src/creaImageIODicomImageReader2.cpp

   1 #include <creaImageIODicomImageReader2.h>
   2 #include "gdcmStringFilter.h"
   3
   4
   5 #include <creaImageIOSystem.h>
   6 #include "boost/filesystem/path.hpp"
   7
   8 #include <creaImageIOTreeAttributeDescriptor.h>
   9 #include <vtkStringArray.h>
  10 #include <creaImageIOGimmick.h>
  11
  12
  13 #ifdef _DEBUG
  14 #define new DEBUG_NEW
  15 #endif
  16 namespace creaImageIO
  17 {
  18
  19   //=====================================================================
  20   DicomImageReader::DicomImageReader()
  21   {
  22       mReader =  vtkGDCMImageReader::New();
  23       SetName ( "Dicom" );
  24
  25   };
  26   //=====================================================================
  27
  28   //=====================================================================
  29   DicomImageReader::~DicomImageReader()
  30   {
  31       mReader->Delete();
  32   }
  33   //=====================================================================
  34
  35   //=====================================================================
  36   bool DicomImageReader::CanRead(const std::string& filename)
  37   {
  38       gdcm::Reader reader;
  39       reader.SetFileName( filename.c_str() );
  40       return  reader.Read();
  41
  42   }
  43   //=====================================================================
  44
  45   //=====================================================================
  46   vtkImageData* DicomImageReader::ReadImage(const std::string& filename)
  47   {
  48     vtkImageData* im = 0;
  49     try
  50       {
  51         mReader->SetFileName(filename.c_str());
  52         mReader->Update();
  53         im = vtkImageData::New();
  54         im->ShallowCopy(mReader->GetOutput());
  55       }
  56     catch (...)
  57       {
  58         if (im!=0) im->Delete();
  59           im = 0;
  60       }
  61     return im;
  62   }
  63
  64   //=====================================================================
  65   void DicomImageReader::PushBackExtensions(std::vector<std::string>& v)
  66   {
  67     v.push_back("dcm");
  68     v.push_back("");
  69   }
  70
  71   //========================================================================
  72   std::string irclean(const std::string& str)
  73   {
  74           if(str.size() > 0)
  75           {
  76                 if (str == "GDCM::Unfound")
  77                   {
  78                 return "";
  79                   }
  80                 if (str[str.size()-1]==' ')
  81                   {
  82                 return irclean(str.substr(0,str.size()-1));
  83                   }
  84                 if (str[str.size()-1]==0)
  85                   {
  86                 return irclean(str.substr(0,str.size()-1));
  87                   }
  88           }
  89
  90     return str;
  91   }
  92   //========================================================================
  93   //=====================================================================
  94
  95
  96         void DicomImageReader::getAttributes(const std::string filename,
  97                 std::map <std::string , std::string> &infos, std::vector<std::string> i_attr)
  98         {
  99                 gdcm::Reader reader;
 100                 reader.SetFileName( filename.c_str() );
 101                 if (reader.Read())
 102                 {
 103                         std::vector<std::string>::iterator it = i_attr.begin();
 104                         for(;it != i_attr.end(); it++)
 105                         {
 106                                 unsigned short el;
 107                                 unsigned short gr;
 108                                 sscanf((*it).c_str(),"D%04hx_%04hx",&gr,&el);
 109                                 if ( ( gr!=0 ) && ( el!=0 ) )
 110                                 {
 111                                         infos[(*it)] =  ( GetStringValueFromTag(reader.GetFile().GetDataSet().GetDataElement(gdcm::Tag(gr,el))) );
 112                                 }
 113                         }
 114                 }
 115         }
 116
 117   //=====================================================================
 118   void DicomImageReader::ReadAttributes(const std::string& filename,
 119                       std::map<std::string,std::string>& attr)
 120   {
 121     GimmickMessage(2,"Reading attributes from DICOM file '"
 122                    <<filename<<"'"<<std::endl);
 123
 124
 125       gdcm::Reader reader;
 126       reader.SetFileName( filename.c_str() );
 127       if (reader.Read())
 128       {
 129                   gdcm::StringFilter sf;
 130                   sf.SetFile(reader.GetFile());
 131                   std::map<std::string,std::string>::iterator i;
 132                   for (i=attr.begin();i!=attr.end();++i)
 133               {
 134                           if ( i->first == "D0004_1500" )
 135                           {
 136                                   boost::filesystem::path full_path(filename);
 137                                   std::string f = full_path.leaf();
 138                                   i->second = f;
 139                           }
 140                           else if ( i->first == "FullFileName" )
 141                           {
 142                                 i->second = filename;
 143                           }
 144                           else if ( i->first == "FullFileDirectory" )
 145                           {
 146                                  std::string::size_type last_pos = filename.find_last_of("//");
 147                                  //find first separator
 148                                  i->second = filename.substr(0, last_pos);
 149                           }
 150                           else
 151                           {
 152                                   uint16_t el;
 153                                   uint16_t gr;
 154                                   tree::AttributeDescriptor::GetDicomGroupElementFromKey(i->first,gr,el);
 155                                   //if ( ( gr!=0 ) && ( el!=0 ) )
 156                                   const gdcm::Tag tag(gr, el);
 157                                   if( reader.GetFile().GetDataSet().FindDataElement( tag ) )
 158                                   {
 159                                           i->second = irclean(sf.ToString(tag));
 160                                   }
 161                                   else
 162                                   {
 163                                           i->second = "";
 164                                   }
 165                           }
 166                   }
 167           }
 168   }
 169
 170 void DicomImageReader::ReadAttributes2(const std::string& filename,
 171                       std::map<std::string,std::string>& attr)
 172   {
 173         if(!b_loaded)
 174         {
 175                 std::map<std::string,std::string>::iterator i;
 176                 for (i=attr.begin();i!=attr.end();++i)
 177                   {
 178                         if ( i->first == "D0004_1500" ||  i->first == "FullFileName" || i->first == "FullFileDirectory" )
 179                         {
 180
 181                         }
 182                         else
 183                         {
 184                         uint16_t el;
 185                         uint16_t gr;
 186
 187                         tree::AttributeDescriptor::GetDicomGroupElementFromKey(i->first,gr,el);
 188                         mscan.AddTag(gdcm::Tag(gr,el) );
 189                         }
 190                 }
 191                 b_loaded = true;
 192         }
 193          bool b = mscan.IsKey(filename.c_str());
 194      if( b )
 195       {
 196                   const gdcm::Scanner::TagToValue &mapping = mscan.GetMapping(filename.c_str());
 197                   gdcm::Scanner::TagToValue::const_iterator it = mapping.begin();
 198                   std::map<std::string, std::string>::iterator i;
 199                 for (i=attr.begin();i!=attr.end();++i, ++it)
 200                 {
 201                         if ( i->first == "D0004_1500" )
 202                         {
 203                                 boost::filesystem::path full_path(filename);
 204                                 std::string f = full_path.leaf();
 205                                 i->second = f;
 206                         }
 207                         else if ( i->first == "FullFileName" )
 208                         {
 209                                 i->second = filename;
 210                         }
 211                         else if ( i->first == "FullFileDirectory" )
 212                         {
 213                                   std::string::size_type last_pos = filename.find_last_of("//");
 214                                   //find first separator
 215                                   i->second = filename.substr(0, last_pos);
 216                         }
 217                         else
 218                         {
 219                                 const char *value = it->second;
 220                                 i->second = irclean(it->second);
 221                         }
 222                 }
 223          }
 224 }
 225
 226 const std::string DicomImageReader::GetStringValueFromTag(const gdcm::DataElement& de)
 227 {
 228   static std::string buffer;
 229   buffer = "";  // cleanup previous call
 230
 231
 232     const gdcm::ByteValue *bv = de.GetByteValue();
 233     if( bv ) // Can be Type 2
 234       {
 235       buffer = std::string( bv->GetPointer(), bv->GetLength() );
 236       // Will be padded with at least one \0
 237       }
 238
 239   // Since return is a const char* the very first \0 will be considered
 240   return buffer.c_str();
 241 }
 242   //=====================================================================
 243
 244 } // namespace creaImageIO
 245