# 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.niftyseg import no_niftyseg, get_custom_path, CalcTopNCC from nipype.testing import skipif, example_data import pytest @skipif(no_niftyseg(cmd='seg_CalcTopNCC')) def test_seg_calctopncc(): # Create a node object calctopncc = CalcTopNCC() # Check if the command is properly defined assert calctopncc.cmd == get_custom_path('seg_CalcTopNCC') # test raising error with mandatory args absent with pytest.raises(ValueError): calctopncc.run() # Assign some input data in_file = example_data('im1.nii') file1 = example_data('im2.nii') file2 = example_data('im3.nii') calctopncc.inputs.in_file = in_file calctopncc.inputs.num_templates = 2 calctopncc.inputs.in_templates = [file1, file2] calctopncc.inputs.top_templates = 1 cmd_tmp = '{cmd} -target {in_file} -templates 2 {file1} {file2} -n 1'
# 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.niftyseg import (no_niftyseg, get_custom_path, PatchMatch) from nipype.testing import assert_equal, skipif, example_data @skipif(no_niftyseg(cmd='seg_PatchMatch')) def test_seg_patchmatch(): # Create a reg_aladin object seg_patchmatch = PatchMatch() # Check if the command is properly defined yield assert_equal, seg_patchmatch.cmd, get_custom_path('seg_PatchMatch') # Assign some input data in_file = example_data('im1.nii') seg_patchmatch.inputs.in_file = in_file seg_patchmatch.inputs.mask_file = in_file seg_patchmatch.inputs.database_file = in_file cmd_tmp = '{cmd} -i {in_file} -m {mask_file} -db {db} -o {out_file}' expected_cmd = cmd_tmp.format( cmd=get_custom_path('seg_PatchMatch'), in_file=in_file, mask_file=in_file, db=in_file, out_file=os.path.join(os.getcwd(), 'im1_pm.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.niftyseg import (no_niftyseg, get_custom_path, UnaryStats, BinaryStats) from nipype.testing import example_data import pytest @pytest.mark.skipif(no_niftyseg(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 assert unarys.cmd == get_custom_path('seg_stats') # 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( cmd=get_custom_path('seg_stats'), 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.niftyseg import no_niftyseg, get_custom_path, PatchMatch from nipype.testing import example_data import os import pytest @pytest.mark.skipif(no_niftyseg(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 assert seg_patchmatch.cmd == get_custom_path('seg_PatchMatch') # 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 seg_patchmatch.inputs.database_file = db_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.niftyseg import (no_niftyseg, get_custom_path, FillLesions) from nipype.testing import skipif, example_data import os import pytest @skipif(no_niftyseg(cmd='seg_FillLesions')) def test_seg_filllesions(): # Create a node object seg_fill = FillLesions() # Check if the command is properly defined assert seg_fill.cmd == get_custom_path('seg_FillLesions') # 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 expected_cmd = '{cmd} -i {in_file} -l {lesion_mask} -o {out_file}'.format( cmd=get_custom_path('seg_FillLesions'),
# 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.niftyseg import (no_niftyseg, get_custom_path, LabelFusion, CalcTopNCC) from nipype.testing import example_data import os import pytest @pytest.mark.skipif(no_niftyseg(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 assert steps.cmd == get_custom_path('seg_LabFusion') # 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 steps.inputs.file_to_seg = file_to_seg
# 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.niftyseg import no_niftyseg, get_custom_path, PatchMatch from nipype.testing import skipif, example_data import os import pytest @skipif(no_niftyseg(cmd='seg_PatchMatch')) def test_seg_patchmatch(): # Create a node object seg_patchmatch = PatchMatch() # Check if the command is properly defined assert seg_patchmatch.cmd == get_custom_path('seg_PatchMatch') # 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 seg_patchmatch.inputs.database_file = db_file cmd_tmp = '{cmd} -i {in_file} -m {mask_file} -db {db} -o {out_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.niftyseg import (no_niftyseg, get_custom_path, UnaryMaths, BinaryMaths, BinaryMathsInteger, TupleMaths, Merge) from nipype.testing import example_data import os import pytest @pytest.mark.skipif(no_niftyseg(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 assert unarym.cmd == get_custom_path('seg_maths') # 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'
# 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.niftyseg import (no_niftyseg, get_custom_path, UnaryMaths, BinaryMaths) from nipype.testing import (assert_equal, skipif, example_data) @skipif(no_niftyseg(cmd='seg_maths')) def test_seg_maths(): # Create a reg_aladin object unarym = UnaryMaths() # Check if the command is properly defined yield assert_equal, unarym.cmd, get_custom_path('seg_maths') # Assign some input data in_file = example_data('im1.nii') unarym.inputs.in_file = in_file unarym.inputs.operation = 'otsu' expected_cmd = '{cmd} {in_file} -otsu {out_file}'.format( cmd=get_custom_path('seg_maths'), in_file=in_file, out_file=os.path.join(os.getcwd(), 'im1_otsu.nii')) yield assert_equal, unarym.cmdline, expected_cmd # Create a reg_aladin object
# 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.niftyseg import (no_niftyseg, get_custom_path, FillLesions) from nipype.testing import example_data import os import pytest @pytest.mark.skipif(no_niftyseg(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 assert seg_fill.cmd == get_custom_path('seg_FillLesions') # 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 expected_cmd = '{cmd} -i {in_file} -l {lesion_mask} -o {out_file}'.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.niftyseg import no_niftyseg, get_custom_path, EM from nipype.testing import skipif, example_data import os import pytest @skipif(no_niftyseg(cmd='seg_EM')) def test_seg_em(): # Create a node object seg_em = EM() # Check if the command is properly defined assert seg_em.cmd == get_custom_path('seg_EM') # 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 \ {out_file} -out_outlier {out_outlier}' expected_cmd = cmd_tmp.format( cmd=get_custom_path('seg_EM'),
# 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.niftyseg import (no_niftyseg, get_custom_path, LabelFusion) from nipype.testing import skipif, example_data import os import pytest @skipif(no_niftyseg(cmd='seg_LabFusion')) def test_steps(): # Create a node object steps = LabelFusion() # Check if the command is properly defined assert steps.cmd == get_custom_path('seg_LabFusion') # 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 steps.inputs.file_to_seg = file_to_seg steps.inputs.template_file = template_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.niftyseg import (no_niftyseg, get_custom_path, CalcTopNCC) from nipype.testing import assert_equal, skipif, example_data @skipif(no_niftyseg(cmd='seg_CalcTopNCC')) def test_seg_patchmatch(): # Create a reg_aladin object calctopncc = CalcTopNCC() # Check if the command is properly defined yield assert_equal, calctopncc.cmd, get_custom_path('seg_CalcTopNCC') # Assign some input data in_file = example_data('im1.nii') calctopncc.inputs.in_file = in_file calctopncc.inputs.num_templates = 2 calctopncc.inputs.in_templates = [in_file, in_file] calctopncc.inputs.top_templates = 1 cmd_tmp = '{cmd} -target {in_file} -templates 2 {file1} {file2} -n 1' expected_cmd = cmd_tmp.format( cmd=get_custom_path('seg_CalcTopNCC'), in_file=in_file, file1=in_file, file2=in_file) # out_file=os.path.join(os.getcwd(), 'im1_pm.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.niftyseg import (no_niftyseg, get_custom_path, UnaryStats, BinaryStats) from nipype.testing import skipif, example_data import pytest @skipif(no_niftyseg(cmd='seg_stats')) def test_unary_stats(): # Create a node object unarys = UnaryStats() # Check if the command is properly defined assert unarys.cmd == get_custom_path('seg_stats') # 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( cmd=get_custom_path('seg_stats'), 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 os from nipype.interfaces.niftyseg import no_niftyseg, get_custom_path, FillLesions from nipype.testing import assert_equal, skipif, example_data @skipif(no_niftyseg(cmd="seg_FillLesions")) def test_seg_filllesions(): # Create a reg_aladin object seg_fill = FillLesions() # Check if the command is properly defined yield assert_equal, seg_fill.cmd, get_custom_path("seg_FillLesions") # Assign some input data in_file = example_data("im1.nii") seg_fill.inputs.in_file = in_file seg_fill.inputs.lesion_mask = in_file expected_cmd = "{cmd} -i {in_file} -l {lesion_mask} -o {out_file}".format( cmd=get_custom_path("seg_FillLesions"), in_file=in_file, lesion_mask=in_file, out_file=os.path.join(os.getcwd(), "im1_lesions_filled.nii"), ) yield assert_equal, seg_fill.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.niftyseg import no_niftyseg, get_custom_path, EM from nipype.testing import assert_equal, skipif, example_data @skipif(no_niftyseg(cmd='seg_EM')) def test_seg_em(): # Create a reg_aladin object seg_em = EM() # Check if the command is properly defined yield assert_equal, seg_em.cmd, get_custom_path('seg_EM') # 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 {out_file} \ -out_outlier {out_outlier}' expected_cmd = cmd_tmp.format( cmd=get_custom_path('seg_EM'), in_file=in_file, out_file=os.path.join(os.getcwd(), 'im1_em.nii'), bc_out=os.path.join(os.getcwd(), 'im1_bc_em.nii'), out_outlier=os.path.join(os.getcwd(), 'im1_outlier_em.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.niftyseg import (no_niftyseg, get_custom_path, UnaryStats, BinaryStats) from nipype.testing import skipif, example_data import pytest @skipif(no_niftyseg(cmd='seg_stats')) def test_unary_stats(): # Create a node object unarys = UnaryStats() # Check if the command is properly defined assert unarys.cmd == get_custom_path('seg_stats') # 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( cmd=get_custom_path('seg_stats'), in_file=in_file) assert unarys.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.niftyseg import (no_niftyseg, get_custom_path, UnaryMaths, BinaryMaths, BinaryMathsInteger, TupleMaths, Merge) from nipype.testing import skipif, example_data import os import pytest @skipif(no_niftyseg(cmd='seg_maths')) def test_unary_maths(): # Create a node object unarym = UnaryMaths() # Check if the command is properly defined assert unarym.cmd == get_custom_path('seg_maths') # 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' expected_cmd = '{cmd} {in_file} -otsu -odt float {out_file}'.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.niftyseg import no_niftyseg, get_custom_path, EM from nipype.testing import example_data import os import pytest @pytest.mark.skipif(no_niftyseg(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 assert seg_em.cmd == get_custom_path('seg_EM') # 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 \ {out_file} -out_outlier {out_outlier}' expected_cmd = cmd_tmp.format(