Merge pull request dipy#3228 from jhlegarreta/FixCombinedWorkflowExam…

…pleWarning

STYLE: Fix unused loop control variable warning

doc/examples/combined_workflow_creation.py

@@ -10,6 +10,8 @@
 file is usually located in the ``dipy/workflows`` directory.
 """
 
+import os
+
 from dipy.workflows.combined_workflow import CombinedWorkflow
 
 ###############################################################################
@@ -37,7 +39,14 @@ def _get_sub_flows(self):
         sub workflows parameters available in commandline.
         """
 
-    def run(self, input_files, out_dir="", out_file="processed.nii.gz"):
+    def run(
+        self,
+        input_files,
+        out_dir="",
+        out_denoised="processed.nii.gz",
+        out_mask="brain_mask.nii.gz",
+        out_masked="dwi_masked.nii.gz",
+    ):
         """
         Parameters
         ----------
@@ -48,8 +57,14 @@ def run(self, input_files, out_dir="", out_file="processed.nii.gz"):
         out_dir : string, optional
             Where the resulting file will be saved. (default '')
 
-        out_file : string, optional
-            Name of the result file to be saved. (default 'processed.nii.gz')
+        out_denoised : string, optional
+            Name of the denoised file to be saved.
+
+        out_mask : string, optional
+            Name of the Otsu mask file to be saved.
+
+        out_masked : string, optional
+            Name of the Otsu masked file to be saved.
         """
 
         """
@@ -65,13 +80,26 @@ def run(self, input_files, out_dir="", out_file="processed.nii.gz"):
 
         io_it = self.get_io_iterator()
 
-        for in_file, out_file in io_it:
+        for fnames in io_it:
+            in_fname = fnames[0]
+            _out_denoised = os.path.basename(fnames[1])
+            _out_mask = os.path.basename(fnames[2])
+            _out_masked = os.path.basename(fnames[3])
+
             nl_flow = NLMeansFlow()
-            self.run_sub_flow(nl_flow, in_file, out_dir=out_dir)
+            self.run_sub_flow(
+                nl_flow, in_fname, out_dir=out_dir, out_denoised=_out_denoised
+            )
             denoised = nl_flow.last_generated_outputs["out_denoised"]
 
             me_flow = MedianOtsuFlow()
-            self.run_sub_flow(me_flow, denoised, out_dir=out_dir)
+            self.run_sub_flow(
+                me_flow,
+                denoised,
+                out_dir=out_dir,
+                out_mask=_out_mask,
+                out_masked=_out_masked,
+            )
 
 
 ###############################################################################