1 | # Set of routines to normalise WISH data |
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2 | from mantidsimple import * |
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3 | import matplotlib.pyplot as p |
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4 | import numpy as n |
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5 | wish_dir="" |
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6 | |
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7 | # Get the valid wavelength range, i.e. excluding regions where choppers cut |
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8 | def WISH_getlambdarange(): |
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9 | return 0.7,10.35 |
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10 | |
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11 | def WISH_setuser(usern): |
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12 | global username |
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13 | username=usern |
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14 | |
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15 | def WISH_setdatadir(directory="/archive/ndxwish/Instrument/data/cycle_09_5/"): |
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16 | global wish_datadir |
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17 | wish_datadir=directory |
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18 | |
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19 | def WISH_setuserdir(directory): |
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20 | global wish_userdir |
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21 | wish_userdir=directory |
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22 | |
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23 | def WISH_datadir(): |
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24 | return wish_datadir |
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25 | |
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26 | def WISH_userdir(cycle='cycle_10_1'): |
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27 | return wish_userdir |
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28 | |
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29 | def WISH_calibration(cycle="11_4"): |
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30 | #return "/home/mp43/Calibration/Cycle_"+cycle+"/" |
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31 | return "/home/hqs74821/work/mantid_stuff/DockWidget/" |
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32 | |
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33 | def WISH_startup(usern,cycle='10_1'): |
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34 | global userdatadir |
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35 | global userdataprocessed |
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36 | global mtdplt |
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37 | import sys |
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38 | sys.path.append('/home/hqs74821/work/mantid_stuff/DockWidget/') |
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39 | import Mantid_plotting as mtdplt |
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40 | userdatadir="/archive/ndxwish/Instrument/data/cycle_"+cycle+'/' |
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41 | WISH_setdatadir(userdatadir) |
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42 | print "Raw Data in : ", userdatadir |
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43 | userdataprocessed="/home/hqs74821/work/mantid_stuff/DockWidget/ProcessedData/" |
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44 | WISH_setuserdir(directory=userdataprocessed) |
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45 | print "Processed Data in : ",userdataprocessed |
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46 | return |
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47 | |
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48 | |
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49 | #Returns the calibration filename |
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50 | def WISH_cal(panel): |
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51 | return WISH_calibration()+"WISH_cycle_10_3_noends_9to9.cal" |
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52 | |
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53 | # Returns the grouping filename |
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54 | def WISH_group(): |
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55 | return WISH_calibration()+"WISH_cycle_10_3_noends_9to9.cal" |
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56 | |
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57 | def WISH_getvana(panel,SE="candlestick",cycle="09_4"): |
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58 | if (SE=="candlestick"): |
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59 | if (cycle=="09_2"): |
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60 | return WISH_calibration()+"vana318-"+str(panel)+"foc-rmbins-smooth50.nx5" |
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61 | if (cycle=="09_3"): |
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62 | return WISH_calibration(cycle)+"vana935-"+str(panel)+"foc-SS.nx5" |
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63 | if (cycle=="09_4"): |
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64 | return WISH_calibration(cycle)+"vana3123-"+str(panel)+"foc-SS.nx5" |
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65 | if (cycle=="09_5"): |
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66 | return WISH_calibration(cycle)+"vana3123-"+str(panel)+"foc-SS.nx5" |
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67 | if (cycle=="11_4"): |
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68 | return WISH_calibration(cycle)+"vana19612-"+str(panel)+"foc-SF-SS.nxs" |
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69 | if (SE=="WISHcryo"): |
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70 | if (cycle=="09_2"): |
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71 | return WISH_calibration()+"vana318-"+str(panel)+"foc-rmbins-smooth50.nx5" |
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72 | if (cycle=="09_3"): |
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73 | return WISH_calibration(cycle)+"vana935-"+str(panel)+"foc-SS.nx5" |
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74 | if (cycle=="09_4"): |
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75 | return WISH_calibration(cycle)+"vana3123-"+str(panel)+"foc-SS.nx5" |
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76 | if (cycle=="11_1"): |
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77 | return WISH_calibration(cycle)+"vana17718-"+str(panel)+"foc-SS.nxs" |
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78 | if (cycle=="11_2"): |
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79 | return WISH_calibration(cycle)+"vana16812-"+str(panel)+"foc-SS.nx5" |
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80 | if (cycle=="11_3"): |
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81 | return WISH_calibration(cycle)+"vana18590-"+str(panel)+"foc-SS-new.nxs" |
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82 | |
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83 | |
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84 | def split_string(t): |
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85 | indxp=0 |
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86 | for i in range(0,len(t)): |
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87 | if (t[i]=="+"): |
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88 | indxp=i |
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89 | if (indxp!=0): |
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90 | return int(t[0:indxp]),int(t[indxp+1:len(t)]) |
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91 | |
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92 | def WISH_getemptyinstrument(panel,cycle="09_4"): |
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93 | if (cycle=="09_4"): |
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94 | return WISH_calibration(cycle)+"emptyinst3120-"+str(panel)+"foc.nx5" |
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95 | |
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96 | def WISH_getempty(panel,SE="WISHcryo",cycle="09_4"): |
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97 | if (SE=="WISHcryo"): |
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98 | if (cycle=="09_2"): |
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99 | return WISH_calibration(cycle)+"emptycryo322-"+str(panel)+"-smooth50.nx5" |
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100 | if (cycle=="09_3"): |
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101 | return WISH_calibration(cycle)+"emptycryo1725-"+str(panel)+"foc.nx5" |
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102 | if (cycle=="09_4"): |
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103 | return WISH_calibration(cycle)+"emptycryo3307-"+str(panel)+"foc.nx5" |
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104 | if (cycle=="09_5"): |
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105 | return WISH_calibration(cycle)+"emptycryo16759-"+str(panel)+"foc.nx5" |
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106 | if (cycle=="11_1"): |
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107 | return WISH_calibration(cycle)+"emptycryo17712-"+str(panel)+"foc-SS.nxs" |
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108 | if (cycle=="11_2"): |
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109 | return WISH_calibration(cycle)+"emptycryo16759-"+str(panel)+"foc-SS.nx5" |
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110 | if (cycle=="11_3"): |
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111 | return WISH_calibration(cycle)+"emptycryo17712-"+str(panel)+"foc-SS-new.nxs" |
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112 | if (cycle=="11_4"): |
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113 | return WISH_calibration(cycle)+"empty_mag20620-"+str(panel)+"foc-HR-SF.nxs" |
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114 | if (SE=="candlestick"): |
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115 | if (cycle=="09_4"): |
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116 | return WISH_calibration(cycle)+"emptyinst3120-"+str(panel)+"foc.nxs" |
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117 | if (cycle=="09_3"): |
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118 | return WISH_calibration(cycle)+"emptyinst1726-"+str(panel)+"foc-monitor.nxs" |
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119 | if (cycle=="11_4"): |
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120 | return WISH_calibration(cycle)+"emptyinst19618-"+str(panel)+"foc-SF-S.nxs" |
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121 | |
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122 | def WISH_getfilename(run_number,ext): |
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123 | if (ext[0]!='s'): |
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124 | data_dir=WISH_datadir() |
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125 | else: |
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126 | #data_dir="/datad/ndxwish/" |
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127 | data_dir=WISH_datadir() |
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128 | digit=len(str(run_number)) |
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129 | filename=data_dir+"WISH" |
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130 | for i in range(0,8-digit): |
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131 | filename=filename+"0" |
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132 | filename+=str(run_number)+"."+ext |
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133 | return filename |
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134 | |
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135 | def WISH_returnpanel(panel): |
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136 | if (panel==1): |
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137 | min=6 |
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138 | max=19461 |
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139 | elif (panel==2): |
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140 | min=19462 |
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141 | max=38917 |
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142 | elif( panel==3): |
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143 | min=38918 |
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144 | max=58373 |
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145 | elif (panel==4): |
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146 | min=58374 |
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147 | max=77829 |
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148 | elif (panel==5): |
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149 | min=77830 |
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150 | max=97285 |
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151 | elif (panel==6): |
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152 | min=97286 |
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153 | max=116741 |
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154 | elif (panel==7): |
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155 | min=116742 |
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156 | max=136197 |
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157 | elif (panel==8): |
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158 | min=136198 |
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159 | max=155653 |
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160 | elif (panel==9): |
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161 | min=155654 |
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162 | max=175109 |
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163 | elif (panel==0): |
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164 | min=6 |
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165 | max=175109 |
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166 | return min,max |
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167 | |
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168 | # Reads a wish data file return a workspace with a short name |
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169 | def WISH_read(number,panel,ext): |
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170 | if type(number) is int: |
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171 | filename=WISH_getfilename(number,ext) |
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172 | if (ext[0:9]=="nxs_event"): |
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173 | filename=WISH_getfilename(number,"nxs") |
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174 | print "will be reading filename..."+filename |
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175 | min,max=WISH_returnpanel(panel) |
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176 | if (panel!=0): |
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177 | output="w"+str(number)+"-"+str(panel) |
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178 | else: |
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179 | output="w"+str(number) |
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180 | if (ext=="raw"): |
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181 | LoadRaw(Filename=filename,OutputWorkspace=output,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0") |
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182 | MaskBins(output,output,XMin=99900,XMax=106000) |
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183 | print "standard raw file loaded" |
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184 | if (ext[0]=="s"): |
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185 | LoadRaw(Filename=filename,OutputWorkspace=output,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0") |
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186 | MaskBins(output,output,XMin=99900,XMax=106000) |
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187 | print "sav file loaded" |
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188 | if (ext=="nxs_event"): |
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189 | LoadEventNexus(Filename=filename,OutputWorkspace=output,LoadMonitors='1') |
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190 | RenameWorkspace(output+"_monitors","w"+str(number)+"_monitors") |
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191 | Rebin(InputWorkspace=output,OutputWorkspace=output,Params='6000,-0.00063,110000') |
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192 | ConvertToMatrixWorkspace(output,output) |
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193 | min,max=WISH_returnpanel(panel) |
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194 | CropWorkspace(InputWorkspace=output,OutputWorkspace=output,StartWorkspaceIndex=min-6,EndWorkspaceIndex=max-6) |
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195 | MaskBins(output,output,XMin=99900,XMax=106000) |
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196 | print "full nexus eventfile loaded" |
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197 | if (ext[0:10]=="nxs_event_"): |
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198 | label,tmin,tmax=split_string_event(ext) |
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199 | output=output+"_"+label |
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200 | if (tmax=="end"): |
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201 | LoadEventNexus(Filename=filename,OutputWorkspace=output,FilterByTimeStart=tmin,LoadMonitors='1',MonitorsAsEvents='1',FilterMonByTimeStart=tmin) |
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202 | else: |
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203 | LoadEventNexus(Filename=filename,OutputWorkspace=output,FilterByTimeStart=tmin,FilterByTimeStop=tmax,LoadMonitors='1',MonitorsAsEvents='1',FilterMonByTimeStart=tmin,FilterMonByTimeStop=tmax) |
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204 | RenameWorkspace(output+"_monitors","w"+str(number)+"_monitors") |
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205 | print "renaming monitors done!" |
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206 | Rebin(InputWorkspace=output,OutputWorkspace=output,Params='6000,-0.00063,110000') |
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207 | ConvertToMatrixWorkspace(output,output) |
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208 | min,max=WISH_returnpanel(panel) |
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209 | CropWorkspace(InputWorkspace=output,OutputWorkspace=output,StartWorkspaceIndex=min-6,EndWorkspaceIndex=max-6) |
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210 | MaskBins(output,output,XMin=99900,XMax=106000) |
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211 | print "nexus event file chopped" |
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212 | if (ext=="nxs"): |
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213 | LoadNexus(Filename=filename,OutputWorkspace=output) |
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214 | print "standard histo nxs file loaded" |
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215 | else: |
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216 | n1,n2=split_string(number) |
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217 | output="w"+str(n1)+"_"+str(n2)+"-"+str(panel) |
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218 | filename=WISH_getfilename(n1,ext) |
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219 | print "reading filename..."+filename |
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220 | min,max=WISH_returnpanel(panel) |
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221 | output1="w"+str(n1)+"-"+str(panel) |
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222 | LoadRaw(Filename=filename,OutputWorkspace=output1,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0") |
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223 | filename=WISH_getfilename(n2,ext) |
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224 | print "reading filename..."+filename |
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225 | min,max=WISH_returnpanel(panel) |
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226 | output2="w"+str(n2)+"-"+str(panel) |
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227 | LoadRaw(Filename=filename,OutputWorkspace=output2,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0") |
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228 | MergeRuns(output1+","+output2,output) |
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229 | mantid.deleteWorkspace(output1) |
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230 | mantid.deleteWorkspace(output2) |
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231 | ConvertUnits(output,output,"Wavelength") |
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232 | lmin,lmax=WISH_getlambdarange() |
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233 | CropWorkspace(output,output,XMin=lmin,XMax=lmax) |
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234 | monitor=WISH_process_incidentmon(number,ext,spline_terms=70,debug=False) |
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235 | print "first norm to be done" |
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236 | NormaliseToMonitor(InputWorkspace=output,OutputWorkspace=output+"norm1",MonitorWorkspace=monitor) |
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237 | print "second norm to be done" |
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238 | NormaliseToMonitor(InputWorkspace=output+"norm1",OutputWorkspace=output+"norm2",MonitorWorkspace=monitor,IntegrationRangeMin=0.7,IntegrationRangeMax=10.35) |
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239 | DeleteWorkspace(output) |
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240 | DeleteWorkspace(output+"norm1") |
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241 | RenameWorkspace(output+"norm2",output) |
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242 | ConvertUnits(output,output,"TOF") |
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243 | ReplaceSpecialValues(output,output,NaNValue=0.0,NaNError=0.0,InfinityValue=0.0,InfinityError=0.0) |
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244 | return output |
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245 | |
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246 | #Focus dataset for a given panel and return the workspace |
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247 | def WISH_focus_onepanel(work,focus,panel): |
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248 | AlignDetectors(work,work,WISH_cal(panel)) |
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249 | DiffractionFocussing(work,focus,WISH_group()) |
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250 | if (panel==5): |
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251 | CropWorkspace(focus,focus,XMin=0.3) |
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252 | mantid.deleteWorkspace(work) |
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253 | return focus |
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254 | |
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255 | def WISH_split(focus): |
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256 | for i in range(0,10): |
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257 | out=focus[0:len(focus)-3]+"-"+str(i+1)+"foc" |
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258 | ExtractSingleSpectrum(focus,out,i) |
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259 | mantid.deleteWorkspace(focus) |
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260 | return |
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261 | |
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262 | def WISH_focus(work,panel): |
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263 | focus=work+"foc" |
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264 | if (panel!=0): |
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265 | WISH_focus_onepanel(work,focus,panel) |
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266 | else: |
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267 | WISH_focus_onepanel(work,focus,panel) |
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268 | WISH_split(focus) |
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269 | |
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270 | def WISH_process(number,panel,ext,SEsample="WISHcryo",emptySEcycle="09_4",SEvana="candlestick",cyclevana="09_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0): |
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271 | w=WISH_read(number,panel,ext) |
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272 | print "file read and normalized" |
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273 | if (absorb): |
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274 | ConvertUnits(w,w,"Wavelength") |
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275 | CylinderAbsorption(InputWorkspace=w,OutputWorkspace="T", |
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276 | CylinderSampleHeight=h,CylinderSampleRadius=r,AttenuationXSection=Xa, |
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277 | ScatteringXSection=Xs,SampleNumberDensity=nd, |
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278 | NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="25",ExpMethod="Normal") |
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279 | Divide(w,"T",w) |
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280 | mantid.deleteWorkspace("T") |
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281 | ConvertUnits(w,w,"TOF") |
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282 | wfoc=WISH_focus(w,panel) |
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283 | print "focussing done!" |
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284 | if type(number) is int: |
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285 | wfocname="w"+str(number)+"-"+str(panel)+"foc" |
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286 | if (len(ext)>9): |
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287 | label,tmin,tmax=split_string_event(ext) |
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288 | wfocname="w"+str(number)+"-"+str(panel)+"_"+label+"foc" |
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289 | else: |
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290 | n1,n2=split_string(number) |
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291 | wfocname="w"+str(n1)+"_"+str(n2)+"-"+str(panel)+"foc" |
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292 | if (panel==1): |
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293 | CropWorkspace(wfocname,wfocname,XMin=0.80,XMax=53.3) |
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294 | elif(panel==2): |
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295 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1) |
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296 | elif(panel==3): |
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297 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77) |
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298 | elif(panel==4): |
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299 | CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86) |
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300 | elif(panel==5): |
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301 | CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99) |
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302 | elif(panel==6): |
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303 | CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99) |
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304 | elif(panel==7): |
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305 | CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86) |
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306 | elif(panel==8): |
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307 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77) |
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308 | elif(panel==9): |
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309 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1) |
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310 | |
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311 | if (panel==0): |
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312 | for i in range(1,10): |
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313 | wfocname="w"+str(number)+"-"+str(i)+"foc" |
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314 | CropWorkspace(wfocname,wfocname,XMin=0.80,XMax=53.3) |
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315 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1) |
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316 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77) |
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317 | CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86) |
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318 | CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99) |
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319 | CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99) |
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320 | CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86) |
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321 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77) |
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322 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1) |
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323 | #print "will try to load an empty with the name:" |
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324 | print WISH_getempty(panel,SEsample,emptySEcycle) |
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325 | if (panel==0): |
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326 | for i in range(1,10): |
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327 | wfocname="w"+str(number)+"-"+str(i)+"foc" |
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328 | LoadNexusProcessed(Filename=WISH_getempty(i,SEsample,emptySEcycle),OutputWorkspace="empty") |
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329 | RebinToWorkspace("empty",wfocname,"empty") |
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330 | Minus(wfocname,"empty",wfocname) |
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331 | mantid.deleteWorkspace("empty") |
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332 | print "will try to load a vanadium with the name:"+WISH_getvana(i,SEvana,cyclevana) |
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333 | LoadNexusProcessed(Filename=WISH_getvana(i,SEvana,cyclevana),OutputWorkspace="vana") |
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334 | RebinToWorkspace("vana",wfocname,"vana") |
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335 | Divide(wfocname,"vana",wfocname) |
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336 | mantid.deleteWorkspace("vana") |
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337 | ConvertUnits(wfocname,wfocname,"TOF") |
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338 | ReplaceSpecialValues(wfocname,wfocname,NaNValue=0.0,NaNError=0.0,InfinityValue=0.0,InfinityError=0.0) |
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339 | SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(i)+ext+".gss",Append=False,Bank=1) |
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340 | SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(i)+ext+".dat") |
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341 | SaveNexusProcessed(wfocname,WISH_userdir()+str(number)+"-"+str(i)+ext+".nxs") |
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342 | else: |
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343 | LoadNexusProcessed(Filename=WISH_getempty(panel,SEsample,emptySEcycle),OutputWorkspace="empty") |
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344 | RebinToWorkspace("empty",wfocname,"empty") |
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345 | Minus(wfocname,"empty",wfocname) |
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346 | mantid.deleteWorkspace("empty") |
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347 | print "will try to load a vanadium with the name:"+WISH_getvana(panel,SEvana,cyclevana) |
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348 | LoadNexusProcessed(Filename=WISH_getvana(panel,SEvana,cyclevana),OutputWorkspace="vana") |
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349 | RebinToWorkspace("vana",wfocname,"vana") |
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350 | Divide(wfocname,"vana",wfocname) |
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351 | mantid.deleteWorkspace("vana") |
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352 | ConvertUnits(wfocname,wfocname,"TOF") |
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353 | ReplaceSpecialValues(wfocname,wfocname,NaNValue=0.0,NaNError=0.0,InfinityValue=0.0,InfinityError=0.0) |
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354 | SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(panel)+ext+".gss",Append=False,Bank=1) |
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355 | SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(panel)+ext+".dat") |
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356 | SaveNexusProcessed(wfocname,WISH_userdir()+str(number)+"-"+str(panel)+ext+".nxs") |
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357 | return wfocname |
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358 | #Create a corrected vanadium (normalise,corrected for attenuation and empty, strip peaks) and |
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359 | # save a a nexus processed file. |
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360 | # It looks like smoothing of 100 works quite well |
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361 | def WISH_createvan(van,empty,panel,smoothing,vh,vr,cycle_van="09_3",cycle_empty="09_3"): |
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362 | WISH_setdatadir("/archive/ndxwish/Instrument/data/cycle_"+cycle_van+"/") |
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363 | wvan=WISH_read(van,panel,"nxs_event") |
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364 | WISH_setdatadir("/archive/ndxwish/Instrument/data/cycle_"+cycle_empty+"/") |
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365 | wempty=WISH_read(empty,panel,"nxs_event") |
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366 | Minus(wvan,wempty,wvan) |
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367 | print "read van and empty" |
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368 | mantid.deleteWorkspace(wempty) |
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369 | ConvertUnits(wvan,wvan,"Wavelength") |
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370 | CylinderAbsorption(InputWorkspace=wvan,OutputWorkspace="T", |
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371 | CylinderSampleHeight=str(vh),CylinderSampleRadius=str(vr),AttenuationXSection="4.8756", |
---|
372 | ScatteringXSection="5.16",SampleNumberDensity="0.07118", |
---|
373 | NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="25",ExpMethod="Normal") |
---|
374 | Divide(wvan,"T",wvan) |
---|
375 | mantid.deleteWorkspace("T") |
---|
376 | ConvertUnits(wvan,wvan,"TOF") |
---|
377 | vanfoc=WISH_focus(wvan,panel) |
---|
378 | mantid.deleteWorkspace(wvan) |
---|
379 | #StripPeaks(vanfoc,vanfoc) |
---|
380 | #SmoothData(vanfoc,vanfoc,str(smoothing)) |
---|
381 | return |
---|
382 | |
---|
383 | def WISH_createempty(empty,panel): |
---|
384 | wempty=WISH_read(empty,panel,"raw") |
---|
385 | emptyfoc=WISH_focus(wempty,panel) |
---|
386 | return emptyfoc |
---|
387 | |
---|
388 | def WISH_monitors(rb,ext): |
---|
389 | data_dir=WISH_dir() |
---|
390 | file=WISH_getfilename(rb,ext) |
---|
391 | wout="w"+str(rb) |
---|
392 | print "reading File..."+file |
---|
393 | LoadRaw(Filename=file,OutputWorkspace=wout,SpectrumMin=str(1),SpectrumMax=str(5),LoadLogFiles="0") |
---|
394 | NormaliseByCurrent(wout,wout) |
---|
395 | ConvertToDistribution(wout) |
---|
396 | return wout |
---|
397 | |
---|
398 | def WISH_PH_TOF(runnumber,tubemin): |
---|
399 | min=6+(tubenumber-1)*128 |
---|
400 | max=min+128 |
---|
401 | file=WISH_getfilename(runnumber,tubemin) |
---|
402 | output="Run"+str(runnumber)+"tube"+str(tubenumber) |
---|
403 | w=WISH_read(number,panel,ext) |
---|
404 | print "file read and normalized" |
---|
405 | if (absorb): |
---|
406 | ConvertUnits(w,w,"Wavelength") |
---|
407 | CylinderAbsorption(InputWorkspace=w,OutputWorkspace="T", |
---|
408 | CylinderSampleHeight=h,CylinderSampleRadius=r,AttenuationXSection=Xa, |
---|
409 | ScatteringXSection=Xs,SampleNumberDensity=nd, |
---|
410 | NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="25",ExpMethod="Normal") |
---|
411 | Divide(w,"T",w) |
---|
412 | mantid.deleteWorkspace("T") |
---|
413 | ConvertUnits(w,w,"TOF") |
---|
414 | wfoc=WISH_focus(w,panel) |
---|
415 | print "focussing done!" |
---|
416 | if type(number) is int: |
---|
417 | wfocname="w"+str(number)+"-"+str(panel)+"foc" |
---|
418 | if (len(ext)>9): |
---|
419 | label,tmin,tmax=split_string_event(ext) |
---|
420 | wfocname="w"+str(number)+"-"+str(panel)+"_"+label+"foc" |
---|
421 | else: |
---|
422 | n1,n2=split_string(number) |
---|
423 | wfocname="w"+str(n1)+"_"+str(n2)+"-"+str(panel)+"foc" |
---|
424 | if (panel==1): |
---|
425 | CropWorkspace(wfocname,wfocname,XMin=0.80,XMax=53.3) |
---|
426 | elif(panel==2): |
---|
427 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1) |
---|
428 | elif(panel==3): |
---|
429 | CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77) |
---|
430 | elif(panel==4): |
---|
431 | CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86) |
---|
432 | elif(panel==5): |
---|
433 | CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99) |
---|
434 | #print "will try to load an empty with the name:" |
---|
435 | print WISH_getempty(panel,SEsample,emptySEcycle) |
---|
436 | if (panel==0): |
---|
437 | for i in range(1,6): |
---|
438 | LoadNexusProcessed(Filename=WISH_getempty(i,SEsample,emptySEcycle),OutputWorkspace="empty") |
---|
439 | RebinToWorkspace("empty",wfocname,"empty") |
---|
440 | Minus(wfocname,"empty",wfocname) |
---|
441 | mantid.deleteWorkspace("empty") |
---|
442 | print "will try to load a vanadium with the name:"+WISH_getvana(i,SEvana,cyclevana) |
---|
443 | LoadNexusProcessed(Filename=WISH_getvana(i,SEvana,cyclevana),OutputWorkspace="vana") |
---|
444 | RebinToWorkspace("vana",wfocname,"vana") |
---|
445 | Divide(wfocname,"vana",wfocname) |
---|
446 | mantid.deleteWorkspace("vana") |
---|
447 | ConvertUnits(wfocname,wfocname,"TOF") |
---|
448 | # SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(i)+ext+".gss",Append=False,Bank=1) |
---|
449 | # SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(i)+ext+".dat") |
---|
450 | else: |
---|
451 | LoadNexusProcessed(Filename=WISH_getempty(panel,SEsample,emptySEcycle),OutputWorkspace="empty") |
---|
452 | RebinToWorkspace("empty",wfocname,"empty") |
---|
453 | Minus(wfocname,"empty",wfocname) |
---|
454 | mantid.deleteWorkspace("empty") |
---|
455 | print "will try to load a vanadium with the name:"+WISH_getvana(panel,SEvana,cyclevana) |
---|
456 | LoadNexusProcessed(Filename=WISH_getvana(panel,SEvana,cyclevana),OutputWorkspace="vana") |
---|
457 | RebinToWorkspace("vana",wfocname,"vana") |
---|
458 | Divide(wfocname,"vana",wfocname) |
---|
459 | mantid.deleteWorkspace("vana") |
---|
460 | ConvertUnits(wfocname,wfocname,"TOF") |
---|
461 | # SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(panel)+ext+".gss",Append=False,Bank=1) |
---|
462 | # SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(panel)+ext+".dat") |
---|
463 | return wfocname |
---|
464 | LoadRaw(Filename=file,OutputWorkspace=output,spectrummin=str(min),spectrummax=str(max),LoadLogFiles="0") |
---|
465 | Integration(output,output+"int") |
---|
466 | g=plotTimeBin(output+"int",0) |
---|
467 | |
---|
468 | # Smoothing the incident beam monitor using a spline function. Regions around Bragg edges are masked, before fitting with a spline function. |
---|
469 | # Returns a smooth monitor spectrum |
---|
470 | |
---|
471 | |
---|
472 | def WISH_process_incidentmon(number,ext,spline_terms=20,debug=False): |
---|
473 | if type(number) is int: |
---|
474 | fname=WISH_getfilename(number,ext) |
---|
475 | works="monitor"+str(number) |
---|
476 | if (ext=="raw"): |
---|
477 | works="monitor"+str(number) |
---|
478 | LoadRaw(Filename=fname,OutputWorkspace=works,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0") |
---|
479 | if (ext[0]=="s"): |
---|
480 | works="monitor"+str(number) |
---|
481 | LoadRaw(Filename=fname,OutputWorkspace=works,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0") |
---|
482 | if (ext=="nxs"): |
---|
483 | works="monitor"+str(number) |
---|
484 | LoadNexus(Filename=fname,OutputWorkspace=works,SpectrumMin=4,SpectrumMax=4) |
---|
485 | if (ext[0:9]=="nxs_event"): |
---|
486 | temp="w"+str(number)+"_monitors" |
---|
487 | works="w"+str(number)+"_monitor4" |
---|
488 | Rebin(temp,temp,Params='6000,-0.00063,110000',PreserveEvents=False) |
---|
489 | ExtractSingleSpectrum(temp,works,3) |
---|
490 | else: |
---|
491 | n1,n2=split_string(number) |
---|
492 | works="monitor"+str(n1)+"_"+str(n2) |
---|
493 | fname=WISH_getfilename(n1,ext) |
---|
494 | works1="monitor"+str(n1) |
---|
495 | LoadRaw(Filename=fname,OutputWorkspace=works1,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0") |
---|
496 | fname=WISH_getfilename(n2,ext) |
---|
497 | works2="monitor"+str(n2) |
---|
498 | LoadRaw(Filename=fname,OutputWorkspace=works2,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0") |
---|
499 | MergeRuns(works1+","+works2,works) |
---|
500 | mantid.deleteWorkspace(works1) |
---|
501 | mantid.deleteWorkspace(works2) |
---|
502 | ConvertUnits(works,works,"Wavelength") |
---|
503 | lmin,lmax=WISH_getlambdarange() |
---|
504 | CropWorkspace(works,works,XMin=lmin,XMax=lmax) |
---|
505 | ex_regions=n.zeros((2,4)) |
---|
506 | ex_regions[:,0]=[4.57,4.76] |
---|
507 | ex_regions[:,1]=[3.87,4.12] |
---|
508 | ex_regions[:,2]=[2.75,2.91] |
---|
509 | ex_regions[:,3]=[2.24,2.50] |
---|
510 | ConvertToDistribution(works) |
---|
511 | if (debug): |
---|
512 | x,y,z=mtdplt.getnarray(works,0) |
---|
513 | p.plot(x,y) |
---|
514 | for reg in range(0,4): |
---|
515 | MaskBins(works,works,XMin=ex_regions[0,reg],XMax=ex_regions[1,reg]) |
---|
516 | if (debug): |
---|
517 | x,y,z=mtdplt.getnarray(works,LoadRaw0) |
---|
518 | p.plot(x,y) |
---|
519 | SplineBackground(works,works,0,spline_terms) |
---|
520 | if (debug): |
---|
521 | x,y,z=mtdplt.getnarray(works,0) |
---|
522 | p.plot(x,y) |
---|
523 | p.show() |
---|
524 | SmoothData(works,works,40) |
---|
525 | ConvertFromDistribution(works) |
---|
526 | return works |
---|
527 | |
---|
528 | #removes the peaks in a vanadium run, then performs a spline and a smooth |
---|
529 | def Removepeaks_spline_smooth_empty(works,panel,debug=False): |
---|
530 | if (panel==1): |
---|
531 | splineterms=0 |
---|
532 | smoothterms=30 |
---|
533 | if (panel==2): |
---|
534 | splineterms=0 |
---|
535 | smoothterms=10 |
---|
536 | if (panel==3): |
---|
537 | splineterms=0 |
---|
538 | smoothterms=15 |
---|
539 | if (panel==4): |
---|
540 | splineterms=0 |
---|
541 | smoothterms=15 |
---|
542 | if (panel==5): |
---|
543 | splineterms=0 |
---|
544 | smoothterms=10 |
---|
545 | if (debug): |
---|
546 | x,y,z=getnarray(works,0) |
---|
547 | p.plot(x,y) |
---|
548 | if (splineterms!=0): |
---|
549 | SplineBackground(works,works,0,splineterms) |
---|
550 | if (debug): |
---|
551 | x,y,z=getnarray(works,0) |
---|
552 | p.plot(x,y) |
---|
553 | SmoothData(works,works,smoothterms) |
---|
554 | if (debug): |
---|
555 | x,y,z=getnarray(works,0) |
---|
556 | p.plot(x,y) |
---|
557 | p.show() |
---|
558 | return works |
---|
559 | |
---|
560 | def split_string_event(t): |
---|
561 | #this assumes the form nxs_event_label_tmin_tmax |
---|
562 | indx_=[] |
---|
563 | for i in range(10,len(t)): |
---|
564 | if (t[i]=="_"): |
---|
565 | indx_.append(i) |
---|
566 | label=t[10:indx_[0]] |
---|
567 | tmin=t[indx_[0]+1:indx_[1]] |
---|
568 | tmax=t[indx_[1]+1:len(t)] |
---|
569 | return label,tmin,tmax |
---|
570 | |
---|
571 | #test="nxs_event_1_300.00_600.00" |
---|
572 | #print split_string_event(test) |
---|
573 | |
---|
574 | # ##################################################################### |
---|
575 | # ##### USER SPECIFIC PART STARTS BELOW ## |
---|
576 | # ##### IN CASE LINES ABOVE HAVE BEEN EDITED AND SCRIPTS NO LONGER WORK ## |
---|
577 | # ##### LOG OUT AND BACK IN TO THE MACHINE ## |
---|
578 | # ##################################################################### |
---|
579 | # ########### SETTING the paths automatically : WISH_startup(username,cycle_name) ############## |
---|
580 | WISH_startup("mp43","13_3") |
---|
581 | # # WISH PROCESS ROUTINES TO EDIT (penultimate line optional but useful for recovering data later on) # |
---|
582 | # To add two raw files together, replace runno (integer, eg. 16800) by a string "int1+int2" (eg "16800+16801" note quotes) |
---|
583 | # ############################################################################################## |
---|
584 | #beg=0 |
---|
585 | #end=1800 |
---|
586 | #nbslices=int(end/180) |
---|
587 | #suffix=[] |
---|
588 | #for k in range(0,nbslices): |
---|
589 | # suffix.append("nxs_event_slice"+str(k)+"_"+str(int(k*180))+"_"+str((k+1)*180)) |
---|
590 | |
---|
591 | #print len(suffix) |
---|
592 | #print suffix[0], suffix[k] |
---|
593 | |
---|
594 | #for i in range(24901,24902): |
---|
595 | # for j in range(2,3): |
---|
596 | # for k in range(0,len(suffix)): |
---|
597 | # wout=WISH_process(i,j,suffix[k],"candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
598 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
599 | # ############################################################################################## |
---|
600 | #for i in range(24895,24896): |
---|
601 | # for j in range(5,6): |
---|
602 | # wout=WISH_process(i,j,"nxs_event_slice1_0_300","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
603 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
604 | # wout=WISH_process(i,j,"nxs_event_slice2_300_600","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
605 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
606 | # wout=WISH_process(i,j,"nxs_event_slice3_600_900","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
607 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
608 | # wout=WISH_process(i,j,"nxs_event_slice4_900_1200","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
609 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
610 | # wout=WISH_process(i,j,"nxs_event_slice5_1200_1500","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
611 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
612 | # wout=WISH_process(i,j,"nxs_event_slice6_1500_1800","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
613 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
614 | # wout=WISH_process(i,j,"nxs_event_slice7_1800_2100","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
615 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
616 | # wout=WISH_process(i,j,"nxs_event_slice8_2100_2400","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
617 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
618 | # wout=WISH_process(i,j,"nxs_event_slice9_2400_2700","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
619 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
620 | # wout=WISH_process(i,j,"nxs_event_slice10_2700_3000","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
621 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
622 | # wout=WISH_process(i,j,"nxs_event_slice11_3000_3300","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
623 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
624 | # wout=WISH_process(i,j,"nxs_event_slice12_3300_end","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
625 | |
---|
626 | for i in range(25449,25450): |
---|
627 | for j in range(1,10): |
---|
628 | wout=WISH_process(i,j,"raw","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
629 | ConvertUnits(wout,wout+"-d","dSpacing") |
---|
630 | # SaveGSS("w"+str(i)+"-1foc",WISH_userdir()+str(i)+"-1foc"+".gss",Append=False,Bank=1) |
---|
631 | # SaveFocusedXYE("w"+str(i)+"-1foc",WISH_userdir()+str(i)+"-1foc"+".dat") |
---|
632 | # SaveGSS("w"+str(i)+"-2foc",WISH_userdir()+str(i)+"-2foc"+".gss",Append=False,Bank=1) |
---|
633 | # SaveFocusedXYE("w"+str(i)+"-2foc",WISH_userdir()+str(i)+"-2foc"+".dat") |
---|
634 | RebinToWorkspace("w"+str(i)+"-6foc","w"+str(i)+"-5foc","w"+str(i)+"-6foc") |
---|
635 | Plus("w"+str(i)+"-5foc","w"+str(i)+"-6foc","w"+str(i)+"-5_6foc") |
---|
636 | ConvertUnits("w"+str(i)+"-5_6foc","w"+str(i)+"-5_6foc"+"-d","dSpacing") |
---|
637 | SaveGSS("w"+str(i)+"-5_6foc",WISH_userdir()+str(i)+"-5_6foc"+".gss",Append=False,Bank=1) |
---|
638 | SaveFocusedXYE("w"+str(i)+"-5_6foc",WISH_userdir()+str(i)+"-5_6foc"+".dat") |
---|
639 | SaveNexusProcessed("w"+str(i)+"-5_6foc",WISH_userdir()+str(i)+"-5_6foc"+".nxs") |
---|
640 | RebinToWorkspace("w"+str(i)+"-7foc","w"+str(i)+"-4foc","w"+str(i)+"-7foc") |
---|
641 | Plus("w"+str(i)+"-4foc","w"+str(i)+"-7foc","w"+str(i)+"-4_7foc") |
---|
642 | ConvertUnits("w"+str(i)+"-4_7foc","w"+str(i)+"-4_7foc"+"-d","dSpacing") |
---|
643 | SaveGSS("w"+str(i)+"-4_7foc",WISH_userdir()+str(i)+"-4_7foc"+".gss",Append=False,Bank=1) |
---|
644 | SaveFocusedXYE("w"+str(i)+"-4_7foc",WISH_userdir()+str(i)+"-4_7foc"+".dat") |
---|
645 | SaveNexusProcessed("w"+str(i)+"-4_7foc",WISH_userdir()+str(i)+"-4_7foc"+".nxs") |
---|
646 | RebinToWorkspace("w"+str(i)+"-8foc","w"+str(i)+"-3foc","w"+str(i)+"-8foc") |
---|
647 | Plus("w"+str(i)+"-3foc","w"+str(i)+"-8foc","w"+str(i)+"-3_8foc") |
---|
648 | ConvertUnits("w"+str(i)+"-3_8foc","w"+str(i)+"-3_8foc"+"-d","dSpacing") |
---|
649 | SaveGSS("w"+str(i)+"-3_8foc",WISH_userdir()+str(i)+"-3_8foc"+".gss",Append=False,Bank=1) |
---|
650 | SaveFocusedXYE("w"+str(i)+"-3_8foc",WISH_userdir()+str(i)+"-3_8foc"+".dat") |
---|
651 | SaveNexusProcessed("w"+str(i)+"-3_8foc",WISH_userdir()+str(i)+"-3_8foc"+".nxs") |
---|
652 | RebinToWorkspace("w"+str(i)+"-9foc","w"+str(i)+"-2foc","w"+str(i)+"-9foc") |
---|
653 | Plus("w"+str(i)+"-2foc","w"+str(i)+"-9foc","w"+str(i)+"-2_9foc") |
---|
654 | ConvertUnits("w"+str(i)+"-2_9foc","w"+str(i)+"-2_9foc"+"-d","dSpacing") |
---|
655 | SaveGSS("w"+str(i)+"-2_9foc",WISH_userdir()+str(i)+"-2_9foc"+".gss",Append=False,Bank=1) |
---|
656 | SaveFocusedXYE("w"+str(i)+"-2_9foc",WISH_userdir()+str(i)+"-2_9foc"+".dat") |
---|
657 | SaveNexusProcessed("w"+str(i)+"-2_9foc",WISH_userdir()+str(i)+"-2_9foc"+".nxs") |
---|
658 | # ############################################################################################# |
---|
659 | #for i in range(23840,23841): |
---|
660 | # for j in range(5,0,-1): |
---|
661 | # wout=WISH_process(i,j,"raw","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0) |
---|
662 | # SaveNexusProcessed(wout,WISH_userdir()+wout+".nxs") |
---|
663 | # ConvertUnits(wout,wout+"-d","dSpacing") |
---|
664 | |
---|
665 | |
---|
666 | # ########################################################################################### |
---|
667 | #for i in range(18880,18881): |
---|
668 | # for j in range(1,6): |
---|
669 | # wout=WISH_process(i,j,"raw","WISHcryo","11_3","WISHcryo","11_3",absorb=True,nd=0.0035,Xs=62.27,Xa=429.95,h=4.0,r=0.15) |
---|
670 | # ########################################################################################### |
---|
671 | # ######### END OF WISH PROCESS ROUTINES ################## |
---|
672 | |
---|
673 | # ##################################################################### |
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674 | # How to retrieve already processed Data without having to reprocess it (in case Mantid session has been closed # |
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675 | #for runno in range(24122,24130): |
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676 | # for j in range(1,6): |
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677 | # wr=str(runno)+"-"+str(j)+"raw-0" |
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678 | # LoadNexusProcessed(WISH_userdir()+wr+".nxs",wr) |
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679 | # ConvertUnits(wr,wr+"-d","dSpacing") |
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680 | |
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681 | ##################################################################### |
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682 | #for runno in range(22678,22686): |
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683 | #for j in range(1,6): |
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684 | #wr="w"+str(runno)+"-"+str(j)+"foc" |
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685 | |
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686 | #for j in range(1,6): |
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687 | # Plus("w22663"+"-"+str(j)+"foc","w22664"+"-"+str(j)+"foc","vancan"+"-"+str(j)+"foc") |
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688 | # SaveGSS(InputWorkspace="vancan"+"-"+str(j)+"foc",Filename=WISH_userdir()+"vancan"+"-"+str(j)+"foc.gss",Append=False,Bank=1) |
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689 | |
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690 | |
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691 | |
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692 | |
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693 | # #################################################################### |
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694 | # If you don't have a correct empty, either use the most suitable one or use the lines below #### |
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695 | #for i in range(1197,1410): |
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696 | # for j in range(1,6): |
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697 | # wout=WISH_read(i,j,"raw") |
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698 | # wfoc=WISH_focus(wout,j) |
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699 | # #################################################################### |
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700 | # use the lines below to manually set the paths if needed |
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701 | #WISH_setdatadir("/archive/ndxwish/Instrument/data/cycle_10_1/") |
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702 | #WISH_setuserdir("/home/mp43/ProcessedData/")WISHcryo |
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703 | # ######### use the lines below to process a LoadRawvanadium run ################## |
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704 | #for j in range(1,2): |
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705 | # WISH_createvan(19612,19618,j,100,4.0,0.15,cycle_van="11_4",cycle_empty="11_4") |
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706 | # CropWorkspace(InputWorkspace="w19612-"+str(j)+"foc",OutputWorkspace="w19612-"+str(j)+"foc",XMin='0.35',XMax='5.0') |
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707 | # Removepeaks_spline_smooth_vana("w18904-"+str(j)+"foc",j,debug=False) |
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708 | # SaveNexusProcessed("w16847-"+str(i)+"foc",WISH_userdir()+"vana16847-"+str(i)+"foc.nx5") |
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709 | # ######## use the lines below to create a processed empty (instrument, cryostat, can..) run ######## |
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710 | #for i in range(4,5): |
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711 | # WISH_createempty(20620,i) |
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712 | #SaveNexusProcessed("w16748-"+str(i)+"foc",WISH_userdir()+"emptyinst16748-"+str(i)+"foc.nx5") |
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713 | |
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714 | |
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