dim_nanoscope_format_io.cpp

Digital Notebook Source Code v1.1.0 [

/*****************************************************************************
  NANOSCOPE 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:
    01/10/2005 12:17 - First creation
    02/08/2005 22:30 - Support for incomplete image sections
        
  Ver : 2
*****************************************************************************/

#include <string>

#include "dim_nanoscope_format.h"

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

#include <math.h>
#if defined(WIN32)
#include <limits.h>
#endif

#ifndef USHRT_MAX
  #define USHRT_MAX 0xffff
#endif



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

static int read_nanoscope_image(TDimFormatHandle *fmtHndl)
{
  if (fmtHndl == NULL) return 1;
  if (fmtHndl->internalParams == NULL) return 1;
  TDimNanoscopeParams *nanoPar = (TDimNanoscopeParams *) fmtHndl->internalParams;
  TDimImageInfo *info = &nanoPar->i; 
  if (fmtHndl->stream == NULL) return 1;
  
  TDimNanoscopeImg nimg = nanoPar->imgs.at(0);
  if (fmtHndl->pageNumber < nanoPar->imgs.size())
    nimg = nanoPar->imgs.at( fmtHndl->pageNumber );

  TDimImageBitmap *img = fmtHndl->image;
  info->width  = nimg.width;
  info->height = nimg.height;
  info->imageMode = DIM_GRAYSCALE;
  info->samples = 1;
  info->depth = 16;
  unsigned long img_size_bytes = nimg.width * nimg.height * 2;

  // init the image
  if ( allocImg( fmtHndl, info, img) != 0 ) return 1;

  if ( dimSeek(fmtHndl, nimg.data_offset, SEEK_SET) != 0) return 1;
  if (dimRead( fmtHndl, img->bits[0], img_size_bytes, 1 ) != 1) return 1;
  if ( (img->i.depth == 16) && (dimBigendian) ) 
    dimSwapArrayOfShort((DIM_UINT16*) img->bits[0], img_size_bytes/2);

  
  // now convert from SHORT to USHORT
  if (img->i.depth == 16)
  {
    DIM_INT16 *pS  = (DIM_INT16 *)  img->bits[0];
    DIM_UINT16 *pU = (DIM_UINT16 *) img->bits[0];
    unsigned int x;
    for (x=0; x<img_size_bytes/2; x++)
      pU[x] = (unsigned short) (pS[x] + SHRT_MAX);
  }

  // now convert from bottom-top to top-bottom
  register int y;
  int line_size = getLineSizeInBytes(img);
  unsigned char *pbuf = new unsigned char [ line_size ];
  unsigned char *pt = ((unsigned char*) img->bits[0] ) + (line_size * (nimg.height-1));
  unsigned char *pb = (unsigned char*) img->bits[0];

  for (y=0; y<floor(info->height/2.0); y++) 
  {
    memcpy( pbuf, pb, line_size );
    memcpy( pb, pt, line_size );
    memcpy( pt, pbuf, line_size );
    pb+=line_size;
    pt-=line_size;
  }
  delete [] pbuf;

  return 0;
}


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

DIM_UINT nanoscope_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_nanoscope_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;
  
  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)
  {
     //int disp_level = * (DIM_INT16 *) (note + 0);
     //int is_last    = * (DIM_INT32 *) (note + 2);
     int note_type  = * (DIM_INT16 *) (note + 10);
     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;
  group; tag; type;
}

char* read_text_nanoscope_metadata ( TDimFormatHandle *fmtHndl )
{
  if (fmtHndl == NULL) return NULL;
  if (fmtHndl->internalParams == NULL) return NULL;
  TDimNanoscopeParams *nanoPar = (TDimNanoscopeParams *) fmtHndl->internalParams;
  
  TDimNanoscopeImg nimg = nanoPar->imgs.at(0);
  if (fmtHndl->pageNumber < nanoPar->imgs.size())
    nimg = nanoPar->imgs.at( fmtHndl->pageNumber );


  char *buf = NULL;
  std::string str = "";
  char cstr[1024], *line, *l2, p1[1024], p2[1024];

  

  str += "[Nanoscope page properties]\n";

  sprintf( cstr, "Width: %.2f um\n", nimg.width * nimg.xR );
  str += cstr;

  sprintf( cstr, "Height: %.2f um\n", nimg.height * nimg.yR );
  str += cstr;

  // Microscope mode 
  //  \@MicroscopeList: S [TMMode] "Tapping"
  //  \@MicroscopeList: S [AFMMode] "Contact"
  line = strstr( (char*) nanoPar->metaText.c_str(), "@MicroscopeList: S [" );
  if (line != NULL) {
    sscanf( line, "@MicroscopeList: S [%s ""%s""", p1, p2 );
    sprintf( cstr, "Microscope mode: %s\n", p2 );
    if (cstr != NULL) str += cstr;
  }

  // Depth
  
  
  // Deflection


  // \Date: 06:32:07 PM Thu Dec 09 2004
  line = strstr( (char*) nanoPar->metaText.c_str(), "Date: " );
  if (line != NULL) {
    l2 = strstr( line, "\n" );
    memset( p1, 0, 1024 );
    strncpy( p1, line, l2-line );
    if (l2 != NULL) str += p1;
    str += "\n";
  }


  str += "\n";

  str += nimg.metaText;
  str += "\n";
  str += nanoPar->metaText;

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

  return NULL;
}