X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvToolSegmentation.cxx;h=63ff9b150f6cac958826bb87e83b9473310b9c0a;hb=d55f025b18f68066a52b8f33c2dc6481e82c2580;hp=9bd9365e105eff6babee4b76147a2727be54e4ff;hpb=e34e0e0eb662c6c7fa3681f53aac959fef4b4f73;p=clitk.git

diff --git a/vv/vvToolSegmentation.cxx b/vv/vvToolSegmentation.cxx
index 9bd9365..63ff9b1 100644
--- a/vv/vvToolSegmentation.cxx
+++ b/vv/vvToolSegmentation.cxx
@@ -26,12 +26,17 @@
 // 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"
@@ -69,6 +74,9 @@ vvToolSegmentation::vvToolSegmentation(vvMainWindowBase * parent, Qt::WindowFlag
   AddInputSelector("Select one image");
   
   // Init
+  mCurrentLabelUnderMousePointer = 0.0;
+  mCurrentMousePositionInMM.resize(3);
+  //  mCurrentMousePositionInPixel.resize(3);
   mRefMaskImage = NULL;
   mCurrentState = State_Default;
   mKernelValue = 3; // FIXME must be odd. If even -> not symmetrical
@@ -96,7 +104,6 @@ bool vvToolSegmentation::close()
   DD("remo mask");
   if (mCurrentMaskActor) mCurrentMaskActor->RemoveActors();
   for(int i=0; i<mCurrentCCLActors.size(); i++) {
-    DD(i);
     if (mCurrentCCLActors[i]) mCurrentCCLActors[i]->RemoveActors();
   }
   DD("wclose");
@@ -200,6 +207,7 @@ void vvToolSegmentation::OpenBinaryImage()
   // 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);
@@ -208,6 +216,48 @@ void vvToolSegmentation::OpenBinaryImage()
   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);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+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;
 }
 //------------------------------------------------------------------------------
 
@@ -215,6 +265,9 @@ void vvToolSegmentation::OpenBinaryImage()
 //------------------------------------------------------------------------------
 void vvToolSegmentation::KeyPressed(std::string KeyPress)
 { 
+  if (KeyPress == "G") {
+    RegionGrowing();
+  }
   if (KeyPress == "e") {
     Erode();
   }
@@ -226,6 +279,7 @@ void vvToolSegmentation::KeyPressed(std::string KeyPress)
   }
   if (KeyPress == "m") {
     Merge(); 
+    UpdateAndRenderNewMask();
   }
   if (KeyPress == "s") { // Supress "Remove" one label
     if (mCurrentState == State_CCL) RemoveLabel();
@@ -245,6 +299,63 @@ void vvToolSegmentation::KeyPressed(std::string KeyPress)
 //------------------------------------------------------------------------------
 
 
+//------------------------------------------------------------------------------
+void vvToolSegmentation::RegionGrowing()
+{
+  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");
+  
+  // mouse pointer
+  QApplication::restoreOverrideCursor();
+}  
+//------------------------------------------------------------------------------
+
+
 //------------------------------------------------------------------------------
 void vvToolSegmentation::Merge()
 {
@@ -266,7 +377,7 @@ void vvToolSegmentation::Merge()
   int * pCCL = (int*)ccl->GetScalarPointer();
   char * pPix = (char*)mask->GetScalarPointer();
   for(uint i=0; i<ccl->GetNumberOfPoints(); i++) {
-    if (pCCL[i] == 0) pPix[i] = 0; // copy BG
+    if (pCCL[i] == 0) pPix[i] = GetBackgroundValue(); // copy BG. In CCL BG is always 0
   }
 
   // Display new mask and remove ccl
@@ -275,7 +386,7 @@ void vvToolSegmentation::Merge()
   mCurrentMaskActor = CreateMaskActor(mCurrentMaskImage, 1, 0, false); // renew
   mCurrentMaskActor->Update();
   mCurrentMaskActor->SetVisible(true); 
-  mCurrentSlicerManager->Render();
+  // mCurrentSlicerManager->Render();
   mCurrentState = State_Default;
 }
 //------------------------------------------------------------------------------
@@ -291,10 +402,18 @@ void vvToolSegmentation::Erode()
   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();
@@ -312,10 +431,18 @@ void vvToolSegmentation::Dilate()
   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();
@@ -335,6 +462,8 @@ void vvToolSegmentation::UpdateAndRenderNewMask()
   mCurrentMaskActor->SetContourVisible(cvisible);
 
   mCurrentSlicerManager->Render();
+  UpdateMaskSize(mCurrentMaskImage, mCurrentMaskSizeInPixels, mCurrentMaskSizeInCC);
+  UpdateMaskSizeLabels();
 }
 //------------------------------------------------------------------------------
 
@@ -352,7 +481,7 @@ void vvToolSegmentation::Labelize()
   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;
@@ -426,34 +555,72 @@ QSharedPointer<vvROIActor> vvToolSegmentation::CreateMaskActor(vvImage::Pointer
 //------------------------------------------------------------------------------
 void vvToolSegmentation::MousePositionChanged(int slicer)
 {
-  if (mCurrentState == State_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]) {
-    mCurrentLabelUnderMousePointer = 
-      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;
+    mCurrentLabelUnderMousePointer = 0; // BG is always 0 in CCL
   }
-  // DD(mCurrentLabelUnderMousePointer);
+#endif
 }
 //------------------------------------------------------------------------------
 
@@ -470,8 +637,14 @@ void vvToolSegmentation::RemoveLabel() {
   // 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();
 }
 //------------------------------------------------------------------------------