X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FcreaImageIOGimmickView.cpp;h=4ada3a9c54277a33230e0bee464de9bc514f3f3f;hb=bebe9cec5af89cf1461b3230c9aa31e930d49fb8;hp=02d18a7d490af03bb2eab27f1540d000f6b5aea3;hpb=a881ab2fb97d10dd3cff975444f81b0b497b2ad7;p=creaImageIO.git diff --git a/src/creaImageIOGimmickView.cpp b/src/creaImageIOGimmickView.cpp index 02d18a7..4ada3a9 100644 --- a/src/creaImageIOGimmickView.cpp +++ b/src/creaImageIOGimmickView.cpp @@ -1,5 +1,33 @@ +/* +# --------------------------------------------------------------------- +# +# 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 -#include + #include "boost/filesystem.hpp" #if defined(USE_GDCM) @@ -10,16 +38,18 @@ #include #endif -#if defined(USE_GDCM2) +/*#if defined(USE_GDCM2) #include #include "gdcmSystem.h" #include "gdcmCryptographicMessageSyntax.h" #include "gdcmUIDGenerator.h" #include "gdcmAnonymizer.h" #include "gdcmGlobal.h" +#endif*/ +#if defined(_WIN32) +#pragma warning(disable: 4996) #endif - namespace fs = boost::filesystem; namespace creaImageIO { @@ -354,11 +384,11 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect if(ext[5] == 0) { - ext[5] = im.size()-1; + ext[5] = (int)im.size()-1; } else { - ext[5] = ext[5] * im.size()-1; // to deal with multiframes - JPR + ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes - JPR } out->SetExtent(ext); @@ -367,7 +397,7 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect int dim[3]; first->GetDimensions(dim); - out->SetDimensions(dim[0], dim[1], im.size() ); + out->SetDimensions(dim[0], dim[1], (int)im.size() ); out->AllocateScalars(); out->Update(); @@ -456,20 +486,37 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect void GimmickView::readImages1(std::vector& o_output, std::vector im, OutputAttr i_attr) { + + i_attr.outside.push_back("D0019_100a"); // simens Number Of Images In Mosaic + +//EED Borrame + int i,isize=i_attr.outside.size(); + for (i=0;i::iterator it; for (it=im.begin(); it!=im.end(); ++it) { OutStrGimmick out; out.img = vtkImageData::New(); out.img->ShallowCopy(mReader.GetImage(*it)); - if(i_attr.mult) +printf("EED GimmickView::readImages1 A\n "); + if(i_attr.mult) + { getAttributes((*it),out.infos,i_attr); +printf("EED GimmickView::readImages1 B %s \n ", out.infos.find("D0019_100a")->second.c_str() ); + } o_output.push_back(out); } // If we want only one output information structure, we set it outside the loop if(!i_attr.mult) { getAttributes(im.front(), o_output.front().infos, i_attr); +printf("EED GimmickView::readImages1 C %s \n ", o_output.front().infos.find("D0019_100a")->second.c_str() ); } } @@ -489,11 +536,9 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect first->GetWholeExtent(ext); // send also 0,0 in Z if(ext[5] == 0) { - ext[5] = im.size()-1; - } - else - { - ext[5] = ext[5] * im.size()-1; // to deal with multiframes + ext[5] = (int)im.size()-1; + } else { + ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes } out.img->SetExtent(ext); int dim[3]; @@ -501,7 +546,7 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect first->GetDimensions(dim); first->GetSpacing(spac); out.img->SetSpacing(spac); - out.img->SetDimensions(dim[0], dim[1], im.size() ); + out.img->SetDimensions(dim[0], dim[1], (int)im.size() ); out.img->AllocateScalars(); out.img->Update(); unsigned long imsize = dim[0] * dim[1]; @@ -545,7 +590,7 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect std::vector::iterator it; std::vector::iterator it_out = o_output.begin(); - for (it=im.begin(); it!=im.end(); ++it, it_out += dim[2]) + for (it=im.begin(); it!=im.end(); ++it)//, it_out ++) { vtkImageData* cur = mReader.GetImage( (*it) ); for (int slice= 0 ; slice & s, std::vect memcpy(out.img->GetScalarPointer(0,0,0), cur->GetScalarPointer(0,0,slice), imsize); o_output.push_back(out); } - if(i_attr.mult) - getAttributes((*it),(*it_out).infos,i_attr); + // if(i_attr.mult) + // getAttributes((*it),(*it_out).infos,i_attr); } if(!i_attr.mult) { @@ -602,7 +647,7 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect out.img->SetExtent(ext); first->GetSpacing(spac); out.img->SetSpacing(spac); - out.img->SetDimensions(dim[0], dim[1], im.size() ); + out.img->SetDimensions(dim[0], dim[1], (int)im.size() ); out.img->AllocateScalars(); out.img->Update(); unsigned long imsize = dim[0] * dim[1]; @@ -631,28 +676,21 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect void GimmickView::readImages(std::vector& o_output, std::vector im, OutputAttr i_attr, int i_dim, double i_zspc) { - int size = im.size(); + int size = (int)im.size(); if ( size == 0) { return; - } - else if (size == 1) - { + } else if (size == 1) { // Simplest case // Only one image : give it // But take in count multiframe possibility if ( isSingle(im.front()) || i_dim != 1) { readImages1(o_output,im, i_attr); - } - else - { - readImages2(o_output,im, i_attr,i_zspc); - } - - } - else - { + } else { + readImages2(o_output,im, i_attr,i_zspc); + } + } else { // multiple or single frame if ( isSingle(im.front()) ) { @@ -661,40 +699,33 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect { // 2D to 3D readImages3(o_output,im, i_attr,i_zspc); - } - else - { + } else { readImages1(o_output,im, i_attr); } - } - else - { + } else { // we deal with multiple frames n x (2D x T) // Differents outputs are avaialable if(i_dim == 1) { // put all in one output readImages3(o_output,im, i_attr,i_zspc); - - } - else if( i_dim == 2) - { + } else if( i_dim == 2) { // put in a vector of n x T (2D) readImages2(o_output,im, i_attr,i_zspc); - } - else if( i_dim == 3) - { + } else if( i_dim == 3) { // put in a vector of n (2D x T) // No transformations. readImages1(o_output,im, i_attr); - } - else - { + } else { // put in a vector of T (2D x n) readImages4(o_output,im, i_attr); - } - } - } + } // i_dim + } //isSingle(im.front()) + } // if size + +//EED UnMosaic step... +//How to verifie if is a mosaic file , with how many images inside?? + } @@ -715,7 +746,7 @@ void GimmickView::ReadImagesNotThreadedInVector(std::vector& s, s else if (im.size()>1) // Test inutile ? JPR { /// \TODO fix unused variable 'first' - vtkImageData* first = mReader.GetImage( im.front()); +// vtkImageData* first = mReader.GetImage( im.front()); if (dimension == 2) { // n3D @@ -725,10 +756,8 @@ void GimmickView::ReadImagesNotThreadedInVector(std::vector& s, s vtkImageData* out = vtkImageData::New(); out->ShallowCopy(mReader.GetImage(*it)); s.push_back(out); - } - } - else - { + } // for + } else { // n2D to 3D // NO! // n *2D + T in a vector : @@ -737,9 +766,9 @@ void GimmickView::ReadImagesNotThreadedInVector(std::vector& s, s { vtkImageData* out = mReader.GetImage( (*it)); s.push_back(out); - } - } - } + } // for + } // if dimension + } // if im.size } //====================================================================== @@ -840,7 +869,7 @@ void GimmickView::ReadImagesNotThreadedInVector(std::vector& s, s } - +#if defined(USE_GDCM) //////////////////////////////////////////////////////////////////////// void GimmickView::Anonymize(std::vector i_filenames, int type) { @@ -870,8 +899,9 @@ void GimmickView::Anonymize(std::vector i_filenames, int type) // We need a gdcm::FileHelper, since we want to load the pixels GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(file); - - uint8_t *imageData = fh->GetImageData(); + +//Borrame +//EED uint8_t *imageData = fh->GetImageData(); // Institution name file->AddAnonymizeElement(0x0008, 0x0080, "*"); @@ -895,12 +925,18 @@ void GimmickView::Anonymize(std::vector i_filenames, int type) fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE); fh->WriteDcmExplVR(file->GetFileName() +".ano1" ); - std::cout << i <<" End Anonymize" << std::cout; + std::cout << i <<" End Anonymize" << std::endl; file->ClearAnonymizeList(); file->Delete(); fh->Delete(); } } +#endif +#if defined(USE_GDCM2) +void GimmickView::Anonymize(std::vector i_filenames, int type) +{ +} +#endif //////////////////////////////////////////////////////////////////////// //void GimmickView::Anonymize(std::vector i_filenames, int type) //{