dim_biorad_pic_format_io.cpp

Digital Notebook Source Code v1.1.0 [

/*****************************************************************************
  BIORAD PIC IO
  UCSB/BioITR property
  Copyright (c) 2004 by Dmitry V. Fedorov <www.dimin.net> <[e-mail]>

  IMPLEMENTATION
  
  Programmer: Dima V. Fedorov <mailto:[e-mail]> <http://www.dimin.net/>
    

  History:
    03/29/2004 22:23 - First creation
    05/10/2004 14:55 - Big endian support
    08/04/2004 22:25 - Update to FMT_IFS 1.2, support for io protorypes
        
  Ver : 3
*****************************************************************************/

#include <string>

// Disables Visual Studio 2005 warnings for deprecated code
#ifdef WIN32
   #pragma warning(disable:4996)
#endif

#include "dim_biorad_pic_format.h"

//#include "memio.h"
//extern void* DimMalloc(DIM_ULONG size);
//extern void* DimFree(void *p); 

TDimBioRadPicParams initTDimBioRadPicParams()
{
  TDimBioRadPicParams r;

  r.i = initTDimImageInfo();
  r.i.depth  = 8;

  r.page_size_bytes = 0;
  r.data_offset     = 76;
  r.notes_offset    = 0;
  r.has_notes       = 0;

  r.metaData.magnification = 0;
  sprintf(r.metaData.datetime, "0000-00-00 00:00:00");

  return r;
}

//----------------------------------------------------------------------------
// READ PROC
//----------------------------------------------------------------------------

static int read_biorad_image(TDimFormatHandle *fmtHndl)
{
  if (fmtHndl == NULL) return 1;
  if (fmtHndl->internalParams == NULL) return 1;
  TDimBioRadPicParams *picPar = (TDimBioRadPicParams *) fmtHndl->internalParams;
  TDimImageInfo *info = &picPar->i;  
  TDimImageBitmap *img = fmtHndl->image;

  // init the image
  if ( allocImg( fmtHndl, info, img) != 0 ) return 1;
  long offset = picPar->data_offset + fmtHndl->pageNumber * picPar->page_size_bytes;

  if (fmtHndl->stream == NULL) return 1;
  if ( dimSeek(fmtHndl, offset, SEEK_SET) != 0) return 1;
  if (dimRead( fmtHndl, img->bits[0], picPar->page_size_bytes, 1 ) != 1) return 1;
  if ( (img->i.depth == 16) && (dimBigendian) ) 
    dimSwapArrayOfShort((DIM_UINT16*) img->bits[0], picPar->page_size_bytes/2);
  
  if (info->imageMode == DIM_RGB)
  { // rgb mode, three pages are considered RGB channels

    offset += picPar->page_size_bytes;
    if (dimSeek( fmtHndl, offset, SEEK_SET) != 0) return 1;
    if (dimRead( fmtHndl, img->bits[1], picPar->page_size_bytes, 1 ) != 1) return 1;

    if ( (img->i.depth == 16) && (dimBigendian) ) 
      dimSwapArrayOfShort((DIM_UINT16*) img->bits[1], picPar->page_size_bytes/2);

    if (picPar->num_images > 2)
    {
      offset += picPar->page_size_bytes;
      if (dimSeek( fmtHndl, offset, SEEK_SET) != 0) return 1;
      if (dimRead( fmtHndl, img->bits[2], picPar->page_size_bytes, 1 ) != 1) return 1;

      if ( (img->i.depth == 16) && (dimBigendian) ) 
        dimSwapArrayOfShort((DIM_UINT16*) img->bits[2], picPar->page_size_bytes/2);
    }
    else
    {
      memset( img->bits[2], 0, picPar->page_size_bytes );
    }
  }

  return 0;
}


//----------------------------------------------------------------------------
// META DATA PROC
//----------------------------------------------------------------------------

DIM_UINT add_one_tag (TDimFormatHandle *fmtHndl, int tag, const char* str)
{
  DIM_UCHAR *buf = NULL;
  DIM_UINT32 buf_size = strlen(str);
  DIM_UINT32 buf_type = DIM_TAG_ASCII;

  if ( (buf_size == 0) || (str == NULL) ) return 1;
  else
  {
    // now add tag into structure
    TDimTagItem item;

    buf = (unsigned char *) dimMalloc(fmtHndl, buf_size + 1);
    strncpy((char *) buf, str, buf_size);
    buf[buf_size] = '\0';

    item.tagGroup  = DIM_META_BIORAD;
    item.tagId     = tag;
    item.tagType   = buf_type;
    item.tagLength = buf_size;
    item.tagData   = buf;

    addMetaTag( &fmtHndl->metaData, item);
  }

  return 0;
}

DIM_UINT read_biorad_metadata (TDimFormatHandle *fmtHndl, int group, int tag, int type)
{
  if (fmtHndl == NULL) return 1;
  if (fmtHndl->internalParams == NULL) return 1;
  TDimBioRadPicParams *picPar = (TDimBioRadPicParams *) fmtHndl->internalParams;
  tag; type;
  
  if ( (group != DIM_META_BIORAD) && (group != -1) ) return 1;

  std::string note01 = "";  
  std::string note20 = "";
  std::string note21 = "";
  unsigned char note[96];

  // print biorad notes into the file
  dimSeek(fmtHndl, picPar->notes_offset, SEEK_SET);

  while ( dimRead( fmtHndl, note, 1, 96 ) == 96) {
     short note_type  = * (DIM_INT16 *) (note + 10);
     if (dimBigendian) dimSwapShort ( (DIM_UINT16*) &note_type );
     char *text     = (char *) (note + 16);
     if (text[0] == '\0') continue; 

     if (note_type == 01) { note01 += text; note01 += "\n"; }
     if (note_type == 20) { note20 += text; note20 += "\n"; }
     if (note_type == 21) { note21 += text; note21 += "\n"; }
  }
 
  if (note01.size() > 0) 
    add_one_tag ( fmtHndl, 01, note01.c_str() );
  if (note20.size() > 0) 
    add_one_tag ( fmtHndl, 20, note20.c_str() );
  if (note21.size() > 0) 
    add_one_tag ( fmtHndl, 21, note21.c_str() );

  return 0;
}

char* read_text_biorad_metadata ( TDimFormatHandle *fmtHndl )
{
  if (fmtHndl == NULL) return NULL;
  if (fmtHndl->internalParams == NULL) return NULL;
  TDimBioRadPicParams *picPar = (TDimBioRadPicParams *) fmtHndl->internalParams; 
  TDimImageInfo *info = &picPar->i;
  
  char *buf = NULL;
  std::string str = ""; 
  std::string note01 = ""; 
  std::string note20 = ""; 
  std::string note21 = ""; 
  unsigned char note[96];

  // print biorad notes into the file
  dimSeek(fmtHndl, picPar->notes_offset, SEEK_SET);
  while (dimRead( fmtHndl, note, 1, 96 ) == 96) {
     short note_type  = * (DIM_INT16 *) (note + 10);
     if (dimBigendian) dimSwapShort ( (DIM_UINT16*) &note_type );
     char *text     = (char *) (note + 16);

     if (note_type == 1) {
       if (text[0] == '\0') continue;
       note01 += text;
       note01 += '\n';
     }

     if (note_type == 20) {
       if (text[0] == '\0') continue;       
       note20 += text;
       note20 += '\n';
     }

     if (note_type == 21) {
       if (text[0] == '\0') continue;       
       note21 += text;
       note21 += '\n';
     }
  }

  str += "[BioRad PIC Metadata]\n\n";
  
  sprintf((char*) note, "Number of frames: %d\n", info->number_pages );
  str += (char*) note;

  if ( picPar->metaData.pixel_size[0] > 0) {  
    sprintf((char*)note, "X Resolution: %.6f microns\n", picPar->metaData.pixel_size[0] );
    str += (char*) note;
  }
  
  if ( picPar->metaData.pixel_size[1] > 0) {  
    sprintf((char*)note, "Y Resolution: %.6f microns\n", picPar->metaData.pixel_size[1] );
    str += (char*) note;
  }

  if ( (picPar->metaData.pixel_size[2] > 0) && (info->number_pages > 1) ) {
    sprintf((char*)note, "Z Resolution: %.6f microns\n", picPar->metaData.pixel_size[2] );
    str += (char*) note;
  }
  str += "\n";


  if (note01.size() > 0) {
    str += "\n[NOTE 1]\n";
    str += note01;
    str += "\n";
  }

  if (note20.size() > 0) {
    str += "\n[NOTE 20]\n";
    str += note20;
    str += "\n";
  }

  if (note21.size() > 0) {
    str += "\n[NOTE 21]\n";
    str += note21;
    str += "\n";
  }

  buf = new char [str.size()+1];
  buf[str.size()] = '\0';
  memcpy( buf, str.c_str(), str.size() );
  
  return buf;
}