inversion_state.py @ 332c10d

Last change on this file since 332c10d was 5251ec6, checked in by Paul Kienzle <pkienzle@…>, 6 years ago
improved support for py37 in sasgui
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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
21	from sas.sasgui.guiframe.dataFitting import Data1D
22	from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader
23	from sas.sascalc.dataloader.readers.cansas_reader import get_content
24
25	logger = logging.getLogger(__name__)
26
27	PRNODE_NAME = 'pr_inversion'
28	CANSAS_NS = "cansas1d/1.0"
29
30	# Translation of names between stored and object data
31	## List of P(r) inversion inputs
32	in_list = [["nterms", "nfunc"],
33	["d_max", "d_max"],
34	["alpha", "alpha"],
35	["slit_width", "width"],
36	["slit_height", "height"],
37	["qmin", "qmin"],
38	["qmax", "qmax"],
39	["estimate_bck", "estimate_bck"],
40	["bck_value", "bck_value"]]
41
42	## List of P(r) inversion outputs
43	out_list = [["elapsed", "elapsed"],
44	["rg", "rg"],
45	["iq0", "iq0"],
46	["bck", "bck"],
47	["chi2", "chi2"],
48	["osc", "osc"],
49	["pos", "pos"],
50	["pos_err", "pos_err"],
51	["alpha_estimate", "alpha_estimate"],
52	["nterms_estimate", "nterms_estimate"]]
53
54	class InversionState(object):
55	"""
56	Class to hold the state information of the InversionControl panel.
57	"""
58	def __init__(self):
59	"""
60	Default values
61	"""
62	# Input
63	self.file = None
64	self.estimate_bck = False
65	self.timestamp = time.time()
66	self.bck_value = 0.0
67
68	# Inversion parameters
69	self.nfunc = None
70	self.d_max = None
71	self.alpha = None
72
73	# Slit parameters
74	self.height = None
75	self.width = None
76
77	# Q range
78	self.qmin = None
79	self.qmax = None
80
81	# Outputs
82	self.elapsed = None
83	self.rg = None
84	self.iq0 = None
85	self.bck = None
86	self.chi2 = None
87	self.osc = None
88	self.pos = None
89	self.pos_err = None
90
91	# Estimates
92	self.alpha_estimate = None
93	self.nterms_estimate = None
94
95	# Data
96	self.q = None
97	self.iq_obs = None
98	self.iq_calc = None
99
100	# Coefficients
101	self.coefficients = None
102	self.covariance = None
103
104	def __str__(self):
105	"""
106	Pretty print
107
108	:return: string representing the state
109
110	"""
111	state = "File: %s\n" % self.file
112	state += "Timestamp: %s\n" % self.timestamp
113	state += "Estimate bck: %s\n" % str(self.estimate_bck)
114	state += "Bck Value: %s\n" % str(self.bck_value)
115	state += "No. terms: %s\n" % str(self.nfunc)
116	state += "D_max: %s\n" % str(self.d_max)
117	state += "Alpha: %s\n" % str(self.alpha)
118
119	state += "Slit height: %s\n" % str(self.height)
120	state += "Slit width: %s\n" % str(self.width)
121
122	state += "Qmin: %s\n" % str(self.qmin)
123	state += "Qmax: %s\n" % str(self.qmax)
124
125	state += "\nEstimates:\n"
126	state += " Alpha: %s\n" % str(self.alpha_estimate)
127	state += " Nterms: %s\n" % str(self.nterms_estimate)
128
129	state += "\nOutputs:\n"
130	state += " Elapsed: %s\n" % str(self.elapsed)
131	state += " Rg: %s\n" % str(self.rg)
132	state += " I(q=0): %s\n" % str(self.iq0)
133	state += " Bck: %s\n" % str(self.bck)
134	state += " Chi^2: %s\n" % str(self.chi2)
135	state += " Oscillation:%s\n" % str(self.osc)
136	state += " Positive: %s\n" % str(self.pos)
137	state += " 1-sigma pos:%s\n" % str(self.pos_err)
138
139	return state
140
141	def toXML(self, file="pr_state.prv", doc=None, entry_node=None):
142	"""
143	Writes the state of the InversionControl panel to file, as XML.
144
145	Compatible with standalone writing, or appending to an
146	already existing XML document. In that case, the XML document
147	is required. An optional entry node in the XML document
148	may also be given.
149
150	:param file: file to write to
151	:param doc: XML document object [optional]
152	:param entry_node: XML node within the XML document at which
153	we will append the data [optional]
154
155	"""
156	#TODO: Get this to work
157	from xml.dom.minidom import getDOMImplementation
158
159	# Check whether we have to write a standalone XML file
160	if doc is None:
161	impl = getDOMImplementation()
162
163	doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0")
164
165	newdoc = impl.createDocument(None, PRNODE_NAME, doc_type)
166	top_element = newdoc.documentElement
167	else:
168	# We are appending to an existing document
169	newdoc = doc
170	top_element = newdoc.createElement(PRNODE_NAME)
171	if entry_node is None:
172	newdoc.documentElement.appendChild(top_element)
173	else:
174	entry_node.appendChild(top_element)
175
176	attr = newdoc.createAttribute("version")
177	attr.nodeValue = '1.0'
178	top_element.setAttributeNode(attr)
179
180	# File name
181	element = newdoc.createElement("filename")
182	if self.file is not None:
183	element.appendChild(newdoc.createTextNode(str(self.file)))
184	else:
185	element.appendChild(newdoc.createTextNode(str(file)))
186	top_element.appendChild(element)
187
188	element = newdoc.createElement("timestamp")
189	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
190	attr = newdoc.createAttribute("epoch")
191	attr.nodeValue = str(self.timestamp)
192	element.setAttributeNode(attr)
193	top_element.appendChild(element)
194
195	# Inputs
196	inputs = newdoc.createElement("inputs")
197	top_element.appendChild(inputs)
198
199	for item in in_list:
200	element = newdoc.createElement(item[0])
201	element.appendChild(newdoc.createTextNode(str(getattr(self, item[1]))))
202	inputs.appendChild(element)
203
204	# Outputs
205	outputs = newdoc.createElement("outputs")
206	top_element.appendChild(outputs)
207
208	for item in out_list:
209	element = newdoc.createElement(item[0])
210	element.appendChild(newdoc.createTextNode(str(getattr(self, item[1]))))
211	outputs.appendChild(element)
212
213	# Save output coefficients and its covariance matrix
214	element = newdoc.createElement("coefficients")
215	element.appendChild(newdoc.createTextNode(str(self.coefficients)))
216	outputs.appendChild(element)
217	element = newdoc.createElement("covariance")
218	element.appendChild(newdoc.createTextNode(str(self.covariance)))
219	outputs.appendChild(element)
220
221	# Save the file
222	if doc is None:
223	fd = open(file, 'w')
224	fd.write(newdoc.toprettyxml())
225	fd.close()
226	return None
227	else:
228	return newdoc
229
230	def fromXML(self, file=None, node=None):
231	"""
232	Load a P(r) inversion state from a file
233
234	:param file: .prv file
235	:param node: node of a XML document to read from
236
237	"""
238	if file is not None:
239	msg = "InversionState no longer supports non-CanSAS"
240	msg += " format for P(r) files"
241	raise RuntimeError(msg)
242
243	if node.get('version') and node.get('version') == '1.0':
244
245	# Get file name
246	entry = get_content('ns:filename', node)
247	if entry is not None:
248	self.file = entry.text.strip()
249
250	# Get time stamp
251	entry = get_content('ns:timestamp', node)
252	if entry is not None and entry.get('epoch'):
253	try:
254	self.timestamp = float(entry.get('epoch'))
255	except Exception as exc:
256	msg = "InversionState.fromXML: Could not read "
257	msg += "timestamp\n %s" % exc
258	logger.error(msg)
259
260	# Parse inversion inputs
261	entry = get_content('ns:inputs', node)
262	if entry is not None:
263	for item in in_list:
264	input_field = get_content('ns:%s' % item[0], entry)
265	if input_field is not None:
266	try:
267	setattr(self, item[1], float(input_field.text.strip()))
268	except:
269	setattr(self, item[1], None)
270	input_field = get_content('ns:estimate_bck', entry)
271	if input_field is not None:
272	try:
273	self.estimate_bck = input_field.text.strip() == 'True'
274	except:
275	self.estimate_bck = False
276
277	# Parse inversion outputs
278	entry = get_content('ns:outputs', node)
279	if entry is not None:
280	# Output parameters (scalars)
281	for item in out_list:
282	input_field = get_content('ns:%s' % item[0], entry)
283	if input_field is not None:
284	try:
285	setattr(self, item[1], float(input_field.text.strip()))
286	except:
287	setattr(self, item[1], None)
288
289	# Look for coefficients
290	# Format is [value, value, value, value]
291	coeff = get_content('ns:coefficients', entry)
292	if coeff is not None:
293	# Remove brackets
294	c_values = coeff.text.strip().replace('[', '')
295	c_values = c_values.replace(']', '')
296	toks = c_values.split()
297	self.coefficients = []
298	for c in toks:
299	try:
300	self.coefficients.append(float(c))
301	except:
302	# Bad data, skip. We will count the number of
303	# coefficients at the very end and deal with
304	# inconsistencies then.
305	pass
306	# Sanity check
307	if not len(self.coefficients) == self.nfunc:
308	# Inconsistent number of coefficients.
309	# Don't keep the data.
310	err_msg = "InversionState.fromXML: inconsistant "
311	err_msg += "number of coefficients: "
312	err_msg += "%d %d" % (len(self.coefficients),
313	self.nfunc)
314	logger.error(err_msg)
315	self.coefficients = None
316
317	# Look for covariance matrix
318	# Format is [ [value, value], [value, value] ]
319	coeff = get_content('ns:covariance', entry)
320	if coeff is not None:
321	# Parse rows
322	rows = coeff.text.strip().split('[')
323	self.covariance = []
324	for row in rows:
325	row = row.strip()
326	if len(row) == 0: continue
327	# Remove end bracket
328	row = row.replace(']', '')
329	c_values = row.split()
330	cov_row = []
331	for c in c_values:
332	try:
333	cov_row.append(float(c))
334	except:
335	# Bad data, skip. We will count the number of
336	# coefficients at the very end and deal with
337	# inconsistencies then.
338	pass
339	# Sanity check: check the number of entries in the row
340	if len(cov_row) == self.nfunc:
341	self.covariance.append(cov_row)
342	# Sanity check: check the number of rows in the covariance
343	# matrix
344	if not len(self.covariance) == self.nfunc:
345	# Inconsistent dimensions of the covariance matrix.
346	# Don't keep the data.
347	err_msg = "InversionState.fromXML: "
348	err_msg += "inconsistant dimensions of the "
349	err_msg += " covariance matrix: "
350	err_msg += "%d %d" % (len(self.covariance), self.nfunc)
351	logger.error(err_msg)
352	self.covariance = None
353
354	class Reader(CansasReader):
355	"""
356	Class to load a .prv P(r) inversion file
357	"""
358	## File type
359	type_name = "P(r)"
360
361	## Wildcards
362	type = ["P(r) files (.prv)\|.prv",
363	"SASView files (.svs)\|.svs"]
364	## List of allowed extensions
365	ext = ['.prv', '.PRV', '.svs', '.SVS']
366
367	def __init__(self, call_back, cansas=True):
368	"""
369	Initialize the call-back method to be called
370	after we load a file
371
372	:param call_back: call-back method
373	:param cansas: True = files will be written/read in CanSAS format
374	False = write CanSAS format
375
376	"""
377	## Call back method to be executed after a file is read
378	self.call_back = call_back
379	## CanSAS format flag
380	self.cansas = cansas
381	self.state = None
382
383	def read(self, path):
384	"""
385	Load a new P(r) inversion state from file
386
387	:param path: file path
388
389	:return: None
390
391	"""
392	if self.cansas:
393	return self._read_cansas(path)
394	else:
395	return self._read_standalone(path)
396
397	def _read_standalone(self, path):
398	"""
399	Load a new P(r) inversion state from file.
400	The P(r) node is assumed to be the top element.
401
402	:param path: file path
403
404	:return: None
405
406	"""
407	# Read the new state from file
408	state = InversionState()
409	state.fromXML(file=path)
410
411	# Call back to post the new state
412	self.state = state
413	#self.call_back(state)
414	return None
415
416	def _parse_prstate(self, entry):
417	"""
418	Read a p(r) inversion result from an XML node
419
420	:param entry: XML node to read from
421
422	:return: InversionState object
423
424	"""
425	state = None
426
427	# Locate the P(r) node
428	try:
429	nodes = entry.xpath('ns:%s' % PRNODE_NAME,
430	namespaces={'ns': CANSAS_NS})
431	if nodes != []:
432	# Create an empty state
433	state = InversionState()
434	state.fromXML(node=nodes[0])
435	except Exception as exc:
436	msg = "XML document does not contain P(r) "
437	msg += "information.\n %s" % exc
438	logger.info(msg)
439
440	return state
441
442	def _read_cansas(self, path):
443	"""
444	Load data and P(r) information from a CanSAS XML file.
445
446	:param path: file path
447
448	:return: Data1D object if a single SASentry was found,
449	or a list of Data1D objects if multiple entries were found,
450	or None of nothing was found
451
452	:raise RuntimeError: when the file can't be opened
453	:raise ValueError: when the length of the data vectors are inconsistent
454
455	"""
456	output = []
457
458	if os.path.isfile(path):
459	basename = os.path.basename(path)
460	root, extension = os.path.splitext(basename)
461	#TODO: eventually remove the check for .xml once
462	# the P(r) writer/reader is truly complete.
463	if extension.lower() in self.ext or extension.lower() == '.xml':
464
465	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
466	# Check the format version number
467	# Specifying the namespace will take care of the file
468	#format version
469	root = tree.getroot()
470
471	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
472	namespaces={'ns': CANSAS_NS})
473
474	for entry in entry_list:
475	prstate = self._parse_prstate(entry)
476	#prstate could be None when .svs file is loaded
477	#in this case, skip appending to output
478	if prstate is not None:
479	sas_entry, _ = self._parse_entry(entry)
480	sas_entry.meta_data['prstate'] = prstate
481	sas_entry.filename = prstate.file
482	output.append(sas_entry)
483	else:
484	raise RuntimeError("%s is not a file" % path)
485
486	# Return output consistent with the loader's api
487	if len(output) == 0:
488	return None
489	elif len(output) == 1:
490	# Call back to post the new state
491	self.call_back(output[0].meta_data['prstate'], datainfo=output[0])
492	#self.state = output[0].meta_data['prstate']
493	return output[0]
494	else:
495	return output
496
497
498	def write(self, filename, datainfo=None, prstate=None):
499	"""
500	Write the content of a Data1D as a CanSAS XML file
501
502	:param filename: name of the file to write
503	:param datainfo: Data1D object
504	:param prstate: InversionState object
505
506	"""
507	# Sanity check
508	if self.cansas:
509	doc = self.write_toXML(datainfo, prstate)
510	# Write the XML document
511	fd = open(filename, 'w')
512	fd.write(doc.toprettyxml())
513	fd.close()
514	else:
515	prstate.toXML(file=filename)
516
517	def write_toXML(self, datainfo=None, state=None):
518	"""
519	Write toXML, a helper for write()
520
521	: return: xml doc
522	"""
523	if datainfo is None:
524	datainfo = Data1D(x=[], y=[])
525	elif not issubclass(datainfo.__class__, Data1D):
526	msg = "The cansas writer expects a Data1D "
527	msg += "instance: %s" % str(datainfo.__class__.__name__)
528	raise RuntimeError(msg)
529
530	# Create basic XML document
531	doc, sasentry = self._to_xml_doc(datainfo)
532
533	# Add the invariant information to the XML document
534	if state is not None:
535	doc = state.toXML(doc=doc, entry_node=sasentry)
536
537	return doc

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source: sasview/src/sas/sasgui/perspectives/pr/inversion_state.py @ 332c10d

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