Context Navigation

source: trunk/GSASIIfiles.py @ 4408

Last change on this file since 4408 was 4388, checked in by vondreele, 5 years ago
Add warning for using type=2 TOF instrument profile function in old gsas iparm files
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 45.1 KB

Line
1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2020-04-02 15:48:25 +0000 (Thu, 02 Apr 2020) $
4	# $Author: toby $
5	# $Revision: 4388 $
6	# $URL: trunk/GSASIIfiles.py $
7	# $Id: GSASIIfiles.py 4388 2020-04-02 15:48:25Z 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: 4388 $")
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	print('''*WARNING gsas profile function #2 does not give valid GSAS-II diffractometer/profile coefficients *
223	you should request GSAS-II instparm file from Instrument responsible''')
224	data.extend([sfloat(s[1]),0.0,1./sfloat(s[3])]) #alpha, beta-0, beta-1
225	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
226	else:
227	s = Iparm['INS 1PRCF1 '].split()
228	pfType = int(s[0])
229	s = Iparm['INS 1PRCF11'].split()
230	if abs(pfType) == 1:
231	data.extend([sfloat(s[1]),sfloat(s[2]),sfloat(s[3])]) #alpha, beta-0, beta-1
232	s = Iparm['INS 1PRCF12'].split()
233	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
234	elif abs(pfType) in [3,4,5]:
235	data.extend([sfloat(s[0]),sfloat(s[1]),sfloat(s[2])]) #alpha, beta-0, beta-1
236	if abs(pfType) == 4:
237	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
238	else:
239	s = Iparm['INS 1PRCF12'].split()
240	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
241	Inst1 = makeInstDict(names,data,codes)
242	Inst1['Bank'] = [Bank,Bank,0]
243	Inst2 = {}
244	if pfType < 0:
245	Ipab = 'INS 1PAB'+str(-pfType)
246	Npab = int(Iparm[Ipab+' '].strip())
247	Inst2['Pdabc'] = []
248	for i in range(Npab):
249	k = Ipab+str(i+1).rjust(2)
250	s = Iparm[k].split()
251	Inst2['Pdabc'].append([float(t) for t in s])
252	Inst2['Pdabc'] = np.array(Inst2['Pdabc'])
253	Inst2['Pdabc'].T[3] += Inst2['Pdabc'].T[0]*Inst1['difC'][0] #turn 3rd col into TOF
254	if 'INS 1I ITYP' in Iparm:
255	s = Iparm['INS 1I ITYP'].split()
256	Ityp = int(s[0])
257	Tminmax = [float(s[1])1000.,float(s[2])1000.]
258	Itypes = ['Exponential','Maxwell/Exponential','','Maxwell/Chebyschev','']
259	if Ityp in [1,2,4]:
260	Inst2['Itype'] = Itypes[Ityp-1]
261	Inst2['Tminmax'] = Tminmax
262	Icoeff = []
263	Iesd = []
264	Icovar = []
265	for i in range(3):
266	s = Iparm['INS 1ICOFF'+str(i+1)].split()
267	Icoeff += [float(S) for S in s]
268	s = Iparm['INS 1IECOF'+str(i+1)].split()
269	Iesd += [float(S) for S in s]
270	NT = 10
271	for i in range(8):
272	s = Iparm['INS 1IECOR'+str(i+1)]
273	if i == 7:
274	NT = 8
275	Icovar += [float(s[6j:6j+6]) for j in range(NT)]
276	Inst2['Icoeff'] = Icoeff
277	Inst2['Iesd'] = Iesd
278	Inst2['Icovar'] = Icovar
279	return [Inst1,Inst2]
280
281	def ReadPowderInstprm(instLines, bank, databanks, rd):
282	'''Read lines from a GSAS-II (new) instrument parameter file
283	similar to G2pwdGUI.OnLoad
284	If instprm file has multiple banks each with header #Bank n: ..., this
285	finds matching bank no. to load - problem with nonmatches?
286
287	Note that this routine performs a similar role to :meth:`GSASIIdataGUI.GSASII.ReadPowderInstprm`,
288	but that will call a GUI routine for selection when needed. This routine will raise exceptions
289	on errors and will select the first bank when a choice might be appropriate.
290	TODO: refactor to combine the two routines.
291
292	:param list instLines: strings from GSAS-II parameter file; can be concatenated with ';'
293	:param int bank: bank number to check when instprm file has '#BANK n:...' strings
294	when bank = n then use parameters; otherwise skip that set. Ignored if BANK n:
295	not present. NB: this kind of instprm file made by a Save all profile command in Instrument Par ameters
296	:return dict: Inst instrument parameter dict if OK, or
297	str: Error message if failed
298
299	(transliterated from GSASIIdataGUI.py:1235 (rev 3008), function of the same name)
300	'''
301	if 'GSAS-II' not in instLines[0]:
302	raise ValueError("Not a valid GSAS-II instprm file")
303
304	newItems = []
305	newVals = []
306	Found = False
307	il = 0
308	if bank is None:
309	banklist = set()
310	for S in instLines:
311	if S[0] == '#' and 'Bank' in S:
312	banklist.add(int(S.split(':')[0].split()[1]))
313	# Picks the first bank by default
314	if len(banklist) > 1:
315	bank = sorted(banklist)[0]
316	else:
317	bank = 1
318	rd.powderentry[2] = bank
319	while il < len(instLines):
320	S = instLines[il]
321	if S[0] == '#':
322	if Found:
323	break
324	if 'Bank' in S:
325	if bank == int(S.split(':')[0].split()[1]):
326	il += 1
327	S = instLines[il]
328	else:
329	il += 1
330	S = instLines[il]
331	while il < len(instLines) and '#Bank' not in S:
332	il += 1
333	if il == len(instLines):
334	raise ValueError("Bank {} not found in instprm file".format(bank))
335	S = instLines[il]
336	continue
337	else:
338	il += 1
339	S = instLines[il]
340	Found = True
341	if '"""' in S:
342	delim = '"""'
343	elif "'''" in S:
344	delim = "'''"
345	else:
346	S = S.replace(' ', '')
347	SS = S.strip().split(';')
348	for s in SS:
349	item, val = s.split(':', 1)
350	newItems.append(item)
351	try:
352	newVals.append(float(val))
353	except ValueError:
354	newVals.append(val)
355	il += 1
356	continue
357	# read multiline values, delimited by ''' or """
358	item, val = S.strip().split(':', 1)
359	val = val.replace(delim, '').rstrip()
360	val += '\n'
361	while True:
362	il += 1
363	if il >= len(instLines):
364	break
365	S = instLines[il]
366	if delim in S:
367	val += S.replace(delim, '').rstrip()
368	val += '\n'
369	break
370	else:
371	val += S.rstrip()
372	val += '\n'
373	newItems.append(item)
374	newVals.append(val)
375	il += 1
376	if 'Lam1' in newItems:
377	rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
378	'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
379	else:
380	rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],'DisplaceY':[0.,False]})
381	return [makeInstDict(newItems, newVals, len(newVals)*[False]), {}]
382
383	def LoadImportRoutines(prefix, errprefix=None, traceback=False):
384	'''Routine to locate GSASII importers matching a prefix string
385	'''
386	if errprefix is None:
387	errprefix = prefix
388
389	readerlist = []
390	pathlist = sys.path[:]
391	if '.' not in pathlist:
392	pathlist.append('.')
393
394	potential_files = []
395	for path in pathlist:
396	for filename in glob.iglob(os.path.join(path, 'G2'+prefix+'*.py')):
397	potential_files.append(filename)
398
399	potential_files = sorted(list(set(potential_files)))
400	for filename in potential_files:
401	path, rootname = os.path.split(filename)
402	pkg = os.path.splitext(rootname)[0]
403
404	try:
405	fp = None
406	fp, fppath, desc = imp.find_module(pkg, [path])
407	pkg = imp.load_module(pkg, fp, fppath, desc)
408	for name, value in inspect.getmembers(pkg):
409	if name.startswith('_'):
410	continue
411	if inspect.isclass(value):
412	for method in 'Reader', 'ExtensionValidator', 'ContentsValidator':
413	if not hasattr(value, method):
414	break
415	if not callable(getattr(value, method)):
416	break
417	else:
418	reader = value()
419	if reader.UseReader:
420	readerlist.append(reader)
421	except AttributeError:
422	G2Print ('Import_' + errprefix + ': Attribute Error ' + filename)
423	if traceback:
424	traceback.print_exc(file=sys.stdout)
425	except Exception as exc:
426	G2Print ('\nImport_' + errprefix + ': Error importing file ' + filename)
427	G2Print (u'Error message: {}\n'.format(exc))
428	if traceback:
429	traceback.print_exc(file=sys.stdout)
430	finally:
431	if fp:
432	fp.close()
433
434	return readerlist
435
436	def LoadExportRoutines(parent, traceback=False):
437	'''Routine to locate GSASII exporters
438	'''
439	exporterlist = []
440	pathlist = sys.path
441	filelist = []
442	for path in pathlist:
443	for filename in glob.iglob(os.path.join(path,"G2export*.py")):
444	filelist.append(filename)
445	filelist = sorted(list(set(filelist))) # remove duplicates
446	# go through the routines and import them, saving objects that
447	# have export routines (method Exporter)
448	for filename in filelist:
449	path,rootname = os.path.split(filename)
450	pkg = os.path.splitext(rootname)[0]
451	try:
452	fp = None
453	fp, fppath,desc = imp.find_module(pkg,[path,])
454	pkg = imp.load_module(pkg,fp,fppath,desc)
455	for clss in inspect.getmembers(pkg): # find classes defined in package
456	if clss[0].startswith('_'): continue
457	if not inspect.isclass(clss[1]): continue
458	# check if we have the required methods
459	if not hasattr(clss[1],'Exporter'): continue
460	if not callable(getattr(clss[1],'Exporter')): continue
461	if parent is None:
462	if not hasattr(clss[1],'Writer'): continue
463	else:
464	if not hasattr(clss[1],'loadParmDict'): continue
465	if not callable(getattr(clss[1],'loadParmDict')): continue
466	try:
467	exporter = clss[1](parent) # create an export instance
468	except AttributeError:
469	pass
470	except Exception as exc:
471	G2Print ('\nExport init: Error substantiating class ' + clss[0])
472	G2Print (u'Error message: {}\n'.format(exc))
473	if traceback:
474	traceback.print_exc(file=sys.stdout)
475	continue
476	exporterlist.append(exporter)
477	except AttributeError:
478	G2Print ('Export Attribute Error ' + filename)
479	if traceback:
480	traceback.print_exc(file=sys.stdout)
481	except Exception as exc:
482	G2Print ('\nExport init: Error importing file ' + filename)
483	G2Print (u'Error message: {}\n'.format(exc))
484	if traceback:
485	traceback.print_exc(file=sys.stdout)
486	finally:
487	if fp:
488	fp.close()
489	return exporterlist
490
491	def readColMetadata(imagefile):
492	'''Reads image metadata from a column-oriented metadata table
493	(1-ID style .par file). Called by :func:`GetColumnMetadata`
494
495	The .par file has any number of columns separated by spaces.
496	The directory for the file must be specified in
497	Config variable :data:`config_example.Column_Metadata_directory`.
498	As an index to the .par file a second "label file" must be specified with the
499	same file root name as the .par file but the extension must be .XXX_lbls (where
500	.XXX is the extension of the image) or if that is not present extension
501	.lbls.
502
503	:param str imagefile: the full name of the image file (with extension, directory optional)
504
505	:returns: a dict with parameter values. Named parameters will have the type based on
506	the specified Python function, named columns will be character strings
507
508	The contents of the label file will look like this::
509
510	# define keywords
511	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
512	distance: float \| 75
513	wavelength:lambda keV: 12.398425/float(keV)\|9
514	pixelSize:lambda x: [74.8, 74.8]\|0
515	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
516	Temperature: float\|53
517	FreePrm2: int \| 34 \| Free Parm2 Label
518	# define other variables
519	0:day
520	1:month
521	2:date
522	3:time
523	4:year
524	7:I_ring
525
526	This file contains three types of lines in any order.
527	* Named parameters are evaluated with user-supplied Python code (see
528	subsequent information). Specific named parameters are used
529	to determine values that are used for image interpretation (see table,
530	below). Any others are copied to the Comments subsection of the Image
531	tree item.
532	* Column labels are defined with a column number (integer) followed by
533	a colon (:) and a label to be assigned to that column. All labeled
534	columns are copied to the Image's Comments subsection.
535	* Comments are any line that does not contain a colon.
536
537	Note that columns are numbered starting at zero.
538
539	Any named parameter may be defined provided it is not a valid integer,
540	but the named parameters in the table have special meanings, as descibed.
541	The parameter name is followed by a colon. After the colon, specify
542	Python code that defines or specifies a function that will be called to
543	generate a value for that parameter.
544
545	Note that several keywords, if defined in the Comments, will be found and
546	placed in the appropriate section of the powder histogram(s)'s Sample
547	Parameters after an integration: ``Temperature``, ``Pressure``, ``Time``,
548	``FreePrm1``, ``FreePrm2``, ``FreePrm3``, ``Omega``, ``Chi``, and ``Phi``.
549
550	After the Python code, supply a vertical bar (\|) and then a list of one
551	more more columns that will be supplied as arguments to that function.
552
553	Note that the labels for the three FreePrm items can be changed by
554	including that label as a third item with an additional vertical bar. Labels
555	will be ignored for any other named parameters.
556
557	The examples above are discussed here:
558
559	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
560	Here the function to be used is defined with a lambda statement::
561
562	lambda x,y: "{}_{:0>6}".format(x,y)
563
564	This function will use the format function to create a file name from the
565	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
566	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
567	which will be left-padded with zeros to six characters (format directive ``:0>6``).
568
569	When there will be more than one image generated per line in the .par file, an alternate way to
570	generate list of file names takes into account the number of images generated::
571
572	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
573
574	Here a third parameter is used to specify the number of images generated, where
575	the image number is incremented for each image.
576
577	``distance: float \| 75``
578	Here the contents of column 75 will be converted to a floating point number
579	by calling float on it. Note that the spaces here are ignored.
580
581	``wavelength:lambda keV: 12.398425/float(keV)\|9``
582	Here we define an algebraic expression to convert an energy in keV to a
583	wavelength and pass the contents of column 9 as that input energy
584
585	``pixelSize:lambda x: [74.8, 74.8]\|0``
586	In this case the pixel size is a constant (a list of two numbers). The first
587	column is passed as an argument as at least one argument is required, but that
588	value is not used in the expression.
589
590	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
591	This example defines a parameter that takes items in the first five columns
592	and formats them in a different way. This parameter is not one of the pre-defined
593	parameter names below. Some external code could be used to change the month string
594	(argument ``m``) to a integer from 1 to 12.
595
596	``FreePrm2: int \| 34 \| Free Parm2 Label``
597	In this example, the contents of column 34 will be converted to an integer and
598	placed as the second free-named parameter in the Sample Parameters after an
599	integration. The label for this parameter will be changed to "Free Parm2 Label".
600
601	Pre-defined parameter names
602
603	============= ========= ======== =====================================================
604	keyword required type Description
605	============= ========= ======== =====================================================
606	filename yes str or generates the file name prefix for the matching image
607	list file (MyImage001 for file /tmp/MyImage001.tif) or
608	a list of file names.
609	polarization no float generates the polarization expected based on the
610	monochromator angle, defaults to 0.99.
611	center no list of generates the approximate beam center on the detector
612	2 floats in mm, such as [204.8, 204.8].
613	distance yes float generates the distance from the sample to the detector
614	in mm
615	pixelSize no list of generates the size of the pixels in microns such as
616	2 floats [200.0, 200.0].
617	wavelength yes float generates the wavelength in Angstroms
618	============= ========= ======== =====================================================
619
620	'''
621	dir,fil = os.path.split(os.path.abspath(imagefile))
622	imageName,ext = os.path.splitext(fil)
623	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
624	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
625	if len(parfiles) == 0:
626	G2Print('Sorry, No Column metadata (.par) file found in '+
627	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
628	return {}
629	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
630	parRoot = os.path.splitext(parFil)[0]
631	for e in (ext+'_lbls','.lbls'):
632	if os.path.exists(parRoot+e):
633	lblFil = parRoot+e
634	break
635	else:
636	G2Print('Warning: No labels definitions found for '+parFil)
637	continue
638	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
639	if errors:
640	print('Errors in labels file '+lblFil)
641	for i in errors: print(' '+i)
642	continue
643	else:
644	G2Print('Read '+lblFil)
645	# scan through each line in this .par file, looking for the matching image rootname
646	fp = open(parFil,'Ur')
647	for iline,line in enumerate(fp):
648	items = line.strip().split(' ')
649	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
650	if type(nameList) is str:
651	if nameList != imageName: continue
652	name = nameList
653	else:
654	for name in nameList:
655	if name == imageName: break # got a match
656	else:
657	continue
658	# parse the line and finish
659	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
660	metadata['par file'] = parFil
661	metadata['lbls file'] = lblFil
662	G2Print("Metadata read from {} line {}".format(parFil,iline+1))
663	fp.close()
664	return metadata
665	else:
666	G2Print("Image {} not found in {}".format(imageName,parFil))
667	fp.close()
668	continue
669	fp.close()
670	else:
671	G2Print("Warning: No .par metadata for image {}".format(imageName))
672	return {}
673
674	def readColMetadataLabels(lblFil):
675	'''Read the .*lbls file and setup for metadata assignments
676	'''
677	lbldict = {}
678	keyExp = {}
679	keyCols = {}
680	labels = {}
681	errors = []
682	fp = open(lblFil,'Ur') # read column labels
683	for iline,line in enumerate(fp): # read label definitions
684	line = line.strip()
685	if not line or line[0] == '#': continue # comments
686	items = line.split(':')
687	if len(items) < 2: continue # lines with no colon are also comments
688	# does this line a definition for a named parameter?
689	key = items[0]
690	try:
691	int(key)
692	except ValueError: # try as named parameter since not a valid number
693	items = line.split(':',1)[1].split('\|')
694	try:
695	f = eval(items[0]) # compile the expression
696	if not callable(f):
697	errors += ['Expression "{}" for key {} is not a function (line {})'.
698	format(items[0],key,iline)]
699	continue
700	keyExp[key] = f
701	except Exception as msg:
702	errors += ['Expression "{}" for key {} is not valid (line {})'.
703	format(items[0],key,iline)]
704	errors += [str(msg)]
705	continue
706	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
707	if key.lower().startswith('freeprm') and len(items) > 2:
708	labels[key] = items[2]
709	continue
710	if len(items) == 2: # simple column definition
711	lbldict[int(items[0])] = items[1]
712	fp.close()
713	if 'filename' not in keyExp:
714	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
715	return labels,lbldict,keyCols,keyExp,errors
716
717	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
718	'''Evaluate the metadata for a line in the .par file
719	'''
720	metadata = {lbldict[j]:items[j] for j in lbldict}
721	named = {}
722	for key in keyExp:
723	try:
724	res = keyExp[key](*[items[j] for j in keyCols[key]])
725	except:
726	if ShowError:
727	res = "* error *"
728	else:
729	continue
730	named[key] = res
731	metadata.update(named)
732	for lbl in labels: # add labels for FreePrm's
733	metadata['label_'+lbl[4:].lower()] = labels[lbl]
734	return metadata
735
736	def GetColumnMetadata(reader):
737	'''Add metadata to an image from a column-type metadata file
738	using :func:`readColMetadata`
739
740	:param reader: a reader object from reading an image
741
742	'''
743	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
744	parParms = readColMetadata(reader.readfilename)
745	if not parParms: return # check for read failure
746	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
747	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
748	for key in parParms:
749	if key in specialKeys+('par file','lbls file'): continue
750	reader.Comments += ["{} = {}".format(key,parParms[key])]
751	if "polarization" in parParms:
752	reader.Data['PolaVal'][0] = parParms["polarization"]
753	else:
754	reader.Data['PolaVal'][0] = 0.99
755	if "center" in parParms:
756	reader.Data['center'] = parParms["center"]
757	if "pixelSize" in parParms:
758	reader.Data['pixelSize'] = parParms["pixelSize"]
759	if "wavelength" in parParms:
760	reader.Data['wavelength'] = parParms['wavelength']
761	else:
762	G2Print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
763	if "distance" in parParms:
764	reader.Data['distance'] = parParms['distance']
765	reader.Data['setdist'] = parParms['distance']
766	else:
767	G2Print('Error: distance not defined in {}'.format(parParms['lbls file']))
768
769	def LoadControls(Slines,data):
770	'Read values from a .imctrl (Image Controls) file'
771	cntlList = ['color','wavelength','distance','tilt','invert_x','invert_y','type','Oblique',
772	'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth',
773	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList','setdist',
774	'PolaVal','SampleAbs','dark image','background image','twoth']
775	save = {}
776	for S in Slines:
777	if S[0] == '#':
778	continue
779	[key,val] = S.strip().split(':',1)
780	if key in ['type','calibrant','binType','SampleShape','color',]: #strings
781	save[key] = val
782	elif key in ['varyList',]:
783	save[key] = eval(val) #dictionary
784	elif key in ['rotation']:
785	save[key] = float(val)
786	elif key in ['center',]:
787	if ',' in val:
788	save[key] = eval(val)
789	else:
790	vals = val.strip('[] ').split()
791	save[key] = [float(vals[0]),float(vals[1])]
792	elif key in cntlList:
793	save[key] = eval(val)
794	data.update(save)
795
796	def WriteControls(filename,data):
797	'Write current values to a .imctrl (Image Controls) file'
798	File = open(filename,'w')
799	keys = ['type','color','wavelength','calibrant','distance','center','Oblique',
800	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth','setdist',
801	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
802	'calibskip','pixLimit','cutoff','calibdmin','Flat Bkg','varyList',
803	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image',
804	'twoth']
805	for key in keys:
806	if key not in data: #uncalibrated!
807	continue
808	File.write(key+':'+str(data[key])+'\n')
809	File.close()
810
811	def RereadImageData(ImageReaderlist,imagefile,ImageTag=None,FormatName=''):
812	'''Read a single image with an image importer. This is called to
813	reread an image after it has already been imported, so it is not
814	necessary to reload metadata.
815
816	Based on :func:`GetImageData.GetImageData` which this can replace
817	where imageOnly=True
818
819	:param list ImageReaderlist: list of Reader objects for images
820	:param str imagefile: name of image file
821	:param int/str ImageTag: specifies a particular image to be read from a file.
822	First image is read if None (default).
823	:param str formatName: the image reader formatName
824
825	:returns: an image as a numpy array
826	'''
827	# determine which formats are compatible with this file
828	primaryReaders = []
829	secondaryReaders = []
830	for rd in ImageReaderlist:
831	flag = rd.ExtensionValidator(imagefile)
832	if flag is None:
833	secondaryReaders.append(rd)
834	elif flag:
835	if not FormatName:
836	primaryReaders.append(rd)
837	elif FormatName == rd.formatName:
838	primaryReaders.append(rd)
839	if len(secondaryReaders) + len(primaryReaders) == 0:
840	G2Print('Error: No matching format for file '+imagefile)
841	raise Exception('No image read')
842	errorReport = ''
843	if not imagefile:
844	return
845	for rd in primaryReaders+secondaryReaders:
846	rd.ReInitialize() # purge anything from a previous read
847	rd.errors = "" # clear out any old errors
848	if not rd.ContentsValidator(imagefile): # rejected on cursory check
849	errorReport += "\n "+rd.formatName + ' validator error'
850	if rd.errors:
851	errorReport += ': '+rd.errors
852	continue
853	flag = rd.Reader(imagefile,None,blocknum=ImageTag)
854	if flag: # this read succeeded
855	if rd.Image is None:
856	raise Exception('No image read. Strange!')
857	if GSASIIpath.GetConfigValue('Transpose'):
858	G2Print ('Warning: Transposing Image!')
859	rd.Image = rd.Image.T
860	#rd.readfilename = imagefile
861	return rd.Image
862	else:
863	G2Print('Error reading file '+imagefile)
864	G2Print('Error messages(s)\n'+errorReport)
865	raise Exception('No image read')
866
867	def readMasks(filename,masks,ignoreThreshold):
868	'''Read a GSAS-II masks file'''
869	File = open(filename,'r')
870	save = {}
871	oldThreshold = masks['Thresholds'][0]
872	S = File.readline()
873	while S:
874	if S[0] == '#':
875	S = File.readline()
876	continue
877	[key,val] = S.strip().split(':',1)
878	if key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
879	if ignoreThreshold and key == 'Thresholds':
880	S = File.readline()
881	continue
882	save[key] = eval(val)
883	if key == 'Thresholds':
884	save[key][0] = oldThreshold
885	save[key][1][1] = min(oldThreshold[1],save[key][1][1])
886	S = File.readline()
887	File.close()
888	masks.update(save)
889	# CleanupMasks
890	for key in ['Points','Rings','Arcs','Polygons']:
891	masks[key] = masks.get(key,[])
892	masks[key] = [i for i in masks[key] if len(i)]
893
894	def PDFWrite(PDFentry,fileroot,PDFsaves,PDFControls,Inst={},Limits=[]):
895	'''Write PDF-related data (G(r), S(Q),...) into files, as
896	selected.
897
898	:param str PDFentry: name of the PDF entry in the tree. This is
899	used for comments in the file specifying where it came from;
900	it can be arbitrary
901	:param str fileroot: name of file(s) to be written. The extension
902	will be ignored.
903	:param list PDFsaves: flags that determine what type of file will be
904	written:
905	PDFsaves[0], if True writes a I(Q) file with a .iq extension
906	PDFsaves[1], if True writes a S(Q) file with a .sq extension
907	PDFsaves[2], if True writes a F(Q) file with a .fq extension
908	PDFsaves[3], if True writes a G(r) file with a .gr extension
909	PDFsaves[4], if True writes G(r) in a pdfGUI input file with
910	a .gr extension. Note that if PDFsaves[3] and PDFsaves[4] are
911	both True, the pdfGUI overwrites the G(r) file.
912	PDFsaves[5], if True writes F(Q) & g(R) with .fq & .gr extensions
913	overwrites these if selected by option 2, 3 or 4
914	:param dict PDFControls: The PDF parameters and computed results
915	:param dict Inst: Instrument parameters from the PDWR entry used
916	to compute the PDF. Needed only when PDFsaves[4] is True.
917	:param list Limits: Computation limits from the PDWR entry used
918	to compute the PDF. Needed only when PDFsaves[4] is True.
919	'''
920	import scipy.interpolate as scintp
921	fileroot = os.path.splitext(fileroot)[0]
922	if PDFsaves[0]: #I(Q)
923	iqfilename = fileroot+'.iq'
924	iqdata = PDFControls['I(Q)'][1]
925	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
926	iqfile = open(iqfilename,'w')
927	iqfile.write('#T I(Q) %s\n'%(PDFentry))
928	iqfile.write('#L Q I(Q)\n')
929	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
930	iqnew = zip(qnew,iqfxn(qnew))
931	for q,iq in iqnew:
932	iqfile.write("%15.6g %15.6g\n" % (q,iq))
933	iqfile.close()
934	G2Print (' I(Q) saved to: '+iqfilename)
935
936	if PDFsaves[1]: #S(Q)
937	sqfilename = fileroot+'.sq'
938	sqdata = PDFControls['S(Q)'][1]
939	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
940	sqfile = open(sqfilename,'w')
941	sqfile.write('#T S(Q) %s\n'%(PDFentry))
942	sqfile.write('#L Q S(Q)\n')
943	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
944	sqnew = zip(qnew,sqfxn(qnew))
945	for q,sq in sqnew:
946	sqfile.write("%15.6g %15.6g\n" % (q,sq))
947	sqfile.close()
948	G2Print (' S(Q) saved to: '+sqfilename)
949
950	if PDFsaves[2]: #F(Q)
951	fqfilename = fileroot+'.fq'
952	fqdata = PDFControls['F(Q)'][1]
953	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
954	fqfile = open(fqfilename,'w')
955	fqfile.write('#T F(Q) %s\n'%(PDFentry))
956	fqfile.write('#L Q F(Q)\n')
957	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
958	fqnew = zip(qnew,fqfxn(qnew))
959	for q,fq in fqnew:
960	fqfile.write("%15.6g %15.6g\n" % (q,fq))
961	fqfile.close()
962	G2Print (' F(Q) saved to: '+fqfilename)
963
964	if PDFsaves[3]: #G(R)
965	grfilename = fileroot+'.gr'
966	grdata = PDFControls['G(R)'][1]
967	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
968	grfile = open(grfilename,'w')
969	grfile.write('#T G(R) %s\n'%(PDFentry))
970	grfile.write('#L R G(R)\n')
971	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
972	grnew = zip(rnew,grfxn(rnew))
973	for r,gr in grnew:
974	grfile.write("%15.6g %15.6g\n" % (r,gr))
975	grfile.close()
976	G2Print (' G(R) saved to: '+grfilename)
977
978	if PDFsaves[4]: #pdfGUI file for G(R)
979	import GSASIImath as G2mth
980	import GSASIIlattice as G2lat
981	grfilename = fileroot+'.gr'
982	grdata = PDFControls['G(R)'][1]
983	qdata = PDFControls['I(Q)'][1][0]
984	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
985	grfile = open(grfilename,'w')
986	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
987	grnew = zip(rnew,grfxn(rnew))
988
989	grfile.write('[DEFAULT]\n')
990	grfile.write('\n')
991	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
992	grfile.write('\n')
993	grfile.write('# input and output specifications\n')
994	grfile.write('dataformat = Qnm\n')
995	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
996	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
997	grfile.write('outputtype = gr\n')
998	grfile.write('\n')
999	grfile.write('# PDF calculation setup\n')
1000	if 'x' in Inst['Type']:
1001	grfile.write('mode = %s\n'%('xray'))
1002	elif 'N' in Inst['Type']:
1003	grfile.write('mode = %s\n'%('neutron'))
1004	wave = G2mth.getMeanWave(Inst)
1005	grfile.write('wavelength = %.5f\n'%(wave))
1006	formula = ''
1007	for el in PDFControls['ElList']:
1008	formula += el
1009	num = PDFControls['ElList'][el]['FormulaNo']
1010	if num == round(num):
1011	formula += '%d'%(int(num))
1012	else:
1013	formula += '%.2f'%(num)
1014	grfile.write('composition = %s\n'%(formula))
1015	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
1016	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
1017	grfile.write('qmaxinst = %.2f\n'%(highQ))
1018	grfile.write('qmin = %.5f\n'%(qdata[0]))
1019	grfile.write('qmax = %.4f\n'%(qdata[-1]))
1020	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
1021	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
1022	grfile.write('rstep = 0.01\n')
1023
1024
1025	grfile.write('\n')
1026	grfile.write('# End of config '+63*'-')
1027	grfile.write('\n')
1028	grfile.write('#### start data\n')
1029	grfile.write('#S 1\n')
1030	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
1031	for r,gr in grnew:
1032	grfile.write("%15.2F %15.6F\n" % (r,gr))
1033	grfile.close()
1034	G2Print (' G(R) saved to: '+grfilename)
1035
1036	if PDFsaves[5]: #RMCProfile files for F(Q) & g(r) overwrites any above
1037
1038	fqfilename = fileroot+'.fq'
1039	fqdata = PDFControls['F(Q)'][1]
1040	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
1041	fqfile = open(fqfilename,'w')
1042	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
1043	nq = qnew.shape[0]
1044	fqfile.write('%20d\n'%nq-1)
1045	fqfile.write(fqfilename+'\n')
1046	fqnew = zip(qnew,fqfxn(qnew))
1047	for q,fq in fqnew[1:]:
1048	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1049	fqfile.close()
1050	G2Print (' F(Q) saved to: '+fqfilename)
1051
1052	grfilename = fileroot+'.gr'
1053	grdata = PDFControls['g(r)'][1]
1054	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1055	grfile = open(grfilename,'w')
1056	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1057	nr = rnew.shape[0]
1058	grfile.write('%20d\n'%nr-1)
1059	grfile.write(grfilename+'\n')
1060	grnew = zip(rnew,grfxn(rnew))
1061	for r,gr in grnew[1:]:
1062	grfile.write("%15.6g %15.6g\n" % (r,gr))
1063	grfile.close()
1064	G2Print (' G(R) saved to: '+grfilename)
1065

Note: See TracBrowser for help on using the repository browser.

Download in other formats: