qviewio.c File Reference

I/O functions for QView TAC file format. More...

#include "tpcclibConfig.h"
#include "tpcift.h"
#include "tpcisotope.h"
#include "tpccsv.h"
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <string.h>
#include "tpctac.h"

Go to the source code of this file.

Functions
int	tacReadQView (TAC *tac, CSV *csv, const int grouponly, TPCSTATUS *status)

Detailed Description

I/O functions for QView TAC file format.

Definition in file qviewio.c.

Function Documentation

tacReadQView()

int tacReadQView	(	TAC *	tac,
		CSV *	csv,
		const int	grouponly,
		TPCSTATUS *	status )

Read QView format from CSV struct into TAC struct.

Note that QView TAC format does not contain frame times.

Returns

enum tpcerror (TPCERROR_OK when successful).

Author

Vesa Oikonen

See also

tacRead, tacWrite, tacInit

Parameters

tac	Pointer to TAC structure, contents of which are to be written.
csv	Pointer to CSV from which data is read.
grouponly	Read TACs of all ROIs (0), or only group means (1).
status	Pointer to status data; enter NULL if not needed.

Definition at line 27 of file qviewio.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(tac==NULL) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_FAIL);
    return TPCERROR_FAIL;
  }
  if(verbose>0) {printf("%s()\n", __func__); fflush(stdout);}
 
  tacFree(tac);
 
  if(csv==NULL || csv->row_nr<2 || csv->col_nr<12) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_DATA);
    return TPCERROR_NO_DATA;
  }
 
  int ret=0;
 
  /* Check from the first line (title) that data indeed is QView data */
  if(strcasecmp(csv->c[0].content, "directory")!=0 || 
     strcasecmp(csv->c[11].content, "group")!=0)
  {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FORMAT);
    return TPCERROR_INVALID_FORMAT;
  }
 
  /* Find the highest frame number from parens in 'num' field */
  int maxFrameNr=0;
  {
    int fn;
    char *cptr, *cptr2;
    for(int ri=1; ri<csv->row_nr; ri++) {
      cptr=csvCell(csv, ri, 2); if(cptr==NULL) continue;
      if(verbose>50) printf("  '%s'\n", cptr);
      cptr2=strchr(cptr, '('); if(cptr2==NULL) continue;
      fn=atoi(cptr2+1); if(fn>maxFrameNr) maxFrameNr=fn;
    }
  }
  if(verbose>1) printf("maxFrameNr := %d\n", maxFrameNr);
  if(maxFrameNr<1) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FORMAT);
    return TPCERROR_INVALID_FORMAT;
  }
  /* Estimate the number of TACs */
  int maxTacNr=(csv->row_nr-1)/maxFrameNr; // row_nr includes the title line
  if(verbose>1) printf("maxTacNr := %d\n", maxTacNr);
  if(maxFrameNr<1) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FORMAT);
    return TPCERROR_INVALID_FORMAT;
  }
 
  /* Allocate memory for TAC data; and to be on the safe side, for one extra TAC */
  ret=tacAllocate(tac, maxFrameNr, maxTacNr);
  statusSet(status, __func__, __FILE__, __LINE__, ret);
  if(ret!=TPCERROR_OK) return(ret);
  tac->isframe=0;
 
  /* Copy data from CSV into TAC structure */
  ret=0;
  for(int i=1; i<csv->row_nr; i++) {
    /* Read the cells of this CSV line */
    char *cnum, *cslice, *cmean, *cpixel, *cgroup;
    cnum=csvCell(csv, i, 2); if(cnum==NULL) continue;
    cslice=csvCell(csv, i, 3); if(cslice==NULL) continue;
    cmean=csvCell(csv, i, 4); if(cmean==NULL) continue;
    cpixel=csvCell(csv, i, 9); if(cpixel==NULL) continue;
    cgroup=csvCell(csv, i, 11); if(cgroup==NULL) continue;
    /* Get slice number; if missing, then this is group ROI */
    int slice;
    ret=atoiCheck(cslice, &slice);
    if(ret!=0) {slice=-1; ret=0;}
    /* If only group ROIs were requested, and this is not group */
    if(slice>0 && grouponly!=0) continue;
    /* Depending on previous, get frame number and group name, or frame and ROI number */
    char *cptr=strchr(cnum, '('); if(cptr==NULL) continue;
    int fn=atoi(cptr+1); if(fn<1 || fn>maxFrameNr) {ret=1; break;}
    char tacname[MAX_TACNAME_LEN+1];
    if(slice<1) { // this is group
      /* Check group name, and use it as TAC name */
      if(strnlen(cgroup, 2)<1) {ret=2; break;}
      strlcpy(tacname, cgroup, MAX_TACNAME_LEN);
    } else { // this is one roi at one image slice
      /* Get ROI number */
      int roinr=atoi(cnum); if(roinr<1) {ret=3; break;}
      /* If group name exists, the use that and ROI number and slice number to construct TAC name */
      if(strnlen(cgroup, 2)>0 && strnlen(cgroup, 2)<12) {
        sprintf(tacname, "%s_roi%d__pl%d", cgroup, roinr, slice);
      } else {
        /* Otherwise use ROI number and slice number to construct TAC name */
        sprintf(tacname, "roi%d__pl%d", roinr, slice);
      }
    }
    /* Get the number of pixels */
    int pxlnr;
    ret=atoiCheck(cpixel, &pxlnr); if(ret) {pxlnr=0; ret=0;}
    /* Get the ROI concentration */
    double conc=atofVerified(cmean);
    if(verbose>20) printf("tacname='%s' pxlnr=%d fn=%d conc=%g\n", tacname, pxlnr, fn, conc);
    /* Determine the TAC index for this; first check if this TAC already is added */
    int ri;
    for(ri=0; ri<tac->tacNr; ri++) {
      if(strcmp(tac->c[ri].name, tacname)==0 && doubleMatch(tac->c[ri].size, (double)pxlnr, 0.1))
        break;
      /* if TAC is not yet added, then ri will be set to the first free index */
    }
    /* check that ri is not too big */
    if(ri>=maxTacNr) {ret=4; break;}
    /* Put value in place */
    tac->c[ri].y[fn-1]=conc;
    /* If this was first encounter of this TAC, then set other info, and increase tacNr */
    if(ri>=tac->tacNr) {
      strcpy(tac->c[ri].name, tacname);
      tac->c[ri].size=(double)pxlnr;
      tac->tacNr++;
    }
    /* Increase also sampleNr when necessary */
    if(fn>tac->sampleNr) tac->sampleNr=fn;
  }
  if(ret) {
    if(verbose>1) printf("  error %d\n", ret);
    tacFree(tac);
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FORMAT);
    return TPCERROR_INVALID_FORMAT;
  }
 
  if(tac->sampleNr<1 || tac->tacNr<1) {
    tacFree(tac);
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FORMAT);
    return TPCERROR_INVALID_FORMAT;
  }
 
  for(int i=0; i<tac->sampleNr; i++) tac->x[i]=tac->x1[i]=tac->x2[i]=0.0;
 
  tac->format=TAC_FORMAT_QVIEW;
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(TPCERROR_OK);
}

Referenced by tacRead().