Merge pull request #1806 from mgxd/fix/mnibias

fix: MNIBiasCorrection smart out_file

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -1503,11 +1503,11 @@ class MNIBiasCorrectionInputSpec(FSTraitedSpec):
     # mandatory
     in_file = File(exists=True, mandatory=True, argstr="--i %s",
                    desc="input volume. Input can be any format accepted by mri_convert.")
+    # optional
     out_file = File(argstr="--o %s", name_source=['in_file'],
                     name_template='%s_output', hash_files=False, keep_extension=True,
                     desc="output volume. Output can be any format accepted by mri_convert. " +
                     "If the output format is COR, then the directory must exist.")
-    # optional
     iterations = traits.Int(4, argstr="--n %d",
                             desc="Number of iterations to run nu_correct. Default is 4. This is the number of times " +
                             "that nu_correct is repeated (ie, using the output from the previous run as the input for " +
@@ -1528,7 +1528,7 @@ class MNIBiasCorrectionInputSpec(FSTraitedSpec):
                         desc="Shrink parameter for finer sampling (default is 4)")
 
 class MNIBiasCorrectionOutputSpec(TraitedSpec):
-    out_file = File(desc="output volume")
+    out_file = File(exists=True, desc="output volume")
 
 
 class MNIBiasCorrection(FSCommand):
@@ -1563,11 +1563,6 @@ class MNIBiasCorrection(FSCommand):
     input_spec = MNIBiasCorrectionInputSpec
     output_spec = MNIBiasCorrectionOutputSpec
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
-        return outputs
-
 
 class WatershedSkullStripInputSpec(FSTraitedSpec):
     # required

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -85,3 +85,31 @@ def test_synthesizeflash(create_files_in_directory):
     syn2 = freesurfer.SynthesizeFLASH(t1_image=filelist[0], pd_image=filelist[1], flip_angle=20, te=5, tr=25)
     assert syn2.cmdline == ('mri_synthesize 25.00 20.00 5.000 %s %s %s'
                             % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_20.mgz')))
+
+@pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+def test_mandatory_outvol(create_files_in_directory):
+    filelist, outdir = create_files_in_directory
+    mni = freesurfer.MNIBiasCorrection()
+
+    # make sure command gets called
+    assert mni.cmd == "mri_nu_correct.mni"
+
+    # test raising error with mandatory args absent
+    with pytest.raises(ValueError): mni.cmdline
+
+    # test with minimal args
+    mni.inputs.in_file = filelist[0] 
+    assert mni.cmdline == ('mri_nu_correct.mni --i %s --o %s_output.mgz'
+                           % (filelist[0], filelist[0].replace('.mgz', '')))
+
+    # test with custom outfile
+    mni.inputs.out_file = 'new_corrected_file.mgz'
+    assert mni.cmdline == ('mri_nu_correct.mni --i %s --o new_corrected_file.mgz'
+                           % (filelist[0]))
+
+    # constructor based tests
+    mni2 = freesurfer.MNIBiasCorrection(in_file=filelist[0], 
+                                        out_file='bias_corrected_output',
+                                        iterations=4)
+    assert mni2.cmdline == ('mri_nu_correct.mni --i %s --n 4 --o bias_corrected_output.mgz'
+                             % filelist[0])