inversion_state.py @ 3600c12

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 3600c12 was 5777106, checked in by Mathieu Doucet <doucetm@…>, 11 years ago
Moving things around. Will definitely not build.
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1	"""
2	Handling of P(r) inversion states
3	"""
4	################################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#
9	#See the license text in license.txt
10	#
11	#copyright 2009, University of Tennessee
12	################################################################################
13
14
15	import time
16	import os
17	import sys
18	import logging
19	from lxml import etree
20	from sans.guiframe.dataFitting import Data1D
21	from sans.dataloader.readers.cansas_reader import Reader as CansasReader
22	from sans.dataloader.readers.cansas_reader import get_content
23
24	PRNODE_NAME = 'pr_inversion'
25	CANSAS_NS = "cansas1d/1.0"
26
27	# Translation of names between stored and object data
28	## List of P(r) inversion inputs
29	in_list = [["nterms", "nfunc"],
30	["d_max", "d_max"],
31	["alpha", "alpha"],
32	["slit_width", "width"],
33	["slit_height", "height"],
34	["qmin", "qmin"],
35	["qmax", "qmax"],
36	["estimate_bck", "estimate_bck"]]
37
38	## List of P(r) inversion outputs
39	out_list = [["elapsed", "elapsed"],
40	["rg", "rg"],
41	["iq0", "iq0"],
42	["bck", "bck"],
43	["chi2", "chi2"],
44	["osc", "osc"],
45	["pos", "pos"],
46	["pos_err", "pos_err"],
47	["alpha_estimate", "alpha_estimate"],
48	["nterms_estimate", "nterms_estimate"]]
49
50	class InversionState(object):
51	"""
52	Class to hold the state information of the InversionControl panel.
53	"""
54	def __init__(self):
55	"""
56	Default values
57	"""
58	# Input
59	self.file = None
60	self.estimate_bck = False
61	self.timestamp = time.time()
62
63	# Inversion parameters
64	self.nfunc = None
65	self.d_max = None
66	self.alpha = None
67
68	# Slit parameters
69	self.height = None
70	self.width = None
71
72	# Q range
73	self.qmin = None
74	self.qmax = None
75
76	# Outputs
77	self.elapsed = None
78	self.rg = None
79	self.iq0 = None
80	self.bck = None
81	self.chi2 = None
82	self.osc = None
83	self.pos = None
84	self.pos_err = None
85
86	# Estimates
87	self.alpha_estimate = None
88	self.nterms_estimate = None
89
90	# Data
91	self.q = None
92	self.iq_obs = None
93	self.iq_calc = None
94
95	# Coefficients
96	self.coefficients = None
97	self.covariance = None
98
99	def __str__(self):
100	"""
101	Pretty print
102
103	:return: string representing the state
104
105	"""
106	state = "File: %s\n" % self.file
107	state += "Timestamp: %s\n" % self.timestamp
108	state += "Estimate bck: %s\n" % str(self.estimate_bck)
109	state += "No. terms: %s\n" % str(self.nfunc)
110	state += "D_max: %s\n" % str(self.d_max)
111	state += "Alpha: %s\n" % str(self.alpha)
112
113	state += "Slit height: %s\n" % str(self.height)
114	state += "Slit width: %s\n" % str(self.width)
115
116	state += "Qmin: %s\n" % str(self.qmin)
117	state += "Qmax: %s\n" % str(self.qmax)
118
119	state += "\nEstimates:\n"
120	state += " Alpha: %s\n" % str(self.alpha_estimate)
121	state += " Nterms: %s\n" % str(self.nterms_estimate)
122
123	state += "\nOutputs:\n"
124	state += " Elapsed: %s\n" % str(self.elapsed)
125	state += " Rg: %s\n" % str(self.rg)
126	state += " I(q=0): %s\n" % str(self.iq0)
127	state += " Bck: %s\n" % str(self.bck)
128	state += " Chi^2: %s\n" % str(self.chi2)
129	state += " Oscillation:%s\n" % str(self.osc)
130	state += " Positive: %s\n" % str(self.pos)
131	state += " 1-sigma pos:%s\n" % str(self.pos_err)
132
133	return state
134
135	def toXML(self, file="pr_state.prv", doc=None, entry_node=None):
136	"""
137	Writes the state of the InversionControl panel to file, as XML.
138
139	Compatible with standalone writing, or appending to an
140	already existing XML document. In that case, the XML document
141	is required. An optional entry node in the XML document
142	may also be given.
143
144	:param file: file to write to
145	:param doc: XML document object [optional]
146	:param entry_node: XML node within the XML document at which
147	we will append the data [optional]
148
149	"""
150	from xml.dom.minidom import getDOMImplementation
151
152	# Check whether we have to write a standalone XML file
153	if doc is None:
154	impl = getDOMImplementation()
155
156	doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0")
157
158	newdoc = impl.createDocument(None, PRNODE_NAME, doc_type)
159	top_element = newdoc.documentElement
160	else:
161	# We are appending to an existing document
162	newdoc = doc
163	top_element = newdoc.createElement(PRNODE_NAME)
164	if entry_node is None:
165	newdoc.documentElement.appendChild(top_element)
166	else:
167	entry_node.appendChild(top_element)
168
169	attr = newdoc.createAttribute("version")
170	attr.nodeValue = '1.0'
171	top_element.setAttributeNode(attr)
172
173	# File name
174	element = newdoc.createElement("filename")
175	if self.file is not None:
176	element.appendChild(newdoc.createTextNode(str(self.file)))
177	else:
178	element.appendChild(newdoc.createTextNode(str(file)))
179	top_element.appendChild(element)
180
181	element = newdoc.createElement("timestamp")
182	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
183	attr = newdoc.createAttribute("epoch")
184	attr.nodeValue = str(self.timestamp)
185	element.setAttributeNode(attr)
186	top_element.appendChild(element)
187
188	# Inputs
189	inputs = newdoc.createElement("inputs")
190	top_element.appendChild(inputs)
191
192	for item in in_list:
193	element = newdoc.createElement(item[0])
194	cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))"
195	exec cmd % item[1]
196	inputs.appendChild(element)
197
198	# Outputs
199	outputs = newdoc.createElement("outputs")
200	top_element.appendChild(outputs)
201
202	for item in out_list:
203	element = newdoc.createElement(item[0])
204	cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))"
205	exec cmd % item[1]
206	outputs.appendChild(element)
207
208	# Save output coefficients and its covariance matrix
209	element = newdoc.createElement("coefficients")
210	element.appendChild(newdoc.createTextNode(str(self.coefficients)))
211	outputs.appendChild(element)
212	element = newdoc.createElement("covariance")
213	element.appendChild(newdoc.createTextNode(str(self.covariance)))
214	outputs.appendChild(element)
215
216	# Save the file
217	if doc is None:
218	fd = open(file, 'w')
219	fd.write(newdoc.toprettyxml())
220	fd.close()
221	return None
222	else:
223	return newdoc.toprettyxml()
224
225	def fromXML(self, file=None, node=None):
226	"""
227	Load a P(r) inversion state from a file
228
229	:param file: .prv file
230	:param node: node of a XML document to read from
231
232	"""
233	if file is not None:
234	msg = "InversionState no longer supports non-CanSAS"
235	msg += " format for P(r) files"
236	raise RuntimeError, msg
237
238	if node.get('version') and node.get('version') == '1.0':
239
240	# Get file name
241	entry = get_content('ns:filename', node)
242	if entry is not None:
243	self.file = entry.text.strip()
244
245	# Get time stamp
246	entry = get_content('ns:timestamp', node)
247	if entry is not None and entry.get('epoch'):
248	try:
249	self.timestamp = float(entry.get('epoch'))
250	except:
251	msg = "InversionState.fromXML: Could not read "
252	msg += "timestamp\n %s" % sys.exc_value
253	logging.error(msg)
254
255	# Parse inversion inputs
256	entry = get_content('ns:inputs', node)
257	if entry is not None:
258	for item in in_list:
259	input_field = get_content('ns:%s' % item[0], entry)
260	if input_field is not None:
261	try:
262	cmd = 'self.%s = float(input_field.text.strip())'
263	exec cmd % item[1]
264	except:
265	exec 'self.%s = None' % item[1]
266	input_field = get_content('ns:estimate_bck', entry)
267	if input_field is not None:
268	try:
269	self.estimate_bck = input_field.text.strip()=='True'
270	except:
271	self.estimate_bck = False
272
273	# Parse inversion outputs
274	entry = get_content('ns:outputs', node)
275	if entry is not None:
276	# Output parameters (scalars)
277	for item in out_list:
278	input_field = get_content('ns:%s' % item[0], entry)
279	if input_field is not None:
280	try:
281	cmd = 'self.%s = float(input_field.text.strip())'
282	exec cmd % item[1]
283	except:
284	exec 'self.%s = None' % item[1]
285
286	# Look for coefficients
287	# Format is [value, value, value, value]
288	coeff = get_content('ns:coefficients', entry)
289	if coeff is not None:
290	# Remove brackets
291	c_values = coeff.text.strip().replace('[','')
292	c_values = c_values.replace(']','')
293	toks = c_values.split()
294	self.coefficients = []
295	for c in toks:
296	try:
297	self.coefficients.append(float(c))
298	except:
299	# Bad data, skip. We will count the number of
300	# coefficients at the very end and deal with
301	# inconsistencies then.
302	pass
303	# Sanity check
304	if not len(self.coefficients) == self.nfunc:
305	# Inconsistent number of coefficients.
306	# Don't keep the data.
307	err_msg = "InversionState.fromXML: inconsistant "
308	err_msg += "number of coefficients: "
309	err_msg += "%d %d" % (len(self.coefficients),
310	self.nfunc)
311	logging.error(err_msg)
312	self.coefficients = None
313
314	# Look for covariance matrix
315	# Format is [ [value, value], [value, value] ]
316	coeff = get_content('ns:covariance', entry)
317	if coeff is not None:
318	# Parse rows
319	rows = coeff.text.strip().split('[')
320	self.covariance = []
321	for row in rows:
322	row = row.strip()
323	if len(row) == 0: continue
324	# Remove end bracket
325	row = row.replace(']','')
326	c_values = row.split()
327	cov_row = []
328	for c in c_values:
329	try:
330	cov_row.append(float(c))
331	except:
332	# Bad data, skip. We will count the number of
333	# coefficients at the very end and deal with
334	# inconsistencies then.
335	pass
336	# Sanity check: check the number of entries in the row
337	if len(cov_row) == self.nfunc:
338	self.covariance.append(cov_row)
339	# Sanity check: check the number of rows in the covariance
340	# matrix
341	if not len(self.covariance) == self.nfunc:
342	# Inconsistent dimensions of the covariance matrix.
343	# Don't keep the data.
344	err_msg = "InversionState.fromXML: "
345	err_msg += "inconsistant dimensions of the "
346	err_msg += " covariance matrix: "
347	err_msg += "%d %d" % (len(self.covariance), self.nfunc)
348	logging.error(err_msg)
349	self.covariance = None
350
351	class Reader(CansasReader):
352	"""
353	Class to load a .prv P(r) inversion file
354	"""
355	## File type
356	type_name = "P(r)"
357
358	## Wildcards
359	type = ["P(r) files (.prv)\|.prv",
360	"SANSView files (.svs)\|.svs"]
361	## List of allowed extensions
362	ext = ['.prv', '.PRV', '.svs', '.SVS']
363
364	def __init__(self, call_back, cansas=True):
365	"""
366	Initialize the call-back method to be called
367	after we load a file
368
369	:param call_back: call-back method
370	:param cansas: True = files will be written/read in CanSAS format
371	False = write CanSAS format
372
373	"""
374	## Call back method to be executed after a file is read
375	self.call_back = call_back
376	## CanSAS format flag
377	self.cansas = cansas
378	self.state = None
379
380	def read(self, path):
381	"""
382	Load a new P(r) inversion state from file
383
384	:param path: file path
385
386	:return: None
387
388	"""
389	if self.cansas==True:
390	return self._read_cansas(path)
391	else:
392	return self._read_standalone(path)
393
394	def _read_standalone(self, path):
395	"""
396	Load a new P(r) inversion state from file.
397	The P(r) node is assumed to be the top element.
398
399	:param path: file path
400
401	:return: None
402
403	"""
404	# Read the new state from file
405	state = InversionState()
406	state.fromXML(file=path)
407
408	# Call back to post the new state
409	self.state = state
410	#self.call_back(state)
411	return None
412
413	def _parse_prstate(self, entry):
414	"""
415	Read a p(r) inversion result from an XML node
416
417	:param entry: XML node to read from
418
419	:return: InversionState object
420
421	"""
422	state = None
423
424	# Locate the P(r) node
425	try:
426	nodes = entry.xpath('ns:%s' % PRNODE_NAME,
427	namespaces={'ns': CANSAS_NS})
428	if nodes !=[]:
429	# Create an empty state
430	state = InversionState()
431	state.fromXML(node=nodes[0])
432	except:
433	msg = "XML document does not contain P(r) "
434	msg += "information.\n %s" % sys.exc_value
435	logging.info(msg)
436
437	return state
438
439	def _read_cansas(self, path):
440	"""
441	Load data and P(r) information from a CanSAS XML file.
442
443	:param path: file path
444
445	:return: Data1D object if a single SASentry was found,
446	or a list of Data1D objects if multiple entries were found,
447	or None of nothing was found
448
449	:raise RuntimeError: when the file can't be opened
450	:raise ValueError: when the length of the data vectors are inconsistent
451
452	"""
453	output = []
454
455	if os.path.isfile(path):
456	basename = os.path.basename(path)
457	root, extension = os.path.splitext(basename)
458	#TODO: eventually remove the check for .xml once
459	# the P(r) writer/reader is truly complete.
460	if extension.lower() in self.ext or extension.lower() == '.xml':
461
462	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
463	# Check the format version number
464	# Specifying the namespace will take care of the file
465	#format version
466	root = tree.getroot()
467
468	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
469	namespaces={'ns': CANSAS_NS})
470
471	for entry in entry_list:
472	sas_entry = self._parse_entry(entry)
473	prstate = self._parse_prstate(entry)
474	#prstate could be None when .svs file is loaded
475	#in this case, skip appending to output
476	if prstate != None:
477	sas_entry.meta_data['prstate'] = prstate
478	sas_entry.filename = prstate.file
479	output.append(sas_entry)
480	else:
481	raise RuntimeError, "%s is not a file" % path
482
483	# Return output consistent with the loader's api
484	if len(output) == 0:
485	return None
486	elif len(output) == 1:
487	# Call back to post the new state
488	self.call_back(output[0].meta_data['prstate'], datainfo = output[0])
489	#self.state = output[0].meta_data['prstate']
490	return output[0]
491	else:
492	return output
493
494
495	def write(self, filename, datainfo=None, prstate=None):
496	"""
497	Write the content of a Data1D as a CanSAS XML file
498
499	:param filename: name of the file to write
500	:param datainfo: Data1D object
501	:param prstate: InversionState object
502
503	"""
504	# Sanity check
505	if self.cansas == True:
506	doc =self.write_toXML(datainfo, prstate)
507	# Write the XML document
508	fd = open(filename, 'w')
509	fd.write(doc.toprettyxml())
510	fd.close()
511	else:
512	prstate.toXML(file=filename)
513
514	def write_toXML(self, datainfo=None, state=None):
515	"""
516	Write toXML, a helper for write()
517
518	: return: xml doc
519	"""
520	if datainfo is None:
521	datainfo = Data1D(x=[], y=[])
522	elif not issubclass(datainfo.__class__, Data1D):
523	msg = "The cansas writer expects a Data1D "
524	msg += "instance: %s" % str(datainfo.__class__.__name__)
525	raise RuntimeError, msg
526
527	# Create basic XML document
528	doc, sasentry = self._to_xml_doc(datainfo)
529
530	# Add the invariant information to the XML document
531	if state is not None:
532	state.toXML(doc=doc, entry_node=sasentry)
533
534	return doc
535

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source: sasview/src/sans/perspectives/pr/inversion_state.py @ 3600c12

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