inversion_state.py @ 3e41f43

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 3e41f43 was 3e41f43, checked in by Gervaise Alina <gervyh@…>, 14 years ago
make pr plugin inheriting from pluginbase in guiframe
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File size: 19.5 KB

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

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source: sasview/prview/perspectives/pr/inversion_state.py @ 3e41f43

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