--- /dev/null
+*.swp
+build
clitkXdrImageIOFactory.cxx
clitkHndImageIO.cxx
clitkHndImageIOFactory.cxx
+ clitkGateAsciiImageIO.cxx
+ clitkGateAsciiImageIOFactory.cxx
clitkDicomRTDoseIO.cxx
clitkDicomRTDoseIOFactory.cxx
clitkOrientation.cxx
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// std include
+#include <regex.h>
+#include <cstdio>
+#include <sstream>
+#include <iostream>
+using std::cout;
+using std::endl;
+
+// clitk include
+#include "clitkGateAsciiImageIO.h"
+#include "clitkCommon.h"
+
+// itk include
+#include <itkMetaDataObject.h>
+
+std::ostream& operator<<(std::ostream& os, const clitk::GateAsciiImageIO::GateAsciiHeader& header)
+{
+ os << "matrix_size=[" << header.matrix_size[0] << "," << header.matrix_size[1] << "," << header.matrix_size[2] << "]" << endl;
+ os << "resolution=[" << header.resolution[0] << "," << header.resolution[1] << "," << header.resolution[2] << "]" << endl;
+ os << "voxel_size=[" << header.voxel_size[0] << "," << header.voxel_size[1] << "," << header.voxel_size[2] << "]" << endl;
+ os << "nb_value=" << header.nb_value << endl;
+ return os;
+}
+
+//--------------------------------------------------------------------
+// Read Image Information
+void clitk::GateAsciiImageIO::ReadImageInformation()
+{
+ FILE* handle = fopen(m_FileName.c_str(),"r");
+ if (!handle) {
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+ return;
+ }
+
+ GateAsciiHeader header;
+ if (!ReadHeader(handle,header)) {
+ itkGenericExceptionMacro(<< "Could not read header: " << m_FileName);
+ fclose(handle);
+ return;
+ }
+ fclose(handle);
+
+ int real_length = -1;
+ double real_spacing = 0;
+ for (int kk=0; kk<3; kk++) {
+ if (header.resolution[kk]>1) {
+ if (real_length>0) {
+ itkGenericExceptionMacro(<< "Could not image dimension: " << m_FileName);
+ return;
+ }
+ real_length = header.resolution[kk];
+ real_spacing = header.voxel_size[kk];
+ }
+ }
+ assert(real_length == header.nb_value);
+
+ // Set image information
+ SetNumberOfDimensions(2);
+ SetDimensions(0, real_length);
+ SetDimensions(1, 1);
+ SetSpacing(0, real_spacing);
+ SetSpacing(1, 1);
+ SetOrigin(0, 0);
+ SetOrigin(1, 0);
+ SetComponentType(itk::ImageIOBase::DOUBLE);
+}
+
+//--------------------------------------------------------------------
+bool clitk::GateAsciiImageIO::CanReadFile(const char* FileNameToRead)
+{
+ std::string filename(FileNameToRead);
+
+ { // check extension
+ std::string filenameext = GetExtension(filename);
+ if (filenameext != "txt") return false;
+ }
+
+ { // check header
+ FILE* handle = fopen(filename.c_str(),"r");
+ if (!handle) return false;
+
+ GateAsciiHeader header;
+ if (!ReadHeader(handle,header)) { fclose(handle); return false; }
+ fclose(handle);
+ }
+
+ return true;
+}
+
+//--------------------------------------------------------------------
+// Read Line in file
+bool clitk::GateAsciiImageIO::ReadLine(FILE* handle, std::string& line)
+{
+ std::stringstream stream;
+ while (true)
+ {
+ char item;
+ if (ferror(handle)) return false;
+ if (fread(&item,1,1,handle) != 1) return false;
+
+ if (item=='\n' or feof(handle)) {
+ line = stream.str();
+ return true;
+ }
+
+ stream << item;
+ }
+}
+
+std::string ExtractMatch(const std::string& base, const regmatch_t& match)
+{
+ return base.substr(match.rm_so,match.rm_eo-match.rm_so);
+}
+
+template <typename T>
+T ConvertFromString(const std::string& value)
+{
+ std::stringstream stream;
+ stream << value;
+ T converted;
+ stream >> converted;
+ return converted;
+}
+
+//--------------------------------------------------------------------
+// Read Image Header
+bool clitk::GateAsciiImageIO::ReadHeader(FILE* handle, GateAsciiHeader& header)
+{
+ assert(handle);
+ std::string line;
+
+ regex_t re_comment;
+ regex_t re_matrix_size;
+ regex_t re_resol;
+ regex_t re_voxel_size;
+ regex_t re_nb_value;
+ regmatch_t matches[4];
+
+ { // build regex
+ int ret = 0;
+ ret = regcomp(&re_comment,"^#.+$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret == 0);
+ ret = regcomp(&re_matrix_size,"^# +Matrix *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret == 0);
+ ret = regcomp(&re_resol,"^# +Resol *= +\\(([0-9]+),([0-9]+),([0-9]+)\\)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret == 0);
+ ret = regcomp(&re_voxel_size,"^# +Voxel *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret == 0);
+ ret = regcomp(&re_nb_value,"^# +nbVal *= +([0-9]+)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret == 0);
+ }
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_comment,line.c_str(),1,matches,0) == REG_NOMATCH) return false;
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_matrix_size,line.c_str(),4,matches,0) == REG_NOMATCH) return false;
+ header.matrix_size[0] = ConvertFromString<double>(ExtractMatch(line,matches[1]));
+ header.matrix_size[1] = ConvertFromString<double>(ExtractMatch(line,matches[2]));
+ header.matrix_size[2] = ConvertFromString<double>(ExtractMatch(line,matches[3]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_resol,line.c_str(),4,matches,0) == REG_NOMATCH) return false;
+ header.resolution[0] = ConvertFromString<int>(ExtractMatch(line,matches[1]));
+ header.resolution[1] = ConvertFromString<int>(ExtractMatch(line,matches[2]));
+ header.resolution[2] = ConvertFromString<int>(ExtractMatch(line,matches[3]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_voxel_size,line.c_str(),4,matches,0) == REG_NOMATCH) return false;
+ header.voxel_size[0] = ConvertFromString<double>(ExtractMatch(line,matches[1]));
+ header.voxel_size[1] = ConvertFromString<double>(ExtractMatch(line,matches[2]));
+ header.voxel_size[2] = ConvertFromString<double>(ExtractMatch(line,matches[3]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_nb_value,line.c_str(),2,matches,0) == REG_NOMATCH) return false;
+ header.nb_value = ConvertFromString<int>(ExtractMatch(line,matches[1]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_comment,line.c_str(),1,matches,0) == REG_NOMATCH) return false;
+
+ return true;
+}
+
+//--------------------------------------------------------------------
+// Read Image Content
+void clitk::GateAsciiImageIO::Read(void* abstract_buffer)
+{
+ FILE* handle = fopen(m_FileName.c_str(),"r");
+ if (!handle) {
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+ return;
+ }
+
+ GateAsciiHeader header;
+ if (!ReadHeader(handle,header)) {
+ itkGenericExceptionMacro(<< "Could not read header: " << m_FileName);
+ fclose(handle);
+ return;
+ }
+
+ {
+ double* buffer = static_cast<double*>(abstract_buffer);
+ int read_count = 0;
+ while (true) {
+ std::string line;
+ if (!ReadLine(handle,line)) break;
+ *buffer = ConvertFromString<double>(line);
+ read_count++;
+ buffer++;
+ }
+ assert(read_count == header.nb_value);
+ }
+
+ fclose(handle);
+}
+
+//--------------------------------------------------------------------
+bool clitk::GateAsciiImageIO::CanWriteFile(const char* FileNameToWrite)
+{
+ if (GetExtension(std::string(FileNameToWrite)) != "txt") return false;
+ return true;
+}
+
+void clitk::GateAsciiImageIO::WriteImageInformation()
+{
+ cout << GetNumberOfDimensions() << endl;
+}
+
+bool clitk::GateAsciiImageIO::SupportsDimension(unsigned long dim)
+{
+ if (dim==2) return true;
+ return false;
+}
+
+//--------------------------------------------------------------------
+// Write Image
+void clitk::GateAsciiImageIO::Write(const void* abstract_buffer)
+{
+ const unsigned long nb_value = GetDimensions(0)*GetDimensions(1);
+ std::stringstream stream;
+ stream << "######################" << endl;
+ stream << "# Matrix Size= (" << GetSpacing(0)*GetDimensions(0) << "," << GetSpacing(1)*GetDimensions(1) << ",1)" << endl;
+ stream << "# Resol = (" << GetDimensions(0) << "," << GetDimensions(1) << ",1)" << endl;
+ stream << "# VoxelSize = (" << GetSpacing(0) << "," << GetSpacing(1) << ",1)" << endl;
+ stream << "# nbVal = " << nb_value << endl;
+ stream << "######################" << endl;
+
+ const double* buffer = static_cast<const double*>(abstract_buffer);
+ for (unsigned long kk=0; kk<nb_value; kk++) { stream << buffer[kk] << endl; }
+
+ FILE* handle = fopen(m_FileName.c_str(),"w");
+ if (!handle) {
+ itkGenericExceptionMacro(<< "Could not open file (for writing): " << m_FileName);
+ return;
+ }
+
+ fwrite(stream.str().c_str(),1,stream.str().size(),handle);
+
+ fclose(handle);
+}
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKGATEASCIIIMAGEIO_H
+#define CLITKGATEASCIIIMAGEIO_H
+
+// itk include
+#include "itkImageIOBase.h"
+
+#if defined (_MSC_VER) && (_MSC_VER < 1600)
+//SR: taken from
+//#include "msinttypes/stdint.h"
+typedef unsigned int uint32_t;
+#else
+#include <stdint.h>
+#endif
+
+namespace clitk {
+
+ //====================================================================
+ // Class for reading gate ascii Image file format
+ class GateAsciiImageIO: public itk::ImageIOBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef GateAsciiImageIO Self;
+ typedef itk::ImageIOBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef signed short int PixelType;
+
+ struct GateAsciiHeader {
+ double matrix_size[3];
+ int resolution[3];
+ double voxel_size[3];
+ int nb_value;
+ };
+
+ GateAsciiImageIO():Superclass() {;}
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(GateAsciiImageIO, ImageIOBase);
+
+ /*-------- This part of the interface deals with reading data. ------ */
+ virtual void ReadImageInformation();
+ virtual bool CanReadFile( const char* FileNameToRead );
+ virtual void Read(void * buffer);
+
+ /*-------- This part of the interfaces deals with writing data. ----- */
+ virtual void WriteImageInformation();
+ virtual bool CanWriteFile(const char* filename);
+ virtual void Write(const void* buffer);
+
+ virtual bool SupportsDimension(unsigned long dim);
+
+ protected:
+
+ static bool ReadHeader(FILE* handle, GateAsciiHeader& header);
+ static bool ReadLine(FILE* handle, std::string& line);
+
+ }; // end class GateAsciiImageIO
+} // end namespace
+
+// explicit template instantiation
+//template class itk::CreateObjectFunction<clitk::GateAsciiImageIO>;
+
+#endif /* end #define CLITKGATEASCIIIMAGEIO_H */
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#include "clitkGateAsciiImageIOFactory.h"
+
+//====================================================================
+clitk::GateAsciiImageIOFactory::GateAsciiImageIOFactory()
+{
+ this->RegisterOverride("itkImageIOBase",
+ "GateAsciiImageIO",
+ "GateAscii Image IO",
+ 1,
+ itk::CreateObjectFunction<GateAsciiImageIO>::New());
+}
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKGATEASCIIIMAGEIOFACTORY_H
+#define CLITKGATEASCIIIMAGEIOFACTORY_H
+
+// clitk include
+#include "clitkGateAsciiImageIO.h"
+
+// itk include
+#include "itkImageIOBase.h"
+#include "itkObjectFactoryBase.h"
+#include "itkVersion.h"
+
+namespace clitk {
+
+ //====================================================================
+ // Factory for reading GateAscii Image file format
+ class GateAsciiImageIOFactory: public itk::ObjectFactoryBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef GateAsciiImageIOFactory Self;
+ typedef itk::ObjectFactoryBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Class methods used to interface with the registered factories. */
+ const char* GetITKSourceVersion(void) const {
+ return ITK_SOURCE_VERSION;
+ }
+
+ const char* GetDescription(void) const {
+ return "GateAscii ImageIO Factory, allows the loading of gate ascii images into insight";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(GateAsciiImageIOFactory, ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void) {
+ ObjectFactoryBase::RegisterFactory( Self::New() );
+ }
+
+ protected:
+ GateAsciiImageIOFactory();
+ ~GateAsciiImageIOFactory() {};
+
+ private:
+ GateAsciiImageIOFactory(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+ };
+
+} // end namespace
+
+#endif /* end #define CLITKGATEASCIIIMAGEIOFACTORY_H */
+
#include "clitkVfImageIOFactory.h"
#include "clitkXdrImageIOFactory.h"
#include "clitkHndImageIOFactory.h"
+#include "clitkGateAsciiImageIOFactory.h"
//--------------------------------------------------------------------
// Register factories
void clitk::RegisterClitkFactories()
{
+ clitk::GateAsciiImageIOFactory::RegisterOneFactory();
clitk::DicomRTDoseIOFactory::RegisterOneFactory();
#if ITK_VERSION_MAJOR <= 3
itk::ImageIOFactory::RegisterBuiltInFactories();
WRAP_GGO(clitkGammaIndex_GGO_C clitkGammaIndex.ggo)
ADD_EXECUTABLE(clitkGammaIndex clitkGammaIndex.cxx ${clitkGammaIndex_GGO_C})
- TARGET_LINK_LIBRARIES(clitkGammaIndex vtkCommon vtkFiltering vtkGraphics vtkIO vtkImaging)
+ TARGET_LINK_LIBRARIES(clitkGammaIndex clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES} vtkIO)
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGammaIndex)
ADD_EXECUTABLE(clitkImageArithm clitkImageArithm.cxx)
#include "clitkGammaIndex_ggo.h"
-vtkImageData *loadImage(const std::string &filename) {
- vtkImageReader2 *reader = vtkMetaImageReader::New();
- //vtkImageReader2 *reader = vtkPNGReader::New();
- reader->SetFileName(filename.c_str());
- reader->Update();
+#include <clitkIO.h>
+#include <vvImage.h>
+#include <vvImageReader.h>
+#include <vvImageWriter.h>
- vtkImageData *image = reader->GetOutput();
- image->Register(NULL);
- reader->Delete();
+#include <itkImage.h>
+#include <itkImageRegionIterator.h>
+typedef itk::Image<double> OutputImageType;
+typedef itk::ImageRegionIterator<OutputImageType> OutputImageIterator;
- return image;
+vtkImageData* loadImage(const std::string& filename)
+{
+ vvImageReader::Pointer reader = vvImageReader::New();
+ reader->SetInputFilename(filename);
+ reader->Update();
+ vvImage::Pointer vvimage = reader->GetOutput();
+ if (!vvimage) { cerr << "can't load " << filename << endl; return NULL; }
+
+ vtkImageData *image = vtkImageData::New();
+ image->DeepCopy(vvimage->GetFirstVTKImageData());
+ return image;
}
-void saveImage(vtkImageData *image,const std::string &filename) {
- cout << "saving " << filename << endl;
- vtkImageWriter *writer = vtkMetaImageWriter::New();
- writer->SetFileName(filename.c_str());
- writer->SetInput(image);
- writer->Write();
- writer->Delete();
+void saveImage(OutputImageType* image,const std::string &filename) {
+ vvImage::Pointer vvimage = vvImage::New();
+ vvimage->AddItkImage(image);
+
+ vvImageWriter::Pointer writer = vvImageWriter::New();
+ writer->SetOutputFileName(filename.c_str());
+ writer->SetInput(vvimage);
+ writer->Update();
}
+
void insertTriangles(vtkCellArray *cells, vtkPoints *points, const vtkIdType ids[4]) {
- double p0[3]; points->GetPoint(ids[0],p0);
- double p1[3]; points->GetPoint(ids[1],p1);
- double p2[3]; points->GetPoint(ids[2],p2);
- double p3[3]; points->GetPoint(ids[3],p3);
- //cout << "----------------------------------" << endl;
- //cout << "p0=[" << p0[0] << "," << p0[1] << "," << p0[2] << "]" << endl;
- //cout << "p1=[" << p1[0] << "," << p1[1] << "," << p1[2] << "]" << endl;
- //cout << "p2=[" << p2[0] << "," << p2[1] << "," << p2[2] << "]" << endl;
- //cout << "p3=[" << p3[0] << "," << p3[1] << "," << p3[2] << "]" << endl;
-
- double center[] = {0,0,0};
- for (int kk=0; kk<3; kk++) {
- center[kk] += p0[kk];
- center[kk] += p1[kk];
- center[kk] += p2[kk];
- center[kk] += p3[kk];
- center[kk] /= 4.;
- }
-
- vtkIdType center_id = points->InsertNextPoint(center);
- //cout << "center=[" << center[0] << "," << center[1] << "," << center[2] << "]" << endl;
-
- cells->InsertNextCell(3);
- cells->InsertCellPoint(ids[0]);
- cells->InsertCellPoint(ids[1]);
- cells->InsertCellPoint(center_id);
-
- cells->InsertNextCell(3);
- cells->InsertCellPoint(ids[1]);
- cells->InsertCellPoint(ids[3]);
- cells->InsertCellPoint(center_id);
-
- cells->InsertNextCell(3);
- cells->InsertCellPoint(ids[3]);
- cells->InsertCellPoint(ids[2]);
- cells->InsertCellPoint(center_id);
-
- cells->InsertNextCell(3);
- cells->InsertCellPoint(ids[2]);
- cells->InsertCellPoint(ids[0]);
- cells->InsertCellPoint(center_id);
+ double p0[3]; points->GetPoint(ids[0],p0);
+ double p1[3]; points->GetPoint(ids[1],p1);
+ double p2[3]; points->GetPoint(ids[2],p2);
+ double p3[3]; points->GetPoint(ids[3],p3);
+ //cout << "----------------------------------" << endl;
+ //cout << "p0=[" << p0[0] << "," << p0[1] << "," << p0[2] << "]" << endl;
+ //cout << "p1=[" << p1[0] << "," << p1[1] << "," << p1[2] << "]" << endl;
+ //cout << "p2=[" << p2[0] << "," << p2[1] << "," << p2[2] << "]" << endl;
+ //cout << "p3=[" << p3[0] << "," << p3[1] << "," << p3[2] << "]" << endl;
+
+ double center[] = {0,0,0};
+ for (int kk=0; kk<3; kk++) {
+ center[kk] += p0[kk];
+ center[kk] += p1[kk];
+ center[kk] += p2[kk];
+ center[kk] += p3[kk];
+ center[kk] /= 4.;
+ }
+
+ vtkIdType center_id = points->InsertNextPoint(center);
+ //cout << "center=[" << center[0] << "," << center[1] << "," << center[2] << "]" << endl;
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(ids[1]);
+ cells->InsertCellPoint(center_id);
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[1]);
+ cells->InsertCellPoint(ids[3]);
+ cells->InsertCellPoint(center_id);
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[3]);
+ cells->InsertCellPoint(ids[2]);
+ cells->InsertCellPoint(center_id);
+
+ cells->InsertNextCell(3);
+ cells->InsertCellPoint(ids[2]);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(center_id);
+}
+
+void insertLine(vtkCellArray *cells, vtkPoints *points, const vtkIdType ids[2]) {
+ cells->InsertNextCell(2);
+ cells->InsertCellPoint(ids[0]);
+ cells->InsertCellPoint(ids[1]);
}
double getMaximum(vtkImageData *image) {
- bool first = true;
- double maximum = 0;
+ bool first = true;
+ double maximum = 0;
- for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
- double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
+ vtkPointData* point_data = image->GetPointData();
+ assert(point_data);
+ vtkDataArray* scalars = point_data->GetScalars();
+ assert(scalars);
- if (first) {
- maximum = value;
- first = false;
- continue;
- }
+ for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
+ double value = scalars->GetTuple1(kk);
+
+ if (first) {
+ maximum = value;
+ first = false;
+ continue;
+ }
- if (maximum<value) maximum = value;
- }
+ if (maximum<value) maximum = value;
+ }
- return maximum;
+ return maximum;
}
+
vtkPolyData *buildPlane(vtkImageData *image,double spatial_margin,double dose_margin) {
- vtkPoints *points = vtkPoints::New();
- for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
- double *point = image->GetPoint(kk);
- double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
- assert(value>=0);
- assert(point[2]==0);
- point[2] = value;
-
- point[0] /= spatial_margin;
- point[1] /= spatial_margin;
- point[2] /= dose_margin;
+ vtkPoints *points = vtkPoints::New();
+ for (int kk=0; kk<image->GetNumberOfPoints(); kk++) {
+ double *point = image->GetPoint(kk);
+ double value = image->GetPointData()->GetScalars()->GetTuple1(kk);
+ assert(value>=0);
+ assert(point[2]==0);
+ point[2] = value;
+
+ point[0] /= spatial_margin;
+ point[1] /= spatial_margin;
+ point[2] /= dose_margin;
#ifndef NDEBUG
- vtkIdType point_id = points->InsertNextPoint(point);
- assert(kk==point_id);
+ vtkIdType point_id = points->InsertNextPoint(point);
+ assert(kk==point_id);
#else
- points->InsertNextPoint(point);
+ points->InsertNextPoint(point);
#endif
- }
-
- vtkCellArray *cells = vtkCellArray::New();
- for (int kk=0; kk<image->GetNumberOfCells(); kk++) {
- vtkCell *cell = image->GetCell(kk);
- assert(cell->GetNumberOfPoints()==4);
- insertTriangles(cells,points,cell->GetPointIds()->GetPointer(0));
- }
-
- vtkPolyData *data = vtkPolyData::New();
- data->SetPoints(points);
- data->SetPolys(cells);
- points->Delete();
- cells->Delete();
-
- return data;
-}
+ }
-void assert2D(vtkImageData *image) {
-#ifndef NDEBUG
- int *extent = image->GetWholeExtent();
- assert(extent[4]==0);
- assert(extent[5]==0);
-#endif
+ vtkCellArray *cells = vtkCellArray::New();
+ for (int kk=0; kk<image->GetNumberOfCells(); kk++) {
+ vtkCell *cell = image->GetCell(kk);
+
+ if (cell->GetNumberOfPoints()==4) {
+ insertTriangles(cells,points,cell->GetPointIds()->GetPointer(0));
+ continue;
+ }
+
+ if (cell->GetNumberOfPoints()==2) {
+ insertLine(cells,points,cell->GetPointIds()->GetPointer(0));
+ continue;
+ }
+
+ assert(false);
+ }
+
+ vtkPolyData *data = vtkPolyData::New();
+ data->SetPoints(points);
+ data->SetPolys(cells);
+ points->Delete();
+ cells->Delete();
+
+ return data;
}
int main(int argc,char * argv[])
{
- args_info_clitkGammaIndex args_info;
-
- if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
- exit(1);
-
- if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
- std::cerr << "Specify either relative or absolute dose margin" << endl;
- exit(1);
- }
-
- bool verbose = args_info.verbose_flag;
-
- std::string reference_filename(args_info.reference_arg);
- std::string target_filename(args_info.target_arg);
- std::string gamma_filename(args_info.output_arg);
- double space_margin = args_info.spatial_margin_arg;
- double dose_rel_margin = args_info.relative_dose_margin_arg;
- double dose_margin = args_info.absolute_dose_margin_arg;
- bool use_dose_margin = args_info.absolute_dose_margin_given;
-
- if (verbose) {
- cout << "reference_filename=" << reference_filename << endl;
- cout << "target_filename=" << target_filename << endl;
- cout << "gamma_filename=" << gamma_filename << endl;
- cout << "space_margin=" << space_margin << endl;
- if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
- else cout << "dose_rel_margin=" << dose_rel_margin << endl;
- }
-
- // load reference
- vtkImageData *reference = loadImage(reference_filename);
- assert2D(reference);
-
- // intensity normalisation
- if (!use_dose_margin) {
- dose_margin = getMaximum(reference)*dose_rel_margin;
- if (verbose) cout << "dose_margin=" << dose_margin << endl;
- }
-
- // build surface
- vtkPolyData *data = buildPlane(reference,space_margin,dose_margin);
- reference->Delete();
-
- vtkAbstractCellLocator *locator = vtkCellLocator::New();
- locator->SetDataSet(data);
- data->Delete();
- locator->CacheCellBoundsOn();
- locator->AutomaticOn();
- locator->BuildLocator();
-
- // load target
- vtkImageData *target = loadImage(target_filename);
- assert2D(target);
-
- // allocate output
- vtkImageData *output = vtkImageData::New();
- output->SetExtent(target->GetWholeExtent());
- output->SetOrigin(target->GetOrigin());
- output->SetSpacing(target->GetSpacing());
- output->SetScalarTypeToFloat();
- output->AllocateScalars();
-
- // fill output
- unsigned long total = 0;
- unsigned long over_one = 0;
- for (int kk=0; kk<target->GetNumberOfPoints(); kk++) {
- double *point = target->GetPoint(kk);
- double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
- assert(value>=0);
- assert(point[2]==0);
- point[2] = value;
-
- point[0] /= space_margin;
- point[1] /= space_margin;
- point[2] /= dose_margin;
-
- double closest_point[3] = {0,0,0};
- vtkIdType cell_id = 0;
- int foo = 0;
- double squared_distance = 0;
-
- locator->FindClosestPoint(point,closest_point,cell_id,foo,squared_distance);
-
- double distance = sqrt(squared_distance);
- output->GetPointData()->GetScalars()->SetTuple1(kk,distance);
-
- if (value>1) over_one++;
- total++;
-
- }
-
- if (verbose) {
- cout << "total=" << total << endl;
- cout << "over_one=" << over_one << endl;
- cout << "ratio=" << static_cast<float>(over_one)/total << endl;
- }
-
- locator->Delete();
- target->Delete();
-
- saveImage(output,gamma_filename);
- output->Delete();
-
- return 0;
+ clitk::RegisterClitkFactories();
+
+ args_info_clitkGammaIndex args_info;
+
+ if (cmdline_parser_clitkGammaIndex(argc, argv, &args_info) != 0)
+ exit(1);
+
+ if (!args_info.absolute_dose_margin_given && !args_info.relative_dose_margin_given) {
+ std::cerr << "Specify either relative or absolute dose margin" << endl;
+ exit(1);
+ }
+
+ bool verbose = args_info.verbose_flag;
+
+ std::string reference_filename(args_info.reference_arg);
+ std::string target_filename(args_info.target_arg);
+ std::string gamma_filename(args_info.output_arg);
+ double space_margin = args_info.spatial_margin_arg;
+ double dose_rel_margin = args_info.relative_dose_margin_arg;
+ double dose_margin = args_info.absolute_dose_margin_arg;
+ bool use_dose_margin = args_info.absolute_dose_margin_given;
+
+ if (verbose) {
+ cout << "reference_filename=" << reference_filename << endl;
+ cout << "target_filename=" << target_filename << endl;
+ cout << "gamma_filename=" << gamma_filename << endl;
+ cout << "space_margin=" << space_margin << endl;
+ if (use_dose_margin) cout << "dose_margin=" << dose_margin << endl;
+ else cout << "dose_rel_margin=" << dose_rel_margin << endl;
+ }
+
+ // load reference
+ vtkImageData* reference = loadImage(reference_filename);
+ assert(reference);
+
+ // intensity normalisation
+ if (!use_dose_margin) {
+ dose_margin = getMaximum(reference)*dose_rel_margin;
+ if (verbose) cout << "dose_margin=" << dose_margin << endl;
+ }
+
+ // build surface
+ vtkPolyData *data = buildPlane(reference,space_margin,dose_margin);
+ reference->Delete();
+
+ vtkAbstractCellLocator *locator = vtkCellLocator::New();
+ locator->SetDataSet(data);
+ data->Delete();
+ locator->CacheCellBoundsOn();
+ locator->AutomaticOn();
+ locator->BuildLocator();
+
+ // load target
+ vtkImageData* target = loadImage(target_filename);
+ assert(target);
+
+ // allocate output
+ OutputImageType::Pointer output = OutputImageType::New();
+ {
+ OutputImageType::SizeType::SizeValueType output_array_size[2];
+ output_array_size[0] = target->GetDimensions()[0];
+ output_array_size[1] = target->GetDimensions()[1];
+ OutputImageType::SizeType output_size;
+ output_size.SetSize(output_array_size);
+ output->SetRegions(OutputImageType::RegionType(output_size));
+ output->SetOrigin(target->GetOrigin());
+ output->SetSpacing(target->GetSpacing());
+ output->Allocate();
+ }
+
+ // fill output
+ unsigned long kk = 0;
+ unsigned long over_one = 0;
+ OutputImageIterator iter(output,output->GetLargestPossibleRegion());
+ iter.GoToBegin();
+ while (!iter.IsAtEnd()) {
+ double *point = target->GetPoint(kk);
+ double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
+ assert(value>=0);
+ assert(point[2]==0);
+ point[2] = value;
+
+ point[0] /= space_margin;
+ point[1] /= space_margin;
+ point[2] /= dose_margin;
+
+ double closest_point[3] = {0,0,0};
+ vtkIdType cell_id = 0;
+ int foo = 0;
+ double squared_distance = 0;
+
+ locator->FindClosestPoint(point,closest_point,cell_id,foo,squared_distance);
+ double distance = sqrt(squared_distance);
+ iter.Set(distance);
+
+ if (distance>1) over_one++;
+ kk++;
+ ++iter;
+ }
+
+ if (verbose) {
+ cout << "total=" << kk << endl;
+ cout << "over_one=" << over_one << endl;
+ cout << "ratio=" << static_cast<float>(over_one)/kk << endl;
+ }
+
+ locator->Delete();
+ target->Delete();
+
+ saveImage(output,gamma_filename);
+
+ return 0;
}
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff