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

freeview/LayerSurface.cpp

@@ -1221,14 +1221,14 @@ int LayerSurface::GetVertexIndexAtTarget( double* pos, double* distance, int sur
   return m_surfaceSource->FindVertexAtRAS( realRas, distance, surface_type );
 }
 
-bool LayerSurface::GetRASAtVertex( int nVertex, double* ras )
+bool LayerSurface::GetRASAtVertex( int nVertex, double* ras, int surface_type )
 {
   if ( m_surfaceSource == NULL )
   {
     return false;
   }
 
-  return m_surfaceSource->GetRASAtVertex( nVertex, ras );
+  return m_surfaceSource->GetRASAtVertex( nVertex, ras, surface_type );
 }
 
 void LayerSurface::GetSurfaceRASAtTarget( double* pos_in, double* ras_out )
@@ -2282,7 +2282,8 @@ bool LayerSurface::GetCorrelationOverlayDataAtVertex(int nVert, float *output, i
 
 bool LayerSurface::IsInflated()
 {
-  return (GetFileName().toLower().contains("inflated") || GetActiveSurface() == FSSurface::SurfaceInflated);
+  return (QFileInfo(GetFileName()).fileName().toLower().contains("inflated") ||
+          GetActiveSurface() == FSSurface::SurfaceInflated);
 }
 
 bool LayerSurface::GetActiveLabelCentroidPosition(double *pos)
@@ -3203,3 +3204,19 @@ void LayerSurface::GetCenterOfActor(double *pt)
     bbox.GetCenter(pt);
   }
 }
+
+bool LayerSurface::SavePathAsControlPoints(const QString& fn, bool bMarks)
+{
+  SurfacePath* sp = NULL;
+  if (bMarks)
+  {
+    sp = m_marks;
+  }
+  else if (!m_paths.isEmpty())
+    sp = GetActivePath();
+
+  if (sp)
+    return sp->SaveAsControlPoints(fn);
+  else
+    return false;
+}

freeview/LayerSurface.h

@@ -99,7 +99,7 @@ class LayerSurface : public LayerEditable
 
   int GetVertexIndexAtTarget( double* ras, double* distance, int surface_type = -1 );
 
-  bool GetRASAtVertex       ( int nVertex, double* ras_out );
+  bool GetRASAtVertex       ( int nVertex, double* ras_out, int surface_type = -1 );
   bool GetSurfaceRASAtVertex( int nVertex, double* ras_out );
 
   int GetVertexAtSurfaceRAS(double* ras, double* distance );
@@ -456,6 +456,8 @@ public slots:
 
   void GetCenterOfActor(double* pt);
 
+  bool SavePathAsControlPoints(const QString& fn, bool bMarks = false);
+
 Q_SIGNALS:
   void SurfaceAnnotationAdded( SurfaceAnnotation* );
   void SurfaceLabelAdded( SurfaceLabel* );

freeview/RenderView3D.cpp

@@ -30,6 +30,7 @@
 #include "SurfaceRegion.h"
 #include "SurfaceROI.h"
 #include "SurfaceOverlayProperty.h"
+#include "SurfacePath.h"
 #include <vtkProp.h>
 #include <vtkCellPicker.h>
 #include <vtkRenderWindow.h>
@@ -58,12 +59,14 @@
 #include <vtkCubeAxesActor.h>
 #include <vtkTextProperty.h>
 #include <QFileInfo>
+#include <QFileDialog>
 #include "MyUtils.h"
 #include "FSSurface.h"
 #include "Interactor3DPathEdit.h"
 #include <QElapsedTimer>
 #include "vtkInteractorStyleMyTrackballCamera.h"
 #include <vtkCubeAxesActor.h>
+#include <QMessageBox>
 
 #define SLICE_PICKER_PIXEL_TOLERANCE  15
 
@@ -619,7 +622,7 @@ bool RenderView3D::MapInflatedCoords(LayerSurface *surf, double *pos_in, double
     surf->SetCurrentVertex(nVertex);
   else
     surf->SetMouseVertex(nVertex);
-  if (QFileInfo(surf->GetFileName()).fileName().contains("inflated") || surf->GetActiveSurface() == FSSurface::SurfaceInflated)
+  if (surf->IsInflated())
   {
     if (m_cursor3D->IsShown())
       m_cursorInflatedSurf->Show();
@@ -1600,6 +1603,24 @@ void RenderView3D::TriggerContextMenu( QMouseEvent* event )
     menu->addSeparator();
     menu->addAction(act);
   }
+
+  surf = (LayerSurface*)mainwnd->GetActiveLayer("Surface");
+  if (surf)
+  {
+    menu->addSeparator();
+    if (surf->GetMarks() && surf->GetMarks()->GetNumberOfPoints() > 0)
+    {
+      act = new QAction("Save Marked Vertices As Control Points", this);
+      connect(act, SIGNAL(triggered()), SLOT(SaveMarksAsControlPoints()));
+      menu->addAction(act);
+    }
+    if (surf->GetActivePath())
+    {
+      act = new QAction("Save Path As Control Points", this);
+      connect(act, SIGNAL(triggered()), SLOT(SavePathAsControlPoints()));
+      menu->addAction(act);
+    }
+  }
   menu->exec(event->globalPos());
 }
 
@@ -1801,3 +1822,30 @@ int RenderView3D::GetAxesFlyMode()
 {
   return m_actorAxesActor->GetFlyMode();
 }
+
+void RenderView3D::SavePathAsControlPoints()
+{
+  LayerSurface* surf = (LayerSurface*)MainWindow::GetMainWindow()->GetActiveLayer("Surface");
+  if (surf && surf->GetActivePath())
+    SavePathAsControlPoints(surf->GetActivePath());
+}
+
+void RenderView3D::SaveMarksAsControlPoints()
+{
+  LayerSurface* surf = (LayerSurface*)MainWindow::GetMainWindow()->GetActiveLayer("Surface");
+  if (surf && surf->GetMarks())
+    SavePathAsControlPoints(surf->GetMarks());
+}
+
+void RenderView3D::SavePathAsControlPoints(SurfacePath *sp)
+{
+  LayerSurface* surf = (LayerSurface*)MainWindow::GetMainWindow()->GetActiveLayer("Surface");
+  QString fn = QFileDialog::getSaveFileName( this, QString("Save %1 As").arg(sp->IsPathMade()?"Path":"Vertices"),
+                                             "",
+                                             "Control Point files (*)");
+  if ( !fn.isEmpty())
+  {
+    if (!surf->SavePathAsControlPoints(fn, !sp->IsPathMade()))
+      QMessageBox::warning(this, "Error", "Failed to save file " + fn);
+  }
+}

freeview/RenderView3D.h

@@ -42,6 +42,7 @@ class Interactor3DPathEdit;
 class RenderView3D;
 class vtkInteractorStyleMyTrackballCamera;
 class Region3D;
+class SurfacePath;
 
 class RenderView3D : public RenderView
 {
@@ -174,10 +175,13 @@ public slots:
   void SetAxesFlyMode(int n);
   void DeleteCurrent3DRegion();
   void DeleteAll3DRegions();
+  void SavePathAsControlPoints();
+  void SaveMarksAsControlPoints();
 
 protected:
   void DoUpdateRASPosition( int posX, int posY, bool bCursor = false, bool bSlicePickOnly = false );
   void DoUpdateConnectivityDisplay();
+  void SavePathAsControlPoints(SurfacePath* sp);
 
   void HighlightSliceFrame( int n );
 

freeview/SurfacePath.cpp

@@ -486,3 +486,32 @@ double SurfacePath::GetLength()
     else
         return 0;
 }
+
+bool SurfacePath::SaveAsControlPoints(const QString &filename)
+{
+  QFile file( filename );
+  if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
+  {
+    QString strg = file.errorString();
+    if (strg.isEmpty())
+      cerr << "Can not open file for writing\n";
+    else
+      cerr << qPrintable(strg) << "\n";
+    return false;
+  }
+
+  QTextStream out(&file);
+  for (int n = 0; n < m_listVertices.size(); n++)
+  {
+    double pt[3];
+    m_mris->GetRASAtVertex(m_listVertices[n], pt, m_mris->IsInflated()?FSSurface::SurfaceWhite:-1);
+    out << QString("%1 %2 %3\n").arg(pt[0]).arg(pt[1]).arg(pt[2]);
+  }
+  out << QString("info\nnumpoints %1\nuseRealRAS 1\n").arg( m_listVertices.size() );
+  return true;
+}
+
+int SurfacePath::GetNumberOfPoints()
+{
+  return m_listVertices.size();
+}

freeview/SurfacePath.h

@@ -81,6 +81,10 @@ class SurfacePath : public QObject
 
   double GetLength();
 
+  int GetNumberOfPoints();
+
+  bool SaveAsControlPoints(const QString& filename);
+
 signals:
   void ColorChanged( const QColor& );
   void Progress(int n);

packages/dcm2niix/CMakeLists.txt

@@ -207,28 +207,18 @@ if(APPLE)
 endif()
 
 ### start of addition for FREESURFER
-# we should not need this if we use target_compile_definitions()
-#target_link_libraries(dcm2niix nifti ${ZLIB_LIBRARIES})
-
-set(LIBRARY dcm2niix)
-add_library(dcm2niix STATIC
-    dcm2fsWrapper.cpp
+set(DCM2NIIXFSLIB dcm2niixfs)
+add_library(${DCM2NIIXFSLIB} STATIC
+    dcm2niix_fswrapper.cpp
     nii_dicom.cpp
     jpg_0XC3.cpp
     ujpeg.cpp
     nifti1_io_core.cpp
     nii_foreign.cpp
     nii_ortho.cpp
     nii_dicom_batch.cpp)
-target_compile_definitions(${LIBRARY} PUBLIC -DMGH_FREESURFER -DUSING_MGH_NIFTI_IO)
-
-# DON'T build dcm2niixfsexe
-#set(DCM2NIIXFSEXE dcm2niixfsexe)
-#add_executable(${DCM2NIIXFSEXE} dcm2fsmain.cpp)
-#target_link_libraries(${DCM2NIIXFSEXE} dcm2niixfs nifti ${ZLIB_LIBRARIES})
+target_compile_definitions(${DCM2NIIXFSLIB} PUBLIC -DUSING_DCM2NIIXFSWRAPPER -DUSING_MGH_NIFTI_IO)
 ### end of addition for FREESURFER
 
 #install(TARGETS ${PROGRAMS} DESTINATION bin)
-### additions for FREESURFER
-#install(TARGETS ${LIBRARY} DESTINATION bin)
-#install(TARGETS ${DCM2NIIXFSEXE} DESTINATION bin)
+

packages/dcm2niix/dcm2fsWrapper.cpp → packages/dcm2niix/dcm2niix_fswrapper.cpp

@@ -1,12 +1,11 @@
 #include <stdio.h>
 
 #include "nii_dicom.h"
-#include "dcm2fsWrapper.h"
+#include "dcm2niix_fswrapper.h"
 
-struct TDCMopts dcm2fsWrapper::tdcmOpts;
-//MRIFSSTRUCT dcm2fsWrapper::mrifsStruct;
+struct TDCMopts dcm2niix_fswrapper::tdcmOpts;
 
-/* oct06 version
+/* These are the TDCMopts defaults set in dcm2niix
 isIgnoreTriggerTimes = false
 isTestx0021x105E = false
 isAddNamePostFixes = true
@@ -41,17 +40,19 @@ isProgress = 0
 compressFlag = 0
 dirSearchDepth = 5
 gzLevel = 6
-filename = "%s_%p"    // seriesNum_protocol
+filename = "%s_%p"    // seriesNum_protocol -f "%s_%p"
 outdir = "..."
 indir = "..."
 pigzname = '\000'
-optsname = "..."
+optsname = "~/.dcm2nii.ini"
 indirParent = "..."
 imageComments = ""
 seriesNumber = nnn 
 numSeries = 0
  */
-void dcm2fsWrapper::setOpts(const char* dcmindir, const char* niioutdir)
+
+// set TDCMopts defaults, overwrite settings to output in mgz orientation
+void dcm2niix_fswrapper::setOpts(const char* dcmindir, const char* niioutdir)
 {
   memset(&tdcmOpts, 0, sizeof(tdcmOpts));
   setDefaultOpts(&tdcmOpts, NULL);
@@ -61,6 +62,7 @@ void dcm2fsWrapper::setOpts(const char* dcmindir, const char* niioutdir)
   if (niioutdir != NULL)
     strcpy(tdcmOpts.outdir, niioutdir);
 
+  // set the options for freesurfer mgz orientation
   tdcmOpts.isRotate3DAcq = false;
   tdcmOpts.isFlipY = false;
   tdcmOpts.isIgnoreSeriesInstanceUID = true;
@@ -71,57 +73,49 @@ void dcm2fsWrapper::setOpts(const char* dcmindir, const char* niioutdir)
   //tdcmOpts.isForceOnsetTimes = false;
 }
 
-bool dcm2fsWrapper::isDICOM(const char* file)
+// interface to isDICOMfile() in nii_dicom.cpp
+bool dcm2niix_fswrapper::isDICOM(const char* file)
 {
   return isDICOMfile(file);
 }
 
-int dcm2fsWrapper::dcm2NiiOneSeries(const char* dcmfile)
+/*
+ * interface to nii_loadDirCore() to search all dicom files from the directory input file is in,
+ * and convert dicom files with the same series as given file.
+ */
+int dcm2niix_fswrapper::dcm2NiiOneSeries(const char* dcmfile)
 {
+  // get seriesNo for given dicom file
   struct TDICOMdata tdicomData = readDICOM((char*)dcmfile);
 
   double seriesNo = (double)tdicomData.seriesUidCrc;
   if (tdcmOpts.isIgnoreSeriesInstanceUID)
     seriesNo = (double)tdicomData.seriesNum;
 
+  // set TDCMopts to convert just one series
   tdcmOpts.seriesNumber[0] = seriesNo;
   tdcmOpts.numSeries = 1;
 
-  //memset(&mrifsStruct, 0, sizeof(mrifsStruct));
   return nii_loadDirCore(tdcmOpts.indir, &tdcmOpts);
 }
 
-int dcm2fsWrapper::saveNii(const char* nii)
-{
-  FILE *fp = fopen(nii, "wb");
-  if (!fp) 
-    return 1;
-
-  MRIFSSTRUCT* mrifsStruct = getMrifsStruct();
-
-  //if (!opts.isSaveNativeEndian) swapEndian(&hdr, im, true); //byte-swap endian (e.g. little->big)
-  fwrite(&mrifsStruct->hdr0, sizeof(mrifsStruct->hdr0), 1, fp);
-  uint32_t pad = 0;
-  fwrite(&pad, sizeof( pad), 1, fp);
-  fwrite(mrifsStruct->imgM, mrifsStruct->imgsz, 1, fp);
-  fclose(fp);
-
-  return 0;
-}
-
-MRIFSSTRUCT* dcm2fsWrapper::getMrifsStruct(void)
+// interface to nii_getMrifsStruct()
+MRIFSSTRUCT* dcm2niix_fswrapper::getMrifsStruct(void)
 {
   return nii_getMrifsStruct();
 }
 
-nifti_1_header* dcm2fsWrapper::getNiiHeader(void)
+// return nifti header saved in MRIFSSTRUCT
+nifti_1_header* dcm2niix_fswrapper::getNiiHeader(void)
 {
   MRIFSSTRUCT* mrifsStruct = getMrifsStruct();
   return &mrifsStruct->hdr0;
 }
 
-const unsigned char* dcm2fsWrapper::getMRIimg(void)
+// return image data saved in MRIFSSTRUCT
+const unsigned char* dcm2niix_fswrapper::getMRIimg(void)
 {
   MRIFSSTRUCT* mrifsStruct = getMrifsStruct();
   return mrifsStruct->imgM;
 }
+