swh:1:snp:e6d42e6731ce66e3c09de07ac49964c03139e990
Tip revision: 8449484d61814fb6b89eccbdcc29c5d51481966e authored by Konrad Werys on 07 December 2018, 11:08:10 UTC
travis works again
travis works again
Tip revision: 8449484
itkPipeline_test.cpp
/*!
* \file itkPipeline_test.cpp
* \author Konrad Werys
* \date 2018/08/14
*/
#include "CmakeConfigForTomato.h"
#ifdef USE_ITK
#include "OxFunctionsT1Basic.h"
#include "OxFitterAmoebaVnl.h"
#include "OxSignCalculatorNoSign.h"
#include "OxSignCalculatorRealImag.h"
#include "OxStartPointCalculatorDefault3Dims.h"
#include "OxCalculatorT1Molli.h"
#include "itkReadFileListFilter.h"
#include "itkSortInvTimesImageFilter.h"
#include "itkCalculatorT1ImageFilter.h"
#ifdef USE_VTK
#include "QuickView.h"
#endif //USE_VTK
#include "gtest/gtest.h"
TEST(itkPipeline, readAndCalculateT1FromMag) {
bool doVisualise = false; //for debugging
// primitive data types
typedef double InputPixelType;
typedef double OutputPixelType;
// image data types
typedef itk::Image< InputPixelType, 3 > InputImageType3D;
typedef itk::Image< OutputPixelType, 2 > OutputImageType;
typedef itk::ReadFileListFilter<InputImageType3D> ReadFileListFilterType;
typedef itk::SortInvTimesImageFilter < InputImageType3D, InputImageType3D> SortInvTimesImageFilterType;
typedef itk::CalculatorT1ImageFilter < InputImageType3D, OutputImageType > CalculatorT1ImageFilterType;
std::vector<std::string> dcmMagFilePaths;
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0001.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0002.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0003.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0004.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0005.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0006.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0007.dcm");
ReadFileListFilterType::Pointer reader = ReadFileListFilterType::New();
reader->SetFileList(dcmMagFilePaths);
reader->Update();
SortInvTimesImageFilterType::Pointer sorter = SortInvTimesImageFilterType::New();
sorter->SetInvTimesNonSorted(reader->GetInvTimes());
sorter->SetInput(reader->GetOutput());
sorter->Update();
// if I do not store a copy of inversion times like this, vnl_vector does funny things with the data under
// the pointer .data_block();
int nSamples = sorter->GetInvTimesSorted().size();
InputPixelType *invTimes = new InputPixelType[nSamples];
KWUtil::copyArrayToArray(nSamples, invTimes, sorter->GetInvTimesSorted().data_block());
// init the necessary objects
Ox::FunctionsT1Basic<InputPixelType> functionsObject;
Ox::FitterAmoebaVnl<InputPixelType> fitter;
Ox::SignCalculatorNoSign<InputPixelType> signCalculator;
Ox::StartPointCalculatorDefault3Dims<InputPixelType> startPointCalculator;
Ox::CalculatorT1Molli<InputPixelType> calculatorT1;
// configure fitter
fitter.setMaxFunctionEvals(10); // to accelerate the test
// configure calculator
calculatorT1.setFunctionsT1(&functionsObject);
calculatorT1.setFitter(&fitter);
calculatorT1.setSignCalculator(&signCalculator);
calculatorT1.setStartPointCalculator(&startPointCalculator);
calculatorT1.setInvTimes(invTimes);
calculatorT1.setNSamples(nSamples);
// configure calculator itk filter
CalculatorT1ImageFilterType::Pointer imageCalculatorItk = CalculatorT1ImageFilterType::New();
imageCalculatorItk->SetInputMagImage(sorter->GetOutput());
imageCalculatorItk->SetCalculator(&calculatorT1);
//imageCalculatorItk->SetNumberOfThreads(1);
ASSERT_NO_THROW(imageCalculatorItk->Update());
#ifdef USE_VTK
if (doVisualise){
// view
QuickView viewer;
viewer.AddImage(imageCalculatorItk->GetAImage(), true, "A");
viewer.AddImage(imageCalculatorItk->GetBImage(), true, "B");
viewer.AddImage(imageCalculatorItk->GetT1starImage(), true, "T1star");
viewer.Visualize();
}
#endif
delete [] invTimes;
}
TEST(itkPipeline, calculateT1FromMagAndPhase) {
bool doVisualise = false; //for debugging
// primitive data types
typedef double InputPixelType;
typedef double OutputPixelType;
// image data types
typedef itk::Image< InputPixelType, 3 > InputImageType3D;
typedef itk::Image< OutputPixelType, 2 > OutputImageType;
typedef itk::ReadFileListFilter<InputImageType3D> ReadFileListFilterType;
typedef itk::SortInvTimesImageFilter < InputImageType3D, InputImageType3D> SortInvTimesImageFilterType;
typedef itk::CalculatorT1ImageFilter < InputImageType3D, OutputImageType > CalculatorT1ImageFilterType;
std::vector<std::string> dcmMagFilePaths;
std::vector<std::string> dcmPhaFilePaths;
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0001.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0002.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0003.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0004.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0005.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0006.dcm");
dcmMagFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_12/IM-0001-0007.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0001.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0002.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0003.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0004.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0005.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0006.dcm");
dcmPhaFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_13/IM-0002-0007.dcm");
ReadFileListFilterType::Pointer readerMag = ReadFileListFilterType::New();
readerMag->SetFileList(dcmMagFilePaths);
readerMag->Update();
ReadFileListFilterType::Pointer readerPha = ReadFileListFilterType::New();
readerPha->SetFileList(dcmPhaFilePaths);
readerPha->Update();
SortInvTimesImageFilterType::Pointer sorterMag = SortInvTimesImageFilterType::New();
sorterMag->SetInvTimesNonSorted(readerMag->GetInvTimes());
sorterMag->SetInput(readerMag->GetOutput());
sorterMag->Update();
SortInvTimesImageFilterType::Pointer sorterPha = SortInvTimesImageFilterType::New();
sorterPha->SetInvTimesNonSorted(readerPha->GetInvTimes());
sorterPha->SetInput(readerPha->GetOutput());
sorterPha->Update();
// if I do not store a copy of inversion times like this, vnl_vector does funny things with the data under
// the pointer .data_block();
int nSamples = sorterMag->GetInvTimesSorted().size();
InputPixelType *invTimes = new InputPixelType[nSamples];
KWUtil::copyArrayToArray(nSamples, invTimes, sorterMag->GetInvTimesSorted().data_block());
// init the necessary objects
Ox::FunctionsT1Basic<InputPixelType> functionsObject;
Ox::FitterAmoebaVnl<InputPixelType> fitter;
Ox::SignCalculatorRealImag<InputPixelType> signCalculator;
Ox::StartPointCalculatorDefault3Dims<InputPixelType> startPointCalculator;
Ox::CalculatorT1Molli<InputPixelType> calculatorT1;
// configure fitter
fitter.setMaxFunctionEvals(10); // to accelerate the test
// configure calculator
calculatorT1.setFunctionsT1(&functionsObject);
calculatorT1.setFitter(&fitter);
calculatorT1.setSignCalculator(&signCalculator);
calculatorT1.setStartPointCalculator(&startPointCalculator);
calculatorT1.setInvTimes(invTimes);
calculatorT1.setNSamples(nSamples);
// configure calculator itk filter
CalculatorT1ImageFilterType::Pointer imageCalculatorItk = CalculatorT1ImageFilterType::New();
imageCalculatorItk->SetInputMagImage(sorterMag->GetOutput());
imageCalculatorItk->SetInputPhaImage(sorterPha->GetOutput());
imageCalculatorItk->SetCalculator(&calculatorT1);
//imageCalculatorItk->SetNumberOfThreads(1);
ASSERT_NO_THROW(imageCalculatorItk->Update());
delete [] invTimes;
}
#endif // USE_ITK