Merge pull request #3173 from mgxd/enh/euler-number

ENH: Detect values for EulerNumber interface

Author: effigies

nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py

@@ -17,7 +17,7 @@ def test_EulerNumber_inputs():
 
 
 def test_EulerNumber_outputs():
-    output_map = dict(out_file=dict(extensions=None,),)
+    output_map = dict(defects=dict(), euler=dict(),)
     outputs = EulerNumber.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/interfaces/freesurfer/tests/test_utils.py

@@ -230,3 +230,19 @@ def test_mrisexpand(tmpdir):
     assert op.dirname(if_out_file) == op.dirname(fsavginfo["smoothwm"])
     # Node places output in working directory
     assert op.dirname(nd_out_file) == nd_res.runtime.cwd
+
+
+@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
+def test_eulernumber(tmpdir):
+    # grab a surface from fsaverage
+    fssrc = FreeSurferSource(
+        subjects_dir=fs.Info.subjectsdir(), subject_id="fsaverage", hemi="lh"
+    )
+    pial = fssrc.run().outputs.pial
+    assert isinstance(pial, str), "Problem when fetching surface file"
+
+    eu = fs.EulerNumber()
+    eu.inputs.in_file = pial
+    res = eu.run()
+    assert res.outputs.defects == 0
+    assert res.outputs.euler == 2

nipype/interfaces/freesurfer/utils.py

@@ -2592,7 +2592,9 @@ class EulerNumberInputSpec(FSTraitedSpec):
 
 
 class EulerNumberOutputSpec(TraitedSpec):
-    out_file = File(exists=False, desc="Output file for EulerNumber")
+    euler = traits.Int(desc="Euler number of cortical surface. A value of 2 signals a "
+                            "topologically correct surface model with no holes")
+    defects = traits.Int(desc="Number of defects")
 
 
 class EulerNumber(FSCommand):
@@ -2612,9 +2614,22 @@ class EulerNumber(FSCommand):
     input_spec = EulerNumberInputSpec
     output_spec = EulerNumberOutputSpec
 
+    def _run_interface(self, runtime):
+        runtime = super()._run_interface(runtime)
+        self._parse_output(runtime.stdout, runtime.stderr)
+        return runtime
+
+    def _parse_output(self, stdout, stderr):
+        """Parse stdout / stderr and extract defects"""
+        m = re.search(r'(?<=total defect index = )\d+', stdout or stderr)
+        if m is None:
+            raise RuntimeError("Could not fetch defect index")
+        self._defects = int(m.group())
+
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs["out_file"] = os.path.abspath(self.inputs.in_file)
+        outputs["defects"] = self._defects
+        outputs["euler"] = 2 - (2 * self._defects)
         return outputs