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
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@ -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)

161
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>
@ -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()
@ -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();
@ -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(
@ -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;
}

7
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);
@ -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);
}