X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FcreaImageIOSimpleView.cpp;h=98321c132c24fe5f53098a125f85085640d36ec1;hb=3579beef5bd466705bc0431d7347d1150cdffe97;hp=c3d22d4ee0d9d03c36d788c2eb6b7f27a72a1929;hpb=d17451ab47af34069d6dcda617ff6e4a132f3d0f;p=creaImageIO.git diff --git a/src/creaImageIOSimpleView.cpp b/src/creaImageIOSimpleView.cpp index c3d22d4..98321c1 100644 --- a/src/creaImageIOSimpleView.cpp +++ b/src/creaImageIOSimpleView.cpp @@ -1,11 +1,53 @@ -#include "creaImageIOSimpleView.h" +/* +# --------------------------------------------------------------------- +# +# Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image +# pour la Santé) +# Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton +# Previous Authors : Laurent Guigues, Jean-Pierre Roux +# CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil +# +# This software is governed by the CeCILL-B license under French law and +# abiding by the rules of distribution of free software. You can use, +# modify and/ or redistribute the software under the terms of the CeCILL-B +# license as circulated by CEA, CNRS and INRIA at the following URL +# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html +# or in the file LICENSE.txt. +# +# As a counterpart to the access to the source code and rights to copy, +# modify and redistribute granted by the license, users are provided only +# with a limited warranty and the software's author, the holder of the +# economic rights, and the successive licensors have only limited +# liability. +# +# The fact that you are presently reading this means that you have had +# knowledge of the CeCILL-B license and that you accept its terms. +# ------------------------------------------------------------------------ +*/ + #include "boost/filesystem/operations.hpp" #include "boost/filesystem/fstream.hpp" +#include "creaImageIOSimpleView.h" +#include "creaImageIOUnMosaicVtkImageData.h" + namespace creaImageIO { - bool SimpleView::readFile(std::vector i_filenames, std::vector &i_img) + bool SimpleView::readFile( std::vector i_filenames, // in information names + std::vector i_attr, // in information attributes names + std::vector > &i_imgAttr, // out information attributes names-values + std::vector &i_img) // out information vtkImageData { + //Mosaic Attribute for Simens + i_attr.push_back("D0019_100a"); // Number of images in mosaic (Simens) + i_attr.push_back("D0018_0088"); // Spacing Between Slices + creaImageIOUnMosaicVtkImageData Mosaic; + vtkImageData* tmpImg1; + vtkImageData* tmpImg2; + int numberOfImagesInMosaic; + double spc[3]; + double spcZ; + bool bresult, bfinal = true; ImageReader *mReader = new ImageReader(); std::vector::iterator it = i_filenames.begin(); @@ -14,18 +56,54 @@ namespace creaImageIO bresult = mReader->CanRead((*it).c_str()); if(bresult) { - i_img.push_back(mReader->ReadImage((*it).c_str())); - } - else - { + std::map mapAttr; + mReader->getAttributes( (*it).c_str() , mapAttr, i_attr ); // filename, outMapAttr-NameValue, inVectAttributeName + i_imgAttr.push_back( mapAttr ); + +//EED borrame +// i_img.push_back( mReader->ReadImage( (*it).c_str() ) ); + + + // EED 18 octt 2014 + std::map ::iterator itMapAttr; + std::string numberOfImagesInMosaicStr=""; + std::string spaceBetweenSliceStr=""; + + itMapAttr = mapAttr.find("D0019_100a"); + if ( itMapAttr!=mapAttr.end() ) numberOfImagesInMosaicStr = itMapAttr->second; + +// std::string numberOfImagesInMosaicStr = mapAttr.find("D0019_100a")->second; + itMapAttr = mapAttr.find("D0018_0088"); + if ( itMapAttr!=mapAttr.end() ) spaceBetweenSliceStr = itMapAttr->second; + +// std::string spaceBetweenSliceStr = mapAttr.find("D0018_0088")->second; + if (numberOfImagesInMosaicStr=="") + { + i_img.push_back( mReader->ReadImage( (*it).c_str() ) ); + } else { + numberOfImagesInMosaic = atoi(numberOfImagesInMosaicStr.c_str()); + spcZ = atoi(spaceBetweenSliceStr.c_str()); + tmpImg1 = mReader->ReadImage( (*it).c_str() ) ; + tmpImg1->GetSpacing( spc ); + tmpImg2 = Mosaic.unMosaic( tmpImg1 , numberOfImagesInMosaic ); + tmpImg2->SetSpacing( spc[0], spc[1], spcZ ); + i_img.push_back( tmpImg2 ); + }// elemet + + } else { + printf("ERROR. Impossible to read file %s\n", (*it).c_str() ); bfinal = false; - } - } + } // if + } // for delete mReader; return bfinal; } - bool SimpleView::readDirectory(const std::string i_pathname, std::vector &i_imgs) + + bool SimpleView::readDirectory( const std::string i_pathname, // in information names + std::vector i_attr, // in information attributes names + std::vector > &i_imgAttr, // out information attributes names-values + std::vector &i_imgs) // out information vtkImageData { bool bresult = true; ImageReader *mReader = new ImageReader(); @@ -39,22 +117,129 @@ namespace creaImageIO { if (!boost::filesystem::is_directory(itr->status())) { - if( mReader->CanRead(itr->string()) ) + if( mReader->CanRead(itr->path().string()) ) { - names.push_back(itr->string()); + names.push_back(itr->path().string()); } } } std::sort (names.begin(), names.end()); // make sure names are in lexicographical order - int lgr = names.size(); + int lgr = (int)names.size(); for(int i=0; i mapAttr; + mReader->getAttributes( names[i] , mapAttr, i_attr ); // filename, outMapAttr-NameValue, inVectAttributeName + i_imgAttr.push_back( mapAttr ); + + //UnMosaic step.. + i_imgs.push_back( mReader->ReadImage(names[i]) ); } } return bresult; } -} - + + + vtkImageData* SimpleView::getVolumeSelected( std::vector lstImages) + { + vtkImageData *result; + +// creaImageIO::WxSimpleDlg dlg(0,crea::std2wx(bbGetInputTitle()),"localdatabase_Descriptor.dscp","Local Database"); +// dlg.SetAttrDicomTags( bbGetInputDicomTags() ); +// dlg.ShowModal(); +// bbSetOutputDicomInfo( dlg.getDicomInfoImagesSelected() ); + + if (lstImages.size()!=0) + { +// bbSetOutputFileName( std::string( dlg.getInfoImage().mb_str() ) ); + if(lstImages.size() ==1) + { + result = lstImages[0] ; + } else { + // FCY: it will be a big problem if we have several kind of data in the same folder. + // creation of a huge vtkImageData!!!! + vtkImageData* first = lstImages[0]; + int dim[3]; + first->GetDimensions(dim); + if (dim[2]==1) + { + vtkImageData *out = vtkImageData::New(); + int ext[6]; +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 + first->GetWholeExtent(ext); +#else + first->GetExtent(ext); +#endif + if(ext[5] == 0) + { + ext[5] = lstImages.size()-1; + } else { + ext[5] = ext[5] * lstImages.size()-1; // to deal with multiframes + } // ext + out->SetExtent(ext); + double spac[3]; + first->GetDimensions(dim); + first->GetSpacing(spac); + if (spac[0]==spac[1]) + { + spac[2]=spac[0]; + } + out->SetSpacing(spac); + out->SetDimensions(dim[0], dim[1], lstImages.size() ); +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 + + out->SetScalarType(first->GetScalarType()); + out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents()); + out->AllocateScalars(); + out->Update(); +#else + out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents()); +#endif + + + unsigned long imsize = dim[0] * dim[1]; + imsize = imsize * dim[2]; // deal with multiframes here + // differents formats char , short, etc... + // differents components 1..3 ex. jpg ->RGB 3 + imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents(); + int slice,sizeImageVector=lstImages.size(); + for (slice=0 ; sliceGetScalarPointer(0,0,slice), img->GetScalarPointer(0,0,0), imsize); + //img->Delete(); + } // for slice + out->Modified(); +//EED This is NOT working. The iteration over the pointer vtkImageData +// int slice=0; +// std::vector::iterator it; +// for (it=dlg.getImagesSelected().begin(); it!=dlg.getImagesSelected().end(); ++it) +// { +// memcpy(out->GetScalarPointer(0,0,slice), (*it)->GetScalarPointer(0,0,0), imsize); +// slice++; +// } +// //for (it=dlg.getImagesSelected().begin(); it!=dlg.getImagesSelected().end(); ++it) +// //{ +// // (*it)->Delete(); +// //} + + result =out; + + } else { + result = first; + } // dim + } // if getImagesSelected size + result->Modified(); + } else { + result = NULL; + } // getImagesSelected().size()!=0 + return result; + } + + +} // NAMESPACE