From: Eduardo DAVILA Date: Wed, 4 Oct 2017 09:45:40 +0000 (+0200) Subject: Merge remote-tracking branch 'origin/changestoITK3and4' into vtk7itk4wx3 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=b52bf19755b9e9f7d4a40abb2c8e881b56d49577;hp=688c28613d4d3f54fb74d55adb653a4a26cebf13;p=creaImageIO.git Merge remote-tracking branch 'origin/changestoITK3and4' into vtk7itk4wx3 --- diff --git a/appli/TestWxGimmickReaderDialog/CMakeLists.txt b/appli/TestWxGimmickReaderDialog/CMakeLists.txt index fa7307b..255ab8f 100644 --- a/appli/TestWxGimmickReaderDialog/CMakeLists.txt +++ b/appli/TestWxGimmickReaderDialog/CMakeLists.txt @@ -30,6 +30,6 @@ ELSE(WIN32) ADD_EXECUTABLE(creaImageIOApp MACOSX_BUNDLE main) ENDIF(WIN32) -TARGET_LINK_LIBRARIES( creaImageIOApp creaImageIO ) +TARGET_LINK_LIBRARIES( creaImageIOApp creaImageIO ${ITK_LIBRARIES} ) INSTALL_TARGETS(/bin/ creaImageIOApp ) diff --git a/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h b/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h index 3b98bfd..d099ff2 100644 --- a/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h +++ b/bbtk/src/bbcreaImageIOGetDicomAttributesFromMaps.h @@ -32,11 +32,11 @@ class bbcreaImageIO_EXPORT GetDicomAttributesFromMaps BBTK_BEGIN_DESCRIBE_BLACK_BOX(GetDicomAttributesFromMaps,bbtk::AtomicBlackBox); BBTK_NAME("GetDicomAttributesFromMaps"); -BBTK_AUTHOR("Info-Dev, Eduardo DAVIL"); +BBTK_AUTHOR("Info-Dev, Eduardo DAVILA"); BBTK_DESCRIPTION("eduardo.davila[at]creatis.insa-lyon.fr -"); BBTK_CATEGORY("empty"); BBTK_INPUT(GetDicomAttributesFromMaps,In,"Vector of maps with DICOM attributes",std::vector< mapString >,""); - BBTK_INPUT(GetDicomAttributesFromMaps,KeyDicom,"Key DICOM",std::string ,""); + BBTK_INPUT(GetDicomAttributesFromMaps,KeyDicom,"Key DICOM ex: D0028_0030 ",std::string ,""); BBTK_OUTPUT(GetDicomAttributesFromMaps,Out,"Vector of the attribute asked.",std::vector ,""); BBTK_END_DESCRIBE_BLACK_BOX(GetDicomAttributesFromMaps); //===== diff --git a/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.cxx b/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.cxx index b3b8552..e0c2a1e 100644 --- a/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.cxx +++ b/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.cxx @@ -1,28 +1,28 @@ /* - # --------------------------------------------------------------------- - # - # 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. - # ------------------------------------------------------------------------ + # --------------------------------------------------------------------- + # + # 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. + # ------------------------------------------------------------------------ */ //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) @@ -31,6 +31,32 @@ #include "bbcreaImageIOItkImagesChooserDialogBox.h" #include "bbcreaImageIOPackage.h" +#include "itkImage.h" +#include "itkImportImageFilter.h" + +/* +// ------------------------------------------------------------------------- +// LFV: avoid itk::Concept check on 4d or superior images +#define BBCREAIMAGEIO_ChooserDlg_Template( t, ty, di ) \ + if( t == typeid( itk::Image< ty, di >* ) ) \ + { \ + this->Export< itk::Image< ty, di > >( ); \ + this->ExportVTK< itk::Image< ty, di > >( ); \ + } +*/ + +// ------------------------------------------------------------------------- +// LFV: avoid itk::Concept check on 4d or superior images +#define BBCREAIMAGEIO_ChooserDlg_Template( t, ty, di ) \ + if( t == typeid( itk::Image< ty, di >* ) ) \ + { \ + this->Export< ty , di >( ); \ + this->ExportVTK< itk::Image< ty, di > >( ); \ + } + + +// ------------------------------------------------------------------------- + namespace bbcreaImageIO { @@ -46,47 +72,115 @@ void ItkImagesChooserDialogBox::Process() dlg->ShowModal(); bbtk::TypeInfo typ = bbitk::GetITKImagePtrTypeInfoFromPixelTypeInfoAndDimension(*dlg->getTypes().front(), dlg->getDims().front()); - BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, Export); - BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, ExportVTK); + + BBCREAIMAGEIO_ChooserDlg_Template( typ, char, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, short, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, int, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, long, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, float, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, double, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned char, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned short, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned int, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned long, 1 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, char, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, short, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, int, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, long, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, float, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, double, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned char, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned short, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned int, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned long, 2 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, char, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, short, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, int, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, long, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, float, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, double, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned char, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned short, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned int, 3 ) + else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned long, 3 ); + + + /* Deprecated + BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, Export); + BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, ExportVTK); + */ delete dlg; } -template + +//template +template void ItkImagesChooserDialogBox::Export() { - if (dlg->getImagesSelected().size() == 1) - { + typedef itk::Image TImage; + if (dlg->getImagesSelected().size() == 1) + { bbSetOutputOut( dlg->getTemplatedImagesSelected().front().GetPointer() ); - } - else if (dlg->getImagesSelected().size() > 1) - { - OutputImagesITKType outVect; - - typename std::vector tempImgs= dlg->getTemplatedImagesSelected(); - typename std::vector::iterator it = tempImgs.begin(); - for(;it != tempImgs.end(); ++it) - { - outVect.push_back( (*it).GetPointer() ); - } - bbSetOutputOutIImages( outVect); - } - else - { + } else if (dlg->getImagesSelected().size() > 1){ + OutputImagesITKType outVect; + typename std::vector tempImgs= dlg->getTemplatedImagesSelected(); + typename std::vector::iterator it = tempImgs.begin(); + for(;it != tempImgs.end(); ++it) + { + outVect.push_back( (*it).GetPointer() ); + } // for + bbSetOutputOutIImages( outVect); + + typedef ty RGBPixelType; + typedef itk::ImportImageFilter< ty , di > ImportFilterType; + typename ImportFilterType::Pointer importFilter = ImportFilterType::New(); + + typename TImage::SizeType imsize; + imsize[0] = tempImgs[0].GetPointer()->GetLargestPossibleRegion().GetSize()[0]; + imsize[1] = tempImgs[0].GetPointer()->GetLargestPossibleRegion().GetSize()[1]; + imsize[2] = tempImgs.size(); + + typename ImportFilterType::IndexType start; + start.Fill( 0 ); + typename ImportFilterType::RegionType region; + region.SetIndex( start ); + region.SetSize( imsize ); + importFilter->SetRegion( region ); + + const itk::SpacePrecisionType origin[ 3 ] = { 0.0, 0.0, 0.0 }; + importFilter->SetOrigin( origin ); + + const itk::SpacePrecisionType spacing[ 3 ] = { 1.0, 1.0, 1.0 }; + importFilter->SetSpacing( spacing ); + const unsigned long int numberOfPixels2D = imsize[0]*imsize[1]; + const unsigned long int numberOfPixels2DInBytes = imsize[0]*imsize[1]*sizeof(ty); + const unsigned long int numberOfPixels3D = imsize[0]*imsize[1]*imsize[2]*sizeof(ty); + + RGBPixelType * localBuffer = new RGBPixelType[ numberOfPixels3D ]; + RGBPixelType * tmpLocalBuffer = localBuffer; + + it = tempImgs.begin(); + for(;it != tempImgs.end(); ++it) + { + memcpy(tmpLocalBuffer, (*it).GetPointer()->GetBufferPointer(), numberOfPixels2DInBytes); + tmpLocalBuffer = tmpLocalBuffer + numberOfPixels2D; + } // for + + const bool importImageFilterWillOwnTheBuffer = true; + importFilter->SetImportPointer( localBuffer , numberOfPixels3D , importImageFilterWillOwnTheBuffer ); + importFilter->Update(); + importFilter->Register(); + bbSetOutputOut( importFilter->GetOutput() ); + + } else { // warning: passing NULL to non-pointer //bbSetOutputOut( NULL); bbSetOutputOut(0); // JPR } - // FCY To test the Output - //typedef itk::Image ImageType; - //typedef itk::ImageFileReader< ImageType > itkReaderType; - // typename itkReaderType::Pointer reader = itkReaderType::New(); - // - // reader->SetFileName("d:\test.hdr"); - // reader->Update(); - //reader->GetOutput()->Register(); - // this->bbSetOutputOut(reader->GetOutput()); } + + template void ItkImagesChooserDialogBox::ExportVTK() { @@ -100,40 +194,34 @@ void ItkImagesChooserDialogBox::ExportVTK() dlg->split3Din3Dvtk( (*it) ); } bbSetOutputOutVImages( dlg->getVtkImagesSelected() ); - } - else if (dlg->getDims().front() == 4) - { + } else if (dlg->getDims().front() == 4) { // To Test // dlg->split4Din3Dvtk("d:/temp2"); // bbSetOutputOutVImages( dlg->getVtkImagesSelected()); - } - else - { - // NOT IMPLEMENTED YET FOR DIMENSIONS > 4 - - } - + } else { + // NOT IMPLEMENTED YET FOR DIMENSIONS > 4 + } // if dlg } + //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== void ItkImagesChooserDialogBox::bbUserSetDefaultValues() -{ - +{ } + //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== void ItkImagesChooserDialogBox::bbUserInitializeProcessing() { - } + //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== void ItkImagesChooserDialogBox::bbUserFinalizeProcessing() { - } -} -// EO namespace bbcreaImageIO + +} // EO namespace bbcreaImageIO diff --git a/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.h b/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.h index fa1d910..b492390 100644 --- a/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.h +++ b/bbtk/src/bbcreaImageIOItkImagesChooserDialogBox.h @@ -75,7 +75,9 @@ class bbcreaImageIO_EXPORT ItkImagesChooserDialogBox private: // Template read method - template void Export(); + +//EED template void Export(); +template void Export(); // Template export vtk Images template void ExportVTK(); diff --git a/src/creaImageIOWxAnySimpleDlg.cpp b/src/creaImageIOWxAnySimpleDlg.cpp index 926e118..a8db5f7 100644 --- a/src/creaImageIOWxAnySimpleDlg.cpp +++ b/src/creaImageIOWxAnySimpleDlg.cpp @@ -29,13 +29,19 @@ #include "creaImageIOWxAnySimpleDlg.h" #include "creaImageIOWxGimmickReaderDialog.h" -#include + +#if ITK_VERSION_MAJOR < 4 // : WARNING: deprecated in ITK 4.0 +# include +# include +#else // ITK_VERSION_MAJOR < 4 +# include +#endif // ITK_VERSION_MAJOR < 4 + #include #include #include #include #include -#include #include #include #include @@ -102,25 +108,28 @@ namespace creaImageIO std::string name = crea::wx2std(wxArray[i]); // FOR THE MOMENT ONLY short 3D et short 4D readImg(name); - } - } - else { + } // for + } else { // TO DO WARNING MESSAGES - } - } + } // if + } // if SetReturnCode( resultShowModal ); // Close(); EndModal( resultShowModal ); } + +///////////////////////////////////////////////////////////////////// +// // +////////////////////////////////////////////////////////////////////// void WxAnySimpleDlg::setExts(std::vector i_exts) { m_exts = i_exts; } - ///////////////////////////////////////////////////////////////////// + +///////////////////////////////////////////////////////////////////// // // ////////////////////////////////////////////////////////////////////// - void WxAnySimpleDlg::OnReadDirectory(wxCommandEvent &event) { int resultShowModal; @@ -132,33 +141,55 @@ namespace creaImageIO if ( resultShowModal==wxID_OK ) { std::string path = crea::wx2std(dirDlg->GetPath()); + +/* typedef boost::filesystem::directory_iterator dir_it; dir_it itr(path); dir_it end_itr; - /*if (boost::filesystem::exists(path)) - {*/ +// if (boost::filesystem::exists(path)) +// { for(;itr != end_itr; ++itr) { - bvalid = m_exts.size() == 0? true : false; - std::vector::iterator it = m_exts.begin(); - std::string ext = itr->path().filename().string().substr(itr->path().filename().string().find_last_of(".")); - for(; it != m_exts.end(); it++) - { - if(ext == (*it) ) - { - bvalid = true; - break; - } - } +//EED +// All files have the same extention +// bvalid = m_exts.size() == 0? true : false; +// std::vector::iterator it = m_exts.begin(); +// std::string ext = itr->path().filename().string().substr(itr->path().filename().string().find_last_of(".")); +// for(; it != m_exts.end(); it++) +// { +// if(ext == (*it) ) +// { +// bvalid = true; +// break; +// } +// } // for +bvalid=true; if (!boost::filesystem::is_directory(itr->status()) && bvalid) { - readImg(itr->path().string().c_str()); - } - } - } +printf("EED WxAnySimpleDlg::OnReadDirectory Each file %s \n", itr->path().string().c_str() ); + readImg( itr->path().string().c_str() ); + } // if + } // for itr +*/ + + typedef vector vec; // store paths + vec v; // so we can sort them later + copy(boost::filesystem::directory_iterator(path), boost::filesystem::directory_iterator(), back_inserter(v)); + sort(v.begin(), v.end()); // sort, since directory iteration + // is not ordered on some file systems + for (vec::const_iterator it (v.begin()); it != v.end(); ++it) + { + readImg( it->string().c_str() ); + } // for + + + + + } // if OK SetReturnCode( resultShowModal ); // Close(); EndModal( resultShowModal ); + } ////////////////////////////////////////////////////////////////////// @@ -230,9 +261,11 @@ namespace creaImageIO return imageIO->GetNumberOfDimensions(); } + void WxAnySimpleDlg::readImg(const std::string &i_name) { size_t dims = getNumberOfDimensions(i_name); + //const std::type_info *type= &getType(i_name); switch(dims) { @@ -339,6 +372,7 @@ namespace creaImageIO } else { + printf("EED WxAnySimpleDlg::readImg Not type found for DIM 3 \n"); //????FCY, so what the type???? } break; @@ -481,6 +515,7 @@ namespace creaImageIO } else { + printf("EED WxAnySimpleDlg::readImg Not type found for DIM 4 \n"); //????FCY, so what the type???? } break; @@ -513,7 +548,11 @@ namespace creaImageIO { typedef itk::Image TImage; typedef itk::GDCMImageIO GDCMType; +#if ITK_VERSION_MAJOR < 4 typedef itk::DICOMSeriesFileNames dicnames; +#else // ITK_VERSION_MAJOR < 4 + typedef itk::GDCMSeriesFileNames dicnames; +#endif // ITK_VERSION_MAJOR < 4 GDCMType::Pointer gdcmIO = GDCMType::New(); dicnames::Pointer generator = dicnames::New(); diff --git a/src/creaImageIOWxAnySimpleDlg.h b/src/creaImageIOWxAnySimpleDlg.h index df24819..65c80a6 100644 --- a/src/creaImageIOWxAnySimpleDlg.h +++ b/src/creaImageIOWxAnySimpleDlg.h @@ -102,13 +102,13 @@ namespace creaImageIO for(; it != m_AnyImages.end(); it++) { imgs.push_back(boost::any_cast (*it)); - } + } // for return imgs; } bool AllSameType(); template void split3Din3Dvtk(TImage* i_Img) - { + { typedef itk::ImageToVTKImageFilter< TImage > ConnectorType; typename ConnectorType::Pointer connector = ConnectorType::New(); connector->SetInput(i_Img); @@ -127,14 +127,11 @@ namespace creaImageIO m_Vresults.push_back(im); } - template void split4Din3Dvtk(TImage* i_Img); - private: - // strange compile error with gcc 4.5.1-4 //JPR std::vector m_AnyDims; //comment out const JPR std::vector m_AnyType; //comment out const JPR @@ -145,7 +142,6 @@ namespace creaImageIO wxString infoimage; std::string m_dir; - bool m_dicom; /// interface to read data SimpleView m_view; @@ -157,6 +153,5 @@ namespace creaImageIO const std::type_info & getType(const std::string &i_name); }; - }// namespace creaImageIO #endif //__creaImageWxAnySimpleDlg_h_INCLUDED__ diff --git a/src/creaImageIOWxGimmickReaderDialog.cpp b/src/creaImageIOWxGimmickReaderDialog.cpp index bce7fc7..1dff6b3 100644 --- a/src/creaImageIOWxGimmickReaderDialog.cpp +++ b/src/creaImageIOWxGimmickReaderDialog.cpp @@ -80,8 +80,7 @@ namespace creaImageIO threads); mView->Initialize(); // Connect the AddProgress callback - mView->ConnectValidationObserver - ( boost::bind( &WxGimmickReaderDialog::OnValid , this, _1 ) ); + mView->ConnectValidationObserver( boost::bind( &WxGimmickReaderDialog::OnValid , this, _1 ) ); } catch (crea::Exception e) {