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Merge branch 'scoutRTUIDevelREG' into 'ScoutRTUIDevel'

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MapTransformToNewOrigin and CalcInternalTransformV3 moved to another file,...

See merge request cpt_bioeng/drt!28
This commit is contained in:
via_r
2023-05-17 11:12:44 +02:00
parent 2a6a8d4922 ab29d81e5e
commit 8d2976ebbc
13 changed files with 1171 additions and 894 deletions
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2
reg23Topograms/itkDTRrecon/CMakeLists.txt
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@ -16,6 +16,7 @@ INCLUDE_DIRECTORIES(${GDCM_INCLUDE_DIRS})
SET(SRCS
itkImageProcessor.cpp
itkImageProcessorHelpers.cpp
vtkContourTopogramProjectionFilter.cxx
DRTMetaInformation.cpp
@ -23,6 +24,7 @@ SET(SRCS
SET(HDR
itkImageProcessor.h
itkImageProcessorHelpers.h
itkQtIterationUpdate.h
itkgSiddonJacobsRayCastInterpolateImageFunction.h
itkgSiddonJacobsRayCastInterpolateImageFunction.hxx

85
reg23Topograms/itkDTRrecon/DRTMetaInformation.cpp
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@ -474,6 +474,8 @@ DRTProjectionGeometryImageMetaInformation(){
this->m_ProjectionCenter.Fill(0.);
this->m_UseRotationsForHiddenTransform = true;
}
void
@ -517,25 +519,98 @@ RTGeometryMetaInformation
}
InternalTransformMetaInformation::InternalTransformMetaInformation(){
m_pCalProjCenter.Fill(0.);
m_pRTIsocenter.Fill(0.);
m_IECtoLPSDirs.SetIdentity();
}
void
InternalTransformMetaInformation
::PrintSelf(std::ostream& os, itk::Indent indent) const
{
Superclass::PrintSelf(os, indent);
}
InternalTransformMetaInformation
::~InternalTransformMetaInformation ()
{
}
R23MetaInformation::
R23MetaInformation (){
m_DegreeOfFreedom = tDegreeOfFreedomEnum::UNKNOWN;
}
void
R23MetaInformation
::PrintSelf(std::ostream& os, itk::Indent indent) const
{
Superclass::PrintSelf(os, indent);
}
R23MetaInformation
::~R23MetaInformation ()
{
}
TransformMetaInformation ::
TransformMetaInformation (){
m_Translations.Fill(0.);
m_HiddenTranslations.Fill(0.);
m_Rotations.Fill(0.);
m_HiddenRotations.Fill(0.);
m_UserRotations.Fill(0.);
m_UserTranslations.Fill(0.);
m_ReferenceTransform.Fill(0.);
//m_ReferenceTransform.Fill(0.);
m_CurrentTransform.Fill(0.);
//m_CurrentTransform.Fill(0.);
m_DegreeOfFreedom = tDegreeOfFreedomEnum::UNKNOWN;
// m_DegreeOfFreedom = tDegreeOfFreedomEnum::UNKNOWN;
}
TransformMetaInformation::PointType
TransformMetaInformation::GetT(){
PointType
pT;
pT[0] = m_UserTranslations[0] + m_HiddenTranslations[0];
pT[1] = m_UserTranslations[1] + m_HiddenTranslations[1];
pT[2] = m_UserTranslations[2] + m_HiddenTranslations[2];
return
pT;
}
TransformMetaInformation::PointType
TransformMetaInformation::TransformMetaInformation::GetR(){
PointType
pR;
pR[0] = m_UserRotations[0] + m_HiddenRotations[0];
pR[1] = m_UserRotations[1] + m_HiddenRotations[1];
pR[2] = m_UserRotations[2] + m_HiddenRotations[2];
return
pR;
}

136
reg23Topograms/itkDTRrecon/DRTMetaInformation.h
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@ -408,6 +408,10 @@ public:
itkSetMacro(ProjectionCenter, PointType);
itkGetMacro(ProjectionCenter, PointType);
itkSetMacro(UseRotationsForHiddenTransform, bool);
itkGetMacro(UseRotationsForHiddenTransform, bool);
protected:
double
@ -447,6 +451,9 @@ protected:
m_ProjectionCenterOffset2;
bool
m_UseRotationsForHiddenTransform;
/** Default Constructor **/
DRTProjectionGeometryImageMetaInformation ();
/** Default Destructor **/
@ -514,6 +521,107 @@ private:
};
class InternalTransformMetaInformation :
public itk::Object{
public:
/** standard typedefs **/
typedef InternalTransformMetaInformation Self;
typedef itk::Object Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::Point<double, 3> PointType;
typedef itk::Matrix<double,3,3> TransformMatrixType;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(InternalTransformMetaInformation, itk::Object);
/** object information streaming **/
void PrintSelf(std::ostream& os, itk::Indent indent) const;
itkSetMacro(pCalProjCenter,PointType);
itkSetMacro(pRTIsocenter,PointType);
itkSetMacro(IECtoLPSDirs,TransformMatrixType);
itkGetMacro(pCalProjCenter,PointType);
itkGetMacro(pRTIsocenter,PointType);
itkGetMacro(IECtoLPSDirs,TransformMatrixType);
protected:
PointType
m_pCalProjCenter,
m_pRTIsocenter;
TransformMatrixType
m_IECtoLPSDirs;
/** Default Constructor **/
InternalTransformMetaInformation ();
/** Default Destructor **/
virtual ~InternalTransformMetaInformation ();
private:
/** purposely not implemented **/
InternalTransformMetaInformation (const Self&);
/** purposely not implemented **/
void operator=(const Self&);
};
class R23MetaInformation :
public itk::Object{
public:
/** standard typedefs **/
typedef R23MetaInformation Self;
typedef itk::Object Superclass;
typedef itk::SmartPointer<Self> Pointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(R23MetaInformation, itk::Object);
/** object information streaming **/
void PrintSelf(std::ostream& os, itk::Indent indent) const;
itkSetEnumMacro(DegreeOfFreedom, tDegreeOfFreedomEnum);
itkGetEnumMacro(DegreeOfFreedom, tDegreeOfFreedomEnum);
protected:
tDegreeOfFreedomEnum
m_DegreeOfFreedom;
/** Default Constructor **/
R23MetaInformation ();
/** Default Destructor **/
virtual ~R23MetaInformation ();
private:
/** purposely not implemented **/
R23MetaInformation (const Self&);
/** purposely not implemented **/
void operator=(const Self&);
};
class TransformMetaInformation :
public itk::Object{
@ -535,11 +643,11 @@ public:
void PrintSelf(std::ostream& os, itk::Indent indent) const;
itkSetMacro(Translations,PointType);
itkGetMacro(Translations,PointType);
itkSetMacro(HiddenTranslations,PointType);
itkGetMacro(HiddenTranslations,PointType);
itkSetMacro(Rotations,PointType);
itkGetMacro(Rotations,PointType);
itkSetMacro(HiddenRotations,PointType);
itkGetMacro(HiddenRotations,PointType);
itkSetMacro(UserTranslations,PointType);
itkGetMacro(UserTranslations,PointType);
@ -547,29 +655,17 @@ public:
itkSetMacro(UserRotations,PointType);
itkGetMacro(UserRotations,PointType);
itkSetMacro(ReferenceTransform,TransformMatrixType);
itkGetMacro(ReferenceTransform,TransformMatrixType);
itkSetMacro(CurrentTransform,TransformMatrixType);
itkGetMacro(CurrentTransform,TransformMatrixType);
itkSetEnumMacro(DegreeOfFreedom, tDegreeOfFreedomEnum);
itkGetEnumMacro(DegreeOfFreedom, tDegreeOfFreedomEnum);
PointType GetT();
PointType GetR();
protected:
PointType
m_Translations,
m_Rotations,
m_HiddenTranslations,
m_HiddenRotations,
m_UserTranslations,
m_UserRotations;
TransformMatrixType
m_ReferenceTransform,
m_CurrentTransform;
tDegreeOfFreedomEnum
m_DegreeOfFreedom;
/** Default Constructor **/
TransformMetaInformation ();

72
reg23Topograms/itkDTRrecon/autoreg/itkMutualInformationTwoImageToOneImageMetric.hxx
View File

@ -93,33 +93,61 @@ MutualInformationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetValue()
itkExceptionMacro(<< "Fixed filter1 has not been assigned");
}
if (!this->m_Transform1) {
itkExceptionMacro(<< "m_Transform1 has not been assigned");
}
if (!this->m_Transform2) {
itkExceptionMacro(<< "m_Transform2 has not been assigned");
}
// std::cout<< "----- itkMutualInformationTwoImage GetValue -----" <<std::endl;
// std::cout<< "Mutual GetValue T1 :: center : " <<
// this->m_Transform1.GetPointer()->GetCenter() <<std::endl;
// std::cout<< "Mutual GetValue T1 :: Pars : " <<
// this->m_Transform1.GetPointer()->GetParameters() <<std::endl;
// std::cout<< "--------------------------------" <<std::endl;
this->m_Interpolator1->SetTransform(this->m_Transform1);
this->m_Interpolator1->Initialize();
this->m_Filter1->Update();
using InternalMetricType = itk::MattesMutualInformationImageToImageMetric<TFixedImage, TMovingImage>;
using NearestNeighborType = itk::NearestNeighborInterpolateImageFunction<TMovingImage, double>;
/*
* NearestNeighborType in our images results in not resolving for the cranio-caudal direction.
* in LPS-Z we are very much bound to the CT resolution, therefore if we take the Nearest Neighbor
* we simply do not explore that direction... and will always have an uncertainty of 1 slice thickness.
* */
//using NearestNeighborType = itk::NearestNeighborInterpolateImageFunction<TMovingImage, double>;
/*
* LinearInterpolateImageFunction performs better for us, performance degradation not noticeable.
* */
using LinearInterpType = itk::LinearInterpolateImageFunction<TMovingImage, double>;
//We need to set transform and parameters.
auto dummyTransform = TransformType::New();
auto dummyParameters = dummyTransform->GetParameters();
auto dummyInterpolator1 = NearestNeighborType::New();
auto dummyInterpolator1 = LinearInterpType::New();
auto metric1 = InternalMetricType::New();
metric1->SetTransform(dummyTransform);
metric1->SetTransformParameters(dummyParameters);
metric1->SetInterpolator(dummyInterpolator1);
auto fixedImageRegion1 = fixedImage1->GetBufferedRegion();
metric1->SetFixedImageRegion(fixedImageRegion1);
//auto fixedImageRegion1 = fixedImage1->GetBufferedRegion();
//metric1->SetFixedImageRegion(fixedImageRegion1);
/* We get the fixed image region from the parent class... */
metric1->SetFixedImageRegion(Superclass::GetFixedImageRegion1());
//std::cout<< "-----> Mutual :: fixedImageRegion1: "<< metric1->GetFixedImageRegion() << std::endl;
auto movingImageRegion = this->m_Filter1->GetOutput()->GetBufferedRegion();
unsigned int numberOfPixels = movingImageRegion.GetNumberOfPixels();
//auto numberOfSamples = static_cast<unsigned int>(numberOfPixels * 0.50); //100%
metric1->UseAllPixelsOn();
metric1->SetNumberOfHistogramBins(30);
// since we have a ROI, then we should not set allPixels to TRUE.
//metric1->UseAllPixelsOn();
metric1->SetNumberOfHistogramBins(50);
metric1->SetFixedImage(fixedImage1);
metric1->SetMovingImage(this->m_Filter1->GetOutput());
@ -132,26 +160,26 @@ MutualInformationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetValue()
this->m_Interpolator2->Initialize();
this->m_Filter2->Update();
auto dummyInterpolator2 = NearestNeighborType::New();
auto dummyInterpolator2 = LinearInterpType::New();
auto metric2 = InternalMetricType::New();
metric2->SetTransform(dummyTransform);
metric2->SetTransformParameters(dummyParameters);
metric2->SetInterpolator(dummyInterpolator2);
auto fixedImageRegion2 = fixedImage1->GetBufferedRegion();
metric2->SetFixedImageRegion(fixedImageRegion2);
// auto fixedImageRegion2 = fixedImage2->GetBufferedRegion();
// metric2->SetFixedImageRegion(fixedImageRegion2);
metric2->SetFixedImageRegion(Superclass::GetFixedImageRegion2());
//std::cout<< "-----> Mutual :: fixedImageRegion2: "<< metric2->GetFixedImageRegion() << std::endl;
movingImageRegion = this->m_Filter2->GetOutput()->GetBufferedRegion();
numberOfPixels = movingImageRegion.GetNumberOfPixels();
//numberOfSamples = static_cast<unsigned int>(numberOfPixels * 0.50); //100%
//%metric2->SetNumberOfSpatialSamples(numberOfSamples);
metric2->UseAllPixelsOn();
metric2->SetNumberOfHistogramBins(30);
//metric2->SetNumberOfSpatialSamples(numberOfSamples);
//metric2->UseAllPixelsOn();
metric2->SetNumberOfHistogramBins(50);
metric2->SetFixedImage(fixedImage2);
metric2->SetMovingImage(this->m_Filter2->GetOutput());
metric2->Initialize();
auto measure2 = metric2->GetValue(dummyParameters);
@ -163,13 +191,13 @@ MutualInformationTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetValue()
auto measure = (measure1 + measure2) / 2.0;
auto oldprecision = std::cout.precision();
std::cout.precision(std::numeric_limits<double>::digits10 + 2);
std::cout << "Measure1: " << measure1 << " Counts: " << this->m_NumberOfPixelsCounted << std::endl;
std::cout << "Measure2: " << measure2 << " Counts: " << this->m_NumberOfPixelsCounted << std::endl;
std::cout << "Measure: " << measure << std::endl;
std::cout << "=======================================================" << std::endl;
std::cout.precision(oldprecision);
// auto oldprecision = std::cout.precision();
// std::cout.precision(std::numeric_limits<double>::digits10 + 2);
// std::cout << "Measure1: " << measure1 << " Counts: " << this->m_NumberOfPixelsCounted << std::endl;
// std::cout << "Measure2: " << measure2 << " Counts: " << this->m_NumberOfPixelsCounted << std::endl;
// std::cout << "Measure: " << measure << std::endl;
// std::cout << "=======================================================" << std::endl;
// std::cout.precision(oldprecision);
return measure;
}

26
reg23Topograms/itkDTRrecon/autoreg/itkTwoProjectionImageRegistrationMethod.h
View File

@ -163,6 +163,10 @@ public:
itkSetObjectMacro(Transform2, TransformType);
itkGetConstObjectMacro(Transform2, TransformType);
/** Set/Get the IsocIECTransform. */
itkSetObjectMacro(IsocIECTransform, TransformType);
itkGetConstObjectMacro(IsocIECTransform, TransformType);
/** Set/Get the Interpolators. */
itkSetObjectMacro(Interpolator1, InterpolatorType);
itkSetObjectMacro(Interpolator2, InterpolatorType);
@ -170,8 +174,14 @@ public:
itkGetConstObjectMacro(Interpolator2, InterpolatorType);
/** Set/Get the Meta informations. */
itkSetObjectMacro(TransformMetaInfo, TransformMetaInformation);
itkGetConstObjectMacro(TransformMetaInfo, TransformMetaInformation);
itkSetObjectMacro(TransformMetaInfo, R23MetaInformation);
itkGetConstObjectMacro(TransformMetaInfo, R23MetaInformation);
itkSetObjectMacro(internalMeta1, InternalTransformMetaInformation);
itkGetConstObjectMacro(internalMeta1, InternalTransformMetaInformation);
itkSetObjectMacro(internalMeta2, InternalTransformMetaInformation);
itkGetConstObjectMacro(internalMeta2, InternalTransformMetaInformation);
/** Set/Get the output filters. */
itkSetObjectMacro(Filter1, ChangeInformationFilterType);
@ -236,8 +246,8 @@ protected:
itkSetMacro(LastOptimizerParameters, ParametersType);
/** Entry-point for internal ITK filter observer. **/
void OnInternalFilterProgressReceptor(itk::Object *caller,
const itk::EventObject &event);
// void OnInternalFilterProgressReceptor(itk::Object *caller,
// const itk::EventObject &event);
private:
@ -248,12 +258,18 @@ private:
FixedImageConstPointer m_FixedImage1;
FixedImageConstPointer m_FixedImage2;
TransformPointer m_IsocIECTransform;
TransformPointer m_Transform1;
TransformPointer m_Transform2;
InterpolatorPointer m_Interpolator1;
InterpolatorPointer m_Interpolator2;
TransformMetaInformation::Pointer
InternalTransformMetaInformation::Pointer
m_internalMeta1,
m_internalMeta2;
R23MetaInformation::Pointer
m_TransformMetaInfo;
ChangeInformationFilterPointer

77
reg23Topograms/itkDTRrecon/autoreg/itkTwoProjectionImageRegistrationMethod.hxx
View File

@ -38,7 +38,10 @@ TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::TwoProjectionIm
m_MovingImage = nullptr; // has to be provided by the user.
m_Transform1 = nullptr; // has to be provided by the user.
m_Transform2 = nullptr; // has to be provided by the user.
m_IsocIECTransform = nullptr;
m_TransformMetaInfo = nullptr; // has to be provided by the user.
m_internalMeta1 = nullptr;
m_internalMeta2 = nullptr;
m_Interpolator1 = nullptr; // has to be provided by the user.
m_Interpolator2 = nullptr; // has to be provided by the user.
m_Metric = nullptr; // has to be provided by the user.
@ -80,6 +83,7 @@ void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::SetFixedIm
m_FixedImageRegionDefined2 = true;
}
/*
* Initialize by setting the interconnects between components.
*/
@ -119,7 +123,8 @@ void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::Initialize
// Connect the transform to the Decorator.
auto* transformOutput = static_cast<TransformOutputType*>(this->ProcessObject::GetOutput(0));
transformOutput->Set(m_Transform1.GetPointer());
//transformOutput->Set(m_Transform1.GetPointer());
transformOutput->Set(m_IsocIECTransform.GetPointer());
if (!m_Interpolator1) {
itkExceptionMacro(<< "Interpolator1 is not present");
@ -141,13 +146,26 @@ void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::Initialize
itkExceptionMacro(<< "TransformMetaInfo is not present");
}
if (!m_internalMeta1) {
itkExceptionMacro(<< "internalMeta1 is not present");
}
if (!m_internalMeta2) {
itkExceptionMacro(<< "internalMeta1 is not present");
}
// Setup the metric
m_Metric->SetMovingImage(m_MovingImage);
m_Metric->SetFixedImage1(m_FixedImage1);
m_Metric->SetFixedImage2(m_FixedImage2);
m_Metric->SetTransform1(m_Transform1);
m_Metric->SetTransform2(m_Transform2);
m_Metric->SetIsocTransf(m_IsocIECTransform);
m_Metric->SetTransformMetaInfo(m_TransformMetaInfo);
m_Metric->SetinternalMeta1(m_internalMeta1);
m_Metric->SetinternalMeta2(m_internalMeta2);
m_Metric->SetFilter1(m_Filter1);
m_Metric->SetFilter2(m_Filter2);
@ -174,36 +192,37 @@ void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::Initialize
m_Optimizer->SetScales(m_Metric->GetWeightings());
m_Optimizer->SetCostFunction(m_Metric);
m_InitialOptimizerParameters = m_Metric->GetParameters();
m_InitialOptimizerParameters =
m_Metric->GetParameters();
m_Optimizer->SetInitialPosition(m_InitialOptimizerParameters);
}
template <typename TFixedImage, typename TMovingImage>
void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::OnInternalFilterProgressReceptor(
itk::Object *caller, const itk::EventObject &event)
{
itk::ProcessObject *filter = dynamic_cast<itk::ProcessObject *>(caller);
//template <typename TFixedImage, typename TMovingImage>
//void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::OnInternalFilterProgressReceptor(
// itk::Object *caller, const itk::EventObject &event)
//{
// itk::ProcessObject *filter = dynamic_cast<itk::ProcessObject *>(caller);
if(!itk::ProgressEvent().CheckEvent(&event) || !filter)
return;
// if(!itk::ProgressEvent().CheckEvent(&event) || !filter)
// return;
if (filter)
{
// double p = m_CurrentProgressStart;
// // filter->GetProgress() in [0;1]
// p += m_CurrentProgressSpan * filter->GetProgress();
// // NOTE: filter is buggy - not in [0;1] if multi-threading is activated!
// if (p > (m_CurrentProgressStart + m_CurrentProgressSpan))
// p = m_CurrentProgressStart + m_CurrentProgressSpan;
// TaskProgressInfo(m_CurrentProgressDirection, p);
// if (filter)
// {
//// double p = m_CurrentProgressStart;
//// // filter->GetProgress() in [0;1]
//// p += m_CurrentProgressSpan * filter->GetProgress();
//// // NOTE: filter is buggy - not in [0;1] if multi-threading is activated!
//// if (p > (m_CurrentProgressStart + m_CurrentProgressSpan))
//// p = m_CurrentProgressStart + m_CurrentProgressSpan;
//// TaskProgressInfo(m_CurrentProgressDirection, p);
// if (m_CancelRequest)
// filter->SetAbortGenerateData(true); // may be handled by filter
//// if (m_CancelRequest)
//// filter->SetAbortGenerateData(true); // may be handled by filter
std::cout << "Porca Madonna " << std::endl;
}
}
// std::cout << "OnInternalFilterProgressReceptor :: filter (TRUE) " << std::endl;
// }
//}
/*
* Starts the Registration Process
@ -212,22 +231,10 @@ template <typename TFixedImage, typename TMovingImage>
void TwoProjectionImageRegistrationMethod<TFixedImage, TMovingImage>::StartRegistration()
{
// typedef itk::MemberCommand<TwoProjectionImageRegistrationMethod> ITKCommandType;
// typedef ITKCommandType::Pointer MemberPointer ;
// ITKCommandType::Pointer cmd = ITKCommandType::New();
// itk::Command cmd= itk::Command::Pointer(this);
// cmd->SetCallbackFunction(this,
// (ITKCommandType::Pointer)&TwoProjectionImageRegistrationMethod::OnInternalFilterProgressReceptor);
itk::ProgressReporter progress(
this,
1, 1000,100);
// this->SetAbortGenerateData(true);
ParametersType empty(1);
empty.Fill(0.0);
try {

25
reg23Topograms/itkDTRrecon/autoreg/itkgTwoImageToOneImageMetric.h
View File

@ -40,6 +40,8 @@
#include <linux/limits.h>
#include <unistd.h>
#include <itkImageProcessorHelpers.h>
namespace itk {
/** \class gTwoImageToOneImageMetric
@ -169,6 +171,10 @@ public:
/** Get a pointer to the Transform2. */
itkGetConstObjectMacro(Transform2, TransformType);
itkSetObjectMacro(IsocTransf, TransformType);
itkGetObjectMacro(IsocTransf, TransformType);
/** Connect the Interpolator. */
itkSetObjectMacro(Interpolator1, InterpolatorType);
@ -185,10 +191,17 @@ public:
itkGetConstReferenceMacro(NumberOfPixelsCounted, unsigned long);
/** Connect the DRTGeometryMetaInfo. */
itkSetObjectMacro(TransformMetaInfo, TransformMetaInformation);
itkSetObjectMacro(TransformMetaInfo, R23MetaInformation);
/** Get a pointer to the DRTGeometryMetaInfo. */
itkGetConstObjectMacro(TransformMetaInfo, TransformMetaInformation);
itkGetConstObjectMacro(TransformMetaInfo, R23MetaInformation);
itkSetObjectMacro(internalMeta1, InternalTransformMetaInformation);
itkGetConstObjectMacro(internalMeta1, InternalTransformMetaInformation);
itkSetObjectMacro(internalMeta2, InternalTransformMetaInformation);
itkGetConstObjectMacro(internalMeta2, InternalTransformMetaInformation);
/** Set the region over which the metric will be computed */
itkSetMacro(FixedImageRegion1, FixedImageRegionType);
@ -261,6 +274,8 @@ protected:
mutable TransformPointer m_Transform1;
mutable TransformPointer m_Transform2;
mutable TransformPointer m_IsocTransf;
InterpolatorPointer m_Interpolator1;
InterpolatorPointer m_Interpolator2;
@ -274,9 +289,13 @@ protected:
mutable FixedImageMaskPointer m_FixedImageMask2;
mutable MovingImageMaskPointer m_MovingImageMask;
TransformMetaInformation::Pointer
R23MetaInformation::Pointer
m_TransformMetaInfo;
InternalTransformMetaInformation::Pointer
m_internalMeta1,
m_internalMeta2;
ChangeInformationFilterPointer
m_Filter1,
m_Filter2;

115
reg23Topograms/itkDTRrecon/autoreg/itkgTwoImageToOneImageMetric.hxx
View File

@ -32,6 +32,8 @@ gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::gTwoImageToOneImageMetric(
m_Transform1 = nullptr; // has to be provided by the user.
m_Transform2 = nullptr; // has to be provided by the user.
m_TransformMetaInfo = nullptr; // has to be provided by the user.
m_internalMeta1 = nullptr;
m_internalMeta2 = nullptr;
m_Interpolator1 = nullptr; // has to be provided by the user.
m_Interpolator2 = nullptr; // has to be provided by the user.
m_GradientImage = nullptr; // will receive the output of the filter;
@ -54,8 +56,18 @@ bool gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::SetTransformParameter
if (!m_Transform2) {
itkExceptionMacro(<< "Transform 2 has not been assigned");
}
if (!m_internalMeta1){
itkExceptionMacro(<< "m_internalMeta1 has not been assigned");
}
if (!m_internalMeta2){
itkExceptionMacro(<< "m_internalMeta2 has not been assigned");
}
if (!m_IsocTransf){
itkExceptionMacro(<< "m_IsocTransf has not been assigned");
}
auto transformParameters = m_Transform1->GetParameters();
//auto transformParameters = m_Transform1->GetParameters();
auto transformParameters = m_IsocTransf->GetParameters();
double TranslationAlongX = transformParameters[3];
double TranslationAlongY = transformParameters[4];
double TranslationAlongZ = transformParameters[5];
@ -63,6 +75,8 @@ bool gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::SetTransformParameter
double RotationAlongY = transformParameters[1];
double RotationAlongZ = transformParameters[2];
//std::cout << "m_IsocTransf PARS: "<< transformParameters <<std::endl;
switch (m_TransformMetaInfo->GetDegreeOfFreedom()) {
case X_ONLY:
TranslationAlongX = parameters[0];
@ -97,31 +111,82 @@ bool gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::SetTransformParameter
break;
}
// std::cout << "New Transform Parameters = " << std::endl;
// std::cout << "New Transform Parameters ISOC IEC = " << std::endl;
// std::cout << " Translation X = " << TranslationAlongX << " mm" << std::endl;
// std::cout << " Translation Y = " << TranslationAlongY << " mm" << std::endl;
// std::cout << " Translation Z = " << TranslationAlongZ << " mm" << std::endl;
// std::cout << " Rotation Along X = " << RotationAlongX / dtr << " deg" << std::endl;
// std::cout << " Rotation Along Y = " << RotationAlongY / dtr << " deg" << std::endl;
// std::cout << " Rotation Along Z = " << RotationAlongZ / dtr << " deg" << std::endl;
// std::cout << " Rotation Along X = " << RotationAlongX /*/ dtr*/ << " deg" << std::endl;
// std::cout << " Rotation Along Y = " << RotationAlongY /*/ dtr*/ << " deg" << std::endl;
// std::cout << " Rotation Along Z = " << RotationAlongZ /*/ dtr*/ << " deg" << std::endl;
// std::cout << "+++++++++++++++++++++++++++++++++++++++++++++++++++++++" << std::endl;
transformParameters[0] = RotationAlongX;
transformParameters[1] = RotationAlongY;
transformParameters[2] = RotationAlongZ;
transformParameters[3] = TranslationAlongX;
transformParameters[4] = TranslationAlongY;
transformParameters[5] = TranslationAlongZ;
bool transformValid = (std::abs(TranslationAlongX) < m_MaxTranslation) && (std::abs(TranslationAlongY) < m_MaxTranslation) && (std::abs(TranslationAlongZ) < m_MaxTranslation);
// individual R and T components of the IsoC transform
ImageType3D::PointType
pT;
pT[0] = TranslationAlongX;
pT[1] = TranslationAlongY;
pT[2] = TranslationAlongZ;
ImageType3D::PointType
pR;
pR[0] = RotationAlongX;
pR[1] = RotationAlongY;
pR[2] = RotationAlongZ;
// check if we are within tolerance
bool transformValid =
(std::abs(pT[0]) < m_MaxTranslation) &&
(std::abs(pT[1]) < m_MaxTranslation) &&
(std::abs(pT[2]) < m_MaxTranslation);
if (transformValid) {
m_Transform1->SetParameters(transformParameters);
m_Transform2->SetParameters(transformParameters);
/*
Here we calculate the transform for eack projection corresponding to the isocentric
one we are optimizing.
This calculation takes into account calibrated center of projection for each view.
*/
// Calculate internal transform1
TransformType::Pointer CurrTransform;
CurrTransform = CalculateInternalTransformV3(
pT,
pR,
m_internalMeta1->GetpCalProjCenter(),
m_internalMeta1->GetpRTIsocenter(),
m_internalMeta1->GetIECtoLPSDirs());
m_Transform1->SetIdentity();
m_Transform1->SetParameters(
CurrTransform->GetParameters());
m_Transform1->SetCenter(
m_internalMeta1->GetpCalProjCenter());
// std::cout<<"----- itkgTwoImageToOne SetTransformParameters -----"<<std::endl;
// std::cout << "m_Transform1 :: Center: "<< m_Transform1->GetCenter()<<std::endl;
// std::cout << "m_Transform1 :: Pars: "<< m_Transform1->GetParameters()<<std::endl;
// std::cout<< "--------------------------------" <<std::endl;
// Calculate internal transform2
CurrTransform = CalculateInternalTransformV3(
pT,
pR,
m_internalMeta2->GetpCalProjCenter(),
m_internalMeta2->GetpRTIsocenter(),
m_internalMeta2->GetIECtoLPSDirs());
m_Transform2->SetIdentity();
m_Transform2->SetParameters(
CurrTransform->GetParameters());
m_Transform2->SetCenter(
m_internalMeta2->GetpCalProjCenter());
} else {
std::cout << " Transform invalid, out of range!" << std::endl;
std::cout << "+++++++++++++++++++++++++++++++++++++++++++++++++++++++" << std::endl;
}
return transformValid;
}
@ -129,16 +194,23 @@ template <typename TFixedImage, typename TMovingImage>
void gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::Initialize()
{
if (!m_Transform1) {
if (!m_IsocTransf) {
itkExceptionMacro(<< "Transform is not present");
}
if (!m_Transform1) {
itkExceptionMacro(<< "Transform is not present");
itkExceptionMacro(<< "Transform1 is not present");
}
if (!m_Transform2) {
itkExceptionMacro(<< "Transform is not present");
itkExceptionMacro(<< "Transform2 is not present");
}
if(!m_internalMeta1) {
itkExceptionMacro(<< "m_internalMeta1 is not present");
}
if(!m_internalMeta2) {
itkExceptionMacro(<< "m_internalMeta2 is not present");
}
if (!m_Interpolator1) {
@ -237,7 +309,7 @@ unsigned int gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetNumberOfPa
break;
}
return m_Transform1->GetNumberOfParameters();
return m_IsocTransf->GetNumberOfParameters();
}
template <typename TFixedImage, typename TMovingImage>
@ -263,6 +335,7 @@ itk::Optimizer::ScalesType gTwoImageToOneImageMetric<TFixedImage, TMovingImage>:
weightings[2] = 1. / dtr;
break;
case SIX_DOF:
//G: ITHINKTHOSEARE FLIPPED!!
weightings[0] = 1.;
weightings[1] = 1.;
weightings[2] = 1.;
@ -279,10 +352,12 @@ itk::Optimizer::ScalesType gTwoImageToOneImageMetric<TFixedImage, TMovingImage>:
}
template <typename TFixedImage, typename TMovingImage>
typename gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::ParametersType gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetParameters() const
typename gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::
ParametersType gTwoImageToOneImageMetric<TFixedImage, TMovingImage>::GetParameters() const
{
ParametersType parametersTransform = m_Transform1->GetParameters(); //angleX, angleY, angleZ, transX, transY, transZ
// ParametersType parametersTransform = m_Transform1->GetParameters(); //angleX, angleY, angleZ, transX, transY, transZ
ParametersType parametersTransform = m_IsocTransf->GetParameters(); //angleX, angleY, angleZ, transX, transY, transZ
ParametersType parameters(this->GetNumberOfParameters());
switch (m_TransformMetaInfo->GetDegreeOfFreedom()) {
case X_ONLY:

1156
reg23Topograms/itkDTRrecon/itkImageProcessor.cpp
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131
reg23Topograms/itkDTRrecon/itkImageProcessor.h
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@ -51,6 +51,8 @@ gfattori 08.11.2021
#include "itkQtIterationUpdate.h"
#include "itkImageProcessorHelpers.h"
namespace itk
{
@ -76,15 +78,16 @@ public:
CommandIterationUpdate::Pointer
optimizerObserver;
/** Set number of logic CPU to be made available to interpolators*/
void SetNumberOfWorkingUnits(int iN);
/** Input data load methods*/
int load3DSerieFromFolder(const char* );
int load3DSerieFromFiles( std::vector<std::string> );
int unload3DVolumeAndMeta();
int load2D(const char *);
int unload2DAndMeta(int);
int query2DimageReconstructionDiameter(const char*);
//int query2DimageReconstructionDiameter(const char*);
void loadRTPlanInfo(double, double, double, double, double ,double);
int unloadRTPlanAndMeta();
@ -118,7 +121,6 @@ public:
tDegreeOfFreedomEnum GetDegreeOfFreedom();
void SetCustom_ProjectionCenterOffsetFixedAxes_IEC(double,double,double,double,double,double);
void SetCustom_ProjectionCenterFixedAxes_IEC(double,double,double);
/** Intensity threshold used for image projection,
@ -128,8 +130,16 @@ public:
/** Custom settings of the projection images */
void SetCustom_2Dres(double,double,double,double);
void SetCustom_2Dsize(int,int,int,int);
/** Custom transform to map IEC of imaging device into IEC-Support
* Tx Ty Tz [mm] Rx Ry Rz [deg]
*/
void SetCustom_ImportTransform(double, double, double,
double, double, double);
/** Should rotations be used when computing import offset and hidden transform? */
void SetUseRotationsForImportOffset(bool bVal);
void SetCustom_UpdateMetaInfo();
@ -137,21 +147,42 @@ public:
void SetInitialTranslations(double, double, double);
void SetInitialRotations(double, double, double);
/** Get transform parameters for 3D Volume */
void GetFinalTranslations(double&, double&, double&);
void GetFinalRotations(double&, double&, double&);
/** Set user transform parameters for 3D Volume in LPS*/
void SetUserTranslationsLPS(double, double, double);
void SetUserRotationsLPS(double, double, double);
/** Returns user components only of the autoReg
* */
Optimizer::ParametersType
GetFinalR23Parameters();
/** Initialize the registration pipeline*/
void InitializeRegistration(double, double, eDegreeOfFreedomType);
/** Start the registration process*/
int StartRegistration(std::string extraInfo);
/** Get transform parameters for 3D Volume */
double* GetTransformParameters();
///** Get transform parameters for 3D Volume */
/** Get the complete transform, likely for export to SRO.
* This includes user and hidden contributions.
* Transform center has to be specified, Zero would result
* in Isocentric transform with center at the RT Iso.
*/
TransformType::Pointer
GetCompleteIsocentricTransform(/*ImageType3D::PointType TransformCenter*/);
/** Get only the User component of the transform
* as parameters' list. Import offset and hidden not included.
* This can be use to update UI transform display
* ParametersType :: Rx Ry Rz Tx Ty Tz
*/
Optimizer::ParametersType
GetUserIsocentricTransform();
/** Return useful meta info for external use
* Consumer should check for nullptr...
*/
const CTVolumeImageMetaInformation::Pointer
GetCTMetaInfo();
const RTGeometryMetaInformation::Pointer
GetRTMetaInfo();
const DRTProjectionGeometryImageMetaInformation::Pointer
GetDRTGeoMetaInfo();
/** Initialize projection geometry */
void InitializeProjector();
@ -184,24 +215,26 @@ public:
void WriteProjectionImages();
void Write2DImages();
/** Auto Reg23 methods */
/** Get the current cost function value from the optimizer*/
double GetOptimizerValue();
/** Get the cost function value for the current transform*/
double GetCurrentMetricValue();
void SetROI(double, double, double, double);
/** Set Optimizer type */
void SetOptimizer(std::string);
/** Set Metric type */
void SetMetric(std::string);
/** Use full image as ROI */
void SetFullROI(bool);
/** Maximum number of iterations for the optimizer */
void SetMaxNumberOfIterations(int);
/** Define the region to be used as ROI on fixed images */
void SetRegionFixed1(int,int,int,int);
void SetRegionFixed2(int,int,int,int);
/** Optimizer which tries to find the minimn (Powell Optimizer)*/
using OptimizerType = itk::PowellOptimizer;
protected:
/** Various pixel types */
using InternalPixelType = float;
@ -232,10 +265,11 @@ private:
/** The following lines define each of the components used in the
registration: The transform, optimizer, metric, interpolator and
the registration method itself. */
using TransformType = itk::Euler3DTransform<double>;
using InterpolatorType = itk::gSiddonJacobsRayCastInterpolateImageFunction<InternalImageType, double>;
using ResampleFilterType = itk::ResampleImageFilter<InternalImageType, InternalImageType>;
/** Optimizer which tries to find the minimun (Powell Optimizer)*/
using OptimizerType = itk::PowellOptimizer;
/** Optimizer which tries to find the minimn (Powell Optimizer)*/
using AmoebaOptimizerType = itk::AmoebaOptimizer;
/** Optimizer which samples the whol space */
@ -264,41 +298,10 @@ private:
/** ITK to VTK filter */
using ITKtoVTKFilterType = itk::ImageToVTKImageFilter<OutputImageType>;
void
CalculateExternalUserTransform(
TransformType::Pointer transform,
DRTImageMetaInformation::Pointer imageMetaInfo);
// TransformType::Pointer
// CalculateInternalTransform(
// ImageType3D::PointType m_TranslationOffset,
// ImageType3D::PointType m_RotationOffset,
// ImageType3D::PointType m_TranslationUser,
// ImageType3D::PointType m_RotationUser,
// ImageType3D::PointType m_ProjectionTransformCenter,
// ImageType3D::PointType m_UserTransformCenter,
// ImageType3D::PointType m_OffsetTransformCenter,
// InternalImageType::DirectionType m_IECtoLPSDirections
// );
/* Calculate the transform used in siddon.
* The isocentric transform is mapped to the calibrated center of projection */
TransformType::Pointer
CalculateInternalTransformV2(
ImageType3D::PointType m_TranslationOffset,
ImageType3D::PointType m_RotationOffset,
ImageType3D::PointType m_TranslationUser,
ImageType3D::PointType m_RotationUser,
ImageType3D::PointType m_CalibratedProjectionCenter,
ImageType3D::PointType m_RTIsocenter,
InternalImageType::DirectionType m_IECtoLPSDirections
);
TransformType::Pointer
transform1,
transform2;
transform2,
IsocTransf;
InterpolatorType::Pointer
interpolator1,
@ -360,20 +363,6 @@ private:
);
// ImageType3D::PointType
// CalcDRTImageOffset(
// ImageType3D::PointType m_DRTOffset,
// double dAngle,
// InternalImageType::DirectionType stdDRT2LPS
// );
TransformType::Pointer
MapTransformToNewOrigin(
ImageType3D::PointType m_COR,
ImageType3D::PointType m_Translations,
ImageType3D::PointType m_Rotations
);
double
CalcProjectionAngleLPS(
tPatOrientation pOrient,
@ -407,9 +396,6 @@ private:
* m_Projection1VTKTransform,
* m_Projection2VTKTransform;
/*Transformation Parameters */
double dTransfParam[6];
/**
* Many meta containers
*/
@ -433,6 +419,12 @@ private:
TransformMetaInformation::Pointer
m_TransformMetaInfo;
R23MetaInformation::Pointer
m_r23MetaInfo;
InternalTransformMetaInformation::Pointer
m_InternalTransf1,
m_InternalTransf2;
double m_OptmizerValue;
int m_MaxNumberOfIterations;
@ -448,6 +440,9 @@ private:
bool m_UseMutualInformation;
bool m_UseDumptoFile;
int
iNWUnits;
};

165
reg23Topograms/itkDTRrecon/itkImageProcessorHelpers.cpp Normal file
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@ -0,0 +1,165 @@
#include "itkImageProcessorHelpers.h"
#include <gdcmReader.h>
#include <stdio.h>
namespace itk {
TransformType::Pointer
MapTransformToNewOrigin(
ImageType3D::PointType m_COR, // Center of rotation for the proj geometry. this is my new origin.
ImageType3D::PointType m_Translations,
ImageType3D::PointType m_Rotations
){
TransformType::Pointer InputTransform = TransformType::New();
InputTransform->SetComputeZYX(true);
InputTransform->SetIdentity();
TransformType::OutputVectorType translation;
translation[0] = m_Translations[0];
translation[1] = m_Translations[1];
translation[2] = m_Translations[2];
InputTransform->SetTranslation(translation);
const double dtr = (atan(1.0) * 4.0) / 180.0;
InputTransform->SetRotation(
dtr * m_Rotations[0],
dtr * m_Rotations[1],
dtr * m_Rotations[2]);
ImageType3D::PointType m_TransformOrigin;
m_TransformOrigin.Fill(0.);
InputTransform->SetCenter(
m_TransformOrigin );
ImageType3D::PointType NewOriginTranslations =
InputTransform->TransformPoint(m_COR);
ImageType3D::PointType DeltaNewOrigin =
NewOriginTranslations - m_COR;
TransformType::Pointer m_OutputTransform =
TransformType::New();
m_OutputTransform ->SetComputeZYX(true);
m_OutputTransform ->SetIdentity();
translation[0] = DeltaNewOrigin[0];
translation[1] = DeltaNewOrigin[1];
translation[2] = DeltaNewOrigin[2];
m_OutputTransform->SetTranslation(translation);
m_OutputTransform->SetRotation(
dtr * m_Rotations[0],
dtr * m_Rotations[1],
dtr * m_Rotations[2]);
m_OutputTransform->SetCenter(m_COR);
InputTransform = NULL;
return m_OutputTransform;
}
TransformType::Pointer
CalculateInternalTransformV3(
ImageType3D::PointType m_Translation, //IEC
ImageType3D::PointType m_Rotation, //IEC
ImageType3D::PointType m_CalibratedProjectionCenter, //LPS
ImageType3D::PointType m_RTIsocenter, //LPS
InternalImageType::DirectionType m_IECtoLPSDirections
)
{
//Convert all inputs into LPS
ImageType3D::PointType m_TLPS =
m_IECtoLPSDirections * m_Translation;
ImageType3D::PointType m_RLPS =
m_IECtoLPSDirections * m_Rotation;
// Map offset to the projection center
TransformType::Pointer m_outputTransform =
MapTransformToNewOrigin (
m_CalibratedProjectionCenter - m_RTIsocenter,
m_TLPS,
m_RLPS
);
m_outputTransform->SetCenter(m_CalibratedProjectionCenter);
return m_outputTransform;
}
const char* queryStationName(const char* pcFName){
static std::string buffer;
/* Check if we can open the file */
gdcm::Reader R;
R.SetFileName(pcFName);
if(!R.Read())
{std::cerr<<"ERROR: cannot read file: "<<pcFName<<std::endl;
return "\n";
}
const gdcm::File &file = R.GetFile();
const gdcm::DataSet &ds = file.GetDataSet();
std::string s (gGetStringValueFromTag(gdcm::Tag(0x0008,0x1010), ds));
std::copy(s.rbegin(), s.rend(), std::back_inserter(buffer));
std::reverse(buffer.begin(),buffer.end());
return buffer.c_str();
}
int query2DimageReconstructionDiameter(const char *pcFName){
/* Check if we can open the file */
gdcm::Reader R;
R.SetFileName(pcFName);
if(!R.Read())
{std::cerr<<"ERROR: cannot read file: "<<pcFName<<std::endl;
return -1;
}
const gdcm::File &file = R.GetFile();
const gdcm::DataSet &ds = file.GetDataSet();
char* sTmpString = new char [255];
strcpy( sTmpString,gGetStringValueFromTag(gdcm::Tag(0x0018,0x1100), ds));
return std::atoi(sTmpString);
}
//FUNCTION DECLARATION NECESSARY FOR COPY/PASTE FROM vtkGDCMImageReader
// const char *gGetStringValueFromTag(const gdcm::Tag& t, const gdcm::DataSet& ds);
const char *gGetStringValueFromTag(const gdcm::Tag& t, const gdcm::DataSet& ds)
{
static std::string buffer;
buffer = ""; // cleanup previous call
if( ds.FindDataElement( t ) )
{
const gdcm::DataElement& de = ds.GetDataElement( t );
const gdcm::ByteValue *bv = de.GetByteValue();
if( bv ) // Can be Type 2
{
buffer = std::string( bv->GetPointer(), bv->GetLength() );
// Will be padded with at least one \0
}
}
// Since return is a const char* the very first \0 will be considered
return buffer.c_str();
}
}

55
reg23Topograms/itkDTRrecon/itkImageProcessorHelpers.h Normal file
View File

@ -0,0 +1,55 @@
#ifndef ITKIMAGEPROCESSORHELPERS_H
#define ITKIMAGEPROCESSORHELPERS_H
#include "itkEuler3DTransform.h"
#include "itkImage.h"
#include "itkEuler3DTransform.h"
#include "itkCommand.h"
#include "itkObject.h"
#include "itkObjectFactory.h"
#include <gdcmTag.h>
#include <gdcmDataSet.h>
namespace itk
{
using TransformType = itk::Euler3DTransform<double>;
constexpr static unsigned int Dimension = 3;
using PixelType3D = short;
using InternalPixelType = float;
using ImageType3D = itk::Image<PixelType3D, Dimension>;
using InternalImageType = itk::Image<InternalPixelType, Dimension>;
TransformType::Pointer
MapTransformToNewOrigin(
ImageType3D::PointType m_COR,
ImageType3D::PointType m_Translations,
ImageType3D::PointType m_Rotations
);
TransformType::Pointer
CalculateInternalTransformV3(
ImageType3D::PointType m_Translation,
ImageType3D::PointType m_Rotation,
ImageType3D::PointType m_CalibratedProjectionCenter,
ImageType3D::PointType m_RTIsocenter,
InternalImageType::DirectionType m_IECtoLPSDirections
);
const char *gGetStringValueFromTag(const gdcm::Tag& t, const gdcm::DataSet& ds);
int query2DimageReconstructionDiameter(const char*);
const char* queryStationName(const char*);
}
#endif

14
reg23Topograms/itkDTRrecon/itkQtIterationUpdate.h
View File

@ -118,11 +118,17 @@ public:
std::cout.precision(oldprecision);
std::cout << "Position: " << optimizer->GetCurrentPosition() << std::endl;
// objIterUpdate->onIteration(
// optimizer->GetCurrentIteration()+1,
// optimizer->GetCurrentPosition()[0],
// optimizer->GetCurrentPosition()[2],
// -optimizer->GetCurrentPosition()[1]
// );
objIterUpdate->onIteration(
optimizer->GetCurrentIteration()+1,
optimizer->GetCurrentPosition()[0],
optimizer->GetCurrentPosition()[2],
-optimizer->GetCurrentPosition()[1]
optimizer->GetCurrentPosition()[1],
optimizer->GetCurrentPosition()[2]
);
}
return;
@ -172,7 +178,9 @@ public:
os->precision(std::numeric_limits<double>::digits10 + 2);
*os << optimizer->GetCurrentValue();
os->precision(oldprecision);
*os << "\t" << position[0] << "\t" << position[2] << "\t" << -position[1] << std::endl;
//*os << "\t" << position[0] << "\t" << position[2] << "\t" << -position[1] << std::endl;
*os << "\t" << position[0] << "\t" << position[1] << "\t" << position[2] << std::endl;
}
return;
}