cansas_reader.py @ c3e4e213

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 c3e4e213 was 83b6408, checked in by krzywon, 8 years ago
Modified Cansas XML reader to attempt to load data that doesn't fully meet the cansas format.
Property mode set to `100644`
File size: 50.1 KB

Rev	Line
[d26dea0]	1	"""
	2	CanSAS data reader - new recursive cansas_version.
	3	"""
	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	#If you use DANSE applications to do scientific research that leads to
	9	#publication, we ask that you acknowledge the use of the software with the
	10	#following sentence:
	11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
	12	#copyright 2008,2009 University of Tennessee
	13	#############################################################################
[0f1e140]	14
[d26dea0]	15	import logging
	16	import numpy
	17	import os
	18	import sys
	19	import datetime
	20	import inspect
	21	# For saving individual sections of data
[b699768]	22	from sas.sascalc.dataloader.data_info import Data1D
	23	from sas.sascalc.dataloader.data_info import Collimation
	24	from sas.sascalc.dataloader.data_info import TransmissionSpectrum
	25	from sas.sascalc.dataloader.data_info import Detector
	26	from sas.sascalc.dataloader.data_info import Process
	27	from sas.sascalc.dataloader.data_info import Aperture
	28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
	30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants
[d26dea0]	31
[682c432]	32	# The following 2 imports ARE used. Do not remove either.
	33	import xml.dom.minidom
	34	from xml.dom.minidom import parseString
	35
[83b6408]	36	## TODO: Refactor to load multiple <SASData> as separate Data1D objects
	37	## TODO: Refactor to allow invalid XML, but give a useful warning when loaded
	38
[d26dea0]	39	_ZERO = 1e-16
	40	PREPROCESS = "xmlpreprocess"
	41	ENCODING = "encoding"
	42	RUN_NAME_DEFAULT = "None"
	43	HAS_CONVERTER = True
	44	try:
[b699768]	45	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	46	except ImportError:
	47	HAS_CONVERTER = False
	48
	49	CONSTANTS = CansasConstants()
	50	CANSAS_FORMAT = CONSTANTS.format
	51	CANSAS_NS = CONSTANTS.names
	52	ALLOW_ALL = True
	53
[682c432]	54	# DO NOT REMOVE Called by outside packages:
[d85c194]	55	# sas.sasgui.perspectives.invariant.invariant_state
	56	# sas.sasgui.perspectives.fitting.pagestate
[d26dea0]	57	def get_content(location, node):
	58	"""
	59	Get the first instance of the content of a xpath location.
	60
	61	:param location: xpath location
	62	:param node: node to start at
	63
	64	:return: Element, or None
	65	"""
	66	nodes = node.xpath(location,
	67	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	68	if len(nodes) > 0:
	69	return nodes[0]
	70	else:
	71	return None
	72
[682c432]	73	# DO NOT REMOVE Called by outside packages:
[d85c194]	74	# sas.sasgui.perspectives.fitting.pagestate
[d26dea0]	75	def write_node(doc, parent, name, value, attr=None):
	76	"""
	77	:param doc: document DOM
	78	:param parent: parent node
	79	:param name: tag of the element
	80	:param value: value of the child text node
	81	:param attr: attribute dictionary
	82
	83	:return: True if something was appended, otherwise False
	84	"""
	85	if attr is None:
	86	attr = {}
	87	if value is not None:
	88	node = doc.createElement(name)
	89	node.appendChild(doc.createTextNode(str(value)))
	90	for item in attr:
	91	node.setAttribute(item, attr[item])
	92	parent.appendChild(node)
	93	return True
	94	return False
	95
	96	class Reader(XMLreader):
	97	"""
	98	Class to load cansas 1D XML files
	99
	100	:Dependencies:
	101	The CanSAS reader requires PyXML 0.8.4 or later.
	102	"""
	103	##CanSAS version - defaults to version 1.0
	104	cansas_version = "1.0"
	105	base_ns = "{cansas1d/1.0}"
	106	logging = None
	107	errors = None
	108	type_name = "canSAS"
	109	## Wildcards
	110	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
	111	## List of allowed extensions
	112	ext = ['.xml', '.XML', '.svs', '.SVS']
	113	## Flag to bypass extension check
	114	allow_all = True
	115
	116	def __init__(self):
	117	## List of errors
	118	self.errors = set()
	119	self.logging = []
	120	self.encoding = None
	121
	122	def is_cansas(self, ext="xml"):
	123	"""
	124	Checks to see if the xml file is a CanSAS file
	125
	126	:param ext: The file extension of the data file
	127	"""
	128	if self.validate_xml():
	129	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	130	value = self.xmlroot.get(name)
	131	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	132	value.rsplit(" ")[0]:
	133	return True
	134	if ext == "svs":
	135	return True
	136	return False
	137
[83b6408]	138	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	139	"""
	140	Loads the file and associates a schema, if a known schema exists
	141
	142	:param xml_file: The xml file path sent to Reader.read
	143	"""
	144	base_name = xml_reader.__file__
	145	base_name = base_name.replace("\\", "/")
	146	base = base_name.split("/sas/")[0]
	147
	148	# Load in xml file and get the cansas version from the header
	149	self.set_xml_file(xml_file)
	150	self.cansas_version = self.xmlroot.get("version", "1.0")
	151
	152	# Generic values for the cansas file based on the version
	153	cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	154	if schema_path == "":
	155	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format\
[d26dea0]	156	(base, cansas_defaults.get("schema")).replace("\\", "/")
	157
	158	# Link a schema to the XML file.
	159	self.set_schema(schema_path)
	160	return cansas_defaults
	161
[83b6408]	162	## TODO: Test loading invalid CanSAS XML files and see if this works
	163	## TODO: Once works, try adding a warning that the data is invalid
	164	def read(self, xml_file, schema_path=""):
[d26dea0]	165	"""
	166	Validate and read in an xml_file file in the canSAS format.
	167
	168	:param xml_file: A canSAS file path in proper XML format
	169	"""
	170	# output - Final list of Data1D objects
	171	output = []
	172	# ns - Namespace hierarchy for current xml_file object
	173	ns_list = []
	174
	175	# Check that the file exists
	176	if os.path.isfile(xml_file):
	177	basename = os.path.basename(xml_file)
	178	_, extension = os.path.splitext(basename)
	179	# If the file type is not allowed, return nothing
	180	if extension in self.ext or self.allow_all:
	181	# Get the file location of
[83b6408]	182	cansas_defaults = self.load_file_and_schema(xml_file, schema_path)
[d26dea0]	183
	184	# Try to load the file, but raise an error if unable to.
	185	# Check the file matches the XML schema
	186	try:
	187	if self.is_cansas(extension):
	188	# Get each SASentry from XML file and add it to a list.
	189	entry_list = self.xmlroot.xpath(
	190	'/ns:SASroot/ns:SASentry',
	191	namespaces={'ns': cansas_defaults.get("ns")})
	192	ns_list.append("SASentry")
	193
	194	# If multiple files, modify the name for each is unique
	195	increment = 0
	196	# Parse each SASentry item
	197	for entry in entry_list:
	198	# Define a new Data1D object with zeroes for
	199	# x_vals and y_vals
	200	data1d = Data1D(numpy.empty(0), numpy.empty(0),
	201	numpy.empty(0), numpy.empty(0))
	202	data1d.dxl = numpy.empty(0)
	203	data1d.dxw = numpy.empty(0)
	204
	205	# If more than one SASentry, increment each in order
	206	name = basename
	207	if len(entry_list) - 1 > 0:
	208	name += "_{0}".format(increment)
	209	increment += 1
	210
	211	# Set the Data1D name and then parse the entry.
	212	# The entry is appended to a list of entry values
	213	data1d.filename = name
	214	data1d.meta_data["loader"] = "CanSAS 1D"
	215
	216	# Get all preprocessing events and encoding
	217	self.set_processing_instructions()
	218	data1d.meta_data[PREPROCESS] = \
	219	self.processing_instructions
	220
	221	# Parse the XML file
	222	return_value, extras = \
	223	self._parse_entry(entry, ns_list, data1d)
	224	del extras[:]
	225
	226	return_value = self._final_cleanup(return_value)
	227	output.append(return_value)
	228	else:
[af09f48]	229	raise RuntimeError, "Invalid XML at: {0}".format(\
	230	self.find_invalid_xml())
[d26dea0]	231	except:
	232	# If the file does not match the schema, raise this error
[83b6408]	233	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid.xsd"
	234	invalid_xml = self.find_invalid_xml()
	235	invalid_xml = "\n\nThe loaded xml file does not fully meet the CanSAS v1.x specification. SasView " + \
	236	"loaded as much of the data as possible.\n\n" + invalid_xml
	237	self.errors.add(invalid_xml)
	238	self.set_schema(schema_path)
	239	if self.is_cansas():
	240	output = self.read(xml_file, schema_path)
	241	else:
	242	raise RuntimeError, "%s cannot be read" % xml_file
[d26dea0]	243	return output
	244	# Return a list of parsed entries that dataloader can manage
	245	return None
	246
	247	def _final_cleanup(self, data1d):
	248	"""
	249	Final cleanup of the Data1D object to be sure it has all the
	250	appropriate information needed for perspectives
	251
	252	:param data1d: Data1D object that has been populated
	253	"""
	254	# Final cleanup
	255	# Remove empty nodes, verify array sizes are correct
	256	for error in self.errors:
	257	data1d.errors.append(error)
	258	self.errors.clear()
	259	numpy.trim_zeros(data1d.x)
	260	numpy.trim_zeros(data1d.y)
	261	numpy.trim_zeros(data1d.dy)
	262	size_dx = data1d.dx.size
	263	size_dxl = data1d.dxl.size
	264	size_dxw = data1d.dxw.size
[682c432]	265	if data1d._xunit != data1d.x_unit:
	266	data1d.x_unit = data1d._xunit
	267	if data1d._yunit != data1d.y_unit:
	268	data1d.y_unit = data1d._yunit
[d26dea0]	269	if size_dxl == 0 and size_dxw == 0:
	270	data1d.dxl = None
	271	data1d.dxw = None
	272	numpy.trim_zeros(data1d.dx)
	273	elif size_dx == 0:
	274	data1d.dx = None
	275	size_dx = size_dxl
	276	numpy.trim_zeros(data1d.dxl)
	277	numpy.trim_zeros(data1d.dxw)
	278	return data1d
	279
	280	def _create_unique_key(self, dictionary, name, numb=0):
	281	"""
	282	Create a unique key value for any dictionary to prevent overwriting
	283	Recurses until a unique key value is found.
	284
	285	:param dictionary: A dictionary with any number of entries
	286	:param name: The index of the item to be added to dictionary
	287	:param numb: The number to be appended to the name, starts at 0
	288	"""
	289	if dictionary.get(name) is not None:
	290	numb += 1
	291	name = name.split("_")[0]
	292	name += "_{0}".format(numb)
	293	name = self._create_unique_key(dictionary, name, numb)
	294	return name
	295
	296	def _unit_conversion(self, node, new_current_level, data1d, \
	297	tagname, node_value):
	298	"""
	299	A unit converter method used to convert the data included in the file
	300	to the default units listed in data_info
	301
	302	:param new_current_level: cansas_constants level as returned by
	303	iterate_namespace
	304	:param attr: The attributes of the node
	305	:param data1d: Where the values will be saved
	306	:param node_value: The value of the current dom node
	307	"""
	308	attr = node.attrib
	309	value_unit = ''
	310	err_msg = None
[682c432]	311	default_unit = None
[d26dea0]	312	if 'unit' in attr and new_current_level.get('unit') is not None:
	313	try:
	314	local_unit = attr['unit']
	315	if isinstance(node_value, float) is False:
	316	exec("node_value = float({0})".format(node_value))
	317	unitname = new_current_level.get("unit")
	318	exec "default_unit = data1d.{0}".format(unitname)
	319	if local_unit is not None and default_unit is not None and \
	320	local_unit.lower() != default_unit.lower() \
	321	and local_unit.lower() != "none":
	322	if HAS_CONVERTER == True:
	323	## Check local units - bad units raise KeyError
	324	data_conv_q = Converter(local_unit)
	325	value_unit = default_unit
[682c432]	326	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	327	else:
	328	value_unit = local_unit
	329	err_msg = "Unit converter is not available.\n"
	330	else:
	331	value_unit = local_unit
	332	except KeyError:
	333	err_msg = "CanSAS reader: unexpected "
	334	err_msg += "\"{0}\" unit [{1}]; "
	335	err_msg = err_msg.format(tagname, local_unit)
[682c432]	336	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	337	value_unit = local_unit
	338	except:
	339	err_msg = "CanSAS reader: unknown error converting "
	340	err_msg += "\"{0}\" unit [{1}]"
	341	err_msg = err_msg.format(tagname, local_unit)
	342	value_unit = local_unit
	343	elif 'unit' in attr:
	344	value_unit = attr['unit']
	345	if err_msg:
	346	self.errors.add(err_msg)
	347	node_value = "float({0})".format(node_value)
	348	return node_value, value_unit
	349
	350	def _check_for_empty_data(self, data1d):
	351	"""
	352	Creates an empty data set if no data is passed to the reader
	353
	354	:param data1d: presumably a Data1D object
	355	"""
	356	if data1d == None:
	357	self.errors = set()
	358	x_vals = numpy.empty(0)
	359	y_vals = numpy.empty(0)
	360	dx_vals = numpy.empty(0)
	361	dy_vals = numpy.empty(0)
	362	dxl = numpy.empty(0)
	363	dxw = numpy.empty(0)
	364	data1d = Data1D(x_vals, y_vals, dx_vals, dy_vals)
	365	data1d.dxl = dxl
	366	data1d.dxw = dxw
	367	return data1d
	368
	369	def _handle_special_cases(self, tagname, data1d, children):
	370	"""
	371	Handle cases where the data type in Data1D is a dictionary or list
	372
	373	:param tagname: XML tagname in use
	374	:param data1d: The original Data1D object
	375	:param children: Child nodes of node
	376	:param node: existing node with tag name 'tagname'
	377	"""
	378	if tagname == "SASdetector":
	379	data1d = Detector()
	380	elif tagname == "SAScollimation":
	381	data1d = Collimation()
	382	elif tagname == "SAStransmission_spectrum":
	383	data1d = TransmissionSpectrum()
	384	elif tagname == "SASprocess":
	385	data1d = Process()
	386	for child in children:
	387	if child.tag.replace(self.base_ns, "") == "term":
	388	term_attr = {}
	389	for attr in child.keys():
	390	term_attr[attr] = \
	391	' '.join(child.get(attr).split())
	392	if child.text is not None:
	393	term_attr['value'] = \
	394	' '.join(child.text.split())
	395	data1d.term.append(term_attr)
	396	elif tagname == "aperture":
	397	data1d = Aperture()
	398	if tagname == "Idata" and children is not None:
	399	data1d = self._check_for_empty_resolution(data1d, children)
	400	return data1d
	401
	402	def _check_for_empty_resolution(self, data1d, children):
	403	"""
	404	A method to check all resolution data sets are the same size as I and Q
	405	"""
	406	dql_exists = False
	407	dqw_exists = False
	408	dq_exists = False
	409	di_exists = False
	410	for child in children:
	411	tag = child.tag.replace(self.base_ns, "")
	412	if tag == "dQl":
	413	dql_exists = True
	414	if tag == "dQw":
	415	dqw_exists = True
	416	if tag == "Qdev":
	417	dq_exists = True
	418	if tag == "Idev":
	419	di_exists = True
	420	if dqw_exists and dql_exists == False:
	421	data1d.dxl = numpy.append(data1d.dxl, 0.0)
	422	elif dql_exists and dqw_exists == False:
	423	data1d.dxw = numpy.append(data1d.dxw, 0.0)
	424	elif dql_exists == False and dqw_exists == False \
	425	and dq_exists == False:
	426	data1d.dx = numpy.append(data1d.dx, 0.0)
	427	if di_exists == False:
	428	data1d.dy = numpy.append(data1d.dy, 0.0)
	429	return data1d
	430
	431	def _restore_original_case(self,
	432	tagname_original,
	433	tagname,
	434	save_data1d,
	435	data1d):
	436	"""
	437	Save the special case data to the appropriate location and restore
	438	the original Data1D object
	439
	440	:param tagname_original: Unmodified tagname for the node
	441	:param tagname: modified tagname for the node
	442	:param save_data1d: The original Data1D object
	443	:param data1d: If a special case was handled, an object of that type
	444	"""
	445	if tagname_original == "SASdetector":
	446	save_data1d.detector.append(data1d)
	447	elif tagname_original == "SAScollimation":
	448	save_data1d.collimation.append(data1d)
	449	elif tagname == "SAStransmission_spectrum":
	450	save_data1d.trans_spectrum.append(data1d)
	451	elif tagname_original == "SASprocess":
	452	save_data1d.process.append(data1d)
	453	elif tagname_original == "aperture":
	454	save_data1d.aperture.append(data1d)
	455	else:
	456	save_data1d = data1d
	457	return save_data1d
	458
	459	def _handle_attributes(self, node, data1d, cs_values, tagname):
	460	"""
	461	Process all of the attributes for a node
	462	"""
	463	attr = node.attrib
	464	if attr is not None:
	465	for key in node.keys():
	466	try:
	467	node_value, unit = self._get_node_value(node, cs_values, \
	468	data1d, tagname)
	469	cansas_attrib = \
	470	cs_values.current_level.get("attributes").get(key)
	471	attrib_variable = cansas_attrib.get("variable")
	472	if key == 'unit' and unit != '':
	473	attrib_value = unit
	474	else:
	475	attrib_value = node.attrib[key]
[682c432]	476	store_attr = attrib_variable.format("data1d",
	477	attrib_value,
	478	key,
	479	node_value)
[d26dea0]	480	exec store_attr
	481	except AttributeError:
	482	pass
	483	return data1d
	484
	485	def _get_node_value(self, node, cs_values, data1d, tagname):
	486	"""
	487	Get the value of a node and any applicable units
	488
	489	:param node: The XML node to get the value of
	490	:param cs_values: A CansasConstants.CurrentLevel object
	491	:param attr: The node attributes
	492	:param dataid: The working object to be modified
	493	:param tagname: The tagname of the node
	494	"""
	495	#Get the text from the node and convert all whitespace to spaces
	496	units = ''
	497	node_value = node.text
	498	if node_value == "":
	499	node_value = None
	500	if node_value is not None:
	501	node_value = ' '.join(node_value.split())
	502
	503	# If the value is a float, compile with units.
	504	if cs_values.ns_datatype == "float":
	505	# If an empty value is given, set as zero.
	506	if node_value is None or node_value.isspace() \
	507	or node_value.lower() == "nan":
	508	node_value = "0.0"
	509	#Convert the value to the base units
	510	node_value, units = self._unit_conversion(node, \
	511	cs_values.current_level, data1d, tagname, node_value)
	512
	513	# If the value is a timestamp, convert to a datetime object
	514	elif cs_values.ns_datatype == "timestamp":
	515	if node_value is None or node_value.isspace():
	516	pass
	517	else:
	518	try:
	519	node_value = \
	520	datetime.datetime.fromtimestamp(node_value)
	521	except ValueError:
	522	node_value = None
	523	return node_value, units
	524
	525	def _parse_entry(self, dom, names=None, data1d=None, extras=None):
	526	"""
	527	Parse a SASEntry - new recursive method for parsing the dom of
	528	the CanSAS data format. This will allow multiple data files
	529	and extra nodes to be read in simultaneously.
	530
	531	:param dom: dom object with a namespace base of names
	532	:param names: A list of element names that lead up to the dom object
	533	:param data1d: The data1d object that will be modified
	534	:param extras: Any values that should go into meta_data when data1d
	535	is not a Data1D object
	536	"""
	537
	538	if extras is None:
	539	extras = []
	540	if names is None or names == []:
	541	names = ["SASentry"]
	542
	543	data1d = self._check_for_empty_data(data1d)
	544
	545	self.base_ns = "{0}{1}{2}".format("{", \
	546	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
	547	tagname = ''
	548	tagname_original = ''
	549
	550	# Go through each child in the parent element
	551	for node in dom:
	552	try:
	553	# Get the element name and set the current names level
	554	tagname = node.tag.replace(self.base_ns, "")
	555	tagname_original = tagname
	556	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or\
	557	tagname == "invariant":
	558	continue
	559	names.append(tagname)
	560	children = node.getchildren()
	561	if len(children) == 0:
	562	children = None
	563	save_data1d = data1d
	564
	565	# Look for special cases
	566	data1d = self._handle_special_cases(tagname, data1d, children)
	567
	568	# Get where to store content
	569	cs_values = CONSTANTS.iterate_namespace(names)
	570	# If the element is a child element, recurse
	571	if children is not None:
	572	# Returned value is new Data1D object with all previous and
	573	# new values in it.
	574	data1d, extras = self._parse_entry(node,
	575	names, data1d, extras)
	576
	577	#Get the information from the node
	578	node_value, _ = self._get_node_value(node, cs_values, \
	579	data1d, tagname)
	580
	581	# If appending to a dictionary (meta_data \| run_name)
	582	# make sure the key is unique
	583	if cs_values.ns_variable == "{0}.meta_data[\"{2}\"] = \"{1}\"":
	584	# If we are within a Process, Detector, Collimation or
	585	# Aperture instance, pull out old data1d
	586	tagname = self._create_unique_key(data1d.meta_data, \
	587	tagname, 0)
	588	if isinstance(data1d, Data1D) == False:
	589	store_me = cs_values.ns_variable.format("data1d", \
	590	node_value, tagname)
	591	extras.append(store_me)
	592	cs_values.ns_variable = None
	593	if cs_values.ns_variable == "{0}.run_name[\"{2}\"] = \"{1}\"":
	594	tagname = self._create_unique_key(data1d.run_name, \
	595	tagname, 0)
	596
	597	# Check for Data1D object and any extra commands to save
	598	if isinstance(data1d, Data1D):
	599	for item in extras:
	600	exec item
	601	# Don't bother saving empty information unless it is a float
	602	if cs_values.ns_variable is not None and \
	603	node_value is not None and \
	604	node_value.isspace() == False:
	605	# Format a string and then execute it.
	606	store_me = cs_values.ns_variable.format("data1d", \
	607	node_value, tagname)
	608	exec store_me
	609	# Get attributes and process them
	610	data1d = self._handle_attributes(node, data1d, cs_values, \
	611	tagname)
	612
	613	except TypeError:
	614	pass
	615	except Exception as excep:
	616	exc_type, exc_obj, exc_tb = sys.exc_info()
	617	fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
	618	print(excep, exc_type, fname, exc_tb.tb_lineno, \
	619	tagname, exc_obj)
	620	finally:
	621	# Save special cases in original data1d object
	622	# then restore the data1d
	623	save_data1d = self._restore_original_case(tagname_original, \
	624	tagname, save_data1d, data1d)
	625	if tagname_original == "fitting_plug_in" or \
	626	tagname_original == "invariant" or \
	627	tagname_original == "pr_inversion":
	628	pass
	629	else:
	630	data1d = save_data1d
	631	# Remove tagname from names to restore original base
	632	names.remove(tagname_original)
	633	return data1d, extras
	634
	635	def _get_pi_string(self):
	636	"""
	637	Creates the processing instructions header for writing to file
	638	"""
	639	pis = self.return_processing_instructions()
	640	if len(pis) > 0:
	641	pi_tree = self.create_tree(pis[0])
	642	i = 1
	643	for i in range(1, len(pis) - 1):
	644	pi_tree = self.append(pis[i], pi_tree)
	645	pi_string = self.to_string(pi_tree)
	646	else:
	647	pi_string = ""
	648	return pi_string
	649
	650	def _create_main_node(self):
	651	"""
	652	Creates the primary xml header used when writing to file
	653	"""
	654	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	655	version = self.cansas_version
	656	n_s = CANSAS_NS.get(version).get("ns")
	657	if version == "1.1":
	658	url = "http://www.cansas.org/formats/1.1/"
	659	else:
	660	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	661	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	662	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	663	"version" : version}
	664	nsmap = {'xsi' : xsi, None: n_s}
	665
	666	main_node = self.create_element("{" + n_s + "}SASroot",
	667	attrib=attrib, nsmap=nsmap)
	668	return main_node
	669
	670	def _write_run_names(self, datainfo, entry_node):
	671	"""
	672	Writes the run names to the XML file
	673
	674	:param datainfo: The Data1D object the information is coming from
	675	:param entry_node: lxml node ElementTree object to be appended to
	676	"""
	677	if datainfo.run == None or datainfo.run == []:
	678	datainfo.run.append(RUN_NAME_DEFAULT)
	679	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	680	for item in datainfo.run:
	681	runname = {}
	682	if item in datainfo.run_name and \
	683	len(str(datainfo.run_name[item])) > 1:
	684	runname = {'name': datainfo.run_name[item]}
	685	self.write_node(entry_node, "Run", item, runname)
	686
	687	def _write_data(self, datainfo, entry_node):
	688	"""
	689	Writes the I and Q data to the XML file
	690
	691	:param datainfo: The Data1D object the information is coming from
	692	:param entry_node: lxml node ElementTree object to be appended to
	693	"""
	694	node = self.create_element("SASdata")
	695	self.append(node, entry_node)
	696
	697	for i in range(len(datainfo.x)):
	698	point = self.create_element("Idata")
	699	node.append(point)
	700	self.write_node(point, "Q", datainfo.x[i],
[682c432]	701	{'unit': datainfo.x_unit})
[d26dea0]	702	if len(datainfo.y) >= i:
	703	self.write_node(point, "I", datainfo.y[i],
[682c432]	704	{'unit': datainfo.y_unit})
[d26dea0]	705	if datainfo.dy != None and len(datainfo.dy) > i:
	706	self.write_node(point, "Idev", datainfo.dy[i],
[682c432]	707	{'unit': datainfo.y_unit})
[d26dea0]	708	if datainfo.dx != None and len(datainfo.dx) > i:
	709	self.write_node(point, "Qdev", datainfo.dx[i],
[682c432]	710	{'unit': datainfo.x_unit})
[d26dea0]	711	if datainfo.dxw != None and len(datainfo.dxw) > i:
	712	self.write_node(point, "dQw", datainfo.dxw[i],
[682c432]	713	{'unit': datainfo.x_unit})
[d26dea0]	714	if datainfo.dxl != None and len(datainfo.dxl) > i:
	715	self.write_node(point, "dQl", datainfo.dxl[i],
[682c432]	716	{'unit': datainfo.x_unit})
[d26dea0]	717
	718	def _write_trans_spectrum(self, datainfo, entry_node):
	719	"""
	720	Writes the transmission spectrum data to the XML file
	721
	722	:param datainfo: The Data1D object the information is coming from
	723	:param entry_node: lxml node ElementTree object to be appended to
	724	"""
	725	for i in range(len(datainfo.trans_spectrum)):
	726	spectrum = datainfo.trans_spectrum[i]
	727	node = self.create_element("SAStransmission_spectrum",
	728	{"name" : spectrum.name})
	729	self.append(node, entry_node)
	730	if isinstance(spectrum.timestamp, datetime.datetime):
	731	node.setAttribute("timestamp", spectrum.timestamp)
	732	for i in range(len(spectrum.wavelength)):
	733	point = self.create_element("Tdata")
	734	node.append(point)
	735	self.write_node(point, "Lambda", spectrum.wavelength[i],
	736	{'unit': spectrum.wavelength_unit})
	737	self.write_node(point, "T", spectrum.transmission[i],
	738	{'unit': spectrum.transmission_unit})
	739	if spectrum.transmission_deviation != None \
	740	and len(spectrum.transmission_deviation) >= i:
	741	self.write_node(point, "Tdev",
	742	spectrum.transmission_deviation[i],
	743	{'unit':
	744	spectrum.transmission_deviation_unit})
	745
	746	def _write_sample_info(self, datainfo, entry_node):
	747	"""
	748	Writes the sample information to the XML file
	749
	750	:param datainfo: The Data1D object the information is coming from
	751	:param entry_node: lxml node ElementTree object to be appended to
	752	"""
	753	sample = self.create_element("SASsample")
	754	if datainfo.sample.name is not None:
	755	self.write_attribute(sample, "name",
	756	str(datainfo.sample.name))
	757	self.append(sample, entry_node)
	758	self.write_node(sample, "ID", str(datainfo.sample.ID))
	759	self.write_node(sample, "thickness", datainfo.sample.thickness,
	760	{"unit": datainfo.sample.thickness_unit})
	761	self.write_node(sample, "transmission", datainfo.sample.transmission)
	762	self.write_node(sample, "temperature", datainfo.sample.temperature,
	763	{"unit": datainfo.sample.temperature_unit})
	764
	765	pos = self.create_element("position")
	766	written = self.write_node(pos,
	767	"x",
	768	datainfo.sample.position.x,
	769	{"unit": datainfo.sample.position_unit})
	770	written = written \| self.write_node( \
	771	pos, "y", datainfo.sample.position.y,
	772	{"unit": datainfo.sample.position_unit})
	773	written = written \| self.write_node( \
	774	pos, "z", datainfo.sample.position.z,
	775	{"unit": datainfo.sample.position_unit})
	776	if written == True:
	777	self.append(pos, sample)
	778
	779	ori = self.create_element("orientation")
	780	written = self.write_node(ori, "roll",
	781	datainfo.sample.orientation.x,
	782	{"unit": datainfo.sample.orientation_unit})
	783	written = written \| self.write_node( \
	784	ori, "pitch", datainfo.sample.orientation.y,
	785	{"unit": datainfo.sample.orientation_unit})
	786	written = written \| self.write_node( \
	787	ori, "yaw", datainfo.sample.orientation.z,
	788	{"unit": datainfo.sample.orientation_unit})
	789	if written == True:
	790	self.append(ori, sample)
	791
	792	for item in datainfo.sample.details:
	793	self.write_node(sample, "details", item)
	794
	795	def _write_instrument(self, datainfo, entry_node):
	796	"""
	797	Writes the instrumental information to the XML file
	798
	799	:param datainfo: The Data1D object the information is coming from
	800	:param entry_node: lxml node ElementTree object to be appended to
	801	"""
	802	instr = self.create_element("SASinstrument")
	803	self.append(instr, entry_node)
	804	self.write_node(instr, "name", datainfo.instrument)
	805	return instr
	806
	807	def _write_source(self, datainfo, instr):
	808	"""
	809	Writes the source information to the XML file
	810
	811	:param datainfo: The Data1D object the information is coming from
	812	:param instr: instrument node to be appended to
	813	"""
	814	source = self.create_element("SASsource")
	815	if datainfo.source.name is not None:
	816	self.write_attribute(source, "name",
	817	str(datainfo.source.name))
	818	self.append(source, instr)
	819	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	820	datainfo.source.radiation = "neutron"
	821	self.write_node(source, "radiation", datainfo.source.radiation)
	822
	823	size = self.create_element("beam_size")
	824	if datainfo.source.beam_size_name is not None:
	825	self.write_attribute(size, "name",
	826	str(datainfo.source.beam_size_name))
	827	written = self.write_node( \
	828	size, "x", datainfo.source.beam_size.x,
	829	{"unit": datainfo.source.beam_size_unit})
	830	written = written \| self.write_node( \
	831	size, "y", datainfo.source.beam_size.y,
	832	{"unit": datainfo.source.beam_size_unit})
	833	written = written \| self.write_node( \
	834	size, "z", datainfo.source.beam_size.z,
	835	{"unit": datainfo.source.beam_size_unit})
	836	if written == True:
	837	self.append(size, source)
	838
	839	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	840	self.write_node(source, "wavelength",
	841	datainfo.source.wavelength,
	842	{"unit": datainfo.source.wavelength_unit})
	843	self.write_node(source, "wavelength_min",
	844	datainfo.source.wavelength_min,
	845	{"unit": datainfo.source.wavelength_min_unit})
	846	self.write_node(source, "wavelength_max",
	847	datainfo.source.wavelength_max,
	848	{"unit": datainfo.source.wavelength_max_unit})
	849	self.write_node(source, "wavelength_spread",
	850	datainfo.source.wavelength_spread,
	851	{"unit": datainfo.source.wavelength_spread_unit})
	852
	853	def _write_collimation(self, datainfo, instr):
	854	"""
	855	Writes the collimation information to the XML file
	856
	857	:param datainfo: The Data1D object the information is coming from
	858	:param instr: lxml node ElementTree object to be appended to
	859	"""
	860	if datainfo.collimation == [] or datainfo.collimation == None:
	861	coll = Collimation()
	862	datainfo.collimation.append(coll)
	863	for item in datainfo.collimation:
	864	coll = self.create_element("SAScollimation")
	865	if item.name is not None:
	866	self.write_attribute(coll, "name", str(item.name))
	867	self.append(coll, instr)
	868
	869	self.write_node(coll, "length", item.length,
	870	{"unit": item.length_unit})
	871
	872	for aperture in item.aperture:
	873	apert = self.create_element("aperture")
	874	if aperture.name is not None:
	875	self.write_attribute(apert, "name", str(aperture.name))
	876	if aperture.type is not None:
	877	self.write_attribute(apert, "type", str(aperture.type))
	878	self.append(apert, coll)
	879
	880	size = self.create_element("size")
	881	if aperture.size_name is not None:
	882	self.write_attribute(size, "name",
	883	str(aperture.size_name))
	884	written = self.write_node(size, "x", aperture.size.x,
	885	{"unit": aperture.size_unit})
	886	written = written \| self.write_node( \
	887	size, "y", aperture.size.y,
	888	{"unit": aperture.size_unit})
	889	written = written \| self.write_node( \
	890	size, "z", aperture.size.z,
	891	{"unit": aperture.size_unit})
	892	if written == True:
	893	self.append(size, apert)
	894
	895	self.write_node(apert, "distance", aperture.distance,
	896	{"unit": aperture.distance_unit})
	897
	898	def _write_detectors(self, datainfo, instr):
	899	"""
	900	Writes the detector information to the XML file
	901
	902	:param datainfo: The Data1D object the information is coming from
	903	:param inst: lxml instrument node to be appended to
	904	"""
	905	if datainfo.detector == None or datainfo.detector == []:
	906	det = Detector()
	907	det.name = ""
	908	datainfo.detector.append(det)
	909
	910	for item in datainfo.detector:
	911	det = self.create_element("SASdetector")
	912	written = self.write_node(det, "name", item.name)
	913	written = written \| self.write_node(det, "SDD", item.distance,
	914	{"unit": item.distance_unit})
	915	if written == True:
	916	self.append(det, instr)
	917
	918	off = self.create_element("offset")
	919	written = self.write_node(off, "x", item.offset.x,
	920	{"unit": item.offset_unit})
	921	written = written \| self.write_node(off, "y", item.offset.y,
	922	{"unit": item.offset_unit})
	923	written = written \| self.write_node(off, "z", item.offset.z,
	924	{"unit": item.offset_unit})
	925	if written == True:
	926	self.append(off, det)
	927
	928	ori = self.create_element("orientation")
	929	written = self.write_node(ori, "roll", item.orientation.x,
	930	{"unit": item.orientation_unit})
	931	written = written \| self.write_node(ori, "pitch",
	932	item.orientation.y,
	933	{"unit": item.orientation_unit})
	934	written = written \| self.write_node(ori, "yaw",
	935	item.orientation.z,
	936	{"unit": item.orientation_unit})
	937	if written == True:
	938	self.append(ori, det)
	939
	940	center = self.create_element("beam_center")
	941	written = self.write_node(center, "x", item.beam_center.x,
	942	{"unit": item.beam_center_unit})
	943	written = written \| self.write_node(center, "y",
	944	item.beam_center.y,
	945	{"unit": item.beam_center_unit})
	946	written = written \| self.write_node(center, "z",
	947	item.beam_center.z,
	948	{"unit": item.beam_center_unit})
	949	if written == True:
	950	self.append(center, det)
	951
	952	pix = self.create_element("pixel_size")
	953	written = self.write_node(pix, "x", item.pixel_size.x,
	954	{"unit": item.pixel_size_unit})
	955	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	956	{"unit": item.pixel_size_unit})
	957	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	958	{"unit": item.pixel_size_unit})
	959	written = written \| self.write_node(det, "slit_length",
	960	item.slit_length,
	961	{"unit": item.slit_length_unit})
	962	if written == True:
	963	self.append(pix, det)
	964
	965	def _write_process_notes(self, datainfo, entry_node):
	966	"""
	967	Writes the process notes to the XML file
	968
	969	:param datainfo: The Data1D object the information is coming from
	970	:param entry_node: lxml node ElementTree object to be appended to
	971
	972	"""
	973	for item in datainfo.process:
	974	node = self.create_element("SASprocess")
	975	self.append(node, entry_node)
	976	self.write_node(node, "name", item.name)
	977	self.write_node(node, "date", item.date)
	978	self.write_node(node, "description", item.description)
	979	for term in item.term:
	980	value = term['value']
	981	del term['value']
	982	self.write_node(node, "term", value, term)
	983	for note in item.notes:
	984	self.write_node(node, "SASprocessnote", note)
	985	if len(item.notes) == 0:
	986	self.write_node(node, "SASprocessnote", "")
	987
	988	def _write_notes(self, datainfo, entry_node):
	989	"""
	990	Writes the notes to the XML file and creates an empty note if none
	991	exist
	992
	993	:param datainfo: The Data1D object the information is coming from
	994	:param entry_node: lxml node ElementTree object to be appended to
	995
	996	"""
	997	if len(datainfo.notes) == 0:
	998	node = self.create_element("SASnote")
	999	self.append(node, entry_node)
	1000	else:
	1001	for item in datainfo.notes:
	1002	node = self.create_element("SASnote")
	1003	self.write_text(node, item)
	1004	self.append(node, entry_node)
	1005
[5ce7f17]	1006	def _check_origin(self, entry_node, doc, frm):
[d26dea0]	1007	"""
	1008	Return the document, and the SASentry node associated with
	1009	the data we just wrote.
	1010	If the calling function was not the cansas reader, return a minidom
	1011	object rather than an lxml object.
	1012
	1013	:param entry_node: lxml node ElementTree object to be appended to
	1014	:param doc: entire xml tree
	1015	"""
[5ce7f17]	1016	if not frm:
	1017	frm = inspect.stack()[1]
[d26dea0]	1018	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
	1019	mod_name = mod_name.replace(".py", "")
	1020	mod = mod_name.split("sas/")
	1021	mod_name = mod[1]
[45d90b9]	1022	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1023	string = self.to_string(doc, pretty_print=False)
	1024	doc = parseString(string)
	1025	node_name = entry_node.tag
	1026	node_list = doc.getElementsByTagName(node_name)
	1027	entry_node = node_list.item(0)
[5ce7f17]	1028	return doc, entry_node
[d26dea0]	1029
	1030	def _to_xml_doc(self, datainfo):
	1031	"""
	1032	Create an XML document to contain the content of a Data1D
	1033
	1034	:param datainfo: Data1D object
	1035	"""
	1036	if not issubclass(datainfo.__class__, Data1D):
	1037	raise RuntimeError, "The cansas writer expects a Data1D instance"
	1038
	1039	# Get PIs and create root element
	1040	pi_string = self._get_pi_string()
	1041	# Define namespaces and create SASroot object
	1042	main_node = self._create_main_node()
	1043	# Create ElementTree, append SASroot and apply processing instructions
	1044	base_string = pi_string + self.to_string(main_node)
	1045	base_element = self.create_element_from_string(base_string)
	1046	doc = self.create_tree(base_element)
	1047	# Create SASentry Element
	1048	entry_node = self.create_element("SASentry")
	1049	root = doc.getroot()
	1050	root.append(entry_node)
	1051
	1052	# Add Title to SASentry
	1053	self.write_node(entry_node, "Title", datainfo.title)
	1054	# Add Run to SASentry
	1055	self._write_run_names(datainfo, entry_node)
	1056	# Add Data info to SASEntry
	1057	self._write_data(datainfo, entry_node)
	1058	# Transmission Spectrum Info
	1059	self._write_trans_spectrum(datainfo, entry_node)
	1060	# Sample info
	1061	self._write_sample_info(datainfo, entry_node)
	1062	# Instrument info
	1063	instr = self._write_instrument(datainfo, entry_node)
	1064	# Source
	1065	self._write_source(datainfo, instr)
	1066	# Collimation
	1067	self._write_collimation(datainfo, instr)
	1068	# Detectors
	1069	self._write_detectors(datainfo, instr)
	1070	# Processes info
	1071	self._write_process_notes(datainfo, entry_node)
	1072	# Note info
	1073	self._write_notes(datainfo, entry_node)
	1074	# Return the document, and the SASentry node associated with
	1075	# the data we just wrote
	1076	# If the calling function was not the cansas reader, return a minidom
	1077	# object rather than an lxml object.
[5ce7f17]	1078	frm = inspect.stack()[1]
	1079	doc, entry_node = self._check_origin(entry_node, doc, frm)
[d26dea0]	1080	return doc, entry_node
	1081
	1082	def write_node(self, parent, name, value, attr=None):
	1083	"""
	1084	:param doc: document DOM
	1085	:param parent: parent node
	1086	:param name: tag of the element
	1087	:param value: value of the child text node
	1088	:param attr: attribute dictionary
	1089
	1090	:return: True if something was appended, otherwise False
	1091	"""
	1092	if value is not None:
	1093	parent = self.ebuilder(parent, name, value, attr)
	1094	return True
	1095	return False
	1096
	1097	def write(self, filename, datainfo):
	1098	"""
	1099	Write the content of a Data1D as a CanSAS XML file
	1100
	1101	:param filename: name of the file to write
	1102	:param datainfo: Data1D object
	1103	"""
	1104	# Create XML document
	1105	doc, _ = self._to_xml_doc(datainfo)
	1106	# Write the file
	1107	file_ref = open(filename, 'w')
	1108	if self.encoding == None:
	1109	self.encoding = "UTF-8"
	1110	doc.write(file_ref, encoding=self.encoding,
	1111	pretty_print=True, xml_declaration=True)
	1112	file_ref.close()
	1113
	1114	# DO NOT REMOVE - used in saving and loading panel states.
	1115	def _store_float(self, location, node, variable, storage, optional=True):
	1116	"""
	1117	Get the content of a xpath location and store
	1118	the result. Check that the units are compatible
	1119	with the destination. The value is expected to
	1120	be a float.
	1121
	1122	The xpath location might or might not exist.
	1123	If it does not exist, nothing is done
	1124
	1125	:param location: xpath location to fetch
	1126	:param node: node to read the data from
	1127	:param variable: name of the data member to store it in [string]
	1128	:param storage: data object that has the 'variable' data member
	1129	:param optional: if True, no exception will be raised
	1130	if unit conversion can't be done
	1131
	1132	:raise ValueError: raised when the units are not recognized
	1133	"""
	1134	entry = get_content(location, node)
	1135	try:
	1136	value = float(entry.text)
	1137	except:
	1138	value = None
	1139
	1140	if value is not None:
	1141	# If the entry has units, check to see that they are
	1142	# compatible with what we currently have in the data object
	1143	units = entry.get('unit')
	1144	if units is not None:
	1145	toks = variable.split('.')
	1146	local_unit = None
	1147	exec "local_unit = storage.%s_unit" % toks[0]
	1148	if local_unit != None and units.lower() != local_unit.lower():
	1149	if HAS_CONVERTER == True:
	1150	try:
	1151	conv = Converter(units)
	1152	exec "storage.%s = %g" % \
	1153	(variable, conv(value, units=local_unit))
	1154	except:
	1155	_, exc_value, _ = sys.exc_info()
	1156	err_mess = "CanSAS reader: could not convert"
	1157	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1158	% (variable, units, local_unit, exc_value)
	1159	self.errors.add(err_mess)
	1160	if optional:
	1161	logging.info(err_mess)
	1162	else:
	1163	raise ValueError, err_mess
	1164	else:
	1165	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1166	% (variable, units)
	1167	err_mess += " expecting [%s]" % local_unit
	1168	self.errors.add(err_mess)
	1169	if optional:
	1170	logging.info(err_mess)
	1171	else:
	1172	raise ValueError, err_mess
	1173	else:
	1174	exec "storage.%s = value" % variable
	1175	else:
	1176	exec "storage.%s = value" % variable
	1177
	1178	# DO NOT REMOVE - used in saving and loading panel states.
	1179	def _store_content(self, location, node, variable, storage):
	1180	"""
	1181	Get the content of a xpath location and store
	1182	the result. The value is treated as a string.
	1183
	1184	The xpath location might or might not exist.
	1185	If it does not exist, nothing is done
	1186
	1187	:param location: xpath location to fetch
	1188	:param node: node to read the data from
	1189	:param variable: name of the data member to store it in [string]
	1190	:param storage: data object that has the 'variable' data member
	1191
	1192	:return: return a list of errors
	1193	"""
	1194	entry = get_content(location, node)
	1195	if entry is not None and entry.text is not None:
	1196	exec "storage.%s = entry.text.strip()" % variable

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ c3e4e213

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