From a87ee77b44bbd70eaeaf197ae649203564f657c1 Mon Sep 17 00:00:00 2001
From: Daljit Singh <daljit7991@gmail.com>
Date: Wed, 21 Jun 2023 12:32:32 +0100
Subject: [PATCH] Fix generation of list of config file options

---
 docs/format_config_options                   |  2 +-
 docs/generate_user_docs.sh                   |  2 +-
 docs/reference/config_file_options.rst       | 14 +++++++++-----
 src/gui/mrview/tool/connectome/selection.cpp |  6 +++---
 src/registration/linear.h                    |  2 +-
 5 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/docs/format_config_options b/docs/format_config_options
index 048ef85e68..c93b0e12af 100755
--- a/docs/format_config_options
+++ b/docs/format_config_options
@@ -20,7 +20,7 @@ import sys
 optionlist =  [ ]
 
 for line in sys.stdin:
-  line = line.split ('//CONF')[1][1:]
+  line = line.split ('// CONF')[1][1:]
   if line.startswith ('option:'):
     optionlist += [ [ line[8:].strip(), '', '' ] ]
   elif line.startswith ('default:'):
diff --git a/docs/generate_user_docs.sh b/docs/generate_user_docs.sh
index 7a2ae23ef8..44239ae9fc 100755
--- a/docs/generate_user_docs.sh
+++ b/docs/generate_user_docs.sh
@@ -110,7 +110,7 @@ echo "
 
 # Generating list of configuration file options
 
-grep -rn --include=\*.h --include=\*.cpp '^\s*//CONF\b' "${mrtrix_root}" |\
+grep -rn --include=\*.h --include=\*.cpp '^\s*//\sCONF\b' "${mrtrix_root}" |\
   "${mrtrix_root}"/docs/format_config_options > ${mrtrix_root}/docs/reference/config_file_options.rst
 
 
diff --git a/docs/reference/config_file_options.rst b/docs/reference/config_file_options.rst
index bf53cc4a80..4f494f33e6 100644
--- a/docs/reference/config_file_options.rst
+++ b/docs/reference/config_file_options.rst
@@ -109,7 +109,8 @@ List of MRtrix3 configuration file options
 
     *default: 0.5*
 
-     The fraction of the colour of an edge connected to two selected nodes determined by the fixed selection highlight colour.
+     The fraction of the colour of an edge connected to two selected nodes determined by the fixed selection
+     highlight colour.
 
 .. option:: ConnectomeEdgeSelectedSizeMultiplier
 
@@ -151,7 +152,8 @@ List of MRtrix3 configuration file options
 
     *default: 1.0*
 
-     The multiplicative factor to apply to the transparency of nodes not currently selected nor associated with a selected node.
+     The multiplicative factor to apply to the transparency of nodes not currently selected nor associated with a
+     selected node.
 
 .. option:: ConnectomeNodeOtherColour
 
@@ -163,13 +165,14 @@ List of MRtrix3 configuration file options
 
     *default: 0.75*
 
-     The fraction of the colour of an unselected, non-associated node determined by the fixed not-selected highlight colour.
+     The fraction of the colour of an unselected, non-associated node determined by the fixed not-selected
 
 .. option:: ConnectomeNodeOtherSizeMultiplier
 
     *default: 1.0*
 
-     The multiplicative factor to apply to the size of nodes not currently selected nor associated with a selected node.
+     The multiplicative factor to apply to the size of nodes not currently selected nor associated with a selected
+     node.
 
 .. option:: ConnectomeNodeOtherVisibilityOverride
 
@@ -638,7 +641,8 @@ List of MRtrix3 configuration file options
 
     *default: 0.0001*
 
-     Linear registration: smallest gradient descent step measured in fraction of a voxel at which to stop registration.
+     Linear registration: smallest gradient descent step measured in fraction of a voxel at which to stop
+     registration.
 
 .. option:: ScriptScratchDir
 
diff --git a/src/gui/mrview/tool/connectome/selection.cpp b/src/gui/mrview/tool/connectome/selection.cpp
index 01d3d7d52b..fa399cdb9d 100644
--- a/src/gui/mrview/tool/connectome/selection.cpp
+++ b/src/gui/mrview/tool/connectome/selection.cpp
@@ -82,7 +82,7 @@ NodeSelectionSettings::NodeSelectionSettings()
   // CONF option: ConnectomeEdgeSelectedColourFade
   // CONF default: 0.5
   // CONF The fraction of the colour of an edge connected to two selected nodes determined by the fixed selection
-  // highlight colour.
+  // CONF highlight colour.
   edge_selected_colour_fade = File::Config::get_float("ConnectomeEdgeSelectedColourFade", 0.5f);
   // CONF option: ConnectomeEdgeSelectedColour
   // CONF default: 0.9,0.9,1.0
@@ -151,12 +151,12 @@ NodeSelectionSettings::NodeSelectionSettings()
   // CONF option: ConnectomeNodeOtherSizeMultiplier
   // CONF default: 1.0
   // CONF The multiplicative factor to apply to the size of nodes not currently selected nor associated with a selected
-  // node.
+  // CONF node.
   node_other_size_multiplier = File::Config::get_float("ConnectomeNodeOtherSizeMultiplier", 1.0f);
   // CONF option: ConnectomeNodeOtherAlphaMultiplier
   // CONF default: 1.0
   // CONF The multiplicative factor to apply to the transparency of nodes not currently selected nor associated with a
-  // selected node.
+  // CONF selected node.
   node_other_alpha_multiplier = File::Config::get_float("ConnectomeNodeOtherAlphaMultiplier", 1.0f);
 
   // CONF option: ConnectomeEdgeOtherVisibilityOverride
diff --git a/src/registration/linear.h b/src/registration/linear.h
index f6eb77c21f..4d7cc4c3e6 100644
--- a/src/registration/linear.h
+++ b/src/registration/linear.h
@@ -455,7 +455,7 @@ class Linear {
       // CONF option: RegStopLen
       // CONF default: 0.0001
       // CONF Linear registration: smallest gradient descent step measured in fraction of a voxel at which to stop
-      // registration.
+      // CONF registration.
       default_type reg_stop_len = File::Config::get_float("RegStopLen", 0.0001);
       stop.array() *= reg_stop_len;
       DEBUG("coherence length: " + str(coherence));