X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FcreaImageIOGimmickView.cpp;h=0a76936736294655e38f4d77fa54c0a5790b89f9;hb=bae8afe7ee037a3368be7060c3a0708582e7d413;hp=3e1224b66c44f786abf094b46a218eb2db91f47b;hpb=2e07001ca19daa5e58e0af4a6e5ebfbe75de91c5;p=creaImageIO.git diff --git a/src/creaImageIOGimmickView.cpp b/src/creaImageIOGimmickView.cpp index 3e1224b..0a76936 100644 --- a/src/creaImageIOGimmickView.cpp +++ b/src/creaImageIOGimmickView.cpp @@ -1,23 +1,55 @@ +/* +# --------------------------------------------------------------------- +# +# 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) #include #include +#include +#include #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 { @@ -28,20 +60,20 @@ namespace creaImageIO public: ImageExtent(const std::string& x, const std::string& y, const std::string& z, const std::string& t) { - sscanf(x.c_str(),"%d",&mExtent[0]); - sscanf(y.c_str(),"%d",&mExtent[1]); - sscanf(z.c_str(),"%d",&mExtent[2]); - sscanf(t.c_str(),"%d",&mExtent[3]); - if(x==""){mExtent[0]=1;} - if(y==""){mExtent[1]=1;} - if(z==""){mExtent[2]=1;} - if(t==""){mExtent[3]=1;} - - if (mExtent[3]>1) mDim=4; - else if (mExtent[2]>1) mDim=3; - else if (mExtent[1]>1) mDim=2; - else if (mExtent[0]>1) mDim=1; - else mDim=0; + sscanf(x.c_str(),"%d",&mExtent[0]); + sscanf(y.c_str(),"%d",&mExtent[1]); + sscanf(z.c_str(),"%d",&mExtent[2]); + sscanf(t.c_str(),"%d",&mExtent[3]); + if(x==""){mExtent[0]=1;} + if(y==""){mExtent[1]=1;} + if(z==""){mExtent[2]=1;} + if(t==""){mExtent[3]=1;} + + if (mExtent[3]>1) mDim=4; + else if (mExtent[2]>1) mDim=3; + else if (mExtent[1]>1) mDim=2; + else if (mExtent[0]>1) mDim=1; + else mDim=0; } @@ -296,11 +328,16 @@ namespace creaImageIO mValidationSignal(ivalid); } + void GimmickView::stopReader() + { + mReader.Stop(); + } + //====================================================================== ///Reads Images (Non Threaded) void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vector im, int dimension) { - mReader.Stop(); + stopReader(); /* remember! #define GIMMICK_NO_IMAGE_SELECTION 0 @@ -347,11 +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); @@ -360,7 +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(); @@ -482,16 +519,19 @@ 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; + ext[5] = (int)im.size()-1; } else { - ext[5] = ext[5] * im.size()-1; // to deal with multiframes + ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes } out.img->SetExtent(ext); int dim[3]; + double spac[3]; first->GetDimensions(dim); - out.img->SetDimensions(dim[0], dim[1], im.size() ); + first->GetSpacing(spac); + out.img->SetSpacing(spac); + out.img->SetDimensions(dim[0], dim[1], (int)im.size() ); out.img->AllocateScalars(); out.img->Update(); unsigned long imsize = dim[0] * dim[1]; @@ -523,7 +563,9 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect { vtkImageData* first = mReader.GetImage( im.front()); int dim[3]; + double spac[3]; first->GetDimensions(dim); + first->GetSpacing(spac); // differents formats char , short, etc... // differents components 1..3 ex. jpg ->RGB 3 unsigned long imsize = dim[0] * dim[1]; @@ -533,7 +575,7 @@ 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 OutStrGimmick out; out.img = vtkImageData::New(); out.img->SetScalarType(first->GetScalarType()); - + out.img->SetSpacing(spac); out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents()); int ext[6]; first->GetWholeExtent(ext); // send also 0,0 in Z @@ -554,8 +596,8 @@ void GimmickView::ReadImagesNotThreaded(std::vector& 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) { @@ -584,11 +626,13 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents()); int ext[6]; + double spac[6]; first->GetWholeExtent(ext); // send also 0,0 in Z ext[5] = 0; out.img->SetExtent(ext); - - out.img->SetDimensions(dim[0], dim[1], im.size() ); + first->GetSpacing(spac); + out.img->SetSpacing(spac); + out.img->SetDimensions(dim[0], dim[1], (int)im.size() ); out.img->AllocateScalars(); out.img->Update(); unsigned long imsize = dim[0] * dim[1]; @@ -617,7 +661,7 @@ 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; @@ -634,11 +678,8 @@ void GimmickView::ReadImagesNotThreaded(std::vector& s, std::vect else { readImages2(o_output,im, i_attr,i_zspc); - } - - } - else - { + } + } else { // multiple or single frame if ( isSingle(im.front()) ) { @@ -700,6 +741,7 @@ 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()); if (dimension == 2) { @@ -825,7 +867,73 @@ void GimmickView::ReadImagesNotThreadedInVector(std::vector& s, s } - +#if defined(USE_GDCM) +//////////////////////////////////////////////////////////////////////// +void GimmickView::Anonymize(std::vector i_filenames, int type) +{ + bool res = true; + std::vector filesH; + std::vector suid; + std::map msuid; + std::string tempuid = GDCM_NAME_SPACE::Util::CreateUniqueUID(); + int i = 1; + std::vector::iterator it = i_filenames.begin(); + for(; it != i_filenames.end(); it++) + { + + GDCM_NAME_SPACE::File *file; + file = GDCM_NAME_SPACE::File::New( ); + file->SetLoadMode( GDCM_NAME_SPACE::LD_ALL ); + file->SetFileName( (*it).c_str() ); + res = file->Load(); + if ( !res ) + { + std::cerr << "Sorry, " << (*it).c_str() <<" not a gdcm-readable " + << "DICOM / ACR File" <Delete(); + //return 0; + } + std::cout << " ... is readable " << std::endl; + + // 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(); + + // Institution name + file->AddAnonymizeElement(0x0008, 0x0080, "*"); + // Patient's name + file->AddAnonymizeElement(0x0010, 0x0010, "*"); + // Patient's ID + file->AddAnonymizeElement( 0x0010, 0x0020,"1515" ); + // Study Instance UID + file->AddAnonymizeElement(0x0020, 0x000d, tempuid ); + // Telephone + file->AddAnonymizeElement(0x0010, 0x2154, "3615" ); + + // Aware user will add here more fields to anonymize here + + // The gdcm::File is modified in memory + + file->AnonymizeFile(); + + + i++; + fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE); + + fh->WriteDcmExplVR(file->GetFileName() +".ano1" ); + std::cout << i <<" End Anonymize" << std::cout; + 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) //{