gdcm_conv 0.2.0

/*
zipstream Library License:
--------------------------

The zlib/libpng License Copyright (c) 2003 Jonathan de Halleux.

This software is provided 'as-is', without any express or implied warranty. In
no event will the authors be held liable for any damages arising from the use
of this software.

Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it freely,
subject to the following restrictions:

1. The origin of this software must not be misrepresented; you must not claim
   that you wrote the original software. If you use this software in a
   product, an acknowledgment in the product documentation would be
   appreciated but is not required.

2. Altered source versions must be plainly marked as such, and must not be
   misrepresented as being the original software.

3. This notice may not be removed or altered from any source distribution

Author: Jonathan de Halleux, dehalleux@pelikhan.com, 2003

Altered by: Andreas Zieringer 2003 for OpenSG project
            made it platform independent, gzip conform, fixed gzip footer

Altered by: Geoffrey Hutchison 2005 for Open Babel project
            minor namespace modifications, VC++ compatibility

Altered by: Mathieu Malaterre 2008, for GDCM project
            when reading deflate bit stream in DICOM special handling of \0 is needed
            also when writing deflate back to disk, the add_footer must be called
*/

//*****************************************************************************
//  template class basic_zip_streambuf
//*****************************************************************************

//-----------------------------------------------------------------------------
// PUBLIC
//-----------------------------------------------------------------------------

/** Construct a zip stream
 * More info on the following parameters can be found in the zlib documentation.
 */

template <class charT, class traits>
basic_zip_streambuf<charT, traits>::basic_zip_streambuf(ostream_reference ostream,
                                                        int level,
                                                        EStrategy strategy,
                                                        int window_size,
                                                        int memory_level,
                                                        size_t buffer_size)
    : _ostream(ostream),
      _output_buffer(buffer_size, 0),
      _buffer(buffer_size, 0),
      _crc(0)
{
    _zip_stream.zalloc = (alloc_func) nullptr;
    _zip_stream.zfree = (free_func) nullptr;

    _zip_stream.next_in = nullptr;
    _zip_stream.avail_in = 0;
    _zip_stream.avail_out = 0;
    _zip_stream.next_out = nullptr;

    if(level > 9)
        level = 9;

    if(memory_level > 9)
        memory_level = 9;

    _err=deflateInit2(&_zip_stream, level, Z_DEFLATED,
                      window_size, memory_level,
                      static_cast<int>(strategy));
    this->setp( &(_buffer[0]), &(_buffer[_buffer.size()-1]));
}

/** Destructor
 */
template <class charT, class traits>
basic_zip_streambuf<charT, traits>::~basic_zip_streambuf()
{
    flush();
 //   _ostream.flush(); CM already done in flush()
    _err=deflateEnd(&_zip_stream);
}

/** Do the synchronization
 * @todo
 * document correctly!
 */
template <class charT, class traits>
int basic_zip_streambuf<charT, traits>::sync()
{
    if(this->pptr() && this->pptr() > this->pbase())
    {
        /*int c =*/ overflow(EOF);

        // ACHTUNG wenn das drin ist hoert er nach dem ersten endl auf!
        /*
          if ( c == EOF)
          return -1;
        */
    }

    return 0;
}

/** <unknown purpose>
 * @todo
 * document correctly!
 */
template <class charT, class traits>
typename basic_zip_streambuf<charT, traits>::int_type
basic_zip_streambuf<charT, traits>::overflow(int_type c)
{
    int w = static_cast<int>(this->pptr() - this->pbase());
    if (c != EOF)
    {
        *this->pptr() = (char)c;
        ++w;
    }
    if (zip_to_stream(this->pbase(), w))
    {
        this->setp(this->pbase(), this->epptr() - 1);
        return c;
    }
    else
    {
        return EOF;
    }
}

/** flushes the zip buffer and output buffer.
 *
 *    This method should be called at the end of the compression. Calling flush
 *    multiple times, will lower the compression ratio.
 */
template <class charT, class traits>
std::streamsize basic_zip_streambuf<charT, traits>::flush()
{
    std::streamsize total_written_byte_size = 0;

    // updating crc
    _crc = crc32(_crc,  _zip_stream.next_in,
                 _zip_stream.avail_in);

    do
    {
        _err = deflate(&_zip_stream, Z_FINISH);
        if(_err == Z_OK || _err == Z_STREAM_END)
        {
            std::streamsize written_byte_size = static_cast<std::streamsize>(_output_buffer.size()) - _zip_stream.avail_out;
            total_written_byte_size += written_byte_size;
            // output buffer is full, dumping to ostream
            _ostream.write( (const char_type*) &(_output_buffer[0]),
                            static_cast<std::streamsize>(written_byte_size/sizeof(char_type)*sizeof(char)));

            // checking if some bytes were not written.
            size_t remainder = written_byte_size%sizeof(char_type);
            if(remainder != 0)
            {
                // copy to the beginning of the stream
				std::streamsize theDiff = written_byte_size-remainder;
				//assert (theDiff > 0 && theDiff < std::numeric_limits<unsigned int>::max());

                memcpy(&(_output_buffer[0]),
                       &(_output_buffer[(unsigned int)theDiff]), remainder);

            }

            _zip_stream.avail_out = static_cast<uInt>(_output_buffer.size() - remainder);
            _zip_stream.next_out = &_output_buffer[remainder];
        }
    }
    while(_err == Z_OK);

    _ostream.flush();

    return total_written_byte_size;
}

/** returns a reference to the output stream
 */
template <class charT, class traits> inline
typename basic_zip_streambuf<charT, traits>::ostream_reference
basic_zip_streambuf<charT, traits>::get_ostream() const
{
    return _ostream;
}

/** returns the latest zlib error status
 */
template <class charT, class traits> inline
int basic_zip_streambuf<charT, traits>::get_zerr() const
{
    return _err;
}

/** returns the crc of the input data compressed so far.
 */
template <class charT, class traits> inline
unsigned long
basic_zip_streambuf<charT, traits>:: get_crc() const
{
    return _crc;
}

/**  returns the size (bytes) of the input data compressed so far.
 */
template <class charT, class traits> inline
unsigned long
basic_zip_streambuf<charT, traits>::get_in_size() const
{
    return _zip_stream.total_in;
}

/**  returns the size (bytes) of the compressed data so far.
 */
template <class charT, class traits> inline
long
basic_zip_streambuf<charT, traits>::get_out_size() const
{
    return _zip_stream.total_out;
}

//-----------------------------------------------------------------------------
// PRIVATE
//-----------------------------------------------------------------------------

/** <undocumented>
 * @todo
 * document!
 */
template <class charT, class traits>
bool basic_zip_streambuf<charT, traits>::zip_to_stream(
    char_type *buffer,
    std::streamsize buffer_size)
{
    std::streamsize total_written_byte_size = 0;

    _zip_stream.next_in = (byte_buffer_type) buffer;
    _zip_stream.avail_in = static_cast<uInt>(buffer_size * sizeof(char_type));
    _zip_stream.avail_out = static_cast<uInt>(_output_buffer.size());
    _zip_stream.next_out = &_output_buffer[0];

    // updating crc
    _crc = crc32(_crc, _zip_stream.next_in,
                 _zip_stream.avail_in);

    do
    {
        _err = deflate(&_zip_stream, 0);

        if (_err == Z_OK  || _err == Z_STREAM_END)
        {
            std::streamsize written_byte_size = static_cast<std::streamsize>(_output_buffer.size()) -
                _zip_stream.avail_out;
            total_written_byte_size += written_byte_size;
            // output buffer is full, dumping to ostream

            _ostream.write((const char_type*) &_output_buffer[0],
                           static_cast<std::streamsize>(written_byte_size / sizeof(char_type)));

            // checking if some bytes were not written.
            size_t remainder = written_byte_size % sizeof(char_type);
            if(remainder != 0)
            {
                // copy to the beginning of the stream
				std::streamsize theDiff = written_byte_size-remainder;
				//gdcm_assert(theDiff > 0 && theDiff < std::numeric_limits<unsigned int>::max());
                memcpy(&_output_buffer[0],
                       &_output_buffer[(unsigned int)theDiff],
                       remainder);
            }

            _zip_stream.avail_out = static_cast<uInt>(_output_buffer.size()-remainder);
            _zip_stream.next_out = &_output_buffer[remainder];
        }
    }
    while(_zip_stream.avail_in != 0 && _err == Z_OK);

    (void)total_written_byte_size;
    
    return _err == Z_OK;
}







//*****************************************************************************
//  template class basic_unzip_streambuf
//*****************************************************************************

//-----------------------------------------------------------------------------
// PUBLIC
//-----------------------------------------------------------------------------

/** Constructor
 */
template <class charT, class traits>
basic_unzip_streambuf<charT, traits>::basic_unzip_streambuf(istream_reference istream,
                                                            int window_size,
                                                            size_t read_buffer_size,
                                                            size_t input_buffer_size)
    : _istream(istream),
      _input_buffer(input_buffer_size),
      _buffer(read_buffer_size),
      _crc(0)
{
    // setting zalloc, zfree and opaque
    _zip_stream.zalloc = (alloc_func) nullptr;
    _zip_stream.zfree = (free_func) nullptr;

    _zip_stream.next_in = nullptr;
    _zip_stream.avail_in = 0;
    _zip_stream.avail_out = 0;
    _zip_stream.next_out = nullptr;

    _err = inflateInit2(&_zip_stream, window_size);

    this->setg(&_buffer[0] + 4,     // beginning of putback area
               &_buffer[0] + 4,     // read position
               &_buffer[0] + 4);    // end position
}

/**
 * @todo document!
 */
template <class charT, class traits>
basic_unzip_streambuf<charT, traits>::~basic_unzip_streambuf()
{
    inflateEnd(&_zip_stream);
}


/**
 * @todo document!
 */
template <class charT, class traits>
typename basic_unzip_streambuf<charT, traits>::int_type
basic_unzip_streambuf<charT, traits>::underflow()
{
    if(this->gptr() && ( this->gptr() < this->egptr()))
        return * reinterpret_cast<unsigned char *>(this->gptr());

    int n_putback = static_cast<int>(this->gptr() - this->eback());
    if(n_putback > 4)
        n_putback = 4;

    memcpy(&_buffer[0] + (4 - n_putback),
           this->gptr() - n_putback,
           n_putback * sizeof(char_type));

    std::streamsize num =
        unzip_from_stream(&_buffer[0] + 4,
                          static_cast<std::streamsize>((_buffer.size() - 4) *
                                                       sizeof(char_type)));

    if(num <= 0) // ERROR or EOF
        return EOF;

    // reset buffer pointers
    this->setg(&_buffer[0] + (4 - n_putback),   // beginning of putback area
               &_buffer[0] + 4,                 // read position
               &_buffer[0] + 4 + num);          // end of buffer

    // return next character
    return * reinterpret_cast<unsigned char *>(this->gptr());
}

/** returns the compressed input istream
 */
template <class charT, class traits> inline
typename basic_unzip_streambuf<charT, traits>::istream_reference
basic_unzip_streambuf<charT, traits>::get_istream()
{
    return _istream;
}

/** returns the zlib stream structure
 */
template <class charT, class traits> inline
z_stream &
basic_unzip_streambuf<charT, traits>::get_zip_stream()
{
    return _zip_stream;
}

/** returns the latest zlib error state
 */
template <class charT, class traits> inline
int
basic_unzip_streambuf<charT, traits>::get_zerr() const
{
    return _err;
}

/** returns the crc of the uncompressed data so far
 */
template <class charT, class traits> inline
unsigned long
basic_unzip_streambuf<charT, traits>::get_crc() const
{
    return _crc;
}

/** returns the number of uncompressed bytes
 */
template <class charT, class traits> inline
long
basic_unzip_streambuf<charT, traits>::get_out_size() const
{
    return _zip_stream.total_out;
}

/** returns the number of read compressed bytes
 */
template <class charT, class traits> inline
long
basic_unzip_streambuf<charT, traits>::get_in_size() const
{
    return _zip_stream.total_in;
}


//-----------------------------------------------------------------------------
// PRIVATE
//-----------------------------------------------------------------------------

/**
 */
template <class charT, class traits> inline
void
basic_unzip_streambuf<charT, traits>::put_back_from_zip_stream()
{
    if(_zip_stream.avail_in == 0)
        return;

    _istream.clear(std::ios::goodbit);
    _istream.seekg(-intf(_zip_stream.avail_in),
                   std::ios_base::cur);

    _zip_stream.avail_in = 0;
}

/**
 */
template <class charT, class traits> inline
std::streamsize
basic_unzip_streambuf<charT, traits>::unzip_from_stream(char_type* buffer,
                                                        std::streamsize buffer_size)
{
    _zip_stream.next_out  =
        (byte_buffer_type) buffer;
    _zip_stream.avail_out =
        static_cast<uInt>(buffer_size * sizeof(char_type));
    size_t count = _zip_stream.avail_in;

    do
    {
        if(_zip_stream.avail_in == 0)
            count=fill_input_buffer();

        if(_zip_stream.avail_in)
        {
            _err = inflate(&_zip_stream,  Z_SYNC_FLUSH);
        }
    }
    while(_err==Z_OK && _zip_stream.avail_out != 0 && count != 0);

	std::streamsize theSize = buffer_size - ((std::streamsize)_zip_stream.avail_out) / sizeof(char_type);
//	assert (theSize >= 0 && theSize < std::numeric_limits<uInt>::max());

    // updating crc
    _crc = crc32(_crc, (byte_buffer_type) buffer,(uInt)theSize);

    std::streamsize n_read =
        buffer_size - _zip_stream.avail_out / sizeof(char_type);

    // check if it is the end
    if (_err == Z_STREAM_END)
        put_back_from_zip_stream();

    return n_read;
}


/**
 */
template <class charT, class traits> inline
size_t
basic_unzip_streambuf<charT, traits>::fill_input_buffer()
{
    _zip_stream.next_in = &_input_buffer[0];
    _istream.read((char_type*) &_input_buffer[0],
                  static_cast<std::streamsize>(_input_buffer.size() /
                                               sizeof(char_type)));
    std::streamsize nbytesread = _istream.gcount()*sizeof(char_type);
    if( !_istream )
      {
      if( _istream.eof() )
        {
        // Ok so we reached the end of file, since we did not read no header
        // we have to explicitly tell zlib the compress stream ends, therefore
        // we add an extra \0 character...it may not always be needed...
        gdcm_assert( nbytesread < (std::streamsize)(_input_buffer.size() / sizeof(char_type)) );
        _input_buffer[ (unsigned int)nbytesread ] = 0;
        ++nbytesread;
        }
      }

    return _zip_stream.avail_in = (uInt)nbytesread;
}







//*****************************************************************************
//  template class basic_zip_ostream
//*****************************************************************************

//-----------------------------------------------------------------------------
// PUBLIC
//-----------------------------------------------------------------------------

#if defined(_MSC_VER)
# pragma warning (push)
# pragma warning (disable:4355)
#endif

/**
 */
template <class charT, class traits> inline
basic_zip_ostream<charT, traits>::basic_zip_ostream(ostream_reference ostream,
                                                    bool isgzip,
                                                    int level,
                                                    EStrategy strategy,
                                                    int window_size,
                                                    int memory_level,
                                                    size_t buffer_size) :
    basic_zip_streambuf<charT, traits>(ostream, level, strategy, window_size,
                                       memory_level, buffer_size),
    std::basic_ostream<charT, traits>(this),
    _is_gzip(isgzip),
    _added_footer(false)
{
    if(_is_gzip)
        add_header();
}

#if defined(_MSC_VER)
# pragma warning (pop)
#endif

/** Destructor
 */
template <class charT, class traits>
basic_zip_ostream<charT, traits>::~basic_zip_ostream()
{
    //if(_is_gzip)
        add_footer();
}

/** returns true if it is a gzip
 */
template <class charT, class traits> inline
bool basic_zip_ostream<charT, traits>::is_gzip() const
{
    return _is_gzip;
}

/** flush inner buffer and zipper buffer
 */

template <class charT, class traits> inline
basic_zip_ostream<charT, traits>& basic_zip_ostream<charT, traits>::zflush()
{
    static_cast<std::basic_ostream<charT, traits> *>(this)->flush();
    static_cast<basic_zip_streambuf<charT, traits> *>(this)->flush();
    return *this;
}

template <class charT, class traits> inline
void basic_zip_ostream<charT, traits>::finished()
{
    if(_is_gzip)
        add_footer();
    else
        zflush();
}


//-----------------------------------------------------------------------------
// PRIVATE
//-----------------------------------------------------------------------------

/**
 * @todo document!
 */
template <class charT, class traits>
basic_zip_ostream<charT,traits>& basic_zip_ostream<charT, traits>::add_header()
{
    char_type zero = 0;

    this->get_ostream() << static_cast<char_type>(detail::gz_magic[0])
                        << static_cast<char_type>(detail::gz_magic[1])
                        << static_cast<char_type>(Z_DEFLATED)
                        << zero //flags
                        << zero<<zero<<zero<<zero // time
                        << zero //xflags
                        << static_cast<char_type>(OS_CODE);

    return *this;
}

/**
 * @todo document!
 */
template <class charT, class traits>
basic_zip_ostream<charT,traits>& basic_zip_ostream<charT, traits>::add_footer()
{
    if(_added_footer)
        return *this;

    zflush();

    _added_footer = true;

    // Writes crc and length in LSB order to the stream.
    unsigned long crc = this->get_crc();
    for(int n=0;n<4;++n)
    {
        this->get_ostream().put((char)(crc & 0xff));
        crc >>= 8;
    }

    unsigned long length = this->get_in_size();
    for(int m=0;m<4;++m)
    {
        this->get_ostream().put((char)(length & 0xff));
        length >>= 8;
    }

    return *this;
}






//*****************************************************************************
//  template class basic_zip_istream
//*****************************************************************************

//-----------------------------------------------------------------------------
// PUBLIC
//-----------------------------------------------------------------------------

#if defined(_MSC_VER)
# pragma warning (push)
# pragma warning (disable:4355)
#endif

/** Constructor
 */
template <class charT, class traits>
basic_zip_istream<charT, traits>::basic_zip_istream(istream_reference istream,
                                                    int window_size,
                                                    size_t read_buffer_size,
                                                    size_t input_buffer_size)
    : basic_unzip_streambuf<charT, traits>(istream, window_size,
                                           read_buffer_size, input_buffer_size),
      std::basic_istream<charT, traits>(this),
      _is_gzip(false),
      _gzip_crc(0),
      _gzip_data_size(0)
{
  if(this->get_zerr() == Z_OK)
    {
    int check = check_header();(void)check;
    //std::cerr << "check_header:" << check << std::endl;
    }
}

#if defined(_MSC_VER)
# pragma warning (pop)
#endif

/** returns true if it is a gzip file
 */
template <class charT, class traits> inline
bool
basic_zip_istream<charT, traits>::is_gzip() const
{
    return _is_gzip;
}

/** return crc check result
 *
 * This must be called after the reading of compressed data is finished!  This
 * method compares it to the crc of the uncompressed data.
 *
 *    \return true if crc check is successful
 */
template <class charT, class traits> inline
bool
basic_zip_istream<charT, traits>::check_crc()
{
    read_footer();
    return this->get_crc() == _gzip_crc;
}

/** return data size check
 */
template <class charT, class traits> inline
bool
basic_zip_istream<charT, traits>::check_data_size() const
{
    return this->get_out_size() == _gzip_data_size;
}

/** return the crc value in the file
 */
template <class charT, class traits> inline
long
basic_zip_istream<charT, traits>::get_gzip_crc() const
{
    return _gzip_crc;
}

/** return the data size in the file
 */
template <class charT, class traits> inline
long
basic_zip_istream<charT, traits>::get_gzip_data_size() const
{
    return _gzip_data_size;
}

//-----------------------------------------------------------------------------
// PROTECTED
//-----------------------------------------------------------------------------

/**
 * @todo document!
 */
template <class charT, class traits>
int
basic_zip_istream<charT, traits>::check_header()
{
    int method; /* method byte */
    int flagsbyte;  /* flags byte */
    uInt len;
    int c;
    int err=0;
    z_stream &zip_stream = this->get_zip_stream();

    /* Check the gzip magic header */
    for(len = 0; len < 2; len++)
    {
        c = (int)this->get_istream().get();
        if (c != detail::gz_magic[len])
        {
            if (len != 0)
                this->get_istream().unget();
            if (c!= EOF)
            {
                this->get_istream().unget();
            }

            err = zip_stream.avail_in != 0 ? Z_OK : Z_STREAM_END;
            _is_gzip = false;
            return err;
        }
    }

    _is_gzip = true;
    method = (int)this->get_istream().get();
    flagsbyte = (int)this->get_istream().get();
    if (method != Z_DEFLATED || (flagsbyte & detail::gz_reserved) != 0)
    {
        err = Z_DATA_ERROR;
        return err;
    }

    /* Discard time, xflags and OS code: */
    for (len = 0; len < 6; len++)
        this->get_istream().get();

    if ((flagsbyte & detail::gz_extra_field) != 0)
    {
        /* skip the extra field */
        len  =  (uInt)this->get_istream().get();
        len += ((uInt)this->get_istream().get())<<8;
        /* len is garbage if EOF but the loop below will quit anyway */
        while (len-- != 0 && this->get_istream().get() != EOF) ;
    }
    if ((flagsbyte & detail::gz_orig_name) != 0)
    {
        /* skip the original file name */
        while ((c = this->get_istream().get()) != 0 && c != EOF) ;
    }
    if ((flagsbyte & detail::gz_comment) != 0)
    {
        /* skip the .gz file comment */
        while ((c = this->get_istream().get()) != 0 && c != EOF) ;
    }
    if ((flagsbyte & detail::gz_head_crc) != 0)
    {  /* skip the header crc */
        for (len = 0; len < 2; len++)
            this->get_istream().get();
    }
    err = this->get_istream().eof() ? Z_DATA_ERROR : Z_OK;

    return err;
}

/**
 * @todo document!
 */
template <class charT, class traits>
void
basic_zip_istream<charT, traits>::read_footer()
{
    if(_is_gzip)
    {
        _gzip_crc = 0;
        for(int n=0;n<4;++n)
            _gzip_crc += ((((int) this->get_istream().get()) & 0xff) << (8*n));

        _gzip_data_size = 0;
        for(int n=0;n<4;++n)
            _gzip_data_size +=
                ((((int) this->get_istream().get()) & 0xff) << (8*n));
    }
}