Added command-line option to set overlay threshold offset

Author: rpwang17

freeview/MainWindow.cpp

@@ -2013,6 +2013,10 @@ void MainWindow::RunScript()
   {
     CommandSetSurfaceOverlayOpacity( sa );
   }
+  else if ( cmd == "setsurfaceoverlayoffset")
+  {
+    CommandSetSurfaceOverlayOffset(sa);
+  }
   else if ( cmd == "setsurfaceoverlayframe")
   {
     CommandSetSurfaceOverlayFrame( sa );
@@ -3603,7 +3607,7 @@ void MainWindow::CommandLoadSurface( const QStringList& cmd )
   QVariantMap sup_options;
   valid_overlay_options << "overlay_reg" << "overlay_method" << "overlay_threshold" << "overlay_color"
                         << "overlay_rh" << "overlay_opacity" << "overlay_frame" << "overlay_smooth" << "overlay_custom"
-                        << "overlay_mask";
+                        << "overlay_mask" << "overlay_offset";
   bool bNoAutoLoad = m_defaultSettings["no_autoload"].toBool();
   for (int nOverlay = 0; nOverlay < overlay_list.size(); nOverlay++)
   {
@@ -3622,6 +3626,7 @@ void MainWindow::CommandLoadSurface( const QStringList& cmd )
     QStringList overlay_thresholds;
     QStringList overlay_custom;
     QStringList overlay_mask;
+    QString overlay_offset;
     bool bSecondHalfData = false;
     for ( int k = sa_fn.size()-1; k >= 0; k-- )
     {
@@ -3650,6 +3655,8 @@ void MainWindow::CommandLoadSurface( const QStringList& cmd )
           overlay_custom = subArgu.split(",", MD_SkipEmptyParts);
         else if (subOption == "overlay_mask")
           overlay_mask = subArgu.split(",", MD_SkipEmptyParts);
+        else if (subOption == "overlay_offset")
+          overlay_offset = subArgu;
       }
     }
     if (overlay_reg.isEmpty())
@@ -3764,6 +3771,9 @@ void MainWindow::CommandLoadSurface( const QStringList& cmd )
 
           if (!overlay_mask.isEmpty())
             m_scripts.insert(1, QStringList("setsurfaceoverlaymask") << overlay_mask);
+
+          if (!overlay_offset.isEmpty())
+            m_scripts.insert(1, QStringList("setsurfaceoverlayoffset") << overlay_offset);
         }
         else if ( subOption == "mrisps" )
         {
@@ -4077,6 +4087,30 @@ void MainWindow::CommandSetSurfaceOverlayOpacity(const QStringList &cmd)
   }
 }
 
+void MainWindow::CommandSetSurfaceOverlayOffset(const QStringList &cmd)
+{
+  LayerSurface* surf = (LayerSurface*)GetLayerCollection( "Surface" )->GetActiveLayer();
+  if ( surf )
+  {
+    SurfaceOverlay* overlay = surf->GetActiveOverlay();
+    if ( overlay )
+    {
+      bool ok;
+      double val = cmd[1].toDouble(&ok);
+      if (ok)
+      {
+        overlay->GetProperty()->SetOffset(val);
+        surf->UpdateOverlay(true);
+        overlay->EmitDataUpdated();
+      }
+      else
+      {
+        cerr << "Invalid input for overlay offset.\n";
+      }
+    }
+  }
+}
+
 void MainWindow::CommandSetSurfaceOverlayFrame(const QStringList &cmd)
 {
   LayerSurface* surf = (LayerSurface*)GetLayerCollection( "Surface" )->GetActiveLayer();

freeview/MainWindow.h

@@ -404,6 +404,7 @@ public slots:
   void CommandSetSurfaceOverlaySmooth     ( const QStringList& cmd );
   void CommandSetSurfaceOverlayMask      ( const QStringList& cmd );
   void CommandSetSurfaceOverlayCustom     ( const QStringList& cmd );
+  void CommandSetSurfaceOverlayOffset    ( const QStringList& cmd );
   void CommandSetSurfaceColor   ( const QStringList& cmd );
   void CommandSetSurfaceEdgeColor ( const QStringList& cmd );
   void CommandSetSurfaceEdgeThickness ( const QStringList& cmd );

freeview/RenderView3D.cpp

@@ -558,7 +558,7 @@ void RenderView3D::DoUpdateRASPosition( int posX, int posY, bool bCursor, bool b
         lc_mri->SetCursorRASPosition( pos );
         MainWindow::GetMainWindow()->SetSlicePosition( pos );
       }
-      else if ( lc_mri->HasProp( prop ) || lc_roi->HasProp( prop ) )
+      else if ( mri_sel || lc_roi->HasProp( prop ) )
       {
         if ( bCursor )
         {

freeview/main.cpp

@@ -200,6 +200,7 @@ int main(int argc, char *argv[])
     "':overlay_custom=[filename]val,r,g,b,val2,r2,g2,b2...' Set customized overlay color. If only given one argument as filename, customized color scale will be loaded from the given file.\n\n"
     "':overlay_opacity=opacity' Set opacity of overlay.\n\n"
     "':overlay_threshold=low,(mid,)high(,percentile)' Set overlay threshold values, separated by comma. When overlay method is linear or linearopaque, only 2 numbers (low and high) are needed. When method is piecewise, 3 numbers are needed. If last element is 'percentile', use the give numbers as percentile.\n\n"
+    "':overlay_offset=offset' Set the offset for overlay threshold setting.\n\n"
     "':overlay_mask=filename(,invert)' Use given label file as mask for overlay. If invert is specified, use the inverted mask.\n\n"
     "':overlay_frame=frame_number' Set active frame of multi-frame overlay.\n\n"
     "':overlay_smooth=smooth_steps' Set smooth steps for overlay.\n\n"