cmd,
in_file=in_file,
lesion_mask=lesion_mask,
out_file='im1_lesions_filled.nii.gz',
)
assert seg_fill.cmdline == expected_cmd
def test_reg_transform_def():
# Create a reg_transform object
nr = RegTransform()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_transform')
# Assign some input data
trans_file = example_data('warpfield.nii')
nr.inputs.def_input = trans_file
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_transform') + ' -omp 4 ' +\
'-def ' + trans_file + ' ' + os.getcwd() + os.sep + 'warpfield_trans.nii.gz'
yield assert_equal, nr.cmdline, expected_cmd
def test_seg_em():
# Create a node object
seg_em = EM()
# Check if the command is properly defined
cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')
assert seg_em.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
seg_em.run()
# Assign some input data
in_file = example_data('im1.nii')
seg_em.inputs.in_file = in_file
seg_em.inputs.no_prior = 4
cmd_tmp = '{cmd} -in {in_file} -nopriors 4 -bc_out {bc_out} -out \
{out_file} -out_outlier {out_outlier}'
expected_cmd = cmd_tmp.format(
cmd=cmd,
in_file=in_file,
out_file='im1_em.nii.gz',
bc_out='im1_bc_em.nii.gz',
out_outlier='im1_outlier_em.nii.gz',
)
assert seg_em.cmdline == expected_cmd
def test_tuple_maths():
# Create a node object
tuplem = TupleMaths()
# Check if the command is properly defined
cmd = get_custom_path('seg_maths', env_dir='NIFTYSEGDIR')
assert tuplem.cmd == cmd
# 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=cmd,
in_file=in_file,
op=op_file,
out_file='im1_lncc.nii')
assert tuplem.cmdline == expected_cmd
def test_reg_tools_iso():
# Create a reg_tools object
nr = RegTools()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_tools')
# Assign some input data
in_file = example_data('im1.nii')
nr.inputs.in_file = in_file
nr.inputs.iso_flag = True
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_tools') + ' ' + '-in ' + in_file + ' -iso ' +\
'-omp 4 ' + '-out ' + os.getcwd() + os.sep + 'im1_tools.nii.gz'
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_average_demean3():
# 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
ref_file = example_data('anatomical.nii')
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
aff1_file = example_data('TransformParameters.0.txt')
aff2_file = example_data('ants_Affine.txt')
aff3_file = example_data('elastix.txt')
trans1_file = example_data('roi01.nii')
trans2_file = example_data('roi02.nii')
trans3_file = example_data('roi03.nii')
nr.inputs.warp_files = [aff1_file, trans1_file, one_file,
aff2_file, trans2_file, two_file,
aff3_file, trans3_file, three_file]
nr.inputs.demean3_ref_file = ref_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 -demean3 %s %s %s %s %s %s %s %s %s %s'
% (get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.nii.gz'),
ref_file,
aff1_file, trans1_file, one_file,
aff2_file, trans2_file, two_file,
aff3_file, trans3_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_transform_comp_txt():
# Create a reg_transform object
nr = RegTransform()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_transform')
# Assign some input data
aff1_file = example_data('ants_Affine.txt')
aff2_file = example_data('elastix.txt')
nr.inputs.comp_input2 = aff2_file
nr.inputs.comp_input = aff1_file
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_transform') + ' -omp 4 ' +\
'-comp ' + aff1_file + ' ' + aff2_file + ' ' + os.getcwd() + os.sep + 'ants_Affine_trans.txt'
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_jacobian_jac():
# Create a reg_jacobian object
nr = RegJacobian()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_jacobian')
# 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.omp_core_val = 4
expected_cmd = get_custom_path('reg_jacobian') + ' -omp 4 ' + '-ref ' + ref_file + ' ' +\
'-trans ' + trans_file + ' -jac ' + os.getcwd() + os.sep + 'warpfield_jac.nii.gz'
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_average_demean3():
# 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
ref_file = example_data('anatomical.nii')
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
aff1_file = example_data('TransformParameters.0.txt')
aff2_file = example_data('ants_Affine.txt')
aff3_file = example_data('elastix.txt')
trans1_file = example_data('roi01.nii')
trans2_file = example_data('roi02.nii')
trans3_file = example_data('roi03.nii')
nr.inputs.warp_files = [
aff1_file, trans1_file, one_file, aff2_file, trans2_file, two_file,
aff3_file, trans3_file, three_file
]
nr.inputs.demean3_ref_file = ref_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 -demean3 %s %s %s %s %s %s %s %s %s %s' %
(get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.nii.gz'), ref_file,
aff1_file, trans1_file, one_file, aff2_file, trans2_file,
two_file, aff3_file, trans3_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():
# Create a reg_measure object
nr = RegMeasure()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_measure')
# Assign some input data
ref_file = example_data('im1.nii')
flo_file = example_data('im2.nii')
nr.inputs.ref_file = ref_file
nr.inputs.flo_file = flo_file
nr.inputs.measure_type = 'lncc'
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_measure') + ' ' + '-flo ' + flo_file + ' ' + '-lncc ' + '-omp 4 '+\
'-out ' + os.getcwd() + os.sep + 'im2_lncc.txt ' + '-ref ' + ref_file
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_transform_flirt():
# Create a reg_transform object
nr = RegTransform()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_transform')
# Assign some input data
aff_file = example_data('elastix.txt')
ref_file = example_data('im1.nii')
in_file = example_data('im2.nii')
nr.inputs.flirt_2_nr_input = (aff_file, ref_file, in_file)
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_transform') + ' -omp 4 ' +\
'-flirtAff2NR ' + '%s %s %s' % (aff_file, ref_file, in_file) + ' ' +\
os.getcwd() + os.sep + 'elastix_trans.txt'
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_transform_def():
# 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
trans_file = example_data('warpfield.nii')
nr.inputs.def_input = trans_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -def {trans_file} {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_transform'),
trans_file=trans_file,
out_file=os.path.join(os.getcwd(), 'warpfield_trans.nii.gz'))
assert nr.cmdline == expected_cmd
def test_reg_transform_def():
# 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
trans_file = example_data('warpfield.nii')
nr.inputs.def_input = trans_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -def {trans_file} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
trans_file=trans_file,
out_file=os.path.join(
os.getcwd(), 'warpfield_trans.nii.gz'))
assert nr.cmdline == expected_cmd
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_reg_average_avg_ref():
# 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
ref_file = example_data('anatomical.nii')
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
trans1_file = example_data('roi01.nii')
trans2_file = example_data('roi02.nii')
trans3_file = example_data('roi03.nii')
nr.inputs.warp_files = [trans1_file, one_file,
trans2_file, two_file,
trans3_file, three_file]
nr.inputs.avg_ref_file = ref_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_tran %s %s %s %s %s %s %s'
% (get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.nii.gz'),
ref_file, trans1_file, one_file, trans2_file, two_file,
trans3_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_aladin():
# Create a reg_aladin object
nr = RegAladin()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path("reg_aladin")
# 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
expected_cmd = (
get_custom_path("reg_aladin")
+ " "
+ "-aff "
+ os.getcwd()
+ os.sep
+ "im2_aff.txt "
+ "-flo "
+ flo_file
+ " "
+ "-omp 4 "
+ "-ref "
+ ref_file
+ " "
+ "-res "
+ os.getcwd()
+ os.sep
+ "im2_res.nii.gz "
+ "-rmask "
+ rmask_file
)
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_resample_res():
# Create a reg_resample object
nr = RegResample()
# Check if the command is properly defined
yield assert_equal, nr.cmd, get_custom_path('reg_resample')
# 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.inter_val = 'LIN'
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_resample') + ' ' + '-flo ' + flo_file + ' ' + '-inter 1 -omp 4 ' +\
'-ref ' + ref_file + ' ' + '-trans ' + trans_file + ' ' +\
'-res ' + os.getcwd() + os.sep + 'im2_res.nii.gz'
yield assert_equal, nr.cmdline, expected_cmd
def test_reg_tools_mul():
""" tests for reg_tools interface """
# Create a reg_tools object
nr_tools = RegTools()
# Check if the command is properly defined
assert nr_tools.cmd == get_custom_path('reg_tools')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_tools.run()
# Test reg_tools: mul
in_file = example_data('im1.nii')
nr_tools.inputs.in_file = in_file
nr_tools.inputs.mul_val = 4
nr_tools.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -in {in_file} -mul 4.0 -omp 4 -out {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_tools'),
in_file=in_file,
out_file=os.path.join(
os.getcwd(), 'im1_tools.nii.gz'))
assert nr_tools.cmdline == expected_cmd
# Test reg_tools: iso
nr_tools_2 = RegTools(iso_flag=True, omp_core_val=4)
in_file = example_data('im1.nii')
nr_tools_2.inputs.in_file = in_file
cmd_tmp = '{cmd} -in {in_file} -iso -omp 4 -out {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_tools'),
in_file=in_file,
out_file=os.path.join(
os.getcwd(), 'im1_tools.nii.gz'))
assert nr_tools_2.cmdline == expected_cmd
def test_reg_tools_mul():
""" tests for reg_tools interface """
# Create a reg_tools object
nr_tools = RegTools()
# Check if the command is properly defined
assert nr_tools.cmd == get_custom_path('reg_tools')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
nr_tools.run()
# Test reg_tools: mul
in_file = example_data('im1.nii')
nr_tools.inputs.in_file = in_file
nr_tools.inputs.mul_val = 4
nr_tools.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -in {in_file} -mul 4.0 -omp 4 -out {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_tools'),
in_file=in_file,
out_file='im1_tools.nii.gz')
assert nr_tools.cmdline == expected_cmd
# Test reg_tools: iso
nr_tools_2 = RegTools(iso_flag=True, omp_core_val=4)
in_file = example_data('im1.nii')
nr_tools_2.inputs.in_file = in_file
cmd_tmp = '{cmd} -in {in_file} -iso -omp 4 -out {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_tools'),
in_file=in_file,
out_file='im1_tools.nii.gz')
assert nr_tools_2.cmdline == expected_cmd
def test_reg_transform_comp_txt():
# 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
aff1_file = example_data('ants_Affine.txt')
aff2_file = example_data('elastix.txt')
nr.inputs.comp_input2 = aff2_file
nr.inputs.comp_input = aff1_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -comp {aff1} {aff2} {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_transform'),
aff1=aff1_file,
aff2=aff2_file,
out_file=os.path.join(os.getcwd(), 'ants_Affine_trans.txt'))
assert nr.cmdline == expected_cmd
def test_reg_transform_comp_txt():
# 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
aff1_file = example_data('ants_Affine.txt')
aff2_file = example_data('elastix.txt')
nr.inputs.comp_input2 = aff2_file
nr.inputs.comp_input = aff1_file
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -comp {aff1} {aff2} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
aff1=aff1_file,
aff2=aff2_file,
out_file=os.path.join(
os.getcwd(), 'ants_Affine_trans.txt'))
assert nr.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='im2_cpp.nii.gz',
flo=flo_file,
ref=ref_file,
res='im2_res.nii.gz',
rmask=rmask_file,
)
assert nr_f3d.cmdline == expected_cmd
def test_reg_transform_flirt():
# 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
aff_file = example_data('elastix.txt')
ref_file = example_data('im1.nii')
in_file = example_data('im2.nii')
nr.inputs.flirt_2_nr_input = (aff_file, ref_file, in_file)
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -flirtAff2NR {aff} {ref} {in_file} {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('reg_transform'),
aff=aff_file,
ref=ref_file,
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'elastix_trans.txt'))
assert nr.cmdline == expected_cmd
def test_reg_transform_flirt():
# 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
aff_file = example_data('elastix.txt')
ref_file = example_data('im1.nii')
in_file = example_data('im2.nii')
nr.inputs.flirt_2_nr_input = (aff_file, ref_file, in_file)
nr.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -flirtAff2NR {aff} {ref} {in_file} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
aff=aff_file,
ref=ref_file,
in_file=in_file,
out_file=os.path.join(
os.getcwd(), 'elastix_trans.txt'))
assert nr.cmdline == expected_cmd
def test_dwi_tool():
""" Testing DwiTool interface."""
# Create a node object
dwi_tool = DwiTool()
# Check if the command is properly defined
cmd = get_custom_path('dwi_tool', env_dir='NIFTYFITDIR')
assert dwi_tool.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
dwi_tool.run()
# Assign some input data
in_file = example_data('dwi.nii.gz')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii.gz')
dwi_tool.inputs.source_file = in_file
dwi_tool.inputs.mask_file = mask_file
dwi_tool.inputs.bval_file = bval_file
dwi_tool.inputs.bvec_file = bvec_file
dwi_tool.inputs.b0_file = b0_file
dwi_tool.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -b0 {b0} \
-mask {mask} -dti -famap {fa} -logdti2 {log} -mcmap {mc} -mdmap {md} \
-rgbmap {rgb} -syn {syn} -v1map {v1}'
expected_cmd = cmd_tmp.format(cmd=cmd,
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
b0=b0_file,
mask=mask_file,
fa='dwi_famap.nii.gz',
log='dwi_logdti2.nii.gz',
mc='dwi_mcmap.nii.gz',
md='dwi_mdmap.nii.gz',
rgb='dwi_rgbmap.nii.gz',
syn='dwi_syn.nii.gz',
v1='dwi_v1map.nii.gz')
assert dwi_tool.cmdline == expected_cmd
def test_fit_dwi():
""" Testing FitDwi interface."""
# Create a node object
fit_dwi = FitDwi()
# Check if the command is properly defined
cmd = get_custom_path('fit_dwi', env_dir='NIFTYFITDIR')
assert fit_dwi.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_dwi.run()
# Assign some input data
in_file = example_data('dwi.nii.gz')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
fit_dwi.inputs.source_file = in_file
fit_dwi.inputs.bval_file = bval_file
fit_dwi.inputs.bvec_file = bvec_file
fit_dwi.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -dti \
-error {error} -famap {fa} -mcmap {mc} -mcout {mcout} -mdmap {md} -nodiff \
{nodiff} -res {res} -rgbmap {rgb} -syn {syn} -tenmap2 {ten2} -v1map {v1}'
expected_cmd = cmd_tmp.format(cmd=cmd,
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
error='dwi_error.nii.gz',
fa='dwi_famap.nii.gz',
mc='dwi_mcmap.nii.gz',
md='dwi_mdmap.nii.gz',
nodiff='dwi_no_diff.nii.gz',
res='dwi_resmap.nii.gz',
rgb='dwi_rgbmap.nii.gz',
syn='dwi_syn.nii.gz',
ten2='dwi_tenmap2.nii.gz',
v1='dwi_v1map.nii.gz',
mcout='dwi_mcout.txt')
assert fit_dwi.cmdline == expected_cmd
def test_unary_stats():
""" Test for the seg_stats interfaces """
# Create a node object
unarys = UnaryStats()
# Check if the command is properly defined
cmd = get_custom_path('seg_stats', env_dir='NIFTYSEGDIR')
assert unarys.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
unarys.run()
# Assign some input data
in_file = example_data('im1.nii')
unarys.inputs.in_file = in_file
unarys.inputs.operation = 'a'
expected_cmd = '{cmd} {in_file} -a'.format(cmd=cmd, in_file=in_file)
assert unarys.cmdline == expected_cmd
def test_unary_maths():
# Create a node object
unarym = UnaryMaths()
# Check if the command is properly defined
cmd = get_custom_path('seg_maths', env_dir='NIFTYSEGDIR')
assert unarym.cmd == cmd
# test raising error with mandatory args absent
with pytest.raises(ValueError):
unarym.run()
# Assign some input data
in_file = example_data('im1.nii')
unarym.inputs.in_file = in_file
unarym.inputs.operation = 'otsu'
unarym.inputs.output_datatype = 'float'
expected_cmd = '{cmd} {in_file} -otsu -odt float {out_file}'.format(
cmd=cmd, in_file=in_file, out_file='im1_otsu.nii')
assert unarym.cmdline == expected_cmd
def test_reg_transform_def():
""" tests for reg_transform interface """
# Create a reg_transform object
nr_transform = RegTransform()
# Check if the command is properly defined
assert nr_transform.cmd == get_custom_path('reg_transform')
# Assign some input data
trans_file = example_data('warpfield.nii')
nr_transform.inputs.def_input = trans_file
nr_transform.inputs.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -def {trans_file} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
trans_file=trans_file,
out_file=os.path.join(
os.getcwd(), 'warpfield_trans.nii.gz'))
assert nr_transform.cmdline == expected_cmd
# Test reg_transform: def ref
nr_transform_2 = RegTransform(omp_core_val=4)
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
nr_transform_2.inputs.ref1_file = ref_file
nr_transform_2.inputs.def_input = trans_file
cmd_tmp = '{cmd} -ref {ref_file} -omp 4 -def {trans_file} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
ref_file=ref_file,
trans_file=trans_file,
out_file=os.path.join(
os.getcwd(), 'warpfield_trans.nii.gz'))
assert nr_transform_2.cmdline == expected_cmd
# Test reg_transform: comp nii
nr_transform_3 = RegTransform(omp_core_val=4)
ref_file = example_data('im1.nii')
trans_file = example_data('warpfield.nii')
trans2_file = example_data('anatomical.nii')
nr_transform_3.inputs.ref1_file = ref_file
nr_transform_3.inputs.comp_input2 = trans2_file
nr_transform_3.inputs.comp_input = trans_file
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_transform_3.cmdline == expected_cmd
# Test reg_transform: comp txt
nr_transform_4 = RegTransform(omp_core_val=4)
aff1_file = example_data('ants_Affine.txt')
aff2_file = example_data('elastix.txt')
nr_transform_4.inputs.comp_input2 = aff2_file
nr_transform_4.inputs.comp_input = aff1_file
cmd_tmp = '{cmd} -omp 4 -comp {aff1} {aff2} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
aff1=aff1_file,
aff2=aff2_file,
out_file=os.path.join(
os.getcwd(), 'ants_Affine_trans.txt'))
assert nr_transform_4.cmdline == expected_cmd
# Test reg_transform: comp
nr_transform_5 = RegTransform(omp_core_val=4)
trans_file = example_data('warpfield.nii')
aff_file = example_data('elastix.txt')
nr_transform_5.inputs.comp_input2 = trans_file
nr_transform_5.inputs.comp_input = aff_file
cmd_tmp = '{cmd} -omp 4 -comp {aff} {trans} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
aff=aff_file,
trans=trans_file,
out_file=os.path.join(
os.getcwd(), 'elastix_trans.nii.gz'))
assert nr_transform_5.cmdline == expected_cmd
# Test reg_transform: flirt
nr_transform_6 = RegTransform(omp_core_val=4)
aff_file = example_data('elastix.txt')
ref_file = example_data('im1.nii')
in_file = example_data('im2.nii')
nr_transform_6.inputs.flirt_2_nr_input = (aff_file, ref_file, in_file)
cmd_tmp = '{cmd} -omp 4 -flirtAff2NR {aff} {ref} {in_file} {out_file}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('reg_transform'),
aff=aff_file,
ref=ref_file,
in_file=in_file,
out_file=os.path.join(
os.getcwd(), 'elastix_trans.txt'))
assert nr_transform_6.cmdline == expected_cmd
def test_reg_average():
""" tests for reg_average interface """
# Create a reg_average object
nr_average = RegAverage()
# Check if the command is properly defined
assert nr_average.cmd == get_custom_path('reg_average')
# Average niis
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
nr_average.inputs.avg_files = [one_file, two_file, three_file]
generated_cmd = nr_average.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_obj:
argv = f_obj.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.decode('utf-8') == expected_argv
# Test command line with text file
expected_cmd = ('%s --cmd_file %s' %
(get_custom_path('reg_average'), reg_average_cmd))
assert generated_cmd == expected_cmd
# Test Reg Average: average txt
nr_average_2 = RegAverage()
one_file = example_data('TransformParameters.0.txt')
two_file = example_data('ants_Affine.txt')
three_file = example_data('elastix.txt')
nr_average_2.inputs.avg_files = [one_file, two_file, three_file]
generated_cmd = nr_average_2.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_obj:
argv = f_obj.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.txt'), one_file, two_file, three_file)
assert argv.decode('utf-8') == expected_argv
# Test Reg Average: average list
nr_average_3 = RegAverage()
one_file = example_data('TransformParameters.0.txt')
two_file = example_data('ants_Affine.txt')
three_file = example_data('elastix.txt')
nr_average_3.inputs.avg_lts_files = [one_file, two_file, three_file]
generated_cmd = nr_average_3.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_obj:
argv = f_obj.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.decode('utf-8') == expected_argv
# Test Reg Average: average ref
nr_average_4 = RegAverage()
ref_file = example_data('anatomical.nii')
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
trans1_file = example_data('roi01.nii')
trans2_file = example_data('roi02.nii')
trans3_file = example_data('roi03.nii')
nr_average_4.inputs.warp_files = [
trans1_file, one_file, trans2_file, two_file, trans3_file, three_file
]
nr_average_4.inputs.avg_ref_file = ref_file
generated_cmd = nr_average_4.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_obj:
argv = f_obj.read()
os.remove(reg_average_cmd)
expected_argv = (
'%s %s -avg_tran %s %s %s %s %s %s %s' %
(get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.nii.gz'), ref_file, trans1_file,
one_file, trans2_file, two_file, trans3_file, three_file))
assert argv.decode('utf-8') == expected_argv
# Test Reg Average: demean3
nr_average_5 = RegAverage()
ref_file = example_data('anatomical.nii')
one_file = example_data('im1.nii')
two_file = example_data('im2.nii')
three_file = example_data('im3.nii')
aff1_file = example_data('TransformParameters.0.txt')
aff2_file = example_data('ants_Affine.txt')
aff3_file = example_data('elastix.txt')
trans1_file = example_data('roi01.nii')
trans2_file = example_data('roi02.nii')
trans3_file = example_data('roi03.nii')
nr_average_5.inputs.warp_files = [
aff1_file, trans1_file, one_file, aff2_file, trans2_file, two_file,
aff3_file, trans3_file, three_file
]
nr_average_5.inputs.demean3_ref_file = ref_file
generated_cmd = nr_average_5.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_obj:
argv = f_obj.read()
os.remove(reg_average_cmd)
expected_argv = ('%s %s -demean3 %s %s %s %s %s %s %s %s %s %s' %
(get_custom_path('reg_average'),
os.path.join(os.getcwd(), 'avg_out.nii.gz'), ref_file,
aff1_file, trans1_file, one_file, aff2_file, trans2_file,
two_file, aff3_file, trans3_file, three_file))
assert argv.decode('utf-8') == expected_argv
