/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  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.
 *
 *=========================================================================*/
/*=========================================================================
 *
 *  Portions of this file are subject to the VTK Toolkit Version 3 copyright.
 *
 *  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
 *
 *  For complete copyright, license and disclaimer of warranty information
 *  please refer to the NOTICE file at the top of the ITK source tree.
 *
 *=========================================================================*/
#include "itkLSMImageIO.h"
#include "itkByteSwapper.h"

#include "itk_kwiml.h"
#include "itk_tiff.h"

/* Structure with LSM-specific data ( only in the first image directory). */
#define TIF_CZ_LSMINFO 34412 /* 0x866c, Type: TIF_BYTE, Length: 512 */
#define TIF_CZ_LSMINFO_SIZE_RESERVED 90 + 6
#define TIF_CZ_LSMINFO_SIZE 512

namespace itk
{
extern "C"
{
static void TagExtender(TIFF *tiff)
{
  static ITK_CONSTEXPR TIFFFieldInfo xtiffFieldInfo[] = {
          { TIF_CZ_LSMINFO, TIFF_VARIABLE, TIFF_VARIABLE, TIFF_BYTE,
          FIELD_CUSTOM, 0, 1, const_cast< char * >( "LSM Private Tag" ) }
    };

  TIFFMergeFieldInfo( tiff, xtiffFieldInfo,
                      sizeof( xtiffFieldInfo ) / sizeof( xtiffFieldInfo[0] ) );
}
}

typedef KWIML_INT_int32_t  Int32_t;
typedef KWIML_INT_uint32_t UInt32_t;

typedef float       Float32_t;
typedef double      Float64_t;
typedef long double Float96_t;

typedef struct {
  UInt32_t U32MagicNumber;
  Int32_t S32StructureSize;
  Int32_t S32DimensionX;
  Int32_t S32DimensionY;
  Int32_t S32DimensionZ;
  Int32_t S32DimensionChannels;
  Int32_t S32DimensionTime;
  Int32_t S32DataType;
  Int32_t S32ThumbnailX;
  Int32_t S32ThumbnailY;
  Float64_t F64VoxelSizeX;
  Float64_t F64VoxelSizeY;
  Float64_t F64VoxelSizeZ;
  UInt32_t u32ScanType;
  UInt32_t u32DataType;
  UInt32_t u32OffsetVectorOverlay;
  UInt32_t u32OffsetInputLut;
  UInt32_t u32OffsetOutputLut;
  UInt32_t u32OffsetChannelColors;
  Float64_t F64TimeIntervall;
  UInt32_t u32OffsetChannelDataTypes;
  UInt32_t u32OffsetScanInformation;
  UInt32_t u32OffsetKsData;
  UInt32_t u32OffsetTimeStamps;
  UInt32_t u32OffsetEventList;
  UInt32_t u32OffsetRoi;
  UInt32_t u32OffsetBleachRoi;
  UInt32_t u32OffsetNextRecording;
  UInt32_t u32Reserved[TIF_CZ_LSMINFO_SIZE_RESERVED];
} zeiss_info;

LSMImageIO::LSMImageIO()
{
  m_ByteOrder = LittleEndian;
  m_FileType = Binary;

  this->AddSupportedWriteExtension(".lsm");
  this->AddSupportedWriteExtension(".LSM");

  this->AddSupportedReadExtension(".lsm");
  this->AddSupportedReadExtension(".LSM");
}

LSMImageIO::~LSMImageIO()
{}

// This method will only test if the header looks like a
// LSM image file.
bool LSMImageIO::CanReadFile(const char *filename)
{
  std::string   fname(filename);

  if ( fname == "" )
    {
    itkDebugMacro(<< "No filename specified.");
    return false;
    }

  bool                   extensionFound = false;
  std::string::size_type sprPos = fname.rfind(".lsm");
  if ( ( sprPos != std::string::npos )
       && ( sprPos == fname.length() - 4 ) )
    {
    extensionFound = true;
    }
  sprPos = fname.rfind(".LSM");
  if ( ( sprPos != std::string::npos )
       && ( sprPos == fname.length() - 4 ) )
    {
    extensionFound = true;
    }

  if ( !extensionFound )
    {
    itkDebugMacro(<< "The filename extension is not recognized");
    return false;
    }

  // Check that TIFFImageIO can read this file:
  TIFFErrorHandler save = TIFFSetWarningHandler(ITK_NULLPTR); // get rid of warning about
                                                    // Zeiss tag
  if ( !this->TIFFImageIO::CanReadFile(filename) )
    {
    return false;
    }
  TIFFSetWarningHandler(save);

  // Check this is indeed a LSM file
  if ( !this->CanFindTIFFTag(TIF_CZ_LSMINFO) )
    {
    return false;
    }

  // everything was ok
  return true;
}

void LSMImageIO::Read(void *buffer)
{
  this->TIFFImageIO::Read(buffer);
}

void LSMImageIO::ReadImageInformation()
{
  // this really should be a compile time assert
  itkAssertInDebugAndIgnoreInReleaseMacro( sizeof( zeiss_info ) == TIF_CZ_LSMINFO_SIZE );

  this->TIFFImageIO::ReadImageInformation();

  // Now is a good time to check what was read and replaced it with LSM
  // information
  unsigned int tif_cz_lsminfo_size;
  void *praw = this->TIFFImageIO::ReadRawByteFromTag(TIF_CZ_LSMINFO, tif_cz_lsminfo_size);
  zeiss_info *zi = reinterpret_cast< zeiss_info * >( praw );
  if ( praw == ITK_NULLPTR
       || tif_cz_lsminfo_size != TIF_CZ_LSMINFO_SIZE )
    {
    // no zeiss info, just use tiff spacing
    return;
    }
  // FIXME byte swap, when should it happen? writting?
  ByteSwapper<double>::SwapFromSystemToLittleEndian( &zi->F64VoxelSizeX );
  ByteSwapper<double>::SwapFromSystemToLittleEndian( &zi->F64VoxelSizeY );
  ByteSwapper<double>::SwapFromSystemToLittleEndian( &zi->F64VoxelSizeZ );
  m_Spacing[0] = zi->F64VoxelSizeX;
  m_Spacing[1] = zi->F64VoxelSizeY;
  // TIFF only support 2 or 3 dimension:
  if ( m_NumberOfDimensions == 3 )
    {
    m_Spacing[2] = zi->F64VoxelSizeZ;
    }
}

bool LSMImageIO::CanWriteFile(const char *name)
{
  std::string filename = name;

  if ( filename == "" )
    {
    return false;
    }

  std::string::size_type pos = filename.rfind(".lsm");
  if ( ( pos != std::string::npos )
       && ( pos == filename.length() - 4 ) )
    {
    return true;
    }

  pos = filename.rfind(".LSM");
  if ( ( pos != std::string::npos )
       && ( pos == filename.length() - 4 ) )
    {
    return true;
    }

  return false;
}

void LSMImageIO::FillZeissStruct(char *cz)
{
  memset(cz, 0, TIF_CZ_LSMINFO_SIZE); // fill with 0
  zeiss_info *z = reinterpret_cast< zeiss_info * >( cz );
  z->U32MagicNumber = 0x0400494c;
  z->S32StructureSize = TIF_CZ_LSMINFO_SIZE;
  z->S32DimensionX = m_Dimensions[0];
  z->S32DimensionY = m_Dimensions[1];
  if ( m_NumberOfDimensions == 3 )
    {
    z->S32DimensionZ = m_Dimensions[2];
    }
  z->S32DimensionChannels = m_NumberOfComponents;
  z->S32DimensionTime = 1;
  z->S32DataType = 0;
  z->S32ThumbnailX = 128 * m_Dimensions[0] / m_Dimensions[1];
  z->S32ThumbnailY = 128;
  z->F64VoxelSizeX = m_Spacing[0];
  z->F64VoxelSizeY = m_Spacing[1];
  if ( m_NumberOfDimensions == 3 )
    {
    z->F64VoxelSizeZ = m_Spacing[2];
    }
}

void LSMImageIO::Write(const void *buffer)
{
  const unsigned char *outPtr = (const unsigned char *)buffer;

  unsigned int width, height, page, pages = 1;

  width =  m_Dimensions[0];
  height = m_Dimensions[1];
  if ( m_NumberOfDimensions == 3 )
    {
    pages = m_Dimensions[2];
    }

  uint16_t    scomponents = this->GetNumberOfComponents();
  float resolution = -1;
  uint16_t    bps;

  switch ( this->GetComponentType() )
    {
    case UCHAR:
      bps = 8;
      break;

    case USHORT:
      bps = 16;
      break;

    default:
      itkExceptionMacro(<< "TIFF supports unsigned char and unsigned short");
    }

  uint16_t predictor;

  TIFF *tif = TIFFOpen(m_FileName.c_str(), "w");
  if ( !tif )
    {
    itkDebugMacro(<< "Returning");
    return;
    }

  uint32 w = width;
  uint32 h = height;

  TIFFSetTagExtender(TagExtender);
  if ( m_NumberOfDimensions == 3 )
    {
    TIFFCreateDirectory(tif);
    }
  for ( page = 0; page < pages; page++ )
    {
    TIFFSetDirectory(tif, page);
    TIFFSetField(tif, TIFFTAG_IMAGEWIDTH, w);
    TIFFSetField(tif, TIFFTAG_IMAGELENGTH, h);
    TIFFSetField(tif, TIFFTAG_SAMPLESPERPIXEL, scomponents);
    TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, bps); // Fix for stype
    TIFFSetField(tif, TIFFTAG_PLANARCONFIG, PLANARCONFIG_CONTIG);
    char zeiss[TIF_CZ_LSMINFO_SIZE];
    FillZeissStruct(zeiss);
    unsigned int iCount = sizeof( zeiss ) / sizeof( zeiss[0] );
    // Zeiss field is only on the first TIFF image
    if ( page == 0 )
      {
      TIFFSetField(tif, TIF_CZ_LSMINFO, iCount, zeiss);
      }

    if ( scomponents > 3 )
      {
      // if number of scalar components is greater than 3, that means we assume
      // there is alpha.
      uint16  extra_samples = scomponents - 3;
      uint16 *sample_info = new uint16[scomponents - 3];
      sample_info[0] = EXTRASAMPLE_ASSOCALPHA;
      int cc;
      for ( cc = 1; cc < scomponents - 3; cc++ )
        {
        sample_info[cc] = EXTRASAMPLE_UNSPECIFIED;
        }
      TIFFSetField(tif, TIFFTAG_EXTRASAMPLES, extra_samples,
                   sample_info);
      delete[] sample_info;
      }

    uint16_t compression;

    if ( m_UseCompression )
      {
      switch ( m_Compression )
        {
        case TIFFImageIO::PackBits:
          compression = COMPRESSION_PACKBITS; break;
        case TIFFImageIO::JPEG:
          compression = COMPRESSION_JPEG; break;
        case TIFFImageIO::Deflate:
          compression = COMPRESSION_DEFLATE; break;
        case TIFFImageIO::LZW:
          compression = COMPRESSION_LZW; break;
        default:
          compression = COMPRESSION_NONE;
        }
      }
    else
      {
      compression = COMPRESSION_NONE;
      }

    TIFFSetField(tif, TIFFTAG_COMPRESSION, compression); // Fix for compression

    uint16 photometric = ( scomponents == 1 ) ? PHOTOMETRIC_MINISBLACK : PHOTOMETRIC_RGB;

    if ( compression == COMPRESSION_JPEG )
      {
      TIFFSetField(tif, TIFFTAG_JPEGQUALITY, 75); // Parameter
      TIFFSetField(tif, TIFFTAG_JPEGCOLORMODE, JPEGCOLORMODE_RGB);
      photometric = PHOTOMETRIC_YCBCR;
      }
    else if ( compression == COMPRESSION_LZW )
      {
      predictor = 2;
      TIFFSetField(tif, TIFFTAG_PREDICTOR, predictor);
      itkDebugMacro(<< "LZW compression is patented outside US so it is disabled");
      }
    else if ( compression == COMPRESSION_DEFLATE )
      {
      predictor = 2;
      TIFFSetField(tif, TIFFTAG_PREDICTOR, predictor);
      }

    TIFFSetField(tif, TIFFTAG_PHOTOMETRIC, photometric); // Fix for scomponents

    if ( resolution > 0 )
      {
      TIFFSetField(tif, TIFFTAG_XRESOLUTION, resolution);
      TIFFSetField(tif, TIFFTAG_YRESOLUTION, resolution);
      TIFFSetField(tif, TIFFTAG_RESOLUTIONUNIT, RESUNIT_INCH);
      }

    if ( m_NumberOfDimensions == 3 )
      {
      // We are writing single page of the multipage file
      TIFFSetField(tif, TIFFTAG_SUBFILETYPE, FILETYPE_PAGE);
      }
    int rowLength; // in bytes

    switch ( this->GetComponentType() )
      {
      case UCHAR:
        rowLength = sizeof( unsigned char );
        break;
      case USHORT:
        rowLength = sizeof( unsigned short );
        break;
      default:
        itkExceptionMacro(<< "TIFF supports unsigned char and unsigned short");
      }

    rowLength *= this->GetNumberOfComponents();
    rowLength *= width;

    int row = 0;
    for ( unsigned int idx2 = 0; idx2 < height; idx2++ )
      {
      if ( TIFFWriteScanline(tif, const_cast< unsigned char * >( outPtr ), row, 0) < 0 )
        {
        itkExceptionMacro(<< "TIFFImageIO: error out of disk space");
        }
      outPtr += rowLength;
      row++;
      }

    if ( m_NumberOfDimensions == 3 )
      {
      TIFFWriteDirectory(tif);
      }
    }
  TIFFClose(tif);
}

void LSMImageIO::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);
}
} // end namespace itk
