diff --git a/apps/VoxelizerTool/VoxelizerToolHelper.cpp b/apps/VoxelizerTool/VoxelizerToolHelper.cpp
index 5eda333..cbeb35c 100644
--- a/apps/VoxelizerTool/VoxelizerToolHelper.cpp
+++ b/apps/VoxelizerTool/VoxelizerToolHelper.cpp
@@ -1,227 +1,216 @@
// -----------------------------------------------------------------------
// RTToolbox - DKFZ radiotherapy quantitative evaluation library
//
// Copyright (c) German Cancer Research Center (DKFZ),
// Software development for Integrated Diagnostics and Therapy (SIDT).
// ALL RIGHTS RESERVED.
// See rttbCopyright.txt or
// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notices for more information.
//
//------------------------------------------------------------------------
/*!
// @file
// @version $Revision: 1127 $ (last changed revision)
// @date $Date: 2015-10-01 13:33:33 +0200 (Do, 01 Okt 2015) $ (last change date)
// @author $Author: hentsch $ (last changed by)
*/
#include <iostream>
#include "rttbBoostMaskAccessor.h"
#include "itkMacro.h"
#include "VoxelizerToolHelper.h"
#include "VoxelizerToolApplicationData.h"
#include "rttbITKImageMaskAccessorConverter.h"
#include "rttbImageWriter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkAddImageFilter.h"
#include <regex>
#include <boost/algorithm/string/case_conv.hpp>
-#include <boost/filesystem.hpp>
+
+#include "rttbUtils.h"
#include "rttbDicomFileStructureSetGenerator.h"
void rttb::apps::voxelizerTool::removeSpecialCharacters(std::string& label)
{
//Replace / to avoid problems with directories (struct "Magen/DD" --> Magen/DD.mhd), delete trailing . to avoid filenames with two trailing points (Niere re. --> Niere re..mhd)
while (label.find("/") != std::string::npos)
{
label.replace(label.find("/"), 1, "_");
}
if (*label.rbegin() == '.')
{
label.replace(label.size() - 1, 1, "");
}
}
-std::string rttb::apps::voxelizerTool::getFilenameWithoutEnding(const std::string& outfilename)
-{
- boost::filesystem::path p(outfilename);
- return p.replace_extension("").string();
-}
-
-std::string rttb::apps::voxelizerTool::getFileEnding(const std::string& outfilename)
-{
- boost::filesystem::path p(outfilename);
- return p.extension().string();
-}
-
rttb::core::MaskAccessorInterface::MaskAccessorPointer rttb::apps::voxelizerTool::createMask(
rttb::core::DoseAccessorInterface::DoseAccessorPointer doseAccessorPtr,
rttb::core::Structure::StructTypePointer structurePtr,
bool strict)
{
rttb::core::MaskAccessorInterface::MaskAccessorPointer maskAccessorPtr;
if (doseAccessorPtr != nullptr && structurePtr != nullptr)
{
maskAccessorPtr = boost::make_shared<rttb::masks::boost::BoostMaskAccessor>
(structurePtr, doseAccessorPtr->getGeometricInfo(),
strict);
maskAccessorPtr->updateMask();
}
return maskAccessorPtr;
}
void rttb::apps::voxelizerTool::writeMaskToFile(std::vector<core::MaskAccessorInterface::MaskAccessorPointer> maskVector,
const std::string& outputFileName, bool voxelization)
{
if (!maskVector.empty())
{
io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer itkImage;
if (maskVector.size() > 1)
{
itkImage = addMultipleStructsToImage(maskVector);
}
else
{
io::itk::ITKImageMaskAccessorConverter maskAccessorConverter(maskVector.at(0));
maskAccessorConverter.process();
itkImage = maskAccessorConverter.getITKImage();
}
if (voxelization)
{
itkImage = applyThresholdFilter(itkImage);
}
io::itk::ImageWriter writer(outputFileName, itkImage);
writer.writeFile();
}
}
rttb::io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer rttb::apps::voxelizerTool::addMultipleStructsToImage(
std::vector<core::MaskAccessorInterface::MaskAccessorPointer> maskVector)
{
std::vector<io::itk::ITKImageMaskAccessor::ITKMaskImageType::Pointer> listOfITKImages;
for (const auto & i : maskVector)
{
io::itk::ITKImageMaskAccessorConverter maskAccessorConverter(i);
maskAccessorConverter.process();
listOfITKImages.push_back(maskAccessorConverter.getITKImage());
}
itk::AddImageFilter <itk::Image<rttb::DoseTypeGy, 3>, itk::Image<rttb::DoseTypeGy, 3>>::Pointer addFilter =
itk::AddImageFilter <itk::Image<rttb::DoseTypeGy, 3>, itk::Image<rttb::DoseTypeGy, 3>>::New();
io::itk::ITKImageMaskAccessor::ITKMaskImageType::Pointer filterResult;
for (int k = 1; k < listOfITKImages.size(); k++)
{
if (k == 1)
{
addFilter->SetInput1(listOfITKImages.at(0));
}
else
{
addFilter->SetInput1(filterResult);
}
addFilter->SetInput2(listOfITKImages.at(k));
addFilter->Update();
filterResult = addFilter->GetOutput();
}
return filterResult.GetPointer();
}
rttb::io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer rttb::apps::voxelizerTool::applyThresholdFilter(
io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer itkImage)
{
itk::BinaryThresholdImageFilter< itk::Image<rttb::DoseTypeGy, 3>, itk::Image<rttb::DoseTypeGy, 3> >::Pointer filter =
itk::BinaryThresholdImageFilter< itk::Image<rttb::DoseTypeGy, 3>, itk::Image<rttb::DoseTypeGy, 3> >::New();
filter->SetInput(itkImage);
filter->SetLowerThreshold(0.5);
filter->SetUpperThreshold(1.0);
filter->SetInsideValue(1.0);
filter->Update();
return filter->GetOutput();
}
void rttb::apps::voxelizerTool::processData(rttb::apps::voxelizerTool::ApplicationData& appData) {
if (appData._struct->getNumberOfStructures()>0)
{
std::vector<core::MaskAccessorInterface::MaskAccessorPointer> maskVector;
if (appData._addStructures)
{
for (size_t i=0; i<appData._struct->getNumberOfStructures(); i++ )
{
std::cout << "creating mask #" << i << "...";
maskVector.push_back(createMask(appData._dose, appData._struct->getStructure(i),
!appData._noStrictVoxelization));
std::cout << "done" << std::endl;
}
std::cout << "writing mask to file...";
writeMaskToFile(maskVector, appData._outputFilename, appData._binaryVoxelization);
std::cout << "done" << std::endl;
}
else
{
//default behavior: read only first struct that matches the regex
unsigned int maxIterationCount = 1;
//only if specified: read all structs that matches the regex
if (appData._multipleStructs)
{
maxIterationCount = appData._struct->getNumberOfStructures();
}
for (size_t i = 0; i<maxIterationCount; i++)
{
std::cout << "creating mask #" << i << "...";
auto currentMask = createMask(appData._dose, appData._struct->getStructure(i),
!appData._noStrictVoxelization);
std::cout << "done" << std::endl;
std::string labelOfInterest = appData._struct->getStructure(i)->getLabel();
removeSpecialCharacters(labelOfInterest);
std::string outputName = appData._outputFilename;
if (appData._multipleStructs)
{
- std::string fileName = getFilenameWithoutEnding(
+ std::string fileName = rttb::core::getFilenameWithoutEnding(
appData._outputFilename);
- std::string fileEnding = getFileEnding(appData._outputFilename);
+ std::string fileEnding = rttb::core::getFileEnding(appData._outputFilename);
outputName = fileName + "_" + labelOfInterest + fileEnding;
}
std::vector<rttb::core::MaskAccessorInterface::MaskAccessorPointer> currenMaskVector{ currentMask };
std::cout << "writing mask #" << i << " to file...";
writeMaskToFile(currenMaskVector, outputName, appData._binaryVoxelization);
std::cout << "done" << std::endl;
}
}
}
else
{
std::cout << "No struct found" << std::endl;
}
}
\ No newline at end of file
diff --git a/apps/VoxelizerTool/VoxelizerToolHelper.h b/apps/VoxelizerTool/VoxelizerToolHelper.h
index 429046e..312777a 100644
--- a/apps/VoxelizerTool/VoxelizerToolHelper.h
+++ b/apps/VoxelizerTool/VoxelizerToolHelper.h
@@ -1,69 +1,67 @@
// -----------------------------------------------------------------------
// RTToolbox - DKFZ radiotherapy quantitative evaluation library
//
// Copyright (c) German Cancer Research Center (DKFZ),
// Software development for Integrated Diagnostics and Therapy (SIDT).
// ALL RIGHTS RESERVED.
// See rttbCopyright.txt or
// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notices for more information.
//
//------------------------------------------------------------------------
/*!
// @file
// @version $Revision: 1127 $ (last changed revision)
// @date $Date: 2015-10-01 13:33:33 +0200 (Do, 01 Okt 2015) $ (last change date)
// @author $Author: hentsch $ (last changed by)
*/
#include <string>
#include <vector>
#include "rttbStructure.h"
#include "rttbMaskAccessorInterface.h"
#include "rttbITKImageMaskAccessor.h"
#include "rttbDoseAccessorInterface.h"
namespace rttb
{
namespace apps
{
namespace voxelizerTool
{
class ApplicationData;
void processData(ApplicationData& appData);
/**@brief Search the label with the position from index
@return a label from the list as string
*/
void removeSpecialCharacters(std::string& label);
/**@brief create a mask with _rtStructureSet and _doseAccessor object.
@return a mask object
*/
core::MaskAccessorInterface::MaskAccessorPointer createMask(
core::DoseAccessorInterface::DoseAccessorPointer doseAccessorPtr,
rttb::core::Structure::StructTypePointer structurePtr,
bool strict);
/**@brief write the mask into the outputfile
@param Outputfilename
*/
void writeMaskToFile(std::vector<core::MaskAccessorInterface::MaskAccessorPointer> maskVector,
const std::string& outputFileName, bool voxelization);
io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer addMultipleStructsToImage(
std::vector<core::MaskAccessorInterface::MaskAccessorPointer> maskVector);
io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer applyThresholdFilter(
io::itk::ITKImageMaskAccessor::ITKMaskImageType::ConstPointer itkImage);
- std::string getFilenameWithoutEnding(const std::string& outfilename);
- std::string getFileEnding(const std::string& outfilename);
}
}
}
\ No newline at end of file
diff --git a/code/core/rttbUtils.cpp b/code/core/rttbUtils.cpp
index 364ef90..853f5c6 100644
--- a/code/core/rttbUtils.cpp
+++ b/code/core/rttbUtils.cpp
@@ -1,51 +1,66 @@
// -----------------------------------------------------------------------
// RTToolbox - DKFZ radiotherapy quantitative evaluation library
//
// Copyright (c) German Cancer Research Center (DKFZ),
// Software development for Integrated Diagnostics and Therapy (SIDT).
// ALL RIGHTS RESERVED.
// See rttbCopyright.txt or
// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notices for more information.
//
//------------------------------------------------------------------------
/*!
// @file
// @version $Revision: 1674 $ (last changed revision)
// @date $Date: 2017-01-27 10:34:46 +0100 (Fr, 27 Jan 2017) $ (last change date)
// @author $Author: hentsch $ (last changed by)
*/
#include <rttbUtils.h>
+#include <boost/filesystem.hpp>
namespace rttb {
namespace core {
- bool isKey(const std::map<double, double>& values, const double value) {
+ bool isKey(const std::map<double, double>& values, const double value) {
for (auto const& collectionElements : values) {
if (std::abs(collectionElements.first - value) <= errorConstant)
{
return true;
}
}
return false;
}
bool isKey(const std::vector<double>& values, double value) {
for (auto const& collectionElement : values) {
if (std::abs(collectionElement - value) <= errorConstant)
{
return true;
}
}
return false;
}
bool valueIsClose(double value1, double value2, double specificErrorConstant) {
return std::abs(value1 - value2) < specificErrorConstant;
}
+
+
+ std::string getFilenameWithoutEnding(const std::string& outfilename)
+ {
+ boost::filesystem::path p(outfilename);
+ return p.replace_extension("").string();
+ }
+
+ std::string getFileEnding(const std::string& outfilename)
+ {
+ boost::filesystem::path p(outfilename);
+ return p.extension().string();
+ }
+
}
}
diff --git a/code/core/rttbUtils.h b/code/core/rttbUtils.h
index 22e3d6b..878b5f3 100644
--- a/code/core/rttbUtils.h
+++ b/code/core/rttbUtils.h
@@ -1,44 +1,49 @@
// -----------------------------------------------------------------------
// RTToolbox - DKFZ radiotherapy quantitative evaluation library
//
// Copyright (c) German Cancer Research Center (DKFZ),
// Software development for Integrated Diagnostics and Therapy (SIDT).
// ALL RIGHTS RESERVED.
// See rttbCopyright.txt or
// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notices for more information.
//
//------------------------------------------------------------------------
/*!
// @file
// @version $Revision: 1674 $ (last changed revision)
// @date $Date: 2017-01-27 10:34:46 +0100 (Fr, 27 Jan 2017) $ (last change date)
// @author $Author: hentsch $ (last changed by)
*/
#ifndef __RTTB_UTILS_H
#define __RTTB_UTILS_H
#include <map>
#include <vector>
#include <rttbBaseType.h>
#include "RTTBCoreExports.h"
namespace rttb
{
namespace core
{
bool RTTBCore_EXPORT isKey(const std::map<double, double>& values, double value);
- bool RTTBCore_EXPORT isKey(const std::vector<double>& values, double value);
+ bool RTTBCore_EXPORT isKey(const std::vector<double>& values, double value);
- bool RTTBCore_EXPORT valueIsClose(double value1, double value2, double specificErrorConstant = 1e-5);
+ bool RTTBCore_EXPORT valueIsClose(double value1, double value2, double specificErrorConstant = 1e-5);
+
+ std::string RTTBCore_EXPORT getFilenameWithoutEnding(const std::string& outfilename);
+
+ std::string RTTBCore_EXPORT getFileEnding(const std::string& outfilename);
+
}
}
#endif