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: 2014-03-24 22:22:41 +0000 (Mon, 24 Mar 2014) $ |
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5 | # $Author: toby $ |
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6 | # $Revision: 1261 $ |
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7 | # $URL: trunk/exports/G2export_map.py $ |
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8 | # $Id: G2export_map.py 1261 2014-03-24 22:22:41Z toby $ |
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9 | ########### SVN repository information ################### |
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10 | ''' |
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11 | *Module G2export_map: Map export* |
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12 | ------------------------------------------- |
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13 | |
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14 | Code to write Fourier/Charge-Flip atomic density maps out in formats that |
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15 | can be read by external programs. At present a GSAS format |
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16 | that is supported by FOX and DrawXTL |
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17 | (:class:`ExportMapASCII`) and the CCP4 format that |
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18 | is used by COOT (:class:`ExportMapCCP4`) are implemented. |
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19 | ''' |
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20 | import os |
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21 | import GSASIIpath |
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22 | import numpy as np |
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23 | GSASIIpath.SetVersionNumber("$Revision: 1261 $") |
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24 | import GSASIIIO as G2IO |
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25 | #import GSASIIgrid as G2gd |
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26 | #import GSASIIstrIO as G2stIO |
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27 | #import GSASIImath as G2mth |
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28 | #import GSASIIlattice as G2lat |
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29 | #import GSASIIspc as G2spc |
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30 | #import GSASIIphsGUI as G2pg |
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31 | #import GSASIIstrMain as G2stMn |
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32 | |
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33 | class ExportMapASCII(G2IO.ExportBaseclass): |
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34 | '''Used to create a text file for a phase |
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35 | |
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36 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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37 | ''' |
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38 | def __init__(self,G2frame): |
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39 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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40 | G2frame=G2frame, |
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41 | formatName = 'FOX/DrawXTL file', |
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42 | extension='.grd', |
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43 | longFormatName = 'Export map as text (.grd) file' |
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44 | ) |
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45 | self.exporttype = ['map'] |
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46 | self.multiple = False |
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47 | |
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48 | def Exporter(self,event=None): |
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49 | '''Export a map as a text file |
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50 | ''' |
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51 | # the export process starts here |
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52 | self.InitExport(event) |
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53 | # load all of the tree into a set of dicts |
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54 | self.loadTree() |
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55 | if self.ExportSelect(): return # set export parameters, get file name |
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56 | filename = self.filename |
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57 | for phasenam in self.phasenam: |
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58 | phasedict = self.Phases[phasenam] # pointer to current phase info |
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59 | rho = phasedict['General']['Map'].get('rho',[]) |
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60 | if not len(rho): |
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61 | print "There is no map for phase "+str(phasenam) |
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62 | continue |
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63 | if len(self.phasenam) > 1: # if more than one filename is written, add a phase # -- not in use yet |
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64 | i = self.Phases[phasenam]['pId'] |
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65 | self.filename = os.path.splitext(filename)[1] + "_" + mapData['MapType'] + str(i) + self.extension |
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66 | self.OpenFile() |
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67 | self.Write("Map of Phase "+str(phasenam)+" from "+str(self.G2frame.GSASprojectfile)) |
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68 | # get cell parameters & print them |
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69 | cellList,cellSig = self.GetCell(phasenam) |
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70 | fmt = 3*" {:9.5f}" + 3*" {:9.3f}" |
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71 | self.Write(fmt.format(*cellList[:6])) |
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72 | nx,ny,nz = rho.shape |
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73 | self.Write(" {:3d} {:3d} {:3d}".format(nx,ny,nz)) |
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74 | for i in range(nx): |
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75 | for j in range(ny): |
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76 | for k in range(nz): |
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77 | self.Write(str(rho[i,j,k])) |
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78 | self.CloseFile() |
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79 | print('map from Phase '+str(phasenam)+' written to file '+str(self.fullpath)) |
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80 | |
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81 | class ExportMapCCP4(G2IO.ExportBaseclass): |
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82 | '''Used to create a text file for a phase |
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83 | |
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84 | :param wx.Frame G2frame: reference to main GSAS-II frame |
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85 | ''' |
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86 | def __init__(self,G2frame): |
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87 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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88 | G2frame=G2frame, |
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89 | formatName = 'CCP4 map file', |
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90 | extension='.map', |
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91 | longFormatName = 'Export CCP4 .map file' |
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92 | ) |
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93 | self.exporttype = ['map'] |
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94 | self.multiple = False |
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95 | |
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96 | # Tools for file writing. |
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97 | def Write(self,data,dtype): |
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98 | import struct |
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99 | '''write a block of output |
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100 | |
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101 | :param data: the data to be written. |
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102 | ''' |
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103 | self.fp.write(struct.pack(dtype,data)) |
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104 | |
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105 | def Exporter(self,event=None): |
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106 | '''Export a map as a text file |
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107 | ''' |
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108 | # the export process starts here |
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109 | self.InitExport(event) |
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110 | # load all of the tree into a set of dicts |
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111 | self.loadTree() |
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112 | if self.ExportSelect(): return # set export parameters, get file name |
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113 | filename = self.filename |
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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 | mapData = phasedict['General']['Map'] |
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117 | rho = mapData.get('rho',[]) |
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118 | |
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119 | if not len(rho): |
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120 | print "There is no map for phase "+str(phasenam) |
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121 | continue |
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122 | if len(self.phasenam) > 1: # if more than one filename is written, add a phase # -- not in use yet |
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123 | i = self.Phases[phasenam]['pId'] |
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124 | self.filename = os.path.splitext(filename)[1] + "_" + mapData['MapType'] + str(i) + self.extension |
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125 | cell = phasedict['General']['Cell'][1:7] |
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126 | nx,ny,nz = rho.shape |
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127 | self.OpenFile(mode='wb') |
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128 | for n in rho.shape: self.Write(n,'i') #nX,nY,nZ |
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129 | self.Write(2,'i') #mode=2 float map |
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130 | for i in [0,0,0]: self.Write(i,'i') #1st position on x,y,z |
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131 | for n in rho.shape: self.Write(n,'i') #nX,nY,nZ |
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132 | for c in cell: self.Write(c,'f') |
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133 | for i in [1,2,3]: self.Write(i,'i') #axes order = x,y,z |
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134 | self.Write(np.min(rho),'f') |
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135 | self.Write(np.max(rho),'f') |
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136 | self.Write(np.mean(rho),'f') |
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137 | self.Write(0,'i') |
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138 | for i in range(24,53): |
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139 | self.Write(0,'i') |
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140 | for s in ['M','A','P',' ']: self.Write(s,'s') |
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141 | self.Write(0x44410000,'i') |
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142 | self.Write(np.std(rho),'f') |
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143 | for i in range(56,257): |
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144 | self.Write(0,'i') |
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145 | for x in rho.flatten('F'): |
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146 | self.Write(x,'f') |
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147 | self.CloseFile() |
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148 | print('map from Phase '+str(phasenam)+' written to file '+str(self.fullpath)) |
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