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source: trunk/GSASIIfiles.py @ 5360

Last change on this file since 5360 was 5112, checked in by vondreele, 3 years ago
implement energy dispersive x-ray data as a new type 'PXE'; assume Gaussian peak shape only; no sample broadening considered. Peak resolution is only ~0.5% not good enough to see sample broadening import, plotting, peak fitting, indexing & cell refinement from peak positions "complete" data is old (from ~20 yrs ago) so no idea about modern ED data. Start on use in Pawley/LeBail? refinement - Rietveld excluded; currently not working Some work on ISODISTORT implementation
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File size: 45.6 KB

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2021-12-15 22:56:41 +0000 (Wed, 15 Dec 2021) $
4	# $Author: toby $
5	# $Revision: 5112 $
6	# $URL: trunk/GSASIIfiles.py $
7	# $Id: GSASIIfiles.py 5112 2021-12-15 22:56:41Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIfiles: data (non-GUI) I/O routines
11	==========================================
12
13	Module with miscellaneous routines for input and output from files.
14
15	This module should not contain any references to wxPython so that it
16	can be imported for scriptable use or potentially on clients where
17	wx is not installed.
18
19	Future refactoring: This module and GSASIIIO.py needs some work to
20	move non-wx routines here. It may will likely make sense to rename the module(s)
21	at that point.
22	'''
23	from __future__ import division, print_function
24	import platform
25	import os
26	import sys
27	import glob
28	import inspect
29	import numpy as np
30
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 5112 $")
33
34	# N.B. This is duplicated in G2IO
35	def sfloat(S):
36	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
37	if S.strip():
38	try:
39	return float(S)
40	except ValueError:
41	pass
42	return 0.0
43
44	G2printLevel = 'all'
45	'''This defines the level of output from calls to :func:`G2Print`,
46	which should be used in place of print() within this module.
47	Settings for this are 'all', 'warn', 'error' or 'none'. Also see:
48	:func:`G2Print` and :func:`G2SetPrintLevel`.
49	'''
50
51	def G2SetPrintLevel(level):
52	'''Set the level of output from calls to :func:`G2Print`, which should
53	be used in place of print() within GSASII. Settings for the mode are
54	'all', 'warn', 'error' or 'none'
55
56	:param str level: a string used to set the print level, which may be
57	'all', 'warn', 'error' or 'none'.
58	Note that capitalization and extra letters in level are ignored, so
59	'Warn', 'warnings', etc. will all set the mode to 'warn'
60	'''
61	global G2printLevel
62	for mode in 'all', 'warn', 'error', 'none':
63	if mode in level.lower():
64	G2printLevel = mode
65	return
66	else:
67	G2Print('G2SetPrintLevel Error: level={} cannot be interpreted.',
68	'Use all, warn, error or none.')
69
70	def find(name, path):
71	'''find 1st occurance of file in path
72	'''
73	for root, dirs, files in os.walk(path):
74	if name in files:
75	return os.path.join(root, name)
76
77	def G2Print(args,*kwargs):
78	'''Print with filtering based level of output (see :func:`G2SetPrintLevel`).
79	Use G2Print() as replacement for print().
80
81	:param str mode: if specified, this should contain the mode for printing
82	('error', 'warn' or anything else). If not specified, the first argument
83	of the print command (args[0]) should contain the string 'error' for
84	error messages and 'warn' for warning messages
85	(capitalization and additional letters ignored.)
86	'''
87	if G2printLevel == 'none': return
88	if kwargs.get('mode') is None:
89	testStr = str(args[0]).lower()
90	else:
91	testStr = kwargs['mode'][:].lower()
92	del kwargs['mode']
93	level = 2
94	for i,mode in enumerate(('error', 'warn')):
95	if mode in testStr:
96	level = i
97	break
98	if G2printLevel == 'error' and level > 0: return
99	if G2printLevel == 'warn' and level > 1: return
100	print(args,*kwargs)
101
102	def get_python_versions(packagelist):
103	versions = [['Python', sys.version.split()[0]]]
104	for pack in packagelist:
105	try:
106	versions.append([pack.__name__, pack.__version__])
107	except:
108	pass
109	versions.append(['Platform',
110	sys.platform + ' ' + platform.architecture()[0] +
111	' ' + platform.machine()])
112	return versions
113
114	def makeInstDict(names,data,codes):
115	inst = dict(zip(names,zip(data,data,codes)))
116	for item in inst:
117	inst[item] = list(inst[item])
118	return inst
119
120	def SetPowderInstParms(Iparm, rd):
121	'''extracts values from instrument parameters in rd.instdict
122	or in array Iparm.
123	Create and return the contents of the instrument parameter tree entry.
124	'''
125	Irads = {0:' ',1:'CrKa',2:'FeKa',3:'CuKa',4:'MoKa',5:'AgKa',6:'TiKa',7:'CoKa'}
126	DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars
127	# override inst values with values read from data file
128	Bank = rd.powderentry[2] #should be used in multibank iparm files
129	if rd.instdict.get('type'):
130	DataType = rd.instdict.get('type')
131	data = [DataType,]
132	instname = Iparm.get('INS 1INAME ')
133	irad = int(Iparm.get('INS 1 IRAD ','0'))
134	if instname:
135	rd.Sample['InstrName'] = instname.strip()
136	if 'C' in DataType:
137	wave1 = None
138	wave2 = 0.0
139	if rd.instdict.get('wave'):
140	wl = rd.instdict.get('wave')
141	wave1 = wl[0]
142	if len(wl) > 1: wave2 = wl[1]
143	s = Iparm['INS 1 ICONS']
144	if not wave1:
145	wave1 = sfloat(s[:10])
146	wave2 = sfloat(s[10:20])
147	v = (wave1,wave2,
148	sfloat(s[20:30])/100.,sfloat(s[55:65]),sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
149	if not v[1]:
150	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
151	v = (v[0],v[2],v[4])
152	codes = [0,0,0,0,0]
153	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
154	else:
155	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
156	codes = [0,0,0,0,0,0,0]
157	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
158	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
159	data.extend(v)
160	if 'INS 1PRCF ' in Iparm:
161	v1 = Iparm['INS 1PRCF '].split()
162	v = Iparm['INS 1PRCF 1'].split()
163	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
164	azm = float(Iparm.get('INS 1DETAZM','0.0'))
165	v = Iparm['INS 1PRCF 2'].split()
166	if v1[0] == 3:
167	data.extend([float(v[0]),float(v[1]),0.0,float(v[2])+float(v[3],azm)]) #get LX, LY, Z, S+H/L & azimuth
168	else:
169	data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
170	else:
171	v1 = Iparm['INS 1PRCF1 '].split()
172	v = Iparm['INS 1PRCF11'].split()
173	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
174	azm = float(Iparm.get('INS 1DETAZM','0.0'))
175	v = Iparm['INS 1PRCF12'].split()
176	if v1[0] == 3:
177	data.extend([float(v[0]),float(v[1]),0.0,float(v[2])+float(v[3],azm)]) #get LX, LY, Z, S+H/L & azimuth
178	else:
179	data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
180	codes.extend([0,0,0,0,0,0,0])
181	Iparm1 = makeInstDict(names,data,codes)
182	Iparm1['Source'] = [Irads[irad],Irads[irad]]
183	Iparm1['Bank'] = [Bank,Bank,0]
184	return [Iparm1,{}]
185	elif 'T' in DataType:
186	names = ['Type','fltPath','2-theta','difC','difA', 'difB','Zero','alpha','beta-0','beta-1',
187	'beta-q','sig-0','sig-1','sig-2','sig-q', 'X','Y','Z','Azimuth',]
188	codes = [0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,]
189	azm = 0.
190	if 'INS 1DETAZM' in Iparm:
191	azm = float(Iparm['INS 1DETAZM'])
192	rd.Sample['Azimuth'] = azm
193	fltPath0 = 20. #arbitrary
194	if 'INS FPATH1' in Iparm:
195	s = Iparm['INS FPATH1'].split()
196	fltPath0 = sfloat(s[0])
197	if 'INS 1BNKPAR' not in Iparm: #bank missing from Iparm file
198	return []
199	s = Iparm['INS 1BNKPAR'].split()
200	fltPath1 = sfloat(s[0])
201	data.extend([fltPath0+fltPath1,]) #Flight path source-sample-detector
202	data.extend([sfloat(s[1]),]) #2-theta for bank
203	s = Iparm['INS 1 ICONS'].split()
204	data.extend([sfloat(s[0]),sfloat(s[1]),0.0,sfloat(s[2])]) #difC,difA,difB,Zero
205	if 'INS 1PRCF ' in Iparm:
206	s = Iparm['INS 1PRCF '].split()
207	pfType = int(s[0])
208	s = Iparm['INS 1PRCF 1'].split()
209	if abs(pfType) == 1:
210	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
211	s = Iparm['INS 1PRCF 2'].split()
212	data.extend([0.0,0.0,sfloat(s[1]),sfloat(s[2]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
213	elif abs(pfType) in [3,4,5]:
214	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
215	if abs(pfType) == 4:
216	data.extend([0.0,0.0,sfloat(s[3]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
217	else:
218	s = Iparm['INS 1PRCF 2'].split()
219	data.extend([0.0,0.0,sfloat(s[0]),sfloat(s[1]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
220	elif abs(pfType) == 2:
221	print('''*WARNING gsas profile function #2 does not give valid GSAS-II diffractometer/profile coefficients *
222	you should request GSAS-II instparm file from Instrument responsible''')
223	data.extend([sfloat(s[1]),0.0,1./sfloat(s[3])]) #alpha, beta-0, beta-1
224	data.extend([0.0,0.0,sfloat(s[1]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
225	else:
226	s = Iparm['INS 1PRCF1 '].split()
227	pfType = int(s[0])
228	s = Iparm['INS 1PRCF11'].split()
229	if abs(pfType) == 1:
230	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
231	s = Iparm['INS 1PRCF12'].split()
232	data.extend([0.0,0.0,sfloat(s[1]),sfloat(s[2]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
233	elif abs(pfType) in [3,4,5]:
234	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
235	if abs(pfType) == 4:
236	data.extend([0.0,0.0,sfloat(s[3]),0.0,0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
237	else:
238	s = Iparm['INS 1PRCF12'].split()
239	data.extend([0.0,0.0,sfloat(s[0]),sfloat(s[1]),0.0,0.0,0.0,0.0,azm]) #beta-q, sig-0, sig-1, sig-2, sig-q, X, Y, Z
240	Inst1 = makeInstDict(names,data,codes)
241	Inst1['Bank'] = [Bank,Bank,0]
242	Inst2 = {}
243	if pfType < 0:
244	Ipab = 'INS 1PAB'+str(-pfType)
245	Npab = int(Iparm[Ipab+' '].strip())
246	Inst2['Pdabc'] = []
247	for i in range(Npab):
248	k = Ipab+str(i+1).rjust(2)
249	s = Iparm[k].split()
250	Inst2['Pdabc'].append([float(t) for t in s])
251	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
252	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
253	if 'INS 1I ITYP' in Iparm:
254	s = Iparm['INS 1I ITYP'].split()
255	Ityp = int(s[0])
256	Tminmax = [float(s[1])1000.,float(s[2])1000.]
257	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
258	if Ityp in [1,2,4]:
259	Inst2['Itype'] = Itypes[Ityp-1]
260	Inst2['Tminmax'] = Tminmax
261	Icoeff = []
262	Iesd = []
263	Icovar = []
264	for i in range(3):
265	s = Iparm['INS 1ICOFF'+str(i+1)].split()
266	Icoeff += [float(S) for S in s]
267	s = Iparm['INS 1IECOF'+str(i+1)].split()
268	Iesd += [float(S) for S in s]
269	NT = 10
270	for i in range(8):
271	s = Iparm['INS 1IECOR'+str(i+1)]
272	if i == 7:
273	NT = 8
274	Icovar += [float(s[6j:6j+6]) for j in range(NT)]
275	Inst2['Icoeff'] = Icoeff
276	Inst2['Iesd'] = Iesd
277	Inst2['Icovar'] = Icovar
278	return [Inst1,Inst2]
279	elif 'E' in DataType:
280	tth = float(Iparm['INS 1 ICONS'])
281	s = Iparm['INS 1PRCF11'].split()
282	names = ['Type','2-theta','XE','YE','ZE','A','B', 'C']
283	codes = [0,0,0,0,0,0,0,0]
284	data.extend([tth,0.0,0.0,0.0,sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #A,B,C
285	Iparm1 = makeInstDict(names,data,codes)
286	Iparm1['Bank'] = [Bank,Bank,0]
287	return [Iparm1,{}]
288
289	def ReadPowderInstprm(instLines, bank, databanks, rd):
290	'''Read lines from a GSAS-II (new) instrument parameter file
291	similar to G2pwdGUI.OnLoad
292	If instprm file has multiple banks each with header #Bank n: ..., this
293	finds matching bank no. to load - problem with nonmatches?
294
295	Note that this routine performs a similar role to :meth:`GSASIIdataGUI.GSASII.ReadPowderInstprm`,
296	but that will call a GUI routine for selection when needed. This routine will raise exceptions
297	on errors and will select the first bank when a choice might be appropriate.
298	TODO: refactor to combine the two routines.
299
300	:param list instLines: strings from GSAS-II parameter file; can be concatenated with ';'
301	:param int bank: bank number to check when instprm file has '#BANK n:...' strings
302	when bank = n then use parameters; otherwise skip that set. Ignored if BANK n:
303	not present. NB: this kind of instprm file made by a Save all profile command in Instrument Par ameters
304	:return dict: Inst instrument parameter dict if OK, or
305	str: Error message if failed
306
307	(transliterated from GSASIIdataGUI.py:1235 (rev 3008), function of the same name)
308	'''
309	if 'GSAS-II' not in instLines[0]:
310	raise ValueError("Not a valid GSAS-II instprm file")
311
312	newItems = []
313	newVals = []
314	Found = False
315	il = 0
316	if bank is None:
317	banklist = set()
318	for S in instLines:
319	if S[0] == '#' and 'Bank' in S:
320	banklist.add(int(S.split(':')[0].split()[1]))
321	# Picks the first bank by default
322	if len(banklist) > 1:
323	bank = sorted(banklist)[0]
324	else:
325	bank = 1
326	rd.powderentry[2] = bank
327	while il < len(instLines):
328	S = instLines[il]
329	if S[0] == '#':
330	if Found:
331	break
332	if 'Bank' in S:
333	if bank == int(S.split(':')[0].split()[1]):
334	il += 1
335	S = instLines[il]
336	else:
337	il += 1
338	S = instLines[il]
339	while il < len(instLines) and '#Bank' not in S:
340	il += 1
341	if il == len(instLines):
342	raise ValueError("Bank {} not found in instprm file".format(bank))
343	S = instLines[il]
344	continue
345	else:
346	il += 1
347	S = instLines[il]
348	Found = True
349	if '"""' in S:
350	delim = '"""'
351	elif "'''" in S:
352	delim = "'''"
353	else:
354	S = S.replace(' ', '')
355	SS = S.strip().split(';')
356	for s in SS:
357	item, val = s.split(':', 1)
358	newItems.append(item)
359	try:
360	newVals.append(float(val))
361	except ValueError:
362	newVals.append(val)
363	il += 1
364	continue
365	# read multiline values, delimited by ''' or """
366	item, val = S.strip().split(':', 1)
367	val = val.replace(delim, '').rstrip()
368	val += '\n'
369	while True:
370	il += 1
371	if il >= len(instLines):
372	break
373	S = instLines[il]
374	if delim in S:
375	val += S.replace(delim, '').rstrip()
376	val += '\n'
377	break
378	else:
379	val += S.rstrip()
380	val += '\n'
381	newItems.append(item)
382	newVals.append(val)
383	il += 1
384	if 'Lam1' in newItems:
385	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
386	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
387	else:
388	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
389	return [makeInstDict(newItems, newVals, len(newVals)*[False]), {}]
390
391	def LoadImportRoutines(prefix, errprefix=None, traceback=False):
392	'''Routine to locate GSASII importers matching a prefix string
393	'''
394	if errprefix is None:
395	errprefix = prefix
396
397	readerlist = []
398	import_files = {}
399	if '.' not in sys.path: sys.path.append('.')
400	for path in sys.path:
401	for filename in glob.iglob(os.path.join(path, 'G2'+prefix+'*.py')):
402	pkg = os.path.splitext(os.path.split(filename)[1])[0]
403	if pkg in import_files:
404	G2Print('Warning: file {} hidden by {}'.format(os.path.abspath(filename),import_files[pkg]))
405	else:
406	import_files[pkg] = filename
407
408	for pkg in sorted(import_files.keys()):
409	try:
410	exec('import '+pkg)
411	for name, value in inspect.getmembers(eval(pkg)):
412	if name.startswith('_'):
413	continue
414	if inspect.isclass(value):
415	for method in 'Reader', 'ExtensionValidator', 'ContentsValidator':
416	if not hasattr(value, method):
417	break
418	if not callable(getattr(value, method)):
419	break
420	else:
421	reader = value()
422	if reader.UseReader:
423	readerlist.append(reader)
424	except AttributeError:
425	G2Print ('Import_' + errprefix + ': Attribute Error ' + import_files[pkg])
426	if traceback:
427	traceback.print_exc(file=sys.stdout)
428	except Exception as exc:
429	G2Print ('\nImport_' + errprefix + ': Error importing file ' + import_files[pkg])
430	G2Print (u'Error message: {}\n'.format(exc))
431	if traceback:
432	traceback.print_exc(file=sys.stdout)
433	return readerlist
434
435	def LoadExportRoutines(parent, traceback=False):
436	'''Routine to locate GSASII exporters
437	'''
438	exporterlist = []
439	import_files = {}
440	if '.' not in sys.path: sys.path.append('.')
441	for path in sys.path:
442	for filename in glob.iglob(os.path.join(path,"G2export*.py")):
443	pkg = os.path.splitext(os.path.split(filename)[1])[0]
444	if pkg in import_files:
445	G2Print('Warning: file {} hidden by {}'
446	.format(os.path.abspath(filename),import_files[pkg]))
447	else:
448	import_files[pkg] = filename
449	# go through the routines and import them, saving objects that
450	# have export routines (method Exporter)
451	for pkg in sorted(import_files.keys()):
452	try:
453	exec('import '+pkg)
454	for clss in inspect.getmembers(eval(pkg)): # find classes defined in package
455	if clss[0].startswith('_'): continue
456	if not inspect.isclass(clss[1]): continue
457	# check if we have the required methods
458	if not hasattr(clss[1],'Exporter'): continue
459	if not callable(getattr(clss[1],'Exporter')): continue
460	if parent is None:
461	if not hasattr(clss[1],'Writer'): continue
462	else:
463	if not hasattr(clss[1],'loadParmDict'): continue
464	if not callable(getattr(clss[1],'loadParmDict')): continue
465	try:
466	exporter = clss[1](parent) # create an export instance
467	except AttributeError:
468	pass
469	except Exception as exc:
470	G2Print ('\nExport init: Error substantiating class ' + clss[0])
471	G2Print (u'Error message: {}\n'.format(exc))
472	if traceback:
473	traceback.print_exc(file=sys.stdout)
474	continue
475	exporterlist.append(exporter)
476	except AttributeError:
477	G2Print ('Export Attribute Error ' + import_files[pkg])
478	if traceback:
479	traceback.print_exc(file=sys.stdout)
480	except Exception as exc:
481	G2Print ('\nExport init: Error importing file ' + import_files[pkg])
482	G2Print (u'Error message: {}\n'.format(exc))
483	if traceback:
484	traceback.print_exc(file=sys.stdout)
485	return exporterlist
486
487	def readColMetadata(imagefile):
488	'''Reads image metadata from a column-oriented metadata table
489	(1-ID style .par file). Called by :func:`GetColumnMetadata`
490
491	The .par file has any number of columns separated by spaces.
492	The directory for the file must be specified in
493	Config variable :data:`config_example.Column_Metadata_directory`.
494	As an index to the .par file a second "label file" must be specified with the
495	same file root name as the .par file but the extension must be .XXX_lbls (where
496	.XXX is the extension of the image) or if that is not present extension
497	.lbls.
498
499	:param str imagefile: the full name of the image file (with extension, directory optional)
500
501	:returns: a dict with parameter values. Named parameters will have the type based on
502	the specified Python function, named columns will be character strings
503
504	The contents of the label file will look like this::
505
506	# define keywords
507	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
508	distance: float \| 75
509	wavelength:lambda keV: 12.398425/float(keV)\|9
510	pixelSize:lambda x: [74.8, 74.8]\|0
511	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
512	Temperature: float\|53
513	FreePrm2: int \| 34 \| Free Parm2 Label
514	# define other variables
515	0:day
516	1:month
517	2:date
518	3:time
519	4:year
520	7:I_ring
521
522	This file contains three types of lines in any order.
523	* Named parameters are evaluated with user-supplied Python code (see
524	subsequent information). Specific named parameters are used
525	to determine values that are used for image interpretation (see table,
526	below). Any others are copied to the Comments subsection of the Image
527	tree item.
528	* Column labels are defined with a column number (integer) followed by
529	a colon (:) and a label to be assigned to that column. All labeled
530	columns are copied to the Image's Comments subsection.
531	* Comments are any line that does not contain a colon.
532
533	Note that columns are numbered starting at zero.
534
535	Any named parameter may be defined provided it is not a valid integer,
536	but the named parameters in the table have special meanings, as descibed.
537	The parameter name is followed by a colon. After the colon, specify
538	Python code that defines or specifies a function that will be called to
539	generate a value for that parameter.
540
541	Note that several keywords, if defined in the Comments, will be found and
542	placed in the appropriate section of the powder histogram(s)'s Sample
543	Parameters after an integration: ``Temperature``, ``Pressure``, ``Time``,
544	``FreePrm1``, ``FreePrm2``, ``FreePrm3``, ``Omega``, ``Chi``, and ``Phi``.
545
546	After the Python code, supply a vertical bar (\|) and then a list of one
547	more more columns that will be supplied as arguments to that function.
548
549	Note that the labels for the three FreePrm items can be changed by
550	including that label as a third item with an additional vertical bar. Labels
551	will be ignored for any other named parameters.
552
553	The examples above are discussed here:
554
555	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
556	Here the function to be used is defined with a lambda statement::
557
558	lambda x,y: "{}_{:0>6}".format(x,y)
559
560	This function will use the format function to create a file name from the
561	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
562	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
563	which will be left-padded with zeros to six characters (format directive ``:0>6``).
564
565	When there will be more than one image generated per line in the .par file, an alternate way to
566	generate list of file names takes into account the number of images generated::
567
568	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
569
570	Here a third parameter is used to specify the number of images generated, where
571	the image number is incremented for each image.
572
573	``distance: float \| 75``
574	Here the contents of column 75 will be converted to a floating point number
575	by calling float on it. Note that the spaces here are ignored.
576
577	``wavelength:lambda keV: 12.398425/float(keV)\|9``
578	Here we define an algebraic expression to convert an energy in keV to a
579	wavelength and pass the contents of column 9 as that input energy
580
581	``pixelSize:lambda x: [74.8, 74.8]\|0``
582	In this case the pixel size is a constant (a list of two numbers). The first
583	column is passed as an argument as at least one argument is required, but that
584	value is not used in the expression.
585
586	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
587	This example defines a parameter that takes items in the first five columns
588	and formats them in a different way. This parameter is not one of the pre-defined
589	parameter names below. Some external code could be used to change the month string
590	(argument ``m``) to a integer from 1 to 12.
591
592	``FreePrm2: int \| 34 \| Free Parm2 Label``
593	In this example, the contents of column 34 will be converted to an integer and
594	placed as the second free-named parameter in the Sample Parameters after an
595	integration. The label for this parameter will be changed to "Free Parm2 Label".
596
597	Pre-defined parameter names
598
599	============= ========= ======== =====================================================
600	keyword required type Description
601	============= ========= ======== =====================================================
602	filename yes str or generates the file name prefix for the matching image
603	list file (MyImage001 for file /tmp/MyImage001.tif) or
604	a list of file names.
605	polarization no float generates the polarization expected based on the
606	monochromator angle, defaults to 0.99.
607	center no list of generates the approximate beam center on the detector
608	2 floats in mm, such as [204.8, 204.8].
609	distance yes float generates the distance from the sample to the detector
610	in mm
611	pixelSize no list of generates the size of the pixels in microns such as
612	2 floats [200.0, 200.0].
613	wavelength yes float generates the wavelength in Angstroms
614	============= ========= ======== =====================================================
615
616	'''
617	dir,fil = os.path.split(os.path.abspath(imagefile))
618	imageName,ext = os.path.splitext(fil)
619	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
620	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
621	if len(parfiles) == 0:
622	G2Print('Sorry, No Column metadata (.par) file found in '+
623	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
624	return {}
625	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
626	parRoot = os.path.splitext(parFil)[0]
627	for e in (ext+'_lbls','.lbls'):
628	if os.path.exists(parRoot+e):
629	lblFil = parRoot+e
630	break
631	else:
632	G2Print('Warning: No labels definitions found for '+parFil)
633	continue
634	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
635	if errors:
636	print('Errors in labels file '+lblFil)
637	for i in errors: print(' '+i)
638	continue
639	else:
640	G2Print('Read '+lblFil)
641	# scan through each line in this .par file, looking for the matching image rootname
642	fp = open(parFil,'r')
643	for iline,line in enumerate(fp):
644	items = line.strip().split(' ')
645	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
646	if type(nameList) is str:
647	if nameList != imageName: continue
648	name = nameList
649	else:
650	for name in nameList:
651	if name == imageName: break # got a match
652	else:
653	continue
654	# parse the line and finish
655	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
656	metadata['par file'] = parFil
657	metadata['lbls file'] = lblFil
658	G2Print("Metadata read from {} line {}".format(parFil,iline+1))
659	fp.close()
660	return metadata
661	else:
662	G2Print("Image {} not found in {}".format(imageName,parFil))
663	fp.close()
664	continue
665	fp.close()
666	else:
667	G2Print("Warning: No .par metadata for image {}".format(imageName))
668	return {}
669
670	def readColMetadataLabels(lblFil):
671	'''Read the .*lbls file and setup for metadata assignments
672	'''
673	lbldict = {}
674	keyExp = {}
675	keyCols = {}
676	labels = {}
677	errors = []
678	fp = open(lblFil,'r') # read column labels
679	for iline,line in enumerate(fp): # read label definitions
680	line = line.strip()
681	if not line or line[0] == '#': continue # comments
682	items = line.split(':')
683	if len(items) < 2: continue # lines with no colon are also comments
684	# does this line a definition for a named parameter?
685	key = items[0]
686	try:
687	int(key)
688	except ValueError: # try as named parameter since not a valid number
689	items = line.split(':',1)[1].split('\|')
690	try:
691	f = eval(items[0]) # compile the expression
692	if not callable(f):
693	errors += ['Expression "{}" for key {} is not a function (line {})'.
694	format(items[0],key,iline)]
695	continue
696	keyExp[key] = f
697	except Exception as msg:
698	errors += ['Expression "{}" for key {} is not valid (line {})'.
699	format(items[0],key,iline)]
700	errors += [str(msg)]
701	continue
702	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
703	if key.lower().startswith('freeprm') and len(items) > 2:
704	labels[key] = items[2]
705	continue
706	if len(items) == 2: # simple column definition
707	lbldict[int(items[0])] = items[1]
708	fp.close()
709	if 'filename' not in keyExp:
710	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
711	return labels,lbldict,keyCols,keyExp,errors
712
713	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
714	'''Evaluate the metadata for a line in the .par file
715	'''
716	metadata = {lbldict[j]:items[j] for j in lbldict}
717	named = {}
718	for key in keyExp:
719	try:
720	res = keyExp[key](*[items[j] for j in keyCols[key]])
721	except:
722	if ShowError:
723	res = "* error *"
724	else:
725	continue
726	named[key] = res
727	metadata.update(named)
728	for lbl in labels: # add labels for FreePrm's
729	metadata['label_'+lbl[4:].lower()] = labels[lbl]
730	return metadata
731
732	def GetColumnMetadata(reader):
733	'''Add metadata to an image from a column-type metadata file
734	using :func:`readColMetadata`
735
736	:param reader: a reader object from reading an image
737
738	'''
739	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
740	parParms = readColMetadata(reader.readfilename)
741	if not parParms: return # check for read failure
742	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
743	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
744	for key in parParms:
745	if key in specialKeys+('par file','lbls file'): continue
746	reader.Comments += ["{} = {}".format(key,parParms[key])]
747	if "polarization" in parParms:
748	reader.Data['PolaVal'][0] = parParms["polarization"]
749	else:
750	reader.Data['PolaVal'][0] = 0.99
751	if "center" in parParms:
752	reader.Data['center'] = parParms["center"]
753	if "pixelSize" in parParms:
754	reader.Data['pixelSize'] = parParms["pixelSize"]
755	if "wavelength" in parParms:
756	reader.Data['wavelength'] = parParms['wavelength']
757	else:
758	G2Print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
759	if "distance" in parParms:
760	reader.Data['distance'] = parParms['distance']
761	reader.Data['setdist'] = parParms['distance']
762	else:
763	G2Print('Error: distance not defined in {}'.format(parParms['lbls file']))
764
765	def LoadControls(Slines,data):
766	'Read values from a .imctrl (Image Controls) file'
767	cntlList = ['color','wavelength','distance','tilt','invert_x','invert_y','type','Oblique',
768	'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth',
769	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList','setdist',
770	'PolaVal','SampleAbs','dark image','background image','twoth']
771	save = {}
772	for S in Slines:
773	if S[0] == '#':
774	continue
775	[key,val] = S.strip().split(':',1)
776	if key in ['type','calibrant','binType','SampleShape','color',]: #strings
777	save[key] = val
778	elif key in ['varyList',]:
779	save[key] = eval(val) #dictionary
780	elif key in ['rotation']:
781	save[key] = float(val)
782	elif key in ['center',]:
783	if ',' in val:
784	save[key] = eval(val)
785	else:
786	vals = val.strip('[] ').split()
787	save[key] = [float(vals[0]),float(vals[1])]
788	elif key in cntlList:
789	save[key] = eval(val)
790	data.update(save)
791
792	def WriteControls(filename,data):
793	'Write current values to a .imctrl (Image Controls) file'
794	File = open(filename,'w')
795	keys = ['type','color','wavelength','calibrant','distance','center','Oblique',
796	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth','setdist',
797	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
798	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList',
799	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image',
800	'twoth']
801	for key in keys:
802	if key not in data: #uncalibrated!
803	continue
804	File.write(key+':'+str(data[key])+'\n')
805	File.close()
806
807	def RereadImageData(ImageReaderlist,imagefile,ImageTag=None,FormatName=''):
808	'''Read a single image with an image importer. This is called to
809	reread an image after it has already been imported, so it is not
810	necessary to reload metadata.
811
812	Based on :func:`GetImageData.GetImageData` which this can replace
813	where imageOnly=True
814
815	:param list ImageReaderlist: list of Reader objects for images
816	:param str imagefile: name of image file
817	:param int/str ImageTag: specifies a particular image to be read from a file.
818	First image is read if None (default).
819	:param str formatName: the image reader formatName
820
821	:returns: an image as a numpy array
822	'''
823	# determine which formats are compatible with this file
824	primaryReaders = []
825	secondaryReaders = []
826	for rd in ImageReaderlist:
827	flag = rd.ExtensionValidator(imagefile)
828	if flag is None:
829	secondaryReaders.append(rd)
830	elif flag:
831	if not FormatName:
832	primaryReaders.append(rd)
833	elif FormatName == rd.formatName:
834	primaryReaders.append(rd)
835	if len(secondaryReaders) + len(primaryReaders) == 0:
836	G2Print('Error: No matching format for file '+imagefile)
837	raise Exception('No image read')
838	errorReport = ''
839	if not imagefile:
840	return
841	for rd in primaryReaders+secondaryReaders:
842	rd.ReInitialize() # purge anything from a previous read
843	rd.errors = "" # clear out any old errors
844	if not rd.ContentsValidator(imagefile): # rejected on cursory check
845	errorReport += "\n "+rd.formatName + ' validator error'
846	if rd.errors:
847	errorReport += ': '+rd.errors
848	continue
849	flag = rd.Reader(imagefile,None,blocknum=ImageTag)
850	if flag: # this read succeeded
851	if rd.Image is None:
852	raise Exception('No image read. Strange!')
853	if GSASIIpath.GetConfigValue('Transpose'):
854	G2Print ('Warning: Transposing Image!')
855	rd.Image = rd.Image.T
856	#rd.readfilename = imagefile
857	return rd.Image
858	else:
859	G2Print('Error reading file '+imagefile)
860	G2Print('Error messages(s)\n'+errorReport)
861	raise Exception('No image read')
862
863	def readMasks(filename,masks,ignoreThreshold):
864	'''Read a GSAS-II masks file'''
865	File = open(filename,'r')
866	save = {}
867	oldThreshold = masks['Thresholds'][0]
868	S = File.readline()
869	while S:
870	if S[0] == '#':
871	S = File.readline()
872	continue
873	[key,val] = S.strip().split(':',1)
874	if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
875	if ignoreThreshold and key == 'Thresholds':
876	S = File.readline()
877	continue
878	save[key] = eval(val)
879	if key == 'Thresholds':
880	save[key][0] = oldThreshold
881	save[key][1][1] = min(oldThreshold[1],save[key][1][1])
882	S = File.readline()
883	File.close()
884	masks.update(save)
885	# CleanupMasks
886	for key in ['Points','Rings','Arcs','Polygons']:
887	masks[key] = masks.get(key,[])
888	masks[key] = [i for i in masks[key] if len(i)]
889
890	def PDFWrite(PDFentry,fileroot,PDFsaves,PDFControls,Inst={},Limits=[]):
891	'''Write PDF-related data (G(r), S(Q),...) into files, as
892	selected.
893
894	:param str PDFentry: name of the PDF entry in the tree. This is
895	used for comments in the file specifying where it came from;
896	it can be arbitrary
897	:param str fileroot: name of file(s) to be written. The extension
898	will be ignored.
899	:param list PDFsaves: flags that determine what type of file will be
900	written:
901	PDFsaves[0], if True writes a I(Q) file with a .iq extension
902	PDFsaves[1], if True writes a S(Q) file with a .sq extension
903	PDFsaves[2], if True writes a F(Q) file with a .fq extension
904	PDFsaves[3], if True writes a G(r) file with a .gr extension
905	PDFsaves[4], if True writes G(r) in a pdfGUI input file with
906	a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are
907	both True, the pdfGUI overwrites the G(r) file.
908	PDFsaves[5], if True writes F(Q) & g(R) with .fq & .gr extensions
909	overwrites these if selected by option 2, 3 or 4
910	:param dict PDFControls: The PDF parameters and computed results
911	:param dict Inst: Instrument parameters from the PDWR entry used
912	to compute the PDF. Needed only when PDFsaves[4] is True.
913	:param list Limits: Computation limits from the PDWR entry used
914	to compute the PDF. Needed only when PDFsaves[4] is True.
915	'''
916	import scipy.interpolate as scintp
917	fileroot = os.path.splitext(fileroot)[0]
918	if PDFsaves[0]: #I(Q)
919	iqfilename = fileroot+'.iq'
920	iqdata = PDFControls['I(Q)'][1]
921	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
922	iqfile = open(iqfilename,'w')
923	iqfile.write('#T I(Q) %s\n'%(PDFentry))
924	iqfile.write('#L Q I(Q)\n')
925	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
926	iqnew = zip(qnew,iqfxn(qnew))
927	for q,iq in iqnew:
928	iqfile.write("%15.6g %15.6g\n" % (q,iq))
929	iqfile.close()
930	G2Print (' I(Q) saved to: '+iqfilename)
931
932	if PDFsaves[1]: #S(Q)
933	sqfilename = fileroot+'.sq'
934	sqdata = PDFControls['S(Q)'][1]
935	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
936	sqfile = open(sqfilename,'w')
937	sqfile.write('#T S(Q) %s\n'%(PDFentry))
938	sqfile.write('#L Q S(Q)\n')
939	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
940	sqnew = zip(qnew,sqfxn(qnew))
941	for q,sq in sqnew:
942	sqfile.write("%15.6g %15.6g\n" % (q,sq))
943	sqfile.close()
944	G2Print (' S(Q) saved to: '+sqfilename)
945
946	if PDFsaves[2]: #F(Q)
947	fqfilename = fileroot+'.fq'
948	fqdata = PDFControls['F(Q)'][1]
949	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
950	fqfile = open(fqfilename,'w')
951	fqfile.write('#T F(Q) %s\n'%(PDFentry))
952	fqfile.write('#L Q F(Q)\n')
953	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
954	fqnew = zip(qnew,fqfxn(qnew))
955	for q,fq in fqnew:
956	fqfile.write("%15.6g %15.6g\n" % (q,fq))
957	fqfile.close()
958	G2Print (' F(Q) saved to: '+fqfilename)
959
960	if PDFsaves[3]: #G(R)
961	grfilename = fileroot+'.gr'
962	grdata = PDFControls['G(R)'][1]
963	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
964	grfile = open(grfilename,'w')
965	grfile.write('#T G(R) %s\n'%(PDFentry))
966	grfile.write('#L R G(R)\n')
967	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
968	grnew = zip(rnew,grfxn(rnew))
969	for r,gr in grnew:
970	grfile.write("%15.6g %15.6g\n" % (r,gr))
971	grfile.close()
972	G2Print (' G(R) saved to: '+grfilename)
973
974	if PDFsaves[4]: #pdfGUI file for G(R)
975	import GSASIImath as G2mth
976	import GSASIIlattice as G2lat
977	grfilename = fileroot+'.gr'
978	grdata = PDFControls['G(R)'][1]
979	qdata = PDFControls['I(Q)'][1][0]
980	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
981	grfile = open(grfilename,'w')
982	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
983	grnew = zip(rnew,grfxn(rnew))
984
985	grfile.write('[DEFAULT]\n')
986	grfile.write('\n')
987	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
988	grfile.write('\n')
989	grfile.write('# input and output specifications\n')
990	grfile.write('dataformat = Qnm\n')
991	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
992	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
993	grfile.write('outputtype = gr\n')
994	grfile.write('\n')
995	grfile.write('# PDF calculation setup\n')
996	if 'x' in Inst['Type']:
997	grfile.write('mode = %s\n'%('xray'))
998	elif 'N' in Inst['Type']:
999	grfile.write('mode = %s\n'%('neutron'))
1000	wave = G2mth.getMeanWave(Inst)
1001	grfile.write('wavelength = %.5f\n'%(wave))
1002	formula = ''
1003	for el in PDFControls['ElList']:
1004	formula += el
1005	num = PDFControls['ElList'][el]['FormulaNo']
1006	if num == round(num):
1007	formula += '%d'%(int(num))
1008	else:
1009	formula += '%.2f'%(num)
1010	grfile.write('composition = %s\n'%(formula))
1011	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
1012	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
1013	grfile.write('qmaxinst = %.2f\n'%(highQ))
1014	grfile.write('qmin = %.5f\n'%(qdata[0]))
1015	grfile.write('qmax = %.4f\n'%(qdata[-1]))
1016	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
1017	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
1018	grfile.write('rstep = 0.01\n')
1019	grfile.write('\n')
1020	grfile.write('# End of config '+63*'-')
1021	grfile.write('\n')
1022	grfile.write('#### start data\n')
1023	grfile.write('#S 1\n')
1024	grfile.write('#L r($\\AA$) G($\\AA^{-2}$)\n')
1025	for r,gr in grnew:
1026	grfile.write("%15.2F %15.6F\n" % (r,gr))
1027	grfile.close()
1028	G2Print (' G(R) saved to: '+grfilename)
1029
1030	if len(PDFsaves) > 5 and PDFsaves[5]: #RMCProfile files for F(Q) & g(r) overwrites any above
1031
1032	fqfilename = fileroot+'.fq'
1033	fqdata = PDFControls['F(Q)'][1]
1034	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
1035	fqfile = open(fqfilename,'w')
1036	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
1037	nq = qnew.shape[0]
1038	fqfile.write('%20d\n'%(nq-1))
1039	fqfile.write(fqfilename+'\n')
1040	fqnew = zip(qnew,fqfxn(qnew))
1041	for q,fq in fqnew:
1042	if not q:
1043	continue
1044	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1045	fqfile.close()
1046	G2Print (' F(Q) saved to: '+fqfilename)
1047
1048	grfilename = fileroot+'.gr'
1049	grdata = PDFControls['g(r)'][1]
1050	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1051	grfile = open(grfilename,'w')
1052	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1053	nr = rnew.shape[0]
1054	grfile.write('%20d\n'%(nr-1))
1055	grfile.write(grfilename+'\n')
1056	grnew = zip(rnew,grfxn(rnew))
1057	for r,gr in grnew:
1058	if not r:
1059	continue
1060	grfile.write("%15.6g %15.6g\n" % (r,gr))
1061	grfile.close()
1062	G2Print (' G(R) saved to: '+grfilename)
1063

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