inversion_state.py @ bacc04b

Last change on this file since bacc04b was d85c194, checked in by Piotr Rozyczko <piotr.rozyczko@…>, 9 years ago
Remaining modules refactored
Property mode set to `100644`
File size: 18.8 KB

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

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SasView

source: sasview/src/sas/sasgui/perspectives/pr/inversion_state.py @ bacc04b

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