| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2020-03-03 21:01:43 +0000 (Tue, 03 Mar 2020) $ |
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| 4 | # $Author: toby $ |
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| 5 | # $Revision: 4339 $ |
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| 6 | # $URL: trunk/imports/G2pwd_Panalytical.py $ |
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| 7 | # $Id: G2pwd_Panalytical.py 4339 2020-03-03 21:01:43Z toby $ |
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| 8 | ########### SVN repository information ################### |
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| 9 | |
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| 10 | from __future__ import division, print_function |
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| 11 | import os.path as ospath |
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| 12 | import xml.etree.ElementTree as ET |
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| 13 | import numpy as np |
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| 14 | import GSASIIobj as G2obj |
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| 15 | import GSASIIpath |
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| 16 | GSASIIpath.SetVersionNumber("$Revision: 4339 $") |
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| 17 | class Panalytical_ReaderClass(G2obj.ImportPowderData): |
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| 18 | '''Routines to import powder data from a Pananalytical.xrdm (xml) file. |
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| 19 | |
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| 20 | ''' |
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| 21 | def __init__(self): |
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| 22 | super(self.__class__,self).__init__( # fancy way to self-reference |
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| 23 | extensionlist=('.xrdml','.xml'), |
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| 24 | strictExtension=True, |
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| 25 | formatName = 'Panalytical xrdml (xml)', |
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| 26 | longFormatName = 'Panalytical powder data as *.xrdml' |
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| 27 | ) |
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| 28 | self.scriptable = True |
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| 29 | self.vals = None |
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| 30 | self.stepsize = None |
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| 31 | self.skip = 0 |
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| 32 | self.root = None |
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| 33 | |
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| 34 | # Validate the contents -- make sure we only have valid lines and set |
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| 35 | # values we will need for later read. |
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| 36 | def ContentsValidator(self, filename): |
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| 37 | fp = open(filename,'r') |
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| 38 | self.vals = None |
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| 39 | self.stepsize = None |
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| 40 | fp.seek(0) |
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| 41 | try: |
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| 42 | self.root = ET.parse(fp).getroot() |
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| 43 | tag = self.root.tag |
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| 44 | tag = tag.split('}')[0]+'}' |
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| 45 | self.root.find(tag+'comment') |
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| 46 | except: |
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| 47 | self.errors = 'Bad xml file' |
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| 48 | fp.close() |
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| 49 | return False |
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| 50 | fp.close() |
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| 51 | return True |
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| 52 | |
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| 53 | def Reader(self,filename, ParentFrame=None, **kwarg): |
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| 54 | 'Read a Panalytical .xrdml (.xml) file; already in self.root' |
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| 55 | blockNum = kwarg.get('blocknum',0) |
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| 56 | self.idstring = ospath.basename(filename) + ' Scan '+str(blockNum) |
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| 57 | x = [] |
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| 58 | y = [] |
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| 59 | w = [] |
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| 60 | tag = self.root.tag |
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| 61 | tag = tag.split('}')[0]+'}' |
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| 62 | sample = self.root.find(tag+'sample') |
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| 63 | self.idstring = ospath.basename(filename) + ' Scan '+str(blockNum) |
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| 64 | blks = self.root.findall(tag+'xrdMeasurement') |
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| 65 | scans = [] |
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| 66 | for data in blks: |
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| 67 | scans += data.findall(tag+'scan') |
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| 68 | data = self.root.find(tag+'xrdMeasurement') |
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| 69 | wave = data.find(tag+'usedWavelength') |
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| 70 | incident = data.find(tag+'incidentBeamPath') |
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| 71 | radius = float(incident.find(tag+'radius').text) |
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| 72 | tube = incident.find(tag+'xRayTube') |
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| 73 | if len(scans) > 1: |
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| 74 | self.repeat = True |
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| 75 | if blockNum-1 == len(scans): |
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| 76 | self.repeat = False |
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| 77 | return False |
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| 78 | scan = scans[blockNum-1] |
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| 79 | header = scan.find(tag+'header') |
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| 80 | dataPoints = scan.find(tag+'dataPoints') |
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| 81 | self.comments.append('Gonio. radius=%.2f'%(radius)) |
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| 82 | self.Sample['Gonio. radius'] = radius |
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| 83 | if sample.find(tag+'id').text: |
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| 84 | self.comments.append('Sample name='+sample.find(tag+'id').text) |
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| 85 | try: |
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| 86 | self.comments.append('Date/TimeStart='+header.find(tag+'startTimeStamp').text) |
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| 87 | self.comments.append('Date/TimeEnd='+header.find(tag+'endTimeStamp').text) |
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| 88 | self.comments.append('xray tube='+tube.attrib['name']) |
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| 89 | except AttributeError: |
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| 90 | pass |
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| 91 | self.comments.append('Ka1=%s'%(wave.find(tag+'kAlpha1').text)) |
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| 92 | self.comments.append('Ka2=%s'%(wave.find(tag+'kAlpha2').text)) |
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| 93 | self.comments.append('Ka2/Ka1=%s'%(wave.find(tag+'ratioKAlpha2KAlpha1').text)) |
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| 94 | self.comments.append('Kb=%s'%(wave.find(tag+'kBeta').text)) |
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| 95 | self.comments.append('Voltage='+tube.find(tag+'tension').text) |
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| 96 | self.comments.append('Current='+tube.find(tag+'current').text) |
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| 97 | limits = dataPoints.find(tag+'positions') |
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| 98 | startPos = float(limits.find(tag+'startPosition').text) |
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| 99 | endPos= float(limits.find(tag+'endPosition').text) |
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| 100 | for seclbl in 'intensities','counts': |
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| 101 | sec = dataPoints.find(tag+seclbl) |
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| 102 | if sec is None: continue |
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| 103 | y = np.fromstring(sec.text,sep=' ') |
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| 104 | break |
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| 105 | else: |
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| 106 | print('Panalytical read error: Intensities could not be located') |
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| 107 | return False |
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| 108 | N = y.shape[0] |
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| 109 | x = np.linspace(startPos,endPos,N) |
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| 110 | w = np.where(y>0,1./y,1.) |
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| 111 | self.powderdata = [ |
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| 112 | np.array(x), # x-axis values |
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| 113 | np.array(y), # powder pattern intensities |
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| 114 | np.array(w), # 1/sig(intensity)^2 values (weights) |
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| 115 | np.zeros(N), # calc. intensities (zero) |
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| 116 | np.zeros(N), # calc. background (zero) |
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| 117 | np.zeros(N), # obs-calc profiles |
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| 118 | ] |
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| 119 | conditions = scan.find(tag+'nonAmbientPoints') |
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| 120 | if conditions is not None: |
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| 121 | kind = conditions.attrib['type'] |
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| 122 | if kind == 'Temperature': |
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| 123 | Temperature = float(conditions.find(tag+'nonAmbientValues').text.split()[-1]) |
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| 124 | self.Sample['Temperature'] = Temperature |
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| 125 | return True |
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