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; NAME:
; MPFITPEAK
;
; AUTHOR:
; Craig B. Markwardt, NASA/GSFC Code 662, Greenbelt, MD 20770
; craigm@lheamail.gsfc.nasa.gov
; UPDATED VERSIONs can be found on my WEB PAGE:
; http://cow.physics.wisc.edu/~craigm/idl/idl.html
;
; PURPOSE:
; Fit a gaussian, lorentzian or Moffat model to data
;
; MAJOR TOPICS:
; Curve and Surface Fitting
;
; CALLING SEQUENCE:
; yfit = MPFITPEAK(X, Y, A, NTERMS=nterms, ...)
;
; DESCRIPTION:
;
; MPFITPEAK fits a gaussian, lorentzian or Moffat model using the
; non-linear least squares fitter MPFIT. MPFITPEAK is meant to be a
; drop-in replacement for IDL's GAUSSFIT function (and requires
; MPFIT and MPFITFUN).
;
; The choice of the fitting function is determined by the keywords
; GAUSSIAN, LORENTZIAN and MOFFAT. By default the gaussian model
; function is used. [ The Moffat function is a modified Lorentzian
; with variable power law index. (Moffat, A. F. J. 1969, Astronomy &
; Astrophysics, v. 3, p. 455-461) ]
;
; The functional form of the baseline is determined by NTERMS and
; the function to be fitted. NTERMS represents the total number of
; parameters, A, to be fitted. The functional forms and the
; meanings of the parameters are described in this table:
;
; GAUSSIAN# Lorentzian# Moffat#
;
; Model A[0]*exp(-0.5*u^2) A[0]/(u^2 + 1) A[0]/(u^2 + 1)^A[3]
;
; A[0] Peak Value Peak Value Peak Value
; A[1] Peak Centroid Peak Centroid Peak Centroid
; A[2] Gaussian Sigma HWHM% HWHM%
; A[3] + A[3] * + A[3] * Moffat Index
; A[4] + A[4]*x * + A[4]*x * + A[4] *
; A[5] + A[5]*x *
;
; Notes: # u = (x - A[1])/A[2]
; % Half-width at half maximum
; * Optional depending on NTERMS
;
; By default the initial starting values for the parameters A are
; estimated from the data. However, explicit starting values can be
; supplied using the ESTIMATES keyword. Also, error or weighting
; values can optionally be provided; otherwise the fit is
; unweighted.
;
; MPFITPEAK fits the peak value of the curve. The area under a
; gaussian peak is A[0]*A[2]*SQRT(2*!DPI); the area under a
; lorentzian peak is A[0]*A[2]*!DPI.
;
; Data values of NaN or Infinity for "Y", "ERROR" or "WEIGHTS" will
; be ignored as missing data if the NAN keyword is set. Otherwise,
; they may cause the fitting loop to halt with an error message.
; Note that the fit will still halt if the model function, or its
; derivatives, produces infinite or NaN values, or if an "X" value is
; missing.
;
; RESTRICTIONS:
;
; If no starting parameter ESTIMATES are provided, then MPFITPEAK
; attempts to estimate them from the data. This is not a perfect
; science; however, the author believes that the technique
; implemented here is more robust than the one used in IDL's
; GAUSSFIT. The author has tested cases of strong peaks, noisy
; peaks and broad peaks, all with success.
;
; Users should be aware that if the baseline term contains a strong
; linear component then the automatic estimation may fail. For
; automatic estimation to work the peak amplitude should dominate
; over the the maximum baseline.
;
; COMPATIBILITY
;
; This function is designed to work with IDL 5.0 or greater.
;
; Because TIED parameters rely on the EXECUTE() function, they cannot
; be used with the free version of the IDL Virtual Machine.
;
;
; INPUTS:
; X - Array of independent variable values, whose values should
; monotonically increase.
;
; Y - Array of "measured" dependent variable values. Y should have
; the same data type and dimension as X.
; NOTE: the following special cases apply:
; * if Y is NaN or Infinite, and the NAN keyword is
; set, then the corresponding data point is ignored
;
; OUTPUTS:
; A - Upon return, an array of NTERMS best fit parameter values.
; See the table above for the meanings of each parameter
; element.
;
;
; RETURNS:
;
; Returns the best fitting model function.
;
; KEYWORDS:
;
; ** NOTE ** Additional keywords such as PARINFO, BESTNORM, and
; STATUS are accepted by MPFITPEAK but not documented
; here. Please see the documentation for MPFIT for the
; description of these advanced options.
;
; AUTODERIV - Set to 1 to have MPFIT compute the derivatives numerically.
; Default is 0 - derivatives are computed analytically, which is
; generally faster. (Prior to Jan 2011, the default was 1)
;
; CHISQ - the value of the summed squared residuals for the
; returned parameter values.
;
; DOF - number of degrees of freedom, computed as
; DOF = N_ELEMENTS(DEVIATES) - NFREE
; Note that this doesn't account for pegged parameters (see
; NPEGGED).
;
; ERROR - upon input, the measured 1-sigma uncertainties in the "Y"
; values. If no ERROR or WEIGHTS are given, then the fit is
; unweighted.
; NOTE: the following special cases apply:
; * if ERROR is zero, then the corresponding data point
; is ignored
; * if ERROR is NaN or Infinite, and the NAN keyword is
; set, then the corresponding data point is ignored
; * if ERROR is negative, then the absolute value of
; ERROR is used.
;
; ESTIMATES - Array of starting values for each parameter of the
; model. The number of parameters should at least be
; three (four for Moffat), and if less than NTERMS, will
; be extended with zeroes. If ESTIMATES is not set,
; then the starting values are estimated from the data
; directly, before fitting. (This also means that
; PARINFO.VALUES is ignored.)
; Default: not set - parameter values are estimated from data.
;
; GAUSSIAN - if set, fit a gaussian model function. The Default.
; LORENTZIAN - if set, fit a lorentzian model function.
; MOFFAT - if set, fit a Moffat model function.
;
; MEASURE_ERRORS - synonym for ERRORS, for consistency with built-in
; IDL fitting routines.
;
; NAN - ignore infinite or NaN values in the Y, ERR or WEIGHTS
; parameters. These values will be treated as missing data.
; However, the fit will still halt with an error condition if
; the model function becomes infinite, or if X has missing
; values.
;
; NEGATIVE / POSITIVE - if set, and ESTIMATES is not provided, then
; MPFITPEAK will assume that a
; negative/positive peak is present.
; Default: determined automatically
;
; NFREE - the number of free parameters in the fit. This includes
; parameters which are not FIXED and not TIED, but it does
; include parameters which are pegged at LIMITS.
;
; NO_FIT - if set, then return only the initial estimates without
; fitting. Useful to find out what the estimates the
; automatic guessing algorithm produced. If NO_FIT is set,
; then SIGMA and CHISQ values are not produced. The
; routine returns, NAN, and STATUS=5.
;
; NTERMS - An integer describing the number of fitting terms.
; NTERMS must have a minimum value, but can optionally be
; larger depending on the desired baseline.
;
; For gaussian and lorentzian models, NTERMS must be three
; (zero baseline), four (constant baseline) or five (linear
; baseline). Default: 4
;
; For the Moffat model, NTERMS must be four (zero
; baseline), five (constant baseline), or six (linear
; baseline). Default: 5
;
; PERROR - upon return, the 1-sigma uncertainties of the parameter
; values A. These values are only meaningful if the ERRORS
; or WEIGHTS keywords are specified properly.
;
; If the fit is unweighted (i.e. no errors were given, or
; the weights were uniformly set to unity), then PERROR
; will probably not represent the true parameter
; uncertainties.
;
; *If* you can assume that the true reduced chi-squared
; value is unity -- meaning that the fit is implicitly
; assumed to be of good quality -- then the estimated
; parameter uncertainties can be computed by scaling PERROR
; by the measured chi-squared value.
;
; DOF = N_ELEMENTS(X) - N_ELEMENTS(PARMS) ; deg of freedom
; PCERROR = PERROR * SQRT(BESTNORM / DOF) ; scaled uncertainties
;
; QUIET - if set then diagnostic fitting messages are suppressed.
; Default: QUIET=1 (i.e., no diagnostics)
;
; SIGMA - synonym for PERROR (1-sigma parameter uncertainties), for
; compatibility with GAUSSFIT. Do not confuse this with the
; Gaussian "sigma" width parameter.
;
; WEIGHTS - Array of weights to be used in calculating the
; chi-squared value. If WEIGHTS is specified then the ERROR
; keyword is ignored. The chi-squared value is computed
; as follows:
;
; CHISQ = TOTAL( (Y-MYFUNCT(X,P))^2 * ABS(WEIGHTS) )
;
; Here are common values of WEIGHTS:
;
; 1D/ERR^2 - Normal weighting (ERR is the measurement error)
; 1D/Y - Poisson weighting (counting statistics)
; 1D - Unweighted
;
; The ERROR keyword takes precedence over any WEIGHTS
; keyword values. If no ERROR or WEIGHTS are given, then
; the fit is unweighted.
; NOTE: the following special cases apply:
; * if WEIGHTS is zero, then the corresponding data point
; is ignored
; * if WEIGHTS is NaN or Infinite, and the NAN keyword is
; set, then the corresponding data point is ignored
; * if WEIGHTS is negative, then the absolute value of
; WEIGHTS is used.
;
; YERROR - upon return, the root-mean-square variance of the
; residuals.
;
;
; EXAMPLE:
;
; ; First, generate some synthetic data
; npts = 200
; x = dindgen(npts) * 0.1 - 10. ; Independent variable
; yi = gauss1(x, [2.2D, 1.4, 3000.]) + 1000 ; "Ideal" Y variable
; y = yi + randomn(seed, npts) * sqrt(1000. + yi); Measured, w/ noise
; sy = sqrt(1000.D + y) ; Poisson errors
;
; ; Now fit a Gaussian to see how well we can recover the original
; yfit = mpfitpeak(x, y, a, error=sy)
; print, p
;
; Generates a synthetic data set with a Gaussian peak, and Poisson
; statistical uncertainty. Then the same function is fitted to the
; data.
;
; REFERENCES:
;
; MINPACK-1, Jorge More', available from netlib (www.netlib.org).
; "Optimization Software Guide," Jorge More' and Stephen Wright,
; SIAM, *Frontiers in Applied Mathematics*, Number 14.
;
; MODIFICATION HISTORY:
;
; New algorithm for estimating starting values, CM, 31 Oct 1999
; Documented, 02 Nov 1999
; Small documentation fixes, 02 Nov 1999
; Slight correction to calculation of dx, CM, 02 Nov 1999
; Documented PERROR for unweighted fits, 03 Nov 1999, CM
; Copying permission terms have been liberalized, 26 Mar 2000, CM
; Change requirements on # elements in X and Y, 20 Jul 2000, CM
; (thanks to David Schlegel <schlegel@astro.princeton.edu>)
; Added documentation on area under curve, 29 Aug 2000, CM
; Added POSITIVE and NEGATIVE keywords, 17 Nov 2000, CM
; Added reference to Moffat paper, 10 Jan 2001, CM
; Added usage message, 26 Jul 2001, CM
; Documentation clarification, 05 Sep 2001, CM
; Make more consistent with comparable IDL routines, 30 Jun 2003, CM
; Assumption of sorted data was removed, CM, 06 Sep 2003, CM
; Add some defensive code against divide by zero, 30 Nov 2005, CM
; Add some defensive code against all Y values equal to each other,
; 17 Apr 2005, CM
; Convert to IDL 5 array syntax (!), 16 Jul 2006, CM
; Move STRICTARR compile option inside each function/procedure, 9 Oct 2006
; Add COMPATIBILITY section, CM, 13 Dec 2007
; Missed some old IDL 4 () array syntax, now corrected, 13 Jun 2008
; Slightly more error checking for pathalogical case, CM, 11 Nov 2008
; Clarify documentation regarding what happens when ESTIMATES is not
; set, CM, 14 Dec 2008
; Add the NAN keyword, document how NAN, WEIGHTS and ERROR interact,
; CM, 30 Mar 2009
; Correct one case of old IDL 4 () array syntax (thanks to I. Urra),
; CM, 25 Jan 2010
; Improve performance by analytic derivative computation, added AUTODERIV
; keyword, W. Landsman, 2011-01-21
; Move estimation code to its own function; allow the user to compute
; only the estimate and return immediately without fitting,
; C. Markwardt, 2011-07-12
;
; $Id: mpfitpeak.pro,v 1.19 2011/12/08 17:51:33 cmarkwar Exp $
;-
; Copyright (C) 1997-2001, 2003, 2005, 2007, 2008, 2009, 2010, Craig Markwardt
; This software is provided as is without any warranty whatsoever.
; Permission to use, copy, modify, and distribute modified or
; unmodified copies is granted, provided this copyright and disclaimer
; are included unchanged.
;-
forward_function mpfit, mpfitfun, mpfitpeak, mpfitpeak_gauss, $
mpfitpeak_lorentz, mpfitpeak_moffat, mpfitpeak_u
function mpfitpeak_u, x, p
COMPILE_OPT strictarr
wid = abs(p[2]) > 1e-20
return, ((x-p[1])/wid)
end
; Gaussian Function
function mpfitpeak_gauss, x, p, pder, _extra=extra
COMPILE_OPT strictarr,hidden
sz = size(x,/type)
if sz EQ 5 then smax = 26D else smax = 13.
u = mpfitpeak_u(x, p)
mask = abs(u) LT smax ;; Prevents floating underflow
Np = N_elements(p)
if Np GE 4 then f = p[3] else f = 0
if Np GE 5 then f = f + p[4]*x
uz = mask*exp(-0.5 * u^2 * mask)
if N_params() GT 2 then begin ;; Compute derivatives if asked
pder = make_array(N_elements(x), Np,type= size(p,/type) )
pder[*,0] = uz
if p[2] NE 0 then pder[*,1] = p[0]*uz*u/p[2]
pder[*,2] = pder[*,1]*u
if Np GE 4 then pder[*,3] = 1.
if Np GE 5 then pder[*,4] = x
endif
return, f + p[0] * uz
end
; Lorentzian Function
function mpfitpeak_lorentz, x, p, pder, _extra=extra
COMPILE_OPT strictarr,hidden
u = mpfitpeak_u(x, p)
Np = N_elements(p)
if Np GE 4 then f = p[3] else f = 0
if Np GE 5 then f = f + p[4]*x
denom = 1/(u^2 + 1)
if N_params() GT 2 then begin ;; Compute derivatives if asked
pder = make_array(N_elements(x), Np,type= size(p,/type) )
pder[*,0] = denom
if p[2] NE 0 then pder[*,1] = 2*p[0]*u*denom*denom/p[2]
pder[*,2] = pder[*,1]*u
if Np GE 4 then pder[*,3] = 1.
if Np GE 5 then pder[*,4] = x
endif
return, f + p[0] *denom
end
; Moffat Function
function mpfitpeak_moffat, x, p, pder,_extra=extra
COMPILE_OPT strictarr
u = mpfitpeak_u(x, p)
Np = N_elements(p)
if Np GE 5 then f = p[4] else f = 0
if Np GE 6 then f = f + p[5]*x
denom0 = (u^2 +1)
denom = denom0^(-p[3])
if N_params() GT 2 then begin ;; Compute derivatives if asked
pder = make_array(N_elements(x), Np,type= size(p,/type) )
pder[*,0] = denom
if p[2] NE 0 then pder[*,1] = 2*p[3]*p[0]*u*denom/p[2]/denom0
pder[*,2] = pder[*,1]*u
pder[*,3] = -alog(denom0)*p[0]*denom
if Np GE 5 then pder[*,4] = 1.
if Np GE 6 then pder[*,5] = x
endif
return, f + p[0]* denom
end
;
; Utility function to estimate peak parameters from an X,Y dataset
;
; X - independent variable
; Y - dependent variable (possibly noisy)
; NAN - if set, then ignore NAN values
; POSITIVE_PEAK - if set, search for positive peak
; NEGATIVE_PEAK - if set, search for negative peak
; (if neither POSITIVE_PEAK nor NEGATIVE_PEAK is set, then search
; for the largest magnitude peak)
; ERRMSG - upon return, set to an error code if an error occurred
;
function mpfitpeak_est, x, y, nan=nan, $
positive_peak=pos, negative_peak=neg, $
errmsg=errmsg
;; Here is the secret - the width is estimated based on the area
;; above/below the average. Thus, as the signal becomes more
;; noisy the width automatically broadens as it should.
nx = n_elements(x)
is = sort(x)
xs = x[is] & ys = y[is]
maxx = max(xs, min=minx) & maxy = max(ys, min=miny, nan=nan)
dx = 0.5 * [xs[1]-xs[0], xs[2:*] - xs, xs[nx-1] - xs[nx-2]]
totarea = total(dx*ys, nan=nan) ;; Total area under curve
av = totarea/(maxx - minx) ;; Average height
;; Degenerate case: all flat with no noise
if miny EQ maxy then begin
est = ys[0]*0.0 + [0,xs[nx/2],(xs[nx-1]-xs[0])/2, ys[0]]
guess = 1
return, est
endif
;; Compute the spread in values above and below average... we
;; take the narrowest one as the one with the peak
wh1 = where(y GE av, ct1)
wh2 = where(y LE av, ct2)
if ct1 EQ 0 OR ct2 EQ 0 then begin
errmsg = 'ERROR: average Y value should fall within the range of Y data values but does not'
return, !values.d_nan
endif
sd1 = total(x[wh1]^2)/ct1 - (total(x[wh1])/ct1)^2
sd2 = total(x[wh2]^2)/ct2 - (total(x[wh2])/ct2)^2
;; Compute area above/below average
if keyword_set(pos) then goto, POS_PEAK
if keyword_set(neg) then goto, NEG_PEAK
if sd1 LT sd2 then begin ;; This is a positive peak
POS_PEAK:
cent = x[where(y EQ maxy)] & cent = cent[0]
peak = maxy - av
endif else begin ;; This is a negative peak
NEG_PEAK:
cent = x[where(y EQ miny)] & cent = cent[0]
peak = miny - av
endelse
peakarea = totarea - total(dx*(ys<av), nan=nan)
if peak EQ 0 then peak = 0.5*peakarea
width = peakarea / (2*abs(peak))
if width EQ 0 OR finite(width) EQ 0 then width = median(dx)
est = [peak, cent, width, av]
return, est
end
function mpfitpeak, x, y, a, estimates=est, nterms=nterms, $
gaussian=gauss, lorentzian=lorentz, moffat=moffat, $
perror=perror, sigma=sigma, yerror=yerror, $
chisq=chisq, bestnorm=bestnorm, niter=iter, nfev=nfev, $
error=dy, weights=weights, measure_errors=dym, $
nfree=nfree, dof=dof, nan=nan, $
no_fit=no_fit, $
negative=neg, positive=pos, parinfo=parinfo, $
best_fjac=best_fjac, pfree_index=pfree_index, covar=covar,$
errmsg=errmsg, status=status, autoderiv=autoderiv0, $
query=query, quiet=quiet, _extra=extra
COMPILE_OPT strictarr
status = 0L
errmsg = ''
if n_params() EQ 0 then begin
message, 'USAGE: yfit = MPFITPEAK(X, Y, A, ...)', /info
return, !values.d_nan
endif
;; Detect MPFIT and crash if it was not found
catch, catcherror
if catcherror NE 0 then begin
MPFIT_NOTFOUND:
catch, /cancel
message, 'ERROR: the required functions MPFIT and MPFITFUN ' + $
'must be in your IDL path', /info
return, !values.d_nan
endif
if mpfit(/query) NE 1 then goto, MPFIT_NOTFOUND
if mpfitfun(/query) NE 1 then goto, MPFIT_NOTFOUND
catch, /cancel
if keyword_set(query) then return, 1
;; Check the number of parameter estimates
if n_elements(quiet) EQ 0 then quiet = 1
if n_elements(nterms) EQ 0 then nterms = 4
if n_elements(autoderiv0) EQ 0 then autoderiv = 0 else autoderiv = keyword_set(autoderiv0)
;; Reject data vectors that are too simple
if n_elements(x) LT nterms OR n_elements(y) LT nterms then begin
errmsg = 'ERROR: X and Y must have at least NTERMS elements'
message, errmsg, /cont
status = 0
return, !values.d_nan
endif
;; Compute the weighting factors to use
if (n_elements(dy) EQ 0 AND n_elements(weights) EQ 0 AND $
n_elements(dym) EQ 0) then begin
weights = x*0+1 ;; Unweighted by default
endif else if n_elements(dy) GT 0 then begin
weights = dy * 0 ;; Avoid division by zero
wh = where(dy NE 0, ct)
if ct GT 0 then weights[wh] = 1./dy[wh]^2
endif else if n_elements(dym) GT 0 then begin
weights = dym * 0 ;; Avoid division by zero
wh = where(dym NE 0, ct)
if ct GT 0 then weights[wh] = 1./dym[wh]^2
endif
;; If the user did not supply an estimate of the parameter values,
;; then try to guestimate them.
if n_elements(est) EQ 0 then begin
guess = 1
est = mpfitpeak_est(x, y, nan=nan, pos=pos, neg=neg, $
errmsg=errmsg)
if errmsg NE '' then begin
message, errmsg, /cont
status = 0
endif
endif
;; Parameter checking for individual function types
np = 3
if keyword_set(moffat) then begin ;; MOFFAT
fun = 'mpfitpeak_moffat'
if keyword_set(guess) then est = [est[0:2], 1, est[3:*]]
np = 4
endif else if keyword_set(lorentz) then begin ;; LORENTZIAN
fun = 'mpfitpeak_lorentz'
endif else begin ;; GAUSSIAN
fun = 'mpfitpeak_gauss'
endelse
if n_elements(est) LT np then begin
errmsg = 'ERROR: parameter ESTIMATES must have at least '+strtrim(np,2)+$
' elements'
message, errmsg, /cont
return, !values.d_nan
endif
if nterms[0] LT np then begin
errmsg = 'ERROR: NTERMS must be at least '+strtrim(np,2)
message, errmsg, /cont
return, !values.d_nan
endif
p0 = replicate(est[0]*0, nterms[0] > n_elements(est))
p0[0] = est
;; If the user wanted only to get an estimate, then return here
if keyword_set(no_fit) then begin
status = 5
a = est
return, !values.d_nan
endif
;; Function call
a = mpfitfun(fun, x, y, 0, p0[0:nterms[0]-1], weights=weights, $
bestnorm=bestnorm, nfev=nfev, status=status, $
nfree=nfree, dof=dof, nan=nan, $
parinfo=parinfo, perror=perror, niter=iter, yfit=yfit, $
best_fjac=best_fjac, pfree_index=pfree_index, covar=covar, $
quiet=quiet, errmsg=errmsg, autoderiv=autoderiv, _EXTRA=extra)
;; Print error message if there is one.
if NOT keyword_set(quiet) AND errmsg NE '' then $
message, errmsg, /cont
if status NE 0 then begin
;; Make sure the width is positive
a[2] = abs(a[2])
;; For compatibility with GAUSSFIT
if n_elements(perror) GT 0 then sigma = perror
if n_elements(bestnorm) GT 0 then chisq = bestnorm
;; Root mean squared of residuals
yerror = a[0]*0
if n_elements(dof) GT 0 AND dof[0] GT 0 then begin
yerror[0] = sqrt( total( (y-yfit)^2, nan=nan ) / dof[0])
endif
return, yfit
endif
return, !values.d_nan
end
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