dftio.c File Reference

Contains I/O functions for DFT files. More...

#include "libtpccurveio.h"
#include <unistd.h>

Go to the source code of this file.

Functions
int	dftRead (char *filename, DFT *data)
int	dftFormat (char *fname)
int	dftType (FILE *fp)
void	dftPrint (DFT *data)
int	dftWrite (DFT *data, char *filename)
int	dftWriteHTML (DFT *dft, char *fname, int orientation)
int	dftWriteXHTML11_doctype (FILE *fp)
int	dftWriteXHTML11_head (FILE *fp, char *author_name)
int	dft_fill_hdr_from_IFT (DFT *dft, IFT *ift)
int	dftGetPmodTitle (DFT *dft, char *title_line)

Variables
int	DFT_NR_OF_DECIMALS = 3

Detailed Description

Contains I/O functions for DFT files.

Author

Vesa Oikonen

Bug

Line length cannot be larger than max int value, but this is not taken into consideration. This may limit the curve number in some systems.

Definition in file dftio.c.

Function Documentation

dft_fill_hdr_from_IFT()

int dft_fill_hdr_from_IFT	(	DFT *	dft,
		IFT *	ift )

Read certain keys from IFT and set DFT fields accordingly.

Returns

Returns the nr of identified keys.

Parameters

dft	Pointer to allocated DFT struct where information will be written
ift	Pointer to IFT struct from where information is retrieved

Definition at line 971 of file dftio.c.

  {
  int ki, ri, ok_nr=0, ret;
  char keystr[256], *cptr;
 
  //printf("dft_fill_hdr_from_IFT()\n");
 
  /* Check for study number */
  strcpy(keystr, "studynr"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "study number"); ki=iftGet(ift, keystr, 0);}
  if(ki==-1) {strcpy(keystr, "study_number"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0) {
    strlcpy(dft->studynr, ift->item[ki].value, MAX_STUDYNR_LEN);
    ok_nr++;
  }
 
  /* Check for time unit */
  strcpy(keystr, "timeunit"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "time unit"); ki=iftGet(ift, keystr, 0);}
  if(ki==-1) {strcpy(keystr, "time_unit"); ki=iftGet(ift, keystr, 0);}
  if(ki==-1) {strcpy(keystr, "Time units"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0) {
    ret=petTunitId(ift->item[ki].value);
    if(ret>=0 && ret!=TUNIT_UNKNOWN) {dft->timeunit=ret; ok_nr++;}
  }
 
  /* Check for sample unit */
  strcpy(keystr, "unit"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "Activity units"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0) {
    strncpy(dft->unit, ift->item[ki].value, 12); dft->unit[12]=(char)0;
    ok_nr++;
  }
 
  /* Check for region names */
  ri=0;
  do {
    strcpy(keystr, "voiname"); ki=iftGetNth(ift, keystr, ri+1, 0);
    if(ki>=0) {
      strncpy(dft->voi[ri].name, ift->item[ki].value, MAX_REGIONNAME_LEN);
      dft->voi[ri].name[MAX_REGIONNAME_LEN]=(char)0;
      rnameSplit(ift->item[ki].value, dft->voi[ri].voiname,
        dft->voi[ri].hemisphere, dft->voi[ri].place, MAX_REGIONSUBNAME_LEN);
    }
    ri++; ok_nr++;
  } while(ki>=0 && ri<dft->_voidataNr);
 
  /* Check for region volumes */
  strcpy(keystr, "sizes"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "volumes"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0 && strlen(ift->item[ki].value)) {
    ri=0; cptr=strtok(ift->item[ki].value, " ;\t");
    while(cptr!=NULL && ri<dft->_voidataNr) {
      if(strcmp(cptr, ".")==0) {ri++; continue;}
      dft->voi[ri++].size=atof_dpi(cptr);
      cptr=strtok(NULL, " ;\t");
    }
    ok_nr++;
  }
 
  /* Check for the name of radiopharmaceutical */
  strcpy(keystr, "radiopharmaceutical"); ki=iftGet(ift, keystr, 0);
  if(ki>=0 && strlen(ift->item[ki].value)) {
    strncpy(dft->radiopharmaceutical, ift->item[ki].value, 31);
    dft->radiopharmaceutical[31]=(char)0;
    ok_nr++;
  }
 
  /* Check for isotope name */
  strcpy(keystr, "isotope"); ki=iftGet(ift, keystr, 0);
  if(ki>=0 && strlen(ift->item[ki].value)) {
    strncpy(dft->isotope, ift->item[ki].value, 6); dft->isotope[6]=(char)0;
    ok_nr++;
  }
 
  /* Check if there is anything about correction for physical decay */
  strcpy(keystr, "decay_correction"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "decay correction"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0 && strlen(ift->item[ki].value)) {
    if(strncasecmp(ift->item[ki].value, "Yes", 1)==0) {
      dft->decayCorrected=DFT_DECAY_CORRECTED; ok_nr++;
    } else if(strncasecmp(ift->item[ki].value, "No", 1)==0) {
      dft->decayCorrected=DFT_DECAY_NOTCORRECTED; ok_nr++;
    }
  }
 
  /* Check for injection time */
  strcpy(keystr, "injection time"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "injection_time"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0 && strlen(ift->item[ki].value)) {
    /* check if time is in correct format; otherwise try to correct it */
    if(ift->item[ki].value[4]=='-' && ift->item[ki].value[7]=='-' &&
       ift->item[ki].value[13]==':' && ift->item[ki].value[16]==':') {
      strncpy(dft->injectionTime, ift->item[ki].value, 19);
      dft->injectionTime[19]=(char)0; ok_nr++;
    } else if(ift->item[ki].value[2]=='.' && ift->item[ki].value[5]=='.' &&
              ift->item[ki].value[13]==':' && ift->item[ki].value[16]==':') {
      sprintf(dft->injectionTime, "%4.4s-%2.2s-%2.2s %8.8s",
        ift->item[ki].value+6, ift->item[ki].value+3, ift->item[ki].value,
        ift->item[ki].value+11);
      ok_nr++;
    }
  }
 
  /* Check for scan start time */
  strcpy(keystr, "scan start time"); ki=iftGet(ift, keystr, 0);
  if(ki==-1) {strcpy(keystr, "scan_start_time"); ki=iftGet(ift, keystr, 0);}
  if(ki==-1) {strcpy(keystr, "scan_start"); ki=iftGet(ift, keystr, 0);}
  if(ki==-1) {strcpy(keystr, "scan start"); ki=iftGet(ift, keystr, 0);}
  if(ki>=0 && strlen(ift->item[ki].value)) {
    /* check if time is in correct format; otherwise try to correct it */
    if(ift->item[ki].value[4]=='-' && ift->item[ki].value[7]=='-' &&
       ift->item[ki].value[13]==':' && ift->item[ki].value[16]==':') {
      strncpy(dft->scanStartTime, ift->item[ki].value, 19);
      dft->scanStartTime[19]=(char)0; ok_nr++;
    } else if(ift->item[ki].value[2]=='.' && ift->item[ki].value[5]=='.' &&
              ift->item[ki].value[13]==':' && ift->item[ki].value[16]==':') {
      sprintf(dft->scanStartTime, "%4.4s-%2.2s-%2.2s %8.8s",
        ift->item[ki].value+6, ift->item[ki].value+3, ift->item[ki].value,
        ift->item[ki].value+11);
      ok_nr++;
    }
  }
 
  return(ok_nr);
}

Referenced by dftRead().

dftFormat()

int dftFormat

(

char *

fname

)

Determine the type of DFT file. This will replace dftType().

Note that only some of formats are currently identified, and identification does not mean that dftRead() supports the format.

Returns

Returns DFT_FORMAT_UNKNOWN or other format id defined in dft.h.

See also

dftRead, dftWrite

Parameters

fname

Pointer to file name; this string is not modified.

Definition at line 422 of file dftio.c.

  {
  if(CSV_TEST>0) {printf("%s('%s')\n", __func__, fname); fflush(stdout);}
 
  FILE *fp;
  char tmp[256];
  int c;
 
 
  /* Open file */
  fp=fopen(fname, "r"); if(fp==NULL) return DFT_FORMAT_UNKNOWN;
 
  /* Binary data? */
  while((c=fgetc(fp))!=EOF) {
    if(isalnum(c) || isspace(c) || isgraph(c)) continue;
    if(c>=160) continue;
    if(CSV_TEST>1) {printf("  invalid character %d\n", c); fflush(stdout);}
    fclose(fp); return DFT_FORMAT_UNKNOWN;
  }
  rewind(fp);
 
  /* File with one title line without comment mark? */
  while(fgets(tmp, 10, fp) != NULL) {if(strlen(tmp)) break;}
  if(strncasecmp(tmp, "Time[", 5)==0) {fclose(fp); return DFT_FORMAT_PMOD;}
  if(strncasecmp(tmp, "Start[", 6)==0) {fclose(fp); return DFT_FORMAT_PMOD;}
  if(strcasestr(tmp, "Start\tEnd\t")!=NULL) {fclose(fp); return DFT_FORMAT_PMOD;}
  rewind(fp);
 
  /* Read the first line that is not empty or comment line */
  while(fgets(tmp, 32, fp) != NULL) {
    if(strlen(tmp)==0) continue;
    if(tmp[0]=='#') continue;
    if(strncmp(tmp, "//", 2)==0) continue;
    break;
  }
  rewind(fp);
 
  /* Check for identification strings */
  if(strncasecmp(tmp, "DFT", 3)==0) {fclose(fp); return DFT_FORMAT_STANDARD;}
  else if(strncasecmp(tmp, "FIT1", 3)==0) {fclose(fp); return DFT_FORMAT_FIT;}
  else if(strncasecmp(tmp, "cpt", 3)==0) {fclose(fp); return DFT_FORMAT_NCI;}
 
  /* Identify certain file name extensions */
  if(fncasematch(fname, "*.idwc")==1 || fncasematch(fname, "*.idw")==1) {
    fclose(fp); return DFT_FORMAT_IDWC;}
  if(fncasematch(fname, "*.if")==1) {fclose(fp); return DFT_FORMAT_IF;}
 
  fclose(fp);
 
  /* Try to read as CSV */
  CSV csv; csvInit(&csv);
  if(csvRead(&csv, fname)==0) {
    int format=DFT_FORMAT_UNKNOWN;
    if(csv.separator==';') format=DFT_FORMAT_CSV_INT;
    else if(csv.separator==',') format=DFT_FORMAT_CSV_UK;
    else if(csv.separator=='\t') {
      int i, commas=0, dots=0;
      for(i=0; i<csv.nr; i++) {
        if(strchr(csv.c[i].content, ',')!=NULL) commas++;
        else if(strchr(csv.c[i].content, '.')!=NULL) dots++;
      }
      if(dots>commas) format=DFT_FORMAT_CSV_UK; else format=DFT_FORMAT_CSV_INT;
    }
    if(CSV_TEST>1) printf("  format=%d\n", format);
    csvEmpty(&csv);
    if(format!=DFT_FORMAT_UNKNOWN) return(format);
  }
 
  return DFT_FORMAT_PLAIN;
}

Referenced by dftRead(), dftReadinput(), and dftReadReference().

dftGetPmodTitle()

int dftGetPmodTitle	(	DFT *	dft,
		char *	title_line )

Read single title line from PMOD files and set DFT fields accordingly. Alternatively, reads the number of regions in PMOD title line.

Returns

Returns 0 if title contents were successfully saved in DFT struct; if pointer to DFT struct is not specified, then the number of regions is returned.

Parameters

dft	Pointer to allocated DFT struct where information will be written; Enter NULL, if only the nr of regions is to be returned.
title_line	Pointer to string containing the title line; string is not modified

Definition at line 1109 of file dftio.c.

  {
  //printf("dftGetPmodTitle()\n");
  //printf(" '%s'\n", title_line);
  //if(dft==NULL) printf(" dft=NULL\n");
 
  int ti=0, ri, ret, tabs=0, timetype=DFT_TIME_MIDDLE;
  char *cptr, *cptr2, rname[MAX_REGIONNAME_LEN+1];
  char unit[MAX_UNITS_LEN+1], separs[8];
 
  /* Check the input */
  if(strlen(title_line)<1) return 1;
 
  /* Count the nr of tabs in title line */
  cptr=title_line; while(*cptr) {if(*cptr=='\t') tabs++; cptr++;}
  /* If tabs found, then do not use space as field separator */
  if(tabs>0) strcpy(separs, "\t\n\r"); else strcpy(separs, " \t\n\r");
 
  /* Make a copy of title line */
  char ntl[1+strlen(title_line)], *tl;
  strcpy(ntl, title_line); tl=ntl;
  cptr=strtok(tl, separs); if(cptr==NULL) return 2;
  ti=ri=0;
  while(cptr!=NULL) {
    if(ti==0) {
      if(strlen(cptr)>6 && strncasecmp(cptr, "Time[", 5)==0) {
        strncpy(unit, cptr+5, MAX_UNITS_LEN); unit[MAX_UNITS_LEN]=(char)0;
        cptr2=strchr(unit, ']'); if(cptr2!=NULL) *cptr2=(char)0;
        if(dft!=NULL) dft->timeunit=petTunitId(unit);
        timetype=DFT_TIME_MIDDLE;
      } else if(strlen(cptr)>6 && strncasecmp(cptr, "start[", 6)==0) {
        strncpy(unit, cptr+6, MAX_UNITS_LEN); unit[MAX_UNITS_LEN]=(char)0;
        cptr2=strchr(unit, ']'); if(cptr2!=NULL) *cptr2=(char)0;
        if(dft!=NULL) dft->timeunit=petTunitId(unit);
        timetype=DFT_TIME_STARTEND;
      }
    } else if(ti==1 && timetype==DFT_TIME_STARTEND) {
      if(strlen(cptr)>5 && strncasecmp(cptr, "end[", 4)==0) {
        strncpy(unit, cptr+4, MAX_UNITS_LEN); unit[MAX_UNITS_LEN]=(char)0;
        cptr2=strchr(unit, ']'); if(cptr2!=NULL) *cptr2=(char)0;
        ret=petCunitId(unit);
        if(ret!=CUNIT_UNKNOWN && dft!=NULL) strcpy(dft->unit, petCunit(ret));
      }
    } else {
      // get tac name
      strncpy(rname, cptr, MAX_REGIONNAME_LEN);
      rname[MAX_REGIONNAME_LEN]=(char)0;
      cptr2=strchr(rname, '['); if(cptr2!=NULL) *cptr2=(char)0;
      while((cptr2=strchr(rname, '_'))!=NULL) *cptr2=' ';
      if(dft!=NULL && ri<dft->_voidataNr) strcpy(dft->voi[ri].name, rname);
      // get unit
      cptr2=strchr(cptr, '['); 
      if(cptr2!=NULL) {
        strncpy(unit, cptr2+1, MAX_UNITS_LEN); unit[MAX_UNITS_LEN]=(char)0;
        cptr2=strchr(unit, ']'); if(cptr2!=NULL) *cptr2=(char)0;
        ret=petCunitId(unit);
        if(ret!=CUNIT_UNKNOWN && dft!=NULL) strcpy(dft->unit, petCunit(ret));
      }
      ri++;
    }
    ti++;
    cptr=strtok(NULL, separs);
  }
  if(dft==NULL) {
    return(ri);
  }
 
  dft->timetype=timetype;
  
  //for(int i=0; i<dft->_voidataNr; i++) printf("    '%s'\n", dft->voi[i].name);  
  
  /* Split ROI names */
  ti=ri;
  for(ri=0; ri<ti; ri++)
    rnameSplit(dft->voi[ri].name, dft->voi[ri].voiname,
          dft->voi[ri].hemisphere, dft->voi[ri].place, MAX_REGIONSUBNAME_LEN);
 
  return(0);
}

Referenced by dftRead().

dftPrint()

void dftPrint

(

DFT *

data

)

Prints to stdout the contents of DFT data structure. Mainly for testing purposes.

See also

dftWrite

Definition at line 538 of file dftio.c.

{
  int voi, frame;
 
  printf("Number of curves: %d     Number of data points: %d\n",
    data->voiNr, data->frameNr);
  printf("Study: '%s'  Unit: '%s'\n", data->studynr, data->unit);
  printf("Time unit and type: %d %d\n", data->timeunit, data->timetype);
  if(strlen(data->radiopharmaceutical))
    printf("Radiopharmaceutical: %s\n", data->radiopharmaceutical);
  if(strlen(data->isotope)) printf("Isotope: %s\n", data->isotope);
  if(strlen(data->scanStartTime))
    printf("Scan start time: %s\n", data->scanStartTime);
  if(strlen(data->injectionTime))
    printf("Injection time: %s\n", data->injectionTime);
  if(data->decayCorrected==DFT_DECAY_CORRECTED)
    printf("Corrected for physical decay: yes\n");
  else if(data->decayCorrected==DFT_DECAY_NOTCORRECTED)
    printf("Corrected for physical decay: no\n");
  printf("_datasize = %d\n", data->_dataSize);
  for(voi=0; voi<data->voiNr; voi++) {
    if(strlen(data->voi[voi].name)>0)
      printf("\nROI name: '%s' Size: %g\n",
        data->voi[voi].name, data->voi[voi].size);
    else
      printf("\nROI name: '%s' '%s' '%s'  Size: %g\n",
        data->voi[voi].voiname, data->voi[voi].hemisphere, data->voi[voi].place,
        data->voi[voi].size);
    for(frame=0; frame<data->frameNr; frame++) {
      printf("%03d:  %11.3e %11.3e %11.3e    %11.3e %11.3e %11.3e\n",
        frame+1, data->x[frame], data->x1[frame], data->x2[frame],
        data->voi[voi].y[frame], data->voi[voi].y2[frame],
        data->voi[voi].y3[frame]);
    }
  }
  printf("Comments:\n");
  if(strlen(data->comments)>0) printf("%s\n", data->comments);
  printf("Weights:\n");
  if(data->isweight)
    for(frame=0; frame<data->frameNr; frame++)
      printf(" %03d  %11.3e %11.3e  %11.3e\n", frame+1,
        data->x1[frame], data->x2[frame], data->w[frame]);
  else
    printf(" contains no weights.\n");
  return;
}

Referenced by csv2dft(), dftRead(), img_k1_using_ki(), img_logan(), and img_patlak().

dftRead()

int dftRead	(	char *	filename,
		DFT *	data )

Read TAC file contents into specified DFT data structure. Reads standard DFT files, plain DFT files, and some other formats.

See also

dftFormat, dftWrite

Returns

Returns 0 when successful, in case of error sets dfterrmsg.

Parameters

filename	Name of file to be read.
data	Pointer to initiated DFT struct where data will be written; any old content is deleted.

Definition at line 22 of file dftio.c.

  {
  const int verbose=0;
  if(verbose>0) {printf("%s(%s, dft)\n", __func__, filename); fflush(stdout);}
 
  FILE *fp;
  char *cptr, *line, *lptr, temp[128];
  int ret, i, j, c, type=0, voiNr=0, frameNr=0, longest=0;
  double f;
  IFT ift;
 
 
  /* Empty data */
  if(data==NULL) {strcpy(dfterrmsg, "invalid data"); return 1;}
  dftEmpty(data);
 
  /* Check if file can be opened for read; then close it for now */
  if(verbose>1) {printf("opening file\n"); fflush(stdout);}
  fp=fopen(filename, "r");
  if(fp==NULL) {strcpy(dfterrmsg, "cannot open file"); return 1;}
  fclose(fp);
 
  /* Try to identify the file format */
  type=dftFormat(filename); if(verbose>1) printf("  type := %d\n", type);
  if(type==DFT_FORMAT_UNKNOWN) {
    strcpy(dfterrmsg, "unknown file format"); return 1;
  } else if(type==DFT_FORMAT_FIT) {
    strcpy(dfterrmsg, "cannot read fit file"); return 1;
  }
 
  /* Read some special formats */
  if(type==DFT_FORMAT_NCI) { // TPC format before DFT
    if(verbose>1) {printf("calling roikbqRead()\n"); fflush(stdout);}
    ret=roikbqRead(filename, data); if(ret!=0) return ret;
    dftFrametimes(data);
    return(0);
  } else if(type==DFT_FORMAT_IDWC) {
    if(verbose>1) {printf("calling idwcRead()\n"); fflush(stdout);}
    ret=idwcRead(filename, data); if(ret!=0) return ret;
    if(strlen(data->studynr)==0) studynr_from_fname(filename, data->studynr);
    return(0);
  } else if(type==DFT_FORMAT_IF) {
    if(verbose>1) {printf("calling iftRead()\n"); fflush(stdout);}
    ret=ifRead(filename, data); if(ret!=0) return ret;
    if(strlen(data->studynr)==0) studynr_from_fname(filename, data->studynr);
    return(0);
  } else if(type==DFT_FORMAT_CSV_INT || type==DFT_FORMAT_CSV_UK) {
    CSV csv;
    csvInit(&csv); //CSV_TEST=100;
    if(verbose>1) {printf("calling csvRead()\n"); fflush(stdout);}
    ret=csvRead(&csv, filename);
    if(ret==0) ret=csv2dft(&csv, data);
    csvEmpty(&csv);
    if(ret==0) {
      /* Try to read information from an interfile-type header */
      IFT ift; iftInit(&ift);
      if(iftRead(&ift, filename, 1, 0)==0 && ift.keyNr>0) dft_fill_hdr_from_IFT(data, &ift);
      iftEmpty(&ift);
      /* study number, too */
      if(strlen(data->studynr)==0) studynr_from_fname(filename, data->studynr);
      /* Set DFT comments */
      dftSetComments(data);
      return(0);
    }
    // if not ok, then just drop through with plain format
    type=DFT_FORMAT_PLAIN;
  }
 
  /* Try to read supported TAC formats, not the others */
  if(type!=DFT_FORMAT_PLAIN && type!=DFT_FORMAT_STANDARD &&
     type!=DFT_FORMAT_IFT && type!=DFT_FORMAT_PMOD
  ) {
    strcpy(dfterrmsg, "unsupported file format"); return 1;
  }
 
  /* Try to read information from an interfile-type header */
  if(verbose>1) {printf("calling iftRead()\n"); fflush(stdout);}
  iftInit(&ift);
  if(iftRead(&ift, filename, 1, 0)!=0) iftEmpty(&ift);
 
  /* Open file */
  if(verbose>1) {printf("re-opening file\n"); fflush(stdout);}
  fp=fopen(filename, "r");
  if(fp==NULL) {
    strcpy(dfterrmsg, "cannot open file"); iftEmpty(&ift); return 1;
  }
 
  /* Get the length of the longest line */
  i=0; while((c=fgetc(fp))!=EOF) {
    if(c==10 || c==13) {if(i>longest) longest=i; i=0;} else i++;}
  if(i>longest) longest=i;
  rewind(fp); longest+=2;
  if(verbose>1) {printf("  longest := %d\n", longest); fflush(stdout);}
 
  /* and allocate memory for string of that length */
  line=(char*)malloc((longest+1)*sizeof(char));
  if(line==NULL) {strcpy(dfterrmsg, "out of memory"); iftEmpty(&ift); fclose(fp); return 2;}
 
  /* Get the frame number */
  i=0; while(fgets(line, longest, fp)!=NULL && *line) {
    if(line[0]=='#') continue;
    cptr=strchr(line, '#'); if(cptr!=NULL) *cptr=(char)0;
    for(j=0; j<(int)strlen(line); j++)
      if(isalnum((int)line[j]) || line[j]=='.') {i++; break;}
  }
  rewind(fp); frameNr=i;
  if(type==DFT_FORMAT_STANDARD) frameNr-=4; /* title lines */
  if(type==DFT_FORMAT_PMOD) frameNr-=1;
  if(verbose>1) {printf("frameNr := %d\n", frameNr); fflush(stdout);}
  if(frameNr<1) {
    strcpy(dfterrmsg, "contains no data");
    iftEmpty(&ift); free(line); fclose(fp); return 1;
  }
 
  /* Get the number of curves */
  /* find first line that is not an empty or a comment line */
  while(fgets(line, longest, fp)!=NULL) {
    if(line[0]=='#') continue;
    /* If PMOD file, then read it from the title */
    if(type==DFT_FORMAT_PMOD) {voiNr=dftGetPmodTitle(NULL, line); break;}
    /* In plain data file that is first frame, which starts with time */
    /* In normal DFT file that is 1st title line, which starts with 'DFT' */
    char *nline; nline=strdup(line); lptr=nline;
    cptr=strtok(lptr, " \t\n\r"); if(cptr==NULL) {free(nline); continue;}
    voiNr=0; while((cptr=strtok(NULL, " \t\n\r"))!=NULL) voiNr++;
    free(nline);
    break;
  }
  rewind(fp);
  if(verbose>1) {printf("voiNr := %d\n", voiNr); fflush(stdout);}
  if(voiNr<1) {
    strcpy(dfterrmsg, "contains no curves");
    iftEmpty(&ift); free(line); fclose(fp); return 1;
  }
 
  /* Allocate memory for data */
  if(verbose>1) {printf("allocating memory\n"); fflush(stdout);}
  if(dftSetmem(data, frameNr, voiNr)) {
    strcpy(dfterrmsg, "out of memory");
    iftEmpty(&ift); free(line); fclose(fp); return 2;
  }
 
  /* For plain data files, set defaults for title data */
  if(type==DFT_FORMAT_PLAIN || type==DFT_FORMAT_IFT) {
    if(verbose>1) {printf("setting title defaults for plain data\n"); fflush(stdout);}
    int u, n; u=voiNr; n=1; while((u/=10)>=1) n++;
    if(n>MAX_REGIONSUBNAME_LEN) n=MAX_REGIONSUBNAME_LEN;
    for(i=0; i<voiNr; i++) {
      snprintf(data->voi[i].voiname, MAX_REGIONSUBNAME_LEN+1, "%0*d", n, i+1);
      strcpy(data->voi[i].name, data->voi[i].voiname);
    }
    /* Default: times in minutes, and frame mid time */
    data->timeunit=TUNIT_UNKNOWN; data->timetype=DFT_TIME_MIDDLE;
  }
 
  /*
   *  Try to read information from an interfile-type header
   */
  if(ift.keyNr>0) {
    if(verbose>1) {printf("calling dft_fill_hdr_from_IFT\n"); fflush(stdout);}
    dft_fill_hdr_from_IFT(data, &ift);
  }
  iftEmpty(&ift);
 
  /* Try to read information from a single title line in PMOD files */
  if(type==DFT_FORMAT_PMOD) {
    if(fgets(line, longest, fp)==NULL) {
      strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 101;}
    if(verbose>1) {printf("calling dftGetPmodTitle\n"); fflush(stdout);}
    dftGetPmodTitle(data, line);
    // do not rewind!
  }
 
  /* 
   *  Read DFT title lines, if they exist
   */
  i=0; 
  if(type==DFT_FORMAT_STANDARD) {
    if(verbose>1) {printf("reading DFT title lines\n"); fflush(stdout);}
    do {
      if(fgets(line, longest, fp)==NULL) {
        strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 102;}
      lptr=line;
      /* Check for comment line */
      if(line[0]=='#') { /* Read comment only if there is space left */
        strlcat(data->comments, line, _DFT_COMMENT_LEN);
        continue;
      }
      cptr=strchr(line, '#'); if(cptr!=NULL) *cptr=(char)0;
      /* Read first token, and check for empty lines as well */
      cptr=strtok(lptr, " \t\n\r"); if(cptr==NULL) continue; else i++;
      if(i==1) { /* VOI names */
        for(j=0; j<voiNr; j++) {
          cptr=strtok(NULL, " \t\n\r");
          if(cptr==NULL) {strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 103;}
          if(strlen(cptr)>1 || *cptr!='.') {
            strncpy(data->voi[j].name, cptr, MAX_REGIONNAME_LEN);
            data->voi[j].name[MAX_REGIONNAME_LEN]=(char)0;
            strncpy(data->voi[j].voiname, cptr, MAX_REGIONSUBNAME_LEN);
            data->voi[j].voiname[MAX_REGIONSUBNAME_LEN]=(char)0;
            /* if name is long, then divide it into name subfields */
            if(strlen(cptr)>MAX_REGIONSUBNAME_LEN) { 
              strncpy(data->voi[j].hemisphere, cptr+MAX_REGIONSUBNAME_LEN, MAX_REGIONSUBNAME_LEN);
              data->voi[j].hemisphere[MAX_REGIONSUBNAME_LEN]=(char)0;
              if(strlen(cptr)>2*MAX_REGIONSUBNAME_LEN) {
                strncpy(data->voi[j].place, cptr+2*MAX_REGIONSUBNAME_LEN, MAX_REGIONSUBNAME_LEN);
                data->voi[j].place[MAX_REGIONSUBNAME_LEN]=(char)0;
              }
            }
          } else {
            int u, n; u=voiNr; n=1; while((u/=10)>=1) n++; if(n>6) n=6;
            snprintf(data->voi[j].voiname, 7, "%0*d", n, j+1);
            strcpy(data->voi[j].name, data->voi[j].voiname);
          }
        }
      } else if(i==2) { /* 2nd VOI names (hemispheres) */
        if(strcmp(cptr, ".")!=0) {
          strlcpy(data->studynr, cptr, MAX_STUDYNR_LEN);
        } else strcpy(data->studynr, "");
        for(j=0; j<voiNr; j++) {
          if((cptr=strtok(NULL, " \t\n\r"))==NULL) {
            strcpy(dfterrmsg, "missing field on 2nd line");
            free(line); fclose(fp); return 104;
          }
          if(strlen(cptr)>1 || *cptr!='.') {
            strncpy(data->voi[j].hemisphere, cptr, MAX_REGIONSUBNAME_LEN);
            data->voi[j].hemisphere[MAX_REGIONSUBNAME_LEN]=(char)0;
            strcat(data->voi[j].name, " ");
            strlcat(data->voi[j].name, data->voi[j].hemisphere, MAX_REGIONNAME_LEN);
          } else {
            strlcat(data->voi[j].name, " .", MAX_REGIONNAME_LEN+1);
          }
        }
        /* check that there are no more contents */
        if((cptr=strtok(NULL, " \t\n\r"))!=NULL) {
          strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 105;}
      } else if(i==3) { /* unit and VOI place (planes) */
        /* first, copy the unit */
        strlcpy(data->unit, cptr, 13); //data->unit[12]=(char)0;
        /* then, copy the names */
        int len, ii=0;
        j=0;
        while(j<voiNr) {
          if((cptr=strtok(NULL, " \t\n\r"))==NULL) {
            strcpy(dfterrmsg, "missing field on 3rd line");
            free(line); fclose(fp); return 106;
          }
          len=strlen(cptr);
          /* check if cunit consists of two parts */
          if(ii==0 && cptr[0]=='(' && cptr[len-1]==')') {ii++; continue;}
          /* copy the name */
          if(len>1 || *cptr!='.') {
            strlcpy(data->voi[j].place, cptr, MAX_REGIONSUBNAME_LEN+1);
            //data->voi[j].place[MAX_REGIONSUBNAME_LEN]=(char)0;
            strcat(data->voi[j].name, " ");
            strlcat(data->voi[j].name, data->voi[j].place, MAX_REGIONNAME_LEN+1);
          } else {
            strlcat(data->voi[j].name, " .", MAX_REGIONNAME_LEN+1);
          }
          j++; ii++;
        }
      } else if(i==4) { /* time type, time unit, and VOI sizes */
        /* time type */
        if(strcasecmp(cptr, "Time")==0) data->timetype=DFT_TIME_MIDDLE;
        else if(strcasecmp(cptr, "Times")==0) data->timetype=DFT_TIME_STARTEND;
        else if(strcasecmp(cptr, "Start")==0) data->timetype=DFT_TIME_START;
        else if(strcasecmp(cptr, "End")==0) data->timetype=DFT_TIME_END;
        else if(strcasecmp(cptr, "Distance")==0) data->timetype=DFT_TIME_MIDDLE;
        else if(strcasecmp(cptr, "Distances")==3) data->timetype=DFT_TIME_STARTEND;
        else {strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 108;}
        /* time unit */
        if((cptr=strtok(NULL, " \t\n\r"))==NULL) {
          strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 109;}
        strcpy(temp, ""); j=sscanf(cptr, "(%127s)", temp);
        j=strlen(temp)-1; if(j>=0 && temp[j]==')') temp[j]=(char)0;
        data->timeunit=petTunitId(temp);
        if(data->timeunit<0) {
          strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 110;}
        /* volumes */
        for(j=0; j<voiNr; j++) {
          if((cptr=strtok(NULL, " \t\n\r"))==NULL) {
            strcpy(dfterrmsg, "wrong format"); free(line); fclose(fp); return 111;}
          if(strlen(cptr)==1 && *cptr=='.') data->voi[j].size=0.0;
          else data->voi[j].size=atof_dpi(cptr);
        }
      }
    } while(i<4); // Standard DFT title lines are now read
  }
 
  /* Read data lines */
  if(verbose>1) {printf("reading data lines\n"); fflush(stdout);}
  i=0; while(fgets(line, longest, fp)!=NULL) {
 
    /* Check for comment line */
    if(line[0]=='#') { /* Read comment only if there is space left */
      strlcat(data->comments, line, _DFT_COMMENT_LEN);
      continue;
    }
    // remove end-of-line comment    
    cptr=strchr(line, '#'); if(cptr!=NULL) *cptr=(char)0;
 
    /* Read first token, and check for empty lines as well */
    char *nline; nline=strdup(line); lptr=nline;
    cptr=strtok(lptr, " \t\n\r"); if(cptr==NULL) {free(nline); continue;}
    if(i<frameNr) {
      /* Read time(s) */
      if(atof_with_check(cptr, &f)!=0) {
        strcpy(dfterrmsg, "wrong format"); 
        free(line); free(nline); fclose(fp); return 130;
      }
      if(data->timetype==DFT_TIME_STARTEND) {
        data->x1[i]=f; cptr=strtok(NULL, " \t\n\r");
        if(atof_with_check(cptr, &data->x2[i])!=0) {
          strcpy(dfterrmsg, "wrong format"); 
          free(line); free(nline); fclose(fp); return 131;
        }
        data->x[i]=0.5*(data->x1[i]+data->x2[i]);
      } else data->x[i]=f;
      /* curve data */
      for(j=0; j<voiNr; j++) {
        if((cptr=strtok(NULL, " \t\n\r"))==NULL) {
          strcpy(dfterrmsg, "wrong format"); 
          free(line); free(nline); fclose(fp); return 132;
        }
        if(strlen(cptr)==1 && *cptr=='.') 
          data->voi[j].y[i]=nan("");
        else {
          if(atof_with_check(cptr, &data->voi[j].y[i])!=0) {
            strcpy(dfterrmsg, "wrong format"); 
            free(line); free(nline); fclose(fp); return 133;
          }
          c=dec_nr(cptr);
          if(c>DFT_NR_OF_DECIMALS && c<11) DFT_NR_OF_DECIMALS=c;
        }
      }
    }
    free(nline);
    i++;
  }
  if(i!=frameNr) {strcpy(dfterrmsg, "wrong format"); fclose(fp); free((char*)line); return 134;}
 
  /* Close file */
  fclose(fp); free((char*)line);
 
  /* Set voiNr and frameNr, and type */
  data->voiNr=voiNr; data->frameNr=frameNr;
  if(type==DFT_FORMAT_IFT) {
    data->_type=DFT_FORMAT_PLAIN;
  } else if(type==DFT_FORMAT_PMOD) {
    data->_type=type; // keeping PMOD format
    // unless TAC names could not be read
    for(i=0; i<data->voiNr; i++) if(strlen(data->voi[i].name)<1) {
      data->_type=DFT_FORMAT_PLAIN; break;} 
  } else {
    data->_type=type;
  }
 
  /* Set study number from file name, if necessary */
  if(strlen(data->studynr)==0) studynr_from_fname(filename, data->studynr);
 
  /* If weight 'voi' was read, move it to its own place */
  for(i=0; i<data->voiNr; i++) if(!strcasecmp(data->voi[i].voiname, "weight")) {
    data->isweight=1;
    for(j=0; j<data->frameNr; j++) data->w[j]=data->voi[i].y[j];
    /* Move the following VOIs one step backwards */
    for(c=i+1; c<data->voiNr; c++) if(dftCopyvoi(data, c, c-1)) {
      strcpy(dfterrmsg, "cannot read weight"); return 4;}
    data->voiNr--;
    break;
  }
  /* If no weights were found, set uniform weight */
  if(!data->isweight) for(i=0; i<data->frameNr; i++) data->w[i]=1.0;
 
  /* Calculate frame mid times, or frame start and end times;
     this works only if time units are known */
  dftFrametimes(data);
 
  /* Make again the full ROI names from the separate sub parts */
  for(i=0; i<data->voiNr; i++)
    rnameCatenate(data->voi[i].name, MAX_REGIONNAME_LEN, data->voi[i].voiname, 
                  data->voi[i].hemisphere, data->voi[i].place, ' ');
 
 
  if(CSV_TEST>100) dftPrint(data);
  return(0);
}

Referenced by dftReadinput(), dftReadModelingData(), dftReadReference(), and imgReadModelingData().

dftType()

int dftType

(

FILE *

fp

)

Determine the type of DFT file.

Deprecated

Replace calls to dftType() by dftFormat(), but note that return values have changed.

See also

dftFormat

Returns

0=unknown; 1=normal DFT; 2=plain data; 3=fit file; 4=nci file; 5=KI file

Definition at line 503 of file dftio.c.

{
  char tmp[256];
  int c;
 
  /* Find first line that is not empty or comment line */
  rewind(fp);
  while(fgets(tmp, 4, fp) != NULL) {if(strlen(tmp) && tmp[0]!='#') break;}
  rewind(fp);
 
  /* Check for identification strings */
  if(strncasecmp(tmp, "DFT", 3)==0) return 1;
  else if(strncasecmp(tmp, "FIT1", 3)==0) return 3;
  else if(strncasecmp(tmp, "cpt", 3)==0) return 4;
 
  /* Binary data? */
  while((c=fgetc(fp))!=EOF) 
    if(!isalnum(c) && !isspace(c) && !isgraph(c) && c!=169) {
      rewind(fp); return 0;
    }
 
  /* File with one title line without comment mark? */
  rewind(fp);
  while(fgets(tmp, 10, fp) != NULL) {if(strlen(tmp)) break;}
  if(strncasecmp(tmp, "Time", 4)==0) {rewind(fp); return 5;}
 
  rewind(fp); return 2;
}

dftWrite()

int dftWrite	(	DFT *	data,
		char *	filename )

Write DFT data, usually containing regional time-activity curves (TACs) into specified file.

The file format specified in data is applied. Number of decimals can be determined by changing global variable DFT_NR_OF_DECIMALS.

See also

dftRead, resWrite

Returns

Returns 0 when successful, in case of error sets dfterrmsg.

Parameters

data	Pointer to DFT structure which contents are to be written.
filename	File name where DFT contents are written. If file exists, original file is renamed to a backup file.

Definition at line 594 of file dftio.c.

  {
  int i, j, n, sw, mfw, prec;
  char tmp[1024], tmp2[128], is_stdout=0;
  FILE *fp;
 
 
  /* Check that there is some data to write */
  if(data->voiNr<1 || data->frameNr<1) {strcpy(dfterrmsg, "no data"); return 1;}
 
  /* If format if DFT_FORMAT_HTML or extension is *.HTM(L),
     write in HTML format */
  if(data->_type==DFT_FORMAT_HTML || fncasematch(filename, "*.htm")==1 || fncasematch(filename, "*.html")==1) {
    return(dftWriteHTML(data, filename, 1));
  }
 
  /* Check if writing to stdout */
  if(!strcasecmp(filename, "stdout")) is_stdout=1;
 
  /* Set minimum field width and precision for concentrations */
  mfw=11; if(DFT_NR_OF_DECIMALS>3) mfw+=DFT_NR_OF_DECIMALS-3;
  prec=0; if(DFT_NR_OF_DECIMALS>prec) prec=DFT_NR_OF_DECIMALS;
 
  /* Check if file exists; backup, if necessary */
  if(!is_stdout) (void)backupExistingFile(filename, NULL, NULL);
 
  /* Open output file */
  if(is_stdout) fp=(FILE*)stdout;
  else if((fp = fopen(filename, "w")) == NULL) {strcpy(dfterrmsg, "cannot open file"); return 2;}
 
  /* Write title lines */
  if(data->_type==DFT_FORMAT_STANDARD) {
    /* 1st line with filetype identification string and region names */
    n=fprintf(fp, "%s", DFT_VER);
    if(n==0) {strcpy(dfterrmsg, "disk full"); if(!is_stdout) fclose(fp); return 3;}
    for(i=0; i<data->voiNr; i++) fprintf(fp,"\t%s", data->voi[i].voiname);
    if(data->isweight) fprintf(fp,"\t%s", "weight");
    fprintf(fp, "\n");
    /* 2nd line with study identification and 2nd name (hemisphere) */
    if(strlen(data->studynr)) strlcpy(tmp, data->studynr, 11); else strcpy(tmp, ".");
    fprintf(fp, "%s", tmp);
    for(i=0; i<data->voiNr; i++) {
      if(strlen(data->voi[i].hemisphere)) strcpy(tmp, data->voi[i].hemisphere);
      else strcpy(tmp, ".");
      fprintf(fp, "\t%s", tmp);
    }
    if(data->isweight) fprintf(fp,"\t%s", ".");
    fprintf(fp, "\n");
    /* 3rd line with unit and plane names */
    if(strlen(data->unit)) strcpy(tmp, data->unit); else strcpy(tmp, ".");
    fprintf(fp, "%s", tmp);
    for(i=0; i<data->voiNr; i++) {
      if(strlen(data->voi[i].place)) strcpy(tmp, data->voi[i].place);
      else strcpy(tmp, ".");
      fprintf(fp, "\t%s", tmp);
    }
    if(data->isweight) fprintf(fp,"\t%s", ".");
    fprintf(fp, "\n");
    /* 4th line with time type & unit and region volumes */
    switch(data->timetype) {
      case DFT_TIME_MIDDLE:
        if(data->timeunit==TUNIT_MM || data->timeunit==TUNIT_UM || data->timeunit==TUNIT_CM)
          strcpy(tmp, "Distance ");
        else
          strcpy(tmp, "Time ");
        break;
      case DFT_TIME_START: strcpy(tmp, "Start "); break;
      case DFT_TIME_END: strcpy(tmp, "End "); break;
      case DFT_TIME_STARTEND:
        if(data->timeunit==TUNIT_MM || data->timeunit==TUNIT_UM || data->timeunit==TUNIT_CM)
          strcpy(tmp, "Distances ");
        else
          strcpy(tmp, "Times ");
        break;
    }
    snprintf(tmp2, 128, "(%s)", petTunit(data->timeunit)); strcat(tmp, tmp2);
    fprintf(fp, "%s", tmp);
    for(i=0; i<data->voiNr; i++) {
      if(data->voi[i].size>=0.0) sprintf(tmp, "%.*e", prec, data->voi[i].size);
      else strcpy(tmp, ".");
      fprintf(fp, "\t%s", tmp);
    }
    if(data->isweight) fprintf(fp,"\t%s", ".");
    fprintf(fp, "\n");
  } else if(data->_type==DFT_FORMAT_PMOD) { // write PMOD title line
    char *cptr, tunit[128], cunit[128]; // Set units to format accepted by PMOD
    if(data->timeunit==TUNIT_SEC) strcpy(tunit, "seconds");
    else if(data->timeunit==TUNIT_MIN) strcpy(tunit, "minutes");
    else strcpy(tunit, petTunit(data->timeunit));
    if(petCunitId(data->unit)==CUNIT_UNITLESS) strcpy(cunit, "1/1"); else strcpy(cunit, data->unit); 
    cptr=strstr(cunit, "mL"); if(cptr!=NULL) {*cptr='c'; cptr++; *cptr='c';}
    if(data->timetype==DFT_TIME_STARTEND) fprintf(fp, "start[%s]\tend[%s]", tunit, cunit);
    else fprintf(fp, "time[%s]", tunit);
    for(i=0; i<data->voiNr; i++) {
      /* write roi names, must not include spaces */
      char *s=strdup(data->voi[i].name);
      strReplaceChar(s, ' ', '-'); fprintf(fp, "\t%s", s); free(s);
      /* write calibration unit when necessary */
      if(i==0 && data->timetype!=DFT_TIME_STARTEND) fprintf(fp, "[%s]", cunit);
    }
    if(data->isweight) fprintf(fp,"\t%s", "weight");
    fprintf(fp, "\n");
  }
 
  /* Make sure that only frame mid times are saved without titles */
  if(data->_type==DFT_FORMAT_PLAIN && data->timetype!=DFT_TIME_MIDDLE) sw=0;
  else sw=data->timetype;
 
  /* Write data */
  for(j=0; j<data->frameNr; j++) {
    /* Time(s) */
    switch(sw) {
      case 0: fprintf(fp, "%.5f", data->x[j]); break;
      case 1: fprintf(fp, "%.5f", data->x1[j]); break;
      case 2: fprintf(fp, "%.5f", data->x2[j]); break;
      case 3: fprintf(fp, "%.5f\t%.5f", data->x1[j], data->x2[j]); break;
    }
    /* y values */
    for(i=0; i<data->voiNr; i++) {
      if(!isnan(data->voi[i].y[j])) sprintf(tmp, "%.*e", prec, data->voi[i].y[j]);
      else strcpy(tmp, ".");
      fprintf(fp, "\t%s", tmp);
    }
    if(data->isweight) {
      if(data->_type==DFT_FORMAT_STANDARD || data->_type==DFT_FORMAT_PMOD) {
        if(!isnan(data->w[j])) sprintf(tmp, "%.*e", prec, data->w[j]);
        else strcpy(tmp, "."); 
        fprintf(fp,"\t%s", tmp);
      }
    }
    n=fprintf(fp, "\n");
    if(n==0) {strcpy(dfterrmsg, "disk full"); if(!is_stdout) fclose(fp); return 3;}
  }
 
  /* Write comments */
  if(1) { //data->_type!=DFT_FORMAT_PMOD) {
    n=strnlen(data->comments, _DFT_COMMENT_LEN);
    if(n) for(i=0; i<n; i++) {
      if(i>0 && data->comments[i]=='#' && (data->comments[i-1]!='\n' && data->comments[i-1]!='\r'))
        fputc('\n', fp);
      fputc(data->comments[i], fp);
    }
  }
 
  /* Close file */
  if(!is_stdout) {fflush(fp); fclose(fp);}
 
  return 0;
}

Referenced by plotdata_as_dft().

dftWriteHTML()

int dftWriteHTML	(	DFT *	dft,
		char *	fname,
		int	orientation )

Write DFT contents in HTML table format If file exists, a backup file (+BACKUP_EXTENSION) is written also. If "stdout" is given as filename, output is directed to stdout In case of an error, description is written in dfterrmsg.

Returns

Returns 0 if ok.

Parameters

dft	Input DFT
fname	HTML filename
orientation	Table orientation: 1=original, 2=transposed

Definition at line 757 of file dftio.c.

  {
  int ri, fi, is_stdout=0, ret;
  char tmp[FILENAME_MAX];
  FILE *fp;
 
 
  /* Check input */
  strcpy(dfterrmsg, "invalid input to dftWriteHTML()");
  if(dft==NULL || dft->frameNr<1 || dft->voiNr<1) return(1);
  if(fname==NULL || strlen(fname)<1) return(1);
  strcpy(dfterrmsg, "");
  /* Check if writing to stdout */
  if(!strcasecmp(fname, "stdout")) is_stdout=1;
 
  /* Check if file exists; backup, if necessary */
  if(!is_stdout && access(fname, 0) != -1) {
    strcpy(tmp, fname); strcat(tmp, BACKUP_EXTENSION); rename(fname, tmp);}
  strcpy(dfterrmsg, "cannot write file");
 
  /* Open output file */
  if(is_stdout) fp=(FILE*)stdout;
  else if((fp=fopen(fname, "w"))==NULL) {strcpy(dfterrmsg, "cannot open file"); return(2);}
 
  /* Write XHTML 1.1 doctype and head */
  if(dftWriteXHTML11_doctype(fp) || dftWriteXHTML11_head(fp, "")) {
    strcpy(dfterrmsg, "disk full"); if(!is_stdout) fclose(fp); return(3);
  }
 
  /* Start writing the body of the HTML file */
  ret=fprintf(fp, "<body>\n");
  if(ret==0) {strcpy(dfterrmsg, "disk full"); if(!is_stdout) fclose(fp); return(3);}
 
  /* Start the div for table, and the table */
  fprintf(fp, "\n<div id=\"table\">\n");
  fprintf(fp, "<table>\n");
 
  /* Write the title lines, if there are titles, into the head of the table */
  if(dft->_type!=DFT_FORMAT_PLAIN) {
    fprintf(fp, "<thead>\n");
    if(orientation!=2) {
      /* Empty cell and Region names */
      fprintf(fp, "<tr><td> </td>\n");
      for(ri=0; ri<dft->voiNr; ri++) {
        char *senc=strEncodeForXML(dft->voi[ri].voiname);
        if(senc==NULL) fprintf(fp, "<th>%s</th>\n", dft->voi[ri].voiname);
        else {fprintf(fp, "<th>%s</th>\n", senc); free(senc);}
      }
      fprintf(fp, "</tr>\n");
      /* Study number and Hemispheres */
      fprintf(fp, "<tr><th>%s</th>\n", dft->studynr);
      for(ri=0; ri<dft->voiNr; ri++) {
        char *senc=strEncodeForXML(dft->voi[ri].hemisphere);
        if(senc==NULL) fprintf(fp, "<th>%s</th>\n", dft->voi[ri].hemisphere);
        else {fprintf(fp, "<th>%s</th>\n", senc); free(senc);}
      }
      fprintf(fp, "</tr>\n");
      /* Unit and Places */
      fprintf(fp, "<tr><th>%s</th>\n", dft->unit);
      for(ri=0; ri<dft->voiNr; ri++) {
        char *senc=strEncodeForXML(dft->voi[ri].place);
        if(senc==NULL) fprintf(fp, "<th>%s</th>\n", dft->voi[ri].place);
        else {fprintf(fp, "<th>%s</th>\n", senc); free(senc);}
      }
      fprintf(fp, "</tr>\n");
      /* Time unit and Volumes */
      fprintf(fp, "<tr><th>%s</th>\n", petTunit(dft->timeunit));
      for(ri=0; ri<dft->voiNr; ri++)
        fprintf(fp, "<th>%g</th>\n", dft->voi[ri].size);
      fprintf(fp, "</tr>\n");
    } else if(orientation==2) {
      /* Study number and Unit */
      fprintf(fp, "<tr><th>%s</th>\n", dft->studynr);
      fprintf(fp, "<th>%s</th></tr>\n", dft->unit);  
    }
    /* End the head of table */
    fprintf(fp, "</thead>\n");
  }
 
  /* Write the DFT data into the body of the table */
  fprintf(fp, "<tbody>\n");
 
  /* If transposed, write titles */
  if(orientation==2) {
    fprintf(fp, "<tr><th>Region</th><th>Hemisphere</th><th>Plane</th>\n");
    fprintf(fp, "<th>Volume</th></tr>\n");
  }
  if(orientation!=2) { /* Not transposed */
    for(fi=0; fi<dft->frameNr; fi++) {
      if(fi%2) strcpy(tmp, "evenframe"); else strcpy(tmp, "oddframe");
      /* Time */
      fprintf(fp, "<tr class=\"%s\"><th>%g</th>\n", tmp, dft->x[fi]);
      /* Values */
      for(ri=0; ri<dft->voiNr; ri++)
        fprintf(fp, "<th>%g</th>", dft->voi[ri].y[fi]);
      fprintf(fp, "</tr>\n");
    }
  } else { /* transposed */
    for(ri=0; ri<dft->voiNr; ri++) {
      if(ri%2) strcpy(tmp, "evenframe"); else strcpy(tmp, "oddframe");
      fprintf(fp, "<tr class=\"%s\">", tmp);
      /* Region names */
      char *senc;
      senc=strEncodeForXML(dft->voi[ri].voiname);
      if(senc==NULL) fprintf(fp, "<th>%s</th>", dft->voi[ri].voiname);
      else {fprintf(fp, "<th>%s</th>", senc); free(senc);}
      senc=strEncodeForXML(dft->voi[ri].hemisphere);
      if(senc==NULL) fprintf(fp, "<th>%s</th>", dft->voi[ri].hemisphere);
      else {fprintf(fp, "<th>%s</th>", senc); free(senc);}
      senc=strEncodeForXML(dft->voi[ri].place);
      if(senc==NULL) fprintf(fp, "<th>%s</th>\n", dft->voi[ri].place);
      else {fprintf(fp, "<th>%s</th>\n", senc); free(senc);}
      /* Region volume */
      fprintf(fp, "<td>%g</td>\n", dft->voi[ri].size);
      /* Values */
      for(fi=0; fi<dft->frameNr; fi++) {
        fprintf(fp, "<td>%g</td>", dft->voi[ri].y[fi]);
      }
      fprintf(fp, "</tr>\n");
    }
  }
  /* End the table body and table */
  fprintf(fp, "</tbody></table>\n");
 
  /* Stop writing the body of the HTML file, and end the file */
  fprintf(fp, "</div>\n");
  ret=fprintf(fp, "</body></html>\n\n");
  if(ret==0) {
    strcpy(dfterrmsg, "disk full");
    if(!is_stdout) fclose(fp);
    return(3);
  }
 
  /* Close file */
  if(!is_stdout) {fflush(fp); fclose(fp);}
  strcpy(dfterrmsg, "");
 
  return(0);
}

Referenced by dftWrite().

dftWriteXHTML11_doctype()

int dftWriteXHTML11_doctype

(

FILE *

fp

)

Write XHTML 1.1 doctype into an opened file pointer.

Returns

Returns 0 if successful, non-zero in case of a failure.

Definition at line 908 of file dftio.c.

  {
  int n;
  if(fp==NULL) return(1);
  n=fprintf(fp, "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.1//EN\" ");
  n+=fprintf(fp, "\"https://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd\">\n");
  if(n<20) return(2);
  n=fprintf(fp, "<html xmlns=\"https://www.w3.org/1999/xhtml\" xml:lang=\"en\">\n\n");
  if(n<20) return(2);
  return(0);
}

Referenced by dftWriteHTML().

dftWriteXHTML11_head()

int dftWriteXHTML11_head	(	FILE *	fp,
		char *	author_name )

Write XHTML 1.1 head for DFT file into an opened file pointer.

Returns

Returns 0 if successful, non-zero in case of a failure.

Parameters

fp	File pointer where to write
author_name	Author name, for example software name

Definition at line 926 of file dftio.c.

  {
  int n;
  if(fp==NULL) return(1);
 
  n=fprintf(fp, "<head>\n"); if(n<6) return(2);
  fprintf(fp, "  <title>PET data</title>\n");
  fprintf(fp, "  <meta http-equiv=\"content-type\" content=\"text/html; charset=iso-8859-1\" />\n");
  fprintf(fp, "  <meta http-equiv=\"content-language\" content=\"en-gb\" />\n");
  fprintf(fp, "  <meta name=\"author\" content=\"%s\" />\n", author_name);
  fprintf(fp, "  <meta name=\"ProgId\" content=\"Excel.Sheet\" />\n");
  fprintf(fp, "  <link rel=\"icon\" href=\"https://www.turkupetcentre.net/favicon.ico\" type=\"image/x-icon\" />\n");
  fprintf(fp, "  <link rel=\"shortcut icon\" href=\"https://www.turkupetcentre.net/favicon.ico\" type=\"image/x-icon\" />\n");
  /* write local CSS with basic settings in case that external CSS is not available */
  fprintf(fp, "  <style type=\"text/css\">\n");
  fprintf(fp, "    thead {background-color:#999999; color:black;}\n");
  fprintf(fp, "    table {text-align:left; width:100%%; border-collapse:collapse; empty-cells:show;}\n");
  fprintf(fp, "    td {border:1px solid black;}\n");
  fprintf(fp, "    .oddframe {background-color:#FFFFFF; color:black;}\n");
  fprintf(fp, "    .evenframe {background-color:#CCCCCC; color:black;}\n");
  fprintf(fp, "    #regcontainer ul {margin-left:0; padding-left:0;}\n");
  fprintf(fp, "    #regcontainer ul li {display:inline; list-style-type:none;}\n");
  fprintf(fp, "    #regcontainer a {padding:2px 4px;}\n");
  fprintf(fp, "    <!--table\n");
  fprintf(fp, "     {mso-displayed-decimal-separator:\"\\.\";\n");
  fprintf(fp, "     mso-displayed-thousand-separator:\" \";}\n");
  fprintf(fp, "    -->\n");
  fprintf(fp, "  </style>\n");
  /* load external CSS with more fancy settings */
  fprintf(fp, "  <link rel=\"stylesheet\" type=\"text/css\" ");
  fprintf(fp, "href=\"https://www.turkupetcentre.net/dft.css\" />\n");
  fprintf(fp, "</head>\n");
  if(n<7) return(2);
  return(0);
}

Referenced by dftWriteHTML().

Variable Documentation

DFT_NR_OF_DECIMALS

int DFT_NR_OF_DECIMALS = 3

Nr of decimals for concentration values

Definition at line 13 of file dftio.c.

Referenced by dftRead(), and dftWrite().