cansas_reader.py @ eb38181

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 eb38181 was 5f26aa4, checked in by krzywon, 8 years ago
Fix cansas XML reader issues to resolve broken unit tests.
Property mode set to `100644`
File size: 61.5 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
[250fec92]	16	import numpy as np
[d26dea0]	17	import os
	18	import sys
	19	import datetime
	20	import inspect
	21	# For saving individual sections of data
[250fec92]	22	from sas.sascalc.dataloader.data_info import Data1D, DataInfo, plottable_1D
	23	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, Detector, Process, Aperture
	24	from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable as combine_data
[b699768]	25	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	26	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
[250fec92]	27	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
[d26dea0]	28
[682c432]	29	# The following 2 imports ARE used. Do not remove either.
	30	import xml.dom.minidom
	31	from xml.dom.minidom import parseString
	32
[d26dea0]	33	PREPROCESS = "xmlpreprocess"
	34	ENCODING = "encoding"
	35	RUN_NAME_DEFAULT = "None"
[250fec92]	36	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	37	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	38	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	39	"as much of the data as possible.\n\n"
[d26dea0]	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
	51	class Reader(XMLreader):
	52	"""
	53	Class to load cansas 1D XML files
	54
	55	:Dependencies:
	56	The CanSAS reader requires PyXML 0.8.4 or later.
	57	"""
[250fec92]	58	## CanSAS version - defaults to version 1.0
[d26dea0]	59	cansas_version = "1.0"
	60	base_ns = "{cansas1d/1.0}"
[250fec92]	61	cansas_defaults = None
[d26dea0]	62	type_name = "canSAS"
[250fec92]	63	invalid = True
	64	## Log messages and errors
	65	logging = None
	66	errors = set()
	67	## Namespace hierarchy for current xml_file object
	68	names = None
	69	ns_list = None
	70	## Temporary storage location for loading multiple data sets in a single file
	71	current_datainfo = None
	72	current_dataset = None
	73	current_data1d = None
	74	data = None
	75	## List of data1D objects to be sent back to SasView
	76	output = None
[d26dea0]	77	## Wildcards
	78	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
	79	## List of allowed extensions
	80	ext = ['.xml', '.XML', '.svs', '.SVS']
	81	## Flag to bypass extension check
	82	allow_all = True
	83
[250fec92]	84	def reset_state(self):
	85	"""
	86	Resets the class state to a base case when loading a new data file so previous
	87	data files do not appear a second time
	88	"""
	89	self.current_datainfo = None
	90	self.current_dataset = None
	91	self.current_data1d = None
	92	self.data = []
	93	self.process = Process()
	94	self.transspectrum = TransmissionSpectrum()
	95	self.aperture = Aperture()
	96	self.collimation = Collimation()
	97	self.detector = Detector()
	98	self.names = []
	99	self.cansas_defaults = {}
	100	self.output = []
	101	self.ns_list = None
[d26dea0]	102	self.logging = []
	103	self.encoding = None
	104
[250fec92]	105	def read(self, xml_file, schema_path="", invalid=True):
	106	"""
	107	Validate and read in an xml_file file in the canSAS format.
	108
	109	:param xml_file: A canSAS file path in proper XML format
	110	:param schema_path: A file path to an XML schema to validate the xml_file against
	111	"""
	112	# For every file loaded, reset everything to a base state
	113	self.reset_state()
	114	self.invalid = invalid
	115	# Check that the file exists
	116	if os.path.isfile(xml_file):
	117	basename, extension = os.path.splitext(os.path.basename(xml_file))
	118	# If the file type is not allowed, return nothing
	119	if extension in self.ext or self.allow_all:
	120	# Get the file location of
	121	self.load_file_and_schema(xml_file, schema_path)
	122	self.add_data_set()
	123	# Try to load the file, but raise an error if unable to.
	124	# Check the file matches the XML schema
	125	try:
	126	self.is_cansas(extension)
	127	self.invalid = False
	128	# Get each SASentry from XML file and add it to a list.
	129	entry_list = self.xmlroot.xpath(
	130	'/ns:SASroot/ns:SASentry',
	131	namespaces={'ns': self.cansas_defaults.get("ns")})
	132	self.names.append("SASentry")
	133
	134	# Get all preprocessing events and encoding
	135	self.set_processing_instructions()
	136
	137	# Parse each <SASentry> item
	138	for entry in entry_list:
	139	# Create a new DataInfo object for every <SASentry>
	140
	141
	142	# Set the file name and then parse the entry.
	143	self.current_datainfo.filename = basename + extension
	144	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
	145	self.current_datainfo.meta_data[PREPROCESS] = \
	146	self.processing_instructions
	147
	148	# Parse the XML SASentry
	149	self._parse_entry(entry)
	150	# Combine datasets with datainfo
	151	self.add_data_set()
	152	except RuntimeError:
	153	# If the file does not match the schema, raise this error
	154	invalid_xml = self.find_invalid_xml()
	155	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
	156	self.errors.add(invalid_xml)
	157	# Try again with an invalid CanSAS schema, that requires only a data set in each
	158	base_name = xml_reader.__file__
	159	base_name = base_name.replace("\\", "/")
	160	base = base_name.split("/sas/")[0]
	161	if self.cansas_version == "1.1":
	162	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	163	else:
	164	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	165	self.set_schema(invalid_schema)
	166	try:
	167	if self.invalid:
	168	if self.is_cansas():
	169	self.output = self.read(xml_file, invalid_schema, False)
	170	else:
	171	raise RuntimeError
	172	else:
	173	raise RuntimeError
	174	except RuntimeError:
	175	x = np.zeros(1)
	176	y = np.zeros(1)
	177	self.current_data1d = Data1D(x,y)
	178	self.current_data1d.errors = self.errors
	179	return [self.current_data1d]
	180	else:
	181	self.output.append("Not a valid file path.")
	182	# Return a list of parsed entries that dataloader can manage
	183	return self.output
	184
	185	def _parse_entry(self, dom):
	186	"""
	187	Parse a SASEntry - new recursive method for parsing the dom of
	188	the CanSAS data format. This will allow multiple data files
	189	and extra nodes to be read in simultaneously.
	190
	191	:param dom: dom object with a namespace base of names
	192	"""
	193
[1686a333]	194	frm = inspect.stack()[1]
	195	if not self._is_call_local(frm):
	196	self.reset_state()
	197	self.add_data_set()
	198	self.names.append("SASentry")
	199	self.parent_class = "SASentry"
[250fec92]	200	self._check_for_empty_data()
	201	self.base_ns = "{0}{1}{2}".format("{", \
	202	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
	203	tagname = ''
	204	tagname_original = ''
	205
	206	# Go through each child in the parent element
	207	for node in dom:
[5f26aa4]	208	attr = node.attrib
	209	name = attr.get("name", "")
	210	type = attr.get("type", "")
[250fec92]	211	# Get the element name and set the current names level
	212	tagname = node.tag.replace(self.base_ns, "")
	213	tagname_original = tagname
	214	# Skip this iteration when loading in save state information
	215	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	216	continue
	217
	218	# Get where to store content
	219	self.names.append(tagname_original)
	220	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	221	# If the element is a child element, recurse
	222	if len(node.getchildren()) > 0:
	223	self.parent_class = tagname_original
	224	if tagname == 'SASdata':
	225	self._initialize_new_data_set()
	226	## Recursion step to access data within the group
	227	self._parse_entry(node)
[5f26aa4]	228	if tagname == "SASsample":
	229	self.current_datainfo.sample.name = name
	230	elif tagname == "beam_size":
	231	self.current_datainfo.source.beam_size_name = name
	232	elif tagname == "SAScollimation":
	233	self.collimation.name = name
	234	elif tagname == "aperture":
	235	self.aperture.name = name
	236	self.aperture.type = type
[250fec92]	237	self.add_intermediate()
	238	else:
	239	data_point, unit = self._get_node_value(node, tagname)
	240
	241	## If this is a dataset, store the data appropriately
	242	if tagname == 'Run':
[5f26aa4]	243	self.current_datainfo.run_name[data_point] = name
[250fec92]	244	self.current_datainfo.run.append(data_point)
	245	elif tagname == 'Title':
	246	self.current_datainfo.title = data_point
	247	elif tagname == 'SASnote':
	248	self.current_datainfo.notes.append(data_point)
	249
	250	## I and Q Data
	251	elif tagname == 'I':
	252	self.current_dataset.yaxis("Intensity", unit)
	253	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
	254	elif tagname == 'Idev':
	255	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	256	elif tagname == 'Q':
	257	self.current_dataset.xaxis("Q", unit)
	258	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	259	elif tagname == 'Qdev':
	260	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	261	elif tagname == 'dQw':
	262	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	263	elif tagname == 'dQl':
	264	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	265	elif tagname == 'Qmean':
	266	pass
	267	elif tagname == 'Shadowfactor':
	268	pass
[250fec92]	269
	270	## Sample Information
	271	elif tagname == 'ID' and self.parent_class == 'SASsample':
	272	self.current_datainfo.sample.ID = data_point
	273	elif tagname == 'Title' and self.parent_class == 'SASsample':
	274	self.current_datainfo.sample.name = data_point
	275	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	276	self.current_datainfo.sample.thickness = data_point
	277	self.current_datainfo.sample.thickness_unit = unit
	278	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	279	self.current_datainfo.sample.transmission = data_point
	280	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	281	self.current_datainfo.sample.temperature = data_point
	282	self.current_datainfo.sample.temperature_unit = unit
	283	elif tagname == 'details' and self.parent_class == 'SASsample':
	284	self.current_datainfo.sample.details.append(data_point)
	285	elif tagname == 'x' and self.parent_class == 'position':
	286	self.current_datainfo.sample.position.x = data_point
	287	self.current_datainfo.sample.position_unit = unit
	288	elif tagname == 'y' and self.parent_class == 'position':
	289	self.current_datainfo.sample.position.y = data_point
	290	self.current_datainfo.sample.position_unit = unit
	291	elif tagname == 'z' and self.parent_class == 'position':
	292	self.current_datainfo.sample.position.z = data_point
	293	self.current_datainfo.sample.position_unit = unit
	294	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	295	self.current_datainfo.sample.orientation.x = data_point
	296	self.current_datainfo.sample.orientation_unit = unit
	297	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	298	self.current_datainfo.sample.orientation.y = data_point
	299	self.current_datainfo.sample.orientation_unit = unit
	300	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	301	self.current_datainfo.sample.orientation.z = data_point
	302	self.current_datainfo.sample.orientation_unit = unit
	303
	304	## Instrumental Information
	305	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	306	self.current_datainfo.instrument = data_point
	307	## Detector Information
	308	elif tagname == 'name' and self.parent_class == 'SASdetector':
	309	self.detector.name = data_point
	310	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	311	self.detector.distance = data_point
	312	self.detector.distance_unit = unit
	313	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	314	self.detector.slit_length = data_point
	315	self.detector.slit_length_unit = unit
	316	elif tagname == 'x' and self.parent_class == 'offset':
	317	self.detector.offset.x = data_point
	318	self.detector.offset_unit = unit
	319	elif tagname == 'y' and self.parent_class == 'offset':
	320	self.detector.offset.y = data_point
	321	self.detector.offset_unit = unit
	322	elif tagname == 'z' and self.parent_class == 'offset':
	323	self.detector.offset.z = data_point
	324	self.detector.offset_unit = unit
	325	elif tagname == 'x' and self.parent_class == 'beam_center':
	326	self.detector.beam_center.x = data_point
	327	self.detector.beam_center_unit = unit
	328	elif tagname == 'y' and self.parent_class == 'beam_center':
	329	self.detector.beam_center.y = data_point
	330	self.detector.beam_center_unit = unit
	331	elif tagname == 'z' and self.parent_class == 'beam_center':
	332	self.detector.beam_center.z = data_point
	333	self.detector.beam_center_unit = unit
	334	elif tagname == 'x' and self.parent_class == 'pixel_size':
	335	self.detector.pixel_size.x = data_point
	336	self.detector.pixel_size_unit = unit
	337	elif tagname == 'y' and self.parent_class == 'pixel_size':
	338	self.detector.pixel_size.y = data_point
	339	self.detector.pixel_size_unit = unit
	340	elif tagname == 'z' and self.parent_class == 'pixel_size':
	341	self.detector.pixel_size.z = data_point
	342	self.detector.pixel_size_unit = unit
	343	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	344	self.detector.orientation.x = data_point
	345	self.detector.orientation_unit = unit
	346	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	347	self.detector.orientation.y = data_point
	348	self.detector.orientation_unit = unit
	349	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	350	self.detector.orientation.z = data_point
	351	self.detector.orientation_unit = unit
	352	## Collimation and Aperture
	353	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	354	self.collimation.length = data_point
	355	self.collimation.length_unit = unit
	356	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	357	self.collimation.name = data_point
	358	elif tagname == 'distance' and self.parent_class == 'aperture':
	359	self.aperture.distance = data_point
	360	self.aperture.distance_unit = unit
	361	elif tagname == 'x' and self.parent_class == 'size':
	362	self.aperture.size.x = data_point
	363	self.collimation.size_unit = unit
	364	elif tagname == 'y' and self.parent_class == 'size':
	365	self.aperture.size.y = data_point
	366	self.collimation.size_unit = unit
	367	elif tagname == 'z' and self.parent_class == 'size':
	368	self.aperture.size.z = data_point
	369	self.collimation.size_unit = unit
	370
	371	## Process Information
	372	elif tagname == 'name' and self.parent_class == 'SASprocess':
	373	self.process.name = data_point
	374	elif tagname == 'description' and self.parent_class == 'SASprocess':
	375	self.process.description = data_point
	376	elif tagname == 'date' and self.parent_class == 'SASprocess':
	377	try:
	378	self.process.date = datetime.datetime.fromtimestamp(data_point)
	379	except:
	380	self.process.date = data_point
	381	elif tagname == 'SASprocessnote':
	382	self.process.notes.append(data_point)
	383	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	384	unit = attr.get("unit", "")
	385	dic = {}
	386	dic["name"] = name
	387	dic["value"] = data_point
	388	dic["unit"] = unit
	389	self.process.term.append(dic)
[250fec92]	390
	391	## Transmission Spectrum
	392	elif tagname == 'T' and self.parent_class == 'Tdata':
	393	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	394	self.transspectrum.transmission_unit = unit
	395	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	396	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	397	self.transspectrum.transmission_deviation_unit = unit
	398	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	399	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	400	self.transspectrum.wavelength_unit = unit
	401
	402	## Source Information
	403	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	404	self.current_datainfo.source.wavelength = data_point
	405	self.current_datainfo.source.wavelength_unit = unit
	406	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	407	self.current_datainfo.source.wavelength_min = data_point
	408	self.current_datainfo.source.wavelength_min_unit = unit
	409	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	410	self.current_datainfo.source.wavelength_max = data_point
	411	self.current_datainfo.source.wavelength_max_unit = unit
	412	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	413	self.current_datainfo.source.wavelength_spread = data_point
	414	self.current_datainfo.source.wavelength_spread_unit = unit
	415	elif tagname == 'x' and self.parent_class == 'beam_size':
	416	self.current_datainfo.source.beam_size.x = data_point
	417	self.current_datainfo.source.beam_size_unit = unit
	418	elif tagname == 'y' and self.parent_class == 'beam_size':
	419	self.current_datainfo.source.beam_size.y = data_point
	420	self.current_datainfo.source.beam_size_unit = unit
	421	elif tagname == 'z' and self.parent_class == 'pixel_size':
	422	self.current_datainfo.source.data_point.z = data_point
	423	self.current_datainfo.source.beam_size_unit = unit
	424	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	425	self.current_datainfo.source.radiation = data_point
	426	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	427	self.current_datainfo.source.beam_shape = data_point
	428
	429	## Everything else goes in meta_data
	430	else:
	431	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	432	self.current_datainfo.meta_data[new_key] = data_point
	433
	434	self.names.remove(tagname_original)
	435	length = 0
	436	if len(self.names) > 1:
	437	length = len(self.names) - 1
	438	self.parent_class = self.names[length]
[1686a333]	439	if not self._is_call_local(frm):
	440	self.add_data_set()
	441	empty = None
	442	if self.output[0].dx is not None:
	443	self.output[0].dxl = np.empty(0)
	444	self.output[0].dxw = np.empty(0)
	445	else:
	446	self.output[0].dx = np.empty(0)
	447	return self.output[0], empty
[250fec92]	448
	449
[1686a333]	450	def _is_call_local(self, frm=""):
	451	"""
	452
	453	:return:
	454	"""
	455	if frm == "":
	456	frm = inspect.stack()[1]
	457	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
	458	mod_name = mod_name.replace(".py", "")
	459	mod = mod_name.split("sas/")
	460	mod_name = mod[1]
	461	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	462	return False
	463	return True
	464
[d26dea0]	465	def is_cansas(self, ext="xml"):
	466	"""
	467	Checks to see if the xml file is a CanSAS file
	468
	469	:param ext: The file extension of the data file
	470	"""
	471	if self.validate_xml():
	472	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	473	value = self.xmlroot.get(name)
	474	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	475	value.rsplit(" ")[0]:
	476	return True
	477	if ext == "svs":
	478	return True
[250fec92]	479	raise RuntimeError
[d26dea0]	480
[83b6408]	481	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	482	"""
[250fec92]	483	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	484
	485	:param xml_file: The xml file path sent to Reader.read
[250fec92]	486	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	487	"""
	488	base_name = xml_reader.__file__
	489	base_name = base_name.replace("\\", "/")
	490	base = base_name.split("/sas/")[0]
	491
	492	# Load in xml file and get the cansas version from the header
	493	self.set_xml_file(xml_file)
	494	self.cansas_version = self.xmlroot.get("version", "1.0")
	495
	496	# Generic values for the cansas file based on the version
[250fec92]	497	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	498	if schema_path == "":
[250fec92]	499	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	500	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	501
	502	# Link a schema to the XML file.
	503	self.set_schema(schema_path)
	504
[250fec92]	505	def add_data_set(self):
[d26dea0]	506	"""
[250fec92]	507	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	508	private method to generate a new data set.
[d26dea0]	509
[250fec92]	510	:param key: NeXus group name for current tree level
[d26dea0]	511	"""
	512
[250fec92]	513	if self.current_datainfo and self.current_dataset:
	514	self._final_cleanup()
	515	self.data = []
	516	self.current_datainfo = DataInfo()
[d26dea0]	517
[250fec92]	518	def _initialize_new_data_set(self, parent_list=None):
	519	"""
	520	A private class method to generate a new 1D data object.
	521	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	522
	523	:param parent_list: List of names of parent elements
	524	"""
	525
	526	if parent_list is None:
	527	parent_list = []
	528	x = np.array(0)
	529	y = np.array(0)
	530	self.current_dataset = plottable_1D(x, y)
[d26dea0]	531
[250fec92]	532	def add_intermediate(self):
	533	"""
	534	This method stores any intermediate objects within the final data set after fully reading the set.
	535
	536	:param parent: The NXclass name for the h5py Group object that just finished being processed
	537	"""
	538
	539	if self.parent_class == 'SASprocess':
	540	self.current_datainfo.process.append(self.process)
	541	self.process = Process()
	542	elif self.parent_class == 'SASdetector':
	543	self.current_datainfo.detector.append(self.detector)
	544	self.detector = Detector()
	545	elif self.parent_class == 'SAStransmission_spectrum':
	546	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	547	self.transspectrum = TransmissionSpectrum()
	548	elif self.parent_class == 'SAScollimation':
	549	self.current_datainfo.collimation.append(self.collimation)
	550	self.collimation = Collimation()
[5f26aa4]	551	elif self.parent_class == 'aperture':
[250fec92]	552	self.collimation.aperture.append(self.aperture)
	553	self.aperture = Aperture()
	554	elif self.parent_class == 'SASdata':
	555	self._check_for_empty_resolution()
	556	self.data.append(self.current_dataset)
	557
	558	def _final_cleanup(self):
[d26dea0]	559	"""
	560	Final cleanup of the Data1D object to be sure it has all the
	561	appropriate information needed for perspectives
	562	"""
[250fec92]	563
	564	## Append errors to dataset and reset class errors
	565	self.current_datainfo.errors = set()
[d26dea0]	566	for error in self.errors:
[250fec92]	567	self.current_datainfo.errors.add(error)
[d26dea0]	568	self.errors.clear()
[250fec92]	569
	570	## Combine all plottables with datainfo and append each to output
	571	## Type cast data arrays to float64 and find min/max as appropriate
	572	for dataset in self.data:
	573	if dataset.x is not None:
	574	dataset.x = np.delete(dataset.x, [0])
	575	dataset.x = dataset.x.astype(np.float64)
	576	dataset.xmin = np.min(dataset.x)
	577	dataset.xmax = np.max(dataset.x)
	578	if dataset.y is not None:
	579	dataset.y = np.delete(dataset.y, [0])
	580	dataset.y = dataset.y.astype(np.float64)
	581	dataset.ymin = np.min(dataset.y)
	582	dataset.ymax = np.max(dataset.y)
	583	if dataset.dx is not None:
	584	dataset.dx = np.delete(dataset.dx, [0])
	585	dataset.dx = dataset.dx.astype(np.float64)
	586	if dataset.dxl is not None:
	587	dataset.dxl = np.delete(dataset.dxl, [0])
	588	dataset.dxl = dataset.dxl.astype(np.float64)
	589	if dataset.dxw is not None:
	590	dataset.dxw = np.delete(dataset.dxw, [0])
	591	dataset.dxw = dataset.dxw.astype(np.float64)
	592	if dataset.dy is not None:
	593	dataset.dy = np.delete(dataset.dy, [0])
	594	dataset.dy = dataset.dy.astype(np.float64)
	595	np.trim_zeros(dataset.x)
	596	np.trim_zeros(dataset.y)
	597	np.trim_zeros(dataset.dy)
	598	final_dataset = combine_data(dataset, self.current_datainfo)
	599	self.output.append(final_dataset)
[d26dea0]	600
	601	def _create_unique_key(self, dictionary, name, numb=0):
	602	"""
	603	Create a unique key value for any dictionary to prevent overwriting
[250fec92]	604	Recurse until a unique key value is found.
[d26dea0]	605
	606	:param dictionary: A dictionary with any number of entries
	607	:param name: The index of the item to be added to dictionary
	608	:param numb: The number to be appended to the name, starts at 0
	609	"""
	610	if dictionary.get(name) is not None:
	611	numb += 1
	612	name = name.split("_")[0]
	613	name += "_{0}".format(numb)
	614	name = self._create_unique_key(dictionary, name, numb)
	615	return name
	616
[250fec92]	617	def _get_node_value(self, node, tagname):
	618	"""
	619	Get the value of a node and any applicable units
	620
	621	:param node: The XML node to get the value of
	622	:param tagname: The tagname of the node
	623	"""
	624	#Get the text from the node and convert all whitespace to spaces
	625	units = ''
	626	node_value = node.text
	627	if node_value is not None:
	628	node_value = ' '.join(node_value.split())
	629	else:
	630	node_value = ""
	631
	632	# If the value is a float, compile with units.
	633	if self.ns_list.ns_datatype == "float":
	634	# If an empty value is given, set as zero.
	635	if node_value is None or node_value.isspace() \
	636	or node_value.lower() == "nan":
	637	node_value = "0.0"
	638	#Convert the value to the base units
	639	node_value, units = self._unit_conversion(node, tagname, node_value)
	640
	641	# If the value is a timestamp, convert to a datetime object
	642	elif self.ns_list.ns_datatype == "timestamp":
	643	if node_value is None or node_value.isspace():
	644	pass
	645	else:
	646	try:
	647	node_value = \
	648	datetime.datetime.fromtimestamp(node_value)
	649	except ValueError:
	650	node_value = None
	651	return node_value, units
	652
	653	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	654	"""
	655	A unit converter method used to convert the data included in the file
	656	to the default units listed in data_info
	657
[250fec92]	658	:param node: XML node
	659	:param tagname: name of the node
[d26dea0]	660	:param node_value: The value of the current dom node
	661	"""
	662	attr = node.attrib
	663	value_unit = ''
	664	err_msg = None
[682c432]	665	default_unit = None
[5f26aa4]	666	if not isinstance(node_value, float):
	667	node_value = float(node_value)
	668	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	669	try:
	670	local_unit = attr['unit']
[250fec92]	671	unitname = self.ns_list.current_level.get("unit", "")
	672	if "SASdetector" in self.names:
	673	save_in = "detector"
	674	elif "aperture" in self.names:
	675	save_in = "aperture"
	676	elif "SAScollimation" in self.names:
	677	save_in = "collimation"
	678	elif "SAStransmission_spectrum" in self.names:
	679	save_in = "transspectrum"
	680	elif "SASdata" in self.names:
	681	x = np.zeros(1)
	682	y = np.zeros(1)
	683	self.current_data1d = Data1D(x, y)
	684	save_in = "current_data1d"
	685	elif "SASsource" in self.names:
	686	save_in = "current_datainfo.source"
	687	elif "SASsample" in self.names:
	688	save_in = "current_datainfo.sample"
	689	elif "SASprocess" in self.names:
	690	save_in = "process"
	691	else:
	692	save_in = "current_datainfo"
	693	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	694	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	695	and local_unit.lower() != "none":
	696	if HAS_CONVERTER == True:
	697	## Check local units - bad units raise KeyError
	698	data_conv_q = Converter(local_unit)
	699	value_unit = default_unit
[682c432]	700	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	701	else:
	702	value_unit = local_unit
	703	err_msg = "Unit converter is not available.\n"
	704	else:
	705	value_unit = local_unit
	706	except KeyError:
	707	err_msg = "CanSAS reader: unexpected "
	708	err_msg += "\"{0}\" unit [{1}]; "
	709	err_msg = err_msg.format(tagname, local_unit)
[682c432]	710	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	711	value_unit = local_unit
	712	except:
	713	err_msg = "CanSAS reader: unknown error converting "
	714	err_msg += "\"{0}\" unit [{1}]"
	715	err_msg = err_msg.format(tagname, local_unit)
	716	value_unit = local_unit
	717	elif 'unit' in attr:
	718	value_unit = attr['unit']
	719	if err_msg:
	720	self.errors.add(err_msg)
	721	return node_value, value_unit
	722
[250fec92]	723	def _check_for_empty_data(self):
[d26dea0]	724	"""
	725	Creates an empty data set if no data is passed to the reader
	726
	727	:param data1d: presumably a Data1D object
	728	"""
[250fec92]	729	if self.current_dataset == None:
	730	x_vals = np.empty(0)
	731	y_vals = np.empty(0)
	732	dx_vals = np.empty(0)
	733	dy_vals = np.empty(0)
	734	dxl = np.empty(0)
	735	dxw = np.empty(0)
	736	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	737	self.current_dataset.dxl = dxl
	738	self.current_dataset.dxw = dxw
	739
	740	def _check_for_empty_resolution(self):
[d26dea0]	741	"""
	742	A method to check all resolution data sets are the same size as I and Q
	743	"""
	744	dql_exists = False
	745	dqw_exists = False
	746	dq_exists = False
	747	di_exists = False
[250fec92]	748	if self.current_dataset.dxl is not None:
	749	dql_exists = True
	750	if self.current_dataset.dxw is not None:
	751	dqw_exists = True
	752	if self.current_dataset.dx is not None:
	753	dq_exists = True
	754	if self.current_dataset.dy is not None:
	755	di_exists = True
	756	if dqw_exists and not dql_exists:
	757	array_size = self.current_dataset.dxw.size - 1
	758	self.current_dataset.dxl = np.append(self.current_dataset.dxl, np.zeros([array_size]))
	759	elif dql_exists and not dqw_exists:
	760	array_size = self.current_dataset.dxl.size - 1
	761	self.current_dataset.dxw = np.append(self.current_dataset.dxw, np.zeros([array_size]))
	762	elif not dql_exists and not dqw_exists and not dq_exists:
	763	array_size = self.current_dataset.x.size - 1
	764	self.current_dataset.dx = np.append(self.current_dataset.dx, np.zeros([array_size]))
	765	if not di_exists:
	766	array_size = self.current_dataset.y.size - 1
	767	self.current_dataset.dy = np.append(self.current_dataset.dy, np.zeros([array_size]))
	768
	769
	770	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	771
	772
[250fec92]	773	def write(self, filename, datainfo):
[d26dea0]	774	"""
[250fec92]	775	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	776
[250fec92]	777	:param filename: name of the file to write
	778	:param datainfo: Data1D object
	779	"""
	780	# Create XML document
	781	doc, _ = self._to_xml_doc(datainfo)
	782	# Write the file
	783	file_ref = open(filename, 'w')
	784	if self.encoding == None:
	785	self.encoding = "UTF-8"
	786	doc.write(file_ref, encoding=self.encoding,
	787	pretty_print=True, xml_declaration=True)
	788	file_ref.close()
[d26dea0]	789
[250fec92]	790	def _to_xml_doc(self, datainfo):
[d26dea0]	791	"""
[250fec92]	792	Create an XML document to contain the content of a Data1D
[d26dea0]	793
[250fec92]	794	:param datainfo: Data1D object
[d26dea0]	795	"""
[250fec92]	796	if not issubclass(datainfo.__class__, Data1D):
	797	raise RuntimeError, "The cansas writer expects a Data1D instance"
[d26dea0]	798
[250fec92]	799	# Get PIs and create root element
	800	pi_string = self._get_pi_string()
	801	# Define namespaces and create SASroot object
	802	main_node = self._create_main_node()
	803	# Create ElementTree, append SASroot and apply processing instructions
	804	base_string = pi_string + self.to_string(main_node)
	805	base_element = self.create_element_from_string(base_string)
	806	doc = self.create_tree(base_element)
	807	# Create SASentry Element
	808	entry_node = self.create_element("SASentry")
	809	root = doc.getroot()
	810	root.append(entry_node)
[d26dea0]	811
[250fec92]	812	# Add Title to SASentry
	813	self.write_node(entry_node, "Title", datainfo.title)
	814	# Add Run to SASentry
	815	self._write_run_names(datainfo, entry_node)
	816	# Add Data info to SASEntry
	817	self._write_data(datainfo, entry_node)
	818	# Transmission Spectrum Info
	819	self._write_trans_spectrum(datainfo, entry_node)
	820	# Sample info
	821	self._write_sample_info(datainfo, entry_node)
	822	# Instrument info
	823	instr = self._write_instrument(datainfo, entry_node)
	824	# Source
	825	self._write_source(datainfo, instr)
	826	# Collimation
	827	self._write_collimation(datainfo, instr)
	828	# Detectors
	829	self._write_detectors(datainfo, instr)
	830	# Processes info
	831	self._write_process_notes(datainfo, entry_node)
	832	# Note info
	833	self._write_notes(datainfo, entry_node)
	834	# Return the document, and the SASentry node associated with
	835	# the data we just wrote
	836	# If the calling function was not the cansas reader, return a minidom
	837	# object rather than an lxml object.
	838	frm = inspect.stack()[1]
	839	doc, entry_node = self._check_origin(entry_node, doc, frm)
	840	return doc, entry_node
[d26dea0]	841
[250fec92]	842	def write_node(self, parent, name, value, attr=None):
	843	"""
	844	:param doc: document DOM
	845	:param parent: parent node
	846	:param name: tag of the element
	847	:param value: value of the child text node
	848	:param attr: attribute dictionary
[d26dea0]	849
[250fec92]	850	:return: True if something was appended, otherwise False
	851	"""
	852	if value is not None:
	853	parent = self.ebuilder(parent, name, value, attr)
	854	return True
	855	return False
[d26dea0]	856
	857	def _get_pi_string(self):
	858	"""
	859	Creates the processing instructions header for writing to file
	860	"""
	861	pis = self.return_processing_instructions()
	862	if len(pis) > 0:
	863	pi_tree = self.create_tree(pis[0])
	864	i = 1
	865	for i in range(1, len(pis) - 1):
	866	pi_tree = self.append(pis[i], pi_tree)
	867	pi_string = self.to_string(pi_tree)
	868	else:
	869	pi_string = ""
	870	return pi_string
	871
	872	def _create_main_node(self):
	873	"""
	874	Creates the primary xml header used when writing to file
	875	"""
	876	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	877	version = self.cansas_version
	878	n_s = CANSAS_NS.get(version).get("ns")
	879	if version == "1.1":
	880	url = "http://www.cansas.org/formats/1.1/"
	881	else:
	882	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	883	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	884	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	885	"version" : version}
	886	nsmap = {'xsi' : xsi, None: n_s}
	887
	888	main_node = self.create_element("{" + n_s + "}SASroot",
	889	attrib=attrib, nsmap=nsmap)
	890	return main_node
	891
	892	def _write_run_names(self, datainfo, entry_node):
	893	"""
	894	Writes the run names to the XML file
	895
	896	:param datainfo: The Data1D object the information is coming from
	897	:param entry_node: lxml node ElementTree object to be appended to
	898	"""
	899	if datainfo.run == None or datainfo.run == []:
	900	datainfo.run.append(RUN_NAME_DEFAULT)
	901	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	902	for item in datainfo.run:
	903	runname = {}
	904	if item in datainfo.run_name and \
	905	len(str(datainfo.run_name[item])) > 1:
	906	runname = {'name': datainfo.run_name[item]}
	907	self.write_node(entry_node, "Run", item, runname)
	908
	909	def _write_data(self, datainfo, entry_node):
	910	"""
	911	Writes the I and Q data to the XML file
	912
	913	:param datainfo: The Data1D object the information is coming from
	914	:param entry_node: lxml node ElementTree object to be appended to
	915	"""
	916	node = self.create_element("SASdata")
	917	self.append(node, entry_node)
	918
	919	for i in range(len(datainfo.x)):
	920	point = self.create_element("Idata")
	921	node.append(point)
	922	self.write_node(point, "Q", datainfo.x[i],
[682c432]	923	{'unit': datainfo.x_unit})
[d26dea0]	924	if len(datainfo.y) >= i:
	925	self.write_node(point, "I", datainfo.y[i],
[682c432]	926	{'unit': datainfo.y_unit})
[5f26aa4]	927	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	928	self.write_node(point, "Idev", datainfo.dy[i],
[682c432]	929	{'unit': datainfo.y_unit})
[5f26aa4]	930	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	931	self.write_node(point, "Qdev", datainfo.dx[i],
[682c432]	932	{'unit': datainfo.x_unit})
[5f26aa4]	933	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	934	self.write_node(point, "dQw", datainfo.dxw[i],
[682c432]	935	{'unit': datainfo.x_unit})
[5f26aa4]	936	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	937	self.write_node(point, "dQl", datainfo.dxl[i],
[682c432]	938	{'unit': datainfo.x_unit})
[d26dea0]	939
	940	def _write_trans_spectrum(self, datainfo, entry_node):
	941	"""
	942	Writes the transmission spectrum data to the XML file
	943
	944	:param datainfo: The Data1D object the information is coming from
	945	:param entry_node: lxml node ElementTree object to be appended to
	946	"""
	947	for i in range(len(datainfo.trans_spectrum)):
	948	spectrum = datainfo.trans_spectrum[i]
	949	node = self.create_element("SAStransmission_spectrum",
	950	{"name" : spectrum.name})
	951	self.append(node, entry_node)
	952	if isinstance(spectrum.timestamp, datetime.datetime):
	953	node.setAttribute("timestamp", spectrum.timestamp)
	954	for i in range(len(spectrum.wavelength)):
	955	point = self.create_element("Tdata")
	956	node.append(point)
	957	self.write_node(point, "Lambda", spectrum.wavelength[i],
	958	{'unit': spectrum.wavelength_unit})
	959	self.write_node(point, "T", spectrum.transmission[i],
	960	{'unit': spectrum.transmission_unit})
	961	if spectrum.transmission_deviation != None \
	962	and len(spectrum.transmission_deviation) >= i:
	963	self.write_node(point, "Tdev",
	964	spectrum.transmission_deviation[i],
	965	{'unit':
	966	spectrum.transmission_deviation_unit})
	967
	968	def _write_sample_info(self, datainfo, entry_node):
	969	"""
	970	Writes the sample information to the XML file
	971
	972	:param datainfo: The Data1D object the information is coming from
	973	:param entry_node: lxml node ElementTree object to be appended to
	974	"""
	975	sample = self.create_element("SASsample")
	976	if datainfo.sample.name is not None:
	977	self.write_attribute(sample, "name",
	978	str(datainfo.sample.name))
	979	self.append(sample, entry_node)
	980	self.write_node(sample, "ID", str(datainfo.sample.ID))
	981	self.write_node(sample, "thickness", datainfo.sample.thickness,
	982	{"unit": datainfo.sample.thickness_unit})
	983	self.write_node(sample, "transmission", datainfo.sample.transmission)
	984	self.write_node(sample, "temperature", datainfo.sample.temperature,
	985	{"unit": datainfo.sample.temperature_unit})
	986
	987	pos = self.create_element("position")
	988	written = self.write_node(pos,
	989	"x",
	990	datainfo.sample.position.x,
	991	{"unit": datainfo.sample.position_unit})
	992	written = written \| self.write_node( \
	993	pos, "y", datainfo.sample.position.y,
	994	{"unit": datainfo.sample.position_unit})
	995	written = written \| self.write_node( \
	996	pos, "z", datainfo.sample.position.z,
	997	{"unit": datainfo.sample.position_unit})
	998	if written == True:
	999	self.append(pos, sample)
	1000
	1001	ori = self.create_element("orientation")
	1002	written = self.write_node(ori, "roll",
	1003	datainfo.sample.orientation.x,
	1004	{"unit": datainfo.sample.orientation_unit})
	1005	written = written \| self.write_node( \
	1006	ori, "pitch", datainfo.sample.orientation.y,
	1007	{"unit": datainfo.sample.orientation_unit})
	1008	written = written \| self.write_node( \
	1009	ori, "yaw", datainfo.sample.orientation.z,
	1010	{"unit": datainfo.sample.orientation_unit})
	1011	if written == True:
	1012	self.append(ori, sample)
	1013
	1014	for item in datainfo.sample.details:
	1015	self.write_node(sample, "details", item)
	1016
	1017	def _write_instrument(self, datainfo, entry_node):
	1018	"""
	1019	Writes the instrumental information to the XML file
	1020
	1021	:param datainfo: The Data1D object the information is coming from
	1022	:param entry_node: lxml node ElementTree object to be appended to
	1023	"""
	1024	instr = self.create_element("SASinstrument")
	1025	self.append(instr, entry_node)
	1026	self.write_node(instr, "name", datainfo.instrument)
	1027	return instr
	1028
	1029	def _write_source(self, datainfo, instr):
	1030	"""
	1031	Writes the source information to the XML file
	1032
	1033	:param datainfo: The Data1D object the information is coming from
	1034	:param instr: instrument node to be appended to
	1035	"""
	1036	source = self.create_element("SASsource")
	1037	if datainfo.source.name is not None:
	1038	self.write_attribute(source, "name",
	1039	str(datainfo.source.name))
	1040	self.append(source, instr)
	1041	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	1042	datainfo.source.radiation = "neutron"
	1043	self.write_node(source, "radiation", datainfo.source.radiation)
	1044
	1045	size = self.create_element("beam_size")
	1046	if datainfo.source.beam_size_name is not None:
	1047	self.write_attribute(size, "name",
	1048	str(datainfo.source.beam_size_name))
	1049	written = self.write_node( \
	1050	size, "x", datainfo.source.beam_size.x,
	1051	{"unit": datainfo.source.beam_size_unit})
	1052	written = written \| self.write_node( \
	1053	size, "y", datainfo.source.beam_size.y,
	1054	{"unit": datainfo.source.beam_size_unit})
	1055	written = written \| self.write_node( \
	1056	size, "z", datainfo.source.beam_size.z,
	1057	{"unit": datainfo.source.beam_size_unit})
	1058	if written == True:
	1059	self.append(size, source)
	1060
	1061	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1062	self.write_node(source, "wavelength",
	1063	datainfo.source.wavelength,
	1064	{"unit": datainfo.source.wavelength_unit})
	1065	self.write_node(source, "wavelength_min",
	1066	datainfo.source.wavelength_min,
	1067	{"unit": datainfo.source.wavelength_min_unit})
	1068	self.write_node(source, "wavelength_max",
	1069	datainfo.source.wavelength_max,
	1070	{"unit": datainfo.source.wavelength_max_unit})
	1071	self.write_node(source, "wavelength_spread",
	1072	datainfo.source.wavelength_spread,
	1073	{"unit": datainfo.source.wavelength_spread_unit})
	1074
	1075	def _write_collimation(self, datainfo, instr):
	1076	"""
	1077	Writes the collimation information to the XML file
	1078
	1079	:param datainfo: The Data1D object the information is coming from
	1080	:param instr: lxml node ElementTree object to be appended to
	1081	"""
	1082	if datainfo.collimation == [] or datainfo.collimation == None:
	1083	coll = Collimation()
	1084	datainfo.collimation.append(coll)
	1085	for item in datainfo.collimation:
	1086	coll = self.create_element("SAScollimation")
	1087	if item.name is not None:
	1088	self.write_attribute(coll, "name", str(item.name))
	1089	self.append(coll, instr)
	1090
	1091	self.write_node(coll, "length", item.length,
	1092	{"unit": item.length_unit})
	1093
	1094	for aperture in item.aperture:
	1095	apert = self.create_element("aperture")
	1096	if aperture.name is not None:
	1097	self.write_attribute(apert, "name", str(aperture.name))
	1098	if aperture.type is not None:
	1099	self.write_attribute(apert, "type", str(aperture.type))
	1100	self.append(apert, coll)
	1101
	1102	size = self.create_element("size")
	1103	if aperture.size_name is not None:
	1104	self.write_attribute(size, "name",
	1105	str(aperture.size_name))
	1106	written = self.write_node(size, "x", aperture.size.x,
	1107	{"unit": aperture.size_unit})
	1108	written = written \| self.write_node( \
	1109	size, "y", aperture.size.y,
	1110	{"unit": aperture.size_unit})
	1111	written = written \| self.write_node( \
	1112	size, "z", aperture.size.z,
	1113	{"unit": aperture.size_unit})
	1114	if written == True:
	1115	self.append(size, apert)
	1116
	1117	self.write_node(apert, "distance", aperture.distance,
	1118	{"unit": aperture.distance_unit})
	1119
	1120	def _write_detectors(self, datainfo, instr):
	1121	"""
	1122	Writes the detector information to the XML file
	1123
	1124	:param datainfo: The Data1D object the information is coming from
	1125	:param inst: lxml instrument node to be appended to
	1126	"""
	1127	if datainfo.detector == None or datainfo.detector == []:
	1128	det = Detector()
	1129	det.name = ""
	1130	datainfo.detector.append(det)
	1131
	1132	for item in datainfo.detector:
	1133	det = self.create_element("SASdetector")
	1134	written = self.write_node(det, "name", item.name)
	1135	written = written \| self.write_node(det, "SDD", item.distance,
	1136	{"unit": item.distance_unit})
	1137	if written == True:
	1138	self.append(det, instr)
	1139
	1140	off = self.create_element("offset")
	1141	written = self.write_node(off, "x", item.offset.x,
	1142	{"unit": item.offset_unit})
	1143	written = written \| self.write_node(off, "y", item.offset.y,
	1144	{"unit": item.offset_unit})
	1145	written = written \| self.write_node(off, "z", item.offset.z,
	1146	{"unit": item.offset_unit})
	1147	if written == True:
	1148	self.append(off, det)
	1149
	1150	ori = self.create_element("orientation")
	1151	written = self.write_node(ori, "roll", item.orientation.x,
	1152	{"unit": item.orientation_unit})
	1153	written = written \| self.write_node(ori, "pitch",
	1154	item.orientation.y,
	1155	{"unit": item.orientation_unit})
	1156	written = written \| self.write_node(ori, "yaw",
	1157	item.orientation.z,
	1158	{"unit": item.orientation_unit})
	1159	if written == True:
	1160	self.append(ori, det)
	1161
	1162	center = self.create_element("beam_center")
	1163	written = self.write_node(center, "x", item.beam_center.x,
	1164	{"unit": item.beam_center_unit})
	1165	written = written \| self.write_node(center, "y",
	1166	item.beam_center.y,
	1167	{"unit": item.beam_center_unit})
	1168	written = written \| self.write_node(center, "z",
	1169	item.beam_center.z,
	1170	{"unit": item.beam_center_unit})
	1171	if written == True:
	1172	self.append(center, det)
	1173
	1174	pix = self.create_element("pixel_size")
	1175	written = self.write_node(pix, "x", item.pixel_size.x,
	1176	{"unit": item.pixel_size_unit})
	1177	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1178	{"unit": item.pixel_size_unit})
	1179	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1180	{"unit": item.pixel_size_unit})
	1181	written = written \| self.write_node(det, "slit_length",
	1182	item.slit_length,
	1183	{"unit": item.slit_length_unit})
	1184	if written == True:
	1185	self.append(pix, det)
	1186
	1187	def _write_process_notes(self, datainfo, entry_node):
	1188	"""
	1189	Writes the process notes to the XML file
	1190
	1191	:param datainfo: The Data1D object the information is coming from
	1192	:param entry_node: lxml node ElementTree object to be appended to
	1193
	1194	"""
	1195	for item in datainfo.process:
	1196	node = self.create_element("SASprocess")
	1197	self.append(node, entry_node)
	1198	self.write_node(node, "name", item.name)
	1199	self.write_node(node, "date", item.date)
	1200	self.write_node(node, "description", item.description)
	1201	for term in item.term:
[1686a333]	1202	if isinstance(term, list):
	1203	value = term['value']
	1204	del term['value']
[5f26aa4]	1205	elif isinstance(term, dict):
	1206	value = term.get("value")
	1207	del term['value']
[1686a333]	1208	else:
	1209	value = term
[d26dea0]	1210	self.write_node(node, "term", value, term)
	1211	for note in item.notes:
	1212	self.write_node(node, "SASprocessnote", note)
	1213	if len(item.notes) == 0:
	1214	self.write_node(node, "SASprocessnote", "")
	1215
	1216	def _write_notes(self, datainfo, entry_node):
	1217	"""
	1218	Writes the notes to the XML file and creates an empty note if none
	1219	exist
	1220
	1221	:param datainfo: The Data1D object the information is coming from
	1222	:param entry_node: lxml node ElementTree object to be appended to
	1223
	1224	"""
	1225	if len(datainfo.notes) == 0:
	1226	node = self.create_element("SASnote")
	1227	self.append(node, entry_node)
	1228	else:
	1229	for item in datainfo.notes:
	1230	node = self.create_element("SASnote")
	1231	self.write_text(node, item)
	1232	self.append(node, entry_node)
	1233
[5ce7f17]	1234	def _check_origin(self, entry_node, doc, frm):
[d26dea0]	1235	"""
	1236	Return the document, and the SASentry node associated with
	1237	the data we just wrote.
	1238	If the calling function was not the cansas reader, return a minidom
	1239	object rather than an lxml object.
	1240
	1241	:param entry_node: lxml node ElementTree object to be appended to
	1242	:param doc: entire xml tree
	1243	"""
[5ce7f17]	1244	if not frm:
	1245	frm = inspect.stack()[1]
[d26dea0]	1246	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
	1247	mod_name = mod_name.replace(".py", "")
	1248	mod = mod_name.split("sas/")
	1249	mod_name = mod[1]
[45d90b9]	1250	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1251	string = self.to_string(doc, pretty_print=False)
	1252	doc = parseString(string)
	1253	node_name = entry_node.tag
	1254	node_list = doc.getElementsByTagName(node_name)
	1255	entry_node = node_list.item(0)
[5ce7f17]	1256	return doc, entry_node
[d26dea0]	1257
	1258	# DO NOT REMOVE - used in saving and loading panel states.
	1259	def _store_float(self, location, node, variable, storage, optional=True):
	1260	"""
	1261	Get the content of a xpath location and store
	1262	the result. Check that the units are compatible
	1263	with the destination. The value is expected to
	1264	be a float.
	1265
	1266	The xpath location might or might not exist.
	1267	If it does not exist, nothing is done
	1268
	1269	:param location: xpath location to fetch
	1270	:param node: node to read the data from
	1271	:param variable: name of the data member to store it in [string]
	1272	:param storage: data object that has the 'variable' data member
	1273	:param optional: if True, no exception will be raised
	1274	if unit conversion can't be done
	1275
	1276	:raise ValueError: raised when the units are not recognized
	1277	"""
	1278	entry = get_content(location, node)
	1279	try:
	1280	value = float(entry.text)
	1281	except:
	1282	value = None
	1283
	1284	if value is not None:
	1285	# If the entry has units, check to see that they are
	1286	# compatible with what we currently have in the data object
	1287	units = entry.get('unit')
	1288	if units is not None:
	1289	toks = variable.split('.')
	1290	local_unit = None
	1291	exec "local_unit = storage.%s_unit" % toks[0]
	1292	if local_unit != None and units.lower() != local_unit.lower():
	1293	if HAS_CONVERTER == True:
	1294	try:
	1295	conv = Converter(units)
	1296	exec "storage.%s = %g" % \
	1297	(variable, conv(value, units=local_unit))
	1298	except:
	1299	_, exc_value, _ = sys.exc_info()
	1300	err_mess = "CanSAS reader: could not convert"
	1301	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1302	% (variable, units, local_unit, exc_value)
	1303	self.errors.add(err_mess)
	1304	if optional:
	1305	logging.info(err_mess)
	1306	else:
	1307	raise ValueError, err_mess
	1308	else:
	1309	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1310	% (variable, units)
	1311	err_mess += " expecting [%s]" % local_unit
	1312	self.errors.add(err_mess)
	1313	if optional:
	1314	logging.info(err_mess)
	1315	else:
	1316	raise ValueError, err_mess
	1317	else:
	1318	exec "storage.%s = value" % variable
	1319	else:
	1320	exec "storage.%s = value" % variable
	1321
	1322	# DO NOT REMOVE - used in saving and loading panel states.
	1323	def _store_content(self, location, node, variable, storage):
	1324	"""
	1325	Get the content of a xpath location and store
	1326	the result. The value is treated as a string.
	1327
	1328	The xpath location might or might not exist.
	1329	If it does not exist, nothing is done
	1330
	1331	:param location: xpath location to fetch
	1332	:param node: node to read the data from
	1333	:param variable: name of the data member to store it in [string]
	1334	:param storage: data object that has the 'variable' data member
	1335
	1336	:return: return a list of errors
	1337	"""
	1338	entry = get_content(location, node)
	1339	if entry is not None and entry.text is not None:
	1340	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1341
	1342
	1343	# DO NOT REMOVE Called by outside packages:
	1344	# sas.sasgui.perspectives.invariant.invariant_state
	1345	# sas.sasgui.perspectives.fitting.pagestate
	1346	def get_content(location, node):
	1347	"""
	1348	Get the first instance of the content of a xpath location.
	1349
	1350	:param location: xpath location
	1351	:param node: node to start at
	1352
	1353	:return: Element, or None
	1354	"""
	1355	nodes = node.xpath(location,
	1356	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1357	if len(nodes) > 0:
	1358	return nodes[0]
	1359	else:
	1360	return None
	1361
	1362	# DO NOT REMOVE Called by outside packages:
	1363	# sas.sasgui.perspectives.fitting.pagestate
	1364	def write_node(doc, parent, name, value, attr=None):
	1365	"""
	1366	:param doc: document DOM
	1367	:param parent: parent node
	1368	:param name: tag of the element
	1369	:param value: value of the child text node
	1370	:param attr: attribute dictionary
	1371
	1372	:return: True if something was appended, otherwise False
	1373	"""
	1374	if attr is None:
	1375	attr = {}
	1376	if value is not None:
	1377	node = doc.createElement(name)
	1378	node.appendChild(doc.createTextNode(str(value)))
	1379	for item in attr:
	1380	node.setAttribute(item, attr[item])
	1381	parent.appendChild(node)
	1382	return True
	1383	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ eb38181

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