cansas_reader.py @ 251ef684

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 251ef684 was 7432acb, checked in by andyfaff, 8 years ago
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[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
[83c09af]	22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
[af08e55]	23	plottable_1D, plottable_2D
[83c09af]	24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
	25	Detector, Process, Aperture
	26	from sas.sascalc.dataloader.data_info import \
	27	combine_data_info_with_plottable as combine_data
[b699768]	28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
[250fec92]	30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
[d26dea0]	31
[682c432]	32	# The following 2 imports ARE used. Do not remove either.
	33	import xml.dom.minidom
	34	from xml.dom.minidom import parseString
	35
[463e7ffc]	36	logger = logging.getLogger(__name__)
[c155a16]	37
[d26dea0]	38	PREPROCESS = "xmlpreprocess"
	39	ENCODING = "encoding"
	40	RUN_NAME_DEFAULT = "None"
[250fec92]	41	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	42	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	43	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	44	"as much of the data as possible.\n\n"
[d26dea0]	45	HAS_CONVERTER = True
	46	try:
[b699768]	47	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	48	except ImportError:
	49	HAS_CONVERTER = False
	50
	51	CONSTANTS = CansasConstants()
	52	CANSAS_FORMAT = CONSTANTS.format
	53	CANSAS_NS = CONSTANTS.names
	54	ALLOW_ALL = True
	55
	56	class Reader(XMLreader):
	57	"""
	58	Class to load cansas 1D XML files
	59
	60	:Dependencies:
	61	The CanSAS reader requires PyXML 0.8.4 or later.
	62	"""
[af08e55]	63	# CanSAS version - defaults to version 1.0
[d26dea0]	64	cansas_version = "1.0"
	65	base_ns = "{cansas1d/1.0}"
[250fec92]	66	cansas_defaults = None
[d26dea0]	67	type_name = "canSAS"
[250fec92]	68	invalid = True
[654e8e0]	69	frm = ""
[af08e55]	70	# Log messages and errors
[250fec92]	71	logging = None
	72	errors = set()
[af08e55]	73	# Namespace hierarchy for current xml_file object
[250fec92]	74	names = None
	75	ns_list = None
[af08e55]	76	# Temporary storage location for loading multiple data sets in a single file
[250fec92]	77	current_datainfo = None
	78	current_dataset = None
	79	current_data1d = None
	80	data = None
[af08e55]	81	# List of data1D objects to be sent back to SasView
[250fec92]	82	output = None
[af08e55]	83	# Wildcards
[d26dea0]	84	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
[af08e55]	85	# List of allowed extensions
[d26dea0]	86	ext = ['.xml', '.XML', '.svs', '.SVS']
[af08e55]	87	# Flag to bypass extension check
[d26dea0]	88	allow_all = True
	89
[250fec92]	90	def reset_state(self):
	91	"""
	92	Resets the class state to a base case when loading a new data file so previous
	93	data files do not appear a second time
	94	"""
	95	self.current_datainfo = None
	96	self.current_dataset = None
	97	self.current_data1d = None
	98	self.data = []
	99	self.process = Process()
	100	self.transspectrum = TransmissionSpectrum()
	101	self.aperture = Aperture()
	102	self.collimation = Collimation()
	103	self.detector = Detector()
	104	self.names = []
	105	self.cansas_defaults = {}
	106	self.output = []
	107	self.ns_list = None
[d26dea0]	108	self.logging = []
	109	self.encoding = None
	110
[250fec92]	111	def read(self, xml_file, schema_path="", invalid=True):
	112	"""
	113	Validate and read in an xml_file file in the canSAS format.
	114
	115	:param xml_file: A canSAS file path in proper XML format
	116	:param schema_path: A file path to an XML schema to validate the xml_file against
	117	"""
	118	# For every file loaded, reset everything to a base state
	119	self.reset_state()
	120	self.invalid = invalid
	121	# Check that the file exists
	122	if os.path.isfile(xml_file):
	123	basename, extension = os.path.splitext(os.path.basename(xml_file))
	124	# If the file type is not allowed, return nothing
	125	if extension in self.ext or self.allow_all:
	126	# Get the file location of
	127	self.load_file_and_schema(xml_file, schema_path)
	128	self.add_data_set()
	129	# Try to load the file, but raise an error if unable to.
	130	# Check the file matches the XML schema
	131	try:
	132	self.is_cansas(extension)
	133	self.invalid = False
	134	# Get each SASentry from XML file and add it to a list.
	135	entry_list = self.xmlroot.xpath(
	136	'/ns:SASroot/ns:SASentry',
	137	namespaces={'ns': self.cansas_defaults.get("ns")})
	138	self.names.append("SASentry")
	139
	140	# Get all preprocessing events and encoding
	141	self.set_processing_instructions()
	142
	143	# Parse each <SASentry> item
	144	for entry in entry_list:
	145	# Create a new DataInfo object for every <SASentry>
	146
	147	# Set the file name and then parse the entry.
	148	self.current_datainfo.filename = basename + extension
	149	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
	150	self.current_datainfo.meta_data[PREPROCESS] = \
	151	self.processing_instructions
	152
	153	# Parse the XML SASentry
	154	self._parse_entry(entry)
	155	# Combine datasets with datainfo
	156	self.add_data_set()
	157	except RuntimeError:
	158	# If the file does not match the schema, raise this error
	159	invalid_xml = self.find_invalid_xml()
	160	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
	161	self.errors.add(invalid_xml)
	162	# Try again with an invalid CanSAS schema, that requires only a data set in each
	163	base_name = xml_reader.__file__
	164	base_name = base_name.replace("\\", "/")
	165	base = base_name.split("/sas/")[0]
	166	if self.cansas_version == "1.1":
	167	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	168	else:
	169	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	170	self.set_schema(invalid_schema)
	171	try:
	172	if self.invalid:
	173	if self.is_cansas():
	174	self.output = self.read(xml_file, invalid_schema, False)
	175	else:
	176	raise RuntimeError
	177	else:
	178	raise RuntimeError
	179	except RuntimeError:
	180	x = np.zeros(1)
	181	y = np.zeros(1)
	182	self.current_data1d = Data1D(x,y)
	183	self.current_data1d.errors = self.errors
	184	return [self.current_data1d]
	185	else:
	186	self.output.append("Not a valid file path.")
	187	# Return a list of parsed entries that dataloader can manage
	188	return self.output
	189
[654e8e0]	190	def _parse_entry(self, dom, recurse=False):
[250fec92]	191	"""
	192	Parse a SASEntry - new recursive method for parsing the dom of
	193	the CanSAS data format. This will allow multiple data files
	194	and extra nodes to be read in simultaneously.
	195
	196	:param dom: dom object with a namespace base of names
	197	"""
	198
[654e8e0]	199	if not self._is_call_local() and not recurse:
[1686a333]	200	self.reset_state()
	201	self.add_data_set()
	202	self.names.append("SASentry")
	203	self.parent_class = "SASentry"
[250fec92]	204	self._check_for_empty_data()
	205	self.base_ns = "{0}{1}{2}".format("{", \
	206	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
	207
	208	# Go through each child in the parent element
	209	for node in dom:
[5f26aa4]	210	attr = node.attrib
	211	name = attr.get("name", "")
	212	type = attr.get("type", "")
[250fec92]	213	# Get the element name and set the current names level
	214	tagname = node.tag.replace(self.base_ns, "")
	215	tagname_original = tagname
	216	# Skip this iteration when loading in save state information
	217	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	218	continue
	219
	220	# Get where to store content
	221	self.names.append(tagname_original)
	222	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	223	# If the element is a child element, recurse
	224	if len(node.getchildren()) > 0:
	225	self.parent_class = tagname_original
	226	if tagname == 'SASdata':
[af08e55]	227	self._initialize_new_data_set(node)
	228	if isinstance(self.current_dataset, plottable_2D):
	229	x_bins = attr.get("x_bins", "")
	230	y_bins = attr.get("y_bins", "")
	231	if x_bins is not "" and y_bins is not "":
	232	self.current_dataset.shape = (x_bins, y_bins)
	233	else:
	234	self.current_dataset.shape = ()
	235	# Recursion step to access data within the group
[654e8e0]	236	self._parse_entry(node, True)
[5f26aa4]	237	if tagname == "SASsample":
	238	self.current_datainfo.sample.name = name
	239	elif tagname == "beam_size":
	240	self.current_datainfo.source.beam_size_name = name
	241	elif tagname == "SAScollimation":
	242	self.collimation.name = name
	243	elif tagname == "aperture":
	244	self.aperture.name = name
	245	self.aperture.type = type
[250fec92]	246	self.add_intermediate()
	247	else:
[1905128]	248	if isinstance(self.current_dataset, plottable_2D):
	249	data_point = node.text
	250	unit = attr.get('unit', '')
	251	else:
	252	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	253
[af08e55]	254	# If this is a dataset, store the data appropriately
[250fec92]	255	if tagname == 'Run':
[5f26aa4]	256	self.current_datainfo.run_name[data_point] = name
[250fec92]	257	self.current_datainfo.run.append(data_point)
	258	elif tagname == 'Title':
	259	self.current_datainfo.title = data_point
	260	elif tagname == 'SASnote':
	261	self.current_datainfo.notes.append(data_point)
	262
[af08e55]	263	# I and Q - 1D data
	264	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[c221349]	265	unit_list = unit.split("\|")
[ad4632c]	266	if len(unit_list) > 1:
[c221349]	267	self.current_dataset.yaxis(unit_list[0].strip(),
	268	unit_list[1].strip())
[ad4632c]	269	else:
	270	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	271	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	272	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	273	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	274	elif tagname == 'Q':
[c221349]	275	unit_list = unit.split("\|")
[ad4632c]	276	if len(unit_list) > 1:
[c221349]	277	self.current_dataset.xaxis(unit_list[0].strip(),
	278	unit_list[1].strip())
[ad4632c]	279	else:
	280	self.current_dataset.xaxis("Q", unit)
[250fec92]	281	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	282	elif tagname == 'Qdev':
	283	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	284	elif tagname == 'dQw':
	285	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	286	elif tagname == 'dQl':
	287	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	288	elif tagname == 'Qmean':
	289	pass
	290	elif tagname == 'Shadowfactor':
	291	pass
[ad4632c]	292	elif tagname == 'Sesans':
	293	self.current_datainfo.isSesans = bool(data_point)
[63d773c]	294	elif tagname == 'yacceptance':
	295	self.current_datainfo.sample.yacceptance = (data_point, unit)
[ad4632c]	296	elif tagname == 'zacceptance':
	297	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	298
[af08e55]	299	# I and Qx, Qy - 2D data
	300	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	301	self.current_dataset.yaxis("Intensity", unit)
[1905128]	302	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	303	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	304	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	305	elif tagname == 'Qx':
	306	self.current_dataset.xaxis("Qx", unit)
[1905128]	307	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	308	elif tagname == 'Qy':
	309	self.current_dataset.yaxis("Qy", unit)
[1905128]	310	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	311	elif tagname == 'Qxdev':
	312	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	313	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	314	elif tagname == 'Qydev':
	315	self.current_dataset.yaxis("Qydev", unit)
[1905128]	316	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	317	elif tagname == 'Mask':
[bcabf4e]	318	inter = [item == "1" for item in data_point.split(",")]
[1905128]	319	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	320
	321	# Sample Information
[250fec92]	322	elif tagname == 'ID' and self.parent_class == 'SASsample':
	323	self.current_datainfo.sample.ID = data_point
	324	elif tagname == 'Title' and self.parent_class == 'SASsample':
	325	self.current_datainfo.sample.name = data_point
	326	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	327	self.current_datainfo.sample.thickness = data_point
	328	self.current_datainfo.sample.thickness_unit = unit
	329	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	330	self.current_datainfo.sample.transmission = data_point
	331	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	332	self.current_datainfo.sample.temperature = data_point
	333	self.current_datainfo.sample.temperature_unit = unit
	334	elif tagname == 'details' and self.parent_class == 'SASsample':
	335	self.current_datainfo.sample.details.append(data_point)
	336	elif tagname == 'x' and self.parent_class == 'position':
	337	self.current_datainfo.sample.position.x = data_point
	338	self.current_datainfo.sample.position_unit = unit
	339	elif tagname == 'y' and self.parent_class == 'position':
	340	self.current_datainfo.sample.position.y = data_point
	341	self.current_datainfo.sample.position_unit = unit
	342	elif tagname == 'z' and self.parent_class == 'position':
	343	self.current_datainfo.sample.position.z = data_point
	344	self.current_datainfo.sample.position_unit = unit
	345	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	346	self.current_datainfo.sample.orientation.x = data_point
	347	self.current_datainfo.sample.orientation_unit = unit
	348	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	349	self.current_datainfo.sample.orientation.y = data_point
	350	self.current_datainfo.sample.orientation_unit = unit
	351	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	352	self.current_datainfo.sample.orientation.z = data_point
	353	self.current_datainfo.sample.orientation_unit = unit
	354
[af08e55]	355	# Instrumental Information
[250fec92]	356	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	357	self.current_datainfo.instrument = data_point
[af08e55]	358	# Detector Information
[250fec92]	359	elif tagname == 'name' and self.parent_class == 'SASdetector':
	360	self.detector.name = data_point
	361	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	362	self.detector.distance = data_point
	363	self.detector.distance_unit = unit
	364	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	365	self.detector.slit_length = data_point
	366	self.detector.slit_length_unit = unit
	367	elif tagname == 'x' and self.parent_class == 'offset':
	368	self.detector.offset.x = data_point
	369	self.detector.offset_unit = unit
	370	elif tagname == 'y' and self.parent_class == 'offset':
	371	self.detector.offset.y = data_point
	372	self.detector.offset_unit = unit
	373	elif tagname == 'z' and self.parent_class == 'offset':
	374	self.detector.offset.z = data_point
	375	self.detector.offset_unit = unit
	376	elif tagname == 'x' and self.parent_class == 'beam_center':
	377	self.detector.beam_center.x = data_point
	378	self.detector.beam_center_unit = unit
	379	elif tagname == 'y' and self.parent_class == 'beam_center':
	380	self.detector.beam_center.y = data_point
	381	self.detector.beam_center_unit = unit
	382	elif tagname == 'z' and self.parent_class == 'beam_center':
	383	self.detector.beam_center.z = data_point
	384	self.detector.beam_center_unit = unit
	385	elif tagname == 'x' and self.parent_class == 'pixel_size':
	386	self.detector.pixel_size.x = data_point
	387	self.detector.pixel_size_unit = unit
	388	elif tagname == 'y' and self.parent_class == 'pixel_size':
	389	self.detector.pixel_size.y = data_point
	390	self.detector.pixel_size_unit = unit
	391	elif tagname == 'z' and self.parent_class == 'pixel_size':
	392	self.detector.pixel_size.z = data_point
	393	self.detector.pixel_size_unit = unit
	394	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	395	self.detector.orientation.x = data_point
	396	self.detector.orientation_unit = unit
	397	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	398	self.detector.orientation.y = data_point
	399	self.detector.orientation_unit = unit
	400	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	401	self.detector.orientation.z = data_point
	402	self.detector.orientation_unit = unit
[af08e55]	403	# Collimation and Aperture
[250fec92]	404	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	405	self.collimation.length = data_point
	406	self.collimation.length_unit = unit
	407	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	408	self.collimation.name = data_point
	409	elif tagname == 'distance' and self.parent_class == 'aperture':
	410	self.aperture.distance = data_point
	411	self.aperture.distance_unit = unit
	412	elif tagname == 'x' and self.parent_class == 'size':
	413	self.aperture.size.x = data_point
	414	self.collimation.size_unit = unit
	415	elif tagname == 'y' and self.parent_class == 'size':
	416	self.aperture.size.y = data_point
	417	self.collimation.size_unit = unit
	418	elif tagname == 'z' and self.parent_class == 'size':
	419	self.aperture.size.z = data_point
	420	self.collimation.size_unit = unit
	421
[af08e55]	422	# Process Information
[250fec92]	423	elif tagname == 'name' and self.parent_class == 'SASprocess':
	424	self.process.name = data_point
	425	elif tagname == 'description' and self.parent_class == 'SASprocess':
	426	self.process.description = data_point
	427	elif tagname == 'date' and self.parent_class == 'SASprocess':
	428	try:
	429	self.process.date = datetime.datetime.fromtimestamp(data_point)
	430	except:
	431	self.process.date = data_point
	432	elif tagname == 'SASprocessnote':
	433	self.process.notes.append(data_point)
	434	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	435	unit = attr.get("unit", "")
	436	dic = {}
	437	dic["name"] = name
	438	dic["value"] = data_point
	439	dic["unit"] = unit
	440	self.process.term.append(dic)
[250fec92]	441
[af08e55]	442	# Transmission Spectrum
[250fec92]	443	elif tagname == 'T' and self.parent_class == 'Tdata':
	444	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	445	self.transspectrum.transmission_unit = unit
	446	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	447	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	448	self.transspectrum.transmission_deviation_unit = unit
	449	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	450	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	451	self.transspectrum.wavelength_unit = unit
	452
[af08e55]	453	# Source Information
[250fec92]	454	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	455	self.current_datainfo.source.wavelength = data_point
	456	self.current_datainfo.source.wavelength_unit = unit
	457	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	458	self.current_datainfo.source.wavelength_min = data_point
	459	self.current_datainfo.source.wavelength_min_unit = unit
	460	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	461	self.current_datainfo.source.wavelength_max = data_point
	462	self.current_datainfo.source.wavelength_max_unit = unit
	463	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	464	self.current_datainfo.source.wavelength_spread = data_point
	465	self.current_datainfo.source.wavelength_spread_unit = unit
	466	elif tagname == 'x' and self.parent_class == 'beam_size':
	467	self.current_datainfo.source.beam_size.x = data_point
	468	self.current_datainfo.source.beam_size_unit = unit
	469	elif tagname == 'y' and self.parent_class == 'beam_size':
	470	self.current_datainfo.source.beam_size.y = data_point
	471	self.current_datainfo.source.beam_size_unit = unit
	472	elif tagname == 'z' and self.parent_class == 'pixel_size':
	473	self.current_datainfo.source.data_point.z = data_point
	474	self.current_datainfo.source.beam_size_unit = unit
	475	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	476	self.current_datainfo.source.radiation = data_point
	477	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	478	self.current_datainfo.source.beam_shape = data_point
	479
[af08e55]	480	# Everything else goes in meta_data
[250fec92]	481	else:
	482	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	483	self.current_datainfo.meta_data[new_key] = data_point
	484
	485	self.names.remove(tagname_original)
	486	length = 0
	487	if len(self.names) > 1:
	488	length = len(self.names) - 1
	489	self.parent_class = self.names[length]
[654e8e0]	490	if not self._is_call_local() and not recurse:
	491	self.frm = ""
[1686a333]	492	self.add_data_set()
	493	empty = None
	494	return self.output[0], empty
[250fec92]	495
	496
[654e8e0]	497	def _is_call_local(self):
[1686a333]	498	"""
	499
	500	"""
[654e8e0]	501	if self.frm == "":
	502	inter = inspect.stack()
	503	self.frm = inter[2]
	504	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	505	mod_name = mod_name.replace(".py", "")
	506	mod = mod_name.split("sas/")
	507	mod_name = mod[1]
	508	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	509	return False
	510	return True
	511
[d26dea0]	512	def is_cansas(self, ext="xml"):
	513	"""
	514	Checks to see if the xml file is a CanSAS file
	515
	516	:param ext: The file extension of the data file
	517	"""
	518	if self.validate_xml():
	519	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	520	value = self.xmlroot.get(name)
	521	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	522	value.rsplit(" ")[0]:
	523	return True
	524	if ext == "svs":
	525	return True
[250fec92]	526	raise RuntimeError
[d26dea0]	527
[83b6408]	528	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	529	"""
[250fec92]	530	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	531
	532	:param xml_file: The xml file path sent to Reader.read
[250fec92]	533	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	534	"""
	535	base_name = xml_reader.__file__
	536	base_name = base_name.replace("\\", "/")
	537	base = base_name.split("/sas/")[0]
	538
	539	# Load in xml file and get the cansas version from the header
	540	self.set_xml_file(xml_file)
	541	self.cansas_version = self.xmlroot.get("version", "1.0")
	542
	543	# Generic values for the cansas file based on the version
[250fec92]	544	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	545	if schema_path == "":
[250fec92]	546	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	547	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	548
	549	# Link a schema to the XML file.
	550	self.set_schema(schema_path)
	551
[250fec92]	552	def add_data_set(self):
[d26dea0]	553	"""
[250fec92]	554	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	555	private method to generate a new data set.
[d26dea0]	556
[250fec92]	557	:param key: NeXus group name for current tree level
[d26dea0]	558	"""
	559
[250fec92]	560	if self.current_datainfo and self.current_dataset:
	561	self._final_cleanup()
	562	self.data = []
	563	self.current_datainfo = DataInfo()
[d26dea0]	564
[af08e55]	565	def _initialize_new_data_set(self, node=None):
[250fec92]	566	"""
	567	A private class method to generate a new 1D data object.
	568	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	569
[af08e55]	570	:param node: XML node to determine if 1D or 2D data
[250fec92]	571	"""
	572	x = np.array(0)
	573	y = np.array(0)
[af08e55]	574	for child in node:
	575	if child.tag.replace(self.base_ns, "") == "Idata":
	576	for i_child in child:
	577	if i_child.tag.replace(self.base_ns, "") == "Qx":
	578	self.current_dataset = plottable_2D()
	579	return
[250fec92]	580	self.current_dataset = plottable_1D(x, y)
[d26dea0]	581
[250fec92]	582	def add_intermediate(self):
	583	"""
	584	This method stores any intermediate objects within the final data set after fully reading the set.
	585
	586	:param parent: The NXclass name for the h5py Group object that just finished being processed
	587	"""
	588
	589	if self.parent_class == 'SASprocess':
	590	self.current_datainfo.process.append(self.process)
	591	self.process = Process()
	592	elif self.parent_class == 'SASdetector':
	593	self.current_datainfo.detector.append(self.detector)
	594	self.detector = Detector()
	595	elif self.parent_class == 'SAStransmission_spectrum':
	596	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	597	self.transspectrum = TransmissionSpectrum()
	598	elif self.parent_class == 'SAScollimation':
	599	self.current_datainfo.collimation.append(self.collimation)
	600	self.collimation = Collimation()
[5f26aa4]	601	elif self.parent_class == 'aperture':
[250fec92]	602	self.collimation.aperture.append(self.aperture)
	603	self.aperture = Aperture()
	604	elif self.parent_class == 'SASdata':
	605	self._check_for_empty_resolution()
	606	self.data.append(self.current_dataset)
	607
	608	def _final_cleanup(self):
[d26dea0]	609	"""
	610	Final cleanup of the Data1D object to be sure it has all the
	611	appropriate information needed for perspectives
	612	"""
[250fec92]	613
[af08e55]	614	# Append errors to dataset and reset class errors
[250fec92]	615	self.current_datainfo.errors = set()
[d26dea0]	616	for error in self.errors:
[250fec92]	617	self.current_datainfo.errors.add(error)
[d26dea0]	618	self.errors.clear()
[250fec92]	619
[af08e55]	620	# Combine all plottables with datainfo and append each to output
	621	# Type cast data arrays to float64 and find min/max as appropriate
[250fec92]	622	for dataset in self.data:
[af08e55]	623	if isinstance(dataset, plottable_1D):
	624	if dataset.x is not None:
	625	dataset.x = np.delete(dataset.x, [0])
	626	dataset.x = dataset.x.astype(np.float64)
	627	dataset.xmin = np.min(dataset.x)
	628	dataset.xmax = np.max(dataset.x)
	629	if dataset.y is not None:
	630	dataset.y = np.delete(dataset.y, [0])
	631	dataset.y = dataset.y.astype(np.float64)
	632	dataset.ymin = np.min(dataset.y)
	633	dataset.ymax = np.max(dataset.y)
	634	if dataset.dx is not None:
	635	dataset.dx = np.delete(dataset.dx, [0])
	636	dataset.dx = dataset.dx.astype(np.float64)
	637	if dataset.dxl is not None:
	638	dataset.dxl = np.delete(dataset.dxl, [0])
	639	dataset.dxl = dataset.dxl.astype(np.float64)
	640	if dataset.dxw is not None:
	641	dataset.dxw = np.delete(dataset.dxw, [0])
	642	dataset.dxw = dataset.dxw.astype(np.float64)
	643	if dataset.dy is not None:
	644	dataset.dy = np.delete(dataset.dy, [0])
	645	dataset.dy = dataset.dy.astype(np.float64)
	646	np.trim_zeros(dataset.x)
	647	np.trim_zeros(dataset.y)
	648	np.trim_zeros(dataset.dy)
	649	elif isinstance(dataset, plottable_2D):
	650	dataset.data = dataset.data.astype(np.float64)
	651	dataset.qx_data = dataset.qx_data.astype(np.float64)
	652	dataset.xmin = np.min(dataset.qx_data)
	653	dataset.xmax = np.max(dataset.qx_data)
	654	dataset.qy_data = dataset.qy_data.astype(np.float64)
	655	dataset.ymin = np.min(dataset.qy_data)
	656	dataset.ymax = np.max(dataset.qy_data)
	657	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
	658	+ dataset.qy_data * dataset.qy_data)
	659	if dataset.err_data is not None:
	660	dataset.err_data = dataset.err_data.astype(np.float64)
	661	if dataset.dqx_data is not None:
	662	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
	663	if dataset.dqy_data is not None:
	664	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
	665	if dataset.mask is not None:
	666	dataset.mask = dataset.mask.astype(dtype=bool)
	667
	668	if len(dataset.shape) == 2:
	669	n_rows, n_cols = dataset.shape
	670	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
	671	dataset.x_bins = dataset.qx_data[:int(n_cols)]
	672	dataset.data = dataset.data.flatten()
	673	else:
	674	dataset.y_bins = []
	675	dataset.x_bins = []
	676	dataset.data = dataset.data.flatten()
	677
[250fec92]	678	final_dataset = combine_data(dataset, self.current_datainfo)
	679	self.output.append(final_dataset)
[d26dea0]	680
	681	def _create_unique_key(self, dictionary, name, numb=0):
	682	"""
	683	Create a unique key value for any dictionary to prevent overwriting
[250fec92]	684	Recurse until a unique key value is found.
[d26dea0]	685
	686	:param dictionary: A dictionary with any number of entries
	687	:param name: The index of the item to be added to dictionary
	688	:param numb: The number to be appended to the name, starts at 0
	689	"""
	690	if dictionary.get(name) is not None:
	691	numb += 1
	692	name = name.split("_")[0]
	693	name += "_{0}".format(numb)
	694	name = self._create_unique_key(dictionary, name, numb)
	695	return name
	696
[250fec92]	697	def _get_node_value(self, node, tagname):
	698	"""
	699	Get the value of a node and any applicable units
	700
	701	:param node: The XML node to get the value of
	702	:param tagname: The tagname of the node
	703	"""
	704	#Get the text from the node and convert all whitespace to spaces
	705	units = ''
	706	node_value = node.text
	707	if node_value is not None:
	708	node_value = ' '.join(node_value.split())
	709	else:
	710	node_value = ""
	711
	712	# If the value is a float, compile with units.
	713	if self.ns_list.ns_datatype == "float":
	714	# If an empty value is given, set as zero.
	715	if node_value is None or node_value.isspace() \
	716	or node_value.lower() == "nan":
	717	node_value = "0.0"
	718	#Convert the value to the base units
	719	node_value, units = self._unit_conversion(node, tagname, node_value)
	720
	721	# If the value is a timestamp, convert to a datetime object
	722	elif self.ns_list.ns_datatype == "timestamp":
	723	if node_value is None or node_value.isspace():
	724	pass
	725	else:
	726	try:
	727	node_value = \
	728	datetime.datetime.fromtimestamp(node_value)
	729	except ValueError:
	730	node_value = None
	731	return node_value, units
	732
	733	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	734	"""
	735	A unit converter method used to convert the data included in the file
	736	to the default units listed in data_info
	737
[250fec92]	738	:param node: XML node
	739	:param tagname: name of the node
[d26dea0]	740	:param node_value: The value of the current dom node
	741	"""
	742	attr = node.attrib
	743	value_unit = ''
	744	err_msg = None
[682c432]	745	default_unit = None
[5f26aa4]	746	if not isinstance(node_value, float):
	747	node_value = float(node_value)
	748	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	749	try:
	750	local_unit = attr['unit']
[250fec92]	751	unitname = self.ns_list.current_level.get("unit", "")
	752	if "SASdetector" in self.names:
	753	save_in = "detector"
	754	elif "aperture" in self.names:
	755	save_in = "aperture"
	756	elif "SAScollimation" in self.names:
	757	save_in = "collimation"
	758	elif "SAStransmission_spectrum" in self.names:
	759	save_in = "transspectrum"
	760	elif "SASdata" in self.names:
	761	x = np.zeros(1)
	762	y = np.zeros(1)
	763	self.current_data1d = Data1D(x, y)
	764	save_in = "current_data1d"
	765	elif "SASsource" in self.names:
	766	save_in = "current_datainfo.source"
	767	elif "SASsample" in self.names:
	768	save_in = "current_datainfo.sample"
	769	elif "SASprocess" in self.names:
	770	save_in = "process"
	771	else:
	772	save_in = "current_datainfo"
	773	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	774	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	775	and local_unit.lower() != "none":
	776	if HAS_CONVERTER == True:
[af08e55]	777	# Check local units - bad units raise KeyError
[d26dea0]	778	data_conv_q = Converter(local_unit)
	779	value_unit = default_unit
[682c432]	780	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	781	else:
	782	value_unit = local_unit
	783	err_msg = "Unit converter is not available.\n"
	784	else:
	785	value_unit = local_unit
	786	except KeyError:
	787	err_msg = "CanSAS reader: unexpected "
	788	err_msg += "\"{0}\" unit [{1}]; "
	789	err_msg = err_msg.format(tagname, local_unit)
[682c432]	790	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	791	value_unit = local_unit
	792	except:
	793	err_msg = "CanSAS reader: unknown error converting "
	794	err_msg += "\"{0}\" unit [{1}]"
	795	err_msg = err_msg.format(tagname, local_unit)
	796	value_unit = local_unit
	797	elif 'unit' in attr:
	798	value_unit = attr['unit']
	799	if err_msg:
	800	self.errors.add(err_msg)
	801	return node_value, value_unit
	802
[250fec92]	803	def _check_for_empty_data(self):
[d26dea0]	804	"""
	805	Creates an empty data set if no data is passed to the reader
	806
	807	:param data1d: presumably a Data1D object
	808	"""
[235f514]	809	if self.current_dataset is None:
[250fec92]	810	x_vals = np.empty(0)
	811	y_vals = np.empty(0)
	812	dx_vals = np.empty(0)
	813	dy_vals = np.empty(0)
	814	dxl = np.empty(0)
	815	dxw = np.empty(0)
	816	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	817	self.current_dataset.dxl = dxl
	818	self.current_dataset.dxw = dxw
	819
	820	def _check_for_empty_resolution(self):
[d26dea0]	821	"""
	822	A method to check all resolution data sets are the same size as I and Q
	823	"""
[af08e55]	824	if isinstance(self.current_dataset, plottable_1D):
	825	dql_exists = False
	826	dqw_exists = False
	827	dq_exists = False
	828	di_exists = False
	829	if self.current_dataset.dxl is not None:
	830	dql_exists = True
	831	if self.current_dataset.dxw is not None:
	832	dqw_exists = True
	833	if self.current_dataset.dx is not None:
	834	dq_exists = True
	835	if self.current_dataset.dy is not None:
	836	di_exists = True
	837	if dqw_exists and not dql_exists:
	838	array_size = self.current_dataset.dxw.size - 1
	839	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
	840	np.zeros([array_size]))
	841	elif dql_exists and not dqw_exists:
	842	array_size = self.current_dataset.dxl.size - 1
	843	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
	844	np.zeros([array_size]))
	845	elif not dql_exists and not dqw_exists and not dq_exists:
	846	array_size = self.current_dataset.x.size - 1
	847	self.current_dataset.dx = np.append(self.current_dataset.dx,
	848	np.zeros([array_size]))
	849	if not di_exists:
	850	array_size = self.current_dataset.y.size - 1
	851	self.current_dataset.dy = np.append(self.current_dataset.dy,
	852	np.zeros([array_size]))
	853	elif isinstance(self.current_dataset, plottable_2D):
	854	dqx_exists = False
	855	dqy_exists = False
	856	di_exists = False
	857	mask_exists = False
	858	if self.current_dataset.dqx_data is not None:
	859	dqx_exists = True
	860	if self.current_dataset.dqy_data is not None:
	861	dqy_exists = True
	862	if self.current_dataset.err_data is not None:
	863	di_exists = True
	864	if self.current_dataset.mask is not None:
	865	mask_exists = True
	866	if not dqy_exists:
	867	array_size = self.current_dataset.qy_data.size - 1
	868	self.current_dataset.dqy_data = np.append(
	869	self.current_dataset.dqy_data, np.zeros([array_size]))
	870	if not dqx_exists:
	871	array_size = self.current_dataset.qx_data.size - 1
	872	self.current_dataset.dqx_data = np.append(
	873	self.current_dataset.dqx_data, np.zeros([array_size]))
	874	if not di_exists:
	875	array_size = self.current_dataset.data.size - 1
	876	self.current_dataset.err_data = np.append(
	877	self.current_dataset.err_data, np.zeros([array_size]))
	878	if not mask_exists:
	879	array_size = self.current_dataset.data.size - 1
	880	self.current_dataset.mask = np.append(
	881	self.current_dataset.mask,
	882	np.ones([array_size] ,dtype=bool))
[250fec92]	883
	884	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	885
[250fec92]	886	def write(self, filename, datainfo):
[d26dea0]	887	"""
[250fec92]	888	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	889
[250fec92]	890	:param filename: name of the file to write
	891	:param datainfo: Data1D object
	892	"""
	893	# Create XML document
	894	doc, _ = self._to_xml_doc(datainfo)
	895	# Write the file
	896	file_ref = open(filename, 'w')
[235f514]	897	if self.encoding is None:
[250fec92]	898	self.encoding = "UTF-8"
	899	doc.write(file_ref, encoding=self.encoding,
	900	pretty_print=True, xml_declaration=True)
	901	file_ref.close()
[d26dea0]	902
[250fec92]	903	def _to_xml_doc(self, datainfo):
[d26dea0]	904	"""
[250fec92]	905	Create an XML document to contain the content of a Data1D
[d26dea0]	906
[250fec92]	907	:param datainfo: Data1D object
[d26dea0]	908	"""
[af08e55]	909	is_2d = False
[83c09af]	910	if issubclass(datainfo.__class__, Data2D):
	911	is_2d = True
[d26dea0]	912
[250fec92]	913	# Get PIs and create root element
	914	pi_string = self._get_pi_string()
	915	# Define namespaces and create SASroot object
	916	main_node = self._create_main_node()
	917	# Create ElementTree, append SASroot and apply processing instructions
	918	base_string = pi_string + self.to_string(main_node)
	919	base_element = self.create_element_from_string(base_string)
	920	doc = self.create_tree(base_element)
	921	# Create SASentry Element
	922	entry_node = self.create_element("SASentry")
	923	root = doc.getroot()
	924	root.append(entry_node)
[d26dea0]	925
[250fec92]	926	# Add Title to SASentry
	927	self.write_node(entry_node, "Title", datainfo.title)
	928	# Add Run to SASentry
	929	self._write_run_names(datainfo, entry_node)
	930	# Add Data info to SASEntry
[83c09af]	931	if is_2d:
	932	self._write_data_2d(datainfo, entry_node)
	933	else:
	934	self._write_data(datainfo, entry_node)
[250fec92]	935	# Transmission Spectrum Info
[8434365]	936	# TODO: fix the writer to linearize all data, including T_spectrum
	937	# self._write_trans_spectrum(datainfo, entry_node)
[250fec92]	938	# Sample info
	939	self._write_sample_info(datainfo, entry_node)
	940	# Instrument info
	941	instr = self._write_instrument(datainfo, entry_node)
	942	# Source
	943	self._write_source(datainfo, instr)
	944	# Collimation
	945	self._write_collimation(datainfo, instr)
	946	# Detectors
	947	self._write_detectors(datainfo, instr)
	948	# Processes info
	949	self._write_process_notes(datainfo, entry_node)
	950	# Note info
	951	self._write_notes(datainfo, entry_node)
	952	# Return the document, and the SASentry node associated with
	953	# the data we just wrote
	954	# If the calling function was not the cansas reader, return a minidom
	955	# object rather than an lxml object.
[654e8e0]	956	self.frm = inspect.stack()[1]
	957	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	958	return doc, entry_node
[d26dea0]	959
[250fec92]	960	def write_node(self, parent, name, value, attr=None):
	961	"""
	962	:param doc: document DOM
	963	:param parent: parent node
	964	:param name: tag of the element
	965	:param value: value of the child text node
	966	:param attr: attribute dictionary
[d26dea0]	967
[250fec92]	968	:return: True if something was appended, otherwise False
	969	"""
	970	if value is not None:
	971	parent = self.ebuilder(parent, name, value, attr)
	972	return True
	973	return False
[d26dea0]	974
	975	def _get_pi_string(self):
	976	"""
	977	Creates the processing instructions header for writing to file
	978	"""
	979	pis = self.return_processing_instructions()
	980	if len(pis) > 0:
	981	pi_tree = self.create_tree(pis[0])
	982	i = 1
	983	for i in range(1, len(pis) - 1):
	984	pi_tree = self.append(pis[i], pi_tree)
	985	pi_string = self.to_string(pi_tree)
	986	else:
	987	pi_string = ""
	988	return pi_string
	989
	990	def _create_main_node(self):
	991	"""
	992	Creates the primary xml header used when writing to file
	993	"""
	994	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	995	version = self.cansas_version
	996	n_s = CANSAS_NS.get(version).get("ns")
	997	if version == "1.1":
	998	url = "http://www.cansas.org/formats/1.1/"
	999	else:
	1000	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	1001	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	1002	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	1003	"version" : version}
	1004	nsmap = {'xsi' : xsi, None: n_s}
	1005
	1006	main_node = self.create_element("{" + n_s + "}SASroot",
	1007	attrib=attrib, nsmap=nsmap)
	1008	return main_node
	1009
	1010	def _write_run_names(self, datainfo, entry_node):
	1011	"""
	1012	Writes the run names to the XML file
	1013
	1014	:param datainfo: The Data1D object the information is coming from
	1015	:param entry_node: lxml node ElementTree object to be appended to
	1016	"""
[235f514]	1017	if datainfo.run is None or datainfo.run == []:
[d26dea0]	1018	datainfo.run.append(RUN_NAME_DEFAULT)
	1019	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	1020	for item in datainfo.run:
	1021	runname = {}
	1022	if item in datainfo.run_name and \
	1023	len(str(datainfo.run_name[item])) > 1:
	1024	runname = {'name': datainfo.run_name[item]}
	1025	self.write_node(entry_node, "Run", item, runname)
	1026
	1027	def _write_data(self, datainfo, entry_node):
	1028	"""
[83c09af]	1029	Writes 1D I and Q data to the XML file
[d26dea0]	1030
	1031	:param datainfo: The Data1D object the information is coming from
	1032	:param entry_node: lxml node ElementTree object to be appended to
	1033	"""
	1034	node = self.create_element("SASdata")
	1035	self.append(node, entry_node)
	1036
	1037	for i in range(len(datainfo.x)):
	1038	point = self.create_element("Idata")
	1039	node.append(point)
	1040	self.write_node(point, "Q", datainfo.x[i],
[ad4632c]	1041	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[d26dea0]	1042	if len(datainfo.y) >= i:
	1043	self.write_node(point, "I", datainfo.y[i],
[ad4632c]	1044	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	1045	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	1046	self.write_node(point, "Idev", datainfo.dy[i],
[ad4632c]	1047	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	1048	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	1049	self.write_node(point, "Qdev", datainfo.dx[i],
[ad4632c]	1050	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	1051	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	1052	self.write_node(point, "dQw", datainfo.dxw[i],
[ad4632c]	1053	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	1054	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	1055	self.write_node(point, "dQl", datainfo.dxl[i],
[ad4632c]	1056	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
	1057	if datainfo.isSesans:
	1058	sesans = self.create_element("Sesans")
	1059	sesans.text = str(datainfo.isSesans)
	1060	node.append(sesans)
[63d773c]	1061	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
	1062	{'unit': datainfo.sample.yacceptance[1]})
[ad4632c]	1063	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
	1064	{'unit': datainfo.sample.zacceptance[1]})
	1065
[d26dea0]	1066
[83c09af]	1067	def _write_data_2d(self, datainfo, entry_node):
	1068	"""
	1069	Writes 2D data to the XML file
	1070
	1071	:param datainfo: The Data2D object the information is coming from
	1072	:param entry_node: lxml node ElementTree object to be appended to
	1073	"""
[af08e55]	1074	attr = {}
	1075	if datainfo.data.shape:
[1905128]	1076	attr["x_bins"] = str(len(datainfo.x_bins))
	1077	attr["y_bins"] = str(len(datainfo.y_bins))
	1078	node = self.create_element("SASdata", attr)
[83c09af]	1079	self.append(node, entry_node)
	1080
[1905128]	1081	point = self.create_element("Idata")
	1082	node.append(point)
	1083	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
	1084	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
	1085	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
	1086
	1087	self.write_node(point, "Qx", qx,
	1088	{'unit': datainfo._xunit})
	1089	self.write_node(point, "Qy", qy,
	1090	{'unit': datainfo._yunit})
	1091	self.write_node(point, "I", intensity,
	1092	{'unit': datainfo._zunit})
	1093	if datainfo.err_data is not None:
[5e6df0e]	1094	err = ','.join([str(datainfo.err_data[i]) for i in
	1095	xrange(len(datainfo.err_data))])
[1905128]	1096	self.write_node(point, "Idev", err,
[83c09af]	1097	{'unit': datainfo._zunit})
[1905128]	1098	if datainfo.dqy_data is not None:
[5e6df0e]	1099	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
	1100	xrange(len(datainfo.dqy_data))])
[1905128]	1101	self.write_node(point, "Qydev", dqy,
	1102	{'unit': datainfo._yunit})
	1103	if datainfo.dqx_data is not None:
[5e6df0e]	1104	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
	1105	xrange(len(datainfo.dqx_data))])
[1905128]	1106	self.write_node(point, "Qxdev", dqx,
	1107	{'unit': datainfo._xunit})
	1108	if datainfo.mask is not None:
[5e6df0e]	1109	mask = ','.join(
[bcabf4e]	1110	["1" if datainfo.mask[i] else "0"
	1111	for i in xrange(len(datainfo.mask))])
[1905128]	1112	self.write_node(point, "Mask", mask)
[83c09af]	1113
[d26dea0]	1114	def _write_trans_spectrum(self, datainfo, entry_node):
	1115	"""
	1116	Writes the transmission spectrum data to the XML file
	1117
	1118	:param datainfo: The Data1D object the information is coming from
	1119	:param entry_node: lxml node ElementTree object to be appended to
	1120	"""
	1121	for i in range(len(datainfo.trans_spectrum)):
	1122	spectrum = datainfo.trans_spectrum[i]
	1123	node = self.create_element("SAStransmission_spectrum",
	1124	{"name" : spectrum.name})
	1125	self.append(node, entry_node)
	1126	if isinstance(spectrum.timestamp, datetime.datetime):
	1127	node.setAttribute("timestamp", spectrum.timestamp)
	1128	for i in range(len(spectrum.wavelength)):
	1129	point = self.create_element("Tdata")
	1130	node.append(point)
	1131	self.write_node(point, "Lambda", spectrum.wavelength[i],
	1132	{'unit': spectrum.wavelength_unit})
	1133	self.write_node(point, "T", spectrum.transmission[i],
	1134	{'unit': spectrum.transmission_unit})
[7432acb]	1135	if spectrum.transmission_deviation is not None \
[d26dea0]	1136	and len(spectrum.transmission_deviation) >= i:
	1137	self.write_node(point, "Tdev",
	1138	spectrum.transmission_deviation[i],
	1139	{'unit':
	1140	spectrum.transmission_deviation_unit})
	1141
	1142	def _write_sample_info(self, datainfo, entry_node):
	1143	"""
	1144	Writes the sample information to the XML file
	1145
	1146	:param datainfo: The Data1D object the information is coming from
	1147	:param entry_node: lxml node ElementTree object to be appended to
	1148	"""
	1149	sample = self.create_element("SASsample")
	1150	if datainfo.sample.name is not None:
	1151	self.write_attribute(sample, "name",
	1152	str(datainfo.sample.name))
	1153	self.append(sample, entry_node)
	1154	self.write_node(sample, "ID", str(datainfo.sample.ID))
	1155	self.write_node(sample, "thickness", datainfo.sample.thickness,
	1156	{"unit": datainfo.sample.thickness_unit})
	1157	self.write_node(sample, "transmission", datainfo.sample.transmission)
	1158	self.write_node(sample, "temperature", datainfo.sample.temperature,
	1159	{"unit": datainfo.sample.temperature_unit})
	1160
	1161	pos = self.create_element("position")
	1162	written = self.write_node(pos,
	1163	"x",
	1164	datainfo.sample.position.x,
	1165	{"unit": datainfo.sample.position_unit})
	1166	written = written \| self.write_node( \
	1167	pos, "y", datainfo.sample.position.y,
	1168	{"unit": datainfo.sample.position_unit})
	1169	written = written \| self.write_node( \
	1170	pos, "z", datainfo.sample.position.z,
	1171	{"unit": datainfo.sample.position_unit})
	1172	if written == True:
	1173	self.append(pos, sample)
	1174
	1175	ori = self.create_element("orientation")
	1176	written = self.write_node(ori, "roll",
	1177	datainfo.sample.orientation.x,
	1178	{"unit": datainfo.sample.orientation_unit})
	1179	written = written \| self.write_node( \
	1180	ori, "pitch", datainfo.sample.orientation.y,
	1181	{"unit": datainfo.sample.orientation_unit})
	1182	written = written \| self.write_node( \
	1183	ori, "yaw", datainfo.sample.orientation.z,
	1184	{"unit": datainfo.sample.orientation_unit})
	1185	if written == True:
	1186	self.append(ori, sample)
	1187
	1188	for item in datainfo.sample.details:
	1189	self.write_node(sample, "details", item)
	1190
	1191	def _write_instrument(self, datainfo, entry_node):
	1192	"""
	1193	Writes the instrumental information to the XML file
	1194
	1195	:param datainfo: The Data1D object the information is coming from
	1196	:param entry_node: lxml node ElementTree object to be appended to
	1197	"""
	1198	instr = self.create_element("SASinstrument")
	1199	self.append(instr, entry_node)
	1200	self.write_node(instr, "name", datainfo.instrument)
	1201	return instr
	1202
	1203	def _write_source(self, datainfo, instr):
	1204	"""
	1205	Writes the source information to the XML file
	1206
	1207	:param datainfo: The Data1D object the information is coming from
	1208	:param instr: instrument node to be appended to
	1209	"""
	1210	source = self.create_element("SASsource")
	1211	if datainfo.source.name is not None:
	1212	self.write_attribute(source, "name",
	1213	str(datainfo.source.name))
	1214	self.append(source, instr)
[235f514]	1215	if datainfo.source.radiation is None or datainfo.source.radiation == '':
[d26dea0]	1216	datainfo.source.radiation = "neutron"
	1217	self.write_node(source, "radiation", datainfo.source.radiation)
	1218
	1219	size = self.create_element("beam_size")
	1220	if datainfo.source.beam_size_name is not None:
	1221	self.write_attribute(size, "name",
	1222	str(datainfo.source.beam_size_name))
	1223	written = self.write_node( \
	1224	size, "x", datainfo.source.beam_size.x,
	1225	{"unit": datainfo.source.beam_size_unit})
	1226	written = written \| self.write_node( \
	1227	size, "y", datainfo.source.beam_size.y,
	1228	{"unit": datainfo.source.beam_size_unit})
	1229	written = written \| self.write_node( \
	1230	size, "z", datainfo.source.beam_size.z,
	1231	{"unit": datainfo.source.beam_size_unit})
	1232	if written == True:
	1233	self.append(size, source)
	1234
	1235	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1236	self.write_node(source, "wavelength",
	1237	datainfo.source.wavelength,
	1238	{"unit": datainfo.source.wavelength_unit})
	1239	self.write_node(source, "wavelength_min",
	1240	datainfo.source.wavelength_min,
	1241	{"unit": datainfo.source.wavelength_min_unit})
	1242	self.write_node(source, "wavelength_max",
	1243	datainfo.source.wavelength_max,
	1244	{"unit": datainfo.source.wavelength_max_unit})
	1245	self.write_node(source, "wavelength_spread",
	1246	datainfo.source.wavelength_spread,
	1247	{"unit": datainfo.source.wavelength_spread_unit})
	1248
	1249	def _write_collimation(self, datainfo, instr):
	1250	"""
	1251	Writes the collimation information to the XML file
	1252
	1253	:param datainfo: The Data1D object the information is coming from
	1254	:param instr: lxml node ElementTree object to be appended to
	1255	"""
[235f514]	1256	if datainfo.collimation == [] or datainfo.collimation is None:
[d26dea0]	1257	coll = Collimation()
	1258	datainfo.collimation.append(coll)
	1259	for item in datainfo.collimation:
	1260	coll = self.create_element("SAScollimation")
	1261	if item.name is not None:
	1262	self.write_attribute(coll, "name", str(item.name))
	1263	self.append(coll, instr)
	1264
	1265	self.write_node(coll, "length", item.length,
	1266	{"unit": item.length_unit})
	1267
	1268	for aperture in item.aperture:
	1269	apert = self.create_element("aperture")
	1270	if aperture.name is not None:
	1271	self.write_attribute(apert, "name", str(aperture.name))
	1272	if aperture.type is not None:
	1273	self.write_attribute(apert, "type", str(aperture.type))
	1274	self.append(apert, coll)
	1275
	1276	size = self.create_element("size")
	1277	if aperture.size_name is not None:
	1278	self.write_attribute(size, "name",
	1279	str(aperture.size_name))
	1280	written = self.write_node(size, "x", aperture.size.x,
	1281	{"unit": aperture.size_unit})
	1282	written = written \| self.write_node( \
	1283	size, "y", aperture.size.y,
	1284	{"unit": aperture.size_unit})
	1285	written = written \| self.write_node( \
	1286	size, "z", aperture.size.z,
	1287	{"unit": aperture.size_unit})
	1288	if written == True:
	1289	self.append(size, apert)
	1290
	1291	self.write_node(apert, "distance", aperture.distance,
	1292	{"unit": aperture.distance_unit})
	1293
	1294	def _write_detectors(self, datainfo, instr):
	1295	"""
	1296	Writes the detector information to the XML file
	1297
	1298	:param datainfo: The Data1D object the information is coming from
	1299	:param inst: lxml instrument node to be appended to
	1300	"""
[235f514]	1301	if datainfo.detector is None or datainfo.detector == []:
[d26dea0]	1302	det = Detector()
	1303	det.name = ""
	1304	datainfo.detector.append(det)
	1305
	1306	for item in datainfo.detector:
	1307	det = self.create_element("SASdetector")
	1308	written = self.write_node(det, "name", item.name)
	1309	written = written \| self.write_node(det, "SDD", item.distance,
	1310	{"unit": item.distance_unit})
	1311	if written == True:
	1312	self.append(det, instr)
	1313
	1314	off = self.create_element("offset")
	1315	written = self.write_node(off, "x", item.offset.x,
	1316	{"unit": item.offset_unit})
	1317	written = written \| self.write_node(off, "y", item.offset.y,
	1318	{"unit": item.offset_unit})
	1319	written = written \| self.write_node(off, "z", item.offset.z,
	1320	{"unit": item.offset_unit})
	1321	if written == True:
	1322	self.append(off, det)
	1323
	1324	ori = self.create_element("orientation")
	1325	written = self.write_node(ori, "roll", item.orientation.x,
	1326	{"unit": item.orientation_unit})
	1327	written = written \| self.write_node(ori, "pitch",
	1328	item.orientation.y,
	1329	{"unit": item.orientation_unit})
	1330	written = written \| self.write_node(ori, "yaw",
	1331	item.orientation.z,
	1332	{"unit": item.orientation_unit})
	1333	if written == True:
	1334	self.append(ori, det)
	1335
	1336	center = self.create_element("beam_center")
	1337	written = self.write_node(center, "x", item.beam_center.x,
	1338	{"unit": item.beam_center_unit})
	1339	written = written \| self.write_node(center, "y",
	1340	item.beam_center.y,
	1341	{"unit": item.beam_center_unit})
	1342	written = written \| self.write_node(center, "z",
	1343	item.beam_center.z,
	1344	{"unit": item.beam_center_unit})
	1345	if written == True:
	1346	self.append(center, det)
	1347
	1348	pix = self.create_element("pixel_size")
	1349	written = self.write_node(pix, "x", item.pixel_size.x,
	1350	{"unit": item.pixel_size_unit})
	1351	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1352	{"unit": item.pixel_size_unit})
	1353	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1354	{"unit": item.pixel_size_unit})
	1355	if written == True:
	1356	self.append(pix, det)
[3a9801f]	1357	self.write_node(det, "slit_length", item.slit_length,
	1358	{"unit": item.slit_length_unit})
	1359
[d26dea0]	1360
	1361	def _write_process_notes(self, datainfo, entry_node):
	1362	"""
	1363	Writes the process notes to the XML file
	1364
	1365	:param datainfo: The Data1D object the information is coming from
	1366	:param entry_node: lxml node ElementTree object to be appended to
	1367
	1368	"""
	1369	for item in datainfo.process:
	1370	node = self.create_element("SASprocess")
	1371	self.append(node, entry_node)
	1372	self.write_node(node, "name", item.name)
	1373	self.write_node(node, "date", item.date)
	1374	self.write_node(node, "description", item.description)
	1375	for term in item.term:
[1686a333]	1376	if isinstance(term, list):
	1377	value = term['value']
	1378	del term['value']
[5f26aa4]	1379	elif isinstance(term, dict):
	1380	value = term.get("value")
	1381	del term['value']
[1686a333]	1382	else:
	1383	value = term
[d26dea0]	1384	self.write_node(node, "term", value, term)
	1385	for note in item.notes:
	1386	self.write_node(node, "SASprocessnote", note)
	1387	if len(item.notes) == 0:
	1388	self.write_node(node, "SASprocessnote", "")
	1389
	1390	def _write_notes(self, datainfo, entry_node):
	1391	"""
	1392	Writes the notes to the XML file and creates an empty note if none
	1393	exist
	1394
	1395	:param datainfo: The Data1D object the information is coming from
	1396	:param entry_node: lxml node ElementTree object to be appended to
	1397
	1398	"""
	1399	if len(datainfo.notes) == 0:
	1400	node = self.create_element("SASnote")
	1401	self.append(node, entry_node)
	1402	else:
	1403	for item in datainfo.notes:
	1404	node = self.create_element("SASnote")
	1405	self.write_text(node, item)
	1406	self.append(node, entry_node)
	1407
[654e8e0]	1408	def _check_origin(self, entry_node, doc):
[d26dea0]	1409	"""
	1410	Return the document, and the SASentry node associated with
	1411	the data we just wrote.
	1412	If the calling function was not the cansas reader, return a minidom
	1413	object rather than an lxml object.
	1414
	1415	:param entry_node: lxml node ElementTree object to be appended to
	1416	:param doc: entire xml tree
	1417	"""
[654e8e0]	1418	if not self.frm:
	1419	self.frm = inspect.stack()[1]
	1420	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1421	mod_name = mod_name.replace(".py", "")
	1422	mod = mod_name.split("sas/")
	1423	mod_name = mod[1]
[45d90b9]	1424	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1425	string = self.to_string(doc, pretty_print=False)
	1426	doc = parseString(string)
	1427	node_name = entry_node.tag
	1428	node_list = doc.getElementsByTagName(node_name)
	1429	entry_node = node_list.item(0)
[5ce7f17]	1430	return doc, entry_node
[d26dea0]	1431
	1432	# DO NOT REMOVE - used in saving and loading panel states.
	1433	def _store_float(self, location, node, variable, storage, optional=True):
	1434	"""
	1435	Get the content of a xpath location and store
	1436	the result. Check that the units are compatible
	1437	with the destination. The value is expected to
	1438	be a float.
	1439
	1440	The xpath location might or might not exist.
	1441	If it does not exist, nothing is done
	1442
	1443	:param location: xpath location to fetch
	1444	:param node: node to read the data from
	1445	:param variable: name of the data member to store it in [string]
	1446	:param storage: data object that has the 'variable' data member
	1447	:param optional: if True, no exception will be raised
	1448	if unit conversion can't be done
	1449
	1450	:raise ValueError: raised when the units are not recognized
	1451	"""
	1452	entry = get_content(location, node)
	1453	try:
	1454	value = float(entry.text)
	1455	except:
	1456	value = None
	1457
	1458	if value is not None:
	1459	# If the entry has units, check to see that they are
	1460	# compatible with what we currently have in the data object
	1461	units = entry.get('unit')
	1462	if units is not None:
	1463	toks = variable.split('.')
	1464	local_unit = None
	1465	exec "local_unit = storage.%s_unit" % toks[0]
[7432acb]	1466	if local_unit is not None and units.lower() != local_unit.lower():
[d26dea0]	1467	if HAS_CONVERTER == True:
	1468	try:
	1469	conv = Converter(units)
	1470	exec "storage.%s = %g" % \
	1471	(variable, conv(value, units=local_unit))
	1472	except:
	1473	_, exc_value, _ = sys.exc_info()
	1474	err_mess = "CanSAS reader: could not convert"
	1475	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1476	% (variable, units, local_unit, exc_value)
	1477	self.errors.add(err_mess)
	1478	if optional:
[c155a16]	1479	logger.info(err_mess)
[d26dea0]	1480	else:
	1481	raise ValueError, err_mess
	1482	else:
	1483	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1484	% (variable, units)
	1485	err_mess += " expecting [%s]" % local_unit
	1486	self.errors.add(err_mess)
	1487	if optional:
[c155a16]	1488	logger.info(err_mess)
[d26dea0]	1489	else:
	1490	raise ValueError, err_mess
	1491	else:
	1492	exec "storage.%s = value" % variable
	1493	else:
	1494	exec "storage.%s = value" % variable
	1495
	1496	# DO NOT REMOVE - used in saving and loading panel states.
	1497	def _store_content(self, location, node, variable, storage):
	1498	"""
	1499	Get the content of a xpath location and store
	1500	the result. The value is treated as a string.
	1501
	1502	The xpath location might or might not exist.
	1503	If it does not exist, nothing is done
	1504
	1505	:param location: xpath location to fetch
	1506	:param node: node to read the data from
	1507	:param variable: name of the data member to store it in [string]
	1508	:param storage: data object that has the 'variable' data member
	1509
	1510	:return: return a list of errors
	1511	"""
	1512	entry = get_content(location, node)
	1513	if entry is not None and entry.text is not None:
	1514	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1515
	1516
	1517	# DO NOT REMOVE Called by outside packages:
	1518	# sas.sasgui.perspectives.invariant.invariant_state
	1519	# sas.sasgui.perspectives.fitting.pagestate
	1520	def get_content(location, node):
	1521	"""
	1522	Get the first instance of the content of a xpath location.
	1523
	1524	:param location: xpath location
	1525	:param node: node to start at
	1526
	1527	:return: Element, or None
	1528	"""
	1529	nodes = node.xpath(location,
	1530	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1531	if len(nodes) > 0:
	1532	return nodes[0]
	1533	else:
	1534	return None
	1535
	1536	# DO NOT REMOVE Called by outside packages:
	1537	# sas.sasgui.perspectives.fitting.pagestate
	1538	def write_node(doc, parent, name, value, attr=None):
	1539	"""
	1540	:param doc: document DOM
	1541	:param parent: parent node
	1542	:param name: tag of the element
	1543	:param value: value of the child text node
	1544	:param attr: attribute dictionary
	1545
	1546	:return: True if something was appended, otherwise False
	1547	"""
	1548	if attr is None:
	1549	attr = {}
	1550	if value is not None:
	1551	node = doc.createElement(name)
	1552	node.appendChild(doc.createTextNode(str(value)))
	1553	for item in attr:
	1554	node.setAttribute(item, attr[item])
	1555	parent.appendChild(node)
	1556	return True
	1557	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 251ef684

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