cansas_reader.py @ 15fd91b

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since 15fd91b was 158cb9e, checked in by Piotr Rozyczko <rozyczko@…>, 8 years ago
Added compatibility with save/load projects and analysis.
Property mode set to `100644`
File size: 60.6 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	#############################################################################
	14
	15	import logging
[a40be8c]	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
[a40be8c]	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
[a40be8c]	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"
[a40be8c]	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	"""
[a40be8c]	58	## CanSAS version - defaults to version 1.0
[d26dea0]	59	cansas_version = "1.0"
	60	base_ns = "{cansas1d/1.0}"
[a40be8c]	61	cansas_defaults = None
[d26dea0]	62	type_name = "canSAS"
[a40be8c]	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
[a40be8c]	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
[a40be8c]	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
[158cb9e]	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"
[a40be8c]	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:
	208	# Get the element name and set the current names level
	209	tagname = node.tag.replace(self.base_ns, "")
	210	tagname_original = tagname
	211	# Skip this iteration when loading in save state information
	212	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	213	continue
	214
	215	# Get where to store content
	216	self.names.append(tagname_original)
	217	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	218	# If the element is a child element, recurse
	219	if len(node.getchildren()) > 0:
	220	self.parent_class = tagname_original
	221	if tagname == 'SASdata':
	222	self._initialize_new_data_set()
	223	## Recursion step to access data within the group
	224	self._parse_entry(node)
	225	self.add_intermediate()
	226	else:
	227	data_point, unit = self._get_node_value(node, tagname)
	228
	229	## If this is a dataset, store the data appropriately
	230	if tagname == 'Run':
	231	self.current_datainfo.run.append(data_point)
	232	elif tagname == 'Title':
	233	self.current_datainfo.title = data_point
	234	elif tagname == 'SASnote':
	235	self.current_datainfo.notes.append(data_point)
	236
	237	## I and Q Data
	238	elif tagname == 'I':
	239	self.current_dataset.yaxis("Intensity", unit)
	240	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
	241	elif tagname == 'Idev':
	242	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	243	elif tagname == 'Q':
	244	self.current_dataset.xaxis("Q", unit)
	245	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	246	elif tagname == 'Qdev':
	247	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	248	elif tagname == 'dQw':
	249	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	250	elif tagname == 'dQl':
	251	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[158cb9e]	252	elif tagname == 'Qmean':
	253	pass
	254	elif tagname == 'Shadowfactor':
	255	pass
[a40be8c]	256
	257	## Sample Information
	258	elif tagname == 'ID' and self.parent_class == 'SASsample':
	259	self.current_datainfo.sample.ID = data_point
	260	elif tagname == 'Title' and self.parent_class == 'SASsample':
	261	self.current_datainfo.sample.name = data_point
	262	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	263	self.current_datainfo.sample.thickness = data_point
	264	self.current_datainfo.sample.thickness_unit = unit
	265	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	266	self.current_datainfo.sample.transmission = data_point
	267	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	268	self.current_datainfo.sample.temperature = data_point
	269	self.current_datainfo.sample.temperature_unit = unit
	270	elif tagname == 'details' and self.parent_class == 'SASsample':
	271	self.current_datainfo.sample.details.append(data_point)
	272	elif tagname == 'x' and self.parent_class == 'position':
	273	self.current_datainfo.sample.position.x = data_point
	274	self.current_datainfo.sample.position_unit = unit
	275	elif tagname == 'y' and self.parent_class == 'position':
	276	self.current_datainfo.sample.position.y = data_point
	277	self.current_datainfo.sample.position_unit = unit
	278	elif tagname == 'z' and self.parent_class == 'position':
	279	self.current_datainfo.sample.position.z = data_point
	280	self.current_datainfo.sample.position_unit = unit
	281	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	282	self.current_datainfo.sample.orientation.x = data_point
	283	self.current_datainfo.sample.orientation_unit = unit
	284	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	285	self.current_datainfo.sample.orientation.y = data_point
	286	self.current_datainfo.sample.orientation_unit = unit
	287	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	288	self.current_datainfo.sample.orientation.z = data_point
	289	self.current_datainfo.sample.orientation_unit = unit
	290
	291	## Instrumental Information
	292	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	293	self.current_datainfo.instrument = data_point
	294	## Detector Information
	295	elif tagname == 'name' and self.parent_class == 'SASdetector':
	296	self.detector.name = data_point
	297	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	298	self.detector.distance = data_point
	299	self.detector.distance_unit = unit
	300	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	301	self.detector.slit_length = data_point
	302	self.detector.slit_length_unit = unit
	303	elif tagname == 'x' and self.parent_class == 'offset':
	304	self.detector.offset.x = data_point
	305	self.detector.offset_unit = unit
	306	elif tagname == 'y' and self.parent_class == 'offset':
	307	self.detector.offset.y = data_point
	308	self.detector.offset_unit = unit
	309	elif tagname == 'z' and self.parent_class == 'offset':
	310	self.detector.offset.z = data_point
	311	self.detector.offset_unit = unit
	312	elif tagname == 'x' and self.parent_class == 'beam_center':
	313	self.detector.beam_center.x = data_point
	314	self.detector.beam_center_unit = unit
	315	elif tagname == 'y' and self.parent_class == 'beam_center':
	316	self.detector.beam_center.y = data_point
	317	self.detector.beam_center_unit = unit
	318	elif tagname == 'z' and self.parent_class == 'beam_center':
	319	self.detector.beam_center.z = data_point
	320	self.detector.beam_center_unit = unit
	321	elif tagname == 'x' and self.parent_class == 'pixel_size':
	322	self.detector.pixel_size.x = data_point
	323	self.detector.pixel_size_unit = unit
	324	elif tagname == 'y' and self.parent_class == 'pixel_size':
	325	self.detector.pixel_size.y = data_point
	326	self.detector.pixel_size_unit = unit
	327	elif tagname == 'z' and self.parent_class == 'pixel_size':
	328	self.detector.pixel_size.z = data_point
	329	self.detector.pixel_size_unit = unit
	330	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	331	self.detector.orientation.x = data_point
	332	self.detector.orientation_unit = unit
	333	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	334	self.detector.orientation.y = data_point
	335	self.detector.orientation_unit = unit
	336	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	337	self.detector.orientation.z = data_point
	338	self.detector.orientation_unit = unit
	339	## Collimation and Aperture
	340	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	341	self.collimation.length = data_point
	342	self.collimation.length_unit = unit
	343	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	344	self.collimation.name = data_point
	345	elif tagname == 'distance' and self.parent_class == 'aperture':
	346	self.aperture.distance = data_point
	347	self.aperture.distance_unit = unit
	348	elif tagname == 'x' and self.parent_class == 'size':
	349	self.aperture.size.x = data_point
	350	self.collimation.size_unit = unit
	351	elif tagname == 'y' and self.parent_class == 'size':
	352	self.aperture.size.y = data_point
	353	self.collimation.size_unit = unit
	354	elif tagname == 'z' and self.parent_class == 'size':
	355	self.aperture.size.z = data_point
	356	self.collimation.size_unit = unit
	357
	358	## Process Information
	359	elif tagname == 'name' and self.parent_class == 'SASprocess':
	360	self.process.name = data_point
	361	elif tagname == 'description' and self.parent_class == 'SASprocess':
	362	self.process.description = data_point
	363	elif tagname == 'date' and self.parent_class == 'SASprocess':
	364	try:
	365	self.process.date = datetime.datetime.fromtimestamp(data_point)
	366	except:
	367	self.process.date = data_point
	368	elif tagname == 'SASprocessnote':
	369	self.process.notes.append(data_point)
	370	elif tagname == 'term' and self.parent_class == 'SASprocess':
	371	self.process.term.append(data_point)
	372
	373	## Transmission Spectrum
	374	elif tagname == 'T' and self.parent_class == 'Tdata':
	375	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	376	self.transspectrum.transmission_unit = unit
	377	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	378	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	379	self.transspectrum.transmission_deviation_unit = unit
	380	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	381	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	382	self.transspectrum.wavelength_unit = unit
	383
	384	## Source Information
	385	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	386	self.current_datainfo.source.wavelength = data_point
	387	self.current_datainfo.source.wavelength_unit = unit
	388	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	389	self.current_datainfo.source.wavelength_min = data_point
	390	self.current_datainfo.source.wavelength_min_unit = unit
	391	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	392	self.current_datainfo.source.wavelength_max = data_point
	393	self.current_datainfo.source.wavelength_max_unit = unit
	394	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	395	self.current_datainfo.source.wavelength_spread = data_point
	396	self.current_datainfo.source.wavelength_spread_unit = unit
	397	elif tagname == 'x' and self.parent_class == 'beam_size':
	398	self.current_datainfo.source.beam_size.x = data_point
	399	self.current_datainfo.source.beam_size_unit = unit
	400	elif tagname == 'y' and self.parent_class == 'beam_size':
	401	self.current_datainfo.source.beam_size.y = data_point
	402	self.current_datainfo.source.beam_size_unit = unit
	403	elif tagname == 'z' and self.parent_class == 'pixel_size':
	404	self.current_datainfo.source.data_point.z = data_point
	405	self.current_datainfo.source.beam_size_unit = unit
	406	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	407	self.current_datainfo.source.radiation = data_point
	408	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	409	self.current_datainfo.source.beam_shape = data_point
	410
	411	## Everything else goes in meta_data
	412	else:
	413	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	414	self.current_datainfo.meta_data[new_key] = data_point
	415
	416	self.names.remove(tagname_original)
	417	length = 0
	418	if len(self.names) > 1:
	419	length = len(self.names) - 1
	420	self.parent_class = self.names[length]
[158cb9e]	421	if not self._is_call_local(frm):
	422	self.add_data_set()
	423	empty = None
	424	if self.output[0].dx is not None:
	425	self.output[0].dxl = np.empty(0)
	426	self.output[0].dxw = np.empty(0)
	427	else:
	428	self.output[0].dx = np.empty(0)
	429	return self.output[0], empty
[a40be8c]	430
	431
[158cb9e]	432	def _is_call_local(self, frm=""):
	433	"""
	434
	435	:return:
	436	"""
	437	if frm == "":
	438	frm = inspect.stack()[1]
	439	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
	440	mod_name = mod_name.replace(".py", "")
	441	mod = mod_name.split("sas/")
	442	mod_name = mod[1]
	443	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	444	return False
	445	return True
	446
[d26dea0]	447	def is_cansas(self, ext="xml"):
	448	"""
	449	Checks to see if the xml file is a CanSAS file
	450
	451	:param ext: The file extension of the data file
	452	"""
	453	if self.validate_xml():
	454	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	455	value = self.xmlroot.get(name)
	456	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	457	value.rsplit(" ")[0]:
	458	return True
	459	if ext == "svs":
	460	return True
[a40be8c]	461	raise RuntimeError
[d26dea0]	462
[ef51b63]	463	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	464	"""
[a40be8c]	465	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	466
	467	:param xml_file: The xml file path sent to Reader.read
[a40be8c]	468	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	469	"""
	470	base_name = xml_reader.__file__
	471	base_name = base_name.replace("\\", "/")
	472	base = base_name.split("/sas/")[0]
	473
	474	# Load in xml file and get the cansas version from the header
	475	self.set_xml_file(xml_file)
	476	self.cansas_version = self.xmlroot.get("version", "1.0")
	477
	478	# Generic values for the cansas file based on the version
[a40be8c]	479	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[ef51b63]	480	if schema_path == "":
[a40be8c]	481	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	482	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	483
	484	# Link a schema to the XML file.
	485	self.set_schema(schema_path)
	486
[a40be8c]	487	def add_data_set(self):
[d26dea0]	488	"""
[a40be8c]	489	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	490	private method to generate a new data set.
[d26dea0]	491
[a40be8c]	492	:param key: NeXus group name for current tree level
[d26dea0]	493	"""
	494
[a40be8c]	495	if self.current_datainfo and self.current_dataset:
	496	self._final_cleanup()
	497	self.data = []
	498	self.current_datainfo = DataInfo()
[d26dea0]	499
[a40be8c]	500	def _initialize_new_data_set(self, parent_list=None):
	501	"""
	502	A private class method to generate a new 1D data object.
	503	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	504
	505	:param parent_list: List of names of parent elements
	506	"""
	507
	508	if parent_list is None:
	509	parent_list = []
	510	x = np.array(0)
	511	y = np.array(0)
	512	self.current_dataset = plottable_1D(x, y)
[d26dea0]	513
[a40be8c]	514	def add_intermediate(self):
	515	"""
	516	This method stores any intermediate objects within the final data set after fully reading the set.
	517
	518	:param parent: The NXclass name for the h5py Group object that just finished being processed
	519	"""
	520
	521	if self.parent_class == 'SASprocess':
	522	self.current_datainfo.process.append(self.process)
	523	self.process = Process()
	524	elif self.parent_class == 'SASdetector':
	525	self.current_datainfo.detector.append(self.detector)
	526	self.detector = Detector()
	527	elif self.parent_class == 'SAStransmission_spectrum':
	528	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	529	self.transspectrum = TransmissionSpectrum()
	530	elif self.parent_class == 'SAScollimation':
	531	self.current_datainfo.collimation.append(self.collimation)
	532	self.collimation = Collimation()
	533	elif self.parent_class == 'SASaperture':
	534	self.collimation.aperture.append(self.aperture)
	535	self.aperture = Aperture()
	536	elif self.parent_class == 'SASdata':
	537	self._check_for_empty_resolution()
	538	self.data.append(self.current_dataset)
	539
	540	def _final_cleanup(self):
[d26dea0]	541	"""
	542	Final cleanup of the Data1D object to be sure it has all the
	543	appropriate information needed for perspectives
	544	"""
[a40be8c]	545
	546	## Append errors to dataset and reset class errors
	547	self.current_datainfo.errors = set()
[d26dea0]	548	for error in self.errors:
[a40be8c]	549	self.current_datainfo.errors.add(error)
[d26dea0]	550	self.errors.clear()
[a40be8c]	551
	552	## Combine all plottables with datainfo and append each to output
	553	## Type cast data arrays to float64 and find min/max as appropriate
	554	for dataset in self.data:
	555	if dataset.x is not None:
	556	dataset.x = np.delete(dataset.x, [0])
	557	dataset.x = dataset.x.astype(np.float64)
	558	dataset.xmin = np.min(dataset.x)
	559	dataset.xmax = np.max(dataset.x)
	560	if dataset.y is not None:
	561	dataset.y = np.delete(dataset.y, [0])
	562	dataset.y = dataset.y.astype(np.float64)
	563	dataset.ymin = np.min(dataset.y)
	564	dataset.ymax = np.max(dataset.y)
	565	if dataset.dx is not None:
	566	dataset.dx = np.delete(dataset.dx, [0])
	567	dataset.dx = dataset.dx.astype(np.float64)
	568	if dataset.dxl is not None:
	569	dataset.dxl = np.delete(dataset.dxl, [0])
	570	dataset.dxl = dataset.dxl.astype(np.float64)
	571	if dataset.dxw is not None:
	572	dataset.dxw = np.delete(dataset.dxw, [0])
	573	dataset.dxw = dataset.dxw.astype(np.float64)
	574	if dataset.dy is not None:
	575	dataset.dy = np.delete(dataset.dy, [0])
	576	dataset.dy = dataset.dy.astype(np.float64)
	577	np.trim_zeros(dataset.x)
	578	np.trim_zeros(dataset.y)
	579	np.trim_zeros(dataset.dy)
	580	final_dataset = combine_data(dataset, self.current_datainfo)
	581	self.output.append(final_dataset)
[d26dea0]	582
	583	def _create_unique_key(self, dictionary, name, numb=0):
	584	"""
	585	Create a unique key value for any dictionary to prevent overwriting
[a40be8c]	586	Recurse until a unique key value is found.
[d26dea0]	587
	588	:param dictionary: A dictionary with any number of entries
	589	:param name: The index of the item to be added to dictionary
	590	:param numb: The number to be appended to the name, starts at 0
	591	"""
	592	if dictionary.get(name) is not None:
	593	numb += 1
	594	name = name.split("_")[0]
	595	name += "_{0}".format(numb)
	596	name = self._create_unique_key(dictionary, name, numb)
	597	return name
	598
[a40be8c]	599	def _get_node_value(self, node, tagname):
	600	"""
	601	Get the value of a node and any applicable units
	602
	603	:param node: The XML node to get the value of
	604	:param tagname: The tagname of the node
	605	"""
	606	#Get the text from the node and convert all whitespace to spaces
	607	units = ''
	608	node_value = node.text
	609	if node_value is not None:
	610	node_value = ' '.join(node_value.split())
	611	else:
	612	node_value = ""
	613
	614	# If the value is a float, compile with units.
	615	if self.ns_list.ns_datatype == "float":
	616	# If an empty value is given, set as zero.
	617	if node_value is None or node_value.isspace() \
	618	or node_value.lower() == "nan":
	619	node_value = "0.0"
	620	#Convert the value to the base units
	621	node_value, units = self._unit_conversion(node, tagname, node_value)
	622
	623	# If the value is a timestamp, convert to a datetime object
	624	elif self.ns_list.ns_datatype == "timestamp":
	625	if node_value is None or node_value.isspace():
	626	pass
	627	else:
	628	try:
	629	node_value = \
	630	datetime.datetime.fromtimestamp(node_value)
	631	except ValueError:
	632	node_value = None
	633	return node_value, units
	634
	635	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	636	"""
	637	A unit converter method used to convert the data included in the file
	638	to the default units listed in data_info
	639
[a40be8c]	640	:param node: XML node
	641	:param tagname: name of the node
[d26dea0]	642	:param node_value: The value of the current dom node
	643	"""
	644	attr = node.attrib
	645	value_unit = ''
	646	err_msg = None
[682c432]	647	default_unit = None
[a40be8c]	648	if 'unit' in attr and attr.get('unit') is not None and not self.ns_list.ns_optional:
[d26dea0]	649	try:
	650	local_unit = attr['unit']
[a40be8c]	651	if not isinstance(node_value, float):
	652	node_value = float(node_value)
	653	unitname = self.ns_list.current_level.get("unit", "")
	654	if "SASdetector" in self.names:
	655	save_in = "detector"
	656	elif "aperture" in self.names:
	657	save_in = "aperture"
	658	elif "SAScollimation" in self.names:
	659	save_in = "collimation"
	660	elif "SAStransmission_spectrum" in self.names:
	661	save_in = "transspectrum"
	662	elif "SASdata" in self.names:
	663	x = np.zeros(1)
	664	y = np.zeros(1)
	665	self.current_data1d = Data1D(x, y)
	666	save_in = "current_data1d"
	667	elif "SASsource" in self.names:
	668	save_in = "current_datainfo.source"
	669	elif "SASsample" in self.names:
	670	save_in = "current_datainfo.sample"
	671	elif "SASprocess" in self.names:
	672	save_in = "process"
	673	else:
	674	save_in = "current_datainfo"
	675	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	676	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	677	and local_unit.lower() != "none":
	678	if HAS_CONVERTER == True:
	679	## Check local units - bad units raise KeyError
	680	data_conv_q = Converter(local_unit)
	681	value_unit = default_unit
[682c432]	682	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	683	else:
	684	value_unit = local_unit
	685	err_msg = "Unit converter is not available.\n"
	686	else:
	687	value_unit = local_unit
	688	except KeyError:
	689	err_msg = "CanSAS reader: unexpected "
	690	err_msg += "\"{0}\" unit [{1}]; "
	691	err_msg = err_msg.format(tagname, local_unit)
[682c432]	692	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	693	value_unit = local_unit
	694	except:
	695	err_msg = "CanSAS reader: unknown error converting "
	696	err_msg += "\"{0}\" unit [{1}]"
	697	err_msg = err_msg.format(tagname, local_unit)
	698	value_unit = local_unit
	699	elif 'unit' in attr:
	700	value_unit = attr['unit']
	701	if err_msg:
	702	self.errors.add(err_msg)
	703	return node_value, value_unit
	704
[a40be8c]	705	def _check_for_empty_data(self):
[d26dea0]	706	"""
	707	Creates an empty data set if no data is passed to the reader
	708
	709	:param data1d: presumably a Data1D object
	710	"""
[a40be8c]	711	if self.current_dataset == None:
	712	x_vals = np.empty(0)
	713	y_vals = np.empty(0)
	714	dx_vals = np.empty(0)
	715	dy_vals = np.empty(0)
	716	dxl = np.empty(0)
	717	dxw = np.empty(0)
	718	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	719	self.current_dataset.dxl = dxl
	720	self.current_dataset.dxw = dxw
	721
	722	def _check_for_empty_resolution(self):
[d26dea0]	723	"""
	724	A method to check all resolution data sets are the same size as I and Q
	725	"""
	726	dql_exists = False
	727	dqw_exists = False
	728	dq_exists = False
	729	di_exists = False
[a40be8c]	730	if self.current_dataset.dxl is not None:
	731	dql_exists = True
	732	if self.current_dataset.dxw is not None:
	733	dqw_exists = True
	734	if self.current_dataset.dx is not None:
	735	dq_exists = True
	736	if self.current_dataset.dy is not None:
	737	di_exists = True
	738	if dqw_exists and not dql_exists:
	739	array_size = self.current_dataset.dxw.size - 1
	740	self.current_dataset.dxl = np.append(self.current_dataset.dxl, np.zeros([array_size]))
	741	elif dql_exists and not dqw_exists:
	742	array_size = self.current_dataset.dxl.size - 1
	743	self.current_dataset.dxw = np.append(self.current_dataset.dxw, np.zeros([array_size]))
	744	elif not dql_exists and not dqw_exists and not dq_exists:
	745	array_size = self.current_dataset.x.size - 1
	746	self.current_dataset.dx = np.append(self.current_dataset.dx, np.zeros([array_size]))
	747	if not di_exists:
	748	array_size = self.current_dataset.y.size - 1
	749	self.current_dataset.dy = np.append(self.current_dataset.dy, np.zeros([array_size]))
	750
	751
	752	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	753
	754
[a40be8c]	755	def write(self, filename, datainfo):
[d26dea0]	756	"""
[a40be8c]	757	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	758
[a40be8c]	759	:param filename: name of the file to write
	760	:param datainfo: Data1D object
	761	"""
	762	# Create XML document
	763	doc, _ = self._to_xml_doc(datainfo)
	764	# Write the file
	765	file_ref = open(filename, 'w')
	766	if self.encoding == None:
	767	self.encoding = "UTF-8"
	768	doc.write(file_ref, encoding=self.encoding,
	769	pretty_print=True, xml_declaration=True)
	770	file_ref.close()
[d26dea0]	771
[a40be8c]	772	def _to_xml_doc(self, datainfo):
[d26dea0]	773	"""
[a40be8c]	774	Create an XML document to contain the content of a Data1D
[d26dea0]	775
[a40be8c]	776	:param datainfo: Data1D object
[d26dea0]	777	"""
[a40be8c]	778	if not issubclass(datainfo.__class__, Data1D):
	779	raise RuntimeError, "The cansas writer expects a Data1D instance"
[d26dea0]	780
[a40be8c]	781	# Get PIs and create root element
	782	pi_string = self._get_pi_string()
	783	# Define namespaces and create SASroot object
	784	main_node = self._create_main_node()
	785	# Create ElementTree, append SASroot and apply processing instructions
	786	base_string = pi_string + self.to_string(main_node)
	787	base_element = self.create_element_from_string(base_string)
	788	doc = self.create_tree(base_element)
	789	# Create SASentry Element
	790	entry_node = self.create_element("SASentry")
	791	root = doc.getroot()
	792	root.append(entry_node)
[d26dea0]	793
[a40be8c]	794	# Add Title to SASentry
	795	self.write_node(entry_node, "Title", datainfo.title)
	796	# Add Run to SASentry
	797	self._write_run_names(datainfo, entry_node)
	798	# Add Data info to SASEntry
	799	self._write_data(datainfo, entry_node)
	800	# Transmission Spectrum Info
	801	self._write_trans_spectrum(datainfo, entry_node)
	802	# Sample info
	803	self._write_sample_info(datainfo, entry_node)
	804	# Instrument info
	805	instr = self._write_instrument(datainfo, entry_node)
	806	# Source
	807	self._write_source(datainfo, instr)
	808	# Collimation
	809	self._write_collimation(datainfo, instr)
	810	# Detectors
	811	self._write_detectors(datainfo, instr)
	812	# Processes info
	813	self._write_process_notes(datainfo, entry_node)
	814	# Note info
	815	self._write_notes(datainfo, entry_node)
	816	# Return the document, and the SASentry node associated with
	817	# the data we just wrote
	818	# If the calling function was not the cansas reader, return a minidom
	819	# object rather than an lxml object.
	820	frm = inspect.stack()[1]
	821	doc, entry_node = self._check_origin(entry_node, doc, frm)
	822	return doc, entry_node
[d26dea0]	823
[a40be8c]	824	def write_node(self, parent, name, value, attr=None):
	825	"""
	826	:param doc: document DOM
	827	:param parent: parent node
	828	:param name: tag of the element
	829	:param value: value of the child text node
	830	:param attr: attribute dictionary
[d26dea0]	831
[a40be8c]	832	:return: True if something was appended, otherwise False
	833	"""
	834	if value is not None:
	835	parent = self.ebuilder(parent, name, value, attr)
	836	return True
	837	return False
[d26dea0]	838
	839	def _get_pi_string(self):
	840	"""
	841	Creates the processing instructions header for writing to file
	842	"""
	843	pis = self.return_processing_instructions()
	844	if len(pis) > 0:
	845	pi_tree = self.create_tree(pis[0])
	846	i = 1
	847	for i in range(1, len(pis) - 1):
	848	pi_tree = self.append(pis[i], pi_tree)
	849	pi_string = self.to_string(pi_tree)
	850	else:
	851	pi_string = ""
	852	return pi_string
	853
	854	def _create_main_node(self):
	855	"""
	856	Creates the primary xml header used when writing to file
	857	"""
	858	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	859	version = self.cansas_version
	860	n_s = CANSAS_NS.get(version).get("ns")
	861	if version == "1.1":
	862	url = "http://www.cansas.org/formats/1.1/"
	863	else:
	864	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	865	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	866	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	867	"version" : version}
	868	nsmap = {'xsi' : xsi, None: n_s}
	869
	870	main_node = self.create_element("{" + n_s + "}SASroot",
	871	attrib=attrib, nsmap=nsmap)
	872	return main_node
	873
	874	def _write_run_names(self, datainfo, entry_node):
	875	"""
	876	Writes the run names to the XML file
	877
	878	:param datainfo: The Data1D object the information is coming from
	879	:param entry_node: lxml node ElementTree object to be appended to
	880	"""
	881	if datainfo.run == None or datainfo.run == []:
	882	datainfo.run.append(RUN_NAME_DEFAULT)
	883	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	884	for item in datainfo.run:
	885	runname = {}
	886	if item in datainfo.run_name and \
	887	len(str(datainfo.run_name[item])) > 1:
	888	runname = {'name': datainfo.run_name[item]}
	889	self.write_node(entry_node, "Run", item, runname)
	890
	891	def _write_data(self, datainfo, entry_node):
	892	"""
	893	Writes the I and Q data to the XML file
	894
	895	:param datainfo: The Data1D object the information is coming from
	896	:param entry_node: lxml node ElementTree object to be appended to
	897	"""
	898	node = self.create_element("SASdata")
	899	self.append(node, entry_node)
	900
	901	for i in range(len(datainfo.x)):
	902	point = self.create_element("Idata")
	903	node.append(point)
	904	self.write_node(point, "Q", datainfo.x[i],
[682c432]	905	{'unit': datainfo.x_unit})
[d26dea0]	906	if len(datainfo.y) >= i:
	907	self.write_node(point, "I", datainfo.y[i],
[682c432]	908	{'unit': datainfo.y_unit})
[d26dea0]	909	if datainfo.dy != None and len(datainfo.dy) > i:
	910	self.write_node(point, "Idev", datainfo.dy[i],
[682c432]	911	{'unit': datainfo.y_unit})
[d26dea0]	912	if datainfo.dx != None and len(datainfo.dx) > i:
	913	self.write_node(point, "Qdev", datainfo.dx[i],
[682c432]	914	{'unit': datainfo.x_unit})
[d26dea0]	915	if datainfo.dxw != None and len(datainfo.dxw) > i:
	916	self.write_node(point, "dQw", datainfo.dxw[i],
[682c432]	917	{'unit': datainfo.x_unit})
[d26dea0]	918	if datainfo.dxl != None and len(datainfo.dxl) > i:
	919	self.write_node(point, "dQl", datainfo.dxl[i],
[682c432]	920	{'unit': datainfo.x_unit})
[d26dea0]	921
	922	def _write_trans_spectrum(self, datainfo, entry_node):
	923	"""
	924	Writes the transmission spectrum data to the XML file
	925
	926	:param datainfo: The Data1D object the information is coming from
	927	:param entry_node: lxml node ElementTree object to be appended to
	928	"""
	929	for i in range(len(datainfo.trans_spectrum)):
	930	spectrum = datainfo.trans_spectrum[i]
	931	node = self.create_element("SAStransmission_spectrum",
	932	{"name" : spectrum.name})
	933	self.append(node, entry_node)
	934	if isinstance(spectrum.timestamp, datetime.datetime):
	935	node.setAttribute("timestamp", spectrum.timestamp)
	936	for i in range(len(spectrum.wavelength)):
	937	point = self.create_element("Tdata")
	938	node.append(point)
	939	self.write_node(point, "Lambda", spectrum.wavelength[i],
	940	{'unit': spectrum.wavelength_unit})
	941	self.write_node(point, "T", spectrum.transmission[i],
	942	{'unit': spectrum.transmission_unit})
	943	if spectrum.transmission_deviation != None \
	944	and len(spectrum.transmission_deviation) >= i:
	945	self.write_node(point, "Tdev",
	946	spectrum.transmission_deviation[i],
	947	{'unit':
	948	spectrum.transmission_deviation_unit})
	949
	950	def _write_sample_info(self, datainfo, entry_node):
	951	"""
	952	Writes the sample information 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	sample = self.create_element("SASsample")
	958	if datainfo.sample.name is not None:
	959	self.write_attribute(sample, "name",
	960	str(datainfo.sample.name))
	961	self.append(sample, entry_node)
	962	self.write_node(sample, "ID", str(datainfo.sample.ID))
	963	self.write_node(sample, "thickness", datainfo.sample.thickness,
	964	{"unit": datainfo.sample.thickness_unit})
	965	self.write_node(sample, "transmission", datainfo.sample.transmission)
	966	self.write_node(sample, "temperature", datainfo.sample.temperature,
	967	{"unit": datainfo.sample.temperature_unit})
	968
	969	pos = self.create_element("position")
	970	written = self.write_node(pos,
	971	"x",
	972	datainfo.sample.position.x,
	973	{"unit": datainfo.sample.position_unit})
	974	written = written \| self.write_node( \
	975	pos, "y", datainfo.sample.position.y,
	976	{"unit": datainfo.sample.position_unit})
	977	written = written \| self.write_node( \
	978	pos, "z", datainfo.sample.position.z,
	979	{"unit": datainfo.sample.position_unit})
	980	if written == True:
	981	self.append(pos, sample)
	982
	983	ori = self.create_element("orientation")
	984	written = self.write_node(ori, "roll",
	985	datainfo.sample.orientation.x,
	986	{"unit": datainfo.sample.orientation_unit})
	987	written = written \| self.write_node( \
	988	ori, "pitch", datainfo.sample.orientation.y,
	989	{"unit": datainfo.sample.orientation_unit})
	990	written = written \| self.write_node( \
	991	ori, "yaw", datainfo.sample.orientation.z,
	992	{"unit": datainfo.sample.orientation_unit})
	993	if written == True:
	994	self.append(ori, sample)
	995
	996	for item in datainfo.sample.details:
	997	self.write_node(sample, "details", item)
	998
	999	def _write_instrument(self, datainfo, entry_node):
	1000	"""
	1001	Writes the instrumental information to the XML file
	1002
	1003	:param datainfo: The Data1D object the information is coming from
	1004	:param entry_node: lxml node ElementTree object to be appended to
	1005	"""
	1006	instr = self.create_element("SASinstrument")
	1007	self.append(instr, entry_node)
	1008	self.write_node(instr, "name", datainfo.instrument)
	1009	return instr
	1010
	1011	def _write_source(self, datainfo, instr):
	1012	"""
	1013	Writes the source information to the XML file
	1014
	1015	:param datainfo: The Data1D object the information is coming from
	1016	:param instr: instrument node to be appended to
	1017	"""
	1018	source = self.create_element("SASsource")
	1019	if datainfo.source.name is not None:
	1020	self.write_attribute(source, "name",
	1021	str(datainfo.source.name))
	1022	self.append(source, instr)
	1023	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	1024	datainfo.source.radiation = "neutron"
	1025	self.write_node(source, "radiation", datainfo.source.radiation)
	1026
	1027	size = self.create_element("beam_size")
	1028	if datainfo.source.beam_size_name is not None:
	1029	self.write_attribute(size, "name",
	1030	str(datainfo.source.beam_size_name))
	1031	written = self.write_node( \
	1032	size, "x", datainfo.source.beam_size.x,
	1033	{"unit": datainfo.source.beam_size_unit})
	1034	written = written \| self.write_node( \
	1035	size, "y", datainfo.source.beam_size.y,
	1036	{"unit": datainfo.source.beam_size_unit})
	1037	written = written \| self.write_node( \
	1038	size, "z", datainfo.source.beam_size.z,
	1039	{"unit": datainfo.source.beam_size_unit})
	1040	if written == True:
	1041	self.append(size, source)
	1042
	1043	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1044	self.write_node(source, "wavelength",
	1045	datainfo.source.wavelength,
	1046	{"unit": datainfo.source.wavelength_unit})
	1047	self.write_node(source, "wavelength_min",
	1048	datainfo.source.wavelength_min,
	1049	{"unit": datainfo.source.wavelength_min_unit})
	1050	self.write_node(source, "wavelength_max",
	1051	datainfo.source.wavelength_max,
	1052	{"unit": datainfo.source.wavelength_max_unit})
	1053	self.write_node(source, "wavelength_spread",
	1054	datainfo.source.wavelength_spread,
	1055	{"unit": datainfo.source.wavelength_spread_unit})
	1056
	1057	def _write_collimation(self, datainfo, instr):
	1058	"""
	1059	Writes the collimation information to the XML file
	1060
	1061	:param datainfo: The Data1D object the information is coming from
	1062	:param instr: lxml node ElementTree object to be appended to
	1063	"""
	1064	if datainfo.collimation == [] or datainfo.collimation == None:
	1065	coll = Collimation()
	1066	datainfo.collimation.append(coll)
	1067	for item in datainfo.collimation:
	1068	coll = self.create_element("SAScollimation")
	1069	if item.name is not None:
	1070	self.write_attribute(coll, "name", str(item.name))
	1071	self.append(coll, instr)
	1072
	1073	self.write_node(coll, "length", item.length,
	1074	{"unit": item.length_unit})
	1075
	1076	for aperture in item.aperture:
	1077	apert = self.create_element("aperture")
	1078	if aperture.name is not None:
	1079	self.write_attribute(apert, "name", str(aperture.name))
	1080	if aperture.type is not None:
	1081	self.write_attribute(apert, "type", str(aperture.type))
	1082	self.append(apert, coll)
	1083
	1084	size = self.create_element("size")
	1085	if aperture.size_name is not None:
	1086	self.write_attribute(size, "name",
	1087	str(aperture.size_name))
	1088	written = self.write_node(size, "x", aperture.size.x,
	1089	{"unit": aperture.size_unit})
	1090	written = written \| self.write_node( \
	1091	size, "y", aperture.size.y,
	1092	{"unit": aperture.size_unit})
	1093	written = written \| self.write_node( \
	1094	size, "z", aperture.size.z,
	1095	{"unit": aperture.size_unit})
	1096	if written == True:
	1097	self.append(size, apert)
	1098
	1099	self.write_node(apert, "distance", aperture.distance,
	1100	{"unit": aperture.distance_unit})
	1101
	1102	def _write_detectors(self, datainfo, instr):
	1103	"""
	1104	Writes the detector information to the XML file
	1105
	1106	:param datainfo: The Data1D object the information is coming from
	1107	:param inst: lxml instrument node to be appended to
	1108	"""
	1109	if datainfo.detector == None or datainfo.detector == []:
	1110	det = Detector()
	1111	det.name = ""
	1112	datainfo.detector.append(det)
	1113
	1114	for item in datainfo.detector:
	1115	det = self.create_element("SASdetector")
	1116	written = self.write_node(det, "name", item.name)
	1117	written = written \| self.write_node(det, "SDD", item.distance,
	1118	{"unit": item.distance_unit})
	1119	if written == True:
	1120	self.append(det, instr)
	1121
	1122	off = self.create_element("offset")
	1123	written = self.write_node(off, "x", item.offset.x,
	1124	{"unit": item.offset_unit})
	1125	written = written \| self.write_node(off, "y", item.offset.y,
	1126	{"unit": item.offset_unit})
	1127	written = written \| self.write_node(off, "z", item.offset.z,
	1128	{"unit": item.offset_unit})
	1129	if written == True:
	1130	self.append(off, det)
	1131
	1132	ori = self.create_element("orientation")
	1133	written = self.write_node(ori, "roll", item.orientation.x,
	1134	{"unit": item.orientation_unit})
	1135	written = written \| self.write_node(ori, "pitch",
	1136	item.orientation.y,
	1137	{"unit": item.orientation_unit})
	1138	written = written \| self.write_node(ori, "yaw",
	1139	item.orientation.z,
	1140	{"unit": item.orientation_unit})
	1141	if written == True:
	1142	self.append(ori, det)
	1143
	1144	center = self.create_element("beam_center")
	1145	written = self.write_node(center, "x", item.beam_center.x,
	1146	{"unit": item.beam_center_unit})
	1147	written = written \| self.write_node(center, "y",
	1148	item.beam_center.y,
	1149	{"unit": item.beam_center_unit})
	1150	written = written \| self.write_node(center, "z",
	1151	item.beam_center.z,
	1152	{"unit": item.beam_center_unit})
	1153	if written == True:
	1154	self.append(center, det)
	1155
	1156	pix = self.create_element("pixel_size")
	1157	written = self.write_node(pix, "x", item.pixel_size.x,
	1158	{"unit": item.pixel_size_unit})
	1159	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1160	{"unit": item.pixel_size_unit})
	1161	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1162	{"unit": item.pixel_size_unit})
	1163	written = written \| self.write_node(det, "slit_length",
	1164	item.slit_length,
	1165	{"unit": item.slit_length_unit})
	1166	if written == True:
	1167	self.append(pix, det)
	1168
	1169	def _write_process_notes(self, datainfo, entry_node):
	1170	"""
	1171	Writes the process notes to the XML file
	1172
	1173	:param datainfo: The Data1D object the information is coming from
	1174	:param entry_node: lxml node ElementTree object to be appended to
	1175
	1176	"""
	1177	for item in datainfo.process:
	1178	node = self.create_element("SASprocess")
	1179	self.append(node, entry_node)
	1180	self.write_node(node, "name", item.name)
	1181	self.write_node(node, "date", item.date)
	1182	self.write_node(node, "description", item.description)
	1183	for term in item.term:
[158cb9e]	1184	if isinstance(term, list):
	1185	value = term['value']
	1186	del term['value']
	1187	else:
	1188	value = term
[d26dea0]	1189	self.write_node(node, "term", value, term)
	1190	for note in item.notes:
	1191	self.write_node(node, "SASprocessnote", note)
	1192	if len(item.notes) == 0:
	1193	self.write_node(node, "SASprocessnote", "")
	1194
	1195	def _write_notes(self, datainfo, entry_node):
	1196	"""
	1197	Writes the notes to the XML file and creates an empty note if none
	1198	exist
	1199
	1200	:param datainfo: The Data1D object the information is coming from
	1201	:param entry_node: lxml node ElementTree object to be appended to
	1202
	1203	"""
	1204	if len(datainfo.notes) == 0:
	1205	node = self.create_element("SASnote")
	1206	self.append(node, entry_node)
	1207	else:
	1208	for item in datainfo.notes:
	1209	node = self.create_element("SASnote")
	1210	self.write_text(node, item)
	1211	self.append(node, entry_node)
	1212
[5ce7f17]	1213	def _check_origin(self, entry_node, doc, frm):
[d26dea0]	1214	"""
	1215	Return the document, and the SASentry node associated with
	1216	the data we just wrote.
	1217	If the calling function was not the cansas reader, return a minidom
	1218	object rather than an lxml object.
	1219
	1220	:param entry_node: lxml node ElementTree object to be appended to
	1221	:param doc: entire xml tree
	1222	"""
[5ce7f17]	1223	if not frm:
	1224	frm = inspect.stack()[1]
[d26dea0]	1225	mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
	1226	mod_name = mod_name.replace(".py", "")
	1227	mod = mod_name.split("sas/")
	1228	mod_name = mod[1]
[45d90b9]	1229	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1230	string = self.to_string(doc, pretty_print=False)
	1231	doc = parseString(string)
	1232	node_name = entry_node.tag
	1233	node_list = doc.getElementsByTagName(node_name)
	1234	entry_node = node_list.item(0)
[5ce7f17]	1235	return doc, entry_node
[d26dea0]	1236
	1237	# DO NOT REMOVE - used in saving and loading panel states.
	1238	def _store_float(self, location, node, variable, storage, optional=True):
	1239	"""
	1240	Get the content of a xpath location and store
	1241	the result. Check that the units are compatible
	1242	with the destination. The value is expected to
	1243	be a float.
	1244
	1245	The xpath location might or might not exist.
	1246	If it does not exist, nothing is done
	1247
	1248	:param location: xpath location to fetch
	1249	:param node: node to read the data from
	1250	:param variable: name of the data member to store it in [string]
	1251	:param storage: data object that has the 'variable' data member
	1252	:param optional: if True, no exception will be raised
	1253	if unit conversion can't be done
	1254
	1255	:raise ValueError: raised when the units are not recognized
	1256	"""
	1257	entry = get_content(location, node)
	1258	try:
	1259	value = float(entry.text)
	1260	except:
	1261	value = None
	1262
	1263	if value is not None:
	1264	# If the entry has units, check to see that they are
	1265	# compatible with what we currently have in the data object
	1266	units = entry.get('unit')
	1267	if units is not None:
	1268	toks = variable.split('.')
	1269	local_unit = None
	1270	exec "local_unit = storage.%s_unit" % toks[0]
	1271	if local_unit != None and units.lower() != local_unit.lower():
	1272	if HAS_CONVERTER == True:
	1273	try:
	1274	conv = Converter(units)
	1275	exec "storage.%s = %g" % \
	1276	(variable, conv(value, units=local_unit))
	1277	except:
	1278	_, exc_value, _ = sys.exc_info()
	1279	err_mess = "CanSAS reader: could not convert"
	1280	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1281	% (variable, units, local_unit, exc_value)
	1282	self.errors.add(err_mess)
	1283	if optional:
	1284	logging.info(err_mess)
	1285	else:
	1286	raise ValueError, err_mess
	1287	else:
	1288	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1289	% (variable, units)
	1290	err_mess += " expecting [%s]" % local_unit
	1291	self.errors.add(err_mess)
	1292	if optional:
	1293	logging.info(err_mess)
	1294	else:
	1295	raise ValueError, err_mess
	1296	else:
	1297	exec "storage.%s = value" % variable
	1298	else:
	1299	exec "storage.%s = value" % variable
	1300
	1301	# DO NOT REMOVE - used in saving and loading panel states.
	1302	def _store_content(self, location, node, variable, storage):
	1303	"""
	1304	Get the content of a xpath location and store
	1305	the result. The value is treated as a string.
	1306
	1307	The xpath location might or might not exist.
	1308	If it does not exist, nothing is done
	1309
	1310	:param location: xpath location to fetch
	1311	:param node: node to read the data from
	1312	:param variable: name of the data member to store it in [string]
	1313	:param storage: data object that has the 'variable' data member
	1314
	1315	:return: return a list of errors
	1316	"""
	1317	entry = get_content(location, node)
	1318	if entry is not None and entry.text is not None:
	1319	exec "storage.%s = entry.text.strip()" % variable
[a40be8c]	1320
	1321
	1322	# DO NOT REMOVE Called by outside packages:
	1323	# sas.sasgui.perspectives.invariant.invariant_state
	1324	# sas.sasgui.perspectives.fitting.pagestate
	1325	def get_content(location, node):
	1326	"""
	1327	Get the first instance of the content of a xpath location.
	1328
	1329	:param location: xpath location
	1330	:param node: node to start at
	1331
	1332	:return: Element, or None
	1333	"""
	1334	nodes = node.xpath(location,
	1335	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1336	if len(nodes) > 0:
	1337	return nodes[0]
	1338	else:
	1339	return None
	1340
	1341	# DO NOT REMOVE Called by outside packages:
	1342	# sas.sasgui.perspectives.fitting.pagestate
	1343	def write_node(doc, parent, name, value, attr=None):
	1344	"""
	1345	:param doc: document DOM
	1346	:param parent: parent node
	1347	:param name: tag of the element
	1348	:param value: value of the child text node
	1349	:param attr: attribute dictionary
	1350
	1351	:return: True if something was appended, otherwise False
	1352	"""
	1353	if attr is None:
	1354	attr = {}
	1355	if value is not None:
	1356	node = doc.createElement(name)
	1357	node.appendChild(doc.createTextNode(str(value)))
	1358	for item in attr:
	1359	node.setAttribute(item, attr[item])
	1360	parent.appendChild(node)
	1361	return True
	1362	return False

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 15fd91b

Download in other formats: