# 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.niftyfit import no_niftyfit, get_custom_path, DwiTool
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyfit(cmd="dwi_tool"))
def test_seg_em():
# Create a reg_aladin object
test_node = DwiTool()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path("dwi_tool")
# Assign some input data
in_file = example_data("diffusion.nii")
test_node.inputs.source_file = in_file
cmd_tmp = "{cmd} -famap dwifit__famap -logdti2 dwifit__logdti2 -mdmap \
dwifit__mdmap -rgbmap dwifit__rgbmap -source {in_file} -v1map dwifit__v1map"
expected_cmd = cmd_tmp.format(cmd=get_custom_path("dwi_tool"), in_file=in_file)
yield assert_equal, test_node.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.niftyfit import no_niftyfit, get_custom_path, FitAsl
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyfit(cmd='fit_asl'))
def test_seg_em():
# Create a reg_aladin object
test_node = FitAsl()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_asl')
# Assign some input data
in_file = example_data('im1.nii')
test_node.inputs.source_file = in_file
cmd_tmp = '{cmd} -cbf im1_cbf -error im1_error -source {in_file} \
-syn im1_syn'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_asl'),
in_file=in_file)
yield assert_equal, test_node.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.niftyfit import no_niftyfit, get_custom_path, FitQt1
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyfit(cmd='fit_qt1'))
def test_seg_em():
# Create a reg_aladin object
test_node = FitQt1()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_qt1')
# Assign some input data
in_file = example_data('im1.nii')
test_node.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -error im1_error -m0map im1_m0map \
-mcmap im1_mcmap -res im1_res -syn im1_syn -t1map im1_t1map'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file)
yield assert_equal, test_node.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.niftyfit import no_niftyfit, get_custom_path, DwiTool
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyfit(cmd='dwi_tool'))
def test_dwi_tool():
# Create a node object
test_node = DwiTool()
# Check if the command is properly defined
assert test_node.cmd == get_custom_path('dwi_tool')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
test_node.run()
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii')
test_node.inputs.source_file = in_file
test_node.inputs.mask_file = mask_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_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.niftyfit import no_niftyfit, get_custom_path, FitAsl
from nipype.testing import example_data
@pytest.mark.skipif(no_niftyfit(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
assert fit_asl.cmd == get_custom_path('fit_asl')
# 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(
# -*- 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.niftyfit import no_niftyfit, get_custom_path, FitQt1
from nipype.testing import example_data
@pytest.mark.skipif(no_niftyfit(cmd='fit_qt1'),
reason="niftyfit is not installed")
def test_fit_qt1():
""" Testing FitQt1 interface."""
# Create a node object
fit_qt1 = FitQt1()
# Check if the command is properly defined
assert fit_qt1.cmd == get_custom_path('fit_qt1')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_qt1.run()
# Regular test:
in_file = example_data('TI4D.nii.gz')
fit_qt1.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} -m0map \
{map0} -mcmap {cmap} -res {res} -syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.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.niftyfit import no_niftyfit, get_custom_path, FitDwi
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyfit(cmd='fit_dwi'))
def test_seg_em():
# Create a reg_aladin object
test_node = FitDwi()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_dwi')
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
test_node.inputs.source_file = in_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_file
cmd_tmp = '{cmd} -bval {bval} -bvec {bvec} -famap dwifit__famap -mcmap \
dwifit__mcmap -mdmap dwifit__mdmap -res dwifit__resmap -rgbmap dwifit__rgbmap \
-source {in_file} -syn dwifit__syn -tenmap2 dwifit__tenmap2 -v1map \
dwifit__v1map'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_dwi'),
in_file=in_file,
# 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 (no_niftyfit, get_custom_path, FitDwi,
DwiTool)
from nipype.testing import example_data
@pytest.mark.skipif(no_niftyfit(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
assert fit_dwi.cmd == get_custom_path('fit_dwi')
# 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
# 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.niftyfit import no_niftyfit, get_custom_path, DwiTool
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyfit(cmd='dwi_tool'))
def test_dwi_tool():
# Create a node object
test_node = DwiTool()
# Check if the command is properly defined
assert test_node.cmd == get_custom_path('dwi_tool')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
test_node.run()
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii')
test_node.inputs.source_file = in_file
test_node.inputs.mask_file = mask_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_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.niftyfit import no_niftyfit, get_custom_path, FitQt1
from nipype.testing import example_data
@pytest.mark.skipif(no_niftyfit(cmd='fit_qt1'),
reason="niftyfit is not installed")
def test_fit_qt1():
""" Testing FitQt1 interface."""
# Create a node object
fit_qt1 = FitQt1()
# Check if the command is properly defined
assert fit_qt1.cmd == get_custom_path('fit_qt1')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_qt1.run()
# Regular test:
in_file = example_data('TI4D.nii.gz')
fit_qt1.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} -m0map \
{map0} -mcmap {cmap} -res {res} -syn {syn} -t1map {t1map}'
# -*- 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.niftyfit import no_niftyfit, get_custom_path, FitAsl
from nipype.testing import example_data
@pytest.mark.skipif(no_niftyfit(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
assert fit_asl.cmd == get_custom_path('fit_asl')
# 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(
# 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 (no_niftyfit, get_custom_path, FitDwi,
DwiTool)
from nipype.testing import example_data
@pytest.mark.skipif(no_niftyfit(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
assert fit_dwi.cmd == get_custom_path('fit_dwi')
# 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
