cansas_reader.py @ 9a5097c

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

Last change on this file since 9a5097c was c221349, checked in by krzywon, 8 years ago
Split unit axis and label on "\|" and then strip whitespace.
Property mode set to `100644`
File size: 70.4 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):
[c221349]	263	unit_list = unit.split("\|")
[ad4632c]	264	if len(unit_list) > 1:
[c221349]	265	self.current_dataset.yaxis(unit_list[0].strip(),
	266	unit_list[1].strip())
[ad4632c]	267	else:
	268	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	269	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	270	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	271	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	272	elif tagname == 'Q':
[c221349]	273	unit_list = unit.split("\|")
[ad4632c]	274	if len(unit_list) > 1:
[c221349]	275	self.current_dataset.xaxis(unit_list[0].strip(),
	276	unit_list[1].strip())
[ad4632c]	277	else:
	278	self.current_dataset.xaxis("Q", unit)
[250fec92]	279	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	280	elif tagname == 'Qdev':
	281	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	282	elif tagname == 'dQw':
	283	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	284	elif tagname == 'dQl':
	285	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	286	elif tagname == 'Qmean':
	287	pass
	288	elif tagname == 'Shadowfactor':
	289	pass
[ad4632c]	290	elif tagname == 'Sesans':
	291	self.current_datainfo.isSesans = bool(data_point)
	292	elif tagname == 'zacceptance':
	293	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	294
[af08e55]	295	# I and Qx, Qy - 2D data
	296	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	297	self.current_dataset.yaxis("Intensity", unit)
[1905128]	298	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	299	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	300	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	301	elif tagname == 'Qx':
	302	self.current_dataset.xaxis("Qx", unit)
[1905128]	303	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	304	elif tagname == 'Qy':
	305	self.current_dataset.yaxis("Qy", unit)
[1905128]	306	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	307	elif tagname == 'Qxdev':
	308	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	309	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	310	elif tagname == 'Qydev':
	311	self.current_dataset.yaxis("Qydev", unit)
[1905128]	312	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	313	elif tagname == 'Mask':
[bcabf4e]	314	inter = [item == "1" for item in data_point.split(",")]
[1905128]	315	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	316
	317	# Sample Information
[250fec92]	318	elif tagname == 'ID' and self.parent_class == 'SASsample':
	319	self.current_datainfo.sample.ID = data_point
	320	elif tagname == 'Title' and self.parent_class == 'SASsample':
	321	self.current_datainfo.sample.name = data_point
	322	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	323	self.current_datainfo.sample.thickness = data_point
	324	self.current_datainfo.sample.thickness_unit = unit
	325	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	326	self.current_datainfo.sample.transmission = data_point
	327	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	328	self.current_datainfo.sample.temperature = data_point
	329	self.current_datainfo.sample.temperature_unit = unit
	330	elif tagname == 'details' and self.parent_class == 'SASsample':
	331	self.current_datainfo.sample.details.append(data_point)
	332	elif tagname == 'x' and self.parent_class == 'position':
	333	self.current_datainfo.sample.position.x = data_point
	334	self.current_datainfo.sample.position_unit = unit
	335	elif tagname == 'y' and self.parent_class == 'position':
	336	self.current_datainfo.sample.position.y = data_point
	337	self.current_datainfo.sample.position_unit = unit
	338	elif tagname == 'z' and self.parent_class == 'position':
	339	self.current_datainfo.sample.position.z = data_point
	340	self.current_datainfo.sample.position_unit = unit
	341	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	342	self.current_datainfo.sample.orientation.x = data_point
	343	self.current_datainfo.sample.orientation_unit = unit
	344	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	345	self.current_datainfo.sample.orientation.y = data_point
	346	self.current_datainfo.sample.orientation_unit = unit
	347	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	348	self.current_datainfo.sample.orientation.z = data_point
	349	self.current_datainfo.sample.orientation_unit = unit
	350
[af08e55]	351	# Instrumental Information
[250fec92]	352	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	353	self.current_datainfo.instrument = data_point
[af08e55]	354	# Detector Information
[250fec92]	355	elif tagname == 'name' and self.parent_class == 'SASdetector':
	356	self.detector.name = data_point
	357	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	358	self.detector.distance = data_point
	359	self.detector.distance_unit = unit
	360	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	361	self.detector.slit_length = data_point
	362	self.detector.slit_length_unit = unit
	363	elif tagname == 'x' and self.parent_class == 'offset':
	364	self.detector.offset.x = data_point
	365	self.detector.offset_unit = unit
	366	elif tagname == 'y' and self.parent_class == 'offset':
	367	self.detector.offset.y = data_point
	368	self.detector.offset_unit = unit
	369	elif tagname == 'z' and self.parent_class == 'offset':
	370	self.detector.offset.z = data_point
	371	self.detector.offset_unit = unit
	372	elif tagname == 'x' and self.parent_class == 'beam_center':
	373	self.detector.beam_center.x = data_point
	374	self.detector.beam_center_unit = unit
	375	elif tagname == 'y' and self.parent_class == 'beam_center':
	376	self.detector.beam_center.y = data_point
	377	self.detector.beam_center_unit = unit
	378	elif tagname == 'z' and self.parent_class == 'beam_center':
	379	self.detector.beam_center.z = data_point
	380	self.detector.beam_center_unit = unit
	381	elif tagname == 'x' and self.parent_class == 'pixel_size':
	382	self.detector.pixel_size.x = data_point
	383	self.detector.pixel_size_unit = unit
	384	elif tagname == 'y' and self.parent_class == 'pixel_size':
	385	self.detector.pixel_size.y = data_point
	386	self.detector.pixel_size_unit = unit
	387	elif tagname == 'z' and self.parent_class == 'pixel_size':
	388	self.detector.pixel_size.z = data_point
	389	self.detector.pixel_size_unit = unit
	390	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	391	self.detector.orientation.x = data_point
	392	self.detector.orientation_unit = unit
	393	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	394	self.detector.orientation.y = data_point
	395	self.detector.orientation_unit = unit
	396	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	397	self.detector.orientation.z = data_point
	398	self.detector.orientation_unit = unit
[af08e55]	399	# Collimation and Aperture
[250fec92]	400	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	401	self.collimation.length = data_point
	402	self.collimation.length_unit = unit
	403	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	404	self.collimation.name = data_point
	405	elif tagname == 'distance' and self.parent_class == 'aperture':
	406	self.aperture.distance = data_point
	407	self.aperture.distance_unit = unit
	408	elif tagname == 'x' and self.parent_class == 'size':
	409	self.aperture.size.x = data_point
	410	self.collimation.size_unit = unit
	411	elif tagname == 'y' and self.parent_class == 'size':
	412	self.aperture.size.y = data_point
	413	self.collimation.size_unit = unit
	414	elif tagname == 'z' and self.parent_class == 'size':
	415	self.aperture.size.z = data_point
	416	self.collimation.size_unit = unit
	417
[af08e55]	418	# Process Information
[250fec92]	419	elif tagname == 'name' and self.parent_class == 'SASprocess':
	420	self.process.name = data_point
	421	elif tagname == 'description' and self.parent_class == 'SASprocess':
	422	self.process.description = data_point
	423	elif tagname == 'date' and self.parent_class == 'SASprocess':
	424	try:
	425	self.process.date = datetime.datetime.fromtimestamp(data_point)
	426	except:
	427	self.process.date = data_point
	428	elif tagname == 'SASprocessnote':
	429	self.process.notes.append(data_point)
	430	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	431	unit = attr.get("unit", "")
	432	dic = {}
	433	dic["name"] = name
	434	dic["value"] = data_point
	435	dic["unit"] = unit
	436	self.process.term.append(dic)
[250fec92]	437
[af08e55]	438	# Transmission Spectrum
[250fec92]	439	elif tagname == 'T' and self.parent_class == 'Tdata':
	440	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	441	self.transspectrum.transmission_unit = unit
	442	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	443	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	444	self.transspectrum.transmission_deviation_unit = unit
	445	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	446	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	447	self.transspectrum.wavelength_unit = unit
	448
[af08e55]	449	# Source Information
[250fec92]	450	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	451	self.current_datainfo.source.wavelength = data_point
	452	self.current_datainfo.source.wavelength_unit = unit
	453	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	454	self.current_datainfo.source.wavelength_min = data_point
	455	self.current_datainfo.source.wavelength_min_unit = unit
	456	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	457	self.current_datainfo.source.wavelength_max = data_point
	458	self.current_datainfo.source.wavelength_max_unit = unit
	459	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	460	self.current_datainfo.source.wavelength_spread = data_point
	461	self.current_datainfo.source.wavelength_spread_unit = unit
	462	elif tagname == 'x' and self.parent_class == 'beam_size':
	463	self.current_datainfo.source.beam_size.x = data_point
	464	self.current_datainfo.source.beam_size_unit = unit
	465	elif tagname == 'y' and self.parent_class == 'beam_size':
	466	self.current_datainfo.source.beam_size.y = data_point
	467	self.current_datainfo.source.beam_size_unit = unit
	468	elif tagname == 'z' and self.parent_class == 'pixel_size':
	469	self.current_datainfo.source.data_point.z = data_point
	470	self.current_datainfo.source.beam_size_unit = unit
	471	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	472	self.current_datainfo.source.radiation = data_point
	473	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	474	self.current_datainfo.source.beam_shape = data_point
	475
[af08e55]	476	# Everything else goes in meta_data
[250fec92]	477	else:
	478	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	479	self.current_datainfo.meta_data[new_key] = data_point
	480
	481	self.names.remove(tagname_original)
	482	length = 0
	483	if len(self.names) > 1:
	484	length = len(self.names) - 1
	485	self.parent_class = self.names[length]
[654e8e0]	486	if not self._is_call_local() and not recurse:
	487	self.frm = ""
[1686a333]	488	self.add_data_set()
	489	empty = None
	490	return self.output[0], empty
[250fec92]	491
	492
[654e8e0]	493	def _is_call_local(self):
[1686a333]	494	"""
	495
	496	"""
[654e8e0]	497	if self.frm == "":
	498	inter = inspect.stack()
	499	self.frm = inter[2]
	500	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	501	mod_name = mod_name.replace(".py", "")
	502	mod = mod_name.split("sas/")
	503	mod_name = mod[1]
	504	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	505	return False
	506	return True
	507
[d26dea0]	508	def is_cansas(self, ext="xml"):
	509	"""
	510	Checks to see if the xml file is a CanSAS file
	511
	512	:param ext: The file extension of the data file
	513	"""
	514	if self.validate_xml():
	515	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	516	value = self.xmlroot.get(name)
	517	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	518	value.rsplit(" ")[0]:
	519	return True
	520	if ext == "svs":
	521	return True
[250fec92]	522	raise RuntimeError
[d26dea0]	523
[83b6408]	524	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	525	"""
[250fec92]	526	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	527
	528	:param xml_file: The xml file path sent to Reader.read
[250fec92]	529	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	530	"""
	531	base_name = xml_reader.__file__
	532	base_name = base_name.replace("\\", "/")
	533	base = base_name.split("/sas/")[0]
	534
	535	# Load in xml file and get the cansas version from the header
	536	self.set_xml_file(xml_file)
	537	self.cansas_version = self.xmlroot.get("version", "1.0")
	538
	539	# Generic values for the cansas file based on the version
[250fec92]	540	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	541	if schema_path == "":
[250fec92]	542	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	543	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	544
	545	# Link a schema to the XML file.
	546	self.set_schema(schema_path)
	547
[250fec92]	548	def add_data_set(self):
[d26dea0]	549	"""
[250fec92]	550	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	551	private method to generate a new data set.
[d26dea0]	552
[250fec92]	553	:param key: NeXus group name for current tree level
[d26dea0]	554	"""
	555
[250fec92]	556	if self.current_datainfo and self.current_dataset:
	557	self._final_cleanup()
	558	self.data = []
	559	self.current_datainfo = DataInfo()
[d26dea0]	560
[af08e55]	561	def _initialize_new_data_set(self, node=None):
[250fec92]	562	"""
	563	A private class method to generate a new 1D data object.
	564	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	565
[af08e55]	566	:param node: XML node to determine if 1D or 2D data
[250fec92]	567	"""
	568	x = np.array(0)
	569	y = np.array(0)
[af08e55]	570	for child in node:
	571	if child.tag.replace(self.base_ns, "") == "Idata":
	572	for i_child in child:
	573	if i_child.tag.replace(self.base_ns, "") == "Qx":
	574	self.current_dataset = plottable_2D()
	575	return
[250fec92]	576	self.current_dataset = plottable_1D(x, y)
[d26dea0]	577
[250fec92]	578	def add_intermediate(self):
	579	"""
	580	This method stores any intermediate objects within the final data set after fully reading the set.
	581
	582	:param parent: The NXclass name for the h5py Group object that just finished being processed
	583	"""
	584
	585	if self.parent_class == 'SASprocess':
	586	self.current_datainfo.process.append(self.process)
	587	self.process = Process()
	588	elif self.parent_class == 'SASdetector':
	589	self.current_datainfo.detector.append(self.detector)
	590	self.detector = Detector()
	591	elif self.parent_class == 'SAStransmission_spectrum':
	592	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	593	self.transspectrum = TransmissionSpectrum()
	594	elif self.parent_class == 'SAScollimation':
	595	self.current_datainfo.collimation.append(self.collimation)
	596	self.collimation = Collimation()
[5f26aa4]	597	elif self.parent_class == 'aperture':
[250fec92]	598	self.collimation.aperture.append(self.aperture)
	599	self.aperture = Aperture()
	600	elif self.parent_class == 'SASdata':
	601	self._check_for_empty_resolution()
	602	self.data.append(self.current_dataset)
	603
	604	def _final_cleanup(self):
[d26dea0]	605	"""
	606	Final cleanup of the Data1D object to be sure it has all the
	607	appropriate information needed for perspectives
	608	"""
[250fec92]	609
[af08e55]	610	# Append errors to dataset and reset class errors
[250fec92]	611	self.current_datainfo.errors = set()
[d26dea0]	612	for error in self.errors:
[250fec92]	613	self.current_datainfo.errors.add(error)
[d26dea0]	614	self.errors.clear()
[250fec92]	615
[af08e55]	616	# Combine all plottables with datainfo and append each to output
	617	# Type cast data arrays to float64 and find min/max as appropriate
[250fec92]	618	for dataset in self.data:
[af08e55]	619	if isinstance(dataset, plottable_1D):
	620	if dataset.x is not None:
	621	dataset.x = np.delete(dataset.x, [0])
	622	dataset.x = dataset.x.astype(np.float64)
	623	dataset.xmin = np.min(dataset.x)
	624	dataset.xmax = np.max(dataset.x)
	625	if dataset.y is not None:
	626	dataset.y = np.delete(dataset.y, [0])
	627	dataset.y = dataset.y.astype(np.float64)
	628	dataset.ymin = np.min(dataset.y)
	629	dataset.ymax = np.max(dataset.y)
	630	if dataset.dx is not None:
	631	dataset.dx = np.delete(dataset.dx, [0])
	632	dataset.dx = dataset.dx.astype(np.float64)
	633	if dataset.dxl is not None:
	634	dataset.dxl = np.delete(dataset.dxl, [0])
	635	dataset.dxl = dataset.dxl.astype(np.float64)
	636	if dataset.dxw is not None:
	637	dataset.dxw = np.delete(dataset.dxw, [0])
	638	dataset.dxw = dataset.dxw.astype(np.float64)
	639	if dataset.dy is not None:
	640	dataset.dy = np.delete(dataset.dy, [0])
	641	dataset.dy = dataset.dy.astype(np.float64)
	642	np.trim_zeros(dataset.x)
	643	np.trim_zeros(dataset.y)
	644	np.trim_zeros(dataset.dy)
	645	elif isinstance(dataset, plottable_2D):
	646	dataset.data = dataset.data.astype(np.float64)
	647	dataset.qx_data = dataset.qx_data.astype(np.float64)
	648	dataset.xmin = np.min(dataset.qx_data)
	649	dataset.xmax = np.max(dataset.qx_data)
	650	dataset.qy_data = dataset.qy_data.astype(np.float64)
	651	dataset.ymin = np.min(dataset.qy_data)
	652	dataset.ymax = np.max(dataset.qy_data)
	653	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
	654	+ dataset.qy_data * dataset.qy_data)
	655	if dataset.err_data is not None:
	656	dataset.err_data = dataset.err_data.astype(np.float64)
	657	if dataset.dqx_data is not None:
	658	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
	659	if dataset.dqy_data is not None:
	660	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
	661	if dataset.mask is not None:
	662	dataset.mask = dataset.mask.astype(dtype=bool)
	663
	664	if len(dataset.shape) == 2:
	665	n_rows, n_cols = dataset.shape
	666	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
	667	dataset.x_bins = dataset.qx_data[:int(n_cols)]
	668	dataset.data = dataset.data.flatten()
	669	else:
	670	dataset.y_bins = []
	671	dataset.x_bins = []
	672	dataset.data = dataset.data.flatten()
	673
[250fec92]	674	final_dataset = combine_data(dataset, self.current_datainfo)
	675	self.output.append(final_dataset)
[d26dea0]	676
	677	def _create_unique_key(self, dictionary, name, numb=0):
	678	"""
	679	Create a unique key value for any dictionary to prevent overwriting
[250fec92]	680	Recurse until a unique key value is found.
[d26dea0]	681
	682	:param dictionary: A dictionary with any number of entries
	683	:param name: The index of the item to be added to dictionary
	684	:param numb: The number to be appended to the name, starts at 0
	685	"""
	686	if dictionary.get(name) is not None:
	687	numb += 1
	688	name = name.split("_")[0]
	689	name += "_{0}".format(numb)
	690	name = self._create_unique_key(dictionary, name, numb)
	691	return name
	692
[250fec92]	693	def _get_node_value(self, node, tagname):
	694	"""
	695	Get the value of a node and any applicable units
	696
	697	:param node: The XML node to get the value of
	698	:param tagname: The tagname of the node
	699	"""
	700	#Get the text from the node and convert all whitespace to spaces
	701	units = ''
	702	node_value = node.text
	703	if node_value is not None:
	704	node_value = ' '.join(node_value.split())
	705	else:
	706	node_value = ""
	707
	708	# If the value is a float, compile with units.
	709	if self.ns_list.ns_datatype == "float":
	710	# If an empty value is given, set as zero.
	711	if node_value is None or node_value.isspace() \
	712	or node_value.lower() == "nan":
	713	node_value = "0.0"
	714	#Convert the value to the base units
	715	node_value, units = self._unit_conversion(node, tagname, node_value)
	716
	717	# If the value is a timestamp, convert to a datetime object
	718	elif self.ns_list.ns_datatype == "timestamp":
	719	if node_value is None or node_value.isspace():
	720	pass
	721	else:
	722	try:
	723	node_value = \
	724	datetime.datetime.fromtimestamp(node_value)
	725	except ValueError:
	726	node_value = None
	727	return node_value, units
	728
	729	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	730	"""
	731	A unit converter method used to convert the data included in the file
	732	to the default units listed in data_info
	733
[250fec92]	734	:param node: XML node
	735	:param tagname: name of the node
[d26dea0]	736	:param node_value: The value of the current dom node
	737	"""
	738	attr = node.attrib
	739	value_unit = ''
	740	err_msg = None
[682c432]	741	default_unit = None
[5f26aa4]	742	if not isinstance(node_value, float):
	743	node_value = float(node_value)
	744	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	745	try:
	746	local_unit = attr['unit']
[250fec92]	747	unitname = self.ns_list.current_level.get("unit", "")
	748	if "SASdetector" in self.names:
	749	save_in = "detector"
	750	elif "aperture" in self.names:
	751	save_in = "aperture"
	752	elif "SAScollimation" in self.names:
	753	save_in = "collimation"
	754	elif "SAStransmission_spectrum" in self.names:
	755	save_in = "transspectrum"
	756	elif "SASdata" in self.names:
	757	x = np.zeros(1)
	758	y = np.zeros(1)
	759	self.current_data1d = Data1D(x, y)
	760	save_in = "current_data1d"
	761	elif "SASsource" in self.names:
	762	save_in = "current_datainfo.source"
	763	elif "SASsample" in self.names:
	764	save_in = "current_datainfo.sample"
	765	elif "SASprocess" in self.names:
	766	save_in = "process"
	767	else:
	768	save_in = "current_datainfo"
	769	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	770	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	771	and local_unit.lower() != "none":
	772	if HAS_CONVERTER == True:
[af08e55]	773	# Check local units - bad units raise KeyError
[d26dea0]	774	data_conv_q = Converter(local_unit)
	775	value_unit = default_unit
[682c432]	776	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	777	else:
	778	value_unit = local_unit
	779	err_msg = "Unit converter is not available.\n"
	780	else:
	781	value_unit = local_unit
	782	except KeyError:
	783	err_msg = "CanSAS reader: unexpected "
	784	err_msg += "\"{0}\" unit [{1}]; "
	785	err_msg = err_msg.format(tagname, local_unit)
[682c432]	786	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	787	value_unit = local_unit
	788	except:
	789	err_msg = "CanSAS reader: unknown error converting "
	790	err_msg += "\"{0}\" unit [{1}]"
	791	err_msg = err_msg.format(tagname, local_unit)
	792	value_unit = local_unit
	793	elif 'unit' in attr:
	794	value_unit = attr['unit']
	795	if err_msg:
	796	self.errors.add(err_msg)
	797	return node_value, value_unit
	798
[250fec92]	799	def _check_for_empty_data(self):
[d26dea0]	800	"""
	801	Creates an empty data set if no data is passed to the reader
	802
	803	:param data1d: presumably a Data1D object
	804	"""
[250fec92]	805	if self.current_dataset == None:
	806	x_vals = np.empty(0)
	807	y_vals = np.empty(0)
	808	dx_vals = np.empty(0)
	809	dy_vals = np.empty(0)
	810	dxl = np.empty(0)
	811	dxw = np.empty(0)
	812	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	813	self.current_dataset.dxl = dxl
	814	self.current_dataset.dxw = dxw
	815
	816	def _check_for_empty_resolution(self):
[d26dea0]	817	"""
	818	A method to check all resolution data sets are the same size as I and Q
	819	"""
[af08e55]	820	if isinstance(self.current_dataset, plottable_1D):
	821	dql_exists = False
	822	dqw_exists = False
	823	dq_exists = False
	824	di_exists = False
	825	if self.current_dataset.dxl is not None:
	826	dql_exists = True
	827	if self.current_dataset.dxw is not None:
	828	dqw_exists = True
	829	if self.current_dataset.dx is not None:
	830	dq_exists = True
	831	if self.current_dataset.dy is not None:
	832	di_exists = True
	833	if dqw_exists and not dql_exists:
	834	array_size = self.current_dataset.dxw.size - 1
	835	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
	836	np.zeros([array_size]))
	837	elif dql_exists and not dqw_exists:
	838	array_size = self.current_dataset.dxl.size - 1
	839	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
	840	np.zeros([array_size]))
	841	elif not dql_exists and not dqw_exists and not dq_exists:
	842	array_size = self.current_dataset.x.size - 1
	843	self.current_dataset.dx = np.append(self.current_dataset.dx,
	844	np.zeros([array_size]))
	845	if not di_exists:
	846	array_size = self.current_dataset.y.size - 1
	847	self.current_dataset.dy = np.append(self.current_dataset.dy,
	848	np.zeros([array_size]))
	849	elif isinstance(self.current_dataset, plottable_2D):
	850	dqx_exists = False
	851	dqy_exists = False
	852	di_exists = False
	853	mask_exists = False
	854	if self.current_dataset.dqx_data is not None:
	855	dqx_exists = True
	856	if self.current_dataset.dqy_data is not None:
	857	dqy_exists = True
	858	if self.current_dataset.err_data is not None:
	859	di_exists = True
	860	if self.current_dataset.mask is not None:
	861	mask_exists = True
	862	if not dqy_exists:
	863	array_size = self.current_dataset.qy_data.size - 1
	864	self.current_dataset.dqy_data = np.append(
	865	self.current_dataset.dqy_data, np.zeros([array_size]))
	866	if not dqx_exists:
	867	array_size = self.current_dataset.qx_data.size - 1
	868	self.current_dataset.dqx_data = np.append(
	869	self.current_dataset.dqx_data, np.zeros([array_size]))
	870	if not di_exists:
	871	array_size = self.current_dataset.data.size - 1
	872	self.current_dataset.err_data = np.append(
	873	self.current_dataset.err_data, np.zeros([array_size]))
	874	if not mask_exists:
	875	array_size = self.current_dataset.data.size - 1
	876	self.current_dataset.mask = np.append(
	877	self.current_dataset.mask,
	878	np.ones([array_size] ,dtype=bool))
[250fec92]	879
	880	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	881
[250fec92]	882	def write(self, filename, datainfo):
[d26dea0]	883	"""
[250fec92]	884	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	885
[250fec92]	886	:param filename: name of the file to write
	887	:param datainfo: Data1D object
	888	"""
	889	# Create XML document
	890	doc, _ = self._to_xml_doc(datainfo)
	891	# Write the file
	892	file_ref = open(filename, 'w')
	893	if self.encoding == None:
	894	self.encoding = "UTF-8"
	895	doc.write(file_ref, encoding=self.encoding,
	896	pretty_print=True, xml_declaration=True)
	897	file_ref.close()
[d26dea0]	898
[250fec92]	899	def _to_xml_doc(self, datainfo):
[d26dea0]	900	"""
[250fec92]	901	Create an XML document to contain the content of a Data1D
[d26dea0]	902
[250fec92]	903	:param datainfo: Data1D object
[d26dea0]	904	"""
[af08e55]	905	is_2d = False
[83c09af]	906	if issubclass(datainfo.__class__, Data2D):
	907	is_2d = True
[d26dea0]	908
[250fec92]	909	# Get PIs and create root element
	910	pi_string = self._get_pi_string()
	911	# Define namespaces and create SASroot object
	912	main_node = self._create_main_node()
	913	# Create ElementTree, append SASroot and apply processing instructions
	914	base_string = pi_string + self.to_string(main_node)
	915	base_element = self.create_element_from_string(base_string)
	916	doc = self.create_tree(base_element)
	917	# Create SASentry Element
	918	entry_node = self.create_element("SASentry")
	919	root = doc.getroot()
	920	root.append(entry_node)
[d26dea0]	921
[250fec92]	922	# Add Title to SASentry
	923	self.write_node(entry_node, "Title", datainfo.title)
	924	# Add Run to SASentry
	925	self._write_run_names(datainfo, entry_node)
	926	# Add Data info to SASEntry
[83c09af]	927	if is_2d:
	928	self._write_data_2d(datainfo, entry_node)
	929	else:
	930	self._write_data(datainfo, entry_node)
[250fec92]	931	# Transmission Spectrum Info
	932	self._write_trans_spectrum(datainfo, entry_node)
	933	# Sample info
	934	self._write_sample_info(datainfo, entry_node)
	935	# Instrument info
	936	instr = self._write_instrument(datainfo, entry_node)
	937	# Source
	938	self._write_source(datainfo, instr)
	939	# Collimation
	940	self._write_collimation(datainfo, instr)
	941	# Detectors
	942	self._write_detectors(datainfo, instr)
	943	# Processes info
	944	self._write_process_notes(datainfo, entry_node)
	945	# Note info
	946	self._write_notes(datainfo, entry_node)
	947	# Return the document, and the SASentry node associated with
	948	# the data we just wrote
	949	# If the calling function was not the cansas reader, return a minidom
	950	# object rather than an lxml object.
[654e8e0]	951	self.frm = inspect.stack()[1]
	952	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	953	return doc, entry_node
[d26dea0]	954
[250fec92]	955	def write_node(self, parent, name, value, attr=None):
	956	"""
	957	:param doc: document DOM
	958	:param parent: parent node
	959	:param name: tag of the element
	960	:param value: value of the child text node
	961	:param attr: attribute dictionary
[d26dea0]	962
[250fec92]	963	:return: True if something was appended, otherwise False
	964	"""
	965	if value is not None:
	966	parent = self.ebuilder(parent, name, value, attr)
	967	return True
	968	return False
[d26dea0]	969
	970	def _get_pi_string(self):
	971	"""
	972	Creates the processing instructions header for writing to file
	973	"""
	974	pis = self.return_processing_instructions()
	975	if len(pis) > 0:
	976	pi_tree = self.create_tree(pis[0])
	977	i = 1
	978	for i in range(1, len(pis) - 1):
	979	pi_tree = self.append(pis[i], pi_tree)
	980	pi_string = self.to_string(pi_tree)
	981	else:
	982	pi_string = ""
	983	return pi_string
	984
	985	def _create_main_node(self):
	986	"""
	987	Creates the primary xml header used when writing to file
	988	"""
	989	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	990	version = self.cansas_version
	991	n_s = CANSAS_NS.get(version).get("ns")
	992	if version == "1.1":
	993	url = "http://www.cansas.org/formats/1.1/"
	994	else:
	995	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	996	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	997	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	998	"version" : version}
	999	nsmap = {'xsi' : xsi, None: n_s}
	1000
	1001	main_node = self.create_element("{" + n_s + "}SASroot",
	1002	attrib=attrib, nsmap=nsmap)
	1003	return main_node
	1004
	1005	def _write_run_names(self, datainfo, entry_node):
	1006	"""
	1007	Writes the run names to the XML file
	1008
	1009	:param datainfo: The Data1D object the information is coming from
	1010	:param entry_node: lxml node ElementTree object to be appended to
	1011	"""
	1012	if datainfo.run == None or datainfo.run == []:
	1013	datainfo.run.append(RUN_NAME_DEFAULT)
	1014	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	1015	for item in datainfo.run:
	1016	runname = {}
	1017	if item in datainfo.run_name and \
	1018	len(str(datainfo.run_name[item])) > 1:
	1019	runname = {'name': datainfo.run_name[item]}
	1020	self.write_node(entry_node, "Run", item, runname)
	1021
	1022	def _write_data(self, datainfo, entry_node):
	1023	"""
[83c09af]	1024	Writes 1D I and Q data to the XML file
[d26dea0]	1025
	1026	:param datainfo: The Data1D object the information is coming from
	1027	:param entry_node: lxml node ElementTree object to be appended to
	1028	"""
	1029	node = self.create_element("SASdata")
	1030	self.append(node, entry_node)
	1031
	1032	for i in range(len(datainfo.x)):
	1033	point = self.create_element("Idata")
	1034	node.append(point)
	1035	self.write_node(point, "Q", datainfo.x[i],
[ad4632c]	1036	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[d26dea0]	1037	if len(datainfo.y) >= i:
	1038	self.write_node(point, "I", datainfo.y[i],
[ad4632c]	1039	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	1040	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	1041	self.write_node(point, "Idev", datainfo.dy[i],
[ad4632c]	1042	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	1043	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	1044	self.write_node(point, "Qdev", datainfo.dx[i],
[ad4632c]	1045	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	1046	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	1047	self.write_node(point, "dQw", datainfo.dxw[i],
[ad4632c]	1048	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	1049	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	1050	self.write_node(point, "dQl", datainfo.dxl[i],
[ad4632c]	1051	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
	1052	if datainfo.isSesans:
	1053	sesans = self.create_element("Sesans")
	1054	sesans.text = str(datainfo.isSesans)
	1055	node.append(sesans)
	1056	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
	1057	{'unit': datainfo.sample.zacceptance[1]})
	1058
[d26dea0]	1059
[83c09af]	1060	def _write_data_2d(self, datainfo, entry_node):
	1061	"""
	1062	Writes 2D data to the XML file
	1063
	1064	:param datainfo: The Data2D object the information is coming from
	1065	:param entry_node: lxml node ElementTree object to be appended to
	1066	"""
[af08e55]	1067	attr = {}
	1068	if datainfo.data.shape:
[1905128]	1069	attr["x_bins"] = str(len(datainfo.x_bins))
	1070	attr["y_bins"] = str(len(datainfo.y_bins))
	1071	node = self.create_element("SASdata", attr)
[83c09af]	1072	self.append(node, entry_node)
	1073
[1905128]	1074	point = self.create_element("Idata")
	1075	node.append(point)
	1076	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
	1077	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
	1078	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
	1079
	1080	self.write_node(point, "Qx", qx,
	1081	{'unit': datainfo._xunit})
	1082	self.write_node(point, "Qy", qy,
	1083	{'unit': datainfo._yunit})
	1084	self.write_node(point, "I", intensity,
	1085	{'unit': datainfo._zunit})
	1086	if datainfo.err_data is not None:
[5e6df0e]	1087	err = ','.join([str(datainfo.err_data[i]) for i in
	1088	xrange(len(datainfo.err_data))])
[1905128]	1089	self.write_node(point, "Idev", err,
[83c09af]	1090	{'unit': datainfo._zunit})
[1905128]	1091	if datainfo.dqy_data is not None:
[5e6df0e]	1092	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
	1093	xrange(len(datainfo.dqy_data))])
[1905128]	1094	self.write_node(point, "Qydev", dqy,
	1095	{'unit': datainfo._yunit})
	1096	if datainfo.dqx_data is not None:
[5e6df0e]	1097	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
	1098	xrange(len(datainfo.dqx_data))])
[1905128]	1099	self.write_node(point, "Qxdev", dqx,
	1100	{'unit': datainfo._xunit})
	1101	if datainfo.mask is not None:
[5e6df0e]	1102	mask = ','.join(
[bcabf4e]	1103	["1" if datainfo.mask[i] else "0"
	1104	for i in xrange(len(datainfo.mask))])
[1905128]	1105	self.write_node(point, "Mask", mask)
[83c09af]	1106
[d26dea0]	1107	def _write_trans_spectrum(self, datainfo, entry_node):
	1108	"""
	1109	Writes the transmission spectrum data to the XML file
	1110
	1111	:param datainfo: The Data1D object the information is coming from
	1112	:param entry_node: lxml node ElementTree object to be appended to
	1113	"""
	1114	for i in range(len(datainfo.trans_spectrum)):
	1115	spectrum = datainfo.trans_spectrum[i]
	1116	node = self.create_element("SAStransmission_spectrum",
	1117	{"name" : spectrum.name})
	1118	self.append(node, entry_node)
	1119	if isinstance(spectrum.timestamp, datetime.datetime):
	1120	node.setAttribute("timestamp", spectrum.timestamp)
	1121	for i in range(len(spectrum.wavelength)):
	1122	point = self.create_element("Tdata")
	1123	node.append(point)
	1124	self.write_node(point, "Lambda", spectrum.wavelength[i],
	1125	{'unit': spectrum.wavelength_unit})
	1126	self.write_node(point, "T", spectrum.transmission[i],
	1127	{'unit': spectrum.transmission_unit})
	1128	if spectrum.transmission_deviation != None \
	1129	and len(spectrum.transmission_deviation) >= i:
	1130	self.write_node(point, "Tdev",
	1131	spectrum.transmission_deviation[i],
	1132	{'unit':
	1133	spectrum.transmission_deviation_unit})
	1134
	1135	def _write_sample_info(self, datainfo, entry_node):
	1136	"""
	1137	Writes the sample information to the XML file
	1138
	1139	:param datainfo: The Data1D object the information is coming from
	1140	:param entry_node: lxml node ElementTree object to be appended to
	1141	"""
	1142	sample = self.create_element("SASsample")
	1143	if datainfo.sample.name is not None:
	1144	self.write_attribute(sample, "name",
	1145	str(datainfo.sample.name))
	1146	self.append(sample, entry_node)
	1147	self.write_node(sample, "ID", str(datainfo.sample.ID))
	1148	self.write_node(sample, "thickness", datainfo.sample.thickness,
	1149	{"unit": datainfo.sample.thickness_unit})
	1150	self.write_node(sample, "transmission", datainfo.sample.transmission)
	1151	self.write_node(sample, "temperature", datainfo.sample.temperature,
	1152	{"unit": datainfo.sample.temperature_unit})
	1153
	1154	pos = self.create_element("position")
	1155	written = self.write_node(pos,
	1156	"x",
	1157	datainfo.sample.position.x,
	1158	{"unit": datainfo.sample.position_unit})
	1159	written = written \| self.write_node( \
	1160	pos, "y", datainfo.sample.position.y,
	1161	{"unit": datainfo.sample.position_unit})
	1162	written = written \| self.write_node( \
	1163	pos, "z", datainfo.sample.position.z,
	1164	{"unit": datainfo.sample.position_unit})
	1165	if written == True:
	1166	self.append(pos, sample)
	1167
	1168	ori = self.create_element("orientation")
	1169	written = self.write_node(ori, "roll",
	1170	datainfo.sample.orientation.x,
	1171	{"unit": datainfo.sample.orientation_unit})
	1172	written = written \| self.write_node( \
	1173	ori, "pitch", datainfo.sample.orientation.y,
	1174	{"unit": datainfo.sample.orientation_unit})
	1175	written = written \| self.write_node( \
	1176	ori, "yaw", datainfo.sample.orientation.z,
	1177	{"unit": datainfo.sample.orientation_unit})
	1178	if written == True:
	1179	self.append(ori, sample)
	1180
	1181	for item in datainfo.sample.details:
	1182	self.write_node(sample, "details", item)
	1183
	1184	def _write_instrument(self, datainfo, entry_node):
	1185	"""
	1186	Writes the instrumental information to the XML file
	1187
	1188	:param datainfo: The Data1D object the information is coming from
	1189	:param entry_node: lxml node ElementTree object to be appended to
	1190	"""
	1191	instr = self.create_element("SASinstrument")
	1192	self.append(instr, entry_node)
	1193	self.write_node(instr, "name", datainfo.instrument)
	1194	return instr
	1195
	1196	def _write_source(self, datainfo, instr):
	1197	"""
	1198	Writes the source information to the XML file
	1199
	1200	:param datainfo: The Data1D object the information is coming from
	1201	:param instr: instrument node to be appended to
	1202	"""
	1203	source = self.create_element("SASsource")
	1204	if datainfo.source.name is not None:
	1205	self.write_attribute(source, "name",
	1206	str(datainfo.source.name))
	1207	self.append(source, instr)
	1208	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	1209	datainfo.source.radiation = "neutron"
	1210	self.write_node(source, "radiation", datainfo.source.radiation)
	1211
	1212	size = self.create_element("beam_size")
	1213	if datainfo.source.beam_size_name is not None:
	1214	self.write_attribute(size, "name",
	1215	str(datainfo.source.beam_size_name))
	1216	written = self.write_node( \
	1217	size, "x", datainfo.source.beam_size.x,
	1218	{"unit": datainfo.source.beam_size_unit})
	1219	written = written \| self.write_node( \
	1220	size, "y", datainfo.source.beam_size.y,
	1221	{"unit": datainfo.source.beam_size_unit})
	1222	written = written \| self.write_node( \
	1223	size, "z", datainfo.source.beam_size.z,
	1224	{"unit": datainfo.source.beam_size_unit})
	1225	if written == True:
	1226	self.append(size, source)
	1227
	1228	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1229	self.write_node(source, "wavelength",
	1230	datainfo.source.wavelength,
	1231	{"unit": datainfo.source.wavelength_unit})
	1232	self.write_node(source, "wavelength_min",
	1233	datainfo.source.wavelength_min,
	1234	{"unit": datainfo.source.wavelength_min_unit})
	1235	self.write_node(source, "wavelength_max",
	1236	datainfo.source.wavelength_max,
	1237	{"unit": datainfo.source.wavelength_max_unit})
	1238	self.write_node(source, "wavelength_spread",
	1239	datainfo.source.wavelength_spread,
	1240	{"unit": datainfo.source.wavelength_spread_unit})
	1241
	1242	def _write_collimation(self, datainfo, instr):
	1243	"""
	1244	Writes the collimation information to the XML file
	1245
	1246	:param datainfo: The Data1D object the information is coming from
	1247	:param instr: lxml node ElementTree object to be appended to
	1248	"""
	1249	if datainfo.collimation == [] or datainfo.collimation == None:
	1250	coll = Collimation()
	1251	datainfo.collimation.append(coll)
	1252	for item in datainfo.collimation:
	1253	coll = self.create_element("SAScollimation")
	1254	if item.name is not None:
	1255	self.write_attribute(coll, "name", str(item.name))
	1256	self.append(coll, instr)
	1257
	1258	self.write_node(coll, "length", item.length,
	1259	{"unit": item.length_unit})
	1260
	1261	for aperture in item.aperture:
	1262	apert = self.create_element("aperture")
	1263	if aperture.name is not None:
	1264	self.write_attribute(apert, "name", str(aperture.name))
	1265	if aperture.type is not None:
	1266	self.write_attribute(apert, "type", str(aperture.type))
	1267	self.append(apert, coll)
	1268
	1269	size = self.create_element("size")
	1270	if aperture.size_name is not None:
	1271	self.write_attribute(size, "name",
	1272	str(aperture.size_name))
	1273	written = self.write_node(size, "x", aperture.size.x,
	1274	{"unit": aperture.size_unit})
	1275	written = written \| self.write_node( \
	1276	size, "y", aperture.size.y,
	1277	{"unit": aperture.size_unit})
	1278	written = written \| self.write_node( \
	1279	size, "z", aperture.size.z,
	1280	{"unit": aperture.size_unit})
	1281	if written == True:
	1282	self.append(size, apert)
	1283
	1284	self.write_node(apert, "distance", aperture.distance,
	1285	{"unit": aperture.distance_unit})
	1286
	1287	def _write_detectors(self, datainfo, instr):
	1288	"""
	1289	Writes the detector information to the XML file
	1290
	1291	:param datainfo: The Data1D object the information is coming from
	1292	:param inst: lxml instrument node to be appended to
	1293	"""
	1294	if datainfo.detector == None or datainfo.detector == []:
	1295	det = Detector()
	1296	det.name = ""
	1297	datainfo.detector.append(det)
	1298
	1299	for item in datainfo.detector:
	1300	det = self.create_element("SASdetector")
	1301	written = self.write_node(det, "name", item.name)
	1302	written = written \| self.write_node(det, "SDD", item.distance,
	1303	{"unit": item.distance_unit})
	1304	if written == True:
	1305	self.append(det, instr)
	1306
	1307	off = self.create_element("offset")
	1308	written = self.write_node(off, "x", item.offset.x,
	1309	{"unit": item.offset_unit})
	1310	written = written \| self.write_node(off, "y", item.offset.y,
	1311	{"unit": item.offset_unit})
	1312	written = written \| self.write_node(off, "z", item.offset.z,
	1313	{"unit": item.offset_unit})
	1314	if written == True:
	1315	self.append(off, det)
	1316
	1317	ori = self.create_element("orientation")
	1318	written = self.write_node(ori, "roll", item.orientation.x,
	1319	{"unit": item.orientation_unit})
	1320	written = written \| self.write_node(ori, "pitch",
	1321	item.orientation.y,
	1322	{"unit": item.orientation_unit})
	1323	written = written \| self.write_node(ori, "yaw",
	1324	item.orientation.z,
	1325	{"unit": item.orientation_unit})
	1326	if written == True:
	1327	self.append(ori, det)
	1328
	1329	center = self.create_element("beam_center")
	1330	written = self.write_node(center, "x", item.beam_center.x,
	1331	{"unit": item.beam_center_unit})
	1332	written = written \| self.write_node(center, "y",
	1333	item.beam_center.y,
	1334	{"unit": item.beam_center_unit})
	1335	written = written \| self.write_node(center, "z",
	1336	item.beam_center.z,
	1337	{"unit": item.beam_center_unit})
	1338	if written == True:
	1339	self.append(center, det)
	1340
	1341	pix = self.create_element("pixel_size")
	1342	written = self.write_node(pix, "x", item.pixel_size.x,
	1343	{"unit": item.pixel_size_unit})
	1344	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1345	{"unit": item.pixel_size_unit})
	1346	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1347	{"unit": item.pixel_size_unit})
	1348	if written == True:
	1349	self.append(pix, det)
[3a9801f]	1350	self.write_node(det, "slit_length", item.slit_length,
	1351	{"unit": item.slit_length_unit})
	1352
[d26dea0]	1353
	1354	def _write_process_notes(self, datainfo, entry_node):
	1355	"""
	1356	Writes the process notes to the XML file
	1357
	1358	:param datainfo: The Data1D object the information is coming from
	1359	:param entry_node: lxml node ElementTree object to be appended to
	1360
	1361	"""
	1362	for item in datainfo.process:
	1363	node = self.create_element("SASprocess")
	1364	self.append(node, entry_node)
	1365	self.write_node(node, "name", item.name)
	1366	self.write_node(node, "date", item.date)
	1367	self.write_node(node, "description", item.description)
	1368	for term in item.term:
[1686a333]	1369	if isinstance(term, list):
	1370	value = term['value']
	1371	del term['value']
[5f26aa4]	1372	elif isinstance(term, dict):
	1373	value = term.get("value")
	1374	del term['value']
[1686a333]	1375	else:
	1376	value = term
[d26dea0]	1377	self.write_node(node, "term", value, term)
	1378	for note in item.notes:
	1379	self.write_node(node, "SASprocessnote", note)
	1380	if len(item.notes) == 0:
	1381	self.write_node(node, "SASprocessnote", "")
	1382
	1383	def _write_notes(self, datainfo, entry_node):
	1384	"""
	1385	Writes the notes to the XML file and creates an empty note if none
	1386	exist
	1387
	1388	:param datainfo: The Data1D object the information is coming from
	1389	:param entry_node: lxml node ElementTree object to be appended to
	1390
	1391	"""
	1392	if len(datainfo.notes) == 0:
	1393	node = self.create_element("SASnote")
	1394	self.append(node, entry_node)
	1395	else:
	1396	for item in datainfo.notes:
	1397	node = self.create_element("SASnote")
	1398	self.write_text(node, item)
	1399	self.append(node, entry_node)
	1400
[654e8e0]	1401	def _check_origin(self, entry_node, doc):
[d26dea0]	1402	"""
	1403	Return the document, and the SASentry node associated with
	1404	the data we just wrote.
	1405	If the calling function was not the cansas reader, return a minidom
	1406	object rather than an lxml object.
	1407
	1408	:param entry_node: lxml node ElementTree object to be appended to
	1409	:param doc: entire xml tree
	1410	"""
[654e8e0]	1411	if not self.frm:
	1412	self.frm = inspect.stack()[1]
	1413	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1414	mod_name = mod_name.replace(".py", "")
	1415	mod = mod_name.split("sas/")
	1416	mod_name = mod[1]
[45d90b9]	1417	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1418	string = self.to_string(doc, pretty_print=False)
	1419	doc = parseString(string)
	1420	node_name = entry_node.tag
	1421	node_list = doc.getElementsByTagName(node_name)
	1422	entry_node = node_list.item(0)
[5ce7f17]	1423	return doc, entry_node
[d26dea0]	1424
	1425	# DO NOT REMOVE - used in saving and loading panel states.
	1426	def _store_float(self, location, node, variable, storage, optional=True):
	1427	"""
	1428	Get the content of a xpath location and store
	1429	the result. Check that the units are compatible
	1430	with the destination. The value is expected to
	1431	be a float.
	1432
	1433	The xpath location might or might not exist.
	1434	If it does not exist, nothing is done
	1435
	1436	:param location: xpath location to fetch
	1437	:param node: node to read the data from
	1438	:param variable: name of the data member to store it in [string]
	1439	:param storage: data object that has the 'variable' data member
	1440	:param optional: if True, no exception will be raised
	1441	if unit conversion can't be done
	1442
	1443	:raise ValueError: raised when the units are not recognized
	1444	"""
	1445	entry = get_content(location, node)
	1446	try:
	1447	value = float(entry.text)
	1448	except:
	1449	value = None
	1450
	1451	if value is not None:
	1452	# If the entry has units, check to see that they are
	1453	# compatible with what we currently have in the data object
	1454	units = entry.get('unit')
	1455	if units is not None:
	1456	toks = variable.split('.')
	1457	local_unit = None
	1458	exec "local_unit = storage.%s_unit" % toks[0]
	1459	if local_unit != None and units.lower() != local_unit.lower():
	1460	if HAS_CONVERTER == True:
	1461	try:
	1462	conv = Converter(units)
	1463	exec "storage.%s = %g" % \
	1464	(variable, conv(value, units=local_unit))
	1465	except:
	1466	_, exc_value, _ = sys.exc_info()
	1467	err_mess = "CanSAS reader: could not convert"
	1468	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1469	% (variable, units, local_unit, exc_value)
	1470	self.errors.add(err_mess)
	1471	if optional:
	1472	logging.info(err_mess)
	1473	else:
	1474	raise ValueError, err_mess
	1475	else:
	1476	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1477	% (variable, units)
	1478	err_mess += " expecting [%s]" % local_unit
	1479	self.errors.add(err_mess)
	1480	if optional:
	1481	logging.info(err_mess)
	1482	else:
	1483	raise ValueError, err_mess
	1484	else:
	1485	exec "storage.%s = value" % variable
	1486	else:
	1487	exec "storage.%s = value" % variable
	1488
	1489	# DO NOT REMOVE - used in saving and loading panel states.
	1490	def _store_content(self, location, node, variable, storage):
	1491	"""
	1492	Get the content of a xpath location and store
	1493	the result. The value is treated as a string.
	1494
	1495	The xpath location might or might not exist.
	1496	If it does not exist, nothing is done
	1497
	1498	:param location: xpath location to fetch
	1499	:param node: node to read the data from
	1500	:param variable: name of the data member to store it in [string]
	1501	:param storage: data object that has the 'variable' data member
	1502
	1503	:return: return a list of errors
	1504	"""
	1505	entry = get_content(location, node)
	1506	if entry is not None and entry.text is not None:
	1507	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1508
	1509
	1510	# DO NOT REMOVE Called by outside packages:
	1511	# sas.sasgui.perspectives.invariant.invariant_state
	1512	# sas.sasgui.perspectives.fitting.pagestate
	1513	def get_content(location, node):
	1514	"""
	1515	Get the first instance of the content of a xpath location.
	1516
	1517	:param location: xpath location
	1518	:param node: node to start at
	1519
	1520	:return: Element, or None
	1521	"""
	1522	nodes = node.xpath(location,
	1523	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1524	if len(nodes) > 0:
	1525	return nodes[0]
	1526	else:
	1527	return None
	1528
	1529	# DO NOT REMOVE Called by outside packages:
	1530	# sas.sasgui.perspectives.fitting.pagestate
	1531	def write_node(doc, parent, name, value, attr=None):
	1532	"""
	1533	:param doc: document DOM
	1534	:param parent: parent node
	1535	:param name: tag of the element
	1536	:param value: value of the child text node
	1537	:param attr: attribute dictionary
	1538
	1539	:return: True if something was appended, otherwise False
	1540	"""
	1541	if attr is None:
	1542	attr = {}
	1543	if value is not None:
	1544	node = doc.createElement(name)
	1545	node.appendChild(doc.createTextNode(str(value)))
	1546	for item in attr:
	1547	node.setAttribute(item, attr[item])
	1548	parent.appendChild(node)
	1549	return True
	1550	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 9a5097c

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