X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvImageReader.cxx;h=5c6eba3ef40d7ffb3e8da0b5dc3b2a2ae54a2709;hb=fe61abeb6e452e5f54bef60a287aa104e4e02d70;hp=faa22b85b73b3ba9868e749742f5cf4e7ebfd2ec;hpb=424c311bc966bc93f73022d7371a6249b00a51b6;p=clitk.git diff --git a/vv/vvImageReader.cxx b/vv/vvImageReader.cxx index faa22b8..5c6eba3 100644 --- a/vv/vvImageReader.cxx +++ b/vv/vvImageReader.cxx @@ -1,119 +1,157 @@ /*========================================================================= + Program: vv http://www.creatis.insa-lyon.fr/rio/vv - Program: vv - Module: $RCSfile: vvImageReader.cxx,v $ - Language: C++ - Date: $Date: 2010/01/26 15:04:33 $ - Version: $Revision: 1.2 $ - Author : Pierre Seroul (pierre.seroul@gmail.com) + 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 -Copyright (C) 2008 -Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr -CREATIS-LRMN 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. -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, version 3 of the License. + It is distributed under dual licence -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=========================================================================*/ -#ifndef vvImageReader_CXX -#define vvImageReader_CXX + - 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 #include #include #include "vvImageReader.h" #include "vvImageReader.txx" - -//==================================================================== +//------------------------------------------------------------------------------ vvImageReader::vvImageReader() { - mImage = NULL; - mInputFilenames.resize(0); - mLastError = ""; - mType = UNDEFINEDIMAGETYPE; + mImage = NULL; + mInputFilenames.resize(0); + mLastError = ""; + mType = UNDEFINEDIMAGETYPE; } +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ 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()) + //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); + 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 & filenames) { - mInputFilenames = filenames; + mInputFilenames = filenames; } -//==================================================================== +//------------------------------------------------------------------------------ + +//------------------------------------------------------------------------------ +//Read transformation in NKI format (Xdr, transposed, cm) +void vvImageReader::ReadNkiImageTransform() +{ + bool bRead=true; + typedef itk::ImageFileReader< itk::Image< double, 2 > > MatrixReaderType; + MatrixReaderType::Pointer readerTransfo = MatrixReaderType::New(); + readerTransfo->SetFileName(mInputFilenames[0]+".MACHINEORIENTATION"); + try + { readerTransfo->Update(); + } + catch( itk::ExceptionObject & err ) + { bRead=false; + } + + if (bRead) + { double mat[16]; + + //Transpose matrix (NKI format) + for(int j=0; j<4; j++) + for(int i=0; i<4; i++) + mat[4*j+i]=readerTransfo->GetOutput()->GetBufferPointer()[4*i+j]; + + //From cm to mm + for(int i=0; i<3; i++) + mat[4*i+3]*=10; + + //Set Transformation + vtkSmartPointer pt = vtkSmartPointer::New(); + pt->SetMatrix( mat ); + pt->Inverse(); + mImage->SetTransform( pt ); + } +} +//------------------------------------------------------------------------------ #endif