Fraxinus  17.12-rc4
An IGT application
cxtestSyntheticReconstructInput.cpp
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1 /*=========================================================================
2 This file is part of CustusX, an Image Guided Therapy Application.
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32 
34 #include "cxDummyTool.h"
37 #include "cxTypeConversions.h"
38 #include "cxMathUtils.h"
39 
40 
41 namespace cxtest
42 {
43 
45 {
46  mBounds = cx::Vector3D(99,99,99);
47 
48  mProbeMovementDefinition.mRangeNormalizedTranslation = cx::Vector3D::UnitX();
49 // mProbeMovementDefinition.mRangeAngle = M_PI/8;
50 // mProbeMovementDefinition.mSteps = 100;
51  mProbeMovementDefinition.mRangeAngle = 0;
52  mProbeMovementDefinition.mSteps = 200;
53 
54  mProbe = cx::DummyToolTestUtilities::createProbeDefinitionLinear(100, 100, Eigen::Array2i(200,200));
55 }
56 
58 {
59  mProbeMovementDefinition.mRangeNormalizedTranslation = cx::Vector3D::UnitX() * range;
60 }
62 {
63  mProbeMovementDefinition.mRangeAngle = range;
64 }
66 {
67  mProbeMovementDefinition.mSteps = steps;
68 }
70 {
71  mProbe = probe;
72 }
73 
75 {
76  // factors controlling sample rate:
77  // - output volume spacing
78  // - probe plane in-plane spacing
79  // - probe planes spacing (between the planes)
80  //
81  // set all these rates to the input spacing:
82 
83  mBounds = cx::Vector3D::Ones() * size;
84  mProbe = cx::DummyToolTestUtilities::createProbeDefinitionLinear(size, size, Eigen::Array2i(1,1)*(int(cx::roundAwayFromZero(size/spacing))+1));
85  mProbeMovementDefinition.mRangeNormalizedTranslation = cx::Vector3D::UnitX();
86  mProbeMovementDefinition.mRangeAngle = 0;
87  mProbeMovementDefinition.mSteps = size/spacing+1;
88 }
89 
91 {
92  QString indent("");
93  mPhantom->printInfo();
94  std::cout << indent << "Probe:\n" << streamXml2String(mProbe) << std::endl;
95  std::cout << indent << "ProbeMovement RangeNormalizedTranslation: " << mProbeMovementDefinition.mRangeNormalizedTranslation << std::endl;
96  std::cout << indent << "ProbeMovement RangeAngle: " << mProbeMovementDefinition.mRangeAngle << std::endl;
97  std::cout << indent << "ProbeMovement Steps: " << mProbeMovementDefinition.mSteps<< std::endl;
98 }
99 
101 {
102  mPhantom.reset(new cx::cxSimpleSyntheticVolume(mBounds));
103 }
104 
106 {
107  mPhantom.reset(new cxtest::SphereSyntheticVolume(mBounds));
108 }
109 
111 {
112 
113 }
114 
115 std::vector<cx::Transform3D> SyntheticReconstructInput::generateFrames_rMt_tilted()
116 {
117  cx::Vector3D p0(mBounds[0]/2, mBounds[1]/2, 0); //probe starting point. pointing along z
118  cx::Vector3D range_translation = mBounds[0] * mProbeMovementDefinition.mRangeNormalizedTranslation;
119  double range_angle = mProbeMovementDefinition.mRangeAngle;
120  int steps = mProbeMovementDefinition.mSteps;
121 
122  // generate transforms from tool to reference.
123  return this->generateFrames(p0,
124  range_translation,
125  range_angle,
126  Eigen::Vector3d::UnitY(),
127  steps);
128 }
129 
134 std::vector<cx::Transform3D> SyntheticReconstructInput::generateFrames(cx::Vector3D p0,
135  cx::Vector3D range_translation,
136  double range_angle,
137  cx::Vector3D rotation_axis,
138  int steps)
139 {
140  // generate transforms from tool to reference.
141  std::vector<cx::Transform3D> planes;
142  for(int i = 0; i < steps; ++i)
143  {
144  double R = steps-1;
145  double t = (i-R/2)/R; // range [-0.5 .. 0.5]
146  cx::Transform3D transform = cx::Transform3D::Identity();
147  transform.translation() = p0 + range_translation*t;
148  transform.rotate(Eigen::AngleAxisd(t*range_angle, rotation_axis));
149  planes.push_back(transform);
150  }
151  return planes;
152 }
153 
155 {
156  cx::Vector3D p0(mBounds[0]/2, mBounds[1]/2, 0); //probe starting point. pointing along z
157  cx::Vector3D range_translation = mBounds[0] * mProbeMovementDefinition.mRangeNormalizedTranslation;
158  double range_angle = mProbeMovementDefinition.mRangeAngle;
159  int steps_full = 3*mProbeMovementDefinition.mSteps;
160 
161  // generate oversampled list of positions, for use both in tracking and imaging.
162  std::vector<cx::Transform3D> rMt_full;
163  rMt_full = this->generateFrames(p0,
164  range_translation,
165  range_angle,
166  Eigen::Vector3d::UnitY(),
167  steps_full);
168 
170 
171  // sample out tracking positions from the full list
172  for (unsigned i=0; i<steps_full; i+=2)
173  {
174  cx::TimedPosition pos;
175  pos.mTime = i;
176  pos.mPos = rMt_full[i]; // TODO: skrell av rMpr
177  result.mPositions.push_back(pos);
178  }
179 
180  // sample out image frames from the full list
181  std::vector<vtkImageDataPtr> frames;
182  for (unsigned i=0; i<steps_full; i+=3)
183  {
184  cx::TimedPosition pos;
185  pos.mTime = i;
186  result.mFrames.push_back(pos);
187 
188  frames.push_back(mPhantom->sampleUsData(rMt_full[i], mProbe));
189  }
190  result.mUsRaw = cx::USFrameData::create("virtual", frames);
191 
192  // fill rest of info
193  result.rMpr = cx::Transform3D::Identity(); // if <>Identity, remember to also change mPositions
194  result.mProbeUid = "testProbe";
195  result.mProbeDefinition.setData(mProbe);
196 
197  return result;
198 }
199 
201 {
202  std::vector<cx::Transform3D> planes = this->generateFrames_rMt_tilted();
203 // std::cout << "Starting sampling\n";
205  retval = mPhantom->sampleUsData(planes, mProbe, dMr);
206 // std::cout << "Done sampling\n";
207  return retval;
208 }
209 
210 
211 } // namespace cxtest
212 
One position with timestamp.
Transform3D Transform3D
Transform3D is a representation of an affine 3D transform.
cx::USReconstructInputData generateSynthetic_USReconstructInputData()
std::vector< TimedPosition > mFrames
void setOverallBoundsAndSpacing(double size, double spacing)
double roundAwayFromZero(double val)
Definition: cxMathUtils.cpp:35
cx::ProcessedUSInputDataPtr generateSynthetic_ProcessedUSInputData(cx::Transform3D dMr)
Transform3D rMpr
patient registration
std::vector< TimedPosition > mPositions
Eigen::Vector3d Vector3D
Vector3D is a representation of a point or vector in 3D.
Definition: cxVector3D.h:63
Definition of characteristics for an Ultrasound Probe Sector.
QString streamXml2String(T &val)
boost::shared_ptr< class ProcessedUSInputData > ProcessedUSInputDataPtr
USFrameDataPtr mUsRaw
All imported US data frames with pointers to each frame.
static USFrameDataPtr create(ImagePtr inputFrameData)
float4 transform(float16 matrix, float4 voxel)
static ProbeDefinition createProbeDefinitionLinear(double depth=40, double width=50, Eigen::Array2i frameSize=Eigen::Array2i(80, 40))
Definition: cxDummyTool.cpp:67
void setData(ProbeDefinition data)