# 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
# -*- 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}'