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watershed_morph_nX.cxx
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watershed_morph_nX.cxx
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////program for iterative itkMorphologicalWatershedFromMarkersImageFilter
//01: based on template_02.cxx
#include <string>
#include <sstream>
#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkCommand.h>
#include <itkShiftScaleImageFilter.h>
#include <itkHMinimaImageFilter.h>
#include <itkRegionalMinimaImageFilter.h>
#include <itkConnectedComponentImageFilter.h>
#include <itkMorphologicalWatershedFromMarkersImageFilter.h>
#include <itkBinaryThresholdImageFilter.h>
#include <itkAddImageFilter.h>
#include <itkGradientMagnitudeImageFilter.h>
#include <itkChangeLabelImageFilter.h>
int dispatch_cT(itk::ImageIOBase::IOPixelType, itk::ImageIOBase::IOComponentType, size_t, int, char **);
template<typename InputComponentType>
int dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t, int, char **);
template<typename InputComponentType, typename InputPixelType>
int dispatch_D(size_t, int, char **);
template<typename InputComponentType, typename InputPixelType, size_t Dimension>
int DoIt(int, char *argv[]);
template<typename ReaderImageType, typename WriterImageType>
void FilterEventHandlerITK(itk::Object *caller, const itk::EventObject &event, void*){
const itk::ProcessObject* filter = static_cast<const itk::ProcessObject*>(caller);
if(itk::ProgressEvent().CheckEvent(&event))
fprintf(stderr, "\r%s progress: %5.1f%%", filter->GetNameOfClass(), 100.0 * filter->GetProgress());//stderr is flushed directly
else if(itk::StartEvent().CheckEvent(&event)){
if(strstr(filter->GetNameOfClass(), "ImageFileReader"))
std::cerr << "Reading: " << (dynamic_cast<itk::ImageFileReader<ReaderImageType> *>(caller))->GetFileName();//cast only works if reader was instanciated for ReaderImageType!
else if(strstr(filter->GetNameOfClass(), "ImageFileWriter"))
std::cerr << "Writing: " << (dynamic_cast<itk::ImageFileWriter<WriterImageType> *>(caller))->GetFileName() << std::endl;//cast only works if writer was instanciated for WriterImageType!
}
else if(itk::EndEvent().CheckEvent(&event))
std::cerr << std::endl;
}
template<typename InputComponentType, typename InputPixelType, size_t Dimension>
int DoIt(int argc, char *argv[]){
typedef uint32_t OutputPixelType;
typedef uint8_t MaskType;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::Image<double, Dimension> GreyImageType;
typedef itk::Image<OutputPixelType, Dimension> LabelImageType;
typedef itk::Image<MaskType, Dimension> MaskImageType;
itk::CStyleCommand::Pointer eventCallbackITK;
eventCallbackITK = itk::CStyleCommand::New();
eventCallbackITK->SetCallback(FilterEventHandlerITK<InputImageType,LabelImageType>);
typedef itk::ImageFileReader<InputImageType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->AddObserver(itk::AnyEvent(), eventCallbackITK);
try{
reader->Update();
}
catch(itk::ExceptionObject &ex){
std::cerr << ex << std::endl;
return EXIT_FAILURE;
}
typename GreyImageType::Pointer input;
bool ws0_conn= true;//true reduces amount of watersheds
bool ws_conn= false;
double MinRelFacetSize= atof(argv[5]);
uint8_t NumberOfExtraWS= atoi(argv[6]);
char* interMedOutPrefix= NULL;
if(argc == 8)
interMedOutPrefix= argv[7];
typename LabelImageType::Pointer markerImg;
typename LabelImageType::Pointer borderImg;
typename GreyImageType::Pointer gradientImg;
typename LabelImageType::Pointer labelImg;
typename LabelImageType::PixelType labelCnt;
typedef itk::ImageFileWriter<LabelImageType> LWriterType;
typename LWriterType::Pointer lwriter = LWriterType::New();
lwriter->SetUseCompression(atoi(argv[3]));
lwriter->AddObserver(itk::AnyEvent(), eventCallbackITK);
//lwriter->SetInput(labelImg);//doing that before each update to not get confused
typedef itk::ShiftScaleImageFilter<InputImageType, GreyImageType> SSType;
typename SSType::Pointer ss = SSType::New();
if(atoi(argv[4]))
ss->SetScale(-1); //invert by mul. with -1
else
ss->SetScale(1); //just convert to GreyImageType
//ss->SetScale(atof(argv[4]));//abs(scaling) > 1 does not help gm to be more pronounced!
ss->SetInput(reader->GetOutput());
ss->Update();
input= ss->GetOutput();
{//scoped for better consistency
typedef itk::HMinimaImageFilter<GreyImageType, GreyImageType> HMType; //seems for hmin in-type==out-type!!!
typename HMType::Pointer hm= HMType::New();
hm->SetHeight(MinRelFacetSize);
hm->SetFullyConnected(ws0_conn);
hm->SetInput(input);
hm->AddObserver(itk::AnyEvent(), eventCallbackITK);
hm->Update();
typedef itk::RegionalMinimaImageFilter<GreyImageType, MaskImageType> RegMinType;
typename RegMinType::Pointer rm = RegMinType::New();
rm->SetFullyConnected(ws0_conn);
rm->SetInput(hm->GetOutput());
rm->AddObserver(itk::AnyEvent(), eventCallbackITK);
rm->Update();
// connected component labelling
typedef itk::ConnectedComponentImageFilter<MaskImageType, LabelImageType> CCType;
typename CCType::Pointer labeller = CCType::New();
labeller->SetFullyConnected(ws0_conn);
labeller->SetInput(rm->GetOutput());
labeller->AddObserver(itk::AnyEvent(), eventCallbackITK);
labeller->Update();
labelImg= labeller->GetOutput();
labelImg->DisconnectPipeline();
labelCnt= labeller->GetObjectCount();
}
if(interMedOutPrefix){
lwriter->SetFileName(std::string(interMedOutPrefix) + "_limg.mha");
lwriter->SetInput(labelImg);
lwriter->Update();
}
typedef itk::MorphologicalWatershedFromMarkersImageFilter<GreyImageType, LabelImageType> MWatershedType;
typename MWatershedType::Pointer ws = MWatershedType::New();
ws->SetMarkWatershedLine(NumberOfExtraWS); //use borders if higher order WS are wanted
ws->SetFullyConnected(ws0_conn);
ws->SetInput(input);
ws->SetMarkerImage(labelImg);
ws->AddObserver(itk::AnyEvent(), eventCallbackITK);
ws->Update();
if(NumberOfExtraWS > 0){
if(interMedOutPrefix){
lwriter->SetFileName(std::string(interMedOutPrefix) + "_ws0.mha");
lwriter->SetInput(ws->GetOutput());
lwriter->Update();
}
{//scoped for better consistency
// extract the watershed lines and combine with the orginal markers
typedef itk::BinaryThresholdImageFilter<LabelImageType, LabelImageType> ThreshType;
typename ThreshType::Pointer th = ThreshType::New();
th->SetUpperThreshold(0);
th->SetOutsideValue(0);
// set the inside value to the number of markers + 1
th->SetInsideValue(labelCnt + 1);
th->SetInput(ws->GetOutput());
th->Update();
borderImg= th->GetOutput();
borderImg->DisconnectPipeline();
}
// to combine the markers again
typedef itk::AddImageFilter<LabelImageType, LabelImageType, LabelImageType> AddType;
typename AddType::Pointer adder = AddType::New();
// to create gradient magnitude image
typedef itk::GradientMagnitudeImageFilter<GreyImageType, GreyImageType> GMType;
typename GMType::Pointer gm = GMType::New();
gm->AddObserver(itk::AnyEvent(), eventCallbackITK);
gradientImg= input;
ws->SetMarkWatershedLine(false); //no use for a border in higher stages
ws->SetFullyConnected(ws_conn);
// to delete the background label
typedef itk::ChangeLabelImageFilter<LabelImageType, LabelImageType> ChangeLabType;
typename ChangeLabType::Pointer ch= ChangeLabType::New();
ch->SetChange(labelCnt + 1, 0);
for(char i= 0; i < NumberOfExtraWS; i++){
// Add the marker image to the watershed line image
adder->SetInput1(borderImg);
adder->SetInput2(labelImg);
adder->Update();
markerImg= adder->GetOutput();
markerImg->DisconnectPipeline();
// compute a gradient
gm->SetInput(gradientImg);
gm->Update();
gradientImg= gm->GetOutput();
gradientImg->DisconnectPipeline();
// Now apply higher order watershed
ws->SetInput(gradientImg);
ws->SetMarkerImage(markerImg);
ws->Update();
// delete the background label
ch->SetInput(ws->GetOutput());
ch->Update();
labelImg= ch->GetOutput();
labelImg->DisconnectPipeline();
if(interMedOutPrefix){
std::stringstream sss;
sss << interMedOutPrefix << "_ws" << i+1 << ".mha";
lwriter->SetFileName(sss.str().c_str());
//lwriter->SetFileName(std::string(interMedOutPrefix) + "_ws" + std::to_string(i+1) + ".mha");//c++11: std::to_string
lwriter->SetInput(labelImg);
lwriter->Update();
}
}
}
else
labelImg= ws->GetOutput();
typedef itk::ImageFileWriter<LabelImageType> WriterType;
typename WriterType::Pointer writer = WriterType::New();
writer->SetFileName(argv[2]);
writer->SetInput(labelImg);
writer->SetUseCompression(atoi(argv[3]));
writer->AddObserver(itk::AnyEvent(), eventCallbackITK);
try{
writer->Update();
}
catch(itk::ExceptionObject &ex){
std::cerr << ex << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
int dispatch_cT(itk::ImageIOBase::IOComponentType componentType, itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc, char *argv[]){
int res= 0;
//http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#a8dc783055a0af6f0a5a26cb080feb178
//http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00107
//IOComponentType: UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT, INT, ULONG, LONG, FLOAT, DOUBLE
switch (componentType){
case itk::ImageIOBase::UCHAR:{
typedef unsigned char InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::CHAR:{
typedef char InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::USHORT:{
typedef unsigned short InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::SHORT:{
typedef short InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::UINT:{
typedef unsigned int InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::INT:{
typedef int InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::ULONG:{
typedef unsigned long InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::LONG:{
typedef long InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::FLOAT:{
typedef float InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::DOUBLE:{
typedef double InputComponentType;
res= dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
} break;
case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
default:
std::cout << "unknown component type" << std::endl;
break;
}//switch
return res;
}
template<typename InputComponentType>
int dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc, char *argv[]){
int res= 0;
//http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#abd189f096c2a1b3ea559bc3e4849f658
//http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00099
//IOPixelType:: UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX
switch (pixelType){
case itk::ImageIOBase::SCALAR:{
typedef InputComponentType InputPixelType;
res= dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc, argv);
} break;
case itk::ImageIOBase::UNKNOWNPIXELTYPE:
default:
std::cerr << std::endl << "Error: Pixel type not handled!" << std::endl;
break;
}//switch
return res;
}
template<typename InputComponentType, typename InputPixelType>
int dispatch_D(size_t dimensionType, int argc, char *argv[]){
int res= 0;
switch (dimensionType){
// case 1:
// res= DoIt<InputComponentType, InputPixelType, 1>(argc, argv);
// break;
case 2:
res= DoIt<InputComponentType, InputPixelType, 2>(argc, argv);
break;
case 3:
res= DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
break;
default:
std::cerr << "Error: Images of dimension " << dimensionType << " are not handled!" << std::endl;
break;
}//switch
return res;
}
////from http://itk-users.7.n7.nabble.com/Pad-image-with-0-but-keep-its-type-what-ever-it-is-td27442.html
//namespace itk{
// Description:
// Get the PixelType and ComponentType from fileName
void GetImageType (std::string fileName,
itk::ImageIOBase::IOPixelType &pixelType,
itk::ImageIOBase::IOComponentType &componentType,
size_t &dimensionType
){
typedef itk::Image<unsigned char, 3> ImageType;
itk::ImageFileReader<ImageType>::Pointer imageReader= itk::ImageFileReader<ImageType>::New();
imageReader->SetFileName(fileName.c_str());
imageReader->UpdateOutputInformation();
pixelType = imageReader->GetImageIO()->GetPixelType();
componentType = imageReader->GetImageIO()->GetComponentType();
dimensionType= imageReader->GetImageIO()->GetNumberOfDimensions();
std::cerr << std::endl << "dimensions: " << dimensionType << std::endl;
std::cerr << "component type: " << imageReader->GetImageIO()->GetComponentTypeAsString(componentType) << std::endl;
std::cerr << "component size: " << imageReader->GetImageIO()->GetComponentSize() << std::endl;
std::cerr << "pixel type (string): " << imageReader->GetImageIO()->GetPixelTypeAsString(imageReader->GetImageIO()->GetPixelType()) << std::endl;
std::cerr << "pixel type: " << pixelType << std::endl << std::endl;
}
int main(int argc, char *argv[]){
if ( argc < 7 ){
std::cerr << "Missing Parameters: "
<< argv[0]
<< " Input_Image"
<< " Output_Image"
<< " compress"
<< " invert level WS-extra-runs"
<< " interMedOutPrefix"
<< std::endl;
return EXIT_FAILURE;
}
itk::ImageIOBase::IOPixelType pixelType;
typename itk::ImageIOBase::IOComponentType componentType;
size_t dimensionType;
try {
GetImageType(argv[1], pixelType, componentType, dimensionType);
}//try
catch( itk::ExceptionObject &excep){
std::cerr << argv[0] << ": exception caught !" << std::endl;
std::cerr << excep << std::endl;
return EXIT_FAILURE;
}
return dispatch_cT(componentType, pixelType, dimensionType, argc, argv);
}