Tomato_sameAsShmolli_test.cpp
/*!
* \file Tomato_sameAsShmolli_test.cpp
* \author Konrad Werys
* \date 2018/08/20
*/
#include "CmakeConfigForTomato.h"
#ifdef USE_PRIVATE_NR2
#ifdef USE_ITK
#include "gtest/gtest.h"
#include "Tomato.h"
#include "itkImageFileReader.h"
#include "itkTestingComparisonImageFilter.h"
// TODO: make sure all SNR give the same results
// TODO: make sure all nAmoebaFinalCall give the same results
/**
* \class ActeptanceTests_TomatoTest
* \brief based on https://github.com/google/googletest/blob/master/googletest/docs/advanced.md#sharing-resources-between-tests-in-the-same-test-case
*/
class ActeptanceTests_TomatoFixtureTest : public ::testing::Test {
// primitive data types
typedef int16_t PixelType;
// image data types
typedef itk::Image< PixelType, 2 > ImageType2D;
typedef itk::ImageFileReader<ImageType2D> ReadImage2dFilterType;
typedef itk::Testing::ComparisonImageFilter<ImageType2D, ImageType2D> ComparisonImageFilter2dType;
protected:
// Per-test-case set-up.
// Called before the first test in this test case.
// Can be omitted if not needed.
static void SetUpTestCase() {
std::string configFilePath = "testData/tomatoConfig_Shmolli_inputFilePaths.yaml";
_tomato_object = new Ox::Tomato<double>(configFilePath);
_tomato_object->readAndSort();
_tomato_object->calculate();
_tomato_object->exportToDicom();
std::string output_map_series_number = KWUtil::NumberToString(_tomato_object->_opts->output_map_series_number);
std::string output_fitparams_series_number = KWUtil::NumberToString(_tomato_object->_opts->output_fitparams_series_number);
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_map + KWUtil::PathSeparator() + output_map_series_number + "_T1.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_R2.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_A.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_B.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_T1star.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_ShMolliRange.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_RelSNRFinal.dcm");
_calculatedFilePaths.push_back(_tomato_object->_opts->dir_output_fitparams + KWUtil::PathSeparator() + output_fitparams_series_number + "_nAmebaCallFinal.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_T1MAP_14/IM-0003-0001.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0001.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0002.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0003.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0004.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0005.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0006.dcm");
_originalFilePaths.push_back("testData/dicom/Hcmr_Phantom_1916_260C/Konrad_Shmolli/ShMOLLI_192i_e11_FITPARAMS_15/IM-0004-0007.dcm");
}
// Per-test-case tear-down.
// Called after the last test in this test case.
// Can be omitted if not needed.
static void TearDownTestCase() {
delete _tomato_object;
_tomato_object = NULL;
}
// You can define per-test set-up logic as usual.
virtual void SetUp() {
readerOriginalT1Map = ReadImage2dFilterType::New();
readerCalculatedT1Map = ReadImage2dFilterType::New();
diff = ComparisonImageFilter2dType::New();
}
// You can define per-test tear-down logic as usual.
virtual void TearDown() { }
public:
// Some expensive resource shared by all tests.
static Ox::Tomato<double>* _tomato_object;
static std::vector<std::string> _originalFilePaths;
static std::vector<std::string> _calculatedFilePaths;
ReadImage2dFilterType::Pointer readerOriginalT1Map;
ReadImage2dFilterType::Pointer readerCalculatedT1Map;
ComparisonImageFilter2dType::Pointer diff;
};
Ox::Tomato<double>* ActeptanceTests_TomatoFixtureTest::_tomato_object = NULL;
std::vector<std::string> ActeptanceTests_TomatoFixtureTest::_originalFilePaths;
std::vector<std::string> ActeptanceTests_TomatoFixtureTest::_calculatedFilePaths;
TEST_F(ActeptanceTests_TomatoFixtureTest, sameAsShmolli_T1) {
int i = 0; // T1 map
readerOriginalT1Map->SetFileName(_originalFilePaths.at(i));
readerCalculatedT1Map->SetFileName(_calculatedFilePaths.at(i));
// for comparing the images
diff->SetValidInput(readerOriginalT1Map->GetOutput());
diff->SetTestInput(readerCalculatedT1Map->GetOutput());
diff->Update();
// compare
diff->UpdateLargestPossibleRegion();
double tolerance = 2;
if (diff->GetMaximumDifference() > tolerance)
std::cout << "Number of unequal pixels = " << diff->GetNumberOfPixelsWithDifferences() << std::endl;
ASSERT_LE(diff->GetMaximumDifference(), tolerance);
}
TEST_F(ActeptanceTests_TomatoFixtureTest, sameAsShmolli_R2) {
int i = 1; // R2 map
readerOriginalT1Map->SetFileName(_originalFilePaths.at(i));
readerCalculatedT1Map->SetFileName(_calculatedFilePaths.at(i));
// for comparing the images
diff->SetValidInput(readerOriginalT1Map->GetOutput());
diff->SetTestInput(readerCalculatedT1Map->GetOutput());
diff->Update();
// compare
diff->UpdateLargestPossibleRegion();
ASSERT_LE(diff->GetNumberOfPixelsWithDifferences(), 300); // max allowed error is 2
}
TEST_F(ActeptanceTests_TomatoFixtureTest, sameAsShmolli_A) {
int i = 2; // A map
readerOriginalT1Map->SetFileName(_originalFilePaths.at(i));
readerCalculatedT1Map->SetFileName(_calculatedFilePaths.at(i));
// for comparing the images
diff->SetValidInput(readerOriginalT1Map->GetOutput());
diff->SetTestInput(readerCalculatedT1Map->GetOutput());
diff->Update();
// compare
diff->UpdateLargestPossibleRegion();
ASSERT_LE(diff->GetMaximumDifference(), 2); // max allowed error is 2
}
TEST_F(ActeptanceTests_TomatoFixtureTest, sameAsShmolli_B) {
int i = 3; // B map
readerOriginalT1Map->SetFileName(_originalFilePaths.at(i));
readerCalculatedT1Map->SetFileName(_calculatedFilePaths.at(i));
// for comparing the images
diff->SetValidInput(readerOriginalT1Map->GetOutput());
diff->SetTestInput(readerCalculatedT1Map->GetOutput());
diff->Update();
// compare
diff->UpdateLargestPossibleRegion();
ASSERT_LE(diff->GetMaximumDifference(), 2); // max allowed error is 2
}
TEST_F(ActeptanceTests_TomatoFixtureTest, sameAsShmolli_T1star) {
int i = 4; // T1star map
readerOriginalT1Map->SetFileName(_originalFilePaths.at(i));
readerCalculatedT1Map->SetFileName(_calculatedFilePaths.at(i));
// for comparing the images
diff->SetValidInput(readerOriginalT1Map->GetOutput());
diff->SetTestInput(readerCalculatedT1Map->GetOutput());
diff->Update();
// compare
diff->UpdateLargestPossibleRegion();
ASSERT_LE(diff->GetMaximumDifference(), 2); // max allowed error is 2
}
TEST_F(ActeptanceTests_TomatoFixtureTest, sameAsShmolli_ShmolliRange) {
int i = 5; // ShmolliRange map
readerOriginalT1Map->SetFileName(_originalFilePaths.at(i));
readerCalculatedT1Map->SetFileName(_calculatedFilePaths.at(i));
// for comparing the images
diff->SetValidInput(readerOriginalT1Map->GetOutput());
diff->SetTestInput(readerCalculatedT1Map->GetOutput());
diff->Update();
// compare
diff->UpdateLargestPossibleRegion();
ASSERT_LE(diff->GetMaximumDifference(), 2); // max allowed error is 2
}
#endif // USE_PRIVATE_NR2
#endif // USE_ITK