/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/



#include "gdcmStreamImageWriter.h"
#include "gdcmTag.h"
#include "gdcmMediaStorage.h"
#include <algorithm>
#include "gdcmImageHelper.h"
#include "gdcmRAWCodec.h"

namespace gdcm
{

StreamImageWriter::StreamImageWriter():mspFile(new File)
{
  //set these values to be the opposite ends of possible,
  //so that if the extent is not defined, read can fail properly.
  mXMin = mYMin = mZMin = std::numeric_limits<uint16_t>::max();
  mXMax = mYMax = mZMax = std::numeric_limits<uint16_t>::min();
  mElementOffsets = 0;
  mElementOffsets1 = 0;
}
StreamImageWriter::~StreamImageWriter()
{
}


/// One of either SetFileName or SetStream must be called prior
/// to any other functions.
void StreamImageWriter::SetFileName(const char* inFileName){
  mWriter.SetFileName(inFileName);
  mElementOffsets = 0;//changing to a new file, should make sure that we're starting again
}
void StreamImageWriter::SetStream(std::ostream& inStream){
  mWriter.SetStream(inStream);
}


/// Defines an image extent for the Read function.
/// DICOM states that an image can have no more than 2^16 pixels per edge (as of 2009)
/// In this case, the pixel extents ignore the direction cosines entirely, and
/// assumes that the origin of the image is at location 0,0 (regardless of the definition
/// in space per the tags).  So, if the first 100 pixels of the first row are to be read in,
/// this function should be called with DefinePixelExtent(0, 100, 0, 1), regardless
/// of pixel size or orientation.
void StreamImageWriter::DefinePixelExtent(uint16_t inXMin, uint16_t inXMax,
                                          uint16_t inYMin, uint16_t inYMax,
                                          uint16_t inZMin, uint16_t inZMax){
  mXMin = inXMin;
  mYMin = inYMin;
  mXMax = inXMax;
  mYMax = inYMax;
  mZMin = inZMin;
  mZMax = inZMax;
}

/// Read the DICOM image. There are two reason for failure:
/// 1. The extent is not set
/// 2. The output buffer is not set
/// This method has been implemented to look similar to the metaimageio in itk
bool StreamImageWriter::Write(void* inReadBuffer, const std::size_t& inBufferLength){

  //need to have some kind of extent defined.
  if (mXMin > mXMax || mYMin > mYMax || mZMin > mZMax)
    return false; //for now


//  OneShotReadBuf osrb(inReadBuffer, inBufferLength);
//  std::ostream ostr(&osrb);

  //put the codec interpretation here

//  return ReadImageSubregionRAW(ostr);
  //just do memcpys instead of doing this stream shenanigans
  return WriteImageSubregionRAW((char*)inReadBuffer, inBufferLength);

}
/// Paying attention to the pixel format and so forth, define the proper buffer length for the user.
/// The return amount is in bytes.
/// If the return is 0, then that means that the pixel extent was not defined prior
/// this return is for RAW inputs which are then encoded by the writer, but are used
/// to ensure that the writer gets the proper buffer size
uint32_t StreamImageWriter::DefineProperBufferLength() {
  if (mXMax < mXMin || mYMax < mYMin || mZMax < mZMin) return 0;
  PixelFormat pixelInfo = ImageHelper::GetPixelFormatValue(mWriter.GetFile());
  //unsigned short samplesPerPixel = pixelInfo.GetSamplesPerPixel();
  int bytesPerPixel = pixelInfo.GetPixelSize();
  return (mYMax - mYMin)*(mXMax - mXMin)*(mZMax - mZMin)*bytesPerPixel;
}

/// when writing a raw file, we know the full extent, and can just write the first
/// 12 bytes out (the tag, the VR, and the size)
/// when we do compressed files, we'll do it in chunks, as described in
/// 2009-3, part 5, Annex A, section 4.
/// Pass the raw codec so that in the rare case of a bigendian explicit raw,
/// the first 12 bytes written out should still be kosher.
/// returns -1 if there's any failure, or the complete offset (12 bytes)
/// if it works.  Those 12 bytes are then added to the position in order to determine
/// where to write.
int StreamImageWriter::WriteRawHeader(RAWCodec* inCodec, std::ostream* inStream)
{
  //if this is the first time writing the file out, then
  //the first few header bytes need to be written out; the tags, the length, etc
  //that information is found at 2009, section 5, annex A, table 4-1 and 4-2
  //for now, just writing out straight raw, which means that the first 12 bytes are
  //07fe, 0010, OB, 00, 32 bit length
  //and must be written in little endian (for now-- could do big endian raw, but not atm)
  //so, we set those 12 bytes up, send them through the codec, and then write them directly to disk
  //because this is raw, we know exactly the size that will be written.  So, let's do that.
  if(mElementOffsets == 0)
    {
    uint16_t firstTag = 0x7fe0;
    uint16_t secondTag = 0x0010;
    //uint16_t thirdTag = 0x4f42;
    uint16_t thirdTag = 0x424f; // OB
    uint16_t fourthTag = 0x0000;
    //uint16_t fourthTag = 0x0000;

    uint32_t fifthTag = 0xffffffff;

    uint16_t sixthTag = 0xfffe;
    uint16_t seventhTag = 0xe000;
    uint32_t eightthTag = 0x00000000;

    const int theBufferSize = 4*sizeof(uint16_t)+sizeof(uint32_t)+2*sizeof(uint16_t)+sizeof(uint32_t);
    char* tmpBuffer1 = new char[theBufferSize];

    memcpy(&(tmpBuffer1[0]), &firstTag, sizeof(uint16_t));
    memcpy(&(tmpBuffer1[sizeof(uint16_t)]), &secondTag, sizeof(uint16_t));
    memcpy(&(tmpBuffer1[2*sizeof(uint16_t)]), &thirdTag, sizeof(uint16_t));
    memcpy(&(tmpBuffer1[3*sizeof(uint16_t)]), &fourthTag, sizeof(uint16_t));

    //Addition by Manoj
    memcpy(&(tmpBuffer1[4*sizeof(uint16_t)]), &fifthTag, sizeof(uint32_t));// Data Element Length 4 bytes

    // Basic OffSet Table with No Item Value
    memcpy(&(tmpBuffer1[4*sizeof(uint16_t)+sizeof(uint32_t)]), &sixthTag, sizeof(uint16_t)); //fffe
    memcpy(&(tmpBuffer1[5*sizeof(uint16_t)+sizeof(uint32_t)]), &seventhTag, sizeof(uint16_t));//e000
    memcpy(&(tmpBuffer1[6*sizeof(uint16_t)+sizeof(uint32_t)]), &eightthTag, sizeof(uint32_t));//00000000H

    gdcm_assert( inStream && *inStream && !inStream->eof() && inStream->good() );
    inStream->write(tmpBuffer1, theBufferSize);
    inStream->flush();
    gdcm_assert( inStream && *inStream );
    }

  uint16_t NinthTag = 0xfffe;
  uint16_t TenthTag = 0xe000;

  std::vector<unsigned int> extent = ImageHelper::GetDimensionsValue(mWriter.GetFile());
  PixelFormat pixelInfo = ImageHelper::GetPixelFormatValue(mWriter.GetFile());
  int bytesPerPixel = pixelInfo.GetPixelSize();
  uint32_t sizeTag = extent[0]*extent[1]*extent[2]*bytesPerPixel;

  const int theBufferSize1 = 2*sizeof(uint16_t)+sizeof(uint32_t);

  char* tmpBuffer3 = new char[theBufferSize1];
  char* tmpBuffer4 = new char[theBufferSize1];
  //  std::streamoff theOffset;

  try {

    //First Fragment (Single Frame) of Pixel Data
    memcpy(&(tmpBuffer3[0]), &NinthTag, sizeof(uint16_t)); //fffe
    memcpy(&(tmpBuffer3[sizeof(uint16_t)]), &TenthTag, sizeof(uint16_t)); //e000

    memcpy(&(tmpBuffer3[2*sizeof(uint16_t)]), &sizeTag, sizeof(uint32_t));//Item Length
    //run that through the codec

    if (!inCodec->DecodeBytes(tmpBuffer3, theBufferSize1,
        tmpBuffer4, theBufferSize1)){
      delete [] tmpBuffer3;
      gdcmErrorMacro( "Problems in Header" );
      delete [] tmpBuffer4;
      return -1;
    }

    //write that chunk to the end of the file, ie, this function
    //requires that it be called with a stream in append mode
    //    inStream->seekp(std::ios::beg);
    //    theOffset = mFileOffset;
    //    inStream->seekp(theOffset);
    gdcm_assert( inStream && *inStream && !inStream->eof() && inStream->good() );
    inStream->write(tmpBuffer4, theBufferSize1);
    inStream->flush();
    gdcm_assert( inStream && *inStream );

  } catch(...){
    delete [] tmpBuffer3;
    delete [] tmpBuffer4;
    return -1;
  }
  delete [] tmpBuffer3;
  delete [] tmpBuffer4;
  return sizeTag;
}

/** Read a particular subregion, using the stored mFileOffset as the beginning of the stream.
    This class reads uncompressed data; other subclasses will reimplement this function for compression.
    Assumes that the given buffer is the size in bytes returned from DefineProperBufferLength.
    */
bool StreamImageWriter::WriteImageSubregionRAW(char* inWriteBuffer, const std::size_t& inBufferLength)
{
  (void)inBufferLength;
  //assumes that the file is organized in row-major format, with each row rastering across
//  gdcm_assert( mFileOffset != -1 );
  int y, z;
//  std::streamoff theOffset;

  //need to get the pixel size information
  //should that come from the header?
  //most likely  that's a tag in the header
  std::vector<unsigned int> extent = ImageHelper::GetDimensionsValue(mWriter.GetFile());
  PixelFormat pixelInfo = ImageHelper::GetPixelFormatValue(mWriter.GetFile());
  //unsigned short samplesPerPixel = pixelInfo.GetSamplesPerPixel();
  int bytesPerPixel = pixelInfo.GetPixelSize();
  int SubRowSize = mXMax - mXMin;
  int SubColSize = mYMax - mYMin;

  //set up the codec prior to resetting the file, just in case that affects the way that
  //files are handled by the ImageHelper

  const FileMetaInformation &header = mWriter.GetFile().GetHeader();
  const TransferSyntax &ts = header.GetDataSetTransferSyntax();
  bool needbyteswap = (ts == TransferSyntax::ImplicitVRBigEndianPrivateGE);

  RAWCodec theCodec;
  if( !theCodec.CanDecode(ts) || ts == TransferSyntax::ExplicitVRBigEndian)
    {
    gdcmErrorMacro( "Only RAW for now" );
    return false;
    }

  theCodec.SetNeedByteSwap( needbyteswap );
  theCodec.SetDimensions(ImageHelper::GetDimensionsValue(mWriter.GetFile()));
  theCodec.SetPlanarConfiguration(
  ImageHelper::GetPlanarConfigurationValue(mWriter.GetFile()));
  theCodec.SetPhotometricInterpretation(
    ImageHelper::GetPhotometricInterpretationValue(mWriter.GetFile()));
  //how do I handle byte swapping here?  where is it set?

  //have to reset the stream to the proper position
  //first, reopen the stream,then the loop should set the right position
  //MM: you have to reopen the stream, by default, the writer closes it each time it writes.
//  mWriter.SetFileName(mWriter.GetFileName().c_str(), true);//open in file append mode
  std::ostream* theStream = mWriter.GetStreamPtr();//probably going to need a copy of this
  //to ensure thread safety; if the stream ptr handler gets used simultaneously by different threads,
  //that would be BAD
  //tmpBuffer is for a single raster
  gdcm_assert( theStream && *theStream );
  char* tmpBuffer = new char[SubRowSize*bytesPerPixel];
  char* tmpBuffer2 = new char[SubRowSize*bytesPerPixel];
  try {
    if (mElementOffsets == 0 || mElementOffsets1 ==0 ){
      mElementOffsets = WriteRawHeader(&theCodec, theStream);
      mElementOffsets1 = mElementOffsets;
    }
    if (mElementOffsets < 0){//something broke during writing
      gdcmErrorMacro( "Broke" );
      delete [] tmpBuffer;
      delete [] tmpBuffer2;
      return false;
    }
    //only need to seek to the location once, and then write sequentially
    //may be trickier with compressed images, but should work for RAW
   // theStream->seekp(std::ios::end);
    //seeking to the end should be sufficient, if we're guaranteed to get chunks in order
//    theOffset = mFileOffset + (mZMin * (int)(extent[1]*extent[0]) + mYMin*(int)extent[0] + mXMin)*bytesPerPixel + mElementOffsets;
  //  theStream->seekp(mElementOffsets);
    for (z = mZMin; z < mZMax; ++z){
      for (y = mYMin; y < mYMax; ++y){
        //this next line may require a bit of finagling...
        //std::copy(tmpBuffer2, &(tmpBuffer2[SubRowSize*bytesPerPixel]), std::ostream_iterator<char>(os));
        //make sure to have a test that will test different x, y, and z mins and maxes
        memcpy(tmpBuffer, &(inWriteBuffer[((z-mZMin)*SubRowSize*SubColSize +
          (y-mYMin)*SubRowSize)// + mXMin)//shouldn't need mXMin
          *bytesPerPixel]), SubRowSize*bytesPerPixel);


        if (!theCodec.DecodeBytes(tmpBuffer, SubRowSize*bytesPerPixel,
          tmpBuffer2, SubRowSize*bytesPerPixel)){
          delete [] tmpBuffer;
          delete [] tmpBuffer2;
          return false;
        }
        //should be appending
           //gdcm_assert( theStream && *theStream && !theStream->eof() && theStream->good() );
          theStream->write(tmpBuffer2, SubRowSize*bytesPerPixel);
          theStream->flush();
          //gdcm_assert( theStream && *theStream );
      }
    }
  }
  catch (std::exception & ex){
    (void)ex;
    gdcmWarningMacro( "Failed to write with ex:" << ex.what() );
    delete [] tmpBuffer;
    delete [] tmpBuffer2;
    return false;
  }
  catch (...){
    gdcmWarningMacro( "Failed to write with unknown error." );
    delete [] tmpBuffer;
    delete [] tmpBuffer2;
    return false;
  }
  delete [] tmpBuffer;
  delete [] tmpBuffer2;
  return true;
}

/// Set the spacing and dimension information for the set filename.
/// returns false if the file is not initialized or not an image,
/// with the pixel 0x7fe0, 0x0010 tag.
bool StreamImageWriter::WriteImageInformation(){

  //ok, the writer has a file in it, and so we place the dataset that we're given into
  //the file
  File &mFile = *mspFile;
  mWriter.SetFile(mFile);
  mElementOffsets = 0;//changing to a new file, should make sure that we're starting again
  //filename needs to be set prior to this function
  try
  {
    //question! is this file a copy of the file that was given in, or a reference?
     mFile.GetDataSet().Remove( Tag(0x7fe0,0x0010) ); // FIXME
     gdcm_assert( !mFile.GetDataSet().FindDataElement( Tag(0x7fe0,0x0010) ) );
    if( !mWriter.Write() )//should write everything BUT the image tag.  right?
      {
      //gdcm_assert( 0 );//this assert fires when the image is not writeable, ie, doesn't have
        //tags 2,3 and 8,18
        //if the writer can't write, then this should return false.
        return false;
      }
    //this is where to start writing zeros for the image.
    //BUT! do we know here if it's compressed for writing out?  If so, shouldn't that require forcing
    //the datasets to be presented sequentially?
    //at this point, we should be at the end of the dataset, and the pointer should be set to eof
    //which is good, because otherwise, we have a problem (write is inherited, and I can't easily
    //do the trick where I return the stream location
    //no longer really using the mFileLocation anyway, because always appending.
 /*   mWriter.SetFileName(mWriter.GetFileName().c_str());//MM: we must call setfilename in order to open
    //the stream.  Otherwise, the position information will be wrong.
    std::ostream* theStreamPtr = mWriter.GetStreamPtr();
    theStreamPtr->seekp(std::ios::end);
    mFileOffset = theStreamPtr->tellp();
    std::ofstream* theFileStreamPtr = dynamic_cast<std::ofstream*>(theStreamPtr);
    if (theFileStreamPtr!= NULL){
      theFileStreamPtr->close();
    }
    */
  }
  catch(std::exception & ex)
  {
    (void)ex;
    gdcmWarningMacro( "Failed to write with ex:" << ex.what() );
  }
  catch(...)
  {
    gdcmWarningMacro( "Failed to write with unknown error" );
  }

  // eg. ELSCINT1_PMSCT_RLE1.dcm
//  if( mFileOffset == -1 ) return false;

  // postcondition
//  gdcm_assert( mFileOffset != -1 );
  return true;
}

//this function determines if a file can even be written using the streaming writer
//unlike the reader, can be called before WriteImageInformation, but must be called
//after SetFile.
bool StreamImageWriter::CanWriteFile() const
{
  File &mFile = *mspFile;
  if (mspFile == NULL)
    {
    return false;
    }

  bool hasTag23 = mFile.GetDataSet().FindDataElement(Tag(0x02,0x03));
  bool hasTag818 = mFile.GetDataSet().FindDataElement(Tag(0x08,0x18));
  if (!hasTag23 && !hasTag818){
    // std::cout << "It is good";
    return false; //need both tags to be able to write out to disk
  }
  
  
  const FileMetaInformation &header = mFile.GetHeader();
  const TransferSyntax &ts = header.GetDataSetTransferSyntax();
  //std::cout<< ts;
  RAWCodec theCodec;
//  bool canDecodeWithRaw = !theCodec.CanDecode(ts);
  bool canDecodeWithRaw = theCodec.CanDecode(ts);
  if (!canDecodeWithRaw)
    {
    //std::cout << "It is not good";
    return false; 
    }

  return true;
}

  /// Set the image information to be written to disk that is everything but
  /// the pixel information.  Copies the data into a new dataset, except for the pixel element
///This way, writing the image information will just write everything else.
void StreamImageWriter::SetFile(const File& inFile)
{
  mspFile = inFile;
  File &mFile = *mspFile;
  mWriter.SetFile(mFile);
  mElementOffsets1 = 0;
}

} // end namespace gdcm
