[798] | 1 | #pragma rtGlobals=1 // Use modern global access method. |
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| 2 | #pragma IgorVersion=6.1 |
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| 3 | |
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| 4 | //////////////////////////////////////////////// |
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| 5 | // |
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| 6 | // This is a proof of principle to convert a structure built of spheres |
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| 7 | // into a fitting function |
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| 8 | // |
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| 9 | //////////////////////////////////////////////// |
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| 10 | |
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| 11 | Proc PlotThreeCylKR(num,qmin,qmax) |
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| 12 | Variable num=100,qmin=0.004,qmax=0.4 |
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| 13 | Prompt num "Enter number of data points for model: " |
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| 14 | Prompt qmin "Enter minimum q-value (A^-1) for model: " |
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| 15 | Prompt qmax "Enter maximum q-value (A^-1) for model: " |
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| 16 | |
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| 17 | |
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| 18 | // make the needed waves, three rows for this case |
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| 19 | Make/O/D/N=3 xCtr_KR,yCtr_KR,zCtr_KR,rad_KR,len_KR,sph_KR,rotx_KR,roty_KR,SLD_KR |
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| 20 | |
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| 21 | make/o/D/n=(num) xwave_c3KR,ywave_c3KR |
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| 22 | xwave_c3KR = alog(log(qmin) + x*((log(qmax)-log(qmin))/num)) |
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| 23 | make/o/D coef_c3KR = {0.01,40,32,26,34,26,34,1e-6,2e-6,0.01} |
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| 24 | make/o/t parameters_c3KR = {"scale","radius 1 (A)","length 1 (A)","radius 2 (A)","length 2 (A)","radius 3 (A)","length 3 (A)","SLD cylinder (A^-2)","SLD solvent (A^-2)","incoh. bkg (cm^-1)"} |
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| 25 | Edit parameters_c3KR,coef_c3KR |
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| 26 | Variable/G root:g_c3KR |
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| 27 | g_c3KR := ThreeCylKR(coef_c3KR,ywave_c3KR,xwave_c3KR) |
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| 28 | |
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| 29 | Display ywave_c3KR vs xwave_c3KR |
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| 30 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
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| 31 | Label bottom "q (A\\S-1\\M)" |
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| 32 | Label left "Intensity (cm\\S-1\\M)" |
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| 33 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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| 34 | |
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| 35 | AddModelToStrings("ThreeCylKR","coef_c3KR","parameters_c3KR","c3KR") |
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| 36 | End |
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| 37 | |
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| 38 | ///////////////////////////////////////////////////////////// |
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| 39 | //// - sets up a dependency to a wrapper, not the actual SmearedModelFunction |
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| 40 | Proc PlotSmearedThreeCylKR(str) |
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| 41 | String str |
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| 42 | Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4) |
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| 43 | |
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| 44 | // if any of the resolution waves are missing => abort |
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| 45 | if(ResolutionWavesMissingDF(str)) //updated to NOT use global strings (in GaussUtils) |
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| 46 | Abort |
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| 47 | endif |
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| 48 | |
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| 49 | // make the needed waves, three rows for this case |
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| 50 | Make/O/D/N=3 xCtr_KR,yCtr_KR,zCtr_KR,rad_KR,len_KR,sph_KR,rotx_KR,roty_KR,SLD_KR |
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| 51 | |
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| 52 | SetDataFolder $("root:"+str) |
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| 53 | |
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| 54 | // Setup parameter table for model function |
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| 55 | make/o/D smear_coef_c3KR = {0.01,40,32,26,34,26,34,1e-6,2e-6,0.01} |
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| 56 | make/o/t smear_parameters_c3KR = {"scale","radius 1 (A)","length 1 (A)","radius 2 (A)","length 2 (A)","radius 3 (A)","length 3 (A)","SLD cylinder (A^-2)","SLD solvent (A^-2)","incoh. bkg (cm^-1)"} |
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| 57 | Edit smear_parameters_c3KR,smear_coef_c3KR |
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| 58 | |
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| 59 | // output smeared intensity wave, dimensions are identical to experimental QSIG values |
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| 60 | // make extra copy of experimental q-values for easy plotting |
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| 61 | Duplicate/O $(str+"_q") smeared_c3KR,smeared_qvals |
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| 62 | SetScale d,0,0,"1/cm",smeared_c3KR |
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| 63 | |
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| 64 | Variable/G gs_c3KR=0 |
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| 65 | gs_c3KR := fSmearedThreeCylKR(smear_coef_c3KR,smeared_c3KR,smeared_qvals) //this wrapper fills the STRUCT |
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| 66 | |
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| 67 | Display smeared_c3KR vs smeared_qvals |
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| 68 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
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| 69 | Label bottom "q (A\\S-1\\M)" |
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| 70 | Label left "Intensity (cm\\S-1\\M)" |
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| 71 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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| 72 | |
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| 73 | SetDataFolder root: |
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| 74 | AddModelToStrings("SmearedThreeCylKR","smear_coef_c3KR","smear_parameters_c3KR","c3KR") |
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| 75 | End |
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| 76 | |
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| 77 | // The calculation is inherently AAO, so it's all done here, not passed to another FitFunc |
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| 78 | // |
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| 79 | // not quite sure how to handle the SLDs yet, since I'm treating them as 1 or 2 digit integers |
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| 80 | // |
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| 81 | Function ThreeCylKR(cw,yw,xw) : FitFunc |
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| 82 | Wave cw,yw,xw |
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| 83 | |
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| 84 | // Variable t1=StopMSTimer(-2) |
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| 85 | |
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| 86 | //The input variables are (and output) |
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| 87 | //[0] scale |
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| 88 | //[1] cylinder RADIUS (A) |
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| 89 | //[2] total cylinder LENGTH (A) |
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| 90 | //[3] sld cylinder (A^-2) |
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| 91 | //[4] sld solvent |
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| 92 | //[5] background (cm^-1) |
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| 93 | Variable scale,delrho,bkg,sldCyl,sldSolv,ctr,fill |
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| 94 | Variable r0,r1,r2,l0,l1,l2 |
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| 95 | scale = cw[0] |
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| 96 | r0 = cw[1] |
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| 97 | l0 = cw[2] |
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| 98 | r1 = cw[3] |
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| 99 | l1 = cw[4] |
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| 100 | r2 = cw[5] |
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| 101 | l2 = cw[6] |
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| 102 | sldCyl = cw[7] |
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| 103 | sldSolv = cw[8] |
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| 104 | bkg = cw[9] |
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| 105 | |
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| 106 | |
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| 107 | // make sure all of the globals are set correctly |
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| 108 | NVAR FFT_T = root:FFT_T |
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| 109 | NVAR FFT_N = root:FFT_N |
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| 110 | NVAR FFT_SolventSLD = root:FFT_SolventSLD |
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[838] | 111 | NVAR FFT_delRho = root:FFT_delRho //the SLD multiplier, should have been initialized to 1e-7 |
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[798] | 112 | |
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[838] | 113 | FFT_SolventSLD = trunc(sldSolv/FFT_delRho) //spits back an integer, maybe not correct |
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[798] | 114 | |
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| 115 | // generate the matrix and erase it |
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| 116 | // FFT_MakeMatrixButtonProc("") |
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| 117 | // FFTEraseMatrixButtonProc("") |
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| 118 | // Wave m=root:mat |
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| 119 | |
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| 120 | // fill the matrix with solvent |
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| 121 | // FFTFillSolventMatrixProc("") |
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| 122 | |
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| 123 | // waves to pass to parsing routine |
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| 124 | WAVE xCtr_KR=root:xCtr_KR |
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| 125 | WAVE yCtr_KR=root:yCtr_KR |
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| 126 | WAVE zCtr_KR=root:zCtr_KR |
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| 127 | WAVE rad_KR=root:rad_KR |
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| 128 | WAVE len_KR=root:len_KR |
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| 129 | WAVE sph_KR=root:sph_KR |
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| 130 | WAVE rotx_KR=root:rotx_KR |
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| 131 | WAVE roty_KR=root:roty_KR |
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| 132 | WAVE SLD_KR=root:SLD_KR |
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| 133 | |
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| 134 | |
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| 135 | |
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| 136 | // with the input parameters, build the structure |
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| 137 | // the first cylinder is at 0,0,0 |
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| 138 | // the second cylinder is on "top" (Z) |
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| 139 | // the third cylinder is on the "bottom" (-Z) |
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| 140 | xCtr_KR[0] = 0 |
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| 141 | yCtr_KR[0] = 0 |
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| 142 | zCtr_KR[0] = 0 |
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| 143 | rad_KR[0] = r0 |
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| 144 | len_KR[0] = l0 |
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| 145 | |
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| 146 | xCtr_KR[1] = 0 |
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| 147 | yCtr_KR[1] = 0 |
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| 148 | zCtr_KR[1] = l0/2 + l1/2 |
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| 149 | rad_KR[1] = r1 |
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| 150 | len_KR[1] = l1 |
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| 151 | |
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| 152 | xCtr_KR[2] = 0 |
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| 153 | yCtr_KR[2] = 0 |
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| 154 | zCtr_KR[2] = -(l0/2 + l2/2) |
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| 155 | rad_KR[2] = r2 |
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| 156 | len_KR[2] = l2 |
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| 157 | |
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| 158 | //no rotation here, only one SLD |
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| 159 | sph_KR = FFT_T //use the global |
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| 160 | rotx_KR = 0 |
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| 161 | roty_KR = 0 |
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| 162 | SLD_KR = trunc(sldCyl*1e6) |
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| 163 | |
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| 164 | |
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| 165 | |
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| 166 | // this parses the information and generates xoutW, youtW, zoutW, sldW in the root folder |
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| 167 | KR_MultiCylinder(xCtr_KR,yCtr_KR,zCtr_KR,rad_KR,len_KR,sph_KR,rotx_KR,roty_KR,SLD_KR) |
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| 168 | |
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| 169 | |
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| 170 | // these are really just for display, or if the FFT of mat is wanted later. |
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| 171 | WAVE xoutW=root:xoutW |
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| 172 | WAVE youtW=root:youtW |
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| 173 | WAVE zoutW=root:zoutW |
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| 174 | WAVE sldW=root:sldW |
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| 175 | |
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| 176 | XYZV_FillMat(xoutW,youtW,ZoutW,sldW,1) //last 1 will erase the matrix |
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| 177 | MakeTriplet(xoutW,youtW,zoutW) |
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| 178 | |
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| 179 | |
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| 180 | |
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| 181 | // do the calculation (use the binned if only one SLD, or bin+SLD if the model requires this) |
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| 182 | fDoCalc(xw,yw,FFT_T,12,0) //the binned calculation |
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[940] | 183 | // fDoCalc(xw,yw,FFT_T,13,0) //the binned + multiple SLD calculation |
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[798] | 184 | |
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| 185 | // reset the volume fraction to get the proper scaling |
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| 186 | // the calculation is normalized to the volume fraction of spheres filling the matrix |
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| 187 | Variable frac |
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| 188 | Wave m=root:mat |
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| 189 | |
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| 190 | frac = VolumeFraction_Occ(m) |
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| 191 | |
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| 192 | yw /= frac |
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| 193 | yw *= scale |
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| 194 | yw += bkg |
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| 195 | |
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| 196 | // Print "elapsed time = ",(StopMSTimer(-2) - t1)/1e6 |
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| 197 | |
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| 198 | return(0) |
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| 199 | End |
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| 200 | |
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| 201 | |
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| 202 | // |
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| 203 | //// this is all there is to the smeared calculation! |
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| 204 | Function SmearedThreeCylKR(s) :FitFunc |
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| 205 | Struct ResSmearAAOStruct &s |
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| 206 | |
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| 207 | ////the name of your unsmeared model is the first argument |
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| 208 | Smear_Model_20(ThreeCylKR,s.coefW,s.xW,s.yW,s.resW) |
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| 209 | |
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| 210 | return(0) |
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| 211 | End |
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| 212 | // |
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| 213 | // |
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| 214 | ////wrapper to calculate the smeared model as an AAO-Struct |
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| 215 | //// fills the struct and calls the ususal function with the STRUCT parameter |
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| 216 | //// |
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| 217 | //// used only for the dependency, not for fitting |
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| 218 | //// |
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| 219 | Function fSmearedThreeCylKR(coefW,yW,xW) |
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| 220 | Wave coefW,yW,xW |
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| 221 | |
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| 222 | String str = getWavesDataFolder(yW,0) |
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| 223 | String DF="root:"+str+":" |
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| 224 | |
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| 225 | WAVE resW = $(DF+str+"_res") |
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| 226 | |
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| 227 | STRUCT ResSmearAAOStruct fs |
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| 228 | WAVE fs.coefW = coefW |
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| 229 | WAVE fs.yW = yW |
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| 230 | WAVE fs.xW = xW |
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| 231 | WAVE fs.resW = resW |
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| 232 | |
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| 233 | Variable err |
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| 234 | err = SmearedThreeCylKR(fs) |
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| 235 | |
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| 236 | return (0) |
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| 237 | End |
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