pearl-scienta-preprocess.ipf

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#pragma rtGlobals=3// Use modern global access method and strict wave access.
#pragma IgorVersion = 6.1
#pragma ModuleName = PearlScientaPreprocess
#pragma version = 1.03
#include "mm-fitfuncs"

// $Id$
// author: matthias.muntwiler@psi.ch
// Copyright (c) 2013-17 Paul Scherrer Institut

// Licensed under the Apache License, Version 2.0 (the "License");
//   you may not use this file except in compliance with the License.
//   You may obtain a copy of the License at
//   http://www.apache.org/licenses/LICENSE-2.0



variable prompt_int_linbg_reduction(string* param){
    string &param

    variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
    variable Lsize = NumberByKey("Lsize", param, "=", ";")
    variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
    variable Hsize = NumberByKey("Hsize", param, "=", ";")
    variable Cpos = NumberByKey("Cpos", param, "=", ";")
    variable Csize = NumberByKey("Csize", param, "=", ";")
    
    prompt Lcrop, "Lower cropping region"
    prompt Hcrop, "Upper cropping region"
    prompt Lsize, "Lower background region"
    prompt Hsize, "Upper background region"
    prompt Cpos, "Center position"
    prompt Csize, "Center integration region"
    
    doprompt "int_linbg_reduction Parameters", lcrop, hcrop, lsize, hsize, cpos, csize
    if (v_flag == 0)
        param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
        param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
        param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
        param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
        param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
        param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
    endif

    return v_flag
};

string capture_int_linbg_cursors(){
    // this function is for testing only, until we implement a proper interface
    string param = csr_int_linbg_reduction("")
    svar /z global_params = root:packages:pearl_explorer:s_reduction_params
    if (svar_exists(global_params))
        global_params = param
    endif
    return param
};

string csr_int_linbg_reduction(string win){
    // PRELIMINARY - function arguments may change
    
    // sets reduction parameters from cursors in a graph.
    // an even number of cursors (2 or more) must be set on the image.
    // cursor names and order do not matter,
    // except that the alphabetically first cursor which is attached to an image selects the image.
    // the cursors mark the following positions, from innermost to outermost pair:
    // 1) low and high limits of peak region.
    // 2) peak-side boundary of lower and upper background region.
    // 3) lower and upper cropping region.
    
    string win

    // read all cursor positions
    variable ic
    string sc
    variable nc = 10
    make /n=(nc) /free positions
    variable np = 0
    wave /z image = $""
    string imagename = ""
    string tracename = ""
    string info
    
    for (ic = 0; ic < nc; ic += 1)
        sc = num2char(char2num("A") + ic)
        wave /z wc = CsrWaveRef($sc, win)
        info = CsrInfo($sc, win)
        tracename = StringByKey("TNAME", info, ":", ";")
        if (waveexists(wc) && (wavedims(wc) == 2))
            if (!waveexists(image))
                wave image = wc
                imagename = tracename
            endif
            if (cmpstr(tracename, imagename) == 0)
                positions[np] = pcsr($sc, win)
                np += 1
            endif
        endif
    endfor

    np = floor(np / 2) * 2// ignore odd cursor
    redimension /n=(np) positions
    sort positions, positions
    // shift upper positions by one so that the rightmost pixel becomes 1.0
    positions = p >= np / 2 ? positions + 1 : positions
    positions = positions / dimsize(image, 0)
    
    // map innermost cursor pair to peak center and size
    variable ip2 = np / 2
    variable ip1 = ip2 - 1
    variable Cpos = (positions[ip1] + positions[ip2]) / 2
    variable Csize = positions[ip2] - positions[ip1]
    if (ip1 >= 0)
        Cpos = (positions[ip1] + positions[ip2]) / 2
        Csize = positions[ip2] - positions[ip1]
    else
        // default: a small region in the center
        Cpos = 0.5
        Csize = 0.2
    endif
    
    // background region
    ip1 -= 1
    ip2 += 1
    variable Lsize
    variable Hsize
    if (ip1 >= 0)
        Lsize = positions[ip1]
        Hsize = 1 - positions[ip2]
    else
        // default: everything outside the peak region
        Lsize = Cpos - Csize / 2
        Hsize = 1 - (Cpos + Csize / 2)
    endif
    
    // crop region
    ip1 -= 1
    ip2 += 1
    variable Lcrop
    variable Hcrop
    if (ip1 >= 0)
        Lcrop = positions[ip1]
        Hcrop = 1 - positions[ip2]
    else
        // default: dead corners of the EW4000 at PEARL
        Lcrop = 0.11
        Hcrop = 0.11
    endif
    Lsize = max(Lsize - Lcrop, 0)
    Hsize = max(Hsize - Hcrop, 0)
    
    string param = ""
    param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
    param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
    param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
    param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
    param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
    param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")

    return param
};

variable test_int_linbg(wave image){
    // useful for testing or manual processing
    // since the int_linbg_reduction function cannot be called from the command line directly.
    wave image
    
    string param = ""
    prompt_int_linbg_reduction(param)
    
    string data1_name = "test_data1"
    string data2_name = "test_data2"
    duplicate /o image, $data1_name, $data2_name
    wave w_data1 = $data1_name
    wave w_data2 = $data2_name
    
    int_linbg_reduction(image, w_data1, w_data2, param)
};

threadsafe variable int_linbg_reduction(wave source, wave dest1, wave dest2, string* param){
    // data reduction function for adh5_load_reduced_detector
    // calculates the average pixel value of each angular slice
    // in one center and two background intervals.
    // a background value is calculated at the center position 
    // by linear interpolation from the two background values.
    // returns the center minus linear background in dest1.
    // returns the Poisson one-sigma error in dest2.
    wave source// source wave
        // Scienta detector image, energy axis along X, angle axis along Y
    wave dest1, dest2// destination waves
        // each wave is a one-dimensional intensity distribution
        // the function may redimension these waves to one of the image dimensions
        // (it must be clear to the user which dimension this is).
        // the meaning of dest1 and dest2 is up to the particular function,
        // e.g. dest1 could hold the mean value and dest2 the one-sigma error,
        // or dest1 could hold the X-profile, and dest2 the Y-profile.
    string &param// parameters in a key1=value1;key2=value2;... list
        // all region parameters are relative to the image size (0...1)
        // Lcrop = size of the lower cropping region
        // Hcrop = size of the upper cropping region
        // Lsize = size of the lower background integration region
        // Hsize = size of the upper background integration region
        // Cpos = center position of the of the peak integration region
        // Csize = size of the peak integration region
        
        // typical values (peak centered on detector, FWHM ~ 20 % of image)
        // Lcrop=0.11;Hcrop=0.11;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.2
    
    variable nx = dimsize(source, 0)
    variable ny = dimsize(source, 1)
    
    // read parameters
    variable lcrop = NumberByKey("Lcrop", param, "=", ";")
    variable lsize = NumberByKey("Lsize", param, "=", ";")
    variable hcrop = NumberByKey("Hcrop", param, "=", ";")
    variable hsize = NumberByKey("Hsize", param, "=", ";")
    variable cpos = NumberByKey("Cpos", param, "=", ";")
    variable csize = NumberByKey("Csize", param, "=", ";")
    
    // validate parameters
    // background parameters are optional, center parameter is required.
    if (numtype(lcrop) != 0)
        lcrop = 0
    endif
    if (numtype(lsize) != 0)
        lsize = 0
    endif
    if (numtype(hcrop) != 0)
        hcrop = 0
    endif
    if (numtype(hsize) != 0)
        hsize = 0
    endif
    if (numtype(Cpos) != 0)
        return 1// Cpos parameter missing
    endif
    if (numtype(Csize) != 0)
        return 2// Csize parameter missing
    endif

    variable lpos = lcrop + lsize / 2
    variable hpos = 1 - (hcrop + hsize / 2)

    variable p0
    variable p1
    
    adh5_setup_profile(source, dest1, 1)
    adh5_setup_profile(source, dest2, 1)
    
    duplicate /free dest1, lbg, hbg
    if (lsize > 0)
        p0 = round(lcrop * nx)
        p1 = round((lcrop + lsize) * nx)
        ad_profile_y_w(source, p0, p1, lbg)
    else
        lbg = 0
    endif
    if (hsize > 0)
        p0 = round((1 - hcrop - hsize) * nx)
        p1 = round((1 - hcrop) * nx)
        ad_profile_y_w(source, p0, p1, hbg)
    else
        hbg = 0
    endif
    if (csize > 0)
        p0 = round((cpos - csize/2) * nx)
        p1 = round((cpos + csize/2) * nx)
        ad_profile_y_w(source, p0, p1, dest1)
    else
        dest1 = 0
    endif
    
    variable scale = (cpos - lpos) / (hpos - lpos)
    dest2 = dest1
    dest1 -= scale * (hbg - lbg) + lbg
    dest2 = sqrt(dest2 + scale^2 * (hbg + lbg))
    return 0// return zero if successful, non-zero if an error occurs
};

variable test_shockley_anglefit(wave image, variable branch){
    // apply the Shockley_anglefit function to a single image
    // useful for testing or manual processing
    // since the Shockley_anglefit function cannot be called from the command line directly.
    wave image
    variable branch// +1 or -1
    
    string param = ""
    param = ReplaceStringByKey("branch", param, num2str(branch), "=", ";")
    
    string s_branch
    if (branch >= 0)
        s_branch = "p"
    else
        s_branch = "n"
    endif
    string pkpos_name = "saf_pkpos_" + s_branch
    string pkwid_name = "saf_pkwid_" + s_branch
    duplicate /o image, $pkpos_name, $pkwid_name
    wave w_pkpos = $pkpos_name
    wave w_pkwid = $pkwid_name
    
    shockley_anglefit(image, w_pkpos, w_pkwid, param)
};

variable prompt_Shockley_anglefit(string* param){
    string &param

    variable branch = NumberByKey("branch", param, "=", ";")
    
    prompt branch, "Branch (-1 or +1)"
    
    doprompt "Shockley_anglefit_reduction Parameters", branch
    if (v_flag == 0)
        param = ReplaceNumberByKey("branch", param, branch, "=", ";")
    endif

    return v_flag
};

threadsafe variable Shockley_anglefit(wave source, wave dest1, wave dest2, string* param){
    // data reduction function for adh5_load_reduced_detector
    // specialized for analysing the Cu(111) Shockley surface state
    // do curve fitting of one branch of the surface state
    // the result is peak position versus energy
    // TODO: this function contains hard-coded parameters. please generalize as necessary.
    wave source// source wave
        // Scienta detector image, energy axis along X, angle axis along Y
        // the apex of the surface state must be at angle 0
    wave dest1, dest2// destination waves
        // dest1: peak position
        // dest2: peak width (sigma)
    string &param// parameters in a key1=value1;key2=value2;... list
        // branch=-1 or +1: select negative (positive) angles for the fit interval, respectively
        
    variable nx = dimsize(source, 0)
    variable ny = dimsize(source, 1)
    
    // read parameters
    variable branch = NumberByKey("branch", param, "=", ";")
    
    // validate parameters
    if (numtype(branch) != 0)
        branch = +1
    endif

    // prepare output
    adh5_setup_profile(source, dest1, 0)
    adh5_setup_profile(source, dest2, 0)
    dest1 = nan
    dest2 = nan
    
    // select angle range
    // hard-coded for a particular measurement series
    variable y0
    variable y1
    if (branch < 0)
        y0 = -5
        y1 = 0
    else
        y0 = 0
        y1 = 5
    endif
    
    // select energy range
    // start at the point of highest intensity and go up 0.45 eV
    variable p0
    variable p1
    variable q0
    variable q1
    duplicate /free dest1, center
    q0 = round((y0 - dimoffset(source, 1)) / dimdelta(source, 1))
    q1 = round((y1 - dimoffset(source, 1)) / dimdelta(source, 1))
    ad_profile_x_w(source, q0, q1, center)
    wavestats /q/m=1 center
    p0 = round((v_maxloc - dimoffset(source, 0)) / dimdelta(source, 0))
    p1 = round((v_maxloc + 0.4 - dimoffset(source, 0)) / dimdelta(source, 0))
    
    // prepare intermediate data buffer
    make /n=(ny)/d/free profile
    setscale /p x dimoffset(source,1), dimdelta(source,1), waveunits(source,1), profile
    
    variable pp
    for (pp = p0; pp <= p1; pp += 1)
        profile = source[pp][p]
        curvefit /Q /NTHR=1 /W=2 gauss profile(y0,y1)
        wave w_coef
        dest1[pp] = w_coef[2]
        dest2[pp] = w_coef[3]
    endfor
    return 0// return zero if successful, non-zero if an error occurs
};

variable prompt_int_quadbg_reduction(string* param){
    string &param

    variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
    variable Lsize = NumberByKey("Lsize", param, "=", ";")
    variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
    variable Hsize = NumberByKey("Hsize", param, "=", ";")
    variable Cpos = NumberByKey("Cpos", param, "=", ";")
    variable Csize = NumberByKey("Csize", param, "=", ";")
    
    prompt Lcrop, "Lower cropping region"
    prompt Hcrop, "Upper cropping region"
    prompt Lsize, "Lower background region"
    prompt Hsize, "Upper background region"
    prompt Cpos, "Center position"
    prompt Csize, "Center integration region"
    
    doprompt "int_quadbg_reduction Parameters", lcrop, hcrop, lsize, hsize, cpos, csize
    if (v_flag == 0)
        param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
        param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
        param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
        param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
        param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
        param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
    endif

    return v_flag
};

variable test_int_quadbg(wave image){
    // useful for testing or manual processing
    // since the int_quadbg_reduction function cannot be called from the command line directly.
    wave image
    
    string param = ""
    prompt_int_quadbg_reduction(param)
    
    string data1_name = "test_data1"
    string data2_name = "test_data2"
    duplicate /o image, $data1_name, $data2_name
    wave w_data1 = $data1_name
    wave w_data2 = $data2_name
    
    int_quadbg_reduction(image, w_data1, w_data2, param)
};

threadsafe variable int_quadbg_reduction(wave source, wave dest1, wave dest2, string* param){
    // data reduction function for adh5_load_reduced_detector
    // integrates peak area minus a quadratic backgrouind
    wave source// source wave
        // Scienta detector image, energy axis along X, angle axis along Y
    wave dest1, dest2// destination waves
    string &param// parameters in a key1=value1;key2=value2;... list
        // all region parameters are relative to the image size (0...1)
        // Lcrop = size of the lower cropping region
        // Hcrop = size of the upper cropping region
        // Lsize = size of the lower background integration region
        // Hsize = size of the upper background integration region
        // Cpos = center position of the of the peak integration region
        // Csize = size of the peak integration region
        
        // typical values (peak centered on detector, FWHM ~ 20 % of image)
        // Lcrop=0.11;Hcrop=0.11;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.2
    
    variable nx = dimsize(source, 0)
    variable ny = dimsize(source, 1)
    
    // read parameters
    variable lcrop = NumberByKey("Lcrop", param, "=", ";")
    variable lsize = NumberByKey("Lsize", param, "=", ";")
    variable hcrop = NumberByKey("Hcrop", param, "=", ";")
    variable hsize = NumberByKey("Hsize", param, "=", ";")
    variable cpos = NumberByKey("Cpos", param, "=", ";")
    variable csize = NumberByKey("Csize", param, "=", ";")
    
    // validate parameters
    // background parameters are optional, center parameter is required.
    if (numtype(lcrop) != 0)
        lcrop = 0
    endif
    if (numtype(lsize) != 0)
        lsize = 0
    endif
    if (numtype(hcrop) != 0)
        hcrop = 0
    endif
    if (numtype(hsize) != 0)
        hsize = 0
    endif
    if (numtype(Cpos) != 0)
        return 1// Cpos parameter missing
    endif
    if (numtype(Csize) != 0)
        return 2// Csize parameter missing
    endif

    // crop boundaries
    variable pcl = round(lcrop * nx)
    variable pch = round((1 - hcrop) * nx)
    // fit boundaries
    variable pfl = round((lcrop + lsize) * nx)
    variable pfh = round((1 - hcrop - hsize) * nx)
    // integration boundaries
    variable pil = round((cpos - csize/2) * nx)
    variable pih = round((cpos + csize/2) * nx)
    
    adh5_setup_profile(source, dest1, 0)
    adh5_setup_profile(source, dest2, 0)
    
    // prepare intermediate data buffer
    make /n=(nx) /d /free profile, mask, fit
    setscale /p x dimoffset(source,0), dimdelta(source,0), waveunits(source,0), profile, mask, fit
    mask = ((p >= pcl) && (p < pfl)) || ((p >= pfh) && (p < pch))
    
    variable qq
    variable sp, sf
    variable xil = x2pnt(profile, pil)
    variable xih = x2pnt(profile, pih)
    
    make /n=3 /free /d w_coef
    for (qq = 0; qq < ny; qq += 1)
        profile = source[p][qq]
        curvefit /Q /NTHR=1 /W=2 poly 3, kwCWave=w_coef, profile /M=mask
        fit = poly(w_coef, x)
        sp = sum(profile, xil, xih)
        sf = sum(fit, xil, xih)
        dest1[qq] = sp - sf
        dest2[qq] = sqrt(sp)
    endfor
    
    return 0// return zero if successful, non-zero if an error occurs
};

variable scienta_norm(wave w, variable x){
    wave w
    variable x
    
    return w[0] * (x^2 - w[1]^2)
};

wave fit_scienta_ang_transm(wave data, wave params){
    wave data// measured angular distribution (1D)
    wave /z params
    
    if (!waveexists(params))
        make /n=12 /o params
    endif
    redimension /n=12/d params
    
    variable h = wavemax(data) - wavemin(data)
    params[0] = h / 2
    params[1] = 0
    params[2] = 7
    params[3] = h / 4
    params[4] = -23
    params[5] = 4
    params[6] = h / 4
    params[7] = +23
    params[8] = 4
    params[9] = h / 2
    params[10] = 0
    params[11] = -0.001
    FuncFit /NTHR=0 /q scienta_ang_transm params data
    
    return params
};

threadsafe variable scienta_ang_transm(wave w, variable x){
    // parameterized angular transmission function of the analyser
    wave w// coefficients
        // w[0] = amplitude gauss 1
        // w[1] = position gauss 1
        // w[2] = width gauss 1
        // w[3] = amplitude gauss 2
        // w[4] = position gauss 2
        // w[5] = width gauss 2
        // w[6] = amplitude gauss 3
        // w[7] = position gauss 3
        // w[8] = width gauss 3
        // w[9] = constant background
        // w[10] = linear background
        // w[11] = quadratic background
    variable x
    
    make /free /n=4 /d w_int
    w_int[0] = 0
    w_int[1,] = w[p - 1]
    variable pk1 = gauss1d(w_int, x)
    w_int[1,] = w[p + 2]
    variable pk2 = gauss1d(w_int, x)
    w_int[1,] = w[p + 5]
    variable pk3 = gauss1d(w_int, x)
    w_int[0,2] = w[9 + p]
    w_int[3] = 0
    variable bg = poly(w_int, x)
    
    return bg + pk1 + pk2 + pk3
};

wave fit_scienta_poly_bg(wave data, wave params, variable bgterms){
    wave data// measured distribution (2D)
    wave /z params// wave, will be redimensioned for the correct size
    variable bgterms// number of terms in the polynomial background: 2, 3, or 4
    
    if (!waveexists(params))
        make /n=15 /o params
    endif
    redimension /n=15 /d params
    
    variable wmax = wavemax(data)
    variable wmin = wavemin(data)
    params[0] = 0
    params[1] = 7
    params[2] = 1 / 2
    params[3] = -23
    params[4] = 4
    params[5] = 1 / 2
    params[6] = +23
    params[7] = 4
    params[8] = 1
    params[9] = 0
    params[10] = -0.001
    params[11] = wmin
    params[12] = (wmax - wmin) / dimdelta(data,1) / dimsize(data,1)
    params[13] = 0
    params[14] = 0
    
    string h = "0000000000000"
    if (bgterms < 3)
        h = h + "1"
    else
        h = h + "0"
    endif
    if (bgterms < 4)
        h = h + "1"
    else
        h = h + "0"
    endif
    FuncFitMD /NTHR=1 /q /h=h scienta_poly_bg params data
    
    return params
};

variable scienta_poly_bg(wave w, variable e, variable a){
    // polynomial background with
    // parameterized angular transmission function of the analyser
    wave w// coefficients
        // angular transmission, varies with a
        // amplitude of gauss 1 = 1 constant
        // other peak amplitudes and linear terms are relative to gauss 1
        // w[0] = position gauss 1
        // w[1] = width gauss 1
        // w[2] = amplitude gauss 2, relative to gauss 1
        // w[3] = position gauss 2
        // w[4] = width gauss 2
        // w[5] = amplitude gauss 3, relative to gauss 1
        // w[6] = position gauss 3
        // w[7] = width gauss 3
        // w[8] = constant term
        // w[9] = linear term
        // w[10] = quadratic term
        // spectral background, varies with e
        // w[11] = constant term
        // w[12] = linear term
        // w[13] = quadratic term
        // w[14] = cubic term
    variable a// detection angle
    variable e// electron energy
    
    make /free /n=4 /d w_int
    variable p0 = 0
    
    w_int[0] = 0
    w_int[1] = 1
    w_int[2,] = w[p0 + p - 2]
    variable pk1 = gauss1d(w_int, a)
    p0 += 2

    w_int[1,] = w[p0 + p - 1]
    variable pk2 = gauss1d(w_int, a)
    p0 += 3

    w_int[1,] = w[p0 + p - 1]
    variable pk3 = gauss1d(w_int, a)
    p0 += 3

    w_int[0,2] = w[p0 + p]
    w_int[3] = 0
    variable base = poly(w_int, a)
    p0 += 3

    w_int[0,3] = w[p0 + p]
    variable bg = poly(w_int, e)
    
    return bg * (base + pk1 + pk2 + pk3)
};

variable prompt_redim_linbg_reduction(string* param){
    string &param

    variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
    variable Lsize = NumberByKey("Lsize", param, "=", ";")
    variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
    variable Hsize = NumberByKey("Hsize", param, "=", ";")
    variable Cpos = NumberByKey("Cpos", param, "=", ";")
    variable Csize = NumberByKey("Csize", param, "=", ";")
    
    prompt Lcrop, "Lower cropping region"
    prompt Hcrop, "Upper cropping region"
    prompt Lsize, "Lower background region"
    prompt Hsize, "Upper background region"
    prompt Cpos, "Center position"
    prompt Csize, "Center integration region"
    
    doprompt "redim_linbg_reduction Parameters", lcrop, hcrop, lsize, hsize, cpos, csize
    if (v_flag == 0)
        param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
        param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
        param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
        param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
        param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
        param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
    endif

    return v_flag
};

threadsafe variable redim_linbg_reduction(wave source, wave dest1, wave dest2, string* param){
    wave source
    wave dest1, dest2
    string &param
    
    variable nx = dimsize(source, 0)
    variable ny = dimsize(source, 1)
    
    duplicate /free source, source_redim
    redimension /n=(nx * ny) source_redim
    nx += 1
    redimension /n=(nx, ny) source_redim
    
    return int_linbg_reduction(source_redim, dest1, dest2, param)
};

// DblGaussLinBG function fit reduction

variable test_gauss2_reduction(wave image){
    wave image
    
    string param = ""
    param = ReplaceNumberByKey("rngl", param, -inf, "=", ";")
    param = ReplaceNumberByKey("rngh", param, inf, "=", ";")
    param = ReplaceNumberByKey("pos1", param, 113.70, "=", ";")
    param = ReplaceNumberByKey("wid1", param, 1.46, "=", ";")
    param = ReplaceNumberByKey("pos2", param, 126.53, "=", ";")
    param = ReplaceNumberByKey("wid2", param, 1.63, "=", ";")
    param = ReplaceNumberByKey("ybox", param, 1, "=", ";")
    param = ReplaceStringByKey("return", param, "amp1", "=", ";")

    make /o test1
    make /o test2
    
    gauss2_reduction(image, test1, test2, param)
};

variable prompt_gauss2_reduction(string* param){
    string &param

    variable rngl = NumberByKey("rngl", param, "=", ";")
    variable rngh = NumberByKey("rngh", param, "=", ";")
    variable pos1 = NumberByKey("pos1", param, "=", ";")
    variable wid1 = NumberByKey("wid1", param, "=", ";")
    variable pos2 = NumberByKey("pos2", param, "=", ";")
    variable wid2 = NumberByKey("wid2", param, "=", ";")
    variable ybox = NumberByKey("ybox", param, "=", ";")
    string retpar = StringByKey("return", param, "=", ";")

    prompt rngl, "range low"
    prompt rngh, "range high"
    prompt pos1, "position 1"
    prompt wid1, "width 1"
    prompt pos2, "position 2"
    prompt wid2, "width 2"
    prompt ybox, "ybox (1 or 3)"
    prompt retpar, "return", popup "amp1;amp2;"
    
    doprompt "gauss2_reduction reduction parameters", rngl, rngh, pos1, wid1, pos2, wid2, ybox, retpar
    if (v_flag == 0)
        param = ReplaceNumberByKey("rngl", param, rngl, "=", ";")
        param = ReplaceNumberByKey("rngh", param, rngh, "=", ";")
        param = ReplaceNumberByKey("pos1", param, pos1, "=", ";")
        param = ReplaceNumberByKey("wid1", param, wid1, "=", ";")
        param = ReplaceNumberByKey("pos2", param, pos2, "=", ";")
        param = ReplaceNumberByKey("wid2", param, wid2, "=", ";")
        param = ReplaceStringByKey("return", param, retpar, "=", ";")
        param = ReplaceNumberByKey("ybox", param, ybox, "=", ";")
    endif
    
    return v_flag
};

threadsafe variable gauss2_reduction(wave source, wave dest1, wave dest2, string* param){
    wave source
    wave dest1, dest2
    string &param
        
    variable nx = dimsize(source, 0)
    variable ny = dimsize(source, 1)
    
    // prepare output
    adh5_setup_profile(source, dest1, 1)
    adh5_setup_profile(source, dest2, 1)
    dest1 = 0
    dest2 = 0

    // read parameters
    variable rngl = NumberByKey("rngl", param, "=", ";")
    variable rngh = NumberByKey("rngh", param, "=", ";")
    variable pos1 = NumberByKey("pos1", param, "=", ";")
    variable wid1 = NumberByKey("wid1", param, "=", ";")
    variable pos2 = NumberByKey("pos2", param, "=", ";")
    variable wid2 = NumberByKey("wid2", param, "=", ";")
    variable ybox = NumberByKey("ybox", param, "=", ";")
    string retpar = StringByKey("return", param, "=", ";")

    variable idestcoef
    if (cmpstr(retpar, "amp2") == 0)
        idestcoef = 3
    else
        idestcoef = 0
    endif

    // prepare curve fit
    make /free xprof
    adh5_setup_profile(source, xprof, 0)
    duplicate /free xprof, xprof_sig
    make /free /d /n=8 w_coef, W_sigma
    w_coef[0] = {1, pos1, wid1, 1, pos2, wid2, 0, 0}
    
    variable pl = max(x2pnt(xprof, rngl), 0)
    variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
    
    // text constraints cannot be used in threadsafe functions.
    // the following matrix-vector forumlation is equivalent to:
    // make /free /T /N=4 constraints
    // constraints[0] = {"K0 >= 0", "K3 >= 0", "K6 <= 0", "K7 => 0"}
    make /free /n=(4,8) cmat
    make /free /n=4 cvec
    cmat = 0
    cmat[0][0] = -1
    cmat[1][3] = -1
    cmat[2][6] = 1
    cmat[3][7] = -1
    cvec = 0

    // loop over angle scale    
    variable p0 = 0
    variable p1 = numpnts(dest1) - 1
    variable pp
    variable wmin
    variable wmax
    if (ybox > 1)
        p0 += ceil((ybox - 1) / 2)
        p1 -= ceil((ybox - 1) / 2)
    endif
    variable V_FitNumIters
    
    for (pp = p0; pp <= p1; pp += 1)
        xprof = source[p][pp]
        if (ybox > 1)
            xprof += source[p][pp-1] + source[p][pp+1]
        endif
        xprof_sig = max(sqrt(xprof), 1)
        xprof /= ybox
        xprof_sig /= ybox
        
        wmin = wavemin(xprof)
        wmax = wavemax(xprof)
        w_coef[0] = wmax - wmin
        w_coef[3] = w_coef[0]
        w_coef[6] = 0
        w_coef[7] = wmin
        FuncFit /H="01101100" /Q /NTHR=1 /N /W=2 DblGaussLinBG w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
        wave w_sigma
    
        if (V_FitNumIters < 40)
            dest1[pp] = max(w_coef[idestcoef], 0)
            dest2[pp] = max(w_sigma[idestcoef], 0)
        endif
    endfor
    
    dest1 *= w_coef[idestcoef+2] * sqrt(pi)
    dest2 *= w_coef[idestcoef+2] * sqrt(pi)
    
    return 0
};