img_sif.c File Reference

Copying data from IMG to SIF and vice versa. More...

#include "libtpcimgio.h"

Go to the source code of this file.

Functions
int	sif2img (SIF *sif, IMG *img, int copy_header, int copy_frames, int copy_counts, int verbose)
int	img2sif (IMG *img, SIF *sif, int copy_header, int copy_frames, int copy_counts, int verbose)

Detailed Description

Copying data from IMG to SIF and vice versa.

Author

Vesa Oikonen

Definition in file img_sif.c.

Function Documentation

img2sif()

int img2sif	(	IMG *	img,
		SIF *	sif,
		int	copy_header,
		int	copy_frames,
		int	copy_counts,
		int	verbose )

Set SIF contents based on data in IMG.

Returns

Returns 0 if successful.

Parameters

img	Pointer to IMG struct from which content is copied to SIF.
sif	Pointer to SIF. Must be initiated with sifInit(), but SIF is allocated here if necessary.
copy_header	Select whether header contents are copied (1) or not copied (0) to SIF.
copy_frames	Select whether frame times are copied (1) or not copied (0) to SIF.
copy_counts	Select whether counts are copied (1) or not copied (0) to SIF, or created if they do not exist (2).
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout.

Definition at line 71 of file img_sif.c.

  {
  if(verbose>0)
    printf("img2sif(img, sif, %d, %d, %d, ...)\n", copy_header, copy_frames, copy_counts);
 
  /* Check the arguments */
  if(img==NULL || sif==NULL) return(1);
  if(img->dimt<1) return(1);
 
  /* Verify that IMG contains frame times */
  if(!imgExistentTimes(img)) {
    if(verbose>0) printf("  image does not contain frame times.\n");
    /* If not, then frame times cannot be copied */
    copy_frames=0;
    /* and counts can not be created */
    if(copy_counts==2) copy_counts=1;
  }
 
  /* Check if count data needs to be created */
  if(copy_counts==2 && imgExistentCounts(img)!=0)
    copy_counts=1;
 
  /* Verify that IMG contains isotope information */
  if(img->isotopeHalflife<=0.0) {
    if(verbose>0) printf("  image does not contain isotope halflife.\n");
    /* not, then count data can not be created */
    if(copy_counts==2) copy_counts=1;
  }
 
  /* Allocate memory for SIF if necessary */
  if((copy_frames || copy_counts) && sif->frameNr!=img->dimt) {
    if(sifSetmem(sif, img->dimt)!=0) return(3);
  }
 
  /* copy SIF header */
  if(copy_header) {
    if(verbose>1) printf("  copying header fields.\n");
    sif->scantime=img->scanStart;
    sif->colNr=4;
    sif->version=1;
    strcpy(sif->isotope_name, imgIsotope(img));
    if(strlen(img->studyNr)>0 && strcmp(img->studyNr, ".")!=0)
      strlcpy(sif->studynr, img->studyNr, MAX_STUDYNR_LEN+1);
    else
      strcpy(sif->studynr, "");
  }
 
  /* copy frame times */
  if(copy_frames) {
    if(verbose>1) printf("  copying frame times.\n");
    for(int fi=0; fi<img->dimt; fi++) {
      sif->x1[fi]=img->start[fi]; sif->x2[fi]=img->end[fi];
    }
  }
 
  /* copy or create counts, if required */
  if(copy_counts==2) {
    if(verbose>1) printf("  creating count data.\n");
    /* Calculate average of pixel values */
    long long pxlNr=0;
    for(int fi=0; fi<img->dimt; fi++) {
      double v=0.0;
      for(int k=0; k<img->dimz; k++)
        for(int j=0; j<img->dimy; j++)
          for(int i=0; i<img->dimx; i++) if(isfinite(img->m[k][j][i][fi])) {
            v+=img->m[k][j][i][fi];
            pxlNr++;
          }
      if(pxlNr>0) v/=(double)pxlNr;
      sif->trues[fi]=v;
    }
    /* Multiply by frame durations, unless we have raw data */
    if(img->type!=IMG_TYPE_RAW)
      for(int fi=0; fi<img->dimt; fi++)
        sif->trues[fi]*=(img->end[fi]-img->start[fi]);
    /* Remove decay correction, unless we have raw data */
    if(img->type!=IMG_TYPE_RAW 
         && (img->decayCorrection==IMG_DC_UNKNOWN || img->decayCorrection==IMG_DC_CORRECTED)) {
      double lambda, cf, dur;
      lambda=-hl2lambda(img->isotopeHalflife);
      for(int fi=0; fi<img->dimt; fi++) {
        dur=img->end[fi]-img->start[fi];
        cf=hlLambda2factor(lambda, img->start[fi], dur);
        if(cf>0.0) sif->trues[fi]*=cf;
      }
    }
    /* Scale values to a realistic level */
    double v=sif->trues[0];
    for(int fi=1; fi<sif->frameNr; fi++) if(sif->trues[fi]>v) v=sif->trues[fi];
    v=2.0E+07/v;
    for(int fi=0; fi<sif->frameNr; fi++) sif->trues[fi]*=v;
    /* Prompts are set to Trues and Randoms are set to zero */
    for(int fi=0; fi<sif->frameNr; fi++) {
      sif->prompts[fi]=sif->trues[fi];
      sif->randoms[fi]=0.0;
      if(sif->trues[fi]<1.0) sif->trues[fi]=1.0;
      sif->weights[fi]=img->weight[fi];
    }
  } else if(copy_counts!=0) {
    if(verbose>1) printf("  copying count data.\n");
    for(int fi=0; fi<img->dimt; fi++) {
      sif->prompts[fi]=img->prompts[fi];
      sif->randoms[fi]=img->randoms[fi];
      sif->trues[fi]=sif->prompts[fi]-sif->randoms[fi];
      if(sif->trues[fi]<1.0) sif->trues[fi]=1.0;
      sif->weights[fi]=img->weight[fi];
    }
  }
 
  return(0);
}

Referenced by imgWriteAnalyze(), and imgWriteNifti().

sif2img()

int sif2img	(	SIF *	sif,
		IMG *	img,
		int	copy_header,
		int	copy_frames,
		int	copy_counts,
		int	verbose )

Set IMG contents based on data in SIF.

Returns

Returns 0 if successful.

Parameters

sif	Pointer to SIF struct from which content is copied to IMG.
img	Pointer to IMG. Must be initiated with imgInit(), and allocated if frame time or count information is to be copied.
copy_header	Select whether SIF header contents are copied (1) or not (0)
copy_frames	Select whether SIF frame times are copied (1) or not (0).
copy_counts	Select whether SIF count contents are copied (1) or not (0).
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout.

Definition at line 13 of file img_sif.c.

  {
  if(verbose>0)
    printf("sif2img(sif, img, %d, %d, %d, ...)\n", copy_header, copy_frames, copy_counts);
  if(img==NULL || sif==NULL) return 1;
 
  if(copy_header) {
    if(verbose>1) printf("  copying header.\n");
    img->scanStart=sif->scantime;
    img->isotopeHalflife=60.0*hlFromIsotope(sif->isotope_name);
    if(strlen(sif->studynr)>0 && strcmp(sif->studynr, ".")!=0)
      strlcpy(img->studyNr, sif->studynr, MAX_STUDYNR_LEN+1);
    else
      strcpy(img->studyNr, "");
  }
 
  if(copy_frames) {
    if(verbose>1) printf("  copying frame times.\n");
    if(sif->frameNr!=img->dimt) return(3);
    for(int fi=0; fi<img->dimt; fi++) {
      img->start[fi]=sif->x1[fi];
      img->end[fi]=sif->x2[fi];
      img->mid[fi]=0.5*(img->start[fi]+img->end[fi]);
    }
  }
 
  if(copy_counts) {
    if(verbose>1) printf("  copying count data.\n");
    if(sif->frameNr!=img->dimt) return(3);
    if(sif->colNr<4) return(4);
    for(int fi=0; fi<img->dimt; fi++) {
      img->prompts[fi]=sif->prompts[fi];
      img->randoms[fi]=sif->randoms[fi];
      img->weight[fi]=sif->weights[fi];
    }
  }
 
  return 0;
}

Referenced by imgReadAnalyze().