/*=========================================================================
                                                                                
  Program:   gdcm
  Module:    $RCSfile: ReWrite.cxx,v $
  Language:  C++
  Date:      $Date: 2006/04/19 10:23:56 $
  Version:   $Revision: 1.20 $
                                                                                
  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 "gdcmFile.h"
#include "gdcmFileHelper.h"
#include "gdcmDebug.h"

#include "gdcmArgMgr.h"

#include <iostream>

int main(int argc, char *argv[])
{
   START_USAGE(usage)
   " \n ReWrite :\n",
   " Re write a full gdcm-readable Dicom image                              ",
   "     (usefull when the file header is not very straight).               ",
   "                                                                        ",
   " usage: ReWrite filein=inputFileName fileout=outputFileName             ", 
   "       [mode=write mode] [noshadow] [noseq][debug]                      ",
   "       [rubout=xBegin,xEnd,yBegin,yEnd [ruboutvalue=n (<255)] ]         ",
   "                                                                        ",
   "        mode = a (ACR), x (Explicit VR Dicom), r (RAW : only pixels)    ",
   "        noshadowseq: user doesn't want to load Private Sequences        ",
   "        noshadow : user doesn't want to load Private groups (odd number)",
   "        noseq    : user doesn't want to load Sequences                  ",
   "        rgb      : user wants to tranform LUT (if any) to RGB pixels    ",
   "        debug    : user wants to run the program in 'debug mode'        ",
   FINISH_USAGE

   // ----- Initialize Arguments Manager ------   
   gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
  
   if (argc == 1 || am->ArgMgrDefined("usage")) 
   {
      am->ArgMgrUsage(usage); // Display 'usage'
      delete am;
      return 0;
   }
   char *fileName = am->ArgMgrWantString("filein",usage);
   if ( fileName == NULL )
   {
      std::cout << "'filein= ...' is mandatory" << std::endl;
      delete am;
      return 0;
   }

   char *outputFileName = am->ArgMgrWantString("fileout",usage);
   if ( outputFileName == NULL )
   {
      std::cout << "'fileout= ...' is mandatory" << std::endl;
      delete am;
      return 0;
   }

   const char *mode = am->ArgMgrGetString("mode","X");

   int loadMode = gdcm::LD_ALL;
   if ( am->ArgMgrDefined("noshadowseq") )
      loadMode |= gdcm::LD_NOSHADOWSEQ;
   else 
   {
   if ( am->ArgMgrDefined("noshadow") )
         loadMode |= gdcm::LD_NOSHADOW;
      if ( am->ArgMgrDefined("noseq") )
         loadMode |= gdcm::LD_NOSEQ;
   }

   bool rgb = ( 0 != am->ArgMgrDefined("RGB") );

   if (am->ArgMgrDefined("debug"))
      gdcm::Debug::DebugOn();
      
   bool fail = false;
   int *boundVal;
   int ruboutVal;
   bool rubout = false; 
   if (am->ArgMgrDefined("rubout"))
   {
      int nbBound;
      boundVal = am->ArgMgrGetListOfInt("rubout", &nbBound);

      if (nbBound !=4)
      {
         std::cout << "Illegal number of 'rubout' boundary values (expected : 4, found:" 
                   << nbBound << "); 'rubout' ignored" << std::endl;
         fail = true;
      }
            
      ruboutVal = am->ArgMgrGetInt("ruboutvalue", 0);
      rubout = true;   
   }

 
   // if unused Params we give up
   if ( am->ArgMgrPrintUnusedLabels() )
   { 
      am->ArgMgrUsage(usage);
      delete am;
      return 0;
   }

   delete am;  // we don't need Argument Manager any longer

   // ----------- End Arguments Manager ---------

   gdcm::File *f = gdcm::File::New();
   f->SetLoadMode( loadMode );
   f->SetFileName( fileName );
   bool res = f->Load();  
   if ( !res )
   {
      f->Delete();
      return 0;
   }
  
   if (!f->IsReadable())
   {
       std::cerr << "Sorry, not a Readable DICOM / ACR File"  <<std::endl;
       f->Delete();
       return 0;
   }
   
   gdcm::FileHelper *fh = gdcm::FileHelper::New(f);
   void *imageData; 
   int dataSize;
  
   if (rgb)
   {
      dataSize  = fh->GetImageDataSize();
      imageData = fh->GetImageData(); // somewhat important... can't remember
      fh->SetWriteModeToRGB();
   }
   else
   {
      dataSize  = fh->GetImageDataRawSize();
      imageData = fh->GetImageDataRaw();// somewhat important... can't remember
      fh->SetWriteModeToRaw();
   }

   if ( imageData == 0 ) // to avoid warning
   {
      std::cout << "Was unable to read pixels " << std::endl;
   }
   std::cout <<std::endl <<" dataSize " << dataSize << std::endl;
   int nX,nY,nZ,sPP,planarConfig;
   std::string pixelType, transferSyntaxName;
   nX=f->GetXSize();
   nY=f->GetYSize();
   nZ=f->GetZSize();
   std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << std::endl;

   pixelType    = f->GetPixelType();
   sPP          = f->GetSamplesPerPixel();
   planarConfig = f->GetPlanarConfiguration();
   
   std::cout << " pixelType="           << pixelType 
             << " SampleserPixel="      << sPP
             << " PlanarConfiguration=" << planarConfig 
             << " PhotometricInterpretation=" 
             << f->GetEntryString(0x0028,0x0004) 
             << std::endl;

   int numberOfScalarComponents=f->GetNumberOfScalarComponents();
   std::cout << "NumberOfScalarComponents " << numberOfScalarComponents 
             <<std::endl;
   transferSyntaxName = f->GetTransferSyntaxName();
   std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]" 
             << std::endl;

   // Since we just ReWrite the image, we know no modification 
   // was performed on the pixels.
   // We don't want this image appears as a 'Secondary Captured image'
   fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
   

   if (rubout)
   {     
      if (boundVal[0]<0 || boundVal[0]>nX)
      { 
         std::cout << "xBegin out of bounds; 'rubout' ignored" << std::endl;
         fail = true;      
      }
      if (boundVal[1]<0 || boundVal[1]>nX)
      { 
         std::cout << "xEnd out of bounds; 'rubout' ignored" << std::endl;
         fail = true;      
      }
      if (boundVal[0] > boundVal[1])
      { 
         std::cout << "xBegin greater than xEnd; 'rubout' ignored" << std::endl;
         fail = true;      
      }       
      if (boundVal[2]<0 || boundVal[2]>nY)
      { 
         std::cout << "yBegin out of bounds; 'rubout' ignored" << std::endl;
         fail = true;      
      }
      if (boundVal[3]<0 || boundVal[3]>nY)
      { 
         std::cout << "yEnd out of bounds; 'rubout' ignored" << std::endl;
         fail = true;      
      }
      if (boundVal[2] > boundVal[3])
      { 
         std::cout << "yBegin greater than yEnd; 'rubout' ignored" << std::endl;
         fail = true;      
      }  
      if (!fail)
      {
         int pixelLength = f->GetBitsAllocated()/8;
         int lineLength = nX * sPP * pixelLength;
         size_t lengthToRubout = (boundVal[1]-boundVal[0])*sPP*pixelLength;
         int offsetToBeginOfRubout = boundVal[0]*sPP*pixelLength+lineLength*boundVal[2];
      
         for(int rbl=boundVal[2]; rbl<boundVal[3];rbl++)
         {
            memset((char *)imageData+offsetToBeginOfRubout, ruboutVal, lengthToRubout);
            offsetToBeginOfRubout += lineLength; 
         }
      }   
   } 

   switch (mode[0])
   {
      case 'A' :
      case 'a' :
      // Writting an ACR file
      // from a full gdcm readable File
         std::cout << "WriteACR" << std::endl;
         fh->WriteAcr(outputFileName);
         break;

      case 'D' : // Not documented in the 'usage', because the method 
      case 'd' : //                             is known to be bugged. 
      // Writting a DICOM Implicit VR file
      // from a full gdcm readable File
         std::cout << "WriteDCM Implicit VR" << std::endl;
         fh->WriteDcmImplVR(outputFileName);
         break;

      case 'X' :
      case 'x' :
      // writting a DICOM Explicit VR 
      // from a full gdcm readable File
         std::cout << "WriteDCM Explicit VR" << std::endl;
         // fh->WriteDcmExplVR(outputFileName);
         // Try this one :
         fh->SetWriteTypeToDcmExplVR();
         fh->Write(outputFileName);
         break;

      case 'R' :
      case 'r' :
      //  Writting a Raw File, 
         std::cout << "WriteRaw" << std::endl;
         fh->WriteRawData(outputFileName);
         break;
 
 // Just for fun :
 // Write a 'Video inverse' version of the file.
 // *Not* described, on purpose,  in the USAGE  
      case 'V' :
      case 'v' :
         if ( fh->GetFile()->GetBitsAllocated() == 8)
         {
            std::cout << "videoinv for 8 bits" << std::endl;
            for (int i=0; i<dataSize; i++) 
            {
               ((uint8_t*)imageData)[i] = 255 - ((uint8_t*)imageData)[i];
            }
         }
         else
         {
            std::cout << "videoinv for 16 bits" << std::endl;    
            for (int i=0; i<dataSize/2; i++) 
            {
               ((uint16_t*)imageData)[i] =  65535 - ((uint16_t*)imageData)[i];
            }
         }
         std::cout << "WriteDCM Explicit VR + VideoInv" << std::endl;
         fh->WriteDcmExplVR(outputFileName);
         break;
   }

   f->Delete();
   fh->Delete();
   return 0;
}