inversion_state.py @ ba69349

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 ba69349 was 80d2872, checked in by Mathieu Doucet <doucetm@…>, 15 years ago
prview: ensure that data selected for inversion are of the right class.
Property mode set to `100644`
File size: 18.3 KB

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

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source: sasview/prview/perspectives/pr/inversion_state.py @ ba69349

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