# 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_niftyreg, get_custom_path,
RegResample)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyreg(cmd='reg_resample'))
def test_reg_resample_res():
# 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.inter_val = 'LIN'
# 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.niftyreg import (no_niftyreg, get_custom_path, RegTransform)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyreg(cmd='reg_transform'))
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
@skipif(no_niftyreg(cmd='reg_transform'))
def test_reg_transform_def_ref():
# 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.niftyreg import (no_niftyreg, get_custom_path, RegJacobian)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyreg(cmd='reg_jacobian'))
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
@skipif(no_niftyreg(cmd='reg_jacobian'))
# 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.niftyreg import (no_niftyreg, get_custom_path,
RegAverage)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyreg(cmd='reg_average'))
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)
# 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.niftyreg import (no_niftyreg, get_custom_path, RegTools)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyreg(cmd='reg_tools'))
def test_reg_tools_mul():
# 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.mul_val = 4
nr.inputs.omp_core_val = 4
expected_cmd = get_custom_path('reg_tools') + ' ' + '-in ' + in_file + ' -mul 4.0 ' +\
'-omp 4 ' + '-out ' + os.getcwd() + os.sep + 'im1_tools.nii.gz'
yield assert_equal, nr.cmdline, expected_cmd
@skipif(no_niftyreg(cmd='reg_tools'))
def test_reg_tools_iso():
# -*- 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_niftyreg, get_custom_path,
RegAladin, RegF3D)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyreg(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
# -*- 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_niftyreg, get_custom_path,
RegAladin, RegF3D)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(
no_niftyreg(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:
from nipype.interfaces.niftyreg import no_niftyreg, get_custom_path, RegTools
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyreg(cmd='reg_tools'))
def test_reg_tools_mul():
# 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.mul_val = 4
nr.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,
# 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_niftyreg, get_custom_path,
RegResample)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyreg(cmd='reg_resample'))
def test_reg_resample_res():
# 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.inter_val = 'LIN'
# 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.niftyreg import (no_niftyreg, get_custom_path, RegMeasure)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyreg(cmd='reg_measure'))
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
# 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_niftyreg, get_custom_path,
RegTransform)
from nipype.testing import skipif, example_data
import os
@skipif(no_niftyreg(cmd='reg_transform'))
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
# 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.niftyreg import (no_niftyreg, get_custom_path, RegF3D)
from nipype.testing import (assert_equal, skipif, example_data)
@skipif(no_niftyreg(cmd='reg_f3d'))
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 ' +\
# -*- 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_niftyreg, get_custom_path,
RegAverage, RegResample, RegJacobian,
RegTools, RegMeasure, RegTransform)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(
no_niftyreg(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 os
from nipype.interfaces.niftyreg import no_niftyreg, get_custom_path, RegAladin
from nipype.testing import assert_equal, skipif, example_data
@skipif(no_niftyreg(cmd="reg_aladin"))
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 "
# 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_niftyreg, get_custom_path,
RegAladin)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyreg(cmd='reg_aladin'))
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
# -*- 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_niftyreg, get_custom_path,
RegAverage, RegResample, RegJacobian,
RegTools, RegMeasure, RegTransform)
from nipype.testing import example_data
import os
import pytest
@pytest.mark.skipif(no_niftyreg(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:
from nipype.interfaces.niftyreg import (no_niftyreg, get_custom_path,
RegJacobian)
from nipype.testing import skipif, example_data
import os
import pytest
@skipif(no_niftyreg(cmd='reg_jacobian'))
def test_reg_jacobian_jac():
# 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.omp_core_val = 4
cmd_tmp = '{cmd} -omp 4 -ref {ref} -trans {trans} -jac {jac}'
# 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_niftyreg, get_custom_path,
RegAverage)
from nipype.testing import skipif, example_data
import os
@skipif(no_niftyreg(cmd='reg_average'))
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)
# 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_niftyreg, get_custom_path,
RegMeasure)
from nipype.testing import skipif, example_data
import pytest
import os
@skipif(no_niftyreg(cmd='reg_measure'))
def test_reg_measure():
# Create a reg_measure object
nr = RegMeasure()
# Check if the command is properly defined
assert nr.cmd == get_custom_path('reg_measure')
# 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')
nr.inputs.ref_file = ref_file
nr.inputs.flo_file = flo_file
nr.inputs.measure_type = 'lncc'
nr.inputs.omp_core_val = 4