Medical Imaging Interaction Toolkit  2018.4.99-08619e4f
Medical Imaging Interaction Toolkit
mitkGIFFirstOrderHistogramStatisticsTest.cpp
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1 /*============================================================================
2 
3 The Medical Imaging Interaction Toolkit (MITK)
4 
5 Copyright (c) German Cancer Research Center (DKFZ)
6 All rights reserved.
7 
8 Use of this source code is governed by a 3-clause BSD license that can be
9 found in the LICENSE file.
10 
11 ============================================================================*/
12 
13 #include <mitkTestingMacros.h>
14 #include <mitkTestFixture.h>
15 #include "mitkIOUtil.h"
16 #include <cmath>
17 
19 
20 class mitkGIFFirstOrderHistogramStatisticsTestSuite : public mitk::TestFixture
21 {
22  CPPUNIT_TEST_SUITE(mitkGIFFirstOrderHistogramStatisticsTestSuite);
23 
24  MITK_TEST(ImageDescription_PhantomTest);
25 
26  CPPUNIT_TEST_SUITE_END();
27 
28 private:
29  mitk::Image::Pointer m_IBSI_Phantom_Image_Small;
30  mitk::Image::Pointer m_IBSI_Phantom_Image_Large;
31  mitk::Image::Pointer m_IBSI_Phantom_Mask_Small;
32  mitk::Image::Pointer m_IBSI_Phantom_Mask_Large;
33 
34 public:
35 
36  void setUp(void) override
37  {
38  m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd"));
39  m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd"));
40  m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd"));
41  m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd"));
42  }
43 
44  void ImageDescription_PhantomTest()
45  {
47 
48  featureCalculator->SetUseBinsize(true);
49  featureCalculator->SetBinsize(1.0);
50  featureCalculator->SetUseMinimumIntensity(true);
51  featureCalculator->SetUseMaximumIntensity(true);
52  featureCalculator->SetMinimumIntensity(0.5);
53  featureCalculator->SetMaximumIntensity(6.5);
54 
55  auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large);
56 
57  std::map<std::string, double> results;
58  for (auto valuePair : featureList)
59  {
60  MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second;
61  results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second;
62  }
63  CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 46 features.", std::size_t(46), featureList.size());
64 
65  // These values are obtained by a run of the filter.
66  // The might be wrong!
67  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Value should be 2.15 with Large IBSI Phantom Image", 2.15, results["First Order Histogram::Mean Value"], 0.01);
68  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Variance Value should be 3.05 with Large IBSI Phantom Image", 3.05, results["First Order Histogram::Variance Value"], 0.01);
69  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Skewness Value should be 1.08 with Large IBSI Phantom Image", 1.08, results["First Order Histogram::Skewness Value"], 0.01);
70  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Excess Kurtosis Value should be -0.355 with Large IBSI Phantom Image", -0.355, results["First Order Histogram::Excess Kurtosis Value"], 0.01);
71  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Value should be 1 with Large IBSI Phantom Image", 1.0, results["First Order Histogram::Median Value"], 0.01);
72  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Value should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Minimum Value"], 0.01);
73  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 10 Value should be 0.648 with Large IBSI Phantom Image", 0.648, results["First Order Histogram::Percentile 10 Value"], 0.01);
74  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 90 Value should be 4.475 with Large IBSI Phantom Image", 4.475, results["First Order Histogram::Percentile 90 Value"], 0.01);
75  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Value should be 6 with Large IBSI Phantom Image", 6, results["First Order Histogram::Maximum Value"], 0.01);
76  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mode Value should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Mode Value"], 0.01);
77  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Interquantile Range Value should be 2.9 with Large IBSI Phantom Image", 2.911, results["First Order Histogram::Interquantile Range Value"], 0.01);
78 
79  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Range Value should be 5 with Large IBSI Phantom Image", 5, results["First Order Histogram::Range Value"], 0.01);
80  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Absolute Deviation Value should be 1.55 with Large IBSI Phantom Image", 1.55, results["First Order Histogram::Mean Absolute Deviation Value"], 0.01);
81  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Absolute Deviation Value should be 1.11 with Large IBSI Phantom Image", 1.11, results["First Order Histogram::Robust Mean Absolute Deviation Value"], 0.01);
82  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Absolute Deviation Value should be 1.14 with Large IBSI Phantom Image", 1.14, results["First Order Histogram::Median Absolute Deviation Value"], 0.01);
83  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Coefficient of Variation Value should be 0.812 with Large IBSI Phantom Image", 0.812, results["First Order Histogram::Coefficient of Variation Value"], 0.01);
84  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Quantile coefficient of Dispersion Value should be 0.626 with Large IBSI Phantom Image", 0.626, results["First Order Histogram::Quantile coefficient of Dispersion Value"], 0.01);
85  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Entropy Value should be 1.27 with Large IBSI Phantom Image", 1.27, results["First Order Histogram::Entropy Value"], 0.01);
86  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Uniformity Value should be 0.512 with Large IBSI Phantom Image", 0.512, results["First Order Histogram::Uniformity Value"], 0.01);
87 
88  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Index should be 0.746 with Large IBSI Phantom Image", 0.746, results["First Order Histogram::Robust Mean Index"], 0.01);
89  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Value should be 1.746 with Large IBSI Phantom Image", 1.746, results["First Order Histogram::Robust Mean Value"], 0.01);
90  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Number of Bins should be 6", 6, results["First Order Histogram::Number of Bins"], 0.01);
91  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Bin Size should be 1", 1, results["First Order Histogram::Bin Size"], 0.01);
92 
93  // These values are taken from the IBSI Initiative to ensure compatibility
94  // The values are given with an accuracy of 0.01
95  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Index should be 2.15 with Large IBSI Phantom Image", 2.15, results["First Order Histogram::Mean Index"], 0.01);
96  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Variance Index should be 3.05 with Large IBSI Phantom Image", 3.05, results["First Order Histogram::Variance Index"], 0.01);
97  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Skewness Index should be 1.08 with Large IBSI Phantom Image", 1.08, results["First Order Histogram::Skewness Index"], 0.01);
98  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Excess Kurtosis Index should be -0.355 with Large IBSI Phantom Image", -0.355, results["First Order Histogram::Excess Kurtosis Index"], 0.01);
99  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Index should be 1 with Large IBSI Phantom Image", 1.0, results["First Order Histogram::Median Index"], 0.01);
100  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Index should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Minimum Index"], 0.01);
101  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 10 Index should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Percentile 10 Index"], 0.01);
102  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 90 Index should be 2.15 with Large IBSI Phantom Image", 4, results["First Order Histogram::Percentile 90 Index"], 0.01);
103  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Index should be 6 with Large IBSI Phantom Image", 6, results["First Order Histogram::Maximum Index"], 0.01);
104  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mode Index should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Mode Index"], 0.01);
105  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Interquantile Range Index should be 3 with Large IBSI Phantom Image", 3, results["First Order Histogram::Interquantile Range Index"], 0.01);
106 
107  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Range Index should be 5 with Large IBSI Phantom Image", 5, results["First Order Histogram::Range Index"], 0.01);
108  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Absolute Deviation Index should be 3 with Large IBSI Phantom Image", 1.55, results["First Order Histogram::Mean Absolute Deviation Index"], 0.01);
109  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Absolute Deviation Index should be 1.11 with Large IBSI Phantom Image", 1.11, results["First Order Histogram::Robust Mean Absolute Deviation Index"], 0.01);
110  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Absolute Deviation Index should be 1.14 with Large IBSI Phantom Image", 1.14, results["First Order Histogram::Median Absolute Deviation Index"], 0.01);
111  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Coefficient of Variation Index should be 0.812 with Large IBSI Phantom Image", 0.812, results["First Order Histogram::Coefficient of Variation Index"], 0.01);
112  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Quantile coefficient of Dispersion Index should be 0.6 with Large IBSI Phantom Image", 0.6, results["First Order Histogram::Quantile coefficient of Dispersion Index"], 0.01);
113  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Entropy Index should be 1.27 with Large IBSI Phantom Image", 1.27, results["First Order Histogram::Entropy Index"], 0.01);
114  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Uniformity Index should be 0.512 with Large IBSI Phantom Image", 0.512, results["First Order Histogram::Uniformity Index"], 0.01);
115  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Gradient should be 8 with Large IBSI Phantom Image", 8, results["First Order Histogram::Maximum Gradient"], 0.01);
116  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Gradient Index should be 3 with Large IBSI Phantom Image", 3, results["First Order Histogram::Maximum Gradient Index"], 0.01);
117  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Gradient should be -50 with Large IBSI Phantom Image", -50, results["First Order Histogram::Minimum Gradient"], 0.01);
118  CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Gradient Index should be 3 with Large IBSI Phantom Image", 1, results["First Order Histogram::Minimum Gradient Index"], 0.01);
119  }
120 
121 };
122 
123 MITK_TEST_SUITE_REGISTRATION(mitkGIFFirstOrderHistogramStatistics )
MITK_TEST_SUITE_REGISTRATION(mitkImageToItk)
#define MITK_INFO
Definition: mitkLogMacros.h:18
#define MITK_TEST(TESTMETHOD)
Adds a test to the current test suite.
static std::string GetTestDataFilePath(const std::string &testData)
Get the absolute path for test data.
static std::string GenerateLegacyFeatureNameWOEncoding(const FeatureID &id)
Test fixture for parameterized tests.