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cxtestSyntheticVolumeComparer.cpp
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
3 
4 Copyright (c) 2008-2014, SINTEF Department of Medical Technology
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32 
34 #include "cxVolumeHelpers.h"
35 #include "catch.hpp"
36 #include "cxImage.h"
37 #include "cxtestUtilities.h"
38 #include <vtkImageData.h>
40 #include "cxDataReaderWriter.h"
41 #include <QDir>
42 #include <QString>
43 #include "cxTypeConversions.h"
44 
45 namespace cxtest
46 {
47 
49 {
50 }
51 
53 {
54  mPhantom = phantom;
55  mNominalImage.reset();
56 }
57 
59 {
60  mTestImage = image;
61  mNominalImage.reset();
62 }
63 
64 //vtkImageDataPtr Utilities::create3DVtkImageData(Eigen::Array3i dim, const unsigned int voxelValue)
65 //{
66 // return cx::generateVtkImageData(dim, cx::Vector3D(1,1,1), voxelValue);
67 //}
68 
69 //cx::ImagePtr Utilities::create3DImage(Eigen::Array3i dim, const unsigned int voxelValue)
70 //{
71 // vtkImageDataPtr vtkImageData = create3DVtkImageData(dim, voxelValue);
72 // QString unique_string = qstring_cast(reinterpret_cast<long>(vtkImageData.GetPointer()));
73 // QString imagesUid = QString("TESTUID_%2_%1").arg(unique_string);
74 // cx::ImagePtr image(new cx::Image(imagesUid, vtkImageData));
75 
76 // return image;
77 //}
78 
79 
80 cx::ImagePtr SyntheticVolumeComparer::getNominalOutputImage() const
81 {
82  REQUIRE(mTestImage);
83 
84  if (!mNominalImage)
85  {
86  Eigen::Array3i dim(mTestImage->getBaseVtkImageData()->GetDimensions());
87  cx::Vector3D spacing(mTestImage->getBaseVtkImageData()->GetSpacing());
88  mNominalImage = cxtest::Utilities::create3DImage(dim, spacing, 0);
89  mNominalImage->get_rMd_History()->setRegistration(mTestImage->get_rMd());
90 
91  mPhantom->fillVolume(mNominalImage);
92  }
93 
94  return mNominalImage;
95 }
96 
98 {
99  float sse = this->getRMS();
100  if (this->getVerbose())
101  std::cout << "RMS value: " << sse << std::endl;
102  CHECK(sse < threshold);
103 }
104 
105 double SyntheticVolumeComparer::getRMS() const
106 {
107  double sse = cx::calculateRMSError(mTestImage->getBaseVtkImageData(), this->getNominalOutputImage()->getBaseVtkImageData());
108 // float sse = mPhantom->computeRMSError(mOutputData);
109 // std::cout << "RMS value: " << sse << std::endl;
110  return sse;
111 }
112 
114 {
115  cx::Vector3D c_n = calculateCentroid(this->getNominalOutputImage());
116  cx::Vector3D c_r = calculateCentroid(mTestImage);
117 
118  double difference = (c_n-c_r).norm();
119 
120  if (this->getVerbose())
121  std::cout << "c_n=[" << c_n << "] c_r=[" << c_r << "] diff=[" << difference << "]" << std::endl;
122 
123  CHECK(difference < val);
124 }
125 
127 {
128  double v_n = calculateMass(this->getNominalOutputImage());
129  double v_r = calculateMass(mTestImage);
130  double normalized_difference = fabs(v_n-v_r)/(v_n+v_r);
131 
132  if (this->getVerbose())
133  std::cout << "v_n=[" << v_n << "] v_r=[" << v_r << "] diff=[" << normalized_difference << "]" << std::endl;
134 
135  CHECK(normalized_difference<val);
136 }
137 
138 void SyntheticVolumeComparer::checkValueWithin(cx::Vector3D p_r, int lowerLimit, int upperLimit)
139 {
140  int val = this->getValue(mTestImage, p_r);
141  if (this->getVerbose())
142  std::cout << QString("p_r[%1]=%2, limit=[%3, %4]").arg(qstring_cast(p_r)).arg(val).arg(lowerLimit).arg(upperLimit) << std::endl;
143  CHECK(val>=lowerLimit);
144  CHECK(val<=upperLimit);
145 }
146 
147 double SyntheticVolumeComparer::getValue(cx::ImagePtr image, cx::Vector3D p_r)
148 {
149  vtkImageDataPtr raw = image->getBaseVtkImageData();
150  cx::Vector3D p_d = image->get_rMd().inv().coord(p_r);
151  Eigen::Array3d spacing(raw->GetSpacing());
152  Eigen::Array3i voxel = cx::round(p_r.array() / spacing).cast<int>();
153  double val = raw->GetScalarComponentAsDouble(voxel.data()[0],voxel.data()[1],voxel.data()[2], 0);
154  return val;
155 }
156 
158 {
159  cx::MetaImageReader().saveImage(this->getNominalOutputImage(), this->addFullPath(filename));
160 }
161 
163 {
164  cx::MetaImageReader().saveImage(mTestImage, this->addFullPath(filename));
165 }
166 
167 QString SyntheticVolumeComparer::addFullPath(QString filename)
168 {
169  QDir dir(QDir::homePath() + "/test/");
170  dir.mkdir(".");
171  QString fullFilename = dir.absoluteFilePath(filename);
172  return fullFilename;
173 }
174 
175 } // namespace cxtest
176 
177 
QString qstring_cast(const T &val)
double calculateMass(cx::ImagePtr image)
boost::shared_ptr< class Image > ImagePtr
Definition: cxDicomWidget.h:48
static cx::ImagePtr create3DImage(Eigen::Array3i dim=Eigen::Array3i(3, 3, 3), const unsigned int voxelValue=100)
void checkValueWithin(cx::Vector3D p_r, int lowerLimit, int upperLimit)
boost::shared_ptr< cxSyntheticVolume > cxSyntheticVolumePtr
cx::Vector3D calculateCentroid(cx::ImagePtr image)
void setPhantom(cx::cxSyntheticVolumePtr phantom)
double calculateRMSError(vtkImageDataPtr a, vtkImageDataPtr b)
void saveImage(ImagePtr image, const QString &filename)
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
vtkSmartPointer< class vtkImageData > vtkImageDataPtr
Reader for metaheader .mhd files.
Vector3D round(const Vector3D &a)
Definition: cxVector3D.cpp:96