/*=========================================================================
                                                                                
  Program:   gdcm
  Module:    $RCSfile: gdcmSerieHelper.cxx,v $
  Language:  C++
  Date:      $Date: 2006/01/18 15:25:07 $
  Version:   $Revision: 1.42 $
                                                                                
  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
  l'Image). All rights reserved. See Doc/License.txt or
  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
                                                                                
     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.
                                                                                
=========================================================================*/

#include "gdcmSerieHelper.h"
#include "gdcmDirList.h"
#include "gdcmFile.h"
#include "gdcmDictEntry.h" // for TranslateToKey
#include "gdcmDebug.h"
#include "gdcmUtil.h"

#include <math.h>
#include <vector>
#include <map>
#include <algorithm>
#include <stdio.h>  //for sscanf

namespace gdcm 
{
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
 * \brief   Constructor from a given SerieHelper
 */
SerieHelper::SerieHelper()
{
   m_UseSeriesDetails = false;
   ClearAll();
   UserLessThanFunction = 0;
   DirectOrder = true;
}

/**
 * \brief   Canonical destructor.
 */
SerieHelper::~SerieHelper()
{
   ClearAll();
}

/**
 * \brief  Preventively, clear everything at constructor time.
 *         ( use it at destructor time.)
 */
void SerieHelper::ClearAll()
{
   // For all the 'Single SerieUID' Filesets that may already exist 
   FileList *l = GetFirstSingleSerieUIDFileSet();
   while (l)
   { 
      // For all the gdcm::File of a File set
      for (gdcm::FileList::iterator it  = l->begin();
                                    it != l->end(); 
                                  ++it)
      {
         (*it)->Delete(); // remove each entry
      }
      l->clear();
      delete l;     // remove the container
      l = GetNextSingleSerieUIDFileSet();
   }
}

//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------

// Public
/**
 * \brief add a gdcm::File to the Fileset corresponding to its Serie UID
 * @param   filename Name of the file to deal with
 */
void SerieHelper::AddFileName(std::string const &filename)
{
   // Create a DICOM file
   File *header = File::New();
   header->SetLoadMode(LoadMode);
   header->SetFileName( filename ); 
   header->Load();

   if ( header->IsReadable() )
   {
      int allrules = 1;
      // First step : the user defined a set of rules for the DICOM file
      // he is looking for.
      // Make sure the file corresponds to his set of rules:

      std::string s;
      for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
          it2 != ExRestrictions.end();
          ++it2)
      {
         const ExRule &r = *it2;
         s = header->GetEntryString( r.group, r.elem );
         if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
         {
           // Argh ! This rule is unmatched; let's just quit

           allrules = 0;
           break;
         }
      }

      if ( allrules ) // all rules are respected:
      {
         // Allright! we have a found a DICOM that matches the user expectation. 
         // Let's add it!

         // 0020 000e UI REL Series Instance UID
         const std::string &uid = header->GetEntryString(0x0020, 0x000e);
         // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
         // no need here to do anything special


         if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
         {
            gdcmDebugMacro(" New Serie UID :[" << uid << "]");
            // create a std::list in 'uid' position
            SingleSerieUIDFileSetHT[uid] = new FileList;
         }
         // Current Serie UID and DICOM header seems to match; add the file:
         SingleSerieUIDFileSetHT[uid]->push_back( header );
      }
      else
      {
         // at least one rule was unmatched we need to deallocate the file:
         header->Delete();
      }
   }
   else
   {
      gdcmWarningMacro("Could not read file: " << filename );
      header->Delete();
   }
}

/**
 * \brief add a gdcm::File to the first (and supposed to be unique) file set
 *        of the gdcm::SerieHelper.
 * \warning : this method should be used by aware users only!
 *           Passing a gdcm::File* has the same effect than passing a file name!
 * \todo : decide which one is wrong (the method, or the commentary)!
 *           the following comment doesn't match the method :-(
 *            User is supposed to know the files he want to deal with
 *           and consider them they belong to the same Serie
 *           (even if their Serie UID is different)
 *           user will probabely OrderFileList() this list (actually, ordering
 *           user choosen gdm::File is the sole interest of this method)
 *           Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
 *           vtkGdcmReader parsing twice the same files. 
 *           *no* coherence check is performed, but those specified
 *           by SerieHelper::AddRestriction()
 * @param   header gdcm::File* of the file to deal with
 */
void SerieHelper::AddGdcmFile(File *header)
{
      int allrules = 1;
      // First step the user has defined a set of rules for the DICOM 
      // he is looking for.
      // make sure the file correspond to his set of rules:
      for(SerieRestrictions::iterator it =  Restrictions.begin();
                                      it != Restrictions.end();
                                    ++it)
      {
         const Rule &r = *it;
         const std::string s;// = header->GetEntryString( r.first );
         if ( !Util::DicomStringEqual(s, r.second.c_str()) )
         {
           // Argh ! This rule is unmatch let's just quit
           allrules = 0;
           break;
         }
      }
      if ( allrules ) // all rules are respected:
      {
         // Allright ! we have a found a DICOM that match the user expectation. 
         // Let's add it !

         const std::string &uid = "0";
         // Serie UID of the gdcm::File* may be different.
         // User is supposed to know what he wants

         if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
         {
            gdcmDebugMacro(" New Serie UID :[" << uid << "]");
            // create a std::list in 'uid' position
            SingleSerieUIDFileSetHT[uid] = new FileList;
         }
         // Current Serie UID and DICOM header seems to match; add the file:
         SingleSerieUIDFileSetHT[uid]->push_back( header );
      }
         // Even if a rule was unmatch we don't deallocate the gdcm::File:
}

/**
 * \brief add a rule for restricting a DICOM file to be in the serie we are
 * trying to find. For example you can select only the DICOM files from a
 * directory which would have a particular EchoTime==4.0.
 * This method is a user level, value is not required to be formatted as a DICOM
 * string
 * \todo find a trick to allow user to say if he wants the Rectrictions 
 *       to be *ored* (and not only *anded*)
 * @param   key  Target tag we want restrict on a given value
 * @param value value to be checked to exclude File
 * @param op  operator we want to use to check
 */
void SerieHelper::AddRestriction(TagKey const &key, 
                                 std::string const &value, int op)
{
   ExRule r;
   r.group = key[0];
   r.elem  = key[1];
   r.value = value;
   r.op    = op;
   ExRestrictions.push_back( r ); 
}

/**
 * \brief add a rule for restricting a DICOM file to be in the serie we are
 * trying to find. For example you can select only the DICOM file from a
 * directory which would have a particular EchoTime==4.0.
 * This method is a user level, value is not required to be formatted as a DICOM
 * string
 * \todo find a trick to allow user if he wants the Rectrictions to be *ored*
 *       (and not only *anded*)
 * @param   group tag group number we want restrict on a given value
 * @param   elem  tag element number we want restrict on a given value 
 * @param value value to be checked to exclude File
 * @param op  operator we want to use to check
 */
void SerieHelper::AddRestriction(uint16_t group, uint16_t elem, 
                                 std::string const &value, int op)
{
   ExRule r;
   r.group = group;
   r.elem  = elem;
   r.value = value;
   r.op    = op;
   ExRestrictions.push_back( r ); 
}

/**
 * \brief add an extra  'SerieDetail' for building a 'Serie Identifier'
 *        that ensures (hope so) File constistency (Series Instance UID doesn't.
 * @param   group tag group number we want restrict on a given value
 * @param   elem  tag element number we want restrict on a given value
 * @param  convert wether we want 'convertion', to allow further ordering
 *         e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK 
 */
void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert)
{
   
   ExDetail d;
   d.group   = group;
   d.elem    = elem;
   d.convert = convert;
   ExDetails.push_back( d ); 
}
/**
 * \brief Sets the root Directory
 * @param   dir Name of the directory to deal with
 * @param recursive whether we want explore recursively the root Directory
 */
void SerieHelper::SetDirectory(std::string const &dir, bool recursive)
{
   DirList dirList(dir, recursive); // OS specific
  
   DirListType filenames_list = dirList.GetFilenames();
   for( DirListType::const_iterator it = filenames_list.begin(); 
        it != filenames_list.end(); ++it)
   {
      AddFileName( *it );
   }
}

/**
 * \brief Sorts the given Fileset
 * \warning This could be implemented in a 'Strategy Pattern' approach
 *          But as I don't know how to do it, I leave it this way
 *          BTW, this is also a Strategy, I don't know this is 
 *          the best approach :)
 */
void SerieHelper::OrderFileList(FileList *fileSet)
{

   if ( SerieHelper::UserLessThanFunction )
   {
      UserOrdering( fileSet );
      return; 
   }
   else if ( ImagePositionPatientOrdering( fileSet ) )
   {
      return ;
   }
   else if ( ImageNumberOrdering(fileSet ) )
   {
      return ;
   }
   else  
   {
      FileNameOrdering(fileSet );
   }
}

/**
 * \brief Elementary coherence checking of the files with the same Serie UID
 * Only sizes and pixel type are checked right now ...
 */ 
bool SerieHelper::IsCoherent(FileList *fileSet)
{
   if(fileSet->size() == 1)
   return true;

   FileList::const_iterator it = fileSet->begin();

   int nX =               (*it)->GetXSize();
   int nY =               (*it)->GetYSize();
   int pixelSize =        (*it)->GetPixelSize();
   bool signedPixelData = (*it)->IsSignedPixelData();
   it ++;
   for ( ;
         it != fileSet->end();
       ++it)
   {
      if ( (*it)->GetXSize() != nX )
         return false;
      if ( (*it)->GetYSize() != nY )
         return false;
      if ( (*it)->GetPixelSize() != pixelSize )
         return false;
      if ( (*it)->IsSignedPixelData() != signedPixelData )
         return false;
      // probabely more is to be checked (?)      
   }
   return true;
}

#ifndef GDCM_LEGACY_REMOVE

FileList *SerieHelper::GetFirstCoherentFileList()
{
   ItFileSetHt = SingleSerieUIDFileSetHT.begin();
   if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
      return ItFileSetHt->second;
   return NULL;
}


FileList *SerieHelper::GetNextCoherentFileList()
{
   gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
  
   ++ItFileSetHt;
   if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
      return ItFileSetHt->second;
   return NULL;
}


FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
{
   if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
      return 0;     
   return SingleSerieUIDFileSetHT[SerieUID];
}
#endif


/**
 * \brief   Get the first Fileset while visiting the SingleSerieUIDFileSetmap
 * @return  The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
 */
FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
{
   ItFileSetHt = SingleSerieUIDFileSetHT.begin();
   if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
      return ItFileSetHt->second;
   return NULL;
}

/**
 * \brief   Get the next Fileset while visiting the SingleSerieUIDFileSetmap
 * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called 
 * @return  The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
 */
FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
{
   gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
  
   ++ItFileSetHt;
   if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
      return ItFileSetHt->second;
   return NULL;
}

/**
 * \brief   Get the SingleSerieUIDFileSet according to its Serie UID
 * @param SerieUID SerieUID to retrieve
 * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
 */
FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
{
   if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
      return 0;     
   return SingleSerieUIDFileSetHT[SerieUID];
}

/**
 * \brief   Splits a Single SerieUID Fileset according to the Orientations
 * @param fileSet File Set to be splitted
 * \return  std::map of 'Xcoherent' File sets
 */

XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
{
   XCoherentFileSetmap CoherentFileSet;

   int nb = fileSet->size();
   if (nb == 0 )
      return CoherentFileSet;
   float iop[6];

   std::string strOrient;
   std::ostringstream ossOrient;   
   FileList::const_iterator it = fileSet->begin();
   it ++;
   for ( ;
         it != fileSet->end();
       ++it)
   {     
      // Information is in :      
      // 0020 0037 : Image Orientation (Patient) or
      // 0020 0035 : Image Orientation (RET)

      // Let's build again the 'cosines' string, to be sure of it's format      
      (*it)->GetImageOrientationPatient(iop);

      ossOrient << iop[0];      
      for (int i = 1; i < 6; i++)
      {
        ossOrient << "\\";
        ossOrient << iop[i]; 
      }      
      strOrient = ossOrient.str();
      ossOrient.str("");
      // FIXME : is it a 'cleaner' way to initialize an ostringstream? 

      if ( CoherentFileSet.count(strOrient) == 0 )
      {
         gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
         // create a File set in 'orientation' position
         CoherentFileSet[strOrient] = new FileList;
      }
      // Current Orientation and DICOM header match; add the file:
      CoherentFileSet[strOrient]->push_back( (*it) );
   } 
   return CoherentFileSet;
}

/**
 * \brief   Splits a 'Single SerieUID' Fileset according to the Positions
 * @param fileSet File Set to be splitted
 * \return  std::map of 'Xcoherent' File sets
 */

XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
{
   XCoherentFileSetmap CoherentFileSet;

   int nb = fileSet->size();
   if (nb == 0 )
      return CoherentFileSet;
   float pos[3];
   std::string strImPos;  // read on disc
   std::ostringstream ossPosition;
   std::string strPosition; // re computed
   FileList::const_iterator it = fileSet->begin();
   it ++;
   for ( ;
         it != fileSet->end();
       ++it)
   {     
      // Information is in :      
      // 0020,0032 : Image Position Patient
      // 0020,0030 : Image Position (RET)

      strImPos = (*it)->GetEntryString(0x0020,0x0032);
      if ( strImPos == GDCM_UNFOUND)
      {
         gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
         strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
         if ( strImPos == GDCM_UNFOUND )
         {
            gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
            // User wants to split on the 'Position'
            // No 'Position' info found.
            // We return an empty Htable !
            return CoherentFileSet;
         }  
      }

      if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", 
                                              &pos[0], &pos[1], &pos[2]) != 3 )
      {
            gdcmWarningMacro( "Wrong number for Position : ["
                       << strImPos << "]" );
             return CoherentFileSet;
      }

      // Let's build again the 'position' string, to be sure of it's format      

      ossPosition << pos[0];      
      for (int i = 1; i < 3; i++)
      {
        ossPosition << "\\";
        ossPosition << pos[i]; 
      }      
      strPosition = ossPosition.str();
      ossPosition.str("");
            
      if ( CoherentFileSet.count(strPosition) == 0 )
      {
         gdcmDebugMacro(" New Position :[" << strPosition << "]");
         // create a File set in 'position' position
         CoherentFileSet[strPosition] = new FileList;
      }
      // Current Position and DICOM header match; add the file:
      CoherentFileSet[strPosition]->push_back( (*it) );
   }   
   return CoherentFileSet;
}

/**
 * \brief   Splits a 'Single SerieUID' File set Coherent according to the
 *          value of a given Tag
 * @param fileSet File Set to be splitted
 * @param   group  group number of the target Element
 * @param   elem element number of the target Element
 * \return  std::map of 'Xcoherent' File sets
 */

XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, 
                                               uint16_t group, uint16_t elem)
{
   XCoherentFileSetmap CoherentFileSet;

   int nb = fileSet->size();
   if (nb == 0 )
      return CoherentFileSet;

   std::string strTagValue;  // read on disc

   FileList::const_iterator it = fileSet->begin();
   it ++;
   for ( ;
         it != fileSet->end();
       ++it)
   {     
      // Information is in :      
      // 0020,0032 : Image Position Patient
      // 0020,0030 : Image Position (RET)

      strTagValue = (*it)->GetEntryString(group,elem);
      
      if ( CoherentFileSet.count(strTagValue) == 0 )
      {
         gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
         // create a File set in 'position' position
         CoherentFileSet[strTagValue] = new FileList;
      }
      // Current Tag value and DICOM header match; add the file:
      CoherentFileSet[strTagValue]->push_back( (*it) );
   }
   return CoherentFileSet;
}

//-----------------------------------------------------------------------------
// Protected

//-----------------------------------------------------------------------------
// Private
/**
 * \brief sorts the images, according to their Patient Position.
 *
 *  We may order, considering :
 *   -# Image Position Patient
 *   -# Image Number
 *   -# file name
 *   -# More to come :-)
 * \note : FileList = std::vector<File* >
 * @param fileList Coherent File list (same Serie UID) to sort
 * @return false only if the header is bugged !
 */
bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
//based on Jolinda Smith's algorithm
{
   //iop is calculated based on the file file
   float cosines[6];
   double normal[3];
   double ipp[3];
   double dist;
   double min = 0, max = 0;
   bool first = true;

   std::multimap<double,File *> distmultimap;
   // Use a multimap to sort the distances from 0,0,0
   for ( FileList::const_iterator 
         it = fileList->begin();
         it != fileList->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 ("Image Position Patient") 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];
         }
    
         distmultimap.insert(std::pair<const double,File *>(dist, *it));

         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];
         }

         distmultimap.insert(std::pair<const double,File *>(dist, *it));

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

   }

   // Find out if min/max are coherent
   if ( min == max )
   {
     gdcmWarningMacro("Looks like all images have the exact same image position"
                      << ". No PositionPatientOrdering sort performed" );
     return false;
   }

   // Check to see if image shares a common position
    bool ok = true;
    for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
                                                 it2 != distmultimap.end();
                                                 ++it2)
    {
       if (distmultimap.count((*it2).first) != 1)
       {
          gdcmErrorMacro("File: "
               << ((*it2).second->GetFileName())
               << " Distance: "
               << (*it2).first
               << " position is not unique");
          ok = false;
       } 
    }
    if (!ok)
    {
       return false;
    }
  
   fileList->clear();  // doesn't delete list elements, only nodes

   if (DirectOrder)
   {  
      for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
                                                   it3 != distmultimap.end();
                                                 ++it3)
      {
         fileList->push_back( (*it3).second );
      }
   }
   else // user asked for reverse order
   {
      std::multimap<double, File *>::const_iterator it4;
      it4 = distmultimap.end();
      do
      {
         it4--;
         fileList->push_back( (*it4).second );
      } while (it4 != distmultimap.begin() );
   } 

   distmultimap.clear();

   return true;
}

bool SerieHelper::ImageNumberLessThan(File *file1, File *file2)
{
  return file1->GetImageNumber() < file2->GetImageNumber();
}

bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
{
  return file1->GetImageNumber() > file2->GetImageNumber();
}

/**
 * \brief sorts the images, according to their Image Number
 * \note Works only on bona fide files  (i.e image number is a character string
 *                                      corresponding to an integer)
 *             within a bona fide serie (i.e image numbers are consecutive)
 * @param fileList  File set (same Serie UID) to sort 
 * @return false if non bona fide stuff encountered
 */
bool SerieHelper::ImageNumberOrdering(FileList *fileList) 
{
   int min, max, pos;
   int n = fileList->size();

   FileList::const_iterator it = fileList->begin();
   min = max = (*it)->GetImageNumber();

   for (; it != fileList->end(); ++it, ++n)
   {
      pos = (*it)->GetImageNumber();
      min = (min < pos) ? min : pos;
      max = (max > pos) ? max : pos;
   }

   // Find out if image numbers are coherent (consecutive)
   if ( min == max || max == 0 || max >= (n+min) )
   {
      gdcmWarningMacro( " 'Image numbers' not coherent. "
                        << " No ImageNumberOrdering sort performed.");
      return false;
   }
   if (DirectOrder) 
        Sort(fileList,SerieHelper::ImageNumberLessThan);
//      std::sort(fileList->begin(), fileList->end(), 
//                                          SerieHelper::ImageNumberLessThan );
   else
        Sort(fileList,SerieHelper::ImageNumberGreaterThan);
//      std::sort(fileList->begin(), fileList->end(),
//                                          SerieHelper::ImageNumberGreaterThan );

   return true;
}

bool SerieHelper::FileNameLessThan(File *file1, File *file2)
{
   return file1->GetFileName() < file2->GetFileName();
}

bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
{
   return file1->GetFileName() > file2->GetFileName();
}
/**
 * \brief sorts the images, according to their File Name
 * @param fileList Coherent File list (same Serie UID) to sort
 * @return false only if the header is bugged !
 */
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
   if (DirectOrder) 
        Sort(fileList,SerieHelper::FileNameLessThan);
//      std::sort(fileList->begin(), fileList->end(), 
//                                       SerieHelper::FileNameLessThan);
   else
        Sort(fileList,SerieHelper::FileNameGreaterThan);   
//      std::sort(fileList->begin(), fileList->end(), 
//                                       SerieHelper::FileNameGreaterThan);

   return true;
}

/**
 * \brief sorts the images, according to user supplied function
 * @param fileList Coherent File list (same Serie UID) to sort
 * @return false only if the header is bugged !
 */
bool SerieHelper::UserOrdering(FileList *fileList)
{
        Sort(fileList,SerieHelper::UserLessThanFunction);   
//   std::sort(fileList->begin(), fileList->end(), 
//                                             SerieHelper::UserLessThanFunction);
   if (!DirectOrder) 
   {
      std::reverse(fileList->begin(), fileList->end());
   }
   return true;
}

/**
 * \brief Heuristics to *try* to build a Serie Identifier that would ensure
 *        all the images are coherent.
 *
 * By default, uses the SeriesUID.  If UseSeriesDetails(true) has been called,
 *         then additional identifying information is used.
 *  We allow user to add his own critierions, using AddSeriesDetail
 *        (he knows more than we do about his images!)
 *        ex : in tagging series, the only pertnent tag is
 *        0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN
 * @param inFile gdcm::File we want to build a Serie Identifier for.
 * @return the SeriesIdentifier
 */
std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile )
{
   if( inFile->IsReadable() )
   {
     // 0020 000e UI REL Series Instance UID
    std::string uid =  inFile->GetEntryString (0x0020, 0x000e);
    std::string id = uid.c_str();
    if(m_UseSeriesDetails)
    {
    // If the user requests, additional information can be appended
    // to the SeriesUID to further differentiate volumes in the DICOM
    // objects being processed.
 
   // 0020 0011 Series Number
   // A scout scan prior to a CT volume scan can share the same
   // SeriesUID, but they will sometimes have a different Series Number
       std::string sNum = inFile->GetEntryString(0x0020, 0x0011);
       if( sNum == gdcm::GDCM_UNFOUND )
       {
           sNum = "";
       }
 // 0018 0024 Sequence Name
 // For T1-map and phase-contrast MRA, the different flip angles and
 // directions are only distinguished by the Sequence Name
         std::string sName = inFile->GetEntryString(0x0018, 0x0024);
         if( sName == gdcm::GDCM_UNFOUND )
         {
           sName = "";
         }
 
  // You can think on checking Image Orientation (0020,0037), as well.
  

  // 0018 0050 Slice Thickness
  // On some CT systems, scout scans and subsequence volume scans will
  // have the same SeriesUID and Series Number - YET the slice
  // thickness will differ from the scout slice and the volume slices.
         std::string sThick = inFile->GetEntryString (0x0018, 0x0050);
         if( sThick == gdcm::GDCM_UNFOUND )
         {
           sThick = "";
         }
  // 0028 0010 Rows
  // If the 2D images in a sequence don't have the same number of rows,
  // then it is difficult to reconstruct them into a 3D volume.
         std::string sRows = inFile->GetEntryString (0x0028, 0x0010);
         if( sRows == gdcm::GDCM_UNFOUND )
         {
           sRows = "";
         }
  // 0028 0011 Columns
  // If the 2D images in a sequence don't have the same number of columns,
  // then it is difficult to reconstruct them into a 3D volume.
         std::string sColumns = inFile->GetEntryString (0x0028, 0x0011);
         if( sColumns == gdcm::GDCM_UNFOUND )
         {
           sColumns = "";
         }

  // Concat the new info
         std::string num = sNum.c_str();
         num += sName.c_str();
         num += sThick.c_str();
         num += sRows.c_str();
         num += sColumns.c_str();
 
  // Add a loop, here, to deal with any extra user supplied tag.
  //      We allow user to add his own critierions 
  //      (he knows more than we do about his images!)
  //      ex : in tagging series, the only pertinent tag is
  //          0018|1312 [In-plane Phase Encoding Direction] values : ROW/COLUMN
  
      std::string s; 
      for(SeriesExDetails::iterator it2 = ExDetails.begin();
          it2 != ExDetails.end();
          ++it2)
      {
         const ExDetail &r = *it2;
         s = inFile->GetEntryString( r.group, r.elem );      
         num += s.c_str();
      }
   
  // Append the new info to the SeriesUID
         id += ".";
         id += num.c_str();
       }
   
  // Eliminate non-alphanum characters, including whitespace...
  // that may have been introduced by concats.
       for(unsigned int i=0; i<id.size(); i++)
       {
         while(i<id.size()
               && !( id[i] == '.' || id[i] == '-' || id[i] == '_'
                    || (id[i] >= 'a' && id[i] <= 'z')
                    || (id[i] >= '0' && id[i] <= '9')
                    || (id[i] >= 'A' && id[i] <= 'Z')))
         {
           id.erase(i, 1);
         }
       }
       return id;
     }
     else // Could not open inFile
     {
       gdcmWarningMacro("Could not parse series info.");
       std::string id = gdcm::GDCM_UNFOUND;
       return id;
     }
}

/**
 * \brief Allow user to build is own File Identifier (to be able to sort
 *        temporal series just as he wants)
 *        Criterions will be set with AddSeriesDetail.
 *        (Maybe the method should be moved elsewhere 
 *       -File class? FileHelper class?-
 * @return FileIdentifier (Tokenizable on '_')
 */
std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile )
{
  //     Deal with all user supplied tags.
  //      (user knows more than we do about his images!)
  
   float converted;
   std::string id;
   std::string s; 
   char charConverted[17]; 
   
   for(SeriesExDetails::iterator it2 = ExDetails.begin();
      it2 != ExDetails.end();
      ++it2)
   {
      const ExDetail &r = *it2;
      s = inFile->GetEntryString( r.group, r.elem );
      
      // User is allowed to ask 'convertion', to allow further ordering
      // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
      if (it2->convert)
      {
         converted = atof(s.c_str());
         // probabely something much more complicated is possible, 
         // using C++ features
         /// \todo check the behaviour when there are >0 and <0 numbers
         sprintf(charConverted, "%016.6f",converted);
         s = charConverted;
      }
      // Eliminate non-alphanum characters, including whitespace.
      for(unsigned int i=0; i<s.size(); i++)
      {
         while(i<s.size()
            && !( s[i] == '.' || s[i] == '-'
                    || (s[i] >= 'a' && s[i] <= 'z')
                    || (s[i] >= '0' && s[i] <= '9')
                    || (s[i] >= 'A' && s[i] <= 'Z')))
         {
            s.erase(i, 1);
         }
      }
      
      id += s.c_str();
      id += "_"; // make the FileIdentifier Tokenizable
   }
   
   return id;             
}
//-----------------------------------------------------------------------------
// Print
/**
 * \brief   Canonical printer.
 */
void SerieHelper::Print(std::ostream &os, std::string const &indent)
{
   // For all the Coherent File lists of the gdcm::Serie
   SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
   if ( itl == SingleSerieUIDFileSetHT.end() )
   {
      gdcmWarningMacro( "No SingleSerieUID File set found" );
      return;
   }
   while (itl != SingleSerieUIDFileSetHT.end())
   { 
      os << "Serie UID :[" << itl->first << "]" << std::endl;

      // For all the files of a SingleSerieUID File set
      for (FileList::iterator it =  (itl->second)->begin();
                                  it != (itl->second)->end(); 
                                ++it)
      {
         os << indent << " --- " << (*it)->GetFileName() << std::endl;
      }
      ++itl;
   }
}

//-----------------------------------------------------------------------------
// Sort
/**
 * \brief   Sort FileList.
 */
void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) )
{
 std::sort(fileList->begin(), fileList->end(), pt2Func );
}

//-----------------------------------------------------------------------------
} // end namespace gdcm