# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, CalcTopNCC
from nipype.testing import skipif, example_data
import pytest
@skipif(no_niftyseg(cmd='seg_CalcTopNCC'))
def test_seg_calctopncc():
# 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'
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
PatchMatch)
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyseg(cmd='seg_PatchMatch'))
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'))
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryStats, BinaryStats)
from nipype.testing import example_data
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_stats'),
reason="niftyseg is not installed")
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)
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, PatchMatch
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_PatchMatch'),
reason="niftyseg is not installed")
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
FillLesions)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyseg(cmd='seg_FillLesions'))
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'),
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
LabelFusion, CalcTopNCC)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_LabFusion'),
reason="niftyseg is not installed")
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
LabelFusion, CalcTopNCC)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_LabFusion'),
reason="niftyseg is not installed")
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, PatchMatch
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyseg(cmd='seg_PatchMatch'))
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}'
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryMaths, BinaryMaths,
BinaryMathsInteger, TupleMaths,
Merge)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_maths'),
reason="niftyseg is not installed")
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'
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryMaths, BinaryMaths)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyseg(cmd='seg_maths'))
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
FillLesions)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_FillLesions'),
reason="niftyseg is not installed")
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(
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, EM
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyseg(cmd='seg_EM'))
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'),
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
LabelFusion)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyseg(cmd='seg_LabFusion'))
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
CalcTopNCC)
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyseg(cmd='seg_CalcTopNCC'))
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'))
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryStats, BinaryStats)
from nipype.testing import skipif, example_data
import pytest
@skipif(no_niftyseg(cmd='seg_stats'))
def test_unary_stats():
# 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)
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryMaths, BinaryMaths,
BinaryMathsInteger, TupleMaths, Merge)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_maths'),
reason="niftyseg is not installed")
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'
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, FillLesions
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyseg(cmd="seg_FillLesions"))
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, EM
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyseg(cmd='seg_EM'))
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'))
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryStats, BinaryStats)
from nipype.testing import skipif, example_data
import pytest
@skipif(no_niftyseg(cmd='seg_stats'))
def test_unary_stats():
# 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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
LabelFusion)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyseg(cmd='seg_LabFusion'))
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import (no_niftyseg, get_custom_path,
UnaryMaths, BinaryMaths,
BinaryMathsInteger, TupleMaths, Merge)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyseg(cmd='seg_maths'))
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(
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, EM
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyseg(cmd='seg_EM'),
reason="niftyseg is not installed")
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(
