inversion_state.py @ 302510b

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 302510b was 302510b, checked in by Mathieu Doucet <doucetm@…>, 15 years ago
prview: minor change to load saved inversions as a separate (time-stamped) problem and avoid confusion with data set that was previously loaded.
Property mode set to `100644`
File size: 21.7 KB

Rev	Line
[6f1f129]	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
[91128648]	11	import logging
	12	import DataLoader
	13	from DataLoader.readers.cansas_reader import Reader as CansasReader
	14
	15	PRNODE_NAME = 'pr_inversion'
[6f1f129]	16
	17	## List of P(r) inversion inputs
	18	in_list= [["nterms", "self.nfunc"],
	19	["d_max", "self.d_max"],
	20	["alpha", "self.alpha"],
	21	["slit_width", "self.width"],
	22	["slit_height", "self.height"],
	23	["qmin", "self.qmin"],
	24	["qmax", "self.qmax"]]
	25
	26	## List of P(r) inversion outputs
	27	out_list= [["elapsed", "self.elapsed"],
	28	["rg", "self.rg"],
	29	["iq0", "self.iq0"],
	30	["bck", "self.bck"],
	31	["chi2", "self.chi2"],
	32	["osc", "self.osc"],
	33	["pos", "self.pos"],
	34	["pos_err", "self.pos_err"],
	35	["alpha_estimate", "self.alpha_estimate"],
	36	["nterms_estimate", "self.nterms_estimate"]]
	37
	38	class InversionState(object):
	39	"""
	40	Class to hold the state information of the InversionControl panel.
	41	"""
	42	def __init__(self):
	43	"""
	44	Default values
	45	"""
	46	# Input
	47	self.file = None
	48	self.estimate_bck = False
	49	self.timestamp = time.time()
	50
	51	# Inversion parameters
	52	self.nfunc = None
	53	self.d_max = None
	54	self.alpha = None
	55
	56	# Slit parameters
	57	self.height = None
	58	self.width = None
	59
	60	# Q range
	61	self.qmin = None
	62	self.qmax = None
	63
	64	# Outputs
	65	self.elapsed = None
	66	self.rg = None
	67	self.iq0 = None
	68	self.bck = None
	69	self.chi2 = None
	70	self.osc = None
	71	self.pos = None
	72	self.pos_err = None
	73
	74	# Estimates
	75	self.alpha_estimate = None
	76	self.nterms_estimate = None
	77
	78	# Data
	79	self.q = None
	80	self.iq_obs = None
	81	self.iq_calc = None
[410aad8]	82
	83	# Coefficients
	84	self.coefficients = None
	85	self.covariance = None
[6f1f129]	86
	87	def __str__(self):
	88	"""
	89	Pretty print
	90
	91	@return: string representing the state
	92	"""
	93	state = "File: %s\n" % self.file
	94	state += "Timestamp: %s\n" % self.timestamp
	95	state += "Estimate bck: %s\n" % str(self.estimate_bck)
	96	state += "No. terms: %s\n" % str(self.nfunc)
	97	state += "D_max: %s\n" % str(self.d_max)
	98	state += "Alpha: %s\n" % str(self.alpha)
	99
	100	state += "Slit height: %s\n" % str(self.height)
	101	state += "Slit width: %s\n" % str(self.width)
	102
	103	state += "Qmin: %s\n" % str(self.qmin)
	104	state += "Qmax: %s\n" % str(self.qmax)
	105
	106	state += "\nEstimates:\n"
	107	state += " Alpha: %s\n" % str(self.alpha_estimate)
	108	state += " Nterms: %s\n" % str(self.nterms_estimate)
	109
	110	state += "\nOutputs:\n"
	111	state += " Elapsed: %s\n" % str(self.elapsed)
	112	state += " Rg: %s\n" % str(self.rg)
	113	state += " I(q=0): %s\n" % str(self.iq0)
	114	state += " Bck: %s\n" % str(self.bck)
	115	state += " Chi^2: %s\n" % str(self.chi2)
	116	state += " Oscillation:%s\n" % str(self.osc)
	117	state += " Positive: %s\n" % str(self.pos)
	118	state += " 1-sigma pos:%s\n" % str(self.pos_err)
	119
	120	return state
	121
[91128648]	122	def toXML(self, file="pr_state.prv", doc=None, entry_node=None):
[6f1f129]	123	"""
	124	Writes the state of the InversionControl panel to file, as XML.
	125
[91128648]	126	Compatible with standalone writing, or appending to an
	127	already existing XML document. In that case, the XML document
	128	is required. An optional entry node in the XML document may also be given.
	129
[6f1f129]	130	@param file: file to write to
[91128648]	131	@param doc: XML document object [optional]
	132	@param entry_node: XML node within the XML document at which we will append the data [optional]
[6f1f129]	133	"""
	134	from xml.dom.minidom import getDOMImplementation
	135
[91128648]	136	# Check whether we have to write a standalone XML file
	137	if doc is None:
	138	impl = getDOMImplementation()
[6f1f129]	139
[91128648]	140	doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0")
[6f1f129]	141
[91128648]	142	newdoc = impl.createDocument(None, PRNODE_NAME, doc_type)
	143	top_element = newdoc.documentElement
	144	else:
	145	# We are appending to an existing document
	146	newdoc = doc
	147	top_element = newdoc.createElement(PRNODE_NAME)
	148	if entry_node is None:
	149	newdoc.documentElement.appendChild(top_element)
	150	else:
	151	entry_node.appendChild(top_element)
	152
[6f1f129]	153	attr = newdoc.createAttribute("version")
	154	attr.nodeValue = '1.0'
	155	top_element.setAttributeNode(attr)
	156
	157	# File name
[410aad8]	158	element = newdoc.createElement("filename")
[91128648]	159	if self.file is not None:
	160	element.appendChild(newdoc.createTextNode(str(self.file)))
[410aad8]	161	else:
	162	element.appendChild(newdoc.createTextNode(str(file)))
	163	top_element.appendChild(element)
[6f1f129]	164
	165	element = newdoc.createElement("timestamp")
	166	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	167	attr = newdoc.createAttribute("epoch")
	168	attr.nodeValue = str(self.timestamp)
	169	element.setAttributeNode(attr)
	170	top_element.appendChild(element)
	171
	172	# Inputs
	173	inputs = newdoc.createElement("inputs")
	174	top_element.appendChild(inputs)
	175
	176	for item in in_list:
	177	element = newdoc.createElement(item[0])
	178	exec "element.appendChild(newdoc.createTextNode(str(%s)))" % item[1]
	179	inputs.appendChild(element)
	180
	181	# Outputs
	182	outputs = newdoc.createElement("outputs")
	183	top_element.appendChild(outputs)
	184
	185	for item in out_list:
	186	element = newdoc.createElement(item[0])
	187	exec "element.appendChild(newdoc.createTextNode(str(%s)))" % item[1]
	188	outputs.appendChild(element)
	189
[410aad8]	190	# Save output coefficients and its covariance matrix
	191	element = newdoc.createElement("coefficients")
	192	element.appendChild(newdoc.createTextNode(str(self.coefficients)))
	193	outputs.appendChild(element)
	194	element = newdoc.createElement("covariance")
	195	element.appendChild(newdoc.createTextNode(str(self.covariance)))
	196	outputs.appendChild(element)
	197
[6f1f129]	198	# Save the file
[91128648]	199	if doc is None:
	200	fd = open(file, 'w')
	201	fd.write(newdoc.toprettyxml())
	202	fd.close()
	203	return None
	204	else:
	205	return newdoc.toprettyxml()
[6f1f129]	206
[91128648]	207	def fromXML(self, file=None, node=None):
[6f1f129]	208	"""
	209	Load a P(r) inversion state from a file
	210
	211	@param file: .prv file
[91128648]	212	@param node: node of a XML document to read from
[6f1f129]	213	"""
[91128648]	214	if file is not None:
	215	# Check whether the file is valid
	216	if not os.path.isfile(file):
	217	raise RuntimeError, "P(r) reader: cannot open %s" % file
[6f1f129]	218
[91128648]	219	from xml.dom.minidom import parse
	220	doc = parse(file)
	221	node = doc.documentElement
	222
	223	if node.tagName == PRNODE_NAME:
	224	if node.hasAttribute('version')\
	225	and node.getAttribute('version') == '1.0':
[6f1f129]	226
[91128648]	227	if node.hasChildNodes():
	228	for node in node.childNodes:
[6f1f129]	229	if node.nodeName == 'filename':
	230	if node.hasChildNodes():
	231	self.file = node.childNodes[0].nodeValue.strip()
	232	elif node.nodeName == 'timestamp':
	233	if node.hasAttribute('epoch'):
	234	try:
	235	self.timestamp = float(node.getAttribute('epoch'))
	236	except:
	237	# Could not read timestamp: pass
	238	pass
	239
	240	# Parse inversion inputs
	241	elif node.nodeName == 'inputs':
	242	if node.hasChildNodes():
	243	for item in node.childNodes:
	244	for out in in_list:
	245	if item.nodeName == out[0]:
	246	try:
	247	exec '%s = float(item.childNodes[0].nodeValue.strip())' % out[1]
	248	except:
	249	exec '%s = None' % out[1]
	250	elif item.nodeName == 'estimate_bck':
	251	try:
	252	self.estimate_bck = item.childNodes[0].nodeValue.strip()=='True'
	253	except:
	254	self.estimate_bck = False
	255
	256	# Parse inversion outputs
	257	elif node.nodeName == 'outputs':
	258	if node.hasChildNodes():
	259	for item in node.childNodes:
[410aad8]	260	# Look for standard outputs
[6f1f129]	261	for out in out_list:
	262	if item.nodeName == out[0]:
	263	try:
	264	exec '%s = float(item.childNodes[0].nodeValue.strip())' % out[1]
	265	except:
	266	exec '%s = None' % out[1]
[410aad8]	267
	268	# Look for coefficients
	269	# Format is [value, value, value, value]
	270	if item.nodeName == 'coefficients':
	271	# Remove brackets
	272	c_values = item.childNodes[0].nodeValue.strip().replace('[','')
	273	c_values = c_values.replace(']','')
	274	toks = c_values.split()
	275	self.coefficients = []
	276	for c in toks:
	277	try:
	278	self.coefficients.append(float(c))
	279	except:
	280	# Bad data, skip. We will count the number of
	281	# coefficients at the very end and deal with
	282	# inconsistencies then.
	283	pass
	284	# Sanity check
	285	if not len(self.coefficients) == self.nfunc:
	286	# Inconsistent number of coefficients. Don't keep the data.
	287	err_msg = "InversionState.fromXML: inconsistant number of coefficients: "
	288	err_msg += "%d %d" % (len(self.coefficients), self.nfunc)
	289	logging.error(err_msg)
	290	self.coefficients = None
	291
	292	# Look for covariance matrix
	293	# Format is [ [value, value], [value, value] ]
	294	elif item.nodeName == "covariance":
	295	# Parse rows
	296	rows = item.childNodes[0].nodeValue.strip().split('[')
	297	self.covariance = []
	298	for row in rows:
	299	row = row.strip()
	300	if len(row) == 0: continue
	301	# Remove end bracket
	302	row = row.replace(']','')
	303	c_values = row.split()
	304	cov_row = []
	305	for c in c_values:
	306	try:
	307	cov_row.append(float(c))
	308	except:
	309	# Bad data, skip. We will count the number of
	310	# coefficients at the very end and deal with
	311	# inconsistencies then.
	312	pass
	313	# Sanity check: check the number of entries in the row
	314	if len(cov_row) == self.nfunc:
	315	self.covariance.append(cov_row)
	316	# Sanity check: check the number of rows in the covariance
	317	# matrix
	318	if not len(self.covariance) == self.nfunc:
	319	# Inconsistent dimensions of the covariance matrix.
	320	# Don't keep the data.
	321	err_msg = "InversionState.fromXML: inconsistant dimensions of the covariance matrix: "
	322	err_msg += "%d %d" % (len(self.covariance), self.nfunc)
	323	logging.error(err_msg)
	324	self.covariance = None
[6f1f129]	325	else:
[91128648]	326	raise RuntimeError, "Unsupported P(r) file version"
[6f1f129]	327
	328
[91128648]	329	class Reader(CansasReader):
[6f1f129]	330	"""
	331	Class to load a .prv P(r) inversion file
	332	"""
	333	## File type
	334	type_name = "P(r)"
	335
	336	## Wildcards
	337	type = ["P(r) files (.prv)\|.prv"]
	338	## List of allowed extensions
	339	ext=['.prv', '.PRV']
	340
[91128648]	341	def __init__(self, call_back, cansas=False):
[6f1f129]	342	"""
	343	Initialize the call-back method to be called
	344	after we load a file
	345	@param call_back: call-back method
[91128648]	346	@param cansas: True = files will be written/read in CanSAS format
	347	False = standalone mode
	348
[6f1f129]	349	"""
[91128648]	350	## Call back method to be executed after a file is read
[6f1f129]	351	self.call_back = call_back
[91128648]	352	## CanSAS format flag
	353	self.cansas = cansas
[6f1f129]	354
	355	def read(self, path):
	356	"""
	357	Load a new P(r) inversion state from file
	358
	359	@param path: file path
	360	@return: None
	361	"""
[91128648]	362	if self.cansas==True:
	363	return self._read_cansas(path)
	364	else:
	365	return self._read_standalone(path)
	366
	367	def _read_standalone(self, path):
	368	"""
	369	Load a new P(r) inversion state from file.
	370	The P(r) node is assumed to be the top element.
	371
	372	@param path: file path
	373	@return: None
	374	"""
[6f1f129]	375	# Read the new state from file
	376	state = InversionState()
[91128648]	377	state.fromXML(file=path)
[6f1f129]	378
	379	# Call back to post the new state
	380	self.call_back(state)
	381	return None
[91128648]	382
	383	def _parse_prstate(self, entry):
	384	"""
	385	Read a p(r) inversion result from an XML node
	386	@param entry: XML node to read from
	387	@return: InversionState object
	388	"""
	389	from xml import xpath
	390
	391	# Create an empty state
	392	state = InversionState()
	393
	394	# Locate the P(r) node
	395	try:
	396	nodes = xpath.Evaluate(PRNODE_NAME, entry)
	397	state.fromXML(node=nodes[0])
	398	except:
	399	#raise RuntimeError, "%s is not a file with P(r) information." % path
	400	logging.info("XML document does not contain P(r) information.")
	401	import sys
	402	print sys.exc_value
	403
	404	return state
	405
	406	def _read_cansas(self, path):
	407	"""
	408	Load data and P(r) information from a CanSAS XML file.
	409
	410	@param path: file path
	411	@return: Data1D object if a single SASentry was found,
	412	or a list of Data1D objects if multiple entries were found,
	413	or None of nothing was found
	414	@raise RuntimeError: when the file can't be opened
	415	@raise ValueError: when the length of the data vectors are inconsistent
	416	"""
	417	from xml.dom.minidom import parse
	418	from xml import xpath
	419	output = []
	420
	421	if os.path.isfile(path):
	422	basename = os.path.basename(path)
	423	root, extension = os.path.splitext(basename)
[410aad8]	424	#TODO: eventually remove the check for .xml once
	425	# the P(r) writer/reader is truly complete.
[91128648]	426	if extension.lower() in self.ext or \
	427	extension.lower() == '.xml':
	428
	429	dom = parse(path)
	430
	431	# Format 1: check whether we have a CanSAS file
	432	nodes = xpath.Evaluate('SASroot', dom)
	433	# Check the format version number
	434	if nodes[0].hasAttributes():
	435	for i in range(nodes[0].attributes.length):
	436	if nodes[0].attributes.item(i).nodeName=='version':
	437	if nodes[0].attributes.item(i).nodeValue != self.version:
	438	raise ValueError, "cansas_reader: unrecognized version number %s" % \
	439	nodes[0].attributes.item(i).nodeValue
	440
	441	entry_list = xpath.Evaluate('SASroot/SASentry', dom)
	442	for entry in entry_list:
	443	sas_entry = self._parse_entry(entry)
	444	prstate = self._parse_prstate(entry)
	445	sas_entry.meta_data['prstate'] = prstate
[410aad8]	446	sas_entry.filename = prstate.file
[91128648]	447	output.append(sas_entry)
	448	else:
	449	raise RuntimeError, "%s is not a file" % path
	450
	451	# Return output consistent with the loader's api
	452	if len(output)==0:
	453	return None
	454	elif len(output)==1:
[410aad8]	455	# Call back to post the new state
	456	self.call_back(output[0].meta_data['prstate'], datainfo = output[0])
[91128648]	457	return output[0]
	458	else:
	459	return output
	460
	461
	462	def write(self, filename, datainfo=None, prstate=None):
	463	"""
	464	Write the content of a Data1D as a CanSAS XML file
	465
	466	@param filename: name of the file to write
	467	@param datainfo: Data1D object
	468	@param prstate: InversionState object
	469	"""
	470
	471	# Sanity check
	472	if self.cansas == True:
	473	if datainfo is None:
	474	datainfo = DataLoader.data_info.Data1D(x=[], y=[])
[410aad8]	475	elif not issubclass(datainfo.__class__, DataLoader.data_info.Data1D):
	476	raise RuntimeError, "The cansas writer expects a Data1D instance: %s" % str(datainfo.__class__.__name__)
[91128648]	477
	478	# Create basic XML document
	479	doc, sasentry = self._to_xml_doc(datainfo)
	480
	481	# Add the P(r) information to the XML document
	482	if prstate is not None:
	483	prstate.toXML(doc=doc, entry_node=sasentry)
	484
	485	# Write the XML document
	486	fd = open(filename, 'w')
	487	fd.write(doc.toprettyxml())
	488	fd.close()
	489	else:
	490	prstate.toXML(file=filename)
	491
[6f1f129]	492
	493	if __name__ == "__main__":
[91128648]	494	#TODO: turn all this into unit tests
	495
[6f1f129]	496	state = InversionState()
	497	#print state.fromXML('../../test/pr_state.prv')
	498	print state.fromXML('../../test/test.prv')
[91128648]	499	print state
	500	state.toXML('test_copy.prv')
	501
	502	from DataLoader.loader import Loader
	503	l = Loader()
	504	datainfo = l.load("../../test/cansas1d.xml")
	505
[302510b]	506	def call_back(state, datainfo=None):
[91128648]	507	print state
	508
	509	reader = Reader(call_back)
	510	reader.cansas = False
	511	reader.write("test_copy_from_reader.prv", prstate=state)
	512	reader.cansas = True
	513	reader.write("testout.prv", datainfo, state)
	514	reader.write("testout_wo_datainfo.prv", prstate=state)
	515
	516	# Now try to load things back
	517	reader.cansas = False
	518	#print reader.read("test_copy_from_reader.prv")
	519	reader.cansas = True
	520	#data = reader.read("testout.prv")
	521	data = reader.read("testout_wo_datainfo.prv")
	522	print data
	523	print data.meta_data['prstate']
	524
	525

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source: sasview/prview/perspectives/pr/inversion_state.py @ 302510b

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