inversion_state.py @ b9a5f0e

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

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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 sas.guiframe.dataFitting import Data1D
21	from sas.dataloader.readers.cansas_reader import Reader as CansasReader
22	from sas.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	#TODO: Get this to work
151	from xml.dom.minidom import getDOMImplementation
152
153	# Check whether we have to write a standalone XML file
154	if doc is None:
155	impl = getDOMImplementation()
156
157	doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0")
158
159	newdoc = impl.createDocument(None, PRNODE_NAME, doc_type)
160	top_element = newdoc.documentElement
161	else:
162	# We are appending to an existing document
163	newdoc = doc
164	top_element = newdoc.createElement(PRNODE_NAME)
165	if entry_node is None:
166	newdoc.documentElement.appendChild(top_element)
167	else:
168	entry_node.appendChild(top_element)
169
170	attr = newdoc.createAttribute("version")
171	attr.nodeValue = '1.0'
172	top_element.setAttributeNode(attr)
173
174	# File name
175	element = newdoc.createElement("filename")
176	if self.file is not None:
177	element.appendChild(newdoc.createTextNode(str(self.file)))
178	else:
179	element.appendChild(newdoc.createTextNode(str(file)))
180	top_element.appendChild(element)
181
182	element = newdoc.createElement("timestamp")
183	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
184	attr = newdoc.createAttribute("epoch")
185	attr.nodeValue = str(self.timestamp)
186	element.setAttributeNode(attr)
187	top_element.appendChild(element)
188
189	# Inputs
190	inputs = newdoc.createElement("inputs")
191	top_element.appendChild(inputs)
192
193	for item in in_list:
194	element = newdoc.createElement(item[0])
195	cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))"
196	exec cmd % item[1]
197	inputs.appendChild(element)
198
199	# Outputs
200	outputs = newdoc.createElement("outputs")
201	top_element.appendChild(outputs)
202
203	for item in out_list:
204	element = newdoc.createElement(item[0])
205	cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))"
206	exec cmd % item[1]
207	outputs.appendChild(element)
208
209	# Save output coefficients and its covariance matrix
210	element = newdoc.createElement("coefficients")
211	element.appendChild(newdoc.createTextNode(str(self.coefficients)))
212	outputs.appendChild(element)
213	element = newdoc.createElement("covariance")
214	element.appendChild(newdoc.createTextNode(str(self.covariance)))
215	outputs.appendChild(element)
216
217	# Save the file
218	if doc is None:
219	fd = open(file, 'w')
220	fd.write(newdoc.toprettyxml())
221	fd.close()
222	return None
223	else:
224	return newdoc
225
226	def fromXML(self, file=None, node=None):
227	"""
228	Load a P(r) inversion state from a file
229
230	:param file: .prv file
231	:param node: node of a XML document to read from
232
233	"""
234	if file is not None:
235	msg = "InversionState no longer supports non-CanSAS"
236	msg += " format for P(r) files"
237	raise RuntimeError, msg
238
239	if node.get('version') and node.get('version') == '1.0':
240
241	# Get file name
242	entry = get_content('ns:filename', node)
243	if entry is not None:
244	self.file = entry.text.strip()
245
246	# Get time stamp
247	entry = get_content('ns:timestamp', node)
248	if entry is not None and entry.get('epoch'):
249	try:
250	self.timestamp = float(entry.get('epoch'))
251	except:
252	msg = "InversionState.fromXML: Could not read "
253	msg += "timestamp\n %s" % sys.exc_value
254	logging.error(msg)
255
256	# Parse inversion inputs
257	entry = get_content('ns:inputs', node)
258	if entry is not None:
259	for item in in_list:
260	input_field = get_content('ns:%s' % item[0], entry)
261	if input_field is not None:
262	try:
263	cmd = 'self.%s = float(input_field.text.strip())'
264	exec cmd % item[1]
265	except:
266	exec 'self.%s = None' % item[1]
267	input_field = get_content('ns:estimate_bck', entry)
268	if input_field is not None:
269	try:
270	self.estimate_bck = input_field.text.strip()=='True'
271	except:
272	self.estimate_bck = False
273
274	# Parse inversion outputs
275	entry = get_content('ns:outputs', node)
276	if entry is not None:
277	# Output parameters (scalars)
278	for item in out_list:
279	input_field = get_content('ns:%s' % item[0], entry)
280	if input_field is not None:
281	try:
282	cmd = 'self.%s = float(input_field.text.strip())'
283	exec cmd % item[1]
284	except:
285	exec 'self.%s = None' % item[1]
286
287	# Look for coefficients
288	# Format is [value, value, value, value]
289	coeff = get_content('ns:coefficients', entry)
290	if coeff is not None:
291	# Remove brackets
292	c_values = coeff.text.strip().replace('[','')
293	c_values = c_values.replace(']','')
294	toks = c_values.split()
295	self.coefficients = []
296	for c in toks:
297	try:
298	self.coefficients.append(float(c))
299	except:
300	# Bad data, skip. We will count the number of
301	# coefficients at the very end and deal with
302	# inconsistencies then.
303	pass
304	# Sanity check
305	if not len(self.coefficients) == self.nfunc:
306	# Inconsistent number of coefficients.
307	# Don't keep the data.
308	err_msg = "InversionState.fromXML: inconsistant "
309	err_msg += "number of coefficients: "
310	err_msg += "%d %d" % (len(self.coefficients),
311	self.nfunc)
312	logging.error(err_msg)
313	self.coefficients = None
314
315	# Look for covariance matrix
316	# Format is [ [value, value], [value, value] ]
317	coeff = get_content('ns:covariance', entry)
318	if coeff is not None:
319	# Parse rows
320	rows = coeff.text.strip().split('[')
321	self.covariance = []
322	for row in rows:
323	row = row.strip()
324	if len(row) == 0: continue
325	# Remove end bracket
326	row = row.replace(']','')
327	c_values = row.split()
328	cov_row = []
329	for c in c_values:
330	try:
331	cov_row.append(float(c))
332	except:
333	# Bad data, skip. We will count the number of
334	# coefficients at the very end and deal with
335	# inconsistencies then.
336	pass
337	# Sanity check: check the number of entries in the row
338	if len(cov_row) == self.nfunc:
339	self.covariance.append(cov_row)
340	# Sanity check: check the number of rows in the covariance
341	# matrix
342	if not len(self.covariance) == self.nfunc:
343	# Inconsistent dimensions of the covariance matrix.
344	# Don't keep the data.
345	err_msg = "InversionState.fromXML: "
346	err_msg += "inconsistant dimensions of the "
347	err_msg += " covariance matrix: "
348	err_msg += "%d %d" % (len(self.covariance), self.nfunc)
349	logging.error(err_msg)
350	self.covariance = None
351
352	class Reader(CansasReader):
353	"""
354	Class to load a .prv P(r) inversion file
355	"""
356	## File type
357	type_name = "P(r)"
358
359	## Wildcards
360	type = ["P(r) files (.prv)\|.prv",
361	"SASView files (.svs)\|.svs"]
362	## List of allowed extensions
363	ext = ['.prv', '.PRV', '.svs', '.SVS']
364
365	def __init__(self, call_back, cansas=True):
366	"""
367	Initialize the call-back method to be called
368	after we load a file
369
370	:param call_back: call-back method
371	:param cansas: True = files will be written/read in CanSAS format
372	False = write CanSAS format
373
374	"""
375	## Call back method to be executed after a file is read
376	self.call_back = call_back
377	## CanSAS format flag
378	self.cansas = cansas
379	self.state = None
380
381	def read(self, path):
382	"""
383	Load a new P(r) inversion state from file
384
385	:param path: file path
386
387	:return: None
388
389	"""
390	if self.cansas==True:
391	return self._read_cansas(path)
392	else:
393	return self._read_standalone(path)
394
395	def _read_standalone(self, path):
396	"""
397	Load a new P(r) inversion state from file.
398	The P(r) node is assumed to be the top element.
399
400	:param path: file path
401
402	:return: None
403
404	"""
405	# Read the new state from file
406	state = InversionState()
407	state.fromXML(file=path)
408
409	# Call back to post the new state
410	self.state = state
411	#self.call_back(state)
412	return None
413
414	def _parse_prstate(self, entry):
415	"""
416	Read a p(r) inversion result from an XML node
417
418	:param entry: XML node to read from
419
420	:return: InversionState object
421
422	"""
423	state = None
424
425	# Locate the P(r) node
426	try:
427	nodes = entry.xpath('ns:%s' % PRNODE_NAME,
428	namespaces={'ns': CANSAS_NS})
429	if nodes !=[]:
430	# Create an empty state
431	state = InversionState()
432	state.fromXML(node=nodes[0])
433	except:
434	msg = "XML document does not contain P(r) "
435	msg += "information.\n %s" % sys.exc_value
436	logging.info(msg)
437
438	return state
439
440	def _read_cansas(self, path):
441	"""
442	Load data and P(r) information from a CanSAS XML file.
443
444	:param path: file path
445
446	:return: Data1D object if a single SASentry was found,
447	or a list of Data1D objects if multiple entries were found,
448	or None of nothing was found
449
450	:raise RuntimeError: when the file can't be opened
451	:raise ValueError: when the length of the data vectors are inconsistent
452
453	"""
454	output = []
455
456	if os.path.isfile(path):
457	basename = os.path.basename(path)
458	root, extension = os.path.splitext(basename)
459	#TODO: eventually remove the check for .xml once
460	# the P(r) writer/reader is truly complete.
461	if extension.lower() in self.ext or extension.lower() == '.xml':
462
463	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
464	# Check the format version number
465	# Specifying the namespace will take care of the file
466	#format version
467	root = tree.getroot()
468
469	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
470	namespaces={'ns': CANSAS_NS})
471
472	for entry in entry_list:
473	sas_entry, _ = self._parse_entry(entry)
474	prstate = self._parse_prstate(entry)
475	#prstate could be None when .svs file is loaded
476	#in this case, skip appending to output
477	if prstate != None:
478	sas_entry.meta_data['prstate'] = prstate
479	sas_entry.filename = prstate.file
480	output.append(sas_entry)
481	else:
482	raise RuntimeError, "%s is not a file" % path
483
484	# Return output consistent with the loader's api
485	if len(output) == 0:
486	return None
487	elif len(output) == 1:
488	# Call back to post the new state
489	self.call_back(output[0].meta_data['prstate'], datainfo = output[0])
490	#self.state = output[0].meta_data['prstate']
491	return output[0]
492	else:
493	return output
494
495
496	def write(self, filename, datainfo=None, prstate=None):
497	"""
498	Write the content of a Data1D as a CanSAS XML file
499
500	:param filename: name of the file to write
501	:param datainfo: Data1D object
502	:param prstate: InversionState object
503
504	"""
505	# Sanity check
506	if self.cansas == True:
507	doc = self.write_toXML(datainfo, prstate)
508	# Write the XML document
509	fd = open(filename, 'w')
510	fd.write(doc.toprettyxml())
511	fd.close()
512	else:
513	prstate.toXML(file=filename)
514
515	def write_toXML(self, datainfo=None, state=None):
516	"""
517	Write toXML, a helper for write()
518
519	: return: xml doc
520	"""
521	if datainfo is None:
522	datainfo = Data1D(x=[], y=[])
523	elif not issubclass(datainfo.__class__, Data1D):
524	msg = "The cansas writer expects a Data1D "
525	msg += "instance: %s" % str(datainfo.__class__.__name__)
526	raise RuntimeError, msg
527
528	# Create basic XML document
529	doc, sasentry = self._to_xml_doc(datainfo)
530
531	# Add the invariant information to the XML document
532	if state is not None:
533	doc = state.toXML(doc=doc, entry_node=sasentry)
534
535	return doc
536

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SasView

source: sasview/src/sas/perspectives/pr/inversion_state.py @ b9a5f0e

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