X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvToolSegmentation.cxx;h=63ff9b150f6cac958826bb87e83b9473310b9c0a;hb=0722e563db4e7b4493e4c697f75fb6f6aee93ebb;hp=873a099af18b4a398da00394bed01c45df0daead;hpb=6f76702afbff9ce0af70f887cd8a4e4d4bdd173a;p=clitk.git

diff --git a/vv/vvToolSegmentation.cxx b/vv/vvToolSegmentation.cxx
index 873a099..63ff9b1 100644
--- a/vv/vvToolSegmentation.cxx
+++ b/vv/vvToolSegmentation.cxx
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
+  ===========================================================================**/
 
 // vv
 #include "vvToolSegmentation.h"
@@ -26,14 +26,20 @@
 // clitk
 #include "clitkConnectedComponentLabeling_ggo.h"
 #include "clitkConnectedComponentLabelingGenericFilter.h"
+#include "clitkRegionGrowing_ggo.h"
+#include "clitkRegionGrowingGenericFilter.h"
 
 // Qt
 #include <QFileDialog>
 #include <QMessageBox>
 
 // vtk
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
 #include "vtkImageContinuousErode3D.h"
 #include "vtkImageContinuousDilate3D.h"
+#include "vtkRenderWindow.h"
 
 //------------------------------------------------------------------------------
 // Create the tool and automagically (I like this word) insert it in
@@ -68,8 +74,11 @@ vvToolSegmentation::vvToolSegmentation(vvMainWindowBase * parent, Qt::WindowFlag
   AddInputSelector("Select one image");
   
   // Init
+  mCurrentLabelUnderMousePointer = 0.0;
+  mCurrentMousePositionInMM.resize(3);
+  //  mCurrentMousePositionInPixel.resize(3);
   mRefMaskImage = NULL;
-  mCurrentMode = Mode_Default;
+  mCurrentState = State_Default;
   mKernelValue = 3; // FIXME must be odd. If even -> not symmetrical
   mDefaultLUTColor = vtkSmartPointer<vtkLookupTable>::New();
   mDefaultLUTColor->SetNumberOfTableValues(256);
@@ -90,13 +99,15 @@ vvToolSegmentation::~vvToolSegmentation()
 //------------------------------------------------------------------------------
 bool vvToolSegmentation::close()
 {
-  DD("close");
-  mRefMaskActor->RemoveActors();
-  DD("la");
-  mCurrentMaskActor->RemoveActors();
-  DD("here");
+  DD("remo ref");
+  if (mRefMaskActor) mRefMaskActor->RemoveActors();
+  DD("remo mask");
+  if (mCurrentMaskActor) mCurrentMaskActor->RemoveActors();
+  for(int i=0; i<mCurrentCCLActors.size(); i++) {
+    if (mCurrentCCLActors[i]) mCurrentCCLActors[i]->RemoveActors();
+  }
+  DD("wclose");
   QWidget::close();  
-  DD("toto");
   mCurrentSlicerManager->Render();
   return true;
 }
@@ -135,6 +146,8 @@ void vvToolSegmentation::InputIsSelected(vvSlicerManager * m)
   // Connect mouse position
   connect(mCurrentSlicerManager, SIGNAL(MousePositionUpdatedSignal(int)),
           this, SLOT(MousePositionChanged(int)));
+  connect(mCurrentSlicerManager, SIGNAL(KeyPressedSignal(std::string)),
+          this, SLOT(KeyPressed(std::string)));
 }
 //------------------------------------------------------------------------------
 
@@ -191,60 +204,190 @@ void vvToolSegmentation::OpenBinaryImage()
   reader->Update(vvImageReader::IMAGE);
   mCurrentMaskImage = reader->GetOutput();
 
-  // Add a new roi actor
-  mRefMaskActor = CreateMaskActor(mRefMaskImage, 0, 0, true);
+  // Add a new roi actor for the current mask
+  mCurrentMaskActor = CreateMaskActor(mCurrentMaskImage, 1, 0, false);
+  mCurrentMaskActor->Update(); // default color is red
+  UpdateMaskSize(mCurrentMaskImage, mCurrentMaskSizeInPixels, mCurrentMaskSizeInCC);  
+
+  // Add a mask actor for the reference
+  mRefMaskActor = CreateMaskActor(mRefMaskImage, 0, 1, true);
   mRefMaskActor->SetContourVisible(true);
   mRefMaskActor->SetVisible(false);
   mRefMaskActor->SetContourColor(0,1,0); // green contour
   mRefMaskActor->UpdateColor();
   mRefMaskActor->Update();
+  UpdateMaskSize(mRefMaskImage, mRefMaskSizeInPixels, mRefMaskSizeInCC);  
+
+  // Update GUI
+  UpdateMaskSizeLabels();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::UpdateMaskSizeLabels()
+{
+  QString s("%1 pix (%2 cm3)");
+  s = s.arg(mRefMaskSizeInPixels).arg(mRefMaskSizeInCC);
+  mRefMaskSizeLabel->setText(s);
+  QString s2("%1 pix (%2 cm3)");
+  s2 = s2.arg(mCurrentMaskSizeInPixels).arg(mCurrentMaskSizeInCC);
+  mCurrentMaskSizeLabel->setText(s2);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::UpdateMaskSize(vvImage::Pointer image, long & pix, double & cc)
+{
+  pix = ComputeNumberOfPixels(image, GetForegroundValue());
+  double vol = image->GetSpacing()[0]*image->GetSpacing()[1]*image->GetSpacing()[2];
+  cc = pix * vol / (10*10*10);
+}
+//------------------------------------------------------------------------------
 
-  mCurrentMaskActor = CreateMaskActor(mCurrentMaskImage, 1, 1, false);
-  mCurrentMaskActor->SetOverlayColor(1,0,0); // red roi
-  mRefMaskActor->UpdateColor();
-  mCurrentMaskActor->Update();
 
-  // Prepare widget to get keyboard event. With this method, the key
-  //  only work when the mouse focus is on the dialog
-  DD("here installe");
-  this->installEventFilter(this);
-  //grabKeyboard();
+//------------------------------------------------------------------------------
+long vvToolSegmentation::ComputeNumberOfPixels(vvImage::Pointer image, double value) 
+{
+  int n=0;
+  vtkImageData * im = image->GetFirstVTKImageData();
+  char * pPix = (char*)im->GetScalarPointer(); // FIXME char ?
+  for(uint i=0; i<im->GetNumberOfPoints(); i++) {
+    if (pPix[i] == value) n++;
+  }
+  DD(n);
+  return n;
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::KeyPressed(std::string KeyPress)
+{ 
+  if (KeyPress == "G") {
+    RegionGrowing();
+  }
+  if (KeyPress == "e") {
+    Erode();
+  }
+  if (KeyPress == "d") {
+    Dilate(); // FIXME -> extend image BB !!
+  }
+  if (KeyPress == "L") {
+    Labelize(); 
+  }
+  if (KeyPress == "m") {
+    Merge(); 
+    UpdateAndRenderNewMask();
+  }
+  if (KeyPress == "s") { // Supress "Remove" one label
+    if (mCurrentState == State_CCL) RemoveLabel();
+  }
+  if (KeyPress == "t") { // display remove ref contour
+    mRefMaskActor->SetContourVisible(!mRefMaskActor->IsContourVisible());
+    mRefMaskActor->UpdateColor();
+    mCurrentSlicerManager->Render();
+  }
+  if (KeyPress == "w") {
+    vvImageWriter::Pointer writer = vvImageWriter::New();
+    writer->SetOutputFileName("a.mha");
+    writer->SetInput(mCurrentMaskImage);
+    writer->Update();
+  }
 }
 //------------------------------------------------------------------------------
 
 
 //------------------------------------------------------------------------------
-//void vvToolSegmentation::keyPressEvent(QKeyEvent * event)
-bool vvToolSegmentation::eventFilter(QObject *object, QEvent * e)
+void vvToolSegmentation::RegionGrowing()
 {
-  // DD("key");
-  //vvToolWidgetBase::keyPressEvent(event);
+  DD("RegionGrowing");
+  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  // Merge labels if needed
+  Merge();
+  // Get mouse location
+  DD(mCurrentLabelUnderMousePointer); 
+  DDV(mCurrentMousePositionInMM, 3);
+  //  DDV(mCurrentMousePositionInPixel, 3);
+
+  // Build RG filter parameters
+  typedef args_info_clitkRegionGrowing ArgsInfoType;
+  ArgsInfoType a;
+  cmdline_parser_clitkRegionGrowing_init(&a);
+  // FIXME parameters
+  a.type_arg = 4;  // FIXME set by gui 
+  DD(a.lower_arg);
+  a.lower_arg = 200;
+  a.upper_arg = 3000;
+  a.seed_given = 3;
+  a.seed_arg = new int[3];
+
+  DDV(mCurrentMousePositionInMM, 3);
+  vtkImageData * image = mCurrentImage->GetFirstVTKImageData();
+  double x = (mCurrentMousePositionInMM[0] - image->GetOrigin()[0]) / image->GetSpacing()[0];
+  double y = (mCurrentMousePositionInMM[1] - image->GetOrigin()[1]) / image->GetSpacing()[1];
+  double z = (mCurrentMousePositionInMM[2] - image->GetOrigin()[2]) / image->GetSpacing()[2];
+  a.seed_arg[0] = x;
+  a.seed_arg[1] = y;
+  a.seed_arg[2] = z;
+  a.verbose_flag = 1;
+
+  // Build RG filter parameters
+  typedef clitk::RegionGrowingGenericFilter<args_info_clitkRegionGrowing> FilterType;
+  FilterType::Pointer filter = FilterType::New();
+  filter->SetArgsInfo(a);
+  filter->SetInputVVImage(mCurrentImage);
+  filter->SetIOVerbose(true);  
+  filter->Update();
+  mCurrentMaskImage = filter->GetOutputVVImage();
+  DD("filter done");
+
+  mCurrentMaskActor->RemoveActors();
+  mCurrentMaskActor = CreateMaskActor(mCurrentMaskImage, 1, 0, false);
+  mCurrentMaskActor->Update(); // default color is red
+  UpdateAndRenderNewMask();
+  UpdateMaskSizeLabels();
+  DD("end");
   
-  if (/*object == form &&*/ e->type() == QEvent::KeyPress) {
-    QKeyEvent * event = static_cast<QKeyEvent *>(e);
-    
-    if (event->text() == "e") {
-      Erode();
-    }
-    if (event->text() == "d") {
-      Dilate(); // FIXME -> extend image BB !!
-    }
-    if (event->text() == "l") {
-      Labelize(); 
-    }
-    if (event->text() == "r") { // "Remove" one label
-      if (mCurrentMode == Mode_CCL) RemoveLabel();
-    }
-    if (event->text() == "s") {
-      vvImageWriter::Pointer writer = vvImageWriter::New();
-      writer->SetOutputFileName("a.mha");
-      writer->SetInput(mCurrentMaskImage);
-      writer->Update();
+  // mouse pointer
+  QApplication::restoreOverrideCursor();
+}  
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::Merge()
+{
+  if (mCurrentState != State_CCL) return;
+  
+  DD("Merge");
+  // Remove actors
+  for(int i=0; i<mCurrentCCLActors.size(); i++) {
+    if (mCurrentCCLActors[i]) {
+      mCurrentCCLActors[i]->SetVisible(false);
+      mCurrentCCLActors[i]->RemoveActors();
     }
-    //mMainWindow->keyPressEvent(event);
-    vvToolWidgetBase::keyPressEvent(event);
-  }         
-  return QObject::eventFilter(object, e);
+  }
+  mCurrentCCLActors.clear();
+
+  // Compute new mask
+  vtkImageData * ccl  = mCurrentCCLImage->GetFirstVTKImageData();
+  vtkImageData * mask = mCurrentMaskImage->GetFirstVTKImageData();
+  int * pCCL = (int*)ccl->GetScalarPointer();
+  char * pPix = (char*)mask->GetScalarPointer();
+  for(uint i=0; i<ccl->GetNumberOfPoints(); i++) {
+    if (pCCL[i] == 0) pPix[i] = GetBackgroundValue(); // copy BG. In CCL BG is always 0
+  }
+
+  // Display new mask and remove ccl
+  mCurrentCCLImage->Reset();
+  mCurrentMaskActor->RemoveActors(); // kill it
+  mCurrentMaskActor = CreateMaskActor(mCurrentMaskImage, 1, 0, false); // renew
+  mCurrentMaskActor->Update();
+  mCurrentMaskActor->SetVisible(true); 
+  // mCurrentSlicerManager->Render();
+  mCurrentState = State_Default;
 }
 //------------------------------------------------------------------------------
 
@@ -253,13 +396,24 @@ bool vvToolSegmentation::eventFilter(QObject *object, QEvent * e)
 void vvToolSegmentation::Erode()
 {
   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  // Merge labels if needed
+  Merge();
+  // Get image and start erosion
   vtkImageContinuousErode3D* erode = vtkImageContinuousErode3D::New();
   erode->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
   vtkImageData* image = mCurrentMaskImage->GetVTKImages()[0];
+#if VTK_MAJOR_VERSION <= 5
   erode->SetInput(image);
+#else
+  erode->SetInputData(image);
+#endif
   erode->Update();
   image->DeepCopy(erode->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
   image->Update();
+#else
+  //image->Update();
+#endif
   UpdateAndRenderNewMask();
   erode->Delete();
   QApplication::restoreOverrideCursor();
@@ -271,13 +425,24 @@ void vvToolSegmentation::Erode()
 void vvToolSegmentation::Dilate()
 {
   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  // Merge labels if needed
+  Merge();
+  // Get image and start dilatation
   vtkImageContinuousDilate3D* dilate = vtkImageContinuousDilate3D::New();
   dilate->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
   vtkImageData* image = mCurrentMaskImage->GetVTKImages()[0];
+#if VTK_MAJOR_VERSION <= 5
   dilate->SetInput(image);
+#else
+  dilate->SetInputData(image);
+#endif
   dilate->Update();
   image->DeepCopy(dilate->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
   image->Update();
+#else
+  //image->Update();
+#endif
   UpdateAndRenderNewMask();
   dilate->Delete();
   QApplication::restoreOverrideCursor();
@@ -297,28 +462,32 @@ void vvToolSegmentation::UpdateAndRenderNewMask()
   mCurrentMaskActor->SetContourVisible(cvisible);
 
   mCurrentSlicerManager->Render();
+  UpdateMaskSize(mCurrentMaskImage, mCurrentMaskSizeInPixels, mCurrentMaskSizeInCC);
+  UpdateMaskSizeLabels();
 }
 //------------------------------------------------------------------------------
 
 //------------------------------------------------------------------------------
 void vvToolSegmentation::Labelize()
 {
+  if (mCurrentState == State_CCL) return; // Do nothing in this case
   DD("Labelize");
   // Waiting cursos
   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  mCurrentMaskActor->SetVisible(false);
   
   // Build CCL filter
   vtkImageData* image = mCurrentMaskImage->GetVTKImages()[0];
   typedef args_info_clitkConnectedComponentLabeling ArgsInfoType;
   ArgsInfoType a;
   cmdline_parser_clitkConnectedComponentLabeling_init(&a);
-  a.inputBG_arg = 0;
+  a.inputBG_arg = GetBackgroundValue();
   a.full_flag = false;  // FIXME set by gui
   a.minSize_arg = 100;  // FIXME set by gui 
   typedef clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType> FilterType;
   FilterType::Pointer filter = FilterType::New();
   filter->SetArgsInfo(a);
-  filter->SetInputVVImage(mCurrentMaskImage);
+  filter->SetInputVVImage(mCurrentMaskImage); // FIXME Check type is ok ? convert float ?
   filter->SetIOVerbose(true);  
   filter->Update();
   DD(filter->GetOriginalNumberOfObjects());
@@ -338,18 +507,17 @@ void vvToolSegmentation::Labelize()
   
   // Create actors 
   int n = filter->GetSizeOfObjectsInPixels().size();
-  for(int i=1; i<std::min(n,10); i++) { // Start at 1 because 0 is BG. FIXME max 10
-    DD(i);
+  mCurrentCCLActors.clear();
+  for(int i=1; i<=std::min(n,10); i++) { // Start at 1 because 0 is BG. FIXME max by gui
     QSharedPointer<vvROIActor> actor = CreateMaskActor(mCurrentCCLImage, i, i+1, false); 
     mCurrentCCLActors.push_back( actor );
     actor->Update();    
   }
-  mCurrentMaskActor->SetVisible(false);
-  mCurrentMaskActor->Update();
+  //  mCurrentMaskActor->Update();
   mCurrentSlicerManager->Render();
   
   // UpdateAndRender();
-  mCurrentMode = Mode_CCL;
+  mCurrentState = State_CCL;
   QApplication::restoreOverrideCursor();
 }
 //------------------------------------------------------------------------------
@@ -371,7 +539,6 @@ QSharedPointer<vvROIActor> vvToolSegmentation::CreateMaskActor(vvImage::Pointer
     actor->SetBGMode(true);
   }
   else {
-    DD("FG mode");
     roi->SetForegroundValueLabelImage(i); // FG mode
     actor->SetBGMode(false); // FG mode
   }
@@ -388,33 +555,72 @@ QSharedPointer<vvROIActor> vvToolSegmentation::CreateMaskActor(vvImage::Pointer
 //------------------------------------------------------------------------------
 void vvToolSegmentation::MousePositionChanged(int slicer)
 {
-  if (mCurrentMode == Mode_Default) return; // Do nothing in this case
-
+  // DD("MousePositionChanged ");
+  // DD(slicer);
   double x = mCurrentSlicerManager->GetSlicer(slicer)->GetCurrentPosition()[0];
   double y = mCurrentSlicerManager->GetSlicer(slicer)->GetCurrentPosition()[1];
   double z = mCurrentSlicerManager->GetSlicer(slicer)->GetCurrentPosition()[2];
-  vtkImageData * image = mCurrentCCLImage->GetFirstVTKImageData();
+  mCurrentMousePositionInMM[0] = x;
+  mCurrentMousePositionInMM[1] = y;
+  mCurrentMousePositionInMM[2] = z;
+  // DDV(mCurrentMousePositionInMM, 3);
+
+  //  vtkImageData * image = mCurrentCCLImage->GetFirstVTKImageData();
+  vtkImageData * image = mCurrentMaskImage->GetFirstVTKImageData();
   double Xover = (x - image->GetOrigin()[0]) / image->GetSpacing()[0];
   double Yover = (y - image->GetOrigin()[1]) / image->GetSpacing()[1];
   double Zover = (z - image->GetOrigin()[2]) / image->GetSpacing()[2];
   int ix, iy, iz;
   
+  // mCurrentMousePositionInPixel[0] = Xover;
+  // mCurrentMousePositionInPixel[1] = Yover;
+  // mCurrentMousePositionInPixel[2] = Zover;
+  // DDV(mCurrentMousePositionInPixel, 3);
+#if VTK_MAJOR_VERSION <= 5
   if (Xover >= image->GetWholeExtent()[0] &&
       Xover <= image->GetWholeExtent()[1] &&
       Yover >= image->GetWholeExtent()[2] &&
       Yover <= image->GetWholeExtent()[3] &&
       Zover >= image->GetWholeExtent()[4] &&
       Zover <= image->GetWholeExtent()[5]) {
-    double valueOver = 
-      mCurrentSlicerManager->GetSlicer(0)->GetScalarComponentAsDouble(image, Xover, Yover, Zover, ix, iy, iz, 0);
-    // DD(Xover); DD(Yover); DD(Zover);
-    // DD(ix); DD(iy); DD(iz);
-    // DD(valueOver);
+    if (mCurrentState == State_Default) { // inside the mask
+      mCurrentLabelUnderMousePointer = 1;
+      return; 
+    }
+    else { // inside the label image
+      vtkImageData * image = mCurrentCCLImage->GetFirstVTKImageData();
+      mCurrentLabelUnderMousePointer = 
+        mCurrentSlicerManager->GetSlicer(0)->GetScalarComponentAsDouble(image, Xover, Yover, Zover, ix, iy, iz, 0);
+      return;
+    }
   }
   else {
     // DD("out of mask");
+    mCurrentLabelUnderMousePointer = 0; // BG is always 0 in CCL
   }
-
+#else
+  if (Xover >= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] &&
+      Xover <= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] &&
+      Yover >= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] &&
+      Yover <= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] &&
+      Zover >= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] &&
+      Zover <= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]) {
+    if (mCurrentState == State_Default) { // inside the mask
+      mCurrentLabelUnderMousePointer = 1;
+      return; 
+    }
+    else { // inside the label image
+      vtkImageData * image = mCurrentCCLImage->GetFirstVTKImageData();
+      mCurrentLabelUnderMousePointer = 
+        mCurrentSlicerManager->GetSlicer(0)->GetScalarComponentAsDouble(image, Xover, Yover, Zover, ix, iy, iz, 0);
+      return;
+    }
+  }
+  else {
+    // DD("out of mask");
+    mCurrentLabelUnderMousePointer = 0; // BG is always 0 in CCL
+  }
+#endif
 }
 //------------------------------------------------------------------------------
 
@@ -422,5 +628,23 @@ void vvToolSegmentation::MousePositionChanged(int slicer)
 //------------------------------------------------------------------------------
 void vvToolSegmentation::RemoveLabel() {
   DD("RemoveLabel");
+  if (mCurrentLabelUnderMousePointer == 0) return;
+  // First actor=0 and is label 1. Label 0 is not an actor, it is BG
+  int actorNumber = mCurrentLabelUnderMousePointer-1; 
+  // Set actor invisible
+  mCurrentCCLActors[actorNumber]->SetVisible(false);
+  mCurrentSlicerManager->Render();
+  // Set image label
+  vtkImageData * image = mCurrentCCLImage->GetFirstVTKImageData();
+  int * pPix = (int*)image->GetScalarPointer();
+  int n = 0;
+  for(uint i=0; i<image->GetNumberOfPoints(); i++) {
+    if (pPix[i] == mCurrentLabelUnderMousePointer) pPix[i] = 0;
+    if (pPix[i] != 0) n++; // count the number of pixels in the foreground
+  }
+  // Update mask size
+  mCurrentMaskSizeInPixels = n;
+  mCurrentMaskSizeInCC = mCurrentMaskImage->GetSpacing()[0] * mCurrentMaskImage->GetSpacing()[1] * mCurrentMaskImage->GetSpacing()[2] * n / (10*10*10);
+  UpdateMaskSizeLabels();
 }
 //------------------------------------------------------------------------------