#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "curveio.h"
#include "imgio.h"
#include "imgproc.h"
#include "integr.h"
#include "nnls.h"
#include "llsqwt.h"
#include "pearson.h"
#include "median.h"
#include "mtga.h"
#include "libtpcsvg.h"

Include dependency graph for libtpcmodext.h:

This graph shows which files directly or indirectly include this file:

Functions
void	libtpcmodext_print_readme (FILE *fp)
void	libtpcmodext_print_history (FILE *fp)
void	libtpcmodext_print_dreadme (FILE *fp)
void	libtpcmodext_print_dhistory (FILE *fp)
void	libtpcmodext_print_build (FILE *fp)
int	bf_srtm (double t, double cr, int n, int bfNr, double t3min, double t3max, DFT *bf)
int	dftReadinput (DFT input, DFT tissue, char filename, int filetype, double ti1, double ti2, char *status)
int	dftReadReference (DFT tissue, char filename, int filetype, int ref_index, char *status)
int	dftReadModelingData (char tissuefile, char inputfile1, char inputfile2, char inputfile3, double fitdur, int fitframeNr, DFT tis, DFT inp, FILE loginfo, int verbose, char status)
int	dftRobustMinMaxTAC (DFT dft, int tacindex, double minx, double maxx, double miny, double maxy, int mini, int *maxi)
int	extrapolate_monoexp (DFT dft, double fittime, int min_nr, int max_nr, double mintime, double extr_to, DFT ext, FILE loginfo, char status)
int	dftAutointerpolate (DFT dft, DFT dft2, double endtime)
int	dftDoubleFrames (DFT dft, DFT dft2)
int	dftDivideFrames (DFT dft, int voi_index, int add_nr, DFT dft2)
int	dft_end_line (DFT dft, double fittime, int min_nr, int max_nr, double mintime, int check_impr, FIT fit, FILE loginfo, char status)
int	dft_ln (DFT dft1, DFT dft2)
int	fittime_from_dft (DFT dft, double startTime, double endTime, int first, int *last)
int	fittime_from_img (IMG img, double fittime)
int	check_times_dft_vs_img (IMG img, DFT dft)
int	check_times_dft_vs_dft (DFT dft1, DFT dft2)
int	copy_times_from_img_to_dft (IMG img, DFT dft)
int	getActualSamplenr (DFT *dft, int ri)
int	img_patlak (DFT input, IMG dyn_img, int start, int end, linefit_range fit_range, IMG ki_img, IMG ic_img, IMG nr_img, char status)
int	img_k1_using_ki (DFT input, IMG dyn_img, int frame_nr, IMG ki_img, IMG k1_img, IMG k2k3_img, char status)
int	dftInterpolateCheckStart (DFT input, DFT output, char *status)
int	dftInterpolateCheckEnd (DFT input, DFT output, char *status)
int	dftInterpolate (DFT input, DFT tissue, DFT output, char status)
int	dftInterpolateInto (DFT inp, DFT tis, char *status)
int	dftDerivative (DFT dft, DFT deriv, char *status)
int	dftDerivative_old (DFT dft, DFT deriv, char *status)
int	dftInterpolateForIMG (DFT input, IMG img, int frame_nr, DFT output, double ti1, double ti2, int verbose, char status)
int	imgTimeIntegral (IMG img, float t1, float t2, IMG iimg, int calc_mode, char *status)
int	dftTimeIntegral (DFT dft, double t1, double t2, DFT idft, int calc_mode, char *status)
int	mrl_between_tacs (double y1, double y2, int n)
int	plot_svg (DFT dft, RES res, int first, int last, char main_title, char x_title, char y_title, char fname)
int	plotdata (DFT dft, RES res, int first, int last, char mtitle, char xtitle, char ytitle, char fname)
int	plotdata_as_dft (DFT dft, char fname)
int	plot_fit_svg (DFT dft1, DFT dft2, char main_title, char fname)
int	plot_fitrange_svg (DFT dft1, DFT dft2, char main_title, double x1, double x2, double y1, double y2, char fname)
int	cunit_check_dft_vs_img (DFT dft, IMG img, char *errmsg)
int	dftWeightByFreq (DFT *dft)
int	clusterTACs (IMG dimg, IMG cimg, int nr, DFT *tac, int verbose)
Variables
int	MODEXT_TEST

Function Documentation

int bf_srtm	(	double *	t,
		double *	cr,
		int	n,
		int	bfNr,
		double	t3min,
		double	t3max,
		DFT *	bf
	)

Calculates set of basis functions for SRTM

Returns:: Returns 0 if successful, otherwise nonzero.

Parameters:

t	PET frame mid times
cr	Non-decay corrected Cr(t)
n	Nr of PET frames
bfNr	Nr of basis functions to calculate
t3min	theta3 min
t3max	theta3 max
bf	data for basis functions is allocated and filled here

Definition at line 54 of file bf.c.

int check_times_dft_vs_dft	(	DFT *	dft1,
		DFT *	dft2
	)

Check whether sample times are the same (or very close to) in two DFT structs. Data sets are not edited. If DFT structs contain different sample number, then only common nr of samples are compared.

Returns:: Returns 0 in case of no match, 1 if times do match, and <1 in case of an error.

Parameters:

dft1	Pointer to first DFT data; times can be both seconds or minutes, if unit is correctly set.
dft2	Pointer to second DFT data; times can be both seconds or minutes, if unit is correctly set; sample nr may be different than in dft1.

Definition at line 209 of file fittime.c.

References MODEXT_TEST.

Referenced by dftInterpolate(), dftInterpolateForIMG(), and dftInterpolateInto().

int check_times_dft_vs_img	(	IMG *	img,
		DFT *	dft
	)

Check whether DFT sample times are the same (or very close to) as the frame times in IMG. This would suggest that DFT data originates from the same or similar PET scan. Specified data sets are not edited. If frame nr is different, then only the commong frames are compared.

Returns:: Returns 0 in case of no match, 1 if times do match, and <1 in case of an error.

Parameters:

img	Pointer to IMG data; times must be in sec as usual
dft	Pointer to DFT data; times can be both seconds or minutes, if unit is correctly set; sample nr may be different than in IMG.

Definition at line 150 of file fittime.c.

References MODEXT_TEST.

Referenced by img_patlak().

int clusterTACs	(	IMG *	dimg,
		IMG *	cimg,
		int	nr,
		DFT *	tac,
		int	verbose
	)

Allocates memory and calculates the values for average TACs for clusters.

Returns:: Returns 0 if ok, and >0 in case of an error.

Parameters:

dimg	Dynamic image
cimg	Cluster image
nr	Highest cluster ID
tac	Pointer to initiated but empty DFT data
verbose	Verbose level; if zero, then only warnings are printed into stderr

Definition at line 44 of file cluster.c.

int copy_times_from_img_to_dft	(	IMG *	img,
		DFT *	dft
	)

Copies frame times (especially start and end times, but also mid times) from an IMG data into DFT data, and sets DFT 'header' to indicate that frame start and end times are present.

Returns:: Returns 0 if successful and <>0 in case of an error.

Parameters:

img	Pointer to IMG data; times must be in sec as usual
dft	Pointer to DFT data; times can be both seconds or minutes, if unit is correctly set; sample nr may be smaller than in IMG.

Definition at line 268 of file fittime.c.

References MODEXT_TEST.

Referenced by dftInterpolateForIMG(), and img_patlak().

int cunit_check_dft_vs_img	(	DFT *	dft,
		IMG *	img,
		char *	errmsg
	)

Check that calibration units in IMG (PET image) and DFT (input TAC) are the same, and if not, then try to convert DFT calibration unit to IMG unit. If input unit is unknown, then assume it is the same as the PET unit.

Returns:: Returns 0 if successful, >0 in case of error, and <0 in case of a warning or error message to user is suggested.

Parameters:

dft	Pointer to DFT
img	Pointer to IMG
errmsg	Char pointer to string (at least of length 128) where possible error description or warning is copied; set to NULL if not necessary

Definition at line 53 of file units.c.

References MODEXT_TEST.

int dft_end_line	(	DFT *	dft,
		double *	fittime,
		int *	min_nr,
		int	max_nr,
		double	mintime,
		int	check_impr,
		FIT *	fit,
		FILE *	loginfo,
		char *	status
	)

Fits line to the end-part of TACs. By default, the included data points are determined based on maximum adjusted R^2 from at least three points; regression to the larger number of points is used in case difference in adjusted R^2 values is not larger than 0.0001.

Returns:: Returns 0 when successful, otherwise <>0.

Parameters:

dft	Pointer to original TAC data
fittime	By default, the search for the best line fit is started from the last sample towards the first sample; set fit time to -1 to use this default. However, if the end phase is unreliable or very noisy, you may want to set fittime to include only certain time range from the beginning. Function will write here the fittime that was actually used.
min_nr	The minimum number of samples used in searching the best fit; at least 2, but 3 is recommended. If data is very noisy, then this number may need to be increased. Function will write here the nr of samples that was actually used. This can be used as an alternative to mintime or in addition to it.
max_nr	The maximum number of samples used in searching the best fit; must be higher than min_nr, or set to -1 to not to limit the number.
mintime	Minimum time range used in searching the best fit. If data is very noisy, then this may need to be set, otherwise setting mintime to -1 will use the default. This can be used as an alternative to min_nr or in addition to it.
check_impr	Linear fitting can be applied to all data subsets in the fit time range (check_impr=0), or fitting is stopped when increasing n does not improve the adjusted R^2 (check_impr=1); the latter mode is for compatibility with WinNonlin.
fit	Pointer to data for fitted parameters. Struct must be initiated. Any existing data is deleted. Additionally, adjusted R^2 is written as 3rd (non-documented) parameter.
loginfo	Give file pointer (for example stdout) where log information is printed; NULL if not needed
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 540 of file extrapolate.c.

int dft_ln	(	DFT *	dft1,
		DFT *	dft2
	)

Natural logarithm (ln) transformation for TAC concentrations.

Returns:: Returns 0 when successful, otherwise <>0.

Parameters:

dft1	Pointer to original TAC data
dft2	Pointer to allocated memory for ln transformed TAC data; enter NULL, if original data is to be overwritten by ln transformed values.

Definition at line 703 of file extrapolate.c.

int dftAutointerpolate	(	DFT *	dft,
		DFT *	dft2,
		double	endtime
	)

Interpolates TACs to automatically determined sample times with smaller intervals in the beginning. Only data in y arrays are interpolated; data in y2 and y3 are not used.

Returns:: Function returns 0 when succesful, else a value >= 1.

Parameters:

dft	Data to be interpolated is read from this struct
dft2	Interpolated data is written in this struct; must be initiated; any previous content is deleted
endtime	The length of interpolated/extrapolated data

Definition at line 306 of file extrapolate.c.

References MODEXT_TEST.

int dftDerivative	(	DFT *	dft,
		DFT *	deriv,
		char *	status
	)

Calculate simple derivatives from regional PET TACs. This must not be used for any quantitative purpose.

Returns:: Returns 0 if successul.

Parameters:

dft	DFT struct containing the regional tissue TACs
deriv	Allocated DFT struct for derivatives
status	Pointer to allocated string where the status or error message is written; set to NULL if not needed

Definition at line 617 of file dftint.c.

int dftDerivative_old	(	DFT *	dft,
		DFT *	deriv,
		char *	status
	)

Calculate simple derivatives from regional PET TACs. Old version. Requires that frame start and end times are known.

Returns:: Returns 0 if successul.

Parameters:

dft	DFT struct containing the regional tissue TACs
deriv	Allocated DFT struct for derivatives
status	Pointer to allocated string where the status or error message is written; set to NULL if not needed

Definition at line 573 of file dftint.c.

int dftDivideFrames	(	DFT *	dft,
		int	voi_index,
		int	add_nr,
		DFT *	dft2
	)

Interpolates TACs to automatically determined sample times with smaller intervals in the beginning. Only data in y arrays are interpolated; data in y2 and y3 are not used.

Returns:: Function returns 0 when succesful, else a value >= 1.

Parameters:

dft	Data to be interpolated into more time frames is read from this struct
voi_index	Region index [0..voiNr-1] that is interpolated; <0 means all VOIs
add_nr	Nr of extra time frames that are created from each original frame; valid numers are 1-100; 1 doubles the frame number
dft2	Interpolated data is written in this struct; must be initiated, may be allocated but do not need to be; any previous content is deleted

Definition at line 434 of file extrapolate.c.

References MODEXT_TEST.

int dftDoubleFrames	(	DFT *	dft,
		DFT *	dft2
	)

Doubles the TAC sample number by making each sample/frame into two by linear interpolation. Only data in y arrays are interpolated; data in y2 and y3 are not used.

Returns:: Function returns 0 when succesful, else a value >= 1.

Parameters:

dft	Data to be interpolated is read from this struct
dft2	Interpolated data is written in this struct; must be initiated; any previous content is deleted

Definition at line 371 of file extrapolate.c.

int dftInterpolate	(	DFT *	input,
		DFT *	tissue,
		DFT *	output,
		char *	status
	)

Interpolate (and integrate) TAC data to sample times that are given with another TAC data. PET frame lengths are taken into account if available in tissue DFT struct. Input frame lengths are taken into account if the framing is same as with tissue data.

Returns:: Returns 0 if successful, and <>0 in case of an error.

Parameters:

input	Data which is interpolated; make sure that time unit is the same as in tissue data; time range is checked to cover the tissue data
tissue	Data to which (sample times) the interpolation is done
output	Pointer to initiated DFT into which interpolated values and integrals will be written
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 173 of file dftint.c.

References check_times_dft_vs_dft(), dftInterpolateCheckEnd(), and dftInterpolateCheckStart().

Referenced by dftReadinput().

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int dftInterpolateCheckEnd	(	DFT *	input,
		DFT *	output,
		char *	status
	)

Verify that data to-be-interpolated does not need too much extrapolation in the end, and that samples are not too sparse.

Returns:: Returns 0 if data is fine, 1 if extrapolation can be done, but there may be too few samples, and -1 if extrapolation in the end is impossible.

Parameters:

input	Data that will be verified for reliable interpolation
output	Data containing sample times for interpolated data
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 104 of file dftint.c.

References MODEXT_TEST.

Referenced by dftInterpolate(), and dftInterpolateInto().

int dftInterpolateCheckStart	(	DFT *	input,
		DFT *	output,
		char *	status
	)

Verify that data to-be-interpolated does not need too much extrapolation in the beginning.

Returns:: Returns 0 if data is fine, 1 if it starts late but extrapolation can be done reliably, and -1 if extrapolation in the beginning would be too risky.

Parameters:

input	Data that will be verified for reliable interpolation
output	Data containing sample times for interpolated data
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 52 of file dftint.c.

References MODEXT_TEST.

Referenced by dftInterpolate(), dftInterpolateForIMG(), and dftInterpolateInto().

int dftInterpolateForIMG	(	DFT *	input,
		IMG *	img,
		int	frame_nr,
		DFT *	output,
		double *	ti1,
		double *	ti2,
		int	verbose,
		char *	status
	)

Interpolate (and integrate) TAC data to sample times that are given with IMG data. Input frame lengths are taken into account if they are available in DFT or if the framing is the same as in IMG data.

Returns:: Returns 0 if successful, and <>0 in case of an error.

Parameters:

input	Data which is interpolated
img	Data to which (sample times) the interpolation is done
frame_nr	Number of IMG frames that are needed; can be set to 0 if all frames can be included
output	Pointer to initiated DFT into which interpolated values and integrals will be written at input sample times and units
ti1	First time of input data before interpolation (in input time units); use this to check that required time range was measured; NULL if not needed
ti2	Last time of input data before interpolation (in input time units); use this to check that required time range was measured; NULL if not needed
verbose	Verbose level; set to zero to not to print any comments
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 110 of file misc.c.

References check_times_dft_vs_dft(), copy_times_from_img_to_dft(), and dftInterpolateCheckStart().

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int dftInterpolateInto	(	DFT *	inp,
		DFT *	tis,
		char *	status
	)

Interpolate (and integrate) TAC data to sample times that are given with another TAC data. New TAC is written into existing TAC data. PET frame lengths are taken into account if available in tissue DFT struct. Input frame lengths are taken into account if the framing is same as with tissue data.

Returns:: Returns 0 if successful, and <>0 in case of an error.

Parameters:

inp	Data which is interpolated; make sure that time unit is the same as in tissue data; time range is checked to cover the tissue data
tis	Data into which the interpolation is done
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 286 of file dftint.c.

References check_times_dft_vs_dft(), dftInterpolateCheckEnd(), and dftInterpolateCheckStart().

Referenced by dftReadModelingData(), and dftReadReference().

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int dftReadinput	(	DFT *	input,
		DFT *	tissue,
		char *	filename,
		int *	filetype,
		double *	ti1,
		double *	ti2,
		char *	status
	)

Read DFT format input TAC data to match the time frames in the specified tissue DFT file. Instead of input filename, a reference region name can be given: then all the matching tacs (based on roi names) are moved from the roi data to the input data, with the best match as first tac. Input data is interpolated (if necessary) and also integrated to y2[]. Input time and concentration units are tried to be converted to be the same as in tissue data.

Returns:: Returns 0 if succesful, and >0 in case of an error.

Parameters:

input	Input data, previous contents are cleared
tissue	PET data containing frames and possible input regions
filename	Input data filename, or region name in PET data
filetype	Type of input, as found out here; 1 and 2 =tac, 3=fit, 5=region name; enter NULL, if not needed
ti1	First time of input data before interpolation (in tissue time units); use this to check that required time range was measured; NULL if not needed
ti2	Last time of input data before interpolation (in tissue time units); use this to check that required time range was measured; NULL if not needed
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 70 of file dftinput.c.

References dftInterpolate(), and MODEXT_TEST.

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int dftReadModelingData	(	char *	tissuefile,
		char *	inputfile1,
		char *	inputfile2,
		char *	inputfile3,
		double *	fitdur,
		int *	fitframeNr,
		DFT *	tis,
		DFT *	inp,
		FILE *	loginfo,
		int	verbose,
		char *	status
	)

Read tissue and input data for modeling. Time units are converted to min and input calibration units to units of tissue data. Input data is NOT interpolated to tissue times. If input data extends much further than fit duration, the last part is removed to save computation time in simulations. Input data is verified not to end too early, and not to start too late.

Returns:: Returns 0 when successful, otherwise a non-zero value.

Parameters:

tissuefile	Tissue data filename; one time sample is sufficient here
inputfile1	1st input data filename
inputfile2	2nd input data filename (or NULL if only not needed)
inputfile3	3rd input data filename (or NULL if only not needed)
fitdur	Fit duration (in minutes); shortened if longer than tissue data
fitframeNr	Nr of time frames (samples) in tissue data that are inside fitdur will be written here
tis	Pointer to initiated DFT into which tissue data will be written
inp	Pointer to initiated DFT into which input data (plasma and/or blood) will be written
loginfo	Give file pointer (for example stdout) where log information is printed; NULL if not needed; warnings will be printed in stderr anyway.
verbose	Verbose level; if zero, then only warnings are printed into stderr
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 365 of file dftinput.c.

References dftInterpolateInto(), and fittime_from_dft().

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int dftReadReference	(	DFT *	tissue,
		char *	filename,
		int *	filetype,
		int *	ref_index,
		char *	status
	)

Read DFT format reference region TAC data and add it into DFT already containing other tissue TACs, if reference region TAC(s) are be given in a separate file. Alternative the reference region name can be given, which will then be selected from existing tissue TACs. Reference TACs are marked in DFT with sw=2 (best name match) or sw=1; if reference region file contains several TACs then the one which contains name 'mean' or 'avg' or has shortest total name length is given value sw=2. When necessary, reference data is interpolated and units converted to match the existing tissue DFT. Reference TAC is also integrated into y2[].

Returns:: Returns the number of reference TACs, and <=0 in case of an error.

Parameters:

tissue	PET data containing existing tissue TACs, possibly also reference regions
filename	Reference TAC filename, or region name in previous data
filetype	Type of input, as found out here; 1 and 2 =tac, 3=fit, 5=region name; enter NULL, if not needed
ref_index	Index of the best reference region; enter NULL if not needed
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 228 of file dftinput.c.

References dftInterpolateInto(), and MODEXT_TEST.

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int dftRobustMinMaxTAC	(	DFT *	dft,
		int	tacindex,
		double *	minx,
		double *	maxx,
		double *	miny,
		double *	maxy,
		int *	mini,
		int *	maxi
	)

Robust search of the min and max values of DFT TAC data. Data may contain NaN's, and indivial outliers are not taken as min or max.

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

Definition at line 631 of file dftinput.c.

int dftTimeIntegral	(	DFT *	dft,
		double	t1,
		double	t2,
		DFT *	idft,
		int	calc_mode,
		char *	status
	)

Integration of regional TAC data from time1 to time2, i.e. AUC(t1,t2). You may want to test the time range before applyin this routine, because this function accepts relatively large extrapolation large.

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

Parameters:

dft	Regional TAC data in DFT struct. Number of samples must be at least one. If only one sample, then the integration time range must match with the possible frame start and times. Frames do not have to be continuous in time.
t1	Time where to start integration (same unit as in TACs)
t2	Time to stop integration (same unit as in TACs); must be higher than t1, except that t1=t2 is acceptable when calc_mode=average
idft	Pointer to initiated but empty AUC DFT data (output)
calc_mode	Calculate integral or average: 0=integral, 1=average
status	Pointer to a string (allocated for at least 128 chars) where error message or other execution status will be written; enter NULL, if not needed

Definition at line 379 of file dftint.c.

References MODEXT_TEST.

int dftWeightByFreq ( DFT * dft )

Add weights based on sample frequency or frame length. Existing weights are overwritten.

Returns:: Returns 0 when successful, otherwise <>0.

Parameters:

dft	Samples/frames must be sorted by sample time, but duplicate samples are allowed

Definition at line 48 of file weight.c.

int extrapolate_monoexp	(	DFT *	dft,
		double *	fittime,
		int *	min_nr,
		int	max_nr,
		double	mintime,
		double	extr_to,
		DFT *	ext,
		FILE *	loginfo,
		char *	status
	)

Extrapolation of exponentially decreasing tail of PET radiotracer plasma curves. This is accomplished by fitting line to the end-part of the plot of the natural logarithm of tracer concentration against time. By default, the included data points are determined based on maximum adjusted R^2 from at least three points; fit to the larger number of points is used in case difference in adjusted R^2 values is not larger than 0.0001. This function is used and tested with program extrapol.

Returns:: Returns 0 when successful, otherwise <>0.

Parameters:

dft	Pointer to original TAC data
fittime	By default, the search for the best line fit is started from the last sample towards the first sample; set fit time to -1 to use this default. However, if the end phase is unreliable or very noisy, you may want to set fittime to include only certain time range from the beginning. Function will write here the fittime that was actually used.
min_nr	The minimum number of samples used in searching the best fit; at least 2, but 3 is recommended. If data is very noisy, then this number may need to be increased. Function will write here the nr of samples that was actually used. This can be used as an alternative to mintime or in addition to it.
max_nr	The maximum number of samples used in searching the best fit; must be higher than min_nr, or set to -1 to not to limit the number.
mintime	Minimum time range used in searching the best fit. If data is very noisy, then this may need to be set, otherwise setting mintime to -1 will use the default. This can be used as an alternative to min_nr or in addition to it.
extr_to	Last extrapolated sample time in same time units than in the data
ext	Pointer to data for extrapolated TACs. Struct must be initiated. Any existing data is deleted.
loginfo	Give file pointer (for example stdout) where log information is printed; NULL if not needed
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 87 of file extrapolate.c.

int fittime_from_dft	(	DFT *	dft,
		double *	startTime,
		double *	endTime,
		int *	first,
		int *	last
	)

Reset user-defined fit time range to comply with DFT data.

Returns:: Returns the number of samples included in the fit range, or <0 in case of an error.

Parameters:

dft	Pointer to DFT containing (regional tissue) data; times can be in minutes or seconds, as long as units are defined.
startTime	Pointer containing originally the requested fit start time (min). This is changed to contain the time of the first included frame. Unit must be minutes. Initially, set to <0 to start from the beginning of the data.
endTime	Pointer containing originally the requested fit end time (min). This is changed to contain the time of the last included frame. Unit must be minutes. Initially, set to <0 or to a very large value to reach to the end of data.
first	Function writes the index of the first included sample (frame) here
last	Function writes the index of the last included sample (frame) here

Definition at line 65 of file fittime.c.

References MODEXT_TEST.

Referenced by dftReadModelingData().

int fittime_from_img	(	IMG *	img,
		double *	fittime
	)

Get the IMG frame end time of the last frame that is inside (mid time before) the specified maximum fittime.

Returns:: Returns the number of IMG frames included in the fittime, or <0 in case of an error.

Parameters:

img	Pointer to IMG
fittime	Pointer containing originally the fit time maximum, after this the last included IMG frame end time. Unit must be seconds. Initially, set to <0 or to a very large value to include all frames.

Definition at line 120 of file fittime.c.

References MODEXT_TEST.

int getActualSamplenr	(	DFT *	dft,
		int	ri
	)

Returns the actual TAC sample number, not including NaNs, samples with negative x, duplicate samples, or samples with zero weights (if data is weighted).

Parameters:

dft	Pointer to TAC data in DFT struct; must be sorted by increasing x
ri	Region index [0..voiNr-1]

Definition at line 307 of file fittime.c.

int img_k1_using_ki	(	DFT *	input,
		IMG *	dyn_img,
		int	frame_nr,
		IMG *	ki_img,
		IMG *	k1_img,
		IMG *	k2k3_img,
		char *	status
	)

Computing pixel-by-pixel the K1 for irreversible PET tracers using previously determined Ki (K1*k3/(k2+k3) and bilinear regression.

Returns:: Returns 0 if succesful, and >1 in case of an error.

Parameters:

input	Pointer to the TAC data to be used as model input. Sample times in minutes. Curve is interpolated to PET frame times, if necessary
dyn_img	Pointer to dynamic PET image data. Image and input data must be in the same calibration units
frame_nr	Nr of frames that will be included in the fit [3-frame_nr]
ki_img	Pointer to previously calculated Ki image
k1_img	Pointer to initiated IMG structure where K1 values will be placed
k2k3_img	Pointer to initiated IMG structure where (k2+k3) values will be placed; enter NULL, if not needed
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 52 of file img_k1.c.

References MODEXT_TEST.

int img_patlak	(	DFT *	input,
		IMG *	dyn_img,
		int	start,
		int	end,
		linefit_range	fit_range,
		IMG *	ki_img,
		IMG *	ic_img,
		IMG *	nr_img,
		char *	status
	)

Computing pixel-by-pixel the graphical analysis for irreversible PET tracers (Gjedde-Patlak plot).

Returns:: Returns 0 if succesful, and >0 in case of an error.

Parameters:

input	Pointer to the TAC data to be used as model input. Sample times in minutes. Curve is interpolated to PET frame times, if necessary
dyn_img	Pointer to dynamic PET image data. Image and input data must be in the same calibration units
start	The range of frames where line is fitted, given as the frame start here and next the end index, i.e. [0..frame_nr-1]
end	The range of frames where line is fitted, given as the frame start above and here the end index, i.e. [0..frame_nr-1]
fit_range	Use the whole range or based on data leave out points from the beginning; PRESET or EXCLUDE_BEGIN
ki_img	Pointer to initiated IMG structure where Ki values will be placed
ic_img	Pointer to initiated IMG structure where plot y axis intercept values will be placed; enter NULL, if not needed
nr_img	Pointer to initiated IMG structure where the number of plot data points actually used in the fit is written; enter NULL, when not needed
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 61 of file img_patlak.c.

References check_times_dft_vs_img(), copy_times_from_img_to_dft(), and MODEXT_TEST.

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int imgTimeIntegral	(	IMG *	img,
		float	t1,
		float	t2,
		IMG *	iimg,
		int	calc_mode,
		char *	status
	)

Integration of dynamic image from time1 to time2, storing integrals in iimg, which is allocated here. Frames do not have to be continuous in time. Time unit in integral is sec. Raw data (sinogram) must be divided by frame durations before calling this. You may want to test the time range before applyin this routine, because this function accepts relatively large extrapolation large.

Returns:: Returns errstatus, which is STATUS_OK (0) when call was successful, and >0 in case of an error.

Parameters:

img	IMG data; preferrably dynamic, if static, then the specified time range must match with the frame time
t1	Time where to start integration (sec)
t2	Time to stop integration (sec); must be higher than t1
iimg	Pointer to initiated but empty AUC IMG data
calc_mode	Calculate integral or average: 0=integral, 1=average
status	Pointer to a string (allocated for at least 128 chars) where error message or other execution status will be written; enter NULL, if not needed

Definition at line 236 of file misc.c.

void libtpcmodext_print_build ( FILE * fp )

Print the build info to specified FILE pointer, use stdout for screen.

Definition at line 340 of file libtpcmodextv.c.

References COPYRIGHT, LIB_NAME, and LIB_VERSION.

Referenced by main(), and print_usage().

void libtpcmodext_print_dhistory ( FILE * fp )

Print the library History to specified FILE pointer with Doxygen tags, use stdout for screen.

Definition at line 330 of file libtpcmodextv.c.

References libtpcmodext_print_history().

Referenced by main().

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void libtpcmodext_print_dreadme ( FILE * fp )

Print the library Readme to specified FILE pointer with Doxygen tags, use stdout for screen.

Definition at line 319 of file libtpcmodextv.c.

References COPYRIGHT, LIB_NAME, LIB_VERSION, and libtpcmodext_print_readme().

Referenced by main().

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void libtpcmodext_print_history ( FILE * fp )

Print the library History to specified FILE pointer, use stdout for screen.

Definition at line 142 of file libtpcmodextv.c.

Referenced by libtpcmodext_print_dhistory(), and main().

void libtpcmodext_print_readme ( FILE * fp )

Print the library readme to specified FILE pointer, use stdout for screen.

Definition at line 54 of file libtpcmodextv.c.

References COPYRIGHT, LIB_NAME, and LIB_VERSION.

Referenced by libtpcmodext_print_dreadme(), and main().

int mrl_between_tacs	(	double *	y1,
		double *	y2,
		int	n
	)

Return the maximum run length between given n length arrays of data

Parameters:

y1	Array of data1; may contain NaNs
y2	Array of data2; may contain NaNs
n	Nr of samples in array 1 and 2

Definition at line 45 of file mrl.c.

int plot_fit_svg	(	DFT *	dft1,
		DFT *	dft2,
		char *	main_title,
		char *	fname
	)

Writes plots of original and fitted TACs in SVG 1.1 format. Data must not contain NaNs.

Returns:: Returns 0 if successful, otherwise nonzero.

Parameters:

dft1	Measured data points
dft2	Fitted data points. Times can be different but unit must be the same.
main_title	String for plot main title, or NULL
fname	SVG filename; existing file is backed up

Definition at line 214 of file plotfit.c.

References MODEXT_TEST.

int plot_fitrange_svg	(	DFT *	dft1,
		DFT *	dft2,
		char *	main_title,
		double	x1,
		double	x2,
		double	y1,
		double	y2,
		char *	fname
	)

Writes specified range of plots of original and fitted TACs in SVG 1.1 format.

Returns:: Returns 0 if successful, otherwise nonzero.

Parameters:

dft1	Measured data points
dft2	Fitted data points. Times can be different but unit must be the same.
main_title	String for plot main title, or NULL
x1	Start time; NaN if determined from data
x2	End time; NaN if determined from data
y1	Minimum y value; NaN if determined from data
y2	Maximum y value; NaN if determined from data
fname	SVG filename; existing file is backed up

Definition at line 57 of file plotfit.c.

References MODEXT_TEST.

int plot_svg	(	DFT *	dft,
		RES *	res,
		int	first,
		int	last,
		char *	main_title,
		char *	x_title,
		char *	y_title,
		char *	fname
	)

Writes graphical analysis plots in SVG 1.1 format. Assumes that line slope and ic are in res->parameter[0] and [1].

Returns:: Returns 0 if successful, otherwise nonzero.

Parameters:

dft	Plot points: X in y2, Y in y3
res	Results containing parameters of line
first	First sample (starting from 0) used in linear fit
last	last sample (starting from 0) used in linear fit
main_title	String for plot main title, or NULL
x_title	String for X axis title, or NULL
y_title	String for Y axis title, or NULL
fname	SVG filename; existing file is renamed as *.bak

Definition at line 70 of file plotdata.c.

int plotdata	(	DFT *	dft,
		RES *	res,
		int	first,
		int	last,
		char *	mtitle,
		char *	xtitle,
		char *	ytitle,
		char *	fname
	)

Write plot and line fit data in XHTML 1.1. Strict table format. Assumes that line slope and ic are in res->parameter[0] and [1].

Returns:: Returns 0 if successful, otherwise nonzero.

Parameters:

dft	Plot points: X in y2, Y in y3
res	Results containing parameters of line
first	First sample (starting from 0) used in linear fit
last	last sample (starting from 0) used in linear fit
mtitle	String for plot main title, or NULL
xtitle	String for X axis title, or NULL
ytitle	String for Y axis title, or NULL
fname	Filename for plot data; existing file is renamed as *%. If extension is .dft, plot data (excluding lines) is written in DFT format with x values as separate columns before corresponding y values.

Definition at line 207 of file plotdata.c.

References plotdata_as_dft().

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int plotdata_as_dft	(	DFT *	dft,
		char *	fname
	)

Write plot data in DFT format with x values as separate columns before corresponding y values.

Returns:: Returns 0 if successful, otherwise nonzero.

Parameters:

dft	Plot points: X in y2, Y in y3
fname	Filename for plot data

Definition at line 379 of file plotdata.c.

Referenced by plotdata().

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