# -*- coding: utf-8 -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyfit import FitAsl
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(cmd='fit_asl'),
reason="niftyfit is not installed")
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import UnaryStats, BinaryStats
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
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(
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import PatchMatch
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
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
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
RegAladin, RegF3D)
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(cmd='reg_aladin'),
reason="niftyreg is not installed. reg_aladin not found.")
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
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import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import LabelFusion, CalcTopNCC
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
cmd = get_custom_path('seg_LabFusion', env_dir='NIFTYSEGDIR')
assert steps.cmd == cmd
# 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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import EM
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
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 \
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import (UnaryMaths, BinaryMaths,
BinaryMathsInteger, TupleMaths, Merge)
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
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'
# -*- coding: utf-8 -*-
# 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.niftyreg import (no_nifty_package, get_custom_path,
RegAverage, RegResample, RegJacobian,
RegTools, RegMeasure, RegTransform)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_nifty_package(cmd='reg_resample'),
reason="niftyreg is not installed. reg_resample not found."
)
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')
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import EM
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
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 \
# -*- coding: utf-8 -*-
# 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.niftyreg import (no_nifty_package, get_custom_path,
RegAverage, RegResample, RegJacobian,
RegTools, RegMeasure, RegTransform)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(
no_nifty_package(cmd='reg_resample'),
reason="niftyreg is not installed. reg_resample not found.")
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')
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
RegAladin, RegF3D)
from nipype.testing import example_data
@pytest.mark.skipif(
no_nifty_package(cmd='reg_aladin'),
reason="niftyreg is not installed. reg_aladin not found.")
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyfit import FitDwi, DwiTool
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(cmd='fit_dwi'),
reason="niftyfit is not installed")
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.interfaces.niftyseg import FillLesions
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(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
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
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import pytest
from nipype.interfaces.niftyfit import FitDwi, DwiTool
from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
from nipype.testing import example_data
@pytest.mark.skipif(no_nifty_package(cmd='fit_dwi'),
reason="niftyfit is not installed")
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