void operator()( const Parameter ¶m )
{
OSLM_DEBUG( "itk::ImageSeriesWriter with PIXELTYPE "<< fwTools::DynamicType::string<PIXELTYPE>() );
::fwData::Image::sptr image = param.m_dataImage;
// VAG attention : ImageFileReader ne notifie AUCUNE progressEvent mais son ImageIO oui!!!! mais ImageFileReader ne permet pas de l'atteindre
// car soit mis a la mano ou alors construit lors de l'Update donc trop tard
// Il faut dont creer une ImageIO a la mano (*1*): affecter l'observation sur IO (*2*) et mettre le IO dans le reader (voir *3*)
// Reader IO (*1*)
typename itk::ImageIOBase::Pointer imageIOWrite = itk::ImageIOFactory::CreateImageIO( "image.jpg", itk::ImageIOFactory::WriteMode);
assert( imageIOWrite.IsNotNull() );
// create writer
typedef itk::Image< PIXELTYPE, 3> itkImageType;
typedef itk::Image< unsigned char, 2 > Image2DType;
typedef typename itk::ImageSeriesWriter< itkImageType, Image2DType > WriterType;
typename WriterType::Pointer writer = WriterType::New();
// set observation (*2*)
itk::LightProcessObject::Pointer castHelper= (itk::LightProcessObject *)(imageIOWrite.GetPointer());
assert( castHelper.IsNotNull() );
Progressor progress(castHelper, param.m_fwWriter, param.m_filename);
// create itk Image
typename itkImageType::Pointer itkImage = ::fwItkIO::itkImageFactory<itkImageType>( image );
typedef ::itk::IntensityWindowingImageFilter< itkImageType, itkImageType > RescaleFilterType;
typename RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
double min, max;
::fwData::Composite::sptr poolTF;
poolTF = image->getField< ::fwData::Composite>( ::fwComEd::Dictionary::m_transferFunctionCompositeId );
if(poolTF)
{
::fwData::Composite::iterator iter = poolTF->find(::fwData::TransferFunction::s_DEFAULT_TF_NAME);
if(iter != poolTF->end())
{
::fwData::TransferFunction::sptr tf;
tf = ::fwData::TransferFunction::dynamicCast(iter->second);
min = tf->getWLMinMax().first;
max = tf->getWLMinMax().second;
}
}
else
{
::fwComEd::fieldHelper::MedicalImageHelpers::getMinMax(image, min, max);
}
rescaleFilter->SetWindowMinimum( min );
rescaleFilter->SetWindowMaximum( max );
rescaleFilter->SetOutputMinimum( 0 );
rescaleFilter->SetOutputMaximum( 255 );
rescaleFilter->InPlaceOff();
rescaleFilter->SetInput( itkImage );
rescaleFilter->Update();
writer->SetInput( rescaleFilter->GetOutput() );
typedef itk::NumericSeriesFileNames NameGeneratorType;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
std::string format = param.m_filename;
format += "/%04d.jpg";
nameGenerator->SetSeriesFormat( format.c_str() );
nameGenerator->SetStartIndex( 1 );
nameGenerator->SetEndIndex( image->getSize()[2] );
nameGenerator->SetIncrementIndex( 1 );
writer->SetFileNames( nameGenerator->GetFileNames() );
writer->SetImageIO( imageIOWrite );
// save image;
writer->Update();
}
/**
* draws the tree from the TreeDrawer into a volumetric 3D
* image as a series of 2D png slices
*/
void drawImage(TreeDrawer * td, const char* rootName){
typedef unsigned char PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::Pointer image = ImageType::New();
ImageType::SizeType size;
size[0] = td->dim[0]; // size along X
size[1] = td->dim[1]; // size along Y
size[2] = td->dim[2]; // size along Z
ImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
ImageType::RegionType region;
region.SetSize( size );
region.SetIndex( start );
image->SetRegions( region );
image->Allocate();
ImageType::IndexType pixelIndex;
pixelIndex[0] = 0; // x position
pixelIndex[1] = 0; // y position
pixelIndex[2] = 0; // z position
for(int i = 0; i < td->dim[0]; i++){
for(int j = 0; j < td->dim[1]; j++){
for(int k = 0 ; k < td->dim[2]; k++){
pixelIndex[0] = i;
pixelIndex[1] = j;
pixelIndex[2] = k;
image->SetPixel(pixelIndex, td->imageAt(i, j, k));
}
}
}
typedef itk::Image< unsigned char, 2 > Image2DType;
typedef itk::ImageSeriesWriter< ImageType, Image2DType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput( image);
typedef itk::NumericSeriesFileNames NameGeneratorType;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
std::string format = rootName;
format += "%03d";
format += ".jpg";
nameGenerator->SetSeriesFormat( format.c_str() );
const unsigned int firstSlice = start[2];
const unsigned int lastSlice = start[2] + size[2] - 1;
nameGenerator->SetStartIndex( firstSlice );
nameGenerator->SetEndIndex( lastSlice );
nameGenerator->SetIncrementIndex( 1 );
writer->SetFileNames( nameGenerator->GetFileNames() );
try{
writer->Update();
}catch( itk::ExceptionObject & excp ){
throw "Exception thrown while reading the image";
}
return;
}
int main(int argc, char *argv[])
{
QCoreApplication a(argc, argv);
// new for itk 4.8
itk::JPEGImageIOFactory::RegisterOneFactory();
// init
m_pInvertIntensityFilter = InvertIntensityFilterType::New();
m_pConnector = FilterType::New();
//////////////////////////
// vtk objects
// QT/VTK interact
m_pRenderer = vtkRenderer::New();
// ui.vtkWidget->GetRenderWindow()->AddRenderer(m_pRenderer);
m_pRenderWindow = vtkRenderWindow::New();
m_pRenderWindow->AddRenderer(m_pRenderer);
m_pRenderWindowInteractor = vtkRenderWindowInteractor::New();
m_pRenderWindowInteractor->SetRenderWindow(m_pRenderWindow);
m_pTissueExtractor = vtkMarchingCubes::New(); //vtkContourFilter::New();
m_pTissueNormals = vtkPolyDataNormals::New();
m_pTissueMapper = vtkPolyDataMapper::New();
m_pTissue = vtkActor::New();
m_pTextActor = vtkActor2D::New();
m_pTextMapper = vtkTextMapper::New();
// read a volume
// QString strVolumeIndex;
//strVolumeIndex.sprintf("../", nZoomOut,
// iWidth, iLength, iHeight);
QString strSeriesFormat;
strSeriesFormat = QString("K:/Projects/TestVol3/%04d.jpg");
//qDebug() << strSeriesFormat;
NameGeneratorType::Pointer pNameGenerator = NameGeneratorType::New();
pNameGenerator->SetSeriesFormat(strSeriesFormat.toStdString());
unsigned int nStartIndex = 1;
pNameGenerator->SetStartIndex(nStartIndex); //0 );
pNameGenerator->SetEndIndex(256);
pNameGenerator->SetIncrementIndex( 2 );
///////////
// optional
//pReader->SetImageIO(itk::JPEGImageIO::New());
ReaderType::Pointer pReader = ReaderType::New();
pReader->SetFileNames(pNameGenerator->GetFileNames());
try
{
pReader->Update();
}
catch (itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
m_pImageData = pReader->GetOutput();
// m_pImageData->DisconnectPipeline();
// execute pipeline
m_pInvertIntensityFilter->SetInput(m_pImageData);
m_pConnector->SetInput(m_pInvertIntensityFilter->GetOutput()); //m_pReader->GetOutput());
#if VTK_MAJOR_VERSION <= 5
m_pTissueExtractor->SetInput(m_pConnector->GetOutput());
#else
m_pConnector->Update();
m_pTissueExtractor->SetInputData(m_pConnector->GetOutput());
#endif
//int nIsoSurface = ui.lineEditValue->text().toInt();
//if(nIsoSurface == 0)
int nIsoSurface = 155;
m_pTissueExtractor->SetValue(0, nIsoSurface);
#if VTK_MAJOR_VERSION <= 5
m_pTissueNormals->SetInput(m_pTissueExtractor->GetOutput());
#else
m_pTissueNormals->SetInputConnection(m_pTissueExtractor->GetOutputPort());
#endif
//m_pTissueNormals->SetFeatureAngle(60.0);
#if VTK_MAJOR_VERSION <= 5
m_pTissueMapper->SetInput(m_pTissueNormals->GetOutput());
#else
m_pTissueMapper->SetInputConnection(m_pTissueNormals->GetOutputPort());
#endif
m_pTissueMapper->ScalarVisibilityOff();
m_pTissue->SetMapper(m_pTissueMapper);
//if(!m_pVolumeMapper)
//{
// m_pVolumeMapper = vtkFixedPointVolumeRayCastMapper::New();
// m_pVolumeMapper->SetInput(m_pConnector->GetOutput());
// m_pVolume = vtkVolume::New();
// m_pVolume->SetMapper(m_pVolumeMapper);
// m_pVolume->Update();
// //m_pRenderer->AddActor(m_pVolume);
m_pRenderer->AddActor(m_pTissue);
m_pRenderer->SetBackground(0.0,0.0,0.4);
m_pRenderer->ResetCamera();
m_pRenderer->GetRenderWindow()->Render();
m_pRenderWindowInteractor->Start();
// save to vtk
vtkPolyDataWriter* pWriter = vtkPolyDataWriter::New();
#if VTK_MAJOR_VERSION <= 5
pWriter->SetInput(m_pTissueNormals->GetOutput());
#else
pWriter->SetInputConnection(m_pTissueNormals->GetOutputPort());
#endif
QString strVTKFileName;
strVTKFileName.sprintf("test2.vtk");
pWriter->SetFileName(strVTKFileName.toStdString().c_str());
pWriter->SetFileTypeToBinary();
pWriter->Write();
// save to stl
vtkSTLWriter* pSTLWriter = vtkSTLWriter::New();
#if VTK_MAJOR_VERSION <= 5
pSTLWriter->SetInput(m_pTissueNormals->GetOutput());
#else
pSTLWriter->SetInputConnection(m_pTissueNormals->GetOutputPort());
#endif
QString strSTLFileName;
strSTLFileName.sprintf("test2.stl");
pSTLWriter->SetFileName(strSTLFileName.toStdString().c_str());
pSTLWriter->SetFileTypeToBinary();
pSTLWriter->Write();
// finalize
m_pRenderer->Delete();
m_pTissueExtractor->Delete();
m_pTissueNormals->Delete();
m_pTissueMapper->Delete();
m_pTissue->Delete();
m_pTextActor->Delete();;
m_pTextMapper->Delete();
pReader->Delete();
pWriter->Delete();
pSTLWriter->Delete();
// TODO: there are missing pointers to be deleted. Add them.
return a.exec();
}
