Hi,
I was trying to write a code for performing image reconstruction using RTK Toolkit. As a beginner, I was modifying the example code in RTK (First Reconstruction). While writing the code an issue occurred regarding "Member not found in rtk::ThreeDCircularProjectionGeometry". My code is:
// RTK includes
#include <rtkConstantImageSource.h>
#include <rtkThreeDCircularProjectionGeometryXMLFileWriter.h>
//#include <rtkRayEllipsoidIntersectionImageFilter.h>
#include <rtkFDKConeBeamReconstructionFilter.h>
#include <rtkFieldOfViewImageFilter.h>
#include <rtkThreeDCircularProjectionGeometry.h>
// ITK includes
#include <itkImageFileWriter.h>
#include <iostream>
#include <fstream>
#include <vector>
// Function to read raw data from a binary file
std::vector<float> readRawData(const std::string& filename, size_t dataSize)
{
std::vector<float> rawData;
rawData.resize(dataSize);
std::ifstream file(filename, std::ios::binary);
if (!file.is_open())
{
std::cerr << "Error opening file: " << filename << std::endl;
// Handle the error, return an empty vector, or throw an exception
return rawData;
}
file.read(reinterpret_cast<char*>(rawData.data()), dataSize * sizeof(float));
if (file.fail())
{
std::cerr << "Error reading file: " << filename << std::endl;
// Handle the error, return an empty vector, or throw an exception
}
file.close();
return rawData;
}
int
main(int argc, char ** argv)
{
if (argc < 3)
{
std::cout << "Usage: FirstReconstruction <outputimage> <outputgeometry>" << std::endl;
return EXIT_FAILURE;
}
// Define geometry parameters
const unsigned int numberOfProjections = 351;
const unsigned int detectorRows = 1536;
const unsigned int detectorColumns = 1536;
const double detectorPixelSize = 0.139;
const unsigned int imageRows = 1536;
const unsigned int imageColumns = 1536;
const double spacingBetweenSlices = 0.5;
const unsigned int numberOfSlices = 512;
const double DSD = 1690.0;
const double DSO = 921.0;
const double detectorShiftX = 0.0;
const double detectorShiftY = 0.0;
const double detectorPixelPitch = 0.139;
// Defines the image type
using ImageType = itk::Image<float, 3>;
// Defines the RTK geometry object
using GeometryType = rtk::ThreeDCircularProjectionGeometry;
GeometryType::Pointer geometry = GeometryType::New();
geometry->SetRadiusCylindricalDetector(detectorColumns * detectorPixelSize / 2.0);
geometry->SetSourceToDetectorDistance(DSD);
geometry->SetSourceToIsocenterDistance(DSO);
geometry->SetProjectionMatrix(1, 0, 0, 0, 1, 0);
// Read angles from angles.txt
std::ifstream anglesFile("D:\\Navami\\CBCT_TIGRE CODE\\Data\\CBCT\\Raw1\\angle.txt");
if (!anglesFile.is_open())
{
std::cerr << "Error opening angles file." << std::endl;
return EXIT_FAILURE;
}
std::vector<double> angles;
double angle;
while (anglesFile >> angle)
{
angles.push_back(angle);
}
anglesFile.close();
if (angles.size() != numberOfProjections)
{
std::cerr << "Error: Number of angles in angles.txt does not match the expected number of projections." << std::endl;
return EXIT_FAILURE;
}
for (unsigned int noProj = 0; noProj < numberOfProjections; noProj++)
{
double angle = noProj * 360.0 / numberOfProjections;
geometry->AddProjection(DSD, DSO, angle, detectorShiftX, detectorShiftY, detectorPixelPitch);
}
// Write the geometry to disk
rtk::ThreeDCircularProjectionGeometryXMLFileWriter::Pointer xmlWriter;
xmlWriter = rtk::ThreeDCircularProjectionGeometryXMLFileWriter::New();
xmlWriter->SetFilename(argv[2]);
xmlWriter->SetObject(geometry);
xmlWriter->WriteFile();
// Create a stack of empty projection images
using ConstantImageSourceType = rtk::ConstantImageSource<ImageType>;
ConstantImageSourceType::Pointer constantImageSource = ConstantImageSourceType::New();
ConstantImageSourceType::PointType origin;
ConstantImageSourceType::SpacingType spacing;
ConstantImageSourceType::SizeType sizeOutput;
// origin[0] = -127;
// origin[1] = -127;
// origin[2] = 0.;
origin[0] = -0.5 * detectorColumns * detectorPixelSize;
origin[1] = -0.5 * detectorRows * detectorPixelSize;
origin[2] = 0.;
// sizeOutput[0] = 128;
// sizeOutput[1] = 128;
// sizeOutput[2] = numberOfProjections;
sizeOutput[0] = imageColumns;
sizeOutput[1] = imageRows;
sizeOutput[2] = numberOfProjections;
//spacing.Fill(2.);
spacing.Fill(spacingBetweenSlices);
constantImageSource->SetOrigin(origin);
constantImageSource->SetSpacing(spacing);
constantImageSource->SetSize(sizeOutput);
constantImageSource->SetConstant(0.);
// Loop through raw data files and reconstruct
for (unsigned int projIndex = 0; projIndex < numberOfProjections; projIndex++)
{
// Read raw data for each projection
std::string rawDataFilename = "D:\\Navami\\CBCT_TIGRE CODE\\Data\\CBCT\\Raw1\\projD1_%d_" + std::to_string(projIndex) + ".bin";
size_t projectionSize = detectorRows * detectorColumns;
std::vector<float> rawData = readRawData(rawDataFilename, projectionSize);
// Set the raw data as the input for ConstantImageSource
std::copy(rawData.begin(), rawData.end(), constantImageSource->GetOutput()->GetBufferPointer());
// Create reconstructed image
ConstantImageSourceType::Pointer constantImageSource2 = ConstantImageSourceType::New();
sizeOutput.Fill(imageColumns);
origin.Fill(-0.5 * imageColumns * spacingBetweenSlices);
spacing.Fill(spacingBetweenSlices);
constantImageSource2->SetOrigin(origin);
constantImageSource2->SetSpacing(spacing);
constantImageSource2->SetSize(sizeOutput);
constantImageSource2->SetConstant(0.);
// FDK reconstruction
std::cout << "Reconstructing..." << std::endl;
using FDKCPUType = rtk::FDKConeBeamReconstructionFilter<ImageType>;
FDKCPUType::Pointer feldkamp = FDKCPUType::New();
feldkamp->SetInput(0, constantImageSource2->GetOutput());
feldkamp->SetInput(1, constantImageSource->GetOutput());
feldkamp->SetGeometry(geometry);
feldkamp->GetRampFilter()->SetTruncationCorrection(0.);
feldkamp->GetRampFilter()->SetHannCutFrequency(0.0);
// Field-of-view masking
using FOVFilterType = rtk::FieldOfViewImageFilter<ImageType, ImageType>;
FOVFilterType::Pointer fieldofview = FOVFilterType::New();
fieldofview->SetInput(0, feldkamp->GetOutput());
fieldofview->SetProjectionsStack(constantImageSource->GetOutput());
fieldofview->SetGeometry(geometry);
// Writer for each slice
for (unsigned int sliceIndex = 0; sliceIndex < numberOfSlices; sliceIndex++)
{
std::cout << "Writing output image for slice " << sliceIndex << "..." << std::endl;
using WriterType = itk::ImageFileWriter<ImageType>;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("output_image_proj_" + std::to_string(projIndex) + "_slice_" + std::to_string(sliceIndex) + ".mha");
// Extract the 2D slice using itk::ExtractImageFilter
using ExtractFilterType = itk::ExtractImageFilter<ImageType, ImageType>;
ExtractFilterType::Pointer extractFilter = ExtractFilterType::New();
extractFilter->SetDirectionCollapseToIdentity();
extractFilter->SetInput(fieldofview->GetOutput());
// Define the extraction region
ExtractFilterType::InputImageRegionType extractionRegion;
extractionRegion.SetSize(2, 0); // Set the size of the third dimension to 0
extractionRegion.SetIndex(2, sliceIndex); // Set the index of the third dimension to the current slice
extractFilter->SetExtractionRegion(extractionRegion);
extractFilter->Update();
// Set the input of the writer to the extracted slice
writer->SetInput(extractFilter->GetOutput());
writer->Update();
}
}
std::cout << "Done!" << std::endl;
return EXIT_SUCCESS;
}
In this code the issue occurs while defining the RTK Geometry Object.
Hi, I was trying to write a code for performing image reconstruction using RTK Toolkit. As a beginner, I was modifying the example code in RTK (First Reconstruction). While writing the code an issue occurred regarding "Member not found in rtk::ThreeDCircularProjectionGeometry". My code is:
In this code the issue occurs while defining the RTK Geometry Object.
The error occurring is attached below.![Issue in RTK](https://github.com/RTKConsortium/RTK/assets/126770219/9a07493d-6c56-4b50-a087-52bfd8332641)
I humbly request for any suggestions or solutions to solve this issue. Thank You.