inversion_state.py @ a0ac888

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 a0ac888 was b35d3d1, checked in by Jae Cho <jhjcho@…>, 14 years ago
save state file: working, but more work to do
Property mode set to `100644`
File size: 18.9 KB

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

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source: sasview/prview/perspectives/pr/inversion_state.py @ a0ac888

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