cansas_reader.py @ 2ffe241

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 2ffe241 was b5e9ce26, checked in by GitHub <noreply@…>, 8 years ago
Merge branch 'master' into sesans41
Property mode set to `100644`
File size: 70.3 KB

Rev	Line
[d26dea0]	1	"""
	2	CanSAS data reader - new recursive cansas_version.
	3	"""
	4	############################################################################
	5	#This software was developed by the University of Tennessee as part of the
	6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	7	#project funded by the US National Science Foundation.
	8	#If you use DANSE applications to do scientific research that leads to
	9	#publication, we ask that you acknowledge the use of the software with the
	10	#following sentence:
	11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
	12	#copyright 2008,2009 University of Tennessee
	13	#############################################################################
[0f1e140]	14
[d26dea0]	15	import logging
[250fec92]	16	import numpy as np
[d26dea0]	17	import os
	18	import sys
	19	import datetime
	20	import inspect
	21	# For saving individual sections of data
[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
[d26dea0]	36	PREPROCESS = "xmlpreprocess"
	37	ENCODING = "encoding"
	38	RUN_NAME_DEFAULT = "None"
[250fec92]	39	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	40	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	41	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	42	"as much of the data as possible.\n\n"
[d26dea0]	43	HAS_CONVERTER = True
	44	try:
[b699768]	45	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	46	except ImportError:
	47	HAS_CONVERTER = False
	48
	49	CONSTANTS = CansasConstants()
	50	CANSAS_FORMAT = CONSTANTS.format
	51	CANSAS_NS = CONSTANTS.names
	52	ALLOW_ALL = True
	53
	54	class Reader(XMLreader):
	55	"""
	56	Class to load cansas 1D XML files
	57
	58	:Dependencies:
	59	The CanSAS reader requires PyXML 0.8.4 or later.
	60	"""
[af08e55]	61	# CanSAS version - defaults to version 1.0
[d26dea0]	62	cansas_version = "1.0"
	63	base_ns = "{cansas1d/1.0}"
[250fec92]	64	cansas_defaults = None
[d26dea0]	65	type_name = "canSAS"
[250fec92]	66	invalid = True
[654e8e0]	67	frm = ""
[af08e55]	68	# Log messages and errors
[250fec92]	69	logging = None
	70	errors = set()
[af08e55]	71	# Namespace hierarchy for current xml_file object
[250fec92]	72	names = None
	73	ns_list = None
[af08e55]	74	# Temporary storage location for loading multiple data sets in a single file
[250fec92]	75	current_datainfo = None
	76	current_dataset = None
	77	current_data1d = None
	78	data = None
[af08e55]	79	# List of data1D objects to be sent back to SasView
[250fec92]	80	output = None
[af08e55]	81	# Wildcards
[d26dea0]	82	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
[af08e55]	83	# List of allowed extensions
[d26dea0]	84	ext = ['.xml', '.XML', '.svs', '.SVS']
[af08e55]	85	# Flag to bypass extension check
[d26dea0]	86	allow_all = True
	87
[250fec92]	88	def reset_state(self):
	89	"""
	90	Resets the class state to a base case when loading a new data file so previous
	91	data files do not appear a second time
	92	"""
	93	self.current_datainfo = None
	94	self.current_dataset = None
	95	self.current_data1d = None
	96	self.data = []
	97	self.process = Process()
	98	self.transspectrum = TransmissionSpectrum()
	99	self.aperture = Aperture()
	100	self.collimation = Collimation()
	101	self.detector = Detector()
	102	self.names = []
	103	self.cansas_defaults = {}
	104	self.output = []
	105	self.ns_list = None
[d26dea0]	106	self.logging = []
	107	self.encoding = None
	108
[250fec92]	109	def read(self, xml_file, schema_path="", invalid=True):
	110	"""
	111	Validate and read in an xml_file file in the canSAS format.
	112
	113	:param xml_file: A canSAS file path in proper XML format
	114	:param schema_path: A file path to an XML schema to validate the xml_file against
	115	"""
	116	# For every file loaded, reset everything to a base state
	117	self.reset_state()
	118	self.invalid = invalid
	119	# Check that the file exists
	120	if os.path.isfile(xml_file):
	121	basename, extension = os.path.splitext(os.path.basename(xml_file))
	122	# If the file type is not allowed, return nothing
	123	if extension in self.ext or self.allow_all:
	124	# Get the file location of
	125	self.load_file_and_schema(xml_file, schema_path)
	126	self.add_data_set()
	127	# Try to load the file, but raise an error if unable to.
	128	# Check the file matches the XML schema
	129	try:
	130	self.is_cansas(extension)
	131	self.invalid = False
	132	# Get each SASentry from XML file and add it to a list.
	133	entry_list = self.xmlroot.xpath(
	134	'/ns:SASroot/ns:SASentry',
	135	namespaces={'ns': self.cansas_defaults.get("ns")})
	136	self.names.append("SASentry")
	137
	138	# Get all preprocessing events and encoding
	139	self.set_processing_instructions()
	140
	141	# Parse each <SASentry> item
	142	for entry in entry_list:
	143	# Create a new DataInfo object for every <SASentry>
	144
	145	# Set the file name and then parse the entry.
	146	self.current_datainfo.filename = basename + extension
	147	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
	148	self.current_datainfo.meta_data[PREPROCESS] = \
	149	self.processing_instructions
	150
	151	# Parse the XML SASentry
	152	self._parse_entry(entry)
	153	# Combine datasets with datainfo
	154	self.add_data_set()
	155	except RuntimeError:
	156	# If the file does not match the schema, raise this error
	157	invalid_xml = self.find_invalid_xml()
	158	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
	159	self.errors.add(invalid_xml)
	160	# Try again with an invalid CanSAS schema, that requires only a data set in each
	161	base_name = xml_reader.__file__
	162	base_name = base_name.replace("\\", "/")
	163	base = base_name.split("/sas/")[0]
	164	if self.cansas_version == "1.1":
	165	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	166	else:
	167	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	168	self.set_schema(invalid_schema)
	169	try:
	170	if self.invalid:
	171	if self.is_cansas():
	172	self.output = self.read(xml_file, invalid_schema, False)
	173	else:
	174	raise RuntimeError
	175	else:
	176	raise RuntimeError
	177	except RuntimeError:
	178	x = np.zeros(1)
	179	y = np.zeros(1)
	180	self.current_data1d = Data1D(x,y)
	181	self.current_data1d.errors = self.errors
	182	return [self.current_data1d]
	183	else:
	184	self.output.append("Not a valid file path.")
	185	# Return a list of parsed entries that dataloader can manage
	186	return self.output
	187
[654e8e0]	188	def _parse_entry(self, dom, recurse=False):
[250fec92]	189	"""
	190	Parse a SASEntry - new recursive method for parsing the dom of
	191	the CanSAS data format. This will allow multiple data files
	192	and extra nodes to be read in simultaneously.
	193
	194	:param dom: dom object with a namespace base of names
	195	"""
	196
[654e8e0]	197	if not self._is_call_local() and not recurse:
[1686a333]	198	self.reset_state()
	199	self.add_data_set()
	200	self.names.append("SASentry")
	201	self.parent_class = "SASentry"
[250fec92]	202	self._check_for_empty_data()
	203	self.base_ns = "{0}{1}{2}".format("{", \
	204	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
	205
	206	# Go through each child in the parent element
	207	for node in dom:
[5f26aa4]	208	attr = node.attrib
	209	name = attr.get("name", "")
	210	type = attr.get("type", "")
[250fec92]	211	# Get the element name and set the current names level
	212	tagname = node.tag.replace(self.base_ns, "")
	213	tagname_original = tagname
	214	# Skip this iteration when loading in save state information
	215	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	216	continue
	217
	218	# Get where to store content
	219	self.names.append(tagname_original)
	220	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	221	# If the element is a child element, recurse
	222	if len(node.getchildren()) > 0:
	223	self.parent_class = tagname_original
	224	if tagname == 'SASdata':
[af08e55]	225	self._initialize_new_data_set(node)
	226	if isinstance(self.current_dataset, plottable_2D):
	227	x_bins = attr.get("x_bins", "")
	228	y_bins = attr.get("y_bins", "")
	229	if x_bins is not "" and y_bins is not "":
	230	self.current_dataset.shape = (x_bins, y_bins)
	231	else:
	232	self.current_dataset.shape = ()
	233	# Recursion step to access data within the group
[654e8e0]	234	self._parse_entry(node, True)
[5f26aa4]	235	if tagname == "SASsample":
	236	self.current_datainfo.sample.name = name
	237	elif tagname == "beam_size":
	238	self.current_datainfo.source.beam_size_name = name
	239	elif tagname == "SAScollimation":
	240	self.collimation.name = name
	241	elif tagname == "aperture":
	242	self.aperture.name = name
	243	self.aperture.type = type
[250fec92]	244	self.add_intermediate()
	245	else:
[1905128]	246	if isinstance(self.current_dataset, plottable_2D):
	247	data_point = node.text
	248	unit = attr.get('unit', '')
	249	else:
	250	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	251
[af08e55]	252	# If this is a dataset, store the data appropriately
[250fec92]	253	if tagname == 'Run':
[5f26aa4]	254	self.current_datainfo.run_name[data_point] = name
[250fec92]	255	self.current_datainfo.run.append(data_point)
	256	elif tagname == 'Title':
	257	self.current_datainfo.title = data_point
	258	elif tagname == 'SASnote':
	259	self.current_datainfo.notes.append(data_point)
	260
[af08e55]	261	# I and Q - 1D data
	262	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[ad4632c]	263	unit_list = unit.split(" \| ")
	264	if len(unit_list) > 1:
	265	self.current_dataset.yaxis(unit_list[0], unit_list[1])
	266	else:
	267	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	268	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	269	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	270	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	271	elif tagname == 'Q':
[ad4632c]	272	unit_list = unit.split(" \| ")
	273	if len(unit_list) > 1:
	274	self.current_dataset.xaxis(unit_list[0], unit_list[1])
	275	else:
	276	self.current_dataset.xaxis("Q", unit)
[250fec92]	277	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	278	elif tagname == 'Qdev':
	279	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	280	elif tagname == 'dQw':
	281	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	282	elif tagname == 'dQl':
	283	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	284	elif tagname == 'Qmean':
	285	pass
	286	elif tagname == 'Shadowfactor':
	287	pass
[ad4632c]	288	elif tagname == 'Sesans':
	289	self.current_datainfo.isSesans = bool(data_point)
	290	elif tagname == 'zacceptance':
	291	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	292
[af08e55]	293	# I and Qx, Qy - 2D data
	294	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	295	self.current_dataset.yaxis("Intensity", unit)
[1905128]	296	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	297	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	298	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	299	elif tagname == 'Qx':
	300	self.current_dataset.xaxis("Qx", unit)
[1905128]	301	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	302	elif tagname == 'Qy':
	303	self.current_dataset.yaxis("Qy", unit)
[1905128]	304	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	305	elif tagname == 'Qxdev':
	306	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	307	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	308	elif tagname == 'Qydev':
	309	self.current_dataset.yaxis("Qydev", unit)
[1905128]	310	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	311	elif tagname == 'Mask':
[bcabf4e]	312	inter = [item == "1" for item in data_point.split(",")]
[1905128]	313	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	314
	315	# Sample Information
[250fec92]	316	elif tagname == 'ID' and self.parent_class == 'SASsample':
	317	self.current_datainfo.sample.ID = data_point
	318	elif tagname == 'Title' and self.parent_class == 'SASsample':
	319	self.current_datainfo.sample.name = data_point
	320	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	321	self.current_datainfo.sample.thickness = data_point
	322	self.current_datainfo.sample.thickness_unit = unit
	323	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	324	self.current_datainfo.sample.transmission = data_point
	325	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	326	self.current_datainfo.sample.temperature = data_point
	327	self.current_datainfo.sample.temperature_unit = unit
	328	elif tagname == 'details' and self.parent_class == 'SASsample':
	329	self.current_datainfo.sample.details.append(data_point)
	330	elif tagname == 'x' and self.parent_class == 'position':
	331	self.current_datainfo.sample.position.x = data_point
	332	self.current_datainfo.sample.position_unit = unit
	333	elif tagname == 'y' and self.parent_class == 'position':
	334	self.current_datainfo.sample.position.y = data_point
	335	self.current_datainfo.sample.position_unit = unit
	336	elif tagname == 'z' and self.parent_class == 'position':
	337	self.current_datainfo.sample.position.z = data_point
	338	self.current_datainfo.sample.position_unit = unit
	339	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	340	self.current_datainfo.sample.orientation.x = data_point
	341	self.current_datainfo.sample.orientation_unit = unit
	342	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	343	self.current_datainfo.sample.orientation.y = data_point
	344	self.current_datainfo.sample.orientation_unit = unit
	345	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	346	self.current_datainfo.sample.orientation.z = data_point
	347	self.current_datainfo.sample.orientation_unit = unit
	348
[af08e55]	349	# Instrumental Information
[250fec92]	350	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	351	self.current_datainfo.instrument = data_point
[af08e55]	352	# Detector Information
[250fec92]	353	elif tagname == 'name' and self.parent_class == 'SASdetector':
	354	self.detector.name = data_point
	355	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	356	self.detector.distance = data_point
	357	self.detector.distance_unit = unit
	358	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	359	self.detector.slit_length = data_point
	360	self.detector.slit_length_unit = unit
	361	elif tagname == 'x' and self.parent_class == 'offset':
	362	self.detector.offset.x = data_point
	363	self.detector.offset_unit = unit
	364	elif tagname == 'y' and self.parent_class == 'offset':
	365	self.detector.offset.y = data_point
	366	self.detector.offset_unit = unit
	367	elif tagname == 'z' and self.parent_class == 'offset':
	368	self.detector.offset.z = data_point
	369	self.detector.offset_unit = unit
	370	elif tagname == 'x' and self.parent_class == 'beam_center':
	371	self.detector.beam_center.x = data_point
	372	self.detector.beam_center_unit = unit
	373	elif tagname == 'y' and self.parent_class == 'beam_center':
	374	self.detector.beam_center.y = data_point
	375	self.detector.beam_center_unit = unit
	376	elif tagname == 'z' and self.parent_class == 'beam_center':
	377	self.detector.beam_center.z = data_point
	378	self.detector.beam_center_unit = unit
	379	elif tagname == 'x' and self.parent_class == 'pixel_size':
	380	self.detector.pixel_size.x = data_point
	381	self.detector.pixel_size_unit = unit
	382	elif tagname == 'y' and self.parent_class == 'pixel_size':
	383	self.detector.pixel_size.y = data_point
	384	self.detector.pixel_size_unit = unit
	385	elif tagname == 'z' and self.parent_class == 'pixel_size':
	386	self.detector.pixel_size.z = data_point
	387	self.detector.pixel_size_unit = unit
	388	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	389	self.detector.orientation.x = data_point
	390	self.detector.orientation_unit = unit
	391	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	392	self.detector.orientation.y = data_point
	393	self.detector.orientation_unit = unit
	394	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	395	self.detector.orientation.z = data_point
	396	self.detector.orientation_unit = unit
[af08e55]	397	# Collimation and Aperture
[250fec92]	398	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	399	self.collimation.length = data_point
	400	self.collimation.length_unit = unit
	401	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	402	self.collimation.name = data_point
	403	elif tagname == 'distance' and self.parent_class == 'aperture':
	404	self.aperture.distance = data_point
	405	self.aperture.distance_unit = unit
	406	elif tagname == 'x' and self.parent_class == 'size':
	407	self.aperture.size.x = data_point
	408	self.collimation.size_unit = unit
	409	elif tagname == 'y' and self.parent_class == 'size':
	410	self.aperture.size.y = data_point
	411	self.collimation.size_unit = unit
	412	elif tagname == 'z' and self.parent_class == 'size':
	413	self.aperture.size.z = data_point
	414	self.collimation.size_unit = unit
	415
[af08e55]	416	# Process Information
[250fec92]	417	elif tagname == 'name' and self.parent_class == 'SASprocess':
	418	self.process.name = data_point
	419	elif tagname == 'description' and self.parent_class == 'SASprocess':
	420	self.process.description = data_point
	421	elif tagname == 'date' and self.parent_class == 'SASprocess':
	422	try:
	423	self.process.date = datetime.datetime.fromtimestamp(data_point)
	424	except:
	425	self.process.date = data_point
	426	elif tagname == 'SASprocessnote':
	427	self.process.notes.append(data_point)
	428	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	429	unit = attr.get("unit", "")
	430	dic = {}
	431	dic["name"] = name
	432	dic["value"] = data_point
	433	dic["unit"] = unit
	434	self.process.term.append(dic)
[250fec92]	435
[af08e55]	436	# Transmission Spectrum
[250fec92]	437	elif tagname == 'T' and self.parent_class == 'Tdata':
	438	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	439	self.transspectrum.transmission_unit = unit
	440	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	441	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	442	self.transspectrum.transmission_deviation_unit = unit
	443	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	444	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	445	self.transspectrum.wavelength_unit = unit
	446
[af08e55]	447	# Source Information
[250fec92]	448	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	449	self.current_datainfo.source.wavelength = data_point
	450	self.current_datainfo.source.wavelength_unit = unit
	451	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	452	self.current_datainfo.source.wavelength_min = data_point
	453	self.current_datainfo.source.wavelength_min_unit = unit
	454	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	455	self.current_datainfo.source.wavelength_max = data_point
	456	self.current_datainfo.source.wavelength_max_unit = unit
	457	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	458	self.current_datainfo.source.wavelength_spread = data_point
	459	self.current_datainfo.source.wavelength_spread_unit = unit
	460	elif tagname == 'x' and self.parent_class == 'beam_size':
	461	self.current_datainfo.source.beam_size.x = data_point
	462	self.current_datainfo.source.beam_size_unit = unit
	463	elif tagname == 'y' and self.parent_class == 'beam_size':
	464	self.current_datainfo.source.beam_size.y = data_point
	465	self.current_datainfo.source.beam_size_unit = unit
	466	elif tagname == 'z' and self.parent_class == 'pixel_size':
	467	self.current_datainfo.source.data_point.z = data_point
	468	self.current_datainfo.source.beam_size_unit = unit
	469	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	470	self.current_datainfo.source.radiation = data_point
	471	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	472	self.current_datainfo.source.beam_shape = data_point
	473
[af08e55]	474	# Everything else goes in meta_data
[250fec92]	475	else:
	476	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	477	self.current_datainfo.meta_data[new_key] = data_point
	478
	479	self.names.remove(tagname_original)
	480	length = 0
	481	if len(self.names) > 1:
	482	length = len(self.names) - 1
	483	self.parent_class = self.names[length]
[654e8e0]	484	if not self._is_call_local() and not recurse:
	485	self.frm = ""
[1686a333]	486	self.add_data_set()
	487	empty = None
	488	return self.output[0], empty
[250fec92]	489
	490
[654e8e0]	491	def _is_call_local(self):
[1686a333]	492	"""
	493
	494	"""
[654e8e0]	495	if self.frm == "":
	496	inter = inspect.stack()
	497	self.frm = inter[2]
	498	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	499	mod_name = mod_name.replace(".py", "")
	500	mod = mod_name.split("sas/")
	501	mod_name = mod[1]
	502	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	503	return False
	504	return True
	505
[d26dea0]	506	def is_cansas(self, ext="xml"):
	507	"""
	508	Checks to see if the xml file is a CanSAS file
	509
	510	:param ext: The file extension of the data file
	511	"""
	512	if self.validate_xml():
	513	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	514	value = self.xmlroot.get(name)
	515	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	516	value.rsplit(" ")[0]:
	517	return True
	518	if ext == "svs":
	519	return True
[250fec92]	520	raise RuntimeError
[d26dea0]	521
[83b6408]	522	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	523	"""
[250fec92]	524	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	525
	526	:param xml_file: The xml file path sent to Reader.read
[250fec92]	527	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	528	"""
	529	base_name = xml_reader.__file__
	530	base_name = base_name.replace("\\", "/")
	531	base = base_name.split("/sas/")[0]
	532
	533	# Load in xml file and get the cansas version from the header
	534	self.set_xml_file(xml_file)
	535	self.cansas_version = self.xmlroot.get("version", "1.0")
	536
	537	# Generic values for the cansas file based on the version
[250fec92]	538	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	539	if schema_path == "":
[250fec92]	540	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	541	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	542
	543	# Link a schema to the XML file.
	544	self.set_schema(schema_path)
	545
[250fec92]	546	def add_data_set(self):
[d26dea0]	547	"""
[250fec92]	548	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	549	private method to generate a new data set.
[d26dea0]	550
[250fec92]	551	:param key: NeXus group name for current tree level
[d26dea0]	552	"""
	553
[250fec92]	554	if self.current_datainfo and self.current_dataset:
	555	self._final_cleanup()
	556	self.data = []
	557	self.current_datainfo = DataInfo()
[d26dea0]	558
[af08e55]	559	def _initialize_new_data_set(self, node=None):
[250fec92]	560	"""
	561	A private class method to generate a new 1D data object.
	562	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	563
[af08e55]	564	:param node: XML node to determine if 1D or 2D data
[250fec92]	565	"""
	566	x = np.array(0)
	567	y = np.array(0)
[af08e55]	568	for child in node:
	569	if child.tag.replace(self.base_ns, "") == "Idata":
	570	for i_child in child:
	571	if i_child.tag.replace(self.base_ns, "") == "Qx":
	572	self.current_dataset = plottable_2D()
	573	return
[250fec92]	574	self.current_dataset = plottable_1D(x, y)
[d26dea0]	575
[250fec92]	576	def add_intermediate(self):
	577	"""
	578	This method stores any intermediate objects within the final data set after fully reading the set.
	579
	580	:param parent: The NXclass name for the h5py Group object that just finished being processed
	581	"""
	582
	583	if self.parent_class == 'SASprocess':
	584	self.current_datainfo.process.append(self.process)
	585	self.process = Process()
	586	elif self.parent_class == 'SASdetector':
	587	self.current_datainfo.detector.append(self.detector)
	588	self.detector = Detector()
	589	elif self.parent_class == 'SAStransmission_spectrum':
	590	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	591	self.transspectrum = TransmissionSpectrum()
	592	elif self.parent_class == 'SAScollimation':
	593	self.current_datainfo.collimation.append(self.collimation)
	594	self.collimation = Collimation()
[5f26aa4]	595	elif self.parent_class == 'aperture':
[250fec92]	596	self.collimation.aperture.append(self.aperture)
	597	self.aperture = Aperture()
	598	elif self.parent_class == 'SASdata':
	599	self._check_for_empty_resolution()
	600	self.data.append(self.current_dataset)
	601
	602	def _final_cleanup(self):
[d26dea0]	603	"""
	604	Final cleanup of the Data1D object to be sure it has all the
	605	appropriate information needed for perspectives
	606	"""
[250fec92]	607
[af08e55]	608	# Append errors to dataset and reset class errors
[250fec92]	609	self.current_datainfo.errors = set()
[d26dea0]	610	for error in self.errors:
[250fec92]	611	self.current_datainfo.errors.add(error)
[d26dea0]	612	self.errors.clear()
[250fec92]	613
[af08e55]	614	# Combine all plottables with datainfo and append each to output
	615	# Type cast data arrays to float64 and find min/max as appropriate
[250fec92]	616	for dataset in self.data:
[af08e55]	617	if isinstance(dataset, plottable_1D):
	618	if dataset.x is not None:
	619	dataset.x = np.delete(dataset.x, [0])
	620	dataset.x = dataset.x.astype(np.float64)
	621	dataset.xmin = np.min(dataset.x)
	622	dataset.xmax = np.max(dataset.x)
	623	if dataset.y is not None:
	624	dataset.y = np.delete(dataset.y, [0])
	625	dataset.y = dataset.y.astype(np.float64)
	626	dataset.ymin = np.min(dataset.y)
	627	dataset.ymax = np.max(dataset.y)
	628	if dataset.dx is not None:
	629	dataset.dx = np.delete(dataset.dx, [0])
	630	dataset.dx = dataset.dx.astype(np.float64)
	631	if dataset.dxl is not None:
	632	dataset.dxl = np.delete(dataset.dxl, [0])
	633	dataset.dxl = dataset.dxl.astype(np.float64)
	634	if dataset.dxw is not None:
	635	dataset.dxw = np.delete(dataset.dxw, [0])
	636	dataset.dxw = dataset.dxw.astype(np.float64)
	637	if dataset.dy is not None:
	638	dataset.dy = np.delete(dataset.dy, [0])
	639	dataset.dy = dataset.dy.astype(np.float64)
	640	np.trim_zeros(dataset.x)
	641	np.trim_zeros(dataset.y)
	642	np.trim_zeros(dataset.dy)
	643	elif isinstance(dataset, plottable_2D):
	644	dataset.data = dataset.data.astype(np.float64)
	645	dataset.qx_data = dataset.qx_data.astype(np.float64)
	646	dataset.xmin = np.min(dataset.qx_data)
	647	dataset.xmax = np.max(dataset.qx_data)
	648	dataset.qy_data = dataset.qy_data.astype(np.float64)
	649	dataset.ymin = np.min(dataset.qy_data)
	650	dataset.ymax = np.max(dataset.qy_data)
	651	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
	652	+ dataset.qy_data * dataset.qy_data)
	653	if dataset.err_data is not None:
	654	dataset.err_data = dataset.err_data.astype(np.float64)
	655	if dataset.dqx_data is not None:
	656	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
	657	if dataset.dqy_data is not None:
	658	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
	659	if dataset.mask is not None:
	660	dataset.mask = dataset.mask.astype(dtype=bool)
	661
	662	if len(dataset.shape) == 2:
	663	n_rows, n_cols = dataset.shape
	664	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
	665	dataset.x_bins = dataset.qx_data[:int(n_cols)]
	666	dataset.data = dataset.data.flatten()
	667	else:
	668	dataset.y_bins = []
	669	dataset.x_bins = []
	670	dataset.data = dataset.data.flatten()
	671
[250fec92]	672	final_dataset = combine_data(dataset, self.current_datainfo)
	673	self.output.append(final_dataset)
[d26dea0]	674
	675	def _create_unique_key(self, dictionary, name, numb=0):
	676	"""
	677	Create a unique key value for any dictionary to prevent overwriting
[250fec92]	678	Recurse until a unique key value is found.
[d26dea0]	679
	680	:param dictionary: A dictionary with any number of entries
	681	:param name: The index of the item to be added to dictionary
	682	:param numb: The number to be appended to the name, starts at 0
	683	"""
	684	if dictionary.get(name) is not None:
	685	numb += 1
	686	name = name.split("_")[0]
	687	name += "_{0}".format(numb)
	688	name = self._create_unique_key(dictionary, name, numb)
	689	return name
	690
[250fec92]	691	def _get_node_value(self, node, tagname):
	692	"""
	693	Get the value of a node and any applicable units
	694
	695	:param node: The XML node to get the value of
	696	:param tagname: The tagname of the node
	697	"""
	698	#Get the text from the node and convert all whitespace to spaces
	699	units = ''
	700	node_value = node.text
	701	if node_value is not None:
	702	node_value = ' '.join(node_value.split())
	703	else:
	704	node_value = ""
	705
	706	# If the value is a float, compile with units.
	707	if self.ns_list.ns_datatype == "float":
	708	# If an empty value is given, set as zero.
	709	if node_value is None or node_value.isspace() \
	710	or node_value.lower() == "nan":
	711	node_value = "0.0"
	712	#Convert the value to the base units
	713	node_value, units = self._unit_conversion(node, tagname, node_value)
	714
	715	# If the value is a timestamp, convert to a datetime object
	716	elif self.ns_list.ns_datatype == "timestamp":
	717	if node_value is None or node_value.isspace():
	718	pass
	719	else:
	720	try:
	721	node_value = \
	722	datetime.datetime.fromtimestamp(node_value)
	723	except ValueError:
	724	node_value = None
	725	return node_value, units
	726
	727	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	728	"""
	729	A unit converter method used to convert the data included in the file
	730	to the default units listed in data_info
	731
[250fec92]	732	:param node: XML node
	733	:param tagname: name of the node
[d26dea0]	734	:param node_value: The value of the current dom node
	735	"""
	736	attr = node.attrib
	737	value_unit = ''
	738	err_msg = None
[682c432]	739	default_unit = None
[5f26aa4]	740	if not isinstance(node_value, float):
	741	node_value = float(node_value)
	742	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	743	try:
	744	local_unit = attr['unit']
[250fec92]	745	unitname = self.ns_list.current_level.get("unit", "")
	746	if "SASdetector" in self.names:
	747	save_in = "detector"
	748	elif "aperture" in self.names:
	749	save_in = "aperture"
	750	elif "SAScollimation" in self.names:
	751	save_in = "collimation"
	752	elif "SAStransmission_spectrum" in self.names:
	753	save_in = "transspectrum"
	754	elif "SASdata" in self.names:
	755	x = np.zeros(1)
	756	y = np.zeros(1)
	757	self.current_data1d = Data1D(x, y)
	758	save_in = "current_data1d"
	759	elif "SASsource" in self.names:
	760	save_in = "current_datainfo.source"
	761	elif "SASsample" in self.names:
	762	save_in = "current_datainfo.sample"
	763	elif "SASprocess" in self.names:
	764	save_in = "process"
	765	else:
	766	save_in = "current_datainfo"
	767	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	768	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	769	and local_unit.lower() != "none":
	770	if HAS_CONVERTER == True:
[af08e55]	771	# Check local units - bad units raise KeyError
[d26dea0]	772	data_conv_q = Converter(local_unit)
	773	value_unit = default_unit
[682c432]	774	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	775	else:
	776	value_unit = local_unit
	777	err_msg = "Unit converter is not available.\n"
	778	else:
	779	value_unit = local_unit
	780	except KeyError:
	781	err_msg = "CanSAS reader: unexpected "
	782	err_msg += "\"{0}\" unit [{1}]; "
	783	err_msg = err_msg.format(tagname, local_unit)
[682c432]	784	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	785	value_unit = local_unit
	786	except:
	787	err_msg = "CanSAS reader: unknown error converting "
	788	err_msg += "\"{0}\" unit [{1}]"
	789	err_msg = err_msg.format(tagname, local_unit)
	790	value_unit = local_unit
	791	elif 'unit' in attr:
	792	value_unit = attr['unit']
	793	if err_msg:
	794	self.errors.add(err_msg)
	795	return node_value, value_unit
	796
[250fec92]	797	def _check_for_empty_data(self):
[d26dea0]	798	"""
	799	Creates an empty data set if no data is passed to the reader
	800
	801	:param data1d: presumably a Data1D object
	802	"""
[250fec92]	803	if self.current_dataset == None:
	804	x_vals = np.empty(0)
	805	y_vals = np.empty(0)
	806	dx_vals = np.empty(0)
	807	dy_vals = np.empty(0)
	808	dxl = np.empty(0)
	809	dxw = np.empty(0)
	810	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	811	self.current_dataset.dxl = dxl
	812	self.current_dataset.dxw = dxw
	813
	814	def _check_for_empty_resolution(self):
[d26dea0]	815	"""
	816	A method to check all resolution data sets are the same size as I and Q
	817	"""
[af08e55]	818	if isinstance(self.current_dataset, plottable_1D):
	819	dql_exists = False
	820	dqw_exists = False
	821	dq_exists = False
	822	di_exists = False
	823	if self.current_dataset.dxl is not None:
	824	dql_exists = True
	825	if self.current_dataset.dxw is not None:
	826	dqw_exists = True
	827	if self.current_dataset.dx is not None:
	828	dq_exists = True
	829	if self.current_dataset.dy is not None:
	830	di_exists = True
	831	if dqw_exists and not dql_exists:
	832	array_size = self.current_dataset.dxw.size - 1
	833	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
	834	np.zeros([array_size]))
	835	elif dql_exists and not dqw_exists:
	836	array_size = self.current_dataset.dxl.size - 1
	837	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
	838	np.zeros([array_size]))
	839	elif not dql_exists and not dqw_exists and not dq_exists:
	840	array_size = self.current_dataset.x.size - 1
	841	self.current_dataset.dx = np.append(self.current_dataset.dx,
	842	np.zeros([array_size]))
	843	if not di_exists:
	844	array_size = self.current_dataset.y.size - 1
	845	self.current_dataset.dy = np.append(self.current_dataset.dy,
	846	np.zeros([array_size]))
	847	elif isinstance(self.current_dataset, plottable_2D):
	848	dqx_exists = False
	849	dqy_exists = False
	850	di_exists = False
	851	mask_exists = False
	852	if self.current_dataset.dqx_data is not None:
	853	dqx_exists = True
	854	if self.current_dataset.dqy_data is not None:
	855	dqy_exists = True
	856	if self.current_dataset.err_data is not None:
	857	di_exists = True
	858	if self.current_dataset.mask is not None:
	859	mask_exists = True
	860	if not dqy_exists:
	861	array_size = self.current_dataset.qy_data.size - 1
	862	self.current_dataset.dqy_data = np.append(
	863	self.current_dataset.dqy_data, np.zeros([array_size]))
	864	if not dqx_exists:
	865	array_size = self.current_dataset.qx_data.size - 1
	866	self.current_dataset.dqx_data = np.append(
	867	self.current_dataset.dqx_data, np.zeros([array_size]))
	868	if not di_exists:
	869	array_size = self.current_dataset.data.size - 1
	870	self.current_dataset.err_data = np.append(
	871	self.current_dataset.err_data, np.zeros([array_size]))
	872	if not mask_exists:
	873	array_size = self.current_dataset.data.size - 1
	874	self.current_dataset.mask = np.append(
	875	self.current_dataset.mask,
	876	np.ones([array_size] ,dtype=bool))
[250fec92]	877
	878	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	879
[250fec92]	880	def write(self, filename, datainfo):
[d26dea0]	881	"""
[250fec92]	882	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	883
[250fec92]	884	:param filename: name of the file to write
	885	:param datainfo: Data1D object
	886	"""
	887	# Create XML document
	888	doc, _ = self._to_xml_doc(datainfo)
	889	# Write the file
	890	file_ref = open(filename, 'w')
	891	if self.encoding == None:
	892	self.encoding = "UTF-8"
	893	doc.write(file_ref, encoding=self.encoding,
	894	pretty_print=True, xml_declaration=True)
	895	file_ref.close()
[d26dea0]	896
[250fec92]	897	def _to_xml_doc(self, datainfo):
[d26dea0]	898	"""
[250fec92]	899	Create an XML document to contain the content of a Data1D
[d26dea0]	900
[250fec92]	901	:param datainfo: Data1D object
[d26dea0]	902	"""
[af08e55]	903	is_2d = False
[83c09af]	904	if issubclass(datainfo.__class__, Data2D):
	905	is_2d = True
[d26dea0]	906
[250fec92]	907	# Get PIs and create root element
	908	pi_string = self._get_pi_string()
	909	# Define namespaces and create SASroot object
	910	main_node = self._create_main_node()
	911	# Create ElementTree, append SASroot and apply processing instructions
	912	base_string = pi_string + self.to_string(main_node)
	913	base_element = self.create_element_from_string(base_string)
	914	doc = self.create_tree(base_element)
	915	# Create SASentry Element
	916	entry_node = self.create_element("SASentry")
	917	root = doc.getroot()
	918	root.append(entry_node)
[d26dea0]	919
[250fec92]	920	# Add Title to SASentry
	921	self.write_node(entry_node, "Title", datainfo.title)
	922	# Add Run to SASentry
	923	self._write_run_names(datainfo, entry_node)
	924	# Add Data info to SASEntry
[83c09af]	925	if is_2d:
	926	self._write_data_2d(datainfo, entry_node)
	927	else:
	928	self._write_data(datainfo, entry_node)
[250fec92]	929	# Transmission Spectrum Info
	930	self._write_trans_spectrum(datainfo, entry_node)
	931	# Sample info
	932	self._write_sample_info(datainfo, entry_node)
	933	# Instrument info
	934	instr = self._write_instrument(datainfo, entry_node)
	935	# Source
	936	self._write_source(datainfo, instr)
	937	# Collimation
	938	self._write_collimation(datainfo, instr)
	939	# Detectors
	940	self._write_detectors(datainfo, instr)
	941	# Processes info
	942	self._write_process_notes(datainfo, entry_node)
	943	# Note info
	944	self._write_notes(datainfo, entry_node)
	945	# Return the document, and the SASentry node associated with
	946	# the data we just wrote
	947	# If the calling function was not the cansas reader, return a minidom
	948	# object rather than an lxml object.
[654e8e0]	949	self.frm = inspect.stack()[1]
	950	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	951	return doc, entry_node
[d26dea0]	952
[250fec92]	953	def write_node(self, parent, name, value, attr=None):
	954	"""
	955	:param doc: document DOM
	956	:param parent: parent node
	957	:param name: tag of the element
	958	:param value: value of the child text node
	959	:param attr: attribute dictionary
[d26dea0]	960
[250fec92]	961	:return: True if something was appended, otherwise False
	962	"""
	963	if value is not None:
	964	parent = self.ebuilder(parent, name, value, attr)
	965	return True
	966	return False
[d26dea0]	967
	968	def _get_pi_string(self):
	969	"""
	970	Creates the processing instructions header for writing to file
	971	"""
	972	pis = self.return_processing_instructions()
	973	if len(pis) > 0:
	974	pi_tree = self.create_tree(pis[0])
	975	i = 1
	976	for i in range(1, len(pis) - 1):
	977	pi_tree = self.append(pis[i], pi_tree)
	978	pi_string = self.to_string(pi_tree)
	979	else:
	980	pi_string = ""
	981	return pi_string
	982
	983	def _create_main_node(self):
	984	"""
	985	Creates the primary xml header used when writing to file
	986	"""
	987	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	988	version = self.cansas_version
	989	n_s = CANSAS_NS.get(version).get("ns")
	990	if version == "1.1":
	991	url = "http://www.cansas.org/formats/1.1/"
	992	else:
	993	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	994	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	995	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	996	"version" : version}
	997	nsmap = {'xsi' : xsi, None: n_s}
	998
	999	main_node = self.create_element("{" + n_s + "}SASroot",
	1000	attrib=attrib, nsmap=nsmap)
	1001	return main_node
	1002
	1003	def _write_run_names(self, datainfo, entry_node):
	1004	"""
	1005	Writes the run names to the XML file
	1006
	1007	:param datainfo: The Data1D object the information is coming from
	1008	:param entry_node: lxml node ElementTree object to be appended to
	1009	"""
	1010	if datainfo.run == None or datainfo.run == []:
	1011	datainfo.run.append(RUN_NAME_DEFAULT)
	1012	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	1013	for item in datainfo.run:
	1014	runname = {}
	1015	if item in datainfo.run_name and \
	1016	len(str(datainfo.run_name[item])) > 1:
	1017	runname = {'name': datainfo.run_name[item]}
	1018	self.write_node(entry_node, "Run", item, runname)
	1019
	1020	def _write_data(self, datainfo, entry_node):
	1021	"""
[83c09af]	1022	Writes 1D I and Q data to the XML file
[d26dea0]	1023
	1024	:param datainfo: The Data1D object the information is coming from
	1025	:param entry_node: lxml node ElementTree object to be appended to
	1026	"""
	1027	node = self.create_element("SASdata")
	1028	self.append(node, entry_node)
	1029
	1030	for i in range(len(datainfo.x)):
	1031	point = self.create_element("Idata")
	1032	node.append(point)
	1033	self.write_node(point, "Q", datainfo.x[i],
[ad4632c]	1034	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[d26dea0]	1035	if len(datainfo.y) >= i:
	1036	self.write_node(point, "I", datainfo.y[i],
[ad4632c]	1037	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	1038	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	1039	self.write_node(point, "Idev", datainfo.dy[i],
[ad4632c]	1040	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	1041	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	1042	self.write_node(point, "Qdev", datainfo.dx[i],
[ad4632c]	1043	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	1044	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	1045	self.write_node(point, "dQw", datainfo.dxw[i],
[ad4632c]	1046	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	1047	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	1048	self.write_node(point, "dQl", datainfo.dxl[i],
[ad4632c]	1049	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
	1050	if datainfo.isSesans:
	1051	sesans = self.create_element("Sesans")
	1052	sesans.text = str(datainfo.isSesans)
	1053	node.append(sesans)
	1054	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
	1055	{'unit': datainfo.sample.zacceptance[1]})
	1056
[d26dea0]	1057
[83c09af]	1058	def _write_data_2d(self, datainfo, entry_node):
	1059	"""
	1060	Writes 2D data to the XML file
	1061
	1062	:param datainfo: The Data2D object the information is coming from
	1063	:param entry_node: lxml node ElementTree object to be appended to
	1064	"""
[af08e55]	1065	attr = {}
	1066	if datainfo.data.shape:
[1905128]	1067	attr["x_bins"] = str(len(datainfo.x_bins))
	1068	attr["y_bins"] = str(len(datainfo.y_bins))
	1069	node = self.create_element("SASdata", attr)
[83c09af]	1070	self.append(node, entry_node)
	1071
[1905128]	1072	point = self.create_element("Idata")
	1073	node.append(point)
	1074	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
	1075	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
	1076	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
	1077
	1078	self.write_node(point, "Qx", qx,
	1079	{'unit': datainfo._xunit})
	1080	self.write_node(point, "Qy", qy,
	1081	{'unit': datainfo._yunit})
	1082	self.write_node(point, "I", intensity,
	1083	{'unit': datainfo._zunit})
	1084	if datainfo.err_data is not None:
[5e6df0e]	1085	err = ','.join([str(datainfo.err_data[i]) for i in
	1086	xrange(len(datainfo.err_data))])
[1905128]	1087	self.write_node(point, "Idev", err,
[83c09af]	1088	{'unit': datainfo._zunit})
[1905128]	1089	if datainfo.dqy_data is not None:
[5e6df0e]	1090	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
	1091	xrange(len(datainfo.dqy_data))])
[1905128]	1092	self.write_node(point, "Qydev", dqy,
	1093	{'unit': datainfo._yunit})
	1094	if datainfo.dqx_data is not None:
[5e6df0e]	1095	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
	1096	xrange(len(datainfo.dqx_data))])
[1905128]	1097	self.write_node(point, "Qxdev", dqx,
	1098	{'unit': datainfo._xunit})
	1099	if datainfo.mask is not None:
[5e6df0e]	1100	mask = ','.join(
[bcabf4e]	1101	["1" if datainfo.mask[i] else "0"
	1102	for i in xrange(len(datainfo.mask))])
[1905128]	1103	self.write_node(point, "Mask", mask)
[83c09af]	1104
[d26dea0]	1105	def _write_trans_spectrum(self, datainfo, entry_node):
	1106	"""
	1107	Writes the transmission spectrum data to the XML file
	1108
	1109	:param datainfo: The Data1D object the information is coming from
	1110	:param entry_node: lxml node ElementTree object to be appended to
	1111	"""
	1112	for i in range(len(datainfo.trans_spectrum)):
	1113	spectrum = datainfo.trans_spectrum[i]
	1114	node = self.create_element("SAStransmission_spectrum",
	1115	{"name" : spectrum.name})
	1116	self.append(node, entry_node)
	1117	if isinstance(spectrum.timestamp, datetime.datetime):
	1118	node.setAttribute("timestamp", spectrum.timestamp)
	1119	for i in range(len(spectrum.wavelength)):
	1120	point = self.create_element("Tdata")
	1121	node.append(point)
	1122	self.write_node(point, "Lambda", spectrum.wavelength[i],
	1123	{'unit': spectrum.wavelength_unit})
	1124	self.write_node(point, "T", spectrum.transmission[i],
	1125	{'unit': spectrum.transmission_unit})
	1126	if spectrum.transmission_deviation != None \
	1127	and len(spectrum.transmission_deviation) >= i:
	1128	self.write_node(point, "Tdev",
	1129	spectrum.transmission_deviation[i],
	1130	{'unit':
	1131	spectrum.transmission_deviation_unit})
	1132
	1133	def _write_sample_info(self, datainfo, entry_node):
	1134	"""
	1135	Writes the sample information to the XML file
	1136
	1137	:param datainfo: The Data1D object the information is coming from
	1138	:param entry_node: lxml node ElementTree object to be appended to
	1139	"""
	1140	sample = self.create_element("SASsample")
	1141	if datainfo.sample.name is not None:
	1142	self.write_attribute(sample, "name",
	1143	str(datainfo.sample.name))
	1144	self.append(sample, entry_node)
	1145	self.write_node(sample, "ID", str(datainfo.sample.ID))
	1146	self.write_node(sample, "thickness", datainfo.sample.thickness,
	1147	{"unit": datainfo.sample.thickness_unit})
	1148	self.write_node(sample, "transmission", datainfo.sample.transmission)
	1149	self.write_node(sample, "temperature", datainfo.sample.temperature,
	1150	{"unit": datainfo.sample.temperature_unit})
	1151
	1152	pos = self.create_element("position")
	1153	written = self.write_node(pos,
	1154	"x",
	1155	datainfo.sample.position.x,
	1156	{"unit": datainfo.sample.position_unit})
	1157	written = written \| self.write_node( \
	1158	pos, "y", datainfo.sample.position.y,
	1159	{"unit": datainfo.sample.position_unit})
	1160	written = written \| self.write_node( \
	1161	pos, "z", datainfo.sample.position.z,
	1162	{"unit": datainfo.sample.position_unit})
	1163	if written == True:
	1164	self.append(pos, sample)
	1165
	1166	ori = self.create_element("orientation")
	1167	written = self.write_node(ori, "roll",
	1168	datainfo.sample.orientation.x,
	1169	{"unit": datainfo.sample.orientation_unit})
	1170	written = written \| self.write_node( \
	1171	ori, "pitch", datainfo.sample.orientation.y,
	1172	{"unit": datainfo.sample.orientation_unit})
	1173	written = written \| self.write_node( \
	1174	ori, "yaw", datainfo.sample.orientation.z,
	1175	{"unit": datainfo.sample.orientation_unit})
	1176	if written == True:
	1177	self.append(ori, sample)
	1178
	1179	for item in datainfo.sample.details:
	1180	self.write_node(sample, "details", item)
	1181
	1182	def _write_instrument(self, datainfo, entry_node):
	1183	"""
	1184	Writes the instrumental information to the XML file
	1185
	1186	:param datainfo: The Data1D object the information is coming from
	1187	:param entry_node: lxml node ElementTree object to be appended to
	1188	"""
	1189	instr = self.create_element("SASinstrument")
	1190	self.append(instr, entry_node)
	1191	self.write_node(instr, "name", datainfo.instrument)
	1192	return instr
	1193
	1194	def _write_source(self, datainfo, instr):
	1195	"""
	1196	Writes the source information to the XML file
	1197
	1198	:param datainfo: The Data1D object the information is coming from
	1199	:param instr: instrument node to be appended to
	1200	"""
	1201	source = self.create_element("SASsource")
	1202	if datainfo.source.name is not None:
	1203	self.write_attribute(source, "name",
	1204	str(datainfo.source.name))
	1205	self.append(source, instr)
	1206	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	1207	datainfo.source.radiation = "neutron"
	1208	self.write_node(source, "radiation", datainfo.source.radiation)
	1209
	1210	size = self.create_element("beam_size")
	1211	if datainfo.source.beam_size_name is not None:
	1212	self.write_attribute(size, "name",
	1213	str(datainfo.source.beam_size_name))
	1214	written = self.write_node( \
	1215	size, "x", datainfo.source.beam_size.x,
	1216	{"unit": datainfo.source.beam_size_unit})
	1217	written = written \| self.write_node( \
	1218	size, "y", datainfo.source.beam_size.y,
	1219	{"unit": datainfo.source.beam_size_unit})
	1220	written = written \| self.write_node( \
	1221	size, "z", datainfo.source.beam_size.z,
	1222	{"unit": datainfo.source.beam_size_unit})
	1223	if written == True:
	1224	self.append(size, source)
	1225
	1226	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1227	self.write_node(source, "wavelength",
	1228	datainfo.source.wavelength,
	1229	{"unit": datainfo.source.wavelength_unit})
	1230	self.write_node(source, "wavelength_min",
	1231	datainfo.source.wavelength_min,
	1232	{"unit": datainfo.source.wavelength_min_unit})
	1233	self.write_node(source, "wavelength_max",
	1234	datainfo.source.wavelength_max,
	1235	{"unit": datainfo.source.wavelength_max_unit})
	1236	self.write_node(source, "wavelength_spread",
	1237	datainfo.source.wavelength_spread,
	1238	{"unit": datainfo.source.wavelength_spread_unit})
	1239
	1240	def _write_collimation(self, datainfo, instr):
	1241	"""
	1242	Writes the collimation information to the XML file
	1243
	1244	:param datainfo: The Data1D object the information is coming from
	1245	:param instr: lxml node ElementTree object to be appended to
	1246	"""
	1247	if datainfo.collimation == [] or datainfo.collimation == None:
	1248	coll = Collimation()
	1249	datainfo.collimation.append(coll)
	1250	for item in datainfo.collimation:
	1251	coll = self.create_element("SAScollimation")
	1252	if item.name is not None:
	1253	self.write_attribute(coll, "name", str(item.name))
	1254	self.append(coll, instr)
	1255
	1256	self.write_node(coll, "length", item.length,
	1257	{"unit": item.length_unit})
	1258
	1259	for aperture in item.aperture:
	1260	apert = self.create_element("aperture")
	1261	if aperture.name is not None:
	1262	self.write_attribute(apert, "name", str(aperture.name))
	1263	if aperture.type is not None:
	1264	self.write_attribute(apert, "type", str(aperture.type))
	1265	self.append(apert, coll)
	1266
	1267	size = self.create_element("size")
	1268	if aperture.size_name is not None:
	1269	self.write_attribute(size, "name",
	1270	str(aperture.size_name))
	1271	written = self.write_node(size, "x", aperture.size.x,
	1272	{"unit": aperture.size_unit})
	1273	written = written \| self.write_node( \
	1274	size, "y", aperture.size.y,
	1275	{"unit": aperture.size_unit})
	1276	written = written \| self.write_node( \
	1277	size, "z", aperture.size.z,
	1278	{"unit": aperture.size_unit})
	1279	if written == True:
	1280	self.append(size, apert)
	1281
	1282	self.write_node(apert, "distance", aperture.distance,
	1283	{"unit": aperture.distance_unit})
	1284
	1285	def _write_detectors(self, datainfo, instr):
	1286	"""
	1287	Writes the detector information to the XML file
	1288
	1289	:param datainfo: The Data1D object the information is coming from
	1290	:param inst: lxml instrument node to be appended to
	1291	"""
	1292	if datainfo.detector == None or datainfo.detector == []:
	1293	det = Detector()
	1294	det.name = ""
	1295	datainfo.detector.append(det)
	1296
	1297	for item in datainfo.detector:
	1298	det = self.create_element("SASdetector")
	1299	written = self.write_node(det, "name", item.name)
	1300	written = written \| self.write_node(det, "SDD", item.distance,
	1301	{"unit": item.distance_unit})
	1302	if written == True:
	1303	self.append(det, instr)
	1304
	1305	off = self.create_element("offset")
	1306	written = self.write_node(off, "x", item.offset.x,
	1307	{"unit": item.offset_unit})
	1308	written = written \| self.write_node(off, "y", item.offset.y,
	1309	{"unit": item.offset_unit})
	1310	written = written \| self.write_node(off, "z", item.offset.z,
	1311	{"unit": item.offset_unit})
	1312	if written == True:
	1313	self.append(off, det)
	1314
	1315	ori = self.create_element("orientation")
	1316	written = self.write_node(ori, "roll", item.orientation.x,
	1317	{"unit": item.orientation_unit})
	1318	written = written \| self.write_node(ori, "pitch",
	1319	item.orientation.y,
	1320	{"unit": item.orientation_unit})
	1321	written = written \| self.write_node(ori, "yaw",
	1322	item.orientation.z,
	1323	{"unit": item.orientation_unit})
	1324	if written == True:
	1325	self.append(ori, det)
	1326
	1327	center = self.create_element("beam_center")
	1328	written = self.write_node(center, "x", item.beam_center.x,
	1329	{"unit": item.beam_center_unit})
	1330	written = written \| self.write_node(center, "y",
	1331	item.beam_center.y,
	1332	{"unit": item.beam_center_unit})
	1333	written = written \| self.write_node(center, "z",
	1334	item.beam_center.z,
	1335	{"unit": item.beam_center_unit})
	1336	if written == True:
	1337	self.append(center, det)
	1338
	1339	pix = self.create_element("pixel_size")
	1340	written = self.write_node(pix, "x", item.pixel_size.x,
	1341	{"unit": item.pixel_size_unit})
	1342	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1343	{"unit": item.pixel_size_unit})
	1344	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1345	{"unit": item.pixel_size_unit})
	1346	if written == True:
	1347	self.append(pix, det)
[3a9801f]	1348	self.write_node(det, "slit_length", item.slit_length,
	1349	{"unit": item.slit_length_unit})
	1350
[d26dea0]	1351
	1352	def _write_process_notes(self, datainfo, entry_node):
	1353	"""
	1354	Writes the process notes to the XML file
	1355
	1356	:param datainfo: The Data1D object the information is coming from
	1357	:param entry_node: lxml node ElementTree object to be appended to
	1358
	1359	"""
	1360	for item in datainfo.process:
	1361	node = self.create_element("SASprocess")
	1362	self.append(node, entry_node)
	1363	self.write_node(node, "name", item.name)
	1364	self.write_node(node, "date", item.date)
	1365	self.write_node(node, "description", item.description)
	1366	for term in item.term:
[1686a333]	1367	if isinstance(term, list):
	1368	value = term['value']
	1369	del term['value']
[5f26aa4]	1370	elif isinstance(term, dict):
	1371	value = term.get("value")
	1372	del term['value']
[1686a333]	1373	else:
	1374	value = term
[d26dea0]	1375	self.write_node(node, "term", value, term)
	1376	for note in item.notes:
	1377	self.write_node(node, "SASprocessnote", note)
	1378	if len(item.notes) == 0:
	1379	self.write_node(node, "SASprocessnote", "")
	1380
	1381	def _write_notes(self, datainfo, entry_node):
	1382	"""
	1383	Writes the notes to the XML file and creates an empty note if none
	1384	exist
	1385
	1386	:param datainfo: The Data1D object the information is coming from
	1387	:param entry_node: lxml node ElementTree object to be appended to
	1388
	1389	"""
	1390	if len(datainfo.notes) == 0:
	1391	node = self.create_element("SASnote")
	1392	self.append(node, entry_node)
	1393	else:
	1394	for item in datainfo.notes:
	1395	node = self.create_element("SASnote")
	1396	self.write_text(node, item)
	1397	self.append(node, entry_node)
	1398
[654e8e0]	1399	def _check_origin(self, entry_node, doc):
[d26dea0]	1400	"""
	1401	Return the document, and the SASentry node associated with
	1402	the data we just wrote.
	1403	If the calling function was not the cansas reader, return a minidom
	1404	object rather than an lxml object.
	1405
	1406	:param entry_node: lxml node ElementTree object to be appended to
	1407	:param doc: entire xml tree
	1408	"""
[654e8e0]	1409	if not self.frm:
	1410	self.frm = inspect.stack()[1]
	1411	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1412	mod_name = mod_name.replace(".py", "")
	1413	mod = mod_name.split("sas/")
	1414	mod_name = mod[1]
[45d90b9]	1415	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1416	string = self.to_string(doc, pretty_print=False)
	1417	doc = parseString(string)
	1418	node_name = entry_node.tag
	1419	node_list = doc.getElementsByTagName(node_name)
	1420	entry_node = node_list.item(0)
[5ce7f17]	1421	return doc, entry_node
[d26dea0]	1422
	1423	# DO NOT REMOVE - used in saving and loading panel states.
	1424	def _store_float(self, location, node, variable, storage, optional=True):
	1425	"""
	1426	Get the content of a xpath location and store
	1427	the result. Check that the units are compatible
	1428	with the destination. The value is expected to
	1429	be a float.
	1430
	1431	The xpath location might or might not exist.
	1432	If it does not exist, nothing is done
	1433
	1434	:param location: xpath location to fetch
	1435	:param node: node to read the data from
	1436	:param variable: name of the data member to store it in [string]
	1437	:param storage: data object that has the 'variable' data member
	1438	:param optional: if True, no exception will be raised
	1439	if unit conversion can't be done
	1440
	1441	:raise ValueError: raised when the units are not recognized
	1442	"""
	1443	entry = get_content(location, node)
	1444	try:
	1445	value = float(entry.text)
	1446	except:
	1447	value = None
	1448
	1449	if value is not None:
	1450	# If the entry has units, check to see that they are
	1451	# compatible with what we currently have in the data object
	1452	units = entry.get('unit')
	1453	if units is not None:
	1454	toks = variable.split('.')
	1455	local_unit = None
	1456	exec "local_unit = storage.%s_unit" % toks[0]
	1457	if local_unit != None and units.lower() != local_unit.lower():
	1458	if HAS_CONVERTER == True:
	1459	try:
	1460	conv = Converter(units)
	1461	exec "storage.%s = %g" % \
	1462	(variable, conv(value, units=local_unit))
	1463	except:
	1464	_, exc_value, _ = sys.exc_info()
	1465	err_mess = "CanSAS reader: could not convert"
	1466	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1467	% (variable, units, local_unit, exc_value)
	1468	self.errors.add(err_mess)
	1469	if optional:
	1470	logging.info(err_mess)
	1471	else:
	1472	raise ValueError, err_mess
	1473	else:
	1474	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1475	% (variable, units)
	1476	err_mess += " expecting [%s]" % local_unit
	1477	self.errors.add(err_mess)
	1478	if optional:
	1479	logging.info(err_mess)
	1480	else:
	1481	raise ValueError, err_mess
	1482	else:
	1483	exec "storage.%s = value" % variable
	1484	else:
	1485	exec "storage.%s = value" % variable
	1486
	1487	# DO NOT REMOVE - used in saving and loading panel states.
	1488	def _store_content(self, location, node, variable, storage):
	1489	"""
	1490	Get the content of a xpath location and store
	1491	the result. The value is treated as a string.
	1492
	1493	The xpath location might or might not exist.
	1494	If it does not exist, nothing is done
	1495
	1496	:param location: xpath location to fetch
	1497	:param node: node to read the data from
	1498	:param variable: name of the data member to store it in [string]
	1499	:param storage: data object that has the 'variable' data member
	1500
	1501	:return: return a list of errors
	1502	"""
	1503	entry = get_content(location, node)
	1504	if entry is not None and entry.text is not None:
	1505	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1506
	1507
	1508	# DO NOT REMOVE Called by outside packages:
	1509	# sas.sasgui.perspectives.invariant.invariant_state
	1510	# sas.sasgui.perspectives.fitting.pagestate
	1511	def get_content(location, node):
	1512	"""
	1513	Get the first instance of the content of a xpath location.
	1514
	1515	:param location: xpath location
	1516	:param node: node to start at
	1517
	1518	:return: Element, or None
	1519	"""
	1520	nodes = node.xpath(location,
	1521	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1522	if len(nodes) > 0:
	1523	return nodes[0]
	1524	else:
	1525	return None
	1526
	1527	# DO NOT REMOVE Called by outside packages:
	1528	# sas.sasgui.perspectives.fitting.pagestate
	1529	def write_node(doc, parent, name, value, attr=None):
	1530	"""
	1531	:param doc: document DOM
	1532	:param parent: parent node
	1533	:param name: tag of the element
	1534	:param value: value of the child text node
	1535	:param attr: attribute dictionary
	1536
	1537	:return: True if something was appended, otherwise False
	1538	"""
	1539	if attr is None:
	1540	attr = {}
	1541	if value is not None:
	1542	node = doc.createElement(name)
	1543	node.appendChild(doc.createTextNode(str(value)))
	1544	for item in attr:
	1545	node.setAttribute(item, attr[item])
	1546	parent.appendChild(node)
	1547	return True
	1548	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 2ffe241

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