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source: trunk/GSASIIfiles.py @ 4211

Last change on this file since 4211 was 4195, checked in by vondreele, 6 years ago
add a find utility to GSASIIfiles for finding a file within a directory tree faster version of ExpandCell? & define SwapItems? in GSASIIlattice changes to RMCProfile interface
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 43.7 KB

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2019-12-03 09:00:37 +0000 (Tue, 03 Dec 2019) $
4	# $Author: toby $
5	# $Revision: 4195 $
6	# $URL: trunk/GSASIIfiles.py $
7	# $Id: GSASIIfiles.py 4195 2019-12-03 09:00:37Z 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 os
25	import sys
26	import glob
27	import imp
28	import inspect
29	import platform
30	import numpy as np
31
32	import GSASIIpath
33	GSASIIpath.SetVersionNumber("$Revision: 4195 $")
34
35	# N.B. This is duplicated in G2IO
36	def sfloat(S):
37	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
38	if S.strip():
39	try:
40	return float(S)
41	except ValueError:
42	pass
43	return 0.0
44
45	G2printLevel = 'all'
46	'''This defines the level of output from calls to :func:`G2Print`,
47	which should be used in place of print() within this module.
48	Settings for this are 'all', 'warn', 'error' or 'none'. Also see:
49	:func:`G2Print` and :func:`G2SetPrintLevel`.
50	'''
51
52	def G2SetPrintLevel(level):
53	'''Set the level of output from calls to :func:`G2Print`, which should
54	be used in place of print() within GSASII. Settings for the mode are
55	'all', 'warn', 'error' or 'none'
56
57	:param str level: a string used to set the print level, which may be
58	'all', 'warn', 'error' or 'none'.
59	Note that capitalization and extra letters in level are ignored, so
60	'Warn', 'warnings', etc. will all set the mode to 'warn'
61	'''
62	global G2printLevel
63	for mode in 'all', 'warn', 'error', 'none':
64	if mode in level.lower():
65	G2printLevel = mode
66	return
67	else:
68	G2Print('G2SetPrintLevel Error: level={} cannot be interpreted.',
69	'Use all, warn, error or none.')
70
71	def find(name, path):
72	'''find 1st occurance of file in path
73	'''
74	for root, dirs, files in os.walk(path):
75	if name in files:
76	return os.path.join(root, name)
77
78	def G2Print(args,*kwargs):
79	'''Print with filtering based level of output (see :func:`G2SetPrintLevel`).
80	Use G2Print() as replacement for print().
81
82	:param str mode: if specified, this should contain the mode for printing
83	('error', 'warn' or anything else). If not specified, the first argument
84	of the print command (args[0]) should contain the string 'error' for
85	error messages and 'warn' for warning messages
86	(capitalization and additional letters ignored.)
87	'''
88	if G2printLevel is 'none': return
89	if kwargs.get('mode') is None:
90	testStr = str(args[0]).lower()
91	else:
92	testStr = kwargs['mode'][:].lower()
93	del kwargs['mode']
94	level = 2
95	for i,mode in enumerate(('error', 'warn')):
96	if mode in testStr:
97	level = i
98	break
99	if G2printLevel == 'error' and level > 0: return
100	if G2printLevel == 'warn' and level > 1: return
101	print(args,*kwargs)
102
103	def get_python_versions(packagelist):
104	versions = [['Python', sys.version.split()[0]]]
105	for pack in packagelist:
106	try:
107	versions.append([pack.__name__, pack.__version__])
108	except:
109	pass
110	versions.append(['Platform',
111	sys.platform + ' ' + platform.architecture()[0] +
112	' ' + platform.machine()])
113	return versions
114
115	def makeInstDict(names,data,codes):
116	inst = dict(zip(names,zip(data,data,codes)))
117	for item in inst:
118	inst[item] = list(inst[item])
119	return inst
120
121	def SetPowderInstParms(Iparm, rd):
122	'''extracts values from instrument parameters in rd.instdict
123	or in array Iparm.
124	Create and return the contents of the instrument parameter tree entry.
125	'''
126	Irads = {0:' ',1:'CrKa',2:'FeKa',3:'CuKa',4:'MoKa',5:'AgKa',6:'TiKa',7:'CoKa'}
127	DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars
128	# override inst values with values read from data file
129	Bank = rd.powderentry[2] #should be used in multibank iparm files
130	if rd.instdict.get('type'):
131	DataType = rd.instdict.get('type')
132	data = [DataType,]
133	instname = Iparm.get('INS 1INAME ')
134	irad = int(Iparm.get('INS 1 IRAD ','0'))
135	if instname:
136	rd.Sample['InstrName'] = instname.strip()
137	if 'C' in DataType:
138	wave1 = None
139	wave2 = 0.0
140	if rd.instdict.get('wave'):
141	wl = rd.instdict.get('wave')
142	wave1 = wl[0]
143	if len(wl) > 1: wave2 = wl[1]
144	s = Iparm['INS 1 ICONS']
145	if not wave1:
146	wave1 = sfloat(s[:10])
147	wave2 = sfloat(s[10:20])
148	v = (wave1,wave2,
149	sfloat(s[20:30])/100.,sfloat(s[55:65]),sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
150	if not v[1]:
151	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
152	v = (v[0],v[2],v[4])
153	codes = [0,0,0,0,0]
154	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
155	else:
156	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
157	codes = [0,0,0,0,0,0,0]
158	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
159	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
160	data.extend(v)
161	if 'INS 1PRCF ' in Iparm:
162	v1 = Iparm['INS 1PRCF '].split()
163	v = Iparm['INS 1PRCF 1'].split()
164	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
165	azm = float(Iparm.get('INS 1DETAZM','0.0'))
166	v = Iparm['INS 1PRCF 2'].split()
167	if v1[0] == 3:
168	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
169	else:
170	data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
171	else:
172	v1 = Iparm['INS 1PRCF1 '].split()
173	v = Iparm['INS 1PRCF11'].split()
174	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
175	azm = float(Iparm.get('INS 1DETAZM','0.0'))
176	v = Iparm['INS 1PRCF12'].split()
177	if v1[0] == 3:
178	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
179	else:
180	data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
181	codes.extend([0,0,0,0,0,0,0])
182	Iparm1 = makeInstDict(names,data,codes)
183	Iparm1['Source'] = [Irads[irad],Irads[irad]]
184	Iparm1['Bank'] = [Bank,Bank,0]
185	return [Iparm1,{}]
186	elif 'T' in DataType:
187	names = ['Type','fltPath','2-theta','difC','difA', 'difB','Zero','alpha','beta-0','beta-1',
188	'beta-q','sig-0','sig-1','sig-2','sig-q', 'X','Y','Z','Azimuth',]
189	codes = [0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,]
190	azm = 0.
191	if 'INS 1DETAZM' in Iparm:
192	azm = float(Iparm['INS 1DETAZM'])
193	rd.Sample['Azimuth'] = azm
194	fltPath0 = 20. #arbitrary
195	if 'INS FPATH1' in Iparm:
196	s = Iparm['INS FPATH1'].split()
197	fltPath0 = sfloat(s[0])
198	if 'INS 1BNKPAR' not in Iparm: #bank missing from Iparm file
199	return []
200	s = Iparm['INS 1BNKPAR'].split()
201	fltPath1 = sfloat(s[0])
202	data.extend([fltPath0+fltPath1,]) #Flight path source-sample-detector
203	data.extend([sfloat(s[1]),]) #2-theta for bank
204	s = Iparm['INS 1 ICONS'].split()
205	data.extend([sfloat(s[0]),sfloat(s[1]),0.0,sfloat(s[2])]) #difC,difA,difB,Zero
206	if 'INS 1PRCF ' in Iparm:
207	s = Iparm['INS 1PRCF '].split()
208	pfType = int(s[0])
209	s = Iparm['INS 1PRCF 1'].split()
210	if abs(pfType) == 1:
211	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
212	s = Iparm['INS 1PRCF 2'].split()
213	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
214	elif abs(pfType) in [3,4,5]:
215	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
216	if abs(pfType) == 4:
217	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
218	else:
219	s = Iparm['INS 1PRCF 2'].split()
220	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
221	elif abs(pfType) == 2:
222	data.extend([sfloat(s[1]),0.0,1./sfloat(s[3])]) #alpha, beta-0, beta-1
223	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
224	else:
225	s = Iparm['INS 1PRCF1 '].split()
226	pfType = int(s[0])
227	s = Iparm['INS 1PRCF11'].split()
228	if abs(pfType) == 1:
229	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
230	s = Iparm['INS 1PRCF12'].split()
231	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
232	elif abs(pfType) in [3,4,5]:
233	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
234	if abs(pfType) == 4:
235	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
236	else:
237	s = Iparm['INS 1PRCF12'].split()
238	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
239	Inst1 = makeInstDict(names,data,codes)
240	Inst1['Bank'] = [Bank,Bank,0]
241	Inst2 = {}
242	if pfType < 0:
243	Ipab = 'INS 1PAB'+str(-pfType)
244	Npab = int(Iparm[Ipab+' '].strip())
245	Inst2['Pdabc'] = []
246	for i in range(Npab):
247	k = Ipab+str(i+1).rjust(2)
248	s = Iparm[k].split()
249	Inst2['Pdabc'].append([float(t) for t in s])
250	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
251	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
252	if 'INS 1I ITYP' in Iparm:
253	s = Iparm['INS 1I ITYP'].split()
254	Ityp = int(s[0])
255	Tminmax = [float(s[1])1000.,float(s[2])1000.]
256	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
257	if Ityp in [1,2,4]:
258	Inst2['Itype'] = Itypes[Ityp-1]
259	Inst2['Tminmax'] = Tminmax
260	Icoeff = []
261	Iesd = []
262	Icovar = []
263	for i in range(3):
264	s = Iparm['INS 1ICOFF'+str(i+1)].split()
265	Icoeff += [float(S) for S in s]
266	s = Iparm['INS 1IECOF'+str(i+1)].split()
267	Iesd += [float(S) for S in s]
268	NT = 10
269	for i in range(8):
270	s = Iparm['INS 1IECOR'+str(i+1)]
271	if i == 7:
272	NT = 8
273	Icovar += [float(s[6j:6j+6]) for j in range(NT)]
274	Inst2['Icoeff'] = Icoeff
275	Inst2['Iesd'] = Iesd
276	Inst2['Icovar'] = Icovar
277	return [Inst1,Inst2]
278
279	def ReadPowderInstprm(instLines, bank, databanks, rd):
280	'''Read lines from a GSAS-II (new) instrument parameter file
281	similar to G2pwdGUI.OnLoad
282	If instprm file has multiple banks each with header #Bank n: ..., this
283	finds matching bank no. to load - problem with nonmatches?
284
285	Note that this routine performs a similar role to :meth:`GSASIIdataGUI.GSASII.ReadPowderInstprm`,
286	but that will call a GUI routine for selection when needed. This routine will raise exceptions
287	on errors and will select the first bank when a choice might be appropriate.
288	TODO: refactor to combine the two routines.
289
290	:param list instLines: strings from GSAS-II parameter file; can be concatenated with ';'
291	:param int bank: bank number to check when instprm file has '#BANK n:...' strings
292	when bank = n then use parameters; otherwise skip that set. Ignored if BANK n:
293	not present. NB: this kind of instprm file made by a Save all profile command in Instrument Par ameters
294	:return dict: Inst instrument parameter dict if OK, or
295	str: Error message if failed
296
297	(transliterated from GSASIIdataGUI.py:1235 (rev 3008), function of the same name)
298	'''
299	if 'GSAS-II' not in instLines[0]:
300	raise ValueError("Not a valid GSAS-II instprm file")
301
302	newItems = []
303	newVals = []
304	Found = False
305	il = 0
306	if bank is None:
307	banklist = set()
308	for S in instLines:
309	if S[0] == '#' and 'Bank' in S:
310	banklist.add(int(S.split(':')[0].split()[1]))
311	# Picks the first bank by default
312	if len(banklist) > 1:
313	bank = sorted(banklist)[0]
314	else:
315	bank = 1
316	rd.powderentry[2] = bank
317	while il < len(instLines):
318	S = instLines[il]
319	if S[0] == '#':
320	if Found:
321	break
322	if 'Bank' in S:
323	if bank == int(S.split(':')[0].split()[1]):
324	il += 1
325	S = instLines[il]
326	else:
327	il += 1
328	S = instLines[il]
329	while il < len(instLines) and '#Bank' not in S:
330	il += 1
331	if il == len(instLines):
332	raise ValueError("Bank {} not found in instprm file".format(bank))
333	S = instLines[il]
334	continue
335	else:
336	il += 1
337	S = instLines[il]
338	Found = True
339	if '"""' in S:
340	delim = '"""'
341	elif "'''" in S:
342	delim = "'''"
343	else:
344	S = S.replace(' ', '')
345	SS = S.strip().split(';')
346	for s in SS:
347	item, val = s.split(':', 1)
348	newItems.append(item)
349	try:
350	newVals.append(float(val))
351	except ValueError:
352	newVals.append(val)
353	il += 1
354	continue
355	# read multiline values, delimited by ''' or """
356	item, val = S.strip().split(':', 1)
357	val = val.replace(delim, '').rstrip()
358	val += '\n'
359	while True:
360	il += 1
361	if il >= len(instLines):
362	break
363	S = instLines[il]
364	if delim in S:
365	val += S.replace(delim, '').rstrip()
366	val += '\n'
367	break
368	else:
369	val += S.rstrip()
370	val += '\n'
371	newItems.append(item)
372	newVals.append(val)
373	il += 1
374	if 'Lam1' in newItems:
375	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
376	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
377	else:
378	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
379	return [makeInstDict(newItems, newVals, len(newVals)*[False]), {}]
380
381	def LoadImportRoutines(prefix, errprefix=None, traceback=False):
382	'''Routine to locate GSASII importers matching a prefix string
383	'''
384	if errprefix is None:
385	errprefix = prefix
386
387	readerlist = []
388	pathlist = sys.path[:]
389	if '.' not in pathlist:
390	pathlist.append('.')
391
392	potential_files = []
393	for path in pathlist:
394	for filename in glob.iglob(os.path.join(path, 'G2'+prefix+'*.py')):
395	potential_files.append(filename)
396
397	potential_files = sorted(list(set(potential_files)))
398	for filename in potential_files:
399	path, rootname = os.path.split(filename)
400	pkg = os.path.splitext(rootname)[0]
401
402	try:
403	fp = None
404	fp, fppath, desc = imp.find_module(pkg, [path])
405	pkg = imp.load_module(pkg, fp, fppath, desc)
406	for name, value in inspect.getmembers(pkg):
407	if name.startswith('_'):
408	continue
409	if inspect.isclass(value):
410	for method in 'Reader', 'ExtensionValidator', 'ContentsValidator':
411	if not hasattr(value, method):
412	break
413	if not callable(getattr(value, method)):
414	break
415	else:
416	reader = value()
417	if reader.UseReader:
418	readerlist.append(reader)
419	except AttributeError:
420	G2Print ('Import_' + errprefix + ': Attribute Error ' + filename)
421	if traceback:
422	traceback.print_exc(file=sys.stdout)
423	except Exception as exc:
424	G2Print ('\nImport_' + errprefix + ': Error importing file ' + filename)
425	G2Print (u'Error message: {}\n'.format(exc))
426	if traceback:
427	traceback.print_exc(file=sys.stdout)
428	finally:
429	if fp:
430	fp.close()
431
432	return readerlist
433
434	def LoadExportRoutines(parent, traceback=False):
435	'''Routine to locate GSASII exporters
436	'''
437	exporterlist = []
438	pathlist = sys.path
439	filelist = []
440	for path in pathlist:
441	for filename in glob.iglob(os.path.join(path,"G2export*.py")):
442	filelist.append(filename)
443	filelist = sorted(list(set(filelist))) # remove duplicates
444	# go through the routines and import them, saving objects that
445	# have export routines (method Exporter)
446	for filename in filelist:
447	path,rootname = os.path.split(filename)
448	pkg = os.path.splitext(rootname)[0]
449	try:
450	fp = None
451	fp, fppath,desc = imp.find_module(pkg,[path,])
452	pkg = imp.load_module(pkg,fp,fppath,desc)
453	for clss in inspect.getmembers(pkg): # find classes defined in package
454	if clss[0].startswith('_'): continue
455	if not inspect.isclass(clss[1]): continue
456	# check if we have the required methods
457	if not hasattr(clss[1],'Exporter'): continue
458	if not callable(getattr(clss[1],'Exporter')): continue
459	if parent is None:
460	if not hasattr(clss[1],'Writer'): continue
461	else:
462	if not hasattr(clss[1],'loadParmDict'): continue
463	if not callable(getattr(clss[1],'loadParmDict')): continue
464	try:
465	exporter = clss[1](parent) # create an export instance
466	except AttributeError:
467	pass
468	except Exception as exc:
469	G2Print ('\nExport init: Error substantiating class ' + clss[0])
470	G2Print (u'Error message: {}\n'.format(exc))
471	if traceback:
472	traceback.print_exc(file=sys.stdout)
473	continue
474	exporterlist.append(exporter)
475	except AttributeError:
476	G2Print ('Export Attribute Error ' + filename)
477	if traceback:
478	traceback.print_exc(file=sys.stdout)
479	except Exception as exc:
480	G2Print ('\nExport init: Error importing file ' + filename)
481	G2Print (u'Error message: {}\n'.format(exc))
482	if traceback:
483	traceback.print_exc(file=sys.stdout)
484	finally:
485	if fp:
486	fp.close()
487	return exporterlist
488
489	def readColMetadata(imagefile):
490	'''Reads image metadata from a column-oriented metadata table
491	(1-ID style .par file). Called by :func:`GetColumnMetadata`
492
493	The .par file has any number of columns separated by spaces.
494	The directory for the file must be specified in
495	Config variable :data:`config_example.Column_Metadata_directory`.
496	As an index to the .par file a second "label file" must be specified with the
497	same file root name as the .par file but the extension must be .XXX_lbls (where
498	.XXX is the extension of the image) or if that is not present extension
499	.lbls.
500
501	:param str imagefile: the full name of the image file (with extension, directory optional)
502
503	:returns: a dict with parameter values. Named parameters will have the type based on
504	the specified Python function, named columns will be character strings
505
506	The contents of the label file will look like this::
507
508	# define keywords
509	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
510	distance: float \| 75
511	wavelength:lambda keV: 12.398425/float(keV)\|9
512	pixelSize:lambda x: [74.8, 74.8]\|0
513	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
514	Temperature: float\|53
515	FreePrm2: int \| 34 \| Free Parm2 Label
516	# define other variables
517	0:day
518	1:month
519	2:date
520	3:time
521	4:year
522	7:I_ring
523
524	This file contains three types of lines in any order.
525	* Named parameters are evaluated with user-supplied Python code (see
526	subsequent information). Specific named parameters are used
527	to determine values that are used for image interpretation (see table,
528	below). Any others are copied to the Comments subsection of the Image
529	tree item.
530	* Column labels are defined with a column number (integer) followed by
531	a colon (:) and a label to be assigned to that column. All labeled
532	columns are copied to the Image's Comments subsection.
533	* Comments are any line that does not contain a colon.
534
535	Note that columns are numbered starting at zero.
536
537	Any named parameter may be defined provided it is not a valid integer,
538	but the named parameters in the table have special meanings, as descibed.
539	The parameter name is followed by a colon. After the colon, specify
540	Python code that defines or specifies a function that will be called to
541	generate a value for that parameter.
542
543	Note that several keywords, if defined in the Comments, will be found and
544	placed in the appropriate section of the powder histogram(s)'s Sample
545	Parameters after an integration: ``Temperature``, ``Pressure``, ``Time``,
546	``FreePrm1``, ``FreePrm2``, ``FreePrm3``, ``Omega``, ``Chi``, and ``Phi``.
547
548	After the Python code, supply a vertical bar (\|) and then a list of one
549	more more columns that will be supplied as arguments to that function.
550
551	Note that the labels for the three FreePrm items can be changed by
552	including that label as a third item with an additional vertical bar. Labels
553	will be ignored for any other named parameters.
554
555	The examples above are discussed here:
556
557	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
558	Here the function to be used is defined with a lambda statement::
559
560	lambda x,y: "{}_{:0>6}".format(x,y)
561
562	This function will use the format function to create a file name from the
563	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
564	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
565	which will be left-padded with zeros to six characters (format directive ``:0>6``).
566
567	When there will be more than one image generated per line in the .par file, an alternate way to
568	generate list of file names takes into account the number of images generated::
569
570	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
571
572	Here a third parameter is used to specify the number of images generated, where
573	the image number is incremented for each image.
574
575	``distance: float \| 75``
576	Here the contents of column 75 will be converted to a floating point number
577	by calling float on it. Note that the spaces here are ignored.
578
579	``wavelength:lambda keV: 12.398425/float(keV)\|9``
580	Here we define an algebraic expression to convert an energy in keV to a
581	wavelength and pass the contents of column 9 as that input energy
582
583	``pixelSize:lambda x: [74.8, 74.8]\|0``
584	In this case the pixel size is a constant (a list of two numbers). The first
585	column is passed as an argument as at least one argument is required, but that
586	value is not used in the expression.
587
588	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
589	This example defines a parameter that takes items in the first five columns
590	and formats them in a different way. This parameter is not one of the pre-defined
591	parameter names below. Some external code could be used to change the month string
592	(argument ``m``) to a integer from 1 to 12.
593
594	``FreePrm2: int \| 34 \| Free Parm2 Label``
595	In this example, the contents of column 34 will be converted to an integer and
596	placed as the second free-named parameter in the Sample Parameters after an
597	integration. The label for this parameter will be changed to "Free Parm2 Label".
598
599	Pre-defined parameter names
600
601	============= ========= ======== =====================================================
602	keyword required type Description
603	============= ========= ======== =====================================================
604	filename yes str or generates the file name prefix for the matching image
605	list file (MyImage001 for file /tmp/MyImage001.tif) or
606	a list of file names.
607	polarization no float generates the polarization expected based on the
608	monochromator angle, defaults to 0.99.
609	center no list of generates the approximate beam center on the detector
610	2 floats in mm, such as [204.8, 204.8].
611	distance yes float generates the distance from the sample to the detector
612	in mm
613	pixelSize no list of generates the size of the pixels in microns such as
614	2 floats [200.0, 200.0].
615	wavelength yes float generates the wavelength in Angstroms
616	============= ========= ======== =====================================================
617
618	'''
619	dir,fil = os.path.split(os.path.abspath(imagefile))
620	imageName,ext = os.path.splitext(fil)
621	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
622	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
623	if len(parfiles) == 0:
624	G2Print('Sorry, No Column metadata (.par) file found in '+
625	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
626	return {}
627	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
628	parRoot = os.path.splitext(parFil)[0]
629	for e in (ext+'_lbls','.lbls'):
630	if os.path.exists(parRoot+e):
631	lblFil = parRoot+e
632	break
633	else:
634	G2Print('Warning: No labels definitions found for '+parFil)
635	continue
636	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
637	if errors:
638	print('Errors in labels file '+lblFil)
639	for i in errors: print(' '+i)
640	continue
641	else:
642	G2Print('Read '+lblFil)
643	# scan through each line in this .par file, looking for the matching image rootname
644	fp = open(parFil,'Ur')
645	for iline,line in enumerate(fp):
646	items = line.strip().split(' ')
647	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
648	if type(nameList) is str:
649	if nameList != imageName: continue
650	name = nameList
651	else:
652	for name in nameList:
653	if name == imageName: break # got a match
654	else:
655	continue
656	# parse the line and finish
657	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
658	metadata['par file'] = parFil
659	metadata['lbls file'] = lblFil
660	G2Print("Metadata read from {} line {}".format(parFil,iline+1))
661	fp.close()
662	return metadata
663	else:
664	G2Print("Image {} not found in {}".format(imageName,parFil))
665	fp.close()
666	continue
667	fp.close()
668	else:
669	G2Print("Warning: No .par metadata for image {}".format(imageName))
670	return {}
671
672	def readColMetadataLabels(lblFil):
673	'''Read the .*lbls file and setup for metadata assignments
674	'''
675	lbldict = {}
676	keyExp = {}
677	keyCols = {}
678	labels = {}
679	errors = []
680	fp = open(lblFil,'Ur') # read column labels
681	for iline,line in enumerate(fp): # read label definitions
682	line = line.strip()
683	if not line or line[0] == '#': continue # comments
684	items = line.split(':')
685	if len(items) < 2: continue # lines with no colon are also comments
686	# does this line a definition for a named parameter?
687	key = items[0]
688	try:
689	int(key)
690	except ValueError: # try as named parameter since not a valid number
691	items = line.split(':',1)[1].split('\|')
692	try:
693	f = eval(items[0]) # compile the expression
694	if not callable(f):
695	errors += ['Expression "{}" for key {} is not a function (line {})'.
696	format(items[0],key,iline)]
697	continue
698	keyExp[key] = f
699	except Exception as msg:
700	errors += ['Expression "{}" for key {} is not valid (line {})'.
701	format(items[0],key,iline)]
702	errors += [str(msg)]
703	continue
704	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
705	if key.lower().startswith('freeprm') and len(items) > 2:
706	labels[key] = items[2]
707	continue
708	if len(items) == 2: # simple column definition
709	lbldict[int(items[0])] = items[1]
710	fp.close()
711	if 'filename' not in keyExp:
712	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
713	return labels,lbldict,keyCols,keyExp,errors
714
715	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
716	'''Evaluate the metadata for a line in the .par file
717	'''
718	metadata = {lbldict[j]:items[j] for j in lbldict}
719	named = {}
720	for key in keyExp:
721	try:
722	res = keyExp[key](*[items[j] for j in keyCols[key]])
723	except:
724	if ShowError:
725	res = "* error *"
726	else:
727	continue
728	named[key] = res
729	metadata.update(named)
730	for lbl in labels: # add labels for FreePrm's
731	metadata['label_'+lbl[4:].lower()] = labels[lbl]
732	return metadata
733
734	def GetColumnMetadata(reader):
735	'''Add metadata to an image from a column-type metadata file
736	using :func:`readColMetadata`
737
738	:param reader: a reader object from reading an image
739
740	'''
741	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
742	parParms = readColMetadata(reader.readfilename)
743	if not parParms: return # check for read failure
744	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
745	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
746	for key in parParms:
747	if key in specialKeys+('par file','lbls file'): continue
748	reader.Comments += ["{} = {}".format(key,parParms[key])]
749	if "polarization" in parParms:
750	reader.Data['PolaVal'][0] = parParms["polarization"]
751	else:
752	reader.Data['PolaVal'][0] = 0.99
753	if "center" in parParms:
754	reader.Data['center'] = parParms["center"]
755	if "pixelSize" in parParms:
756	reader.Data['pixelSize'] = parParms["pixelSize"]
757	if "wavelength" in parParms:
758	reader.Data['wavelength'] = parParms['wavelength']
759	else:
760	G2Print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
761	if "distance" in parParms:
762	reader.Data['distance'] = parParms['distance']
763	reader.Data['setdist'] = parParms['distance']
764	else:
765	G2Print('Error: distance not defined in {}'.format(parParms['lbls file']))
766
767	def LoadControls(Slines,data):
768	'Read values from a .imctrl (Image Controls) file'
769	cntlList = ['color','wavelength','distance','tilt','invert_x','invert_y','type','Oblique',
770	'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth',
771	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList','setdist',
772	'PolaVal','SampleAbs','dark image','background image','twoth']
773	save = {}
774	for S in Slines:
775	if S[0] == '#':
776	continue
777	[key,val] = S.strip().split(':',1)
778	if key in ['type','calibrant','binType','SampleShape','color',]: #strings
779	save[key] = val
780	elif key in ['varyList',]:
781	save[key] = eval(val) #dictionary
782	elif key in ['rotation']:
783	save[key] = float(val)
784	elif key in ['center',]:
785	if ',' in val:
786	save[key] = eval(val)
787	else:
788	vals = val.strip('[] ').split()
789	save[key] = [float(vals[0]),float(vals[1])]
790	elif key in cntlList:
791	save[key] = eval(val)
792	data.update(save)
793
794	def WriteControls(filename,data):
795	'Write current values to a .imctrl (Image Controls) file'
796	File = open(filename,'w')
797	keys = ['type','color','wavelength','calibrant','distance','center','Oblique',
798	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth','setdist',
799	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
800	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList',
801	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image',
802	'twoth']
803	for key in keys:
804	if key not in data: #uncalibrated!
805	continue
806	File.write(key+':'+str(data[key])+'\n')
807	File.close()
808
809	def RereadImageData(ImageReaderlist,imagefile,ImageTag=None,FormatName=''):
810	'''Read a single image with an image importer. This is called to
811	reread an image after it has already been imported, so it is not
812	necessary to reload metadata.
813
814	Based on :func:`GetImageData.GetImageData` which this can replace
815	where imageOnly=True
816
817	:param list ImageReaderlist: list of Reader objects for images
818	:param str imagefile: name of image file
819	:param int/str ImageTag: specifies a particular image to be read from a file.
820	First image is read if None (default).
821	:param str formatName: the image reader formatName
822
823	:returns: an image as a numpy array
824	'''
825	# determine which formats are compatible with this file
826	primaryReaders = []
827	secondaryReaders = []
828	for rd in ImageReaderlist:
829	flag = rd.ExtensionValidator(imagefile)
830	if flag is None:
831	secondaryReaders.append(rd)
832	elif flag:
833	if not FormatName:
834	primaryReaders.append(rd)
835	elif FormatName == rd.formatName:
836	primaryReaders.append(rd)
837	if len(secondaryReaders) + len(primaryReaders) == 0:
838	G2Print('Error: No matching format for file '+imagefile)
839	raise Exception('No image read')
840	errorReport = ''
841	if not imagefile:
842	return
843	for rd in primaryReaders+secondaryReaders:
844	rd.ReInitialize() # purge anything from a previous read
845	rd.errors = "" # clear out any old errors
846	if not rd.ContentsValidator(imagefile): # rejected on cursory check
847	errorReport += "\n "+rd.formatName + ' validator error'
848	if rd.errors:
849	errorReport += ': '+rd.errors
850	continue
851	flag = rd.Reader(imagefile,None,blocknum=ImageTag)
852	if flag: # this read succeeded
853	if rd.Image is None:
854	raise Exception('No image read. Strange!')
855	if GSASIIpath.GetConfigValue('Transpose'):
856	G2Print ('Warning: Transposing Image!')
857	rd.Image = rd.Image.T
858	#rd.readfilename = imagefile
859	return rd.Image
860	else:
861	G2Print('Error reading file '+imagefile)
862	G2Print('Error messages(s)\n'+errorReport)
863	raise Exception('No image read')
864
865	def readMasks(filename,masks,ignoreThreshold):
866	'''Read a GSAS-II masks file'''
867	File = open(filename,'r')
868	save = {}
869	oldThreshold = masks['Thresholds'][0]
870	S = File.readline()
871	while S:
872	if S[0] == '#':
873	S = File.readline()
874	continue
875	[key,val] = S.strip().split(':',1)
876	if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
877	if ignoreThreshold and key == 'Thresholds':
878	S = File.readline()
879	continue
880	save[key] = eval(val)
881	if key == 'Thresholds':
882	save[key][0] = oldThreshold
883	save[key][1][1] = min(oldThreshold[1],save[key][1][1])
884	S = File.readline()
885	File.close()
886	masks.update(save)
887	# CleanupMasks
888	for key in ['Points','Rings','Arcs','Polygons']:
889	masks[key] = masks.get(key,[])
890	masks[key] = [i for i in masks[key] if len(i)]
891
892	def PDFWrite(PDFentry,fileroot,PDFsaves,PDFControls,Inst={},Limits=[]):
893	'''Write PDF-related data (G(r), S(Q),...) into files, as
894	selected.
895
896	:param str PDFentry: name of the PDF entry in the tree. This is
897	used for comments in the file specifying where it came from;
898	it can be arbitrary
899	:param str fileroot: name of file(s) to be written. The extension
900	will be ignored.
901	:param list PDFsaves: flags that determine what type of file will be
902	written:
903	PDFsaves[0], if True writes a I(Q) file with a .iq extension
904	PDFsaves[1], if True writes a S(Q) file with a .sq extension
905	PDFsaves[2], if True writes a F(Q) file with a .fq extension
906	PDFsaves[3], if True writes a G(r) file with a .gr extension
907	PDFsaves[4], if True writes G(r) in a pdfGUI input file with
908	a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are
909	both True, the pdfGUI overwrites the G(r) file.
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
1020
1021	grfile.write('\n')
1022	grfile.write('# End of config '+63*'-')
1023	grfile.write('\n')
1024	grfile.write('#### start data\n')
1025	grfile.write('#S 1\n')
1026	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
1027	for r,gr in grnew:
1028	grfile.write("%15.2F %15.6F\n" % (r,gr))
1029	grfile.close()
1030	G2Print (' G(R) saved to: '+grfilename)

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