fattori_g/reg23Topograms
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Merge branch 'dicomNet' into 'master'

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Basic Functionality - UI, DCMDB, DCMNet

See merge request cpt_bioeng/drt!11
This commit is contained in:
fattori_g
2022-06-29 14:22:50 +00:00
parent 496bb08c27 b91ca7c5e9
commit d05205ca88
4 changed files with 244 additions and 125 deletions
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9
reg23Topograms/itkDTRrecon/CMakeLists.txt
View File

@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8.8)
cmake_minimum_required(VERSION 2.8.12)
SET(LIB_NAME itkDTRrecon)
@ -10,7 +10,6 @@ find_package(VTK REQUIRED)
INCLUDE_DIRECTORIES(${VTK_INCLUDE_DIRS})
FIND_PACKAGE(GDCM REQUIRED)
include(${GDCM_USE_FILE})
INCLUDE_DIRECTORIES(${GDCM_INCLUDE_DIRS})
SET(SRCS
@ -34,7 +33,7 @@ SET(LINK_LIBS
${LIB_NAME}
${VTK_LIBRARIES}
${ITK_LIBRARIES}
${GDCM_LIBRARIES}
gdcmMSFF
)
TARGET_LINK_LIBRARIES(
@ -45,3 +44,7 @@ TARGET_LINK_LIBRARIES(
target_include_directories (${LIB_NAME}
PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}
)
set(EXTRA_LIBS ${EXTRA_LIBS} itkDTRrecon)
set(EXTRA_LIBS ${EXTRA_LIBS} PARENT_SCOPE)

339
reg23Topograms/itkDTRrecon/itkImageProcessor.cpp
View File

@ -22,6 +22,7 @@ gfattori 08.11.2021
#include "itkMatrix.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkOrientImageFilter.h"
#include <gdcmIPPSorter.h>
#include <string>
@ -284,12 +285,12 @@ void itkImageProcessor::SetCustom_ImportTransform(double dTx,
}
void itkImageProcessor::SetCustom_ProjectionCenterOffsetFixedAxes_IEC(
double dX1,
double dY1,
double dZ1,
double dX2,
double dY2,
double dZ2)
double dX1,
double dY1,
double dZ1,
double dX2,
double dY2,
double dZ2)
{
typedef itk::Point<double, 3> PointType;
@ -369,8 +370,108 @@ void itkImageProcessor::SetCustom_2Dsize(int nX1, int nY1,int nX2,int nY2)
//TODO UPDATE TO FOLLOW
}
int itkImageProcessor::load3DSerieFromFiles( std::vector<std::string> v_fnames){
int itkImageProcessor::load3DSerie(const char * pcDirName)
tPatOrientation m_PatOrientation
= tPatOrientation::NotDefined;
/* Since are not sure DB indexer to sort images,
* we run the IPP sorter here. */
using IppSorterType = gdcm::IPPSorter;
IppSorterType ZSorter;
ZSorter.SetComputeZSpacing( true );
ZSorter.SetZSpacingTolerance( 1e-3 );
bool b = ZSorter.Sort(v_fnames);
if( !b )
{
std::cerr << "itkImageProcessor::load3DSerieFromFiles :: Failed to sort files based on IPP." << std::endl;
return EXIT_FAILURE;
}
/* Some debugging output */
//std::cout << "Sorting succeeded:" << std::endl;
//ZSorter.Print( std::cout );
//std::cout << "Found z-spacing:" << std::endl;
//std::cout << ZSorter.GetZSpacing() << std::endl;
const std::vector<std::string> & v_sortedFnames =
ZSorter.GetFilenames();
try
{
using ImageIOType = itk::GDCMImageIO;
ImageIOType::Pointer dicomIO = ImageIOType::New();
ImageSeriesReaderType3D::Pointer
imageSeriesReader3D = ImageSeriesReaderType3D::New();
imageSeriesReader3D->SetImageIO(dicomIO);
imageSeriesReader3D->SetFileNames(v_sortedFnames);
//imageSeriesReader3D->SetNumberOfWorkUnits(8);
imageSeriesReader3D->ForceOrthogonalDirectionOff(); // properly read CTs with gantry tilt
//imageSeriesReader3D->SetSpacingWarningRelThreshold();
imageSeriesReader3D->Update();
if(v_fnames.size()>0){
gdcm::Reader R;
R.SetFileName(v_sortedFnames.at(0).c_str());
if(!R.Read())
{
cerr<<"ERROR: cannot read file: "<<v_sortedFnames.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::load3DSerieFromFolder(const char * pcDirName)
{
using NamesGeneratorType = itk::GDCMSeriesFileNames;
@ -402,7 +503,7 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
else
{
std::cout << "No DICOMs in: " << pcDirName << std::endl;
return EXIT_SUCCESS;
return EXIT_FAILURE;
}
while (seriesItr != seriesEnd)
@ -467,7 +568,7 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
m_PatOrientation = eImageOrientationType::NotDefined;
}
free (sTmpString);
delete [] (sTmpString);
} else {
return -1;
}
@ -493,9 +594,17 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
return EXIT_FAILURE;
}
InternalImageType::Pointer m_InputImage =
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){
@ -597,9 +706,9 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
image3DIn =
m_3DInputChangeInformationToZero->GetOutput();
return EXIT_SUCCESS;
}
const std::vector <double> itkImageProcessor::GetRTImportOffset()
@ -1176,7 +1285,7 @@ void itkImageProcessor::InitializeProjector()
//AAAAAA TODOOOOO CERCA
ImageType3D::PointType pFakeIsoLPS =
m_DRTImage1MetaInfo->GetProjectionOriginLPS();
m_DRTImage1MetaInfo->GetProjectionOriginLPS();
//ImageType3D::PointType pFakeIsoLPS =
// m_CTMetaInfo->GetProjectionOriginLPS(
@ -1249,7 +1358,7 @@ void itkImageProcessor::InitializeProjector()
if(m_RTMetaInfo == NULL)
{
ImageType3D::PointType pFakeIsoLPS =
m_DRTImage2MetaInfo->GetProjectionOriginLPS();
m_DRTImage2MetaInfo->GetProjectionOriginLPS();
//ImageType3D::PointType pFakeIsoLPS =
// m_CTMetaInfo->GetProjectionOriginLPS(
@ -1317,17 +1426,17 @@ void itkImageProcessor::InitializeProjector()
// // 2D Image 2
// interpolator2->SetProjectionAngle(
// dtr *
// m_DRTImage2MetaInfo->GetProjectionAngleLPS() );
// interpolator2->SetFocalPointToIsocenterDistance(
// m_DRTImage2MetaInfo->GetSCD());
// interpolator2->SetThreshold(
// m_DRTGeometryMetaInfo->GetIntensityThreshold()
// );
// interpolator2->SetTransform(transform);
// interpolator2->Initialize();
// // 2D Image 2
// interpolator2->SetProjectionAngle(
// dtr *
// m_DRTImage2MetaInfo->GetProjectionAngleLPS() );
// interpolator2->SetFocalPointToIsocenterDistance(
// m_DRTImage2MetaInfo->GetSCD());
// interpolator2->SetThreshold(
// m_DRTGeometryMetaInfo->GetIntensityThreshold()
// );
// interpolator2->SetTransform(transform);
// interpolator2->Initialize();
@ -1518,10 +1627,10 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
ImageType3D::PointType NominalIsocenterZero_wZcorrectionLPS;
NominalIsocenterZero_wZcorrectionLPS =
m_CTMetaInfo->GetProjectionOriginLPSZero(
m_DRTGeometryMetaInfo->GetProjectionCenter()
);
NominalIsocenterZero_wZcorrectionLPS =
m_CTMetaInfo->GetProjectionOriginLPSZero(
m_DRTGeometryMetaInfo->GetProjectionCenter()
);
std::cout<< "///////////////// PGEOM META BEG ///////////////" <<std::endl;
@ -1571,13 +1680,13 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
NominalIsocenter_wZcorrectionLPS//m_DRTImage1MetaInfo->GetProjectionOriginLPS()
);
std::cout<<"Bounds1: "
std::cout<<"Bounds1: "
<<vBounds.data()[0]<<" "
<<vBounds.data()[1]<<" "
<<vBounds.data()[2]<<" "
<<vBounds.data()[3]<<" "
<<vBounds.data()[4]<<" "
<<vBounds.data()[5]<<std::endl;
<<vBounds.data()[1]<<" "
<<vBounds.data()[2]<<" "
<<vBounds.data()[3]<<" "
<<vBounds.data()[4]<<" "
<<vBounds.data()[5]<<std::endl;
m_DRTImage1MetaInfo->SetSizeWithBounds(
vBounds.data(),
@ -1593,8 +1702,8 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage1MetaInfo->GetCOV(),
NominalIsocenter_wZcorrectionLPS,//m_DRTImage1MetaInfo->GetProjectionOriginLPS(),
this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle1IEC() ),
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle1IEC() ),
//m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),// m_DRTImage1MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS
)
@ -1605,9 +1714,9 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage1MetaInfo->SetImageDirectionsLPS(
CalcDRTImageDirections(
this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle1IEC()),
//m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),//m_DRTImage1MetaInfo->GetProjectionAngleLPS(),
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle1IEC()),
//m_DRTGeometryMetaInfo->GetProjectionAngle1IEC(),//m_DRTImage1MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS)
);
@ -1648,15 +1757,15 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage2MetaInfo->SetProjectionOriginLPS(
CalibratedIsocenterLPS);
// m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter2())
// );
// m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter2())
// );
m_DRTImage2MetaInfo->SetProjectionOriginLPSZero(
CalibratedIsocenterZeroLPS);
// m_CTMetaInfo->GetProjectionOriginLPSZero(
// m_DRTGeometryMetaInfo->GetProjectionCenter2())
// );
// m_CTMetaInfo->GetProjectionOriginLPSZero(
// m_DRTGeometryMetaInfo->GetProjectionCenter2())
// );
vBounds.clear();
vBounds = m_CTMetaInfo->CalculateRegions(
@ -1664,12 +1773,12 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
);
std::cout<<"Bounds2: "
<<vBounds.data()[0]<<" "
<<vBounds.data()[1]<<" "
<<vBounds.data()[2]<<" "
<<vBounds.data()[3]<<" "
<<vBounds.data()[4]<<" "
<<vBounds.data()[5]<<std::endl;
<<vBounds.data()[0]<<" "
<<vBounds.data()[1]<<" "
<<vBounds.data()[2]<<" "
<<vBounds.data()[3]<<" "
<<vBounds.data()[4]<<" "
<<vBounds.data()[5]<<std::endl;
m_DRTImage2MetaInfo->SetSizeWithBounds(
vBounds.data(),
@ -1683,9 +1792,9 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage2MetaInfo->GetCOV(),
NominalIsocenter_wZcorrectionLPS,//m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) ,
//m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(),
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) ,
//m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS
)
);
@ -1693,8 +1802,8 @@ void itkImageProcessor::UpdateProjectionGeometryMeta(){
m_DRTImage2MetaInfo->SetImageDirectionsLPS(
CalcDRTImageDirections(
this->CalcProjectionAngleLPS(
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) ,
m_CTMetaInfo->GetPatientOrientation(),
m_DRTGeometryMetaInfo->GetProjectionAngle2IEC()) ,
//m_DRTGeometryMetaInfo->GetProjectionAngle2IEC(),//m_DRTImage2MetaInfo->GetProjectionAngleLPS(),
Std_DRT2LPS)
);
@ -1773,8 +1882,8 @@ void itkImageProcessor::GetProjectionImages(){
ImageType3D::PointType pFakeIsoLPS =
m_DRTImage1MetaInfo->GetProjectionOriginLPS();
//m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter());
//m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter());
std::cout<<"pFakeIsoLPS: "<<std::endl;
@ -1818,9 +1927,9 @@ void itkImageProcessor::GetProjectionImages(){
CurrTransform->GetAngleZ()
);
std::cout<< "itkImageProcessor::GetProjectionImages" <<std::endl;
std::cout<< "itkImageProcessor::GetProjectionImages" <<std::endl;
// AAAAAAA TODOOO CERCAA
// AAAAAAA TODOOO CERCAA
transform1 ->SetCenter(
m_DRTImage1MetaInfo->GetProjectionOriginLPSZero());
@ -1851,65 +1960,65 @@ void itkImageProcessor::GetProjectionImages(){
//CurrTransform->SetComputeZYX(true);
//CurrTransform->SetIdentity();
if(m_RTMetaInfo == NULL)
{
if(m_RTMetaInfo == NULL)
{
ImageType3D::PointType pFakeIsoLPS =
m_DRTImage2MetaInfo->GetProjectionOriginLPS();
//m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter());
ImageType3D::PointType pFakeIsoLPS =
m_DRTImage2MetaInfo->GetProjectionOriginLPS();
//m_CTMetaInfo->GetProjectionOriginLPS(
// m_DRTGeometryMetaInfo->GetProjectionCenter());
std::cout<<"pFakeIsoLPS: "<<std::endl;
std::cout<<"pFakeIsoLPS: "<<std::endl;
CurrTransform =
CalculateInternalTransform(
ZeroPoint,
ZeroPoint,
m_TransformMetaInfo->GetTranslations(),
m_TransformMetaInfo->GetRotations(),
m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
pFakeIsoLPS,
ZeroPoint,
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()
CurrTransform =
CalculateInternalTransform(
ZeroPoint,
ZeroPoint,
m_TransformMetaInfo->GetTranslations(),
m_TransformMetaInfo->GetRotations(),
m_DRTImage2MetaInfo->GetProjectionOriginLPS(),
pFakeIsoLPS,
ZeroPoint,
IECtoLPS_Directions
);
std::cout<<"pFakeIsoLPS: "<<std::endl;
transform2 ->SetCenter(
m_DRTImage2MetaInfo->GetProjectionOriginLPSZero());
} 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 ->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 +2037,10 @@ void itkImageProcessor::GetProjectionImages(){
imageDRT2In = filter2->GetOutput();
std::cout<< "itkImageProcessor::GetProjectionImages END" <<std::endl;
// std::cout<<"MMMMM: "<<
// interpolator1->GetInverseTransform()->GetMatrix()<<std::endl;
// std::cout<<"MMMMM: "<<
// interpolator1->GetInverseTransform()->GetTranslation()<<std::endl;
// std::cout<<"MMMMM: "<<
// interpolator1->GetInverseTransform()->GetMatrix()<<std::endl;
// std::cout<<"MMMMM: "<<
// interpolator1->GetInverseTransform()->GetTranslation()<<std::endl;
}

19
reg23Topograms/itkDTRrecon/itkImageProcessor.h
View File

@ -72,7 +72,9 @@ public:
itkTypeMacro(itkImageProcessor, Object);
/** Input data load methods*/
int load3DSerie(const char* );
int load3DSerieFromFolder(const char* );
int load3DSerieFromFiles( std::vector<std::string> );
int load2D(const char *);
void loadRTPlanInfo(double, double, double, double, double ,double);
@ -151,13 +153,13 @@ public:
protected:
/** Various pixel types */
using InternalPixelType = float;
using PixelType2D = short;
using PixelType3D = short;
using OutputPixelType = unsigned char;
using InternalPixelType = float;
using PixelType2D = short;
using PixelType3D = short;
using OutputPixelType = unsigned char;
using ImageType3D = itk::Image<PixelType3D, Dimension>;
using InternalImageType = itk::Image<InternalPixelType, Dimension>;
using ImageType3D = itk::Image<PixelType3D, Dimension>;
using InternalImageType = itk::Image<InternalPixelType, Dimension>;
itkImageProcessor();
virtual ~itkImageProcessor();
@ -167,6 +169,9 @@ private:
itkImageProcessor(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 */
using ImageType2D = itk::Image<PixelType3D, Dimension>;

2
reg23Topograms/itkDTRrecon/vtkContourTopogramProjectionFilter.cxx
View File

@ -148,6 +148,8 @@ int vtkContourTopogramProjectionFilter::RequestData(
pp2[1] -= dProjectionLPSOffset [1];
pp2[2] -= dProjectionLPSOffset [2];
// std::cout << ii << " " << pp2[0] << " " << pp2[1] << " " << pp2[2] << std::endl;
PrjPoints->InsertPoint(ii,pp2);
}