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 | #include "FlexibleCylinder_v40" |
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5 | |
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6 | /////////////////////////// |
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7 | // plots the scattering from a flexible cylinder with an |
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8 | // elliptical cross-section |
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9 | // |
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10 | // same chain calculation as flexible cylinder, |
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11 | // correcting for a different cross-section |
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12 | // |
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13 | // Bergstrom / Pedersen reference in Langmuir |
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14 | // |
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15 | // Contains Wei-Ren's corrections for the chain model July 2006 |
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16 | // |
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17 | // |
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18 | Proc PlotFlexCyl_Ellip(num,qmin,qmax) |
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19 | Variable num=128,qmin=0.001,qmax=0.7 |
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20 | Prompt num "Enter number of data points for model: " |
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21 | Prompt qmin "Enter minimum q-value (A^-1) for model: " |
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22 | Prompt qmax "Enter maximum q-value (A^-1) for model: " |
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23 | |
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24 | Make/O/D/n=(num) xwave_fleell,ywave_fleell |
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25 | xwave_fleell = alog(log(qmin) + x*((log(qmax)-log(qmin))/num)) |
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26 | Make/O/D coef_fleell = {1.,1000,100,20,1.5,1e-6,6.3e-6,0.0001} |
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27 | make/o/t parameters_fleell = {"scale","Contour Length (A)","Kuhn Length, b (A)","Minor Radius (a) (A)","Axis Ratio = major/a","SLD cylinder (A^-2)","SLD solvent (A^-2)","bkgd (arb)"} |
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28 | Edit parameters_fleell,coef_fleell |
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29 | |
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30 | Variable/G root:g_fleell |
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31 | g_fleell := FlexCyl_Ellip(coef_fleell,ywave_fleell,xwave_fleell) |
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32 | Display ywave_fleell vs xwave_fleell |
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33 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
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34 | Label bottom "q (A\\S-1\\M)" |
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35 | Label left "Intensity (cm\\S-1\\M)" |
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36 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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37 | |
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38 | AddModelToStrings("FlexCyl_Ellip","coef_fleell","parameters_fleell","fleell") |
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39 | End |
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40 | |
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41 | // - sets up a dependency to a wrapper, not the actual SmearedModelFunction |
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42 | Proc PlotSmearedFlexCyl_Ellip(str) |
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43 | String str |
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44 | Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4) |
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45 | |
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46 | // if any of the resolution waves are missing => abort |
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47 | if(ResolutionWavesMissingDF(str)) //updated to NOT use global strings (in GaussUtils) |
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48 | Abort |
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49 | endif |
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50 | |
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51 | SetDataFolder $("root:"+str) |
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52 | |
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53 | // Setup parameter table for model function |
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54 | Make/O/D smear_coef_fleell = {1.,1000,100,20,1.5,1e-6,6.3e-6,0.0001} |
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55 | make/o/t smear_parameters_fleell = {"scale","Contour Length (A)","Kuhn Length, b (A)","Minor Radius (a) (A)","Axis Ratio = major/a","SLD cylinder (A^-2)","SLD solvent (A^-2)","bkgd (arb)"} |
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56 | Edit smear_parameters_fleell,smear_coef_fleell //display parameters in a table |
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57 | |
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58 | // output smeared intensity wave, dimensions are identical to experimental QSIG values |
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59 | // make extra copy of experimental q-values for easy plotting |
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60 | Duplicate/O $(str+"_q") smeared_fleell,smeared_qvals // |
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61 | SetScale d,0,0,"1/cm",smeared_fleell // |
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62 | |
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63 | Variable/G gs_fleell=0 |
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64 | gs_fleell := fSmearedFlexCyl_Ellip(smear_coef_fleell,smeared_fleell,smeared_qvals) //this wrapper fills the STRUCT |
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65 | |
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66 | Display smeared_fleell vs smeared_qvals // |
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67 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
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68 | Label bottom "q (A\\S-1\\M)" |
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69 | Label left "I(q) (cm\\S-1\\M)" |
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70 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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71 | |
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72 | SetDataFolder root: |
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73 | AddModelToStrings("SmearedFlexCyl_Ellip","smear_coef_fleell","smear_parameters_fleell","fleell") |
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74 | End |
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75 | |
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76 | |
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77 | |
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78 | |
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79 | //AAO version, uses XOP if available |
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80 | // simply calls the original single point calculation with |
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81 | // a wave assignment (this will behave nicely if given point ranges) |
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82 | Function FlexCyl_Ellip(cw,yw,xw) : FitFunc |
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83 | Wave cw,yw,xw |
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84 | |
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85 | #if exists("FlexCyl_EllipX") |
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86 | yw = FlexCyl_EllipX(cw,xw) |
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87 | #else |
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88 | yw = fFlexCyl_Ellip(cw,xw) |
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89 | #endif |
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90 | return(0) |
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91 | End |
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92 | |
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93 | // |
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94 | Function fFlexCyl_Ellip(ww,x) :FitFunc |
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95 | Wave ww |
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96 | Variable x |
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97 | |
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98 | //nice names to the input params |
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99 | //ww[0] = scale |
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100 | //ww[1] = L [A] |
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101 | //ww[2] = B [A] |
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102 | //ww[3] = rad [A] cross-sectional radius |
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103 | //ww[4] = ellRatio = major/minor axis (greater than one) |
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104 | //ww[5] = sld cylinder [A^-2] |
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105 | //ww[6] = sld solvent |
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106 | //ww[7] = bkg [cm-1] |
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107 | Variable scale,L,B,bkg,rad,qr,cont,ellRatio,sldc,slds |
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108 | |
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109 | scale = ww[0] |
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110 | L = ww[1] |
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111 | B = ww[2] |
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112 | rad = ww[3] |
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113 | ellRatio = ww[4] |
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114 | sldc = ww[5] |
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115 | slds = ww[6] |
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116 | bkg = ww[7] |
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117 | |
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118 | cont = sldc-slds |
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119 | qr = x*rad //used for cross section contribution only |
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120 | |
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121 | //local variables |
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122 | Variable flex,crossSect |
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123 | |
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124 | flex = Sk_WR(x,L,B) //Wei-Ren's calculations, do not have cross section |
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125 | |
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126 | //calculate cross section contribution - Eqns.(28) &(29) (approximate) |
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127 | //use elliptical cross-section here |
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128 | crossSect = EllipticalCross_fn(x,rad,(rad*ellRatio)) |
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129 | |
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130 | //normalize form factor by multiplying by cylinder volume * cont^2 |
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131 | // then convert to cm-1 by multiplying by 10^8 |
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132 | // then scale = phi |
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133 | |
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134 | flex *= crossSect |
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135 | flex *= Pi*rad*rad*ellRatio*L |
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136 | flex *= cont^2 |
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137 | flex *= 1.0e8 |
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138 | |
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139 | return (scale*flex + bkg) |
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140 | |
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141 | end |
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142 | ////////////// flex chain - with excluded volume |
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143 | |
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144 | Function EllipticalCross_fn(qq,a,b) |
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145 | Variable qq,a,b |
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146 | |
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147 | Make/O/D/N=100 ellip |
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148 | SetScale x,0,(pi/2),ellip |
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149 | |
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150 | ellip = bessJ(1,(qq*sqrt(a^2*sin(x)^2+b^2*cos(x)^2))) / (qq*sqrt(a^2*sin(x)^2+b^2*cos(x)^2)) |
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151 | ellip *=2 |
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152 | ellip = ellip^2 |
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153 | Integrate/T ellip |
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154 | |
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155 | return(ellip[99]*2/pi) |
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156 | End |
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157 | |
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158 | //wrapper to calculate the smeared model as an AAO-Struct |
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159 | // fills the struct and calls the ususal function with the STRUCT parameter |
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160 | // |
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161 | // used only for the dependency, not for fitting |
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162 | // |
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163 | Function fSmearedFlexCyl_Ellip(coefW,yW,xW) |
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164 | Wave coefW,yW,xW |
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165 | |
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166 | String str = getWavesDataFolder(yW,0) |
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167 | String DF="root:"+str+":" |
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168 | |
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169 | WAVE resW = $(DF+str+"_res") |
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170 | |
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171 | STRUCT ResSmearAAOStruct fs |
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172 | WAVE fs.coefW = coefW |
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173 | WAVE fs.yW = yW |
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174 | WAVE fs.xW = xW |
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175 | WAVE fs.resW = resW |
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176 | |
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177 | Variable err |
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178 | err = SmearedFlexCyl_Ellip(fs) |
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179 | |
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180 | return (0) |
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181 | End |
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182 | |
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183 | // this is all there is to the smeared calculation! |
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184 | Function SmearedFlexCyl_Ellip(s) :FitFunc |
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185 | Struct ResSmearAAOStruct &s |
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186 | |
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187 | // the name of your unsmeared model (AAO) is the first argument |
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188 | Smear_Model_20(FlexCyl_Ellip,s.coefW,s.xW,s.yW,s.resW) |
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189 | |
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190 | return(0) |
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191 | End |
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192 | |
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