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

freeview/LayerMRI.cpp

@@ -4432,3 +4432,13 @@ bool LayerMRI::Load3DRegions( const QString& fn )
   emit Region3DAdded();
   return bSuccess;
 }
+
+
+void LayerMRI::Close3DRegion()
+{
+  if ( m_current3DRegion )
+  {
+    m_current3DRegion->Close();
+    emit ActorUpdated();
+  }
+}

freeview/LayerMRI.h

@@ -366,6 +366,8 @@ class LayerMRI : public LayerVolumeBase
 
   bool Load3DRegions(const QString& fn);
 
+  void Close3DRegion();
+
 public slots:
   virtual void SetModified();
   void SetActiveFrame( int nFrame );

freeview/MyUtils.h

@@ -35,7 +35,7 @@ class MyUtils
   static void FloodFill( char* data, int x, int y, int dim_x, int dim_y, int fill_value, int border_value );
 
   template <class T> static double GetDistance( const T* pt1, const T* pt2 );
-  template <class T> static void GetVector( T* pt1, T* pt2, double* v_out );
+  template <class T> static void GetVector( T* pt1, T* pt2, double* v_out, bool bNormalize = true);
   template <class T> static bool Equal( T* pt1, T* p2, int n = 3 );
   template <class T> static T** AllocateMatrix(int ny, int nx);
   template <class T> static void FreeMatrix(T** p, int ny);
@@ -107,7 +107,7 @@ double MyUtils::Dot( T* v1, T* v2 )
 }
 
 template <class T>
-void MyUtils::GetVector( T* pt1_in, T* pt2_in, double* v_out )
+void MyUtils::GetVector( T* pt1_in, T* pt2_in, double* v_out, bool bNormalize )
 {
   T pt1[3], pt2[3];
   for ( int i = 0; i < 3; i++ )
@@ -124,7 +124,9 @@ void MyUtils::GetVector( T* pt1_in, T* pt2_in, double* v_out )
 
   for ( int i = 0; i < 3; i++ )
   {
-    v_out[i] = ( (double)pt2[i] - (double)pt1[i] ) / dist;
+    v_out[i] = ( (double)pt2[i] - (double)pt1[i] );
+    if (bNormalize)
+      v_out[i] /= dist;
   }
 }
 

freeview/Region3D.cpp

@@ -15,6 +15,9 @@
 #include "LayerMRI.h"
 #include "LayerPropertyMRI.h"
 #include "vtkSplineFilter.h"
+#include <vtkKdTreePointLocator.h>
+#include "vtkCleanPolyData.h"
+#include <QDebug>
 
 Region3D::Region3D(LayerMRI* owner ) : QObject(owner), m_mri(owner)
 {
@@ -28,7 +31,16 @@ Region3D::Region3D(LayerMRI* owner ) : QObject(owner), m_mri(owner)
   m_actor->GetProperty()->SetLineWidth( 5*ratio );
 
   m_points = vtkSmartPointer<vtkPoints>::New();
+  m_interpolatedPoints = vtkSmartPointer<vtkPoints>::New();
   m_color = Qt::blue;
+
+  m_locator = vtkSmartPointer<vtkKdTreePointLocator>::New();
+  QList<vtkActor*> list = m_mri->GetContourActors(true);
+  if (!list.isEmpty())
+  {
+    m_locator->SetDataSet(vtkPolyData::SafeDownCast( list.first()->GetMapper()->GetInput() ));
+    m_locator->BuildLocator();
+  }
 }
 
 Region3D::~Region3D()
@@ -65,7 +77,20 @@ void Region3D::RebuildOutline( bool bInterpolate )
     m_mri->GetVolumeInfo(dim, vs);
     spline->SetSubdivideToLength();
     spline->SetLength(qMin(qMin(vs[0],vs[1]), vs[2])/3);
-    mapper->SetInputConnection(spline->GetOutputPort());
+    spline->Update();
+    m_interpolatedPoints = spline->GetOutput()->GetPoints();
+    polydata = vtkSmartPointer<vtkPolyData>::New();
+    lines = vtkSmartPointer<vtkCellArray>::New();
+    lines->InsertNextCell( m_interpolatedPoints->GetNumberOfPoints() );
+    for ( int i = 0; i < m_interpolatedPoints->GetNumberOfPoints(); i++ )
+    {
+      lines->InsertCellPoint( i );
+    }
+    polydata->SetPoints( m_interpolatedPoints );
+    polydata->SetLines( lines );
+    vtkSmartPointer<vtkCleanPolyData> clean = vtkSmartPointer<vtkCleanPolyData>::New();
+    clean->SetInputData(polydata);
+    mapper->SetInputConnection(clean->GetOutputPort());
   }
   else
   {
@@ -125,9 +150,12 @@ QColor Region3D::GetColor()
 bool Region3D::HasPoint(double *pt, double dist)
 {
   double th = dist*dist;
-  for (int i = 0; i < m_points->GetNumberOfPoints(); i++)
+  vtkPoints* pts = m_points;
+  if (m_interpolatedPoints.GetPointer())
+    pts = m_interpolatedPoints;
+  for (int i = 0; i < pts->GetNumberOfPoints(); i++)
   {
-    if (vtkMath::Distance2BetweenPoints(pt, m_points->GetPoint(i)) < th)
+    if (vtkMath::Distance2BetweenPoints(pt, pts->GetPoint(i)) < th)
       return true;
   }
   return false;
@@ -200,7 +228,7 @@ bool Region3D::Load( FILE* fp )
   }
   m_color = QColor(r, g, b);
 
-  RebuildOutline( false );
+  RebuildOutline( true );
 
   return true;
 }

freeview/Region3D.h

@@ -16,6 +16,7 @@ class vtkClipPolyData;
 class vtkCleanPolyData;
 class RenderView3D;
 class LayerMRI;
+class vtkKdTreePointLocator;
 
 class Region3D : public QObject
 {
@@ -62,6 +63,8 @@ class Region3D : public QObject
 
   vtkSmartPointer<vtkActor>   m_actor;
   vtkSmartPointer<vtkPoints>  m_points;
+  vtkSmartPointer<vtkPoints>  m_interpolatedPoints;
+  vtkSmartPointer<vtkKdTreePointLocator> m_locator;
 
   LayerMRI*   m_mri;
   QColor      m_color;

freeview/RenderView3D.cpp

@@ -1133,6 +1133,8 @@ void RenderView3D::CloseSelectRegion(int nAction)
   {
     if (nAction == Interactor::MM_SurfaceRegion)
       mri->CloseSurfaceRegion();
+    else if (nAction == Interactor::MM_DrawOnSurface)
+      mri->Close3DRegion();
   }
 }
 

trc/blood.cxx

@@ -1570,9 +1570,10 @@ void Blood::MatchStreamlineEnds() {
         ivalid2++;
       }
 
-      if (!mMask.empty())
+      if (!mMask.empty()) {
         imask++;
         iaseg++;
+      }
     }
   }
   else {					// Have labeling ROIs

trc/coffin.cxx

@@ -2678,11 +2678,12 @@ bool Coffin::ProposePathFull() {
     if (!IsInMask(cpoint)) {
       *isrej = true;
 
-      if (mDebug)
+      if (mDebug) {
         mLog << "Reject due to control point " 
              << isrej - mRejectControl.begin() << " off mask at "
              << cpoint[0] << " " << cpoint[1] << " " << cpoint[2] << endl;
         LogObjectiveNaN(0);
+      }
     }
 
     cpoint += 3;

trc/dmri_trk2trk.cxx

@@ -725,9 +725,10 @@ int main(int argc, char **argv) {
       streamlines.erase(streamlines.begin(), streamlines.begin() + kstrmean);
       streamlines.erase(streamlines.begin() + 1, streamlines.end());
 
-      if (!properties.empty())
+      if (!properties.empty()) {
         properties.erase(properties.begin(), properties.begin() + kstrmean);
         properties.erase(properties.begin() + 1, properties.end());
+      }
     }
 
     // Write transformed streamlines to volume