src/creaImageIOSimpleView.cpp

   1 /*
   2 # ---------------------------------------------------------------------
   3 #
   4 # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
   5 #                        pour la Santé)
   6 # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
   7 # Previous Authors : Laurent Guigues, Jean-Pierre Roux
   8 # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
   9 #
  10 #  This software is governed by the CeCILL-B license under French law and
  11 #  abiding by the rules of distribution of free software. You can  use,
  12 #  modify and/ or redistribute the software under the terms of the CeCILL-B
  13 #  license as circulated by CEA, CNRS and INRIA at the following URL
  14 #  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  15 #  or in the file LICENSE.txt.
  16 #
  17 #  As a counterpart to the access to the source code and  rights to copy,
  18 #  modify and redistribute granted by the license, users are provided only
  19 #  with a limited warranty  and the software's author,  the holder of the
  20 #  economic rights,  and the successive licensors  have only  limited
  21 #  liability.
  22 #
  23 #  The fact that you are presently reading this means that you have had
  24 #  knowledge of the CeCILL-B license and that you accept its terms.
  25 # ------------------------------------------------------------------------
  26 */
  27
  28 #include "boost/filesystem/operations.hpp"
  29 #include "boost/filesystem/fstream.hpp"
  30
  31 #include "creaImageIOSimpleView.h"
  32 #include "creaImageIOUnMosaicVtkImageData.h"
  33
  34 namespace creaImageIO
  35 {
  36         bool SimpleView::readFile(      std::vector<std::string> i_filenames,                                                                   // in information names
  37                                                                                 std::vector<std::string> i_attr,                                                                // in information attributes names
  38                                                                                 std::vector<std::map <std::string , std::string> > &i_imgAttr,  // out information attributes names-values
  39                                                                                 std::vector<vtkImageData *> &i_img)                                                     // out information vtkImageData
  40         {
  41
  42                   //Mosaic Attribute for Simens
  43                         i_attr.push_back("D0019_100a");  // Number of images in mosaic (Simens)
  44                         i_attr.push_back("D0018_0088");  // Spacing Between Slices
  45
  46
  47
  48                         creaImageIOUnMosaicVtkImageData Mosaic;
  49                         vtkImageData* tmpImg1;
  50                         vtkImageData* tmpImg2;
  51                         int numberOfImagesInMosaic;
  52                         double spc[3];
  53                         double spcZ;
  54
  55                         bool bresult, bfinal = true;
  56                         ImageReader *mReader = new ImageReader();
  57                         std::vector<std::string>::iterator it = i_filenames.begin();
  58                         for (; it != i_filenames.end(); it++)
  59                         {
  60                                 bresult = mReader->CanRead((*it).c_str());
  61                                 if(bresult)
  62                                 {
  63                                         std::map <std::string , std::string> mapAttr;
  64                                         mReader->getAttributes( (*it).c_str() , mapAttr, i_attr ); //  filename, outMapAttr-NameValue, inVectAttributeName
  65                                         i_imgAttr.push_back( mapAttr );
  66
  67 //EED borrame
  68 //                                      i_img.push_back( mReader->ReadImage( (*it).c_str() ) );
  69
  70
  71                                         // EED 18 octt 2014
  72                                         std::map <std::string , std::string>::iterator itMapAttr;
  73                                         std::string numberOfImagesInMosaicStr="";
  74                                         std::string spaceBetweenSliceStr="";
  75
  76                                         itMapAttr = mapAttr.find("D0019_100a");
  77                                         if ( itMapAttr!=mapAttr.end() ) numberOfImagesInMosaicStr = itMapAttr->second;
  78
  79 //                                      std::string numberOfImagesInMosaicStr = mapAttr.find("D0019_100a")->second;
  80                                         itMapAttr = mapAttr.find("D0018_0088");
  81                                         if ( itMapAttr!=mapAttr.end() ) spaceBetweenSliceStr = itMapAttr->second;
  82
  83 //                                      std::string spaceBetweenSliceStr = mapAttr.find("D0018_0088")->second;
  84                                         if (numberOfImagesInMosaicStr=="")
  85                                         {
  86                                                 i_img.push_back( mReader->ReadImage( (*it).c_str() ) );
  87                                         } else {
  88                                                 numberOfImagesInMosaic = atoi(numberOfImagesInMosaicStr.c_str());
  89                                                 spcZ = atoi(spaceBetweenSliceStr.c_str());
  90                                                 tmpImg1 = mReader->ReadImage( (*it).c_str() ) ;
  91                                                 tmpImg1->GetSpacing( spc );
  92                                                 tmpImg2 = Mosaic.unMosaic( tmpImg1 , numberOfImagesInMosaic );
  93                                                 tmpImg2->SetSpacing( spc[0], spc[1], spcZ );
  94                                                 i_img.push_back( tmpImg2 );
  95                                         }// elemet
  96
  97                                 } else {
  98                                         printf("ERROR. Impossible to read file %s\n", (*it).c_str() );
  99                                         bfinal = false;
 100                                 } // if
 101                         } // for
 102                         delete mReader;
 103
 104                         return bfinal;
 105         }
 106
 107
 108         bool SimpleView::readDirectory( const std::string i_pathname,                                                                                   // in information names
 109                                                                                                 std::vector<std::string> i_attr,                                                                                        // in information attributes names
 110                                                                                                 std::vector<std::map <std::string , std::string> > &i_imgAttr,  // out information attributes names-values
 111                                                                                                 std::vector<vtkImageData *> &i_imgs)                                                                    // out information vtkImageData
 112         {
 113                         bool bresult = true;
 114                         ImageReader *mReader = new ImageReader();
 115                         std::vector<std::string> names;
 116                         bresult = boost::filesystem::exists( i_pathname );
 117                         if (bresult)
 118                         {
 119                                 boost::filesystem::directory_iterator itr(i_pathname);
 120                                 boost::filesystem::directory_iterator end_itr;
 121                                 for(;itr != end_itr; ++itr)
 122                                 {
 123                                         if (!boost::filesystem::is_directory(itr->status()))
 124                                         {
 125                                                 if( mReader->CanRead(itr->path().string()) )
 126                                                 {
 127                                                         names.push_back(itr->path().string());
 128                                                 }
 129                                         }
 130                                 }
 131                                 std::sort (names.begin(), names.end()); // make sure names are in lexicographical order
 132                                 int lgr = (int)names.size();
 133
 134                                 for(int i=0; i<lgr; i++)
 135                                 {
 136                std::cout << names[i] << std::endl;
 137
 138                                         std::map <std::string , std::string> mapAttr;
 139                                         mReader->getAttributes( names[i] , mapAttr, i_attr ); //  filename, outMapAttr-NameValue, inVectAttributeName
 140                                         i_imgAttr.push_back( mapAttr );
 141
 142                                         //UnMosaic step..
 143
 144                                    i_imgs.push_back( mReader->ReadImage(names[i]) );
 145                                 }
 146                         }
 147                         return bresult;
 148         }
 149
 150
 151         vtkImageData* SimpleView::getVolumeSelected( std::vector<vtkImageData*> lstImages)
 152         {
 153                 vtkImageData *result;
 154
 155 //        creaImageIO::WxSimpleDlg dlg(0,crea::std2wx(bbGetInputTitle()),"localdatabase_Descriptor.dscp","Local Database");
 156 //              dlg.SetAttrDicomTags( bbGetInputDicomTags() );
 157 //              dlg.ShowModal();
 158 //              bbSetOutputDicomInfo( dlg.getDicomInfoImagesSelected() );
 159
 160                 if (lstImages.size()!=0){
 161 //                bbSetOutputFileName( std::string( dlg.getInfoImage().mb_str() ) );
 162                   if(lstImages.size() ==1)
 163                   {
 164                         result = lstImages[0] ;
 165                   } else {
 166                                 // FCY: it will be a big problem if we have several kind of data in the same folder.
 167                                 // creation of a huge vtkImageData!!!!
 168                                 vtkImageData* first = lstImages[0];
 169                                 int dim[3];
 170                                 first->GetDimensions(dim);
 171                                 if (dim[2]==1)
 172                                 {
 173                                         vtkImageData *out = vtkImageData::New();
 174                                         int ext[6];
 175 //EED 2017-01-01 Migration VTK7
 176 #if VTK_MAJOR_VERSION <= 5
 177                                         first->GetWholeExtent(ext);
 178 #else
 179                                         first->GetExtent(ext);
 180 #endif
 181                                         if(ext[5] == 0)
 182                                         {
 183                                            ext[5] = lstImages.size()-1;
 184                                          } else {
 185                                                 ext[5] = ext[5] * lstImages.size()-1; // to deal with multiframes
 186                                         } // ext
 187                                         out->SetExtent(ext);
 188                                         double spac[3];
 189                                         first->GetDimensions(dim);
 190                                         first->GetSpacing(spac);
 191                                         if (spac[0]==spac[1])
 192                                         {
 193                                                 spac[2]=spac[0];
 194                                 }
 195                                         out->SetSpacing(spac);
 196                                         out->SetDimensions(dim[0], dim[1], lstImages.size() );
 197 //EED 2017-01-01 Migration VTK7
 198 #if VTK_MAJOR_VERSION <= 5
 199
 200                                         out->SetScalarType(first->GetScalarType());
 201                                         out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 202                                         out->AllocateScalars();
 203                                         out->Update();
 204 #else
 205                                         out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
 206 #endif
 207
 208
 209                                         unsigned long imsize = dim[0] * dim[1];
 210                                         imsize = imsize * dim[2];  // deal with multiframes here
 211                                         // differents formats char , short, etc...
 212                                         // differents components 1..3  ex. jpg ->RGB 3
 213                                         imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 214                                 int slice,sizeImageVector=lstImages.size();
 215                                         for (slice=0 ; slice<sizeImageVector ; slice++)
 216                                         {
 217                                                 vtkImageData *img = lstImages[slice];
 218                                                 memcpy(out->GetScalarPointer(0,0,slice), img->GetScalarPointer(0,0,0), imsize);
 219                                                 //img->Delete();
 220                                         } // for slice
 221                                         out->Modified();
 222 //EED This is NOT working. The iteration over the pointer vtkImageData
 223 //                              int slice=0;
 224 //                              std::vector<vtkImageData*>::iterator it;
 225 //                              for (it=dlg.getImagesSelected().begin(); it!=dlg.getImagesSelected().end(); ++it)
 226 //                                      {
 227 //                                                memcpy(out->GetScalarPointer(0,0,slice), (*it)->GetScalarPointer(0,0,0), imsize);
 228 //                                                slice++;
 229 //                                      }
 230 //                              //for (it=dlg.getImagesSelected().begin(); it!=dlg.getImagesSelected().end(); ++it)
 231 //                                      //{
 232 //                                      //              (*it)->Delete();
 233 //                                      //}
 234
 235                                         result =out;
 236
 237                                 } else {
 238                                         result = first;
 239                                 } // dim
 240                         } // if getImagesSelected size
 241                 } else {
 242                 result = NULL;
 243                 } // getImagesSelected().size()!=0
 244                         result->Modified();
 245         return result;
 246         }
 247
 248
 249 }