// $Header: /cvs/public/gdcm/src/gdcmHeader.h,v 1.34 2003/07/07 10:26:14 regrain Exp $

#include "gdcmHeaderHelper.h"
#include "gdcmUtil.h" //for debug
#include <math.h>
#include <algorithm>

//----------------------------------------------------------------------------
/**
 * \ingroup gdcmHeaderHelper
 * \brief   cstor
 */
gdcmHeaderHelper::gdcmHeaderHelper() : gdcmHeader( )
{
}
//----------------------------------------------------------------------------
/**
 * \ingroup gdcmHeaderHelper
 * \brief   cstor
 */
gdcmHeaderHelper::gdcmHeaderHelper(const char *InFilename, 
    bool exception_on_error) : gdcmHeader( InFilename , exception_on_error)
{
}
//----------------------------------------------------------------------------
/**
 * \ingroup gdcmHeaderHelper
 * \brief   Return the size (in bytes) of a single pixel of data.
 * @return  The size in bytes of a single pixel of data.
 *
 */
int gdcmHeaderHelper::GetPixelSize(void) {
   string PixelType = GetPixelType();
   if (PixelType == "8U"  || PixelType == "8S")
      return 1;
   if (PixelType == "16U" || PixelType == "16S")
      return 2;
   if (PixelType == "32U" || PixelType == "32S")
      return 4;
   dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
   return 0;
}
//----------------------------------------------------------------------------
/**
 * \ingroup gdcmHeaderHelper
 * \brief   Build the Pixel Type of the image.
 *          Possible values are:
 *          - 8U  unsigned  8 bit,
 *          - 8S    signed  8 bit,
 *          - 16U unsigned 16 bit,
 *          - 16S   signed 16 bit,
 *          - 32U unsigned 32 bit,
 *          - 32S   signed 32 bit,
 * \warning 12 bit images appear as 16 bit.
 * @return  
 */
string gdcmHeaderHelper::GetPixelType(void) {
   string BitsAlloc;
   BitsAlloc = GetElValByName("Bits Allocated");
   if (BitsAlloc == "gdcm::Unfound") {
      dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
      BitsAlloc = string("16");
   }
   if (BitsAlloc == "12")
      BitsAlloc = string("16");

   string Signed;
   Signed = GetElValByName("Pixel Representation");
   if (Signed == "gdcm::Unfound") {
      dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
      BitsAlloc = string("0");
   }
   if (Signed == "0")
      Signed = string("U");
   else
      Signed = string("S");

   return( BitsAlloc + Signed);
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0028,0030 : Pixel Spacing
  * \           else 1.
  * @return X dimension of a pixel
  */
float gdcmHeaderHelper::GetXSpacing(void) {
    float xspacing, yspacing;
    string StrSpacing = GetPubElValByNumber(0x0028,0x0030);

    if (StrSpacing == "gdcm::Unfound") {
       dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
       return 1.;
     }
   if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2)
     return 0.;
   //else
   return xspacing;
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0028,0030 : Pixel Spacing
  * \           else 1.
  * @return Y dimension of a pixel
  */
float gdcmHeaderHelper::GetYSpacing(void) {
   float xspacing, yspacing;
   string StrSpacing = GetPubElValByNumber(0x0028,0x0030);
  
   if (StrSpacing == "gdcm::Unfound") {
      dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
      return 1.;
    }
  if( sscanf( StrSpacing.c_str(), "%f\\%f", &xspacing, &yspacing) != 2)
    return 0.;
  if (yspacing == 0.) {
    dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
    // seems to be a bug in the header ...
    sscanf( StrSpacing.c_str(), "%f\\0\\%f", &xspacing, &yspacing);
  }
  return yspacing;
} 

//----------------------------------------------------------------------------
/**
  *\ingroup gdcmHeaderHelper
  *\brief gets the info from 0018,0088 : Space Between Slices
  *\               else from 0018,0050 : Slice Thickness
  *\               else 1.
  * @return Z dimension of a voxel-to be
  */
float gdcmHeaderHelper::GetZSpacing(void) {
   // TODO : translate into English
   // Spacing Between Slices : distance entre le milieu de chaque coupe
   // Les coupes peuvent etre :
   //   jointives     (Spacing between Slices = Slice Thickness)
   //   chevauchantes (Spacing between Slices < Slice Thickness)
   //   disjointes    (Spacing between Slices > Slice Thickness)
   // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
   //   ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
   //   Si le Spacing Between Slices est absent, 
   //   on suppose que les coupes sont jointives
   
   string StrSpacingBSlices = GetPubElValByNumber(0x0018,0x0088);

   if (StrSpacingBSlices == "gdcm::Unfound") {
      dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
      string StrSliceThickness = GetPubElValByNumber(0x0018,0x0050);       
      if (StrSliceThickness == "gdcm::Unfound")
         return 1.;
      else
         // if no 'Spacing Between Slices' is found, 
         // we assume slices join together
         // (no overlapping, no interslice gap)
         // if they don't, we're fucked up
         return atof(StrSliceThickness.c_str());  
   } else {
      return atof(StrSpacingBSlices.c_str());
   }
}

//----------------------------------------------------------------------------
//
// Image Position Patient                              (0020,0032):
// If not found (ACR_NEMA) we try Image Position       (0020,0030)
// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
//                                   or Location       (0020,0050) 
// as the Z coordinate, 
// 0. for all the coordinates if nothing is found

// TODO : find a way to inform the caller nothing was found
// TODO : How to tell the caller a wrong number of values was found?

/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0020,0032 : Image Position Patient
  *\                else from 0020,0030 : Image Position (RET)
  *\                else 0.
  * @return up-left image corner position
  */
float gdcmHeaderHelper::GetXOrigin(void) {
    float xImPos, yImPos, zImPos;  
    string StrImPos = GetPubElValByNumber(0x0020,0x0032);

    if (StrImPos == "gdcm::Unfound") {
       dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
       StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
       if (StrImPos == "gdcm::Unfound") {
          dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
          // How to tell the caller nothing was found ?
       }  
       return 0.;
     }
   if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
     return 0.;
   return xImPos;
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0020,0032 : Image Position Patient
  * \               else from 0020,0030 : Image Position (RET)
  * \               else 0.
  * @return up-left image corner position
  */
float gdcmHeaderHelper::GetYOrigin(void) {
    float xImPos, yImPos, zImPos;
    string StrImPos = GetPubElValByNumber(0x0020,0x0032);

    if (StrImPos == "gdcm::Unfound") {
       dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
       StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
       if (StrImPos == "gdcm::Unfound") {
          dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
       }  
       return 0.;
     }
   if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
     return 0.;
   return yImPos;
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0020,0032 : Image Position Patient
  * \               else from 0020,0030 : Image Position (RET)
  * \               else from 0020,1041 : Slice Location
  * \               else from 0020,0050 : Location
  * \               else 0.
  * @return up-left image corner position
  */
float gdcmHeaderHelper::GetZOrigin(void) {
   float xImPos, yImPos, zImPos; 
   string StrImPos = GetPubElValByNumber(0x0020,0x0032);
   if (StrImPos != "gdcm::Unfound") {
      if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
         dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
         return 0.;  // bug in the element 0x0020,0x0032
      } else {
         return zImPos;
      }    
   }  
   StrImPos = GetPubElValByNumber(0x0020,0x0030); // For ACR-NEMA images
   if (StrImPos != "gdcm::Unfound") {
      if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
         dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
         return 0.;  // bug in the element 0x0020,0x0032
      } else {
         return zImPos;
      }    
   }                
   string StrSliceLocation = GetPubElValByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
   if (StrSliceLocation != "gdcm::Unfound") {
      if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
         dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
         return 0.;  // bug in the element 0x0020,0x1041
      } else {
         return zImPos;
      }
   }   
   dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
   string StrLocation = GetPubElValByNumber(0x0020,0x0050);
   if (StrLocation != "gdcm::Unfound") {
      if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
         dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
         return 0.;  // bug in the element 0x0020,0x0050
      } else {
         return zImPos;
      }
   }
   dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");  
   return 0.; // Hopeless
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0020,0013 : Image Number
  * \               else 0.
  * @return image number
  */
int gdcmHeaderHelper::GetImageNumber(void) {
  int imNb;
  string StrImNumber = GetPubElValByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
  if (StrImNumber != "gdcm::Unfound") {
      if( sscanf( StrImNumber.c_str(), "%i", &imNb) != 1) {
         dbg.Verbose(0, "gdcmHeader::GetImageNumber: no Image Number Information");
         return 0;
      } else {
         return imNb;
      }    
   }
   return 0;   //Hopeless
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0008,0060 : Modality
  * @return ModalityType
  */
ModalityType gdcmHeaderHelper::GetModality(void) {
  string StrModality = GetPubElValByNumber(0x0008,0x0060); //0008 0060 CS ID Modality
  if (StrModality != "gdcm::Unfound") {
    if ( StrModality.find("CR") < text.length())
    {
      return CR;
    }
    else if ( StrModality.find("CT") < StrModality.length() )
    {
      return CT;
    }
    else if ( StrModality.find("MR") < StrModality.length())
    {
      return MR;
    }
    else if ( StrModality.find("NM") < StrModality.length())
    {
      return NM;
    }
    else if ( StrModality.find("OT") < StrModality.length())
    {
      return OT;
    }
    else if ( StrModality.find("US") < StrModality.length())
    {
      return US;
    }
    else if ( StrModality.find("XA") < StrModality.length())
    {
      return XA;
    }
    else
    {
      //throw error return value ???
      // specified <> unknow in our database
      return Unknow;
    }
  }
}
















gdcmSerieHeaderHelper::~gdcmSerieHeaderHelper()
{
  //! \todo
/*  for (list<gdcmHeaderHelper>::iterator it  = CoherentGdcmFileList.begin();
        it != CoherentGdcmFileList.end(); it++)
  {
    delete *it;
  }*/
  CoherentGdcmFileList.clear();
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief gets the info from 0020,0037 : Image Orientation Patient
  * @return cosines of image orientation patient
  */
void gdcmHeaderHelper::GetImageOrientationPatient( float* iop ) {

  //iop is supposed to be float[6]
  iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0;
  
  string StrImOriPat = GetPubElValByNumber(0x0020,0x0037); // 0020 0037 DS REL Image Orientation (Patient)
  if (StrImOriPat != "gdcm::Unfound") {
    if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", 
            &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
         dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0032)");
         return ;  // bug in the element 0x0020,0x0037
    } 
    else
      return ;
  }
}

//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief add a gdcmFile to the list based on file name
  */
void gdcmSerieHeaderHelper::AddFileName(string filename)
{
  gdcmHeaderHelper *GdcmFile = new gdcmHeaderHelper(filename.c_str());
  this->CoherentGdcmFileList.push_back( *GdcmFile );
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief add a gdcmFile to the list
  */
void gdcmSerieHeaderHelper::AddGdcmFile(gdcmHeaderHelper file)
{
  this->CoherentGdcmFileList.push_back( file );
}
//----------------------------------------------------------------------------
/**
  * \ingroup gdcmHeaderHelper
  * \brief \todo
  */
void gdcmSerieHeaderHelper::SetDirectory(string dir)
{
}
//----------------------------------------------------------------------------

/**
  * \ingroup gdcmHeaderHelper
  * \brief 
    We may order, considering :
      -# Image Number
      -# Image Position Patient
      -# More to come :)
*/
void gdcmSerieHeaderHelper::OrderGdcmFileList()
{
  //iop is calculated based on the file file
  float *cosines = new float[6];
  float normal[3];
  float ipp[3];
  float dist;
  float min, max;
  bool first = true;
  int n=0;
  vector<float> distlist;

  for (list<gdcmHeaderHelper>::iterator it  = CoherentGdcmFileList.begin();
        it != CoherentGdcmFileList.end(); it++)
  {
    if(first) {
      it->GetImageOrientationPatient(cosines);

      //You only have to do this once for all slices in the volume. Next, for
      //each slice, calculate the distance along the slice normal using the IPP
      //tag ("dist" is initialized to zero before reading the first slice) :
      normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
      normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
      normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
  
      ipp[0] = it->GetXOrigin();
      ipp[1] = it->GetYOrigin();
      ipp[2] = it->GetZOrigin();

      dist = 0;
      for (int i = 0; i < 3; ++i)
          dist += normal[i]*ipp[i];
  
      distlist.push_back( dist );

      max = min = dist;
      first = false;
    }
    else {
      ipp[0] = it->GetXOrigin();
      ipp[1] = it->GetYOrigin();
      ipp[2] = it->GetZOrigin();
  
      dist = 0;
      for (int i = 0; i < 3; ++i)
          dist += normal[i]*ipp[i];

      distlist.push_back( dist );

      min = (min < dist) ? min : dist;
      max = (max > dist) ? max : dist;
    }
    n++;
  }

    //Then I order the slices according to the value "dist". Finally, once
    //I've read in all the slices, I calculate the z-spacing as the difference
    //between the "dist" values for the first two slices.
    vector<gdcmHeaderHelper> CoherentGdcmFileVector;
    CoherentGdcmFileVector.resize( n );
    assert( CoherentGdcmFileVector.capacity() >= n );

    float step = (max - min)/(n - 1);
    int pos;
    n = 0;

    for (list<gdcmHeaderHelper>::iterator it  = CoherentGdcmFileList.begin();
        it != CoherentGdcmFileList.end(); it++, n++)
    {
      //2*n sort algo !!
      //Assumption: all files are present (no one missing)
      pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
      CoherentGdcmFileVector[pos] = *it;
    }
    
  delete[] cosines;
}