Merge pull request #1884 from effigies/test/bbregister

TEST: Multi-version BBRegister test

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -1038,6 +1038,9 @@ class BBRegisterInputSpec6(BBRegisterInputSpec):
     init = traits.Enum('coreg', 'rr', 'spm', 'fsl', 'header', 'best', argstr='--init-%s',
                        xor=['init_reg_file'],
                        desc='initialize registration with mri_coreg, spm, fsl, or header')
+    init_reg_file = File(exists=True, argstr='--init-reg %s',
+                         desc='existing registration file',
+                         xor=['init'])
 
 
 class BBRegisterOutputSpec(TraitedSpec):

nipype/interfaces/freesurfer/tests/test_BBRegister.py

@@ -0,0 +1,68 @@
+from __future__ import unicode_literals
+from ..preprocess import BBRegister, BBRegisterInputSpec6
+
+
+def test_BBRegister_inputs():
+    input_map_5_3 = dict(
+        args=dict(argstr='%s',),
+        contrast_type=dict(argstr='--%s', mandatory=True,),
+        environ=dict(nohash=True, usedefault=True,),
+        epi_mask=dict(argstr='--epi-mask',),
+        ignore_exception=dict(nohash=True, usedefault=True,),
+        init=dict(argstr='--init-%s', mandatory=True, xor=['init_reg_file'],),
+        init_reg_file=dict(argstr='--init-reg %s', mandatory=True, xor=['init'],),
+        intermediate_file=dict(argstr='--int %s',),
+        out_fsl_file=dict(argstr='--fslmat %s',),
+        out_reg_file=dict(argstr='--reg %s', genfile=True,),
+        reg_frame=dict(argstr='--frame %d', xor=['reg_middle_frame'],),
+        reg_middle_frame=dict(argstr='--mid-frame', xor=['reg_frame'],),
+        registered_file=dict(argstr='--o %s',),
+        source_file=dict(argstr='--mov %s', copyfile=False, mandatory=True,),
+        spm_nifti=dict(argstr='--spm-nii',),
+        subject_id=dict(argstr='--s %s', mandatory=True,),
+        subjects_dir=dict(),
+        terminal_output=dict(nohash=True,),
+        )
+    input_map_6_0 = dict(
+        args=dict(argstr='%s',),
+        contrast_type=dict(argstr='--%s', mandatory=True,),
+        environ=dict(nohash=True, usedefault=True,),
+        epi_mask=dict(argstr='--epi-mask',),
+        ignore_exception=dict(nohash=True, usedefault=True,),
+        init=dict(argstr='--init-%s', xor=['init_reg_file'],),
+        init_reg_file=dict(argstr='--init-reg %s', xor=['init'],),
+        intermediate_file=dict(argstr='--int %s',),
+        out_fsl_file=dict(argstr='--fslmat %s',),
+        out_reg_file=dict(argstr='--reg %s', genfile=True,),
+        reg_frame=dict(argstr='--frame %d', xor=['reg_middle_frame'],),
+        reg_middle_frame=dict(argstr='--mid-frame', xor=['reg_frame'],),
+        registered_file=dict(argstr='--o %s',),
+        source_file=dict(argstr='--mov %s', copyfile=False, mandatory=True,),
+        spm_nifti=dict(argstr='--spm-nii',),
+        subject_id=dict(argstr='--s %s', mandatory=True,),
+        subjects_dir=dict(),
+        terminal_output=dict(nohash=True,),
+        )
+
+    instance = BBRegister()
+    if isinstance(instance.inputs, BBRegisterInputSpec6):
+        input_map = input_map_6_0
+    else:
+        input_map = input_map_5_3
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(instance.inputs.traits()[key], metakey) == value
+
+
+def test_BBRegister_outputs():
+    output_map = dict(min_cost_file=dict(),
+                      out_fsl_file=dict(),
+                      out_reg_file=dict(),
+                      registered_file=dict(),
+                      )
+    outputs = BBRegister.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py

@@ -6,7 +6,9 @@
 import pytest
 from nipype.testing.fixtures import create_files_in_directory
 
-import nipype.interfaces.freesurfer as freesurfer
+from nipype.interfaces import freesurfer
+from nipype.interfaces.freesurfer.preprocess import FSVersion
+from nipype import LooseVersion
 
 
 @pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed")
@@ -118,3 +120,37 @@ def test_mandatory_outvol(create_files_in_directory):
                                         iterations=4)
     assert mni2.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_output'
                              % filelist[0])
+
+@pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+def test_bbregister(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+    bbr = freesurfer.BBRegister()
+
+    # make sure command gets called
+    assert bbr.cmd == "bbregister"
+
+    # test raising error with mandatory args absent
+    with pytest.raises(ValueError):
+        bbr.cmdline
+
+    bbr.inputs.subject_id = 'fsaverage'
+    bbr.inputs.source_file = filelist[0]
+    bbr.inputs.contrast_type = 't2'
+
+    # Check that 'init' is mandatory in FS < 6, but not in 6+
+    if LooseVersion(FSVersion) < LooseVersion("6.0.0"):
+        with pytest.raises(ValueError):
+            bbr.cmdline
+    else:
+        bbr.cmdline
+
+    bbr.inputs.init = 'fsl'
+
+    base, ext = os.path.splitext(os.path.basename(filelist[0]))
+    if ext == '.gz':
+        base, _ = os.path.splitext(base)
+
+    assert bbr.cmdline == ('bbregister --t2 --init-fsl '
+                           '--reg {base}_bbreg_fsaverage.dat '
+                           '--mov {full} --s fsaverage'.format(
+                            full=filelist[0], base=base))