[Insight-users] Adaptive thresholding by region

[Loïc Giraldi]

Hi Lassi,

First of all thanks for your help.

Indeed this filter does perfectly what I want, and even in a better way than
the one I was thinking to. Nevertheless, I would like to understand the
mistake I have done in my code, it would probably help me and others in
future works.

Regards,
Loïc

2010/5/10 Lassi Paavolainen <lassi.paavolainen at jyu.fi>

> Hi Loic,
>
> You might want to have a look at following Insight Journal paper that
> should do exactly what you plan to do:
> http://insight-journal.org/browse/publication/702
>
> Best regards,
> Lassi
>
>
> On Mon, 10 May 2010, Loïc Giraldi wrote:
>
>  Hi all!
>>
>> I'm trying to make an adaptive thresholding using the Otsu method. To do
>> so,
>> I want to process my image by region. The idea is to separate the original
>> picture in several blocks, process each block and reconstruct the final
>> output by gathering the blocks.
>> I am trying to do it using the RegionOfInterestImageFilter, the
>> OtsuThresholdImageFilter and the PasteImageFilter in a loop over regions,
>> I
>> have grabbed some informations in this mailing list but I can't manage to
>> make it working. The process works if I do not loop over regions.
>>
>> Here is my code:
>>
>> #include "itkImage.h"
>> #include "itkImageFileReader.h"
>> #include "itkImageFileWriter.h"
>>
>> #include "itkRegionOfInterestImageFilter.h"
>> #include "itkOtsuThresholdImageFilter.h"
>> #include "itkPasteImageFilter.h"
>>
>> #include <iostream>
>> #include <string>
>> #include <sstream>
>> #include <cstdlib>
>> using namespace std;
>>
>>
>> template <typename T> string toString(T val){
>>     ostringstream oss;
>>     oss << val;
>>     return oss.str();
>> }
>>
>> int main(int argc, char *argv[]){
>>     ////////////////////////////  Usage //////////////////////////////
>>     if (argc<3){
>>         std::cerr << "Missing arguments!" << std::endl;
>>         std::cerr << "Usage : " << argv[0]
>>                   << " InputFile"
>>                   << " Size" << std::endl;
>>         return 1;
>>     }
>>
>>     const char *inputFileName = argv[1];
>>     const unsigned int size = atoi(argv[2]);
>>
>>     //////////////////////  Image definitions ////////////////////////
>>     const int Dimension = 3;
>>
>>     typedef unsigned short InputPixelType;
>>     typedef unsigned char OutputPixelType;
>>
>>     typedef itk::Image< InputPixelType, Dimension > InputImageType;
>>     typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>
>>     ////////////////////////  Image reading //////////////////////////
>>     typedef itk::ImageFileReader< InputImageType > ReaderType;
>>
>>     ReaderType::Pointer reader = ReaderType::New();
>>     reader->SetFileName(inputFileName);
>>     try{
>>         reader->Update();
>>     }
>>     catch( itk::ExceptionObject & excep ){
>>         std::cerr << "Exception caught !" << std::endl;
>>         std::cerr << excep << std::endl;
>>     }
>>
>>     //////////////////////////  Filtering ////////////////////////////
>>     //Output Allocation
>>     OutputImageType::Pointer output = OutputImageType::New();
>>     OutputImageType::IndexType outIndex;
>>     OutputImageType::SizeType outSize;
>>     OutputImageType::RegionType outRegion;
>>
>>     for (int i = 0; i < Dimension; ++i){
>>
>> outIndex[i]=reader->GetOutput()->GetBufferedRegion().GetIndex()[i];
>>         outSize[i]=reader->GetOutput()->GetBufferedRegion().GetSize()[i];
>>     }
>>
>>     outRegion.SetIndex(outIndex);
>>     outRegion.SetSize(outSize);
>>
>>     output->SetRegions(outRegion);
>>     output->Allocate();
>>     output->FillBuffer(0);
>>
>>     //Moving box definition
>>     InputImageType::IndexType boxIndex;
>>     InputImageType::SizeType boxSize;
>>     InputImageType::RegionType boxRegion;
>>
>>     for (int i = 0; i < Dimension; ++i){
>>         boxIndex[i] = outIndex[i];
>>     }
>>     for (int i = 0; i < Dimension; ++i){
>>         boxSize[i] = size;
>>     }
>>
>>     boxRegion.SetIndex(boxIndex);
>>     boxRegion.SetSize(boxSize);
>>
>>     unsigned numberOfBoxes[3];
>>     for (int i = 0; i < Dimension; ++i){
>>         numberOfBoxes[i] = static_cast<unsigned>((outSize[i]/size));
>>     }
>>
>>     //Processing
>>     typedef itk::RegionOfInterestImageFilter< InputImageType,
>> InputImageType> ROIFilterType;
>>     typedef itk::OtsuThresholdImageFilter< InputImageType, OutputImageType
>> >
>> OtsuThresholdFilterType;
>>     typedef itk::PasteImageFilter<OutputImageType> PasteImageFilterType;
>>
>>     ROIFilterType::Pointer roi = ROIFilterType::New();
>>     OtsuThresholdFilterType::Pointer otsu =
>> OtsuThresholdFilterType::New();
>>     PasteImageFilterType::Pointer paste = PasteImageFilterType::New();
>>
>>     for(unsigned i = 0; i < numberOfBoxes[0]; ++i){
>>         for(unsigned j = 0; j < numberOfBoxes[1]; ++j){
>>             for(unsigned k = 0; k < numberOfBoxes[2]; ++k){
>>
>>                 boxIndex[0] += i * size;
>>                 boxIndex[1] += j * size;
>>                 boxIndex[2] += k * size;
>>                 boxRegion.SetIndex(boxIndex);
>>
>>                 roi->SetInput(reader->GetOutput());
>>                 roi->SetRegionOfInterest(boxRegion);
>>
>>                 try{
>>                     roi->UpdateLargestPossibleRegion();
>>                     roi->Update();
>>                 }
>>                 catch( itk::ExceptionObject & excep ){
>>                     std::cerr << "ROI!" << std::endl;
>>                     std::cerr << "Exception caught !" << std::endl;
>>                     std::cerr << excep << std::endl;
>>                 }
>>
>>                 otsu->SetInput(roi->GetOutput());
>>                 otsu->SetNumberOfHistogramBins(128);
>>                 otsu->SetInsideValue(255);
>>                 otsu->SetOutsideValue(0);
>>
>>                 try{
>>                     otsu->UpdateLargestPossibleRegion();
>>                     otsu->Update();
>>                 }
>>                 catch( itk::ExceptionObject & excep ){
>>                     std::cerr << "Otsu!" << std::endl;
>>                     std::cerr << "Exception caught !" << std::endl;
>>                     std::cerr << excep << std::endl;
>>                 }
>>                 otsu->Print(std::cout);
>>
>>                 paste->SetDestinationImage(output);
>>                 paste->SetSourceImage(otsu->GetOutput());
>>                 paste->SetDestinationIndex( boxIndex );
>>                 paste->SetSourceRegion( boxRegion );
>>
>>                 try{
>>                     paste->UpdateLargestPossibleRegion();
>>                     paste->Update();
>>                 }
>>                 catch( itk::ExceptionObject & excep ){
>>                     std::cerr << "Paste!" << std::endl;
>>                     std::cerr << "Exception caught !" << std::endl;
>>                     std::cerr << excep << std::endl;
>>                     std::cerr << "i,j,k = " << i << ',' << j << ',' << k
>> <<
>> std::endl;
>>                     boxRegion.Print(std::cerr);
>>                     paste.Print(std::cerr);
>>                     paste->GetOutput()->Print(std::cerr);
>>                 }
>>                 output = paste->GetOutput();
>>                 output->DisconnectPipeline();
>>             }
>>         }
>>     }
>>
>>     ////////////////////////  Image writing //////////////////////////
>>     typedef itk::ImageFileWriter< OutputImageType > WriterType;
>>
>>     WriterType::Pointer writer = WriterType::New();
>>
>>     string outputFileName(inputFileName);
>>     size_t pos = outputFileName.find_last_of('.');
>>     outputFileName.insert(pos, "_result_"+toString(size));
>>
>>     writer->SetInput(output);
>>     writer->SetFileName(outputFileName.c_str());
>>     writer->Update();
>>     try{
>>         writer->Update();
>>     }
>>     catch( itk::ExceptionObject & excep ){
>>         std::cerr << "Write!" << std::endl;
>>         std::cerr << "Exception caught !" << std::endl;
>>         std::cerr << excep << std::endl;
>>     }
>>     return 0;
>> }
>>
>> Thanks for your help,
>> Regards,
>> Loïc
>>
>>
>>
>>
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