1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
/*!
 * \file itkOxT1ImageFilter_test.cpp
 * \author Konrad Werys
 * \date 2018/08/13
 */


#include "CmakeConfigForTomato.h"
#ifdef USE_ITK

#include "OxTestItkImagesFactory.h"
#include "OxFunctionsT1Basic.h"
#include "OxFitterAmoebaVnl.h"
#include "OxSignCalculatorNoSign.h"
#include "OxSignCalculatorRealImag.h"
#include "OxStartPointCalculatorDefault3Dims.h"
#include "OxCalculatorT1Molli.h"

#include "itkCalculatorT1ImageFilter.h"

#include "itkTestingComparisonImageFilter.h"

#include "gtest/gtest.h"

TEST(itkCalculatorT1ImageFilter, calculate) {

    typedef double TYPE;
    typedef itk::Image <TYPE, 3> TImageIn;
    typedef itk::Image <TYPE, 2> TImageOut;
    typedef itk::CalculatorT1ImageFilter < TImageIn, TImageOut > CalculatorT1ImageFilterType;
    typedef itk::Testing::ComparisonImageFilter<TImageIn, TImageIn> ComparisonImageFilter3dType;
    typedef itk::Testing::ComparisonImageFilter<TImageOut, TImageOut> ComparisonImageFilter2dType;

    std::vector< std::string > filePaths;
    filePaths.push_back("testData/blood.yaml");
    filePaths.push_back("testData/myocardium.yaml");

    int nRows = 2;
    int nCols = 3;

    // test images
    Ox::TestItkImagesFactory<TYPE> itkImagesFactory(nRows, nCols, filePaths);

    TImageIn::Pointer imageMag = itkImagesFactory.generateImageMag();
    TImageIn::Pointer imagePha = itkImagesFactory.generateImagePha();

    TImageOut::Pointer imageMolliA = itkImagesFactory.generateImageResultsMolliA();
    TImageOut::Pointer imageMolliB = itkImagesFactory.generateImageResultsMolliB();
    TImageOut::Pointer imageMolliT1star = itkImagesFactory.generateImageResultsMolliT1star();

    // init the necessary objects
    Ox::FunctionsT1Basic<TYPE> functionsObject;
    Ox::FitterAmoebaVnl<TYPE> fitterAmoebaVnl;
    Ox::SignCalculatorRealImag<TYPE> signCalculator;
    Ox::StartPointCalculatorDefault3Dims<TYPE> startPointCalculator;
    Ox::CalculatorT1Molli<TYPE> calculatorT1Molli;

    // configure calculator
    calculatorT1Molli.setFunctionsT1(&functionsObject);
    calculatorT1Molli.setFitter(&fitterAmoebaVnl);
    calculatorT1Molli.setSignCalculator(&signCalculator);
    calculatorT1Molli.setStartPointCalculator(&startPointCalculator);
    calculatorT1Molli.setInvTimes(itkImagesFactory.getInvTimesPtr());
    calculatorT1Molli.setNSamples(itkImagesFactory.getNSamples());

    // configure calculator itk filter
    CalculatorT1ImageFilterType::Pointer imageCalculatorItk = CalculatorT1ImageFilterType::New();
    imageCalculatorItk->SetInputMagImage(imageMag);
    imageCalculatorItk->SetInputPhaImage(imagePha);
    imageCalculatorItk->SetCalculator(&calculatorT1Molli);
    //imageCalculatorItk->SetNumberOfThreads(1);
    imageCalculatorItk->Update();

    ComparisonImageFilter2dType::Pointer diff = ComparisonImageFilter2dType::New();

    diff->SetValidInput(imageMolliA.GetPointer());
    diff->SetTestInput(imageCalculatorItk->GetAImage());
    diff->UpdateLargestPossibleRegion();

    EXPECT_LE(diff->GetMaximumDifference(), 1e-2);

    diff->SetValidInput(imageMolliB.GetPointer());
    diff->SetTestInput(imageCalculatorItk->GetBImage());
    diff->UpdateLargestPossibleRegion();

    EXPECT_LE(diff->GetMaximumDifference(), 1e-2);

    diff->SetValidInput(imageMolliT1star.GetPointer());
    diff->SetTestInput(imageCalculatorItk->GetT1starImage());
    diff->UpdateLargestPossibleRegion();

    EXPECT_LE(diff->GetMaximumDifference(), 1e-2);

}

TEST(itkCalculatorT1ImageFilter, calculate_no_phase_given) {

    typedef double TYPE;
    typedef itk::Image <TYPE, 3> TImageIn;
    typedef itk::Image <TYPE, 2> TImageOut;
    typedef itk::CalculatorT1ImageFilter < TImageIn, TImageOut > ImageCalculatorItkType;
    typedef itk::Testing::ComparisonImageFilter<TImageIn, TImageIn> ComparisonImageFilter3dType;
    typedef itk::Testing::ComparisonImageFilter<TImageOut, TImageOut> ComparisonImageFilter2dType;

    std::vector< std::string > filePaths;
    filePaths.push_back("testData/blood.yaml");
    filePaths.push_back("testData/myocardium.yaml");

    int nRows = 4;
    int nCols = 5;

    // test images
    Ox::TestItkImagesFactory<TYPE> itkImagesFactory(nRows, nCols, filePaths);

    TImageIn::Pointer imageMag = itkImagesFactory.generateImageMag();
    //TImageIn::Pointer imagePha = itkImagesFactory.generateImagePha();

    TImageOut::Pointer imageMolliA = itkImagesFactory.generateImageResultsMolliA();
    TImageOut::Pointer imageMolliB = itkImagesFactory.generateImageResultsMolliB();
    TImageOut::Pointer imageMolliT1star = itkImagesFactory.generateImageResultsMolliT1star();

    // init the necessary objects
    Ox::FunctionsT1Basic<TYPE> functionsObject;
    Ox::FitterAmoebaVnl<TYPE> fitterAmoebaVnl;
    Ox::SignCalculatorNoSign<TYPE> signCalculator;
    Ox::StartPointCalculatorDefault3Dims<TYPE> startPointCalculator;
    Ox::CalculatorT1Molli<TYPE> calculatorT1Molli;

    // configure calculator
    calculatorT1Molli.setFunctionsT1(&functionsObject);
    calculatorT1Molli.setFitter(&fitterAmoebaVnl);
    calculatorT1Molli.setSignCalculator(&signCalculator);
    calculatorT1Molli.setStartPointCalculator(&startPointCalculator);
    calculatorT1Molli.setInvTimes(itkImagesFactory.getInvTimesPtr());
    calculatorT1Molli.setNSamples(itkImagesFactory.getNSamples());

    // configure calculator itk filter
    ImageCalculatorItkType::Pointer imageCalculatorItk = ImageCalculatorItkType::New();
    imageCalculatorItk->SetInputMagImage(imageMag);
    // imageCalculatorItk->SetInputPhaImage(imagePha);
    imageCalculatorItk->SetCalculator(&calculatorT1Molli);
    //imageCalculatorItk->SetNumberOfThreads(1);
    imageCalculatorItk->Update();

    ComparisonImageFilter2dType::Pointer diff = ComparisonImageFilter2dType::New();

    diff->SetValidInput(imageMolliA.GetPointer());
    diff->SetTestInput(imageCalculatorItk->GetAImage());
    diff->UpdateLargestPossibleRegion();

    EXPECT_LE(diff->GetMaximumDifference(), 1e-2);

    diff->SetValidInput(imageMolliB.GetPointer());
    diff->SetTestInput(imageCalculatorItk->GetBImage());
    diff->UpdateLargestPossibleRegion();

    EXPECT_LE(diff->GetMaximumDifference(), 1e-2);

    diff->SetValidInput(imageMolliT1star.GetPointer());
    diff->SetTestInput(imageCalculatorItk->GetT1starImage());
    diff->UpdateLargestPossibleRegion();

    EXPECT_LE(diff->GetMaximumDifference(), 1e-2);
}

#endif //USE_ITK