creaImageIODicomImageReader2.cpp

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#include <creaImageIODicomImageReader2.h>
#include "gdcmStringFilter.h"
#include "vtkGDCMImageReader.h"

#include <creaImageIOSystem.h>
#include "boost/filesystem/path.hpp"

#include <creaImageIOTreeAttributeDescriptor.h>
#include <vtkStringArray.h>
#include <creaImageIOGimmick.h>

#include "gdcmUIDs.h"
#ifdef _DEBUG
#define new DEBUG_NEW
#endif
namespace creaImageIO
{

  //=====================================================================
  DicomImageReader::DicomImageReader()
  {
      mReader =  vtkGDCMImageReader::New();
      SetName ( "Dicom" );
        
  };
  //=====================================================================
  
  //=====================================================================
  DicomImageReader::~DicomImageReader()
  {
      mReader->Delete();
  }
  //=====================================================================

  //=====================================================================  
  bool DicomImageReader::CanRead(const std::string& filename)
  { 
      gdcm::Reader reader;
      reader.SetFileName( filename.c_str() );
      return  reader.Read();
         
  }
  //=====================================================================

  //=====================================================================
  vtkImageData* DicomImageReader::ReadImage(const std::string& filename)
  {
    vtkImageData* im = 0;
    try
      {
        mReader->SetFileName(filename.c_str());
        mReader->Update();
        im = vtkImageData::New();
        im->ShallowCopy(mReader->GetOutput());
      }
    catch (...)
      {
        if (im!=0) im->Delete();
          im = 0;
      }
    return im;
    //gdcm::Tag grouplength(0x0000,0x0000);
    //gdcm::DataElement de(gdcm::Tag(0x0000, 0x0000));
    //de.SetByteValue("0",gdcm::VR::UL);
    //
    //
    //gdcm::UIDs::GetUIDString(gdcm::UIDS::uid_1_2_840_10008_1_1),gdcm::VR::UI);

    //std::ostream os;
    //de.Write(&os);

  }

  //=====================================================================
  void DicomImageReader::PushBackExtensions(std::vector<std::string>& v)
  {
    v.push_back("dcm");
    v.push_back("");
  }
 
  //========================================================================
  std::string irclean(const std::string& str)
  {
          if(str.size() > 0)
          {
                if (str == "GDCM::Unfound") 
                  {
                return "";
                  }
                if (str[str.size()-1]==' ')
                  {
                return irclean(str.substr(0,str.size()-1));
                  }
                if (str[str.size()-1]==0)
                  {
                return irclean(str.substr(0,str.size()-1));
                  }
          }
    
    return str;
  }
  //========================================================================
  //=====================================================================
  

        void DicomImageReader::getAttributes(const std::string filename, 
                std::map <std::string , std::string> &infos, std::vector<std::string> i_attr)
        {
                gdcm::Reader reader;
                reader.SetFileName( filename.c_str() );
                if (reader.Read())
                {
                        std::vector<std::string>::iterator it = i_attr.begin();
                        for(;it != i_attr.end(); it++)
                        {
                                unsigned short el;
                                unsigned short gr;
                                sscanf((*it).c_str(),"D%04hx_%04hx",&gr,&el);
                                if ( ( gr!=0 ) && ( el!=0 ) )
                                {
                                        infos[(*it)] =  ( GetStringValueFromTag(reader.GetFile().GetDataSet().GetDataElement(gdcm::Tag(gr,el))) );
                                }
                        }
                }
        }

  //=====================================================================
  void DicomImageReader::ReadAttributes(const std::string& filename, 
                      std::map<std::string,std::string>& attr)
  {
    GimmickMessage(2,"Reading attributes from DICOM file '"
                   <<filename<<"'"<<std::endl);

   
      gdcm::Reader reader;
      reader.SetFileName( filename.c_str() );
      if (reader.Read())
      {
                  gdcm::StringFilter sf;
                  sf.SetFile(reader.GetFile());
                  std::map<std::string,std::string>::iterator i;
                  for (i=attr.begin();i!=attr.end();++i)
              {
                          if ( i->first == "D0004_1500" )
                          {
                                  boost::filesystem::path full_path(filename);
                                  std::string f = full_path.leaf();
                                  i->second = f;
                          }
                          else if ( i->first == "FullFileName" )
                          {
                                i->second = filename;
                          }
                          else if ( i->first == "FullFileDirectory" )
                          {
                                 std::string::size_type last_pos = filename.find_last_of("//");
                                 //find first separator
                                 i->second = filename.substr(0, last_pos);
                          }
                          else
                          {
                                  uint16_t el;
                                  uint16_t gr;
                      {
            gdcm::Attribute<  0x0008,0x103e> at;
            std::string sr;
            at.SetValue(sr);
            
        }
                                  tree::AttributeDescriptor::GetDicomGroupElementFromKey(i->first,gr,el);
                                  //if ( ( gr!=0 ) && ( el!=0 ) )
                                  const gdcm::Tag tag(gr, el);
                                  if( reader.GetFile().GetDataSet().FindDataElement( tag ) )
                                  {
                                          i->second = irclean(sf.ToString(tag));
                                  }
                                  else
                                  {
                                          i->second = "";
                                  }
                          }
                  }
          }
  }

void DicomImageReader::ReadAttributes2(const std::string& filename, 
                      std::map<std::string,std::string>& attr)
  {
        if(!b_loaded)
        {
                std::map<std::string,std::string>::iterator i;
                for (i=attr.begin();i!=attr.end();++i)
                  {
                        if ( i->first == "D0004_1500" ||  i->first == "FullFileName" || i->first == "FullFileDirectory" )
                        {
                        
                        }
                        else
                        {
                        uint16_t el;
                        uint16_t gr;
                        
                        tree::AttributeDescriptor::GetDicomGroupElementFromKey(i->first,gr,el);
                        mscan.AddTag(gdcm::Tag(gr,el) );
                        }
                }
                b_loaded = true;
        }
         bool b = mscan.IsKey(filename.c_str());
     if( b )
      {
                  const gdcm::Scanner::TagToValue &mapping = mscan.GetMapping(filename.c_str());
                  gdcm::Scanner::TagToValue::const_iterator it = mapping.begin();
                  std::map<std::string, std::string>::iterator i;
                for (i=attr.begin();i!=attr.end();++i, ++it)
                {
                        if ( i->first == "D0004_1500" )
                        {
                                boost::filesystem::path full_path(filename);
                                std::string f = full_path.leaf();
                                i->second = f;
                        }
                        else if ( i->first == "FullFileName" )
                        {
                                i->second = filename;
                        }
                        else if ( i->first == "FullFileDirectory" )
                        {
                                  std::string::size_type last_pos = filename.find_last_of("//");
                                  //find first separator
                                  i->second = filename.substr(0, last_pos);
                        }
                        else
                        {
                                const char *value = it->second;
                                i->second = irclean(it->second);
                        }
                }
         }
}

const std::string DicomImageReader::GetStringValueFromTag(const gdcm::DataElement& de)
{
  static std::string buffer;
  buffer = "";  // cleanup previous call


    const gdcm::ByteValue *bv = de.GetByteValue();
    if( bv ) // Can be Type 2
      {
      buffer = std::string( bv->GetPointer(), bv->GetLength() );
      // Will be padded with at least one \0
      }

  // Since return is a const char* the very first \0 will be considered
  return buffer.c_str();
}
  //=====================================================================
  
} // namespace creaImageIO