1 | #pragma rtGlobals=1 // Use modern global access method. |
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2 | #pragma version=5.0 |
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3 | #pragma IgorVersion=6.0 |
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4 | |
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5 | //********************************************* |
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6 | // For AVERAGE and for DRAWING |
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7 | // DRAWING routines only use a subset of the total list, since saving, naming, etc. don't apply |
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8 | // (10) possible keywords, some numerical, some string values |
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9 | // AVTYPE=string string from set {Circular,Annular,Rectangular,Sector,2D_ASCII,QxQy_ASCII,PNG_Graphic} |
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10 | // PHI=value azimuthal angle (-90,90) |
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11 | // DPHI=value +/- angular range around phi for average |
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12 | // WIDTH=value total width of rectangular section, in pixels |
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13 | // SIDE=string string from set {left,right,both} **note NOT capitalized |
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14 | // QCENTER=value q-value (1/A) of center of annulus for annular average |
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15 | // QDELTA=value total width of annulus centered at QCENTER |
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16 | // PLOT=string string from set {Yes,No} = truth of generating plot of averaged data |
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17 | // SAVE=string string from set {Yes,No} = truth of saving averaged data to disk |
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18 | // NAME=string string from set {Auto,Manual} = Automatic name generation or Manual(dialog) |
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19 | //*********************************************** |
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20 | |
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21 | |
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22 | // this fuction also does sector averaging |
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23 | //the parameters in the global keyword-string must have already been set somewhere |
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24 | //either directly, from the protocol, or from the Average_Panel |
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25 | //** the keyword-list has already been "pre-parsed" to send only Circular or Sector |
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26 | //averages to this routine. Rectangualr or annular averages get done elsewhere |
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27 | // TYPE parameter determines which data folder to work from |
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28 | // |
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29 | //annnulus (step) size is currently fixed at 1 (variable dr, below) |
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30 | Function CircularAverageTo1D(type) |
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31 | String type |
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32 | |
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33 | SVAR keyListStr = root:myGlobals:Protocols:gAvgInfoStr //this is the list that has it all |
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34 | Variable isCircular = 0 |
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35 | |
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36 | if( cmpstr("Circular",StringByKey("AVTYPE",keyListStr,"=",";")) ==0) |
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37 | isCircular = 1 //set a switch for later |
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38 | Endif |
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39 | |
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40 | //type is the data type to do the averaging on, and will be set as the current folder |
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41 | //get the current displayed data (so the correct folder is used) |
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42 | String destPath = "root:Packages:NIST:"+type |
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43 | |
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44 | // |
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45 | Variable xcenter,ycenter,x0,y0,sx,sx3,sy,sy3,dtsize,dtdist,dr,ddr |
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46 | Variable lambda,trans |
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47 | WAVE reals = $(destPath + ":RealsRead") |
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48 | WAVE/T textread = $(destPath + ":TextRead") |
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49 | String fileStr = textread[3] |
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50 | |
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51 | // center of detector, for non-linear corrections |
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52 | NVAR pixelsX = root:myGlobals:gNPixelsX |
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53 | NVAR pixelsY = root:myGlobals:gNPixelsY |
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54 | |
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55 | xcenter = pixelsX/2 + 0.5 // == 64.5 for 128x128 Ordela |
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56 | ycenter = pixelsY/2 + 0.5 // == 64.5 for 128x128 Ordela |
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57 | |
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58 | // beam center, in pixels |
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59 | x0 = reals[16] |
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60 | y0 = reals[17] |
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61 | //detector calibration constants |
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62 | sx = reals[10] //mm/pixel (x) |
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63 | sx3 = reals[11] //nonlinear coeff |
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64 | sy = reals[13] //mm/pixel (y) |
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65 | sy3 = reals[14] //nonlinear coeff |
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66 | |
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67 | dtsize = 10*reals[20] //det size in mm |
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68 | dtdist = 1000*reals[18] // det distance in mm |
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69 | |
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70 | NVAR binWidth=root:myGlobals:gBinWidth |
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71 | |
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72 | dr = binWidth // ***********annulus width set by user, default is one*********** |
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73 | ddr = dr*sx //step size, in mm (this value should be passed to the resolution calculation, not dr 18NOV03) |
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74 | |
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75 | Variable rcentr,large_num,small_num,dtdis2,nq,xoffst,dxbm,dybm,ii |
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76 | Variable phi_rad,dphi_rad,phi_x,phi_y |
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77 | Variable forward,mirror |
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78 | |
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79 | String side = StringByKey("SIDE",keyListStr,"=",";") |
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80 | // Print "side = ",side |
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81 | |
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82 | if(!isCircular) //must be sector avg (rectangular not sent to this function) |
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83 | //convert from degrees to radians |
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84 | phi_rad = (Pi/180)*NumberByKey("PHI",keyListStr,"=",";") |
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85 | dphi_rad = (Pi/180)*NumberByKey("DPHI",keyListStr,"=",";") |
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86 | //create cartesian values for unit vector in phi direction |
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87 | phi_x = cos(phi_rad) |
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88 | phi_y = sin(phi_rad) |
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89 | Endif |
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90 | |
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91 | /// data wave is data in the current folder which was set at the top of the function |
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92 | WAVE data=$(destPath + ":data") |
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93 | //Check for the existence of the mask, if not, make one (local to this folder) that is null |
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94 | |
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95 | if(WaveExists($"root:Packages:NIST:MSK:data") == 0) |
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96 | Print "There is no mask file loaded (WaveExists)- the data is not masked" |
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97 | Make/O/N=(pixelsX,pixelsY) $(destPath + ":mask") |
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98 | Wave mask = $(destPath + ":mask") |
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99 | mask = 0 |
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100 | else |
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101 | Wave mask=$"root:Packages:NIST:MSK:data" |
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102 | Endif |
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103 | |
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104 | // |
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105 | //pixels within rcentr of beam center are broken into 9 parts (units of mm) |
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106 | rcentr = 100 //original |
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107 | // rcentr = 0 |
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108 | // values for error if unable to estimate value |
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109 | //large_num = 1e10 |
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110 | large_num = 1 //1e10 value (typically sig of last data point) plots poorly, arb set to 1 |
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111 | small_num = 1e-10 |
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112 | |
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113 | // output wave are expected to exist (?) initialized to zero, what length? |
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114 | // 200 points on VAX --- use 300 here, or more if SAXS data is used with 1024x1024 detector (1000 pts seems good) |
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115 | Variable defWavePts=500 |
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116 | Make/O/N=(defWavePts) $(destPath + ":qval"),$(destPath + ":aveint") |
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117 | Make/O/N=(defWavePts) $(destPath + ":ncells"),$(destPath + ":dsq"),$(destPath + ":sigave") |
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118 | Make/O/N=(defWavePts) $(destPath + ":SigmaQ"),$(destPath + ":fSubS"),$(destPath + ":QBar") |
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119 | |
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120 | WAVE qval = $(destPath + ":qval") |
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121 | WAVE aveint = $(destPath + ":aveint") |
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122 | WAVE ncells = $(destPath + ":ncells") |
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123 | WAVE dsq = $(destPath + ":dsq") |
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124 | WAVE sigave = $(destPath + ":sigave") |
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125 | WAVE qbar = $(destPath + ":QBar") |
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126 | WAVE sigmaq = $(destPath + ":SigmaQ") |
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127 | WAVE fsubs = $(destPath + ":fSubS") |
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128 | |
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129 | qval = 0 |
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130 | aveint = 0 |
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131 | ncells = 0 |
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132 | dsq = 0 |
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133 | sigave = 0 |
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134 | qbar = 0 |
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135 | sigmaq = 0 |
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136 | fsubs = 0 |
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137 | |
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138 | dtdis2 = dtdist^2 |
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139 | nq = 1 |
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140 | xoffst=0 |
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141 | //distance of beam center from detector center |
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142 | dxbm = FX(x0,sx3,xcenter,sx) |
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143 | dybm = FY(y0,sy3,ycenter,sy) |
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144 | |
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145 | //BEGIN AVERAGE ********** |
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146 | Variable xi,dxi,dx,jj,data_pixel,yj,dyj,dy,mask_val=0.1 |
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147 | Variable dr2,nd,fd,nd2,ll,kk,dxx,dyy,ir,dphi_p |
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148 | |
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149 | // IGOR arrays are indexed from [0][0], FORTAN from (1,1) (and the detector too) |
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150 | // loop index corresponds to FORTRAN (old code) |
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151 | // and the IGOR array indices must be adjusted (-1) to the correct address |
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152 | ii=1 |
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153 | do |
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154 | xi = ii |
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155 | dxi = FX(xi,sx3,xcenter,sx) |
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156 | dx = dxi-dxbm //dx and dy are in mm |
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157 | |
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158 | jj = 1 |
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159 | do |
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160 | data_pixel = data[ii-1][jj-1] //assign to local variable |
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161 | yj = jj |
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162 | dyj = FY(yj,sy3,ycenter,sy) |
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163 | dy = dyj - dybm |
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164 | if(!(mask[ii-1][jj-1])) //masked pixels = 1, skip if masked (this way works...) |
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165 | dr2 = (dx^2 + dy^2)^(0.5) //distance from beam center NOTE dr2 used here - dr used above |
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166 | if(dr2>rcentr) //keep pixel whole |
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167 | nd = 1 |
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168 | fd = 1 |
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169 | else //break pixel into 9 equal parts |
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170 | nd = 3 |
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171 | fd = 2 |
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172 | endif |
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173 | nd2 = nd^2 |
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174 | ll = 1 //"el-el" loop index |
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175 | do |
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176 | dxx = dx + (ll - fd)*sx/3 |
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177 | kk = 1 |
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178 | do |
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179 | dyy = dy + (kk - fd)*sy/3 |
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180 | if(isCircular) |
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181 | //circular average, use all pixels |
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182 | //(increment) |
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183 | nq = IncrementPixel(data_pixel,ddr,dxx,dyy,aveint,dsq,ncells,nq,nd2) |
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184 | else |
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185 | //a sector average - determine azimuthal angle |
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186 | dphi_p = dphi_pixel(dxx,dyy,phi_x,phi_y) |
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187 | if(dphi_p < dphi_rad) |
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188 | forward = 1 //within forward sector |
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189 | else |
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190 | forward = 0 |
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191 | Endif |
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192 | if((Pi - dphi_p) < dphi_rad) |
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193 | mirror = 1 //within mirror sector |
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194 | else |
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195 | mirror = 0 |
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196 | Endif |
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197 | //check if pixel lies within allowed sector(s) |
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198 | if(cmpstr(side,"both")==0) //both sectors |
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199 | if ( mirror || forward) |
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200 | //increment |
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201 | nq = IncrementPixel(data_pixel,ddr,dxx,dyy,aveint,dsq,ncells,nq,nd2) |
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202 | Endif |
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203 | else |
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204 | if(cmpstr(side,"right")==0) //forward sector only |
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205 | if(forward) |
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206 | //increment |
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207 | nq = IncrementPixel(data_pixel,ddr,dxx,dyy,aveint,dsq,ncells,nq,nd2) |
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208 | Endif |
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209 | else //mirror sector only |
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210 | if(mirror) |
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211 | //increment |
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212 | nq = IncrementPixel(data_pixel,ddr,dxx,dyy,aveint,dsq,ncells,nq,nd2) |
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213 | Endif |
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214 | Endif |
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215 | Endif //allowable sectors |
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216 | Endif //circular or sector check |
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217 | kk+=1 |
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218 | while(kk<=nd) |
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219 | ll += 1 |
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220 | while(ll<=nd) |
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221 | Endif //masked pixel check |
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222 | jj += 1 |
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223 | while (jj<=pixelsY) |
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224 | ii += 1 |
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225 | while(ii<=pixelsX) //end of the averaging |
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226 | |
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227 | //compute q-values and errors |
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228 | Variable ntotal,rr,theta,avesq,aveisq,var |
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229 | |
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230 | lambda = reals[26] |
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231 | ntotal = 0 |
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232 | kk = 1 |
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233 | do |
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234 | rr = (2*kk-1)*ddr/2 |
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235 | theta = 0.5*atan(rr/dtdist) |
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236 | qval[kk-1] = (4*Pi/lambda)*sin(theta) |
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237 | if(ncells[kk-1] == 0) |
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238 | //no pixels in annuli, data unknown |
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239 | aveint[kk-1] = 0 |
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240 | sigave[kk-1] = large_num |
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241 | else |
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242 | if(ncells[kk-1] <= 1) |
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243 | //need more than one pixel to determine error |
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244 | aveint[kk-1] = aveint[kk-1]/ncells[kk-1] |
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245 | sigave[kk-1] = large_num |
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246 | else |
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247 | //assume that the intensity in each pixel in annuli is normally |
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248 | // distributed about mean... |
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249 | aveint[kk-1] = aveint[kk-1]/ncells[kk-1] |
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250 | avesq = aveint[kk-1]^2 |
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251 | aveisq = dsq[kk-1]/ncells[kk-1] |
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252 | var = aveisq-avesq |
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253 | if(var<=0) |
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254 | sigave[kk-1] = small_num |
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255 | else |
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256 | sigave[kk-1] = sqrt(var/(ncells[kk-1] - 1)) |
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257 | endif |
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258 | endif |
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259 | endif |
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260 | ntotal += ncells[kk-1] |
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261 | kk+=1 |
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262 | while(kk<=nq) |
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263 | |
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264 | //Print "NQ = ",nq |
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265 | // data waves were defined as 300 points (=defWavePts), but now have less than that (nq) points |
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266 | // use DeletePoints to remove junk from end of waves |
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267 | //WaveStats would be a more foolproof implementation, to get the # points in the wave |
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268 | Variable startElement,numElements |
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269 | startElement = nq |
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270 | numElements = defWavePts - startElement |
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271 | DeletePoints startElement,numElements, qval,aveint,ncells,dsq,sigave |
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272 | |
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273 | //////////////end of VAX sector_ave() |
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274 | |
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275 | //angle dependent transmission correction |
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276 | Variable uval,arg,cos_th |
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277 | lambda = reals[26] |
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278 | trans = reals[4] |
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279 | |
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280 | // |
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281 | // The transmission correction is now done at the ADD step, in DetCorr() |
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282 | // |
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283 | // ////this section is the trans_correct() VAX routine |
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284 | // if(trans<0.1) |
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285 | // Print "***transmission is less than 0.1*** and is a significant correction" |
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286 | // endif |
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287 | // if(trans==0) |
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288 | // Print "***transmission is ZERO*** and has been reset to 1.0 for the averaging calculation" |
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289 | // trans = 1 |
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290 | // endif |
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291 | // //optical thickness |
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292 | // uval = -ln(trans) //use natural logarithm |
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293 | // //apply correction to aveint[] |
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294 | // //index from zero here, since only working with IGOR waves |
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295 | // ii=0 |
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296 | // do |
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297 | // theta = 2*asin(lambda*qval[ii]/(4*pi)) |
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298 | // cos_th = cos(theta) |
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299 | // arg = (1-cos_th)/cos_th |
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300 | // if((uval<0.01) || (cos_th>0.99)) //OR |
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301 | // //small arg, approx correction |
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302 | // aveint[ii] /= 1-0.5*uval*arg |
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303 | // else |
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304 | // //large arg, exact correction |
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305 | // aveint[ii] /= (1-exp(-uval*arg))/(uval*arg) |
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306 | // endif |
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307 | // ii+=1 |
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308 | // while(ii<nq) |
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309 | // //end of transmission/pathlength correction |
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310 | |
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311 | // *************************************************************** |
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312 | // |
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313 | // Do the extra 3 columns of resolution calculations starting here. |
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314 | // |
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315 | // *************************************************************** |
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316 | |
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317 | Variable L2 = reals[18] |
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318 | Variable BS = reals[21] |
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319 | Variable S1 = reals[23] |
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320 | Variable S2 = reals[24] |
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321 | Variable L1 = reals[25] |
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322 | lambda = reals[26] |
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323 | Variable lambdaWidth = reals[27] |
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324 | String detStr=textRead[9] |
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325 | |
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326 | Variable usingLenses = reals[28] //new 2007 |
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327 | |
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328 | //Two parameters DDET and APOFF are instrument dependent. Determine |
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329 | //these from the instrument name in the header. |
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330 | //From conversation with JB on 01.06.99 these are the current |
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331 | //good values |
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332 | |
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333 | Variable DDet |
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334 | NVAR apOff = root:myGlobals:apOff //in cm |
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335 | |
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336 | // DDet = DetectorPixelResolution(fileStr,detStr) //needs detector type and beamline |
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337 | //note that reading the detector pixel size from the header ASSUMES SQUARE PIXELS! - Jan2008 |
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338 | DDet = reals[10]/10 // header value (X) is in mm, want cm here |
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339 | |
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340 | |
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341 | //Width of annulus used for the average is gotten from the |
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342 | //input dialog before. This also must be passed to the resolution |
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343 | //calculator. Currently the default is dr=1 so just keeping that. |
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344 | |
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345 | //Go from 0 to nq doing the calc for all three values at |
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346 | //every Q value |
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347 | |
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348 | ii=0 |
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349 | |
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350 | Variable ret1,ret2,ret3 |
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351 | do |
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352 | getResolution(qval[ii],lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,ddr,usingLenses,ret1,ret2,ret3) |
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353 | sigmaq[ii] = ret1 |
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354 | qbar[ii] = ret2 |
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355 | fsubs[ii] = ret3 |
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356 | ii+=1 |
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357 | while(ii<nq) |
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358 | DeletePoints startElement,numElements, sigmaq, qbar, fsubs |
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359 | |
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360 | // End of resolution calculations |
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361 | // *************************************************************** |
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362 | |
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363 | //Plot the data in the Plot_1d window |
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364 | Avg_1D_Graph(aveint,qval,sigave) |
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365 | |
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366 | //get rid of the default mask, if one was created (it is in the current folder) |
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367 | //don't just kill "mask" since it might be pointing to the one in the MSK folder |
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368 | Killwaves/Z $(destPath+":mask") |
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369 | |
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370 | //return to root folder (redundant) |
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371 | SetDataFolder root: |
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372 | |
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373 | Return 0 |
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374 | End |
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375 | |
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376 | //returns nq, new number of q-values |
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377 | //arrays aveint,dsq,ncells are also changed by this function |
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378 | // |
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379 | Function IncrementPixel(dataPixel,ddr,dxx,dyy,aveint,dsq,ncells,nq,nd2) |
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380 | Variable dataPixel,ddr,dxx,dyy |
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381 | Wave aveint,dsq,ncells |
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382 | Variable nq,nd2 |
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383 | |
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384 | Variable ir |
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385 | |
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386 | ir = trunc(sqrt(dxx*dxx+dyy*dyy)/ddr)+1 |
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387 | if (ir>nq) |
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388 | nq = ir //resets maximum number of q-values |
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389 | endif |
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390 | aveint[ir-1] += dataPixel/nd2 //ir-1 must be used, since ir is physical |
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391 | dsq[ir-1] += dataPixel*dataPixel/nd2 |
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392 | ncells[ir-1] += 1/nd2 |
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393 | |
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394 | Return nq |
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395 | End |
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396 | |
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397 | //function determines azimuthal angle dphi that a vector connecting |
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398 | //center of detector to pixel makes with respect to vector |
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399 | //at chosen azimuthal angle phi -> [cos(phi),sin(phi)] = [phi_x,phi_y] |
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400 | //dphi is always positive, varying from 0 to Pi |
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401 | // |
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402 | Function dphi_pixel(dxx,dyy,phi_x,phi_y) |
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403 | Variable dxx,dyy,phi_x,phi_y |
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404 | |
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405 | Variable val,rr,dot_prod |
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406 | |
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407 | rr = sqrt(dxx^2 + dyy^2) |
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408 | dot_prod = (dxx*phi_x + dyy*phi_y)/rr |
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409 | //? correct for roundoff error? - is this necessary in IGOR, w/ double precision? |
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410 | if(dot_prod > 1) |
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411 | dot_prod =1 |
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412 | Endif |
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413 | if(dot_prod < -1) |
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414 | dot_prod = -1 |
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415 | Endif |
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416 | |
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417 | val = acos(dot_prod) |
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418 | |
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419 | return val |
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420 | |
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421 | End |
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422 | |
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423 | //calculates the x distance from the center of the detector, w/nonlinear corrections |
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424 | // |
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425 | Function FX(xx,sx3,xcenter,sx) |
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426 | Variable xx,sx3,xcenter,sx |
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427 | |
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428 | Variable retval |
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429 | |
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430 | retval = sx3*tan((xx-xcenter)*sx/sx3) |
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431 | Return retval |
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432 | End |
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433 | |
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434 | //calculates the y distance from the center of the detector, w/nonlinear corrections |
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435 | // |
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436 | Function FY(yy,sy3,ycenter,sy) |
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437 | Variable yy,sy3,ycenter,sy |
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438 | |
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439 | Variable retval |
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440 | |
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441 | retval = sy3*tan((yy-ycenter)*sy/sy3) |
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442 | Return retval |
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443 | End |
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444 | |
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445 | //old function not called anymore, now "ave" button calls routine from AvgGraphics.ipf |
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446 | //to get input from panel rather than large prompt for missing parameters |
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447 | Function Ave_button(button0) : ButtonControl |
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448 | String button0 |
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449 | |
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450 | // the button on the graph will average the currently displayed data |
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451 | SVAR type=root:myGlobals:gDataDisplayType |
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452 | |
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453 | //Check for logscale data in "type" folder |
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454 | SetDataFolder "root:Packages:NIST:"+type //use the full path, so it will always work |
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455 | String dest = "root:Packages:NIST:" + type |
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456 | |
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457 | NVAR isLogScale = $(dest + ":gIsLogScale") |
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458 | if(isLogScale == 1) |
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459 | //data is logscale, convert it back and reset the global |
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460 | Duplicate/O $(dest + ":linear_data") $(dest + ":data") |
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461 | // WAVE vlegend=$(dest + ":vlegend") |
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462 | // Make the color table linear scale |
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463 | // vlegend = y |
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464 | Variable/G $(dest + ":gIsLogScale") = 0 //copy to keep with the current data folder |
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465 | SetDataFolder root: |
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466 | //rename the button to reflect "isLin" - the displayed name must have been isLog |
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467 | Button bisLog,title="isLin",rename=bisLin |
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468 | Endif |
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469 | |
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470 | //set data folder back to root |
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471 | SetDataFolder root: |
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472 | |
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473 | //do the average - ask the user for what type of average |
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474 | //ask the user for averaging paramters |
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475 | Execute "GetAvgInfo()" |
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476 | |
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477 | //dispatch to correct averaging routine |
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478 | //if you want to save the files, see Panel_DoAverageButtonProc(ctrlName) function |
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479 | //for making a fake protocol (needed to write out data) |
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480 | SVAR tempStr = root:myGlobals:Protocols:gAvgInfoStr |
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481 | String choice = StringByKey("AVTYPE",tempStr,"=",";") |
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482 | if(cmpstr("Rectangular",choice)==0) |
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483 | //dispatch to rectangular average |
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484 | RectangularAverageTo1D(type) |
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485 | else |
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486 | if(cmpstr("Annular",choice)==0) |
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487 | AnnularAverageTo1D(type) |
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488 | else |
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489 | //circular or sector |
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490 | CircularAverageTo1D(type) |
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491 | Endif |
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492 | Endif |
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493 | |
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494 | Return 0 |
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495 | End |
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