Exemplo n.º 1
0
# -*- 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 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
Exemplo n.º 2
0
# 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 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(
Exemplo n.º 3
0
# 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 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
Exemplo n.º 4
0
# -*- 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
Exemplo n.º 5
0
# 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 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
Exemplo n.º 6
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# 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 \
Exemplo n.º 7
0
# 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'
Exemplo n.º 8
0
# -*- 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')
Exemplo n.º 9
0
# 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 \
Exemplo n.º 10
0
# -*- 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')
Exemplo n.º 11
0
# -*- 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
Exemplo n.º 12
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# 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
Exemplo n.º 13
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# 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
Exemplo n.º 14
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# 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