From 05de2b66d714e3fe13f7e77c624b310b1ef932f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?=
 <jon.haitz.legarreta@gmail.com>
Date: Sat, 18 May 2024 11:24:49 -0400
Subject: [PATCH] STYLE: Fix unused loop control variable warning

Fix unused loop control variable warning: show how to specify multiple
output filenames for a combined workflow, and provide them to the
corresponding sub-workflows.

Fixes:
```
doc/examples/combined_workflow_creation.py:68:22:
 B007 Loop control variable `out_file` not used within loop body
```

raised for example in:
https://github.com/dipy/dipy/actions/runs/9131684633/job/25111443178#step:4:116
---
 doc/examples/combined_workflow_creation.py | 40 ++++++++++++++++++----
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/doc/examples/combined_workflow_creation.py b/doc/examples/combined_workflow_creation.py
index ff9da26fc1..63a31030ec 100644
--- a/doc/examples/combined_workflow_creation.py
+++ b/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,
+            )
 
 
 ###############################################################################