Esempi in Python per no_freesurfer

Esempio n. 1

# -*- 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 os
import numpy as np
import nibabel as nb

import pytest

from nipype.utils import NUMPY_MMAP
from nipype.interfaces.freesurfer import model, no_freesurfer
import nipype.pipeline.engine as pe


@pytest.mark.skipif(no_freesurfer(), reason="freesurfer is not installed")
def test_concatenate(tmpdir):
    tmpdir.chdir()

    in1 = tmpdir.join("cont1.nii").strpath
    in2 = tmpdir.join("cont2.nii").strpath
    out = "bar.nii"

    data1 = np.zeros((3, 3, 3, 1), dtype=np.float32)
    data2 = np.ones((3, 3, 3, 5), dtype=np.float32)
    out_data = np.concatenate((data1, data2), axis=3)
    mean_data = np.mean(out_data, axis=3)

    nb.Nifti1Image(data1, affine=np.eye(4)).to_filename(in1)
    nb.Nifti1Image(data2, affine=np.eye(4)).to_filename(in2)

Esempio n. 2

File: test_preprocess.py Progetto: tamires-consulting/nipype

# -*- 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 os

import pytest
from nipype.testing.fixtures import create_files_in_directory

from nipype.interfaces import freesurfer
from nipype.interfaces.freesurfer import Info
from nipype import LooseVersion


@pytest.mark.skipif(freesurfer.no_freesurfer(),
                    reason="freesurfer is not installed")
def test_robustregister(create_files_in_directory):
    filelist, outdir = create_files_in_directory

    reg = freesurfer.RobustRegister()
    cwd = os.getcwd()

    # make sure command gets called
    assert reg.cmd == "mri_robust_register"

    # test raising error with mandatory args absent
    with pytest.raises(ValueError):
        reg.run()

    # .inputs based parameters setting
    reg.inputs.source_file = filelist[0]
    reg.inputs.target_file = filelist[1]

Esempio n. 3

File: test_model.py Progetto: shoshber/nipype

# -*- 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 os
import numpy as np
import nibabel as nib

import pytest
from nipype.interfaces.freesurfer import model, no_freesurfer
import nipype.pipeline.engine as pe


@pytest.mark.skipif(no_freesurfer(), reason="freesurfer is not installed")
def test_concatenate(tmpdir):
    tempdir = str(tmpdir)
    os.chdir(tempdir)
    in1 = os.path.join(tempdir, 'cont1.nii')
    in2 = os.path.join(tempdir, 'cont2.nii')
    out = 'bar.nii'

    data1 = np.zeros((3, 3, 3, 1), dtype=np.float32)
    data2 = np.ones((3, 3, 3, 5), dtype=np.float32)
    out_data = np.concatenate((data1, data2), axis=3)
    mean_data = np.mean(out_data, axis=3)

    nib.Nifti1Image(data1, affine=np.eye(4)).to_filename(in1)
    nib.Nifti1Image(data2, affine=np.eye(4)).to_filename(in2)

    # Test default behavior
    res = model.Concatenate(in_files=[in1, in2]).run()

Esempio n. 4

File: test_preprocess.py Progetto: yzw0041/nipype

# -*- 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 builtins import str
import os

import pytest
from nipype.testing.fixtures import create_files_in_directory

from nipype.interfaces import freesurfer
from nipype.interfaces.freesurfer import Info
from nipype import LooseVersion


@pytest.mark.skipif(
    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
def test_robustregister(create_files_in_directory):
    filelist, outdir = create_files_in_directory

    reg = freesurfer.RobustRegister()
    cwd = os.getcwd()

    # make sure command gets called
    assert reg.cmd == 'mri_robust_register'

    # test raising error with mandatory args absent
    with pytest.raises(ValueError):
        reg.run()

    # .inputs based parameters setting
    reg.inputs.source_file = filelist[0]

Esempio n. 5

File: test_preprocess.py Progetto: moloney/nipype

# -*- 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 builtins import str
import os

import pytest
from nipype.testing.fixtures import create_files_in_directory

from nipype.interfaces import freesurfer
from nipype.interfaces.freesurfer import Info
from nipype import LooseVersion


@pytest.mark.skipif(
    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
def test_robustregister(create_files_in_directory):
    filelist, outdir = create_files_in_directory

    reg = freesurfer.RobustRegister()
    cwd = os.getcwd()

    # make sure command gets called
    assert reg.cmd == 'mri_robust_register'

    # test raising error with mandatory args absent
    with pytest.raises(ValueError):
        reg.run()

    # .inputs based parameters setting
    reg.inputs.source_file = filelist[0]