| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2017-05-17 20:06:18 +0000 (Wed, 17 May 2017) $ |
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| 4 | # $Author: vondreele $ |
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| 5 | # $Revision: 2836 $ |
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| 6 | # $URL: trunk/imports/G2pwd_fxye.py $ |
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| 7 | # $Id: G2pwd_fxye.py 2836 2017-05-17 20:06:18Z vondreele $ |
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| 8 | ########### SVN repository information ################### |
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| 9 | ''' |
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| 10 | *Module G2pwd_fxye: GSAS data files* |
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| 11 | ------------------------------------ |
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| 12 | Routine to read in powder data in a variety of formats |
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| 13 | that are defined for GSAS. |
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| 14 | |
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| 15 | ''' |
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| 16 | import os.path as ospath |
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| 17 | import numpy as np |
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| 18 | import GSASIIobj as G2obj |
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| 19 | import GSASIIpath |
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| 20 | GSASIIpath.SetVersionNumber("$Revision: 2836 $") |
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| 21 | |
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| 22 | class GSAS_ReaderClass(G2obj.ImportPowderData): |
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| 23 | 'Routines to import powder data from a GSAS files' |
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| 24 | def __init__(self): |
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| 25 | super(self.__class__,self).__init__( # fancy way to self-reference |
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| 26 | extensionlist=('.fxye','.raw','.gsas','.gda','.gsa','.gss','.RAW','.GSAS','.GDA','.GSA'), |
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| 27 | strictExtension=False, |
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| 28 | formatName = 'GSAS powder data', |
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| 29 | longFormatName = 'GSAS powder data files (.fxye, .raw, .gsas...)' |
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| 30 | ) |
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| 31 | self.clockWd = {} |
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| 32 | self.TimeMap = {} |
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| 33 | self.dnames = [] |
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| 34 | self.scriptable = True |
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| 35 | |
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| 36 | # Validate the contents -- look for a bank line |
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| 37 | def ContentsValidator(self, filepointer): |
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| 38 | 'Validrate by checking to see if the file has BANK lines & count them' |
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| 39 | #print 'ContentsValidator: '+self.formatName |
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| 40 | nBanks= 0 |
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| 41 | fname = ospath.basename(filepointer.name) |
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| 42 | for i,line in enumerate(filepointer): |
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| 43 | self.GSAS = True |
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| 44 | if i==0: # first line is always a comment |
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| 45 | continue |
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| 46 | if i==1 and line[:4].lower() == 'inst': |
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| 47 | # 2nd line is optional instrument parameter file |
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| 48 | continue |
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| 49 | if line[0] == '#': continue |
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| 50 | if line[:4] == 'BANK': |
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| 51 | self.dnames.append(fname+' '+' '.join(line.split()[:2])) |
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| 52 | nBanks += 1 |
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| 53 | continue |
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| 54 | elif line[:7] == 'Monitor': continue |
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| 55 | elif line [:8] == 'TIME_MAP': #LANSCE TOF data |
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| 56 | continue |
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| 57 | # else: |
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| 58 | # if not all(c in ' 0123456789.eE+-' for c in line[:-1]): |
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| 59 | # self.errors = 'Unexpected information in line: '+str(i+1) |
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| 60 | # self.errors += ' '+str(line) |
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| 61 | # return False |
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| 62 | if nBanks: |
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| 63 | if not len(self.selections): |
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| 64 | self.selections = range(nBanks) |
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| 65 | return True |
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| 66 | self.errors = 'No BANK records found' |
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| 67 | return False # no bank records |
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| 68 | |
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| 69 | def Reader(self,filename,filepointer, ParentFrame=None, **kwarg): |
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| 70 | '''Read a GSAS (old formats) file of type FXY, FXYE, ESD or STD types. |
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| 71 | If multiple datasets are requested, use self.repeat and buffer caching. |
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| 72 | ''' |
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| 73 | def GetFXYEdata(File,Pos,Bank): |
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| 74 | File.seek(Pos) |
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| 75 | x = [] |
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| 76 | y = [] |
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| 77 | w = [] |
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| 78 | S = File.readline() |
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| 79 | while S and S[:4] != 'BANK' and S[0] != '#': |
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| 80 | vals = S.split() |
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| 81 | x.append(float(vals[0])/100.) #CW: from centidegrees to degrees |
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| 82 | f = float(vals[1]) |
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| 83 | s = float(vals[2]) |
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| 84 | if f <= 0.0 or s <= 0.0: |
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| 85 | y.append(0.0) |
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| 86 | w.append(0.0) |
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| 87 | else: |
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| 88 | y.append(float(vals[1])) |
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| 89 | w.append(1.0/float(vals[2])**2) |
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| 90 | S = File.readline() |
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| 91 | N = len(x) |
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| 92 | return [np.array(x),np.array(y),np.array(w),np.zeros(N),np.zeros(N),np.zeros(N)] |
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| 93 | |
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| 94 | def GetFXYdata(File,Pos,Bank): |
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| 95 | File.seek(Pos) |
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| 96 | x = [] |
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| 97 | y = [] |
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| 98 | w = [] |
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| 99 | S = File.readline() |
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| 100 | while S and S[:4] != 'BANK' and S[0] != '#': |
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| 101 | vals = S.split() |
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| 102 | x.append(float(vals[0])/100.) #CW: from centidegrees to degrees |
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| 103 | f = float(vals[1]) |
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| 104 | if f > 0.0: |
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| 105 | y.append(f) |
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| 106 | w.append(1.0/f) |
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| 107 | else: |
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| 108 | y.append(0.0) |
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| 109 | w.append(0.0) |
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| 110 | S = File.readline() |
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| 111 | N = len(x) |
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| 112 | return [np.array(x),np.array(y),np.array(w),np.zeros(N),np.zeros(N),np.zeros(N)] |
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| 113 | |
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| 114 | def GetESDdata(File,Pos,Bank): |
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| 115 | File.seek(Pos) |
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| 116 | cons = Bank.split() |
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| 117 | if 'TIME_MAP' == cons[4]: |
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| 118 | start = 0 |
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| 119 | step = 1 |
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| 120 | else: |
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| 121 | start = float(cons[5])/100.0 #CW: from centidegrees to degrees |
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| 122 | step = float(cons[6])/100.0 |
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| 123 | x = [] |
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| 124 | y = [] |
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| 125 | w = [] |
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| 126 | S = File.readline() |
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| 127 | j = 0 |
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| 128 | while S and S[:4] != 'BANK' and S[0] != '#': |
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| 129 | if 'TIME_MAP' in S: |
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| 130 | break |
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| 131 | for i in range(0,80,16): |
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| 132 | if S[i:i+8] == 8*' ': |
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| 133 | break |
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| 134 | xi = start+step*j |
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| 135 | yi = sfloat(S[i:i+8]) |
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| 136 | ei = sfloat(S[i+8:i+16]) |
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| 137 | x.append(xi) |
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| 138 | if yi > 0.0: |
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| 139 | y.append(yi) |
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| 140 | w.append(1.0/ei**2) |
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| 141 | else: |
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| 142 | y.append(0.0) |
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| 143 | w.append(0.0) |
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| 144 | j += 1 |
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| 145 | S = File.readline() |
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| 146 | N = len(x) |
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| 147 | if self.clockWd: |
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| 148 | if len(self.clockWd) == 1: |
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| 149 | x = Tmap2TOF(self.TimeMap['1'],self.clockWd['1']) |
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| 150 | else: |
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| 151 | x = Tmap2TOF(self.TimeMap[cons[5]],self.clockWd[cons[5]]) |
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| 152 | return [np.array(x),np.array(y),np.array(w),np.zeros(N),np.zeros(N),np.zeros(N)] |
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| 153 | |
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| 154 | def GetSTDdata(File,Pos,Bank): |
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| 155 | File.seek(Pos) |
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| 156 | cons = Bank.split() |
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| 157 | Nch = int(cons[2]) |
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| 158 | if self.clockWd: |
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| 159 | start = 0 |
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| 160 | step = 1 |
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| 161 | else: |
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| 162 | start = float(cons[5])/100.0 #CW: from centidegrees to degrees |
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| 163 | step = float(cons[6])/100.0 #NB TOF 0.1*ms! |
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| 164 | x = [] |
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| 165 | y = [] |
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| 166 | w = [] |
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| 167 | S = File.readline() |
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| 168 | j = 0 |
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| 169 | while S and S[:4] != 'BANK' and S[0] != '#': |
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| 170 | if 'TIME_MAP' in S or '\x1a' in S: |
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| 171 | break |
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| 172 | for i in range(0,80,8): |
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| 173 | if S[i:i+10] == 10*' ': |
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| 174 | break |
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| 175 | xi = start+step*j |
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| 176 | ni = max(sint(S[i:i+2]),1) |
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| 177 | yi = max(sfloat(S[i+2:i+8]),0.0) |
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| 178 | if yi: |
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| 179 | vi = yi/ni |
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| 180 | else: |
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| 181 | yi = 0.0 |
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| 182 | vi = 0.0 |
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| 183 | j += 1 |
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| 184 | if j < Nch: |
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| 185 | x.append(xi) |
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| 186 | if vi <= 0.: |
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| 187 | y.append(0.) |
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| 188 | w.append(0.) |
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| 189 | else: |
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| 190 | y.append(yi) |
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| 191 | w.append(1.0/vi) |
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| 192 | S = File.readline() |
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| 193 | N = len(x) |
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| 194 | if self.clockWd: |
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| 195 | if len(self.clockWd) == 1: |
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| 196 | x = Tmap2TOF(self.TimeMap['1'],self.clockWd['1']) |
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| 197 | else: |
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| 198 | x = Tmap2TOF(self.TimeMap[cons[5]],self.clockWd[cons[5]]) |
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| 199 | return [np.array(x),np.array(y),np.array(w),np.zeros(N),np.zeros(N),np.zeros(N)] |
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| 200 | |
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| 201 | def GetALTdata(File,Pos,Bank): |
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| 202 | File.seek(Pos) |
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| 203 | cons = Bank.split() |
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| 204 | x = [] |
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| 205 | y = [] |
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| 206 | w = [] |
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| 207 | S = File.readline() |
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| 208 | j = 0 |
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| 209 | while S and S[:4] != 'BANK' and S[0] != '#': |
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| 210 | for i in range(0,80,20): |
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| 211 | if S[i:i+8] == 9*' ': |
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| 212 | break |
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| 213 | xi = sfloat(S[i:i+9])/3200. |
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| 214 | yi = sfloat(S[i+9:i+16])/1000. |
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| 215 | ei = sfloat(S[i+16:i+21])/1000. |
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| 216 | x.append(xi) |
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| 217 | if yi > 0.0: |
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| 218 | y.append(yi) |
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| 219 | w.append(1.0/ei**2) |
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| 220 | else: |
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| 221 | y.append(0.0) |
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| 222 | w.append(0.0) |
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| 223 | j += 1 |
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| 224 | S = File.readline() |
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| 225 | N = len(x) |
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| 226 | if self.clockWd: |
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| 227 | x = Tmap2TOF(self.TimeMap[cons[5]],self.clockWd[cons[5]]) |
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| 228 | return [np.array(x),np.array(y),np.array(w),np.zeros(N),np.zeros(N),np.zeros(N)] |
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| 229 | |
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| 230 | def GetTimeMap(File,Pos,TimeMap): |
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| 231 | File.seek(Pos) |
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| 232 | cons = TimeMap[8:].split() |
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| 233 | mapNo = cons[0] |
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| 234 | if 'TIME_MAP10' in TimeMap: mapNo = '1' #HIPD cluge! |
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| 235 | Nch = int(cons[1]) |
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| 236 | Nrec = int(cons[2]) |
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| 237 | clockWd = float(cons[4])/1000. #in mus |
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| 238 | TMap = np.zeros(Nch+2,dtype=int) |
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| 239 | ind = 0 |
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| 240 | for i in range(Nrec): |
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| 241 | S = File.readline().rstrip('\n') |
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| 242 | vals = S.split() |
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| 243 | for val in vals: |
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| 244 | TMap[ind] = int(val) |
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| 245 | ind += 1 |
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| 246 | TMap = np.reshape(TMap,(-1,3)) |
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| 247 | TMax = TMap[-1][0] |
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| 248 | Nch = TMap[-2][0]+(TMax-TMap[-2][1]+TMap[-2][2]-1)/TMap[-2][2] |
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| 249 | TMap[-1] = [Nch+1,TMax,0] |
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| 250 | TMap = TMap.T |
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| 251 | TMap[0] -= 1 |
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| 252 | return TMap.T,clockWd,mapNo |
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| 253 | |
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| 254 | def Tmap2TOF(TMap,clockWd): |
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| 255 | TOF = [] |
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| 256 | Tch,T,Step = TMap[0] |
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| 257 | for tmap in TMap[1:]: |
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| 258 | tch,t,step = tmap |
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| 259 | TOF += [T+Step*(i-Tch) for i in range(Tch,tch)] |
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| 260 | Tch,T,Step = tmap |
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| 261 | TOF = np.array(TOF)*clockWd |
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| 262 | return TOF |
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| 263 | |
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| 264 | Banks = [] |
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| 265 | Pos = [] |
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| 266 | rdbuffer = kwarg.get('buffer') |
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| 267 | title = '' |
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| 268 | comments = None |
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| 269 | |
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| 270 | # reload previously saved values - used for multibank reads |
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| 271 | if self.repeat and rdbuffer is not None: |
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| 272 | Banks = rdbuffer.get('Banks') |
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| 273 | Pos = rdbuffer.get('Pos') |
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| 274 | self.selections = rdbuffer.get('selections') |
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| 275 | comments = rdbuffer.get('comments') |
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| 276 | |
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| 277 | # read through the file and find the beginning of each bank |
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| 278 | # Save the offset (Pos), BANK line (Banks), comments for each bank |
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| 279 | # |
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| 280 | # This is going to need a fair amount of work to track line numbers |
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| 281 | # in the input file. |
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| 282 | if len(Banks) != len(Pos) or len(Banks) == 0: |
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| 283 | i = -1 |
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| 284 | while True: |
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| 285 | i += 1 |
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| 286 | S = filepointer.readline() |
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| 287 | if len(S) == 0: break |
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| 288 | |
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| 289 | if i==0: # first line is always a comment |
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| 290 | self.errors = 'Error reading title' |
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| 291 | title = S[:-1] |
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| 292 | comments = [[title,]] |
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| 293 | continue |
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| 294 | if i==1 and S[:4].lower() == 'inst' and ':' in S: |
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| 295 | # 2nd line is instrument parameter file (optional) |
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| 296 | self.errors = 'Error reading instrument parameter filename' |
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| 297 | self.instparm = S.split(':')[1].strip('[]').strip() |
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| 298 | continue |
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| 299 | if S[0] == '#': # allow comments anywhere in the file |
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| 300 | # comments in fact should only preceed BANK lines |
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| 301 | comments[-1].append(S[:-1]) |
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| 302 | continue |
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| 303 | if S[:4] == 'BANK': |
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| 304 | self.errors = 'Error reading bank:' |
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| 305 | self.errors += ' '+str(S) |
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| 306 | comments.append([title,]) |
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| 307 | Banks.append(S) |
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| 308 | Pos.append(filepointer.tell()) |
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| 309 | if S[:8] == 'TIME_MAP': #assumes one time map; HIPPO has multiple time maps |
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| 310 | if len(Banks) == 0: |
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| 311 | self.errors = 'Error reading time map before any bank lines' |
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| 312 | else: |
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| 313 | self.errors = 'Error reading time map after bank:\n '+str(Banks[-1]) |
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| 314 | timemap,clockwd,mapNo = GetTimeMap(filepointer,filepointer.tell(),S) |
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| 315 | self.TimeMap[mapNo] = timemap |
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| 316 | self.clockWd[mapNo] = clockwd |
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| 317 | |
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| 318 | |
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| 319 | # Now select the bank to read |
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| 320 | if not Banks: # use of ContentsValidator should prevent this error |
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| 321 | print self.formatName+' scan error: no BANK records' |
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| 322 | selblk = None # no block to choose |
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| 323 | self.errors = 'No BANK records found (strange!)' |
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| 324 | return False |
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| 325 | elif len(Banks) == 1: # only one Bank, don't ask |
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| 326 | selblk = 0 |
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| 327 | elif self.repeat and self.selections is not None: |
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| 328 | # we were called to repeat the read |
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| 329 | #print 'debug: repeat #',self.repeatcount,'selection',self.selections[self.repeatcount] |
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| 330 | selblk = self.selections[self.repeatcount] |
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| 331 | self.repeatcount += 1 |
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| 332 | if self.repeatcount >= len(self.selections): self.repeat = False |
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| 333 | else: # choose from options |
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| 334 | selblk = self.selections[0] # select first in list |
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| 335 | if len(self.selections) > 1: # prepare to loop through again |
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| 336 | self.repeat = True |
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| 337 | self.repeatcount = 1 |
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| 338 | if rdbuffer is not None: |
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| 339 | rdbuffer['Banks'] = Banks |
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| 340 | rdbuffer['Pos'] = Pos |
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| 341 | rdbuffer['selections'] = self.selections |
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| 342 | rdbuffer['comments'] = comments |
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| 343 | |
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| 344 | # got a selection, now read it |
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| 345 | Bank = Banks[selblk] |
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| 346 | try: |
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| 347 | bnkNo = int(Bank.split()[1]) |
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| 348 | except ValueError: |
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| 349 | bnkNo = 1 |
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| 350 | if 'FXYE' in Bank: |
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| 351 | self.errors = 'Error reading FXYE data in Bank\n '+Banks[selblk] |
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| 352 | self.powderdata = GetFXYEdata(filepointer,Pos[selblk],Banks[selblk]) |
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| 353 | elif 'FXY' in Bank: |
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| 354 | self.errors = 'Error reading FXY data in Bank\n '+Banks[selblk] |
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| 355 | self.powderdata = GetFXYdata(filepointer,Pos[selblk],Banks[selblk]) |
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| 356 | elif 'ESD' in Bank: |
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| 357 | self.errors = 'Error reading ESD data in Bank\n '+Banks[selblk] |
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| 358 | self.powderdata = GetESDdata(filepointer,Pos[selblk],Banks[selblk]) |
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| 359 | elif 'STD' in Bank: |
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| 360 | self.errors = 'Error reading STD data in Bank\n '+Banks[selblk] |
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| 361 | self.powderdata = GetSTDdata(filepointer,Pos[selblk],Banks[selblk]) |
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| 362 | elif 'ALT' in Bank: |
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| 363 | self.errors = 'Error reading ALT data in Bank\n '+Banks[selblk] |
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| 364 | self.powderdata = GetALTdata(filepointer,Pos[selblk],Banks[selblk]) |
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| 365 | else: |
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| 366 | self.errors = 'Error reading STD data in Bank\n '+Banks[selblk] |
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| 367 | self.powderdata = GetSTDdata(filepointer,Pos[selblk],Banks[selblk]) |
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| 368 | |
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| 369 | self.errors = 'Error processing information after read complete' |
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| 370 | if comments is not None: |
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| 371 | self.comments = comments[selblk] |
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| 372 | self.powderentry[0] = filename |
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| 373 | self.powderentry[1] = Pos # position offset (never used, I hope) |
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| 374 | self.powderentry[2] = bnkNo #selblk+1 # bank number |
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| 375 | self.idstring = ospath.basename(filename) + ' Bank '+str(bnkNo) #selblk+1) |
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| 376 | self.numbanks=len(Banks) |
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| 377 | # scan comments for temperature & radius |
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| 378 | Temperature = 300. |
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| 379 | for S in self.comments: |
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| 380 | if 'Temp' in S.split('=')[0]: |
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| 381 | try: |
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| 382 | Temperature = float(S.split('=')[1]) |
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| 383 | except: |
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| 384 | pass |
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| 385 | elif 'Gonio' in S.split('=')[0]: |
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| 386 | try: |
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| 387 | self.Sample['Gonio. radius'] = float(S.split('=')[1]) |
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| 388 | except: |
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| 389 | pass |
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| 390 | elif 'Omega' in S.split('=')[0] or 'Theta' in S.split('=')[0]: #HIPD weirdness |
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| 391 | try: |
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| 392 | self.Sample['Omega'] = 90.-float(S.split('=')[1]) |
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| 393 | except: |
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| 394 | pass |
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| 395 | elif 'Chi' in S.split('=')[0]: |
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| 396 | try: |
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| 397 | self.Sample['Chi'] = -float(S.split('=')[1]) |
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| 398 | except: |
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| 399 | pass |
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| 400 | elif 'Phi' in S.split('=')[0]: |
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| 401 | try: |
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| 402 | self.Sample['Phi'] = float(S.split('=')[1]) |
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| 403 | except: |
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| 404 | pass |
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| 405 | self.Sample['Temperature'] = Temperature |
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| 406 | return True |
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| 407 | |
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| 408 | def sfloat(S): |
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| 409 | 'convert a string to a float, treating an all-blank string as zero' |
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| 410 | if S.strip(): |
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| 411 | return float(S) |
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| 412 | else: |
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| 413 | return 0.0 |
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| 414 | |
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| 415 | def sint(S): |
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| 416 | 'convert a string to an integer, treating an all-blank string as zero' |
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| 417 | if S.strip(): |
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| 418 | return int(S) |
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| 419 | else: |
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| 420 | return 0 |
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| 421 | |
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