cansas_reader.py @ f9fbe99

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 f9fbe99 was 0f1e140, checked in by krzywon, 8 years ago
Fix the broken unit tests.
Property mode set to `100644`
File size: 49.2 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
[d26dea0]	36	_ZERO = 1e-16
	37	PREPROCESS = "xmlpreprocess"
	38	ENCODING = "encoding"
	39	RUN_NAME_DEFAULT = "None"
	40	HAS_CONVERTER = True
	41	try:
[b699768]	42	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	43	except ImportError:
	44	HAS_CONVERTER = False
	45
	46	CONSTANTS = CansasConstants()
	47	CANSAS_FORMAT = CONSTANTS.format
	48	CANSAS_NS = CONSTANTS.names
	49	ALLOW_ALL = True
	50
[682c432]	51	# DO NOT REMOVE Called by outside packages:
[d85c194]	52	# sas.sasgui.perspectives.invariant.invariant_state
	53	# sas.sasgui.perspectives.fitting.pagestate
[d26dea0]	54	def get_content(location, node):
	55	"""
	56	Get the first instance of the content of a xpath location.
	57
	58	:param location: xpath location
	59	:param node: node to start at
	60
	61	:return: Element, or None
	62	"""
	63	nodes = node.xpath(location,
	64	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	65	if len(nodes) > 0:
	66	return nodes[0]
	67	else:
	68	return None
	69
[682c432]	70	# DO NOT REMOVE Called by outside packages:
[d85c194]	71	# sas.sasgui.perspectives.fitting.pagestate
[d26dea0]	72	def write_node(doc, parent, name, value, attr=None):
	73	"""
	74	:param doc: document DOM
	75	:param parent: parent node
	76	:param name: tag of the element
	77	:param value: value of the child text node
	78	:param attr: attribute dictionary
	79
	80	:return: True if something was appended, otherwise False
	81	"""
	82	if attr is None:
	83	attr = {}
	84	if value is not None:
	85	node = doc.createElement(name)
	86	node.appendChild(doc.createTextNode(str(value)))
	87	for item in attr:
	88	node.setAttribute(item, attr[item])
	89	parent.appendChild(node)
	90	return True
	91	return False
	92
	93	class Reader(XMLreader):
	94	"""
	95	Class to load cansas 1D XML files
	96
	97	:Dependencies:
	98	The CanSAS reader requires PyXML 0.8.4 or later.
	99	"""
	100	##CanSAS version - defaults to version 1.0
	101	cansas_version = "1.0"
	102	base_ns = "{cansas1d/1.0}"
	103	logging = None
	104	errors = None
	105	type_name = "canSAS"
	106	## Wildcards
	107	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
	108	## List of allowed extensions
	109	ext = ['.xml', '.XML', '.svs', '.SVS']
	110	## Flag to bypass extension check
	111	allow_all = True
	112
	113	def __init__(self):
	114	## List of errors
	115	self.errors = set()
	116	self.logging = []
	117	self.encoding = None
	118
	119	def is_cansas(self, ext="xml"):
	120	"""
	121	Checks to see if the xml file is a CanSAS file
	122
	123	:param ext: The file extension of the data file
	124	"""
	125	if self.validate_xml():
	126	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	127	value = self.xmlroot.get(name)
	128	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	129	value.rsplit(" ")[0]:
	130	return True
	131	if ext == "svs":
	132	return True
	133	return False
	134
	135	def load_file_and_schema(self, xml_file):
	136	"""
	137	Loads the file and associates a schema, if a known schema exists
	138
	139	:param xml_file: The xml file path sent to Reader.read
	140	"""
	141	base_name = xml_reader.__file__
	142	base_name = base_name.replace("\\", "/")
	143	base = base_name.split("/sas/")[0]
	144
	145	# Load in xml file and get the cansas version from the header
	146	self.set_xml_file(xml_file)
	147	self.cansas_version = self.xmlroot.get("version", "1.0")
	148
	149	# Generic values for the cansas file based on the version
	150	cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[45d90b9]	151	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format\
[d26dea0]	152	(base, cansas_defaults.get("schema")).replace("\\", "/")
	153
	154	# Link a schema to the XML file.
	155	self.set_schema(schema_path)
	156	return cansas_defaults
	157
	158	def read(self, xml_file):
	159	"""
	160	Validate and read in an xml_file file in the canSAS format.
	161
	162	:param xml_file: A canSAS file path in proper XML format
	163	"""
	164	# output - Final list of Data1D objects
	165	output = []
	166	# ns - Namespace hierarchy for current xml_file object
	167	ns_list = []
	168
	169	# Check that the file exists
	170	if os.path.isfile(xml_file):
	171	basename = os.path.basename(xml_file)
	172	_, extension = os.path.splitext(basename)
	173	# If the file type is not allowed, return nothing
	174	if extension in self.ext or self.allow_all:
	175	# Get the file location of
	176	cansas_defaults = self.load_file_and_schema(xml_file)
	177
	178	# Try to load the file, but raise an error if unable to.
	179	# Check the file matches the XML schema
	180	try:
	181	if self.is_cansas(extension):
	182	# Get each SASentry from XML file and add it to a list.
	183	entry_list = self.xmlroot.xpath(
	184	'/ns:SASroot/ns:SASentry',
	185	namespaces={'ns': cansas_defaults.get("ns")})
	186	ns_list.append("SASentry")
	187
	188	# If multiple files, modify the name for each is unique
	189	increment = 0
	190	# Parse each SASentry item
	191	for entry in entry_list:
	192	# Define a new Data1D object with zeroes for
	193	# x_vals and y_vals
	194	data1d = Data1D(numpy.empty(0), numpy.empty(0),
	195	numpy.empty(0), numpy.empty(0))
	196	data1d.dxl = numpy.empty(0)
	197	data1d.dxw = numpy.empty(0)
	198
	199	# If more than one SASentry, increment each in order
	200	name = basename
	201	if len(entry_list) - 1 > 0:
	202	name += "_{0}".format(increment)
	203	increment += 1
	204
	205	# Set the Data1D name and then parse the entry.
	206	# The entry is appended to a list of entry values
	207	data1d.filename = name
	208	data1d.meta_data["loader"] = "CanSAS 1D"
	209
	210	# Get all preprocessing events and encoding
	211	self.set_processing_instructions()
	212	data1d.meta_data[PREPROCESS] = \
	213	self.processing_instructions
	214
	215	# Parse the XML file
	216	return_value, extras = \
	217	self._parse_entry(entry, ns_list, data1d)
	218	del extras[:]
	219
	220	return_value = self._final_cleanup(return_value)
	221	output.append(return_value)
	222	else:
[af09f48]	223	raise RuntimeError, "Invalid XML at: {0}".format(\
	224	self.find_invalid_xml())
[d26dea0]	225	except:
	226	# If the file does not match the schema, raise this error
	227	raise RuntimeError, "%s cannot be read" % xml_file
	228	return output
	229	# Return a list of parsed entries that dataloader can manage
	230	return None
	231
	232	def _final_cleanup(self, data1d):
	233	"""
	234	Final cleanup of the Data1D object to be sure it has all the
	235	appropriate information needed for perspectives
	236
	237	:param data1d: Data1D object that has been populated
	238	"""
	239	# Final cleanup
	240	# Remove empty nodes, verify array sizes are correct
	241	for error in self.errors:
	242	data1d.errors.append(error)
	243	self.errors.clear()
	244	numpy.trim_zeros(data1d.x)
	245	numpy.trim_zeros(data1d.y)
	246	numpy.trim_zeros(data1d.dy)
	247	size_dx = data1d.dx.size
	248	size_dxl = data1d.dxl.size
	249	size_dxw = data1d.dxw.size
[682c432]	250	if data1d._xunit != data1d.x_unit:
	251	data1d.x_unit = data1d._xunit
	252	if data1d._yunit != data1d.y_unit:
	253	data1d.y_unit = data1d._yunit
[d26dea0]	254	if size_dxl == 0 and size_dxw == 0:
	255	data1d.dxl = None
	256	data1d.dxw = None
	257	numpy.trim_zeros(data1d.dx)
	258	elif size_dx == 0:
	259	data1d.dx = None
	260	size_dx = size_dxl
	261	numpy.trim_zeros(data1d.dxl)
	262	numpy.trim_zeros(data1d.dxw)
	263	return data1d
	264
	265	def _create_unique_key(self, dictionary, name, numb=0):
	266	"""
	267	Create a unique key value for any dictionary to prevent overwriting
	268	Recurses until a unique key value is found.
	269
	270	:param dictionary: A dictionary with any number of entries
	271	:param name: The index of the item to be added to dictionary
	272	:param numb: The number to be appended to the name, starts at 0
	273	"""
	274	if dictionary.get(name) is not None:
	275	numb += 1
	276	name = name.split("_")[0]
	277	name += "_{0}".format(numb)
	278	name = self._create_unique_key(dictionary, name, numb)
	279	return name
	280
	281	def _unit_conversion(self, node, new_current_level, data1d, \
	282	tagname, node_value):
	283	"""
	284	A unit converter method used to convert the data included in the file
	285	to the default units listed in data_info
	286
	287	:param new_current_level: cansas_constants level as returned by
	288	iterate_namespace
	289	:param attr: The attributes of the node
	290	:param data1d: Where the values will be saved
	291	:param node_value: The value of the current dom node
	292	"""
	293	attr = node.attrib
	294	value_unit = ''
	295	err_msg = None
[682c432]	296	default_unit = None
[d26dea0]	297	if 'unit' in attr and new_current_level.get('unit') is not None:
	298	try:
	299	local_unit = attr['unit']
	300	if isinstance(node_value, float) is False:
	301	exec("node_value = float({0})".format(node_value))
	302	unitname = new_current_level.get("unit")
	303	exec "default_unit = data1d.{0}".format(unitname)
	304	if local_unit is not None and default_unit is not None and \
	305	local_unit.lower() != default_unit.lower() \
	306	and local_unit.lower() != "none":
	307	if HAS_CONVERTER == True:
	308	## Check local units - bad units raise KeyError
	309	data_conv_q = Converter(local_unit)
	310	value_unit = default_unit
[682c432]	311	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	312	else:
	313	value_unit = local_unit
	314	err_msg = "Unit converter is not available.\n"
	315	else:
	316	value_unit = local_unit
	317	except KeyError:
	318	err_msg = "CanSAS reader: unexpected "
	319	err_msg += "\"{0}\" unit [{1}]; "
	320	err_msg = err_msg.format(tagname, local_unit)
[682c432]	321	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	322	value_unit = local_unit
	323	except:
	324	err_msg = "CanSAS reader: unknown error converting "
	325	err_msg += "\"{0}\" unit [{1}]"
	326	err_msg = err_msg.format(tagname, local_unit)
	327	value_unit = local_unit
	328	elif 'unit' in attr:
	329	value_unit = attr['unit']
	330	if err_msg:
	331	self.errors.add(err_msg)
	332	node_value = "float({0})".format(node_value)
	333	return node_value, value_unit
	334
	335	def _check_for_empty_data(self, data1d):
	336	"""
	337	Creates an empty data set if no data is passed to the reader
	338
	339	:param data1d: presumably a Data1D object
	340	"""
	341	if data1d == None:
	342	self.errors = set()
	343	x_vals = numpy.empty(0)
	344	y_vals = numpy.empty(0)
	345	dx_vals = numpy.empty(0)
	346	dy_vals = numpy.empty(0)
	347	dxl = numpy.empty(0)
	348	dxw = numpy.empty(0)
	349	data1d = Data1D(x_vals, y_vals, dx_vals, dy_vals)
	350	data1d.dxl = dxl
	351	data1d.dxw = dxw
	352	return data1d
	353
	354	def _handle_special_cases(self, tagname, data1d, children):
	355	"""
	356	Handle cases where the data type in Data1D is a dictionary or list
	357
	358	:param tagname: XML tagname in use
	359	:param data1d: The original Data1D object
	360	:param children: Child nodes of node
	361	:param node: existing node with tag name 'tagname'
	362	"""
	363	if tagname == "SASdetector":
	364	data1d = Detector()
	365	elif tagname == "SAScollimation":
	366	data1d = Collimation()
	367	elif tagname == "SAStransmission_spectrum":
	368	data1d = TransmissionSpectrum()
	369	elif tagname == "SASprocess":
	370	data1d = Process()
	371	for child in children:
	372	if child.tag.replace(self.base_ns, "") == "term":
	373	term_attr = {}
	374	for attr in child.keys():
	375	term_attr[attr] = \
	376	' '.join(child.get(attr).split())
	377	if child.text is not None:
	378	term_attr['value'] = \
	379	' '.join(child.text.split())
	380	data1d.term.append(term_attr)
	381	elif tagname == "aperture":
	382	data1d = Aperture()
	383	if tagname == "Idata" and children is not None:
	384	data1d = self._check_for_empty_resolution(data1d, children)
	385	return data1d
	386
	387	def _check_for_empty_resolution(self, data1d, children):
	388	"""
	389	A method to check all resolution data sets are the same size as I and Q
	390	"""
	391	dql_exists = False
	392	dqw_exists = False
	393	dq_exists = False
	394	di_exists = False
	395	for child in children:
	396	tag = child.tag.replace(self.base_ns, "")
	397	if tag == "dQl":
	398	dql_exists = True
	399	if tag == "dQw":
	400	dqw_exists = True
	401	if tag == "Qdev":
	402	dq_exists = True
	403	if tag == "Idev":
	404	di_exists = True
	405	if dqw_exists and dql_exists == False:
	406	data1d.dxl = numpy.append(data1d.dxl, 0.0)
	407	elif dql_exists and dqw_exists == False:
	408	data1d.dxw = numpy.append(data1d.dxw, 0.0)
	409	elif dql_exists == False and dqw_exists == False \
	410	and dq_exists == False:
	411	data1d.dx = numpy.append(data1d.dx, 0.0)
	412	if di_exists == False:
	413	data1d.dy = numpy.append(data1d.dy, 0.0)
	414	return data1d
	415
	416	def _restore_original_case(self,
	417	tagname_original,
	418	tagname,
	419	save_data1d,
	420	data1d):
	421	"""
	422	Save the special case data to the appropriate location and restore
	423	the original Data1D object
	424
	425	:param tagname_original: Unmodified tagname for the node
	426	:param tagname: modified tagname for the node
	427	:param save_data1d: The original Data1D object
	428	:param data1d: If a special case was handled, an object of that type
	429	"""
	430	if tagname_original == "SASdetector":
	431	save_data1d.detector.append(data1d)
	432	elif tagname_original == "SAScollimation":
	433	save_data1d.collimation.append(data1d)
	434	elif tagname == "SAStransmission_spectrum":
	435	save_data1d.trans_spectrum.append(data1d)
	436	elif tagname_original == "SASprocess":
	437	save_data1d.process.append(data1d)
	438	elif tagname_original == "aperture":
	439	save_data1d.aperture.append(data1d)
	440	else:
	441	save_data1d = data1d
	442	return save_data1d
	443
	444	def _handle_attributes(self, node, data1d, cs_values, tagname):
	445	"""
	446	Process all of the attributes for a node
	447	"""
	448	attr = node.attrib
	449	if attr is not None:
	450	for key in node.keys():
	451	try:
	452	node_value, unit = self._get_node_value(node, cs_values, \
	453	data1d, tagname)
	454	cansas_attrib = \
	455	cs_values.current_level.get("attributes").get(key)
	456	attrib_variable = cansas_attrib.get("variable")
	457	if key == 'unit' and unit != '':
	458	attrib_value = unit
	459	else:
	460	attrib_value = node.attrib[key]
[682c432]	461	store_attr = attrib_variable.format("data1d",
	462	attrib_value,
	463	key,
	464	node_value)
[d26dea0]	465	exec store_attr
	466	except AttributeError:
	467	pass
	468	return data1d
	469
	470	def _get_node_value(self, node, cs_values, data1d, tagname):
	471	"""
	472	Get the value of a node and any applicable units
	473
	474	:param node: The XML node to get the value of
	475	:param cs_values: A CansasConstants.CurrentLevel object
	476	:param attr: The node attributes
	477	:param dataid: The working object to be modified
	478	:param tagname: The tagname of the node
	479	"""
	480	#Get the text from the node and convert all whitespace to spaces
	481	units = ''
	482	node_value = node.text
	483	if node_value == "":
	484	node_value = None
	485	if node_value is not None:
	486	node_value = ' '.join(node_value.split())
	487
	488	# If the value is a float, compile with units.
	489	if cs_values.ns_datatype == "float":
	490	# If an empty value is given, set as zero.
	491	if node_value is None or node_value.isspace() \
	492	or node_value.lower() == "nan":
	493	node_value = "0.0"
	494	#Convert the value to the base units
	495	node_value, units = self._unit_conversion(node, \
	496	cs_values.current_level, data1d, tagname, node_value)
	497
	498	# If the value is a timestamp, convert to a datetime object
	499	elif cs_values.ns_datatype == "timestamp":
	500	if node_value is None or node_value.isspace():
	501	pass
	502	else:
	503	try:
	504	node_value = \
	505	datetime.datetime.fromtimestamp(node_value)
	506	except ValueError:
	507	node_value = None
	508	return node_value, units
	509
	510	def _parse_entry(self, dom, names=None, data1d=None, extras=None):
	511	"""
	512	Parse a SASEntry - new recursive method for parsing the dom of
	513	the CanSAS data format. This will allow multiple data files
	514	and extra nodes to be read in simultaneously.
	515
	516	:param dom: dom object with a namespace base of names
	517	:param names: A list of element names that lead up to the dom object
	518	:param data1d: The data1d object that will be modified
	519	:param extras: Any values that should go into meta_data when data1d
	520	is not a Data1D object
	521	"""
	522
	523	if extras is None:
	524	extras = []
	525	if names is None or names == []:
	526	names = ["SASentry"]
	527
	528	data1d = self._check_for_empty_data(data1d)
	529
	530	self.base_ns = "{0}{1}{2}".format("{", \
	531	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
	532	tagname = ''
	533	tagname_original = ''
	534
	535	# Go through each child in the parent element
	536	for node in dom:
	537	try:
	538	# Get the element name and set the current names level
	539	tagname = node.tag.replace(self.base_ns, "")
	540	tagname_original = tagname
	541	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or\
	542	tagname == "invariant":
	543	continue
	544	names.append(tagname)
	545	children = node.getchildren()
	546	if len(children) == 0:
	547	children = None
	548	save_data1d = data1d
	549
	550	# Look for special cases
	551	data1d = self._handle_special_cases(tagname, data1d, children)
	552
	553	# Get where to store content
	554	cs_values = CONSTANTS.iterate_namespace(names)
	555	# If the element is a child element, recurse
	556	if children is not None:
	557	# Returned value is new Data1D object with all previous and
	558	# new values in it.
	559	data1d, extras = self._parse_entry(node,
	560	names, data1d, extras)
	561
	562	#Get the information from the node
	563	node_value, _ = self._get_node_value(node, cs_values, \
	564	data1d, tagname)
	565
	566	# If appending to a dictionary (meta_data \| run_name)
	567	# make sure the key is unique
	568	if cs_values.ns_variable == "{0}.meta_data[\"{2}\"] = \"{1}\"":
	569	# If we are within a Process, Detector, Collimation or
	570	# Aperture instance, pull out old data1d
	571	tagname = self._create_unique_key(data1d.meta_data, \
	572	tagname, 0)
	573	if isinstance(data1d, Data1D) == False:
	574	store_me = cs_values.ns_variable.format("data1d", \
	575	node_value, tagname)
	576	extras.append(store_me)
	577	cs_values.ns_variable = None
	578	if cs_values.ns_variable == "{0}.run_name[\"{2}\"] = \"{1}\"":
	579	tagname = self._create_unique_key(data1d.run_name, \
	580	tagname, 0)
	581
	582	# Check for Data1D object and any extra commands to save
	583	if isinstance(data1d, Data1D):
	584	for item in extras:
	585	exec item
	586	# Don't bother saving empty information unless it is a float
	587	if cs_values.ns_variable is not None and \
	588	node_value is not None and \
	589	node_value.isspace() == False:
	590	# Format a string and then execute it.
	591	store_me = cs_values.ns_variable.format("data1d", \
	592	node_value, tagname)
	593	exec store_me
	594	# Get attributes and process them
	595	data1d = self._handle_attributes(node, data1d, cs_values, \
	596	tagname)
	597
	598	except TypeError:
	599	pass
	600	except Exception as excep:
	601	exc_type, exc_obj, exc_tb = sys.exc_info()
	602	fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
	603	print(excep, exc_type, fname, exc_tb.tb_lineno, \
	604	tagname, exc_obj)
	605	finally:
	606	# Save special cases in original data1d object
	607	# then restore the data1d
	608	save_data1d = self._restore_original_case(tagname_original, \
	609	tagname, save_data1d, data1d)
	610	if tagname_original == "fitting_plug_in" or \
	611	tagname_original == "invariant" or \
	612	tagname_original == "pr_inversion":
	613	pass
	614	else:
	615	data1d = save_data1d
	616	# Remove tagname from names to restore original base
	617	names.remove(tagname_original)
	618	return data1d, extras
	619
	620	def _get_pi_string(self):
	621	"""
	622	Creates the processing instructions header for writing to file
	623	"""
	624	pis = self.return_processing_instructions()
	625	if len(pis) > 0:
	626	pi_tree = self.create_tree(pis[0])
	627	i = 1
	628	for i in range(1, len(pis) - 1):
	629	pi_tree = self.append(pis[i], pi_tree)
	630	pi_string = self.to_string(pi_tree)
	631	else:
	632	pi_string = ""
	633	return pi_string
	634
	635	def _create_main_node(self):
	636	"""
	637	Creates the primary xml header used when writing to file
	638	"""
	639	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	640	version = self.cansas_version
	641	n_s = CANSAS_NS.get(version).get("ns")
	642	if version == "1.1":
	643	url = "http://www.cansas.org/formats/1.1/"
	644	else:
	645	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	646	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	647	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	648	"version" : version}
	649	nsmap = {'xsi' : xsi, None: n_s}
	650
	651	main_node = self.create_element("{" + n_s + "}SASroot",
	652	attrib=attrib, nsmap=nsmap)
	653	return main_node
	654
	655	def _write_run_names(self, datainfo, entry_node):
	656	"""
	657	Writes the run names to the XML file
	658
	659	:param datainfo: The Data1D object the information is coming from
	660	:param entry_node: lxml node ElementTree object to be appended to
	661	"""
	662	if datainfo.run == None or datainfo.run == []:
	663	datainfo.run.append(RUN_NAME_DEFAULT)
	664	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	665	for item in datainfo.run:
	666	runname = {}
	667	if item in datainfo.run_name and \
	668	len(str(datainfo.run_name[item])) > 1:
	669	runname = {'name': datainfo.run_name[item]}
	670	self.write_node(entry_node, "Run", item, runname)
	671
	672	def _write_data(self, datainfo, entry_node):
	673	"""
	674	Writes the I and Q data to the XML file
	675
	676	:param datainfo: The Data1D object the information is coming from
	677	:param entry_node: lxml node ElementTree object to be appended to
	678	"""
	679	node = self.create_element("SASdata")
	680	self.append(node, entry_node)
	681
	682	for i in range(len(datainfo.x)):
	683	point = self.create_element("Idata")
	684	node.append(point)
	685	self.write_node(point, "Q", datainfo.x[i],
[682c432]	686	{'unit': datainfo.x_unit})
[d26dea0]	687	if len(datainfo.y) >= i:
	688	self.write_node(point, "I", datainfo.y[i],
[682c432]	689	{'unit': datainfo.y_unit})
[d26dea0]	690	if datainfo.dy != None and len(datainfo.dy) > i:
	691	self.write_node(point, "Idev", datainfo.dy[i],
[682c432]	692	{'unit': datainfo.y_unit})
[d26dea0]	693	if datainfo.dx != None and len(datainfo.dx) > i:
	694	self.write_node(point, "Qdev", datainfo.dx[i],
[682c432]	695	{'unit': datainfo.x_unit})
[d26dea0]	696	if datainfo.dxw != None and len(datainfo.dxw) > i:
	697	self.write_node(point, "dQw", datainfo.dxw[i],
[682c432]	698	{'unit': datainfo.x_unit})
[d26dea0]	699	if datainfo.dxl != None and len(datainfo.dxl) > i:
	700	self.write_node(point, "dQl", datainfo.dxl[i],
[682c432]	701	{'unit': datainfo.x_unit})
[d26dea0]	702
	703	def _write_trans_spectrum(self, datainfo, entry_node):
	704	"""
	705	Writes the transmission spectrum data to the XML file
	706
	707	:param datainfo: The Data1D object the information is coming from
	708	:param entry_node: lxml node ElementTree object to be appended to
	709	"""
	710	for i in range(len(datainfo.trans_spectrum)):
	711	spectrum = datainfo.trans_spectrum[i]
	712	node = self.create_element("SAStransmission_spectrum",
	713	{"name" : spectrum.name})
	714	self.append(node, entry_node)
	715	if isinstance(spectrum.timestamp, datetime.datetime):
	716	node.setAttribute("timestamp", spectrum.timestamp)
	717	for i in range(len(spectrum.wavelength)):
	718	point = self.create_element("Tdata")
	719	node.append(point)
	720	self.write_node(point, "Lambda", spectrum.wavelength[i],
	721	{'unit': spectrum.wavelength_unit})
	722	self.write_node(point, "T", spectrum.transmission[i],
	723	{'unit': spectrum.transmission_unit})
	724	if spectrum.transmission_deviation != None \
	725	and len(spectrum.transmission_deviation) >= i:
	726	self.write_node(point, "Tdev",
	727	spectrum.transmission_deviation[i],
	728	{'unit':
	729	spectrum.transmission_deviation_unit})
	730
	731	def _write_sample_info(self, datainfo, entry_node):
	732	"""
	733	Writes the sample information to the XML file
	734
	735	:param datainfo: The Data1D object the information is coming from
	736	:param entry_node: lxml node ElementTree object to be appended to
	737	"""
	738	sample = self.create_element("SASsample")
	739	if datainfo.sample.name is not None:
	740	self.write_attribute(sample, "name",
	741	str(datainfo.sample.name))
	742	self.append(sample, entry_node)
	743	self.write_node(sample, "ID", str(datainfo.sample.ID))
	744	self.write_node(sample, "thickness", datainfo.sample.thickness,
	745	{"unit": datainfo.sample.thickness_unit})
	746	self.write_node(sample, "transmission", datainfo.sample.transmission)
	747	self.write_node(sample, "temperature", datainfo.sample.temperature,
	748	{"unit": datainfo.sample.temperature_unit})
	749
	750	pos = self.create_element("position")
	751	written = self.write_node(pos,
	752	"x",
	753	datainfo.sample.position.x,
	754	{"unit": datainfo.sample.position_unit})
	755	written = written \| self.write_node( \
	756	pos, "y", datainfo.sample.position.y,
	757	{"unit": datainfo.sample.position_unit})
	758	written = written \| self.write_node( \
	759	pos, "z", datainfo.sample.position.z,
	760	{"unit": datainfo.sample.position_unit})
	761	if written == True:
	762	self.append(pos, sample)
	763
	764	ori = self.create_element("orientation")
	765	written = self.write_node(ori, "roll",
	766	datainfo.sample.orientation.x,
	767	{"unit": datainfo.sample.orientation_unit})
	768	written = written \| self.write_node( \
	769	ori, "pitch", datainfo.sample.orientation.y,
	770	{"unit": datainfo.sample.orientation_unit})
	771	written = written \| self.write_node( \
	772	ori, "yaw", datainfo.sample.orientation.z,
	773	{"unit": datainfo.sample.orientation_unit})
	774	if written == True:
	775	self.append(ori, sample)
	776
	777	for item in datainfo.sample.details:
	778	self.write_node(sample, "details", item)
	779
	780	def _write_instrument(self, datainfo, entry_node):
	781	"""
	782	Writes the instrumental information to the XML file
	783
	784	:param datainfo: The Data1D object the information is coming from
	785	:param entry_node: lxml node ElementTree object to be appended to
	786	"""
	787	instr = self.create_element("SASinstrument")
	788	self.append(instr, entry_node)
	789	self.write_node(instr, "name", datainfo.instrument)
	790	return instr
	791
	792	def _write_source(self, datainfo, instr):
	793	"""
	794	Writes the source information to the XML file
	795
	796	:param datainfo: The Data1D object the information is coming from
	797	:param instr: instrument node to be appended to
	798	"""
	799	source = self.create_element("SASsource")
	800	if datainfo.source.name is not None:
	801	self.write_attribute(source, "name",
	802	str(datainfo.source.name))
	803	self.append(source, instr)
	804	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	805	datainfo.source.radiation = "neutron"
	806	self.write_node(source, "radiation", datainfo.source.radiation)
	807
	808	size = self.create_element("beam_size")
	809	if datainfo.source.beam_size_name is not None:
	810	self.write_attribute(size, "name",
	811	str(datainfo.source.beam_size_name))
	812	written = self.write_node( \
	813	size, "x", datainfo.source.beam_size.x,
	814	{"unit": datainfo.source.beam_size_unit})
	815	written = written \| self.write_node( \
	816	size, "y", datainfo.source.beam_size.y,
	817	{"unit": datainfo.source.beam_size_unit})
	818	written = written \| self.write_node( \
	819	size, "z", datainfo.source.beam_size.z,
	820	{"unit": datainfo.source.beam_size_unit})
	821	if written == True:
	822	self.append(size, source)
	823
	824	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	825	self.write_node(source, "wavelength",
	826	datainfo.source.wavelength,
	827	{"unit": datainfo.source.wavelength_unit})
	828	self.write_node(source, "wavelength_min",
	829	datainfo.source.wavelength_min,
	830	{"unit": datainfo.source.wavelength_min_unit})
	831	self.write_node(source, "wavelength_max",
	832	datainfo.source.wavelength_max,
	833	{"unit": datainfo.source.wavelength_max_unit})
	834	self.write_node(source, "wavelength_spread",
	835	datainfo.source.wavelength_spread,
	836	{"unit": datainfo.source.wavelength_spread_unit})
	837
	838	def _write_collimation(self, datainfo, instr):
	839	"""
	840	Writes the collimation information to the XML file
	841
	842	:param datainfo: The Data1D object the information is coming from
	843	:param instr: lxml node ElementTree object to be appended to
	844	"""
	845	if datainfo.collimation == [] or datainfo.collimation == None:
	846	coll = Collimation()
	847	datainfo.collimation.append(coll)
	848	for item in datainfo.collimation:
	849	coll = self.create_element("SAScollimation")
	850	if item.name is not None:
	851	self.write_attribute(coll, "name", str(item.name))
	852	self.append(coll, instr)
	853
	854	self.write_node(coll, "length", item.length,
	855	{"unit": item.length_unit})
	856
	857	for aperture in item.aperture:
	858	apert = self.create_element("aperture")
	859	if aperture.name is not None:
	860	self.write_attribute(apert, "name", str(aperture.name))
	861	if aperture.type is not None:
	862	self.write_attribute(apert, "type", str(aperture.type))
	863	self.append(apert, coll)
	864
	865	size = self.create_element("size")
	866	if aperture.size_name is not None:
	867	self.write_attribute(size, "name",
	868	str(aperture.size_name))
	869	written = self.write_node(size, "x", aperture.size.x,
	870	{"unit": aperture.size_unit})
	871	written = written \| self.write_node( \
	872	size, "y", aperture.size.y,
	873	{"unit": aperture.size_unit})
	874	written = written \| self.write_node( \
	875	size, "z", aperture.size.z,
	876	{"unit": aperture.size_unit})
	877	if written == True:
	878	self.append(size, apert)
	879
	880	self.write_node(apert, "distance", aperture.distance,
	881	{"unit": aperture.distance_unit})
	882
	883	def _write_detectors(self, datainfo, instr):
	884	"""
	885	Writes the detector information to the XML file
	886
	887	:param datainfo: The Data1D object the information is coming from
	888	:param inst: lxml instrument node to be appended to
	889	"""
	890	if datainfo.detector == None or datainfo.detector == []:
	891	det = Detector()
	892	det.name = ""
	893	datainfo.detector.append(det)
	894
	895	for item in datainfo.detector:
	896	det = self.create_element("SASdetector")
	897	written = self.write_node(det, "name", item.name)
	898	written = written \| self.write_node(det, "SDD", item.distance,
	899	{"unit": item.distance_unit})
	900	if written == True:
	901	self.append(det, instr)
	902
	903	off = self.create_element("offset")
	904	written = self.write_node(off, "x", item.offset.x,
	905	{"unit": item.offset_unit})
	906	written = written \| self.write_node(off, "y", item.offset.y,
	907	{"unit": item.offset_unit})
	908	written = written \| self.write_node(off, "z", item.offset.z,
	909	{"unit": item.offset_unit})
	910	if written == True:
	911	self.append(off, det)
	912
	913	ori = self.create_element("orientation")
	914	written = self.write_node(ori, "roll", item.orientation.x,
	915	{"unit": item.orientation_unit})
	916	written = written \| self.write_node(ori, "pitch",
	917	item.orientation.y,
	918	{"unit": item.orientation_unit})
	919	written = written \| self.write_node(ori, "yaw",
	920	item.orientation.z,
	921	{"unit": item.orientation_unit})
	922	if written == True:
	923	self.append(ori, det)
	924
	925	center = self.create_element("beam_center")
	926	written = self.write_node(center, "x", item.beam_center.x,
	927	{"unit": item.beam_center_unit})
	928	written = written \| self.write_node(center, "y",
	929	item.beam_center.y,
	930	{"unit": item.beam_center_unit})
	931	written = written \| self.write_node(center, "z",
	932	item.beam_center.z,
	933	{"unit": item.beam_center_unit})
	934	if written == True:
	935	self.append(center, det)
	936
	937	pix = self.create_element("pixel_size")
	938	written = self.write_node(pix, "x", item.pixel_size.x,
	939	{"unit": item.pixel_size_unit})
	940	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	941	{"unit": item.pixel_size_unit})
	942	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	943	{"unit": item.pixel_size_unit})
	944	written = written \| self.write_node(det, "slit_length",
	945	item.slit_length,
	946	{"unit": item.slit_length_unit})
	947	if written == True:
	948	self.append(pix, det)
	949
	950	def _write_process_notes(self, datainfo, entry_node):
	951	"""
	952	Writes the process notes to the XML file
	953
	954	:param datainfo: The Data1D object the information is coming from
	955	:param entry_node: lxml node ElementTree object to be appended to
	956
	957	"""
	958	for item in datainfo.process:
	959	node = self.create_element("SASprocess")
	960	self.append(node, entry_node)
	961	self.write_node(node, "name", item.name)
	962	self.write_node(node, "date", item.date)
	963	self.write_node(node, "description", item.description)
	964	for term in item.term:
	965	value = term['value']
	966	del term['value']
	967	self.write_node(node, "term", value, term)
	968	for note in item.notes:
	969	self.write_node(node, "SASprocessnote", note)
	970	if len(item.notes) == 0:
	971	self.write_node(node, "SASprocessnote", "")
	972
	973	def _write_notes(self, datainfo, entry_node):
	974	"""
	975	Writes the notes to the XML file and creates an empty note if none
	976	exist
	977
	978	:param datainfo: The Data1D object the information is coming from
	979	:param entry_node: lxml node ElementTree object to be appended to
	980
	981	"""
	982	if len(datainfo.notes) == 0:
	983	node = self.create_element("SASnote")
	984	self.append(node, entry_node)
	985	else:
	986	for item in datainfo.notes:
	987	node = self.create_element("SASnote")
	988	self.write_text(node, item)
	989	self.append(node, entry_node)
	990
[5ce7f17]	991	def _check_origin(self, entry_node, doc, frm):
[d26dea0]	992	"""
	993	Return the document, and the SASentry node associated with
	994	the data we just wrote.
	995	If the calling function was not the cansas reader, return a minidom
	996	object rather than an lxml object.
	997
	998	:param entry_node: lxml node ElementTree object to be appended to
	999	:param doc: entire xml tree
	1000	"""
[5ce7f17]	1001	if not frm:
	1002	frm = inspect.stack()[1]
[d26dea0]	1003	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
	1004	mod_name = mod_name.replace(".py", "")
	1005	mod = mod_name.split("sas/")
	1006	mod_name = mod[1]
[45d90b9]	1007	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1008	string = self.to_string(doc, pretty_print=False)
	1009	doc = parseString(string)
	1010	node_name = entry_node.tag
	1011	node_list = doc.getElementsByTagName(node_name)
	1012	entry_node = node_list.item(0)
[5ce7f17]	1013	return doc, entry_node
[d26dea0]	1014
	1015	def _to_xml_doc(self, datainfo):
	1016	"""
	1017	Create an XML document to contain the content of a Data1D
	1018
	1019	:param datainfo: Data1D object
	1020	"""
	1021	if not issubclass(datainfo.__class__, Data1D):
	1022	raise RuntimeError, "The cansas writer expects a Data1D instance"
	1023
	1024	# Get PIs and create root element
	1025	pi_string = self._get_pi_string()
	1026	# Define namespaces and create SASroot object
	1027	main_node = self._create_main_node()
	1028	# Create ElementTree, append SASroot and apply processing instructions
	1029	base_string = pi_string + self.to_string(main_node)
	1030	base_element = self.create_element_from_string(base_string)
	1031	doc = self.create_tree(base_element)
	1032	# Create SASentry Element
	1033	entry_node = self.create_element("SASentry")
	1034	root = doc.getroot()
	1035	root.append(entry_node)
	1036
	1037	# Add Title to SASentry
	1038	self.write_node(entry_node, "Title", datainfo.title)
	1039	# Add Run to SASentry
	1040	self._write_run_names(datainfo, entry_node)
	1041	# Add Data info to SASEntry
	1042	self._write_data(datainfo, entry_node)
	1043	# Transmission Spectrum Info
	1044	self._write_trans_spectrum(datainfo, entry_node)
	1045	# Sample info
	1046	self._write_sample_info(datainfo, entry_node)
	1047	# Instrument info
	1048	instr = self._write_instrument(datainfo, entry_node)
	1049	# Source
	1050	self._write_source(datainfo, instr)
	1051	# Collimation
	1052	self._write_collimation(datainfo, instr)
	1053	# Detectors
	1054	self._write_detectors(datainfo, instr)
	1055	# Processes info
	1056	self._write_process_notes(datainfo, entry_node)
	1057	# Note info
	1058	self._write_notes(datainfo, entry_node)
	1059	# Return the document, and the SASentry node associated with
	1060	# the data we just wrote
	1061	# If the calling function was not the cansas reader, return a minidom
	1062	# object rather than an lxml object.
[5ce7f17]	1063	frm = inspect.stack()[1]
	1064	doc, entry_node = self._check_origin(entry_node, doc, frm)
[d26dea0]	1065	return doc, entry_node
	1066
	1067	def write_node(self, parent, name, value, attr=None):
	1068	"""
	1069	:param doc: document DOM
	1070	:param parent: parent node
	1071	:param name: tag of the element
	1072	:param value: value of the child text node
	1073	:param attr: attribute dictionary
	1074
	1075	:return: True if something was appended, otherwise False
	1076	"""
	1077	if value is not None:
	1078	parent = self.ebuilder(parent, name, value, attr)
	1079	return True
	1080	return False
	1081
	1082	def write(self, filename, datainfo):
	1083	"""
	1084	Write the content of a Data1D as a CanSAS XML file
	1085
	1086	:param filename: name of the file to write
	1087	:param datainfo: Data1D object
	1088	"""
	1089	# Create XML document
	1090	doc, _ = self._to_xml_doc(datainfo)
	1091	# Write the file
	1092	file_ref = open(filename, 'w')
	1093	if self.encoding == None:
	1094	self.encoding = "UTF-8"
	1095	doc.write(file_ref, encoding=self.encoding,
	1096	pretty_print=True, xml_declaration=True)
	1097	file_ref.close()
	1098
	1099	# DO NOT REMOVE - used in saving and loading panel states.
	1100	def _store_float(self, location, node, variable, storage, optional=True):
	1101	"""
	1102	Get the content of a xpath location and store
	1103	the result. Check that the units are compatible
	1104	with the destination. The value is expected to
	1105	be a float.
	1106
	1107	The xpath location might or might not exist.
	1108	If it does not exist, nothing is done
	1109
	1110	:param location: xpath location to fetch
	1111	:param node: node to read the data from
	1112	:param variable: name of the data member to store it in [string]
	1113	:param storage: data object that has the 'variable' data member
	1114	:param optional: if True, no exception will be raised
	1115	if unit conversion can't be done
	1116
	1117	:raise ValueError: raised when the units are not recognized
	1118	"""
	1119	entry = get_content(location, node)
	1120	try:
	1121	value = float(entry.text)
	1122	except:
	1123	value = None
	1124
	1125	if value is not None:
	1126	# If the entry has units, check to see that they are
	1127	# compatible with what we currently have in the data object
	1128	units = entry.get('unit')
	1129	if units is not None:
	1130	toks = variable.split('.')
	1131	local_unit = None
	1132	exec "local_unit = storage.%s_unit" % toks[0]
	1133	if local_unit != None and units.lower() != local_unit.lower():
	1134	if HAS_CONVERTER == True:
	1135	try:
	1136	conv = Converter(units)
	1137	exec "storage.%s = %g" % \
	1138	(variable, conv(value, units=local_unit))
	1139	except:
	1140	_, exc_value, _ = sys.exc_info()
	1141	err_mess = "CanSAS reader: could not convert"
	1142	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1143	% (variable, units, local_unit, exc_value)
	1144	self.errors.add(err_mess)
	1145	if optional:
	1146	logging.info(err_mess)
	1147	else:
	1148	raise ValueError, err_mess
	1149	else:
	1150	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1151	% (variable, units)
	1152	err_mess += " expecting [%s]" % local_unit
	1153	self.errors.add(err_mess)
	1154	if optional:
	1155	logging.info(err_mess)
	1156	else:
	1157	raise ValueError, err_mess
	1158	else:
	1159	exec "storage.%s = value" % variable
	1160	else:
	1161	exec "storage.%s = value" % variable
	1162
	1163	# DO NOT REMOVE - used in saving and loading panel states.
	1164	def _store_content(self, location, node, variable, storage):
	1165	"""
	1166	Get the content of a xpath location and store
	1167	the result. The value is treated as a string.
	1168
	1169	The xpath location might or might not exist.
	1170	If it does not exist, nothing is done
	1171
	1172	:param location: xpath location to fetch
	1173	:param node: node to read the data from
	1174	:param variable: name of the data member to store it in [string]
	1175	:param storage: data object that has the 'variable' data member
	1176
	1177	:return: return a list of errors
	1178	"""
	1179	entry = get_content(location, node)
	1180	if entry is not None and entry.text is not None:
	1181	exec "storage.%s = entry.text.strip()" % variable

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ f9fbe99

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