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 | // Vers 1.2 090501 |
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7 | // |
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8 | //**************************** |
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9 | // |
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10 | // Procedures to perform the "Correct" step during data reduction |
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11 | // |
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12 | // - ther is olny one procedure to perform the subtractions, and a single |
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13 | // parameter flags which subtractions are to be done. Different numbers of |
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14 | // attenuators during scattering runs are corrected as described in John's memo, |
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15 | // with the note that ONLY method (3) is used, which assumes that 'diffuse' scattering |
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16 | // is dominant over 'dark current' (note that 'dark current' = shutter CLOSED) |
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17 | // |
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18 | // |
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19 | //do the CORRECT step based on the answers to emp and bkg subtraction |
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20 | //by setting the proper"mode" |
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21 | //1 = both emp and bgd subtraction |
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22 | //2 = only bgd subtraction |
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23 | //3 = only emp subtraction |
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24 | //4 = no subtraction |
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25 | //additional modes 091301 |
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26 | //11 = emp, bgd, drk |
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27 | //12 = bgd and drk |
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28 | //13 = emp and drk |
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29 | //14 = no subtractions |
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30 | // |
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31 | //******************************** |
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32 | |
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33 | //unused test procedure for Correct() function |
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34 | //must be updated to include "mode" parameter before re-use |
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35 | // |
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36 | Proc CorrectData() |
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37 | |
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38 | Variable err |
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39 | String type |
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40 | |
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41 | err = Correct() |
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42 | |
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43 | if(err) |
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44 | Abort "error in Correct" |
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45 | endif |
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46 | |
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47 | //contents are always dumped to COR |
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48 | type = "COR" |
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49 | |
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50 | //need to update the display with "data" from the correct dataFolder |
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51 | //reset the current displaytype to "type" |
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52 | String/G root:myGlobals:gDataDisplayType=Type |
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53 | |
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54 | fRawWindowHook() |
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55 | |
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56 | End |
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57 | |
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58 | |
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59 | //mode describes the type of subtraction that is to be done |
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60 | //1 = both emp and bgd subtraction |
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61 | //2 = only bgd subtraction |
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62 | //3 = only emp subtraction |
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63 | //4 = no subtraction |
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64 | // |
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65 | // + 10 indicates that WORK.DRK is to be used |
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66 | // |
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67 | //091301 version |
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68 | //now simple dispatches to the correct subtraction - logic was too |
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69 | //involved to do in one function - unclear and error-prone |
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70 | // |
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71 | // 081203 version |
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72 | // checks for trans==1 in SAM and EMP before dispatching |
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73 | // and asks for new value if desired |
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74 | // |
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75 | Function Correct(mode) |
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76 | Variable mode |
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77 | |
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78 | Variable err=0,trans,newTrans |
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79 | |
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80 | //switch and dispatch based on the required subtractions |
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81 | // always check for SAM data |
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82 | err = WorkDataExists("SAM") |
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83 | if(err==1) |
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84 | return(err) |
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85 | endif |
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86 | |
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87 | |
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88 | //check for trans==1 |
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89 | NVAR doCheck=root:myGlobals:gDoTransCheck |
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90 | Wave/Z samR=root:SAM:RealsRead |
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91 | Wave/Z empR=root:EMP:RealsRead |
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92 | if(doCheck) |
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93 | trans = samR[4] |
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94 | newTrans=GetNewTrans(trans,"SAM") //will change value if necessary |
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95 | if(numtype(newTrans)==0) |
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96 | samR[4] = newTrans //avoid user abort assigning NaN |
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97 | endif |
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98 | if(trans != newTrans) |
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99 | print "Using SAM trans = ",samR[4] |
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100 | endif |
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101 | endif |
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102 | |
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103 | //copy SAM information to COR, wiping out the old contents of the COR folder first |
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104 | //do this even if no correction is dispatched (if incorrect mode) |
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105 | err = CopyWorkContents("SAM","COR") |
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106 | if(err==1) |
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107 | Abort "No data in SAM, abort from Correct()" |
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108 | endif |
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109 | |
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110 | // Print "dispatching to mode = ",mode |
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111 | switch(mode) |
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112 | case 1: |
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113 | err = WorkDataExists("EMP") |
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114 | if(err==1) |
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115 | return(err) |
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116 | Endif |
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117 | if(doCheck) |
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118 | trans = empR[4] |
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119 | newTrans=GetNewTrans(trans,"EMP") //will change value if necessary |
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120 | if(numtype(newTrans)==0) |
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121 | empR[4] = newTrans |
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122 | endif |
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123 | if(trans != newTrans) |
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124 | print "Using EMP trans = ",empR[4] |
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125 | endif |
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126 | endif |
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127 | err = WorkDataExists("BGD") |
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128 | if(err==1) |
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129 | return(err) |
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130 | Endif |
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131 | err = CorrectMode_1() |
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132 | break |
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133 | case 2: |
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134 | err = WorkDataExists("BGD") |
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135 | if(err==1) |
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136 | return(err) |
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137 | Endif |
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138 | err = CorrectMode_2() |
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139 | break |
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140 | case 3: |
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141 | err = WorkDataExists("EMP") |
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142 | if(err==1) |
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143 | return(err) |
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144 | Endif |
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145 | if(doCheck) |
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146 | trans = empR[4] |
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147 | newTrans=GetNewTrans(trans,"EMP") //will change value if necessary |
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148 | if(numtype(newTrans)==0) |
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149 | empR[4] = newTrans |
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150 | endif |
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151 | if(trans != newTrans) |
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152 | print "Using EMP trans = ",empR[4] |
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153 | endif |
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154 | endif |
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155 | err = CorrectMode_3() |
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156 | break |
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157 | case 4: |
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158 | err = CorrectMode_4() |
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159 | break |
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160 | case 11: |
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161 | err = WorkDataExists("EMP") |
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162 | if(err==1) |
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163 | return(err) |
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164 | Endif |
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165 | if(doCheck) |
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166 | trans = empR[4] |
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167 | newTrans=GetNewTrans(trans,"EMP") //will change value if necessary |
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168 | if(numtype(newTrans)==0) |
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169 | empR[4] = newTrans |
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170 | endif |
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171 | if(trans != newTrans) |
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172 | print "Using EMP trans = ",empR[4] |
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173 | endif |
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174 | endif |
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175 | err = WorkDataExists("BGD") |
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176 | if(err==1) |
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177 | return(err) |
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178 | Endif |
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179 | err = WorkDataExists("DRK") |
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180 | if(err==1) |
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181 | return(err) |
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182 | Endif |
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183 | err = CorrectMode_11() |
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184 | break |
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185 | case 12: |
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186 | err = WorkDataExists("BGD") |
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187 | if(err==1) |
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188 | return(err) |
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189 | Endif |
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190 | err = WorkDataExists("DRK") |
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191 | if(err==1) |
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192 | return(err) |
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193 | Endif |
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194 | err = CorrectMode_12() |
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195 | break |
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196 | case 13: |
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197 | err = WorkDataExists("EMP") |
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198 | if(err==1) |
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199 | return(err) |
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200 | Endif |
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201 | if(doCheck) |
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202 | trans = empR[4] |
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203 | newTrans=GetNewTrans(trans,"EMP") //will change value if necessary |
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204 | if(numtype(newTrans)==0) |
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205 | empR[4] = newTrans |
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206 | endif |
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207 | if(trans != newTrans) |
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208 | print "Using EMP trans = ",empR[4] |
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209 | endif |
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210 | endif |
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211 | err = WorkDataExists("DRK") |
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212 | if(err==1) |
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213 | return(err) |
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214 | Endif |
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215 | err = CorrectMode_13() |
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216 | break |
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217 | case 14: |
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218 | err = WorkDataExists("DRK") |
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219 | if(err==1) |
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220 | return(err) |
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221 | Endif |
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222 | err = CorrectMode_14() |
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223 | break |
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224 | default: //something wrong |
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225 | Print "Incorrect mode in Correct()" |
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226 | return(1) //error |
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227 | endswitch |
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228 | |
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229 | //calculation attempted, return the result |
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230 | return(err) |
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231 | End |
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232 | |
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233 | // subtraction of bot EMP and BGD from SAM |
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234 | // data exists, checked by dispatch routine |
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235 | // |
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236 | Function CorrectMode_1() |
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237 | |
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238 | //create the necessary wave references |
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239 | WAVE sam_data=$"root:SAM:data" |
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240 | WAVE sam_reals=$"root:SAM:realsread" |
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241 | WAVE sam_ints=$"root:SAM:integersread" |
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242 | WAVE/T sam_text=$"root:SAM:textread" |
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243 | WAVE bgd_data=$"root:BGD:data" |
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244 | WAVE bgd_reals=$"root:BGD:realsread" |
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245 | WAVE bgd_ints=$"root:BGD:integersread" |
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246 | WAVE/T bgd_text=$"root:BGD:textread" |
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247 | WAVE emp_data=$"root:EMP:data" |
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248 | WAVE emp_reals=$"root:EMP:realsread" |
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249 | WAVE emp_ints=$"root:EMP:integersread" |
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250 | WAVE/T emp_text=$"root:EMP:textread" |
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251 | WAVE cor_data=$"root:COR:data" |
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252 | WAVE/T cor_text=$"root:COR:textread" |
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253 | |
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254 | //get sam and bgd attenuation factors |
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255 | String fileStr="" |
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256 | Variable lambda,attenNo,sam_AttenFactor,bgd_attenFactor,emp_AttenFactor |
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257 | Variable tmonsam,fsam,fbgd,xshift,yshift,rsam,csam,rbgd,cbgd,tmonbgd |
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258 | Variable wcen=0.001,tsam,temp,remp,cemp,tmonemp,femp |
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259 | fileStr = sam_text[3] |
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260 | lambda = sam_reals[26] |
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261 | attenNo = sam_reals[3] |
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262 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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263 | fileStr = bgd_text[3] |
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264 | lambda = bgd_reals[26] |
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265 | attenNo = bgd_reals[3] |
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266 | bgd_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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267 | fileStr = emp_text[3] |
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268 | lambda = emp_reals[26] |
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269 | attenNo = emp_reals[3] |
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270 | emp_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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271 | |
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272 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
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273 | tmonsam = sam_reals[0] //monitor count in SAM |
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274 | tsam = sam_reals[4] //SAM transmission |
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275 | csam = sam_reals[16] //x center |
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276 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
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277 | tmonbgd = bgd_reals[0] //monitor count in BGD |
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278 | cbgd = bgd_reals[16] |
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279 | rbgd = bgd_reals[17] |
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280 | tmonemp = emp_reals[0] //monitor count in EMP |
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281 | temp = emp_reals[4] //trans emp |
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282 | cemp = emp_reals[16] //beamcenter of EMP |
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283 | remp = emp_reals[17] |
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284 | |
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285 | if(temp==0) |
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286 | DoAlert 0,"Empty Cell transmission was zero. It has been reset to one for the subtraction" |
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287 | temp=1 |
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288 | Endif |
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289 | |
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290 | NVAR pixelsX = root:myGlobals:gNPixelsX |
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291 | NVAR pixelsY = root:myGlobals:gNPixelsY |
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292 | |
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293 | //get the shifted data arrays, EMP and BGD, each relative to SAM |
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294 | Make/D/O/N=(pixelsX,pixelsY) cor1,bgd_temp,noadd_bgd,emp_temp,noadd_emp |
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295 | xshift = cbgd-csam |
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296 | yshift = rbgd-rsam |
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297 | if(abs(xshift) <= wcen) |
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298 | xshift = 0 |
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299 | Endif |
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300 | if(abs(yshift) <= wcen) |
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301 | yshift = 0 |
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302 | Endif |
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303 | GetShiftedArray(bgd_data,bgd_temp,noadd_bgd,xshift,yshift) //bgd_temp |
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304 | |
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305 | xshift = cemp-csam |
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306 | yshift = remp-rsam |
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307 | if(abs(xshift) <= wcen) |
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308 | xshift = 0 |
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309 | Endif |
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310 | if(abs(yshift) <= wcen) |
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311 | yshift = 0 |
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312 | Endif |
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313 | GetShiftedArray(emp_data,emp_temp,noadd_emp,xshift,yshift) //emp_temp |
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314 | |
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315 | //do the subtraction |
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316 | fsam=1 |
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317 | femp = tmonsam/tmonemp //this should be ==1 since normalized files |
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318 | fbgd = tmonsam/tmonbgd //this should be ==1 since normalized files |
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319 | cor1 = fsam*sam_data/sam_attenFactor - fbgd*bgd_temp/bgd_attenFactor |
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320 | cor1 -= (tsam/temp)*(femp*emp_temp/emp_attenFactor - fbgd*bgd_temp/bgd_attenFactor) |
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321 | cor1 *= noadd_bgd*noadd_emp //zero out the array mismatch values |
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322 | |
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323 | //we're done, get out w/no error |
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324 | //set the COR data to the result |
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325 | cor_data = cor1 |
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326 | //update COR header |
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327 | cor_text[1] = date() + " " + time() //date + time stamp |
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328 | |
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329 | KillWaves/Z cor1,bgd_temp,noadd_bgd,emp_temp,noadd_emp |
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330 | SetDataFolder root: |
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331 | Return(0) |
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332 | End |
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333 | |
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334 | //background only |
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335 | // existence of data checked by dispatching routine |
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336 | // data has already been copied to COR folder |
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337 | Function CorrectMode_2() |
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338 | |
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339 | //create the necessary wave references |
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340 | WAVE sam_data=$"root:SAM:data" |
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341 | WAVE sam_reals=$"root:SAM:realsread" |
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342 | WAVE sam_ints=$"root:SAM:integersread" |
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343 | WAVE/T sam_text=$"root:SAM:textread" |
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344 | WAVE bgd_data=$"root:BGD:data" |
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345 | WAVE bgd_reals=$"root:BGD:realsread" |
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346 | WAVE bgd_ints=$"root:BGD:integersread" |
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347 | WAVE/T bgd_text=$"root:BGD:textread" |
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348 | WAVE cor_data=$"root:COR:data" |
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349 | WAVE/T cor_text=$"root:COR:textread" |
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350 | |
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351 | //get sam and bgd attenuation factors |
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352 | String fileStr="" |
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353 | Variable lambda,attenNo,sam_AttenFactor,bgd_attenFactor |
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354 | Variable tmonsam,fsam,fbgd,xshift,yshift,rsam,csam,rbgd,cbgd,tmonbgd |
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355 | Variable wcen=0.001 |
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356 | fileStr = sam_text[3] |
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357 | lambda = sam_reals[26] |
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358 | attenNo = sam_reals[3] |
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359 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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360 | fileStr = bgd_text[3] |
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361 | lambda = bgd_reals[26] |
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362 | attenNo = bgd_reals[3] |
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363 | bgd_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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364 | |
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365 | //Print "atten = ",sam_attenFactor,bgd_attenFactor |
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366 | |
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367 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
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368 | tmonsam = sam_reals[0] //monitor count in SAM |
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369 | csam = sam_reals[16] //x center |
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370 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
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371 | tmonbgd = bgd_reals[0] //monitor count in BGD |
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372 | cbgd = bgd_reals[16] |
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373 | rbgd = bgd_reals[17] |
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374 | |
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375 | // set up beamcenter shift, relative to SAM |
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376 | xshift = cbgd-csam |
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377 | yshift = rbgd-rsam |
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378 | if(abs(xshift) <= wcen) |
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379 | xshift = 0 |
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380 | Endif |
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381 | if(abs(yshift) <= wcen) |
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382 | yshift = 0 |
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383 | Endif |
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384 | |
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385 | NVAR pixelsX = root:myGlobals:gNPixelsX |
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386 | NVAR pixelsY = root:myGlobals:gNPixelsY |
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387 | //get shifted data arrays, relative to SAM |
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388 | Make/D/O/N=(pixelsX,pixelsY) cor1,bgd_temp,noadd_bgd //temp arrays |
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389 | GetShiftedArray(bgd_data,bgd_temp,noadd_bgd,xshift,yshift) //bgd_temp is the BGD |
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390 | |
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391 | //do the sam-bgd subtraction, deposit result in cor1 |
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392 | fsam = 1 |
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393 | fbgd = tmonsam/tmonbgd //this should be ==1 since normalized files |
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394 | |
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395 | //print "fsam,fbgd = ",fsam,fbgd |
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396 | |
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397 | cor1 = fsam*sam_data/sam_AttenFactor - fbgd*bgd_temp/bgd_AttenFactor |
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398 | cor1 *= noadd_bgd //zeros out regions where arrays do not overlap, one otherwise |
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399 | |
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400 | //we're done, get out w/no error |
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401 | //set the COR_data to the result |
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402 | cor_data = cor1 |
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403 | //update COR header |
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404 | cor_text[1] = date() + " " + time() //date + time stamp |
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405 | |
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406 | KillWaves/Z cor1,bgd_temp,noadd_bgd |
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407 | SetDataFolder root: |
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408 | Return(0) |
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409 | End |
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410 | |
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411 | // empty subtraction only |
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412 | // data does exist, checked by dispatch routine |
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413 | // |
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414 | Function CorrectMode_3() |
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415 | //create the necessary wave references |
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416 | WAVE sam_data=$"root:SAM:data" |
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417 | WAVE sam_reals=$"root:SAM:realsread" |
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418 | WAVE sam_ints=$"root:SAM:integersread" |
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419 | WAVE/T sam_text=$"root:SAM:textread" |
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420 | WAVE emp_data=$"root:EMP:data" |
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421 | WAVE emp_reals=$"root:EMP:realsread" |
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422 | WAVE emp_ints=$"root:EMP:integersread" |
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423 | WAVE/T emp_text=$"root:EMP:textread" |
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424 | WAVE cor_data=$"root:COR:data" |
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425 | WAVE/T cor_text=$"root:COR:textread" |
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426 | |
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427 | //get sam and bgd attenuation factors |
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428 | String fileStr="" |
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429 | Variable lambda,attenNo,sam_AttenFactor,emp_attenFactor |
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430 | Variable tmonsam,fsam,femp,xshift,yshift,rsam,csam,remp,cemp,tmonemp |
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431 | Variable wcen=0.001,tsam,temp |
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432 | fileStr = sam_text[3] |
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433 | lambda = sam_reals[26] |
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434 | attenNo = sam_reals[3] |
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435 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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436 | fileStr = emp_text[3] |
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437 | lambda = emp_reals[26] |
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438 | attenNo = emp_reals[3] |
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439 | emp_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
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440 | |
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441 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
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442 | tmonsam = sam_reals[0] //monitor count in SAM |
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443 | tsam = sam_reals[4] //SAM transmission |
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444 | csam = sam_reals[16] //x center |
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445 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
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446 | tmonemp = emp_reals[0] //monitor count in EMP |
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447 | temp = emp_reals[4] //trans emp |
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448 | cemp = emp_reals[16] //beamcenter of EMP |
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449 | remp = emp_reals[17] |
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450 | |
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451 | if(temp==0) |
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452 | DoAlert 0,"Empty Cell transmission was zero. It has been reset to one for the subtraction" |
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453 | temp=1 |
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454 | Endif |
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455 | |
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456 | //Print "rbgd,cbgd = ",rbgd,cbgd |
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457 | // set up beamcenter shift, relative to SAM |
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458 | xshift = cemp-csam |
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459 | yshift = remp-rsam |
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460 | if(abs(xshift) <= wcen) |
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461 | xshift = 0 |
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462 | Endif |
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463 | if(abs(yshift) <= wcen) |
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464 | yshift = 0 |
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465 | Endif |
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466 | |
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467 | NVAR pixelsX = root:myGlobals:gNPixelsX |
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468 | NVAR pixelsY = root:myGlobals:gNPixelsY |
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469 | //get shifted data arrays, relative to SAM |
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470 | Make/D/O/N=(pixelsX,pixelsY) cor1,emp_temp,noadd_emp //temp arrays |
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471 | GetShiftedArray(emp_data,emp_temp,noadd_emp,xshift,yshift) //emp_temp is the EMP |
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472 | |
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473 | //do the sam-bgd subtraction, deposit result in cor1 |
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474 | fsam = 1 |
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475 | femp = tmonsam/tmonemp //this should be ==1 since normalized files |
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476 | |
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477 | cor1 = fsam*sam_data/sam_AttenFactor - femp*(tsam/temp)*emp_temp/emp_AttenFactor |
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478 | cor1 *= noadd_emp //zeros out regions where arrays do not overlap, one otherwise |
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479 | |
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480 | //we're done, get out w/no error |
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481 | //set the COR data to the result |
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482 | cor_data = cor1 |
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483 | //update COR header |
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484 | cor_text[1] = date() + " " + time() //date + time stamp |
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485 | |
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486 | KillWaves/Z cor1,emp_temp,noadd_emp |
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487 | SetDataFolder root: |
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488 | Return(0) |
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489 | End |
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490 | |
---|
491 | // NO subtraction - simply rescales for attenuators |
---|
492 | // SAM data does exist, checked by dispatch routine |
---|
493 | // |
---|
494 | // !! moves data to COR folder, since the data has been corrected, by rescaling |
---|
495 | // |
---|
496 | Function CorrectMode_4() |
---|
497 | //create the necessary wave references |
---|
498 | WAVE sam_data=$"root:SAM:data" |
---|
499 | WAVE sam_reals=$"root:SAM:realsread" |
---|
500 | WAVE sam_ints=$"root:SAM:integersread" |
---|
501 | WAVE/T sam_text=$"root:SAM:textread" |
---|
502 | |
---|
503 | WAVE cor_data=$"root:COR:data" |
---|
504 | WAVE/T cor_text=$"root:COR:textread" |
---|
505 | |
---|
506 | //get sam and bgd attenuation factors |
---|
507 | String fileStr="" |
---|
508 | Variable lambda,attenNo,sam_AttenFactor |
---|
509 | fileStr = sam_text[3] |
---|
510 | lambda = sam_reals[26] |
---|
511 | attenNo = sam_reals[3] |
---|
512 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
513 | |
---|
514 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
515 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
516 | Make/D/O/N=(pixelsX,pixelsY) cor1 |
---|
517 | |
---|
518 | cor1 = sam_data/sam_AttenFactor //simply rescale the data |
---|
519 | |
---|
520 | //we're done, get out w/no error |
---|
521 | //set the COR data to the result |
---|
522 | cor_data = cor1 |
---|
523 | //update COR header |
---|
524 | cor_text[1] = date() + " " + time() //date + time stamp |
---|
525 | |
---|
526 | KillWaves/Z cor1 |
---|
527 | SetDataFolder root: |
---|
528 | Return(0) |
---|
529 | End |
---|
530 | |
---|
531 | Function CorrectMode_11() |
---|
532 | //create the necessary wave references |
---|
533 | WAVE sam_data=$"root:SAM:data" |
---|
534 | WAVE sam_reals=$"root:SAM:realsread" |
---|
535 | WAVE sam_ints=$"root:SAM:integersread" |
---|
536 | WAVE/T sam_text=$"root:SAM:textread" |
---|
537 | WAVE bgd_data=$"root:BGD:data" |
---|
538 | WAVE bgd_reals=$"root:BGD:realsread" |
---|
539 | WAVE bgd_ints=$"root:BGD:integersread" |
---|
540 | WAVE/T bgd_text=$"root:BGD:textread" |
---|
541 | WAVE emp_data=$"root:EMP:data" |
---|
542 | WAVE emp_reals=$"root:EMP:realsread" |
---|
543 | WAVE emp_ints=$"root:EMP:integersread" |
---|
544 | WAVE/T emp_text=$"root:EMP:textread" |
---|
545 | WAVE drk_data=$"root:DRK:data" |
---|
546 | WAVE drk_reals=$"root:DRK:realsread" |
---|
547 | WAVE drk_ints=$"root:DRK:integersread" |
---|
548 | WAVE/T drk_text=$"root:DRK:textread" |
---|
549 | WAVE cor_data=$"root:COR:data" |
---|
550 | WAVE/T cor_text=$"root:COR:textread" |
---|
551 | |
---|
552 | //get sam and bgd attenuation factors |
---|
553 | String fileStr="" |
---|
554 | Variable lambda,attenNo,sam_AttenFactor,bgd_attenFactor,emp_AttenFactor |
---|
555 | Variable tmonsam,fsam,fbgd,xshift,yshift,rsam,csam,rbgd,cbgd,tmonbgd |
---|
556 | Variable wcen=0.001,tsam,temp,remp,cemp,tmonemp,femp,time_sam,time_drk,savmon_sam |
---|
557 | fileStr = sam_text[3] |
---|
558 | lambda = sam_reals[26] |
---|
559 | attenNo = sam_reals[3] |
---|
560 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
561 | fileStr = bgd_text[3] |
---|
562 | lambda = bgd_reals[26] |
---|
563 | attenNo = bgd_reals[3] |
---|
564 | bgd_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
565 | fileStr = emp_text[3] |
---|
566 | lambda = emp_reals[26] |
---|
567 | attenNo = emp_reals[3] |
---|
568 | emp_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
569 | |
---|
570 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
---|
571 | tmonsam = sam_reals[0] //monitor count in SAM |
---|
572 | tsam = sam_reals[4] //SAM transmission |
---|
573 | csam = sam_reals[16] //x center |
---|
574 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
---|
575 | tmonbgd = bgd_reals[0] //monitor count in BGD |
---|
576 | cbgd = bgd_reals[16] |
---|
577 | rbgd = bgd_reals[17] |
---|
578 | tmonemp = emp_reals[0] //monitor count in EMP |
---|
579 | temp = emp_reals[4] //trans emp |
---|
580 | cemp = emp_reals[16] //beamcenter of EMP |
---|
581 | remp = emp_reals[17] |
---|
582 | savmon_sam=sam_reals[1] //true monitor count in SAM |
---|
583 | time_sam = sam_ints[2] //count time SAM |
---|
584 | time_drk = drk_ints[2] //drk count time |
---|
585 | |
---|
586 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
587 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
588 | //rescale drk to sam cnt time and then multiply by the same monitor scaling as SAM |
---|
589 | Make/D/O/N=(pixelsX,pixelsY) drk_temp |
---|
590 | drk_temp = drk_data*(time_sam/time_drk)*(tmonsam/savmon_sam) |
---|
591 | |
---|
592 | if(temp==0) |
---|
593 | DoAlert 0,"Empty Cell transmission was zero. It has been reset to one for the subtraction" |
---|
594 | temp=1 |
---|
595 | Endif |
---|
596 | |
---|
597 | //get the shifted data arrays, EMP and BGD, each relative to SAM |
---|
598 | Make/D/O/N=(pixelsX,pixelsY) cor1,bgd_temp,noadd_bgd,emp_temp,noadd_emp |
---|
599 | xshift = cbgd-csam |
---|
600 | yshift = rbgd-rsam |
---|
601 | if(abs(xshift) <= wcen) |
---|
602 | xshift = 0 |
---|
603 | Endif |
---|
604 | if(abs(yshift) <= wcen) |
---|
605 | yshift = 0 |
---|
606 | Endif |
---|
607 | GetShiftedArray(bgd_data,bgd_temp,noadd_bgd,xshift,yshift) //bgd_temp |
---|
608 | |
---|
609 | xshift = cemp-csam |
---|
610 | yshift = remp-rsam |
---|
611 | if(abs(xshift) <= wcen) |
---|
612 | xshift = 0 |
---|
613 | Endif |
---|
614 | if(abs(yshift) <= wcen) |
---|
615 | yshift = 0 |
---|
616 | Endif |
---|
617 | GetShiftedArray(emp_data,emp_temp,noadd_emp,xshift,yshift) //emp_temp |
---|
618 | //always ignore the DRK center shift |
---|
619 | |
---|
620 | //do the subtraction |
---|
621 | fsam=1 |
---|
622 | femp = tmonsam/tmonemp //this should be ==1 since normalized files |
---|
623 | fbgd = tmonsam/tmonbgd //this should be ==1 since normalized files |
---|
624 | cor1 = fsam*sam_data/sam_attenFactor |
---|
625 | cor1 -= (tsam/temp)*(femp*emp_temp/emp_attenFactor - fbgd*bgd_temp/bgd_attenFactor) |
---|
626 | cor1 -= (fbgd*bgd_temp/bgd_attenFactor - drk_temp) |
---|
627 | cor1 -= drk_temp/sam_attenFactor |
---|
628 | cor1 *= noadd_bgd*noadd_emp //zero out the array mismatch values |
---|
629 | |
---|
630 | //we're done, get out w/no error |
---|
631 | //set the COR data to the result |
---|
632 | cor_data = cor1 |
---|
633 | //update COR header |
---|
634 | cor_text[1] = date() + " " + time() //date + time stamp |
---|
635 | |
---|
636 | KillWaves/Z cor1,bgd_temp,noadd_bgd,emp_temp,noadd_emp,drk_temp |
---|
637 | SetDataFolder root: |
---|
638 | Return(0) |
---|
639 | End |
---|
640 | |
---|
641 | //bgd and drk subtraction |
---|
642 | // |
---|
643 | Function CorrectMode_12() |
---|
644 | //create the necessary wave references |
---|
645 | WAVE sam_data=$"root:SAM:data" |
---|
646 | WAVE sam_reals=$"root:SAM:realsread" |
---|
647 | WAVE sam_ints=$"root:SAM:integersread" |
---|
648 | WAVE/T sam_text=$"root:SAM:textread" |
---|
649 | WAVE bgd_data=$"root:BGD:data" |
---|
650 | WAVE bgd_reals=$"root:BGD:realsread" |
---|
651 | WAVE bgd_ints=$"root:BGD:integersread" |
---|
652 | WAVE/T bgd_text=$"root:BGD:textread" |
---|
653 | WAVE drk_data=$"root:DRK:data" |
---|
654 | WAVE drk_reals=$"root:DRK:realsread" |
---|
655 | WAVE drk_ints=$"root:DRK:integersread" |
---|
656 | WAVE/T drk_text=$"root:DRK:textread" |
---|
657 | WAVE cor_data=$"root:COR:data" |
---|
658 | WAVE/T cor_text=$"root:COR:textread" |
---|
659 | |
---|
660 | //get sam and bgd attenuation factors |
---|
661 | String fileStr="" |
---|
662 | Variable lambda,attenNo,sam_AttenFactor,bgd_attenFactor |
---|
663 | Variable tmonsam,fsam,fbgd,xshift,yshift,rsam,csam,rbgd,cbgd,tmonbgd |
---|
664 | Variable wcen=0.001,time_drk,time_sam,savmon_sam,tsam |
---|
665 | fileStr = sam_text[3] |
---|
666 | lambda = sam_reals[26] |
---|
667 | attenNo = sam_reals[3] |
---|
668 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
669 | fileStr = bgd_text[3] |
---|
670 | lambda = bgd_reals[26] |
---|
671 | attenNo = bgd_reals[3] |
---|
672 | bgd_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
673 | |
---|
674 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
---|
675 | tmonsam = sam_reals[0] //monitor count in SAM |
---|
676 | tsam = sam_reals[4] //SAM transmission |
---|
677 | csam = sam_reals[16] //x center |
---|
678 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
---|
679 | tmonbgd = bgd_reals[0] //monitor count in BGD |
---|
680 | cbgd = bgd_reals[16] |
---|
681 | rbgd = bgd_reals[17] |
---|
682 | savmon_sam=sam_reals[1] //true monitor count in SAM |
---|
683 | time_sam = sam_ints[2] //count time SAM |
---|
684 | time_drk = drk_ints[2] //drk count time |
---|
685 | |
---|
686 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
687 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
688 | //rescale drk to sam cnt time and then multiply by the same monitor scaling as SAM |
---|
689 | Make/D/O/N=(pixelsX,pixelsY) drk_temp |
---|
690 | drk_temp = drk_data*(time_sam/time_drk)*(tmonsam/savmon_sam) |
---|
691 | |
---|
692 | // set up beamcenter shift, relative to SAM |
---|
693 | xshift = cbgd-csam |
---|
694 | yshift = rbgd-rsam |
---|
695 | if(abs(xshift) <= wcen) |
---|
696 | xshift = 0 |
---|
697 | Endif |
---|
698 | if(abs(yshift) <= wcen) |
---|
699 | yshift = 0 |
---|
700 | Endif |
---|
701 | //get shifted data arrays, relative to SAM |
---|
702 | Make/D/O/N=(pixelsX,pixelsY) cor1,bgd_temp,noadd_bgd //temp arrays |
---|
703 | GetShiftedArray(bgd_data,bgd_temp,noadd_bgd,xshift,yshift) //bgd_temp is the BGD |
---|
704 | //always ignore the DRK center shift |
---|
705 | |
---|
706 | //do the sam-bgd subtraction, deposit result in cor1 |
---|
707 | fsam = 1 |
---|
708 | fbgd = tmonsam/tmonbgd //this should be ==1 since normalized files |
---|
709 | |
---|
710 | cor1 = fsam*sam_data/sam_AttenFactor + fbgd*tsam*bgd_temp/bgd_AttenFactor |
---|
711 | cor1 += -1*(fbgd*bgd_temp/bgd_attenFactor - drk_temp) - drk_temp/sam_attenFactor |
---|
712 | cor1 *= noadd_bgd //zeros out regions where arrays do not overlap, one otherwise |
---|
713 | |
---|
714 | //we're done, get out w/no error |
---|
715 | //set the COR_data to the result |
---|
716 | cor_data = cor1 |
---|
717 | //update COR header |
---|
718 | cor_text[1] = date() + " " + time() //date + time stamp |
---|
719 | |
---|
720 | // KillWaves/Z cor1,bgd_temp,noadd_bgd,drk_temp |
---|
721 | SetDataFolder root: |
---|
722 | Return(0) |
---|
723 | End |
---|
724 | |
---|
725 | //EMP and DRK subtractions |
---|
726 | // all data exists, DRK is on a time basis (noNorm) |
---|
727 | //scale DRK by monitor count scaling factor and the ratio of couting times |
---|
728 | //to place the DRK file on equal footing |
---|
729 | Function CorrectMode_13() |
---|
730 | //create the necessary wave references |
---|
731 | WAVE sam_data=$"root:SAM:data" |
---|
732 | WAVE sam_reals=$"root:SAM:realsread" |
---|
733 | WAVE sam_ints=$"root:SAM:integersread" |
---|
734 | WAVE/T sam_text=$"root:SAM:textread" |
---|
735 | WAVE emp_data=$"root:EMP:data" |
---|
736 | WAVE emp_reals=$"root:EMP:realsread" |
---|
737 | WAVE emp_ints=$"root:EMP:integersread" |
---|
738 | WAVE/T emp_text=$"root:EMP:textread" |
---|
739 | WAVE drk_data=$"root:DRK:data" |
---|
740 | WAVE drk_reals=$"root:DRK:realsread" |
---|
741 | WAVE drk_ints=$"root:DRK:integersread" |
---|
742 | WAVE/T drk_text=$"root:DRK:textread" |
---|
743 | WAVE cor_data=$"root:COR:data" |
---|
744 | WAVE/T cor_text=$"root:COR:textread" |
---|
745 | |
---|
746 | //get sam and bgd attenuation factors (DRK irrelevant) |
---|
747 | String fileStr="" |
---|
748 | Variable lambda,attenNo,sam_AttenFactor,emp_attenFactor |
---|
749 | Variable tmonsam,fsam,femp,xshift,yshift,rsam,csam,remp,cemp,tmonemp |
---|
750 | Variable wcen=0.001,tsam,temp,savmon_sam,time_sam,time_drk |
---|
751 | fileStr = sam_text[3] |
---|
752 | lambda = sam_reals[26] |
---|
753 | attenNo = sam_reals[3] |
---|
754 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
755 | fileStr = emp_text[3] |
---|
756 | lambda = emp_reals[26] |
---|
757 | attenNo = emp_reals[3] |
---|
758 | emp_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
759 | |
---|
760 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
---|
761 | tmonsam = sam_reals[0] //monitor count in SAM |
---|
762 | tsam = sam_reals[4] //SAM transmission |
---|
763 | csam = sam_reals[16] //x center |
---|
764 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
---|
765 | tmonemp = emp_reals[0] //monitor count in EMP |
---|
766 | temp = emp_reals[4] //trans emp |
---|
767 | cemp = emp_reals[16] //beamcenter of EMP |
---|
768 | remp = emp_reals[17] |
---|
769 | savmon_sam=sam_reals[1] //true monitor count in SAM |
---|
770 | time_sam = sam_ints[2] //count time SAM |
---|
771 | time_drk = drk_ints[2] //drk count time |
---|
772 | |
---|
773 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
774 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
775 | //rescale drk to sam cnt time and then multiply by the same monitor scaling as SAM |
---|
776 | Make/D/O/N=(pixelsX,pixelsY) drk_temp |
---|
777 | drk_temp = drk_data*(time_sam/time_drk)*(tmonsam/savmon_sam) |
---|
778 | |
---|
779 | if(temp==0) |
---|
780 | DoAlert 0,"Empty Cell transmission was zero. It has been reset to one for the subtraction" |
---|
781 | temp=1 |
---|
782 | Endif |
---|
783 | |
---|
784 | //Print "rbgd,cbgd = ",rbgd,cbgd |
---|
785 | // set up beamcenter shift, relative to SAM |
---|
786 | xshift = cemp-csam |
---|
787 | yshift = remp-rsam |
---|
788 | if(abs(xshift) <= wcen) |
---|
789 | xshift = 0 |
---|
790 | Endif |
---|
791 | if(abs(yshift) <= wcen) |
---|
792 | yshift = 0 |
---|
793 | Endif |
---|
794 | //get shifted data arrays, relative to SAM |
---|
795 | Make/D/O/N=(pixelsX,pixelsY) cor1,emp_temp,noadd_emp //temp arrays |
---|
796 | GetShiftedArray(emp_data,emp_temp,noadd_emp,xshift,yshift) //emp_temp is the EMP |
---|
797 | //always ignore beamcenter shift for DRK |
---|
798 | |
---|
799 | //do the sam-bgd subtraction, deposit result in cor1 |
---|
800 | fsam = 1 |
---|
801 | femp = tmonsam/tmonemp //this should be ==1 since normalized files |
---|
802 | |
---|
803 | cor1 = fsam*sam_data/sam_AttenFactor - femp*(tsam/temp)*emp_temp/emp_AttenFactor |
---|
804 | cor1 += drk_temp - drk_temp/sam_attenFactor |
---|
805 | cor1 *= noadd_emp //zeros out regions where arrays do not overlap, one otherwise |
---|
806 | |
---|
807 | //we're done, get out w/no error |
---|
808 | //set the COR data to the result |
---|
809 | cor_data = cor1 |
---|
810 | //update COR header |
---|
811 | cor_text[1] = date() + " " + time() //date + time stamp |
---|
812 | |
---|
813 | KillWaves/Z cor1,emp_temp,noadd_emp,drk_temp |
---|
814 | SetDataFolder root: |
---|
815 | Return(0) |
---|
816 | End |
---|
817 | |
---|
818 | // ONLY drk subtraction |
---|
819 | // |
---|
820 | Function CorrectMode_14() |
---|
821 | //create the necessary wave references |
---|
822 | WAVE sam_data=$"root:SAM:data" |
---|
823 | WAVE sam_reals=$"root:SAM:realsread" |
---|
824 | WAVE sam_ints=$"root:SAM:integersread" |
---|
825 | WAVE/T sam_text=$"root:SAM:textread" |
---|
826 | |
---|
827 | WAVE drk_data=$"root:DRK:data" |
---|
828 | WAVE drk_reals=$"root:DRK:realsread" |
---|
829 | WAVE drk_ints=$"root:DRK:integersread" |
---|
830 | WAVE/T drk_text=$"root:DRK:textread" |
---|
831 | WAVE cor_data=$"root:COR:data" |
---|
832 | WAVE/T cor_text=$"root:COR:textread" |
---|
833 | |
---|
834 | //get sam and bgd attenuation factors |
---|
835 | String fileStr="" |
---|
836 | Variable lambda,attenNo,sam_AttenFactor,bgd_attenFactor |
---|
837 | Variable tmonsam,fsam,fbgd,xshift,yshift,rsam,csam,rbgd,cbgd,tmonbgd |
---|
838 | Variable wcen=0.001,time_drk,time_sam,savmon_sam,tsam |
---|
839 | fileStr = sam_text[3] |
---|
840 | lambda = sam_reals[26] |
---|
841 | attenNo = sam_reals[3] |
---|
842 | sam_AttenFactor = AttenuationFactor(fileStr,lambda,AttenNo) |
---|
843 | |
---|
844 | //get relative monitor counts (should all be 10^8, since normalized in add step) |
---|
845 | tmonsam = sam_reals[0] //monitor count in SAM |
---|
846 | tsam = sam_reals[4] //SAM transmission |
---|
847 | csam = sam_reals[16] //x center |
---|
848 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
---|
849 | |
---|
850 | savmon_sam=sam_reals[1] //true monitor count in SAM |
---|
851 | time_sam = sam_ints[2] //count time SAM |
---|
852 | time_drk = drk_ints[2] //drk count time |
---|
853 | |
---|
854 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
855 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
856 | //rescale drk to sam cnt time and then multiply by the same monitor scaling as SAM |
---|
857 | Make/D/O/N=(pixelsX,pixelsY) drk_temp |
---|
858 | drk_temp = drk_data*(time_sam/time_drk)*(tmonsam/savmon_sam) |
---|
859 | |
---|
860 | Make/D/O/N=(pixelsX,pixelsY) cor1 //temp arrays |
---|
861 | //always ignore the DRK center shift |
---|
862 | |
---|
863 | //do the subtraction, deposit result in cor1 |
---|
864 | fsam = 1 |
---|
865 | fbgd = tmonsam/tmonbgd //this should be ==1 since normalized files |
---|
866 | |
---|
867 | //correct sam for attenuators, and do the same to drk, since it was scaled to sam count time |
---|
868 | cor1 = fsam*sam_data/sam_AttenFactor - drk_temp/sam_attenFactor |
---|
869 | |
---|
870 | //we're done, get out w/no error |
---|
871 | //set the COR_data to the result |
---|
872 | cor_data = cor1 |
---|
873 | //update COR header |
---|
874 | cor_text[1] = date() + " " + time() //date + time stamp |
---|
875 | |
---|
876 | // KillWaves/Z cor1,bgd_temp,noadd_bgd,drk_temp |
---|
877 | SetDataFolder root: |
---|
878 | Return(0) |
---|
879 | End |
---|
880 | |
---|
881 | |
---|
882 | //function to return the shifted contents of a data array for subtraction |
---|
883 | //(SLOW) if ShiftSum is called |
---|
884 | //data_in is input |
---|
885 | //data_out is shifted matrix |
---|
886 | //noadd_mat =1 if shift matrix is valid, =0 if no data |
---|
887 | // |
---|
888 | //if no shift is required, data_in is returned and noadd_mat =1 (all valid) |
---|
889 | // |
---|
890 | Function GetShiftedArray(data_in,data_out,noadd_mat,xshift,yshift) |
---|
891 | WAVE data_in,data_out,noadd_mat |
---|
892 | Variable xshift,yshift |
---|
893 | |
---|
894 | Variable ii=0,jj=0 |
---|
895 | noadd_mat = 1 //initialize to 1 |
---|
896 | |
---|
897 | If((xshift != 0) || (yshift != 0)) |
---|
898 | DoAlert 1,"Do you want to ignore the beam center mismatch?" |
---|
899 | if(V_flag==1) //yes -> just go on |
---|
900 | xshift=0 |
---|
901 | yshift=0 |
---|
902 | endif |
---|
903 | endif |
---|
904 | |
---|
905 | If((xshift == 0) && (yshift == 0)) |
---|
906 | data_out=data_in //no change |
---|
907 | noadd_mat = 1 //use all of the data |
---|
908 | return(0) |
---|
909 | endif |
---|
910 | |
---|
911 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
912 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
913 | |
---|
914 | Print "beamcenter shift x,y = ",xshift,yshift |
---|
915 | Make/O/N=1 noadd |
---|
916 | for(ii=0;ii<pixelsX;ii+=1) |
---|
917 | for(jj=0;jj<pixelsY;jj+=1) |
---|
918 | //get the contribution of the shifted data |
---|
919 | data_out[ii][jj] = ShiftSum(data_in,ii,jj,xshift,yshift,noadd) |
---|
920 | if(noadd[0]) |
---|
921 | noadd_mat[ii][jj] = 0 //shift is off the detector |
---|
922 | endif |
---|
923 | endfor |
---|
924 | endfor |
---|
925 | return(0) |
---|
926 | End |
---|
927 | |
---|
928 | //utility function that checks if data exists in a data folder |
---|
929 | //checks only for the existence of DATA - no other waves |
---|
930 | // |
---|
931 | Function WorkDataExists(type) |
---|
932 | String type |
---|
933 | |
---|
934 | String destPath="" |
---|
935 | destPath = "root:"+Type + ":data" |
---|
936 | if(WaveExists($destpath) == 0) |
---|
937 | Print "There is no work file in "+type |
---|
938 | Return(1) //error condition |
---|
939 | else |
---|
940 | //check for log-scaling of the data and adjust if necessary |
---|
941 | ConvertFolderToLinearScale(type) |
---|
942 | return(0) |
---|
943 | Endif |
---|
944 | End |
---|
945 | |
---|
946 | ////////////////// |
---|
947 | // bunch of utility junk to catch |
---|
948 | // sample transmission = 1 |
---|
949 | // and handle (too many) options |
---|
950 | // |
---|
951 | Function GetNewTrans(oldTrans,type) |
---|
952 | Variable oldTrans |
---|
953 | String type |
---|
954 | |
---|
955 | Variable newTrans,newCode |
---|
956 | if (oldTrans!=1) |
---|
957 | return(oldTrans) //get out now if trans != 1, don't change anything |
---|
958 | endif |
---|
959 | //get input from the user |
---|
960 | NewDataFolder/O root:myGlobals:tmp_trans |
---|
961 | Variable/G root:myGlobals:tmp_trans:inputTrans=0.92 |
---|
962 | Variable/G root:myGlobals:tmp_trans:returnCode=0 |
---|
963 | DoTransInput(type) |
---|
964 | NVAR inputTrans=root:myGlobals:tmp_trans:inputTrans |
---|
965 | NVAR code=root:myGlobals:tmp_trans:returnCode |
---|
966 | newTrans=inputTrans //keep a copy before deleting everything |
---|
967 | newCode=code |
---|
968 | if(newCode==4) |
---|
969 | Abort "Aborting correction. Use the Transmission Panel to calculate transmissions" |
---|
970 | Endif |
---|
971 | // printf "You entered %g and the code is %g\r",newTrans,newCode |
---|
972 | // KillDataFolder root:tmp_trans |
---|
973 | |
---|
974 | if(newCode==1) |
---|
975 | Variable/G root:myGlobals:gDoTransCheck=0 //turn off checking |
---|
976 | endif |
---|
977 | |
---|
978 | if(newcode==2) //user changed trans value |
---|
979 | return(newTrans) |
---|
980 | else |
---|
981 | return(oldTrans) //All other cases, user did not change value |
---|
982 | endif |
---|
983 | end |
---|
984 | |
---|
985 | Function IgnoreNowButton(ctrlName) : ButtonControl |
---|
986 | String ctrlName |
---|
987 | |
---|
988 | // Print "ignore now" |
---|
989 | NVAR val=root:myGlobals:tmp_trans:returnCode |
---|
990 | val=0 //code for ignore once |
---|
991 | |
---|
992 | DoWindow/K tmp_GetInputPanel // Kill self |
---|
993 | End |
---|
994 | |
---|
995 | Function DoTransInput(str) |
---|
996 | String str |
---|
997 | |
---|
998 | NewPanel /W=(150,50,361,294) |
---|
999 | DoWindow/C tmp_GetInputPanel // Set to an unlikely name |
---|
1000 | DrawText 15,23,"The "+str+" Transmission = 1" |
---|
1001 | DrawText 15,43,"What do you want to do?" |
---|
1002 | DrawText 15,125,"(Reset this in Preferences)" |
---|
1003 | SetVariable setvar0,pos={20,170},size={160,17},limits={0,1,0.01} |
---|
1004 | SetVariable setvar0,value= root:myGlobals:tmp_trans:inputTrans,title="New Transmission" |
---|
1005 | |
---|
1006 | Button button0,pos={36,56},size={120,20},proc=IgnoreNowButton,title="Ignore This Time" |
---|
1007 | Button button1,pos={36,86},size={120,20},proc=IgnoreAlwaysButtonProc,title="Ignore Always" |
---|
1008 | Button button2,pos={36,143},size={120,20},proc=UseNewValueButtonProc,title="Use New Value" |
---|
1009 | Button button3,pos={36,213},size={120,20},proc=AbortCorrectionButtonProc,title="Abort Correction" |
---|
1010 | PauseForUser tmp_GetInputPanel |
---|
1011 | End |
---|
1012 | |
---|
1013 | Function IgnoreAlwaysButtonProc(ctrlName) : ButtonControl |
---|
1014 | String ctrlName |
---|
1015 | |
---|
1016 | // Print "ignore always" |
---|
1017 | NVAR val=root:myGlobals:tmp_trans:returnCode |
---|
1018 | val=1 //code for ignore always |
---|
1019 | DoWindow/K tmp_GetInputPanel // Kill self |
---|
1020 | End |
---|
1021 | |
---|
1022 | Function UseNewValueButtonProc(ctrlName) : ButtonControl |
---|
1023 | String ctrlName |
---|
1024 | |
---|
1025 | // Print "use new Value" |
---|
1026 | NVAR val=root:myGlobals:tmp_trans:returnCode |
---|
1027 | val=2 //code for use new Value |
---|
1028 | DoWindow/K tmp_GetInputPanel // Kill self |
---|
1029 | End |
---|
1030 | |
---|
1031 | Function AbortCorrectionButtonProc(ctrlName) : ButtonControl |
---|
1032 | String ctrlName |
---|
1033 | |
---|
1034 | // Print "Abort" |
---|
1035 | NVAR val=root:myGlobals:tmp_trans:returnCode |
---|
1036 | val=4 //code for abort |
---|
1037 | DoWindow/K tmp_GetInputPanel // Kill self |
---|
1038 | End |
---|
1039 | |
---|
1040 | ////////////////////////// |
---|
1041 | //**********unused*********** |
---|
1042 | //mode describes the type of subtraction that is to be done |
---|
1043 | //1 = both emp and bgd subtraction |
---|
1044 | //2 = only bgd subtraction |
---|
1045 | //3 = only emp subtraction |
---|
1046 | //4 = no subtraction (handled by ExecuteProtocol(), but implemented here as well) |
---|
1047 | // |
---|
1048 | // + 10 indicates that WORK.DRK is to be used |
---|
1049 | //**********unused*********** |
---|
1050 | //**worse yet, only partially converted to use DRK files!*********** |
---|
1051 | // |
---|
1052 | Function OLD_Correct(mode) |
---|
1053 | Variable mode |
---|
1054 | |
---|
1055 | //Print "mode = ",mode |
---|
1056 | if(mode==4) |
---|
1057 | Print "no subtraction required - Correct(mode) should not have been called" |
---|
1058 | return(1) //error - correct should not have been called |
---|
1059 | Endif |
---|
1060 | |
---|
1061 | // always check for existence of data in SAM |
---|
1062 | // if the desired workfile doesn't exist, let the user know, and abort |
---|
1063 | String destPath |
---|
1064 | String type = "SAM" |
---|
1065 | //check for SAM |
---|
1066 | destPath = "root:"+Type + ":data" |
---|
1067 | if(WaveExists($destpath) == 0) |
---|
1068 | Print "There is no work file in "+type+"--Aborting" |
---|
1069 | Return(1) //error condition |
---|
1070 | else |
---|
1071 | //check for log-scaling of the "SAM" data and adjust if necessary |
---|
1072 | ConvertFolderToLinearScale(type) |
---|
1073 | Wave sam_data = $"root:SAM:data" |
---|
1074 | Endif |
---|
1075 | |
---|
1076 | //check for BGD if mode = 1 or 2 or 11 or 12 |
---|
1077 | if( (mode ==1) || (mode==2) || (mode==11) || (mode==12) ) |
---|
1078 | type = "BGD" |
---|
1079 | destPath = "root:"+Type + ":data" |
---|
1080 | if(WaveExists($destpath) == 0) |
---|
1081 | Print "There is no work file in "+type+"--Aborting" |
---|
1082 | Return(1) //error condition |
---|
1083 | else |
---|
1084 | //check for log-scaling of the "BGD" data and adjust if necessary |
---|
1085 | ConvertFolderToLinearScale(type) |
---|
1086 | Wave bgd_data = $"root:BGD:data" |
---|
1087 | Endif |
---|
1088 | Endif |
---|
1089 | |
---|
1090 | // check for EMP data if type 3 or 1 or 13 or 11 |
---|
1091 | if( (mode==1) || (mode==3) || (mode==11) || (mode==13) ) |
---|
1092 | type = "EMP" |
---|
1093 | destPath = "root:"+Type + ":data" |
---|
1094 | if(WaveExists($destpath) == 0) |
---|
1095 | Print "There is no work file in "+type+"--Aborting" |
---|
1096 | Return(1) //error condition |
---|
1097 | else |
---|
1098 | //check for log-scaling of the "EMP" data and adjust if necessary |
---|
1099 | ConvertFolderToLinearScale(type) |
---|
1100 | Wave emp_data = $"root:EMP:data" |
---|
1101 | Endif |
---|
1102 | Endif |
---|
1103 | |
---|
1104 | // check for DRK data if type 11,12,13, or 14 |
---|
1105 | if( (mode==11) || (mode==12) || (mode==13) || (mode==14) ) |
---|
1106 | type = "DRK" |
---|
1107 | destPath = "root:"+Type + ":data" |
---|
1108 | if(WaveExists($destpath) == 0) |
---|
1109 | Print "There is no work file in "+type+"--Aborting" |
---|
1110 | Return(1) //error condition |
---|
1111 | else |
---|
1112 | //check for log-scaling of the "EMP" data and adjust if necessary |
---|
1113 | ConvertFolderToLinearScale(type) |
---|
1114 | Wave drk_data = $"root:DRK:data" |
---|
1115 | Endif |
---|
1116 | Endif |
---|
1117 | |
---|
1118 | //necessary files exist, proceed |
---|
1119 | |
---|
1120 | //make needed wave references to other folders |
---|
1121 | //NOTE that these references MAY NOT EXIST, depending on the mode |
---|
1122 | WAVE sam_reals = $"root:SAM:realsread" |
---|
1123 | WAVE sam_ints = $"root:SAM:integersread" |
---|
1124 | WAVE/T sam_text = $"root:SAM:textread" |
---|
1125 | WAVE/Z emp_reals = $"root:EMP:realsread" |
---|
1126 | WAVE/Z emp_ints = $"root:EMP:integersread" |
---|
1127 | WAVE/T/Z emp_text = $"root:EMP:textread" |
---|
1128 | WAVE/Z bgd_reals = $"root:BGD:realsread" |
---|
1129 | WAVE/Z bgd_ints = $"root:BGD:integersread" |
---|
1130 | WAVE/T/Z bgd_text = $"root:BGD:textread" |
---|
1131 | |
---|
1132 | //find the attenuation of the sample (if any) |
---|
1133 | Variable SamAttenFactor,lambda,attenNo,err=0 |
---|
1134 | String samfileStr="" |
---|
1135 | samfileStr = sam_text[3] |
---|
1136 | lambda = sam_reals[26] |
---|
1137 | attenNo = sam_reals[3] |
---|
1138 | SamAttenFactor = AttenuationFactor(samFileStr,lambda,AttenNo) |
---|
1139 | //if sample trans is zero, do only SAM-BGD subtraction (notify the user) |
---|
1140 | Variable sam_trans = sam_reals[4] |
---|
1141 | |
---|
1142 | //copy SAM information to COR, wiping out the old contents of the COR folder first |
---|
1143 | err = CopyWorkContents("SAM","COR") |
---|
1144 | if(err==1) |
---|
1145 | Abort "No data in SAM, abort from Correct()" |
---|
1146 | endif |
---|
1147 | |
---|
1148 | //now switch to COR folder |
---|
1149 | DestPath="root:COR" |
---|
1150 | //make appropriate wave references |
---|
1151 | WAVE data=$(destPath + ":data") // these wave references point to the SAM data in COR |
---|
1152 | WAVE/T textread=$(destPath + ":textread") //that are to be directly operated on |
---|
1153 | WAVE integersread=$(destPath + ":integersread") |
---|
1154 | WAVE realsread=$(destPath + ":realsRead") |
---|
1155 | |
---|
1156 | NVAR pixelsX = root:myGlobals:gNPixelsX |
---|
1157 | NVAR pixelsY = root:myGlobals:gNPixelsY |
---|
1158 | |
---|
1159 | //Print "done copying data, starting the correct calculations" |
---|
1160 | |
---|
1161 | // Start the actual "correct" step here |
---|
1162 | Variable wcen=0.001,numsam,tmonsam,tsam,rsam,csam,fsam |
---|
1163 | Variable tmonbgd,fbgd,xshift,yshift,rbgd,cbgd,sh_sum,ii,jj,trans,tmonemp,temp,femp |
---|
1164 | Variable cemp,remp |
---|
1165 | //make temporary waves to hold the intermediate results and the shifted arrays |
---|
1166 | Duplicate/O data cor1,cor2 |
---|
1167 | cor1 = 0 //initialize to zero |
---|
1168 | cor2 = 0 |
---|
1169 | |
---|
1170 | //make needed wave references to other folders |
---|
1171 | Wave sam_reals = $"root:SAM:realsread" |
---|
1172 | Wave bgd_reals = $"root:BGD:realsread" |
---|
1173 | Wave emp_reals = $"root:EMP:realsread" |
---|
1174 | |
---|
1175 | //get counts, trans, etc. from file headers |
---|
1176 | numsam = sam_ints[3] //number of runs in SAM file |
---|
1177 | tmonsam = sam_reals[0] //monitor count in SAM |
---|
1178 | tsam = sam_reals[4] //SAM transmission |
---|
1179 | csam = sam_reals[16] //x center |
---|
1180 | rsam = sam_reals[17] //beam (x,y) define center of corrected field |
---|
1181 | //Print "rsam,csam = ",rsam,csam |
---|
1182 | |
---|
1183 | // |
---|
1184 | //do sam-bgd subtraction if mode (1) or (2) |
---|
1185 | //else (mode 3), set cor1 = sam_data |
---|
1186 | if( (mode==1) || (mode==2) ) |
---|
1187 | fsam = 1 |
---|
1188 | tmonbgd = bgd_reals[0] //monitor count in BGD |
---|
1189 | fbgd = tmonsam/tmonbgd //this should be ==1 since normalized files |
---|
1190 | |
---|
1191 | //set up center shift, relative to SAM |
---|
1192 | cbgd = bgd_reals[16] |
---|
1193 | rbgd = bgd_reals[17] |
---|
1194 | //Print "rbgd,cbgd = ",rbgd,cbgd |
---|
1195 | xshift = cbgd-csam |
---|
1196 | yshift = rbgd-rsam |
---|
1197 | if(abs(xshift) <= wcen) |
---|
1198 | xshift = 0 |
---|
1199 | Endif |
---|
1200 | if(abs(yshift) <= wcen) |
---|
1201 | yshift = 0 |
---|
1202 | Endif |
---|
1203 | |
---|
1204 | If((xshift != 0) || (yshift != 0)) |
---|
1205 | DoAlert 1,"Do you want to ignore the beam center mismatch?" |
---|
1206 | if(V_flag==1) //yes -> just go on |
---|
1207 | xshift=0 |
---|
1208 | yshift=0 |
---|
1209 | endif |
---|
1210 | endif |
---|
1211 | //do the sam-bgd subtraction, deposit result in cor1[][] |
---|
1212 | If((xshift == 0) && (yshift == 0)) |
---|
1213 | //great, no shift required |
---|
1214 | cor1 = fsam*sam_data - fbgd*bgd_data*SamAttenFactor |
---|
1215 | else |
---|
1216 | //shift required, very time-consuming |
---|
1217 | Print "sam-bgd shift x,y = ",xshift,yshift |
---|
1218 | Make/O/N=1 noadd //needed to get noadd condition back from ShiftSum() |
---|
1219 | ii=0 |
---|
1220 | do |
---|
1221 | jj=0 |
---|
1222 | do |
---|
1223 | //get the contribution of shifted data |
---|
1224 | sh_sum = ShiftSum(bgd_data,ii,jj,xshift,yshift,noadd) |
---|
1225 | if(noadd[0]) |
---|
1226 | cor1[ii][jj]=0 |
---|
1227 | else |
---|
1228 | //add the sam_data + shifted sum |
---|
1229 | cor1[ii][jj] = fsam*sam_data[ii][jj] - fbgd*sh_sum*SamAttenFactor |
---|
1230 | Endif |
---|
1231 | jj+=1 |
---|
1232 | while(jj<pixelsY) |
---|
1233 | ii+=1 |
---|
1234 | while(ii<pixelsX) |
---|
1235 | Endif |
---|
1236 | else //switch on mode |
---|
1237 | cor1 = sam_data //setup for just EMP subtraction |
---|
1238 | Endif |
---|
1239 | |
---|
1240 | //Print "sam-bgd done" |
---|
1241 | |
---|
1242 | if(mode == 2) //just a BGD subtraction |
---|
1243 | //we're done, get out w/no error |
---|
1244 | //set the COR data to the result |
---|
1245 | data = cor1 |
---|
1246 | //update COR header |
---|
1247 | textread[1] = date() + " " + time() //date + time stamp |
---|
1248 | SetDataFolder root: |
---|
1249 | KillWaves/Z cor1,cor2 |
---|
1250 | Return(0) |
---|
1251 | Endif |
---|
1252 | |
---|
1253 | //if mode ==1 (ONLY choice left) do the empty-background subtraction |
---|
1254 | //else mode = 3, set cor2 to emp_data |
---|
1255 | if(mode==1) //full subtraction |
---|
1256 | trans = emp_reals[4] //EMP transmission |
---|
1257 | if(trans == 0) |
---|
1258 | trans = 1 |
---|
1259 | DoAlert 0,"Empty cell transmission was zero. It has been reset to one for the calculation" |
---|
1260 | endif |
---|
1261 | tmonemp = emp_reals[0] |
---|
1262 | femp = tmonsam/tmonemp |
---|
1263 | temp = trans |
---|
1264 | |
---|
1265 | //set up center shift, relative to EMP |
---|
1266 | cemp = emp_reals[16] |
---|
1267 | remp = emp_reals[17] |
---|
1268 | //Print "remp,cemp ",remp,cemp |
---|
1269 | xshift = cbgd - cemp |
---|
1270 | yshift = rbgd - remp |
---|
1271 | if(abs(xshift) <= wcen ) |
---|
1272 | xshift = 0 |
---|
1273 | endif |
---|
1274 | if(abs(yshift) <= wcen) |
---|
1275 | yshift = 0 |
---|
1276 | endif |
---|
1277 | |
---|
1278 | If((xshift != 0) || (yshift != 0)) |
---|
1279 | DoAlert 1,"Do you want to ignore the beam center mismatch?" |
---|
1280 | if(V_flag==1) |
---|
1281 | xshift=0 |
---|
1282 | yshift=0 |
---|
1283 | endif |
---|
1284 | endif |
---|
1285 | //do the emp-bgd subtraction, deposit result in cor2[][] |
---|
1286 | If((xshift == 0) && (yshift == 0)) |
---|
1287 | //great, no shift required, DON'T scale this by the attenuation gfactor |
---|
1288 | cor2 = femp*emp_data - fbgd*bgd_data |
---|
1289 | else |
---|
1290 | //shift required, very time-consuming |
---|
1291 | Print "emp-bgd shift x,y = ",xshift,yshift |
---|
1292 | Make/O/N=1 noadd //needed to get noadd condition back from ShiftSum() |
---|
1293 | ii=0 |
---|
1294 | do |
---|
1295 | jj=0 |
---|
1296 | do |
---|
1297 | //get the contribution of shifted data |
---|
1298 | sh_sum = ShiftSum(bgd_data,ii,jj,xshift,yshift,noadd) |
---|
1299 | if(noadd[0]) |
---|
1300 | cor2[ii][jj]=0 |
---|
1301 | else |
---|
1302 | //add the sam_data + shifted sum |
---|
1303 | cor2[ii][jj] = femp*emp_data[ii][jj] - fbgd*sh_sum |
---|
1304 | Endif |
---|
1305 | jj+=1 |
---|
1306 | while(jj<pixelsY) |
---|
1307 | ii+=1 |
---|
1308 | while(ii<pixelsX) |
---|
1309 | Endif |
---|
1310 | else //switch on mode==1 for full subtraction |
---|
1311 | cor2 = emp_data |
---|
1312 | //be sure to set the empty center location... for the shift |
---|
1313 | trans = emp_reals[4] //EMP transmission |
---|
1314 | if(trans == 0) |
---|
1315 | trans = 1 |
---|
1316 | DoAlert 0,"Empty cell transmission was zero. It has been reset to one for the calculation" |
---|
1317 | endif |
---|
1318 | tmonemp = emp_reals[0] |
---|
1319 | femp = tmonsam/tmonemp |
---|
1320 | temp = trans |
---|
1321 | |
---|
1322 | //set up center shift, relative to EMP |
---|
1323 | cemp = emp_reals[16] |
---|
1324 | remp = emp_reals[17] |
---|
1325 | Endif |
---|
1326 | |
---|
1327 | //Print "emp-bgd done" |
---|
1328 | |
---|
1329 | //mode 2 exited, either 1 or 3 apply from here, and are setup properly. |
---|
1330 | |
---|
1331 | //set up for final step, data(COR) = cor1 - Tsam/Temp*cor2 |
---|
1332 | //set up shift, relative to SAM |
---|
1333 | xshift = cemp - csam |
---|
1334 | yshift = remp - rsam |
---|
1335 | if(abs(xshift) <= wcen ) |
---|
1336 | xshift = 0 |
---|
1337 | endif |
---|
1338 | if(abs(yshift) <= wcen) |
---|
1339 | yshift = 0 |
---|
1340 | endif |
---|
1341 | |
---|
1342 | If((xshift != 0) || (yshift != 0)) |
---|
1343 | DoAlert 1,"Do you want to ignore the beam center mismatch?" |
---|
1344 | if(V_flag==1) |
---|
1345 | xshift=0 |
---|
1346 | yshift=0 |
---|
1347 | endif |
---|
1348 | endif |
---|
1349 | //do the cor1-a*cor2 subtraction, deposit result in data[][] (in the COR folder) |
---|
1350 | If((xshift == 0) && (yshift == 0)) |
---|
1351 | //great, no shift required |
---|
1352 | data = cor1 - (tsam/temp)*cor2*SamAttenFactor |
---|
1353 | else |
---|
1354 | //shift required, very time-consuming |
---|
1355 | Print "sam-emp shift x,y = ",xshift,yshift |
---|
1356 | Make/O/N=1 noadd //needed to get noadd condition back from ShiftSum() |
---|
1357 | ii=0 |
---|
1358 | do |
---|
1359 | jj=0 |
---|
1360 | do |
---|
1361 | //get the contribution of shifted data |
---|
1362 | sh_sum = ShiftSum(cor2,ii,jj,xshift,yshift,noadd) |
---|
1363 | if(noadd[0]) |
---|
1364 | data[ii][jj]=0 |
---|
1365 | else |
---|
1366 | //add the sam_data + shifted sum |
---|
1367 | data[ii][jj] = cor1[ii][jj] - (tsam/temp)*sh_sum*SamAttenFactor |
---|
1368 | Endif |
---|
1369 | jj+=1 |
---|
1370 | while(jj<pixelsY) |
---|
1371 | ii+=1 |
---|
1372 | while(ii<pixelsX) |
---|
1373 | Endif |
---|
1374 | |
---|
1375 | //Print "all done" |
---|
1376 | |
---|
1377 | //update COR header |
---|
1378 | textread[1] = date() + " " + time() //date + time stamp |
---|
1379 | |
---|
1380 | //clean up |
---|
1381 | SetDataFolder root:COR |
---|
1382 | SetDataFolder root: |
---|
1383 | KillWaves/Z cor1,cor2,noadd |
---|
1384 | |
---|
1385 | Return(0) //all is ok, if you made it to this point |
---|
1386 | End |
---|