libtpccurveio.h File Reference

Header file for libtpccurveio. More...

#include "tpcclibConfig.h"
#include "libtpcmisc.h"
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <strings.h>
#include <ctype.h>
#include <math.h>
#include <time.h>

Go to the source code of this file.

Data Structures
struct	Voi
struct	DFT
struct	ResVOI
struct	RES
struct	FitVOI
struct	FIT
struct	CSV_item
struct	CSV

Macros
#define	BACKUP_EXTENSION   ".bak"
#define	MAX_RESPARAMS   100
#define	MAX_RESPARNAME_LEN   15
#define	MAX_FITPARAMS   100
#define	DFT_FORMAT_UNKNOWN   -1
#define	DFT_FORMAT_PLAIN   0
#define	DFT_FORMAT_STANDARD   1
#define	DFT_FORMAT_IFT   2
#define	DFT_FORMAT_FIT   3
#define	DFT_FORMAT_NCI   4
#define	DFT_FORMAT_PMOD   5
#define	DFT_FORMAT_CSV_INT   6
#define	DFT_FORMAT_CSV_UK   7
#define	DFT_FORMAT_CPT   8
#define	DFT_FORMAT_IDWC   9
#define	DFT_FORMAT_IF   10
#define	DFT_FORMAT_XML   11
#define	DFT_FORMAT_HTML   12
#define	DFT_FORMAT_XELERIS   13
#define	DFT_TIME_MIDDLE   0
#define	DFT_TIME_START   1
#define	DFT_TIME_END   2
#define	DFT_TIME_STARTEND   3
#define	DFT_DECAY_UNKNOWN   0
#define	DFT_DECAY_CORRECTED   1
#define	DFT_DECAY_NOTCORRECTED   2

Enumerations
enum	mathfuncs {   MF_LEVEL =100 , MF_LINE , MF_POL2 , MF_POL3 ,   MF_POL4 , MF_POL5 , MF_POL6 , MF_POL7 ,   MF_POL8 , MF_POL9 , MF_RATF11 =211 , MF_RATF21 =221 ,   MF_RATF22 =222 , MF_RATF32 =232 , MF_RATF33 =233 , MF_EXP1 =301 ,   MF_EXP2 , MF_EXP3 , MF_EXP4 , MF_EXP5 ,   MF_LUNDQVIST =321 , MF_LUNDQVIST2 , MF_LUNDQVIST3 , MF_EXPBOLUSINF =331 ,   MF_EXPBOLUSINF_RW =332 , MF_MF_EXPBOLUSINF_AZ =334 , MF_PK11195 =351 , MF_PPFIGAM =403 ,   MF_PF_MU =831 , MF_HILL =841 , MF_1MHILL =842 , MF_1MHILL_ADE =843 ,   MF_HILL_B =844 , MF_AMHILL =845 , MF_EHILL_PAR =846 , MF_EHILL_MET =847 ,   MF_EHILL2_PAR =848 , MF_EHILL2_MET =849 , MF_MAMEDE =851 , MF_1MMAMEDE ,   MF_MAYER_PAR =861 , MF_MAYER_MET , MF_EMAYER_PAR =863 , MF_EMAYER_MET ,   MF_HILL3M_PAR =871 , MF_HILL3M_M1 , MF_HILL3M_M2 , MF_HILL3M_M3 ,   MF_PF3M_PAR =881 , MF_PF3M_M1 , MF_PF3M_M2 , MF_PF3M_M3 ,   MF_STEP =1010 , MF_RATF33D =1232 , MF_FENGM2S =1312 , MF_FENGM2 =1313 ,   MF_FENGM2E =1314 , MF_GAMMAV =1401 , MF_GAMMAVB =1402 , MF_GAMMAVR =1403 ,   MF_WEIBULLCDF_D =1421 , MF_WEIBULLCDF_DD =1423 , MF_SURGE =1431 , MF_SURGE_TRAD =1432 ,   MF_SURGE_RECIRC =1433 , MF_P2B_SRC =1434 , MF_SURGE_FDG =1435 , MF_ERLANGPDF =1441 ,   MF_HILL_D =1801 , MF_HILL_DD =1811 , MF_HILL_SDD =1821 , MF_IMGPROFILE =2111 ,   MF_P2B_RF =2233 , MF_P2B_FM2 =2313 , MF_P2B_HILL =2841 , MF_GRAHAM_INP =9501 ,   MF_GRAHAM_EINP , MF_GRAHAM_INPM , MF_HUANG_MET =9601 , MF_CARSON_EMET ,   MF_NEW_MET , MF_MLMCM =9701 }
enum	{   CSV_OK , CSV_ERROR , CSV_CANNOTOPEN , CSV_INVALIDFORMAT ,   CSV_TOOBIG , CSV_OUTOFMEMORY , CSV_NOTABLE }

Functions
int	cptrnameSplit (char *rname, char *name1, char *name2, char *name3, int max_name_len)
int	cptReadOne (char *cptfile, DFT *dft, int verbose)
int	cptWrite (DFT *dft, char *filename, int cpt_format)
void	csvInit (CSV *csv)
void	csvEmpty (CSV *csv)
int	csvRead (CSV *csv, char *fname)
int	csv2dft (CSV *csv, DFT *dft)
int	csv2dft_a (CSV *csv, DFT *dft)
int	csv2dft_b (CSV *csv, DFT *dft)
int	csv2dft_linkset (CSV *csv, DFT *dft)
int	csv2dft_mat (CSV *csv, DFT *dft)
int	csvIsRegular (CSV *csv)
char *	csvCell (CSV *csv, int row, int col)
void	dftInit (DFT *data)
void	dftEmpty (DFT *data)
int	dftSetmem (DFT *data, int frameNr, int voiNr)
int	dftAddmem (DFT *data, int voiNr)
int	dftAdd (DFT *data1, DFT *data2, int voi)
int	dftSelect (DFT *data, char *name)
int	dftSelectRegions (DFT *dft, char *region_name, int reset)
int	dftSelectBestReference (DFT *dft)
void	dftFrametimes (DFT *data)
int	dftOverflow (DFT *data)
int	dftCopyvoi (DFT *data, int from, int to)
int	dftMovevoi (DFT *dft, int from, int to)
int	dftDelete (DFT *dft, int voi)
int	dftCopymainhdr (DFT *dft1, DFT *dft2)
int	dftCopymainhdr2 (DFT *dft1, DFT *dft2, int ow)
int	dftCopyvoihdr (DFT *dft1, int from, DFT *dft2, int to)
int	dftdup (DFT *dft1, DFT *dft2)
int	dftAllocateWithHeader (DFT *dft, int frameNr, int voiNr, DFT *dft_from)
int	dftAddnullframe (DFT *data)
int	dftSort (DFT *data)
int	dftSortPlane (DFT *data)
int	dft_nr_of_NA (DFT *dft)
int	dftNAfill (DFT *dft)
int	dftMinMax (DFT *dft, double *minx, double *maxx, double *miny, double *maxy)
int	dftMinMaxTAC (DFT *dft, int tacindex, double *minx, double *maxx, double *miny, double *maxy, int *mini, int *maxi, int *mins, int *maxs)
int	dftMaxY (DFT *dft, double t1, double t2, double *miny, double *maxy)
double	dft_kBqMin (DFT *data)
double	dft_kBqMax (DFT *data)
int	dftSortByFrame (DFT *dft)
int	dftDeleteFrameOverlap (DFT *dft)
int	dftDeleteFrameOverlap_old (DFT *dft)
int	dftRemoveTimeRange (DFT *dft, double startT, double endT)
void	dftSetComments (DFT *dft)
int	dftFillInitialGap (DFT *dft)
int	dftAddSpaceForFrames (DFT *dft, int nr_to_add)
void	dftRNameSimplify (DFT *dft, int hemisphere, int place)
int	dftMeanTAC (DFT *dft, DFT *mean)
int	dftValidNr (DFT *dft, double tstart, double tstop, int index)
int	dftDecayCorrection (DFT *dft, double hl, int mode, int y, int y2, int y3, char *status, int verbose)
int	dftRead (char *filename, DFT *data)
int	dftWrite (DFT *data, char *filename)
void	dftPrint (DFT *data)
int	dftFormat (char *fname)
int	dftType (FILE *fp)
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)
int	res_allocate_with_dft (RES *res, DFT *dft)
int	dftToResult (DFT *dft, RES *res, char *status)
void	dftUnitToDFT (DFT *dft, int dunit)
int	dftUnitConversion (DFT *dft, int dunit)
int	dftTimeunitToDFT (DFT *dft, const char *timeunit)
int	dftTimeunitConversion (DFT *dft, int tunit)
void	dftMin2sec (DFT *data)
void	dftSec2min (DFT *data)
int	fit_allocate_with_dft (FIT *fit, DFT *dft)
int	fitToResult (FIT *fit, RES *res, char *status)
int	idwcWrite (DFT *dft, char *filename)
int	idwcRead (char *filename, DFT *dft)
int	ifWrite (DFT *dft, char *filename)
int	ifRead (char *filename, DFT *dft)
void	fitEmpty (FIT *fit)
void	fitInit (FIT *fit)
int	fitSetmem (FIT *fit, int voiNr)
void	fitPrint (FIT *fit)
int	fitWrite (FIT *fit, char *filename)
int	fitRead (char *filename, FIT *fit, int verbose)
int	fitEval (FitVOI *r, double x, double *y)
int	fitEvaltac (FitVOI *r, double *x, double *y, int dataNr)
int	fitFunctionname (int type, char *str)
int	fitFunctionformat (int type, char *str)
int	fitIntegralEval (FitVOI *r, double x, double *yi)
int	fitIntegralEvaltac (FitVOI *r, double *x, double *yi, int dataNr)
int	fitDerivEval (FitVOI *r, double x, double *yd)
int	fitDerivEvaltac (FitVOI *r, double *x, double *yd, int dataNr)
unsigned int	factorial (unsigned int n)
unsigned long long int	lfactorial (unsigned long long int n)
double	igam (double a, double x)
double	igamc (double a, double x)
int	roikbqWrite (DFT *dft, char *fname)
int	roikbqRead (char *fname, DFT *dft)
int	res2ift (RES *res, IFT *ift, int verbose)
void	resEmpty (RES *res)
void	resInit (RES *res)
int	resSetmem (RES *res, int voiNr)
void	resFixParnames (RES *res)
void	resPrint (RES *res)
int	resRead (char *filename, RES *res, int verbose)
int	resWrite (RES *res, char *filename, int verbose)
int	resWriteHTML (RES *res, char *fname, int verbose)
int	resFName2study (char *fname, char *studyNumber)
int	resMedian (double *data, int nr, double *median, double *min, double *max)
int	resMean (double *data, int nr, double *mean, double *sd)
void	resSortByName (RES *res)
int	resCopyMHeader (RES *res1, RES *res2)
int	resDelete (RES *res, int voi)
int	resSelect (RES *data, char *name)
int	resSelectRegions (RES *res, char *region_name, int reset)
int	resParameterPrintType (RES *res, int parIndex)
int	resWriteXHTML11_doctype (FILE *fp)
int	resWriteXHTML11_head (FILE *fp, char *author_name)
int	resWriteHTML_table (RES *res, FILE *fp)
int	resIsDuplicateNames (RES *res)
int	resMatchHeader (RES *res1, RES *res2)
int	resMatchRegions (RES *res1, RES *res2)
int	resMatchParameternames (RES *res1, RES *res2)
int	resMatchParameters (RES *res1, RES *res2, int test_par, double test_limit, int test_sd)
int	resMatchParametersAbs (RES *res1, RES *res2, int test_par, double test_limit, int test_sd)
int	resRNameSubfieldExists (RES *res)
int	tsvRead (char *filename, DFT *dft)
int	xelRead (char *filename, DFT *dft)

Variables
char	cpterrmsg [128]
int	CSV_TEST
char	dfterrmsg [64]
int	DFT_NR_OF_DECIMALS
int	MATHFUNC_TEST
char	fiterrmsg [64]
int	RESULT_TEST
char	reserrmsg [64]

Detailed Description

Header file for libtpccurveio.

Author

Vesa Oikonen

Definition in file libtpccurveio.h.

Macro Definition Documentation

BACKUP_EXTENSION

#define BACKUP_EXTENSION   ".bak"

Backup file extension

Definition at line 27 of file libtpccurveio.h.

Referenced by dftWriteHTML(), ecat63Create(), ecat7Create(), idwcWrite(), ifWrite(), resWriteHTML(), and roikbqWrite().

DFT_DECAY_CORRECTED

#define DFT_DECAY_CORRECTED   1

Definition for Decay correction status in DFT structure.

Definition at line 443 of file libtpccurveio.h.

Referenced by dft_fill_hdr_from_IFT(), dftDecayCorrection(), dftPrint(), dftSetComments(), and noiseSD4SimulationFromDFT().

DFT_DECAY_NOTCORRECTED

#define DFT_DECAY_NOTCORRECTED   2

Definition for Decay correction status in DFT structure.

Definition at line 445 of file libtpccurveio.h.

Referenced by dft_fill_hdr_from_IFT(), dftDecayCorrection(), dftPrint(), and dftSetComments().

DFT_DECAY_UNKNOWN

#define DFT_DECAY_UNKNOWN   0

Definition for Decay correction status in DFT structure.

Definition at line 441 of file libtpccurveio.h.

Referenced by dftCopymainhdr2(), dftSetComments(), and noiseSD4SimulationFromDFT().

DFT_FORMAT_CPT

#define DFT_FORMAT_CPT   8

TAC file format (DFT type)

Definition at line 419 of file libtpccurveio.h.

DFT_FORMAT_CSV_INT

#define DFT_FORMAT_CSV_INT   6

TAC file format (DFT type)

Definition at line 415 of file libtpccurveio.h.

Referenced by dftFormat(), and dftRead().

DFT_FORMAT_CSV_UK

#define DFT_FORMAT_CSV_UK   7

TAC file format (DFT type)

Definition at line 417 of file libtpccurveio.h.

Referenced by dftFormat(), and dftRead().

DFT_FORMAT_FIT

#define DFT_FORMAT_FIT   3

TAC file format (DFT type)

Definition at line 409 of file libtpccurveio.h.

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

DFT_FORMAT_HTML

#define DFT_FORMAT_HTML   12

TAC file format (DFT type)

Definition at line 427 of file libtpccurveio.h.

Referenced by dftWrite().

DFT_FORMAT_IDWC

#define DFT_FORMAT_IDWC   9

TAC file format (DFT type)

Definition at line 421 of file libtpccurveio.h.

Referenced by dftFormat(), and dftRead().

DFT_FORMAT_IF

#define DFT_FORMAT_IF   10

TAC file format (DFT type)

Definition at line 423 of file libtpccurveio.h.

Referenced by dftFormat(), and dftRead().

DFT_FORMAT_IFT

#define DFT_FORMAT_IFT   2

TAC file format (DFT type)

Definition at line 407 of file libtpccurveio.h.

Referenced by dftRead().

DFT_FORMAT_NCI

#define DFT_FORMAT_NCI   4

TAC file format (DFT type)

Definition at line 411 of file libtpccurveio.h.

Referenced by dftFormat(), and dftRead().

DFT_FORMAT_PLAIN

#define DFT_FORMAT_PLAIN   0

TAC file format (DFT type)

Definition at line 403 of file libtpccurveio.h.

Referenced by csv2dft(), dftAdd(), dftFormat(), dftRead(), dftWrite(), and dftWriteHTML().

DFT_FORMAT_PMOD

#define DFT_FORMAT_PMOD   5

TAC file format (DFT type)

Definition at line 413 of file libtpccurveio.h.

Referenced by dftFormat(), dftRead(), dftSetComments(), and dftWrite().

DFT_FORMAT_STANDARD

#define DFT_FORMAT_STANDARD   1

TAC file format (DFT type)

Definition at line 405 of file libtpccurveio.h.

Referenced by bf_srtm(), csv2dft_a(), csv2dft_b(), csv2dft_linkset(), csv2dft_mat(), dftAllocateWithIMG(), dftFormat(), dftRead(), dftSetComments(), dftTimeIntegral(), dftWrite(), and sif2dft().

DFT_FORMAT_UNKNOWN

#define DFT_FORMAT_UNKNOWN   -1

TAC file format (DFT type)

Definition at line 401 of file libtpccurveio.h.

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

DFT_FORMAT_XELERIS

#define DFT_FORMAT_XELERIS   13

TAC file format (DFT type)

Definition at line 429 of file libtpccurveio.h.

DFT_FORMAT_XML

#define DFT_FORMAT_XML   11

TAC file format (DFT type)

Definition at line 425 of file libtpccurveio.h.

DFT_TIME_END

#define DFT_TIME_END   2

Definition for DFT (frame) time type

Definition at line 436 of file libtpccurveio.h.

Referenced by check_times_dft_vs_dft(), check_times_dft_vs_img(), dftEndtime(), dftFrametimes(), dftRead(), and dftWrite().

DFT_TIME_MIDDLE

#define DFT_TIME_MIDDLE   0

Definition for DFT (frame) time type

Definition at line 432 of file libtpccurveio.h.

Referenced by check_times_dft_vs_dft(), check_times_dft_vs_img(), csv2dft_a(), csv2dft_linkset(), dftAutointerpolate(), dftDerivative(), dftEndtime(), dftFrametimes(), dftGetPmodTitle(), dftRead(), dftTimeIntegral(), dftWeightByFreq(), dftWrite(), and extrapolate_monoexp().

DFT_TIME_START

#define DFT_TIME_START   1

Definition for DFT (frame) time type

Definition at line 434 of file libtpccurveio.h.

Referenced by check_times_dft_vs_dft(), check_times_dft_vs_img(), dftEndtime(), dftFrametimes(), dftRead(), and dftWrite().

DFT_TIME_STARTEND

#define DFT_TIME_STARTEND   3

Definition for DFT (frame) time type

Definition at line 438 of file libtpccurveio.h.

Referenced by bfIrr2TCM(), bfRadiowater(), check_times_dft_vs_dft(), check_times_dft_vs_img(), clusterTACs(), copy_times_from_img_to_dft(), csv2dft_a(), csv2dft_b(), csv2dft_mat(), dft_nr_of_NA(), dftAllocateWithIMG(), dftAutointerpolate(), dftDecayCorrection(), dftDeleteFrameOverlap(), dftDeleteFrameOverlap_old(), dftDerivative(), dftDivideFrames(), dftDoubleFrames(), dftEndtime(), dftFillInitialGap(), dftFixPeak(), dftFrametimes(), dftGetPmodTitle(), dftInterpolate(), dftInterpolateCheckEnd(), dftInterpolateCheckStart(), dftInterpolateForIMG(), dftInterpolateInto(), dftMaxY(), dftMinMax(), dftMinMaxTAC(), dftRead(), dftReadinput(), dftReadModelingData(), dftReadReference(), dftRobustMinMaxTAC(), dftTimeIntegral(), dftValidNr(), dftVerifyPeak(), dftWeightByFreq(), dftWrite(), fit_allocate_with_dft(), fittime_from_dft(), res_allocate_with_dft(), sif2dft(), and simMyocDiameterCurve().

MAX_FITPARAMS

#define MAX_FITPARAMS   100

Max nr of parameters in FIT

Definition at line 239 of file libtpccurveio.h.

MAX_RESPARAMS

#define MAX_RESPARAMS   100

Max nr of parameters

Definition at line 133 of file libtpccurveio.h.

Referenced by dftToResult(), rescoll_tabulate(), resEmpty(), resFixParnames(), resRead(), resSetmem(), resWrite(), and resWriteHTML_table().

MAX_RESPARNAME_LEN

#define MAX_RESPARNAME_LEN   15

Max length of parameter names and units

Definition at line 137 of file libtpccurveio.h.

Referenced by resFixParnames(), and resRead().

Enumeration Type Documentation

anonymous enum

anonymous enum

CSV structure status.

Definition at line 348 of file libtpccurveio.h.

     {CSV_OK, CSV_ERROR, CSV_CANNOTOPEN, CSV_INVALIDFORMAT, CSV_TOOBIG,
    CSV_OUTOFMEMORY, CSV_NOTABLE
    };

mathfuncs

enum mathfuncs

FIT functions

Definition at line 243 of file libtpccurveio.h.

               {
  MF_LEVEL=100, MF_LINE, MF_POL2, MF_POL3, MF_POL4, MF_POL5, MF_POL6, MF_POL7,
  MF_POL8, MF_POL9,
  MF_RATF11=211, MF_RATF21=221, MF_RATF22=222, MF_RATF32=232, MF_RATF33=233,
  MF_EXP1=301, MF_EXP2, MF_EXP3, MF_EXP4, MF_EXP5,
  MF_LUNDQVIST=321, MF_LUNDQVIST2, MF_LUNDQVIST3,
  MF_EXPBOLUSINF=331, MF_EXPBOLUSINF_RW=332, MF_MF_EXPBOLUSINF_AZ=334,
  MF_PK11195=351,
  MF_PPFIGAM=403,
  MF_PF_MU=831,
  MF_HILL=841, MF_1MHILL=842, MF_1MHILL_ADE=843, MF_HILL_B=844, MF_AMHILL=845,
  MF_EHILL_PAR=846, MF_EHILL_MET=847,
  MF_EHILL2_PAR=848, MF_EHILL2_MET=849,
  MF_MAMEDE=851, MF_1MMAMEDE,
  MF_MAYER_PAR=861, MF_MAYER_MET, MF_EMAYER_PAR=863, MF_EMAYER_MET,
  MF_HILL3M_PAR=871, MF_HILL3M_M1, MF_HILL3M_M2, MF_HILL3M_M3, 
  MF_PF3M_PAR=881, MF_PF3M_M1, MF_PF3M_M2, MF_PF3M_M3, 
  MF_STEP=1010,
  MF_RATF33D=1232,
  MF_FENGM2S=1312, MF_FENGM2=1313, MF_FENGM2E=1314,
  MF_GAMMAV=1401, MF_GAMMAVB=1402, MF_GAMMAVR=1403,
  MF_WEIBULLCDF_D=1421, MF_WEIBULLCDF_DD=1423,
  MF_SURGE=1431, MF_SURGE_TRAD=1432, MF_SURGE_RECIRC=1433, MF_P2B_SRC=1434, MF_SURGE_FDG=1435,
  MF_ERLANGPDF=1441,
  MF_HILL_D=1801, MF_HILL_DD=1811, MF_HILL_SDD=1821,
  MF_IMGPROFILE=2111,
  MF_P2B_RF=2233, MF_P2B_FM2=2313, MF_P2B_HILL=2841,
  MF_GRAHAM_INP=9501, MF_GRAHAM_EINP, MF_GRAHAM_INPM,
  MF_HUANG_MET=9601, MF_CARSON_EMET, MF_NEW_MET,
  MF_MLMCM=9701,
};

Function Documentation

cptReadOne()

int cptReadOne ( char * cptfile, DFT * dft, int verbose )

extern

Read TACs from CPT file into a DFT.

Returns

Returns 0 if successful, sets cpterrmsg in case of an error.

See also

cptWrite, dftInit, cptrnameSplit

Parameters

cptfile	CPT filename
dft	Pointer to DFT where TACs are read; must be empty and initialized
verbose	Verbose level; if zero, then only warnings are printed into stderr

Definition at line 59 of file cpt.c.

  {
  int fi, fj, ri, ii, li, rn, fn, n, ret, colNr=10, lineNr=0;
  char *cptr, tmp[512];
  IFT ift;
  int title_line, roi_col, roi_nr=0, frame_nr=0;
 
  if(verbose>0) printf("%s('%s', *dft)\n", __func__, cptfile);
 
  /* Check input */
  if(cptfile==NULL || strlen(cptfile)<1 || dft==NULL) {
    strcpy(cpterrmsg, "program error"); return(1);
  }
  dftEmpty(dft);
 
  /*
   *  Read CPT file as IFT
   */
  iftInit(&ift);
  ret=iftRead(&ift, cptfile, 0, verbose-1);
  if(ret) {
    strcpy(cpterrmsg, ift.status);
    iftEmpty(&ift); return(4);
  }
  if(verbose>0) iftWrite(&ift, "stdout", 0);
  
  /*
   *  Find the line of data titles
   */
  title_line=iftFindNthValue(&ift, " ROI Avg ", 1, 0);
  if(title_line<0) {
    sprintf(cpterrmsg, "unsupported filetype");
    iftEmpty(&ift); return(6);
  }
  /* From title line, check if data consists of 10 or 11 columns */
  strcpy(tmp, ift.item[title_line].value);
  cptr=strtok(tmp, " \t\n\r");
  if(strcasecmp(cptr, "Frame")!=0) {
    sprintf(cpterrmsg, "unsupported filetype");
    iftEmpty(&ift); return(7);
  }
  cptr=strtok(NULL, " \t\n\r");
  colNr=10; if(strcasecmp(cptr, "ROI")!=0) colNr++;
  if(colNr==10) roi_col=1; else roi_col=2;
  if(verbose>1) printf("title_line=%d colNr=%d\n", title_line, colNr);
 
  /*
   *  Mark data lines with sw=1
   */
  for(ii=lineNr=0; ii<ift.keyNr; ii++) {
    /* Data can not start before title line and the unit line below it */
    if(ii<title_line+2) {ift.item[ii].sw=0; continue;}
    /* Comment lines cannot contain data, or at least we don't read it */
    if(ift.item[ii].type!=' ' && ift.item[ii].type!='\0') {
      ift.item[ii].sw=0; continue;}
    /* and there cannot be any key */
    if(ift.item[ii].key!=NULL && strlen(ift.item[ii].key)>0) {
      ift.item[ii].sw=0; continue;}
    /* Check that column number matches */
    n=0; strncpy(tmp, ift.item[ii].value, 511); tmp[511]=(char)0;
    cptr=strtok(tmp, " \t\n\r");
    while(cptr!=NULL) {n++; cptr=strtok(NULL, " \t\n\r");}
    if(n!=colNr) {ift.item[ii].sw=0; continue;}
    ift.item[ii].sw=1; lineNr++;
  }
  if(lineNr<1)  {
    sprintf(cpterrmsg, "unsupported filetype");
    iftEmpty(&ift); return(8);
  }
  if(verbose>1) printf("lineNr=%d\n", lineNr);
 
  /*
   *  Read the data into a new, local table
   */
  double tactable[colNr][lineNr];
  for(ii=0, n=0; ii<ift.keyNr; ii++) if(ift.item[ii].sw==1) {
    ret=sscanf(ift.item[ii].value, "%lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf",
      &tactable[0][n], &tactable[1][n], &tactable[2][n], &tactable[3][n],
      &tactable[4][n], &tactable[5][n], &tactable[6][n], &tactable[7][n],
      &tactable[8][n], &tactable[9][n], &tactable[10][n] );
    n++; /*printf("ret=%d\n", ret);*/
  }
  if(verbose>2) { /* print the table */
    printf("\n");
    for(fi=0; fi<lineNr; fi++) {
      for(ri=0; ri<colNr; ri++) printf(" %g", tactable[ri][fi]); 
      printf("\n");
    }
    printf("\n");
  }
 
  /*
   *  Compute the number of ROIs and Frames from the data lines
   */
  for(fi=1, roi_nr=frame_nr=1; fi<lineNr; fi++) {
    /* have these been seen before? */
    for(fj=0, fn=rn=0; fj<fi; fj++) {
      if(tactable[roi_col][fj]==tactable[roi_col][fi]) rn++;
      if(tactable[0][fj]==tactable[0][fi]) fn++;
    }
    if(rn==0) roi_nr++;
    if(fn==0) frame_nr++;
  }
  if(verbose>1) printf("roi_nr=%d frame_nr=%d\n", roi_nr, frame_nr);
  /* Also, test that the highest frame number equals number of frames */
  for(fi=0, n=0; fi<lineNr; fi++) if(tactable[0][fi]>n) n=tactable[0][fi];
  if(n!=frame_nr) {
    sprintf(cpterrmsg, "frames are not consequential");
    iftEmpty(&ift); return(9);
  }
  /* And also, test that roi_nr*frame_nr == nr of data lines */
  if(roi_nr*frame_nr!=lineNr) {
    sprintf(cpterrmsg, "missing or extra samples");
    iftEmpty(&ift); return(10);
  }
 
  /*
   *  Copy data into DFT
   */
 
  /* Allocate memory for DFT */
  ret=dftSetmem(dft, frame_nr, roi_nr);
  if(ret) {
    sprintf(cpterrmsg, "cannot allocate memory");
    iftEmpty(&ift); dftEmpty(dft); return(11);
  }
  dft->frameNr=frame_nr; dft->voiNr=roi_nr; dft->_type=1;
 
  /* Make a list of ROI ID numbers */
  int roi_id[roi_nr];
  n=0; roi_id[n++]=tactable[roi_col][0];
  for(fi=1; fi<lineNr; fi++) {
    for(fj=0; fj<fi; fj++)
      if(tactable[roi_col][fj]==tactable[roi_col][fi]) continue;
    roi_id[n++]=(int)(0.5+tactable[roi_col][fi]);
  }
  if(verbose>2) {
    printf("List of ROI ID numbers:\n");
    for(ri=0; ri<roi_nr; ri++) printf("   %d : %d\n", ri+1, roi_id[ri]);
  }
 
  /* Extract data for one ROI at a time */
  for(int ri=0; ri<roi_nr; ri++) {
    fi=0; /* all frames of this ROI */
    for(li=0; li<lineNr; li++) if(roi_id[ri]==(int)(0.5+tactable[roi_col][li])) {
      /* Activity average value */
      dft->voi[ri].y[fi]=tactable[colNr-8][li];
      /* Only once for each ROI */
      if(fi==0) {
        /* ROI volume */
        dft->voi[ri].size=tactable[colNr-1][li];
        /* ROI name (may be changed later) */
        sprintf(dft->voi[ri].voiname, "ROI%03d", roi_id[ri]);
        if(colNr>10) sprintf(dft->voi[ri].place, "Pl%04.0f", tactable[1][ri]);
        snprintf(dft->voi[ri].name, MAX_REGIONNAME_LEN, "%s . %s",
                 dft->voi[ri].voiname, dft->voi[ri].place);
      }
      /* Get frame times from the first ROI */
      if(ri==0) {
        dft->x1[fi]=tactable[colNr-4][li];
        dft->x2[fi]=dft->x1[fi]+tactable[colNr-3][li];
        dft->x[fi]=0.5*(dft->x1[fi]+dft->x2[fi]);
      }
      fi++;
    } /* next frame */
  } /* next ROI */
  /* Convert frame times into minutes */
  dftSec2min(dft); dft->timetype=3;
 
  /*
   *  Get studynumber from filename
   */
  studynr_from_fname(cptfile, dft->studynr);
 
  /*
   *  Try to find the data unit
   */
  ii=iftFindNthValue(&ift, "In units of ", 1, 0);
  if(ii>=0) {
    strncpy(tmp, ift.item[ii].value+12, 511); tmp[511]=(char)0;
    cptr=strtok(tmp, " \t\n\r,;");
    strncpy(dft->unit, cptr, MAX_UNITS_LEN);
    dft->unit[MAX_UNITS_LEN]=(char)0;
  } else {
    strcpy(tmp, "Units"); ii=iftGet(&ift, tmp, 0);
    if(ii>=0) {
      strncpy(dft->unit, ift.item[ii].value, MAX_UNITS_LEN);
      dft->unit[MAX_UNITS_LEN]=(char)0;
    }   
  }
 
  /*
   *  Try to extract the region name (if only one ROI)
   */
  if(dft->voiNr==1) {
    ii=iftFindNthKey(&ift, "Using ROI ", 1, 0);
    if(ii>=0) {
      cptr=strchr(ift.item[ii].key, '\"');
      if(cptr!=NULL) {
        strncpy(dft->voi[0].name, cptr+1, MAX_REGIONNAME_LEN);
        dft->voi[0].name[MAX_REGIONNAME_LEN]=(char)0;
        cptr=strchr(dft->voi[0].name, '\"');
        if(cptr!=NULL) *cptr=(char)0;
      }
    }
    cptrnameSplit(dft->voi[0].name,
      dft->voi[0].voiname, dft->voi[0].hemisphere, dft->voi[0].place,
      MAX_REGIONSUBNAME_LEN);
  }
 
  /*
   *  Try to find the plane number
   */
  ii=iftFindNthKey(&ift, "Plane ", 1, 0);
  if(ii>=0) {
    n=atoi(ift.item[ii].key+6);
    if(verbose>2) printf("Plane %d\n", n);
    if(n>0) for(ri=0; ri<dft->voiNr; ri++) snprintf(dft->voi[ri].place, 7, "Pl%04d", n);
  } else {
    ii=iftFindNthValue(&ift, "Plane ", 1, 0);
    if(ii>=0) {
      n=atoi(ift.item[ii].value+6);
      if(verbose>2) printf("Plane %d\n", n);
      if(n>0) for(ri=0; ri<dft->voiNr; ri++) snprintf(dft->voi[ri].place, 7, "Pl%04d", n);
    }
  }
 
  /* Set weights in DFT to 1.0 */
  dft->isweight=0;
  for(fi=0; fi<dft->frameNr; fi++) dft->w[fi]=1.0;
 
 
  iftEmpty(&ift);
  return(0);
}

cptrnameSplit()

int cptrnameSplit ( char * rname, char * name1, char * name2, char * name3, int max_name_len )

extern

Split region name into 1-3 subparts of given max length.

Returns

Returns the number of subparts.

See also

cptReadOne

Parameters

rname	Region name to split (string is not edited)
name1	Pointer to 1st subname (anatomical region)
name2	Pointer to 2nd subname (usually hemisphere)
name3	Pointer to 3rd subname (usually image plane)
max_name_len	Max lenght of subnames, excluding terminal null

Definition at line 24 of file cpt.c.

  {
  char temp[MAX_REGIONNAME_LEN+1], *cptr, *cptr2;
  int nr=0;
 
  if(rname==NULL || name1==NULL || name2==NULL || name3==NULL) return(0);
  if(max_name_len<1) return(0);
  name1[0]=name2[0]=name3[0]=(char)0;
  strncpy(temp, rname, MAX_REGIONNAME_LEN); temp[MAX_REGIONNAME_LEN]=(char)0;
  cptr=strtok(temp, " _\t\n\r"); if(cptr==NULL) return(nr);
  cptr2=strstr(cptr, "dx"); if(cptr2==NULL) cptr2=strstr(cptr, "sin");
  if(cptr2!=NULL) {strcpy(name2, cptr2); *cptr2=(char)0; nr++;}
  else strcpy(name2, ".");
  strncpy(name1, cptr, max_name_len); name1[max_name_len]=(char)0; nr++;
  cptr=strtok(NULL, " _\t\n\r"); if(cptr==NULL) return(nr);
  strncpy(name3, cptr, max_name_len); name3[max_name_len]=(char)0; nr++;
  return(nr);
}

Referenced by cptReadOne().

cptWrite()

int cptWrite ( DFT * dft, char * filename, int cpt_format )

extern

Write TAC data in CPT (Imagetool) format. If TACs are from different planes, then each plane will be saved in its own file.

Returns

Returns 0 if successful; in case of an error, sets string cpterrmsg.

See also

cptReadOne, dftInit

Parameters

dft	TAC data to write
filename	CPT path and file name without extension, because this function may need to add plane number before .cpt
cpt_format	Specific CPT format: 0=default, others not yet supported

Definition at line 308 of file cpt.c.

  {
  int ri, fi, ret, n, roi_id;
  FILE *fp;
  char cptfile[FILENAME_MAX], tmp[256];
 
  /* Check input */
  if(dft==NULL || dft->voiNr<1 || dft->frameNr<1 || strlen(filename)<1) {
    strcpy(cpterrmsg, "program error"); return(1);
  }
  if(cpt_format!=0) strcpy(cpterrmsg, "cpt format not supported yet");
  /* Sort data by plane */
  ret=dftSortPlane(dft);
  if(ret) {
    strcpy(cpterrmsg, "error in data file"); return(2);
  }
  /* Convert times to seconds if necessary */
  if(dft->timeunit==TUNIT_MIN) dftMin2sec(dft);
 
  
  for(ri=0; ri<dft->voiNr; ri++) {
    /* Construct CPT filename */
    strcpy(cptfile, filename);
    if(strlen(dft->voi[ri].place)>0 && strcmp(dft->voi[ri].place, ".")!=0) {
      snprintf(cptfile, FILENAME_MAX, "%s_%s.cpt", filename, dft->voi[ri].place);
    } else {
      snprintf(cptfile, FILENAME_MAX, "%s.cpt", filename);
    }
    /* Open file */
    fp=fopen(cptfile, "w");
    if(fp==NULL) {
      sprintf(cpterrmsg, "cannot open file for write"); return(5);
    }
    /* Write 1st title */
    if(strlen(dft->unit)==0) strcpy(tmp, "unknown"); else strcpy(tmp, dft->unit);
    //fprintf(fp, "# In units of %s per pixel per second\n", tmp);
    fprintf(fp, "# In units of %s\n", tmp);
    /* Write 2nd title */
    if(strncasecmp(dft->voi[ri].place, "Pl", 2)==0)
      sprintf(tmp, "%d", atoi(dft->voi[ri].place+2));
    else if(strlen(dft->voi[ri].place)==0 || strcmp(dft->voi[ri].place, ".")==0)
      strcpy(tmp, "1");
    else
      strcpy(tmp, dft->voi[ri].place);
    fprintf(fp, "Plane %-6.6s Scan Start Date (d m y): 1 1 1980     Scan Start Time (h m s): 0 0 0\n\n", tmp);
    /* Write 3rd title */
    fprintf(fp, "Frame  ROI ID        ROI Avg    #pixels    ROI Total   %%Stdev    Offset   Duration   ROI Surf.     ROI Vol.\n");
    fprintf(fp, "                                (screen)                          (sec)     (sec)     mmxmm       mmxmmxmm\n");
    /* Write all frames */
    for(fi=0, n=ri; fi<dft->frameNr; fi++) {
      n=ri;
      /* current region */
      strcpy(tmp, dft->voi[ri].voiname);
      if(strlen(dft->voi[ri].hemisphere)>0 && strcmp(dft->voi[ri].hemisphere, ".")!=0) {
        strcat(tmp, " "); strcat(tmp, dft->voi[ri].hemisphere);}
      strcpy(tmp, "");
      if(strncasecmp(dft->voi[ri].voiname, "ROI", 3)==0 && atoi(dft->voi[ri].voiname+3)>0)
        roi_id=atoi(dft->voi[ri].voiname+3); else roi_id=1;
      fprintf(fp, "%-6d %-3d %-8.8s %11.4e %5d     %10.4e %7.1f  %9.1f %9.1f    %10.4e    %10.4e\n", 
        fi+1, roi_id, tmp, dft->voi[ri].y[fi], 0, 0.0, 0.0,
        dft->x1[fi], dft->x2[fi]-dft->x1[fi], 0.0, dft->voi[ri].size );
      /* the rest of regions on the same plane */
      while(n<dft->voiNr-1 && strcasecmp(dft->voi[ri].place, dft->voi[n+1].place)==0) {
        n++; strcpy(tmp, dft->voi[n].voiname);
        if(strlen(dft->voi[n].hemisphere)>0 && strcmp(dft->voi[n].hemisphere, ".")!=0) {
          strcat(tmp, " "); strcat(tmp, dft->voi[n].hemisphere);}
        strcpy(tmp, "");
        if(strncasecmp(dft->voi[n].voiname, "ROI", 3)==0 && atoi(dft->voi[n].voiname+3)>0)
          roi_id=atoi(dft->voi[n].voiname+3); else roi_id=n-ri+1;
        fprintf(fp, "%-6d %-3d %-8.8s %11.4e %5d     %10.4e %7.1f  %9.1f %9.1f    %10.4e    %10.4e\n", 
          fi+1, roi_id, tmp, dft->voi[n].y[fi], 0, 0.0, 0.0,
          dft->x1[fi], dft->x2[fi]-dft->x1[fi], 0.0, dft->voi[n].size );
      }
    }
    ri=n;
#if(0)
    /* DON'T DO THIS; at least "asetaatti" program does not work with this */
    /* In the end, write the number of frames */
    fprintf(fp, "\n# %d Frame(s) analyzed.\n", dft->frameNr);
#endif
    fclose(fp);
  }
 
  return(0);
}

csv2dft()

int csv2dft ( CSV * csv, DFT * dft )

extern

Reads different CSV formats into DFT struct

Returns

Returns 0 when successful, otherwise an error code.

Parameters

csv	Pointer to CSV data to be converted
dft	Pointer to empty DFT struct which will be allocated and filled here

Definition at line 200 of file csv.c.

  {
  int ret, i, u, n, m;
 
  if(CSV_TEST>2) {printf("csv2dft()\n"); fflush(stdout);}
  if(csv==NULL || dft==NULL) return CSV_ERROR;
  if(csv->row_nr<1 || csv->col_nr<1) return CSV_INVALIDFORMAT;
 
  /* Is this LinkSet format? */
  if(strcasecmp(csv->c[0].content, "LinkSet")==0) {
    ret=csv2dft_linkset(csv, dft);
    if(ret!=CSV_OK) {
      if(CSV_TEST>2) printf("reading LinkSet CSV format failed.\n");
    }
    return(ret);
  }
 
  /* Maybe mat file? */
  ret=csv2dft_mat(csv, dft);
  if(ret==CSV_OK) {
    if(CSV_TEST>2) printf("reading Mat CSV format successful.\n");
    return(ret);
  }
 
  /* Many CSV formats are impossible to identify, therefore we will just
     try to convert different formats until one succeeds or all are failed */
  if(CSV_TEST>2) printf("trying to read 1st CSV format\n");
  ret=csv2dft_a(csv, dft);
  if(ret!=CSV_OK) {
    if(CSV_TEST>2) printf("reading 1st CSV format failed; trying 2nd format\n");
    ret=csv2dft_b(csv, dft);
  }
  if(ret!=CSV_OK) {
    if(CSV_TEST>2) printf("2nd CSV format failed\n");
  }
  if(ret!=CSV_OK) {dft->_type=DFT_FORMAT_PLAIN; return ret;}
  /* Make sure that TAC names are filled */
  u=dft->voiNr; n=1; while((u/=10)>=1) n++;
  if(n>MAX_REGIONSUBNAME_LEN) n=MAX_REGIONSUBNAME_LEN;
  for(i=0, m=0; i<dft->voiNr; i++) {
    if(strlen(dft->voi[i].voiname)<1 || strcmp(dft->voi[i].voiname, ".")==0) {
      snprintf(dft->voi[i].voiname, 7, "%0*d", n, i+1);
      strcpy(dft->voi[i].name, dft->voi[i].voiname);
      m++;
    }
  }
  /* If none of TACs had a name, then set DFT plain format */
  if(m==dft->voiNr) dft->_type=DFT_FORMAT_PLAIN;
 
  if(CSV_TEST>3) dftPrint(dft);
  return CSV_OK;
}

Referenced by dftRead().

csv2dft_a()

int csv2dft_a ( CSV * csv, DFT * dft )

extern

Reads simple and Inveon type 1 data into DFT struct

Returns

Returns 0 when successful, otherwise an error code.

Parameters

csv	Pointer to CSV data to be converted
dft	Pointer to empty DFT struct which will be allocated and filled here

Definition at line 262 of file csv.c.

  {
  int ri, ci, sci, ii, ret;
  char *cptr;
 
  if(CSV_TEST>2) {printf("csv2dft_a()\n"); fflush(stdout);}
  if(csv==NULL || dft==NULL) return CSV_ERROR;
  if(csv->row_nr<1 || csv->col_nr<1) return CSV_INVALIDFORMAT;
 
 
  if(CSV_TEST>2)
    for(int i=0; i<csv->nr; i++)
      printf("row=%d col=%d content='%s'\n", csv->c[i].row, csv->c[i].col, csv->c[i].content);
 
 
  /* Allocate memory for DFT */
  dftEmpty(dft);
  if(CSV_TEST>2) {
    printf("frame_nr=%d voi_nr=%d\n", csv->row_nr, csv->col_nr-1); 
    fflush(stdout);
  }
  ret=dftSetmem(dft, csv->row_nr, csv->col_nr-1);
  if(ret!=0) return CSV_OUTOFMEMORY;
  /* Set DFT defaults */
  dft->timetype=DFT_TIME_MIDDLE;
  dft->_type=DFT_FORMAT_STANDARD;
  dft->isweight=0;
  dftUnitToDFT(dft, CUNIT_UNKNOWN);
  dft->timeunit=TUNIT_UNKNOWN;
  for(ri=0; ri<csv->row_nr; ri++) dft->w[ri]=1.0;
  for(ci=0; ci<csv->col_nr-1; ci++) dft->voi[ci].sw=0;
 
  /* Fill DFT */
  ri=0;
  for(ii=0; ii<csv->nr;) {
    // goto start of row
    for(; ii<csv->nr && csv->c[ii].col!=1; ii++) {}
    if(ii==csv->nr) break;
    if(CSV_TEST>10) {
      printf("\nline start at %d\n", ii); 
      printf("  ri=%d\n", ri); 
      fflush(stdout);
    }
    // ignore line with empty first column
    if(csv->c[ii].content==NULL) {
      if(CSV_TEST>11) {printf("  empty first column\n"); fflush(stdout);}
      ii++; continue;
    }
    // ignore comment line
    if(csv->c[ii].content[0]=='#') {
      if(CSV_TEST>11) {printf("  comment line\n"); fflush(stdout);}
      ii++; continue;
    }
    // ignore line that does not start with number
    // unless it contains TAC titles
    if(!isdigit(csv->c[ii].content[0]) && csv->c[ii].content[0]!='-') {
      if(strstr(csv->c[ii].content, "Time")==NULL &&
         strstr(csv->c[ii].content, "TIME")==NULL &&
         strstr(csv->c[ii].content, "time")==NULL)
      {
        if(CSV_TEST>11) {printf("  not a numerical value or title\n"); fflush(stdout);}
        ii++; continue;
      }
      dft->_type=DFT_FORMAT_STANDARD;
      if(strncasecmp(csv->c[ii].content, "Start time", 10)==0 &&
         strncasecmp(csv->c[ii+1].content, "End time", 8)==0) 
      {
        dft->timetype=DFT_TIME_STARTEND;
        if(CSV_TEST>6) printf("timetype := %d\n", dft->timetype);
      }
      if(CSV_TEST>7) {
        printf("first title field := '%s'\n", csv->c[ii].content);
        fflush(stdout);
      }
      if(strstr(csv->c[ii].content, "min")!=NULL) dft->timeunit=TUNIT_MIN;
      else if(strstr(csv->c[ii].content, "sec")!=NULL) dft->timeunit=TUNIT_SEC;
      else dft->timeunit=TUNIT_UNKNOWN;
      ii++;
      
      if(dft->timetype==DFT_TIME_MIDDLE) sci=2; else {sci=3; ii++;}
      for(ci=sci; ci<=csv->col_nr && ii<csv->nr; ci++, ii++) {
        if(CSV_TEST>2) {
          printf("col=%d row=%d\n", csv->c[ii].col, csv->c[ii].row);
          if(CSV_TEST>3) printf("ci=%d ii=%d\n", ci, ii);
          fflush(stdout);
        }
        if(csv->c[ii].col!=ci) {dftEmpty(dft); return CSV_NOTABLE;}
        if(csv->c[ii].content!=NULL) {
          /* Check if this column should be omitted from DFT */
          if(strstr(csv->c[ii].content, " - Time")!=NULL) {
            if(CSV_TEST>2) printf("  ignored time column.\n");
            dft->voi[ci-sci].sw=1; continue;
          }
          if(strstr(csv->c[ii].content, "(upper bound)")!=NULL) {
            if(CSV_TEST>2) printf("  ignored upper bound column.\n");
            dft->voi[ci-sci].sw=2; continue;
          }
          if(strstr(csv->c[ii].content, "(lower bound)")!=NULL) {
            if(CSV_TEST>2) printf("  ignored lower bound column.\n");
            dft->voi[ci-sci].sw=3; continue;
          }
          if(strstr(csv->c[ii].content, "(standard deviation)")!=NULL) {
            if(CSV_TEST>2) printf("  ignored s.d. column.\n");
            dft->voi[ci-sci].sw=4; continue;
          }
          /* Search calibration unit from name */
          if(petCunitId(dft->unit)==CUNIT_UNKNOWN) {
            if(strstr(csv->c[ii].content, "(Bq/ml)")!=NULL)
              dftUnitToDFT(dft, CUNIT_BQ_PER_ML);
            else if(strstr(csv->c[ii].content, "(kBq/ml)")!=NULL)
              dftUnitToDFT(dft, CUNIT_KBQ_PER_ML);
            else if(strstr(csv->c[ii].content, "(MBq/ml)")!=NULL)
              dftUnitToDFT(dft, CUNIT_MBQ_PER_ML);
            else if(strstr(csv->c[ii].content, "(% ID/g)")!=NULL)
              dftUnitToDFT(dft, CUNIT_PIDM);
            else if(strstr(csv->c[ii].content, "Bq/ml")!=NULL)
              dftUnitToDFT(dft, CUNIT_BQ_PER_ML);
            else if(strstr(csv->c[ii].content, "kBq/ml")!=NULL)
              dftUnitToDFT(dft, CUNIT_KBQ_PER_ML);
            else if(strstr(csv->c[ii].content, "MBq/ml")!=NULL)
              dftUnitToDFT(dft, CUNIT_MBQ_PER_ML);
            else if(strstr(csv->c[ii].content, "% ID/g")!=NULL)
              dftUnitToDFT(dft, CUNIT_PIDM);
          }
        }
        if(csv->c[ii].content==NULL) {
          sprintf(dft->voi[ci-sci].name, "%d", ci-sci+1);
          strcpy(dft->voi[ci-sci].voiname, dft->voi[ci-sci].name);
        } else {
          cptr=strstr(csv->c[ii].content, " - "); if(cptr!=NULL) *cptr=(char)0;
          strncpy(dft->voi[ci-sci].name, csv->c[ii].content, MAX_REGIONNAME_LEN);
          dft->voi[ci-sci].name[MAX_REGIONNAME_LEN]=(char)0;
          rnameSplit(csv->c[ii].content, dft->voi[ci-sci].voiname,
                     dft->voi[ci-sci].hemisphere, dft->voi[ci-sci].place, MAX_REGIONSUBNAME_LEN);
        }
        if(CSV_TEST>8) printf("name[%d]=%s\n", ci-sci, dft->voi[ci-sci].name);
      }
    }
    
    // check that allocated DFT frame nr is not exceeded
    if(ri>=csv->row_nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
    // read the sample time
    if(dft->timetype==DFT_TIME_MIDDLE) {
      dft->x[ri]=atof_dpi(csv->c[ii++].content);
      if(CSV_TEST>3) printf("x[%d]=%g\n", ri, dft->x[ri]);
    } else {
      dft->x1[ri]=atof_dpi(csv->c[ii++].content);
      dft->x2[ri]=atof_dpi(csv->c[ii++].content);
      dft->x[ri]=0.5*(dft->x1[ri]+dft->x2[ri]);
      if(CSV_TEST>3) printf("x1[%d]=%g x2[%d]=%g\n", ri, dft->x1[ri], ri, dft->x2[ri]);
    }
    // read the sample values
    if(dft->timetype==DFT_TIME_MIDDLE) sci=2; else sci=3;
    for(ci=sci; ci<=csv->col_nr && ii<csv->nr; ci++, ii++) {
      if(CSV_TEST>2) {
        printf("  col=%d row=%d\n", csv->c[ii].col, csv->c[ii].row);
        if(CSV_TEST>3) printf("  ci=%d ii=%d\n", ci, ii);
        fflush(stdout);
      }
      if(csv->c[ii].col!=ci) {dftEmpty(dft); return CSV_NOTABLE;}
      if(strlen(csv->c[ii].content)==0 || strcmp(csv->c[ii].content, ".")==0)
        dft->voi[ci-sci].y[ri]=nan("");
      else
       dft->voi[ci-sci].y[ri]=atof_dpi(csv->c[ii].content);
      if(CSV_TEST>4)
        printf("  y[%d][%d]=%g\n", ri, ci-sci, dft->voi[ci-sci].y[ri]);
    }
    ri++; //if(ri>csv->row_nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
  }
  if(CSV_TEST>1) printf("  %d frame(s) read from CSV\n", ri);
  if(ri<1) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
  dft->frameNr=ri;
  dft->voiNr=csv->col_nr-1; if(dft->timetype==DFT_TIME_STARTEND) dft->voiNr--;
 
  /* Remove those DFT VOIs which where above set to be deleted (where sw!=0) */
  for(ci=dft->voiNr-1, ret=0; ci>=0; ci--) if(dft->voi[ci].sw!=0) {
    ret=dftDelete(dft, ci); if(ret!=0) break;}
  if(ret!=0) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
  if(dft->voiNr<1) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
 
  /* Calculate frame mid times, or frame start and end times;
     this works only if time units are known */
  dftFrametimes(dft);
 
  return CSV_OK;
}

Referenced by csv2dft().

csv2dft_b()

int csv2dft_b ( CSV * csv, DFT * dft )

extern

Reads Inveon type 2 data into DFT struct

Returns

Returns 0 when successful, otherwise an error code.

Parameters

csv	Pointer to CSV data to be converted
dft	Pointer to empty DFT struct which will be allocated and filled here

Definition at line 458 of file csv.c.

  {
  int ri, fi, fip, ii, ret;
  char *cptr, *cptr2, tmp[256];
  double v1, v2;
 
  if(CSV_TEST>2) {printf("csv2dft_b()\n"); fflush(stdout);}
  if(csv==NULL || dft==NULL) return CSV_ERROR;
  //printf("row_nr=%d col_nr=%d\n", csv->row_nr, csv->col_nr);
  if(csv->row_nr<4 || csv->col_nr!=9) return CSV_INVALIDFORMAT;
  dftEmpty(dft);
 
  /* Check the format; first line (containing titles) */
  if(strcasecmp(csv->c[0].content, "#Subject ID")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[1].content, "Subject Weight")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[2].content, "Subject Sex")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[3].content, "Unique Series ID")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[4].content, "Series Date")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[5].content, "Series Description")!=0) return CSV_INVALIDFORMAT;
 
  /* Check the format; third line (containing titles) */
  if(strcasecmp(csv->c[12].content, "#Name")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[13].content, "Volume (mm^3)")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[14].content, "Mean")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[15].content, "SD")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[16].content, "Min")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[17].content, "Max")!=0) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[18].content, "Frame Index")!=0) return CSV_INVALIDFORMAT;
  if(strncasecmp(csv->c[19].content, "Mid time (sec)", 10)!=0) return CSV_INVALIDFORMAT;
  if(strncasecmp(csv->c[20].content, "Duration (sec)", 10)!=0) return CSV_INVALIDFORMAT;
 
  /* Calculate the number of ROIs and time frames */
  ri=1; fi=0; fip=-1; ii=21; cptr=csv->c[ii].content;
  //printf("cell[%d] := '%s'\n", ii, cptr); fflush(stdout);
  for(; ii<csv->nr; ii+=9) {
    cptr2=csv->c[ii].content;
    //printf("cell[%d] := '%s'\n", ii, cptr2); fflush(stdout);
    if(strcmp(cptr, cptr2)==0) fi++;
    else {
      ri++; cptr=cptr2;
      if(fip<0) fip=fi; else if(fi!=fip) return CSV_INVALIDFORMAT;
      fi=1;
    }
    //printf("ri=%d fi=%d fip=%d\n", ri, fi, fip);
  }
  //printf("ri=%d fi=%d\n", ri, fi);
 
  /* Allocate memory for DFT */
  if(CSV_TEST>2) {printf("frame_nr=%d voi_nr=%d\n", fi, ri); fflush(stdout);}
  ret=dftSetmem(dft, fi, ri);
  if(ret!=0) return CSV_OUTOFMEMORY;
  dft->voiNr=ri; dft->frameNr=fi;
  dft->timetype=DFT_TIME_STARTEND;
  dft->_type=DFT_FORMAT_STANDARD;
  dft->isweight=0;
  dftUnitToDFT(dft, CUNIT_UNKNOWN); dft->timeunit=TUNIT_UNKNOWN;
  for(fi=0; fi<dft->frameNr; fi++) dft->w[fi]=1.0;
 
  /* Fill DFT */
  /* time unit */
  ii=19;
  if(strstr(csv->c[ii].content, "min")!=NULL) dft->timeunit=TUNIT_MIN;
  else if(strstr(csv->c[ii].content, "sec")!=NULL) dft->timeunit=TUNIT_SEC;
  else dft->timeunit=TUNIT_UNKNOWN;
  /* study number */
  ii=6;
  cptr=csv->c[ii].content; strlcpy(dft->studynr, cptr, MAX_STUDYNR_LEN);
  cptr=strchr(dft->studynr, '.'); if(cptr!=NULL) *cptr=(char)0;
  cptr=strchr(dft->studynr, ','); if(cptr!=NULL) *cptr=(char)0;
  cptr=strchr(dft->studynr, ' '); if(cptr!=NULL) *cptr=(char)0;
  /* subject weight */
  ii=7; if(ii>=csv->nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
  v1=atof_dpi(csv->c[ii].content);
  if(v1>0.0) sprintf(dft->comments, "# weight := %g\n", v1);
  /* scan start time */
  ii=10; if(ii>=csv->nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
  if(strlen(csv->c[ii].content)>9) {
    sprintf(tmp, "# scan_start_time := %s\n", csv->c[ii].content);
    strcat(dft->comments, tmp);
  }
  /* frame times */
  for(fi=0; fi<dft->frameNr; fi++) {
    ii= 21 + fi*9 + 7; if(ii>csv->nr-2) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
    //printf("cell[%d] := '%s'\n", ii, csv->c[ii].content); fflush(stdout);
    v1=atof_dpi(csv->c[ii].content); v2=atof_dpi(csv->c[ii+1].content);
    dft->x[fi]=v1; dft->x1[fi]=v1-0.5*v2; dft->x2[fi]=v1+0.5*v2;
  }
  /* region names, volumes, and concentrations */
  for(ri=0; ri<dft->voiNr; ri++) {
    /* ROI name */
    ii= 21 + ri*dft->frameNr*9;
    if(ii>=csv->nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
    //printf("ri=%d cell[%d] := '%s'\n", ri, ii, csv->c[ii].content); fflush(stdout);
    strncpy(dft->voi[ri].name, csv->c[ii].content, MAX_REGIONNAME_LEN);
    dft->voi[ri].name[MAX_REGIONNAME_LEN]=(char)0;
    rnameSplit(csv->c[ii].content, dft->voi[ri].voiname, dft->voi[ri].hemisphere, dft->voi[ri].place,
               MAX_REGIONSUBNAME_LEN);
    /* Volume */
    ii++; if(ii>=csv->nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
    dft->voi[ri].size=atof_dpi(csv->c[ii].content);
    /* Frame concentrations */
    ii++; for(fi=0; fi<dft->frameNr; fi++) {
      if((ii+6)>=csv->nr) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
      /* Get concentration */
      dft->voi[ri].y[fi]=atof_dpi(csv->c[ii].content);
      /* Get concentration SD (probably not needed) */
      dft->voi[ri].y2[fi]=atof_dpi(csv->c[ii+1].content);
      /* check that frame times are correct */
      v1=atof_dpi(csv->c[ii+5].content);
      if(dft->x[fi]!=v1) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
      ii+=9;
    } // next frame
  } // next region
 
  return CSV_OK;
}

Referenced by csv2dft().

csv2dft_linkset()

int csv2dft_linkset ( CSV * csv, DFT * dft )

extern

Reads LinkSet data into DFT struct.

Returns

Returns 0 when successful, otherwise an error code.

Parameters

csv	Pointer to CSV data to be converted
dft	Pointer to empty DFT struct which will be allocated and filled here

Definition at line 584 of file csv.c.

  {
  int ri, ci, fi, sci, ii, ret;
  double v;
  char *cptr;
 
  /* Check input data */
  if(CSV_TEST>2) {printf("csv2dft_linkset()\n"); fflush(stdout);}
  if(csv==NULL || dft==NULL) return CSV_ERROR;
  if(csv->nr<2 || csv->row_nr<1 || csv->col_nr<1) return CSV_INVALIDFORMAT;
  if(strcasecmp(csv->c[0].content, "LinkSet")!=0) return CSV_INVALIDFORMAT;
  /* Get the ROI nr */
  for(ii=1, ri=0; ii<csv->nr; ii++) if(csv->c[ii].col==1) {
    if(csv->c[ii].content==NULL) continue;
    if(strncmp(csv->c[ii].content, "VOI:", 4)==0) ri++; 
  }
  if(CSV_TEST>2) {
    printf("frame_nr=%d voi_nr=%d\n", csv->col_nr-2, ri); 
    fflush(stdout);
  }
  if(ri<1 || csv->col_nr<3) return CSV_INVALIDFORMAT;
  /* Delete previous DFT contents */
  dftEmpty(dft);
  /* Allocate memory for DFT */
  ret=dftSetmem(dft, csv->col_nr-2, ri); if(ret!=0) return CSV_OUTOFMEMORY;
  dft->voiNr=ri;
  dft->frameNr=csv->col_nr-2;
 
  /* Set DFT defaults */
  dft->timetype=DFT_TIME_MIDDLE;
  dft->_type=DFT_FORMAT_STANDARD;
  dft->isweight=0;
  dftUnitToDFT(dft, CUNIT_UNKNOWN);
  dft->timeunit=TUNIT_UNKNOWN;
  for(fi=0; fi<dft->frameNr; fi++) dft->w[fi]=1.0;
  for(ri=0; ri<dft->voiNr; ri++) dft->voi[ri].sw=0;
  
  /* Fill DFT contents */
  for(ri=0; ri<dft->voiNr; ri++) {
    if(CSV_TEST>3) printf("reading VOI %d\n", 1+ri);
    /* Search the (ri+1)th VOI */
    sci=0;
    for(ii=1; ii<csv->nr; ii++) if(csv->c[ii].col==1) {
      if(csv->c[ii].content==NULL) continue;
      if(strncmp(csv->c[ii].content, "VOI:", 4)==0) sci++;
      if(sci==ri+1) break; 
    }
    if(sci!=ri+1) break; // not found
    // ii is not the index of the start of data for one VOI
    if(CSV_TEST>5) printf("  ri=%d ii=%d row=%d col=%d\n", ri, ii, csv->c[ii].row, csv->c[ii].col);
    /* Take the ROI number from there in case better name is not found later */
    strncpy(dft->voi[ri].name, csv->c[ii].content+4, MAX_REGIONNAME_LEN);
    dft->voi[ri].name[MAX_REGIONNAME_LEN]=(char)0;
    /* Read time unit from the next field */
    if(CSV_TEST>4 && ri==0) printf("reading time unit\n");
    cptr=strchr(csv->c[ii+1].content, '(');
    if(cptr!=NULL) {
      ci=petTunitId(cptr+1);
      if(ri==0) {
        dft->timeunit=ci;
      } else if(dft->timeunit!=ci) {
        if(CSV_TEST>0) printf("different time units.\n");
        return CSV_INVALIDFORMAT;
      }
    }
    if(CSV_TEST>4 && ri==0) printf("time unit: %s\n", petTunit(dft->timeunit));
    /* Read the times */
    for(fi=0; fi<dft->frameNr; fi++) {
      ci=ii+fi+2; if(ci>=csv->nr) return CSV_INVALIDFORMAT;
      cptr=csv->c[ci].content;
      if(atof_with_check(cptr, &v)!=0) return CSV_INVALIDFORMAT;
      if(ri==0) {
        dft->x[fi]=v;
      } else {
        if(fabs(v-dft->x[fi])>1.0E-003) return CSV_INVALIDFORMAT;
      }
    } // next frame time
    /* First column on the 2nd row should contain the region name */
    if(CSV_TEST>4) printf("reading VOI name\n");
    ii+=csv->col_nr; if(ii>=csv->nr) return CSV_INVALIDFORMAT;
    cptr=csv->c[ii].content;
    if(cptr!=NULL) {
      strncpy(dft->voi[ri].name, cptr, MAX_REGIONNAME_LEN);
      dft->voi[ri].name[MAX_REGIONNAME_LEN]=(char)0;
    } // default name was set before
    rnameSplit(dft->voi[ri].name, dft->voi[ri].voiname, dft->voi[ri].hemisphere, dft->voi[ri].place,
               MAX_REGIONSUBNAME_LEN);
    /* VOI average values should be two rows below this */
    if(CSV_TEST>4) printf("reading VOI values\n");
    ii+=2*csv->col_nr; if(ii>=csv->nr) return CSV_INVALIDFORMAT;
    /* Check that from 2nd column, and get from there the unit, too */
    ii++; if(ii>=csv->nr) return CSV_INVALIDFORMAT;
    cptr=csv->c[ii].content; if(cptr==NULL) return CSV_INVALIDFORMAT;
    if(strncasecmp(cptr, "Average", 7)!=0) return CSV_INVALIDFORMAT;
    cptr=strchr(csv->c[ii].content, '(');
    if(cptr!=NULL) {
      if(CSV_TEST>4 && ri==0)
        printf("reading activity unit from string: '%s'\n", cptr+1);
      ci=petCunitId(cptr+1);
      if(ri==0) {
        strcpy(dft->unit, petCunit(ci));
      } else if(ci!=petCunitId(dft->unit)) {
        if(CSV_TEST>0) printf("different concentration units.\n");
        return CSV_INVALIDFORMAT;
      }
      if(CSV_TEST>5 && ri==0) printf("unit := %s (%d)\n", petCunit(ci), ci);
    }
    /* then read the concentrations */
    for(fi=0; fi<dft->frameNr; fi++) {
      ci=ii+fi+1; if(ci>=csv->nr) return CSV_INVALIDFORMAT;
      cptr=csv->c[ci].content;
      if(atof_with_check(cptr, &v)!=0) return CSV_INVALIDFORMAT;
      dft->voi[ri].y[fi]=v;
    } // next frame time 
  }
  if(ri<dft->voiNr) return CSV_INVALIDFORMAT;
 
  return CSV_OK;
}

Referenced by csv2dft().

csv2dft_mat()

int csv2dft_mat ( CSV * csv, DFT * dft )

extern

Reads Mat data into DFT struct.

Returns

Returns 0 when successful, otherwise an error code.

Parameters

csv	Pointer to CSV data to be converted
dft	Pointer to empty DFT struct which will be allocated and filled here

Definition at line 713 of file csv.c.

  {
  int ri, fi, ret;
  char *cptr;
 
  /* Check input data */
  if(CSV_TEST>2) {printf("csv2dft_mat()\n"); fflush(stdout);}
  if(csv==NULL || dft==NULL) return CSV_ERROR;
  if(csv->nr<4 || csv->row_nr<2 || csv->col_nr<2) return CSV_INVALIDFORMAT;
  if(!csvIsRegular(csv)) return CSV_INVALIDFORMAT;
 
  /* Delete previous DFT contents */
  dftEmpty(dft);
  /* Allocate memory for DFT */
  ret=dftSetmem(dft, csv->col_nr-1, csv->row_nr-1); if(ret!=0) return CSV_OUTOFMEMORY;
  dft->voiNr=csv->row_nr-1;
  dft->frameNr=csv->col_nr-1;
  if(CSV_TEST>2) {printf("frame_nr=%d voi_nr=%d\n", dft->frameNr, dft->voiNr); fflush(stdout);}
 
  /* Set DFT defaults */
  dft->timetype=DFT_TIME_STARTEND;
  dft->_type=DFT_FORMAT_STANDARD;
  dft->isweight=0;
  dftUnitToDFT(dft, CUNIT_UNKNOWN);
  dft->timeunit=TUNIT_UNKNOWN;
  for(fi=0; fi<dft->frameNr; fi++) dft->w[fi]=1.0;
  for(ri=0; ri<dft->voiNr; ri++) dft->voi[ri].sw=0;
 
  if(CSV_TEST>200)
    for(int i=0; i<csv->nr; i++)
      printf("row=%d col=%d content='%s'\n", csv->c[i].row, csv->c[i].col, csv->c[i].content);
 
  /* First cell may contain study number */
  cptr=csvCell(csv, 1, 1);
  if(cptr!=NULL && cptr[0] && strnlen(cptr, 20)<20) {
    strlcpy(dft->studynr, cptr, MAX_STUDYNR_LEN);
    if(CSV_TEST>3) printf("studynr := %s\n", dft->studynr);
  }
  
  /* Fill DFT contents */
  ret=0;
  for(ri=0; ri<dft->voiNr; ri++) {
    if(CSV_TEST>3) printf("reading VOI %d\n", 1+ri);
    /* Get ROI name */
    cptr=csvCell(csv, ri+2, 1); //printf("cptr='%s'\n", cptr);
    if(cptr==NULL) {ret++; break;}
    int n=strlen(cptr); if(n<3) {ret++; break;}
    if(cptr[n-1]=='\'') {cptr[n-1]=(char)0; n--;} else {ret++; break;}
    if(cptr[0]=='\'') {cptr++; n--;} else {ret++; break;}
    strlcpy(dft->voi[ri].name, cptr, MAX_REGIONNAME_LEN);
    rnameSplit(dft->voi[ri].name, dft->voi[ri].voiname, dft->voi[ri].hemisphere, dft->voi[ri].place,
               MAX_REGIONSUBNAME_LEN);
    /* Get concentrations */
    for(fi=0; fi<dft->frameNr; fi++) {
      cptr=csvCell(csv, ri+2, fi+2); // printf("cptr='%s'\n", cptr);
      ret=atof_with_check(cptr, &dft->voi[ri].y[fi]);
      if(ret) break;
    }
    if(ret!=0) break;
  }
  if(ret!=0) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
 
  /* Get frame times */
  if(CSV_TEST>3) printf("reading frames\n");
  ret=0;
  for(fi=0; fi<dft->frameNr; fi++) {
    cptr=csvCell(csv, 1, fi+2); if(cptr==NULL) {ret++; break;}
    int n=strlen(cptr); if(n<3) {ret++; break;}
    char *cptr2=strchr(cptr+1, '-'); if(cptr2!=NULL) {*cptr2=(char)0; cptr2++;}
    ret=atof_with_check(cptr, &dft->x1[fi]);
    if(ret==0) ret=atof_with_check(cptr2, &dft->x2[fi]);
    if(ret) break;
    dft->x[fi]=0.5*(dft->x1[fi]+dft->x2[fi]);
  }
  if(ret!=0) {dftEmpty(dft); return CSV_INVALIDFORMAT;}
 
  return CSV_OK;
}

Referenced by csv2dft().

csvCell()

char * csvCell ( CSV * csv, int row, int col )

extern

Get the CVS field contents in specified row and column.

Returns

Returns pointer to the content string, or NULL if not found.

Author

Vesa Oikonen

See also

csvRead

Parameters

csv	Pointer to CSV
row	CSV row index
col	CSV column index

Definition at line 827 of file csv.c.

  {
  if(csv==NULL) return((char*)NULL);
  for(int i=0; i<csv->nr; i++) 
    if(csv->c[i].row==row && csv->c[i].col==col)
      return(csv->c[i].content);
  return((char*)NULL); 
}

Referenced by csv2dft_mat().

csvEmpty()

void csvEmpty ( CSV * csv )

extern

Free allocated memory in CSV struct

Parameters

csv	Pointer to CSV struct

Definition at line 24 of file csv.c.

  {
  int i;
  if(csv==NULL) return;
  for(i=0; i<csv->nr; i++)
    if(csv->c[i].content!=NULL) free(csv->c[i].content);
  free(csv->c); csv->c=NULL;
  csv->nr=csv->row_nr=csv->col_nr=0;
  csv->separator=(char)0;
}

Referenced by dftFormat(), and dftRead().

csvInit()

void csvInit ( CSV * csv )

extern

Initiate CSV struct

Parameters

csv	Pointer to CSV struct

Definition at line 13 of file csv.c.

  {
  if(csv==NULL) return;
  csv->c=NULL;
  csv->nr=csv->row_nr=csv->col_nr=0;
  csv->separator=(char)0;
}

Referenced by dftFormat(), and dftRead().

csvIsRegular()

int csvIsRegular ( CSV * csv )

extern

Check whether CSV is regular, that is, each row contain the same number of columns.

Author

Vesa Oikonen

See also

csvRead

Returns

Returns 1 if CSV is regular, 0 if not.

Parameters

csv	Pointer to CSV

Definition at line 803 of file csv.c.

  {
  if(csv==NULL) return(0);
  if(csv->nr<2) return(1);
  int i, r, n=0, m=0;
  i=0; r=csv->c[i].row; m++;
  for(i=1; i<csv->nr; i++) {
    if(r==csv->c[i].row) {m++; continue;}
    if(n>0 && m!=n) return(0);
    r=csv->c[i].row; n=m; m=1;
  }
  if(n>0 && m!=n) return(0);
  return(1);
}

Referenced by csv2dft_mat().

csvRead()

int csvRead ( CSV * csv, char * fname )

extern

Read CSV file.

Returns

Non-zero in case of an error.

Parameters

csv	Pointer to CSV struct
fname	Filename

Definition at line 42 of file csv.c.

  {
  if(CSV_TEST>2) {printf("csvRead('%s')\n", fname); fflush(stdout);}
 
  FILE *fp;
  int i, nr, ret, nonprintable=0, inside_quotes=0, previous, col_nr=0;
  const int MAX_CSV_FIELD_LENGTH=1024;
  char buf[MAX_CSV_FIELD_LENGTH+1];
  int tabnr, spacenr, commanr;
  
  
  if(csv==NULL || fname==NULL) return CSV_ERROR;
  /* Open file */
  fp=fopen(fname, "r"); if(fp==NULL) return CSV_CANNOTOPEN;
 
  /* Check the file size */
  nr=nonprintable=0; while((ret=fgetc(fp))!=EOF) {
    if(iscntrl(ret) && ret!=13 && ret!=10 && ret!=9) {nonprintable=1; break;}
    nr++;
  }
  if(CSV_TEST>0) printf("filesize := %d\n", nr);
  if(nr<2) {fclose(fp); return CSV_INVALIDFORMAT;}
  if(nr>5000000) {fclose(fp); return CSV_TOOBIG;}
  rewind(fp);
 
  /* Determine the field separator (unless set outside) */
  if(csv->separator==(char)0) {
    /* Check if ; or tab or space or comma character is found outside double quotes */
    inside_quotes=0; nr=0; tabnr=0; spacenr=0; commanr=0;
    while((ret=fgetc(fp))!=EOF) {
      if(ret=='"') {
        if(inside_quotes==0) inside_quotes=1; else inside_quotes=0;
        continue;
      }
      if(inside_quotes==1) continue;
      if(ret==';') nr++;
      else if(ret=='\t') tabnr++;
      else if(ret==',') commanr++;
      else if(ret==' ') spacenr++;
    }
    if(CSV_TEST>0) {
      printf("semicolon_nr := %d\n", nr);
      printf("tab_nr := %d\n", tabnr);
      printf("comma_nr := %d\n", commanr);
      printf("space_nr := %d\n", spacenr);
    }
    /* If at least one, then assume that ; is the separator, otherwise , or tab */
    if(nr>0) csv->separator=';';
    else if(tabnr>0) csv->separator='\t'; 
    else if(commanr>spacenr) csv->separator=',';
    else csv->separator=' ';
    rewind(fp);
  }
  if(CSV_TEST>0) printf("separator := '%c'\n", csv->separator);
  /* We will not accept space as separator for CSV */
  if(csv->separator==' ') {fclose(fp); return CSV_INVALIDFORMAT;}
 
 
  /* Determine the number of fields in CSV file */
  inside_quotes=0; nr=0; previous=0;
  while((ret=fgetc(fp))!=EOF) {
    if((previous==13 || previous==10) && (ret==13 || ret==10)) {previous=ret; continue;}
    if(ret=='"') {
      if(inside_quotes==0) inside_quotes=1; else inside_quotes=0;
      previous=ret; continue;
    }
    if(inside_quotes==0) {
      if(ret==csv->separator) {
        nr++; previous=ret;
        continue;
      }
      if( (ret==13 || ret==10) && previous!=13 && previous!=10) {
        nr++; previous=ret;
        continue;
      }
 
      int next=fgetc(fp);
      if(next!=EOF) {
        ungetc(next, fp);
      } else {
        nr++; previous=ret;
        continue;
      }
 
    } //printf("%c", (char)ret);
    previous=ret;
  }
  rewind(fp); if(CSV_TEST>0) printf("field_nr := %d\n", nr);
 
  /* Allocate memory for fields */
  csv->c=(CSV_item*)calloc(nr, sizeof(CSV_item));
  if(csv->c==NULL) {fclose(fp); return CSV_OUTOFMEMORY;}
  csv->nr=nr;
 
  /* Copy field contents from CSV file */
  if(CSV_TEST>0) printf("  copying contents...\n");
  inside_quotes=0; nr=0; previous=0; i=0; col_nr=0;
  while((ret=fgetc(fp))!=EOF) {
    if((previous==13 || previous==10) && (ret==13 || ret==10)) {previous=ret; continue;}
    if(ret=='"') {
      if(inside_quotes==0) inside_quotes=1; else inside_quotes=0;
      previous=ret; continue;
    }
    if(inside_quotes==0) {
      if(ret==csv->separator) {
        buf[i]=(char)0; strCleanSpaces(buf); if(CSV_TEST>10) printf("'%s'\n", buf);
        if(nr>=csv->nr) {printf("  index overflow\n"); break;}
        csv->c[nr].content=strdup(buf);
        csv->c[nr].row=1+csv->row_nr; csv->c[nr].col=1+col_nr;
        i=0; nr++; col_nr++; previous=ret;
        continue;
      }
      if( (ret==13 || ret==10) && previous!=13 && previous!=10) {
        buf[i]=(char)0; strCleanSpaces(buf); if(CSV_TEST>10) printf("'%s'\n", buf); 
        if(nr>=csv->nr) {printf("   index overflow\n"); break;}
        csv->c[nr].content=strdup(buf);
        if(CSV_TEST>10) printf("===\n");
        col_nr++; if(col_nr>csv->col_nr) csv->col_nr=col_nr;
        csv->c[nr].row=1+csv->row_nr; csv->c[nr].col=col_nr;
        i=0; nr++; col_nr=0; previous=ret; csv->row_nr++;
        continue;
      }
 
      int next=fgetc(fp);
      if(next!=EOF) {
        ungetc(next, fp);
      } else {
        buf[i]=(char)0; strCleanSpaces(buf); if(CSV_TEST>10) printf("'%s'\n", buf); 
        if(nr>=csv->nr) {printf("   index overflow\n"); break;}
        csv->c[nr].content=strdup(buf);
        if(CSV_TEST>10) printf("===\n");
        col_nr++; if(col_nr>csv->col_nr) csv->col_nr=col_nr;
        csv->c[nr].row=1+csv->row_nr; csv->c[nr].col=col_nr;
        i=0; nr++; col_nr=0; previous=ret; csv->row_nr++;
        continue;
      }
 
    }
    if(i<MAX_CSV_FIELD_LENGTH) buf[i]=(char)ret;
    i++;
    previous=ret;
  }
  if(CSV_TEST>0) printf("  ... copied: nr=%d\n", nr);
 
 
  fclose(fp);
  return CSV_OK;
}

Referenced by dftFormat(), and dftRead().

dft_fill_hdr_from_IFT()

int dft_fill_hdr_from_IFT ( DFT * dft, IFT * ift )

extern

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().

dft_kBqMax()

double dft_kBqMax ( DFT * data )

extern

Returns the highest activity value in DFT

Parameters

data	Pointer to DFT struct

Definition at line 1148 of file dft.c.

  {
  int i, j;
  double max=-1e+99;
 
  if(data==NULL) return(nan(""));
  for(i=0; i<data->voiNr ;i++){
    for(j=0; j<data->frameNr; j++){
      if(!isnan(data->voi[i].y[j]) && data->voi[i].y[j]>max) max=data->voi[i].y[j];
    }
  }
  return(max);
}

Referenced by dftInterpolateCheckStart().

dft_kBqMin()

double dft_kBqMin ( DFT * data )

extern

Returns the lowest activity value in DFT

Parameters

data	Pointer to DFT struct

Definition at line 1129 of file dft.c.

  {
  int i, j;
  double min=1e+99;
 
  if(data==NULL) return(nan(""));
  for(i=0; i<data->voiNr ;i++) {
    for(j=0; j<data->frameNr; j++) {
      if(!isnan(data->voi[i].y[j]) && data->voi[i].y[j]<min) min=data->voi[i].y[j];
    }
  }
  return(min);
}

dft_nr_of_NA()

int dft_nr_of_NA ( DFT * dft )

extern

Check DFT for NA's in sample times and values.

Returns

Returns the number of NA's that were found.

Parameters

dft	Pointer to DFT struct

Definition at line 905 of file dft.c.

  {
  int ri, fi, na_nr=0;
  if(dft==NULL) return 0;
  for(fi=0; fi<dft->frameNr; fi++) {
    if(dft->timetype==DFT_TIME_STARTEND) {
      if(isnan(dft->x1[fi])) na_nr++;
      if(isnan(dft->x2[fi])) na_nr++;
    } else {
      if(isnan(dft->x[fi])) na_nr++;
    }
    for(ri=0; ri<dft->voiNr; ri++) if(isnan(dft->voi[ri].y[fi])) na_nr++;
  }
  return(na_nr);
}

Referenced by dftInterpolateInto(), dftReadModelingData(), and imgReadModelingData().

dftAdd()

int dftAdd ( DFT * data1, DFT * data2, int voi )

extern

Add the specified voi [0,voiNr-1] from data2 to data1. Allocates memory for additional data VOI, if necessary.

Returns

Returns 0 if ok.

Parameters

data1	Pointer to DFT struct data
data2	Pointer to DFT struct data
voi	Index of TAC in the 2nd DFT

Definition at line 188 of file dft.c.

  {
  int i, n;
 
  if(data1==NULL || data2==NULL) return 1;
  /* Check that voi exists */
  if(data2->voiNr<=voi || voi<0) {
    strcpy(dfterrmsg, "there is no region to combine"); return 8;}
 
  /* Check that frame number etc is the same */
  if(data1->frameNr!=data2->frameNr ||
     (data1->_type!=DFT_FORMAT_PLAIN && data2->_type!=DFT_FORMAT_PLAIN &&
      (data1->timeunit!=data2->timeunit || strcasecmp(data1->unit, data2->unit))
   )) {
    strcpy(dfterrmsg, "data does not match"); return 8;}
 
  /* Allocate more memory if necessary */
  if(data1->_voidataNr==data1->voiNr)
    if(dftAddmem(data1, 1)) {
      strcpy(dfterrmsg, "cannot allocate memory"); return 8;}
 
  /* Copy data */
  n=data1->voiNr;
  (void)dftCopyvoihdr(data2, voi, data1, n);
  for(i=0; i<data1->frameNr; i++) {
    data1->voi[n].y[i]=data2->voi[voi].y[i];
    data1->voi[n].y2[i]=data2->voi[voi].y2[i];
    data1->voi[n].y3[i]=data2->voi[voi].y3[i];
  }
  data1->voiNr+=1;
 
  /* If data2 contains weights and data1 does not, then copy those */
  if(data2->isweight && !data1->isweight)
    for(i=0; i<data1->frameNr; i++) data1->w[i]=data2->w[i];
 
  return 0;
}

dftAddmem()

int dftAddmem ( DFT * dft, int voiNr )

extern

Adds room for additional VOI TAC(s) into DFT data structure.

Old data is left unchanged.

Returns

Returns 0 when successful.

Parameters

dft	Pointer to DFT data structure
voiNr	Nr of additional VOI memory blocks

Definition at line 107 of file dft.c.

  {
  Voi *voi2;
  double *data2, *dptr, *newx, *newx1, *newx2, *neww;
  int ri, fi, dataSize2, voidataNr2;
 
  /* Check the input */
  if(dft==NULL || dft->voi==NULL || dft->frameNr<1 || dft->voiNr<1) return 1;
  if(voiNr<0) return 1; else if(voiNr==0) return 0; 
 
  /* Allocate memory for new set of curve data (plus additional 'frame') */
  voidataNr2=voiNr+dft->_voidataNr;
  voi2=(Voi*)calloc(voidataNr2, sizeof(Voi));
  if(voi2==NULL) return 3;
  dataSize2=(dft->frameNr+1)*(3*voidataNr2+4);
  data2=(double*)calloc(dataSize2, sizeof(double)); if(data2==NULL) return 3;
  /* Set pointers for new curve data */
  dptr=data2; newx=dptr; newx[dft->frameNr]=0.0;
  dptr+=dft->frameNr+1; newx1=dptr; newx1[dft->frameNr]=0.0;
  dptr+=dft->frameNr+1; newx2=dptr; newx2[dft->frameNr]=0.0;
  dptr+=dft->frameNr+1; neww=dptr;  neww[dft->frameNr]=0.0;
  for(ri=0; ri<voidataNr2; ri++) {
    dptr+=dft->frameNr+1; voi2[ri].y = dptr;
    dptr+=dft->frameNr+1; voi2[ri].y2 = dptr;
    dptr+=dft->frameNr+1; voi2[ri].y3 = dptr;
  }
 
  /* Copy the original contents */
  for(ri=0; ri<dft->voiNr; ri++) {
    /* Copy Voi header */
    strcpy(voi2[ri].name, dft->voi[ri].name);
    strcpy(voi2[ri].voiname, dft->voi[ri].voiname);
    strcpy(voi2[ri].hemisphere, dft->voi[ri].hemisphere);
    strcpy(voi2[ri].place, dft->voi[ri].place);
    voi2[ri].size=dft->voi[ri].size;
    voi2[ri].sw=dft->voi[ri].sw;
    voi2[ri].sw2=dft->voi[ri].sw2;
    voi2[ri].sw3=dft->voi[ri].sw3;
    /* Copy Voi data */
    for(fi=0; fi<dft->frameNr; fi++) {
      voi2[ri].y[fi]=dft->voi[ri].y[fi];
      voi2[ri].y2[fi]=dft->voi[ri].y2[fi];
      voi2[ri].y3[fi]=dft->voi[ri].y3[fi];
    }
  }
  for(fi=0; fi<dft->frameNr; fi++) {
    newx[fi]=dft->x[fi]; newx1[fi]=dft->x1[fi]; newx2[fi]=dft->x2[fi];
    neww[fi]=dft->w[fi];
  }
 
  /* Replace original pointers */
  free(dft->_data); dft->_data=data2;
  free(dft->voi); dft->voi=voi2;
  dft->x=newx; dft->x1=newx1; dft->x2=newx2; dft->w=neww;
  dft->_voidataNr=voidataNr2; dft->_dataSize=dataSize2;
 
  /* Initiate values */
  for(ri=dft->voiNr; ri<dft->_voidataNr; ri++) {
    strcpy(dft->voi[ri].name, "");
    strcpy(dft->voi[ri].voiname, "");
    strcpy(dft->voi[ri].hemisphere, "");
    strcpy(dft->voi[ri].place, "");
    dft->voi[ri].size=1.0;
    dft->voi[ri].sw=dft->voi[ri].sw2=dft->voi[ri].sw3=0;
    for(fi=0; fi<dft->frameNr+1; fi++)
      dft->voi[ri].y[fi]=dft->voi[ri].y2[fi]=dft->voi[ri].y3[fi]=0.0;
  }
 
  return 0;
}

Referenced by dftAdd(), dftInterpolateInto(), dftReadModelingData(), and imgReadModelingData().

dftAddnullframe()

int dftAddnullframe ( DFT * data )

extern

Include a frame with time 0, unless one already exists.

Returns

Returns <> 0 in case of an error.

Parameters

data	Pointer to DFT struct

Definition at line 752 of file dft.c.

  {
  int i, j, n;
  DFT temp;
 
 
  /* Check whether nullframe exists */
  if(data==NULL) return 1;
  if(data->frameNr<1 || data->x[0]==0.0) return 0;
 
  /* Allocate memory for temp data */
  dftInit(&temp);
  if(dftSetmem(&temp, data->frameNr, data->voiNr)) return 1;
  temp.frameNr=data->frameNr; temp.voiNr=data->voiNr;
 
  /* Copy data to temp */
  strcpy(temp.studynr, data->studynr);
  strcpy(temp.unit, data->unit);
  temp.timeunit=data->timeunit; temp.timetype=data->timetype;
  temp.isweight=data->isweight; temp._type=data->_type;
  strcpy(temp.comments, data->comments);
  for(j=0; j<data->frameNr; j++) {
    temp.x[j]=data->x[j]; temp.x1[j]=data->x1[j]; temp.x2[j]=data->x2[j];
    temp.w[j]=data->w[j];
    for(i=0; i<data->voiNr; i++) {
      temp.voi[i].y[j]=data->voi[i].y[j];
      temp.voi[i].y2[j]=data->voi[i].y2[j];
      temp.voi[i].y3[j]=data->voi[i].y3[j];
    }
  }
  for(i=0; i<data->voiNr; i++) {
    strcpy(temp.voi[i].name, data->voi[i].name);
    strcpy(temp.voi[i].voiname, data->voi[i].voiname);
    strcpy(temp.voi[i].hemisphere, data->voi[i].hemisphere);
    strcpy(temp.voi[i].place, data->voi[i].place);
    temp.voi[i].size=data->voi[i].size;
    temp.voi[i].sw=data->voi[i].sw;
    temp.voi[i].sw2=data->voi[i].sw2;
    temp.voi[i].sw3=data->voi[i].sw3;
  }
 
  /* Reallocate memory for data */
  dftEmpty(data);
  if(dftSetmem(data, temp.frameNr+1, temp.voiNr)) {dftEmpty(&temp); return 2;}
 
  /* Set nullframe */
  data->x[0]=data->x1[0]=data->x2[0]=0.0; data->w[0]=0.0;
  for(i=0; i<temp.voiNr; i++)
    data->voi[i].y[0]=data->voi[i].y2[0]=data->voi[i].y3[0]=0.0;
 
  /* Copy data back from temp */
  strcpy(data->studynr, temp.studynr);
  data->voiNr=temp.voiNr;
  strcpy(data->unit, temp.unit);
  data->timeunit=temp.timeunit; data->timetype=temp.timetype;
  data->isweight=temp.isweight; data->_type=temp._type;
  strcpy(data->comments, temp.comments);
  for(j=0, n=1; j<temp.frameNr; j++) {
    if(temp.x[j]<0.0) continue;
    if(n==1) data->x2[0]=temp.x1[j];
    data->x[n]=temp.x[j]; data->x1[n]=temp.x1[j]; data->x2[n]=temp.x2[j];
    data->w[n]=temp.w[j];
    for(i=0; i<temp.voiNr; i++) {
      data->voi[i].y[n]=temp.voi[i].y[j];
      data->voi[i].y2[n]=temp.voi[i].y2[j];
      data->voi[i].y3[n]=temp.voi[i].y3[j];
    }
    n++;
  }
  data->frameNr=n;
  for(i=0; i<temp.voiNr; i++) {
    strcpy(data->voi[i].name, temp.voi[i].name);
    strcpy(data->voi[i].voiname, temp.voi[i].voiname);
    strcpy(data->voi[i].hemisphere, temp.voi[i].hemisphere);
    strcpy(data->voi[i].place, temp.voi[i].place);
    data->voi[i].size=temp.voi[i].size;
    data->voi[i].sw=temp.voi[i].sw;
    data->voi[i].sw2=temp.voi[i].sw2;
    data->voi[i].sw3=temp.voi[i].sw3;
  }
 
  dftEmpty(&temp);
 
  return 0;
}

dftAddSpaceForFrames()

int dftAddSpaceForFrames ( DFT * dft, int nr_to_add )

extern

Add space for additional frames into DFT, keeping the existing data. frameNr is increased by nr_to_add, but new last frame(s) are empty.

Returns

Returns zero if successful, otherwise <>0.

Parameters

dft	Allocated and data-filled DFT where new frame(s) are added to the end
nr_to_add	Nr of frames to add

Definition at line 1465 of file dft.c.

  {
  DFT temp;
  int ret, ri, fi;
 
  /* Check input */
  if(dft==NULL || dft->frameNr<1 || dft->voiNr<1) return 1;
  if(nr_to_add<1) return 0;
 
  /* Make a temporary storage of the data */
  dftInit(&temp); ret=dftdup(dft, &temp); if(ret!=0) return 10+ret;
  /* Delete and reallocate the original data pointer */
  dftEmpty(dft); ret=dftSetmem(dft, temp.frameNr+nr_to_add, temp.voiNr);
  if(ret!=0) {
    dftdup(&temp, dft); dftEmpty(&temp);
    return 20+ret;
  }
  /* Copy data back, leaving last frame(s) empty */
  ret=dftCopymainhdr(&temp, dft);
  if(ret!=0) {
    dftdup(&temp, dft); dftEmpty(&temp);
    return 30+ret;
  }
  dft->voiNr=temp.voiNr; dft->frameNr=nr_to_add+temp.frameNr;
  dft->isweight=temp.isweight;
  strcpy(dft->comments, temp.comments);
  for(ri=0; ri<temp.voiNr; ri++) {
    ret=dftCopyvoihdr(&temp, ri, dft, ri);
    if(ret!=0) {
      dftdup(&temp, dft); dftEmpty(&temp);
      return 40+ret;
    }
    for(fi=0; fi<temp.frameNr; fi++) {
      dft->voi[ri].y[fi]=temp.voi[ri].y[fi];
      dft->voi[ri].y2[fi]=temp.voi[ri].y2[fi];
      dft->voi[ri].y3[fi]=temp.voi[ri].y3[fi];
    }
    /* Fill in the first frame */
    dft->voi[ri].y[0]=0.0;
    dft->voi[ri].y2[0]=0.0;
    dft->voi[ri].y3[0]=0.0;
  }
  for(fi=0; fi<temp.frameNr; fi++) {
    dft->x1[fi]=temp.x1[fi];
    dft->x2[fi]=temp.x2[fi];
    dft->x[fi]=temp.x[fi];
    dft->w[fi]=temp.w[fi];
  }
 
  /* Fill the last frames with NAs */
  for(fi=temp.frameNr; fi<dft->frameNr; fi++) {
    dft->w[fi]=1.0;
    dft->x1[fi]=dft->x2[fi]=dft->x[0]=0.0;
    for(ri=0; ri<dft->voiNr; ri++) dft->voi[ri].y[fi]=nan("");
  }
  dftEmpty(&temp);
 
  return 0;
}

dftAllocateWithHeader()

int dftAllocateWithHeader ( DFT * dft, int frameNr, int voiNr, DFT * dft_from )

extern

Allocates a DFT structure with specified size, containing no TAC data but header information as available in another DFT struct.

Any existing content of dft2 will be deleted. Dft2 must be initiated.

Returns

Returns 0 if ok.

Parameters

dft	Pointer to initiated DFT struct which will be allocated here; any previous contents will be deleted.
frameNr	Nr of frames to be allocated
voiNr	Nr of planes to be allocated
dft_from	Pointer to DFT struct where header contents will be copied from

Definition at line 702 of file dft.c.

  {
  int ri, fi, ret;
 
  /* Check the input */
  if(dft==NULL || dft_from==NULL || frameNr<1 || voiNr<0) return 1;
  /* Empty the new data */
  dftEmpty(dft);
  /* Allocate memory for dft */
  ret=dftSetmem(dft, frameNr, voiNr); if(ret) return(ret);
  dft->voiNr=voiNr; dft->frameNr=frameNr;
  /* Copy the contents */
  ret=dftCopymainhdr(dft_from, dft); if(ret) return(ret);
  if(dft->voiNr==dft_from->voiNr) {
    for(ri=0; ri<dft->voiNr; ri++) {
      ret=dftCopyvoihdr(dft_from, ri, dft, ri); if(ret) return(ret);
      if(dft->frameNr==dft_from->frameNr) {
        for(fi=0; fi<dft->frameNr; fi++) {
          dft->voi[ri].y[fi]=dft_from->voi[ri].y[fi];
          dft->voi[ri].y2[fi]=dft_from->voi[ri].y2[fi];
          dft->voi[ri].y3[fi]=dft_from->voi[ri].y3[fi];
        }
      }
    }
  }
  if(dft->frameNr==dft_from->frameNr) {
    for(fi=0; fi<dft->frameNr; fi++) {
      dft->x[fi]=dft_from->x[fi];
      dft->x1[fi]=dft_from->x1[fi]; dft->x2[fi]=dft_from->x2[fi];
      dft->w[fi]=dft_from->w[fi];
    }
    dft->isweight=dft_from->isweight;
  }
  return(0);
}

Referenced by dftInterpolateForIMG(), dftMeanTAC(), and dftTimeIntegral().

dftCopymainhdr()

int dftCopymainhdr ( DFT * dft1, DFT * dft2 )

extern

Copy main header info from dft1 to dft2.

Returns

Returns <> 0 in case of an error.

Parameters

dft1	Pointer to DFT struct from where information is copied
dft2	Pointer to DFT struct into which information is copied to

Definition at line 561 of file dft.c.

  {
  if(dft1==NULL || dft2==NULL) return 1;
  strcpy(dft2->studynr, dft1->studynr);
  strcpy(dft2->unit, dft1->unit);
  dft2->timeunit=dft1->timeunit; dft2->timetype=dft1->timetype;
  strcpy(dft2->comments, dft1->comments);
  strcpy(dft2->radiopharmaceutical, dft1->radiopharmaceutical);
  strcpy(dft2->isotope, dft1->isotope);
  strcpy(dft2->scanStartTime, dft1->scanStartTime);
  strcpy(dft2->injectionTime, dft1->injectionTime);
  dft2->decayCorrected=dft1->decayCorrected;
  dft2->_type=dft1->_type;
  return 0;
}

Referenced by dftAddSpaceForFrames(), dftAllocateWithHeader(), dftAutointerpolate(), dftDivideFrames(), dftDoubleFrames(), dftdup(), dftFillInitialGap(), dftInterpolate(), extrapolate_monoexp(), and plotdata_as_dft().

dftCopymainhdr2()

int dftCopymainhdr2 ( DFT * dft1, DFT * dft2, int ow )

extern

Copy main header info from dft1 to dft2. Comments are not copied, because those may contain outdated units and other information.

Returns

Returns <> 0 in case of an error.

Parameters

dft1	Pointer to DFT struct from where information is copied
dft2	Pointer to DFT struct into which information is copied to
ow	Existing header field content is overwritten (1) or kept (0)

Definition at line 587 of file dft.c.

  {
  if(dft1==NULL || dft2==NULL) return 1;
  if(ow || (strlen(dft2->studynr)<1 && strcmp(dft2->studynr, ".")==0))
    strcpy(dft2->studynr, dft1->studynr);
  if(ow || dftUnitId(dft2->unit)==CUNIT_UNKNOWN)
    strcpy(dft2->unit, dft1->unit);
  if(ow || dft2->timeunit==TUNIT_UNKNOWN)
    dft2->timeunit=dft1->timeunit;
  dft2->timetype=dft1->timetype;
  if(ow || strlen(dft2->radiopharmaceutical)<1)
    strcpy(dft2->radiopharmaceutical, dft1->radiopharmaceutical);
  if(ow || strlen(dft2->isotope)<1)
    strcpy(dft2->isotope, dft1->isotope);
  if(ow || strlen(dft2->scanStartTime)<1)
    strcpy(dft2->scanStartTime, dft1->scanStartTime);
  if(ow || strlen(dft2->injectionTime)<1)
    strcpy(dft2->injectionTime, dft1->injectionTime);
  if(ow || dft2->decayCorrected==DFT_DECAY_UNKNOWN)
    dft2->decayCorrected=dft1->decayCorrected;
  if(ow)
    dft2->_type=dft1->_type;
  return 0;
}

Referenced by bfIrr2TCM(), and bfRadiowater().

dftCopyvoi()

int dftCopyvoi ( DFT * data, int from, int to )

extern

Copy VOI data inside DFT data structure from one place to another.

Parameters

data	Pointer to DFT struct
from	TAC index
to	TAC index

Definition at line 472 of file dft.c.

  {
  int i;
 
  /* Check that required data exists */
  if(data==NULL || to>=data->_voidataNr || from>=data->_voidataNr) return 1;
  if(from==to) return 0;
 
  /* Copy VOI info */
  strcpy(data->voi[to].name, data->voi[from].name);
  strcpy(data->voi[to].voiname, data->voi[from].voiname);
  strcpy(data->voi[to].hemisphere, data->voi[from].hemisphere);
  strcpy(data->voi[to].place, data->voi[from].place);
  data->voi[to].size=data->voi[from].size;
  data->voi[to].sw=data->voi[from].sw;
  data->voi[to].sw2=data->voi[from].sw2;
  data->voi[to].sw3=data->voi[from].sw3;
  /* Copy VOI curves */
  for(i=0; i<data->frameNr; i++) {
    data->voi[to].y[i]=data->voi[from].y[i];
    data->voi[to].y2[i]=data->voi[from].y2[i];
    data->voi[to].y3[i]=data->voi[from].y3[i];
  }
 
  return 0;
}

Referenced by dftRead().

dftCopyvoihdr()

int dftCopyvoihdr ( DFT * dft1, int from, DFT * dft2, int to )

extern

Copy voi header info from dft1.voi[from] to dft2.voi[to].

Returns

Returns <> 0 in case of an error.

Parameters

dft1	Pointer to DFT struct
from	TAC index
dft2	Pointer to DFT struct
to	TAC index

Definition at line 623 of file dft.c.

  {
  /* Check that required data exists */
  if(dft1==NULL || dft2==NULL) return 1;
  if(to>=dft2->_voidataNr || from>=dft1->_voidataNr) return 1;
 
  /* Copy VOI info */
  strcpy(dft2->voi[to].name, dft1->voi[from].name);
  strcpy(dft2->voi[to].voiname, dft1->voi[from].voiname);
  strcpy(dft2->voi[to].hemisphere, dft1->voi[from].hemisphere);
  strcpy(dft2->voi[to].place, dft1->voi[from].place);
  dft2->voi[to].size=dft1->voi[from].size;
  dft2->voi[to].sw=dft1->voi[from].sw;
  dft2->voi[to].sw2=dft1->voi[from].sw2;
  dft2->voi[to].sw3=dft1->voi[from].sw3;
 
  return 0;
}

Referenced by dftAdd(), dftAddSpaceForFrames(), dftAllocateWithHeader(), dftAutointerpolate(), dftDivideFrames(), dftDoubleFrames(), dftdup(), dftFillInitialGap(), dftInterpolate(), dftInterpolateInto(), extrapolate_monoexp(), and plotdata_as_dft().

dftDecayCorrection()

int dftDecayCorrection ( DFT * dft, double hl, int mode, int y, int y2, int y3, char * status, int verbose )

extern

Corrects TAC data for physical decay, or removed the correction.

Weights are not modified.

Returns

Returns 0 if conversion was successful, and <> 0 if failed.

Parameters

dft	Pointer to existing DFT data; status of decay correction in DFT is not verified, but set in this function; DFT must contain valid sample time unit.
hl	Half-life of isotope in minutes; enter <=0, if correct isotope code is given in DFT
mode	0=Remove decay correction; 1=Correct for decay
y	Apply (1) or do not apply (0) correction to y[] data in DFT
y2	Apply (1) or do not apply (0) correction to y2[] data in DFT
y3	Apply (1) or do not apply (0) correction to y3[] data in DFT
status	Pointer to a string (allocated for at least 64 chars) where error message or other execution status will be written; enter NULL, if not needed
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout

Definition at line 16 of file dftdecayc.c.

  {
  int ri, fi, isotopeID=-1;
  double lambda, dc;
 
  if(verbose>0) printf("dftDecayCorrection(dft, %g, %d, %d, %d, %d, ...)\n",
    hl, mode, y, y2, y3);
 
  /* Check the input */
  if(status!=NULL) strcpy(status, "invalid input");
  if(dft==NULL) return(1);
  if(dft->voiNr<1 || dft->frameNr<1) return(1);
  
  /* Check that DFT contains time unit */
  if(dft->timeunit!=TUNIT_SEC && dft->timeunit!=TUNIT_MIN && 
     dft->timeunit!=TUNIT_HOUR) 
  {
    if(verbose>0) printf("dft->timeunit := %d\n", dft->timeunit);
    if(status!=NULL) strcpy(status, "sample time unit is not specified");
    return(2);
  }
  
  /* Check and set isotope code and half-life */
  if(hl>1.0E-10) { 
    /* Try to identify the isotope from given half-life */
    isotopeID=hlIsotopeFromHalflife(hl);
    if(isotopeID>=0) {
      /* If identified, then set the code in DFT */
      strcpy(dft->isotope, hlIsotopeCode(isotopeID));
      if(verbose>1) printf("  isotope := %s\n", dft->isotope);
    } else {
      /* If not identified, that may just be because isotope is not yet listed
         in TPC library, but give a warning */
      fprintf(stderr, "Warning: halflife %g min is not identified.\n", hl);
    }
  } else {
    /* Check that valid isotope code is found in DFT */
    hl=hlFromIsotope(dft->isotope); if(hl<=0.0) {
      if(verbose>0) printf("dft->isotope := %s\n", dft->isotope);
      if(status!=NULL) strcpy(status, "valid isotope is not specified");
      return(11);
    }
    if(verbose>1) printf("  half-life := %g min\n", hl);
  }
  
  /*
   *  Calculate the lambda
   */
  if(dft->timeunit==TUNIT_SEC) hl*=60.0;
  else if(dft->timeunit==TUNIT_HOUR) hl/=60.0;
  lambda=hl2lambda(hl); if(mode==0) lambda=-lambda;
  if(verbose>1) printf("lambda := %e\n", lambda);
 
  /*
   *  Decay correction / removal
   */
  if(verbose>2) {
    if(mode!=0) printf("decay correction\n");
    else printf("removing decay correction\n");
  }
  for(fi=0; fi<dft->frameNr; fi++) {
    /* Calculate decay factor */
    if(dft->timetype==DFT_TIME_STARTEND) {
      if(isnan(dft->x1[fi]) || isnan(dft->x2[fi])) continue;
      dc=hlLambda2factor(lambda, dft->x1[fi], dft->x2[fi]-dft->x1[fi]);
    } else {
      if(isnan(dft->x[fi])) continue;
      dc=hlLambda2factor(lambda, dft->x[fi], 0.0);
    }
    if(verbose>4) printf("  %10.4f  ->  %e\n", dft->x[fi], dc);
    /* Correct all regions */
    for(ri=0; ri<dft->voiNr; ri++) {
      if(y!=0 && !isnan(dft->voi[ri].y[fi])) dft->voi[ri].y[fi]*=dc;
      if(y2!=0 && !isnan(dft->voi[ri].y2[fi])) dft->voi[ri].y2[fi]*=dc;
      if(y3!=0 && !isnan(dft->voi[ri].y3[fi])) dft->voi[ri].y3[fi]*=dc;
    }
  }
  if(mode!=0) {
    dft->decayCorrected=DFT_DECAY_CORRECTED;
    if(status!=NULL) strcpy(status, "decay corrected");
  } else {
    dft->decayCorrected=DFT_DECAY_NOTCORRECTED;
    if(status!=NULL) strcpy(status, "decay correction removed");
  }
  return(0);
} 

dftDelete()

int dftDelete ( DFT * dft, int voi )

extern

Delete specified TAC (0..voiNr-1) from the DFT structure.

Returns

Returns 0 if ok.

Parameters

dft	Pointer to DFT struct
voi	TAC index

Definition at line 538 of file dft.c.

  {
  int ret;
 
  /* Check that region exists */
  if(dft==NULL || voi>dft->voiNr-1 || voi<0) return(1);
  /* If it is the last one, then just decrease the voiNr */
  if(voi==dft->voiNr-1) {dft->voiNr--; return(0);}
  /* Otherwise move it to the last position, and then decrease voiNr */
  ret=dftMovevoi(dft, voi, dft->voiNr-1); if(ret) return(10+ret);
  dft->voiNr--;
  return(0);
}

Referenced by csv2dft_a(), and dftReadinput().

dftDeleteFrameOverlap()

int dftDeleteFrameOverlap ( DFT * dft )

extern

Correct frame start and end times if frames are slightly overlapping or have small gaps in between. Gap before the first time frame is not corrected. Large gap is not corrected and it does not lead to an error.

See also

dftFillInitialGap

Returns

If overlap is considerable (>20%), or another error is encountered, function returns a non-zero value. Otherwise 0 is returned.

Parameters

dft	Pointer to DFT data. Data must be sorted by increasing time. Time unit does not need to be set. Timetype must be DFT_TIME_STARTEND, i.e. both frame start and end time must be present; if not, then return value is always 0 (passed).

Definition at line 1237 of file dft.c.

  {
  int fi;
  double overlap, overlap_limit=0.0, flen1, flen2;
 
  if(dft==NULL) return(1);
  if(dft->timetype!=DFT_TIME_STARTEND) return(0);
  for(fi=0; fi<dft->frameNr-1; fi++) {
    overlap=dft->x2[fi] - dft->x1[fi+1];
    if(overlap==0.0) continue; // no gap or overlap
    /* Calculate the frame length of current frame and the next frame */
    flen1=dft->x2[fi]-dft->x1[fi]; flen2=dft->x2[fi+1]-dft->x1[fi+1];
    if(flen1<0.0 || flen2<0.0) return(1);
    /* Set the limit */
    if(flen1<flen2) overlap_limit=0.2*flen1; else overlap_limit=0.2*flen2;
    /* Check if gap or overlap is too large to be fixed automatically */
    if(overlap<-overlap_limit) continue; // gap is too large, then do nothing
    if(overlap>overlap_limit) return(2); // overlap is too large: error
    /* Correct the small gap/overlap by making frame durations more similar */
    if(overlap>0.0) { // overlap
      if(flen1>flen2) dft->x2[fi]=dft->x1[fi+1]; else dft->x1[fi+1]=dft->x2[fi];
    } else { // gap
      if(flen1>flen2) dft->x1[fi+1]=dft->x2[fi]; else dft->x2[fi]=dft->x1[fi+1];
    }
  }
  return(0);
}

Referenced by dftReadModelingData().

dftDeleteFrameOverlap_old()

int dftDeleteFrameOverlap_old ( DFT * dft )

extern

Correct frame start and end times if frames are slightly overlapping or have small gaps in between. Large gap is not corrected and it does not lead to an error.

Returns

If overlap is considerable (>1 s), or another error is encountered, function returns a non-zero value. Otherwise 0 is returned.

Parameters

dft	Pointer to DFT data. Time unit must be set, otherwise no checking is done. Timetype must be DFT_TIME_STARTEND, i.e. both frame start and end time must be present.

Definition at line 1200 of file dft.c.

  {
  int fi;
  double overlap, overlap_limit=1.8, flen1, flen2;
 
  if(dft==NULL) return(1);
  if(dft->timetype!=DFT_TIME_STARTEND) return(0);
  if(dft->timeunit!=TUNIT_MIN && dft->timeunit!=TUNIT_SEC) return(0);
  if(dft->timeunit==TUNIT_MIN) overlap_limit/=60.0;
  for(fi=0; fi<dft->frameNr-1; fi++) {
    overlap=dft->x2[fi] - dft->x1[fi+1];
    if(overlap==0.0) continue; // no gap or overlap
    else if(overlap<-overlap_limit) continue; // gap is large, then do nothing
    else if(overlap>overlap_limit) return(2); // overlap is large: error
    /* Correct the small gap/overlap by making frame durations more similar */
    flen1=dft->x2[fi]-dft->x1[fi]; flen2=dft->x2[fi+1]-dft->x1[fi+1];
    if(overlap>0.0) { // overlap
      if(flen1>flen2) dft->x2[fi]=dft->x1[fi+1]; else dft->x1[fi+1]=dft->x2[fi];
    } else { // gap
      if(flen1>flen2) dft->x1[fi+1]=dft->x2[fi]; else dft->x2[fi]=dft->x1[fi+1];
    }
  }
  return(0);
}

dftdup()

int dftdup ( DFT * dft1, DFT * dft2 )

extern

Makes a duplicate of DFT structure pointed to by dft1 into dft2.

Returns

Returns 0 if ok.

Parameters

dft1	Pointer to DFT struct
dft2	Pointer to initiated DFT struct; any existing content of dft2 will be deleted.

Definition at line 655 of file dft.c.

  {
  int ri, fi, ret;
 
  if(dft1==NULL || dft2==NULL) return 1;
  /* Empty the new data */
  dftEmpty(dft2);
  /* Is that it? Is there any contents in dft1? */
  if(dft1->voiNr==0 && dft1->frameNr==0) {
    ret=dftCopymainhdr(dft1, dft2); return(ret);
  }
  /* Allocate memory for dft2 */
  ret=dftSetmem(dft2, dft1->frameNr, dft1->voiNr); if(ret) return(ret);
  dft2->voiNr=dft1->voiNr; dft2->frameNr=dft1->frameNr;
  /* Copy the contents */
  ret=dftCopymainhdr(dft1, dft2); if(ret) return(ret);
  for(ri=0; ri<dft1->voiNr; ri++) {
    ret=dftCopyvoihdr(dft1, ri, dft2, ri); if(ret) return(ret);
    for(fi=0; fi<dft1->frameNr; fi++) {
      dft2->voi[ri].y[fi]=dft1->voi[ri].y[fi];
      dft2->voi[ri].y2[fi]=dft1->voi[ri].y2[fi];
      dft2->voi[ri].y3[fi]=dft1->voi[ri].y3[fi];
    }
  }
  for(fi=0; fi<dft1->frameNr; fi++) {
    dft2->x[fi]=dft1->x[fi];
    dft2->x1[fi]=dft1->x1[fi]; dft2->x2[fi]=dft1->x2[fi];
    dft2->w[fi]=dft1->w[fi];
  }
  dft2->isweight=dft1->isweight;
  return(0);
}

Referenced by dftAddSpaceForFrames(), dftFillInitialGap(), dftReadinput(), and imgReadModelingData().

dftEmpty()

void dftEmpty ( DFT * data )

extern

Free memory allocated for DFT. All data is cleared.

Parameters

data	Pointer to initiated DFT struct data

Definition at line 20 of file dft.c.

  {
  if(data==NULL) return;
  if(data->_voidataNr>0) free((char*)(data->voi));
  if(data->_dataSize>0) free((char*)(data->_data));
  data->_dataSize=data->_voidataNr=0;
  data->frameNr=data->voiNr=0;
  data->studynr[0]=data->comments[0]=data->unit[0]=(char)0;
  data->radiopharmaceutical[0]=data->isotope[0]=data->decayCorrected=(char)0;
  data->scanStartTime[0]=data->injectionTime[0]=(char)0;
  data->timeunit=data->timetype=0;
}

Referenced by bfIrr2TCM(), bfRadiowater(), clusterTACs(), cptReadOne(), csv2dft_a(), csv2dft_b(), csv2dft_linkset(), csv2dft_mat(), dftAddnullframe(), dftAddSpaceForFrames(), dftAllocateWithHeader(), dftAutointerpolate(), dftDivideFrames(), dftDoubleFrames(), dftdup(), dftFillInitialGap(), dftInterpolate(), dftInterpolateForIMG(), dftInterpolateInto(), dftMeanTAC(), dftRead(), dftReadinput(), dftReadModelingData(), dftReadReference(), dftSetmem(), extrapolate_monoexp(), idwcRead(), ifRead(), img_k1_using_ki(), img_logan(), img_patlak(), imgMaskPixelTACs(), imgReadModelingData(), noiseSD4SimulationFromDFT(), plotdata_as_dft(), roikbqRead(), and simMyocDiameterCurve().

dftFillInitialGap()

int dftFillInitialGap ( DFT * dft )

extern

Check if there is a time gap between time zero and first sample time; if gap does not exist, then nothing is done; if gap exists, then gap is filled with an extra frame.

See also

dftDeleteFrameOverlap

Returns

Returns zero if successful, otherwise <>0.

Parameters

dft	Pointer to DFT struct

Definition at line 1385 of file dft.c.

  {
  DFT temp;
  int ret, ri, fi;
 
  /* Check input */
  if(dft==NULL) return 1;
  if(dft->frameNr<1 || dft->voiNr<1) return 0;
 
  /* Is there an initial gap? If not then we can finish here */
  if(dft->timetype==DFT_TIME_STARTEND) {
    if(dft->x1[0]<=0.0) return 0;
  } else {
    if(dft->x[0]<=0.0) return 0;
  }
 
  /* Make a temporary storage of the data */
  dftInit(&temp); ret=dftdup(dft, &temp); if(ret!=0) return 10+ret;
  /* Delete and reallocate the original data pointer */
  dftEmpty(dft); ret=dftSetmem(dft, temp.frameNr+1, temp.voiNr);
  if(ret!=0) {
    dftdup(&temp, dft); dftEmpty(&temp);
    return 20+ret;
  }
  /* Copy data back, leaving first frame empty */
  ret=dftCopymainhdr(&temp, dft);
  if(ret!=0) {
    dftdup(&temp, dft); dftEmpty(&temp);
    return 30+ret;
  }
  dft->voiNr=temp.voiNr; dft->frameNr=1+temp.frameNr;
  dft->isweight=temp.isweight;
  strcpy(dft->comments, temp.comments);
  for(ri=0; ri<temp.voiNr; ri++) {
    ret=dftCopyvoihdr(&temp, ri, dft, ri);
    if(ret!=0) {
      dftdup(&temp, dft); dftEmpty(&temp);
      return 40+ret;
    }
    for(fi=0; fi<temp.frameNr; fi++) {
      dft->voi[ri].y[fi+1]=temp.voi[ri].y[fi];
      dft->voi[ri].y2[fi+1]=temp.voi[ri].y2[fi];
      dft->voi[ri].y3[fi+1]=temp.voi[ri].y3[fi];
    }
    /* Fill in the first frame */
    dft->voi[ri].y[0]=0.0;
    dft->voi[ri].y2[0]=0.0;
    dft->voi[ri].y3[0]=0.0;
  }
  for(fi=0; fi<temp.frameNr; fi++) {
    dft->x1[fi+1]=temp.x1[fi];
    dft->x2[fi+1]=temp.x2[fi];
    dft->x[fi+1]=temp.x[fi];
    dft->w[fi+1]=temp.w[fi];
  }
  dftEmpty(&temp);
 
  /* Fill the first frame */
  dft->w[0]=1.0;
  if(dft->timetype==DFT_TIME_STARTEND) {
    dft->x1[0]=0.0;
    dft->x2[0]=dft->x1[1];
    dft->x[0]=0.5*(dft->x1[0]+dft->x2[0]);
  } else {
    dft->x1[0]=0.0;
    dft->x2[0]=dft->x1[1];
    dft->x[0]=0.0;
  }
 
  return 0;
}

Referenced by dftFixPeak().

dftFormat()

int dftFormat ( char * fname )

extern

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().

dftFrametimes()

void dftFrametimes ( DFT * data )

extern

Calculate frame mid or start and end times. Timetype is not changed.

Parameters

data	Pointer to DFT struct

Definition at line 340 of file dft.c.

  {
  int i, j;
  double f, fs;
 
  if(data==NULL) return;
  /* If data is told to contain frame start and end times, then check
     that those really are there, or set to middle times, if necessary */
  if(data->timetype==DFT_TIME_STARTEND) {
    for(i=j=0; i<data->frameNr; i++) {
      fs=data->x2[i]-data->x1[i]; if(fs>1.0E-10) {j=1; break;}
    }
    if(j==0) {
      for(i=0; i<data->frameNr; i++) data->x[i]=0.5*(data->x1[i]+data->x2[i]);
      data->timetype=DFT_TIME_MIDDLE;
    }
  }
 
  /* Decide what to do, and get it done */
  if(data->timetype==DFT_TIME_MIDDLE) {
    /* frame start and end times from mid times */
    /* Easy, if only one frame */
    if(data->frameNr==1) {
      if(data->x[0]<=0.0) {data->x1[0]=data->x[0]; data->x2[0]=0.0;}
      else {data->x1[0]=0.0; data->x2[0]=2.0*data->x[0];}
      return;
    }
    /* Fill start and end times with -999 */
    for(i=0; i<data->frameNr; i++) data->x1[i]=data->x2[i]=-999.;
    /* Search for sequences of nearly same frame lengths */
    for(i=1; i<data->frameNr-1; i++) {
      f=data->x[i]-data->x[i-1]; fs=data->x[i+1]-data->x[i];
      if((f+fs)<=0.0 && fabs(fs-f)>=2.0) continue;
      if((f+fs)>0.0 && (2.0*fabs(fs-f)/(f+fs))>0.1) continue; 
      //if(fabs(f-fs)>=2.0) continue; 
      f=(f+fs)/2.0;
      data->x1[i-1]=data->x[i-1]-f/2.0; data->x2[i-1]=data->x[i-1]+f/2.0;
      data->x1[i]=data->x[i]-f/2.0; data->x2[i]=data->x[i]+f/2.0;
      data->x1[i+1]=data->x[i+1]-f/2.0; data->x2[i+1]=data->x[i+1]+f/2.0;
      /* Check for negatives */
      for(j=i-1; j<i+2; j++) {
        if(data->x1[j]<0.0) data->x1[j]=0.0;
        if(data->x2[j]<0.0) data->x2[j]=0.0;
      }
    }
    /* If out-of-sequence frames were left out, fill those to the nearest one */
    i=0;  /* first frame */
    if(data->x1[i]<0) {
      if(data->x1[i+1]>0) data->x2[i]=data->x1[i+1];
      else data->x2[i]=(data->x[i+1]+data->x[i])/2.0;
      data->x1[i]=2.0*data->x[i]-data->x2[i];
    }
    i=data->frameNr-1;  /* last frame */
    if(data->x1[i]<0) {
      if(data->x2[i-1]>0) data->x1[i]=data->x2[i-1];
      else data->x1[i]=(data->x[i-1]+data->x[i])/2.0;
      data->x2[i]=2.0*data->x[i]-data->x1[i];
    }
    /* other frames */
    for(i=1; i<data->frameNr-1; i++) if(data->x1[i]<0.0) {
      /* which frame is nearest? */
      if(data->x[i]-data->x[i-1] <= data->x[i+1]-data->x[i]) { /* last one */
        if(data->x2[i-1]>0) data->x1[i]=data->x2[i-1];
        else data->x1[i]=(data->x[i-1]+data->x[i])/2.0;
        data->x2[i]=2.*data->x[i]-data->x1[i];
      } else { /* next one */
        if(data->x1[i+1]>0) data->x2[i]=data->x1[i+1];
        else data->x2[i]=(data->x[i+1]+data->x[i])/2.0;
        data->x1[i]=2.0*data->x[i]-data->x2[i];
      }
    }
    /* Check for negatives */
    for(i=0; i<data->frameNr; i++) {
      if(data->x1[i]<0.0) data->x1[i]=0.0;
      if(data->x2[i]<0.0) data->x2[i]=data->x1[i];
    }
    /* Check for overlapping and very small gaps */
    for(i=1; i<data->frameNr; i++) {
      f=data->x1[i]-data->x2[i-1];
      if(f<0.0) {
        if(data->x[i]>data->x2[i-1]) data->x1[i]=data->x2[i-1];
        else if(data->x[i-1]<data->x1[i]) data->x2[i-1]=data->x1[i];
        else data->x1[i]=data->x2[i-1]=(data->x[i]+data->x[i-1])/2.0;
      } else if(f>0.0 && f<1.0) {
        data->x1[i]=data->x2[i-1]=(data->x1[i]+data->x2[i-1])/2.0;
      }
    }
  } else if(data->timetype==DFT_TIME_STARTEND) {
    /* mid times from frame start and end times */
    for(i=0; i<data->frameNr; i++) data->x[i]=0.5*(data->x1[i]+data->x2[i]);
  } else if(data->timetype==DFT_TIME_START) {
    /* frame start times -> end and mid times */
    for(i=0; i<data->frameNr-1; i++) data->x2[i]=data->x1[i+1];
    data->x2[data->frameNr-1]=data->x1[data->frameNr-1]+
      (data->x2[data->frameNr-2]-data->x1[data->frameNr-2]);
    for(i=0; i<data->frameNr; i++) data->x[i]=0.5*(data->x1[i]+data->x2[i]);
  } else if(data->timetype==DFT_TIME_END) {
    /* frame end times -> start and mid times */
    data->x1[0]=0.0;
    for(i=1; i<data->frameNr; i++) data->x1[i]=data->x2[i-1];
    for(i=0; i<data->frameNr; i++) data->x[i]=0.5*(data->x1[i]+data->x2[i]);
  }
 
  return;
}

Referenced by csv2dft_a(), dftRead(), and idwcRead().

dftGetPmodTitle()

int dftGetPmodTitle ( DFT * dft, char * title_line )

extern

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().

dftInit()

void dftInit ( DFT * data )

extern

Initiate DFT structure. This should be called once before use.

Parameters

data	Pointer to initiated DFT struct data

Definition at line 38 of file dft.c.

  {
  if(data==NULL) return;
  memset(data, 0, sizeof(DFT));
  data->_voidataNr=data->_dataSize=0;
  data->frameNr=data->voiNr=0;
  data->studynr[0]=data->comments[0]=data->unit[0]=(char)0;
  data->radiopharmaceutical[0]=data->isotope[0]=data->decayCorrected=(char)0;
  data->scanStartTime[0]=data->injectionTime[0]=(char)0;
  data->timeunit=data->timetype=data->isweight=0;
}

Referenced by dftAddnullframe(), dftAddSpaceForFrames(), dftFillInitialGap(), dftReadinput(), dftReadModelingData(), dftReadReference(), img_k1_using_ki(), img_logan(), img_patlak(), imgReadModelingData(), noiseSD4SimulationFromDFT(), and plotdata_as_dft().

dftMaxY()

int dftMaxY ( DFT * dft, double t1, double t2, double * miny, double * maxy )

extern

Search the min and max values of DFT TAC data inside specified time range.

Data may contain NA's.

Returns

Returns 0 if successful.

Parameters

dft	Pointer to the DFT TAC data to search
t1	Start time
t2	End time
miny	Pointer to min Y; set to NULL if not needed
maxy	Pointer to max Y; set to NULL if not needed

Definition at line 1090 of file dft.c.

  {
  int ri, fi;
  double x1, x2, y1, y2;
 
  if(dft==NULL) return(1);
  y1=y2=nan("");
  for(fi=0; fi<dft->frameNr; fi++) {
    if(dft->timetype==DFT_TIME_STARTEND) {
      if(!isfinite(dft->x1[fi]) || !isfinite(dft->x2[fi])) continue;
      x1=dft->x1[fi]; x2=dft->x2[fi];
    } else {
      if(!isfinite(dft->x[fi])) continue;
      x1=x2=dft->x[fi];
    }
    if(x2<t1 || x1>t2) continue; // outside time range
    for(ri=0; ri<dft->voiNr; ri++) if(!isnan(dft->voi[ri].y[fi])) {
      if(isnan(y1) || y1>dft->voi[ri].y[fi]) y1=dft->voi[ri].y[fi];
      if(isnan(y2) || y2<dft->voi[ri].y[fi]) y2=dft->voi[ri].y[fi];
    }
  }
  if(miny!=NULL) {if(isnan(y1)) return(5); else *miny=y1;}
  if(maxy!=NULL) {if(isnan(y2)) return(6); else *maxy=y2;}
  return(0);
}

Referenced by plot_fitrange_svg().

dftMeanTAC()

int dftMeanTAC ( DFT * dft, DFT * mean )

extern

Calculates mean TAC of all TACs in DFT struct. Mean is NOT weighted by VOI sizes. Also SD and CV for each sample time are calculated.

Returns

Returns 0 if successful.

Parameters

dft	Pointer to TAC data from which mean TAC is calculated; missing values (NaN) are allowed
mean	Pointer to initialized or pre-allocated DFT struct in where mean, SD, and CV will be written in y, y2, and y3, respectively.

Definition at line 1580 of file dft.c.

  {
  int ret, fi, ri, n;
  double sum, ssum;
 
  if(dft==NULL || mean==NULL) return(1);
  if(dft->voiNr<1 || dft->frameNr<1) return(2);
 
  /* Allocate memory for mean data, if necessary */
  if(mean->voiNr<1 || mean->frameNr!=dft->frameNr) {
    dftEmpty(mean); ret=dftAllocateWithHeader(mean, dft->frameNr, 1, dft);
    if(ret!=0) return(100+ret);
  }
  strcpy(mean->voi[0].name, "Mean");
  strcpy(mean->voi[0].voiname, mean->voi[0].name);
 
  /* Calculate the mean TAC */
  ret=0;
  for(fi=0; fi<dft->frameNr; fi++) {
    sum=ssum=0.0; n=0;
    for(ri=0; ri<dft->voiNr; ri++) if(!isnan(dft->voi[ri].y[fi])) {
      sum+=dft->voi[ri].y[fi];
      ssum+=dft->voi[ri].y[fi]*dft->voi[ri].y[fi];
      n++;
    }
    if(n==0) {
      mean->voi[0].y[fi]=mean->voi[0].y2[fi]=mean->voi[0].y3[fi]=nan("");
    } else {
      mean->voi[0].y[fi]=sum/(double)n;
      if(n==1) {
        mean->voi[0].y2[fi]=mean->voi[0].y3[fi]=0.0;
      } else {
        mean->voi[0].y2[fi]=sqrt((ssum-sum*sum/(double)n)/(double)(n-1));
        if(fabs(mean->voi[0].y[fi])>1.0E-25)
          mean->voi[0].y3[fi]=fabs(mean->voi[0].y2[fi]/mean->voi[0].y[fi]);
        else
          mean->voi[0].y3[fi]=0.0;
      }
    }
    if(n>0) ret++;
  }
  /* Check that at least half of frames contained acceptable data */
  if(2*ret<dft->frameNr) {dftEmpty(mean); return(10);}
 
  return(0);
}

Referenced by noiseSD4SimulationFromDFT().

dftMin2sec()

void dftMin2sec ( DFT * dft )

extern

Change time unit from min to sec, without checking original unit.

Definition at line 145 of file dftunit.c.

{
  int i;
 
  for(i=0; i<dft->frameNr; i++) {
    if(!isnan(dft->x[i]))  dft->x[i]*=60.;
    if(!isnan(dft->x1[i])) dft->x1[i]*=60.;
    if(!isnan(dft->x1[i])) dft->x2[i]*=60.;
  }
  dft->timeunit=TUNIT_SEC;
}

Referenced by copy_times_from_img_to_dft(), cptWrite(), and dftTimeunitConversion().

dftMinMax()

int dftMinMax ( DFT * dft, double * minx, double * maxx, double * miny, double * maxy )

extern

Search the min and max values of DFT TAC data. Data may contain NA's.

Note that minx and maxx are the smallest and highest x values in data, not the x values at y minimum and maximum; use dftMinMaxTAC() for that.

See also

dftMinMaxTAC, dftRobustMinMaxTAC

Returns

Returns 0 if successful.

Parameters

dft	Pointer to the DFT TAC data to search
minx	Pointer to min X; set to NULL if not needed
maxx	Pointer to max X; set to NULL if not needed
miny	Pointer to min Y; set to NULL if not needed
maxy	Pointer to max Y; set to NULL if not needed

Definition at line 974 of file dft.c.

  {
  int ri, fi, n;
  double x1, x2, y1, y2;
 
  if(dft==NULL) return(1);
  x1=x2=y1=y2=nan("");
  for(fi=0; fi<dft->frameNr; fi++) {
    for(ri=0, n=0; ri<dft->voiNr; ri++) if(!isnan(dft->voi[ri].y[fi])) {
      if(isnan(y1) || y1>dft->voi[ri].y[fi]) y1=dft->voi[ri].y[fi];
      if(isnan(y2) || y2<dft->voi[ri].y[fi]) y2=dft->voi[ri].y[fi];
      n++;
    }
    if(n==0) continue; // no true y values, thus do not use x either
    if(dft->timetype==DFT_TIME_STARTEND) {
      if(!isnan(dft->x1[fi])) {
        if(isnan(x1) || x1>dft->x1[fi]) x1=dft->x1[fi];
      }
      if(!isnan(dft->x2[fi])) {
        if(isnan(x2) || x2<dft->x2[fi]) x2=dft->x2[fi];
      }
    } else if(!isnan(dft->x[fi])) {
      if(isnan(x1) || x1>dft->x[fi]) x1=dft->x[fi];
      if(isnan(x2) || x2<dft->x[fi]) x2=dft->x[fi];
    }
  }
  if(minx!=NULL) {if(isnan(x1)) return(3); else *minx=x1;}
  if(maxx!=NULL) {if(isnan(x2)) return(4); else *maxx=x2;}
  if(miny!=NULL) {if(isnan(y1)) return(5); else *miny=y1;}
  if(maxy!=NULL) {if(isnan(y2)) return(6); else *maxy=y2;}
  return(0);
}

Referenced by plot_fit_svg(), and plot_fitrange_svg().

dftMinMaxTAC()

int dftMinMaxTAC ( DFT * dft, int tacindex, double * minx, double * maxx, double * miny, double * maxy, int * mini, int * maxi, int * mins, int * maxs )

extern

Search the min and max values of DFT TAC data. Data may contain NA's. This is not a replacement of dftMinMax() which is needed e.g. in plotting functions.

See also

dftMinMax, dftRobustMinMaxTAC

Returns

Returns 0 if successful.

Parameters

dft	Pointer to the DFT TAC data to search
tacindex	Index of the only TAC which is searched for min and max; <0 if all
minx	Pointer to X at TAC min; set to NULL if not needed
maxx	Pointer to X at TAC max; set to NULL if not needed
miny	Pointer to min Y; set to NULL if not needed
maxy	Pointer to max Y; set to NULL if not needed
mini	Index of min TAC; set to NULL if not needed
maxi	Index of max TAC; set to NULL if not needed
mins	Index of min sample; set to NULL if not needed
maxs	Index of max sample; set to NULL if not needed

Definition at line 1024 of file dft.c.

  {
  int ri, fi, i1, i2, s1, s2;
  double x, x1, x2, y1, y2;
 
  if(dft==NULL) return(1);
  if(tacindex>=dft->voiNr) return(2);
  if(dft->voiNr<1 || dft->frameNr<1) return(3);
 
  x1=x2=y1=y2=nan(""); i1=i2=s1=s2=0;
  for(fi=0; fi<dft->frameNr; fi++) {
    if(dft->timetype==DFT_TIME_STARTEND) {
      if(isnan(dft->x1[fi])) continue;
      if(isnan(dft->x2[fi])) continue;
      x=0.5*(dft->x1[fi]+dft->x2[fi]);
    } else {
      if(isnan(dft->x[fi])) continue;
      x=dft->x[fi];
    }
    for(ri=0; ri<dft->voiNr; ri++) if(!isnan(dft->voi[ri].y[fi])) {
      if(tacindex>=0 && ri!=tacindex) continue;
      if(isnan(y1) || y1>dft->voi[ri].y[fi]) {
        y1=dft->voi[ri].y[fi]; i1=ri; x1=x; s1=fi;}
      if(isnan(y2) || y2<dft->voi[ri].y[fi]) {
        y2=dft->voi[ri].y[fi]; i2=ri; x2=x; s2=fi;}
    }
  }
  if(minx!=NULL) {if(isnan(x1)) return(11); else *minx=x1;}
  if(maxx!=NULL) {if(isnan(x2)) return(12); else *maxx=x2;}
  if(miny!=NULL) {if(isnan(y1)) return(13); else *miny=y1;}
  if(maxy!=NULL) {if(isnan(y2)) return(14); else *maxy=y2;}
  if(mini!=NULL) {if(isnan(y1)) return(13); else *mini=i1;}
  if(maxi!=NULL) {if(isnan(y2)) return(14); else *maxi=i2;}
  if(mins!=NULL) {if(isnan(y1)) return(13); else *mins=s1;}
  if(maxs!=NULL) {if(isnan(y2)) return(14); else *maxs=s2;}
  return(0);
}

Referenced by dftFixPeak(), and dftVerifyPeak().

dftMovevoi()

int dftMovevoi ( DFT * dft, int from, int to )

extern

Move VOI in DFT structure from one position to another.

Parameters

dft	Pointer to DFT struct
from	TAC index
to	TAC index

Definition at line 508 of file dft.c.

  {
  int ri;
  size_t voisize;
  Voi voi;
 
  if(dft==NULL || from<0 || to<0) return(1);
  if(from+1>dft->_voidataNr || to+1>dft->_voidataNr) return(2);
  if(from==to) return(0);
  voisize=sizeof(Voi);
  memcpy(&voi, dft->voi+from, voisize);
  if(from>to) for(ri=from; ri>to; ri--)
    memcpy(dft->voi+ri, dft->voi+(ri-1), voisize);
  else for(ri=from; ri<to; ri++)
    memcpy(dft->voi+ri, dft->voi+(ri+1), voisize);
  memcpy(dft->voi+ri, &voi, voisize);
  return(0);
}

Referenced by dftDelete(), and dftReadinput().

dftNAfill()

int dftNAfill ( DFT * dft )

extern

Replace NA's in basic DFT data with interpolated values. If extrapolation is necessary, then the values (0,0) and (Infinity,last measured) are assumed.

Returns

Returns 0, if NA's could be filled with sensible values.

Parameters

dft	Pointer to DFT struct

Definition at line 930 of file dft.c.

  {
  int ri, fi, fj;
  double x1, x2, y1, y2, x, y;
 
  if(dft==NULL || dft->voiNr<1 || dft->frameNr<1) return(1);
  for(ri=0; ri<dft->voiNr; ri++) for(fi=0; fi<dft->frameNr; fi++) {
    if(isnan(dft->x[fi])) return(2);
    if(isnan(dft->voi[ri].y[fi])) {
      /* NA's before zero time are always replaced with 0 */
      if(dft->x[fi]<0.0) {dft->voi[ri].y[fi]=0.0; continue;}
      x=dft->x[fi];
      /* Get the previous data that is not NA */
      for(x1=y1=nan(""), fj=fi-1; fj>=0; fj--) if(!isnan(dft->voi[ri].y[fj])) {
        x1=dft->x[fj]; y1=dft->voi[ri].y[fj]; break;
      }
      if(isnan(x1) || isnan(y1)) x1=y1=0.0;
      /* Get the following data that is not NA */
      for(x2=y2=nan(""), fj=fi+1; fj<dft->frameNr; fj++) if(!isnan(dft->voi[ri].y[fj])) {
        x2=dft->x[fj]; y2=dft->voi[ri].y[fj]; break;
      }
      if(isnan(x2) || isnan(y2)) for(fj=fi-1; fj>=0; fj--) if(!isnan(dft->voi[ri].y[fj])) {
        x2=dft->x[fj]; y2=dft->voi[ri].y[fj]; break;
      }
      if(isnan(x2) || isnan(y2)) return(2);
      /* Calculate new value */
      if(x2==x1) y=0.5*(y1+y2); else y=y2-(x2-x)*(y2-y1)/(x2-x1);
      dft->voi[ri].y[fi]=y;
    }
  }
  return(0);
}

dftOverflow()

int dftOverflow ( DFT * data )

extern

Check for overflows in data structure. Returns 0, if ok.

Parameters

data	Pointer to DFT struct

Definition at line 451 of file dft.c.

  {
  int i;
 
  if(data==NULL || data->frameNr<1 || data->voiNr<1) return 0;
  if(data->x[data->frameNr]!=0.0) return 1;
  if(data->x1[data->frameNr]!=0.0) return 2;
  if(data->x2[data->frameNr]!=0.0) return 3;
  for(i=0; i<data->voiNr; i++) {
    if(data->voi[i].y[data->frameNr]!=0.0) return 4;
    if(data->voi[i].y2[data->frameNr]!=0.0) return 5;
    if(data->voi[i].y3[data->frameNr]!=0.0) return 6;
  }
  return 0;
}

dftPrint()

void dftPrint ( DFT * data )

extern

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 )

extern

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().

dftRemoveTimeRange()

int dftRemoveTimeRange ( DFT * dft, double startT, double endT )

extern

Extract specified sample time interval from TAC data.

Returns

Returns 0 when successful, otherwise <>0.

Parameters

dft	Pointer to DFT struct from where samples outside time range will be removed. Data must be sorted to increasing frame times before calling this function.
startT	Start time of data that is preserved (in same units as in DFT)
endT	End time of data that is preserved (in same units as in DFT)

Definition at line 1275 of file dft.c.

  {
  int i, j, voi, first, origNr;
 
  if(dft==NULL || dft->frameNr<1 || dft->voiNr<1) return(1);
  if(endT<startT) return(2);
  if(startT<=dft->x[0] && endT>=dft->x[dft->frameNr-1]) return(0);
  origNr=dft->frameNr;
 
  /* Delete end frames which are collected later than the end time */
  for(j=dft->frameNr-1; j>=0; j--) if(dft->x[j]<=endT) break;
  dft->frameNr=j+1;
 
  /* Find the first frame that has been collected later than start time */
  for(j=0, first=-1; j<dft->frameNr; j++)
    if(dft->x[j]>=startT) {first=j; break;}
  if(first<0) {
    dft->frameNr=origNr; // undelete the end data
    return(3);
  }
 
  /* Delete first frames */
  if(first>0) for(j=first, i=0; j<dft->frameNr; j++, i++) {
    dft->x[i]=dft->x[j]; dft->x1[i]=dft->x1[j]; dft->x2[i]=dft->x2[j];
    dft->w[i]=dft->w[j];
    for(voi=0; voi<dft->voiNr; voi++) {
      dft->voi[voi].y[i]=dft->voi[voi].y[j];
      dft->voi[voi].y2[i]=dft->voi[voi].y2[j];
      dft->voi[voi].y3[i]=dft->voi[voi].y3[j];
    }
  }
  dft->frameNr-=first;
 
  return(0);
}

dftRNameSimplify()

void dftRNameSimplify ( DFT * dft, int hemisphere, int place )

extern

Simplify TAC names in DFT struct: empty hemisphere and/or place field in case those are the same in all TACs.

Parameters

dft	Pointer to DFT struct
hemisphere	Is hemisphere field simplified (1) or not (0), when possible
place	Is place field simplified (1) or not (0), when possible

Definition at line 1534 of file dft.c.

  {
  int ri, n;
 
  if(dft==NULL || dft->voiNr<1) return;
  if(hemisphere==0 && place==0) return;
 
  /* Check if all TACs have the same field content: if yes, then
     delete the field content */ 
  if(hemisphere!=0) {
    for(ri=n=1; ri<dft->voiNr; ri++)
      if(strcasecmp(dft->voi[0].hemisphere, dft->voi[ri].hemisphere)==0) n++;
    if(n==dft->voiNr)
      for(ri=0; ri<dft->voiNr; ri++)
        strcpy(dft->voi[ri].hemisphere, "");
  }
  if(place!=0) {
    for(ri=n=1; ri<dft->voiNr; ri++)
      if(strcasecmp(dft->voi[0].place, dft->voi[ri].place)==0) n++;
    if(n==dft->voiNr)
      for(ri=0; ri<dft->voiNr; ri++)
        strcpy(dft->voi[ri].place, "");
  }
 
  /* Construct combined TAC names */
  for(ri=0; ri<dft->voiNr; ri++)
    rnameCatenate(dft->voi[ri].name, MAX_REGIONNAME_LEN,
                  dft->voi[ri].voiname, dft->voi[ri].hemisphere,
                  dft->voi[ri].place, '_');
  /* Ready */
  return;
}

dftSec2min()

void dftSec2min ( DFT * dft )

extern

Change time unit from sec to min, without checking original unit.

Definition at line 160 of file dftunit.c.

{
  int i;
 
  for(i=0; i<dft->frameNr; i++) {
    if(!isnan(dft->x[i]))  dft->x[i]/=60.; 
    if(!isnan(dft->x1[i])) dft->x1[i]/=60.; 
    if(!isnan(dft->x1[i])) dft->x2[i]/=60.;
  }
  dft->timeunit=TUNIT_MIN;
}

Referenced by copy_times_from_img_to_dft(), cptReadOne(), and dftTimeunitConversion().

dftSelect()

int dftSelect ( DFT * data, char * name )

extern

Select VOIs (sets sw=1), whose names are matching specified string. If no string is specified, then all VOIs are selected. This function is to replaced by dftSelectRegions().

Returns

Returns the number of matches, or <0, if an error occurred.

Parameters

data	Pointer to DFT struct
name	String to search in TAC name fields

Definition at line 239 of file dft.c.

  {
  unsigned int i, j, n;
  char *p, n1[128], n2[128], n3[128], tmp[128], sname[1024];
 
  if(data==NULL) return -1;
  /* Select all, if no string was specified */
  if(name==NULL || strlen(name)==0) {
    for(i=0; i<(unsigned int)data->voiNr; i++) data->voi[i].sw=1; 
    return data->voiNr;
  }
  /* Make a copy of 'name' and use it */
  strcpy(sname, name);
  /* Check if string contains several substrings (hemisphere and place) */
  n1[0]=n2[0]=n3[0]=(char)0;
  p=strtok(sname, " ,;\n\t|"); if(p!=NULL) strcpy(n1, p); else return -1;
  p=strtok(NULL, " ,;\n\t|"); if(p!=NULL) {
    strcpy(n2, p); p=strtok(NULL, " ,;\n\t|"); if(p!=NULL) strcpy(n3, p);}
  /* Convert strings to lowercase */
  for(i=0; i<strlen(n1); i++) n1[i]=tolower(n1[i]);
  for(i=0; i<strlen(n2); i++) n2[i]=tolower(n2[i]);
  for(i=0; i<strlen(n3); i++) n3[i]=tolower(n3[i]);
  /* Search through the data */
  for(i=0, n=0; i<(unsigned int)data->voiNr; i++) {
    data->voi[i].sw=0;
    snprintf(tmp, 128, "%s%s%s", data->voi[i].voiname, data->voi[i].hemisphere,
                                 data->voi[i].place);
    for(j=0; j<strlen(tmp); j++) tmp[j]=tolower(tmp[j]);
    if(strstr(tmp, n1)==NULL) continue;
    if(n2[0] && strstr(tmp, n2)==NULL) continue;
    if(n3[0] && strstr(tmp, n3)==NULL) continue;
    data->voi[i].sw=1; n++;
  }
  return n;
}

dftSelectBestReference()

int dftSelectBestReference ( DFT * dft )

extern

Select the best reference region in case that several were found with dftSelectRegions.

Returns

Returns the index of best region, or <0 in case of an error.

Parameters

dft	Pointer to DFT struct, after using dftSelectRegions()

Definition at line 314 of file dft.c.

  {
  int ri, len, min_len, i;
  
  if(dft==NULL || dft->voiNr<1) return -1;
  for(ri=0, i=-1, min_len=9999; ri<dft->voiNr; ri++) if(dft->voi[ri].sw) {
    len=strlen(dft->voi[ri].voiname);
    if(strcmp(dft->voi[ri].hemisphere, ".")!=0 &&
       strcasecmp(dft->voi[ri].hemisphere, "AVG")!=0 &&
       strcasecmp(dft->voi[ri].hemisphere, "MEAN")!=0)
      len+=1+strlen(dft->voi[ri].hemisphere);
    if(strcmp(dft->voi[ri].place, ".")!=0 &&
       strcasecmp(dft->voi[ri].place, "ALL")!=0 &&
       strcasecmp(dft->voi[ri].place, "AVG")!=0 &&
       strcasecmp(dft->voi[ri].place, "MEAN")!=0)
      len+=1+strlen(dft->voi[ri].place);
    if(len<min_len) {min_len=len; i=ri;}
  }
  if(i<0) return -2; else return i;
}

Referenced by dftReadinput(), and dftReadReference().

dftSelectRegions()

int dftSelectRegions ( DFT * dft, char * region_name, int reset )

extern

Select the VOIs that have matching region name or number. Sets sw=1 or sw=0. This function will replace dftSelect().

Returns

Returns the number of selected VOIs, or <0 in case of an error.

Parameters

dft	Pointer to DFT data where VOIs are selected
region_name	Name or VOI number which is searched
reset	1=Non-matching VOIs are deselected, 0=Old selections are preserved

Definition at line 285 of file dft.c.

  {
  int ri, match_nr=0;
 
  /* Check the input */
  if(dft==NULL || dft->voiNr<1 || strlen(region_name)<1) return(-1);
  /* Reset all selections if required */
  if(reset!=0) for(ri=0; ri<dft->voiNr; ri++) dft->voi[ri].sw=0;
  /* Check each VOI */
  for(ri=0; ri<dft->voiNr; ri++) {
    if(rnameMatch(dft->voi[ri].name, ri+1, region_name)!=0) {
      dft->voi[ri].sw=1; match_nr++;
    }
  }
  return(match_nr);
}

Referenced by dftReadinput(), and dftReadReference().

dftSetComments()

void dftSetComments ( DFT * dft )

extern

Overwrites DFT comments with information in current DFT header.

If DFT format specifies that titles are to be saved, that information is not included in comments.

Parameters

dft	Pointer to DFT struct

Definition at line 1326 of file dft.c.

  {
  char tmp[512];
 
  if(dft==NULL) return;
  strcpy(dft->comments, "");
  /* Write in comments the information that will not be included in titles */
  if(dft->scanStartTime[0]) {
    sprintf(tmp, "# scan_start_time := %s\n", dft->scanStartTime);
    strcat(dft->comments, tmp);
  }
  if(dft->injectionTime[0]) {
    sprintf(tmp, "# injection_time := %s\n", dft->injectionTime);
    strcat(dft->comments, tmp);
  }
  strcpy(tmp, "# decay_correction := ");
  if(dft->decayCorrected==DFT_DECAY_CORRECTED) strcat(tmp, "Yes\n");
  else if(dft->decayCorrected==DFT_DECAY_NOTCORRECTED) strcat(tmp, "No\n");
  else strcat(tmp, "Unknown\n");
  if(dft->decayCorrected!=DFT_DECAY_UNKNOWN) strcat(dft->comments, tmp);
  if(dft->isotope[0]) {
    sprintf(tmp, "# isotope := %s\n", dft->isotope);
    strcat(dft->comments, tmp);
  }
  if(dft->radiopharmaceutical[0]) {
    sprintf(tmp, "# radiopharmaceutical := %s\n", dft->radiopharmaceutical);
    strcat(dft->comments, tmp);
  }
  /* If titles are set to be saved, then there's no need to put more in comments */
  if(dft->_type==DFT_FORMAT_STANDARD || dft->_type==DFT_FORMAT_PMOD) return;
  
  /* Ok then, lets write even title information in comments */
  if(dft->studynr[0]) {
    sprintf(tmp, "# study_number := %s\n", dft->studynr);
    strcat(dft->comments, tmp);
  }
  if(dft->timeunit!=TUNIT_UNKNOWN) {
    sprintf(tmp, "# timeunit := %s\n", petTunit(dft->timeunit) );
    strcat(dft->comments, tmp);
  }
  if(petCunitId(dft->unit)!=CUNIT_UNKNOWN) {
    sprintf(tmp, "# unit := %s\n", dft->unit );
    strcat(dft->comments, tmp);
  }
  // Region names and volumes are not saved in comments because of space limit
  
  return;
}

Referenced by dftRead().

dftSetmem()

int dftSetmem ( DFT * data, int frameNr, int voiNr )

extern

Allocate memory for DFT data and sets data pointers.

Returns

Returns <> 0 in case of an error.

Parameters

data	Pointer to initiated DFT structure data; any old contents are deleted.
frameNr	Nr of time frames (samples) to allocate
voiNr	Nr of concentration arrays (regional TACs) to allocate

Definition at line 57 of file dft.c.

  {
  int i, n;
  double *d;
 
 
  if(data==NULL) return 1;
  /* Clear previous data */
  dftEmpty(data);
 
  /* Allocate memory for curves */
  data->voi=(Voi*)calloc(voiNr, sizeof(Voi));
  if(data->voi==NULL) return 1;
  data->_voidataNr=voiNr;
 
  /* Allocate memory for frames */
  /* For 3 axes, weights, and for curves (3 for each VOI) */
  /* And one extra 'frame' for overflow testing */
  n=(frameNr+1)*(3+1+3*voiNr);
  data->_data=(double*)calloc(n, sizeof(double));
  if(data->_data==NULL) return 1;
  data->_dataSize=n;
 
  /* Set pointers for curve data */
  d=data->_data; data->x = d;
  d += frameNr + 1; data->x1 = d;
  d += frameNr + 1; data->x2 = d;
  d += frameNr + 1; data->w = d;
  for(i=0; i<voiNr; i++) {
    d += frameNr + 1; data->voi[i].y = d;
    d += frameNr + 1; data->voi[i].y2 = d;
    d += frameNr + 1; data->voi[i].y3 = d;
  }
 
  return 0;
}

Referenced by bf_srtm(), bfIrr2TCM(), bfRadiowater(), clusterTACs(), cptReadOne(), csv2dft_a(), csv2dft_b(), csv2dft_linkset(), csv2dft_mat(), dftAddnullframe(), dftAddSpaceForFrames(), dftAllocateWithHeader(), dftAllocateWithIMG(), dftAutointerpolate(), dftDivideFrames(), dftDoubleFrames(), dftdup(), dftFillInitialGap(), dftInterpolate(), dftRead(), extrapolate_monoexp(), idwcRead(), ifRead(), img_k1_using_ki(), img_logan(), img_patlak(), plotdata_as_dft(), roikbqRead(), sif2dft(), simMyocDiameterCurve(), tsvRead(), and xelRead().

dftSort()

int dftSort ( DFT * data )

extern

Sort DFT regions in alphabetical order by their name.

Returns

Returns <> 0 in case of an error.

Parameters

data	Pointer to DFT struct

Definition at line 845 of file dft.c.

  {
  if(data==NULL) return(1);
  if(data->voiNr<=1) return(0);
  qsort(data->voi, data->voiNr, sizeof(Voi), dftQSortName);
  return(0);
}

dftSortByFrame()

int dftSortByFrame ( DFT * dft )

extern

Sorts TAC frames by increasing sample time.

Returns

Returns 0 if ok.

Parameters

dft	Pointer to DFT struct

Definition at line 1169 of file dft.c.

  {
  int ri, fi, fj;
  double d;
 
  if(dft==NULL || dft->voiNr<1 || dft->frameNr<1) return(1);
  for(fi=0; fi<dft->frameNr-1; fi++) for(fj=fi+1; fj<dft->frameNr; fj++) {
    if(dft->x[fj]>=dft->x[fi]) continue;
    d=dft->x[fi];  dft->x[fi]=dft->x[fj];   dft->x[fj]=d;
    d=dft->x1[fi]; dft->x1[fi]=dft->x1[fj]; dft->x1[fj]=d;
    d=dft->x2[fi]; dft->x2[fi]=dft->x2[fj]; dft->x2[fj]=d;
    d=dft->w[fi];  dft->w[fi]=dft->w[fj];   dft->w[fj]=d;
    for(ri=0; ri<dft->voiNr; ri++) {
      d=dft->voi[ri].y[fi]; dft->voi[ri].y[fi]=dft->voi[ri].y[fj]; dft->voi[ri].y[fj]=d;
      d=dft->voi[ri].y2[fi]; dft->voi[ri].y2[fi]=dft->voi[ri].y2[fj]; dft->voi[ri].y2[fj]=d;
      d=dft->voi[ri].y3[fi]; dft->voi[ri].y3[fi]=dft->voi[ri].y3[fj]; dft->voi[ri].y3[fj]=d;
    }
  }
  return(0);
}

Referenced by dftReadModelingData(), and dftVerifyPeak().

dftSortPlane()

int dftSortPlane ( DFT * data )

extern

Sort DFT regions in alphabetical order by their plane.

Returns

Returns <> 0 in case of an error.

Parameters

data	Pointer to DFT struct

Definition at line 875 of file dft.c.

  {
  if(data==NULL) return(1);
  if(data->voiNr<=1) return(0);
  qsort(data->voi, data->voiNr, sizeof(Voi), dftQSortPlane);
  return(0);
}

Referenced by cptWrite().

dftTimeunitConversion()

int dftTimeunitConversion ( DFT * dft, int tunit )

extern

Conversion of the DFT timeunit. Changes both data values and timeunit code. Currently available conversions are: min <-> sec

Returns

Returns 0 if conversion was successful, and <> 0 if failed.

Parameters

dft	Pointer to existing DFT data, whose timeunit is to be changed
tunit	New timeunit code

Definition at line 119 of file dftunit.c.

  {
  /* Check the input */
  if(dft==NULL || tunit<0) return(1);
  
  /* Check if unit already is as required */
  if(dft->timeunit==tunit) return(0);
  
  /* Do the conversion, if supported */
  if(dft->timeunit==TUNIT_MIN && tunit==TUNIT_SEC)
    dftMin2sec(dft);
  else if(dft->timeunit==TUNIT_SEC && tunit==TUNIT_MIN)
    dftSec2min(dft);
  else
    return(2);
 
  return(0);
} 

Referenced by dftInterpolateCheckEnd(), dftInterpolateCheckStart(), dftMatchTimeunits(), dftReadinput(), dftReadModelingData(), dftReadReference(), img_logan(), img_patlak(), and imgReadModelingData().

dftTimeunitToDFT()

int dftTimeunitToDFT ( DFT * dft, const char * timeunit )

extern

Set DFT timeunit; does not change the sample times.

Returns

Returns 0 if successful, and <> 0 if invalid timeunit.

Definition at line 103 of file dftunit.c.

{
  if(dft==NULL || timeunit==NULL) return(1);
  int tunit=petTunitId(timeunit);
  if(tunit<0) return(2); else dft->timeunit=tunit;
  return(0);
}

Referenced by tsvRead().

dftToResult()

int dftToResult ( DFT * dft, RES * res, char * status )

extern

Copy the contents (both header and data) of DFT struct into RES struct.

See also

fitToResult, res_allocate_with_dft

Returns

Returns 0 if successful, in case of an error >0, and <0 if warning is suggested.

Parameters

dft	Regional data from where necessary information is read.
res	Pointer to initiated RES struct which will be allocated here.
status	Pointer to a string (allocated for at least 64 chars) where error message or other execution status will be written; enter NULL, if not needed.

Definition at line 60 of file dftres.c.

  {
  int ri, fi;
 
  // Check the input data
  if(status!=NULL) sprintf(status, "program error");
  if(res==NULL || dft==NULL || dft->voiNr<1 || dft->frameNr<1) return 1;
  // Allocate memory and copy most of headers
  if(res_allocate_with_dft(res, dft) != 0) {
    if(status!=NULL) sprintf(status, "cannot setup results data");
    return 2;
  }
  res->parNr=dft->frameNr; if(res->parNr>MAX_RESPARAMS) {
    sprintf(status, "only %d frames can be copied to results", MAX_RESPARAMS);
    res->parNr=MAX_RESPARAMS;
  }
  // Set parameter titles and units
  for(fi=0; fi<res->parNr; fi++) {
    sprintf(res->parname[fi], "%d", fi+1);
    strcpy(res->parunit[fi], dft->unit);
  }
  // Copy regional values
  for(ri=0; ri<dft->voiNr; ri++) for(fi=0; fi<res->parNr; fi++)
    res->voi[ri].parameter[fi]=dft->voi[ri].y[fi];
 
  if(dft->frameNr>MAX_RESPARAMS) return -1;
  /* Set also deprecated parameter name and unit representations, for now */
  resFixParnames(res);
  return 0;
}

dftType()

int dftType ( FILE * fp )

extern

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;
}

dftUnitConversion()

int dftUnitConversion ( DFT * dft, int dunit )

extern

Conversion of the DFT calibration unit. Changes both data values and unit string. Currently available conversions are: MBq/cc <-> kBq/cc <-> Bq/cc <-> nCi/cc <-> uCi/cc Bq <-> kBq <-> MBq <-> GBq <-> nCi <-> uCi <-> mCi

Returns

Returns 0 if conversion was successful, and <> 0 if failed.

Parameters

dft	Pointer to existing DFT data, whose calibration unit is to be changed
dunit	New unit code

Definition at line 25 of file dftunit.c.

  {
  int current_dunit=CUNIT_UNKNOWN;
  double f=1.0;
  int ri, fi;
  int unit_type=0; /* 0=unknown; 1=concentration; 2=dose */
 
  /* Check the input */
  if(dft==NULL || dunit<0) return(1);
  
  /* Identify the current unit */
  current_dunit=petCunitId(dft->unit);
  if(current_dunit==CUNIT_UNKNOWN) return(2);
  /* If unit is already the requested one, then return */
  if(current_dunit==dunit) return(0);
 
  /* Determine the conversion factor to kBq/cc or MBq */
  switch(current_dunit) {
    case CUNIT_BQ_PER_ML:  f*=0.001; unit_type=1; break;
    case CUNIT_KBQ_PER_ML: f*=1.0; unit_type=1; break;
    case CUNIT_MBQ_PER_ML: f*=1000.0; unit_type=1; break;
    case CUNIT_NCI_PER_ML: f*=0.037; unit_type=1; break;
    case CUNIT_UCI_PER_ML: f*=37.0; unit_type=1; break;
    case CUNIT_BQ:         f*=0.000001; unit_type=2; break;
    case CUNIT_KBQ:        f*=0.001; unit_type=2; break;
    case CUNIT_MBQ:        f*=1.0; unit_type=2; break;
    case CUNIT_GBQ:        f*=1000.0; unit_type=2; break;
    case CUNIT_NCI:        f*=0.000037; unit_type=2; break;
    case CUNIT_UCI:        f*=0.037; unit_type=2; break;
    case CUNIT_MCI:        f*=37.0; unit_type=2; break;
    default: return(2);
  }
 
  /* Determine the conversion factor from kBq/cc or MBq to the required unit */
  if(unit_type==1) switch(dunit) { // concentrations
    case CUNIT_BQ_PER_ML:  f*=1000.0; break;
    case CUNIT_KBQ_PER_ML: f*=1.0; break;
    case CUNIT_MBQ_PER_ML: f*=0.001; break;
    case CUNIT_NCI_PER_ML: f/=0.037; break;
    case CUNIT_UCI_PER_ML: f/=37.0; break;
    default: return(3);
  } else if(unit_type==2) switch(dunit) { // doses
    case CUNIT_BQ:         f*=1000000.0; break;
    case CUNIT_KBQ:        f*=1000.0; break;
    case CUNIT_MBQ:        f*=1.0; break;
    case CUNIT_GBQ:        f*=0.001; break;
    case CUNIT_NCI:        f/=0.000037; break;
    case CUNIT_UCI:        f/=0.037; break;
    case CUNIT_MCI:        f/=37.0; break;
    default: return(3);
  } else
    return(3);
 
  /* Convert the data values */
  if(f==1.0) return(0);
  for(fi=0; fi<dft->frameNr; fi++) {
    for(ri=0; ri<dft->voiNr; ri++) {
      if(!isnan(dft->voi[ri].y[fi])) dft->voi[ri].y[fi]*=f;
      if(!isnan(dft->voi[ri].y2[fi])) dft->voi[ri].y2[fi]*=f;
      if(!isnan(dft->voi[ri].y3[fi])) dft->voi[ri].y3[fi]*=f;
    }
  }
  
  /* Set the new unit string */
  dftUnitToDFT(dft, dunit);
 
  return(0);
} 

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

dftUnitToDFT()

void dftUnitToDFT ( DFT * dft, int dunit )

extern

Set DFT calibration unit string

Definition at line 11 of file dftunit.c.

{
  strcpy(dft->unit, dftUnit(dunit));
}

Referenced by csv2dft_a(), csv2dft_b(), csv2dft_linkset(), csv2dft_mat(), dftUnitConversion(), and tsvRead().

dftValidNr()

int dftValidNr ( DFT * dft, double tstart, double tstop, int index )

extern

Determine the nr of valid data points inside the given time range.

Returns

The number of valid data points.

Parameters

dft	Pointer to DFT struct
tstart	Time range start
tstop	Time range stop
index	Index of TAC to use; enter <0 to use all, in which case the minimum number of valid points is returned.

Definition at line 1638 of file dft.c.

  {
  if(dft==NULL || dft->voiNr<0 || dft->frameNr<0) return(0);
  if(index>dft->voiNr-1) return(0);
  if(index>=0) { // TAC index given
    int n=0;
    double x;
    for(int i=0; i<dft->frameNr; i++) {
      if(dft->timetype!=DFT_TIME_STARTEND) x=dft->x[i]; 
      else x=0.5*(dft->x1[i]+dft->x2[i]); 
      if(isnan(x) || !isfinite(x)) continue;
      if(x<tstart || x>tstop) continue;
      if(isnan(dft->voi[index].y[i]) || !isfinite(dft->voi[index].y[i])) 
        continue;
      n++;
    }
    return(n);
  }
  /* Get min nr of all TACs */  
  int n=0, minn=0;
  minn=dftValidNr(dft, tstart, tstop, 0);
  for(int j=1; j<dft->voiNr; j++) {
    n=dftValidNr(dft, tstart, tstop, j);
    if(n<minn) minn=n;
  }
  return(minn);
}

Referenced by dftValidNr().

dftWrite()

int dftWrite ( DFT * data, char * filename )

extern

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 )

extern

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 )

extern

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 )

extern

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().

factorial()

unsigned int factorial ( unsigned int n )

extern

Calculate factorial of given number.

See also

lfactorial, igam, igamc

Returns

Returns factorial n!, or zero if factorial would cause wrap-around.

Parameters

n	Integer n, from which the factorial is calculated.

Note

Wrap-around will occur if n>12.

Definition at line 1678 of file mathfunc.c.

  {
  if(n<1) return(1);
  if(n>12) return(0);
  return(n*factorial(n-1));
}

Referenced by factorial().

fit_allocate_with_dft()

int fit_allocate_with_dft ( FIT * fit, DFT * dft )

extern

Allocate memory for regional function fits based on information in DFT.

Returns

Returns 0 if successful, otherwise <>0.

Parameters

fit	Pointer to initiated FIT struct which will be allocated here and filled with ROI names etc.
dft	Regional data from where necessary information is read.

Definition at line 14 of file fitres.c.

  {
  int ri;
 
  //printf("fit_allocate_with_dft()\n"); fflush(stdout);
  // Check the input data
  if(fit==NULL || dft==NULL || dft->voiNr<1) return 1;
  // Allocate memory
  if(fitSetmem(fit, dft->voiNr)!=0) return 2;
  fit->voiNr=dft->voiNr;
  /* Set header contents */
  fit->time=time(NULL); // Set current time to results
  strcpy(fit->unit, dft->unit);
  fit->timeunit=dft->timeunit;
  strcpy(fit->studynr, dft->studynr);
  /* Copy region names, etc */
  for(ri=0; ri<dft->voiNr; ri++) {
    strcpy(fit->voi[ri].name, dft->voi[ri].name);
    strcpy(fit->voi[ri].voiname, dft->voi[ri].voiname);
    strcpy(fit->voi[ri].hemisphere, dft->voi[ri].hemisphere);
    strcpy(fit->voi[ri].place, dft->voi[ri].place);
    fit->voi[ri].dataNr=dft->frameNr;
    if(dft->timetype==DFT_TIME_STARTEND) {
      fit->voi[ri].start=dft->x1[0]; fit->voi[ri].end=dft->x2[dft->frameNr-1];
    } else {
      fit->voi[ri].start=dft->x[0]; fit->voi[ri].end=dft->x[dft->frameNr-1];
    }
  }
 
  return 0;
}

Referenced by dft_end_line().

fitDerivEval()

int fitDerivEval ( FitVOI * r, double x, double * yd )

extern

Evaluates yd=Df(x).

See also

fitEval, fitIntegralEval

Returns

Returns 0, if ok.

Parameters

r	Fit parameters of a single region
x	Time where to evaluate the derivative of the function
yd	The derivative of the function is returned here

Definition at line 1540 of file mathfunc.c.

  {
  double a, f, xt, t;
 
  if(r==NULL || yd==NULL) return 1;
  *yd=nan("");
  switch(r->type) {
    case 301:
      break;
    case 302:
      break;
    case 303:
      break;
    case 304:
      break;
    case 305:
      break;
    case 321:
      f=r->p[0]*r->p[1]*exp(r->p[1]*x)*(1.0-exp(r->p[2]*x)) - r->p[0]*r->p[2]*exp((r->p[1]+r->p[2])*x);
      *yd=f;
      break;
    case 322:
      f=0.0;
      a=r->p[0]*r->p[1]*exp(r->p[1]*x)*(1.0-exp(r->p[2]*x)) - r->p[0]*r->p[2]*exp((r->p[1]+r->p[2])*x); f+=a;
      a=r->p[3]*r->p[4]*exp(r->p[4]*x)*(1.0-exp(r->p[5]*x)) - r->p[3]*r->p[5]*exp((r->p[4]+r->p[5])*x); f+=a;
      *yd=f;
      break;
    case 323:
      f=0.0;
      a=r->p[0]*r->p[1]*exp(r->p[1]*x)*(1.0-exp(r->p[2]*x)) - r->p[0]*r->p[2]*exp((r->p[1]+r->p[2])*x); f+=a;
      a=r->p[3]*r->p[4]*exp(r->p[4]*x)*(1.0-exp(r->p[5]*x)) - r->p[3]*r->p[5]*exp((r->p[4]+r->p[5])*x); f+=a;
      a=r->p[6]*r->p[7]*exp(r->p[7]*x)*(1.0-exp(r->p[8]*x)) - r->p[6]*r->p[8]*exp((r->p[7]+r->p[8])*x); f+=a;
      *yd=f;
      break;
    case 331: break; /* not yet applied */
    case 351: break; /* not yet applied */
    case 1312:
      t=r->p[4]; xt=x-t; f=0.0;
      if(xt>0.0) {
        double A1, A2, L1, L2;
        A1=r->p[0]; L1=r->p[1]; A2=r->p[2]; L2=r->p[3];
        f= A1*exp(L1*xt) + A2*L2*exp(L2*xt) + (A1*xt -A2)*L1*exp(L1*xt);
      }
      *yd=f;
      break;
    case 1313:
      t=r->p[6]; xt=x-t; f=0.0;
      if(xt>0.0) {
        double A1, A2, A3, L1, L2, L3;
        A1=r->p[0]; L1=r->p[1]; A2=r->p[2]; L2=r->p[3]; A3=r->p[4]; L3=r->p[5];
        f= A1*exp(L1*xt) + A2*L2*exp(L2*xt) + A3*L3*exp(L3*xt) +
           (A1*xt -A2 -A3)*L1*exp(L1*xt);
      }
      *yd=f;
      break;
    case 1314: break;
      t=r->p[8]; xt=x-t; f=0.0;
      if(xt>0.0) {
        double A1, A2, A3, A4, L1, L2, L3, L4;
        A1=r->p[0]; L1=r->p[1]; A2=r->p[2]; L2=r->p[3]; A3=r->p[4]; L3=r->p[5];
        A4=r->p[6]; L4=r->p[7];
        f= A1*exp(L1*xt) + A2*L2*exp(L2*xt) + A3*L3*exp(L3*xt) +
           A4*L4*exp(L4*xt) + (A1*xt -A2 -A3 -A4)*L1*exp(L1*xt);
      }
      *yd=f;
      break;
    case 1401:
    case 1402:
      xt=x-r->p[3]; if(xt<=0.0 || r->p[2]==0.0) {
        f=0.0;
      } else {
        f=r->p[0]*pow(xt, r->p[1]-1.0)*exp(-xt/r->p[2])*(r->p[1]-(xt/r->p[2]));
      }
      *yd=f;
      break;
    case 1421:
      xt=x-r->p[0]; if(xt<=0.0) {
        *yd=0.0;
      } else {
        a=pow(xt/r->p[2], r->p[3]-1.0);
        *yd=r->p[1]*r->p[3]*a*exp(-a*xt/r->p[2])/r->p[2];
      }
      break;
    case 1801:
      xt=x-r->p[0]; if(xt<=0.0) {
        *yd=0.0;
      } else {
        a=pow(r->p[2], r->p[3])+pow(xt, r->p[3]);
        *yd=r->p[1]*r->p[3]*(pow(xt, r->p[3]-1.0)/a - pow(xt, 2.0*r->p[3]-1.0)/(a*a));
      }
      break;
    case 2111: *yd=nan(""); break; /* no application */
    case 9501: *yd=nan(""); break; /* cannot be applied to one point only */
    case 9502: *yd=nan(""); break; /* cannot be applied to one point only */
    case 9503: *yd=nan(""); break; /* cannot be applied to one point only */
    case 9701: *yd=nan(""); break; /* cannot be applied to one point only */
    default:
      *yd=nan("");
  }
  if(isnan(*yd)) return(3);
  return(0);
}

Referenced by fitDerivEvaltac().

fitDerivEvaltac()

int fitDerivEvaltac ( FitVOI * r, double * x, double * yd, int dataNr )

extern

Evaluates an array yd[i]=Df(x[i]).

See also

fitEvaltac, fitIntegralEvaltac, fitDerivEvaltac

Returns

Returns 0, if ok.

Parameters

r	Fit parameters of a single region
x	Times where to evaluate the function derivatives
yd	Array for the function derivatives
dataNr	Nr of (x,yd) data

Definition at line 1655 of file mathfunc.c.

  {
  int i;
 
  if(r==NULL || x==NULL || yd==NULL || dataNr<1) return(1);
  for(i=0; i<dataNr; i++) if(fitDerivEval(r, x[i], yd+i)) return(2);
  return(0);
}

fitEmpty()

void fitEmpty ( FIT * fit )

extern

Free memory allocated for FIT. All contents are cleared.

See also

fitInit, fitRead, fitWrite

Parameters

fit	Pointer to FIT struct.

Definition at line 18 of file mathfunc.c.

  {
  if(fit==NULL) return;
  if(fit->_voidataNr>0) {
    free((char*)(fit->voi));
    fit->_voidataNr=0;
  }
  fit->voiNr=0;
  fit->datafile[0]=fit->studynr[0]=fit->unit[0]=fit->program[0]=(char)0;
  fit->timeunit=0;
  fit->time=0;
}

Referenced by fitRead(), and fitSetmem().

fitEval()

int fitEval ( FitVOI * r, double x, double * y )

extern

Evaluate y=f(x).

See also

fitEvaltac, fitIntegralEval, fitDerivEval

Returns

Returns 0, if ok.

Parameters

r	Fit parameters of a single region
x	Time where to evaluate the function
y	The value of the function is returned here

Definition at line 645 of file mathfunc.c.

  {
  double a, b, f, sqrx, cubx, xt;
  int i, j, m, n;
  double mp[3][5];
  double mf[]={0.0,0.0,0.0};
 
  if(r==NULL) return(1);
  if(MATHFUNC_TEST>0) {
    printf("fitEval(r, %g, %g): type=%d ;", x, *y, r->type);
    for(i=0; i<r->parNr; i++) printf(" %g", r->p[i]);
    printf("\n");
  }
  if(y==NULL) return(1);
  *y=nan("");
  switch(r->type) {
    case 100:
    case 101:
    case 102:
    case 103:
    case 104:
    case 105:
    case 106:
    case 107:
    case 108:
    case 109:
      n=r->type-99; f=0.0; for(i=n-1; i>0; i--) {f+=r->p[i]; f*=x;} f+=r->p[0];
      *y=f;
      break;
    case 211:
      a=r->p[0]+r->p[2]*x; b=r->p[1]+r->p[3]*x; if(b==0.0) break;
      f=a/b; *y=f;
      break;
    case 221:
      sqrx=x*x;
      a=r->p[0]+r->p[2]*x+r->p[4]*sqrx; b=r->p[1]+r->p[3]*x; if(b==0.0) break;
      f=a/b; *y=f;
      break;
    case 222:
      sqrx=x*x;
      a=r->p[0]+r->p[2]*x+r->p[4]*sqrx;
      b=r->p[1]+r->p[3]*x+r->p[5]*sqrx; if(b==0.0) break;
      f=a/b; *y=f;
      break;
    case 232:
      sqrx=x*x; cubx=sqrx*x;
      a=r->p[0]+r->p[2]*x+r->p[4]*sqrx+r->p[6]*cubx;
      b=r->p[1]+r->p[3]*x+r->p[5]*sqrx; if(b==0.0) break;
      f=a/b; *y=f;
      break;
    case 233:
      sqrx=x*x; cubx=sqrx*x;
      a=r->p[0]+r->p[2]*x+r->p[4]*sqrx+r->p[6]*cubx;
      b=r->p[1]+r->p[3]*x+r->p[5]*sqrx+r->p[7]*cubx; if(b==0.0) break;
      f=a/b; *y=f;
      break;
    case 301:
      f=r->p[0]*exp(r->p[1]*x); *y=f;
      break;
    case 302:
      f=0;
      a=r->p[0]*exp(r->p[1]*x); f+=a;
      a=r->p[2]*exp(r->p[3]*x); f+=a;
      *y=f;
      break;
    case 303:
      f=0;
      a=r->p[0]*exp(r->p[1]*x); f+=a;
      a=r->p[2]*exp(r->p[3]*x); f+=a;
      a=r->p[4]*exp(r->p[5]*x); f+=a;
      *y=f;
      break;
    case 304:
      f=0;
      a=r->p[0]*exp(r->p[1]*x); f+=a;
      a=r->p[2]*exp(r->p[3]*x); f+=a;
      a=r->p[4]*exp(r->p[5]*x); f+=a;
      a=r->p[6]*exp(r->p[7]*x); f+=a;
      *y=f;
      break;
    case 305:
      f=0;
      a=r->p[0]*exp(r->p[1]*x); f+=a;
      a=r->p[2]*exp(r->p[3]*x); f+=a;
      a=r->p[4]*exp(r->p[5]*x); f+=a;
      a=r->p[6]*exp(r->p[7]*x); f+=a;
      a=r->p[8]*exp(r->p[9]*x); f+=a;
      *y=f;
      break;
    case 321:
      f=r->p[0]*exp(r->p[1]*x)*(1.0-exp(r->p[2]*x));
      *y=f;
      break;
    case 322:
      f=0.0;
      a=r->p[0]*exp(r->p[1]*x)*(1.0-exp(r->p[2]*x)); f+=a;
      a=r->p[3]*exp(r->p[4]*x)*(1.0-exp(r->p[5]*x)); f+=a;
      *y=f;
      break;
    case 323:
      f=0.0;
      a=r->p[0]*exp(r->p[1]*x)*(1.0-exp(r->p[2]*x)); f+=a;
      a=r->p[3]*exp(r->p[4]*x)*(1.0-exp(r->p[5]*x)); f+=a;
      a=r->p[6]*exp(r->p[7]*x)*(1.0-exp(r->p[8]*x)); f+=a;
      *y=f;
      break;
    case 1321:
      /* A=p0 B=p1 C=p2 D=k=p3 dT=p4 */
      xt=x-r->p[4]; if(xt<=0.0) {
        f=0.0;
      } else {
        a=exp(-r->p[2]*xt); f=r->p[0]*exp(-r->p[1]*xt)*(1.0-a);
        if(r->p[3]>0.0)
          f+=r->p[3]*(r->p[0]/(r->p[1]*(r->p[1]+r->p[2])))
             *(r->p[2]-((r->p[1]+r->p[2])/a-r->p[1])*exp(-(r->p[1]+r->p[2])*xt));
      }
      *y=f;
      break;
    case 331:
      n=(r->parNr-2)/2;
      if(x<=r->p[0])
        *y=0.0;
      else if(x<r->p[0]+r->p[1]) {
        for(i=0, f=0.0; i<n; i++) { 
          if(r->p[2*i+3]>1.0E-12) b=r->p[2*i+2]/r->p[2*i+3]; else b=r->p[2*i+2];
          f+=b*(1.0-exp(-r->p[2*i+3]*(x-r->p[0])));
        }
        if(r->p[1]>0.0) f*=(1.0/r->p[1]);
        *y=f;
      } else {
        for(i=0, f=0.0; i<n; i++) {
          if(r->p[2*i+3]>1.0E-12) b=r->p[2*i+2]/r->p[2*i+3]; else b=r->p[2*i+2];
          f+=b*(exp(-r->p[2*i+3]*(x-r->p[0]-r->p[1])) - exp(-r->p[2*i+3]*(x-r->p[0])));
        }
        if(r->p[1]>0.0) f*=(1.0/r->p[1]);
        *y=f;
      }
      break;
    case 332:
      if(x<=r->p[0])
        *y=0.0;
      else if(x<=r->p[0]+r->p[1]) {
        f=exp(-r->p[3]*(x-r->p[0]));
        *y=(r->p[2]/(r->p[3]*r->p[3]))*(1.0-f);
      } else {
        f=exp(-r->p[3]*r->p[1]);
        f+=exp(-r->p[3]*(x-r->p[0]-r->p[1]));
        f-=2.0*exp(-r->p[3]*(x-r->p[0]));
        *y=(r->p[2]/(r->p[3]*r->p[3]))*f;
      }
      break;
    case 334:
      if(x<=r->p[0])
        *y=0.0;
      else if(x>r->p[0] && x<=r->p[1]) {
        *y=r->p[2]*(1.0-exp(r->p[3]*(r->p[0]-x)))/(1.0-exp(r->p[3]*(r->p[0]-r->p[1])));
      } else {
        *y=r->p[2]*(exp(r->p[3]*(r->p[1]-x))-exp(r->p[3]*(r->p[0]-x)))/(1.0-exp(r->p[3]*(r->p[0]-r->p[1])));
      }
      break;
    case 351:
      f=1.0-r->p[0]*(2.0-exp(-r->p[1]*x)-exp(-r->p[2]*x)); *y=f;
      break;
    case 403:
      xt=x-r->p[4]; if(xt<0.0) xt=0.0;
      f=r->p[0]*(1.0 - r->p[1]*igam(r->p[3], r->p[2]*xt));
      *y=f;
      break;
    case 831:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=r->p[1];
      } else {
        f=r->p[2]*exp(-r->p[3]*xt*xt*xt/(xt*xt+r->p[4])) + (1.0-r->p[2])*exp(-r->p[5]*xt);
        f*=r->p[1];
      }
      *y=f;
      break;
    case 841:
      f=r->p[0]*pow(x, r->p[1]) / (pow(x, r->p[1]) + r->p[2]);
      *y=f;
      break;
    case 842:
      f=1.0-r->p[0]*pow(x, r->p[1]) / (pow(x, r->p[1]) + r->p[2]);
      *y=f;
      break;
    case 843:
      f=1.0 - r->p[0]*(1.0+r->p[3]*x)*pow(x, r->p[1]) / (pow(x, r->p[1]) + r->p[2]);
      *y=f;
      break;
    case 844:
      if(r->parNr>4) xt=x-r->p[4]; else xt=x; // delay time accounted, if avail
      if(xt<=0.0) f=r->p[3];
      else {a=pow(xt, r->p[1]);  f=r->p[0]*a/(a + r->p[2]) + r->p[3];}
      *y=f;
      break;
    case 845:
      f=r->p[0] - r->p[0]*pow(x, r->p[1]) / (pow(x, r->p[1]) + r->p[2]);
      *y=f;
      break;
    case 846:
      xt=x-r->p[4]; if(xt<=0.0) {
        f=r->p[3];
      } else {
        a=pow(xt, r->p[1]);
        f=r->p[3]+(r->p[0]-r->p[3])*a/(a+r->p[2]);
      }
      *y=f;
      break;
    case 847:
      xt=x-r->p[4]; if(xt<=0.0) {
        f=1.0-r->p[3];
      } else {
        a=pow(xt, r->p[1]);
        f=1.0-r->p[3]-(r->p[0]-r->p[3])*a/(a+r->p[2]);
      }
      *y=f;
      break;
    case 848:
      xt=x-r->p[4]; if(xt<=0.0) {
        f=r->p[3];
      } else {
        a=pow(xt, r->p[1]);
        f=r->p[3] * (1.0 - (1.0-r->p[0])*a/(r->p[2]+a));
      }
      *y=f;
      break;
    case 849:
      xt=x-r->p[4]; if(xt<=0.0) {
        f=1.0-r->p[3];
      } else {
        a=pow(xt, r->p[1]);
        f=1.0 - r->p[3] * (1.0 - (1.0-r->p[0])*a/(r->p[2]+a));
      }
      *y=f;
      break;
    case 851:
      a=r->p[0]*x; a*=a; f=1.0/pow(1.0+a, r->p[1]);
      *y=f;
      break;
    case 852:
      a=r->p[0]*x; a*=a; f=1.0 - 1.0/pow(1.0+a, r->p[1]);
      *y=f;
      break;
    case 861:
      xt=x-r->p[3]; if(xt<=0.0) {
        f=1.0;
      } else {
        f=pow(1.0+pow(r->p[0]*xt, r->p[1]), -r->p[2]);
      }
      *y=f;
      break;
    case 862:
      xt=x-r->p[3]; if(xt<=0.0) {
        f=1.0;
      } else {
        f=pow(1.0+pow(r->p[0]*xt, r->p[1]), -r->p[2]);
      }
      *y=1.0-f;
      break;
    case 863:
      xt=x-r->p[4]; if(xt<=0.0) {
        f=r->p[3];
      } else {
        f=pow(pow(r->p[3],-1.0/r->p[2])+pow(r->p[0]*xt, r->p[1]), -r->p[2]);
      }
      *y=f;
      break;
    case 864:
      xt=x-r->p[4]; if(xt<=0.0) {
        f=1.0-r->p[3];
      } else {
        f=1.0-pow(pow(r->p[3],-1.0/r->p[2])+pow(r->p[0]*xt, r->p[1]), -r->p[2]);
      }
      *y=f;
      break;
    case 871:
    case 872:
    case 873:
    case 874:
      for(m=0; m<3; m++) for(j=0; j<5; j++) mp[m][j]=0.0;
      for(i=m=j=0; i<r->parNr; i++) {mp[m][j]=r->p[i]; j++; if(j>4) {j=0; m++;}} 
      n=r->parNr/5;
      for(m=0; m<n; m++) {
        xt=x-mp[m][4];
        if(xt<=0.0) mf[m]=1.0-mp[m][3];
        else {
          f=pow(xt, mp[m][1]);
          mf[m]=1.0-(mp[m][3]+(mp[m][0]-mp[m][3])*f/(mp[m][2]+f));
        }
      }
      a=1.0-mf[0]*mf[1]-mf[0]*mf[2]-mf[1]*mf[2]+2.0*mf[0]*mf[1]*mf[2];
      if(r->type==871) {
        f=1.0;
        f-=mf[0]*(1.0-mf[1]-mf[2]+mf[1]*mf[2])/a;
        f-=mf[1]*(1.0-mf[0]-mf[2]+mf[0]*mf[2])/a;
        f-=mf[2]*(1.0-mf[0]-mf[1]+mf[0]*mf[1])/a;
        *y=f;
      } else if(r->type==872) {
        *y=mf[0]*(1.0-mf[1]-mf[2]+mf[1]*mf[2])/a;
      } else if(r->type==873) {
        *y=mf[1]*(1.0-mf[0]-mf[2]+mf[0]*mf[2])/a;
      } else if(r->type==874) {
        *y=mf[2]*(1.0-mf[0]-mf[1]+mf[0]*mf[1])/a;
      }
      break;
    case 881:
    case 882:
    case 883:
    case 884:
      for(m=0; m<3; m++) for(j=0; j<5; j++) mp[m][j]=0.0;
      for(i=m=j=0; i<r->parNr; i++) {mp[m][j]=r->p[i]; j++; if(j>4) {j=0; m++;}} 
      n=r->parNr/5;
      for(m=0; m<n; m++) {
        xt=x-mp[m][4];
        if(xt<=0.0) mf[m]=1.0-mp[m][3];
        else {
          mf[m]=1.0 - pow(pow(mp[m][3], -1.0/mp[m][2]) + pow(mp[m][0]*(xt), mp[m][1]), -mp[m][2]);
        }
      }
      a=1.0-mf[0]*mf[1]-mf[0]*mf[2]-mf[1]*mf[2]+2.0*mf[0]*mf[1]*mf[2];
      if(r->type==881) {
        f=1.0;
        f-=mf[0]*(1.0-mf[1]-mf[2]+mf[1]*mf[2])/a;
        f-=mf[1]*(1.0-mf[0]-mf[2]+mf[0]*mf[2])/a;
        f-=mf[2]*(1.0-mf[0]-mf[1]+mf[0]*mf[1])/a;
        *y=f;
      } else if(r->type==882) {
        *y=mf[0]*(1.0-mf[1]-mf[2]+mf[1]*mf[2])/a;
      } else if(r->type==883) {
        *y=mf[1]*(1.0-mf[0]-mf[2]+mf[0]*mf[2])/a;
      } else if(r->type==884) {
        *y=mf[2]*(1.0-mf[0]-mf[1]+mf[0]*mf[1])/a;
      }
      break;
    case 1010: // step functions
      /* Parameter number must be an even number and >=2 */
      if(r->parNr<2 || r->parNr&1) return(2);
      *y=0.0;
      for(int i=0; i<r->parNr; i+=2) if(x>=r->p[i]) *y=r->p[i+1];
      break;
    case 2111:
      xt=x-r->p[3]; a=sqrt(2.0)*(r->p[2]/2.355);
      f=r->p[4]+(r->p[0]/2.0)*(erf((xt+r->p[1])/a)-erf((xt-r->p[1])/a));
      *y=f;
      break;
    case 1232:
      xt=x; if(r->parNr>7) xt-=r->p[7];
      if(xt<=0.0) {
        f=0.0;
      } else {
        sqrx=xt*xt; cubx=sqrx*xt;
        a=r->p[0]+r->p[2]*xt+r->p[4]*sqrx+r->p[6]*cubx;
        b=r->p[1]+r->p[3]*xt+r->p[5]*sqrx; if(b==0.0) break;
        f=a/b;
      }
      *y=f;
      break;
    case 1312:
      xt=x; if(r->parNr>4) xt-=r->p[4];
      if(xt<=0.0) {
        f=0.0;
      } else {
        f=0.0;
        a=(r->p[0]*(xt)-r->p[2])*exp(r->p[1]*(xt)); f+=a;
        a=r->p[2]*exp(r->p[3]*(xt)); f+=a;
      }
      *y=f;
      break;
    case 1313:
      xt=x; if(r->parNr>6) xt-=r->p[6];
      if(xt<=0.0) {
        f=0.0;
      } else {
        f=0.0;
        a=(r->p[0]*(xt)-r->p[2]-r->p[4])*exp(r->p[1]*(xt)); f+=a;
        a=r->p[2]*exp(r->p[3]*(xt)); f+=a;
        a=r->p[4]*exp(r->p[5]*(xt)); f+=a;
      }
      *y=f;
      break;
    case 1314:
      xt=x; if(r->parNr>8) xt-=r->p[8];
      if(xt<=0.0) {
        f=0.0;
      } else {
        f=0.0;
        a=(r->p[0]*(xt)-r->p[2]-r->p[4]-r->p[6])*exp(r->p[1]*(xt)); f+=a;
        a=r->p[2]*exp(r->p[3]*(xt)); f+=a;
        a=r->p[4]*exp(r->p[5]*(xt)); f+=a;
        a=r->p[6]*exp(r->p[7]*(xt)); f+=a;
      }
      *y=f;
      break;
    case 1401:
      xt=x-r->p[3]; if(xt<=0.0 || r->p[2]==0.0) {
        f=0.0;
      } else {
        f=r->p[0]*pow(xt, r->p[1])*exp(-xt/r->p[2]);
      }
      *y=f;
      break;
    case 1402:
      xt=x-r->p[3]; if(xt<=0.0 || r->p[2]==0.0) {
        f=r->p[4];
      } else {
        f=r->p[0]*pow(xt, r->p[1])*exp(-xt/r->p[2]) + r->p[4];
      }
      *y=f;
      break;
    case 1403:
      xt=x-r->p[0];
      f=0.0;
      if(xt>0.0) {
        a=exp(-xt/r->p[3]);
        if(r->p[1]>0.0) f += r->p[1]*pow(xt, r->p[2])*a;
        if(r->parNr==6 && r->p[4]>0.0) f += r->p[4]*(1.0-a)*exp(-xt/r->p[5]);
      }
      *y=f;
      break;
    case 1421:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=0.0;
      } else {
        f=r->p[1]*(1.0-exp(-pow(xt/r->p[2], r->p[3])));
      }
      *y=f;
      break;
    case 1423:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=0.0;
      } else {
        a=xt/r->p[2]; b=pow(a, r->p[3]-1.0); f=exp(-b*a);
        a=r->p[3]*b*f/r->p[2]; b=1.0-f;
        f=r->p[1]*(a+r->p[4]*b);
      }
      *y=f;
      break;
    case 1431:
      if(x<=0.0) {
        f=0.0;
      } else {
        f=r->p[0]*x*exp(-r->p[1]*x)*r->p[1]*r->p[1];
      }
      *y=f;
      break;
    case 1432:
      if(x<=0.0) {
        f=0.0;
      } else {
        f=r->p[0]*x*exp(-r->p[1]*x);
      }
      *y=f;
      break;
    case 1433:
      if(x<=0.0) {
        f=0.0;
      } else {
        double e=exp(-r->p[1]*x);
        f=x*e + (r->p[2]/(r->p[1]*r->p[1]))*(1.0-(r->p[1]*x+1.0)*e);
        f*=r->p[0];
      }
      *y=f;
      break;
    case 1434:
      if(x<=0.0) {
        f=1.0/(1.0-r->p[0]);
      } else {
        double e=exp(-r->p[2]*x);
        double rcp=x*e + (r->p[3]/(r->p[2]*r->p[2]))*(1.0-(r->p[2]*x+1.0)*e);
        rcp*=r->p[1];
        f=1.0/(1.0-r->p[0]*(1.0-rcp));
      }
      *y=f;
      break;
    case 1435:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=0.0;
      } else {
        f=r->p[2]*(r->p[3]*xt*exp(-r->p[4]*r->p[1]*xt) + exp(-r->p[1]*xt) );
      }
      *y=f;
      break;
    case 1441: /* Probability density function of Erlang distribution */
      f=0.0;
      if(x>=0.0) {
        double A=r->p[0], k=r->p[1]; if(!(k>=0.0)) return(2);
        int N=(int)round(r->p[2]); if(!(N>0)) return(2);
        unsigned long long int f=lfactorial(N-1);
        f = A*pow(k, N)*pow(x, N-1)*exp(-k*x)/f;
      }
      *y=f;
      break;
    case 1801:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=0.0;
      } else {
        f=r->p[1]*pow(xt, r->p[3])/(pow(r->p[2], r->p[3])+pow(xt, r->p[3]));
      }
      *y=f;
      break;
    case 1811:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=0.0;
      } else {
        a=pow(r->p[2], r->p[3])+pow(xt, r->p[3]);
        f=r->p[1]*r->p[3]*
          (pow(xt, r->p[3]-1.0)/a - pow(xt, 2.0*r->p[3]-1.0)/(a*a));
      }
      *y=f;
      break;
    case 1821:
      xt=x-r->p[0]; if(xt<=0.0) {
        f=0.0;
      } else {
        double a, c, b, k, xb, cb, cbxb, hill, hilld;
        a=r->p[1]; c=r->p[2]; b=r->p[3]; k=r->p[4];
        cb=pow(c, b); xb=pow(xt, b); cbxb=cb+xb;
        hilld= b*pow(xt, b-1.0)/cbxb - b*pow(xt, 2.0*b-1.0)/(cbxb*cbxb);
        hill=k*xb/cbxb;
        f=a*(hilld+hill);
      }
      *y=f;
      break;
    case 1833:
      xt=x; if(r->parNr>3) xt-=r->p[3];
      if(xt<=0.0) {
        f=0.0;
      } else {
        double c=0.0; if(r->parNr>2) c=r->p[2];
        double e=exp(-r->p[1]*xt);
        f=xt*e + (c/(r->p[1]*r->p[1]))*(1.0-(r->p[1]*xt+1.0)*e);
        f*=r->p[0];
      }
      *y=f;
      break;
    case 2233:
      if(x<=0.0) {
        f=1.0/(1.0-r->p[0]);
      } else {
        sqrx=x*x; cubx=sqrx*x;
        a=0.0+r->p[1]*x+r->p[3]*sqrx+r->p[5]*cubx;
        b=1.0+r->p[2]*x+r->p[4]*sqrx+r->p[6]*cubx;
        f=1.0/(1.0-r->p[0]*(1.0-(a/b)));
      }
      *y=f;
      break;
    case 2313:
      if(r->parNr<3) return(2);
      if(x<=0.0) {
        f=0.0;
      } else {
        double A1=r->p[1];
        double L1=r->p[2];
        double A2=0.0; if(r->parNr>3) A2=r->p[3];
        double L2=0.0; if(r->parNr>4) L2=r->p[4];
        double A3=0.0; if(r->parNr>5) A3=r->p[5];
        double L3=0.0; if(r->parNr>6) L3=r->p[6];
        f=(A1*x - A2 - A3)*exp(-L1*x) + A2*exp(-L2*x) + A3*exp(-L3*x);
      }
      *y=1.0/(1.0-r->p[0]*(1.0-f));
      break;
    case 2801:
      {
        double top, bottom, ec50, hillslope;
        top=r->p[0]; bottom=r->p[1]; ec50=r->p[2]; hillslope=r->p[3]; 
        if(x<=0.0) f=bottom;
        else f=bottom+(top-bottom)/(1.0+pow(ec50/x,hillslope));
      }
      *y=f;
      break;
    case 2802:
      {
        double top, bottom, logec50, hillslope;
        top=r->p[0]; bottom=r->p[1]; logec50=r->p[2]; hillslope=r->p[3]; 
        f=bottom+(top-bottom)/(1.0+pow(10.0, (logec50-x)*hillslope));
      }
      *y=f;
      break;
    case 2841:
      a=r->p[1]*pow(x, r->p[2]) / (pow(x, r->p[2]) + r->p[3]);
      f=1.0/(1.0-r->p[0]*(1.0-a));
      *y=f;
      break;
    case 3331: *y=nan(""); break; /* cannot be applied to one point only */
    case 9501: *y=nan(""); break; /* cannot be applied to one point only */
    case 9502: *y=nan(""); break; /* cannot be applied to one point only */
    case 9503: *y=nan(""); break; /* cannot be applied to one point only */
    case 9701: *y=nan(""); break; /* cannot be applied to one point only */
    default:
      *y=nan("");
  }
  if(isnan(*y)) return 1;
  return 0;
}

Referenced by fitEvaltac().

fitEvaltac()

int fitEvaltac ( FitVOI * r, double * x, double * y, int dataNr )

extern

Evaluates an array y[i]=f(x[i]).

See also

fitEval, fitIntegralEvaltac, fitDerivEvaltac

Returns

Returns 0, if ok.

Parameters

r	Fit parameters of a single region
x	Times where to evaluate the function
y	Array for the function values
dataNr	Nr of (x,y) data

Definition at line 1252 of file mathfunc.c.

  {
  if(r==NULL || x==NULL || y==NULL || dataNr<1) return(1);
 
  /* Special cases that can only be computed as TACs */
  if(r->type==3331) {
    double Ta=r->p[0]; 
    double Ti=r->p[1];
    double dT=r->p[r->parNr-2]; Ta+=dT;
    double tau=r->p[r->parNr-1];
    int n=(r->parNr-4)/2; if(n<1) return(2);
    for(int i=0; i<dataNr; i++) {
      if(x[i]<=Ta) y[i]=0.0;
      else if(x[i]<Ta+Ti) {
        double f=0.0;
        for(int j=0; j<n; j++) {
          double b; 
          if(r->p[2*j+3]>1.0E-12) b=r->p[2*j+2]/r->p[2*j+3]; else b=r->p[2*j+2];
          f+=b*(1.0-exp(-r->p[2*j+3]*(x[i]-Ta)));
        }
        if(Ti>0.0) f*=(1.0/Ti);
        y[i]=f;
      } else {
        double f=0.0;
        for(int j=0; j<n; j++) {
          double b;
          if(r->p[2*j+3]>1.0E-12) b=r->p[2*j+2]/r->p[2*j+3]; else b=r->p[2*j+2];
          f+=b*(exp(-r->p[2*j+3]*(x[i]-Ta-Ti)) - exp(-r->p[2*j+3]*(x[i]-Ta)));
        }
        if(Ti>0.0) f*=(1.0/Ti);
        y[i]=f;
      }
    }
    if(simDispersion(x, y, dataNr, tau, 0.0, NULL)) return(2);
    return(0);
  }
 
  /* Usual functions */
  for(int i=0; i<dataNr; i++) if(fitEval(r, x[i], y+i)) return(2);
  return 0;
}

fitFunctionformat()

int fitFunctionformat ( int type, char * str )

extern

Copies the description of a function type to the specified string which must have space for >=128 characters.

Parameters

type	The number of function
str	Representation of the format of the function

Definition at line 381 of file mathfunc.c.

  {
  strcpy(str, "");
  switch(type) {
    /* Polynomials, including line */
    case 100: strcpy(str, "f(x)=A"); break;
    case 101: strcpy(str, "f(x)=A+B*x"); break;
    case 102: strcpy(str, "f(x)=A+B*x+C*x^2"); break;
    case 103: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3"); break;
    case 104: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3+E*x^4"); break;
    case 105: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3+E*x^4+F*x^5"); break;
    case 106: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3+E*x^4+F*x^5+G*x^6"); break;
    case 107: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3+E*x^4+F*x^5+G*x^6+H*x^7"); break;
    case 108: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3+E*x^4+F*x^5+G*x^6+H*x^7+I*x^8"); break;
    case 109: strcpy(str, "f(x)=A+B*x+C*x^2+D*x^3+E*x^4+F*x^5+G*x^6+H*x^7+I*x^8+J*x^9"); break;
    /* Rational functions */
    case 211: strcpy(str, "f(x)=(A+C*x)/(B+D*x)"); break;
    case 221: strcpy(str, "f(x)=(A+C*x+E*x^2)/(B+D*x)"); break;
    case 222: strcpy(str, "f(x)=(A+C*x+E*x^2)/(B+D*x+F*x^2)"); break;
    case 232: strcpy(str, "f(x)=(A+C*x+E*x^2+G*x^3)/(B+D*x+F*x^2)"); break;
    case 233: strcpy(str, "f(x)=(A+C*x+E*x^2+G*x^3)/(B+D*x+F*x^2+H*x^3)"); break;
    case 1232: strcpy(str, "f(x)=(A+C*(x-t)+E*(x-t)^2+G*(x-t)^3)/(B+D*(x-t)+F*(x-t)^2)"); break;
    /* Rational function for plasma-to-blood ratio */
    case 2233: strcpy(str, "f(x)=1/(1-H*(1-r(x))), where r(x) is 3/3 order rational function for RBC-to-plasma"); break;
    /* Exponential functions */
    case 301: strcpy(str, "f(x)=A*exp(B*x)"); break;
    case 302: strcpy(str, "f(x)=A*exp(B*x)+C*exp(D*x)"); break;
    case 303: strcpy(str, "f(x)=A*exp(B*x)+C*exp(D*x)+E*exp(F*x)"); break;
    case 304: strcpy(str, "f(x)=A*exp(B*x)+C*exp(D*x)+E*exp(F*x)+G*exp(H*x)"); break;
    case 305: strcpy(str, "f(x)=A*exp(B*x)+C*exp(D*x)+E*exp(F*x)+G*exp(H*x)+I*exp(J*x)"); break;
    /* Feng function */
    case 1312: strcpy(str, "f(x)=(A*(x-t)-C)*exp(B*(x-t))+C*exp(D*(x-t))"); break;
    case 1313: strcpy(str, "f(x)=(A*(x-t)-C-E)*exp(B*(x-t))+C*exp(D*(x-t))+E*exp(F*(x-t))"); break;
    case 1314: strcpy(str, "f(x)=(A*(x-t)-C-E-G)*exp(B*(x-t))+C*exp(D*(x-t))+E*exp(F*(x-t))+G*exp(H*(x-t))"); break;
    case 2313: strcpy(str, "f(x)=1/(1-A*(1-((B*x-D-F)*exp(C*x)+D*exp(E*x)+F*exp(G*x))))"); break;
    /* Lundqvist function */
    case 321: strcpy(str, "f(x)=A*exp(B*x)*(1-exp(C*x))"); break;
    case 322: strcpy(str, "f(x)=A*exp(B*x)*(1-exp(C*x))+D*exp(E*x)*(1-exp(F*x))"); break;
    case 323: strcpy(str, "f(x)=A*exp(B*x)*(1-exp(C*x))+D*exp(E*x)*(1-exp(F*x))+G*exp(H*x)*(1-exp(I*x))"); break;
    case 1321: strcpy(str, "f(x)=A*exp(-B*(x-t))*(1-exp(-C*(x-t))) + D*(A/(B*(B+C)))*(C-((B+C)*exp(C*(x-t))-B)*exp(-(B+C)*(x-t))) "); break;
    /* Exponential bolus infusion functions */
    case 331: strcpy(str, "f(x)=(1/Ti)*Sum[i=1..n, (Ai/Li)*(exp(-Li*(x-tA-Ti)) - exp(-Li*(x-Ta)))], when x>=Ta+Ti\nf(x)=(1/Ti)*Sum[i=1..n, (Ai/Li)*(1-exp(-Li*(t-Ta)))], when x>Ta and x<Ta+Ti\nf(x)=0, when t<=Ta");
      break;
    /* Kudomi's function for radiowater */
    case 332: strcpy(str, "f(x)=0, when x<=Ta \nf(x)=(A/L^2)*(1-exp(-L(x-Ta))), when Ta<x<=Ta+Ti \nf(x)=(A/L^2)*(exp(-L*Ti)+exp(-L(x-Ta-Ti))-2exp(-L(x-t1))), when x>Ta+Ti");
      break;
    /* Bolus infusion approaching zero */
    case 334: strcpy(str, "f(x)=0, when x<=t1 \nf(x)=A*(1-exp(L(t1-x)))/(1-exp(L*(t1-t2))), when t1<x<=t2 \nf(x)=A*(exp(L(t2-x))-exp(L(t1-x)))/(1-exp(L*(t1-t2))), when x>t2");
      break;
    /* Exponential functions for plasma fractions */
    case 351: strcpy(str, "f(x)=1-a*(2-exp(-b*x)-exp(-c*x))"); break;
    /* Inverted gamma cdf for plasma parent fraction */
    case 403: strcpy(str, "f(x)=A*(1-B*gammacdf(D,C*(x-t)))"); break;
    /* Gamma variate function */
    case 1401: strcpy(str, "f(x)=A*((x-D)^B)*exp(-(x-D)/C) , when x>=D, else f(x)=0"); break;
    /* Gamma variate function with background */
    case 1402: strcpy(str, "f(x)=A*((x-D)^B)*exp(-(x-D)/C) + E , when x>=D, else f(x)=E"); break;
    /* Gamma variate bolus plus recirculation function */
    case 1403: strcpy(str, "f(x)=B*((x-A)^C)*exp(-(x-A)/D) + E*(1-exp(-(x-A)/D))*exp(-(x-A)/F) , when x>A, else f(x)=0"); break;
    /* Weibull cdf */
    case 1421: strcpy(str, "f(x)=A*(1-exp(-((x-t)/B)^C) , when x>t, else f(x)=0"); break;
    /* Weibull cdf plus pdf (derivative of cdf) */
    case 1423: strcpy(str, "f(x)=A*[C*((x-t)/B)^(C-1)*exp(-((x-t)/B)^C))/B + k*(1-exp(-((x-t)/B)^C))] , when x>t, else f(x)=0"); break;
    /* Surge function with AUC=A */
    case 1431: strcpy(str, "f(x)=A*x*exp(-B*x)*B^2 , when x>0, else f(x)=0"); break;
    /* Traditional Surge function */
    case 1432: strcpy(str, "f(x)=A*x*exp(-B*x) , when x>0, else f(x)=0"); break;
    /* Surge function with recirculation */
    case 1433: strcpy(str, "f(x)=A*[x*exp(-B*x) + (C/B^2)*(1-(B*x+1)*exp(-B*x))], when x>0, else f(x)=0"); break;
    /* Surge function with recirculation for plasma-to-blood ratio */
    case 1434: strcpy(str, "f(x)=1/(1-H*(1-r(x))), where r(x) is function for RBC-to-plasma"); break;
    /* Surge function for late FDG input */
    case 1435: strcpy(str, "f(x)=b*(m*(x-t)*exp(-n*a*(x-t)) + exp(-a*(-t)x)) , when x>t, else f(x)=0"); break;
    /* Probability density function of Erlang distribution */
    case 1441: strcpy(str, "f(x)=A*(k^n)*(x^(n-1))*exp(-k*x)/(n-1)! , when x>0, else f(x)=0"); break;
    /* Hill functions for TACs */
    case 1801: strcpy(str, "f(x)=[A*(x-t)^B]/[(x-t)^B+C^B]"); break;
    case 1811: strcpy(str, "f(x)=A*{[B*(x-t)^(B-1)]/[C^B+(x-t)^B] - [B*(x-t)^(2*B-1)]/[C^B+(x-t)^B]^2}"); break;
    case 1821: strcpy(str, "f(x)=A*{[B*(x-t)^(B-1)]/[C^B+(x-t)^B] - [B*(x-t)^(2*B-1)]/[C^B+(x-t)^B]^2 + K*(x-t)^B]/[(x-t)^B+C^B}"); break;
    /* Surge function with recirculation and delay */
    case 1833: strcpy(str, "f(x)=A*[(x-D)*exp(-B*(x-D)) + (A*C/B^2)*(1-(B*(x-D)+1)*exp(-B*(x-D)))], when x>D, else f(x)=0"); break;
    /* Hill functions for dose-response curves */
    case 2801: strcpy(str, "f(x)=B+[A-B]/[1+(C/x)^D]"); break;
    case 2802: strcpy(str, "f(x)=B+[A-B]/[1+10^{(C-x)*D}]"); break;
    /* Exponential/power type functions for parent fractions */
    case 831: strcpy(str, "f(x)=B*(C*exp(-D*(x-A)^3/((x-A)^2+E))+(1-C)*exp(-F*(x-A))), when x>A, else f(x)=B"); break;
    /* Hill type functions for fractions */
    case 841: strcpy(str, "f(x)=(A*x^B)/(x^B+C)"); break;
    case 842: strcpy(str, "f(x)=1-((A*x^B)/(x^B+C))"); break;
    case 843: strcpy(str, "f(x)=1-((A*(1+D*x)*x^B)/(x^B+C))"); break;
    case 844: strcpy(str, "f(x)=(A*(x-t)^B)/((x-t)^B+C)+D, when x>t, else f(x)=D"); break;
    case 845: strcpy(str, "f(x)=A-(A*x^B)/(x^B+C))"); break;
    case 846: strcpy(str, "f(x)=D+((A-D)*(x-t)^B)/((x-t)^B+C), when x>t, else f(x)=D"); break;
    case 847: strcpy(str, "f(x)=1-D-((A-D)*(x-t)^B)/((x-t)^B+C), when x>t, else f(x)=1-A"); break;
    case 848: strcpy(str, "f(x)=D*((1-A)*(x-t)^B)/((x-t)^B+C), when x>t, else f(x)=D"); break;
    case 849: strcpy(str, "f(x)=1-D*((1-A)*(x-t)^B)/((x-t)^B+C), when x>t, else f(x)=1-A"); break;
    /* Hill function for plasma-to-blood ratio */
    case 2841: strcpy(str, "f(x)=1/(1-H*(1-r(x))), where r(x) is Hill function for RBC-to-plasma"); break;
    /* Mamede/Watabe function for fractions */
    case 851: strcpy(str, "f(x)=1/(1+(A*x)^2)^B"); break;
    case 852: strcpy(str, "f(x)=1-1/(1+(A*x)^2)^B"); break;
    /* Mamede/Watabe function for fractions, as extended by Meyer */
    case 861: strcpy(str, "f(x)=(1+(A*(x-t))^B)^(-C), when x>t, else f(x)=1"); break;
    case 862: strcpy(str, "f(x)=1-(1+(A*(x-t))^B)^(-C), when x>t, else f(x)=0"); break;
    /* ... and further extended by letting fraction start somewhere between 0 and 1 */ 
    case 863: strcpy(str, "f(x)=(D^(-1/C)+(A*(x-t))^B)^(-C), when x>t, else f(x)=D"); break;
    case 864: strcpy(str, "f(x)=1-(D^(-1/C)+(A*(x-t))^B)^(-C), when x>t, else f(x)=1-D"); break;
    /* Functions for fitting plasma fractions via separate metabolite fractions */
    case 871:
    case 881:
      strcpy(str, "f(x)=1-f1(x)-f2(x)-f3(x)"); break;
    case 872:
    case 882:
      strcpy(str, "f1(x)=a(x)(1-b(x)-c(x)+b(x)c(x))/(1-a(x)b(x)-a(x)c(x)-b(x)c(x)+2a(x)b(x)c(x))"); break;
    case 873:
    case 883:
      strcpy(str, "f2(x)=b(x)(1-a(x)-c(x)+a(x)c(x))/(1-a(x)b(x)-a(x)c(x)-b(x)c(x)+2a(x)b(x)c(x))"); break;
    case 874:
    case 884:
      strcpy(str, "f3(x)=c(x)(1-a(x)-b(x)+a(x)b(x))/(1-a(x)b(x)-a(x)c(x)-b(x)c(x)+2a(x)b(x)c(x))"); break;
    case 1010:
      strcpy(str, "f(x)=p2 when x>=p1, f(x)=p4 when x>=p2, ..."); break;
      break;
    /* PET profile functions */
    case 2111: strcpy(str, "P(x)=(C/2)*(erf((x-d+R)/(sqrt(2)*FWHM/2355))-erf((x-d-R)/(sqrt(2)*FWHM/2355)))+bkg");
      break;
    /* Combined functions and models */
    case 3331: strcpy(str, "f(x)=(1/Ti)*Sum[i=1..n, (Ai/Li)*(exp(-Li*(x-tA-Ti)) - exp(-Li*(x-Ta)))], when x>=Ta+Ti\nf(x)=(1/Ti)*Sum[i=1..n, (Ai/Li)*(1-exp(-Li*(t-Ta)))], when x>Ta and x<Ta+Ti\nf(x)=0, when t<=Ta, with additional delay and dispersion");
      break;
    /* Compartmental model functions */
    /* Graham's plasma curve smoothing function */
    case 9501: strcpy(str, "Cp(t)<=>Ci(t)<=>Ct(t)"); break;
    /* Extended Graham's plasma curve smoothing function */
    case 9502: strcpy(str, "Ce(t)<=>Cp(t)<=>Ci(t)<=>Ct(t)"); break;
    /* Extended Graham's plasma curve smoothing function with metabolite */
    case 9503: strcpy(str, "Cpa(t)<=>Cia(t)<=>Cta(t)->Ctm(t)<=>Cim(t)<=>Cpm(t)"); break;
    /* Huang's plasma metabolite model */
    case 9601: strcpy(str, "C4(t)<=>C3(t)<-C0(t)->C1(t)<=>C2(t)"); break;
    /* Extended Carson's plasma metabolite model */
    case 9602: strcpy(str, "Cpa(t)<=>Cta(t)->Ctm(t)<=>Cpm(t)"); break;
    /* New plasma metabolite model */
    case 9603: strcpy(str, "Cpa(t)->Ct1(t)<=>Cpm(t)<=>Ct2(t)"); break;
    /* Multi-linear multi-compartmental TAC fitting model */
    case 9701: strcpy(str, "Ideal bolus -> n compartments"); break;
    default:  return(1);
  }
  return(0);
}

fitFunctionname()

int fitFunctionname ( int type, char * str )

extern

Copies the name of the function to the specified string which must have space for >=128 characters.

Parameters

type	The number of function
str	Name of the function

Definition at line 539 of file mathfunc.c.

  {
  strcpy(str, "");
  switch(type) {
    case 100: strcpy(str, "f(x)=A"); break;
    case 101: strcpy(str, "line"); break;
    case 102: strcpy(str, "2nd order polynomial"); break;
    case 103: strcpy(str, "3rd order polynomial"); break;
    case 104: strcpy(str, "4th order polynomial"); break;
    case 105: strcpy(str, "5th order polynomial"); break;
    case 106: strcpy(str, "6th order polynomial"); break;
    case 107: strcpy(str, "7th order polynomial"); break;
    case 108: strcpy(str, "8th order polynomial"); break;
    case 109: strcpy(str, "9th order polynomial"); break;
    case 211: strcpy(str, "1/1 order rational function"); break;
    case 221: strcpy(str, "2/1 order rational function"); break;
    case 222: strcpy(str, "2/2 order rational function"); break;
    case 232: strcpy(str, "3/2 order rational function"); break;
    case 233: strcpy(str, "3/3 order rational function"); break;
    case 1232: strcpy(str, "3/2 order rational function with delay"); break;
    case 2233: strcpy(str, "3/3 order rational function for plasma-to-blood ratio"); break;
    case 301: strcpy(str, "exponential function"); break;
    case 302: strcpy(str, "sum of 2 exponential functions"); break;
    case 303: strcpy(str, "sum of 3 exponential functions"); break;
    case 304: strcpy(str, "sum of 4 exponential functions"); break;
    case 305: strcpy(str, "sum of 5 exponential functions"); break;
    case 1312: strcpy(str, "Feng model 2 function with 2 exponentials"); break;
    case 1313: strcpy(str, "Feng model 2 function"); break;
    case 1314: strcpy(str, "Feng model 2 function with 4 exponentials"); break;
    case 2313: strcpy(str, "Feng M2 function for plasma-to-blood ratio"); break;
    case 321: strcpy(str, "Lundqvist function"); break;
    case 322: strcpy(str, "sum of 2 Lundqvist functions"); break;
    case 323: strcpy(str, "sum of 3 Lundqvist functions"); break;
    case 1321: strcpy(str, "Lundqvist function with integral and delay"); break;
    case 331: strcpy(str, "Exponential bolus infusion function"); break;
    case 332: strcpy(str, "Kudomi's exponential bolus infusion function for radiowater"); break;
    case 334: strcpy(str, "Exponential bolus function approaching zero"); break;
    case 351: strcpy(str, "Exponential function for [C-11]PK11195 plasma fractions"); break;
    case 403: strcpy(str, "Inverted gamma cdf for plasma parent fraction"); break;
    case 1401: strcpy(str, "Gamma variate function"); break;
    case 1402: strcpy(str, "Gamma variate with background"); break;
    case 1403: strcpy(str, "Gamma variate bolus plus recirculation"); break;
    case 1421: strcpy(str, "Weibull cdf with delay"); break;
    case 1423: strcpy(str, "Weibull cdf and derivative with delay"); break;
    case 1431: strcpy(str, "Surge function"); break;
    case 1432: strcpy(str, "Surge function (trad)"); break;
    case 1433: strcpy(str, "Surge function with recirculation"); break;
    case 1434: strcpy(str, "Surge function with recirculation for plasma-to-blood ratio"); break;
    case 1435: strcpy(str, "Surge function for late FDG AIF"); break;
    case 1441: strcpy(str, "Probability density function of Erlang distribution"); break;
    case 1801: strcpy(str, "Hill function with delay"); break;
    case 1811: strcpy(str, "Derivative of Hill function with delay"); break;
    case 1821: strcpy(str, "Sum of Hill function and derivative with delay"); break;
    case 1833: strcpy(str, "Surge function with recirculation and delay"); break;
    case 2801: strcpy(str, "Hill function for dose-response curve on linear scale"); break;
    case 2802: strcpy(str, "Hill function for dose-response curve on log scale"); break;
    case 831: strcpy(str, "Exponential/Power function for parent fractions"); break;
    case 841: strcpy(str, "Hill function"); break;
    case 842: strcpy(str, "Hill function (1-f(x))"); break;
    case 843: strcpy(str, "Hill function (1-f(x)) with ascending or descending end"); break;
    case 844: strcpy(str, "Hill function with background"); break;
    case 845: strcpy(str, "Hill function (A-f(x))"); break;
    case 846: strcpy(str, "Extended Hill function for plasma parent fraction"); break;
    case 847: strcpy(str, "Extended Hill function for plasma metabolite fraction"); break;
    case 848: strcpy(str, "Extended Hill function #2 for plasma parent fraction"); break;
    case 849: strcpy(str, "Extended Hill function #2 for plasma metabolite fraction"); break;
    case 851: strcpy(str, "Mamede function"); break;
    case 852: strcpy(str, "Mamede function (1-f(x)"); break;
    case 861: strcpy(str, "Meyer parent fraction function"); break;
    case 862: strcpy(str, "Meyer metabolite fraction function"); break;
    case 863: strcpy(str, "Extended Meyer parent fraction function"); break;
    case 864: strcpy(str, "Extended Meyer metabolite fraction function"); break;
    case 871: strcpy(str, "1-3 metabolite Hill function for parent"); break;
    case 872: strcpy(str, "1-3 metabolite Hill function for metab1"); break;
    case 873: strcpy(str, "1-3 metabolite Hill function for metab2"); break;
    case 874: strcpy(str, "1-3 metabolite Hill function for metab3"); break;
    case 881: strcpy(str, "1-3 metabolite power function for parent"); break;
    case 882: strcpy(str, "1-3 metabolite power function for metab1"); break;
    case 883: strcpy(str, "1-3 metabolite power function for metab2"); break;
    case 884: strcpy(str, "1-3 metabolite power function for metab3"); break;
    case 1010: strcpy(str, "Step function"); break;
    case 2111: strcpy(str, "Image profile function"); break;
    case 2841: strcpy(str, "Hill function for plasma-to-blood ratio"); break;
    case 3331: strcpy(str, "Exponential bolus infusion function with delay and dispersion"); break;
    case 9501: strcpy(str, "Graham's input function"); break;
    case 9502: strcpy(str, "Extended Graham's input function"); break;
    case 9503: strcpy(str, "Graham's input function with metabolite"); break;
    case 9601: strcpy(str, "Huang's plasma metabolite model"); break;
    case 9602: strcpy(str, "Extended Carson's plasma metabolite model"); break;
    case 9603: strcpy(str, "New plasma metabolite model"); break;
    case 9701: strcpy(str, "Multilinear multicompartmental TAC fitting model"); break;
    default:  return(1);
  }
  return(0);
}

fitInit()

void fitInit ( FIT * fit )

extern

Initiate FIT structure. Call this once before first use.

See also

fitEmpty, fitRead, fitWrite

Definition at line 38 of file mathfunc.c.

  {
  if(fit==NULL) return;
  memset(fit, 0, sizeof(FIT));
  fit->_voidataNr=0; fit->voiNr=0;
}

fitIntegralEval()

int fitIntegralEval ( FitVOI * r, double x, double * yi )

extern

Evaluates yi=Integral of f(x) between 0 and x.

See also

fitEval, fitDerivEval, fitIntegralEvaltac

Returns

Returns 0, if ok.

Parameters

r	Fit parameters of a single region
x	Time where to evaluate integral of the function
yi	The integral value of the function is returned here

Definition at line 1308 of file mathfunc.c.

  {
  double a, f, xt, t;
 
  if(r==NULL || yi==NULL) return 1;
  *yi=nan("");
  switch(r->type) {
    case 301:
      if(fabs(r->p[1])>1.0e-12) f=(r->p[0]/r->p[1])*(exp(r->p[1]*x)-1.0);
      else f=r->p[0]*x;
      *yi=f;
      break;
    case 302:
      f=0;
      if(fabs(r->p[1])>1.0e-12) a=(r->p[0]/r->p[1])*(exp(r->p[1]*x)-1.0);
      else a=r->p[0]*x;
      f+=a;
      if(fabs(r->p[3])>1.0e-12) a=(r->p[2]/r->p[3])*(exp(r->p[3]*x)-1.0);
      else a=r->p[2]*x;
      f+=a;
      *yi=f;
      break;
    case 303:
      f=0;
      if(fabs(r->p[1])>1.0e-12) a=(r->p[0]/r->p[1])*(exp(r->p[1]*x)-1.0);
      else a=r->p[0]*x;
      f+=a;
      if(fabs(r->p[3])>1.0e-12) a=(r->p[2]/r->p[3])*(exp(r->p[3]*x)-1.0);
      else a=r->p[2]*x;
      f+=a;
      if(fabs(r->p[5])>1.0e-12) a=(r->p[4]/r->p[5])*(exp(r->p[5]*x)-1.0);
      else a=r->p[4]*x;
      f+=a;
      *yi=f;
      break;
    case 304:
      f=0;
      if(fabs(r->p[1])>1.0e-12) a=(r->p[0]/r->p[1])*(exp(r->p[1]*x)-1.0);
      else a=r->p[0]*x;
      f+=a;
      if(fabs(r->p[3])>1.0e-12) a=(r->p[2]/r->p[3])*(exp(r->p[3]*x)-1.0);
      else a=r->p[2]*x;
      f+=a;
      if(fabs(r->p[5])>1.0e-12) a=(r->p[4]/r->p[5])*(exp(r->p[5]*x)-1.0);
      else a=r->p[4]*x;
      f+=a;
      if(fabs(r->p[7])>1.0e-12) a=(r->p[6]/r->p[7])*(exp(r->p[7]*x)-1.0);
      else a=r->p[6]*x;
      f+=a;
      *yi=f;
      break;
    case 305:
      f=0;
      if(fabs(r->p[1])>1.0e-12) a=(r->p[0]/r->p[1])*(exp(r->p[1]*x)-1.0);
      else a=r->p[0]*x;
      f+=a;
      if(fabs(r->p[3])>1.0e-12) a=(r->p[2]/r->p[3])*(exp(r->p[3]*x)-1.0);
      else a=r->p[2]*x;
      f+=a;
      if(fabs(r->p[5])>1.0e-12) a=(r->p[4]/r->p[5])*(exp(r->p[5]*x)-1.0);
      else a=r->p[4]*x;
      f+=a;
      if(fabs(r->p[7])>1.0e-12) a=(r->p[6]/r->p[7])*(exp(r->p[7]*x)-1.0);
      else a=r->p[6]*x;
      f+=a;
      if(fabs(r->p[9])>1.0e-12) a=(r->p[8]/r->p[9])*(exp(r->p[8]*x)-1.0);
      else a=r->p[8]*x;
      f+=a;
      *yi=f;
      break;
    case 321:
      f=(r->p[0]/r->p[1])*exp(r->p[1]*x)
        - r->p[0]*exp((r->p[1]+r->p[2])*x)/(r->p[1]+r->p[2]);
      *yi=f;
      break;
    case 322:
      f=0.0;
      a=(r->p[0]/r->p[1])*exp(r->p[1]*x)
        - r->p[0]*exp((r->p[1]+r->p[2])*x)/(r->p[1]+r->p[2]); f+=a;
      a=(r->p[3]/r->p[4])*exp(r->p[4]*x)
        - r->p[3]*exp((r->p[4]+r->p[5])*x)/(r->p[4]+r->p[5]); f+=a;
      *yi=f;
      break;
    case 323:
      f=0.0;
      a=(r->p[0]/r->p[1])*exp(r->p[1]*x)
        - r->p[0]*exp((r->p[1]+r->p[2])*x)/(r->p[1]+r->p[2]); f+=a;
      a=(r->p[3]/r->p[4])*exp(r->p[4]*x)
        - r->p[3]*exp((r->p[4]+r->p[5])*x)/(r->p[4]+r->p[5]); f+=a;
      a=(r->p[6]/r->p[7])*exp(r->p[7]*x)
        - r->p[6]*exp((r->p[7]+r->p[8])*x)/(r->p[7]+r->p[8]); f+=a;
      *yi=f;
      break;
    case 331: *yi=nan(""); break; /* not yet applied */
    case 351: *yi=nan(""); break; /* not yet applied */
    case 1312:
      t=r->p[4]; xt=x-t; f=0.0;
      if(xt>0.0) {
        double A1, A2, L1, L2;
        A1=r->p[0]; L1=r->p[1]; A2=r->p[2]; L2=r->p[3];
        if(L1!=0.0) { 
          a=exp(L1*xt);
          f+=(A2/L1)*(1.0 - a);
          f+=(A1/(L1*L1))*(1.0 + a*(L1*xt - 1.0)); 
        }
        if(L2!=0.0) f+=(A2/L2)*(exp(L2*xt) - 1.0); else f+=A2*xt; 
      }
      *yi=f;
      break;
    case 1313:
      t=r->p[6]; xt=x-t; f=0.0;
      if(xt>0.0) {
        double A1, A2, A3, L1, L2, L3;
        A1=r->p[0]; L1=r->p[1]; A2=r->p[2]; L2=r->p[3]; A3=r->p[4]; L3=r->p[5];
        if(L1!=0.0) { 
          a=exp(L1*xt);
          f+=(A2/L1)*(1.0 - a);
          f+=(A3/L1)*(1.0 - a);
          f+=(A1/(L1*L1))*(1.0 + a*(L1*xt - 1.0)); 
        }
        if(L2!=0.0) f+=(A2/L2)*(exp(L2*xt) - 1.0); else f+=A2*xt; 
        if(L3!=0.0) f+=(A3/L3)*(exp(L3*xt) - 1.0); else f+=A3*xt;
      }
      *yi=f;
      break;
    case 1314:
      t=r->p[8]; xt=x-t; f=0.0;
      if(xt>0.0) {
        double A1, A2, A3, A4, L1, L2, L3, L4;
        A1=r->p[0]; L1=r->p[1]; A2=r->p[2]; L2=r->p[3]; A3=r->p[4]; L3=r->p[5];
        A4=r->p[6]; L4=r->p[7];
        if(L1!=0.0) { 
          a=exp(L1*xt);
          f+=(A2/L1)*(1.0 - a);
          f+=(A3/L1)*(1.0 - a);
          f+=(A4/L1)*(1.0 - a);
          f+=(A1/(L1*L1))*(1.0 + a*(L1*xt - 1.0)); 
        }
        if(L2!=0.0) f+=(A2/L2)*(exp(L2*xt) - 1.0); else f+=A2*xt; 
        if(L3!=0.0) f+=(A3/L3)*(exp(L3*xt) - 1.0); else f+=A3*xt; 
        if(L4!=0.0) f+=(A4/L4)*(exp(L4*xt) - 1.0); else f+=A4*xt;
      }
      *yi=f;
      break;
    case 1401: *yi=nan(""); break; /* not yet applied */
    case 1402: *yi=nan(""); break; /* not yet applied */
    case 1431:
      f=0.0;
      if(x>0.0) f=r->p[0]*(1.0 - (r->p[1]*x + 1.0)*exp(-r->p[1]*x));
      *yi=f;
      break;
    case 1432:
      f=0.0;
      if(x>0.0) {
        a=r->p[0]/(r->p[1]*r->p[1]);
        f=a*(1.0 - (r->p[1]*x + 1.0)*exp(-r->p[1]*x));
      }
      *yi=f;
      break;
    case 1435:
      xt=x-r->p[0]; f=0.0;
      if(xt>0.0) {
        double a, b, m, n; a=r->p[1]; b=r->p[2]; m=r->p[3]; n=r->p[4];
        f+=m*((1.0-(n*a*xt+1.0)*exp(-n*a*xt)))/(n*n*a*a) + (1.0-exp(-a*xt))/a;
        f*=b;
      }
      *yi=f;
      break;
    case 1441:  /* Probability density function of Erlang distribution, or actually,
                   its integral is the cumulative distribution function of Erlang distribution */
      f=0.0;
      if(x>=0.0) {
        double A, k; A=r->p[0]; k=r->p[1]; if(!(k>=0.0)) return(2);
        int N=(int)round(r->p[2]); if(!(N>=0) || N>20) return(2); // Supports only N=0,1,2,..,20
        if(N==0) f=A;
        else if(N==1) f=A*(1.0-exp(-k*x));
        else if(N==2) f=A*(1.0 - exp(-k*x) - k*x*exp(-k*x));
        else {
          double s=1.0+k*x;
          for(int j=2; j<N; j++) s+=pow(k*x, j)/lfactorial(j);
          f=A*(1.0-s*exp(-k*x));
        }
      }
      *yi=f;
      break;
    case 2111: *yi=nan(""); break; /* no application */
    case 9501: *yi=nan(""); break; /* cannot be applied to one point only */
    case 9502: *yi=nan(""); break; /* cannot be applied to one point only */
    case 9503: *yi=nan(""); break; /* cannot be applied to one point only */
    case 9701: *yi=nan(""); break; /* cannot be applied to one point only */
    default:
      *yi=nan("");
  }
  if(isnan(*yi)) return 3;
  return 0;
}

Referenced by fitIntegralEvaltac().

fitIntegralEvaltac()

int fitIntegralEvaltac ( FitVOI * r, double * x, double * yi, int dataNr )

extern

Evaluate an array yi[i]=Integral of f(x[i]) between 0 and x.

See also

fitEvaltac, fitIntegralEvaltac, fitDerivEvaltac

Returns

Returns 0, if ok.

Parameters

r	Fit parameters of a single region
x	Times where to evaluate the function integrals
yi	Array for the function integral values
dataNr	Nr of (x,yi) data

Definition at line 1517 of file mathfunc.c.

  {
  int i;
 
  if(r==NULL || x==NULL || yi==NULL || dataNr<1) return(1);
  for(i=0; i<dataNr; i++) if(fitIntegralEval(r, x[i], yi+i)) return(2);
  return(0);
}

fitPrint()

void fitPrint ( FIT * fit )

extern

Print to stdout the contents of FIT data structure.

Mainly for testing purposes.

Parameters

fit	Pointer to FIT struct.

Definition at line 180 of file mathfunc.c.

  {
  if(fit==NULL) {printf("FIT = Null\n"); return;}
  if(MATHFUNC_TEST>0) printf("Number of curves: %d\n", fit->voiNr);
  if(MATHFUNC_TEST>0) printf("_voidataNr = %d\n", fit->_voidataNr);
  fitWrite(fit, "stdout");
}

fitRead()

int fitRead ( char * filename, FIT * fit, int verbose )

extern

Read FIT file contents to the specified data structure, emptying its old contents.

Returns

In case of an error, >0 is returned, and a description is written in fiterrmsg.

See also

fitInit, fitPrint, fitWrite

Parameters

filename	Pointer to file name.
fit	Pointer to initiated FIT struct.
verbose	Verbose level; if <=0, then nothing is printed into stdout.

Definition at line 196 of file mathfunc.c.

  {
  char *cptr, line[1024], *lptr;
  int i, ri, n, type=0;
  struct tm st;
 
 
  if(verbose>0) printf("fitRead(%s)\n", filename);
  if(fit==NULL) return 1;
  /* Empty data */
  fitEmpty(fit);
 
  /* Open file */
  FILE *fp=fopen(filename, "r");
  if(fp==NULL) {strcpy(fiterrmsg, "cannot open file"); return 1;}
 
  /* Read data */
  strcpy(fiterrmsg, "wrong format");
  /* Read file type and program name */
  while(fgets(line, 1024, fp)!=NULL) {
    /* Ignore empty and comment lines */
    if(strlen(line)<4 || line[0]=='#') continue;
    /* Check for id string */
    if(!strncmp(line, FIT_VER, strlen(FIT_VER))) type=1; else type=0;
    break;
  }
  if(type!=1) {fclose(fp); return 3;}
  lptr=line; cptr=strtok(lptr, " \t\n\r");
  if(cptr!=NULL) cptr=strtok(NULL, " \t\n\r");
  if(cptr!=NULL && strlen(cptr)<1024) strcpy(fit->program, cptr);
#if(1)
  /* Read optional fields until "Nr of VOIs:" */
  while(1) {
    /* Read title field */
    while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
    /* Stop when "Nr of VOIs" is reached */
    if(strncasecmp(line, "Nr of VOIs:", 11)==0) break;
    /* Read fit date and time */
    if(strncasecmp(line, "Date:", 5)==0) {
      cptr=line+5; while(*cptr && !isdigit(*cptr)) cptr++;
      if(get_datetime(cptr, &st, verbose-3)==0) fit->time=timegm(&st);
      continue;
    }
    /* Read the name of the original datafile */
    if(strncasecmp(line, "Data file:", 10)==0) {
      lptr=&line[10]; cptr=strtok(lptr, " \t\n\r");
      if(cptr!=NULL && strlen(cptr)<FILENAME_MAX) strcpy(fit->datafile, cptr);
      continue;
    }
    /* Read study number */
    if(strncasecmp(line, "Study number:", 13)==0) {
      lptr=&line[13]; cptr=strtok(lptr, " \t\n\r");
      if(cptr!=NULL && strlen(cptr)<MAX_STUDYNR_LEN+1) strcpy(fit->studynr, cptr);
      continue;
    }
    /* Read the activity unit */
    if(strncasecmp(line, "Data unit:", 10)==0) {
      lptr=&line[10]; cptr=strtok(lptr, " \t\n\r");
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(fit->unit, cptr);
      continue;
    }
    /* Read the time unit */
    if(strncasecmp(line, "Time unit:", 10)==0) {
      lptr=&line[10]; cptr=strtok(lptr, " \t\n\r");
      fit->timeunit=petTunitId(cptr);
      continue;
    }
    if(strncasecmp(line, "Distance unit:", 14)==0) {
      lptr=&line[14]; cptr=strtok(lptr, " \t\n\r");
      fit->timeunit=petTunitId(cptr);
      continue;
    }
    fclose(fp); return 8;
  }
  /* Read the nr of regions */
  if(strncasecmp(line, "Nr of VOIs:", 11)) {fclose(fp); return 8;}
  lptr=&line[11]; cptr=strtok(lptr, " \t\n\r");
  n=atoi(cptr); if(n<1 || n>32000) {fclose(fp); return 8;}
#else
  /* Read fit date and time */
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Date:", 5)) {fclose(fp); return 4;}
  cptr=line+5; while(*cptr && !isdigit(*cptr)) cptr++;
  if(get_datetime(cptr, &st, verbose-3)==0) fit->time=timegm(&st); 
  /* Read the name of the original datafile */
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Data file:", 10)) {fclose(fp); return 5;}
  lptr=&line[10]; cptr=strtok(lptr, " \t\n\r");
  if(cptr!=NULL && strlen(cptr)<FILENAME_MAX) strcpy(fit->datafile, cptr);
  /* Read the activity unit */
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Data unit:", 10)) {fclose(fp); return 6;}
  lptr=&line[10]; cptr=strtok(lptr, " \t\n\r");
  if(cptr!=NULL && strlen(cptr)<1024) strcpy(fit->unit, cptr);
  /* Read the time unit */
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Time unit:", 10)==0) lptr=&line[10];
  else if(strncasecmp(line, "Distance unit:", 14)==0) lptr=&line[14];
  else {fclose(fp); return 7;}
  cptr=strtok(lptr, " \t\n\r");
  fit->timeunit=petTunitId(cptr);
  /* Read the nr of regions */
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Nr of VOIs:", 11)) {fclose(fp); return 8;}
  lptr=&line[11]; cptr=strtok(lptr, " \t\n\r");
  n=atoi(cptr); if(n<1 || n>32000) {fclose(fp); return 8;}
#endif
  /* Allocate memory for regions */
  if(fitSetmem(fit, n)) {strcpy(fiterrmsg, "out of memory"); fclose(fp); return 9;}
  fit->voiNr=n;
  /* Read (and ignore) title line */
  strcpy(fiterrmsg, "wrong format");
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Region", 6)) {fclose(fp); return 10;}
  /* Read regional data */
  for(ri=0; ri<fit->voiNr; ri++) {
    /* Read line of data */
    line[0]=(char)0;
    while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
    if(!line[0]) break;
    int pindx=0; char seps[8];
    int sn=strTokenNr(line, " \t\n\r"); if(sn<8) {fclose(fp); fitEmpty(fit); return 11;}
    int tn=strTokenNr(line, "\t\n\r");
    if(tn==sn || tn==sn-1 || tn==sn-2) { // tab as separator
      strcpy(seps, "\t\n\r"); n=tn;
      char *s=strTokenDup(line, seps, NULL);
      char *cptr=s;
      int i=0, n=strlen(s);
      strReplaceChar(cptr, ' ', (char)0);
      strlcpy(fit->voi[ri].voiname, cptr, MAX_REGIONSUBNAME_LEN+1);
      i+=strlen(fit->voi[ri].voiname);
      cptr=s+i; if(i<n) {cptr++; i++;}
      strReplaceChar(cptr, ' ', (char)0);
      strlcpy(fit->voi[ri].hemisphere, cptr, MAX_REGIONSUBNAME_LEN+1);
      i+=strlen(fit->voi[ri].hemisphere);
      cptr=s+i; if(i<n) {cptr++; i++;}
      strReplaceChar(cptr, ' ', (char)0);
      strlcpy(fit->voi[ri].place, cptr, MAX_REGIONSUBNAME_LEN+1);
      free(s);
      pindx=2;
    } else { // spaces as separators
      strcpy(seps, " \t\n\r"); n=sn;
      strTokenNCpy(line, seps, 1, fit->voi[ri].voiname, MAX_REGIONSUBNAME_LEN+1);
      strTokenNCpy(line, seps, 2, fit->voi[ri].hemisphere, MAX_REGIONSUBNAME_LEN+1);
      strTokenNCpy(line, seps, 3, fit->voi[ri].place, MAX_REGIONSUBNAME_LEN+1);
      pindx=4;
    }
    rnameCatenate(fit->voi[ri].name, MAX_REGIONNAME_LEN+1,
      fit->voi[ri].voiname, fit->voi[ri].hemisphere, fit->voi[ri].place, ' ');
    /* Fit start and end times, and original data nr */
    char s[128];
    strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].start=atof_dpi(s);
    strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].end=atof_dpi(s);
    strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].dataNr=atoi(s);
    /* Fit error, parameter nr and function number (type) */
    strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].wss=atof_dpi(s);
    strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].parNr=atoi(s);
    strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].type=atoi(s);
    /* Parameters */
    for(i=0; i<fit->voi[ri].parNr; i++) {
      strTokenNCpy(line, seps, pindx++, s, 128); fit->voi[ri].p[i]=atof_dpi(s);
    }
  }
  if(ri==0) {fclose(fp); fitEmpty(fit); return(12);}
  if(ri<fit->voiNr) fit->voiNr=ri;
 
  /* Close file */
  fclose(fp);
  strcpy(fiterrmsg, "");
 
  if(verbose>1) printf("done fitRead()\n");
  return(0);
}

fitSetmem()

int fitSetmem ( FIT * fit, int voiNr )

extern

Allocate memory for FIT data. Any previous contents are destroyed.

Returns

Returns 0 when successful, and >0 in case of an error.

See also

fitInit, fitEmpty, fitRead

Parameters

fit	Pointer to FIT struct.
voiNr	Nr of TACs to allocate.

Definition at line 154 of file mathfunc.c.

  {
  /* Check that there is something to do */
  if(fit==NULL || voiNr<1) return 1;
 
  /* Clear previous data, but only if necessary */
  if(fit->_voidataNr>0 || fit->voiNr>0) fitEmpty(fit);
 
  /* Allocate memory for regional curves */
  fit->voi=(FitVOI*)calloc(voiNr, sizeof(FitVOI));
  if(fit->voi==NULL) return 2;
  fit->_voidataNr=voiNr;
 
  return 0;
}

Referenced by fit_allocate_with_dft(), and fitRead().

fitToResult()

int fitToResult ( FIT * fit, RES * res, char * status )

extern

Conversion of FIT contents to RES.

See also

res_allocate_with_dft, dftToResult, res2ift

Returns

Returns 0 when successful.

Parameters

fit	Pointer to FIT structure, contents of which are written to RES struct.
res	Pointer to initiated RES struct where FIT contents are written; any previous contents are removed.
status	Pointer to a string (allocated for at least 64 chars) where error message or other execution status will be written; enter NULL, if not needed.

Definition at line 56 of file fitres.c.

  {
  int pi, ri, maxParNr, ret;
 
 
  //printf("fitToResult()\n"); fflush(stdout);
  /* Check input */
  if(status!=NULL) sprintf(status, "invalid data");
  if(fit==NULL || res==NULL) return 1;
  if(fit->voiNr<1) return 2;
 
  /* Determine max parameter number in fits */
  for(ri=0, maxParNr=0; ri<fit->voiNr; ri++)
    if(fit->voi[ri].parNr>maxParNr) maxParNr=fit->voi[ri].parNr;
  //printf("maxParNr := %d\n", maxParNr); fflush(stdout);
 
  /* Allocate memory for results */
  resEmpty(res); ret=resSetmem(res, fit->voiNr); 
  if(ret) {
    if(status!=NULL) sprintf(status, "cannot allocate memory");
    return 11;
  }
  /* Copy titles & filenames */
  //printf("copy header contents\n"); fflush(stdout);
  if(strlen(fit->program)>0 && strlen(fit->program)<512) 
    snprintf(res->program, 1024, "%.512s (c) 2014", fit->program);
  else 
    strcpy(res->program, "fitToResult (c) 2014");
  strcpy(res->datafile, fit->datafile);
  strcpy(res->studynr, fit->studynr);
  res->time=fit->time;
  /* Copy region names, etc */
  //printf("copy region names\n"); fflush(stdout);
  res->voiNr=fit->voiNr;
  for(ri=0; ri<fit->voiNr; ri++) {
    strcpy(res->voi[ri].name, fit->voi[ri].name);
    strcpy(res->voi[ri].voiname, fit->voi[ri].voiname);
    strcpy(res->voi[ri].hemisphere, fit->voi[ri].hemisphere);
    strcpy(res->voi[ri].place, fit->voi[ri].place);
  }
  /* Copy sample number, if equal in all TACs */
  for(ri=1, ret=0; ri<fit->voiNr; ri++)
    if(fit->voi[ri].dataNr!=fit->voi[0].dataNr) ret++;
  if(ret==0) res->datanr=fit->voi[0].dataNr;
  /* Set parameter names */
  //printf("set parameter names\n"); fflush(stdout);
  res->parNr=maxParNr+2; // function id and wss too
  strcpy(res->parname[0], "Func");
  for(pi=0; pi<maxParNr; pi++) sprintf(res->parname[pi+1], "p%d", pi+1);
  strcpy(res->parname[pi+1], "WSS");
  /* Copy parameter values */
  //printf("copy parameter values\n"); fflush(stdout);
  for(ri=0; ri<fit->voiNr; ri++) {
    res->voi[ri].parameter[0]=fit->voi[ri].type; // function id
    for(pi=0; pi<maxParNr; pi++) { // function parameters
      if(pi>=fit->voi[ri].parNr) res->voi[ri].parameter[pi+1]=0.0;
      else res->voi[ri].parameter[pi+1]=fit->voi[ri].p[pi];
    }
    res->voi[ri].parameter[pi+1]=fit->voi[ri].wss; // wss
  }
  /* Set also deprecated parameter name and unit representations, for now */
  //printf("set deprecated info\n"); fflush(stdout);
  resFixParnames(res);
  return(0);
}

fitWrite()

int fitWrite ( FIT * fit, char * filename )

extern

Write function parameters in FIT into specified file.

If necessary, a backup file (+BACKUP_EXTENSION) is created.

Returns

In case of an error, >0 is returned, and a description is written in fiterrmsg.

See also

fitPrint, fitRead, fitInit

Parameters

fit	Pointer to FIT struct.
filename	Filename.

Definition at line 54 of file mathfunc.c.

  {
  int i, j, n, savedNr=0;
  char tmp[1024], is_stdout=0;
  FILE *fp;
 
 
  if(MATHFUNC_TEST>0) printf("fitWrite(FIT, %s)\n", filename);
  /* Check that there is some data to write */
  if(fit==NULL || fit->voiNr<1) {strcpy(fiterrmsg, "no data"); return 1;}
  for(i=0; i<fit->voiNr; i++)
    if(!isnan(fit->voi[i].wss) && fit->voi[i].type>0) savedNr++;
  if(savedNr<1) {strcpy(fiterrmsg, "no fitted data"); return 1;}
 
  /* Check if writing to stdout */
  if(!strcmp(filename, "stdout")) is_stdout=1;
  if(MATHFUNC_TEST>1) {
    if(is_stdout) printf("  output is stdout()\n");
    else printf("  output in file\n"); 
  }
 
  /* 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(MATHFUNC_TEST>2) printf("opening file %s for write\n", filename);
    if((fp = fopen(filename, "w")) == NULL) {
      strcpy(fiterrmsg, "cannot open file"); return 2;
    }
  }
 
  /* Fit file format */
  n=fprintf(fp, "%-11.11s %s\n", FIT_VER, fit->program);
  if(n==0) {
    strcpy(fiterrmsg, "disk full");
    if(!is_stdout) fclose(fp);
    return 3;
  }
  /* Write fit date and time */
  if(!ctime_r_int(&fit->time, tmp)) strcpy(tmp, "");
  fprintf(fp, "Date:\t%s\n", tmp);
  /* Write the name of the original datafile */
  fprintf(fp, "Data file:\t%s\n", fit->datafile);
  /* Write the studynr */
  if(fit->studynr[0]) fprintf(fp, "Study number:\t%s\n", fit->studynr);
  /* Write the 'activity' unit */
  fprintf(fp, "Data unit:\t%s\n", fit->unit);
  /* Write the time unit */
  if(fit->timeunit==TUNIT_UM || fit->timeunit==TUNIT_MM)
    fprintf(fp, "Distance unit:\t%s\n", petTunit(fit->timeunit));
  else
    fprintf(fp, "Time unit:\t%s\n", petTunit(fit->timeunit));
 
  /* Write the voiNr to be saved */
  fprintf(fp, "Nr of VOIs:\t%d\n", savedNr);
  /* Write the Fit title */
  fprintf(fp, "%s %s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
    "Region", "Plane", "Start", "End", "dataNr", "WSS", "parNr", "Type", "Parameters");
  /* Write regional fits */
  for(i=0; i<fit->voiNr; i++) {
    if(isnan(fit->voi[i].wss) || fit->voi[i].type<=0) continue;
    if(fit->voi[i].voiname[0]) strcpy(tmp, fit->voi[i].voiname);
    else strcpy(tmp, ".");
    fprintf(fp, "%.*s ", MAX_REGIONSUBNAME_LEN, tmp);
    if(fit->voi[i].hemisphere[0]) strcpy(tmp, fit->voi[i].hemisphere);
    else strcpy(tmp, ".");
    fprintf(fp, "%.*s ", MAX_REGIONSUBNAME_LEN, tmp);
    if(fit->voi[i].place[0]) strcpy(tmp, fit->voi[i].place);
    else strcpy(tmp, ".");
    fprintf(fp, "%.*s\t", MAX_REGIONSUBNAME_LEN, tmp);
    fprintf(fp, "%.3f\t%.3f\t%d\t%.2E\t%d\t%04d",
       fit->voi[i].start, fit->voi[i].end, fit->voi[i].dataNr,
       fit->voi[i].wss, fit->voi[i].parNr, fit->voi[i].type );
    for(j=0; j<fit->voi[i].parNr; j++) fprintf(fp, "\t%.6E", fit->voi[i].p[j]);
    fprintf(fp, "\n");
  }
 
  /* Close file */
  if(!is_stdout) {
    if(MATHFUNC_TEST>2) printf("closing file %s\n", filename);
    fflush(fp); fclose(fp);
  }
  strcpy(fiterrmsg, "");
 
  if(MATHFUNC_TEST>0) printf("done with fitWrite()\n");
  return(0);
}

Referenced by fitPrint().

idwcRead()

int idwcRead ( char * filename, DFT * dft )

extern

Read IDWC file into DFT data structure. Any previous content of DFT is deleted.

Returns

Returns nonzero in case an error is encountered and sets dfterrmsg.

Parameters

filename	Name of IDWC file to be read
dft	Pointer to DFT data where to regional TAC data is read

Definition at line 77 of file idwc.c.

  {
  int ri, fi, n;
  char tmp[MAX_IDWC_LINE_LEN], *lptr, *cptr;
  FILE *fp;
 
  /* Check the arguments */
  if(filename==NULL || dft==NULL || strlen(filename)<1) {
    strcpy(dfterrmsg, "program error"); return(1);
  }
 
  /* Open file */
  fp=fopen(filename, "r");
  if(fp==NULL) {
    strcpy(dfterrmsg, "cannot open file"); return(2);
  }
 
  /* Read the line telling the sample number */
  fi=0; do {
    if(fgets(tmp, MAX_IDWC_LINE_LEN, fp)==NULL) {
      strcpy(dfterrmsg, "wrong format"); fclose(fp); return(3);}
    lptr=tmp;
    /* Read first token, and check for empty lines as well */
    cptr=strtok(lptr, "; \t\n\r"); if(cptr==NULL) continue;
    /* Check for comment line */
    if(cptr[0]=='#' || cptr[0]==';') continue;
    /* Read the sample number */
    fi=atoi(cptr); break;
  } while(1);
  if(fi<1) {strcpy(dfterrmsg, "wrong format"); fclose(fp); return(3);}
 
  /* Read the line number */
  n=0; while(fgets(tmp, MAX_IDWC_LINE_LEN, fp)!=NULL) {
    lptr=tmp;
    /* Read first token, and check for empty lines as well */
    cptr=strtok(lptr, "; \t\n\r"); if(cptr==NULL) continue;
    /* Check for comment line */
    if(cptr[0]=='#' || cptr[0]==';') continue;
    n++;
  }
  /* Calculate the number of TACs */
  ri=n/fi;  //printf("frameNr=%d voiNr=%d\n", fi, ri);
  if(ri<1) {strcpy(dfterrmsg, "wrong format"); fclose(fp); return(4);}
 
 
  /* Allocate memory for data */
  if(dftSetmem(dft, fi, ri)) {
    strcpy(dfterrmsg, "out of memory"); fclose(fp); return(11);}
  dft->frameNr=fi; dft->voiNr=ri;
 
  /* Read the data */
  rewind(fp); n=ri=fi=0;
  do {
    if(fgets(tmp, MAX_IDWC_LINE_LEN, fp)==NULL) {
      strcpy(dfterrmsg, "wrong format");
      fclose(fp); dftEmpty(dft); return(3);
    }
    lptr=tmp;
    /* Read first token, and check for empty lines as well */
    cptr=strtok(lptr, "; \t\n\r"); if(cptr==NULL) continue;
    /* Check for comment line */
    if(cptr[0]=='#' || cptr[0]==';') continue;
    n++; //printf("%d (fi=%d, ri=%d): %s\n", n, fi, ri, tmp);
    /* This time forget the sample number */
    if(n==1) {continue;}
    /* read the sample time */
    dft->x[fi]=atof(cptr);
    /* read sample value */
    cptr=strtok(NULL, "; \t\n\r"); if(cptr==NULL) continue;
    dft->voi[ri].y[fi]=atof(cptr);
    /* read sample weight */
    cptr=strtok(NULL, "; \t\n\r"); if(cptr==NULL) continue;
    dft->w[fi]+=atof(cptr);
    /* read TAC number */
    cptr=strtok(NULL, "; \t\n\r"); if(cptr==NULL) continue;
    if(fi==0) sprintf(dft->voi[ri].voiname, "%-*.*s",
       MAX_REGIONSUBNAME_LEN, MAX_REGIONSUBNAME_LEN, cptr);
    else if(strncasecmp(dft->voi[ri].voiname, cptr, strlen(cptr))!=0) {
      strcpy(dfterrmsg, "wrong format");
      //printf("'%s' '%s'\n", dft->voi[ri].voiname, cptr);
      fclose(fp); dftEmpty(dft); return(4);
    }
    fi++;
    if(fi==dft->frameNr) {fi=0; ri++;}
    if(ri==dft->voiNr) break;
  } while(1);
  dft->voiNr=ri;
  for(fi=0; fi<dft->frameNr; fi++) dft->w[fi]/=(double)dft->voiNr;
 
  /* close file */
  fclose(fp);
 
  /* Set DFT "header" */
  dft->_type=1;
  dft->timetype=0; dftFrametimes(dft);
  dft->timeunit=TUNIT_SEC; /* sec */
  dft->isweight=1;
 
  return(0);
}

Referenced by dftRead().

idwcWrite()

int idwcWrite ( DFT * dft, char * filename )

extern

Write DFT data into IDWC file format. If file exists, a backup file (+BACKUP_EXTENSION) is written.

Returns

Returns nonzero in case an error is encountered and sets dfterrmsg.

Parameters

dft	Pointer to DFT data that is written in IDWC format
filename	Name of IDWC file to be written; also "stdout" is accepted

Definition at line 18 of file idwc.c.

  {
  int ri, fi, n;
  char tmp[1024], is_stdout=0;
  FILE *fp;
 
 
  /* Check that there is some data to write */
  if(dft->voiNr<1 || dft->frameNr<1 || filename==NULL) {
    strcpy(dfterrmsg, "no data"); return(1);}
 
  /* Check if writing to stdout */
  if(!strcasecmp(filename, "stdout")) is_stdout=1;
 
  /* Check if file exists; backup, if necessary */
  if(!is_stdout && access(filename, 0) != -1) {
    strcpy(tmp, filename); strcat(tmp, BACKUP_EXTENSION);
    if(access(tmp, 0) != -1) remove(tmp);
    rename(filename, tmp);
  }
 
  /* Open output file */
  if(is_stdout) fp=(FILE*)stdout;
  else if((fp = fopen(filename, "w")) == NULL) {
    strcpy(dfterrmsg, "cannot open file"); return(2);}
 
  /* Write sample number */
  n=fprintf(fp, "%d\n", dft->frameNr);
  if(n<2) {
    strcpy(dfterrmsg, "cannot write file");
    fclose(fp); return(3);
  }
  /* write data lines */
  for(ri=0; ri<dft->voiNr; ri++) {
    for(fi=0; fi<dft->frameNr; fi++) {
      n=fprintf(fp, "%6.1f %18.14f %18.14f %3d\n",
        dft->x[fi], dft->voi[ri].y[fi], dft->w[fi], ri+1);
      if(n<8) {
        strcpy(dfterrmsg, "cannot write file");
        fclose(fp); return(4);
      }
    }
  }
  /* close file */
  fclose(fp);
 
  return(0);
}

ifRead()

int ifRead ( char * filename, DFT * dft )

extern

Read IF file into DFT data structure, metabolite corrected plasma as TAC #1 and whole blood as TAC #2. Any previous content of DFT is deleted.

Returns

Returns nonzero in case an error is encountered and sets dfterrmsg.

Parameters

filename	Name of IDWC file to be read
dft	Pointer to DFT data where to regional TAC data is read

Definition at line 78 of file if.c.

  {
  int fi, n;
  char tmp[MAX_IF_LINE_LEN], *lptr, *cptr;
  FILE *fp;
 
  /* Check the arguments */
  if(filename==NULL || dft==NULL || strlen(filename)<1) {
    strcpy(dfterrmsg, "program error"); return(1);
  }
 
  /* Open file */
  fp=fopen(filename, "r");
  if(fp==NULL) {
    strcpy(dfterrmsg, "cannot open file"); return(2);
  }
 
  /* Read the line telling the sample number */
  fi=n=0; do {
    if(fgets(tmp, MAX_IF_LINE_LEN, fp)==NULL) {
      strcpy(dfterrmsg, "wrong format"); fclose(fp); return(3);}
    lptr=tmp; n++;
    /* Read first token, and check for empty lines as well */
    cptr=strtok(lptr, "; \t\n\r"); if(cptr==NULL) continue;
    /* Check for comment line */
    if(cptr[0]=='#' || cptr[0]==';') continue;
    /* Read the sample number */
    fi=atoi(cptr); break;
  } while(1);
  if(fi<1) {strcpy(dfterrmsg, "wrong format"); fclose(fp); return(3);}
 
  /* Allocate memory for data */
  if(dftSetmem(dft, fi, 2)) {
    strcpy(dfterrmsg, "out of memory"); fclose(fp); return(11);}
  dft->frameNr=fi; dft->voiNr=2;
 
  /* Read the data */
  n=fi=0;
  do {
    if(fgets(tmp, MAX_IF_LINE_LEN, fp)==NULL) {
      strcpy(dfterrmsg, "wrong format");
      fclose(fp); dftEmpty(dft); return(3);
    }
    lptr=tmp;
    /* Read first token, and check for empty lines as well */
    cptr=strtok(lptr, "; \t\n\r"); if(cptr==NULL) continue;
    /* Check for comment line */
    if(cptr[0]=='#' || cptr[0]==';') continue;
    n++; //printf("%d (fi=%d): %s\n", n, fi, tmp);
    /* read the sample time */
    dft->x[fi]=atof(cptr);
    /* read metabolite corrected plasma */
    cptr=strtok(NULL, "; \t\n\r"); if(cptr==NULL) continue;
    dft->voi[0].y[fi]=atof(cptr);
    /* read whole blood */
    cptr=strtok(NULL, "; \t\n\r"); if(cptr==NULL) continue;
    dft->voi[1].y[fi]=atof(cptr);
    fi++;
    if(fi==dft->frameNr) break;
  } while(1);
 
  /* close file */
  fclose(fp);
 
  /* Set DFT "header" */
  dft->_type=1;
  dft->timetype=0;
  dft->timeunit=TUNIT_SEC; /* sec */
  dft->isweight=0;
  strcpy(dft->voi[0].voiname, "Plasma");
  strcpy(dft->voi[1].voiname, "Blood");
 
  return(0);
}

Referenced by dftRead().

ifWrite()

int ifWrite ( DFT * dft, char * filename )

extern

Write metabolite corrected plasma TAC and blood TAC into IF file format. If file exists, a backup file (+BACKUP_EXTENSION) is written.

Returns

Returns nonzero in case an error is encountered and sets dfterrmsg.

Parameters

dft	Pointer to DFT data that will be written in IF format: first TAC must be the metabolite corrected plasma, and the 2nd TAC must be the whole blood TAC.
filename	Name of IF file to be written; also "stdout" is accepted

Definition at line 18 of file if.c.

  {
  int fi, n;
  char tmp[1024], is_stdout=0;
  FILE *fp;
 
 
  /* Check that there is some data to write */
  if(dft->voiNr<2 || dft->frameNr<1 || filename==NULL) {
    strcpy(dfterrmsg, "no data"); return(1);}
 
  /* Check if writing to stdout */
  if(!strcasecmp(filename, "stdout")) is_stdout=1;
 
  /* Check if file exists; backup, if necessary */
  if(!is_stdout && access(filename, 0) != -1) {
    strcpy(tmp, filename); strcat(tmp, BACKUP_EXTENSION);
    if(access(tmp, 0) != -1) remove(tmp);
    rename(filename, tmp);
  }
 
  /* Open output file */
  if(is_stdout) fp=(FILE*)stdout;
  else if((fp = fopen(filename, "w")) == NULL) {
    strcpy(dfterrmsg, "cannot open file"); return(2);}
 
  /* Write sample number */
  n=fprintf(fp, "%d\n", dft->frameNr);
  if(n<2) {
    strcpy(dfterrmsg, "cannot write file");
    fclose(fp); return(3);
  }
  /* Write data lines */
  for(fi=0; fi<dft->frameNr; fi++) {
    n=fprintf(fp, "%f\t%f\t%f\n",
      dft->x[fi], dft->voi[0].y[fi], dft->voi[1].y[fi]);
    if(n<6) {
      strcpy(dfterrmsg, "cannot write file");
      fclose(fp); return(4);
    }
  }
  /* close file */
  fclose(fp);
 
  return(0);
}

igam()

double igam ( double a, double x )

extern

Cumulative gamma distribution, or Regularized gamma function, more specifically, lower incomplete gamma function divided by gamma function.

Standard gamma distribution is assumed (Beta=1). f(a,x) = (1/Gamma(a)) * Integral(0,x)(e^-t * t^(a-1))dt

Returns

Returns the value of regularized gamma function, or NaN in case of an error.

See also

igamc, inverfc, factorial

Parameters

a	Shape parameter alpha; must be > 0.
x	Integral from 0 to x; must be >= 0.

Definition at line 1715 of file mathfunc.c.

  {
  /* Check parameters */
  if(x==0.0) return(0.0);
  if((x<0.0) || (a<=0.0)) return(nan(""));
 
  if((x>1.0) && (x>a)) return(1.0 - igamc(a, x));
 
  /* Left tail of incomplete Gamma function:
    x^a * e^-x * Sum(k=0,Inf)(x^k / Gamma(a+k+1)) */
 
  double ans, ax, c, r;
 
  /* Compute  x**a * exp(-x) / Gamma(a) */
  ax=a*log(x) - x - lgamma(a);
  if(ax<-DBL_MAX_10_EXP) return(0.0); // underflow
  ax=exp(ax);
 
  /* power series */
  r=a; c=1.0; ans=1.0;
  do {
    r+=1.0;
    c*=x/r;
    ans+=c;
  } while(c/ans > DBL_EPSILON);
  return(ans*ax/a);
}

Referenced by fitEval(), and igamc().

igamc()

double igamc ( double a, double x )

extern

Regularized gamma function, more specifically, upper incomplete gamma function divided by gamma function.

f(a,x) = (1/Gamma(a)) * Integral(x,Inf)(e^-t * t^(a-1))dt Standard gamma distribution is assumed (Beta=1).

Returns

Returns the value of regularized gamma function, or NaN in case of an error.

See also

igam, inverfc, factorial

Parameters

a	Shape parameter alpha; must be > 0.
x	Integral from x to infinity; must be >= 0

Definition at line 1756 of file mathfunc.c.

  {
  /* Check parameters */
  if((x<0.0) || (a<=0.0)) return(nan(""));
 
  if((x<1.0) || (x<a)) return(1.0-igam(a, x));
 
  double ans, ax, c, yc, r, t, y, z;
  double pk, pkm1, pkm2, qk, qkm1, qkm2;
  double big=4.503599627370496E+015;
  double biginv=2.22044604925031308085E-016;
 
  ax = a*log(x) - x - lgamma(a);
  if(ax < -DBL_MAX_10_EXP) return(0.0); // underflow
  ax=exp(ax);
 
  /* continued fraction */
  y=1.0-a; z=x+y+1.0; c=0.0;
  pkm2=1.0; qkm2=x; pkm1=x+1.0; qkm1=z*x;
  ans=pkm1/qkm1;
  do {
    c+=1.0; y+=1.0; z+=2.0;
    yc=y*c; pk=pkm1*z - pkm2*yc; qk=qkm1*z - qkm2*yc;
    if(qk!=0.0) {r=pk/qk; t=fabs((ans-r)/r); ans=r;}
    else t=1.0;
    pkm2=pkm1; pkm1=pk; qkm2=qkm1; qkm1=qk;
    if(fabs(pk)>big) {pkm2*=biginv; pkm1*=biginv; qkm2*=biginv; qkm1*=biginv;}
  } while(t>DBL_EPSILON);
  return(ans*ax);
}

Referenced by igam().

lfactorial()

unsigned long long int lfactorial ( unsigned long long int n )

extern

Calculate factorial of given number.

See also

factorial, igam, igamc

Returns

Returns factorial n!, or zero if factorial would cause wrap-around.

Parameters

n	Integer n, from which the factorial is calculated.

Note

Wrap-around will occur if n>20.

Definition at line 1695 of file mathfunc.c.

  {
  if(n<1) return(1);
  if(n>20) return(0);
  return(n*lfactorial(n-1));
}

Referenced by fitEval(), fitIntegralEval(), and lfactorial().

res2ift()

int res2ift ( RES * res, IFT * ift, int verbose )

extern

Copy results in RES structure into IFT structure.

Returns

Returns 0 when successful.

See also

fit2Result, dftToResult

Parameters

res	Pointer to RES structure
ift	Pointer to initiated IFT structure
verbose	Verbose level; if zero, then nothing is printed into stdout or stderr

Definition at line 14 of file resift.c.

  {
  int ri, pi, ret;
  char tmp[1024], tmp2[1024], tmp3[1024];
  struct tm st;
 
  if(verbose>0) printf("res2ift()\n");
 
  /* Check the input */
  if(res==NULL || ift==NULL) {
    if(verbose>0) fprintf(stderr, "Error: invalid input\n");
    return(1);
  }
 
  /* Delete any previous content */
  iftEmpty(ift);
  
  /* Set header info */
  if(strlen(res->program)>0) {
    ret=iftPut(ift, "program", res->program, NULL, 0);
    if(ret!=0) {
      if(verbose>0) fprintf(stderr, "Error: cannot set IFT content\n");
      return(3);
    }
  }
  if(gmtime_r(&res->time, &st)!=NULL) {
    strftime(tmp, 256, "%Y-%m-%d %H:%M:%S", &st);
    iftPut(ift, "date", tmp, NULL, 0);
  }
  if(res->studynr[0]) iftPut(ift, "studynr", res->studynr, NULL, 0);
  if(res->datafile[0]) iftPut(ift, "datafile", res->datafile, NULL, 0);
  if(res->plasmafile[0]) iftPut(ift, "plasmafile", res->plasmafile, NULL, 0);
  if(res->plasmafile2[0]) iftPut(ift, "plasmafile2", res->plasmafile2, NULL, 0);
  if(res->bloodfile[0]) iftPut(ift, "bloodfile", res->bloodfile, NULL, 0);
  if(res->reffile[0]) iftPut(ift, "reffile", res->reffile, NULL, 0);
  if(res->refroi[0]) iftPut(ift, "refroi", res->refroi, NULL, 0);
 
  if(res->datarange[0]) iftPut(ift, "datarange", res->datarange, NULL, 0);
  if(res->datanr>0) {
    snprintf(tmp, 1024, "%d", res->datanr); iftPut(ift, "datanr", tmp, NULL, 0);}
  if(res->fitmethod[0]) iftPut(ift, "fitmethod", res->fitmethod, NULL, 0);
 
  if(res->density>0) {
    snprintf(tmp, 1024, "%g", res->density); iftPut(ift, "density", tmp, NULL, 0);}
  if(res->lc>0) {
    snprintf(tmp, 1024, "%g", res->lc); iftPut(ift, "lc", tmp, NULL, 0);}
  if(res->concentration>0) {
    snprintf(tmp, 1024, "%g", res->concentration);
    iftPut(ift, "concentration", tmp, NULL, 0);
  }
  if(res->beta>0) {
    snprintf(tmp, 1024, "%g", res->beta); iftPut(ift, "beta", tmp, NULL, 0);}
  if(res->Vb>0) {
    snprintf(tmp, 1024, "%g", res->Vb); iftPut(ift, "Vb", tmp, NULL, 0);}
  if(res->fA>0) {
    snprintf(tmp, 1024, "%g", res->fA); iftPut(ift, "fA", tmp, NULL, 0);}
  if(res->E>0) {
    snprintf(tmp, 1024, "%g", res->E); iftPut(ift, "E", tmp, NULL, 0);}
  if(res->isweight>0) strcpy(tmp, "yes");
  else if(res->isweight==0) strcpy(tmp, "no");
  else strcpy(tmp, "unknown");
  iftPut(ift, "weighting", tmp, NULL, 0);
 
  /* Set each ROI and parameter value */
  for(ri=0; ri<res->voiNr; ri++) {
    if(res->voiNr>1) {
      strcpy(tmp, res->voi[ri].name); rnameRmDots(tmp, NULL);
      strcat(tmp, "_");
    } else {
      strcpy(tmp, "");
    }
    for(pi=0; pi<res->parNr; pi++) {
      snprintf(tmp2, 1024, "%s%s", tmp, res->parname[pi]);
      if(isnan(res->voi[ri].parameter[pi])) strcpy(tmp3, "");
      else sprintf(tmp3, "%g", res->voi[ri].parameter[pi]);
      if(strlen(res->parunit[pi])) {
        strcat(tmp3, " "); strcat(tmp3, res->parunit[pi]);}
      iftPut(ift, tmp2, tmp3, NULL, 0);
      if(!isnan(res->voi[ri].sd[pi])) {
        snprintf(tmp2, 1024, "%s%s_%s", tmp, res->parname[pi], "SD");
        snprintf(tmp3, 1024, "%g", res->voi[ri].sd[pi]);
        if(strlen(res->parunit[pi])) {
          strcat(tmp3, " "); strcat(tmp3, res->parunit[pi]);}
        iftPut(ift, tmp2, tmp3, NULL, 0);
      }
      if(!isnan(res->voi[ri].cl1[pi])) {
        snprintf(tmp2, 1024, "%s%s_%s", tmp, res->parname[pi], "CL1");
        snprintf(tmp3, 1024, "%g", res->voi[ri].cl1[pi]);
        if(strlen(res->parunit[pi])) {
          strcat(tmp3, " "); strcat(tmp3, res->parunit[pi]);}
        iftPut(ift, tmp2, tmp3, NULL, 0);
      }
      if(!isnan(res->voi[ri].cl2[pi])) {
        snprintf(tmp2, 1024, "%s%s_%s", tmp, res->parname[pi], "CL2");
        snprintf(tmp3, 1024, "%g", res->voi[ri].cl2[pi]);
        if(strlen(res->parunit[pi])) {
          strcat(tmp3, " "); strcat(tmp3, res->parunit[pi]);}
        iftPut(ift, tmp2, tmp3, NULL, 0);
      }
    }
  }
 
  return(0);
}

res_allocate_with_dft()

int res_allocate_with_dft ( RES * res, DFT * dft )

extern

Allocate memory for regional results based on information in DFT.

See also

fit_allocate_with_dft, dftToResult

Returns

Returns 0 if successful, otherwise <>0.

Parameters

res	Pointer to initiated RES struct which will be allocated here and filled with ROI names etc.
dft	Regional data from where necessary information is read.

Definition at line 14 of file dftres.c.

  {
  int ri;
 
  //printf("res_allocate_with_dft()\n"); fflush(stdout);
  // Check the input data
  if(res==NULL || dft==NULL || dft->voiNr<1) return 1;
  // Allocate memory
  if(resSetmem(res, dft->voiNr)!=0) return 2;
  res->voiNr=dft->voiNr;
  // Copy header information
  strcpy(res->studynr, dft->studynr);
  res->Vb=-1.0;
  res->fA=-1.0;
  res->E=-1.0;
  res->time=time(NULL); // Set current time to results
  res->isweight=dft->isweight;
  /* Copy region names, etc */
  for(ri=0; ri<dft->voiNr; ri++) {
    strcpy(res->voi[ri].name, dft->voi[ri].name);
    strcpy(res->voi[ri].voiname, dft->voi[ri].voiname);
    strcpy(res->voi[ri].hemisphere, dft->voi[ri].hemisphere);
    strcpy(res->voi[ri].place, dft->voi[ri].place);
  }
  /* Set data range */
  if(dft->timetype==DFT_TIME_STARTEND)
    sprintf(res->datarange, "%g - %g %s",
      dft->x1[0], dft->x2[dft->frameNr-1], petTunit(dft->timeunit) );
  else
    sprintf(res->datarange, "%g - %g %s",
      dft->x[0], dft->x[dft->frameNr-1], petTunit(dft->timeunit) );
  res->datanr=dft->frameNr;
 
  return 0;
}

Referenced by dftToResult().

resCopyMHeader()

int resCopyMHeader ( RES * res1, RES * res2 )

extern

Copy result main header information to another result structure.

Returns

Returns 0 if successful.

See also

resRead, resInit

Definition at line 1297 of file result.c.

  {
  int i;
 
  if(res1==NULL || res2==NULL) return(1);
  strcpy(res2->program, res1->program);
  res2->time=res1->time;
  res2->parNr=res1->parNr;
  strcpy(res2->studynr, res1->studynr);
  strcpy(res2->datafile, res1->datafile);
  strcpy(res2->reffile, res1->reffile);
  strcpy(res2->plasmafile, res1->plasmafile);
  strcpy(res2->plasmafile2, res1->plasmafile2);
  strcpy(res2->bloodfile, res1->bloodfile);
  strcpy(res2->refroi, res1->refroi);
  strcpy(res2->datarange, res1->datarange);
  res2->datanr=res1->datanr;
  strcpy(res2->fitmethod, res1->fitmethod);
  res2->density=res1->density;
  res2->lc=res1->lc;
  res2->concentration=res1->concentration;
  res2->beta=res1->beta;
  res2->Vb=res1->Vb;
  res2->fA=res1->fA;
  res2->E=res1->E;
  res2->isweight=res1->isweight;
  for(i=0; i<res1->parNr; i++) {
    strcpy(res2->parname[i], res1->parname[i]);
    strcpy(res2->parunit[i], res1->parunit[i]);
  }
  strcpy(res2->titleline, res1->titleline);
  strcpy(res2->unitline, res1->unitline);
  return(0);
}

resDelete()

int resDelete ( RES * res, int voi )

extern

Delete specified region (0..voiNr-1) from the structure.

Returns

Returns 0 if ok.

See also

resSelectRegions, resRead, resSortByName, resIsDuplicateNames

Parameters

res	Pointer to the result data.
voi	TAC index (0..voiNr-1).

Definition at line 1342 of file result.c.

  {
  int i;
 
  /* Check that region exists */
  if(res==NULL || voi>res->voiNr-1 || voi<0) return(1);
  /* If it is the last one, then just decrease the voiNr */
  if(voi==res->voiNr) {res->voiNr--; return(0);}
  /* Otherwise we have to move the following regions in its place */
  for(i=voi+1; i<res->voiNr; i++)
    memcpy(&res->voi[i-1], &res->voi[i], sizeof(ResVOI));
  res->voiNr--;
  return(0);
}

resEmpty()

void resEmpty ( RES * res )

extern

Free memory allocated for results. All data are cleared.

See also

resInit, resSetmem

Parameters

res	Pointer to RES structure.

Definition at line 22 of file result.c.

  {
  if(res==NULL) return;
  if(res->_voidataNr>0) {
    free((char*)(res->voi));
    res->_voidataNr=0;
  }
  res->voiNr=0;
  res->parNr=0;
  res->studynr[0]=(char)0;
  for(int pi=0; pi<MAX_RESPARAMS; pi++) {
    strcpy(res->parname[pi], ""); strcpy(res->parunit[pi], "");}
  res->titleline[0]=res->unitline[0]=(char)0;
  res->program[0]=(char)0; res->refroi[0]=(char)0; res->datarange[0]=(char)0;
  res->datanr=0; res->fitmethod[0]=(char)0;
  res->datafile[0]=res->reffile[0]=(char)0;
  res->plasmafile[0]=res->plasmafile2[0]=res->bloodfile[0]=(char)0;
  res->density=res->lc=res->concentration=res->beta=0.0;
  res->Vb=-1.0;
  res->fA=-1.0;
  res->E=-1.0;
}

Referenced by fitToResult(), resInit(), resRead(), and resSetmem().

resFixParnames()

void resFixParnames ( RES * res )

extern

Fix result parameter names and units, so that both representations are filled correctly, that is, the new string lists *parname[] and *parunit[], and the deprecated titleline[] and unitline[].

New representation, if filled, always overwrites the deprecated one. Units are assumed to follow parameter name representation.

See also

resRNameSubfieldExists

Parameters

res	Pointer to RES struct.

Definition at line 107 of file result.c.

  {
  int i, len, n;
  char *cptr, tmp[1024], *lptr;
 
  if(RESULT_TEST>0) printf("resFixParnames(*res)\n");
  if(res==NULL) return;
  if(res->parNr<1) return;
  if(res->parNr>MAX_RESPARAMS) res->parNr=MAX_RESPARAMS;
 
  /* If new string lists are filled, then copy those to old representation */
  for(i=n=0; i<res->parNr; i++) {
    len=strlen(res->parname[i]); if(len<1) continue;
    if(strcmp(res->parname[i], ".")==0) continue;
    n++;
  }
  if(n>0) { // copy names and units
    strcpy(res->titleline, "");
    for(i=0; i<res->parNr; i++) {
      if(1023<(1+strlen(res->titleline)+strlen(res->parname[i]))) break;
      if(i>0) strcat(res->titleline, " ");
      len=strlen(res->parname[i]);
      if(len<1) strcat(res->titleline, ".");
      else strcat(res->titleline, res->parname[i]);
    }
    strcpy(res->unitline, "");
    for(i=0; i<res->parNr; i++) {
      if(1023<(1+strlen(res->unitline)+strlen(res->parunit[i]))) break;
      if(i>0) strcat(res->unitline, " ");
      len=strlen(res->parunit[i]);
      if(len<1) strcat(res->unitline, ".");
      else strcat(res->unitline, res->parunit[i]);
    }
    if(RESULT_TEST>1) {
      printf("Parameter names and units:\n");
      for(i=0; i<res->parNr; i++)
        printf("  %d: '%s' '%s'\n", i+1, res->parname[i], res->parunit[i]);
      printf("Created titleline: %s\n", res->titleline);
      printf("Created unitline: %s\n", res->unitline);
    }
    return;
  }
 
  /* If new string lists are not filled, then get them from deprecated strings */
  for(i=0; i<res->parNr; i++) {
    strcpy(res->parname[i], "");
    strcpy(res->parunit[i], "");
  }
  strcpy(tmp, res->titleline); lptr=tmp; cptr=strtok(lptr, " \t\n\r");
  i=0; while(cptr!=NULL && i<res->parNr) {
    if(strcmp(cptr, ".")==0) {i++; continue;}
    strncpy(res->parname[i], cptr, MAX_RESPARNAME_LEN);
    res->parname[i][MAX_RESPARNAME_LEN]=(char)0;
    cptr=strtok(NULL, " \t\n\r"); i++;
  }
  strcpy(tmp, res->unitline); lptr=tmp; cptr=strtok(lptr, " \t\n\r");
  i=0; while(cptr!=NULL && i<res->parNr) {
    if(strcmp(cptr, ".")==0) {i++; continue;}
    strncpy(res->parunit[i], cptr, MAX_RESPARNAME_LEN);
    res->parunit[i][MAX_RESPARNAME_LEN]=(char)0;
    cptr=strtok(NULL, " \t\n\r"); i++;
  }
  if(RESULT_TEST>1) {
    printf("Original titleline: %s\n", res->titleline);
    printf("Original unitline: %s\n", res->unitline);
    printf("Resolved parameter names and units:\n");
    for(i=0; i<res->parNr; i++)
      printf("  %d: '%s' '%s'\n", i+1, res->parname[i], res->parunit[i]);
  }
  return;
}

Referenced by dftToResult(), fitToResult(), resMatchParameternames(), resRead(), resWrite(), and resWriteHTML().

resFName2study()

int resFName2study ( char * fname, char * studyNumber )

extern

Set study number based on file name.

See also

studynr_from_fname

Returns

Non-zero in case of an error.

Definition at line 1169 of file result.c.

  {
  return(studynr_from_fname(fname, studyNumber));
}

resInit()

void resInit ( RES * res )

extern

Initiate RES structure. This should be called once before first use.

See also

resSetmem, resEmpty

Parameters

res	Pointer to RES structure.

Definition at line 52 of file result.c.

  {
  if(res==NULL) return;
  memset(res, 0, sizeof(RES));
  res->_voidataNr=0; res->voiNr=0; res->parNr=0;
  //res->Vb=-1.0;
  //res->fA=-1.0;
  //res->E=-1.0;
  resEmpty(res);
}

resIsDuplicateNames()

int resIsDuplicateNames ( RES * res )

extern

Check if result structure contains duplicate region names.

Returns

Returns 0 if not, 1 if duplicates are found, and <0 in case of an error.

See also

resSortByName, resDelete, resRNameSubfieldExists

Parameters

res	Pointer to the result data.

Definition at line 1473 of file result.c.

  {
  int ri, rj;
  
  if(res==NULL) return(-1);
  if(res->voiNr<2) return(0);
  for(ri=0; ri<res->voiNr-1; ri++) for(rj=ri+1; rj<res->voiNr; rj++)
    if(strcasecmp(res->voi[ri].name, res->voi[rj].name)==0) return(1);
  return(0);
}

resMatchHeader()

int resMatchHeader ( RES * res1, RES * res2 )

extern

Check whether result header field values are the same.

Fields that are not checked: program, time, titleline.

Returns

Returns 0 in case of match, and <>0 if not matching.

See also

resRead, resMatchRegions, resMatchParameternames

Parameters

res1	Pointers to the result data that are tested
res2	Pointers to the result data that are tested

Definition at line 1494 of file result.c.

  {
  if(res1==NULL || res2==NULL) return(1);
  if(res1->voiNr!=res2->voiNr) return(3);
  if(res1->parNr!=res2->parNr) return(4);
  if(strcasecmp(res1->datafile, res2->datafile)!=0) return(6);
  if(strcasecmp(res1->reffile, res2->reffile)!=0) return(7);
  if(strcasecmp(res1->plasmafile, res2->plasmafile)!=0) return(8);
  if(strcasecmp(res1->plasmafile2, res2->plasmafile2)!=0) return(9);
  if(strcasecmp(res1->bloodfile, res2->bloodfile)!=0) return(10);
  if(strcasecmp(res1->refroi, res2->refroi)!=0) return(11);
  if(strcasecmp(res1->datarange, res2->datarange)!=0) return(12);
  if(res1->isweight!=res2->isweight) return(13);
  if(res1->density!=res2->density) return(14);
  if(res1->lc!=res2->lc) return(15);
  if(res1->beta!=res2->beta) return(16);
  if(res1->concentration!=res2->concentration) return(17);
  if(res1->Vb!=res2->Vb) return(18);
  if(res1->datanr!=res2->datanr) return(19);
  if(strcasecmp(res1->fitmethod, res2->fitmethod)!=0) return(20);
  if(res1->fA!=res2->fA) return(21);
  if(res1->E!=res2->E) return(22);
  /* Less important */
  if(strcasecmp(res1->studynr, res2->studynr)!=0) return(5);
  return(0);
}

resMatchParameternames()

int resMatchParameternames ( RES * res1, RES * res2 )

extern

Check whether result parameter names are the same.

Returns

Returns 0 in case of match, and 1 if not matching.

See also

resMatchHeader, resMatchHeader, resMatchParameters

Parameters

res1	Pointers to the result data that are tested.
res2	Pointers to the result data that are tested.

Definition at line 1564 of file result.c.

  {
  int i;
 
  if(res1==NULL || res2==NULL || res1->parNr!=res2->parNr) return(1);
 
  resFixParnames(res1);
  resFixParnames(res2);
 
  for(i=0; i<res1->parNr; i++) {
    if(strcasecmp(res1->parname[i], res2->parname[i])!=0) {
      if(RESULT_TEST>1)
        printf("  Parameter names '%s' and '%s' do not match\n",
               res1->parname[i], res2->parname[i]);
      return(1);
    }
    if(strcasecmp(res1->parunit[i], res2->parunit[i])!=0) {
      if(RESULT_TEST>1)
        printf("  Parameter units '%s' and '%s' do not match\n",
               res1->parunit[i], res2->parunit[i]);
      return(1);
    }
  }
  return(0);
}

resMatchParameters()

int resMatchParameters ( RES * res1, RES * res2, int test_par, double test_limit, int test_sd )

extern

Check whether result parameter values are the same.

Returns

Returns 0 in case of match, and <>0 if not matching.

See also

resMatchParametersAbs, resMatchHeader, resMatchHeader, resMatchParameternames

Parameters

res1	Pointers to the result data that are tested.
res2	Pointers to the result data that are tested.
test_par	Parameter index (0..parNr-1) that is verified; <0, if all.
test_limit	Test limit (how exact match is required).
test_sd	Test (1) or do not test (0) SD and Confidence limits.

Definition at line 1600 of file result.c.

  {
  int ri, pi;
  double s, v1, v2;
 
  if(res1==NULL || res2==NULL || res1->voiNr!=res2->voiNr) return(1);
  if(res1->parNr!=res2->parNr) {
    if(test_par<0) return(1);
    if(test_par+1>res1->parNr || test_par+1>res2->parNr) return(1);
  }
  for(ri=0; ri<res1->voiNr; ri++) {
    for(pi=0; pi<res1->parNr; pi++) {
      if(test_par>=0 && test_par!=pi) continue;
      v1=res1->voi[ri].parameter[pi]; v2=res2->voi[ri].parameter[pi];
      if(isnan(v1) && isnan(v2)) continue; // ok if both are NaN
      /* Parameter values */
      if(RESULT_TEST>5) printf("pi=%d ri=%d\n", pi, ri);
      if(RESULT_TEST>5) printf(" %g vs %g\n", v1, v2);
      s=fabs(v1+v2); if(isnan(s)) return(2); // Either one is NaN
      if(test_limit<=0.0) { // values are requested to match exactly
        if(v1!=v2) return(2);
      } if(s==0.0 || v1==0.0 || v2==0.0) { // relative matching cant be done
        if(fabs(v1-v2)>test_limit) return(2);
      } else { // test relative difference against given limit
        if(fabs((v1-v2)/s)>test_limit) return(2);
      }
      if(test_sd!=0) {
        /* SD */
        v1=res1->voi[ri].sd[pi]; v2=res2->voi[ri].sd[pi];
        if(RESULT_TEST>5) printf(" SD: %g vs %g\n", v1, v2);
        if(isnan(v1) && isnan(v2)) {
          // both are NA, that is ok
        } else if(isnan(v1) || isnan(v2)) {
          // one is NA, that is not ok
          return(3);
        } else if(test_limit<=0.0) { // values are requested to match exactly
          if(v1!=v2) return(3);
        } if(s==0.0) { // relative matching cant be done
          if(fabs(v1-v2)>test_limit) return(3);
        } else { // test relative difference against given limit
          if(fabs((v1-v2)/s)>test_limit) return(3);
        }
        /* CL1 */
        v1=res1->voi[ri].cl1[pi]; v2=res2->voi[ri].cl1[pi];
        if(RESULT_TEST>5) printf(" CL1: %g vs %g\n", v1, v2);
        if(isnan(v1) && isnan(v2)) {
          // both are NA, that is ok
        } else if(isnan(v1) || isnan(v2)) {
          // one is NA, that is not ok
          return(4);
        } else if(test_limit<=0.0) { // values are requested to match exactly
          if(v1!=v2) return(4);
        } if(s==0.0) { // relative matching cant be done
          if(fabs(v1-v2)>test_limit) return(4);
        } else { // test relative difference against given limit
          if(fabs((v1-v2)/s)>test_limit) return(4);
        }
        /* CL2 */
        v1=res1->voi[ri].cl2[pi]; v2=res2->voi[ri].cl2[pi];
        if(RESULT_TEST>5) printf(" CL2: %g vs %g\n", v1, v2);
        if(isnan(v1) && isnan(v2)) {
          // both are NA, that is ok
        } else if(isnan(v1) || isnan(v2)) {
          // one is NA, that is not ok
          return(5);
        } else if(test_limit<=0.0) { // values are requested to match exactly
          if(v1!=v2) return(5);
        } if(s==0.0) { // relative matching cant be done
          if(fabs(v1-v2)>test_limit) return(5);
        } else { // test relative difference against given limit
          if(fabs((v1-v2)/s)>test_limit) return(5);
        }
      }
    }
  }
  return(0);
}

resMatchParametersAbs()

int resMatchParametersAbs ( RES * res1, RES * res2, int test_par, double test_limit, int test_sd )

extern

Check whether the two sets of result parameter values are similar within a given absolute range.

Returns

Returns 0 in case of match, and <>0 if not matching.

See also

resMatchParameters

Parameters

res1	Pointers to the result data that are tested.
res2	Pointers to the result data that are tested.
test_par	Parameter index (0..parNr-1) that is verified; <0, if all.
test_limit	Test limit; positive value, below which the absolute difference must be.
test_sd	Test (1) or do not test (0) SD and Confidence limits.

Definition at line 1694 of file result.c.

  {
  int ri, pi;
  double s, v1, v2;
 
  if(res1==NULL || res2==NULL || res1->voiNr!=res2->voiNr) return(1);
  if(res1->parNr!=res2->parNr) {
    if(test_par<0) return(1);
    if(test_par+1>res1->parNr || test_par+1>res2->parNr) return(1);
  }
  if(test_limit<0.0) return(1);
  for(ri=0; ri<res1->voiNr; ri++) {
    for(pi=0; pi<res1->parNr; pi++) {
      if(test_par>=0 && test_par!=pi) continue;
      v1=res1->voi[ri].parameter[pi]; v2=res2->voi[ri].parameter[pi];
      if(isnan(v1) && isnan(v2)) continue;
      /* Parameter values */
      if(RESULT_TEST>5) printf("pi=%d ri=%d\n", pi, ri);
      if(RESULT_TEST>5) printf(" %g vs %g\n", v1, v2);
      s=fabs(v1-v2);
      if(isnan(s) || s>test_limit) return(2);
      if(test_sd!=0) {
        /* SD */
        v1=res1->voi[ri].sd[pi]; v2=res2->voi[ri].sd[pi];
        if(isnan(v1) && !isnan(v2)) return(3);
        if(!isnan(v1) && isnan(v2)) return(3);
        if(!isnan(v1) && !isnan(v2)) {
          if(RESULT_TEST>8) printf(" SD: %g vs %g\n", v1, v2);
          s=fabs(v1-v2); if(s>test_limit) return(3);
        }
        /* CL1 */
        v1=res1->voi[ri].cl1[pi]; v2=res2->voi[ri].cl1[pi];
        if(isnan(v1) && !isnan(v2)) return(4);
        if(!isnan(v1) && isnan(v2)) return(4);
        if(!isnan(v1) && !isnan(v2)) {
          if(RESULT_TEST>8) printf(" CL1: %g vs %g\n", v1, v2);
          s=fabs(v1-v2); if(s>test_limit) return(4);
        }
        /* CL2 */
        v1=res1->voi[ri].cl2[pi]; v2=res2->voi[ri].cl2[pi];
        if(isnan(v1) && !isnan(v2)) return(5);
        if(!isnan(v1) && isnan(v2)) return(5);
        if(!isnan(v1) && !isnan(v2)) {
          if(RESULT_TEST>8) printf(" CL2: %g vs %g\n", v1, v2);
          s=fabs(v1-v2); if(s>test_limit) return(5);
        }
      }
    }
  }
  return(0);
}

resMatchRegions()

int resMatchRegions ( RES * res1, RES * res2 )

extern

Check whether result region names are the same.

Returns

Returns 0 in case of match, and 1 if not matching.

See also

resRNameSubfieldExists, resMatchHeader, resMatchParameternames

Parameters

res1	Pointers to the result data that are tested.
res2	Pointers to the result data that are tested.

Definition at line 1531 of file result.c.

  {
  int ri, m=0;
 
  if(res1==NULL || res2==NULL || res1->voiNr!=res2->voiNr) return(1);
  for(ri=0; ri<res1->voiNr; ri++) {
    m=0;
//  if(strcmp(res1->voi[ri].name, res2->voi[ri].name)!=0) return(1);
    if(strcmp(res1->voi[ri].voiname, res2->voi[ri].voiname)!=0) m++;
    if(strcmp(res1->voi[ri].hemisphere, res2->voi[ri].hemisphere)!=0) m++;;
    if(strcmp(res1->voi[ri].place, res2->voi[ri].place)!=0) m++;
    if(m>0) {
      if(RESULT_TEST>5) {
        printf("  '%s' vs '%s'\n", res1->voi[ri].voiname, res2->voi[ri].voiname);
        printf("  '%s' vs '%s'\n", res1->voi[ri].hemisphere, res2->voi[ri].hemisphere);
        printf("  '%s' vs '%s'\n", res1->voi[ri].place, res2->voi[ri].place);
      }
      return(1);
    }
  }
  return(0);
}

resMean()

int resMean ( double * data, int nr, double * mean, double * sd )

extern

Calculate the mean and sd in the specified double array data of length nr.

NULL pointer may be specified to function in place of an unwanted return parameter.

Returns

Returns 0 if successful.

See also

resMedian, doubleMean

Parameters

data	Array of data.
nr	Length of data array.
mean	Pointer where mean is written.
sd	Pointer where S.D. is written.

Definition at line 1222 of file result.c.

  {
  int i;
  double sum, ssum, v;
 
  /* Check the arguments */
  if(data==NULL) return(1);
  if(nr<1) return(2);
  /* Calculate avg and sd */
  for(i=0, sum=ssum=0.0; i<nr; i++) {
    sum+=data[i]; ssum+=data[i]*data[i];
  }
  if(mean!=NULL) *mean=sum/(double)nr;
  if(sd!=NULL) {
    if(nr>1) v=(ssum-sum*sum/(double)nr)/(double)(nr-1); else v=0.0;
    if(v>0.0) *sd=sqrt(v); else *sd=0.0;
  }
  return(0);
}

Referenced by rescoll_tabulate().

resMedian()

int resMedian ( double * data, int nr, double * median, double * min, double * max )

extern

Calculate the median and the lowest and highest value in the specified double array data of length nr.

Note that array is sorted in this function. NULL pointer may be specified to function in place of an unwanted return parameter.

Returns

Returns 0 if successful.

See also

resMean, doubleMean

Parameters

data	Array of data.
nr	Length of data array.
median	Pointer where median is written.
min	Pointer where min is written.
max	Pointer where max is written.

Definition at line 1186 of file result.c.

  {
  /* Check the arguments */
  if(data==NULL) return(1);
  if(nr<1) return(2);
  /* Sort data in increasing order */
  qsort(data, nr, sizeof(double), resQSortComp);
  /* Get minimum and maximum */
  if(min!=NULL) *min=data[0];
  if(max!=NULL) *max=data[nr-1];
  /* Calculate median */
  if(median!=NULL) {
    if(nr%2) *median=data[(nr-1)/2];
    else *median=0.5*(data[(nr/2)-1]+data[nr/2]);
  }
  return(0);
}

Referenced by rescoll_tabulate().

resParameterPrintType()

int resParameterPrintType ( RES * res, int parIndex )

extern

Determine whether the result parameter should be printed as integer (0), float (1), or exponential (2).

Returns

Returns the code, or <0 in case of an error.

See also

resWrite

Parameters

res	Pointer to the result struct.
parIndex	Index of the parameter to test.

Definition at line 1447 of file result.c.

  {
  int vi, partype=0;
  double x, m=0.0, pint;
 
  if(res==NULL || res->voiNr<1 || parIndex<0 || parIndex>=res->parNr)
    return(-1);
  for(vi=0; vi<res->voiNr; vi++) {
    x=res->voi[vi].parameter[parIndex];
    if(modf(x, &pint)!=0.0) partype=1;
    x=fabs(x); if(x>m) m=x;
  }
  if(partype==1 && (m>=10.0 || m<0.1)) partype=2;
  return(partype);
}

Referenced by rescoll_tabulate(), resWrite(), and resWriteHTML_table().

resPrint()

void resPrint ( RES * res )

extern

Print to stdout the contents of RES data structure.

See also

resWrite, resInit, resRead

Parameters

res	Pointer to result data.

Definition at line 186 of file result.c.

  {
  resWrite(res, "stdout", 0);
}

resRead()

int resRead ( char * filename, RES * res, int verbose )

extern

Read RES file contents to the specified data structure.

Returns

In case of an error, >0 is returned, and a description is written in reserrmsg.

See also

resWrite, resInit, resPrint, resFixParnames

Parameters

filename	Result file name.
res	Pointer to initiated RES structure; any previous contents are deleted.
verbose	Verbose level; if <=0, then nothing is printed into stdout.

Definition at line 199 of file result.c.

  {
  FILE *fp;
  char *cptr, line[1024], *lptr, tmp[1024];
  int i, n;
  fpos_t file_loc;
 
 
  if(verbose>0) printf("resRead(%s, *res);\n", filename);
  if(res==NULL) return(1);
  /* Empty data */
  resEmpty(res);
  res->isweight=-1; /* unknown */
 
  /* Open file; note that 'b' is required for fgetpos() and fsetpos() to work
     correctly */
  fp=fopen(filename, "rb");
  if(fp==NULL) {strcpy(reserrmsg, "cannot open file"); return(1);}
 
  /*
   * Read data, each result set separately, saving only the first one
   */
  strcpy(reserrmsg, "wrong format");
 
  /* Read program name */
  if(verbose>1) printf("reading program name\n");
  while(fgets(line, 1024, fp)!=NULL) {
    /* Ignore empty and comment lines */
    if(strlen(line)<4 || line[0]=='#') continue; else break;
  }
  /* Check for string (c) or (C) */
  if(strstr(line, "(c)") || strstr(line, "(C)")) {
    i=strlen(line)-1; while(i>0 && isspace(line[i])) i--; line[i+1]=(char)0;
    if(i<4) {fclose(fp); return(2);}
    strcpy(res->program, line);
  } else {fclose(fp); return(2);}
 
  /* Read calculation date and time */
  if(verbose>1) printf("reading date and time\n");
  while(fgets(line, 1024, fp)!=NULL) if(strlen(line)>2 && line[0]!='#') break;
  if(strncasecmp(line, "Date:", 5)) {fclose(fp); return(4);}
  cptr=&line[5]; while(isblank(cptr[0])) cptr++;
  if(cptr!=NULL) {
    if(verbose>3) printf("date_str := %s", cptr);
    struct tm st;
    if(get_datetime(cptr, &st, verbose-3)==0) res->time=timegm(&st);
    else if(get_date(cptr, &st)==0) res->time=timegm(&st);
    else res->time=(time_t)0;
  }
 
  /* Read studynr, datafiles, ref region, data range, etc */
  if(verbose>1) printf("reading headers\n");
  do {
    /* Omit comment and too short lines */
    while((lptr=fgets(line, 1024, fp))!=NULL) {
      if(strlen(line)>2 && line[0]!='#') break;
      if(lptr!=NULL && verbose>6)
        printf("omitted line[%d] := %s", (int)strlen(line), line);
    }
    if(lptr==NULL) break;
    strcpy(tmp, line);
    n=0; if(verbose>3) printf("line[%d] := %s", (int)strlen(line), line); 
    if(strncasecmp(line, "Study", 5)==0) {
      lptr=&tmp[6]; cptr=strtok(lptr, " \t\n\r"); n=1;
      if(cptr!=NULL && strlen(cptr)<1024) {
        strlcpy(res->studynr, cptr, MAX_STUDYNR_LEN+1);
      }  
    } else if(strncasecmp(line, "Data file", 9)==0) {
      lptr=&tmp[10]; cptr=strtok(lptr, " \t\n\r"); n=1;
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(res->datafile, cptr);
    } else if(strncasecmp(line, "ROI file", 8)==0) {
      lptr=&tmp[9]; cptr=strtok(lptr, " \t\n\r"); n=1;
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(res->datafile, cptr);
    } else if(strncasecmp(line, "Plasma file", 11)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(res->plasmafile, cptr);
      cptr=res->plasmafile+strlen(res->plasmafile)-1;
      while(isspace((int)*cptr)) {*cptr=(char)0; cptr--;}
    } else if(strncasecmp(line, "2nd Plasma file", 15)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(res->plasmafile2, cptr);
      cptr=res->plasmafile2+strlen(res->plasmafile2)-1;
      while(isspace((int)*cptr)) {*cptr=(char)0; cptr--;}
    } else if(strncasecmp(line, "Blood file", 10)==0) {
      lptr=&tmp[11]; cptr=strtok(lptr, " \t\n\r"); n=1;
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(res->bloodfile, cptr);
    } else if(strncasecmp(line, "Reference file", 14)==0) {
      lptr=&tmp[15]; cptr=strtok(lptr, " \t\n\r"); n=1;
      if(cptr!=NULL && strlen(cptr)<1024) strcpy(res->reffile, cptr);
    } else if(strncasecmp(line, "Reference region", 16)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL && strlen(cptr)<64) strcpy(res->refroi, cptr);
      cptr=res->refroi+strlen(res->refroi)-1;
      while(isspace((int)*cptr)) {*cptr=(char)0; cptr--;}
    } else if(strncasecmp(line, "Fit time", 8)==0 || strncasecmp(line, "Data range", 10)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL && strlen(cptr)<128) strcpy(res->datarange, cptr);
      cptr=res->datarange+strlen(res->datarange)-1;
      while(isspace((int)*cptr)) {*cptr=(char)0; cptr--;}
    } else if(strncasecmp(line, "Data nr", 7)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->datanr=atoi(cptr);
    } else if(strncasecmp(line, "Fit method", 10)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL && strlen(cptr)<128) strcpy(res->fitmethod, cptr);
      cptr=res->fitmethod+strlen(res->fitmethod)-1;
      while(isspace((int)*cptr)) {*cptr=(char)0; cptr--;}
    } else if(strncasecmp(line, "Tissue density", 14)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->density=atof_dpi(cptr);
    } else if(strncasecmp(line, "Lumped constant", 15)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->lc=atof_dpi(cptr);
    } else if(strncasecmp(line, "Concentration", 13)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->concentration=atof_dpi(cptr);
    } else if(strncasecmp(line, "Beta", 4)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->beta=atof_dpi(cptr);
    } else if(strncasecmp(line, "Vb", 2)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->Vb=atof_dpi(cptr);
    } else if(strncasecmp(line, "fA", 2)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->fA=atof_dpi(cptr);
    } else if(strncasecmp(line, "Extraction", 10)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(cptr!=NULL) res->E=atof_dpi(cptr);
    } else if(strncasecmp(line, "Weighting", 9)==0) {
      cptr=strchr(tmp, ':')+1; while(isspace((int)*cptr)) cptr++; n=1;
      if(strncasecmp(cptr, "yes", 1)==0) res->isweight=1;
      else if(strncasecmp(cptr, "no", 1)==0) res->isweight=0;
      else res->isweight=-1;
    } else if(strncasecmp(line, "Data was weighted", 17)==0) {
      res->isweight=1; n=1;
    } else if(strncasecmp(line, "Data was not weighted", 21)==0) {
      res->isweight=0; n=1;
    } else if(strncasecmp(line, "Region", 6)==0) {
      /* Header end, stop here */
      n=0;
    } else { /* Ignore all other header lines */
      n=1;
    }
  } while(n);
  if(verbose>6) printf("quit reading headers\n");
 
  /* Read the result parameter title line */
  if(verbose>1) printf("reading parameter titles\n");
  if(verbose>6) printf("using previously read line[%d] := %s", (int)strlen(line), line);
  if(strncasecmp(line, "Region", 6)) {fclose(fp); return(10);}
  strcpy(tmp, line);
  lptr=strpbrk(tmp+6, " \n\r\t"); if(lptr==NULL) {fclose(fp); return(10);}
  cptr=strtok(lptr, " \n\r\t");
  n=0;
  if(cptr!=NULL) {
    if(strcmp(cptr, ".")!=0) {
      strncpy(res->parname[n], cptr, MAX_RESPARNAME_LEN);
      res->parname[n][MAX_RESPARNAME_LEN]=(char)0;
    } else {strcpy(res->parname[n], "");}
    if(verbose>5) printf("  parname[%d] := '%s'\n", n, res->parname[n]);
    n++;
  } else {strcpy(res->parname[n], "");}
  while(cptr!=NULL) {
    cptr=strtok(NULL, " \n\r\t");
    if(cptr!=NULL && n<MAX_RESPARAMS) {
      if(strcmp(cptr, ".")!=0) {
        strncpy(res->parname[n], cptr, MAX_RESPARNAME_LEN);
        res->parname[n][MAX_RESPARNAME_LEN]=(char)0;
      } else {strcpy(res->parname[n], "");}
      if(verbose>5) printf("  parname[%d] := '%s'\n", n, res->parname[n]);
      n++;
    }
  }
  res->parNr=n; if(verbose>1) printf("parNr := %d\n", res->parNr);
 
  /* Read the result parameter unit line */
  if(verbose>2) printf("seeking unit line...\n");
  if(fgetpos(fp, &file_loc)!=0) {fclose(fp); return(20);}
  while(fgets(line, 1024, fp)!=NULL && strlen(line)<3) {
    if(verbose>6) printf("omitted line[%d] := %s", (int)strlen(line), line);
    /* save the file position where unit line or results really start */
    if(fgetpos(fp, &file_loc)!=0) {fclose(fp); return(20);}
  }
  if(verbose>5) printf("possible unit line[%d]: %s", (int)strlen(line), line);
  if(strncasecmp(line, "# Units :", 7)==0 ||
     strncasecmp(line, "Units : ", 7)==0 ||
     strncasecmp(line, "# Units: ", 7)==0 ||
     strncasecmp(line, "Units: ", 6)==0)
  {
    if(verbose>1) printf("reading parameter units\n");
    strcpy(tmp, line); lptr=strchr(tmp+5, ':');
    if(lptr!=NULL) lptr++; else lptr=strpbrk(tmp+6, " \n\r\t");
    cptr=strtok(lptr, " \n\r\t"); n=0;
    if(cptr!=NULL) {
      if(strcmp(cptr, ".")!=0) {
        strncpy(res->parunit[n], cptr, MAX_RESPARNAME_LEN);
        res->parunit[n][MAX_RESPARNAME_LEN]=(char)0;
      } else {strcpy(res->parunit[n], "");}
      if(verbose>5) printf("  parunit[%d] := '%s'\n", n, res->parunit[n]);
      n++;
    } else {strcpy(res->parunit[n], "");}
    while(cptr!=NULL) {
      cptr=strtok(NULL, " \n\r\t");
      if(cptr!=NULL && n<MAX_RESPARAMS) {
        if(strcmp(cptr, ".")!=0) {
          strncpy(res->parunit[n], cptr, MAX_RESPARNAME_LEN);
          res->parunit[n][MAX_RESPARNAME_LEN]=(char)0;
        } else strcpy(res->parunit[n], "");
        if(verbose>5) printf("  parunit[%d] := '%s'\n", n, res->parunit[n]);
        n++;
      }
    }
  } else {
    if(verbose>5) printf("  ... not identified as unit line.\n");
    /* move file pointer to the previous place */
    if(fsetpos(fp, &file_loc)!=0) {fclose(fp); return(20);}
  }
 
  /* Read the nr of result lines */
  if(verbose>1) printf("reading nr of results\n");
  /* Set bookmark to the start of result lines */
  if(fgetpos(fp, &file_loc)!=0) {fclose(fp); return(21);}
  n=0;
  while(fgets(line, 1024, fp)!=NULL) {
    if(verbose>6) printf("line[%d] := %s", (int)strlen(line), line);
    if(line[0]=='#' || line[0]==';') continue;
    i=strlen(line); if(i<2) continue; if(i<3) break;
    n++;
  }
  /* Return file pointer to the start of result lines */
  if(fsetpos(fp, &file_loc)!=0) {fclose(fp); return(22);}
  if(verbose>1) printf("nr of result lines is %d\n", n);
  if(n<1) {
    strcpy(reserrmsg, "invalid result lines");
    fclose(fp); return(23);
  }
 
  /* Allocate memory for regional results */
  if(verbose>2) printf("allocating memory\n");
  if(resSetmem(res, n)) {
    strcpy(reserrmsg, "cannot allocate memory");
    fclose(fp); return(25);
  }
 
  /* Read regional results */
  if(verbose>1) printf("reading results to memory\n");
  int separtab=0; // 0=space as separator, 1=tab as separator
  char separstr[12];
  res->voiNr=0;
  while(fgets(line, 1024, fp)!=NULL) {
    if(verbose>6) printf("line[%d] := %s", (int)strlen(line), line);
    if(line[0]=='#' || line[0]==';') continue;
    i=strlen(line); if(i<2) continue; if(i<3) break;
    strcpy(tmp, line);
    if(verbose>2) printf("reading result %d\n", 1+res->voiNr);
 
    /* Read region names */
    if(strchr(tmp, '\t')==NULL) separtab=0; else separtab=1;
    if(separtab) strcpy(separstr, "\t\n\r"); else strcpy(separstr, " \t\n\r");
    int tokenNr=strTokenNr(tmp, separstr);
    if(verbose>20) printf("  tokenNr := %d\n", tokenNr);
    if(!separtab) { // old format with space as separator
      if(verbose>20) printf("separator: space\n");
      n=strTokenNCpy(tmp, separstr, 1, res->voi[res->voiNr].voiname, MAX_REGIONSUBNAME_LEN+1);
      if(n==0) {fclose(fp); return(31);}
      n=strTokenNCpy(tmp, separstr, 2, res->voi[res->voiNr].hemisphere, MAX_REGIONSUBNAME_LEN+1);
      if(n==0) {fclose(fp); return(31);}
      n=strTokenNCpy(tmp, separstr, 3, res->voi[res->voiNr].place, MAX_REGIONSUBNAME_LEN+1);
      if(n==0) {fclose(fp); return(31);}
      rnameCatenate(res->voi[res->voiNr].name, MAX_REGIONNAME_LEN, res->voi[res->voiNr].voiname,
                    res->voi[res->voiNr].hemisphere, res->voi[res->voiNr].place, ' ');
    } else { // space can exist only in TAC name
      if(verbose>20) printf("separator: tab\n");
      n=strTokenNCpy(tmp, separstr, 1, res->voi[res->voiNr].name, MAX_REGIONNAME_LEN+1);
      if(n==0) {fclose(fp); return(31);}
      rnameSplit(res->voi[res->voiNr].name, res->voi[res->voiNr].voiname,
                 res->voi[res->voiNr].hemisphere, res->voi[res->voiNr].place, MAX_REGIONSUBNAME_LEN);
    }
    if(strcmp(res->voi[res->voiNr].voiname, ".")==0) res->voi[res->voiNr].voiname[0]=(char)0;
    if(strcmp(res->voi[res->voiNr].hemisphere, ".")==0) res->voi[res->voiNr].hemisphere[0]=(char)0;
    if(strcmp(res->voi[res->voiNr].place, ".")==0) res->voi[res->voiNr].place[0]=(char)0;
    if(verbose>18) {
      printf("  voiname := '%s'\n", res->voi[res->voiNr].voiname);
      printf("  hemisphere := '%s'\n", res->voi[res->voiNr].hemisphere);
      printf("  place := '%s'\n", res->voi[res->voiNr].place);
    }
 
    /* Read results, continuing from the pointer after region names */
    int tokeni=2; if(!separtab) tokeni=4;
    char buf[128];
    for(i=0; i<MAX_RESPARAMS && tokeni<=tokenNr; i++, tokeni++) {
      n=strTokenNCpy(tmp, separstr, tokeni, buf, 128);
      if(n==0) {fclose(fp); return(32);}
      if(strlen(buf)==1 && buf[0]=='.') res->voi[res->voiNr].parameter[i]=nan("");
      else res->voi[res->voiNr].parameter[i]=atof_dpi(buf);
    }
    if(verbose>5) printf("  for '%s' parNr:=%d\n", res->voi[res->voiNr].name, i);
    //if(res->voiNr==0) {res->parNr=i;} else if(i<res->parNr) res->parNr=i;
    if(i<res->parNr) {
      if(verbose>0)
        printf("Warning: smaller parNr %d on region '%s'\n", i, res->voi[res->voiNr].name);
      res->parNr=i;
    }
 
    /* If 'region' name implies that this was confidence limit or sd, then */
    /* move the values into correct places, and do not increase the voiNr */
    if(res->voiNr==0) {res->voiNr++; continue;}
    if(strcasecmp(res->voi[res->voiNr].voiname, "CL")==0) {
      if(strcmp(res->voi[res->voiNr].hemisphere, "95%")==0) {
        if(strcasecmp(res->voi[res->voiNr].place, "Lower")==0)
          for(i=0; i<res->parNr; i++)
            res->voi[res->voiNr-1].cl1[i]=res->voi[res->voiNr].parameter[i];
        else if(strcasecmp(res->voi[res->voiNr].place, "Upper")==0)
          for(i=0; i<res->parNr; i++)
            res->voi[res->voiNr-1].cl2[i]=res->voi[res->voiNr].parameter[i];
        continue;
      }
    } else if(strcasecmp(res->voi[res->voiNr].voiname, "SD")==0) {
      for(i=0; i<res->parNr; i++)
        res->voi[res->voiNr-1].sd[i]=res->voi[res->voiNr].parameter[i];
      continue;
    }
    res->voiNr++;
  }
  if(res->parNr==0) {fclose(fp); return(33);}
  if(verbose>0) printf("nr of results: %d ; nr of parameters: %d\n", res->voiNr, res->parNr);
 
  /* Seek for other results in the same file */
  while(fgets(line, 1024, fp)!=NULL) {
    /* Ignore empty and comment lines */
    if(strlen(line)<3 || line[0]=='#') continue; else break;
  }
  /* Check again for string (c) or (C) */
  if(strstr(line, "(c)") || strstr(line, "(C)")) {
    fprintf(stderr, 
    "Warning: %s contains more than one set of results; only the 1st one is used.\n", filename);
  }
 
  /* Close file */
  fclose(fp);
  strcpy(reserrmsg, "");
 
  /* Fill studynr if it was not found in file */
  if(!res->studynr[0]) studynr_from_fname(filename, res->studynr);
  /* Set also deprecated parameter name and unit representations, for now */
  resFixParnames(res);
 
  return(0);
}

resRNameSubfieldExists()

int resRNameSubfieldExists ( RES * res )

extern

Check whether region name sub-fields exist in any region.

Returns

Returns 1 if hemisphere exists, 2 if place exists, 3 if both exist, and 0 if neither exists, and <0 in case of an error.

See also

resFixParnames, resSortByName, resIsDuplicateNames

Parameters

res	Pointer to RES struct.

Definition at line 1763 of file result.c.

  {
  int ri, m=0, n=0;
 
  if(res==NULL) return(-1);
  if(res->voiNr<1) return(-1);
  for(ri=0; ri<res->voiNr; ri++) {
    if(strlen(res->voi[ri].hemisphere)>0 &&
       strcmp(res->voi[ri].hemisphere, ".")!=0)
      m++;
    if(strlen(res->voi[ri].place)>0 &&
       strcmp(res->voi[ri].place, ".")!=0)
      n++;
  }
  ri=0; if(m>0) ri+=1; if(n>0) ri+=2;
  return(ri);
}

resSelect()

int resSelect ( RES * data, char * name )

extern

Select VOIs (sets sw=1), whose names are matching specified string.

If no string is specified, then all VOIs are selected.

Returns

Returns the number of matches, or <0, if an error occurred.

See also

resDelete, resSelectRegions

Parameters

data	Pointer to the result data.
name	Region name string.

Definition at line 1369 of file result.c.

  {
  unsigned int i, j, n;
  char *p, n1[128], n2[128], n3[128], tmp[128], sname[1024], *lptr;
 
  if(data==NULL) return(-1);
  /* Select all, if no string was specified */
  if(name==NULL || strlen(name)==0) {
    for(i=0; i<(unsigned int)data->voiNr; i++) data->voi[i].sw=1; 
    return(data->voiNr);
  }
  /* Make a copy of 'name' and use it */
  strcpy(sname, name); lptr=sname;
  /* Check if string contains several substrings (hemisphere and place) */
  n1[0]=n2[0]=n3[0]=(char)0;
  p=strtok(lptr, " ,;\n\t|"); if(p!=NULL) strcpy(n1, p); else return(-1);
  p=strtok(NULL, " ,;\n\t|"); if(p!=NULL) {
    strcpy(n2, p); p=strtok(NULL, " ,;\n\t|"); if(p!=NULL) strcpy(n3, p);}
  /* Convert strings to lowercase */
  for(i=0; i<strlen(n1); i++) n1[i]=tolower(n1[i]);
  for(i=0; i<strlen(n2); i++) n2[i]=tolower(n2[i]);
  for(i=0; i<strlen(n3); i++) n3[i]=tolower(n3[i]);
  /* Search through the data */
  for(i=0, n=0; i<(unsigned int)data->voiNr; i++) {
    data->voi[i].sw=0;
    snprintf(tmp, 128, "%s%s%s", data->voi[i].voiname, data->voi[i].hemisphere,
                           data->voi[i].place);
    for(j=0; j<strlen(tmp); j++) tmp[j]=tolower(tmp[j]);
    if(strstr(tmp, n1)==NULL) continue;
    if(n2[0] && strstr(tmp, n2)==NULL) continue;
    if(n3[0] && strstr(tmp, n3)==NULL) continue;
    data->voi[i].sw=1; n++;
  }
  return(n);
}

resSelectRegions()

int resSelectRegions ( RES * res, char * region_name, int reset )

extern

Select the VOIs that have matching region name or number.

Sets sw=1 or sw=0. This will replace resSelect().

Returns

Returns the number of selected VOIs, or <0 in case of an error.

See also

resRead, resDelete, resIsDuplicateNames

Parameters

res	Pointer to RES data where VOIs are selected
region_name	Name or VOI number which is searched
reset	1=Non-matching VOIs are deselected, 0=Old selections are preserved

Definition at line 1417 of file result.c.

  {
  int ri, match_nr=0;
 
  /* Check the input */
  if(res==NULL || res->voiNr<1 || strlen(region_name)<1) return(-1);
  /* Reset all selections if required */
  if(reset!=0) for(ri=0; ri<res->voiNr; ri++) res->voi[ri].sw=0;
  /* Check each VOI */
  for(ri=0; ri<res->voiNr; ri++) {
    if(rnameMatch(res->voi[ri].name, ri+1, region_name)!=0) {
      res->voi[ri].sw=1; match_nr++;
    }
  }
  return(match_nr);
}

resSetmem()

int resSetmem ( RES * res, int voiNr )

extern

Allocate memory for result data. Old data is destroyed.

See also

resInit, resEmpty

Parameters

res	Pointer to initiated and possibly allocated result data.
voiNr	Nr of regional results.

Definition at line 70 of file result.c.

  {
  int ri, pi;
 
  /* Check that there is something to do */
  if(res==NULL || voiNr<1) return(1);
 
  /* Clear previous data, but only if necessary */
  if(res->_voidataNr>0 || res->voiNr>0) resEmpty(res);
 
  /* Allocate memory for regional curves */
  res->voi=(ResVOI*)calloc(voiNr, sizeof(ResVOI));
  if(res->voi==NULL) return(2);
  res->_voidataNr=voiNr;
 
  /* Set SDs and CLs to NA */
  for(ri=0; ri<res->_voidataNr; ri++) for(pi=0; pi<MAX_RESPARAMS; pi++)
    res->voi[ri].sd[pi]=res->voi[ri].cl1[pi]=res->voi[ri].cl2[pi]=nan("");
 
  return(0);
}

Referenced by fitToResult(), res_allocate_with_dft(), and resRead().

resSortByName()

void resSortByName ( RES * res )

extern

Sort RES regions by region name.

See also

resIsDuplicateNames, resRead, resWrite, resCopyMHeader

Definition at line 1266 of file result.c.

  {
  if(res==NULL || res->voiNr<=1) return;
  qsort(res->voi, res->voiNr, sizeof(ResVOI), resQSortName);
  return;
}

resWrite()

int resWrite ( RES * res, char * filename, int verbose )

extern

Write calculation results into specified file.

If file exists, a backup file (+BACKUP_EXTENSION) is written also. If "stdout" is given as filename, output is directed to stdout. If filename extension is *.htm(l), file is saved in HTML format.

Returns

In case of an error, >0 is returned, and a description is written in reserrmsg.

See also

resInit, resRead, resEmpty, resPrint, resWriteHTML

Parameters

res	Pointer to result data.
filename	Output file name.
verbose	Verbose level; if <=0, then nothing is printed into stdout.

Definition at line 565 of file result.c.

  {
  int i, j, n;
  char tmp[1024], is_stdout=0, *cptr;
  FILE *fp;
  int partype[MAX_RESPARAMS]; /* 0=int, 1=double, 2=exp */
  int colwidth[MAX_RESPARAMS];
  double *p;
 
 
  if(verbose>1) printf("resWrite(*res, %s, %d)\n", filename, verbose);
  /* Check that there is some data to write */
  if(res==NULL) {strcpy(reserrmsg, "error in result data"); return(1);}
  if(res->voiNr<1) {strcpy(reserrmsg, "no result data"); return(1);}
 
  /* Write results in HTML format, if necessary */
  cptr=strrchr(filename, '.');
  if(cptr!=NULL && (!strncasecmp(cptr, ".htm", 4)))
    return(resWriteHTML(res, filename, verbose));
 
  /* Check if writing to stdout */
  if(!strcasecmp(filename, "stdout")) is_stdout=1;
 
  /* Check if file exists; backup, if necessary */
  if(!is_stdout) (void)backupExistingFile(filename, NULL, NULL);
 
  resFixParnames(res);
 
  /* Open output file */
  if(is_stdout) fp=(FILE*)stdout;
  else if((fp = fopen(filename, "w")) == NULL) {
    strcpy(reserrmsg, "cannot open file"); return(2);}
 
  /* Program name */
  n=fprintf(fp, "%s\n\n", res->program);
  if(n==0) {
    strcpy(reserrmsg, "disk full");
    if(!is_stdout) fclose(fp);
    return(3);
  }
 
  /* Write calculation date and time */
  if(!ctime_r_int(&res->time, tmp)) strcpy(tmp, "1900-01-01 00:00:00"); 
  fprintf(fp, "Date:\t%s\n", tmp);
 
  /* Write the studynr */
  if(res->studynr[0]) fprintf(fp, "Study:\t%s\n", res->studynr);
 
  /* Write the names of the original datafiles */
  if(res->datafile[0])   fprintf(fp, "Data file:\t%s\n", res->datafile);
  if(res->plasmafile[0]) fprintf(fp, "Plasma file:\t%s\n", res->plasmafile);
  if(res->plasmafile2[0]) fprintf(fp, "2nd Plasma file:\t%s\n", res->plasmafile2);
  if(res->bloodfile[0])  fprintf(fp, "Blood file:\t%s\n", res->bloodfile);
  if(res->reffile[0])    fprintf(fp, "Reference file:\t%s\n", res->reffile);
  if(res->refroi[0])     fprintf(fp, "Reference region:\t%s\n", res->refroi);
 
  /* Write data range etc */
  if(res->datarange[0])  fprintf(fp, "Data range:\t%s\n", res->datarange);
  if(res->datanr>0)      fprintf(fp, "Data nr:\t%d\n", res->datanr);
  if(res->fitmethod[0])  fprintf(fp, "Fit method:\t%s\n", res->fitmethod);
 
  /* Write constants */
  if(res->density>0.0)   fprintf(fp, "Tissue density:\t%g\n", res->density);
  if(res->lc>0.0)        fprintf(fp, "Lumped constant:\t%g\n", res->lc);
  if(res->concentration>0.0)
                         fprintf(fp, "Concentration:\t%g\n", res->concentration);
  if(res->beta>0.0)      fprintf(fp, "Beta:\t%g\n", res->beta);
  if(res->Vb>=0.0)       fprintf(fp, "Vb:\t%g %%\n", res->Vb);
  if(res->fA>=0.0)       fprintf(fp, "fA:\t%g %%\n", res->fA);
  if(res->E>=0.0)        fprintf(fp, "Extraction:\t%g\n", res->E);
 
  /* Weighting */
  if(res->isweight>0) strcpy(tmp, "yes");
  else if(res->isweight==0) strcpy(tmp, "no");
  else strcpy(tmp, "unknown");
  fprintf(fp, "Weighting:\t%s\n", tmp);
 
  /* Determine column widths: */
  for(j=0; j<res->parNr; j++) colwidth[j]=1;
  /* should column be printed as integers (0), floats (1) or exponentials (2)? */
  for(j=0; j<res->parNr; j++) {
    partype[j]=resParameterPrintType(res, j);
  }
  /* min width required by titles */
  for(j=0; j<res->parNr; j++) colwidth[j]=strlen(res->parname[j]);
  if(verbose>2) {
    printf("col widths after titles were checked:\n");
    for(i=0; i<res->parNr; i++)
      printf("  par%d : partype=%d colwidth=%d\n", i+1, partype[i], colwidth[i]);
  }
  /* min width required by units */
  for(j=0; j<res->parNr; j++) {
    n=strlen(res->parunit[j]); if(n>colwidth[j]) colwidth[j]=n;
  }
  if(verbose>2) {
    printf("col widths after units were checked:\n");
    for(i=0; i<res->parNr; i++)
      printf("  par%d : partype=%d colwidth=%d\n", i+1, partype[i], colwidth[i]);
  }
  /* widths required by result values */
  for(i=0; i<res->voiNr; i++) {
    p=res->voi[i].parameter;
    for(j=0; j<res->parNr; j++) {
      if(isnan(p[j])) continue;
      if(p[j]>=0) n=4; else n=3;
      switch(partype[j]) {
        case 0: sprintf(tmp, "%.0f", p[j]); break;
        case 1: sprintf(tmp, "%.*f", n, p[j]); break;
        case 2:
        default: sprintf(tmp, "%.*e", n, p[j]); break;
      }
      n=strlen(tmp); if(n>colwidth[j]) colwidth[j]=n;
    }
  }
  if(verbose>2) {
    printf("col widths after result values were checked:\n");
    for(i=0; i<res->parNr; i++)
      printf("  par%d : partype=%d colwidth=%d\n", i+1, partype[i], colwidth[i]);
  }
 
  /* Title line */
  if(verbose>4) {
    printf("  writing title line with %d parameter(s)\n", res->parNr); 
    fflush(stdout);
  }
  fprintf(fp, "\n%s\t", "Region");
  for(i=0; i<res->parNr; i++) {
    if(strlen(res->parname[i])<1) strcpy(tmp, ".");
    else strcpy(tmp, res->parname[i]);
    fprintf(fp, "\t%s", tmp);
  }
  fprintf(fp, "\n");
 
  /* Write units, if they exist, currently as comment line */
  for(i=j=0; i<res->parNr; i++) if(strlen(res->parunit[i])>0) j++;
  if(j>0) {
    if(verbose>4) {
      printf("  writing units line with %d parameter(s)\n", j); 
      fflush(stdout);
    }
    fprintf(fp, "%s", "# Units:");
    //fprintf(fp, "%s ", "# Units :");
    for(i=0; i<res->parNr; i++) {
      if(strlen(res->parunit[i])<1) strcpy(tmp, ".");
      else strcpy(tmp, res->parunit[i]);
      fprintf(fp, "\t%s", tmp);
    }
    fprintf(fp, "\n");
  }
  fflush(fp);
 
  /* Write regional results */
  if(verbose>4) {
    printf("  writing %d regional results\n", res->voiNr); fflush(stdout);
  }
  for(i=0; i<res->voiNr; i++) {
    if(verbose>6) {printf("    writing region %d\n", 1+i); fflush(stdout);}
#if(1) // new version
    if(res->voi[i].name[0]) {
      fprintf(fp, "%s", res->voi[i].name);
    } else {
      if(res->voi[i].voiname[0]) strcpy(tmp, res->voi[i].voiname); else strcpy(tmp, ".");
      fprintf(fp, "%.*s ", MAX_REGIONSUBNAME_LEN, tmp);
      if(res->voi[i].hemisphere[0]) strcpy(tmp, res->voi[i].hemisphere); else strcpy(tmp, ".");
      fprintf(fp, "%.*s ", MAX_REGIONSUBNAME_LEN, tmp);
      if(res->voi[i].place[0]) strcpy(tmp, res->voi[i].place); else strcpy(tmp, ".");
      fprintf(fp, "%.*s", MAX_REGIONSUBNAME_LEN, tmp);
    }
#else // previous version
    if(res->voi[i].voiname[0])
      strcpy(tmp, res->voi[i].voiname); else strcpy(tmp, ".");
    fprintf(fp, "%.*s ", MAX_REGIONSUBNAME_LEN, tmp);
    if(res->voi[i].hemisphere[0])
      strcpy(tmp, res->voi[i].hemisphere); else strcpy(tmp, ".");
    fprintf(fp, "%.*s ", MAX_REGIONSUBNAME_LEN, tmp);
    if(res->voi[i].place[0])
      strcpy(tmp, res->voi[i].place); else strcpy(tmp, ".");
    fprintf(fp, "%.*s", MAX_REGIONSUBNAME_LEN, tmp);
#endif
    p=res->voi[i].parameter;
    for(j=0; j<res->parNr; j++) {
      if(verbose>15) {printf("      writing par %d\n", 1+j); fflush(stdout);}
      if(isnan(p[j])) {fprintf(fp, "\t."); continue;}
      switch(partype[j]) {
        case 0: fprintf(fp, "\t%.0f", p[j]); break;
        case 1:
          if(p[j]>=0) n=4; else n=3;
          fprintf(fp, "\t%.*f", n, p[j]);
          break;
        default:
          if(p[j]>=0) n=4; else n=3;
          fprintf(fp, "\t%.*e", n, p[j]);
        break;
      }
    }
    fprintf(fp, "\n"); fflush(fp);
    /* Write SD's, if they exist */
    if(verbose>25) {printf("    sd?\n"); fflush(stdout);}
    //if(res->voi[i].sd==NULL) {printf("NULL\n"); fflush(stdout);}
    if(verbose>25) {printf("    parNr=%d\n", res->parNr); fflush(stdout);}
    n=0; for(int j=0; j<res->parNr; j++) {if(!isnan(res->voi[i].sd[j])) n++;}
    if(verbose>25) {printf("      n=%d\n", n); fflush(stdout);}
    if(n>0) {
      fprintf(fp, "SD . .");
      for(j=0; j<res->parNr; j++) {
        if(verbose>15) {printf("      writing sd %d\n", 1+j); fflush(stdout);}
        if(!isnan(res->voi[i].sd[j])) {
          switch(partype[j]) {
            case 0: fprintf(fp, "\t%.0f", res->voi[i].sd[j]); break;
            case 1:
              if(res->voi[i].sd[j]>=0) n=4; else n=3;
              fprintf(fp, "\t%.*f", n, res->voi[i].sd[j]);
              break;
            default:
              if(res->voi[i].sd[j]>=0) n=4; else n=3;
              fprintf(fp, "\t%.*e", n, res->voi[i].sd[j]);
              break;
          }
        } else {
          fprintf(fp, "\t.");
        }
      }
      fprintf(fp, "\n"); fflush(fp);
    }
    /* Write lower confidence limits, if they exist */
    if(verbose>25) {printf("    cl1?\n"); fflush(stdout);}
    n=0; for(int j=0; j<res->parNr; j++) if(!isnan(res->voi[i].cl1[j])) n++;
    if(verbose>25) {printf("      n=%d\n", n); fflush(stdout);}
    if(n>0) {
      fprintf(fp, "CL 95%% Lower");
      for(j=0; j<res->parNr; j++) {
        if(verbose>15) {printf("      writing CL1 %d\n", 1+j); fflush(stdout);}
        if(!isnan(res->voi[i].cl1[j])) {
          switch(partype[j]) {
            case 0: fprintf(fp, "\t%.0f", res->voi[i].cl1[j]); break;
            case 1:
              if(res->voi[i].cl1[j]>=0) n=4; else n=3;
              fprintf(fp, "\t%.*f", n, res->voi[i].cl1[j]);
              break;
            default:
              if(res->voi[i].cl1[j]>=0) n=4; else n=3;
              fprintf(fp, "\t%.*e", n, res->voi[i].cl1[j]);
              break;
          }
        } else {
          fprintf(fp, "\t.");
        }
      }
      fprintf(fp, "\n");
    }
    /* Write upper confidence limits, if they exist */
    if(verbose>25) {printf("    cl2?\n"); fflush(stdout);}
    n=0; for(int j=0; j<res->parNr; j++) if(!isnan(res->voi[i].cl2[j])) n++;
    if(verbose>25) {printf("      n=%d\n", n); fflush(stdout);}
    if(n>0) {
      fprintf(fp, "CL 95%% Upper");
      for(j=0; j<res->parNr; j++) {
        if(verbose>15) {printf("      writing CL2 %d\n", 1+j); fflush(stdout);}
        if(!isnan(res->voi[i].cl2[j])) {
          switch(partype[j]) {
            case 0: fprintf(fp, "\t%.0f", res->voi[i].cl2[j]); break;
            case 1:
              if(res->voi[i].cl2[j]>=0) n=4; else n=3;
              fprintf(fp, "\t%.*f", n, res->voi[i].cl2[j]);
              break;
            default:
              if(res->voi[i].cl2[j]>=0) n=4; else n=3;
              fprintf(fp, "\t%.*e", n, res->voi[i].cl2[j]);
              break;
          }
        } else {
          fprintf(fp, "\t.");
        }
      }
      fprintf(fp, "\n"); fflush(fp);
    }
  } /* next region */
 
  /* Close file */
  if(!is_stdout) {fflush(fp); fclose(fp);}
  strcpy(reserrmsg, "");
  if(verbose>1) {printf("resWrite() done.\n"); fflush(stdout);}
 
  return(0);
}

Referenced by resPrint().

resWriteHTML()

int resWriteHTML ( RES * res, char * fname, int verbose )

extern

Write calculation results into specied XHTML 1.1 file. If file exists, a backup file (+BACKUP_EXTENSION) is written also. If "stdout" is given as filename, output is directed to stdout.

Returns

In case of an error, >0 is returned, and a description is written in reserrmsg.

See also

resWrite

Parameters

res	Pointer to result data
fname	Output file name
verbose	Verbose level; if <=0, then nothing is printed into stdout

Definition at line 865 of file result.c.

  {
  int n, is_stdout=0;
  char tmp[1024];
  FILE *fp;
 
 
  if(verbose>0) printf("resWriteHTML(*res, %s, %d)\n", fname, verbose);
  /* Check that there is some data to write */
  if(res==NULL) {strcpy(reserrmsg, "error in result data"); return(1);}
  if(res->voiNr<1) {strcpy(reserrmsg, "no result data"); return(1);}
  /* Check if writing to stdout */
  if(!strcasecmp(fname, "stdout")) is_stdout=1;
 
  resFixParnames(res);
 
  /* Check if file exists; backup, if necessary */
  if(!is_stdout && access(fname, 0) != -1) {
    strcpy(tmp, fname); strcat(tmp, BACKUP_EXTENSION);
    if(access(tmp, 0)!=-1) remove(tmp);
    rename(fname, tmp);
  }
  strcpy(reserrmsg, "cannot write file");
 
  /* Open output file */
  if(is_stdout) fp=(FILE*)stdout;
  else if((fp=fopen(fname, "w"))==NULL) {
    strcpy(reserrmsg, "cannot open file"); return(2);}
 
  /* Write XHTML 1.1 doctype and head */
  if(resWriteXHTML11_doctype(fp) || resWriteXHTML11_head(fp, res->program)) {
    strcpy(reserrmsg, "disk full");
    if(!is_stdout) fclose(fp);
    return(3);
  }
 
  /* Start writing the body of the HTML file */
  fprintf(fp, "\n<body>\n");
 
  /* Start the div for tables */
  fprintf(fp, "\n<div id=\"tables\">\n");
 
  /* Write results into a table */
  if(resWriteHTML_table(res, fp)!=0) {
    strcpy(reserrmsg, "disk full");
    if(!is_stdout) fclose(fp);
    return(3);
  }
 
  /* Stop writing the body of the HTML file, and end the file */
  fprintf(fp, "</div>\n");
  n=fprintf(fp, "</body></html>\n\n");
  if(n==0) {
    strcpy(reserrmsg, "disk full");
    if(!is_stdout) fclose(fp);
    return(3);
  }
 
  /* Close file */
  if(!is_stdout) {fflush(fp); fclose(fp);}
  strcpy(reserrmsg, "");
 
  return(0);
}

Referenced by resWrite().

resWriteHTML_table()

int resWriteHTML_table ( RES * res, FILE * fp )

extern

Write calculation results as one HTML table into an opened (X)HTML file.

Returns

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

Parameters

res	Pointer to result data.
fp	Output file pointer.

Definition at line 1013 of file result.c.

  {
  int i, j, n;
  char *cptr, tmp[1024];
  int partype[MAX_RESPARAMS]; /* 0=int, 1=double, 2=exp */
  double *p;
 
  if(RESULT_TEST>0) printf("resWriteHTML_table(*res, fp)\n");
  if(fp==NULL || res==NULL) return(1);
 
  /* Write the title lines to the head of table */
  fprintf(fp, "<table>\n");
  fprintf(fp, "<thead>\n");
  /* Program name */
  strcpy(tmp, res->program);
  cptr=strcasestr(tmp, "(c)");
  if(cptr!=NULL) {
    *cptr=(char)0;
     i=strlen(tmp)-1; while(i>0 && isspace(tmp[i])) i--; tmp[i+1]=(char)0;
  }
  if(tmp[0])
    fprintf(fp, "<tr align=left><th>Program:</th><td>%s</td></tr>\n", tmp);
  /* Write calculation date and time */
  if(!ctime_r_int(&res->time, tmp)) strcpy(tmp, "1900-01-01 00:00:00");
  fprintf(fp, "<tr align=left><th>Date:</th><td>%s</td></tr>\n", tmp);
  /* Write the studynr */
  if(res->studynr[0])
    fprintf(fp, "<tr align=left><th>Study:</th><td>%s</td></tr>\n", res->studynr);
  /* Write the names of the original datafiles */
  if(res->datafile[0])
    fprintf(fp, "<tr align=left><th>Data file:</th><td>%s</td></tr>\n", res->datafile);
  if(res->plasmafile[0])
    fprintf(fp, "<tr align=left><th>Plasma file:</th><td>%s</td></tr>\n", res->plasmafile);
  if(res->plasmafile2[0])
    fprintf(fp, "<tr align=left><th>2nd Plasma file:</th><td>%s</td></tr>\n", res->plasmafile2);
  if(res->bloodfile[0])
    fprintf(fp, "<tr align=left><th>Blood file:</th><td>%s</td></tr>\n", res->bloodfile);
  if(res->reffile[0])
    fprintf(fp, "<tr align=left><th>Reference file:</th><td>%s</td></tr>\n", res->reffile);
  if(res->refroi[0])
    fprintf(fp, "<tr align=left><th>Reference region:</th><td>%s</td></tr>\n", res->refroi);
  /* Write data range etc */
  if(res->datarange[0])
    fprintf(fp, "<tr align=left><th>Data range:</th><td>%s</td></tr>\n", res->datarange);
  if(res->datanr>0)
    fprintf(fp, "<tr align=left><th>Data nr:</th><td>%d</td></tr>\n", res->datanr);
  if(res->fitmethod[0])
    fprintf(fp, "<tr align=left><th>Fit method:</th><td>%s</td></tr>\n", res->fitmethod);
  /* Write constants */
  if(res->density>0.0)
    fprintf(fp, "<tr align=left><th>Tissue density:</th><td>%g</td></tr>\n", res->density);
  if(res->lc>0.0)
    fprintf(fp, "<tr align=left><th>Lumped constant:</th><td>%g</td></tr>\n", res->lc);
  if(res->concentration>0.0)
    fprintf(fp, "<tr align=left><th>Concentration:</th><td>%g</td></tr>\n", res->concentration);
  if(res->beta>0.0)
    fprintf(fp, "<tr align=left><th>Beta:</th><td>%g</td></tr>\n", res->beta);
  if(res->Vb>=0.0)
    fprintf(fp, "<tr align=left><th>Vb:</th><td>%g %%</td></tr>\n", res->Vb);
  if(res->fA>=0.0)
    fprintf(fp, "<tr align=left><th>fA:</th><td>%g %%</td></tr>\n", res->fA);
  if(res->E>0.0)
    fprintf(fp, "<tr align=left><th>Extraction:</th><td>%g</td></tr>\n", res->E);
  /* Weighting */
  if(res->isweight>0) strcpy(tmp, "yes");
  else if(res->isweight==0) strcpy(tmp, "no");
  else strcpy(tmp, "unknown");
  fprintf(fp, "<tr align=left><th>Weighting:</th><td>%s</td></tr>\n", tmp);
  /* End the head of table */
  fprintf(fp, "</thead>\n");
 
  /* Collect info on column types */
  for(j=0; j<res->parNr; j++) {
    /* should column be printed as integers, floats or exponentials? */
    partype[j]=resParameterPrintType(res, j);
  }
 
  /* Write the result data to the table body */
  fprintf(fp, "<tbody>\n");
  /* Write the result title line */
  fprintf(fp,"<tr align=left><th>Region</th>\n");
  for(i=0; i<res->parNr; i++) fprintf(fp, "<th>%s</th>", res->parname[i]);
  fprintf(fp, "</tr>\n");
  /* Write regional results */
  for(i=0; i<res->voiNr; i++) {
    if(i%2) strcpy(tmp, "evenroi"); else strcpy(tmp, "oddroi");
    fprintf(fp, "<tr class=\"%s\">", tmp);
    char *senc=strEncodeForXML(res->voi[i].name);
    if(senc==NULL) fprintf(fp, "<th>%s</th>", res->voi[i].name);
    else {fprintf(fp, "<th>%s</th>", senc); free(senc);}
    p=res->voi[i].parameter;
    for(j=0; j<res->parNr; j++) switch(partype[j]) {
      case 0: fprintf(fp, "<td>%.0f</td>", p[j]); break;
      case 1: fprintf(fp, "<td>%.4f</td>", p[j]); break;
      default: fprintf(fp, "<td>%.4E</td>", p[j]); break;
    }
    fprintf(fp, "</tr>\n");
    /* Write SD's, if they exist */
    p=res->voi[i].sd; for(j=n=0; j<res->parNr; j++) if(!isnan(p[j])) n++;
    if(n>0) {
      fprintf(fp, "<tr class=\"sd\">");
      fprintf(fp, "<th>%s</th>", "SD");
      for(j=0; j<res->parNr; j++) {
        if(!isnan(p[j])) switch(partype[j]) {
          case 0: fprintf(fp, "<td>%.0f</td>", p[j]); break;
          case 1: fprintf(fp, "<td>%.4f</td>", p[j]); break;
          default: fprintf(fp, "<td>%.4E</td>", p[j]); break;
        } else fprintf(fp, "<td></td>");
      }
      fprintf(fp, "</tr>\n");
    }
    /* Write lower confidence limits, if they exist */
    p=res->voi[i].cl1; for(j=n=0; j<res->parNr; j++) if(!isnan(p[j])) n++;
    if(n>0) {
      fprintf(fp, "<tr class=\"cl1\">");
      fprintf(fp, "<th>CL95%%L</th>");
      for(j=0; j<res->parNr; j++) {
        if(!isnan(p[j])) switch(partype[j]) {
          case 0: fprintf(fp, "<td>%.0f</td>", p[j]); break;
          case 1: fprintf(fp, "<td>%.4f</td>", p[j]); break;
          default: fprintf(fp, "<td>%.4E</td>", p[j]); break;
        } else fprintf(fp, "<td></td>");
      }
      fprintf(fp, "</tr>\n");
    }
    /* Write upper confidence limits, if they exist */
    p=res->voi[i].cl2; for(j=n=0; j<res->parNr; j++) if(!isnan(p[j])) n++;
    if(n>0) {
      fprintf(fp, "<tr class=\"cl2\">");
      fprintf(fp, "<th>CL95%%U</th>");
      for(j=0; j<res->parNr; j++) {
        if(!isnan(p[j])) switch(partype[j]) {
          case 0: fprintf(fp, "<td>%.0f</td>", p[j]); break;
          case 1: fprintf(fp, "<td>%.4f</td>", p[j]); break;
          default: fprintf(fp, "<td>%.4E</td>", p[j]); break;
        } else fprintf(fp, "<td></td>");
      }
      fprintf(fp, "</tr>\n");
    }
  }
  /* End the body of the table and table */
  fprintf(fp, "</tbody></table>\n");
 
  return(0);
}

Referenced by resWriteHTML().

resWriteXHTML11_doctype()

int resWriteXHTML11_doctype ( FILE * fp )

extern

Write XHTML 1.1 doctype into an opened file pointer.

Returns

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

Parameters

fp	Output file pointer.

Definition at line 941 of file result.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 resWriteHTML().

resWriteXHTML11_head()

int resWriteXHTML11_head ( FILE * fp, char * author_name )

extern

Write XHTML 1.1 head for PET results 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 960 of file result.c.

  {
  int n;
  if(fp==NULL) return(1);
 
  n=fprintf(fp, "<head>\n"); if(n<6) return(2);
  fprintf(fp, "  <title>Tabulated PET results</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=\"description\" content=\"Regional PET results\" />\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 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:colla");
  fprintf(fp, "    table {text-align:left; border-collapse:collapse; empty-cells:show;}\n");
//fprintf(fp, "    td {border:1px solid black;}\n");
  fprintf(fp, "    .oddroi {background-color:#FFFFFF; color:black;}\n");
  fprintf(fp, "    .evenroi {background-color:#CCCCCC; color:black;}\n");
  fprintf(fp, "    .sd {background-color:#999999; color:blue;}\n");
  fprintf(fp, "    .cl1 {background-color:#999999; color:green;}\n");
  fprintf(fp, "    .cl2 {background-color:#999999; color:green;}\n");
  fprintf(fp, "    .oddstudy {background-color:#FFFFFF; color:black;}\n");
  fprintf(fp, "    .evenstudy {background-color:#CCCCCC; color:black;}\n");
  fprintf(fp, "    .oddsum {background-color:#999999; color:black;}\n");
  fprintf(fp, "    .evensum {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\" href=\"https://www.turkupetcentre.net/result.css\" />\n");
  fprintf(fp, "</head>\n");
  if(n<7) return(2);
  return(0);
}

Referenced by resWriteHTML().

roikbqRead()

int roikbqRead ( char * fname, DFT * dft )

extern

Read an old TAC file in *.roi.kbq / *.roi.nci format.

Returns

Returns 0 if ok.

Parameters

fname	Pointer to filename
dft	Pointer to an empty but initiated DFT structure where data is written

Definition at line 95 of file ncifile.c.

  {
  FILE *fp;
  int i, j, k, l, roi_nr=0, frame_nr=0, ret, nr=0;
  char c, line[ROIKBQ_MAX_LINE_LEN], tmp[25], s1[25], s2[25];
  double a, b;
 
 
  /* Check the arguments */
  if(dft==NULL || fname==NULL) {
    strcpy(dfterrmsg, "program fault"); return(1);}
  /* Empty data */
  dftEmpty(dft);
 
  /* Open file */
  fp=fopen(fname, "r");
  if(fp==NULL) {strcpy(dfterrmsg, "cannot open file"); return(2);}
 
  /* Check file type */
  rewind(fp); i=0;
  while(fgets(line, ROIKBQ_MAX_LINE_LEN-1, fp) != NULL) {
    roikbq_strip_spaces(line); if(!strlen(line) || line[0]=='#') continue;
    if(!isalpha((int)line[0])) continue;
    if(strncasecmp(line, "cpt2nci 3", 9)==0) {i=1; break;}
  }
  if(i==0) {strcpy(dfterrmsg, "unsupported file format"); fclose(fp); return(3);}
 
  /* Get data size */
  rewind(fp); roi_nr=frame_nr=0;
  /* read first title line */
  c=fgetc(fp);
  if(c=='#') roikbq_move_to_next_line(fp); else ungetc(c, fp);
  i=roikbq_fgets(fp, 16, tmp);
  if(i<16) {strcpy(dfterrmsg, "unsupported file format"); fclose(fp); return(3);}
  while(i>13) {
    i=roikbq_fgets(fp, 14, tmp); if(i>11 && isalnum((int)tmp[0])) roi_nr++;
  }
  /* read two title lines more */
  roikbq_move_to_next_line(fp); roikbq_move_to_next_line(fp);
  /* now start reading data lines */
  do {
    c=fgetc(fp); if(c==EOF) break; if(c!='\n') frame_nr++;
    roikbq_move_to_next_line(fp);
  } while(c!=EOF);
  if(roi_nr<1 || frame_nr<1) {
    strcpy(dfterrmsg, "unsupported file format"); fclose(fp); return(3);}
 
  /* Allocate memory for DFT */
  ret=dftSetmem(dft, frame_nr, roi_nr);
  if(ret) {strcpy(dfterrmsg, "out of memory"); fclose(fp); return(4);}
  dft->_type=1;
 
  /* Read data */
  /* Set file pointer to the beginning of first title line */
  rewind(fp); c=fgetc(fp);
  if(c=='#') roikbq_move_to_next_line(fp); else ungetc(c, fp);
  /* Read the names of ROIs and Hemispheres */
  j=roikbq_fgets(fp, 16, tmp);
  if(j<16) {strcpy(dfterrmsg, "unsupported file format"); fclose(fp); return(3);}
  i=0; while (j>13) {
    j=roikbq_fgets(fp, 14, tmp); if(i>=roi_nr) continue;
    k=sscanf(tmp, "%s %s", s1, s2); if(k<1) continue;
    if(k==1) s2[0]='\0';
    strcpy(dft->voi[dft->voiNr+i].voiname, s1);
    strcpy(dft->voi[dft->voiNr+i].hemisphere, s2);
    if(s2[0]!='\0')
      snprintf(dft->voi[dft->voiNr+i].name, MAX_REGIONNAME_LEN, "%s %s", s1, s2);
    else
      snprintf(dft->voi[dft->voiNr+i].name, MAX_REGIONNAME_LEN, "%s .", s1);
    i++;
  }
  nr=i;
  /* Read the name of place (planes) in 2nd title line */
  c=fgetc(fp); if(c=='#') roikbq_move_to_next_line(fp); else ungetc(c, fp);
  j=roikbq_fgets(fp, 16, tmp);
  if(j<16) {strcpy(dfterrmsg, "unsupported file format"); fclose(fp); return(3);}
  strncpy(dft->studynr, tmp, 6); dft->studynr[6]=(char)0;
  roikbq_strip_spaces(dft->studynr);
  i=0; while(j>13) {
    j=roikbq_fgets(fp, 14, tmp); if(i>=nr) continue;
    k=sscanf(tmp, "%s", s1); if(k<1) s1[0]='\0';
    strcpy(dft->voi[dft->voiNr+i].place, s1);
    if(s1[0]!='\0') {
      strcat(dft->voi[dft->voiNr+i].name, " ");
      strcat(dft->voi[dft->voiNr+i].name, s1);
    } else strcat(dft->voi[dft->voiNr+i].name, " .");
    i++;
  }
  for(j=i; j<nr; j++) strcpy(dft->voi[dft->voiNr+j].place, "");
  /* Read the ROI volumes in 3rd title line */
  c=fgetc(fp); if(c=='#') roikbq_move_to_next_line(fp); else ungetc(c, fp);
  j=roikbq_fgets(fp, 16, tmp);
  if(j<16) {strcpy(dfterrmsg, "unsupported file format"); fclose(fp); return(3);}
  if(strstr(tmp, "Times")) dft->timetype=3;
  else if(strstr(tmp, "Start")) dft->timetype=1;
  else if(strstr(tmp, "End")) dft->timetype=2;
  else dft->timetype=0;
  if(strstr(tmp, "sec")) dft->timeunit=TUNIT_SEC; else dft->timeunit=TUNIT_MIN;
  i=0; while(j>13) {
    j=roikbq_fgets(fp, 14, tmp); if(i>=nr) continue;
    if(sscanf(tmp, "%lf", &dft->voi[dft->voiNr+i].size)<1)
      dft->voi[dft->voiNr+i].size=0.;
    i++;
  }
  for(j=i; j<nr; j++) dft->voi[dft->voiNr+j].size=0.;
  /* Read frame data */
  k=0; c=fgetc(fp); if(c=='#') roikbq_move_to_next_line(fp); else ungetc(c, fp);
  while((j=roikbq_fgets(fp, 16, tmp))>15) {
    if(k>=frame_nr) break;
    roikbq_strip_spaces(tmp); if(strlen(tmp)==0) continue;
    if(dft->timetype==0) {
      dft->x[k]=atof(tmp);
      dft->x1[k]=dft->x2[k]=nan("");
    } else if(dft->timetype==3) {
      sscanf(tmp, "%lf %lf", &a, &b); dft->x1[k]=a; dft->x2[k]=b;
      dft->x[k]=0.5*(dft->x1[k] + dft->x2[k]);
    } else if(dft->timetype==1) {
      dft->x1[k]=dft->x[k]=dft->x2[k]=atof(tmp);
    } else if(dft->timetype==2) {
      dft->x2[k]=dft->x[k]=dft->x1[k]=atof(tmp);
    }
    if(dft->x[k]<-3.e38) dft->x[k]=nan("");
    i=0; while(j>13) {
      j=roikbq_fgets(fp, 14, tmp); if(i>=nr || j<13) continue;
      roikbq_strip_spaces(tmp);
      if(!strlen(tmp) || !strcmp(tmp, ".")) dft->voi[dft->voiNr+i].y[k]=nan("");
      else {
        dft->voi[dft->voiNr+i].y[k]=atof(tmp);
        if(dft->voi[dft->voiNr+i].y[k]<-3.e38)
          dft->voi[dft->voiNr+i].y[k]=nan("");
      }
      i++;
    }
    for(l=i; l<nr; l++) dft->voi[dft->voiNr+l].y[k]=nan("");
    k++;
    c=fgetc(fp); if(c=='#') roikbq_move_to_next_line(fp); else ungetc(c, fp);
  }
  for(i=k; i<frame_nr; i++) {
    dft->x[i]=0.;
    for(j=dft->voiNr; j<dft->voiNr+nr; j++) dft->voi[j].y[i]=nan("");
  }
  /* Set voiNr and frameNr and close the file */
  dft->voiNr=nr; dft->frameNr=frame_nr; fclose(fp);
  /* Set data unit based on filename */
  if(strstr(fname, ".nci")==NULL && strstr(fname, ".NCI")==NULL)
    strcpy(dft->unit, "kBq/ml");
  else strcpy(dft->unit, "nCi/ml");
  /* Set weights in DFT to 1.0 */
  dft->isweight=0;
  for(i=0; i<dft->frameNr; i++) dft->w[i]=1.0;
  /* quit */  
  return(0);
}

Referenced by dftRead().

roikbqWrite()

int roikbqWrite ( DFT * dft, char * fname )

extern

Write DFT contents in *.roi.kbq format.

Returns

Returns 0 if ok.

Parameters

dft	Pointer to DFT
fname	Filename

Definition at line 26 of file ncifile.c.

  {
  int ri, fi;
  char tmp[FILENAME_MAX];
  FILE *fp;
 
  /* Check that there is some data to write */
  if(dft->voiNr<1 || dft->frameNr<1) {
    strcpy(dfterrmsg, "no data"); return(1);}
 
  /* Check if file exists; backup, if necessary */
  if(access(fname, 0) != -1) {
    strcpy(tmp, fname); strcat(tmp, BACKUP_EXTENSION);
    if(access(tmp, 0) != -1) remove(tmp);
    rename(fname, tmp);
  }
 
  /* Open output file */
  if((fp = fopen(fname, "w")) == NULL) {strcpy(dfterrmsg, "cannot open file"); return(2);}
 
  /* Write title lines */
 
  /* Write 1st title line (Program name and ROI names) */
  fprintf(fp, "%-15.15s", "cpt2nci 3");
  for(ri=0; ri<dft->voiNr; ri++) {
    fprintf(fp, " %-6.6s", dft->voi[ri].voiname);
    if(strcmp(dft->voi[ri].hemisphere, ".")==0) fprintf(fp, " %-6.6s", " ");
    else fprintf(fp, " %-6.6s", dft->voi[ri].hemisphere);
  }
  fprintf(fp, "\n");
 
  /* Write 2nd title line (Study nr and Planes) */
  fprintf(fp, "%-15.15s", dft->studynr);
  for(ri=0; ri<dft->voiNr; ri++)
    fprintf(fp, " %-13.13s", dft->voi[ri].place);
  fprintf(fp, "\n");
 
  /* Write 3rd title line (ROI volumes) */
  fprintf(fp, "%-15.15s", "Time (min)");
  for(ri=0; ri<dft->voiNr; ri++)
    fprintf(fp, " %-13.1f", dft->voi[ri].size);
  fprintf(fp, "\n");
 
  /* Write times and data of each frame */
  for(fi=0; fi<dft->frameNr; fi++) {
    fprintf(fp, "%8.3f       ", dft->x[fi]);
    for(ri=0; ri<dft->voiNr; ri++)
      if(!isnan(dft->voi[ri].y[fi]))
        fprintf(fp, " %-13.6e", dft->voi[ri].y[fi]);
      else
        fprintf(fp, "       .      ");
    fprintf(fp, "\n");
  }
 
  /* Close file */
  fclose(fp);
 
  return(0);
}

tsvRead()

int tsvRead ( char * filename, DFT * dft )

extern

Read Amide TAC file (*.tsv) into DFT data structure. Any previous content of DFT is deleted.

Returns

Returns nonzero in case an error is encountered and sets dfterrmsg.

See also

dftRead

Parameters

filename	Name of Amide TAC file (*.tsv) to be read
dft	Pointer to DFT data where to regional TAC data is read

Definition at line 15 of file tsv.c.

  {
  int ii, si, ri, fi, n, ret;
  char tmp[1024], tmp2[512], *cptr;
  IFT ift;
  float f[13];
  
 
  /* Check the arguments */
  if(filename==NULL || dft==NULL || strlen(filename)<1) {
    strcpy(dfterrmsg, "program error"); return(1);
  }
  
  /* Read the file contents */
  iftInit(&ift); ret=iftRead(&ift, filename, 0, 0);
  if(ret) {strcpy(dfterrmsg, ift.status); iftEmpty(&ift); return(2);}
 
  /* Check that this actually is a Amide TAC file */
  strcpy(tmp, "amide"); ii=iftGet(&ift, tmp, 0);
  if(ii<0) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(3);}
  if(strncasecmp(ift.item[ii].value, "ROI Analysis File - ", 16)!=0) {
    strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(3);}
  sprintf(dft->comments, "# Amide %s\n# original_filename := %s\n",
    ift.item[ii].value, filename);
 
  /* Get the number of ROIs */
  strcpy(tmp, "ROI");
  ri=0; while((ii=iftGetNth(&ift, tmp, ri+1, 0))>=0) ri++;
  //printf("ri=%d\n", ri);
  if(ri<1) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(4);}
  
  /* Get the max frame number */
  for(ii=0, fi=0; ii<ift.keyNr; ii++) {
    if(ift.item[ii].type=='#') continue;
    n=sscanf(ift.item[ii].value, "%f %f %f %f %f %f %f %f %f %f %f %f %f",
      f, f+1, f+2, f+3, f+4, f+5, f+6, f+7, f+8, f+9, f+10, f+11, f+12);
    if(n<13) continue;
    n=temp_roundf(f[0])+1; // Amide frames start from 0
    if(n>fi) fi=n;
  }
  //printf("fi=%d\n", fi);
  if(fi<1) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(5);}
  
  /* Allocate memory for DFT data */
  if(dftSetmem(dft, fi, ri)) {
    strcpy(dfterrmsg, "out of memory"); iftEmpty(&ift); return(7);}
  dft->frameNr=fi; dft->voiNr=ri;
  
  /*
   *  Read one ROI at a time
   */   
  strcpy(tmp, "ROI"); ri=0;
  while((ii=iftGetNth(&ift, tmp, ri+1, 0))>=0) {
    /* Get ROI name */
    strcpy(tmp2, ift.item[ii].value); cptr=strtok(tmp2, " \t\n\r");
    if(cptr!=NULL) {
      strncpy(dft->voi[ri].voiname, cptr, MAX_REGIONSUBNAME_LEN);
      dft->voi[ri].voiname[MAX_REGIONSUBNAME_LEN]='\0';
    } else {
      char buf[128]; snprintf(buf, 128, "%03d", ri+1);
      char *p=buf+strlen(buf)-3;
      snprintf(dft->voi[ri].voiname, MAX_REGIONSUBNAME_LEN, "VOI%s", p);
    }
    /* Get the next data set (output filename will be based on this) */
    for(si=ii+1; si<ift.keyNr; si++) {
      if(ift.item[si].type!='#') continue;
      if(strcasecmp(ift.item[si].key, "Data Set")==0) break;
    }
    if(si<0) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(8);}
    strcpy(tmp2, ift.item[si].value); cptr=strtok(tmp2, " \t\n\r");
    if(cptr!=NULL) {
      strncpy(dft->voi[ri].name, cptr, MAX_REGIONNAME_LEN);
      dft->voi[ri].name[MAX_REGIONNAME_LEN]='\0';
    }
    /* Read the frame data until the next data set */
    for(ii=si+1, fi=0; ii<ift.keyNr; ii++)
      if(ift.item[ii].type!='#') break;
    for(; ii<ift.keyNr; ii++) {
      if(ift.item[ii].type=='#') break;
      n=sscanf(ift.item[ii].value, "%f %f %f %f %f %f %f %f %f %f %f %f %f",
        f, f+1, f+2, f+3, f+4, f+5, f+6, f+7, f+8, f+9, f+10, f+11, f+12);
      if(n<13) continue;
      /* Get mean activity concentration */
      dft->voi[ri].y[fi]=f[5];
      /* Get VOI size */
      if(fi==0)
        dft->voi[ri].size=f[10];
      /* Get frame times, if this is the first ROI */
      if(ri==0) {
        dft->x[fi]=f[2];
        dft->x1[fi]=f[2]-0.5*f[1];
        dft->x2[fi]=f[2]+0.5*f[1];
      }
      fi++;
    } // next frame
    ri++;
  }
  iftEmpty(&ift);
 
  /* Set the study number based on Data Set */
  (void)studynr_from_fname(dft->voi[0].name, dft->studynr);
 
  /* Set the rest of DFT "header" */
  dft->_type=1;
  dft->isweight=0;
  dftTimeunitToDFT(dft, petTunit(TUNIT_SEC)); // time units are in sec
  dftUnitToDFT(dft, CUNIT_UNKNOWN); // conc units are not known
 
  return(0);
}

xelRead()

int xelRead ( char * filename, DFT * dft )

extern

Read Xeleris TAC file into DFT data structure. Any previous content of DFT is deleted.

Returns

Returns nonzero in case an error is encountered and sets dfterrmsg.

Parameters

filename	Name of Xeleris TAC file to be read
dft	Pointer to DFT data where to regional TAC data is read

Definition at line 14 of file xeleris.c.

  {
  int ii, si, ri, fi, n, ret;
  char tmp[1024], tmp2[512], *cptr;
  IFT ift;
  float f[6];
  
 
  /* Check the arguments */
  if(filename==NULL || dft==NULL || strlen(filename)<1) {
    strcpy(dfterrmsg, "program error"); return(1);
  }
  
  /* Read the file contents */
  iftInit(&ift); ret=iftRead(&ift, filename, 0, 0);
  if(ret) {strcpy(dfterrmsg, ift.status); iftEmpty(&ift); return(2);}
  
  /* Check that this actually is a Xeleris TAC file */
  strcpy(tmp, "Image Position"); ii=iftGet(&ift, tmp, 0);
  if(ii<0) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(3);}
  strcpy(tmp, "XAxis"); ii=iftGet(&ift, tmp, 0);
  if(ii<0) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(3);}
  strcpy(tmp, "YAxis"); ii=iftGet(&ift, tmp, 0);
  if(ii<0) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(3);}
  
  /* Find the data title, and assume that lines after that contain the TACs */
  strcpy(tmp, "Curve     X    Dur    Max    Min   Mean StdDev");
  ii=iftFindNthValue(&ift, tmp, 1, 0);
  if(ii<0) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(4);}
  si=ii+1;
  
  /* Determine the number of TACs and time frames */
  ri=fi=0; strcpy(tmp2, ""); n=1;
  for(ii=si; ii<ift.keyNr; ii++) {
    if(sscanf(ift.item[ii].value, "%s", tmp)!=1) {
      strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(5);}
    if(strcmp(tmp, tmp2)==0) {
      n++; if(n>fi) fi=n;
    } else {
      ri++; strcpy(tmp2, tmp); if(n>fi) fi=n; n=1;
    }
    //printf("tmp=%s tmp2=%s n=%d, ri=%d fi=%d\n", tmp, tmp2, n, ri, fi);
  }
  if(ri<1 || fi<1) {strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(6);}
  
  /* Allocate memory for DFT data */
  if(dftSetmem(dft, fi, ri)) {
    strcpy(dfterrmsg, "out of memory"); iftEmpty(&ift); return(7);}
  dft->frameNr=fi; dft->voiNr=ri;
  
  /* Read TAC data and fill DFT */
  ri=fi=0; strcpy(tmp2, ""); n=1;
  for(ii=si; ii<ift.keyNr; ii++) {
    if(sscanf(ift.item[ii].value, "%s %f %f %f %f %f %f", 
       tmp, f, f+1, f+2, f+3, f+4, f+5)!=7) {
      strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(5);}
    if(strcmp(tmp, tmp2)==0) n++;
    else {ri++; strcpy(tmp2, tmp); if(n>fi) fi=n; n=1;}
    //printf("tmp=%s tmp2=%s n=%d, ri=%d fi=%d\n", tmp, tmp2, n, ri, fi);
    /* TAC name */
    strlcpy(dft->voi[ri-1].voiname, tmp, MAX_REGIONSUBNAME_LEN+1);
    //dft->voi[ri-1].voiname[MAX_REGIONSUBNAME_LEN]='\0';
    /* Frame time */
    if(ri==1) {
      dft->x1[n-1]=f[0]; dft->x2[n-1]=f[0]+f[1];
      dft->x[n-1]=0.5*(dft->x1[n-1]+dft->x2[n-1]);
    } else {
      if(fabs(dft->x1[n-1]-f[0])>1.0E-12 || fabs(dft->x2[n-1]-f[0]-f[1])>1.0E-12) {
        strcpy(dfterrmsg, "wrong format"); iftEmpty(&ift); return(8);}
    }
    /* Concentrations */
    dft->voi[ri-1].y[n-1]=f[4];
  }
  
  /* Add image position to the TAC name, if possible */
  strcpy(tmp, "Image Position"); ii=iftGet(&ift, tmp, 0);
  if(ii>=0) {
    f[0]=atof(ift.item[ii].value); sprintf(tmp, "%-6.0f", f[0]); tmp[6]='\0';
    for(ri=0; ri<dft->voiNr; ri++) {
      strcpy(dft->voi[ri].place, tmp);
      sprintf(dft->voi[ri].name, "%s . %s", dft->voi[ri].voiname, dft->voi[ri].place);
    }
  }
 
  /* Determine the concentration (y axis) unit */
  strcpy(tmp, "YAxis"); ii=iftGet(&ift, tmp, 0);
  if(ii>=0 && strncasecmp(ift.item[ii].value, "Uptake (Bqml)", 8)==0) {
    cptr=ift.item[ii].value+8;
    if(     strncasecmp(cptr, "Bqml", 4)==0) strcpy(dft->unit, "Bq/ml");
    else if(strncasecmp(cptr, "kBqml", 5)==0) strcpy(dft->unit, "kBq/ml");
    else if(strncasecmp(cptr, "MBqml", 5)==0) strcpy(dft->unit, "MBq/ml");
    else if(strncasecmp(cptr, "Bqcc", 4)==0) strcpy(dft->unit, "Bq/ml");
    else if(strncasecmp(cptr, "kBqcc", 5)==0) strcpy(dft->unit, "kBq/ml");
    else if(strncasecmp(cptr, "MBqcc", 5)==0) strcpy(dft->unit, "MBq/ml");
  }
 
  /* Determine the time (x axis) unit */
  dft->timeunit=TUNIT_UNKNOWN;
  strcpy(tmp, "XAxis"); ii=iftGet(&ift, tmp, 0);
  if(ii>=0) {
    if(strcasecmp(ift.item[ii].value, "sec")==0) dft->timeunit=TUNIT_SEC;
    else if(strcasecmp(ift.item[ii].value, "min")==0) dft->timeunit=TUNIT_MIN;
  }
  
  iftEmpty(&ift);
 
  /* Set the study number based on filename */
  (void)studynr_from_fname(filename, dft->studynr);
 
  /* Set the rest of DFT "header" */
  dft->_type=1;
  dft->timetype=3;
  dft->isweight=0;
 
  return(0);
}

Variable Documentation

cpterrmsg

char cpterrmsg[128]

extern

Error message from CPT functions.

Definition at line 6 of file cpt.c.

Referenced by cptReadOne(), and cptWrite().

CSV_TEST

int CSV_TEST

extern

Verbose prints from CSV functions.

Definition at line 6 of file csv.c.

Referenced by csv2dft(), csv2dft_a(), csv2dft_b(), csv2dft_linkset(), csv2dft_mat(), csvRead(), dftFormat(), and dftRead().

DFT_NR_OF_DECIMALS

int DFT_NR_OF_DECIMALS

extern

Nr of decimals for concentration values.

Nr of decimals for concentration values

Definition at line 13 of file dftio.c.

Referenced by dftRead(), and dftWrite().

dfterrmsg

char dfterrmsg[64]

extern

Error message from DFT functions.

Definition at line 6 of file dft.c.

Referenced by dftAdd(), dftRead(), dftReadModelingData(), dftWrite(), dftWriteHTML(), idwcRead(), idwcWrite(), ifRead(), ifWrite(), imgReadModelingData(), roikbqRead(), roikbqWrite(), tsvRead(), and xelRead().

fiterrmsg

char fiterrmsg[64]

extern

Error message from FIT functions

Definition at line 6 of file mathfunc.c.

Referenced by fitRead(), and fitWrite().

MATHFUNC_TEST

int MATHFUNC_TEST

extern

Verbose prints from FIT functions

Definition at line 5 of file mathfunc.c.

Referenced by fitEval(), fitPrint(), and fitWrite().

reserrmsg

char reserrmsg[64]

extern

Error message from RES functions

Definition at line 6 of file result.c.

Referenced by resRead(), resWrite(), and resWriteHTML().

RESULT_TEST

int RESULT_TEST

extern

Verbose prints from RES functions

Definition at line 5 of file result.c.

Referenced by resFixParnames(), resMatchParameternames(), resMatchParameters(), resMatchParametersAbs(), resMatchRegions(), and resWriteHTML_table().