Remove out_ prefix from EddyQuad outputs

Author: Adam Richie-Halford

nipype/interfaces/fsl/epi.py

@@ -1297,44 +1297,44 @@ class EddyQuadInputSpec(FSLCommandInputSpec):
 
 
 class EddyQuadOutputSpec(TraitedSpec):
-    out_qc_json = File(
+    qc_json = File(
         exists=True,
         desc=("Single subject database containing quality metrics and data "
               "info.")
     )
-    out_qc_pdf = File(
+    qc_pdf = File(
         exists=True,
         desc="Single subject QC report."
     )
-    out_avg_b_png = traits.List(
+    avg_b_png = traits.List(
         File(exists=True),
         desc=("Image showing mid-sagittal, -coronal and -axial slices of "
               "each averaged b-shell volume.")
     )
-    out_avg_b0_pe_png = traits.List(
+    avg_b0_pe_png = traits.List(
         File(exists=True),
         desc=("Image showing mid-sagittal, -coronal and -axial slices of "
               "each averaged pe-direction b0 volume. Generated when using "
               "the -f option.")
     )
-    out_cnr_png = traits.List(
+    cnr_png = traits.List(
         File(exists=True),
         desc=("Image showing mid-sagittal, -coronal and -axial slices of "
               "each b-shell CNR volume. Generated when CNR maps are "
               "available.")
     )
-    out_vdm_png = File(
+    vdm_png = File(
         exists=True,
         desc=("Image showing mid-sagittal, -coronal and -axial slices of "
               "the voxel displacement map. Generated when using the -f "
               "option.")
     )
-    out_residuals = File(
+    residuals = File(
         exists=True,
         desc=("Text file containing the volume-wise mask-averaged squared "
               "residuals. Generated when residual maps are available.")
     )
-    out_clean_volumes = File(
+    clean_volumes = File(
         exists=True,
         desc=("Text file containing a list of clean volumes, based on "
               "the eddy squared residuals. To generate a version of the "
@@ -1387,38 +1387,38 @@ def _list_outputs(self):
         else:
             out_dir = os.path.abspath(self.inputs.output_dir)
 
-        outputs['out_qc_json'] = os.path.join(out_dir, 'qc.json')
-        outputs['out_qc_pdf'] = os.path.join(out_dir, 'qc.pdf')
+        outputs['qc_json'] = os.path.join(out_dir, 'qc.json')
+        outputs['qc_pdf'] = os.path.join(out_dir, 'qc.pdf')
 
         # Grab all b* files here. This will also grab the b0_pe* files
         # as well, but only if the field input was provided. So we'll remove
         # them later in the next conditional.
-        outputs['out_avg_b_png'] = sorted(glob(
+        outputs['avg_b_png'] = sorted(glob(
             os.path.join(out_dir, 'avg_b*.png')
         ))
 
         if isdefined(self.inputs.field):
-            outputs['out_avg_b0_pe_png'] = sorted(glob(
+            outputs['avg_b0_pe_png'] = sorted(glob(
                 os.path.join(out_dir, 'avg_b0_pe*.png')
             ))
 
-            # The previous glob for `out_avg_b_png` also grabbed the
-            # `out_avg_b0_pe_png` files so we have to remove them
-            # from `out_avg_b_png`.
-            for fname in outputs['out_avg_b0_pe_png']:
-                outputs['out_avg_b_png'].remove(fname)
+            # The previous glob for `avg_b_png` also grabbed the
+            # `avg_b0_pe_png` files so we have to remove them
+            # from `avg_b_png`.
+            for fname in outputs['avg_b0_pe_png']:
+                outputs['avg_b_png'].remove(fname)
 
-            outputs['out_vdm_png'] = os.path.join(out_dir, 'vdm.png')
+            outputs['vdm_png'] = os.path.join(out_dir, 'vdm.png')
 
-        outputs['out_cnr_png'] = sorted(glob(os.path.join(out_dir, 'cnr*.png')))
+        outputs['cnr_png'] = sorted(glob(os.path.join(out_dir, 'cnr*.png')))
 
         residuals = os.path.join(out_dir, 'eddy_msr.txt')
         if os.path.isfile(residuals):
-            outputs['out_residuals'] = residuals
+            outputs['residuals'] = residuals
 
         clean_volumes = os.path.join(out_dir, 'vols_no_outliers.txt')
         if os.path.isfile(clean_volumes):
-            outputs['out_clean_volumes'] = clean_volumes
+            outputs['clean_volumes'] = clean_volumes
 
         return outputs