def test_seg_patchmatch():
# Create a node object
seg_patchmatch = PatchMatch()
# Check if the command is properly defined
assert seg_patchmatch.cmd == get_custom_path('seg_PatchMatch')
# 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=get_custom_path('seg_PatchMatch'),
in_file=in_file,
mask_file=mask_file,
db=db_file,
out_file=os.path.join(
os.getcwd(), 'im1_pm.nii'))
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
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_int_binary_maths():
# Create a node object
ibinarym = BinaryMathsInteger()
# Check if the command is properly defined
assert ibinarym.cmd == get_custom_path('seg_maths')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
ibinarym.run()
# Assign some input data
in_file = example_data('im1.nii')
ibinarym.inputs.in_file = in_file
ibinarym.inputs.operand_value = 2
ibinarym.inputs.operation = 'dil'
ibinarym.inputs.output_datatype = 'float'
expected_cmd = '{cmd} {in_file} -dil 2 -odt float {out_file}'.format(
cmd=get_custom_path('seg_maths'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_dil.nii'))
assert ibinarym.cmdline == expected_cmd
def test_seg_em():
# Create a node object
seg_em = EM()
# Check if the command is properly defined
assert seg_em.cmd == get_custom_path('seg_EM')
# 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=get_custom_path('seg_EM'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_em.nii'),
bc_out=os.path.join(os.getcwd(), 'im1_bc_em.nii'),
out_outlier=os.path.join(os.getcwd(), 'im1_outlier_em.nii'))
assert seg_em.cmdline == expected_cmd
def test_steps():
# Create a node object
steps = LabelFusion()
# Check if the command is properly defined
assert steps.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
steps.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
steps.inputs.in_file = in_file
steps.inputs.kernel_size = 2.0
steps.inputs.file_to_seg = file_to_seg
steps.inputs.template_file = template_file
steps.inputs.template_num = 2
steps.inputs.classifier_type = 'STEPS'
cmd_tmp = '{cmd} -in {in_file} -STEPS 2.000000 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_steps.nii'))
assert steps.cmdline == expected_cmd
def test_binary_maths():
# Create a node object
binarym = BinaryMaths()
# Check if the command is properly defined
assert binarym.cmd == get_custom_path('seg_maths')
# 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=get_custom_path('seg_maths'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_sub.nii'))
assert binarym.cmdline == expected_cmd
def test_seg_em():
# Create a node object
seg_em = EM()
# Check if the command is properly defined
assert seg_em.cmd == get_custom_path('seg_EM')
# 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=get_custom_path('seg_EM'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_em.nii'),
bc_out=os.path.join(os.getcwd(), 'im1_bc_em.nii'),
out_outlier=os.path.join(os.getcwd(), 'im1_outlier_em.nii')
)
assert seg_em.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_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_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_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_seg_patchmatch():
# Create a reg_aladin object
steps = STEPS()
# Check if the command is properly defined
yield assert_equal, steps.cmd, get_custom_path('seg_LabFusion')
# Assign some input data
in_file = example_data('im1.nii')
steps.inputs.in_file = in_file
steps.inputs.kernel_size = 2
steps.inputs.warped_seg_file = in_file
steps.inputs.warped_img_file = in_file
steps.inputs.template_num = 2
cmd_tmp = '{cmd} -in {warped_img_file} -STEPS 2.000000 2 {in_file} \
{warped_seg_file} -out {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_LabFusion'),
warped_img_file=in_file,
in_file=in_file,
warped_seg_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_steps.nii'))
# out_file=os.path.join(os.getcwd(), 'im1_pm.nii'))
yield assert_equal, steps.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
assert seg_patchmatch.cmd == get_custom_path('seg_PatchMatch')
# 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=get_custom_path('seg_PatchMatch'),
in_file=in_file,
mask_file=mask_file,
db=db_file,
out_file=os.path.join(os.getcwd(), 'im1_pm.nii'))
assert seg_patchmatch.cmdline == expected_cmd
def test_seg_filllesions():
# Create a reg_aladin object
seg_fill = FillLesions()
# Check if the command is properly defined
yield assert_equal, seg_fill.cmd, get_custom_path("seg_FillLesions")
# Assign some input data
in_file = example_data("im1.nii")
seg_fill.inputs.in_file = in_file
seg_fill.inputs.lesion_mask = in_file
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=in_file,
out_file=os.path.join(os.getcwd(), "im1_lesions_filled.nii"),
)
yield assert_equal, seg_fill.cmdline, expected_cmd
def test_binary_stats():
# Create a node object
binarys = BinaryStats()
# Check if the command is properly defined
assert binarys.cmd == get_custom_path('seg_stats')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
binarys.run()
# Assign some input data
in_file = example_data('im1.nii')
binarys.inputs.in_file = in_file
binarys.inputs.operand_value = 2
binarys.inputs.operation = 'sa'
expected_cmd = '{cmd} {in_file} -sa 2.00000000'.format(
cmd=get_custom_path('seg_stats'), in_file=in_file)
assert binarys.cmdline == expected_cmd
def test_binary_stats():
# Create a node object
binarys = BinaryStats()
# Check if the command is properly defined
assert binarys.cmd == get_custom_path('seg_stats')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
binarys.run()
# Assign some input data
in_file = example_data('im1.nii')
binarys.inputs.in_file = in_file
binarys.inputs.operand_value = 2
binarys.inputs.operation = 'sa'
expected_cmd = '{cmd} {in_file} -sa 2.00000000'.format(
cmd=get_custom_path('seg_stats'),
in_file=in_file)
assert binarys.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
assert unarys.cmd == get_custom_path('seg_stats')
# 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=get_custom_path('seg_stats'),
in_file=in_file)
assert unarys.cmdline == expected_cmd
def test_seg_maths():
# Create a reg_aladin object
unarym = UnaryMaths()
# Check if the command is properly defined
yield assert_equal, unarym.cmd, get_custom_path('seg_maths')
# Assign some input data
in_file = example_data('im1.nii')
unarym.inputs.in_file = in_file
unarym.inputs.operation = 'otsu'
expected_cmd = '{cmd} {in_file} -otsu {out_file}'.format(
cmd=get_custom_path('seg_maths'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_otsu.nii'))
yield assert_equal, unarym.cmdline, expected_cmd
# Create a reg_aladin object
binarym = BinaryMaths()
# Check if the command is properly defined
yield assert_equal, binarym.cmd, get_custom_path('seg_maths')
# 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'
expected_cmd = '{cmd} {in_file} -sub 2.00000000 {out_file}'.format(
cmd=get_custom_path('seg_maths'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_maths.nii'))
yield assert_equal, binarym.cmdline, expected_cmd
def test_seg_patchmatch():
# Create a reg_aladin object
seg_patchmatch = PatchMatch()
# Check if the command is properly defined
yield assert_equal, seg_patchmatch.cmd, get_custom_path('seg_PatchMatch')
# Assign some input data
in_file = example_data('im1.nii')
seg_patchmatch.inputs.in_file = in_file
seg_patchmatch.inputs.mask_file = in_file
seg_patchmatch.inputs.database_file = in_file
cmd_tmp = '{cmd} -i {in_file} -m {mask_file} -db {db} -o {out_file}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('seg_PatchMatch'),
in_file=in_file,
mask_file=in_file,
db=in_file,
out_file=os.path.join(os.getcwd(), 'im1_pm.nii'))
yield assert_equal, seg_patchmatch.cmdline, expected_cmd
def test_seg_em():
# Create a reg_aladin object
seg_em = EM()
# Check if the command is properly defined
yield assert_equal, seg_em.cmd, get_custom_path('seg_EM')
# 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=get_custom_path('seg_EM'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_em.nii'),
bc_out=os.path.join(os.getcwd(), 'im1_bc_em.nii'),
out_outlier=os.path.join(os.getcwd(), 'im1_outlier_em.nii'))
yield assert_equal, seg_em.cmdline, expected_cmd
def test_unary_maths():
# Create a node object
unarym = UnaryMaths()
# Check if the command is properly defined
assert unarym.cmd == get_custom_path('seg_maths')
# 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=get_custom_path('seg_maths'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_otsu.nii'))
assert unarym.cmdline == expected_cmd
def test_seg_patchmatch():
# Create a reg_aladin object
calctopncc = CalcTopNCC()
# Check if the command is properly defined
yield assert_equal, calctopncc.cmd, get_custom_path('seg_CalcTopNCC')
# Assign some input data
in_file = example_data('im1.nii')
calctopncc.inputs.in_file = in_file
calctopncc.inputs.num_templates = 2
calctopncc.inputs.in_templates = [in_file, in_file]
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=in_file,
file2=in_file)
# out_file=os.path.join(os.getcwd(), 'im1_pm.nii'))
yield assert_equal, calctopncc.cmdline, expected_cmd
def test_unary_maths():
# Create a node object
unarym = UnaryMaths()
# Check if the command is properly defined
assert unarym.cmd == get_custom_path('seg_maths')
# 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=get_custom_path('seg_maths'),
in_file=in_file,
out_file=os.path.join(os.getcwd(), 'im1_otsu.nii'))
assert unarym.cmdline == expected_cmd
def test_seg_stats():
# Create a reg_aladin object
unarys = UnaryStats()
# Check if the command is properly defined
yield assert_equal, unarys.cmd, get_custom_path('seg_stats')
# 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=get_custom_path('seg_stats'),
in_file=in_file)
yield assert_equal, unarys.cmdline, expected_cmd
# Create a reg_aladin object
binarys = BinaryStats()
# Check if the command is properly defined
yield assert_equal, binarys.cmd, get_custom_path('seg_stats')
# Assign some input data
in_file = example_data('im1.nii')
binarys.inputs.in_file = in_file
binarys.inputs.operand_value = 1
binarys.inputs.operation = 'sa'
expected_cmd = '{cmd} {in_file} -sa 1.00000000'.format(
cmd=get_custom_path('seg_stats'),
in_file=in_file)
yield assert_equal, binarys.cmdline, expected_cmd
def test_seg_lab_fusion():
""" Test interfaces for seg_labfusion"""
# Create a node object
steps = LabelFusion()
# Check if the command is properly defined
assert steps.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
steps.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
steps.inputs.in_file = in_file
steps.inputs.kernel_size = 2.0
steps.inputs.file_to_seg = file_to_seg
steps.inputs.template_file = template_file
steps.inputs.template_num = 2
steps.inputs.classifier_type = 'STEPS'
cmd_tmp = '{cmd} -in {in_file} -STEPS 2.000000 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_steps.nii'))
assert steps.cmdline == expected_cmd
# Staple
staple = LabelFusion(kernel_size=2.0,
template_num=2,
classifier_type='STAPLE')
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.file_to_seg = file_to_seg
staple.inputs.template_file = template_file
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
# Assign some input data
mv_node = LabelFusion(template_num=2,
classifier_type='MV',
sm_ranking='ROINCC',
dilation_roi=2)
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
mv_node.inputs.in_file = in_file
mv_node.inputs.file_to_seg = file_to_seg
mv_node.inputs.template_file = template_file
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_node.cmdline == expected_cmd
def test_seg_lab_fusion():
""" Test interfaces for seg_labfusion"""
# Create a node object
steps = LabelFusion()
# Check if the command is properly defined
assert steps.cmd == get_custom_path('seg_LabFusion')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
steps.run()
# Assign some input data
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
steps.inputs.in_file = in_file
steps.inputs.kernel_size = 2.0
steps.inputs.file_to_seg = file_to_seg
steps.inputs.template_file = template_file
steps.inputs.template_num = 2
steps.inputs.classifier_type = 'STEPS'
cmd_tmp = '{cmd} -in {in_file} -STEPS 2.000000 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_steps.nii')
)
assert steps.cmdline == expected_cmd
# Staple
staple = LabelFusion(kernel_size=2.0, template_num=2,
classifier_type='STAPLE')
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.file_to_seg = file_to_seg
staple.inputs.template_file = template_file
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
# Assign some input data
mv_node = LabelFusion(template_num=2, classifier_type='MV',
sm_ranking='ROINCC', dilation_roi=2)
in_file = example_data('im1.nii')
file_to_seg = example_data('im2.nii')
template_file = example_data('im3.nii')
mv_node.inputs.in_file = in_file
mv_node.inputs.file_to_seg = file_to_seg
mv_node.inputs.template_file = template_file
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_node.cmdline == expected_cmd
