1 | #!/usr/bin/env python |
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2 | # -*- coding: utf-8 -*- |
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3 | ########### SVN repository information ################### |
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4 | # $Date: 2017-05-04 14:14:19 +0000 (Thu, 04 May 2017) $ |
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5 | # $Author: vondreele $ |
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6 | # $Revision: 2819 $ |
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7 | # $URL: trunk/exports/G2export_csv.py $ |
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8 | # $Id: G2export_csv.py 2819 2017-05-04 14:14:19Z vondreele $ |
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9 | ########### SVN repository information ################### |
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10 | ''' |
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11 | *Module G2export_csv: Spreadsheet export* |
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12 | ------------------------------------------- |
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13 | |
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14 | Code to create .csv (comma-separated variable) files for |
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15 | GSAS-II data export to a spreadsheet program, etc. |
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16 | |
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17 | ''' |
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18 | import os.path |
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19 | import numpy as np |
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20 | import GSASIIpath |
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21 | GSASIIpath.SetVersionNumber("$Revision: 2819 $") |
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22 | import GSASIIIO as G2IO |
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23 | import GSASIIpy3 as G2py3 |
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24 | import GSASIIobj as G2obj |
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25 | import GSASIImath as G2mth |
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26 | import GSASIIpwd as G2pwd |
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27 | |
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28 | def WriteList(obj,headerItems): |
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29 | '''Write a CSV header |
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30 | |
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31 | :param object obj: Exporter object |
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32 | :param list headerItems: items to write as a header |
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33 | ''' |
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34 | line = '' |
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35 | for lbl in headerItems: |
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36 | if line: line += ',' |
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37 | line += '"'+lbl+'"' |
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38 | obj.Write(line) |
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39 | |
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40 | class ExportPhaseCSV(G2IO.ExportBaseclass): |
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41 | '''Used to create a csv file for a phase |
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42 | |
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43 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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44 | ''' |
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45 | def __init__(self,G2frame): |
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46 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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47 | G2frame=G2frame, |
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48 | formatName = 'CSV file', |
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49 | extension='.csv', |
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50 | longFormatName = 'Export phase as comma-separated (csv) file' |
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51 | ) |
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52 | self.exporttype = ['phase'] |
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53 | self.multiple = True # allow multiple phases to be selected |
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54 | |
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55 | def Writer(self,hist,phasenam,mode='w'): |
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56 | self.OpenFile(mode=mode) |
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57 | # test for aniso atoms |
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58 | aniso = False |
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59 | AtomsList = self.GetAtoms(phasenam) |
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60 | for lbl,typ,mult,xyz,td in AtomsList: |
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61 | if len(td) != 1: |
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62 | aniso = True |
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63 | break |
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64 | if mode == 'w': |
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65 | lbllist = ['hist','phase','a','b','c','alpha','beta','gamma','volume'] |
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66 | lbllist += ["atm label","elem","mult","x","y","z","frac","Uiso"] |
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67 | if aniso: lbllist += ['U11','U22','U33','U12','U13','U23'] |
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68 | WriteList(self,lbllist) |
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69 | |
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70 | cellList,cellSig = self.GetCell(phasenam) |
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71 | line = '"' + str(hist)+ '","' + str(phasenam) + '"' |
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72 | for defsig,val in zip( |
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73 | 3*[-0.00001] + 3*[-0.001] + [-0.01], # sets sig. figs. |
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74 | cellList |
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75 | ): |
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76 | txt = G2mth.ValEsd(val,defsig) |
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77 | if line: line += ',' |
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78 | line += txt |
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79 | self.Write(line) |
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80 | |
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81 | # get atoms and print separated by commas |
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82 | AtomsList = self.GetAtoms(phasenam) |
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83 | for lbl,typ,mult,xyz,td in AtomsList: |
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84 | line = ",,,,,,,,," |
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85 | line += '"' + lbl + '","' + typ + '",' + str(mult) + ',' |
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86 | for val,sig in xyz: |
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87 | line += G2mth.ValEsd(val,-abs(sig)) |
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88 | line += "," |
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89 | if len(td) == 1: |
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90 | line += G2mth.ValEsd(td[0][0],-abs(td[0][1])) |
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91 | else: |
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92 | line += "," |
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93 | for val,sig in td: |
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94 | line += G2mth.ValEsd(val,-abs(sig)) |
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95 | line += "," |
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96 | self.Write(line) |
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97 | |
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98 | if mode == 'w': |
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99 | print('Phase '+phasenam+' written to file '+self.fullpath) |
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100 | self.CloseFile() |
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101 | |
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102 | def Exporter(self,event=None): |
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103 | '''Export a phase as a csv file |
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104 | ''' |
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105 | # the export process starts here |
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106 | self.InitExport(event) |
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107 | # load all of the tree into a set of dicts |
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108 | self.loadTree() |
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109 | # create a dict with refined values and their uncertainties |
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110 | self.loadParmDict() |
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111 | if self.ExportSelect(): return # set export parameters; get file name |
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112 | self.OpenFile() |
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113 | # if more than one phase is selected, put them into a single file |
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114 | for phasenam in self.phasenam: |
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115 | phasedict = self.Phases[phasenam] # pointer to current phase info |
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116 | i = self.Phases[phasenam]['pId'] |
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117 | self.Write('"'+"Phase "+str(phasenam)+" from "+str(self.G2frame.GSASprojectfile)+'"') |
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118 | self.Write('\n"Space group:","'+str(phasedict['General']['SGData']['SpGrp'].strip())+'"') |
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119 | # get cell parameters & print them |
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120 | cellList,cellSig = self.GetCell(phasenam) |
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121 | WriteList(self,['a','b','c','alpha','beta','gamma','volume']) |
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122 | |
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123 | line = '' |
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124 | for defsig,val in zip( |
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125 | 3*[-0.00001] + 3*[-0.001] + [-0.01], # sign values to use when no sigma |
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126 | cellList |
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127 | ): |
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128 | txt = G2mth.ValEsd(val,defsig) |
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129 | if line: line += ',' |
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130 | line += txt |
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131 | self.Write(line) |
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132 | |
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133 | # get atoms and print separated by commas |
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134 | AtomsList = self.GetAtoms(phasenam) |
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135 | # check for aniso atoms |
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136 | aniso = False |
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137 | for lbl,typ,mult,xyz,td in AtomsList: |
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138 | if len(td) != 1: aniso = True |
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139 | lbllist = ["label","elem","mult","x","y","z","frac","Uiso"] |
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140 | if aniso: lbllist += ['U11','U22','U33','U12','U13','U23'] |
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141 | WriteList(self,lbllist) |
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142 | |
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143 | for lbl,typ,mult,xyz,td in AtomsList: |
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144 | line = '"' + lbl + '","' + typ + '",' + str(mult) + ',' |
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145 | for val,sig in xyz: |
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146 | line += G2mth.ValEsd(val,-abs(sig)) |
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147 | line += "," |
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148 | if len(td) == 1: |
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149 | line += G2mth.ValEsd(td[0][0],-abs(td[0][1])) |
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150 | else: |
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151 | line += "," |
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152 | for val,sig in td: |
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153 | line += G2mth.ValEsd(val,-abs(sig)) |
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154 | line += "," |
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155 | self.Write(line) |
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156 | print('Phase '+phasenam+' written to file '+self.fullpath) |
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157 | self.CloseFile() |
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158 | |
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159 | class ExportPowderCSV(G2IO.ExportBaseclass): |
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160 | '''Used to create a csv file for a powder data set |
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161 | |
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162 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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163 | ''' |
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164 | def __init__(self,G2frame): |
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165 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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166 | G2frame=G2frame, |
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167 | formatName = 'CSV file', |
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168 | extension='.csv', |
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169 | longFormatName = 'Export powder data as comma-separated (csv) file' |
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170 | ) |
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171 | self.exporttype = ['powder'] |
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172 | #self.multiple = False # only allow one histogram to be selected |
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173 | self.multiple = True |
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174 | |
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175 | def Writer(self,TreeName,filename=None): |
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176 | #print filename |
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177 | self.OpenFile(filename) |
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178 | histblk = self.Histograms[TreeName] |
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179 | WriteList(self,("x","y_obs","weight","y_calc","y_bkg")) |
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180 | digitList = 2*((13,3),) + ((13,5),) + 2*((13,3),) |
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181 | for vallist in zip(histblk['Data'][0], |
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182 | histblk['Data'][1], |
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183 | histblk['Data'][2], |
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184 | histblk['Data'][3], |
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185 | histblk['Data'][4], |
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186 | #histblk['Data'][5], |
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187 | ): |
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188 | line = "" |
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189 | for val,digits in zip(vallist,digitList): |
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190 | if line: line += ',' |
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191 | line += G2py3.FormatValue(val,digits) |
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192 | self.Write(line) |
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193 | self.CloseFile() |
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194 | |
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195 | def Exporter(self,event=None): |
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196 | '''Export a set of powder data as a csv file |
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197 | ''' |
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198 | # the export process starts here |
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199 | self.InitExport(event) |
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200 | # load all of the tree into a set of dicts |
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201 | self.loadTree() |
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202 | if self.ExportSelect( # set export parameters |
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203 | AskFile='single' # get a file name/directory to save in |
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204 | ): return |
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205 | filenamelist = [] |
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206 | for hist in self.histnam: |
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207 | # multiple files: create a unique name from the histogram |
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208 | fileroot = G2obj.MakeUniqueLabel(self.MakePWDRfilename(hist),filenamelist) |
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209 | # create an instrument parameter file |
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210 | self.filename = os.path.join(self.dirname,fileroot + self.extension) |
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211 | self.Writer(hist) |
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212 | print('Histogram '+hist+' written to file '+self.fullpath) |
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213 | |
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214 | class ExportMultiPowderCSV(G2IO.ExportBaseclass): |
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215 | '''Used to create a csv file for a stack of powder data sets suitable for display |
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216 | purposes only; no y-calc or weights are exported only x & y-obs |
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217 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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218 | ''' |
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219 | def __init__(self,G2frame): |
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220 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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221 | G2frame=G2frame, |
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222 | formatName = 'stacked CSV file', |
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223 | extension='.csv', |
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224 | longFormatName = 'Export powder data sets as a (csv) file - x,y-o1,y-o2,... only' |
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225 | ) |
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226 | self.exporttype = ['powder'] |
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227 | #self.multiple = False # only allow one histogram to be selected |
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228 | self.multiple = True |
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229 | |
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230 | def Exporter(self,event=None): |
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231 | '''Export a set of powder data as a csv file |
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232 | ''' |
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233 | # the export process starts here |
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234 | self.InitExport(event) |
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235 | # load all of the tree into a set of dicts |
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236 | self.loadTree() |
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237 | if self.ExportSelect( # set export parameters |
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238 | AskFile='single' # get a file name/directory to save in |
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239 | ): return |
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240 | filenamelist = [] |
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241 | csvData = [] |
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242 | headList = ["x",] |
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243 | digitList = [] |
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244 | fileroot = G2obj.MakeUniqueLabel(self.MakePWDRfilename(self.histnam[0]),filenamelist) |
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245 | # create a file |
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246 | self.filename = os.path.join(self.dirname,fileroot + self.extension) |
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247 | for ihst,hist in enumerate(self.histnam): |
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248 | histblk = self.Histograms[hist] |
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249 | headList.append('y_obs_'+str(ihst)) |
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250 | if not ihst: |
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251 | digitList = [(13,3),] |
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252 | csvData.append(histblk['Data'][0]) |
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253 | digitList += [(13,3),] |
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254 | csvData.append(histblk['Data'][1]) |
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255 | print('Histogram '+hist+' written to file '+self.fullpath) |
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256 | self.OpenFile() |
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257 | WriteList(self,headList) |
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258 | for vallist in np.array(csvData).T: |
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259 | line = "" |
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260 | for val,digits in zip(vallist,digitList): |
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261 | if line: line += ',' |
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262 | line += G2py3.FormatValue(val,digits) |
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263 | self.Write(line) |
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264 | self.CloseFile() |
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265 | |
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266 | class ExportPowderReflCSV(G2IO.ExportBaseclass): |
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267 | '''Used to create a csv file of reflections from a powder data set |
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268 | |
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269 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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270 | ''' |
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271 | def __init__(self,G2frame): |
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272 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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273 | G2frame=G2frame, |
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274 | formatName = 'reflection list as CSV', |
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275 | extension='.csv', |
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276 | longFormatName = 'Export powder reflection list as a comma-separated (csv) file' |
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277 | ) |
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278 | self.exporttype = ['powder'] |
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279 | self.multiple = False # only allow one histogram to be selected |
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280 | |
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281 | def Exporter(self,event=None): |
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282 | '''Export a set of powder reflections as a csv file |
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283 | ''' |
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284 | self.InitExport(event) |
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285 | # load all of the tree into a set of dicts |
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286 | self.loadTree() |
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287 | if self.ExportSelect(): return # set export parameters, get file name |
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288 | self.OpenFile() |
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289 | hist = self.histnam[0] # there should only be one histogram, in any case take the 1st |
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290 | histblk = self.Histograms[hist] |
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291 | self.Write('"Histogram"') |
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292 | self.Write('"'+hist+'"') |
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293 | self.Write('') |
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294 | # table of phases |
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295 | self.Write('"Phase name","phase #"') |
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296 | for i,phasenam in enumerate(sorted(histblk['Reflection Lists'])): |
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297 | self.Write('"'+str(phasenam)+'",'+str(i)) |
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298 | self.Write('') |
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299 | # note addition of a phase # flag at end (i) |
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300 | for i,phasenam in enumerate(sorted(histblk['Reflection Lists'])): |
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301 | phasDict = histblk['Reflection Lists'][phasenam] |
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302 | tname = {'T':'TOF','C':'2-theta'}[phasDict['Type'][2]] |
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303 | if phasDict.get('Super',False): |
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304 | WriteList(self,("h","k","l","m",tname,"F_obs","F_calc","phase","mult","sig","gam","FWHM","Prfo","phase #")) |
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305 | if 'T' in phasDict['Type']: |
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306 | fmt = "{:.0f},{:.0f},{:.0f},{:.0f},{:.3f},{:.3f},{:.3f},{:.2f},{:.0f},{:.3f},{:.3f},{:.3f},{:.4f},{:d}" |
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307 | else: |
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308 | fmt = "{:.0f},{:.0f},{:.0f},{:.0f},{:.3f},{:.3f},{:.3f},{:.2f},{:.0f},{:.5f},{:.5f},{:.5f},{:.4f},{:d}" |
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309 | refList = phasDict['RefList'] |
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310 | for refItem in refList: |
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311 | if 'T' in phasDict['Type']: |
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312 | h,k,l,m,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr,x,x,x,Prfo = refItem[:17] |
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313 | FWHM = G2pwd.getgamFW(gam,sig) |
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314 | self.Write(fmt.format(h,k,l,m,pos,Fobs,Fcalc,phase,mult,sig,gam,FWHM,i)) |
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315 | else: #convert to deg |
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316 | h,k,l,m,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr,Prfo = refItem[:14] |
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317 | s = np.sqrt(max(sig,0.0001))/100. #var -> sig in deg |
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318 | g = gam/100. #-> deg |
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319 | FWHM = G2pwd.getgamFW(g,s) |
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320 | self.Write(fmt.format(h,k,l,m,pos,Fobs,Fcalc,phase,mult,s,g,FWHM,i)) |
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321 | else: |
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322 | WriteList(self,("h","k","l",tname,"F_obs","F_calc","phase","mult","sig","gam","FWHM","Prfo","phase #")) |
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323 | if 'T' in phasDict['Type']: |
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324 | fmt = "{:.0f},{:.0f},{:.0f},{:.3f},{:.3f},{:.3f},{:.2f},{:.0f},{:.3f},{:.3f},{:.3f},{:.4f},{:d}" |
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325 | else: |
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326 | fmt = "{:.0f},{:.0f},{:.0f},{:.3f},{:.3f},{:.3f},{:.2f},{:.0f},{:.5f},{:.5f},{:.5f},{:.4f},{:d}" |
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327 | refList = phasDict['RefList'] |
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328 | for refItem in refList: |
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329 | if 'T' in phasDict['Type']: |
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330 | h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr,x,x,x,Prfo = refItem[:16] |
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331 | FWHM = G2pwd.getgamFW(gam,sig) |
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332 | self.Write(fmt.format(h,k,l,pos,Fobs,Fcalc,phase,mult,sig,gam,FWHM,Prfo,i)) |
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333 | else: #convert to deg |
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334 | h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr,Prfo = refItem[:13] |
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335 | g = gam/100. |
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336 | s = np.sqrt(max(sig,0.0001))/100. |
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337 | FWHM = G2pwd.getgamFW(g,s) |
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338 | self.Write(fmt.format(h,k,l,pos,Fobs,Fcalc,phase,mult,s,g,FWHM,Prfo,i)) |
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339 | self.CloseFile() |
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340 | print(hist+'reflections written to file '+self.fullpath) |
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341 | |
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342 | class ExportSingleCSV(G2IO.ExportBaseclass): |
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343 | '''Used to create a csv file with single crystal reflection data |
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344 | |
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345 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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346 | ''' |
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347 | def __init__(self,G2frame): |
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348 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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349 | G2frame=G2frame, |
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350 | formatName = 'CSV file', |
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351 | extension='.csv', |
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352 | longFormatName = 'Export reflection list as a comma-separated (csv) file' |
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353 | ) |
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354 | self.exporttype = ['single'] |
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355 | self.multiple = False # only allow one histogram to be selected |
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356 | |
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357 | def Exporter(self,event=None): |
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358 | '''Export a set of single crystal data as a csv file |
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359 | ''' |
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360 | # the export process starts here |
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361 | self.InitExport(event) |
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362 | # load all of the tree into a set of dicts |
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363 | self.loadTree() |
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364 | if self.ExportSelect(): return # set export parameters, get file name |
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365 | self.OpenFile() |
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366 | hist = self.histnam[0] # there should only be one histogram, in any case take the 1st |
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367 | histblk = self.Histograms[hist] |
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368 | for i,phasenam in enumerate(sorted(histblk['Reflection Lists'])): |
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369 | phasDict = histblk['Reflection Lists'][phasenam] |
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370 | tname = {'T':'TOF','C':'2-theta'}[phasDict['Type'][2]] |
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371 | if phasDict.get('Super',False): |
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372 | WriteList(self,("h","k","l","m",tname,"F_obs","F_calc","phase","mult","phase #")) |
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373 | fmt = "{:.0f},{:.0f},{:.0f},{:.0f},{:.3f},{:.3f},{:.3f},{:.2f},{:.0f},{:d}" |
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374 | refList = phasDict['RefList'] |
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375 | for refItem in refList: |
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376 | h,k,l,m,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr = refItem[:13] |
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377 | self.Write(fmt.format(h,k,l,m,pos,Fobs,Fcalc,phase,mult,i)) |
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378 | else: |
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379 | WriteList(self,("h","k","l",tname,"F_obs","F_calc","phase","mult","phase #")) |
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380 | fmt = "{:.0f},{:.0f},{:.0f},{:.3f},{:.3f},{:.3f},{:.2f},{:.0f},{:d}" |
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381 | refList = phasDict['RefList'] |
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382 | for refItem in refList: |
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383 | h,k,l,mult,dsp,pos,sig,gam,Fobs,Fcalc,phase,Icorr = refItem[:12] |
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384 | self.Write(fmt.format(h,k,l,pos,Fobs,Fcalc,phase,mult,i)) |
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385 | self.CloseFile() |
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386 | print(hist+' written to file '+self.fullname) |
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387 | |
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388 | class ExportStrainCSV(G2IO.ExportBaseclass): |
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389 | '''Used to create a csv file with single crystal reflection data |
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390 | |
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391 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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392 | ''' |
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393 | def __init__(self,G2frame): |
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394 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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395 | G2frame=G2frame, |
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396 | formatName = 'Strain CSV file', |
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397 | extension='.csv', |
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398 | longFormatName = 'Export strain results as a comma-separated (csv) file' |
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399 | ) |
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400 | self.exporttype = ['image'] |
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401 | self.multiple = False # only allow one histogram to be selected |
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402 | |
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403 | def Exporter(self,event=None): |
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404 | '''Export a set of single crystal data as a csv file |
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405 | ''' |
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406 | # the export process starts here |
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407 | self.InitExport(event) |
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408 | # load all of the tree into a set of dicts |
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409 | self.loadTree() |
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410 | if self.ExportSelect(): return # set export parameters, get file name |
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411 | self.OpenFile() |
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412 | hist = self.histnam[0] # there should only be one histogram, in any case take the 1st |
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413 | histblk = self.Histograms[hist] |
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414 | StrSta = histblk['Stress/Strain'] |
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415 | WriteList(self,("Dset","Dcalc","e11","sig(e11)","e12","sig(e12)","e22","sig(e22)")) |
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416 | fmt = 2*"{:.5f},"+6*"{:.0f}," |
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417 | fmt1 = "{:.5f}" |
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418 | fmt2 = "{:.2f},{:.5f},{:.5f}" |
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419 | for item in StrSta['d-zero']: |
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420 | Emat = item['Emat'] |
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421 | Esig = item['Esig'] |
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422 | self.Write(fmt.format(item['Dset'],item['Dcalc'],Emat[0],Esig[0],Emat[1],Esig[1],Emat[2],Esig[2])) |
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423 | for item in StrSta['d-zero']: |
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424 | WriteList(self,("Azm","dobs","dcalc","Dset="+fmt1.format(item['Dset']))) |
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425 | ring = np.vstack((item['ImtaObs'],item['ImtaCalc'])) |
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426 | for dat in ring.T: |
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427 | self.Write(fmt2.format(dat[1],dat[0],dat[2])) |
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428 | self.CloseFile() |
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429 | print(hist+' written to file '+self.fullpath) |
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