ImageType::Pointer SBFilterUtils::RegionGrowing(ImageType::Pointer image, ImageType::IndexType seed, bool fullConnectivity, int lowerThreshold, int upperThreshold, int replaceValue) {
ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();
connectedThreshold->SetInput(image);
connectedThreshold->SetSeed(seed);
connectedThreshold->SetLower(lowerThreshold);
connectedThreshold->SetUpper(upperThreshold);
connectedThreshold->SetReplaceValue(replaceValue);
if(fullConnectivity)
connectedThreshold->SetConnectivity(ConnectedFilterType::FullConnectivity);
connectedThreshold->Update();
return connectedThreshold->GetOutput();
}
InputImageType::Pointer getLargeComponents(InputImageType::Pointer im, int n)
{
printf("Removing small connected components ...");
typedef itk::Image<short int,3> LabelImageType;
typedef itk::ConnectedComponentImageFilter<InputImageType,LabelImageType> ConnectedFilterType;
typedef itk::RelabelComponentImageFilter<LabelImageType,LabelImageType> RelabelFilterType;
ConnectedFilterType::Pointer cfilter = ConnectedFilterType::New();
cfilter->SetInput(im);
cfilter->Update();
RelabelFilterType::Pointer rfilter = RelabelFilterType::New();
rfilter->SetInput(cfilter->GetOutput());
rfilter->InPlaceOn();
rfilter->Update();
std::vector<long unsigned int> sizes = rfilter->GetSizeOfObjectsInPixels();
int threshsize = -1;
for(unsigned int counter=0; counter<sizes.size(); counter++)
{
if(sizes[counter] < (unsigned int)n)
{
threshsize = counter;
break;
}
}
typedef itk::BinaryThresholdImageFilter<LabelImageType,InputImageType> BinFilterType;
BinFilterType::Pointer bfilter = BinFilterType::New();
bfilter->SetInput(rfilter->GetOutput());
bfilter->SetInsideValue(255);
bfilter->SetOutsideValue(0);
bfilter->SetLowerThreshold(1);
if(threshsize>1)
bfilter->SetUpperThreshold(threshsize-1);
else
bfilter->SetUpperThreshold(1);
bfilter->Update();
printf(" Done.\n");
return bfilter->GetOutput();
}
vtkImageData* ROISegmentation::startRegionGrow(){
typedef itk::CastImageFilter< ImageType, ImageType >
CastingFilterType;
CastingFilterType::Pointer caster = CastingFilterType::New();
typedef itk::CurvatureFlowImageFilter< ImageType, ImageType >
CurvatureFlowImageFilterType;
CurvatureFlowImageFilterType::Pointer smoothing =
CurvatureFlowImageFilterType::New();
typedef itk::ConfidenceConnectedImageFilter<ImageType, ImageType>
ConnectedFilterType;
ConnectedFilterType::Pointer confidenceConnected = ConnectedFilterType::New();
smoothing->SetInput(pDCM->getITKRawImage());
confidenceConnected->SetInput(smoothing->GetOutput());
caster->SetInput(confidenceConnected->GetOutput());
//Parameter Settings
smoothing->SetNumberOfIterations(2);
smoothing->SetTimeStep(0.05);
confidenceConnected->SetMultiplier(2.5);
confidenceConnected->SetNumberOfIterations(2);
confidenceConnected->SetInitialNeighborhoodRadius(1);
confidenceConnected->SetReplaceValue(255);
if (!_index.empty()){
ImageType::PointType seedPoint;
ImageType::IndexType seedIndex;
std::vector<CursorDim>::iterator iter = _index.begin();
for (iter; iter != _index.end(); ++iter){
seedPoint[0] = iter->_x;
seedPoint[1] = iter->_y;
seedPoint[2] = iter->_z;
if (pDCM->getITKRawImage()->TransformPhysicalPointToIndex(seedPoint, seedIndex)){
qDebug()<<"SeedIndex: " << seedIndex[0] << " " << seedIndex[1] << " " << seedIndex[2] << endl;
confidenceConnected->AddSeed(seedIndex);
}
}
caster->Update();
typedef itk::ImageToVTKImageFilter<ImageType> ConnectorType;
ConnectorType::Pointer connector = ConnectorType::New();
connector->SetInput(caster->GetOutput());
connector->Update();
vtkImageData * rawImage = vtkImageData::New();
rawImage->DeepCopy(connector->GetOutput());
return rawImage;
}
else{
return NULL;
}
}
int exampleProcessImageFilter::update()
{
typedef unsigned short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
qDebug() << d->inputA->identifier();
if (d->option == optionA)
{
if (d->inputA->identifier()=="itkDataImageUShort3" && d->inputB->identifier()=="itkDataImageUShort3")
{
typedef itk::MaskImageFilter< ImageType,ImageType,ImageType > MaskFilterType;
MaskFilterType::Pointer maskFilter = MaskFilterType::New();
//convert from dtkImages to ItkImages and set as intputs for the itk::MaskImageFilter
maskFilter->SetInput1(dynamic_cast<ImageType*>((itk::Object*)(d->inputA->output())));
maskFilter->SetInput2(dynamic_cast<ImageType*>((itk::Object*)(d->inputB->output())));
//Create an image where the output of the filter is going to be displayed
d->output =dynamic_cast<medAbstractDataImage *>(dtkAbstractDataFactory::instance()->create ("itkDataImageUShort3"));
maskFilter->Update();
//Set the data for the output
d->output->setData(maskFilter->GetOutput());
}
else if(d->inputA->identifier()=="itkDataImageDouble4" && d->inputB->identifier()=="itkDataImageDouble4")
{
typedef double PixelType4;
const unsigned int Dimension4 = 4;
typedef itk::Image< PixelType4, Dimension4 > ImageType4;
typedef itk::MaskImageFilter< ImageType4,ImageType4,ImageType4 > MaskFilterType4;
MaskFilterType4::Pointer maskFilter4 = MaskFilterType4::New();
//convert from dtkImages to ItkImages and set as intputs for the itk::MaskImageFilter
maskFilter4->SetInput1(dynamic_cast<ImageType4*>((itk::Object*)(d->inputA->output())));
maskFilter4->SetInput2(dynamic_cast<ImageType4*>((itk::Object*)(d->inputB->output())));
maskFilter4->Update();
//Create an image where the output of the filter is going to be displayed
d->output =dynamic_cast<medAbstractDataImage *> (dtkAbstractDataFactory::instance()->create ("itkDataImageDouble4"));
//Set the data for the output
d->output->setData(maskFilter4->GetOutput());
typedef itk::ImageFileWriter< ImageType4 > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("/user/jgarciag/home/AnalyzeStuff/headerModify/ResulHalfMask4D.mha");
writer->SetInput(/*dynamic_cast<ImageType4*>((itk::Object*)(d->output->output()))*/maskFilter4->GetOutput());
writer->Update();
}
else
qDebug("Not the right itkDataImageUShort3 type of images");
}
else if (d->option == optionB)
{
if (d->inputA->identifier()=="itkDataImageUShort3" && d->inputB->identifier()=="itkDataImageUShort3")
{
typedef itk::AddImageFilter< ImageType,ImageType,ImageType > AddFilterType;
AddFilterType::Pointer AddFilter = AddFilterType::New();
AddFilter->SetInput1(dynamic_cast<ImageType*>((itk::Object*)(d->inputA->output())));
AddFilter->SetInput2(dynamic_cast<ImageType*>((itk::Object*)(d->inputB->output())));
d->output =dynamic_cast<medAbstractDataImage *> (dtkAbstractDataFactory::instance()->create ("itkDataImageUShort3"));
AddFilter->Update();
d->output->setData(AddFilter->GetOutput());
}
else
qDebug("Not the right itkDataImageUShort3 type of images");
}
else if (d->option == optionC)
{
if (d->inputA->identifier()=="itkDataImageUShort3" && d->inputB->identifier()=="itkDataImageUShort3")
{
typedef itk::ConnectedThresholdImageFilter< ImageType, ImageType > ConnectedFilterType;
ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();
connectedThreshold->SetInput( dynamic_cast<ImageType*>((itk::Object*)(d->inputA->output())) );
connectedThreshold->SetLower((d->lowerThreshold));
connectedThreshold->SetUpper((d->lowerThreshold)+150);
ImageType::IndexType index;
index[0] = d->x;
index[1] = d->y;
index[2] = d->z;
connectedThreshold->SetSeed( index );
connectedThreshold->Update();
d->output =dynamic_cast<medAbstractDataImage *> (dtkAbstractDataFactory::instance()->create ("itkDataImageUShort3"));
d->output->setData(connectedThreshold->GetOutput());
}
else
qDebug("Not the right itkDataImageUShort3 type of image");
}
// emit progressed (100);
qDebug("Adios");
return 0;
}
