- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
+ ===========================================================================**/
// vv
#include "vvToolSegmentation.h"
#include "vvToolInputSelectorWidget.h"
#include "vvImageWriter.h"
+// 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
// the main window menu.
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
+ mDefaultLUTColor = vtkSmartPointer<vtkLookupTable>::New();
+ mDefaultLUTColor->SetNumberOfTableValues(256);
+#include "vvDefaultLut.h"
+
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vvToolSegmentation::~vvToolSegmentation()
{
+ DD("destructor");
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
bool vvToolSegmentation::close()
{
- mRefMaskActor->RemoveActors();
+ 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();
mCurrentSlicerManager->Render();
return true;
// Open mask
OpenBinaryImage();
+
+ // If cancel: stop
+ if (mRefMaskActor == NULL) {
+ close();
+ return;
+ }
+
+ // Update gui
+ mToolInputSelectionWidget->hide();
+
+ // Connect mouse position
+ connect(mCurrentSlicerManager, SIGNAL(MousePositionUpdatedSignal(int)),
+ this, SLOT(MousePositionChanged(int)));
+ connect(mCurrentSlicerManager, SIGNAL(KeyPressedSignal(std::string)),
+ this, SLOT(KeyPressed(std::string)));
}
//------------------------------------------------------------------------------
return;
}
- mMaskImage = reader->GetOutput();
- int dim = mMaskImage->GetNumberOfDimensions();
+ mRefMaskImage = reader->GetOutput();
+ int dim = mRefMaskImage->GetNumberOfDimensions();
if (dim != 3 ) {
QMessageBox::information(this,tr("Sorry only 3D yet"), tr("Sorry only 3D yet"));
close();
return;
}
- // Add a new roi actor
- mRefMaskActor = QSharedPointer<vvROIActor>(new vvROIActor);
- std::vector<double> color;
- color.push_back(1);
- color.push_back(0);
- color.push_back(0);
- clitk::DicomRT_ROI::Pointer roi = clitk::DicomRT_ROI::New();
- roi->SetFromBinaryImage(mMaskImage, 1, std::string("toto"), color, filename.toStdString());
- mRefMaskActor->SetBGMode(true);
- mRefMaskActor->SetROI(roi);
- mRefMaskActor->SetSlicerManager(mCurrentSlicerManager);
- mRefMaskActor->Initialize(10, true);
+ reader = vvImageReader::New();
+ reader->SetInputFilenames(filenames);
+ reader->Update(vvImageReader::IMAGE);
+ mCurrentMaskImage = reader->GetOutput();
+
+ // 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);
- // Prepare widget to get keyboard event
- grabKeyboard();
- //connect(this, SIGNAL(keyPressEvent(QKeyEvent*)), this, SLOT(keyPressed(QKeyEvent*)));
+ // Update GUI
+ UpdateMaskSizeLabels();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolSegmentation::keyPressEvent(QKeyEvent * event)
+void vvToolSegmentation::UpdateMaskSizeLabels()
{
- vvToolWidgetBase::keyPressEvent(event);
- //DD("key");
-
- if (event->text() == "e") {
+ 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;
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::KeyPressed(std::string KeyPress)
+{
+ if (KeyPress == "G") {
+ RegionGrowing();
+ }
+ if (KeyPress == "e") {
Erode();
}
- if (event->text() == "d") {
+ if (KeyPress == "d") {
Dilate(); // FIXME -> extend image BB !!
}
- if (event->text() == "s") {
+ 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(mMaskImage);
+ writer->SetInput(mCurrentMaskImage);
writer->Update();
}
}
//------------------------------------------------------------------------------
+//------------------------------------------------------------------------------
+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()
+{
+ 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();
+ }
+ }
+ 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;
+}
+//------------------------------------------------------------------------------
+
+
//------------------------------------------------------------------------------
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 = mMaskImage->GetVTKImages()[0];
+ 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();
- UpdateAndRender();
+#else
+ //image->Update();
+#endif
+ UpdateAndRenderNewMask();
erode->Delete();
QApplication::restoreOverrideCursor();
}
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 = mMaskImage->GetVTKImages()[0];
+ 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();
- UpdateAndRender();
+#else
+ //image->Update();
+#endif
+ UpdateAndRenderNewMask();
dilate->Delete();
QApplication::restoreOverrideCursor();
}
//------------------------------------------------------------------------------
-void vvToolSegmentation::UpdateAndRender()
+void vvToolSegmentation::UpdateAndRenderNewMask()
{
- bool visible = mRefMaskActor->IsVisible();
- bool cvisible = mRefMaskActor->IsContourVisible();
- mRefMaskActor->SetVisible(false);
- mRefMaskActor->SetContourVisible(false);
+ bool visible = mCurrentMaskActor->IsVisible();
+ bool cvisible = mCurrentMaskActor->IsContourVisible();
+ mCurrentMaskActor->SetVisible(false);
+ mCurrentMaskActor->SetContourVisible(false);
+ mCurrentMaskActor->UpdateImage();
+ mCurrentMaskActor->SetVisible(visible);
+ 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 = 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); // FIXME Check type is ok ? convert float ?
+ filter->SetIOVerbose(true);
+ filter->Update();
+ DD(filter->GetOriginalNumberOfObjects());
+ DD(filter->GetSizeOfObjectsInPixels().size());
+ mCurrentCCLImage = filter->GetOutputVVImage();
+ DDV(filter->GetSizeOfObjectsInPixels(), filter->GetSizeOfObjectsInPixels().size());
+ DD("filter done");
+
+ /*
+ // DEBUG
+ vvImageWriter::Pointer writer = vvImageWriter::New();
+ writer->SetInput(mCurrentCCLImage);
+ writer->SetOutputFileName("bidon-ccl.mha");
+ writer->Update();
+ DD(mCurrentCCLImage->IsScalarTypeInteger());
+ */
+
+ // Create actors
+ int n = filter->GetSizeOfObjectsInPixels().size();
+ 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->Update();
+ mCurrentSlicerManager->Render();
+
+ // UpdateAndRender();
+ mCurrentState = State_CCL;
+ QApplication::restoreOverrideCursor();
+}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+QSharedPointer<vvROIActor> vvToolSegmentation::CreateMaskActor(vvImage::Pointer image, int i, int colorID, bool BGMode)
+{
+ static int depth = 1;
+ depth += 1;
+ QSharedPointer<vvROIActor> actor = QSharedPointer<vvROIActor>(new vvROIActor);
+ double * color = mDefaultLUTColor->GetTableValue(colorID % mDefaultLUTColor->GetNumberOfTableValues ());
+ std::vector<double> c;
+ c.push_back(color[0]);
+ c.push_back(color[1]);
+ c.push_back(color[2]);
+ clitk::DicomRT_ROI::Pointer roi = clitk::DicomRT_ROI::New();
+ roi->SetFromBinaryImage(image, i, std::string("toto"), c, std::string("titi"));
+ if (BGMode) {
+ actor->SetBGMode(true);
+ }
+ else {
+ roi->SetForegroundValueLabelImage(i); // FG mode
+ actor->SetBGMode(false); // FG mode
+ }
+ actor->SetROI(roi);
+ actor->SetSlicerManager(mCurrentSlicerManager);
+ actor->Initialize(depth+i, true); // +1 to start at 1 not 0
+ actor->SetContourVisible(false);
+ actor->SetVisible(true);
+ return actor;
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::MousePositionChanged(int slicer)
+{
+ // 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];
+ 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]) {
+ 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
+}
+//------------------------------------------------------------------------------
- //mRefMaskActor->RemoveActors();
- mRefMaskActor->UpdateImage();
- mRefMaskActor->SetVisible(visible);
- mRefMaskActor->SetContourVisible(cvisible);
+
+//------------------------------------------------------------------------------
+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();
}
//------------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff