/*=========================================================================
                                                                                
  Program:   gdcm
  Module:    $RCSfile: gdcmSerieHelper.cxx,v $
  Language:  C++
  Date:      $Date: 2005/08/30 08:12:40 $
  Version:   $Revision: 1.18 $
                                                                                
  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 <algorithm>

namespace gdcm 
{

//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
 * \brief   Constructor from a given SerieHelper
 */
SerieHelper::SerieHelper()
{
   UserLessThanFunction = 0;

   // For all the File lists that may already exist within the gdcm::Serie
   FileList *l = GetFirstCoherentFileList();
   while (l)
   { 
      // For all the files of a File list
      for (gdcm::FileList::iterator it  = l->begin();
                              it != l->end(); 
                            ++it)
      {
         delete *it; // remove entry
      }
      l->clear();
      delete l;     // remove the list
      l = GetNextCoherentFileList();
   }
   DirectOrder = true;
}

/**
 * \brief   Canonical destructor.
 */
SerieHelper::~SerieHelper()
{
   // For all the Coherent File lists of the gdcm::Serie
   FileList *l = GetFirstCoherentFileList();
   while (l)
   { 
      // For all the files of a Coherent File list
      for (FileList::iterator it  = l->begin();
                              it != l->end(); 
                            ++it)
      {
         delete *it; // remove entry
      }
      l->clear();
      delete l;  // remove the list
      l = GetNextCoherentFileList();
   }
}

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

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

// Public
/**
 * \brief add a gdcm::File to the list 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 = new File ();
   header->SetLoadMode(LoadMode);
   header->SetFileName( filename ); 
   header->Load();

   if ( header->IsReadable() )
   {
      int allrules = 1;
      // First step the user has defined a set of rules for the DICOM file
      // 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;
         // doesn't compile (no matching function...).
         const std::string s;// = header->GetEntryValue( r.first );
         if ( !Util::DicomStringEqual(s, r.second.c_str()) )
         {
           // Argh ! This rule is unmatch let's just quit
           allrules = 0;
           break;
         }
      }
*/
      // Just keep 'new style' for Rules
      std::string s;
      for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
          it2 != ExRestrictions.end();
          ++it2)
      {
         const ExRule &r = *it2;
         s = header->GetEntryValue( r.group, r.elem );
         if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
         {
           // 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 !

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

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

/**
 * \brief add a gdcm::File to the first (and supposed to be unique) list
 *        of the gdcm::SerieHelper.
 * \warning : this method should be used by aware users only!
 *            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->GetEntryValue( 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 ( CoherentFileListHT.count(uid) == 0 )
         {
            gdcmDebugMacro(" New Serie UID :[" << uid << "]");
            // create a std::list in 'uid' position
            CoherentFileListHT[uid] = new FileList;
         }
         // Current Serie UID and DICOM header seems to match; add the file:
         CoherentFileListHT[uid]->push_back( header );
      }
         // Even if a rule was unmatch we don't deallocate the gdcm::File:
}

/**
 * \brief add a rules 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
 */
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 ); 
}

#ifndef GDCM_LEGACY_REMOVE
/**
 * \brief add a rules 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
 * @deprecated use : AddRestriction(uint16_t group, uint16_t elem, 
 *                                 std::string const &value, int op);
 */
void SerieHelper::AddRestriction(TagKey const &key, std::string const &value)
{
   Rule r;
   r.first = key;
   r.second = value;
   Restrictions.push_back( r ); 
}
#endif

/**
 * \brief Sets the root Directory
 * @param   dir Name of the directory to deal with
 * @param recursive whether we want explore recursively the 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 File List
 * \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 *coherentFileList)
{

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

/**
 * \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 *coherentFileList)
{
   if(coherentFileList->size() == 1)
   return true;

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

   int nX = (*it)->GetXSize();
   int nY = (*it)->GetYSize();
   int pixelSize = (*it)->GetPixelSize();

   it ++;
   for ( ;
         it != coherentFileList->end();
       ++it)
   {
      if ( (*it)->GetXSize() != nX )
         return false;
      if ( (*it)->GetYSize() != nY )
         return false;
      if ( (*it)->GetPixelSize() != pixelSize )
         return false;
      // probabely more is to be checked (?)
   }
   return true;
}
/**
 * \brief   Get the first List while visiting the CoherentFileListHT
 * @return  The first FileList if found, otherwhise NULL
 */
FileList *SerieHelper::GetFirstCoherentFileList()
{
   ItListHt = CoherentFileListHT.begin();
   if ( ItListHt != CoherentFileListHT.end() )
      return ItListHt->second;
   return NULL;
}

/**
 * \brief   Get the next List while visiting the CoherentFileListHT
 * \note : meaningfull only if GetFirstCoherentFileList() already called
 * @return  The next FileList if found, otherwhise NULL
 */
FileList *SerieHelper::GetNextCoherentFileList()
{
   gdcmAssertMacro (ItListHt != CoherentFileListHT.end());
  
   ++ItListHt;
   if ( ItListHt != CoherentFileListHT.end() )
      return ItListHt->second;
   return NULL;
}

/**
 * \brief   Get the Coherent Files list according to its Serie UID
 * @param SerieUID SerieUID
 * \return  pointer to the Coherent Files list if found, otherwhise NULL
 */
FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
{
   if ( CoherentFileListHT.count(SerieUID) == 0 )
      return 0;     
   return CoherentFileListHT[SerieUID];
}

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

//-----------------------------------------------------------------------------
// Private
/**
 * \brief sorts the images, according to their Patient Position
 *  We may order, considering :
 *   -# Image Position Patient
 *   -# Image Number
 *   -# More to come :-)
 * WARNING : 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];
   float normal[3];
   float ipp[3];
   float dist;
   float min = 0, max = 0;
   bool first = true;
   int n=0;
   std::vector<float> distlist;

   //!\todo rewrite this for loop.
   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 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.
   FileVector CoherentFileVector(n);
   // CoherentFileVector.reserve( n );
   CoherentFileVector.resize( n );
   // gdcmAssertMacro( CoherentFileVector.capacity() >= n );

   // 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;
     }

   float step = (max - min)/(n - 1);
   int pos;
   n = 0;
    
   //VC++ don't understand what scope is !! it -> it2
   for (FileList::const_iterator it2  = fileList->begin();
        it2 != fileList->end(); ++it2, ++n)
   {
      //2*n sort algo !!
      //Assumption: all files are present (no one missing)
      pos = (int)( fabs( (distlist[n]-min)/step) + .5 );

      // a Dicom 'Serie' may contain scout views
      // and images may have differents directions
      // -> More than one may have the same 'pos'
      // Sorting has then NO meaning !
      if (CoherentFileVector[pos]==NULL)
         CoherentFileVector[pos] = *it2;
      else
      {
         gdcmWarningMacro( "At least 2 files with same position. No PositionPatientOrdering sort performed");
         return false;
      }
   }

   fileList->clear();  // doesn't delete list elements, only nodes

   if (DirectOrder)
   {  
      //VC++ don't understand what scope is !! it -> it3
      for (FileVector::const_iterator it3  = CoherentFileVector.begin();
           it3 != CoherentFileVector.end(); ++it3)
      {
         fileList->push_back( *it3 );
      }
   }
   else // user asked for reverse order
   {
      FileVector::const_iterator it4;
      it4 = CoherentFileVector.end();
      do
      {
         it4--;
         fileList->push_back( *it4 );
      } while (it4 != CoherentFileVector.begin() );
   } 

   distlist.clear();
   CoherentFileVector.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 Coherent File list (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) 
      std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan );
   else
      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) 
      std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan);
   else
      std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan);

   return true;
}

/**
 * \brief sorts the images, according to user supplied function
 * \note Only Direct ordering is allowed
 * @param fileList Coherent File list (same Serie UID) to sort
 * @return false only if the header is bugged !
 */
bool SerieHelper::UserOrdering(FileList *fileList)
{
   if (DirectOrder) 
      std::sort(fileList->begin(), fileList->end(), SerieHelper::UserLessThanFunction);
   else
      gdcmWarningMacro( " Only Direct ordering allowed "
                     << "when user function is supplied");
   return true;
}
//-----------------------------------------------------------------------------
// Print
/**
 * \brief   Canonical printer.
 */
void SerieHelper::Print(std::ostream &os, std::string const &indent)
{
   // For all the Coherent File lists of the gdcm::Serie
   CoherentFileListmap::iterator itl = CoherentFileListHT.begin();
   if ( itl == CoherentFileListHT.end() )
   {
      gdcmWarningMacro( "No Coherent File list found" );
      return;
   }
   while (itl != CoherentFileListHT.end())
   { 
      os << "Serie UID :[" << itl->first << "]" << std::endl;

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

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