Fix generation of list of config file options

MRtrix3 · Jul 5, 2023 · cff5cd8 · cff5cd8
1 parent 3977735
commit cff5cd8
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Showing 5 changed files with 15 additions and 11 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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));