inversion_state.py @ 26500ec

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 26500ec was b9a5f0e, checked in by krzywon, 10 years ago
90% complete with the conversion.
Property mode set to `100644`
File size: 19.7 KB

Rev	Line
[1e62361]	1	"""
	2	Handling of P(r) inversion states
	3	"""
[7116b6e0]	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
[6f1f129]	14
[3e41f43]	15	import time
	16	import os
	17	import sys
[91128648]	18	import logging
[b1f7ec6]	19	from lxml import etree
[79492222]	20	from sas.guiframe.dataFitting import Data1D
	21	from sas.dataloader.readers.cansas_reader import Reader as CansasReader
	22	from sas.dataloader.readers.cansas_reader import get_content
[91128648]	23
	24	PRNODE_NAME = 'pr_inversion'
[b1f7ec6]	25	CANSAS_NS = "cansas1d/1.0"
[6f1f129]	26
[80d2872]	27	# Translation of names between stored and object data
[6f1f129]	28	## List of P(r) inversion inputs
[7116b6e0]	29	in_list = [["nterms", "nfunc"],
[80d2872]	30	["d_max", "d_max"],
	31	["alpha", "alpha"],
	32	["slit_width", "width"],
	33	["slit_height", "height"],
	34	["qmin", "qmin"],
[657e52c]	35	["qmax", "qmax"],
	36	["estimate_bck", "estimate_bck"]]
[6f1f129]	37
	38	## List of P(r) inversion outputs
[7116b6e0]	39	out_list = [["elapsed", "elapsed"],
[80d2872]	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"]]
[6f1f129]	49
	50	class InversionState(object):
	51	"""
[7116b6e0]	52	Class to hold the state information of the InversionControl panel.
[6f1f129]	53	"""
	54	def __init__(self):
	55	"""
[7116b6e0]	56	Default values
[6f1f129]	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
[410aad8]	94
	95	# Coefficients
	96	self.coefficients = None
	97	self.covariance = None
[6f1f129]	98
	99	def __str__(self):
	100	"""
[7116b6e0]	101	Pretty print
	102
	103	:return: string representing the state
	104
[6f1f129]	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
[91128648]	135	def toXML(self, file="pr_state.prv", doc=None, entry_node=None):
[6f1f129]	136	"""
[7116b6e0]	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
[3e41f43]	141	is required. An optional entry node in the XML document
	142	may also be given.
[7116b6e0]	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
[6f1f129]	149	"""
[92a2ecd]	150	#TODO: Get this to work
[6f1f129]	151	from xml.dom.minidom import getDOMImplementation
	152
[91128648]	153	# Check whether we have to write a standalone XML file
	154	if doc is None:
	155	impl = getDOMImplementation()
[6f1f129]	156
[91128648]	157	doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0")
[6f1f129]	158
[91128648]	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
[6f1f129]	170	attr = newdoc.createAttribute("version")
	171	attr.nodeValue = '1.0'
	172	top_element.setAttributeNode(attr)
	173
	174	# File name
[410aad8]	175	element = newdoc.createElement("filename")
[91128648]	176	if self.file is not None:
	177	element.appendChild(newdoc.createTextNode(str(self.file)))
[410aad8]	178	else:
	179	element.appendChild(newdoc.createTextNode(str(file)))
	180	top_element.appendChild(element)
[6f1f129]	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])
[3e41f43]	195	cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))"
	196	exec cmd % item[1]
[6f1f129]	197	inputs.appendChild(element)
	198
	199	# Outputs
	200	outputs = newdoc.createElement("outputs")
	201	top_element.appendChild(outputs)
	202
	203	for item in out_list:
	204	element = newdoc.createElement(item[0])
[3e41f43]	205	cmd = "element.appendChild(newdoc.createTextNode(str(self.%s)))"
	206	exec cmd % item[1]
[6f1f129]	207	outputs.appendChild(element)
	208
[410aad8]	209	# Save output coefficients and its covariance matrix
	210	element = newdoc.createElement("coefficients")
	211	element.appendChild(newdoc.createTextNode(str(self.coefficients)))
	212	outputs.appendChild(element)
	213	element = newdoc.createElement("covariance")
	214	element.appendChild(newdoc.createTextNode(str(self.covariance)))
	215	outputs.appendChild(element)
	216
[6f1f129]	217	# Save the file
[91128648]	218	if doc is None:
	219	fd = open(file, 'w')
	220	fd.write(newdoc.toprettyxml())
	221	fd.close()
	222	return None
	223	else:
[92a2ecd]	224	return newdoc
[6f1f129]	225
[91128648]	226	def fromXML(self, file=None, node=None):
[6f1f129]	227	"""
[7116b6e0]	228	Load a P(r) inversion state from a file
	229
	230	:param file: .prv file
	231	:param node: node of a XML document to read from
	232
[6f1f129]	233	"""
[91128648]	234	if file is not None:
[3e41f43]	235	msg = "InversionState no longer supports non-CanSAS"
	236	msg += " format for P(r) files"
	237	raise RuntimeError, msg
[91128648]	238
[3e41f43]	239	if node.get('version') and node.get('version') == '1.0':
[b1f7ec6]	240
	241	# Get file name
	242	entry = get_content('ns:filename', node)
	243	if entry is not None:
	244	self.file = entry.text.strip()
	245
	246	# Get time stamp
	247	entry = get_content('ns:timestamp', node)
	248	if entry is not None and entry.get('epoch'):
	249	try:
	250	self.timestamp = float(entry.get('epoch'))
	251	except:
[3e41f43]	252	msg = "InversionState.fromXML: Could not read "
	253	msg += "timestamp\n %s" % sys.exc_value
	254	logging.error(msg)
[b1f7ec6]	255
	256	# Parse inversion inputs
	257	entry = get_content('ns:inputs', node)
	258	if entry is not None:
	259	for item in in_list:
	260	input_field = get_content('ns:%s' % item[0], entry)
	261	if input_field is not None:
	262	try:
[3e41f43]	263	cmd = 'self.%s = float(input_field.text.strip())'
	264	exec cmd % item[1]
[b1f7ec6]	265	except:
[80d2872]	266	exec 'self.%s = None' % item[1]
[b1f7ec6]	267	input_field = get_content('ns:estimate_bck', entry)
	268	if input_field is not None:
	269	try:
	270	self.estimate_bck = input_field.text.strip()=='True'
	271	except:
	272	self.estimate_bck = False
[6f1f129]	273
[b1f7ec6]	274	# Parse inversion outputs
	275	entry = get_content('ns:outputs', node)
	276	if entry is not None:
	277	# Output parameters (scalars)
	278	for item in out_list:
	279	input_field = get_content('ns:%s' % item[0], entry)
	280	if input_field is not None:
	281	try:
[3e41f43]	282	cmd = 'self.%s = float(input_field.text.strip())'
	283	exec cmd % item[1]
[b1f7ec6]	284	except:
[80d2872]	285	exec 'self.%s = None' % item[1]
[b1f7ec6]	286
	287	# Look for coefficients
	288	# Format is [value, value, value, value]
	289	coeff = get_content('ns:coefficients', entry)
	290	if coeff is not None:
	291	# Remove brackets
	292	c_values = coeff.text.strip().replace('[','')
	293	c_values = c_values.replace(']','')
	294	toks = c_values.split()
	295	self.coefficients = []
	296	for c in toks:
	297	try:
	298	self.coefficients.append(float(c))
	299	except:
	300	# Bad data, skip. We will count the number of
	301	# coefficients at the very end and deal with
	302	# inconsistencies then.
	303	pass
	304	# Sanity check
	305	if not len(self.coefficients) == self.nfunc:
[3e41f43]	306	# Inconsistent number of coefficients.
	307	# Don't keep the data.
	308	err_msg = "InversionState.fromXML: inconsistant "
	309	err_msg += "number of coefficients: "
	310	err_msg += "%d %d" % (len(self.coefficients),
	311	self.nfunc)
[b1f7ec6]	312	logging.error(err_msg)
	313	self.coefficients = None
	314
	315	# Look for covariance matrix
	316	# Format is [ [value, value], [value, value] ]
	317	coeff = get_content('ns:covariance', entry)
	318	if coeff is not None:
	319	# Parse rows
	320	rows = coeff.text.strip().split('[')
	321	self.covariance = []
	322	for row in rows:
	323	row = row.strip()
	324	if len(row) == 0: continue
	325	# Remove end bracket
	326	row = row.replace(']','')
	327	c_values = row.split()
	328	cov_row = []
	329	for c in c_values:
	330	try:
	331	cov_row.append(float(c))
	332	except:
	333	# Bad data, skip. We will count the number of
	334	# coefficients at the very end and deal with
	335	# inconsistencies then.
	336	pass
	337	# Sanity check: check the number of entries in the row
	338	if len(cov_row) == self.nfunc:
	339	self.covariance.append(cov_row)
	340	# Sanity check: check the number of rows in the covariance
	341	# matrix
	342	if not len(self.covariance) == self.nfunc:
	343	# Inconsistent dimensions of the covariance matrix.
	344	# Don't keep the data.
[3e41f43]	345	err_msg = "InversionState.fromXML: "
	346	err_msg += "inconsistant dimensions of the "
	347	err_msg += " covariance matrix: "
[b1f7ec6]	348	err_msg += "%d %d" % (len(self.covariance), self.nfunc)
	349	logging.error(err_msg)
	350	self.covariance = None
	351
[91128648]	352	class Reader(CansasReader):
[6f1f129]	353	"""
[7116b6e0]	354	Class to load a .prv P(r) inversion file
[6f1f129]	355	"""
	356	## File type
	357	type_name = "P(r)"
	358
	359	## Wildcards
[b35d3d1]	360	type = ["P(r) files (.prv)\|.prv",
[b9a5f0e]	361	"SASView files (.svs)\|.svs"]
[6f1f129]	362	## List of allowed extensions
[3e41f43]	363	ext = ['.prv', '.PRV', '.svs', '.SVS']
[6f1f129]	364
[0d88a09]	365	def __init__(self, call_back, cansas=True):
[6f1f129]	366	"""
[7116b6e0]	367	Initialize the call-back method to be called
	368	after we load a file
	369
	370	:param call_back: call-back method
	371	:param cansas: True = files will be written/read in CanSAS format
	372	False = write CanSAS format
[91128648]	373
[6f1f129]	374	"""
[91128648]	375	## Call back method to be executed after a file is read
[6f1f129]	376	self.call_back = call_back
[91128648]	377	## CanSAS format flag
	378	self.cansas = cansas
[75fbd17]	379	self.state = None
[6f1f129]	380
	381	def read(self, path):
	382	"""
[7116b6e0]	383	Load a new P(r) inversion state from file
	384
	385	:param path: file path
	386
	387	:return: None
	388
[6f1f129]	389	"""
[91128648]	390	if self.cansas==True:
	391	return self._read_cansas(path)
	392	else:
	393	return self._read_standalone(path)
	394
	395	def _read_standalone(self, path):
	396	"""
[7116b6e0]	397	Load a new P(r) inversion state from file.
	398	The P(r) node is assumed to be the top element.
	399
	400	:param path: file path
	401
	402	:return: None
	403
[91128648]	404	"""
[6f1f129]	405	# Read the new state from file
	406	state = InversionState()
[91128648]	407	state.fromXML(file=path)
[6f1f129]	408
	409	# Call back to post the new state
[75fbd17]	410	self.state = state
	411	#self.call_back(state)
[6f1f129]	412	return None
[91128648]	413
	414	def _parse_prstate(self, entry):
	415	"""
[7116b6e0]	416	Read a p(r) inversion result from an XML node
	417
	418	:param entry: XML node to read from
	419
	420	:return: InversionState object
	421
[91128648]	422	"""
[b35d3d1]	423	state = None
[91128648]	424
	425	# Locate the P(r) node
	426	try:
[3e41f43]	427	nodes = entry.xpath('ns:%s' % PRNODE_NAME,
	428	namespaces={'ns': CANSAS_NS})
[b35d3d1]	429	if nodes !=[]:
	430	# Create an empty state
	431	state = InversionState()
	432	state.fromXML(node=nodes[0])
[91128648]	433	except:
[3e41f43]	434	msg = "XML document does not contain P(r) "
	435	msg += "information.\n %s" % sys.exc_value
	436	logging.info(msg)
[91128648]	437
	438	return state
	439
	440	def _read_cansas(self, path):
	441	"""
[7116b6e0]	442	Load data and P(r) information from a CanSAS XML file.
	443
	444	:param path: file path
	445
	446	:return: Data1D object if a single SASentry was found,
	447	or a list of Data1D objects if multiple entries were found,
	448	or None of nothing was found
	449
	450	:raise RuntimeError: when the file can't be opened
	451	:raise ValueError: when the length of the data vectors are inconsistent
	452
[91128648]	453	"""
	454	output = []
	455
	456	if os.path.isfile(path):
	457	basename = os.path.basename(path)
	458	root, extension = os.path.splitext(basename)
[410aad8]	459	#TODO: eventually remove the check for .xml once
	460	# the P(r) writer/reader is truly complete.
[3e41f43]	461	if extension.lower() in self.ext or extension.lower() == '.xml':
[91128648]	462
[b1f7ec6]	463	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
[91128648]	464	# Check the format version number
[3e41f43]	465	# Specifying the namespace will take care of the file
	466	#format version
[b1f7ec6]	467	root = tree.getroot()
[91128648]	468
[3e41f43]	469	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
	470	namespaces={'ns': CANSAS_NS})
[b1f7ec6]	471
[91128648]	472	for entry in entry_list:
[92a2ecd]	473	sas_entry, _ = self._parse_entry(entry)
[91128648]	474	prstate = self._parse_prstate(entry)
[b35d3d1]	475	#prstate could be None when .svs file is loaded
	476	#in this case, skip appending to output
	477	if prstate != None:
	478	sas_entry.meta_data['prstate'] = prstate
	479	sas_entry.filename = prstate.file
	480	output.append(sas_entry)
[91128648]	481	else:
	482	raise RuntimeError, "%s is not a file" % path
	483
	484	# Return output consistent with the loader's api
[3e41f43]	485	if len(output) == 0:
[91128648]	486	return None
[3e41f43]	487	elif len(output) == 1:
[410aad8]	488	# Call back to post the new state
[229da98]	489	self.call_back(output[0].meta_data['prstate'], datainfo = output[0])
	490	#self.state = output[0].meta_data['prstate']
[91128648]	491	return output[0]
	492	else:
	493	return output
	494
	495
	496	def write(self, filename, datainfo=None, prstate=None):
	497	"""
[7116b6e0]	498	Write the content of a Data1D as a CanSAS XML file
	499
	500	:param filename: name of the file to write
	501	:param datainfo: Data1D object
	502	:param prstate: InversionState object
	503
[91128648]	504	"""
	505	# Sanity check
	506	if self.cansas == True:
[92a2ecd]	507	doc = self.write_toXML(datainfo, prstate)
[91128648]	508	# Write the XML document
	509	fd = open(filename, 'w')
	510	fd.write(doc.toprettyxml())
	511	fd.close()
	512	else:
	513	prstate.toXML(file=filename)
	514
[b35d3d1]	515	def write_toXML(self, datainfo=None, state=None):
	516	"""
	517	Write toXML, a helper for write()
	518
	519	: return: xml doc
	520	"""
	521	if datainfo is None:
[a07e72f]	522	datainfo = Data1D(x=[], y=[])
	523	elif not issubclass(datainfo.__class__, Data1D):
[3e41f43]	524	msg = "The cansas writer expects a Data1D "
	525	msg += "instance: %s" % str(datainfo.__class__.__name__)
	526	raise RuntimeError, msg
[91128648]	527
[b35d3d1]	528	# Create basic XML document
	529	doc, sasentry = self._to_xml_doc(datainfo)
[92a2ecd]	530
[b35d3d1]	531	# Add the invariant information to the XML document
	532	if state is not None:
[92a2ecd]	533	doc = state.toXML(doc=doc, entry_node=sasentry)
[b35d3d1]	534
	535	return doc
[91128648]	536

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SasView

source: sasview/src/sas/perspectives/pr/inversion_state.py @ 26500ec

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