1 | ###################################################################### |
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2 | # |
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3 | # This is a partial copy from LeBailFitScript.py |
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4 | # |
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5 | # Python Script as Step 1 of Le Bail Fitting to |
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6 | # 1. Load file |
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7 | # 2. Create LeBailFitInput |
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8 | # 3. Fit Peaks |
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9 | # |
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10 | # Step 1: Load data, model (HKL list) and starting instrument parameters values, |
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11 | # and do an initial LeBailFit/calculation to see how much the starting |
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12 | # values are off; |
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13 | |
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14 | #|------------------------------------------------------------------------------------------- |
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15 | #|Step 2.1: Fit single peaks for TOF_h, Alpha, Beta, and Sigma; |
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16 | #| |
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17 | #|Step 2.2: Plot parameters (TOF_H, Alpha, Beta and Sigma) against d-spacing; |
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18 | #| |
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19 | #|Step 2.3: Remove the peaks with bad fit; |
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20 | #| |
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21 | #|Step 2.4: Refine instrument geometry parameters; |
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22 | #| |
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23 | #| It is possible to loop back to Step 2 to include more peaks with single peaks |
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24 | #|------------------------------------------------------------------------------------------- |
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25 | # |
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26 | # Step 5: Do Le Bail Fit from previous result to see whether the peak parameters are |
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27 | # close enough for Le Bail Fit |
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28 | # |
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29 | # !Step 6: Fit Alpha, Beta and apply the change to |
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30 | # |
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31 | # !Step 7: Save the result files to HDD for Step 6, LeBailFit in random walk; |
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32 | # |
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33 | # Step 8: Save the result files to HDD for Step 6, LeBailFit in random walk; |
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34 | # |
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35 | # Step 7: Not in this script; |
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36 | # |
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37 | # Step 8: Process Monte Carlo results from Step 6 |
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38 | # |
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39 | # |
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40 | ###################################################################### |
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41 | from Calibration_ImportInformation import * |
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42 | |
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43 | #-------------- Definition of Global Variables --------------------- |
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44 | bankid = 0 |
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45 | |
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46 | datafilename = "" |
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47 | hklfilename = "" |
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48 | irffilename = "" |
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49 | |
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50 | # montecarlofilename = "" |
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51 | # expirffilename = "" |
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52 | |
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53 | datawsname = "" |
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54 | instrparamwsname = "" |
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55 | braggpeakparamwsname = "" |
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56 | |
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57 | # outdataws1name = "" |
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58 | |
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59 | minpeakheight = 0.001 |
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60 | |
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61 | # Range for Le Bail Fit of all peaks |
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62 | startx = -1 |
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63 | endx = -1 |
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64 | # Range for fitting single peaks for step 1~3 |
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65 | tofmin_singlepeaks = -1 |
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66 | tofmax_singlepeaks = -1 |
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67 | |
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68 | backgroundtype = "Polynomial" |
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69 | backgroundorder = 6 |
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70 | bkgdtablewsname = "" |
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71 | bkgdwsname = "" |
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72 | bkgdfilename = "" |
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73 | usrbkgdpoints = '' |
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74 | |
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75 | latticesize = 4.1568899999999998 |
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76 | #-------------------------------------------------------------------- |
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77 | |
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78 | |
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79 | def setupGlobals(infofilename): |
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80 | """ Set up globals values |
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81 | """ |
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82 | global datafilename, hklfilename, irffilename |
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83 | global datawsname, instrparamwsname, braggpeakparamwsname |
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84 | global bkgdtablewsname, bkgdwsname, bkgdfilename, backgroundorder |
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85 | global tofmin_singlepeaks, tofmax_singlepeaks, startx, endx |
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86 | global bankid, latticesize |
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87 | global usrbkgdpoints |
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88 | |
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89 | bankid, calibDict = importCalibrationInformation(infofilename) |
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90 | bankid = int(bankid) |
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91 | |
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92 | datafilename = calibDict["DataFileDir"] + calibDict[bankid]["DataFileName"] |
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93 | hklfilename = calibDict["HKLFileDir"] + calibDict[bankid]["HKLFileName"] |
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94 | irffilename = calibDict["IrfFileDir"] + calibDict[bankid]["IrfFileName"] |
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95 | |
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96 | startx = float(calibDict[bankid]["LeBailFitMinTOF"]) |
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97 | endx = float(calibDict[bankid]["LeBailFitMaxTOF"]) |
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98 | |
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99 | # Name of workspaces |
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100 | datawsname = calibDict[bankid]["DataWorkspace"] |
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101 | instrparamwsname = "Bank%sInstrumentParameterTable" % (bankid) |
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102 | braggpeakparamwsname = 'BraggPeakParameterTable' |
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103 | |
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104 | # Background related |
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105 | usrbkgdpoints = calibDict[bankid]["UserSpecifiedBkgdPts"] |
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106 | bkgdwsname = datawsname+"_Background" |
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107 | backgroundtype = calibDict["BackgroundType"] |
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108 | backgroundorder = int(calibDict["BackgroundOrder"]) |
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109 | bkgdfilename = calibDict["WorkingDir"] + datawsname + "_Parameters.bak'" |
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110 | bkgdwsname = datawsname + "_Background" |
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111 | bkgdtablewsname = datawsname + "_Background_Parameters" |
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112 | |
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113 | # Other constants |
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114 | latticesize = calibDict[bankid]["LatticeSize"] |
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115 | |
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116 | return |
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117 | |
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118 | #------------------------------------------------------------------------------ |
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119 | # TableWorkspace Processing |
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120 | #------------------------------------------------------------------------------ |
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121 | def parseRefineGeometryMCResultWorkspace(tablews): |
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122 | """ Parse the refinement result workspac |
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123 | """ |
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124 | numrows = tablews.rowCount() |
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125 | numcols = tablews.columnCount() |
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126 | colnames = tablews.getColumnNames() |
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127 | |
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128 | parameterdict = {} |
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129 | |
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130 | for irow in xrange(numrows): |
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131 | ppdict = {} |
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132 | for icol in xrange(numcols): |
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133 | colname = colnames[icol] |
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134 | value = tablews.cell(irow, icol) |
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135 | ppdict[colname] = value |
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136 | # ENDFOR Column |
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137 | chi2 = ppdict["Chi2"] |
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138 | |
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139 | parameterdict[chi2] = ppdict |
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140 | # ENDFOR |
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141 | |
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142 | return parameterdict |
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143 | |
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144 | |
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145 | #def updateInstrumentParameterValue(tablews, paramdict): |
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146 | # """ Update the value to an instrument parameter table |
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147 | # """ |
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148 | # paramnames = paramdict.keys() |
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149 | # for parname in paramnames: |
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150 | # parvalue = paramdict[parname] |
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151 | # # print "%s = %f" % (parname, parvalue) |
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152 | # if parname.count("Chi2") == 0: |
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153 | # # Only update parameters nothing to do with chi2 |
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154 | # UpdatePeakParameterTableValue(InputWorkspace=tablews, |
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155 | # Column='Value', |
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156 | # ParameterNames=[parname], |
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157 | # NewFloatValue=parvalue) |
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158 | # |
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159 | # return |
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160 | |
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161 | |
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162 | def doStep3(): |
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163 | """ Step 3: to check whether the refinement result is good for low-d region |
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164 | """ |
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165 | global startx, endx |
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166 | global datawsname, instrparamwsname, braggpeakparamwsname |
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167 | global bkgdtablewsname, bkgdwsname, backgroundtype, backgroundorder |
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168 | global bankid |
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169 | global usrbkgdpoints |
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170 | |
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171 | # 1. Process background |
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172 | bkgdwsname = datawsname+"_Background" |
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173 | ProcessBackground(InputWorkspace=datawsname, |
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174 | OutputWorkspace=bkgdwsname, |
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175 | Options='SelectBackgroundPoints', |
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176 | LowerBound=startx, |
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177 | UpperBound=endx, |
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178 | BackgroundType=backgroundtype, |
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179 | BackgroundPoints=usrbkgdpoints, |
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180 | NoiseTolerance='0.10000000000000001') |
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181 | |
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182 | functionstr = "name=%s,n=%d" % (backgroundtype, backgroundorder) |
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183 | for iborder in xrange(backgroundorder+1): |
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184 | functionstr = "%s,A%d=%.5f" % (functionstr, iborder, 0.0) |
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185 | print "Background function: %s" % (functionstr) |
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186 | |
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187 | Fit(Function='name=Polynomial,n=6,A0=0.657699,A1=3.68433e-05,A2=-1.29638e-08,A3=1.16778e-12,A4=-4.71439e-17,A5=8.8499e-22,A6=-6.26573e-27', |
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188 | InputWorkspace=bkgdwsname, |
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189 | MaxIterations='1000', |
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190 | Minimizer='Levenberg-MarquardtMD', |
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191 | CreateOutput='1', |
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192 | Output=bkgdwsname, |
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193 | StartX=startx, |
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194 | EndX=endx) |
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195 | |
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196 | # 2. Do calculation |
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197 | usemcresult = True |
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198 | try: |
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199 | bestmdws = mtd["BestMCResult1"] |
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200 | except KeyError: |
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201 | usemcresult = False |
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202 | |
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203 | outwsname = datawsname + "_Calculated" |
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204 | if usemcresult is True: |
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205 | # Use MC N results |
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206 | paramdict = parseRefineGeometryMCResultWorkspace(bestmtdws) |
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207 | |
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208 | raise NotImplementedError("Case 1") |
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209 | |
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210 | index = 0 |
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211 | maxoutput = 1 |
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212 | for chi2 in sorted(paramdict.keys()): |
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213 | # 1. Update parameter values |
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214 | updateInstrumentParameterValue(mtd["Bank%sInstrumentParameterTable1"%(bankid)], paramdict[chi2]) |
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215 | |
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216 | print "Fit range: %f , %f" % (startx, endx) |
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217 | |
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218 | LeBailFit(InputWorkspace=datawsname, |
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219 | OutputWorkspace=outwsname, |
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220 | InputParameterWorkspace='Bank%dInstrumentParameterTable1'%(bankid), |
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221 | OutputParameterWorkspace='Bank%dInstrumentParameterTable1_%d'%(bankid, index), |
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222 | InputHKLWorkspace='BraggPeakParameterTable1', |
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223 | OutputPeaksWorkspace='BraggPeakParameterTable2_%d'%(index), |
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224 | Function='Calculation', |
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225 | FitRegion = '%f, %f' % (startx, endx), |
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226 | BackgroundType='Polynomial', |
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227 | BackgroundParametersWorkspace=bkgdtablewsname, |
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228 | UseInputPeakHeights='0', |
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229 | PeakRadius='8', |
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230 | Minimizer='Levenberg-Marquardt') |
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231 | |
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232 | print "Pattern %s: Instrumental Geometry Chi^2 = %.5f" % ('CalculatedPattern%d'%(index), chi2) |
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233 | index += 1 |
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234 | if index >= maxoutput: |
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235 | break |
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236 | # ENDFOR |
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237 | else: |
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238 | # Use Version 2 result |
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239 | |
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240 | # data from manually refinement |
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241 | # for pair in [("Dtt1", 22529.600), ("Dtt1t", 22747.400), ("Zerot", 15.792320), ("Width", 1.1072)]: |
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242 | |
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243 | # data from Jason's |
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244 | # for pair in [("Dtt1", 22584.512), ("Dtt1t", 22604.852), ("Zerot", 11.317320), ("Width", 1.0521)]: |
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245 | |
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246 | index = 0 |
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247 | print "Fit range: %f , %f" % (startx, endx) |
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248 | LeBailFit(InputWorkspace=datawsname, |
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249 | OutputWorkspace=outwsname, |
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250 | InputParameterWorkspace='Bank1InstrumentParametersTable', |
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251 | OutputParameterWorkspace='Bank%dInstrumentParameterTable1_%d'%(bankid, index), |
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252 | InputHKLWorkspace='BraggPeakParameterTable1', |
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253 | OutputPeaksWorkspace='BraggPeakParameterTable2_%d'%(index), |
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254 | Function='Calculation', |
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255 | FitRegion = '%f, %f' % (startx, endx), |
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256 | BackgroundType='Polynomial', |
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257 | BackgroundParametersWorkspace=bkgdtablewsname, |
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258 | UseInputPeakHeights='0', |
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259 | PeakRadius='8', |
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260 | Minimizer='Levenberg-Marquardt') |
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261 | |
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262 | return |
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263 | |
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264 | def main(argv): |
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265 | """ Main |
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266 | """ |
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267 | setupGlobals("Calibration_Information.config") |
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268 | |
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269 | print "Le Bail Fit Calibration Instrument... Step 3" |
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270 | doStep3() |
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271 | |
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272 | return |
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273 | |
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274 | |
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275 | if __name__=="__main__": |
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276 | main(["LeBailFitScript"]) |
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