fattori_g/reg23Topograms
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Load CT (3D) volume from database

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* If database contains a CT, that can be imported.
* Full pipeline from DataView to itkImageProcessor.
* No checks on CT selection in DataView.
* No feedback of data loaded from RegistrationView to DataView.
This commit is contained in:
fattori_g
2022-06-24 23:28:36 +02:00
parent f9d3272784
commit 3da8413f4f
2 changed files with 207 additions and 118 deletions
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308
reg23Topograms/itkDTRrecon/itkImageProcessor.cpp
View File

@ -284,12 +284,12 @@ void itkImageProcessor::SetCustom_ImportTransform(double dTx,
} }
void itkImageProcessor::SetCustom_ProjectionCenterOffsetFixedAxes_IEC( void itkImageProcessor::SetCustom_ProjectionCenterOffsetFixedAxes_IEC(
double dX1, double dX1,
double dY1, double dY1,
double dZ1, double dZ1,
double dX2, double dX2,
double dY2, double dY2,
double dZ2) double dZ2)
{ {
typedef itk::Point<double, 3> PointType; typedef itk::Point<double, 3> PointType;
@ -369,6 +369,82 @@ void itkImageProcessor::SetCustom_2Dsize(int nX1, int nY1,int nX2,int nY2)
//TODO UPDATE TO FOLLOW //TODO UPDATE TO FOLLOW
} }
int itkImageProcessor::load3DSerieFromFiles( std::vector<std::string> v_fnames){
tPatOrientation m_PatOrientation
= tPatOrientation::NotDefined;
try
{
using ImageIOType = itk::GDCMImageIO;
ImageIOType::Pointer dicomIO = ImageIOType::New();
ImageSeriesReaderType3D::Pointer
imageSeriesReader3D = ImageSeriesReaderType3D::New();
imageSeriesReader3D->SetImageIO(dicomIO);
imageSeriesReader3D->SetFileNames(v_fnames);
imageSeriesReader3D->SetNumberOfWorkUnits(8);
imageSeriesReader3D->ForceOrthogonalDirectionOff(); // properly read CTs with gantry tilt
imageSeriesReader3D->Update();
if(v_fnames.size()>0){
gdcm::Reader R;
R.SetFileName(v_fnames.at(0).c_str());
if(!R.Read())
{
cerr<<"ERROR: cannot read file: "<<v_fnames.at(0).c_str()<<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(0x0018,0x5100), ds));
*std::remove(sTmpString, sTmpString + strlen(sTmpString), ' ') = 0;
if(!strcmp(sTmpString,ImageOrientationStrings[eImageOrientationType::HFS])){
m_PatOrientation = eImageOrientationType::HFS;
} else if(!strcmp(sTmpString,ImageOrientationStrings[eImageOrientationType::FFS])){
m_PatOrientation = eImageOrientationType::FFS;
} else {
m_PatOrientation = eImageOrientationType::NotDefined;
}
delete [] (sTmpString);
} else {
return -1;
}
CastFilterType3D::Pointer caster3D =
CastFilterType3D::New();
caster3D->SetInput(imageSeriesReader3D->GetOutput());
caster3D->Update();
m_VolumeSourceDupli->SetInputImage(caster3D->GetOutput());
m_VolumeSourceDupli->Update();
caster3D = NULL;
}
catch (itk::ExceptionObject & ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
InternalImageType::Pointer m_InputImage =
m_VolumeSourceDupli->GetOutput();
return
this->fill3DVolumeMeta(m_InputImage, m_PatOrientation);
}
int itkImageProcessor::load3DSerie(const char * pcDirName) int itkImageProcessor::load3DSerie(const char * pcDirName)
{ {
@ -493,9 +569,17 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
return EXIT_FAILURE; return EXIT_FAILURE;
} }
InternalImageType::Pointer m_InputImage = InternalImageType::Pointer m_InputImage =
m_VolumeSourceDupli->GetOutput(); m_VolumeSourceDupli->GetOutput();
return
this->fill3DVolumeMeta(m_InputImage, m_PatOrientation);
}
/** Fill Meta after 3D volume load */
int itkImageProcessor::fill3DVolumeMeta(
InternalImageType::Pointer m_InputImage,
tPatOrientation m_PatOrientation){
if(m_CTMetaInfo != NULL){ if(m_CTMetaInfo != NULL){
@ -597,9 +681,9 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
image3DIn = image3DIn =
m_3DInputChangeInformationToZero->GetOutput(); m_3DInputChangeInformationToZero->GetOutput();
return EXIT_SUCCESS; return EXIT_SUCCESS;
} }
const std::vector <double> itkImageProcessor::GetRTImportOffset() const std::vector <double> itkImageProcessor::GetRTImportOffset()
@ -1176,7 +1260,7 @@ void itkImageProcessor::InitializeProjector()
//AAAAAA TODOOOOO CERCA //AAAAAA TODOOOOO CERCA
ImageType3D::PointType pFakeIsoLPS = ImageType3D::PointType pFakeIsoLPS =
m_DRTImage1MetaInfo->GetProjectionOriginLPS(); m_DRTImage1MetaInfo->GetProjectionOriginLPS();
//ImageType3D::PointType pFakeIsoLPS = //ImageType3D::PointType pFakeIsoLPS =
// m_CTMetaInfo->GetProjectionOriginLPS( // m_CTMetaInfo->GetProjectionOriginLPS(
@ -1249,7 +1333,7 @@ void itkImageProcessor::InitializeProjector()
if(m_RTMetaInfo == NULL) if(m_RTMetaInfo == NULL)
{ {
ImageType3D::PointType pFakeIsoLPS = ImageType3D::PointType pFakeIsoLPS =
m_DRTImage2MetaInfo->GetProjectionOriginLPS(); m_DRTImage2MetaInfo->GetProjectionOriginLPS();
//ImageType3D::PointType pFakeIsoLPS = //ImageType3D::PointType pFakeIsoLPS =
// m_CTMetaInfo->GetProjectionOriginLPS( // m_CTMetaInfo->GetProjectionOriginLPS(
@ -1317,17 +1401,17 @@ void itkImageProcessor::InitializeProjector()
// // 2D Image 2 // // 2D Image 2
// interpolator2->SetProjectionAngle( // interpolator2->SetProjectionAngle(
// dtr * // dtr *
// m_DRTImage2MetaInfo->GetProjectionAngleLPS() ); // m_DRTImage2MetaInfo->GetProjectionAngleLPS() );
// interpolator2->SetFocalPointToIsocenterDistance( // interpolator2->SetFocalPointToIsocenterDistance(
// m_DRTImage2MetaInfo->GetSCD()); // m_DRTImage2MetaInfo->GetSCD());
// interpolator2->SetThreshold( // interpolator2->SetThreshold(
// m_DRTGeometryMetaInfo->GetIntensityThreshold() // m_DRTGeometryMetaInfo->GetIntensityThreshold()
// ); // );
// interpolator2->SetTransform(transform); // interpolator2->SetTransform(transform);
// interpolator2->Initialize(); // interpolator2->Initialize();
@ -1518,10 +1602,10 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
ImageType3D::PointType NominalIsocenterZero_wZcorrectionLPS; ImageType3D::PointType NominalIsocenterZero_wZcorrectionLPS;
NominalIsocenterZero_wZcorrectionLPS = NominalIsocenterZero_wZcorrectionLPS =
m_CTMetaInfo->GetProjectionOriginLPSZero( m_CTMetaInfo->GetProjectionOriginLPSZero(
m_DRTGeometryMetaInfo->GetProjectionCenter() m_DRTGeometryMetaInfo->GetProjectionCenter()
); );
std::cout<< "///////////////// PGEOM META BEG ///////////////" <<std::endl; std::cout<< "///////////////// PGEOM META BEG ///////////////" <<std::endl;
@ -1571,13 +1655,13 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
NominalIsocenter_wZcorrectionLPS//m_DRTImage1MetaInfo->GetProjectionOriginLPS() NominalIsocenter_wZcorrectionLPS//m_DRTImage1MetaInfo->GetProjectionOriginLPS()
); );
std::cout<<"Bounds1: " std::cout<<"Bounds1: "
<<vBounds.data()[0]<<" " <<vBounds.data()[0]<<" "
<<vBounds.data()[1]<<" " <<vBounds.data()[1]<<" "
<<vBounds.data()[2]<<" " <<vBounds.data()[2]<<" "
<<vBounds.data()[3]<<" " <<vBounds.data()[3]<<" "
<<vBounds.data()[4]<<" " <<vBounds.data()[4]<<" "
<<vBounds.data()[5]<<std::endl; <<vBounds.data()[5]<<std::endl;
m_DRTImage1MetaInfo->SetSizeWithBounds( m_DRTImage1MetaInfo->SetSizeWithBounds(
vBounds.data(), vBounds.data(),
@ -1593,8 +1677,8 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage1MetaInfo->GetCOV(), m_DRTImage1MetaInfo->GetCOV(),
NominalIsocenter_wZcorrectionLPS,//m_DRTImage1MetaInfo->GetProjectionOriginLPS(), NominalIsocenter_wZcorrectionLPS,//m_DRTImage1MetaInfo->GetProjectionOriginLPS(),
this->CalcProjectionAngleLPS( this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(), m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle1IEC() ), m_DRTGeometryMetaInfo->GetProjectionAngle1IEC() ),
//m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),// m_DRTImage1MetaInfo->GetProjectionAngleLPS(), //m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),// m_DRTImage1MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS Std_DRT2LPS
) )
@ -1605,9 +1689,9 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage1MetaInfo->SetImageDirectionsLPS( m_DRTImage1MetaInfo->SetImageDirectionsLPS(
CalcDRTImageDirections( CalcDRTImageDirections(
this->CalcProjectionAngleLPS( this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(), m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle1IEC()), m_DRTGeometryMetaInfo->GetProjectionAngle1IEC()),
//m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),//m_DRTImage1MetaInfo->GetProjectionAngleLPS(), //m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),//m_DRTImage1MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS) Std_DRT2LPS)
); );
@ -1648,15 +1732,15 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage2MetaInfo->SetProjectionOriginLPS( m_DRTImage2MetaInfo->SetProjectionOriginLPS(
CalibratedIsocenterLPS); CalibratedIsocenterLPS);
// m_CTMetaInfo->GetProjectionOriginLPS( // m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter2()) // m_DRTGeometryMetaInfo->GetProjectionCenter2())
// ); // );
m_DRTImage2MetaInfo->SetProjectionOriginLPSZero( m_DRTImage2MetaInfo->SetProjectionOriginLPSZero(
CalibratedIsocenterZeroLPS); CalibratedIsocenterZeroLPS);
// m_CTMetaInfo->GetProjectionOriginLPSZero( // m_CTMetaInfo->GetProjectionOriginLPSZero(
// m_DRTGeometryMetaInfo->GetProjectionCenter2()) // m_DRTGeometryMetaInfo->GetProjectionCenter2())
// ); // );
vBounds.clear(); vBounds.clear();
vBounds = m_CTMetaInfo->CalculateRegions( vBounds = m_CTMetaInfo->CalculateRegions(
@ -1664,12 +1748,12 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
); );
std::cout<<"Bounds2: " std::cout<<"Bounds2: "
<<vBounds.data()[0]<<" " <<vBounds.data()[0]<<" "
<<vBounds.data()[1]<<" " <<vBounds.data()[1]<<" "
<<vBounds.data()[2]<<" " <<vBounds.data()[2]<<" "
<<vBounds.data()[3]<<" " <<vBounds.data()[3]<<" "
<<vBounds.data()[4]<<" " <<vBounds.data()[4]<<" "
<<vBounds.data()[5]<<std::endl; <<vBounds.data()[5]<<std::endl;
m_DRTImage2MetaInfo->SetSizeWithBounds( m_DRTImage2MetaInfo->SetSizeWithBounds(
vBounds.data(), vBounds.data(),
@ -1683,9 +1767,9 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage2MetaInfo->GetCOV(), m_DRTImage2MetaInfo->GetCOV(),
NominalIsocenter_wZcorrectionLPS,//m_DRTImage2MetaInfo->GetProjectionOriginLPS(), NominalIsocenter_wZcorrectionLPS,//m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
this->CalcProjectionAngleLPS( this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(), m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) , m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) ,
//m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(), //m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS Std_DRT2LPS
) )
); );
@ -1693,8 +1777,8 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage2MetaInfo->SetImageDirectionsLPS( m_DRTImage2MetaInfo->SetImageDirectionsLPS(
CalcDRTImageDirections( CalcDRTImageDirections(
this->CalcProjectionAngleLPS( this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(), m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) , m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) ,
//m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(), //m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS) Std_DRT2LPS)
); );
@ -1773,8 +1857,8 @@ void itkImageProcessor::GetProjectionImages(){
ImageType3D::PointType pFakeIsoLPS = ImageType3D::PointType pFakeIsoLPS =
m_DRTImage1MetaInfo->GetProjectionOriginLPS(); m_DRTImage1MetaInfo->GetProjectionOriginLPS();
//m_CTMetaInfo->GetProjectionOriginLPS( //m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter()); // m_DRTGeometryMetaInfo->GetProjectionCenter());
std::cout<<"pFakeIsoLPS: "<<std::endl; std::cout<<"pFakeIsoLPS: "<<std::endl;
@ -1818,9 +1902,9 @@ void itkImageProcessor::GetProjectionImages(){
CurrTransform->GetAngleZ() CurrTransform->GetAngleZ()
); );
std::cout<< "itkImageProcessor::GetProjectionImages" <<std::endl; std::cout<< "itkImageProcessor::GetProjectionImages" <<std::endl;
// AAAAAAA TODOOO CERCAA // AAAAAAA TODOOO CERCAA
transform1 ->SetCenter( transform1 ->SetCenter(
m_DRTImage1MetaInfo->GetProjectionOriginLPSZero()); m_DRTImage1MetaInfo->GetProjectionOriginLPSZero());
@ -1851,65 +1935,65 @@ void itkImageProcessor::GetProjectionImages(){
//CurrTransform->SetComputeZYX(true); //CurrTransform->SetComputeZYX(true);
//CurrTransform->SetIdentity(); //CurrTransform->SetIdentity();
if(m_RTMetaInfo == NULL) if(m_RTMetaInfo == NULL)
{ {
ImageType3D::PointType pFakeIsoLPS = ImageType3D::PointType pFakeIsoLPS =
m_DRTImage2MetaInfo->GetProjectionOriginLPS(); m_DRTImage2MetaInfo->GetProjectionOriginLPS();
//m_CTMetaInfo->GetProjectionOriginLPS( //m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter()); // m_DRTGeometryMetaInfo->GetProjectionCenter());
std::cout<<"pFakeIsoLPS: "<<std::endl; std::cout<<"pFakeIsoLPS: "<<std::endl;
CurrTransform = CurrTransform =
CalculateInternalTransform( CalculateInternalTransform(
ZeroPoint, ZeroPoint,
ZeroPoint, ZeroPoint,
m_TransformMetaInfo->GetTranslations(), m_TransformMetaInfo->GetTranslations(),
m_TransformMetaInfo->GetRotations(), m_TransformMetaInfo->GetRotations(),
m_DRTImage2MetaInfo->GetProjectionOriginLPS(), m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
pFakeIsoLPS, pFakeIsoLPS,
ZeroPoint, ZeroPoint,
IECtoLPS_Directions IECtoLPS_Directions
);
std::cout<<"pFakeIsoLPS: "<<std::endl;
} else {
CurrTransform =
CalculateInternalTransform(
ZeroPoint ,
m_DRTGeometryMetaInfo->GetIECS2IECScannerR(),
m_TransformMetaInfo->GetTranslations(),
m_TransformMetaInfo->GetRotations(),
m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
m_RTMetaInfo->GetIsocenterLPS() - m_CTMetaInfo->GetImportOffset(),
m_CTMetaInfo->GetImportOffset(),
IECtoLPS_Directions
);
}
transform2->SetComputeZYX(true);
transform2->SetIdentity();
transform2->SetTranslation(
CurrTransform->GetTranslation());
transform2->SetRotation(
CurrTransform->GetAngleX(),
CurrTransform->GetAngleY(),
CurrTransform->GetAngleZ()
); );
std::cout<<"pFakeIsoLPS: "<<std::endl;
transform2 ->SetCenter( } else {
m_DRTImage2MetaInfo->GetProjectionOriginLPSZero());
CurrTransform =
CalculateInternalTransform(
ZeroPoint ,
m_DRTGeometryMetaInfo->GetIECS2IECScannerR(),
m_TransformMetaInfo->GetTranslations(),
m_TransformMetaInfo->GetRotations(),
m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
m_RTMetaInfo->GetIsocenterLPS() - m_CTMetaInfo->GetImportOffset(),
m_CTMetaInfo->GetImportOffset(),
IECtoLPS_Directions
);
}
//transform2 ->Print(std::cout);
transform2->SetComputeZYX(true);
transform2->SetIdentity();
transform2->SetTranslation(
CurrTransform->GetTranslation());
transform2->SetRotation(
CurrTransform->GetAngleX(),
CurrTransform->GetAngleY(),
CurrTransform->GetAngleZ()
);
transform2 ->SetCenter(
m_DRTImage2MetaInfo->GetProjectionOriginLPSZero());
//transform2 ->Print(std::cout);
@ -1928,10 +2012,10 @@ void itkImageProcessor::GetProjectionImages(){
imageDRT2In = filter2->GetOutput(); imageDRT2In = filter2->GetOutput();
std::cout<< "itkImageProcessor::GetProjectionImages END" <<std::endl; std::cout<< "itkImageProcessor::GetProjectionImages END" <<std::endl;
// std::cout<<"MMMMM: "<< // std::cout<<"MMMMM: "<<
// interpolator1->GetInverseTransform()->GetMatrix()<<std::endl; // interpolator1->GetInverseTransform()->GetMatrix()<<std::endl;
// std::cout<<"MMMMM: "<< // std::cout<<"MMMMM: "<<
// interpolator1->GetInverseTransform()->GetTranslation()<<std::endl; // interpolator1->GetInverseTransform()->GetTranslation()<<std::endl;
} }

17
reg23Topograms/itkDTRrecon/itkImageProcessor.h
View File

@ -73,6 +73,8 @@ public:
/** Input data load methods*/ /** Input data load methods*/
int load3DSerie(const char* ); int load3DSerie(const char* );
int load3DSerieFromFiles( std::vector<std::string> );
int load2D(const char *); int load2D(const char *);
void loadRTPlanInfo(double, double, double, double, double ,double); void loadRTPlanInfo(double, double, double, double, double ,double);
@ -151,13 +153,13 @@ public:
protected: protected:
/** Various pixel types */ /** Various pixel types */
using InternalPixelType = float; using InternalPixelType = float;
using PixelType2D = short; using PixelType2D = short;
using PixelType3D = short; using PixelType3D = short;
using OutputPixelType = unsigned char; using OutputPixelType = unsigned char;
using ImageType3D = itk::Image<PixelType3D, Dimension>; using ImageType3D = itk::Image<PixelType3D, Dimension>;
using InternalImageType = itk::Image<InternalPixelType, Dimension>; using InternalImageType = itk::Image<InternalPixelType, Dimension>;
itkImageProcessor(); itkImageProcessor();
virtual ~itkImageProcessor(); virtual ~itkImageProcessor();
@ -167,6 +169,9 @@ private:
itkImageProcessor(const Self&); //purposely not implemented itkImageProcessor(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented void operator=(const Self&); //purposely not implemented
/** Fill Meta after 3D volume load */
int fill3DVolumeMeta(InternalImageType::Pointer,
tPatOrientation);
/** Image types */ /** Image types */
using ImageType2D = itk::Image<PixelType3D, Dimension>; using ImageType2D = itk::Image<PixelType3D, Dimension>;