Merge branch 'dev' of github.com:freesurfer/freesurfer into dev

ayendiki · Jan 25, 2022 · 8f6aeea · 8f6aeea
2 parents eb82742 + aef1a6b
commit 8f6aeea
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Showing 7 changed files with 311 additions and 254 deletions.
diff --git a/freeview/DialogLoadVolume.cpp b/freeview/DialogLoadVolume.cpp
@@ -62,7 +62,7 @@ void DialogLoadVolume::UpdateLUT()
 void DialogLoadVolume::OnOpen()
 {
   QString fn = ui->comboBoxFilenames->currentText().trimmed();
-  if (fn == "current folder")
+  if (fn.isEmpty() || fn == "current folder")
     fn = QDir::currentPath();
   else
     fn =  QFileInfo(fn).absolutePath();
@@ -107,6 +107,7 @@ void DialogLoadVolume::SetRecentFiles( const QStringList& filenames )
   if ( !filenames.isEmpty() )
   {
     ui->comboBoxFilenames->setCurrentIndex( 0 );
+    ui->comboBoxFilenames->setCurrentText("");
     ui->comboBoxFilenames->lineEdit()->setCursorPosition( ui->comboBoxFilenames->currentText().size() );
   }
 }

diff --git a/freeview/MainWindow.cpp b/freeview/MainWindow.cpp
@@ -1918,7 +1918,11 @@ void MainWindow::RunScript()
   }
   else if ( cmd == "setheatscaleoptions" )
   {
-    CommandSetHeadScaleOptions( sa );
+    CommandSetHeatScaleOptions( sa );
+  }
+  else if ( cmd == "setheatscaleoffset")
+  {
+    CommandSetHeatScaleOffset( sa );
   }
   else if ( cmd == "setlut" )
   {
@@ -2152,6 +2156,10 @@ void MainWindow::RunScript()
   {
     CommandSetActiveFrame(sa);
   }
+  else if (cmd == "setautoadjustframecontrast")
+  {
+    CommandSetAutoAdjustFrameContrast(sa);
+  }
   else if (cmd == "setactivelayer")
   {
     CommandSetActiveLayer(sa);
@@ -2376,12 +2384,18 @@ void MainWindow::CommandLoadVolume( const QStringList& sa )
         scales = subArgu.split(",");
       }
       else if ( subOption == "heatscaleoption" ||
-                subOption == "heatscaleoptions" )
+                subOption == "heatscaleoptions" ||
+                subOption == "heatscale_option" ||
+                subOption == "heatscale_options")
       {
         QStringList script("setheatscaleoptions");
         script << subArgu.split(",");
         m_scripts.insert( 0, script );
       }
+      else if ( subOption == "heatscale_offset" )
+      {
+        m_scripts.insert( 0, QStringList() << "setheatscaleoffset" << subArgu );
+      }
       else if ( subOption == "lut" )
       {
         lut_name = subArgu;
@@ -2584,6 +2598,10 @@ void MainWindow::CommandLoadVolume( const QStringList& sa )
       {
         m_scripts.insert( 0, QStringList() << "setactiveframe" << subArgu );
       }
+      else if ( subOption == "auto_adjust_frame_contrast" )
+      {
+        m_scripts.insert( 0, QStringList() << "setautoadjustframecontrast" << subArgu );
+      }
       else if (subOption == "ignore_header")
       {
         sup_data["IgnoreHeader"] = true;
@@ -2775,7 +2793,7 @@ void MainWindow::CommandSetSelectedLabels(const QStringList &cmd)
   }
 }
 
-void MainWindow::CommandSetHeadScaleOptions( const QStringList& sa )
+void MainWindow::CommandSetHeatScaleOptions( const QStringList& sa )
 {
   if ( GetLayerCollection( "MRI" )->GetActiveLayer() )
   {
@@ -2794,6 +2812,22 @@ void MainWindow::CommandSetHeadScaleOptions( const QStringList& sa )
   }
 }
 
+void MainWindow::CommandSetHeatScaleOffset(const QStringList &sa)
+{
+  if ( GetLayerCollection( "MRI" )->GetActiveLayer() )
+  {
+    bool bOK;
+    double dValue = sa[1].toDouble(&bOK);
+    if ( !bOK )
+    {
+      cerr << "Heatscale offset value is not valid.\n";
+      return;
+    }
+    LayerPropertyMRI* p = ( (LayerMRI*)GetLayerCollection( "MRI" )->GetActiveLayer() )->GetProperty();
+    p->SetHeatScaleOffset(dValue);
+  }
+}
+
 void MainWindow::CommandSetLayerName( const QStringList& cmd )
 {
   if ( cmd.size() > 2 )
@@ -3117,6 +3151,16 @@ void MainWindow::CommandSetActiveFrame( const QStringList& sa )
   }
 }
 
+void MainWindow::CommandSetAutoAdjustFrameContrast( const QStringList& sa )
+{
+  LayerMRI* mri = (LayerMRI*)GetLayerCollection( "MRI" )->GetActiveLayer();
+  if ( mri )
+  {
+    mri->GetProperty()->SetAutoAdjustFrameLevel(sa[1].toLower() == "true" || sa[1] == "1");
+  }
+}
+
+
 void MainWindow::CommandSetDisplayIsoSurface( const QStringList& sa )
 {
   LayerMRI* mri = (LayerMRI*)GetLayerCollection( "MRI" )->GetActiveLayer();

diff --git a/freeview/MainWindow.h b/freeview/MainWindow.h
@@ -390,7 +390,8 @@ public slots:
   void CommandWriteSurfaceIntersection( const QStringList& cmd);
   void CommandSetColorMap       ( const QStringList& cmd );
   void CommandSetLUT            ( const QStringList& cmd );
-  void CommandSetHeadScaleOptions( const QStringList& sa );
+  void CommandSetHeatScaleOptions( const QStringList& sa );
+  void CommandSetHeatScaleOffset ( const QStringList& sa );
   void CommandSetOpacity        ( const QStringList& cmd );
   void CommandSetLabelOutline   ( const QStringList& cmd );
   void CommandSetSelectedLabels (const QStringList& cmd);
@@ -441,6 +442,7 @@ public slots:
   void CommandReorderLayers   ( const QStringList& cmd );
   void CommandUnloadLayers    ( const QStringList& cmd );
   void CommandSetActiveFrame    ( const QStringList& cmd );
+  void CommandSetAutoAdjustFrameContrast ( const QStringList& cmd );
   void CommandSetActiveLayer    ( const QStringList& cmd );
   void CommandExportLineProfileThickness  (const QStringList& cmd);
   void CommandSetVolumeTrackFrame   ( const QStringList& cmd );

diff --git a/freeview/main.cpp b/freeview/main.cpp
@@ -142,7 +142,8 @@ int main(int argc, char *argv[])
     "':colormap=name' Set colormap for display. Valid names are grayscale/lut/heat/jet/gecolor/nih/pet/binary. \n\n"
     "':grayscale=min,max' Set grayscale window values.\n\n"
     "':heatscale=min,mid,max' Set heat scale values. If only 2 values given, min and mid will be set to the same value.\n\n"
-    "':heatscaleoptions=option1[,option2]' Set heat scale options. Options can be 'truncate','invert', or both.\n\n"
+    "':heatscale_options=option1[,option2]' Set heat scale options. Options can be 'truncate','invert', or both.\n\n"
+    "':heatscale_offset=val' Set heat scale offset value.\n\n"
     "':colorscale=min,max' Set generic colorscale values for jet/gecolor/nih/pet.\n\n"
     "':lut=name' Set lookup table to the given name. Name can be the name of a stock color table or the filename of a color table file.\n\n"
     "':binary_color=color' Set the color of the non-zero voxels. Colormap must be set to binary. Color can be a color name such as 'red' or 3 values as RGB components of the color, e.g., '255,0,0'.\n\n"
@@ -176,6 +177,7 @@ int main(int argc, char *argv[])
     "':structure=name_or_value' Move the slice in the main viewport to where it has the most of the given structure.\n\n"
     "':ignore_header=flag' Ignore header information. Use the existing volume's header info. Flag can be '1' or '0' or 'true' or 'false'.\n\n"
     "':frame=number' Set active frame (0 based).\n\n"
+    "':auto_adjust_frame_contrast=flag' Set flag for automatically adjust frame contrast. Flag can be '1' or 'true'.\n\n"
     "':select_label=label_index' When colormap is set as look up table, select and show only the given labels. Multiple labels can be given separated by comma, such as, '5,10,20'.\n\n"
     "Example:\nfreeview -v T1.mgz:colormap=heatscale:heatscale=10,100,200\n", 1, 1000 ),
     CmdLineEntry( CMD_LINE_SWITCH, "r", "resample", "", "Resample oblique data to standard RAS." ),

diff --git a/include/GradUnwarp.h b/include/GradUnwarp.h
@@ -11,38 +11,58 @@ typedef struct
   char xyz;
 } COEFF;
 
+class Siemens_B
+{
+public:
+  Siemens_B(int coeffDim0, int nmax0, float R0, double **normfact0, float X, float Y, float Z);
+  ~Siemens_B();
+
+  float siemens_B_x(float **Alpha_x, float **Beta_x);
+  float siemens_B_y(float **Alpha_y, float **Beta_y);
+  float siemens_B_z(float **Alpha_z, float **Beta_z);
+  float siemens_B(float **Alpha, float **Beta);
+  void  siemens_legendre(int n, double x);
+
+private:
+  int coeffDim;
+  int nmax;
+  float R0_mm;
+
+  double **normfact;
+
+  double **P;
+  float  *F;
+  double *cosPhi, *sinPhi;
+  float R, Theta, Phi;
+};
+
 class GradUnwarp
 {
 public:
   GradUnwarp();
   ~GradUnwarp();
 
-  void  setup();
-  void  list_coeff_files();
+  void  setup() {};
+  void  list_coeff_files() {};
 
   void  read_siemens_coeff(const char *gradfilename);
   void  printCoeff();
 
-  float siemens_B_x();
-  float siemens_B_y();
-  float siemens_B_z();
-  float siemens_B(float **Alpha, float **Beta, float **F2);
-  void  siemens_B0(float X, float Y, float Z);
-  void  siemens_legendre(int n, double x, double **P);
-
+  void initSiemensLegendreNormfact();
   void  spharm_evaluate(float X, float Y, float Z, float *Dx, float *Dy, float *Dz);
 
-  void  initSiemensLegendreNormfact();
-
-  void  unwarp();
-  void  unwap_volume();
-  void  unwarp_surface();
+  void  unwarp() {};
+  void  unwap_volume() {};
+  void  unwarp_surface() {};
 
 private:
   FILE *fgrad;
 
   COEFF coeff[100];
 
+  int nmax;
+  int mmax;
+
   int coeffCount;
   int coeffDim;
 
@@ -56,13 +76,6 @@ class GradUnwarp
   double *factorials;
   double **normfact;
 
-  // these are reset and re-calculated for each (x, y, z) in siemens_B0()  
-  double **P;
-  float **F2_x, **F2_y, **F2_z;
-  float  *F;
-  double *cosPhi, *sinPhi;
-  float R, Theta, Phi;
-
 private:
   void _skipCoeffComment();
   void _initCoeff();