add list outputs

Author: josephmje

nipype/interfaces/mrtrix3/preprocess.py

@@ -38,6 +38,7 @@ class DWIDenoiseInputSpec(MRTrix3BaseInputSpec):
         genfile=True)
 
 class DWIDenoiseOutputSpec(TraitedSpec):
+    noise = File(desc='the output noise map', exists=True)
     out_file = File(desc='the output denoised DWI image', exists=True)
 
 class DWIDenoise(MRTrix3Base):
@@ -75,6 +76,13 @@ class DWIDenoise(MRTrix3Base):
     input_spec = DWIDenoiseInputSpec
     output_spec = DWIDenoiseOutputSpec
 
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        if self.inputs.noise != Undefined:
+            outputs['noise'] = op.abspath(self.inputs.noise)
+        return outputs
+
 
 class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
@@ -204,6 +212,7 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
         genfile=True)
 
 class DWIBiasCorrectOutputSpec(TraitedSpec):
+    bias = File(desc='the output bias field', exists=True)
     out_file = File(desc='the output bias corrected DWI image', exists=True)
 
 class DWIBiasCorrect(MRTrix3Base):
@@ -228,6 +237,13 @@ class DWIBiasCorrect(MRTrix3Base):
     input_spec = DWIBiasCorrectInputSpec
     output_spec = DWIBiasCorrectOutputSpec
 
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        if self.inputs.bias != Undefined:
+            outputs['bias'] = op.abspath(self.inputs.bias)
+        return outputs
+
 
 class ResponseSDInputSpec(MRTrix3BaseInputSpec):
     algorithm = traits.Enum(

nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py

@@ -59,7 +59,10 @@ def test_DWIBiasCorrect_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_DWIBiasCorrect_outputs():
-    output_map = dict(out_file=dict(), )
+    output_map = dict(
+        bias=dict(),
+        out_file=dict(),
+    )
     outputs = DWIBiasCorrect.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py

@@ -45,7 +45,10 @@ def test_DWIDenoise_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_DWIDenoise_outputs():
-    output_map = dict(out_file=dict(), )
+    output_map = dict(
+        noise=dict(),
+        out_file=dict(),
+    )
     outputs = DWIDenoise.output_spec()
 
     for key, metadata in list(output_map.items()):