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source: trunk/GSASIIfiles.py @ 4024

Last change on this file since 4024 was 4024, checked in by toby, 4 years ago
fix for print w/optional mode arg
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2019-06-12 18:00:22 +0000 (Wed, 12 Jun 2019) $
4	# $Author: toby $
5	# $Revision: 4024 $
6	# $URL: trunk/GSASIIfiles.py $
7	# $Id: GSASIIfiles.py 4024 2019-06-12 18:00:22Z 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: 4024 $")
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 G2Print(args,*kwargs):
72	'''Print with filtering based level of output (see :func:`G2SetPrintLevel`).
73	Use G2Print() as replacement for print().
74
75	:param str mode: if specified, this should contain the mode for printing
76	('error', 'warn' or anything else). If not specified, the first argument
77	of the print command (args[0]) should contain the string 'error' for
78	error messages and 'warn' for warning messages
79	(capitalization and additional letters ignored.)
80	'''
81	if G2printLevel is 'none': return
82	if kwargs.get('mode') is None:
83	testStr = args[0].lower()
84	else:
85	testStr = kwargs['mode'][:].lower()
86	del kwargs['mode']
87	level = 2
88	for i,mode in enumerate(('error', 'warn')):
89	if mode in testStr:
90	level = i
91	break
92	if G2printLevel == 'error' and level > 0: return
93	if G2printLevel == 'warn' and level > 1: return
94	print(args,*kwargs)
95
96	def get_python_versions(packagelist):
97	versions = [['Python', sys.version.split()[0]]]
98	for pack in packagelist:
99	try:
100	versions.append([pack.__name__, pack.__version__])
101	except:
102	pass
103	versions.append(['Platform',
104	sys.platform + ' ' + platform.architecture()[0] +
105	' ' + platform.machine()])
106	return versions
107
108	def makeInstDict(names,data,codes):
109	inst = dict(zip(names,zip(data,data,codes)))
110	for item in inst:
111	inst[item] = list(inst[item])
112	return inst
113
114	def SetPowderInstParms(Iparm, rd):
115	'''extracts values from instrument parameters in rd.instdict
116	or in array Iparm.
117	Create and return the contents of the instrument parameter tree entry.
118	'''
119	Irads = {0:' ',1:'CrKa',2:'FeKa',3:'CuKa',4:'MoKa',5:'AgKa',6:'TiKa',7:'CoKa'}
120	DataType = Iparm['INS HTYPE '].strip()[:3] # take 1st 3 chars
121	# override inst values with values read from data file
122	Bank = rd.powderentry[2] #should be used in multibank iparm files
123	if rd.instdict.get('type'):
124	DataType = rd.instdict.get('type')
125	data = [DataType,]
126	instname = Iparm.get('INS 1INAME ')
127	irad = int(Iparm.get('INS 1 IRAD ','0'))
128	if instname:
129	rd.Sample['InstrName'] = instname.strip()
130	if 'C' in DataType:
131	wave1 = None
132	wave2 = 0.0
133	if rd.instdict.get('wave'):
134	wl = rd.instdict.get('wave')
135	wave1 = wl[0]
136	if len(wl) > 1: wave2 = wl[1]
137	s = Iparm['INS 1 ICONS']
138	if not wave1:
139	wave1 = sfloat(s[:10])
140	wave2 = sfloat(s[10:20])
141	v = (wave1,wave2,
142	sfloat(s[20:30])/100.,sfloat(s[55:65]),sfloat(s[40:50])) #get lam1, lam2, zero, pola & ratio
143	if not v[1]:
144	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
145	v = (v[0],v[2],v[4])
146	codes = [0,0,0,0,0]
147	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
148	else:
149	names = ['Type','Lam1','Lam2','Zero','I(L2)/I(L1)','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
150	codes = [0,0,0,0,0,0,0]
151	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
152	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
153	data.extend(v)
154	if 'INS 1PRCF ' in Iparm:
155	v1 = Iparm['INS 1PRCF '].split()
156	v = Iparm['INS 1PRCF 1'].split()
157	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
158	azm = float(Iparm.get('INS 1DETAZM','0.0'))
159	v = Iparm['INS 1PRCF 2'].split()
160	if v1[0] == 3:
161	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
162	else:
163	data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
164	else:
165	v1 = Iparm['INS 1PRCF1 '].split()
166	v = Iparm['INS 1PRCF11'].split()
167	data.extend([float(v[0]),float(v[1]),float(v[2])]) #get GU, GV & GW - always here
168	azm = float(Iparm.get('INS 1DETAZM','0.0'))
169	v = Iparm['INS 1PRCF12'].split()
170	if v1[0] == 3:
171	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
172	else:
173	data.extend([0.0,0.0,0.0,0.002,azm]) #OK defaults if fxn #3 not 1st in iprm file
174	codes.extend([0,0,0,0,0,0,0])
175	Iparm1 = makeInstDict(names,data,codes)
176	Iparm1['Source'] = [Irads[irad],Irads[irad]]
177	Iparm1['Bank'] = [Bank,Bank,0]
178	return [Iparm1,{}]
179	elif 'T' in DataType:
180	names = ['Type','fltPath','2-theta','difC','difA', 'difB','Zero','alpha','beta-0','beta-1',
181	'beta-q','sig-0','sig-1','sig-2','sig-q', 'X','Y','Z','Azimuth',]
182	codes = [0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,]
183	azm = 0.
184	if 'INS 1DETAZM' in Iparm:
185	azm = float(Iparm['INS 1DETAZM'])
186	rd.Sample['Azimuth'] = azm
187	fltPath0 = 20. #arbitrary
188	if 'INS FPATH1' in Iparm:
189	s = Iparm['INS FPATH1'].split()
190	fltPath0 = sfloat(s[0])
191	if 'INS 1BNKPAR' not in Iparm: #bank missing from Iparm file
192	return []
193	s = Iparm['INS 1BNKPAR'].split()
194	fltPath1 = sfloat(s[0])
195	data.extend([fltPath0+fltPath1,]) #Flight path source-sample-detector
196	data.extend([sfloat(s[1]),]) #2-theta for bank
197	s = Iparm['INS 1 ICONS'].split()
198	data.extend([sfloat(s[0]),sfloat(s[1]),0.0,sfloat(s[2])]) #difC,difA,difB,Zero
199	if 'INS 1PRCF ' in Iparm:
200	s = Iparm['INS 1PRCF '].split()
201	pfType = int(s[0])
202	s = Iparm['INS 1PRCF 1'].split()
203	if abs(pfType) == 1:
204	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
205	s = Iparm['INS 1PRCF 2'].split()
206	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
207	elif abs(pfType) in [3,4,5]:
208	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
209	if abs(pfType) == 4:
210	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
211	else:
212	s = Iparm['INS 1PRCF 2'].split()
213	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
214	elif abs(pfType) == 2:
215	data.extend([sfloat(s[1]),0.0,1./sfloat(s[3])]) #alpha, beta-0, beta-1
216	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
217	else:
218	s = Iparm['INS 1PRCF1 '].split()
219	pfType = int(s[0])
220	s = Iparm['INS 1PRCF11'].split()
221	if abs(pfType) == 1:
222	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
223	s = Iparm['INS 1PRCF12'].split()
224	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
225	elif abs(pfType) in [3,4,5]:
226	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
227	if abs(pfType) == 4:
228	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
229	else:
230	s = Iparm['INS 1PRCF12'].split()
231	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
232	Inst1 = makeInstDict(names,data,codes)
233	Inst1['Bank'] = [Bank,Bank,0]
234	Inst2 = {}
235	if pfType < 0:
236	Ipab = 'INS 1PAB'+str(-pfType)
237	Npab = int(Iparm[Ipab+' '].strip())
238	Inst2['Pdabc'] = []
239	for i in range(Npab):
240	k = Ipab+str(i+1).rjust(2)
241	s = Iparm[k].split()
242	Inst2['Pdabc'].append([float(t) for t in s])
243	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
244	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
245	if 'INS 1I ITYP' in Iparm:
246	s = Iparm['INS 1I ITYP'].split()
247	Ityp = int(s[0])
248	Tminmax = [float(s[1])1000.,float(s[2])1000.]
249	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
250	if Ityp in [1,2,4]:
251	Inst2['Itype'] = Itypes[Ityp-1]
252	Inst2['Tminmax'] = Tminmax
253	Icoeff = []
254	Iesd = []
255	Icovar = []
256	for i in range(3):
257	s = Iparm['INS 1ICOFF'+str(i+1)].split()
258	Icoeff += [float(S) for S in s]
259	s = Iparm['INS 1IECOF'+str(i+1)].split()
260	Iesd += [float(S) for S in s]
261	NT = 10
262	for i in range(8):
263	s = Iparm['INS 1IECOR'+str(i+1)]
264	if i == 7:
265	NT = 8
266	Icovar += [float(s[6j:6j+6]) for j in range(NT)]
267	Inst2['Icoeff'] = Icoeff
268	Inst2['Iesd'] = Iesd
269	Inst2['Icovar'] = Icovar
270	return [Inst1,Inst2]
271
272	def ReadPowderInstprm(instLines, bank, databanks, rd):
273	'''Read lines from a GSAS-II (new) instrument parameter file
274	similar to G2pwdGUI.OnLoad
275	If instprm file has multiple banks each with header #Bank n: ..., this
276	finds matching bank no. to load - problem with nonmatches?
277
278	Note that this routine performs a similar role to :meth:`GSASIIdataGUI.GSASII.ReadPowderInstprm`,
279	but that will call a GUI routine for selection when needed. This routine will raise exceptions
280	on errors and will select the first bank when a choice might be appropriate.
281	TODO: refactor to combine the two routines.
282
283	:param list instLines: strings from GSAS-II parameter file; can be concatenated with ';'
284	:param int bank: bank number to check when instprm file has '#BANK n:...' strings
285	when bank = n then use parameters; otherwise skip that set. Ignored if BANK n:
286	not present. NB: this kind of instprm file made by a Save all profile command in Instrument Par ameters
287	:return dict: Inst instrument parameter dict if OK, or
288	str: Error message if failed
289
290	(transliterated from GSASIIdataGUI.py:1235 (rev 3008), function of the same name)
291	'''
292	if 'GSAS-II' not in instLines[0]:
293	raise ValueError("Not a valid GSAS-II instprm file")
294
295	newItems = []
296	newVals = []
297	Found = False
298	il = 0
299	if bank is None:
300	banklist = set()
301	for S in instLines:
302	if S[0] == '#' and 'Bank' in S:
303	banklist.add(int(S.split(':')[0].split()[1]))
304	# Picks the first bank by default
305	if len(banklist) > 1:
306	bank = sorted(banklist)[0]
307	else:
308	bank = 1
309	rd.powderentry[2] = bank
310	while il < len(instLines):
311	S = instLines[il]
312	if S[0] == '#':
313	if Found:
314	break
315	if 'Bank' in S:
316	if bank == int(S.split(':')[0].split()[1]):
317	il += 1
318	S = instLines[il]
319	else:
320	il += 1
321	S = instLines[il]
322	while il < len(instLines) and '#Bank' not in S:
323	il += 1
324	if il == len(instLines):
325	raise ValueError("Bank {} not found in instprm file".format(bank))
326	S = instLines[il]
327	continue
328	else:
329	il += 1
330	S = instLines[il]
331	Found = True
332	if '"""' in S:
333	delim = '"""'
334	elif "'''" in S:
335	delim = "'''"
336	else:
337	S = S.replace(' ', '')
338	SS = S.strip().split(';')
339	for s in SS:
340	item, val = s.split(':', 1)
341	newItems.append(item)
342	try:
343	newVals.append(float(val))
344	except ValueError:
345	newVals.append(val)
346	il += 1
347	continue
348	# read multiline values, delimited by ''' or """
349	item, val = S.strip().split(':', 1)
350	val = val.replace(delim, '').rstrip()
351	val += '\n'
352	while True:
353	il += 1
354	if il >= len(instLines):
355	break
356	S = instLines[il]
357	if delim in S:
358	val += S.replace(delim, '').rstrip()
359	val += '\n'
360	break
361	else:
362	val += S.rstrip()
363	val += '\n'
364	newItems.append(item)
365	newVals.append(val)
366	il += 1
367	if 'Lam1' in newItems:
368	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
369	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
370	else:
371	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
372	return [makeInstDict(newItems, newVals, len(newVals)*[False]), {}]
373
374	def LoadImportRoutines(prefix, errprefix=None, traceback=False):
375	'''Routine to locate GSASII importers matching a prefix string
376	'''
377	if errprefix is None:
378	errprefix = prefix
379
380	readerlist = []
381	pathlist = sys.path[:]
382	if '.' not in pathlist:
383	pathlist.append('.')
384
385	potential_files = []
386	for path in pathlist:
387	for filename in glob.iglob(os.path.join(path, 'G2'+prefix+'*.py')):
388	potential_files.append(filename)
389
390	potential_files = sorted(list(set(potential_files)))
391	for filename in potential_files:
392	path, rootname = os.path.split(filename)
393	pkg = os.path.splitext(rootname)[0]
394
395	try:
396	fp = None
397	fp, fppath, desc = imp.find_module(pkg, [path])
398	pkg = imp.load_module(pkg, fp, fppath, desc)
399	for name, value in inspect.getmembers(pkg):
400	if name.startswith('_'):
401	continue
402	if inspect.isclass(value):
403	for method in 'Reader', 'ExtensionValidator', 'ContentsValidator':
404	if not hasattr(value, method):
405	break
406	if not callable(getattr(value, method)):
407	break
408	else:
409	reader = value()
410	if reader.UseReader:
411	readerlist.append(reader)
412	except AttributeError:
413	G2Print ('Import_' + errprefix + ': Attribute Error ' + filename)
414	if traceback:
415	traceback.print_exc(file=sys.stdout)
416	except Exception as exc:
417	G2Print ('\nImport_' + errprefix + ': Error importing file ' + filename)
418	G2Print (u'Error message: {}\n'.format(exc))
419	if traceback:
420	traceback.print_exc(file=sys.stdout)
421	finally:
422	if fp:
423	fp.close()
424
425	return readerlist
426
427	def LoadExportRoutines(parent, traceback=False):
428	'''Routine to locate GSASII exporters
429	'''
430	exporterlist = []
431	pathlist = sys.path
432	filelist = []
433	for path in pathlist:
434	for filename in glob.iglob(os.path.join(path,"G2export*.py")):
435	filelist.append(filename)
436	filelist = sorted(list(set(filelist))) # remove duplicates
437	# go through the routines and import them, saving objects that
438	# have export routines (method Exporter)
439	for filename in filelist:
440	path,rootname = os.path.split(filename)
441	pkg = os.path.splitext(rootname)[0]
442	try:
443	fp = None
444	fp, fppath,desc = imp.find_module(pkg,[path,])
445	pkg = imp.load_module(pkg,fp,fppath,desc)
446	for clss in inspect.getmembers(pkg): # find classes defined in package
447	if clss[0].startswith('_'): continue
448	if not inspect.isclass(clss[1]): continue
449	# check if we have the required methods
450	if not hasattr(clss[1],'Exporter'): continue
451	if not callable(getattr(clss[1],'Exporter')): continue
452	if parent is None:
453	if not hasattr(clss[1],'Writer'): continue
454	else:
455	if not hasattr(clss[1],'loadParmDict'): continue
456	if not callable(getattr(clss[1],'loadParmDict')): continue
457	try:
458	exporter = clss[1](parent) # create an export instance
459	except AttributeError:
460	pass
461	except Exception as exc:
462	G2Print ('\nExport init: Error substantiating class ' + clss[0])
463	G2Print (u'Error message: {}\n'.format(exc))
464	if traceback:
465	traceback.print_exc(file=sys.stdout)
466	continue
467	exporterlist.append(exporter)
468	except AttributeError:
469	G2Print ('Export Attribute Error ' + filename)
470	if traceback:
471	traceback.print_exc(file=sys.stdout)
472	except Exception as exc:
473	G2Print ('\nExport init: Error importing file ' + filename)
474	G2Print (u'Error message: {}\n'.format(exc))
475	if traceback:
476	traceback.print_exc(file=sys.stdout)
477	finally:
478	if fp:
479	fp.close()
480	return exporterlist
481
482	def readColMetadata(imagefile):
483	'''Reads image metadata from a column-oriented metadata table
484	(1-ID style .par file). Called by :func:`GetColumnMetadata`
485
486	The .par file has any number of columns separated by spaces.
487	The directory for the file must be specified in
488	Config variable :data:`config_example.Column_Metadata_directory`.
489	As an index to the .par file a second "label file" must be specified with the
490	same file root name as the .par file but the extension must be .XXX_lbls (where
491	.XXX is the extension of the image) or if that is not present extension
492	.lbls.
493
494	:param str imagefile: the full name of the image file (with extension, directory optional)
495
496	:returns: a dict with parameter values. Named parameters will have the type based on
497	the specified Python function, named columns will be character strings
498
499	The contents of the label file will look like this::
500
501	# define keywords
502	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
503	distance: float \| 75
504	wavelength:lambda keV: 12.398425/float(keV)\|9
505	pixelSize:lambda x: [74.8, 74.8]\|0
506	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
507	Temperature: float\|53
508	FreePrm2: int \| 34 \| Free Parm2 Label
509	# define other variables
510	0:day
511	1:month
512	2:date
513	3:time
514	4:year
515	7:I_ring
516
517	This file contains three types of lines in any order.
518	* Named parameters are evaluated with user-supplied Python code (see
519	subsequent information). Specific named parameters are used
520	to determine values that are used for image interpretation (see table,
521	below). Any others are copied to the Comments subsection of the Image
522	tree item.
523	* Column labels are defined with a column number (integer) followed by
524	a colon (:) and a label to be assigned to that column. All labeled
525	columns are copied to the Image's Comments subsection.
526	* Comments are any line that does not contain a colon.
527
528	Note that columns are numbered starting at zero.
529
530	Any named parameter may be defined provided it is not a valid integer,
531	but the named parameters in the table have special meanings, as descibed.
532	The parameter name is followed by a colon. After the colon, specify
533	Python code that defines or specifies a function that will be called to
534	generate a value for that parameter.
535
536	Note that several keywords, if defined in the Comments, will be found and
537	placed in the appropriate section of the powder histogram(s)'s Sample
538	Parameters after an integration: ``Temperature``, ``Pressure``, ``Time``,
539	``FreePrm1``, ``FreePrm2``, ``FreePrm3``, ``Omega``, ``Chi``, and ``Phi``.
540
541	After the Python code, supply a vertical bar (\|) and then a list of one
542	more more columns that will be supplied as arguments to that function.
543
544	Note that the labels for the three FreePrm items can be changed by
545	including that label as a third item with an additional vertical bar. Labels
546	will be ignored for any other named parameters.
547
548	The examples above are discussed here:
549
550	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
551	Here the function to be used is defined with a lambda statement::
552
553	lambda x,y: "{}_{:0>6}".format(x,y)
554
555	This function will use the format function to create a file name from the
556	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
557	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
558	which will be left-padded with zeros to six characters (format directive ``:0>6``).
559
560	When there will be more than one image generated per line in the .par file, an alternate way to
561	generate list of file names takes into account the number of images generated::
562
563	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
564
565	Here a third parameter is used to specify the number of images generated, where
566	the image number is incremented for each image.
567
568	``distance: float \| 75``
569	Here the contents of column 75 will be converted to a floating point number
570	by calling float on it. Note that the spaces here are ignored.
571
572	``wavelength:lambda keV: 12.398425/float(keV)\|9``
573	Here we define an algebraic expression to convert an energy in keV to a
574	wavelength and pass the contents of column 9 as that input energy
575
576	``pixelSize:lambda x: [74.8, 74.8]\|0``
577	In this case the pixel size is a constant (a list of two numbers). The first
578	column is passed as an argument as at least one argument is required, but that
579	value is not used in the expression.
580
581	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
582	This example defines a parameter that takes items in the first five columns
583	and formats them in a different way. This parameter is not one of the pre-defined
584	parameter names below. Some external code could be used to change the month string
585	(argument ``m``) to a integer from 1 to 12.
586
587	``FreePrm2: int \| 34 \| Free Parm2 Label``
588	In this example, the contents of column 34 will be converted to an integer and
589	placed as the second free-named parameter in the Sample Parameters after an
590	integration. The label for this parameter will be changed to "Free Parm2 Label".
591
592	Pre-defined parameter names
593
594	============= ========= ======== =====================================================
595	keyword required type Description
596	============= ========= ======== =====================================================
597	filename yes str or generates the file name prefix for the matching image
598	list file (MyImage001 for file /tmp/MyImage001.tif) or
599	a list of file names.
600	polarization no float generates the polarization expected based on the
601	monochromator angle, defaults to 0.99.
602	center no list of generates the approximate beam center on the detector
603	2 floats in mm, such as [204.8, 204.8].
604	distance yes float generates the distance from the sample to the detector
605	in mm
606	pixelSize no list of generates the size of the pixels in microns such as
607	2 floats [200.0, 200.0].
608	wavelength yes float generates the wavelength in Angstroms
609	============= ========= ======== =====================================================
610
611	'''
612	dir,fil = os.path.split(os.path.abspath(imagefile))
613	imageName,ext = os.path.splitext(fil)
614	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
615	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
616	if len(parfiles) == 0:
617	G2Print('Sorry, No Column metadata (.par) file found in '+
618	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
619	return {}
620	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
621	parRoot = os.path.splitext(parFil)[0]
622	for e in (ext+'_lbls','.lbls'):
623	if os.path.exists(parRoot+e):
624	lblFil = parRoot+e
625	break
626	else:
627	G2Print('Warning: No labels definitions found for '+parFil)
628	continue
629	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
630	if errors:
631	print('Errors in labels file '+lblFil)
632	for i in errors: print(' '+i)
633	continue
634	else:
635	G2Print('Read '+lblFil)
636	# scan through each line in this .par file, looking for the matching image rootname
637	fp = open(parFil,'Ur')
638	for iline,line in enumerate(fp):
639	items = line.strip().split(' ')
640	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
641	if type(nameList) is str:
642	if nameList != imageName: continue
643	name = nameList
644	else:
645	for name in nameList:
646	if name == imageName: break # got a match
647	else:
648	continue
649	# parse the line and finish
650	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
651	metadata['par file'] = parFil
652	metadata['lbls file'] = lblFil
653	G2Print("Metadata read from {} line {}".format(parFil,iline+1))
654	fp.close()
655	return metadata
656	else:
657	G2Print("Image {} not found in {}".format(imageName,parFil))
658	fp.close()
659	continue
660	fp.close()
661	else:
662	G2Print("Warning: No .par metadata for image {}".format(imageName))
663	return {}
664
665	def readColMetadataLabels(lblFil):
666	'''Read the .*lbls file and setup for metadata assignments
667	'''
668	lbldict = {}
669	keyExp = {}
670	keyCols = {}
671	labels = {}
672	errors = []
673	fp = open(lblFil,'Ur') # read column labels
674	for iline,line in enumerate(fp): # read label definitions
675	line = line.strip()
676	if not line or line[0] == '#': continue # comments
677	items = line.split(':')
678	if len(items) < 2: continue # lines with no colon are also comments
679	# does this line a definition for a named parameter?
680	key = items[0]
681	try:
682	int(key)
683	except ValueError: # try as named parameter since not a valid number
684	items = line.split(':',1)[1].split('\|')
685	try:
686	f = eval(items[0]) # compile the expression
687	if not callable(f):
688	errors += ['Expression "{}" for key {} is not a function (line {})'.
689	format(items[0],key,iline)]
690	continue
691	keyExp[key] = f
692	except Exception as msg:
693	errors += ['Expression "{}" for key {} is not valid (line {})'.
694	format(items[0],key,iline)]
695	errors += [str(msg)]
696	continue
697	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
698	if key.lower().startswith('freeprm') and len(items) > 2:
699	labels[key] = items[2]
700	continue
701	if len(items) == 2: # simple column definition
702	lbldict[int(items[0])] = items[1]
703	fp.close()
704	if 'filename' not in keyExp:
705	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
706	return labels,lbldict,keyCols,keyExp,errors
707
708	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
709	'''Evaluate the metadata for a line in the .par file
710	'''
711	metadata = {lbldict[j]:items[j] for j in lbldict}
712	named = {}
713	for key in keyExp:
714	try:
715	res = keyExp[key](*[items[j] for j in keyCols[key]])
716	except:
717	if ShowError:
718	res = "* error *"
719	else:
720	continue
721	named[key] = res
722	metadata.update(named)
723	for lbl in labels: # add labels for FreePrm's
724	metadata['label_'+lbl[4:].lower()] = labels[lbl]
725	return metadata
726
727	def GetColumnMetadata(reader):
728	'''Add metadata to an image from a column-type metadata file
729	using :func:`readColMetadata`
730
731	:param reader: a reader object from reading an image
732
733	'''
734	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
735	parParms = readColMetadata(reader.readfilename)
736	if not parParms: return # check for read failure
737	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
738	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
739	for key in parParms:
740	if key in specialKeys+('par file','lbls file'): continue
741	reader.Comments += ["{} = {}".format(key,parParms[key])]
742	if "polarization" in parParms:
743	reader.Data['PolaVal'][0] = parParms["polarization"]
744	else:
745	reader.Data['PolaVal'][0] = 0.99
746	if "center" in parParms:
747	reader.Data['center'] = parParms["center"]
748	if "pixelSize" in parParms:
749	reader.Data['pixelSize'] = parParms["pixelSize"]
750	if "wavelength" in parParms:
751	reader.Data['wavelength'] = parParms['wavelength']
752	else:
753	G2Print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
754	if "distance" in parParms:
755	reader.Data['distance'] = parParms['distance']
756	reader.Data['setdist'] = parParms['distance']
757	else:
758	G2Print('Error: distance not defined in {}'.format(parParms['lbls file']))
759
760	def LoadControls(Slines,data):
761	'Read values from a .imctrl (Image Controls) file'
762	cntlList = ['color','wavelength','distance','tilt','invert_x','invert_y','type','Oblique',
763	'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth',
764	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList','setdist',
765	'PolaVal','SampleAbs','dark image','background image','twoth']
766	save = {}
767	for S in Slines:
768	if S[0] == '#':
769	continue
770	[key,val] = S.strip().split(':',1)
771	if key in ['type','calibrant','binType','SampleShape','color',]: #strings
772	save[key] = val
773	elif key in ['varyList',]:
774	save[key] = eval(val) #dictionary
775	elif key in ['rotation']:
776	save[key] = float(val)
777	elif key in ['center',]:
778	if ',' in val:
779	save[key] = eval(val)
780	else:
781	vals = val.strip('[] ').split()
782	save[key] = [float(vals[0]),float(vals[1])]
783	elif key in cntlList:
784	save[key] = eval(val)
785	data.update(save)
786
787	def WriteControls(filename,data):
788	'Write current values to a .imctrl (Image Controls) file'
789	File = open(filename,'w')
790	keys = ['type','color','wavelength','calibrant','distance','center','Oblique',
791	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth','setdist',
792	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
793	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList',
794	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image',
795	'twoth']
796	for key in keys:
797	if key not in data: #uncalibrated!
798	continue
799	File.write(key+':'+str(data[key])+'\n')
800	File.close()
801
802	def RereadImageData(ImageReaderlist,imagefile,ImageTag=None,FormatName=''):
803	'''Read a single image with an image importer. This is called to
804	reread an image after it has already been imported, so it is not
805	necessary to reload metadata.
806
807	Based on :func:`GetImageData.GetImageData` which this can replace
808	where imageOnly=True
809
810	:param list ImageReaderlist: list of Reader objects for images
811	:param str imagefile: name of image file
812	:param int/str ImageTag: specifies a particular image to be read from a file.
813	First image is read if None (default).
814	:param str formatName: the image reader formatName
815
816	:returns: an image as a numpy array
817	'''
818	# determine which formats are compatible with this file
819	primaryReaders = []
820	secondaryReaders = []
821	for rd in ImageReaderlist:
822	flag = rd.ExtensionValidator(imagefile)
823	if flag is None:
824	secondaryReaders.append(rd)
825	elif flag:
826	if not FormatName:
827	primaryReaders.append(rd)
828	elif FormatName == rd.formatName:
829	primaryReaders.append(rd)
830	if len(secondaryReaders) + len(primaryReaders) == 0:
831	G2Print('Error: No matching format for file '+imagefile)
832	raise Exception('No image read')
833	errorReport = ''
834	if not imagefile:
835	return
836	for rd in primaryReaders+secondaryReaders:
837	rd.ReInitialize() # purge anything from a previous read
838	rd.errors = "" # clear out any old errors
839	if not rd.ContentsValidator(imagefile): # rejected on cursory check
840	errorReport += "\n "+rd.formatName + ' validator error'
841	if rd.errors:
842	errorReport += ': '+rd.errors
843	continue
844	flag = rd.Reader(imagefile,None,blocknum=ImageTag)
845	if flag: # this read succeeded
846	if rd.Image is None:
847	raise Exception('No image read. Strange!')
848	if GSASIIpath.GetConfigValue('Transpose'):
849	G2Print ('Warning: Transposing Image!')
850	rd.Image = rd.Image.T
851	#rd.readfilename = imagefile
852	return rd.Image
853	else:
854	G2Print('Error reading file '+imagefile)
855	G2Print('Error messages(s)\n'+errorReport)
856	raise Exception('No image read')
857
858	def readMasks(filename,masks,ignoreThreshold):
859	'''Read a GSAS-II masks file'''
860	File = open(filename,'r')
861	save = {}
862	oldThreshold = masks['Thresholds'][0]
863	S = File.readline()
864	while S:
865	if S[0] == '#':
866	S = File.readline()
867	continue
868	[key,val] = S.strip().split(':',1)
869	if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
870	if ignoreThreshold and key == 'Thresholds':
871	S = File.readline()
872	continue
873	save[key] = eval(val)
874	if key == 'Thresholds':
875	save[key][0] = oldThreshold
876	save[key][1][1] = min(oldThreshold[1],save[key][1][1])
877	S = File.readline()
878	File.close()
879	masks.update(save)
880	# CleanupMasks
881	for key in ['Points','Rings','Arcs','Polygons']:
882	masks[key] = masks.get(key,[])
883	masks[key] = [i for i in masks[key] if len(i)]
884
885	def PDFWrite(PDFentry,fileroot,PDFsaves,PDFControls,Inst={},Limits=[]):
886	'''Write PDF-related data (G(r), S(Q),...) into files, as
887	selected.
888
889	:param str PDFentry: name of the PDF entry in the tree. This is
890	used for comments in the file specifying where it came from;
891	it can be arbitrary
892	:param str fileroot: name of file(s) to be written. The extension
893	will be ignored.
894	:param list PDFsaves: flags that determine what type of file will be
895	written:
896	PDFsaves[0], if True writes a I(Q) file with a .iq extension
897	PDFsaves[1], if True writes a S(Q) file with a .sq extension
898	PDFsaves[2], if True writes a F(Q) file with a .fq extension
899	PDFsaves[3], if True writes a G(r) file with a .gr extension
900	PDFsaves[4], if True writes G(r) in a pdfGUI input file with
901	a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are
902	both True, the pdfGUI overwrites the G(r) file.
903	:param dict PDFControls: The PDF parameters and computed results
904	:param dict Inst: Instrument parameters from the PDWR entry used
905	to compute the PDF. Needed only when PDFsaves[4] is True.
906	:param list Limits: Computation limits from the PDWR entry used
907	to compute the PDF. Needed only when PDFsaves[4] is True.
908	'''
909	import scipy.interpolate as scintp
910	fileroot = os.path.splitext(fileroot)[0]
911	if PDFsaves[0]: #I(Q)
912	iqfilename = fileroot+'.iq'
913	iqdata = PDFControls['I(Q)'][1]
914	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
915	iqfile = open(iqfilename,'w')
916	iqfile.write('#T I(Q) %s\n'%(PDFentry))
917	iqfile.write('#L Q I(Q)\n')
918	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
919	iqnew = zip(qnew,iqfxn(qnew))
920	for q,iq in iqnew:
921	iqfile.write("%15.6g %15.6g\n" % (q,iq))
922	iqfile.close()
923	G2Print (' I(Q) saved to: '+iqfilename)
924
925	if PDFsaves[1]: #S(Q)
926	sqfilename = fileroot+'.sq'
927	sqdata = PDFControls['S(Q)'][1]
928	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
929	sqfile = open(sqfilename,'w')
930	sqfile.write('#T S(Q) %s\n'%(PDFentry))
931	sqfile.write('#L Q S(Q)\n')
932	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
933	sqnew = zip(qnew,sqfxn(qnew))
934	for q,sq in sqnew:
935	sqfile.write("%15.6g %15.6g\n" % (q,sq))
936	sqfile.close()
937	G2Print (' S(Q) saved to: '+sqfilename)
938
939	if PDFsaves[2]: #F(Q)
940	fqfilename = fileroot+'.fq'
941	fqdata = PDFControls['F(Q)'][1]
942	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
943	fqfile = open(fqfilename,'w')
944	fqfile.write('#T F(Q) %s\n'%(PDFentry))
945	fqfile.write('#L Q F(Q)\n')
946	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
947	fqnew = zip(qnew,fqfxn(qnew))
948	for q,fq in fqnew:
949	fqfile.write("%15.6g %15.6g\n" % (q,fq))
950	fqfile.close()
951	G2Print (' F(Q) saved to: '+fqfilename)
952
953	if PDFsaves[3]: #G(R)
954	grfilename = fileroot+'.gr'
955	grdata = PDFControls['G(R)'][1]
956	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
957	grfile = open(grfilename,'w')
958	grfile.write('#T G(R) %s\n'%(PDFentry))
959	grfile.write('#L R G(R)\n')
960	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
961	grnew = zip(rnew,grfxn(rnew))
962	for r,gr in grnew:
963	grfile.write("%15.6g %15.6g\n" % (r,gr))
964	grfile.close()
965	G2Print (' G(R) saved to: '+grfilename)
966
967	if PDFsaves[4]: #pdfGUI file for G(R)
968	import GSASIImath as G2mth
969	import GSASIIlattice as G2lat
970	grfilename = fileroot+'.gr'
971	grdata = PDFControls['G(R)'][1]
972	qdata = PDFControls['I(Q)'][1][0]
973	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
974	grfile = open(grfilename,'w')
975	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
976	grnew = zip(rnew,grfxn(rnew))
977
978	grfile.write('[DEFAULT]\n')
979	grfile.write('\n')
980	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
981	grfile.write('\n')
982	grfile.write('# input and output specifications\n')
983	grfile.write('dataformat = Qnm\n')
984	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
985	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
986	grfile.write('outputtype = gr\n')
987	grfile.write('\n')
988	grfile.write('# PDF calculation setup\n')
989	if 'x' in Inst['Type']:
990	grfile.write('mode = %s\n'%('xray'))
991	elif 'N' in Inst['Type']:
992	grfile.write('mode = %s\n'%('neutron'))
993	wave = G2mth.getMeanWave(Inst)
994	grfile.write('wavelength = %.5f\n'%(wave))
995	formula = ''
996	for el in PDFControls['ElList']:
997	formula += el
998	num = PDFControls['ElList'][el]['FormulaNo']
999	if num == round(num):
1000	formula += '%d'%(int(num))
1001	else:
1002	formula += '%.2f'%(num)
1003	grfile.write('composition = %s\n'%(formula))
1004	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
1005	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
1006	grfile.write('qmaxinst = %.2f\n'%(highQ))
1007	grfile.write('qmin = %.5f\n'%(qdata[0]))
1008	grfile.write('qmax = %.4f\n'%(qdata[-1]))
1009	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
1010	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
1011	grfile.write('rstep = 0.01\n')
1012
1013
1014	grfile.write('\n')
1015	grfile.write('# End of config '+63*'-')
1016	grfile.write('\n')
1017	grfile.write('#### start data\n')
1018	grfile.write('#S 1\n')
1019	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
1020	for r,gr in grnew:
1021	grfile.write("%15.2F %15.6F\n" % (r,gr))
1022	grfile.close()
1023	G2Print (' G(R) saved to: '+grfilename)

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