/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
-#ifndef vvImageReader_CXX
-#define vvImageReader_CXX
+ ======================================================================-====*/
+#ifndef VVIMAGEREADER_CXX
+#define VVIMAGEREADER_CXX
+
#include <QApplication>
#include <itkImageFileReader.h>
#include "vvImageReader.h"
#include "vvImageReader.txx"
+#include "clitkTransformUtilities.h"
-
-//====================================================================
+//------------------------------------------------------------------------------
vvImageReader::vvImageReader()
{
- mImage = NULL;
- mInputFilenames.resize(0);
- mLastError = "";
- mType = UNDEFINEDIMAGETYPE;
+ mImage = NULL;
+ mInputFilenames.resize(0);
+ mLastError = "";
+ mType = UNDEFINEDIMAGETYPE;
+ mSlice = 0;
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
vvImageReader::~vvImageReader() { }
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvImageReader::Update()
{
- Update(mType);
+ Update(mType);
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvImageReader::Update(LoadedImageType type)
{
- itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(mInputFilenames[0].c_str(), itk::ImageIOFactory::ReadMode);
- if (!reader) {
- mLastError="Unable to read file.";
- }
- else {
- reader->SetFileName(mInputFilenames[0]);
- reader->ReadImageInformation();
- if (mInputFilenames.size() > 1)
- Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
- else
- Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
- }
+ itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(mInputFilenames[0].c_str(), itk::ImageIOFactory::ReadMode);
+ if (!reader) {
+ mLastError="Unable to read file.";
+ } else {
+ reader->SetFileName(mInputFilenames[0]);
+ reader->ReadImageInformation();
+ if (mInputFilenames.size() > 1)
+ Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+ else
+ Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+ }
}
+//------------------------------------------------------------------------------
-//====================================================================
-void vvImageReader::Update(int dim,std::string inputPixelType, LoadedImageType type) {
- //CALL_FOR_ALL_DIMS(dim,UpdateWithDim,inputPixelType);
- mType = type;
- mDim = dim;
- mInputPixelType=inputPixelType;
- this->start(); //Start heavy read operation in a separate thread
- while (this->isRunning())
- {
- qApp->processEvents();
- this->wait(50);
- }
+
+//------------------------------------------------------------------------------
+void vvImageReader::Update(int dim,std::string inputPixelType, LoadedImageType type)
+{
+ //CALL_FOR_ALL_DIMS(dim,UpdateWithDim,inputPixelType);
+ mType = type;
+ mDim = dim;
+ mInputPixelType=inputPixelType;
+ this->start(); //Start heavy read operation in a separate thread
+ while (this->isRunning()) {
+ qApp->processEvents();
+ this->wait(50);
+ }
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvImageReader::run()
{
- switch(mDim)
- {
- case 2:
- UpdateWithDim<2>(mInputPixelType);
- break;;
- case 3:
- UpdateWithDim<3>(mInputPixelType);
- break;;
- case 4:
- UpdateWithDim<4>(mInputPixelType);
- break;;
- default:
- std::cerr << "dimension unknown in Update ! " << std::endl;
- }
+ switch(mDim) {
+ case 2:
+ UpdateWithDim<2>(mInputPixelType);
+ break;;
+ case 3:
+ UpdateWithDim<3>(mInputPixelType);
+ break;;
+ case 4:
+ UpdateWithDim<4>(mInputPixelType);
+ break;;
+ default:
+ std::cerr << "dimension unknown in Update ! " << std::endl;
+ }
}
-//====================================================================
+//------------------------------------------------------------------------------
+
-//====================================================================
-/*void vvImageReader::Extract(int dim, std::string inputPixelType, int slice) {
- CALL_FOR_ALL_DIMS(dim, ExtractWithDim, inputPixelType, slice);
-}*/
-//====================================================================
+//------------------------------------------------------------------------------
void vvImageReader::SetInputFilename(const std::string & filename)
{
- mInputFilenames.resize(0);
- mInputFilenames.push_back(filename);
+ mInputFilenames.resize(0);
+ mInputFilenames.push_back(filename);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvImageReader::SetInputFilenames(const std::vector<std::string> & filenames)
+{
+ mInputFilenames = filenames;
}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+//Read transformation in NKI format (Xdr, transposed, cm)
+void vvImageReader::ReadNkiImageTransform()
+{
+ bool bRead=false;
+ std::string filename = mInputFilenames[0]+".MACHINEORIENTATION";
+ if(itksys::SystemTools::FileExists(filename.c_str())){
+ typedef itk::ImageFileReader< itk::Image< double, 2 > > MatrixReaderType;
+ MatrixReaderType::Pointer readerTransfo = MatrixReaderType::New();
+ readerTransfo->SetFileName(filename);
+ try {
+ bRead = true;
+ readerTransfo->Update();
+ } catch( itk::ExceptionObject & err ) {
+ bRead=false;
+ std::cerr << "Cannot read " << filename << std::endl
+ << "The error is: " << err << std::endl;
+ }
-//====================================================================
-void vvImageReader::SetInputFilenames(const std::vector<std::string> & filenames) {
- mInputFilenames = filenames;
+ if (bRead) {
+ //Transpose matrix (NKI format)
+ for(int j=0; j<4; j++)
+ for(int i=0; i<4; i++)
+ mImage->GetTransform()->GetMatrix()->SetElement(j,i,readerTransfo->GetOutput()->GetBufferPointer()[4*i+j]);
+
+ //From cm to mm
+ for(int i=0; i<3; i++)
+ mImage->GetTransform()->GetMatrix()->SetElement(i,3,10*mImage->GetTransform()->GetMatrix()->GetElement(i,3));
+
+ mImage->GetTransform()->Inverse();
+ }
+ }
}
-//====================================================================
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+//Read transformation in ASCII format
+void vvImageReader::ReadMatImageTransform()
+{
+ std::string filename(mInputFilenames[0]+".mat");
+ std::ifstream f(filename.c_str());
+ if(f.is_open()) {
+ f.close();
+
+ itk::Matrix<double, 4, 4> itkMat = clitk::ReadMatrix3D(filename);
+
+ vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
+ transform->Identity();
+ for(int j=0; j<4; j++)
+ for(int i=0; i<4; i++)
+ transform->GetMatrix()->SetElement(j,i,itkMat[j][i]);
+
+ mImage->GetTransform()->PostMultiply();
+ mImage->GetTransform()->Concatenate(transform->GetMatrix());
+ mImage->GetTransform()->Update();
+ }
+}
+//------------------------------------------------------------------------------
#endif
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff