cansas_reader.py @ 13043af

Last change on this file since 13043af was 0d64713, checked in by GitHub <noreply@…>, 8 years ago
Revert "Sesans41"
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[d26dea0]	1	"""
	2	CanSAS data reader - new recursive cansas_version.
	3	"""
	4	############################################################################
	5	#This software was developed by the University of Tennessee as part of the
	6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	7	#project funded by the US National Science Foundation.
	8	#If you use DANSE applications to do scientific research that leads to
	9	#publication, we ask that you acknowledge the use of the software with the
	10	#following sentence:
	11	#This work benefited from DANSE software developed under NSF award DMR-0520547.
	12	#copyright 2008,2009 University of Tennessee
	13	#############################################################################
[0f1e140]	14
[d26dea0]	15	import logging
[250fec92]	16	import numpy as np
[d26dea0]	17	import os
	18	import sys
	19	import datetime
	20	import inspect
	21	# For saving individual sections of data
[83c09af]	22	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
[af08e55]	23	plottable_1D, plottable_2D
[83c09af]	24	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
	25	Detector, Process, Aperture
	26	from sas.sascalc.dataloader.data_info import \
	27	combine_data_info_with_plottable as combine_data
[b699768]	28	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	29	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
[250fec92]	30	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
[d26dea0]	31
[682c432]	32	# The following 2 imports ARE used. Do not remove either.
	33	import xml.dom.minidom
	34	from xml.dom.minidom import parseString
	35
[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):
[0d64713]	263	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	264	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	265	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	266	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	267	elif tagname == 'Q':
[0d64713]	268	self.current_dataset.xaxis("Q", unit)
[250fec92]	269	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	270	elif tagname == 'Qdev':
	271	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	272	elif tagname == 'dQw':
	273	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	274	elif tagname == 'dQl':
	275	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	276	elif tagname == 'Qmean':
	277	pass
	278	elif tagname == 'Shadowfactor':
	279	pass
[250fec92]	280
[af08e55]	281	# I and Qx, Qy - 2D data
	282	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	283	self.current_dataset.yaxis("Intensity", unit)
[1905128]	284	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	285	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	286	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	287	elif tagname == 'Qx':
	288	self.current_dataset.xaxis("Qx", unit)
[1905128]	289	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	290	elif tagname == 'Qy':
	291	self.current_dataset.yaxis("Qy", unit)
[1905128]	292	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	293	elif tagname == 'Qxdev':
	294	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	295	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	296	elif tagname == 'Qydev':
	297	self.current_dataset.yaxis("Qydev", unit)
[1905128]	298	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	299	elif tagname == 'Mask':
[bcabf4e]	300	inter = [item == "1" for item in data_point.split(",")]
[1905128]	301	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	302
	303	# Sample Information
[250fec92]	304	elif tagname == 'ID' and self.parent_class == 'SASsample':
	305	self.current_datainfo.sample.ID = data_point
	306	elif tagname == 'Title' and self.parent_class == 'SASsample':
	307	self.current_datainfo.sample.name = data_point
	308	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	309	self.current_datainfo.sample.thickness = data_point
	310	self.current_datainfo.sample.thickness_unit = unit
	311	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	312	self.current_datainfo.sample.transmission = data_point
	313	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	314	self.current_datainfo.sample.temperature = data_point
	315	self.current_datainfo.sample.temperature_unit = unit
	316	elif tagname == 'details' and self.parent_class == 'SASsample':
	317	self.current_datainfo.sample.details.append(data_point)
	318	elif tagname == 'x' and self.parent_class == 'position':
	319	self.current_datainfo.sample.position.x = data_point
	320	self.current_datainfo.sample.position_unit = unit
	321	elif tagname == 'y' and self.parent_class == 'position':
	322	self.current_datainfo.sample.position.y = data_point
	323	self.current_datainfo.sample.position_unit = unit
	324	elif tagname == 'z' and self.parent_class == 'position':
	325	self.current_datainfo.sample.position.z = data_point
	326	self.current_datainfo.sample.position_unit = unit
	327	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	328	self.current_datainfo.sample.orientation.x = data_point
	329	self.current_datainfo.sample.orientation_unit = unit
	330	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	331	self.current_datainfo.sample.orientation.y = data_point
	332	self.current_datainfo.sample.orientation_unit = unit
	333	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	334	self.current_datainfo.sample.orientation.z = data_point
	335	self.current_datainfo.sample.orientation_unit = unit
	336
[af08e55]	337	# Instrumental Information
[250fec92]	338	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	339	self.current_datainfo.instrument = data_point
[af08e55]	340	# Detector Information
[250fec92]	341	elif tagname == 'name' and self.parent_class == 'SASdetector':
	342	self.detector.name = data_point
	343	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	344	self.detector.distance = data_point
	345	self.detector.distance_unit = unit
	346	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	347	self.detector.slit_length = data_point
	348	self.detector.slit_length_unit = unit
	349	elif tagname == 'x' and self.parent_class == 'offset':
	350	self.detector.offset.x = data_point
	351	self.detector.offset_unit = unit
	352	elif tagname == 'y' and self.parent_class == 'offset':
	353	self.detector.offset.y = data_point
	354	self.detector.offset_unit = unit
	355	elif tagname == 'z' and self.parent_class == 'offset':
	356	self.detector.offset.z = data_point
	357	self.detector.offset_unit = unit
	358	elif tagname == 'x' and self.parent_class == 'beam_center':
	359	self.detector.beam_center.x = data_point
	360	self.detector.beam_center_unit = unit
	361	elif tagname == 'y' and self.parent_class == 'beam_center':
	362	self.detector.beam_center.y = data_point
	363	self.detector.beam_center_unit = unit
	364	elif tagname == 'z' and self.parent_class == 'beam_center':
	365	self.detector.beam_center.z = data_point
	366	self.detector.beam_center_unit = unit
	367	elif tagname == 'x' and self.parent_class == 'pixel_size':
	368	self.detector.pixel_size.x = data_point
	369	self.detector.pixel_size_unit = unit
	370	elif tagname == 'y' and self.parent_class == 'pixel_size':
	371	self.detector.pixel_size.y = data_point
	372	self.detector.pixel_size_unit = unit
	373	elif tagname == 'z' and self.parent_class == 'pixel_size':
	374	self.detector.pixel_size.z = data_point
	375	self.detector.pixel_size_unit = unit
	376	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	377	self.detector.orientation.x = data_point
	378	self.detector.orientation_unit = unit
	379	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	380	self.detector.orientation.y = data_point
	381	self.detector.orientation_unit = unit
	382	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	383	self.detector.orientation.z = data_point
	384	self.detector.orientation_unit = unit
[af08e55]	385	# Collimation and Aperture
[250fec92]	386	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	387	self.collimation.length = data_point
	388	self.collimation.length_unit = unit
	389	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	390	self.collimation.name = data_point
	391	elif tagname == 'distance' and self.parent_class == 'aperture':
	392	self.aperture.distance = data_point
	393	self.aperture.distance_unit = unit
	394	elif tagname == 'x' and self.parent_class == 'size':
	395	self.aperture.size.x = data_point
	396	self.collimation.size_unit = unit
	397	elif tagname == 'y' and self.parent_class == 'size':
	398	self.aperture.size.y = data_point
	399	self.collimation.size_unit = unit
	400	elif tagname == 'z' and self.parent_class == 'size':
	401	self.aperture.size.z = data_point
	402	self.collimation.size_unit = unit
	403
[af08e55]	404	# Process Information
[250fec92]	405	elif tagname == 'name' and self.parent_class == 'SASprocess':
	406	self.process.name = data_point
	407	elif tagname == 'description' and self.parent_class == 'SASprocess':
	408	self.process.description = data_point
	409	elif tagname == 'date' and self.parent_class == 'SASprocess':
	410	try:
	411	self.process.date = datetime.datetime.fromtimestamp(data_point)
	412	except:
	413	self.process.date = data_point
	414	elif tagname == 'SASprocessnote':
	415	self.process.notes.append(data_point)
	416	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	417	unit = attr.get("unit", "")
	418	dic = {}
	419	dic["name"] = name
	420	dic["value"] = data_point
	421	dic["unit"] = unit
	422	self.process.term.append(dic)
[250fec92]	423
[af08e55]	424	# Transmission Spectrum
[250fec92]	425	elif tagname == 'T' and self.parent_class == 'Tdata':
	426	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	427	self.transspectrum.transmission_unit = unit
	428	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	429	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	430	self.transspectrum.transmission_deviation_unit = unit
	431	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	432	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	433	self.transspectrum.wavelength_unit = unit
	434
[af08e55]	435	# Source Information
[250fec92]	436	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	437	self.current_datainfo.source.wavelength = data_point
	438	self.current_datainfo.source.wavelength_unit = unit
	439	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	440	self.current_datainfo.source.wavelength_min = data_point
	441	self.current_datainfo.source.wavelength_min_unit = unit
	442	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	443	self.current_datainfo.source.wavelength_max = data_point
	444	self.current_datainfo.source.wavelength_max_unit = unit
	445	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	446	self.current_datainfo.source.wavelength_spread = data_point
	447	self.current_datainfo.source.wavelength_spread_unit = unit
	448	elif tagname == 'x' and self.parent_class == 'beam_size':
	449	self.current_datainfo.source.beam_size.x = data_point
	450	self.current_datainfo.source.beam_size_unit = unit
	451	elif tagname == 'y' and self.parent_class == 'beam_size':
	452	self.current_datainfo.source.beam_size.y = data_point
	453	self.current_datainfo.source.beam_size_unit = unit
	454	elif tagname == 'z' and self.parent_class == 'pixel_size':
	455	self.current_datainfo.source.data_point.z = data_point
	456	self.current_datainfo.source.beam_size_unit = unit
	457	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	458	self.current_datainfo.source.radiation = data_point
	459	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	460	self.current_datainfo.source.beam_shape = data_point
	461
[af08e55]	462	# Everything else goes in meta_data
[250fec92]	463	else:
	464	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	465	self.current_datainfo.meta_data[new_key] = data_point
	466
	467	self.names.remove(tagname_original)
	468	length = 0
	469	if len(self.names) > 1:
	470	length = len(self.names) - 1
	471	self.parent_class = self.names[length]
[654e8e0]	472	if not self._is_call_local() and not recurse:
	473	self.frm = ""
[1686a333]	474	self.add_data_set()
	475	empty = None
	476	return self.output[0], empty
[250fec92]	477
	478
[654e8e0]	479	def _is_call_local(self):
[1686a333]	480	"""
	481
	482	"""
[654e8e0]	483	if self.frm == "":
	484	inter = inspect.stack()
	485	self.frm = inter[2]
	486	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	487	mod_name = mod_name.replace(".py", "")
	488	mod = mod_name.split("sas/")
	489	mod_name = mod[1]
	490	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	491	return False
	492	return True
	493
[d26dea0]	494	def is_cansas(self, ext="xml"):
	495	"""
	496	Checks to see if the xml file is a CanSAS file
	497
	498	:param ext: The file extension of the data file
	499	"""
	500	if self.validate_xml():
	501	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	502	value = self.xmlroot.get(name)
	503	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	504	value.rsplit(" ")[0]:
	505	return True
	506	if ext == "svs":
	507	return True
[250fec92]	508	raise RuntimeError
[d26dea0]	509
[83b6408]	510	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	511	"""
[250fec92]	512	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	513
	514	:param xml_file: The xml file path sent to Reader.read
[250fec92]	515	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	516	"""
	517	base_name = xml_reader.__file__
	518	base_name = base_name.replace("\\", "/")
	519	base = base_name.split("/sas/")[0]
	520
	521	# Load in xml file and get the cansas version from the header
	522	self.set_xml_file(xml_file)
	523	self.cansas_version = self.xmlroot.get("version", "1.0")
	524
	525	# Generic values for the cansas file based on the version
[250fec92]	526	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	527	if schema_path == "":
[250fec92]	528	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	529	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	530
	531	# Link a schema to the XML file.
	532	self.set_schema(schema_path)
	533
[250fec92]	534	def add_data_set(self):
[d26dea0]	535	"""
[250fec92]	536	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	537	private method to generate a new data set.
[d26dea0]	538
[250fec92]	539	:param key: NeXus group name for current tree level
[d26dea0]	540	"""
	541
[250fec92]	542	if self.current_datainfo and self.current_dataset:
	543	self._final_cleanup()
	544	self.data = []
	545	self.current_datainfo = DataInfo()
[d26dea0]	546
[af08e55]	547	def _initialize_new_data_set(self, node=None):
[250fec92]	548	"""
	549	A private class method to generate a new 1D data object.
	550	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	551
[af08e55]	552	:param node: XML node to determine if 1D or 2D data
[250fec92]	553	"""
	554	x = np.array(0)
	555	y = np.array(0)
[af08e55]	556	for child in node:
	557	if child.tag.replace(self.base_ns, "") == "Idata":
	558	for i_child in child:
	559	if i_child.tag.replace(self.base_ns, "") == "Qx":
	560	self.current_dataset = plottable_2D()
	561	return
[250fec92]	562	self.current_dataset = plottable_1D(x, y)
[d26dea0]	563
[250fec92]	564	def add_intermediate(self):
	565	"""
	566	This method stores any intermediate objects within the final data set after fully reading the set.
	567
	568	:param parent: The NXclass name for the h5py Group object that just finished being processed
	569	"""
	570
	571	if self.parent_class == 'SASprocess':
	572	self.current_datainfo.process.append(self.process)
	573	self.process = Process()
	574	elif self.parent_class == 'SASdetector':
	575	self.current_datainfo.detector.append(self.detector)
	576	self.detector = Detector()
	577	elif self.parent_class == 'SAStransmission_spectrum':
	578	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	579	self.transspectrum = TransmissionSpectrum()
	580	elif self.parent_class == 'SAScollimation':
	581	self.current_datainfo.collimation.append(self.collimation)
	582	self.collimation = Collimation()
[5f26aa4]	583	elif self.parent_class == 'aperture':
[250fec92]	584	self.collimation.aperture.append(self.aperture)
	585	self.aperture = Aperture()
	586	elif self.parent_class == 'SASdata':
	587	self._check_for_empty_resolution()
	588	self.data.append(self.current_dataset)
	589
	590	def _final_cleanup(self):
[d26dea0]	591	"""
	592	Final cleanup of the Data1D object to be sure it has all the
	593	appropriate information needed for perspectives
	594	"""
[250fec92]	595
[af08e55]	596	# Append errors to dataset and reset class errors
[250fec92]	597	self.current_datainfo.errors = set()
[d26dea0]	598	for error in self.errors:
[250fec92]	599	self.current_datainfo.errors.add(error)
[d26dea0]	600	self.errors.clear()
[250fec92]	601
[af08e55]	602	# Combine all plottables with datainfo and append each to output
	603	# Type cast data arrays to float64 and find min/max as appropriate
[250fec92]	604	for dataset in self.data:
[af08e55]	605	if isinstance(dataset, plottable_1D):
	606	if dataset.x is not None:
	607	dataset.x = np.delete(dataset.x, [0])
	608	dataset.x = dataset.x.astype(np.float64)
	609	dataset.xmin = np.min(dataset.x)
	610	dataset.xmax = np.max(dataset.x)
	611	if dataset.y is not None:
	612	dataset.y = np.delete(dataset.y, [0])
	613	dataset.y = dataset.y.astype(np.float64)
	614	dataset.ymin = np.min(dataset.y)
	615	dataset.ymax = np.max(dataset.y)
	616	if dataset.dx is not None:
	617	dataset.dx = np.delete(dataset.dx, [0])
	618	dataset.dx = dataset.dx.astype(np.float64)
	619	if dataset.dxl is not None:
	620	dataset.dxl = np.delete(dataset.dxl, [0])
	621	dataset.dxl = dataset.dxl.astype(np.float64)
	622	if dataset.dxw is not None:
	623	dataset.dxw = np.delete(dataset.dxw, [0])
	624	dataset.dxw = dataset.dxw.astype(np.float64)
	625	if dataset.dy is not None:
	626	dataset.dy = np.delete(dataset.dy, [0])
	627	dataset.dy = dataset.dy.astype(np.float64)
	628	np.trim_zeros(dataset.x)
	629	np.trim_zeros(dataset.y)
	630	np.trim_zeros(dataset.dy)
	631	elif isinstance(dataset, plottable_2D):
	632	dataset.data = dataset.data.astype(np.float64)
	633	dataset.qx_data = dataset.qx_data.astype(np.float64)
	634	dataset.xmin = np.min(dataset.qx_data)
	635	dataset.xmax = np.max(dataset.qx_data)
	636	dataset.qy_data = dataset.qy_data.astype(np.float64)
	637	dataset.ymin = np.min(dataset.qy_data)
	638	dataset.ymax = np.max(dataset.qy_data)
	639	dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data
	640	+ dataset.qy_data * dataset.qy_data)
	641	if dataset.err_data is not None:
	642	dataset.err_data = dataset.err_data.astype(np.float64)
	643	if dataset.dqx_data is not None:
	644	dataset.dqx_data = dataset.dqx_data.astype(np.float64)
	645	if dataset.dqy_data is not None:
	646	dataset.dqy_data = dataset.dqy_data.astype(np.float64)
	647	if dataset.mask is not None:
	648	dataset.mask = dataset.mask.astype(dtype=bool)
	649
	650	if len(dataset.shape) == 2:
	651	n_rows, n_cols = dataset.shape
	652	dataset.y_bins = dataset.qy_data[0::int(n_cols)]
	653	dataset.x_bins = dataset.qx_data[:int(n_cols)]
	654	dataset.data = dataset.data.flatten()
	655	else:
	656	dataset.y_bins = []
	657	dataset.x_bins = []
	658	dataset.data = dataset.data.flatten()
	659
[250fec92]	660	final_dataset = combine_data(dataset, self.current_datainfo)
	661	self.output.append(final_dataset)
[d26dea0]	662
	663	def _create_unique_key(self, dictionary, name, numb=0):
	664	"""
	665	Create a unique key value for any dictionary to prevent overwriting
[250fec92]	666	Recurse until a unique key value is found.
[d26dea0]	667
	668	:param dictionary: A dictionary with any number of entries
	669	:param name: The index of the item to be added to dictionary
	670	:param numb: The number to be appended to the name, starts at 0
	671	"""
	672	if dictionary.get(name) is not None:
	673	numb += 1
	674	name = name.split("_")[0]
	675	name += "_{0}".format(numb)
	676	name = self._create_unique_key(dictionary, name, numb)
	677	return name
	678
[250fec92]	679	def _get_node_value(self, node, tagname):
	680	"""
	681	Get the value of a node and any applicable units
	682
	683	:param node: The XML node to get the value of
	684	:param tagname: The tagname of the node
	685	"""
	686	#Get the text from the node and convert all whitespace to spaces
	687	units = ''
	688	node_value = node.text
	689	if node_value is not None:
	690	node_value = ' '.join(node_value.split())
	691	else:
	692	node_value = ""
	693
	694	# If the value is a float, compile with units.
	695	if self.ns_list.ns_datatype == "float":
	696	# If an empty value is given, set as zero.
	697	if node_value is None or node_value.isspace() \
	698	or node_value.lower() == "nan":
	699	node_value = "0.0"
	700	#Convert the value to the base units
	701	node_value, units = self._unit_conversion(node, tagname, node_value)
	702
	703	# If the value is a timestamp, convert to a datetime object
	704	elif self.ns_list.ns_datatype == "timestamp":
	705	if node_value is None or node_value.isspace():
	706	pass
	707	else:
	708	try:
	709	node_value = \
	710	datetime.datetime.fromtimestamp(node_value)
	711	except ValueError:
	712	node_value = None
	713	return node_value, units
	714
	715	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	716	"""
	717	A unit converter method used to convert the data included in the file
	718	to the default units listed in data_info
	719
[250fec92]	720	:param node: XML node
	721	:param tagname: name of the node
[d26dea0]	722	:param node_value: The value of the current dom node
	723	"""
	724	attr = node.attrib
	725	value_unit = ''
	726	err_msg = None
[682c432]	727	default_unit = None
[5f26aa4]	728	if not isinstance(node_value, float):
	729	node_value = float(node_value)
	730	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	731	try:
	732	local_unit = attr['unit']
[250fec92]	733	unitname = self.ns_list.current_level.get("unit", "")
	734	if "SASdetector" in self.names:
	735	save_in = "detector"
	736	elif "aperture" in self.names:
	737	save_in = "aperture"
	738	elif "SAScollimation" in self.names:
	739	save_in = "collimation"
	740	elif "SAStransmission_spectrum" in self.names:
	741	save_in = "transspectrum"
	742	elif "SASdata" in self.names:
	743	x = np.zeros(1)
	744	y = np.zeros(1)
	745	self.current_data1d = Data1D(x, y)
	746	save_in = "current_data1d"
	747	elif "SASsource" in self.names:
	748	save_in = "current_datainfo.source"
	749	elif "SASsample" in self.names:
	750	save_in = "current_datainfo.sample"
	751	elif "SASprocess" in self.names:
	752	save_in = "process"
	753	else:
	754	save_in = "current_datainfo"
	755	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	756	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	757	and local_unit.lower() != "none":
	758	if HAS_CONVERTER == True:
[af08e55]	759	# Check local units - bad units raise KeyError
[d26dea0]	760	data_conv_q = Converter(local_unit)
	761	value_unit = default_unit
[682c432]	762	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	763	else:
	764	value_unit = local_unit
	765	err_msg = "Unit converter is not available.\n"
	766	else:
	767	value_unit = local_unit
	768	except KeyError:
	769	err_msg = "CanSAS reader: unexpected "
	770	err_msg += "\"{0}\" unit [{1}]; "
	771	err_msg = err_msg.format(tagname, local_unit)
[682c432]	772	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	773	value_unit = local_unit
	774	except:
	775	err_msg = "CanSAS reader: unknown error converting "
	776	err_msg += "\"{0}\" unit [{1}]"
	777	err_msg = err_msg.format(tagname, local_unit)
	778	value_unit = local_unit
	779	elif 'unit' in attr:
	780	value_unit = attr['unit']
	781	if err_msg:
	782	self.errors.add(err_msg)
	783	return node_value, value_unit
	784
[250fec92]	785	def _check_for_empty_data(self):
[d26dea0]	786	"""
	787	Creates an empty data set if no data is passed to the reader
	788
	789	:param data1d: presumably a Data1D object
	790	"""
[250fec92]	791	if self.current_dataset == None:
	792	x_vals = np.empty(0)
	793	y_vals = np.empty(0)
	794	dx_vals = np.empty(0)
	795	dy_vals = np.empty(0)
	796	dxl = np.empty(0)
	797	dxw = np.empty(0)
	798	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	799	self.current_dataset.dxl = dxl
	800	self.current_dataset.dxw = dxw
	801
	802	def _check_for_empty_resolution(self):
[d26dea0]	803	"""
	804	A method to check all resolution data sets are the same size as I and Q
	805	"""
[af08e55]	806	if isinstance(self.current_dataset, plottable_1D):
	807	dql_exists = False
	808	dqw_exists = False
	809	dq_exists = False
	810	di_exists = False
	811	if self.current_dataset.dxl is not None:
	812	dql_exists = True
	813	if self.current_dataset.dxw is not None:
	814	dqw_exists = True
	815	if self.current_dataset.dx is not None:
	816	dq_exists = True
	817	if self.current_dataset.dy is not None:
	818	di_exists = True
	819	if dqw_exists and not dql_exists:
	820	array_size = self.current_dataset.dxw.size - 1
	821	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
	822	np.zeros([array_size]))
	823	elif dql_exists and not dqw_exists:
	824	array_size = self.current_dataset.dxl.size - 1
	825	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
	826	np.zeros([array_size]))
	827	elif not dql_exists and not dqw_exists and not dq_exists:
	828	array_size = self.current_dataset.x.size - 1
	829	self.current_dataset.dx = np.append(self.current_dataset.dx,
	830	np.zeros([array_size]))
	831	if not di_exists:
	832	array_size = self.current_dataset.y.size - 1
	833	self.current_dataset.dy = np.append(self.current_dataset.dy,
	834	np.zeros([array_size]))
	835	elif isinstance(self.current_dataset, plottable_2D):
	836	dqx_exists = False
	837	dqy_exists = False
	838	di_exists = False
	839	mask_exists = False
	840	if self.current_dataset.dqx_data is not None:
	841	dqx_exists = True
	842	if self.current_dataset.dqy_data is not None:
	843	dqy_exists = True
	844	if self.current_dataset.err_data is not None:
	845	di_exists = True
	846	if self.current_dataset.mask is not None:
	847	mask_exists = True
	848	if not dqy_exists:
	849	array_size = self.current_dataset.qy_data.size - 1
	850	self.current_dataset.dqy_data = np.append(
	851	self.current_dataset.dqy_data, np.zeros([array_size]))
	852	if not dqx_exists:
	853	array_size = self.current_dataset.qx_data.size - 1
	854	self.current_dataset.dqx_data = np.append(
	855	self.current_dataset.dqx_data, np.zeros([array_size]))
	856	if not di_exists:
	857	array_size = self.current_dataset.data.size - 1
	858	self.current_dataset.err_data = np.append(
	859	self.current_dataset.err_data, np.zeros([array_size]))
	860	if not mask_exists:
	861	array_size = self.current_dataset.data.size - 1
	862	self.current_dataset.mask = np.append(
	863	self.current_dataset.mask,
	864	np.ones([array_size] ,dtype=bool))
[250fec92]	865
	866	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	867
[250fec92]	868	def write(self, filename, datainfo):
[d26dea0]	869	"""
[250fec92]	870	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	871
[250fec92]	872	:param filename: name of the file to write
	873	:param datainfo: Data1D object
	874	"""
	875	# Create XML document
	876	doc, _ = self._to_xml_doc(datainfo)
	877	# Write the file
	878	file_ref = open(filename, 'w')
	879	if self.encoding == None:
	880	self.encoding = "UTF-8"
	881	doc.write(file_ref, encoding=self.encoding,
	882	pretty_print=True, xml_declaration=True)
	883	file_ref.close()
[d26dea0]	884
[250fec92]	885	def _to_xml_doc(self, datainfo):
[d26dea0]	886	"""
[250fec92]	887	Create an XML document to contain the content of a Data1D
[d26dea0]	888
[250fec92]	889	:param datainfo: Data1D object
[d26dea0]	890	"""
[af08e55]	891	is_2d = False
[83c09af]	892	if issubclass(datainfo.__class__, Data2D):
	893	is_2d = True
[d26dea0]	894
[250fec92]	895	# Get PIs and create root element
	896	pi_string = self._get_pi_string()
	897	# Define namespaces and create SASroot object
	898	main_node = self._create_main_node()
	899	# Create ElementTree, append SASroot and apply processing instructions
	900	base_string = pi_string + self.to_string(main_node)
	901	base_element = self.create_element_from_string(base_string)
	902	doc = self.create_tree(base_element)
	903	# Create SASentry Element
	904	entry_node = self.create_element("SASentry")
	905	root = doc.getroot()
	906	root.append(entry_node)
[d26dea0]	907
[250fec92]	908	# Add Title to SASentry
	909	self.write_node(entry_node, "Title", datainfo.title)
	910	# Add Run to SASentry
	911	self._write_run_names(datainfo, entry_node)
	912	# Add Data info to SASEntry
[83c09af]	913	if is_2d:
	914	self._write_data_2d(datainfo, entry_node)
	915	else:
	916	self._write_data(datainfo, entry_node)
[250fec92]	917	# Transmission Spectrum Info
	918	self._write_trans_spectrum(datainfo, entry_node)
	919	# Sample info
	920	self._write_sample_info(datainfo, entry_node)
	921	# Instrument info
	922	instr = self._write_instrument(datainfo, entry_node)
	923	# Source
	924	self._write_source(datainfo, instr)
	925	# Collimation
	926	self._write_collimation(datainfo, instr)
	927	# Detectors
	928	self._write_detectors(datainfo, instr)
	929	# Processes info
	930	self._write_process_notes(datainfo, entry_node)
	931	# Note info
	932	self._write_notes(datainfo, entry_node)
	933	# Return the document, and the SASentry node associated with
	934	# the data we just wrote
	935	# If the calling function was not the cansas reader, return a minidom
	936	# object rather than an lxml object.
[654e8e0]	937	self.frm = inspect.stack()[1]
	938	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	939	return doc, entry_node
[d26dea0]	940
[250fec92]	941	def write_node(self, parent, name, value, attr=None):
	942	"""
	943	:param doc: document DOM
	944	:param parent: parent node
	945	:param name: tag of the element
	946	:param value: value of the child text node
	947	:param attr: attribute dictionary
[d26dea0]	948
[250fec92]	949	:return: True if something was appended, otherwise False
	950	"""
	951	if value is not None:
	952	parent = self.ebuilder(parent, name, value, attr)
	953	return True
	954	return False
[d26dea0]	955
	956	def _get_pi_string(self):
	957	"""
	958	Creates the processing instructions header for writing to file
	959	"""
	960	pis = self.return_processing_instructions()
	961	if len(pis) > 0:
	962	pi_tree = self.create_tree(pis[0])
	963	i = 1
	964	for i in range(1, len(pis) - 1):
	965	pi_tree = self.append(pis[i], pi_tree)
	966	pi_string = self.to_string(pi_tree)
	967	else:
	968	pi_string = ""
	969	return pi_string
	970
	971	def _create_main_node(self):
	972	"""
	973	Creates the primary xml header used when writing to file
	974	"""
	975	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	976	version = self.cansas_version
	977	n_s = CANSAS_NS.get(version).get("ns")
	978	if version == "1.1":
	979	url = "http://www.cansas.org/formats/1.1/"
	980	else:
	981	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	982	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	983	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	984	"version" : version}
	985	nsmap = {'xsi' : xsi, None: n_s}
	986
	987	main_node = self.create_element("{" + n_s + "}SASroot",
	988	attrib=attrib, nsmap=nsmap)
	989	return main_node
	990
	991	def _write_run_names(self, datainfo, entry_node):
	992	"""
	993	Writes the run names to the XML file
	994
	995	:param datainfo: The Data1D object the information is coming from
	996	:param entry_node: lxml node ElementTree object to be appended to
	997	"""
	998	if datainfo.run == None or datainfo.run == []:
	999	datainfo.run.append(RUN_NAME_DEFAULT)
	1000	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	1001	for item in datainfo.run:
	1002	runname = {}
	1003	if item in datainfo.run_name and \
	1004	len(str(datainfo.run_name[item])) > 1:
	1005	runname = {'name': datainfo.run_name[item]}
	1006	self.write_node(entry_node, "Run", item, runname)
	1007
	1008	def _write_data(self, datainfo, entry_node):
	1009	"""
[83c09af]	1010	Writes 1D I and Q data to the XML file
[d26dea0]	1011
	1012	:param datainfo: The Data1D object the information is coming from
	1013	:param entry_node: lxml node ElementTree object to be appended to
	1014	"""
	1015	node = self.create_element("SASdata")
	1016	self.append(node, entry_node)
	1017
	1018	for i in range(len(datainfo.x)):
	1019	point = self.create_element("Idata")
	1020	node.append(point)
	1021	self.write_node(point, "Q", datainfo.x[i],
[0d64713]	1022	{'unit': datainfo.x_unit})
[d26dea0]	1023	if len(datainfo.y) >= i:
	1024	self.write_node(point, "I", datainfo.y[i],
[0d64713]	1025	{'unit': datainfo.y_unit})
[5f26aa4]	1026	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	1027	self.write_node(point, "Idev", datainfo.dy[i],
[0d64713]	1028	{'unit': datainfo.y_unit})
[5f26aa4]	1029	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	1030	self.write_node(point, "Qdev", datainfo.dx[i],
[0d64713]	1031	{'unit': datainfo.x_unit})
[5f26aa4]	1032	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	1033	self.write_node(point, "dQw", datainfo.dxw[i],
[0d64713]	1034	{'unit': datainfo.x_unit})
[5f26aa4]	1035	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	1036	self.write_node(point, "dQl", datainfo.dxl[i],
[0d64713]	1037	{'unit': datainfo.x_unit})
[d26dea0]	1038
[83c09af]	1039	def _write_data_2d(self, datainfo, entry_node):
	1040	"""
	1041	Writes 2D data to the XML file
	1042
	1043	:param datainfo: The Data2D object the information is coming from
	1044	:param entry_node: lxml node ElementTree object to be appended to
	1045	"""
[af08e55]	1046	attr = {}
	1047	if datainfo.data.shape:
[1905128]	1048	attr["x_bins"] = str(len(datainfo.x_bins))
	1049	attr["y_bins"] = str(len(datainfo.y_bins))
	1050	node = self.create_element("SASdata", attr)
[83c09af]	1051	self.append(node, entry_node)
	1052
[1905128]	1053	point = self.create_element("Idata")
	1054	node.append(point)
	1055	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
	1056	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
	1057	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
	1058
	1059	self.write_node(point, "Qx", qx,
	1060	{'unit': datainfo._xunit})
	1061	self.write_node(point, "Qy", qy,
	1062	{'unit': datainfo._yunit})
	1063	self.write_node(point, "I", intensity,
	1064	{'unit': datainfo._zunit})
	1065	if datainfo.err_data is not None:
[5e6df0e]	1066	err = ','.join([str(datainfo.err_data[i]) for i in
	1067	xrange(len(datainfo.err_data))])
[1905128]	1068	self.write_node(point, "Idev", err,
[83c09af]	1069	{'unit': datainfo._zunit})
[1905128]	1070	if datainfo.dqy_data is not None:
[5e6df0e]	1071	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
	1072	xrange(len(datainfo.dqy_data))])
[1905128]	1073	self.write_node(point, "Qydev", dqy,
	1074	{'unit': datainfo._yunit})
	1075	if datainfo.dqx_data is not None:
[5e6df0e]	1076	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
	1077	xrange(len(datainfo.dqx_data))])
[1905128]	1078	self.write_node(point, "Qxdev", dqx,
	1079	{'unit': datainfo._xunit})
	1080	if datainfo.mask is not None:
[5e6df0e]	1081	mask = ','.join(
[bcabf4e]	1082	["1" if datainfo.mask[i] else "0"
	1083	for i in xrange(len(datainfo.mask))])
[1905128]	1084	self.write_node(point, "Mask", mask)
[83c09af]	1085
[d26dea0]	1086	def _write_trans_spectrum(self, datainfo, entry_node):
	1087	"""
	1088	Writes the transmission spectrum data to the XML file
	1089
	1090	:param datainfo: The Data1D object the information is coming from
	1091	:param entry_node: lxml node ElementTree object to be appended to
	1092	"""
	1093	for i in range(len(datainfo.trans_spectrum)):
	1094	spectrum = datainfo.trans_spectrum[i]
	1095	node = self.create_element("SAStransmission_spectrum",
	1096	{"name" : spectrum.name})
	1097	self.append(node, entry_node)
	1098	if isinstance(spectrum.timestamp, datetime.datetime):
	1099	node.setAttribute("timestamp", spectrum.timestamp)
	1100	for i in range(len(spectrum.wavelength)):
	1101	point = self.create_element("Tdata")
	1102	node.append(point)
	1103	self.write_node(point, "Lambda", spectrum.wavelength[i],
	1104	{'unit': spectrum.wavelength_unit})
	1105	self.write_node(point, "T", spectrum.transmission[i],
	1106	{'unit': spectrum.transmission_unit})
	1107	if spectrum.transmission_deviation != None \
	1108	and len(spectrum.transmission_deviation) >= i:
	1109	self.write_node(point, "Tdev",
	1110	spectrum.transmission_deviation[i],
	1111	{'unit':
	1112	spectrum.transmission_deviation_unit})
	1113
	1114	def _write_sample_info(self, datainfo, entry_node):
	1115	"""
	1116	Writes the sample information to the XML file
	1117
	1118	:param datainfo: The Data1D object the information is coming from
	1119	:param entry_node: lxml node ElementTree object to be appended to
	1120	"""
	1121	sample = self.create_element("SASsample")
	1122	if datainfo.sample.name is not None:
	1123	self.write_attribute(sample, "name",
	1124	str(datainfo.sample.name))
	1125	self.append(sample, entry_node)
	1126	self.write_node(sample, "ID", str(datainfo.sample.ID))
	1127	self.write_node(sample, "thickness", datainfo.sample.thickness,
	1128	{"unit": datainfo.sample.thickness_unit})
	1129	self.write_node(sample, "transmission", datainfo.sample.transmission)
	1130	self.write_node(sample, "temperature", datainfo.sample.temperature,
	1131	{"unit": datainfo.sample.temperature_unit})
	1132
	1133	pos = self.create_element("position")
	1134	written = self.write_node(pos,
	1135	"x",
	1136	datainfo.sample.position.x,
	1137	{"unit": datainfo.sample.position_unit})
	1138	written = written \| self.write_node( \
	1139	pos, "y", datainfo.sample.position.y,
	1140	{"unit": datainfo.sample.position_unit})
	1141	written = written \| self.write_node( \
	1142	pos, "z", datainfo.sample.position.z,
	1143	{"unit": datainfo.sample.position_unit})
	1144	if written == True:
	1145	self.append(pos, sample)
	1146
	1147	ori = self.create_element("orientation")
	1148	written = self.write_node(ori, "roll",
	1149	datainfo.sample.orientation.x,
	1150	{"unit": datainfo.sample.orientation_unit})
	1151	written = written \| self.write_node( \
	1152	ori, "pitch", datainfo.sample.orientation.y,
	1153	{"unit": datainfo.sample.orientation_unit})
	1154	written = written \| self.write_node( \
	1155	ori, "yaw", datainfo.sample.orientation.z,
	1156	{"unit": datainfo.sample.orientation_unit})
	1157	if written == True:
	1158	self.append(ori, sample)
	1159
	1160	for item in datainfo.sample.details:
	1161	self.write_node(sample, "details", item)
	1162
	1163	def _write_instrument(self, datainfo, entry_node):
	1164	"""
	1165	Writes the instrumental information to the XML file
	1166
	1167	:param datainfo: The Data1D object the information is coming from
	1168	:param entry_node: lxml node ElementTree object to be appended to
	1169	"""
	1170	instr = self.create_element("SASinstrument")
	1171	self.append(instr, entry_node)
	1172	self.write_node(instr, "name", datainfo.instrument)
	1173	return instr
	1174
	1175	def _write_source(self, datainfo, instr):
	1176	"""
	1177	Writes the source information to the XML file
	1178
	1179	:param datainfo: The Data1D object the information is coming from
	1180	:param instr: instrument node to be appended to
	1181	"""
	1182	source = self.create_element("SASsource")
	1183	if datainfo.source.name is not None:
	1184	self.write_attribute(source, "name",
	1185	str(datainfo.source.name))
	1186	self.append(source, instr)
	1187	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	1188	datainfo.source.radiation = "neutron"
	1189	self.write_node(source, "radiation", datainfo.source.radiation)
	1190
	1191	size = self.create_element("beam_size")
	1192	if datainfo.source.beam_size_name is not None:
	1193	self.write_attribute(size, "name",
	1194	str(datainfo.source.beam_size_name))
	1195	written = self.write_node( \
	1196	size, "x", datainfo.source.beam_size.x,
	1197	{"unit": datainfo.source.beam_size_unit})
	1198	written = written \| self.write_node( \
	1199	size, "y", datainfo.source.beam_size.y,
	1200	{"unit": datainfo.source.beam_size_unit})
	1201	written = written \| self.write_node( \
	1202	size, "z", datainfo.source.beam_size.z,
	1203	{"unit": datainfo.source.beam_size_unit})
	1204	if written == True:
	1205	self.append(size, source)
	1206
	1207	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1208	self.write_node(source, "wavelength",
	1209	datainfo.source.wavelength,
	1210	{"unit": datainfo.source.wavelength_unit})
	1211	self.write_node(source, "wavelength_min",
	1212	datainfo.source.wavelength_min,
	1213	{"unit": datainfo.source.wavelength_min_unit})
	1214	self.write_node(source, "wavelength_max",
	1215	datainfo.source.wavelength_max,
	1216	{"unit": datainfo.source.wavelength_max_unit})
	1217	self.write_node(source, "wavelength_spread",
	1218	datainfo.source.wavelength_spread,
	1219	{"unit": datainfo.source.wavelength_spread_unit})
	1220
	1221	def _write_collimation(self, datainfo, instr):
	1222	"""
	1223	Writes the collimation information to the XML file
	1224
	1225	:param datainfo: The Data1D object the information is coming from
	1226	:param instr: lxml node ElementTree object to be appended to
	1227	"""
	1228	if datainfo.collimation == [] or datainfo.collimation == None:
	1229	coll = Collimation()
	1230	datainfo.collimation.append(coll)
	1231	for item in datainfo.collimation:
	1232	coll = self.create_element("SAScollimation")
	1233	if item.name is not None:
	1234	self.write_attribute(coll, "name", str(item.name))
	1235	self.append(coll, instr)
	1236
	1237	self.write_node(coll, "length", item.length,
	1238	{"unit": item.length_unit})
	1239
	1240	for aperture in item.aperture:
	1241	apert = self.create_element("aperture")
	1242	if aperture.name is not None:
	1243	self.write_attribute(apert, "name", str(aperture.name))
	1244	if aperture.type is not None:
	1245	self.write_attribute(apert, "type", str(aperture.type))
	1246	self.append(apert, coll)
	1247
	1248	size = self.create_element("size")
	1249	if aperture.size_name is not None:
	1250	self.write_attribute(size, "name",
	1251	str(aperture.size_name))
	1252	written = self.write_node(size, "x", aperture.size.x,
	1253	{"unit": aperture.size_unit})
	1254	written = written \| self.write_node( \
	1255	size, "y", aperture.size.y,
	1256	{"unit": aperture.size_unit})
	1257	written = written \| self.write_node( \
	1258	size, "z", aperture.size.z,
	1259	{"unit": aperture.size_unit})
	1260	if written == True:
	1261	self.append(size, apert)
	1262
	1263	self.write_node(apert, "distance", aperture.distance,
	1264	{"unit": aperture.distance_unit})
	1265
	1266	def _write_detectors(self, datainfo, instr):
	1267	"""
	1268	Writes the detector information to the XML file
	1269
	1270	:param datainfo: The Data1D object the information is coming from
	1271	:param inst: lxml instrument node to be appended to
	1272	"""
	1273	if datainfo.detector == None or datainfo.detector == []:
	1274	det = Detector()
	1275	det.name = ""
	1276	datainfo.detector.append(det)
	1277
	1278	for item in datainfo.detector:
	1279	det = self.create_element("SASdetector")
	1280	written = self.write_node(det, "name", item.name)
	1281	written = written \| self.write_node(det, "SDD", item.distance,
	1282	{"unit": item.distance_unit})
	1283	if written == True:
	1284	self.append(det, instr)
	1285
	1286	off = self.create_element("offset")
	1287	written = self.write_node(off, "x", item.offset.x,
	1288	{"unit": item.offset_unit})
	1289	written = written \| self.write_node(off, "y", item.offset.y,
	1290	{"unit": item.offset_unit})
	1291	written = written \| self.write_node(off, "z", item.offset.z,
	1292	{"unit": item.offset_unit})
	1293	if written == True:
	1294	self.append(off, det)
	1295
	1296	ori = self.create_element("orientation")
	1297	written = self.write_node(ori, "roll", item.orientation.x,
	1298	{"unit": item.orientation_unit})
	1299	written = written \| self.write_node(ori, "pitch",
	1300	item.orientation.y,
	1301	{"unit": item.orientation_unit})
	1302	written = written \| self.write_node(ori, "yaw",
	1303	item.orientation.z,
	1304	{"unit": item.orientation_unit})
	1305	if written == True:
	1306	self.append(ori, det)
	1307
	1308	center = self.create_element("beam_center")
	1309	written = self.write_node(center, "x", item.beam_center.x,
	1310	{"unit": item.beam_center_unit})
	1311	written = written \| self.write_node(center, "y",
	1312	item.beam_center.y,
	1313	{"unit": item.beam_center_unit})
	1314	written = written \| self.write_node(center, "z",
	1315	item.beam_center.z,
	1316	{"unit": item.beam_center_unit})
	1317	if written == True:
	1318	self.append(center, det)
	1319
	1320	pix = self.create_element("pixel_size")
	1321	written = self.write_node(pix, "x", item.pixel_size.x,
	1322	{"unit": item.pixel_size_unit})
	1323	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1324	{"unit": item.pixel_size_unit})
	1325	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1326	{"unit": item.pixel_size_unit})
	1327	if written == True:
	1328	self.append(pix, det)
[3a9801f]	1329	self.write_node(det, "slit_length", item.slit_length,
	1330	{"unit": item.slit_length_unit})
	1331
[d26dea0]	1332
	1333	def _write_process_notes(self, datainfo, entry_node):
	1334	"""
	1335	Writes the process notes to the XML file
	1336
	1337	:param datainfo: The Data1D object the information is coming from
	1338	:param entry_node: lxml node ElementTree object to be appended to
	1339
	1340	"""
	1341	for item in datainfo.process:
	1342	node = self.create_element("SASprocess")
	1343	self.append(node, entry_node)
	1344	self.write_node(node, "name", item.name)
	1345	self.write_node(node, "date", item.date)
	1346	self.write_node(node, "description", item.description)
	1347	for term in item.term:
[1686a333]	1348	if isinstance(term, list):
	1349	value = term['value']
	1350	del term['value']
[5f26aa4]	1351	elif isinstance(term, dict):
	1352	value = term.get("value")
	1353	del term['value']
[1686a333]	1354	else:
	1355	value = term
[d26dea0]	1356	self.write_node(node, "term", value, term)
	1357	for note in item.notes:
	1358	self.write_node(node, "SASprocessnote", note)
	1359	if len(item.notes) == 0:
	1360	self.write_node(node, "SASprocessnote", "")
	1361
	1362	def _write_notes(self, datainfo, entry_node):
	1363	"""
	1364	Writes the notes to the XML file and creates an empty note if none
	1365	exist
	1366
	1367	:param datainfo: The Data1D object the information is coming from
	1368	:param entry_node: lxml node ElementTree object to be appended to
	1369
	1370	"""
	1371	if len(datainfo.notes) == 0:
	1372	node = self.create_element("SASnote")
	1373	self.append(node, entry_node)
	1374	else:
	1375	for item in datainfo.notes:
	1376	node = self.create_element("SASnote")
	1377	self.write_text(node, item)
	1378	self.append(node, entry_node)
	1379
[654e8e0]	1380	def _check_origin(self, entry_node, doc):
[d26dea0]	1381	"""
	1382	Return the document, and the SASentry node associated with
	1383	the data we just wrote.
	1384	If the calling function was not the cansas reader, return a minidom
	1385	object rather than an lxml object.
	1386
	1387	:param entry_node: lxml node ElementTree object to be appended to
	1388	:param doc: entire xml tree
	1389	"""
[654e8e0]	1390	if not self.frm:
	1391	self.frm = inspect.stack()[1]
	1392	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1393	mod_name = mod_name.replace(".py", "")
	1394	mod = mod_name.split("sas/")
	1395	mod_name = mod[1]
[45d90b9]	1396	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1397	string = self.to_string(doc, pretty_print=False)
	1398	doc = parseString(string)
	1399	node_name = entry_node.tag
	1400	node_list = doc.getElementsByTagName(node_name)
	1401	entry_node = node_list.item(0)
[5ce7f17]	1402	return doc, entry_node
[d26dea0]	1403
	1404	# DO NOT REMOVE - used in saving and loading panel states.
	1405	def _store_float(self, location, node, variable, storage, optional=True):
	1406	"""
	1407	Get the content of a xpath location and store
	1408	the result. Check that the units are compatible
	1409	with the destination. The value is expected to
	1410	be a float.
	1411
	1412	The xpath location might or might not exist.
	1413	If it does not exist, nothing is done
	1414
	1415	:param location: xpath location to fetch
	1416	:param node: node to read the data from
	1417	:param variable: name of the data member to store it in [string]
	1418	:param storage: data object that has the 'variable' data member
	1419	:param optional: if True, no exception will be raised
	1420	if unit conversion can't be done
	1421
	1422	:raise ValueError: raised when the units are not recognized
	1423	"""
	1424	entry = get_content(location, node)
	1425	try:
	1426	value = float(entry.text)
	1427	except:
	1428	value = None
	1429
	1430	if value is not None:
	1431	# If the entry has units, check to see that they are
	1432	# compatible with what we currently have in the data object
	1433	units = entry.get('unit')
	1434	if units is not None:
	1435	toks = variable.split('.')
	1436	local_unit = None
	1437	exec "local_unit = storage.%s_unit" % toks[0]
	1438	if local_unit != None and units.lower() != local_unit.lower():
	1439	if HAS_CONVERTER == True:
	1440	try:
	1441	conv = Converter(units)
	1442	exec "storage.%s = %g" % \
	1443	(variable, conv(value, units=local_unit))
	1444	except:
	1445	_, exc_value, _ = sys.exc_info()
	1446	err_mess = "CanSAS reader: could not convert"
	1447	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1448	% (variable, units, local_unit, exc_value)
	1449	self.errors.add(err_mess)
	1450	if optional:
	1451	logging.info(err_mess)
	1452	else:
	1453	raise ValueError, err_mess
	1454	else:
	1455	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1456	% (variable, units)
	1457	err_mess += " expecting [%s]" % local_unit
	1458	self.errors.add(err_mess)
	1459	if optional:
	1460	logging.info(err_mess)
	1461	else:
	1462	raise ValueError, err_mess
	1463	else:
	1464	exec "storage.%s = value" % variable
	1465	else:
	1466	exec "storage.%s = value" % variable
	1467
	1468	# DO NOT REMOVE - used in saving and loading panel states.
	1469	def _store_content(self, location, node, variable, storage):
	1470	"""
	1471	Get the content of a xpath location and store
	1472	the result. The value is treated as a string.
	1473
	1474	The xpath location might or might not exist.
	1475	If it does not exist, nothing is done
	1476
	1477	:param location: xpath location to fetch
	1478	:param node: node to read the data from
	1479	:param variable: name of the data member to store it in [string]
	1480	:param storage: data object that has the 'variable' data member
	1481
	1482	:return: return a list of errors
	1483	"""
	1484	entry = get_content(location, node)
	1485	if entry is not None and entry.text is not None:
	1486	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1487
	1488
	1489	# DO NOT REMOVE Called by outside packages:
	1490	# sas.sasgui.perspectives.invariant.invariant_state
	1491	# sas.sasgui.perspectives.fitting.pagestate
	1492	def get_content(location, node):
	1493	"""
	1494	Get the first instance of the content of a xpath location.
	1495
	1496	:param location: xpath location
	1497	:param node: node to start at
	1498
	1499	:return: Element, or None
	1500	"""
	1501	nodes = node.xpath(location,
	1502	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1503	if len(nodes) > 0:
	1504	return nodes[0]
	1505	else:
	1506	return None
	1507
	1508	# DO NOT REMOVE Called by outside packages:
	1509	# sas.sasgui.perspectives.fitting.pagestate
	1510	def write_node(doc, parent, name, value, attr=None):
	1511	"""
	1512	:param doc: document DOM
	1513	:param parent: parent node
	1514	:param name: tag of the element
	1515	:param value: value of the child text node
	1516	:param attr: attribute dictionary
	1517
	1518	:return: True if something was appended, otherwise False
	1519	"""
	1520	if attr is None:
	1521	attr = {}
	1522	if value is not None:
	1523	node = doc.createElement(name)
	1524	node.appendChild(doc.createTextNode(str(value)))
	1525	for item in attr:
	1526	node.setAttribute(item, attr[item])
	1527	parent.appendChild(node)
	1528	return True
	1529	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 13043af

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