cansas_reader.py @ 654e8e0

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 654e8e0 was 654e8e0, checked in by krzywon, 8 years ago
Resolves #644 and #642: Improved loading performance for cansas XML data. Loading invariants and fits from save states no longer throw errors or open multiple windows.
Property mode set to `100644`
File size: 61.5 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
[250fec92]	22	from sas.sascalc.dataloader.data_info import Data1D, DataInfo, plottable_1D
	23	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, Detector, Process, Aperture
	24	from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable as combine_data
[b699768]	25	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	26	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
[250fec92]	27	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
[d26dea0]	28
[682c432]	29	# The following 2 imports ARE used. Do not remove either.
	30	import xml.dom.minidom
	31	from xml.dom.minidom import parseString
	32
[d26dea0]	33	PREPROCESS = "xmlpreprocess"
	34	ENCODING = "encoding"
	35	RUN_NAME_DEFAULT = "None"
[250fec92]	36	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	37	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	38	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	39	"as much of the data as possible.\n\n"
[d26dea0]	40	HAS_CONVERTER = True
	41	try:
[b699768]	42	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	43	except ImportError:
	44	HAS_CONVERTER = False
	45
	46	CONSTANTS = CansasConstants()
	47	CANSAS_FORMAT = CONSTANTS.format
	48	CANSAS_NS = CONSTANTS.names
	49	ALLOW_ALL = True
	50
	51	class Reader(XMLreader):
	52	"""
	53	Class to load cansas 1D XML files
	54
	55	:Dependencies:
	56	The CanSAS reader requires PyXML 0.8.4 or later.
	57	"""
[250fec92]	58	## CanSAS version - defaults to version 1.0
[d26dea0]	59	cansas_version = "1.0"
	60	base_ns = "{cansas1d/1.0}"
[250fec92]	61	cansas_defaults = None
[d26dea0]	62	type_name = "canSAS"
[250fec92]	63	invalid = True
[654e8e0]	64	frm = ""
[250fec92]	65	## Log messages and errors
	66	logging = None
	67	errors = set()
	68	## Namespace hierarchy for current xml_file object
	69	names = None
	70	ns_list = None
	71	## Temporary storage location for loading multiple data sets in a single file
	72	current_datainfo = None
	73	current_dataset = None
	74	current_data1d = None
	75	data = None
	76	## List of data1D objects to be sent back to SasView
	77	output = None
[d26dea0]	78	## Wildcards
	79	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
	80	## List of allowed extensions
	81	ext = ['.xml', '.XML', '.svs', '.SVS']
	82	## Flag to bypass extension check
	83	allow_all = True
	84
[250fec92]	85	def reset_state(self):
	86	"""
	87	Resets the class state to a base case when loading a new data file so previous
	88	data files do not appear a second time
	89	"""
	90	self.current_datainfo = None
	91	self.current_dataset = None
	92	self.current_data1d = None
	93	self.data = []
	94	self.process = Process()
	95	self.transspectrum = TransmissionSpectrum()
	96	self.aperture = Aperture()
	97	self.collimation = Collimation()
	98	self.detector = Detector()
	99	self.names = []
	100	self.cansas_defaults = {}
	101	self.output = []
	102	self.ns_list = None
[d26dea0]	103	self.logging = []
	104	self.encoding = None
	105
[250fec92]	106	def read(self, xml_file, schema_path="", invalid=True):
	107	"""
	108	Validate and read in an xml_file file in the canSAS format.
	109
	110	:param xml_file: A canSAS file path in proper XML format
	111	:param schema_path: A file path to an XML schema to validate the xml_file against
	112	"""
	113	# For every file loaded, reset everything to a base state
	114	self.reset_state()
	115	self.invalid = invalid
	116	# Check that the file exists
	117	if os.path.isfile(xml_file):
	118	basename, extension = os.path.splitext(os.path.basename(xml_file))
	119	# If the file type is not allowed, return nothing
	120	if extension in self.ext or self.allow_all:
	121	# Get the file location of
	122	self.load_file_and_schema(xml_file, schema_path)
	123	self.add_data_set()
	124	# Try to load the file, but raise an error if unable to.
	125	# Check the file matches the XML schema
	126	try:
	127	self.is_cansas(extension)
	128	self.invalid = False
	129	# Get each SASentry from XML file and add it to a list.
	130	entry_list = self.xmlroot.xpath(
	131	'/ns:SASroot/ns:SASentry',
	132	namespaces={'ns': self.cansas_defaults.get("ns")})
	133	self.names.append("SASentry")
	134
	135	# Get all preprocessing events and encoding
	136	self.set_processing_instructions()
	137
	138	# Parse each <SASentry> item
	139	for entry in entry_list:
	140	# Create a new DataInfo object for every <SASentry>
	141
	142	# Set the file name and then parse the entry.
	143	self.current_datainfo.filename = basename + extension
	144	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
	145	self.current_datainfo.meta_data[PREPROCESS] = \
	146	self.processing_instructions
	147
	148	# Parse the XML SASentry
	149	self._parse_entry(entry)
	150	# Combine datasets with datainfo
	151	self.add_data_set()
	152	except RuntimeError:
	153	# If the file does not match the schema, raise this error
	154	invalid_xml = self.find_invalid_xml()
	155	invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml
	156	self.errors.add(invalid_xml)
	157	# Try again with an invalid CanSAS schema, that requires only a data set in each
	158	base_name = xml_reader.__file__
	159	base_name = base_name.replace("\\", "/")
	160	base = base_name.split("/sas/")[0]
	161	if self.cansas_version == "1.1":
	162	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	163	else:
	164	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	165	self.set_schema(invalid_schema)
	166	try:
	167	if self.invalid:
	168	if self.is_cansas():
	169	self.output = self.read(xml_file, invalid_schema, False)
	170	else:
	171	raise RuntimeError
	172	else:
	173	raise RuntimeError
	174	except RuntimeError:
	175	x = np.zeros(1)
	176	y = np.zeros(1)
	177	self.current_data1d = Data1D(x,y)
	178	self.current_data1d.errors = self.errors
	179	return [self.current_data1d]
	180	else:
	181	self.output.append("Not a valid file path.")
	182	# Return a list of parsed entries that dataloader can manage
	183	return self.output
	184
[654e8e0]	185	def _parse_entry(self, dom, recurse=False):
[250fec92]	186	"""
	187	Parse a SASEntry - new recursive method for parsing the dom of
	188	the CanSAS data format. This will allow multiple data files
	189	and extra nodes to be read in simultaneously.
	190
	191	:param dom: dom object with a namespace base of names
	192	"""
	193
[654e8e0]	194	if not self._is_call_local() and not recurse:
[1686a333]	195	self.reset_state()
	196	self.add_data_set()
	197	self.names.append("SASentry")
	198	self.parent_class = "SASentry"
[250fec92]	199	self._check_for_empty_data()
	200	self.base_ns = "{0}{1}{2}".format("{", \
	201	CANSAS_NS.get(self.cansas_version).get("ns"), "}")
	202
	203	# Go through each child in the parent element
	204	for node in dom:
[5f26aa4]	205	attr = node.attrib
	206	name = attr.get("name", "")
	207	type = attr.get("type", "")
[250fec92]	208	# Get the element name and set the current names level
	209	tagname = node.tag.replace(self.base_ns, "")
	210	tagname_original = tagname
	211	# Skip this iteration when loading in save state information
	212	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	213	continue
	214
	215	# Get where to store content
	216	self.names.append(tagname_original)
	217	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	218	# If the element is a child element, recurse
	219	if len(node.getchildren()) > 0:
	220	self.parent_class = tagname_original
	221	if tagname == 'SASdata':
	222	self._initialize_new_data_set()
	223	## Recursion step to access data within the group
[654e8e0]	224	self._parse_entry(node, True)
[5f26aa4]	225	if tagname == "SASsample":
	226	self.current_datainfo.sample.name = name
	227	elif tagname == "beam_size":
	228	self.current_datainfo.source.beam_size_name = name
	229	elif tagname == "SAScollimation":
	230	self.collimation.name = name
	231	elif tagname == "aperture":
	232	self.aperture.name = name
	233	self.aperture.type = type
[250fec92]	234	self.add_intermediate()
	235	else:
	236	data_point, unit = self._get_node_value(node, tagname)
	237
	238	## If this is a dataset, store the data appropriately
	239	if tagname == 'Run':
[5f26aa4]	240	self.current_datainfo.run_name[data_point] = name
[250fec92]	241	self.current_datainfo.run.append(data_point)
	242	elif tagname == 'Title':
	243	self.current_datainfo.title = data_point
	244	elif tagname == 'SASnote':
	245	self.current_datainfo.notes.append(data_point)
	246
	247	## I and Q Data
	248	elif tagname == 'I':
	249	self.current_dataset.yaxis("Intensity", unit)
	250	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
	251	elif tagname == 'Idev':
	252	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	253	elif tagname == 'Q':
	254	self.current_dataset.xaxis("Q", unit)
	255	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	256	elif tagname == 'Qdev':
	257	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	258	elif tagname == 'dQw':
	259	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	260	elif tagname == 'dQl':
	261	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	262	elif tagname == 'Qmean':
	263	pass
	264	elif tagname == 'Shadowfactor':
	265	pass
[250fec92]	266
	267	## Sample Information
	268	elif tagname == 'ID' and self.parent_class == 'SASsample':
	269	self.current_datainfo.sample.ID = data_point
	270	elif tagname == 'Title' and self.parent_class == 'SASsample':
	271	self.current_datainfo.sample.name = data_point
	272	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	273	self.current_datainfo.sample.thickness = data_point
	274	self.current_datainfo.sample.thickness_unit = unit
	275	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	276	self.current_datainfo.sample.transmission = data_point
	277	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	278	self.current_datainfo.sample.temperature = data_point
	279	self.current_datainfo.sample.temperature_unit = unit
	280	elif tagname == 'details' and self.parent_class == 'SASsample':
	281	self.current_datainfo.sample.details.append(data_point)
	282	elif tagname == 'x' and self.parent_class == 'position':
	283	self.current_datainfo.sample.position.x = data_point
	284	self.current_datainfo.sample.position_unit = unit
	285	elif tagname == 'y' and self.parent_class == 'position':
	286	self.current_datainfo.sample.position.y = data_point
	287	self.current_datainfo.sample.position_unit = unit
	288	elif tagname == 'z' and self.parent_class == 'position':
	289	self.current_datainfo.sample.position.z = data_point
	290	self.current_datainfo.sample.position_unit = unit
	291	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	292	self.current_datainfo.sample.orientation.x = data_point
	293	self.current_datainfo.sample.orientation_unit = unit
	294	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	295	self.current_datainfo.sample.orientation.y = data_point
	296	self.current_datainfo.sample.orientation_unit = unit
	297	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	298	self.current_datainfo.sample.orientation.z = data_point
	299	self.current_datainfo.sample.orientation_unit = unit
	300
	301	## Instrumental Information
	302	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	303	self.current_datainfo.instrument = data_point
	304	## Detector Information
	305	elif tagname == 'name' and self.parent_class == 'SASdetector':
	306	self.detector.name = data_point
	307	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	308	self.detector.distance = data_point
	309	self.detector.distance_unit = unit
	310	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	311	self.detector.slit_length = data_point
	312	self.detector.slit_length_unit = unit
	313	elif tagname == 'x' and self.parent_class == 'offset':
	314	self.detector.offset.x = data_point
	315	self.detector.offset_unit = unit
	316	elif tagname == 'y' and self.parent_class == 'offset':
	317	self.detector.offset.y = data_point
	318	self.detector.offset_unit = unit
	319	elif tagname == 'z' and self.parent_class == 'offset':
	320	self.detector.offset.z = data_point
	321	self.detector.offset_unit = unit
	322	elif tagname == 'x' and self.parent_class == 'beam_center':
	323	self.detector.beam_center.x = data_point
	324	self.detector.beam_center_unit = unit
	325	elif tagname == 'y' and self.parent_class == 'beam_center':
	326	self.detector.beam_center.y = data_point
	327	self.detector.beam_center_unit = unit
	328	elif tagname == 'z' and self.parent_class == 'beam_center':
	329	self.detector.beam_center.z = data_point
	330	self.detector.beam_center_unit = unit
	331	elif tagname == 'x' and self.parent_class == 'pixel_size':
	332	self.detector.pixel_size.x = data_point
	333	self.detector.pixel_size_unit = unit
	334	elif tagname == 'y' and self.parent_class == 'pixel_size':
	335	self.detector.pixel_size.y = data_point
	336	self.detector.pixel_size_unit = unit
	337	elif tagname == 'z' and self.parent_class == 'pixel_size':
	338	self.detector.pixel_size.z = data_point
	339	self.detector.pixel_size_unit = unit
	340	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	341	self.detector.orientation.x = data_point
	342	self.detector.orientation_unit = unit
	343	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	344	self.detector.orientation.y = data_point
	345	self.detector.orientation_unit = unit
	346	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	347	self.detector.orientation.z = data_point
	348	self.detector.orientation_unit = unit
	349	## Collimation and Aperture
	350	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	351	self.collimation.length = data_point
	352	self.collimation.length_unit = unit
	353	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	354	self.collimation.name = data_point
	355	elif tagname == 'distance' and self.parent_class == 'aperture':
	356	self.aperture.distance = data_point
	357	self.aperture.distance_unit = unit
	358	elif tagname == 'x' and self.parent_class == 'size':
	359	self.aperture.size.x = data_point
	360	self.collimation.size_unit = unit
	361	elif tagname == 'y' and self.parent_class == 'size':
	362	self.aperture.size.y = data_point
	363	self.collimation.size_unit = unit
	364	elif tagname == 'z' and self.parent_class == 'size':
	365	self.aperture.size.z = data_point
	366	self.collimation.size_unit = unit
	367
	368	## Process Information
	369	elif tagname == 'name' and self.parent_class == 'SASprocess':
	370	self.process.name = data_point
	371	elif tagname == 'description' and self.parent_class == 'SASprocess':
	372	self.process.description = data_point
	373	elif tagname == 'date' and self.parent_class == 'SASprocess':
	374	try:
	375	self.process.date = datetime.datetime.fromtimestamp(data_point)
	376	except:
	377	self.process.date = data_point
	378	elif tagname == 'SASprocessnote':
	379	self.process.notes.append(data_point)
	380	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	381	unit = attr.get("unit", "")
	382	dic = {}
	383	dic["name"] = name
	384	dic["value"] = data_point
	385	dic["unit"] = unit
	386	self.process.term.append(dic)
[250fec92]	387
	388	## Transmission Spectrum
	389	elif tagname == 'T' and self.parent_class == 'Tdata':
	390	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	391	self.transspectrum.transmission_unit = unit
	392	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	393	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	394	self.transspectrum.transmission_deviation_unit = unit
	395	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	396	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	397	self.transspectrum.wavelength_unit = unit
	398
	399	## Source Information
	400	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	401	self.current_datainfo.source.wavelength = data_point
	402	self.current_datainfo.source.wavelength_unit = unit
	403	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	404	self.current_datainfo.source.wavelength_min = data_point
	405	self.current_datainfo.source.wavelength_min_unit = unit
	406	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	407	self.current_datainfo.source.wavelength_max = data_point
	408	self.current_datainfo.source.wavelength_max_unit = unit
	409	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	410	self.current_datainfo.source.wavelength_spread = data_point
	411	self.current_datainfo.source.wavelength_spread_unit = unit
	412	elif tagname == 'x' and self.parent_class == 'beam_size':
	413	self.current_datainfo.source.beam_size.x = data_point
	414	self.current_datainfo.source.beam_size_unit = unit
	415	elif tagname == 'y' and self.parent_class == 'beam_size':
	416	self.current_datainfo.source.beam_size.y = data_point
	417	self.current_datainfo.source.beam_size_unit = unit
	418	elif tagname == 'z' and self.parent_class == 'pixel_size':
	419	self.current_datainfo.source.data_point.z = data_point
	420	self.current_datainfo.source.beam_size_unit = unit
	421	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	422	self.current_datainfo.source.radiation = data_point
	423	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	424	self.current_datainfo.source.beam_shape = data_point
	425
	426	## Everything else goes in meta_data
	427	else:
	428	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	429	self.current_datainfo.meta_data[new_key] = data_point
	430
	431	self.names.remove(tagname_original)
	432	length = 0
	433	if len(self.names) > 1:
	434	length = len(self.names) - 1
	435	self.parent_class = self.names[length]
[654e8e0]	436	if not self._is_call_local() and not recurse:
	437	self.frm = ""
[1686a333]	438	self.add_data_set()
	439	empty = None
	440	if self.output[0].dx is not None:
	441	self.output[0].dxl = np.empty(0)
	442	self.output[0].dxw = np.empty(0)
	443	else:
	444	self.output[0].dx = np.empty(0)
	445	return self.output[0], empty
[250fec92]	446
	447
[654e8e0]	448	def _is_call_local(self):
[1686a333]	449	"""
	450
	451	"""
[654e8e0]	452	if self.frm == "":
	453	inter = inspect.stack()
	454	self.frm = inter[2]
	455	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	456	mod_name = mod_name.replace(".py", "")
	457	mod = mod_name.split("sas/")
	458	mod_name = mod[1]
	459	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	460	return False
	461	return True
	462
[d26dea0]	463	def is_cansas(self, ext="xml"):
	464	"""
	465	Checks to see if the xml file is a CanSAS file
	466
	467	:param ext: The file extension of the data file
	468	"""
	469	if self.validate_xml():
	470	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	471	value = self.xmlroot.get(name)
	472	if CANSAS_NS.get(self.cansas_version).get("ns") == \
	473	value.rsplit(" ")[0]:
	474	return True
	475	if ext == "svs":
	476	return True
[250fec92]	477	raise RuntimeError
[d26dea0]	478
[83b6408]	479	def load_file_and_schema(self, xml_file, schema_path=""):
[d26dea0]	480	"""
[250fec92]	481	Loads the file and associates a schema, if a schema is passed in or if one already exists
[d26dea0]	482
	483	:param xml_file: The xml file path sent to Reader.read
[250fec92]	484	:param schema_path: The path to a schema associated with the xml_file, or find one based on the file
[d26dea0]	485	"""
	486	base_name = xml_reader.__file__
	487	base_name = base_name.replace("\\", "/")
	488	base = base_name.split("/sas/")[0]
	489
	490	# Load in xml file and get the cansas version from the header
	491	self.set_xml_file(xml_file)
	492	self.cansas_version = self.xmlroot.get("version", "1.0")
	493
	494	# Generic values for the cansas file based on the version
[250fec92]	495	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
[83b6408]	496	if schema_path == "":
[250fec92]	497	schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \
	498	(base, self.cansas_defaults.get("schema")).replace("\\", "/")
[d26dea0]	499
	500	# Link a schema to the XML file.
	501	self.set_schema(schema_path)
	502
[250fec92]	503	def add_data_set(self):
[d26dea0]	504	"""
[250fec92]	505	Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
	506	private method to generate a new data set.
[d26dea0]	507
[250fec92]	508	:param key: NeXus group name for current tree level
[d26dea0]	509	"""
	510
[250fec92]	511	if self.current_datainfo and self.current_dataset:
	512	self._final_cleanup()
	513	self.data = []
	514	self.current_datainfo = DataInfo()
[d26dea0]	515
[250fec92]	516	def _initialize_new_data_set(self, parent_list=None):
	517	"""
	518	A private class method to generate a new 1D data object.
	519	Outside methods should call add_data_set() to be sure any existing data is stored properly.
	520
	521	:param parent_list: List of names of parent elements
	522	"""
	523
	524	if parent_list is None:
	525	parent_list = []
	526	x = np.array(0)
	527	y = np.array(0)
	528	self.current_dataset = plottable_1D(x, y)
[d26dea0]	529
[250fec92]	530	def add_intermediate(self):
	531	"""
	532	This method stores any intermediate objects within the final data set after fully reading the set.
	533
	534	:param parent: The NXclass name for the h5py Group object that just finished being processed
	535	"""
	536
	537	if self.parent_class == 'SASprocess':
	538	self.current_datainfo.process.append(self.process)
	539	self.process = Process()
	540	elif self.parent_class == 'SASdetector':
	541	self.current_datainfo.detector.append(self.detector)
	542	self.detector = Detector()
	543	elif self.parent_class == 'SAStransmission_spectrum':
	544	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	545	self.transspectrum = TransmissionSpectrum()
	546	elif self.parent_class == 'SAScollimation':
	547	self.current_datainfo.collimation.append(self.collimation)
	548	self.collimation = Collimation()
[5f26aa4]	549	elif self.parent_class == 'aperture':
[250fec92]	550	self.collimation.aperture.append(self.aperture)
	551	self.aperture = Aperture()
	552	elif self.parent_class == 'SASdata':
	553	self._check_for_empty_resolution()
	554	self.data.append(self.current_dataset)
	555
	556	def _final_cleanup(self):
[d26dea0]	557	"""
	558	Final cleanup of the Data1D object to be sure it has all the
	559	appropriate information needed for perspectives
	560	"""
[250fec92]	561
	562	## Append errors to dataset and reset class errors
	563	self.current_datainfo.errors = set()
[d26dea0]	564	for error in self.errors:
[250fec92]	565	self.current_datainfo.errors.add(error)
[d26dea0]	566	self.errors.clear()
[250fec92]	567
	568	## Combine all plottables with datainfo and append each to output
	569	## Type cast data arrays to float64 and find min/max as appropriate
	570	for dataset in self.data:
	571	if dataset.x is not None:
	572	dataset.x = np.delete(dataset.x, [0])
	573	dataset.x = dataset.x.astype(np.float64)
	574	dataset.xmin = np.min(dataset.x)
	575	dataset.xmax = np.max(dataset.x)
	576	if dataset.y is not None:
	577	dataset.y = np.delete(dataset.y, [0])
	578	dataset.y = dataset.y.astype(np.float64)
	579	dataset.ymin = np.min(dataset.y)
	580	dataset.ymax = np.max(dataset.y)
	581	if dataset.dx is not None:
	582	dataset.dx = np.delete(dataset.dx, [0])
	583	dataset.dx = dataset.dx.astype(np.float64)
	584	if dataset.dxl is not None:
	585	dataset.dxl = np.delete(dataset.dxl, [0])
	586	dataset.dxl = dataset.dxl.astype(np.float64)
	587	if dataset.dxw is not None:
	588	dataset.dxw = np.delete(dataset.dxw, [0])
	589	dataset.dxw = dataset.dxw.astype(np.float64)
	590	if dataset.dy is not None:
	591	dataset.dy = np.delete(dataset.dy, [0])
	592	dataset.dy = dataset.dy.astype(np.float64)
	593	np.trim_zeros(dataset.x)
	594	np.trim_zeros(dataset.y)
	595	np.trim_zeros(dataset.dy)
	596	final_dataset = combine_data(dataset, self.current_datainfo)
	597	self.output.append(final_dataset)
[d26dea0]	598
	599	def _create_unique_key(self, dictionary, name, numb=0):
	600	"""
	601	Create a unique key value for any dictionary to prevent overwriting
[250fec92]	602	Recurse until a unique key value is found.
[d26dea0]	603
	604	:param dictionary: A dictionary with any number of entries
	605	:param name: The index of the item to be added to dictionary
	606	:param numb: The number to be appended to the name, starts at 0
	607	"""
	608	if dictionary.get(name) is not None:
	609	numb += 1
	610	name = name.split("_")[0]
	611	name += "_{0}".format(numb)
	612	name = self._create_unique_key(dictionary, name, numb)
	613	return name
	614
[250fec92]	615	def _get_node_value(self, node, tagname):
	616	"""
	617	Get the value of a node and any applicable units
	618
	619	:param node: The XML node to get the value of
	620	:param tagname: The tagname of the node
	621	"""
	622	#Get the text from the node and convert all whitespace to spaces
	623	units = ''
	624	node_value = node.text
	625	if node_value is not None:
	626	node_value = ' '.join(node_value.split())
	627	else:
	628	node_value = ""
	629
	630	# If the value is a float, compile with units.
	631	if self.ns_list.ns_datatype == "float":
	632	# If an empty value is given, set as zero.
	633	if node_value is None or node_value.isspace() \
	634	or node_value.lower() == "nan":
	635	node_value = "0.0"
	636	#Convert the value to the base units
	637	node_value, units = self._unit_conversion(node, tagname, node_value)
	638
	639	# If the value is a timestamp, convert to a datetime object
	640	elif self.ns_list.ns_datatype == "timestamp":
	641	if node_value is None or node_value.isspace():
	642	pass
	643	else:
	644	try:
	645	node_value = \
	646	datetime.datetime.fromtimestamp(node_value)
	647	except ValueError:
	648	node_value = None
	649	return node_value, units
	650
	651	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	652	"""
	653	A unit converter method used to convert the data included in the file
	654	to the default units listed in data_info
	655
[250fec92]	656	:param node: XML node
	657	:param tagname: name of the node
[d26dea0]	658	:param node_value: The value of the current dom node
	659	"""
	660	attr = node.attrib
	661	value_unit = ''
	662	err_msg = None
[682c432]	663	default_unit = None
[5f26aa4]	664	if not isinstance(node_value, float):
	665	node_value = float(node_value)
	666	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	667	try:
	668	local_unit = attr['unit']
[250fec92]	669	unitname = self.ns_list.current_level.get("unit", "")
	670	if "SASdetector" in self.names:
	671	save_in = "detector"
	672	elif "aperture" in self.names:
	673	save_in = "aperture"
	674	elif "SAScollimation" in self.names:
	675	save_in = "collimation"
	676	elif "SAStransmission_spectrum" in self.names:
	677	save_in = "transspectrum"
	678	elif "SASdata" in self.names:
	679	x = np.zeros(1)
	680	y = np.zeros(1)
	681	self.current_data1d = Data1D(x, y)
	682	save_in = "current_data1d"
	683	elif "SASsource" in self.names:
	684	save_in = "current_datainfo.source"
	685	elif "SASsample" in self.names:
	686	save_in = "current_datainfo.sample"
	687	elif "SASprocess" in self.names:
	688	save_in = "process"
	689	else:
	690	save_in = "current_datainfo"
	691	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	692	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	693	and local_unit.lower() != "none":
	694	if HAS_CONVERTER == True:
	695	## Check local units - bad units raise KeyError
	696	data_conv_q = Converter(local_unit)
	697	value_unit = default_unit
[682c432]	698	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	699	else:
	700	value_unit = local_unit
	701	err_msg = "Unit converter is not available.\n"
	702	else:
	703	value_unit = local_unit
	704	except KeyError:
	705	err_msg = "CanSAS reader: unexpected "
	706	err_msg += "\"{0}\" unit [{1}]; "
	707	err_msg = err_msg.format(tagname, local_unit)
[682c432]	708	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	709	value_unit = local_unit
	710	except:
	711	err_msg = "CanSAS reader: unknown error converting "
	712	err_msg += "\"{0}\" unit [{1}]"
	713	err_msg = err_msg.format(tagname, local_unit)
	714	value_unit = local_unit
	715	elif 'unit' in attr:
	716	value_unit = attr['unit']
	717	if err_msg:
	718	self.errors.add(err_msg)
	719	return node_value, value_unit
	720
[250fec92]	721	def _check_for_empty_data(self):
[d26dea0]	722	"""
	723	Creates an empty data set if no data is passed to the reader
	724
	725	:param data1d: presumably a Data1D object
	726	"""
[250fec92]	727	if self.current_dataset == None:
	728	x_vals = np.empty(0)
	729	y_vals = np.empty(0)
	730	dx_vals = np.empty(0)
	731	dy_vals = np.empty(0)
	732	dxl = np.empty(0)
	733	dxw = np.empty(0)
	734	self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals)
	735	self.current_dataset.dxl = dxl
	736	self.current_dataset.dxw = dxw
	737
	738	def _check_for_empty_resolution(self):
[d26dea0]	739	"""
	740	A method to check all resolution data sets are the same size as I and Q
	741	"""
	742	dql_exists = False
	743	dqw_exists = False
	744	dq_exists = False
	745	di_exists = False
[250fec92]	746	if self.current_dataset.dxl is not None:
	747	dql_exists = True
	748	if self.current_dataset.dxw is not None:
	749	dqw_exists = True
	750	if self.current_dataset.dx is not None:
	751	dq_exists = True
	752	if self.current_dataset.dy is not None:
	753	di_exists = True
	754	if dqw_exists and not dql_exists:
	755	array_size = self.current_dataset.dxw.size - 1
	756	self.current_dataset.dxl = np.append(self.current_dataset.dxl, np.zeros([array_size]))
	757	elif dql_exists and not dqw_exists:
	758	array_size = self.current_dataset.dxl.size - 1
	759	self.current_dataset.dxw = np.append(self.current_dataset.dxw, np.zeros([array_size]))
	760	elif not dql_exists and not dqw_exists and not dq_exists:
	761	array_size = self.current_dataset.x.size - 1
	762	self.current_dataset.dx = np.append(self.current_dataset.dx, np.zeros([array_size]))
	763	if not di_exists:
	764	array_size = self.current_dataset.y.size - 1
	765	self.current_dataset.dy = np.append(self.current_dataset.dy, np.zeros([array_size]))
	766
	767
	768	####### All methods below are for writing CanSAS XML files #######
[d26dea0]	769
	770
[250fec92]	771	def write(self, filename, datainfo):
[d26dea0]	772	"""
[250fec92]	773	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	774
[250fec92]	775	:param filename: name of the file to write
	776	:param datainfo: Data1D object
	777	"""
	778	# Create XML document
	779	doc, _ = self._to_xml_doc(datainfo)
	780	# Write the file
	781	file_ref = open(filename, 'w')
	782	if self.encoding == None:
	783	self.encoding = "UTF-8"
	784	doc.write(file_ref, encoding=self.encoding,
	785	pretty_print=True, xml_declaration=True)
	786	file_ref.close()
[d26dea0]	787
[250fec92]	788	def _to_xml_doc(self, datainfo):
[d26dea0]	789	"""
[250fec92]	790	Create an XML document to contain the content of a Data1D
[d26dea0]	791
[250fec92]	792	:param datainfo: Data1D object
[d26dea0]	793	"""
[250fec92]	794	if not issubclass(datainfo.__class__, Data1D):
	795	raise RuntimeError, "The cansas writer expects a Data1D instance"
[d26dea0]	796
[250fec92]	797	# Get PIs and create root element
	798	pi_string = self._get_pi_string()
	799	# Define namespaces and create SASroot object
	800	main_node = self._create_main_node()
	801	# Create ElementTree, append SASroot and apply processing instructions
	802	base_string = pi_string + self.to_string(main_node)
	803	base_element = self.create_element_from_string(base_string)
	804	doc = self.create_tree(base_element)
	805	# Create SASentry Element
	806	entry_node = self.create_element("SASentry")
	807	root = doc.getroot()
	808	root.append(entry_node)
[d26dea0]	809
[250fec92]	810	# Add Title to SASentry
	811	self.write_node(entry_node, "Title", datainfo.title)
	812	# Add Run to SASentry
	813	self._write_run_names(datainfo, entry_node)
	814	# Add Data info to SASEntry
	815	self._write_data(datainfo, entry_node)
	816	# Transmission Spectrum Info
	817	self._write_trans_spectrum(datainfo, entry_node)
	818	# Sample info
	819	self._write_sample_info(datainfo, entry_node)
	820	# Instrument info
	821	instr = self._write_instrument(datainfo, entry_node)
	822	# Source
	823	self._write_source(datainfo, instr)
	824	# Collimation
	825	self._write_collimation(datainfo, instr)
	826	# Detectors
	827	self._write_detectors(datainfo, instr)
	828	# Processes info
	829	self._write_process_notes(datainfo, entry_node)
	830	# Note info
	831	self._write_notes(datainfo, entry_node)
	832	# Return the document, and the SASentry node associated with
	833	# the data we just wrote
	834	# If the calling function was not the cansas reader, return a minidom
	835	# object rather than an lxml object.
[654e8e0]	836	self.frm = inspect.stack()[1]
	837	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	838	return doc, entry_node
[d26dea0]	839
[250fec92]	840	def write_node(self, parent, name, value, attr=None):
	841	"""
	842	:param doc: document DOM
	843	:param parent: parent node
	844	:param name: tag of the element
	845	:param value: value of the child text node
	846	:param attr: attribute dictionary
[d26dea0]	847
[250fec92]	848	:return: True if something was appended, otherwise False
	849	"""
	850	if value is not None:
	851	parent = self.ebuilder(parent, name, value, attr)
	852	return True
	853	return False
[d26dea0]	854
	855	def _get_pi_string(self):
	856	"""
	857	Creates the processing instructions header for writing to file
	858	"""
	859	pis = self.return_processing_instructions()
	860	if len(pis) > 0:
	861	pi_tree = self.create_tree(pis[0])
	862	i = 1
	863	for i in range(1, len(pis) - 1):
	864	pi_tree = self.append(pis[i], pi_tree)
	865	pi_string = self.to_string(pi_tree)
	866	else:
	867	pi_string = ""
	868	return pi_string
	869
	870	def _create_main_node(self):
	871	"""
	872	Creates the primary xml header used when writing to file
	873	"""
	874	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	875	version = self.cansas_version
	876	n_s = CANSAS_NS.get(version).get("ns")
	877	if version == "1.1":
	878	url = "http://www.cansas.org/formats/1.1/"
	879	else:
	880	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	881	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	882	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	883	"version" : version}
	884	nsmap = {'xsi' : xsi, None: n_s}
	885
	886	main_node = self.create_element("{" + n_s + "}SASroot",
	887	attrib=attrib, nsmap=nsmap)
	888	return main_node
	889
	890	def _write_run_names(self, datainfo, entry_node):
	891	"""
	892	Writes the run names to the XML file
	893
	894	:param datainfo: The Data1D object the information is coming from
	895	:param entry_node: lxml node ElementTree object to be appended to
	896	"""
	897	if datainfo.run == None or datainfo.run == []:
	898	datainfo.run.append(RUN_NAME_DEFAULT)
	899	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	900	for item in datainfo.run:
	901	runname = {}
	902	if item in datainfo.run_name and \
	903	len(str(datainfo.run_name[item])) > 1:
	904	runname = {'name': datainfo.run_name[item]}
	905	self.write_node(entry_node, "Run", item, runname)
	906
	907	def _write_data(self, datainfo, entry_node):
	908	"""
	909	Writes the I and Q data to the XML file
	910
	911	:param datainfo: The Data1D object the information is coming from
	912	:param entry_node: lxml node ElementTree object to be appended to
	913	"""
	914	node = self.create_element("SASdata")
	915	self.append(node, entry_node)
	916
	917	for i in range(len(datainfo.x)):
	918	point = self.create_element("Idata")
	919	node.append(point)
	920	self.write_node(point, "Q", datainfo.x[i],
[682c432]	921	{'unit': datainfo.x_unit})
[d26dea0]	922	if len(datainfo.y) >= i:
	923	self.write_node(point, "I", datainfo.y[i],
[682c432]	924	{'unit': datainfo.y_unit})
[5f26aa4]	925	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	926	self.write_node(point, "Idev", datainfo.dy[i],
[682c432]	927	{'unit': datainfo.y_unit})
[5f26aa4]	928	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	929	self.write_node(point, "Qdev", datainfo.dx[i],
[682c432]	930	{'unit': datainfo.x_unit})
[5f26aa4]	931	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	932	self.write_node(point, "dQw", datainfo.dxw[i],
[682c432]	933	{'unit': datainfo.x_unit})
[5f26aa4]	934	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	935	self.write_node(point, "dQl", datainfo.dxl[i],
[682c432]	936	{'unit': datainfo.x_unit})
[d26dea0]	937
	938	def _write_trans_spectrum(self, datainfo, entry_node):
	939	"""
	940	Writes the transmission spectrum data to the XML file
	941
	942	:param datainfo: The Data1D object the information is coming from
	943	:param entry_node: lxml node ElementTree object to be appended to
	944	"""
	945	for i in range(len(datainfo.trans_spectrum)):
	946	spectrum = datainfo.trans_spectrum[i]
	947	node = self.create_element("SAStransmission_spectrum",
	948	{"name" : spectrum.name})
	949	self.append(node, entry_node)
	950	if isinstance(spectrum.timestamp, datetime.datetime):
	951	node.setAttribute("timestamp", spectrum.timestamp)
	952	for i in range(len(spectrum.wavelength)):
	953	point = self.create_element("Tdata")
	954	node.append(point)
	955	self.write_node(point, "Lambda", spectrum.wavelength[i],
	956	{'unit': spectrum.wavelength_unit})
	957	self.write_node(point, "T", spectrum.transmission[i],
	958	{'unit': spectrum.transmission_unit})
	959	if spectrum.transmission_deviation != None \
	960	and len(spectrum.transmission_deviation) >= i:
	961	self.write_node(point, "Tdev",
	962	spectrum.transmission_deviation[i],
	963	{'unit':
	964	spectrum.transmission_deviation_unit})
	965
	966	def _write_sample_info(self, datainfo, entry_node):
	967	"""
	968	Writes the sample information to the XML file
	969
	970	:param datainfo: The Data1D object the information is coming from
	971	:param entry_node: lxml node ElementTree object to be appended to
	972	"""
	973	sample = self.create_element("SASsample")
	974	if datainfo.sample.name is not None:
	975	self.write_attribute(sample, "name",
	976	str(datainfo.sample.name))
	977	self.append(sample, entry_node)
	978	self.write_node(sample, "ID", str(datainfo.sample.ID))
	979	self.write_node(sample, "thickness", datainfo.sample.thickness,
	980	{"unit": datainfo.sample.thickness_unit})
	981	self.write_node(sample, "transmission", datainfo.sample.transmission)
	982	self.write_node(sample, "temperature", datainfo.sample.temperature,
	983	{"unit": datainfo.sample.temperature_unit})
	984
	985	pos = self.create_element("position")
	986	written = self.write_node(pos,
	987	"x",
	988	datainfo.sample.position.x,
	989	{"unit": datainfo.sample.position_unit})
	990	written = written \| self.write_node( \
	991	pos, "y", datainfo.sample.position.y,
	992	{"unit": datainfo.sample.position_unit})
	993	written = written \| self.write_node( \
	994	pos, "z", datainfo.sample.position.z,
	995	{"unit": datainfo.sample.position_unit})
	996	if written == True:
	997	self.append(pos, sample)
	998
	999	ori = self.create_element("orientation")
	1000	written = self.write_node(ori, "roll",
	1001	datainfo.sample.orientation.x,
	1002	{"unit": datainfo.sample.orientation_unit})
	1003	written = written \| self.write_node( \
	1004	ori, "pitch", datainfo.sample.orientation.y,
	1005	{"unit": datainfo.sample.orientation_unit})
	1006	written = written \| self.write_node( \
	1007	ori, "yaw", datainfo.sample.orientation.z,
	1008	{"unit": datainfo.sample.orientation_unit})
	1009	if written == True:
	1010	self.append(ori, sample)
	1011
	1012	for item in datainfo.sample.details:
	1013	self.write_node(sample, "details", item)
	1014
	1015	def _write_instrument(self, datainfo, entry_node):
	1016	"""
	1017	Writes the instrumental information to the XML file
	1018
	1019	:param datainfo: The Data1D object the information is coming from
	1020	:param entry_node: lxml node ElementTree object to be appended to
	1021	"""
	1022	instr = self.create_element("SASinstrument")
	1023	self.append(instr, entry_node)
	1024	self.write_node(instr, "name", datainfo.instrument)
	1025	return instr
	1026
	1027	def _write_source(self, datainfo, instr):
	1028	"""
	1029	Writes the source information to the XML file
	1030
	1031	:param datainfo: The Data1D object the information is coming from
	1032	:param instr: instrument node to be appended to
	1033	"""
	1034	source = self.create_element("SASsource")
	1035	if datainfo.source.name is not None:
	1036	self.write_attribute(source, "name",
	1037	str(datainfo.source.name))
	1038	self.append(source, instr)
	1039	if datainfo.source.radiation == None or datainfo.source.radiation == '':
	1040	datainfo.source.radiation = "neutron"
	1041	self.write_node(source, "radiation", datainfo.source.radiation)
	1042
	1043	size = self.create_element("beam_size")
	1044	if datainfo.source.beam_size_name is not None:
	1045	self.write_attribute(size, "name",
	1046	str(datainfo.source.beam_size_name))
	1047	written = self.write_node( \
	1048	size, "x", datainfo.source.beam_size.x,
	1049	{"unit": datainfo.source.beam_size_unit})
	1050	written = written \| self.write_node( \
	1051	size, "y", datainfo.source.beam_size.y,
	1052	{"unit": datainfo.source.beam_size_unit})
	1053	written = written \| self.write_node( \
	1054	size, "z", datainfo.source.beam_size.z,
	1055	{"unit": datainfo.source.beam_size_unit})
	1056	if written == True:
	1057	self.append(size, source)
	1058
	1059	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1060	self.write_node(source, "wavelength",
	1061	datainfo.source.wavelength,
	1062	{"unit": datainfo.source.wavelength_unit})
	1063	self.write_node(source, "wavelength_min",
	1064	datainfo.source.wavelength_min,
	1065	{"unit": datainfo.source.wavelength_min_unit})
	1066	self.write_node(source, "wavelength_max",
	1067	datainfo.source.wavelength_max,
	1068	{"unit": datainfo.source.wavelength_max_unit})
	1069	self.write_node(source, "wavelength_spread",
	1070	datainfo.source.wavelength_spread,
	1071	{"unit": datainfo.source.wavelength_spread_unit})
	1072
	1073	def _write_collimation(self, datainfo, instr):
	1074	"""
	1075	Writes the collimation information to the XML file
	1076
	1077	:param datainfo: The Data1D object the information is coming from
	1078	:param instr: lxml node ElementTree object to be appended to
	1079	"""
	1080	if datainfo.collimation == [] or datainfo.collimation == None:
	1081	coll = Collimation()
	1082	datainfo.collimation.append(coll)
	1083	for item in datainfo.collimation:
	1084	coll = self.create_element("SAScollimation")
	1085	if item.name is not None:
	1086	self.write_attribute(coll, "name", str(item.name))
	1087	self.append(coll, instr)
	1088
	1089	self.write_node(coll, "length", item.length,
	1090	{"unit": item.length_unit})
	1091
	1092	for aperture in item.aperture:
	1093	apert = self.create_element("aperture")
	1094	if aperture.name is not None:
	1095	self.write_attribute(apert, "name", str(aperture.name))
	1096	if aperture.type is not None:
	1097	self.write_attribute(apert, "type", str(aperture.type))
	1098	self.append(apert, coll)
	1099
	1100	size = self.create_element("size")
	1101	if aperture.size_name is not None:
	1102	self.write_attribute(size, "name",
	1103	str(aperture.size_name))
	1104	written = self.write_node(size, "x", aperture.size.x,
	1105	{"unit": aperture.size_unit})
	1106	written = written \| self.write_node( \
	1107	size, "y", aperture.size.y,
	1108	{"unit": aperture.size_unit})
	1109	written = written \| self.write_node( \
	1110	size, "z", aperture.size.z,
	1111	{"unit": aperture.size_unit})
	1112	if written == True:
	1113	self.append(size, apert)
	1114
	1115	self.write_node(apert, "distance", aperture.distance,
	1116	{"unit": aperture.distance_unit})
	1117
	1118	def _write_detectors(self, datainfo, instr):
	1119	"""
	1120	Writes the detector information to the XML file
	1121
	1122	:param datainfo: The Data1D object the information is coming from
	1123	:param inst: lxml instrument node to be appended to
	1124	"""
	1125	if datainfo.detector == None or datainfo.detector == []:
	1126	det = Detector()
	1127	det.name = ""
	1128	datainfo.detector.append(det)
	1129
	1130	for item in datainfo.detector:
	1131	det = self.create_element("SASdetector")
	1132	written = self.write_node(det, "name", item.name)
	1133	written = written \| self.write_node(det, "SDD", item.distance,
	1134	{"unit": item.distance_unit})
	1135	if written == True:
	1136	self.append(det, instr)
	1137
	1138	off = self.create_element("offset")
	1139	written = self.write_node(off, "x", item.offset.x,
	1140	{"unit": item.offset_unit})
	1141	written = written \| self.write_node(off, "y", item.offset.y,
	1142	{"unit": item.offset_unit})
	1143	written = written \| self.write_node(off, "z", item.offset.z,
	1144	{"unit": item.offset_unit})
	1145	if written == True:
	1146	self.append(off, det)
	1147
	1148	ori = self.create_element("orientation")
	1149	written = self.write_node(ori, "roll", item.orientation.x,
	1150	{"unit": item.orientation_unit})
	1151	written = written \| self.write_node(ori, "pitch",
	1152	item.orientation.y,
	1153	{"unit": item.orientation_unit})
	1154	written = written \| self.write_node(ori, "yaw",
	1155	item.orientation.z,
	1156	{"unit": item.orientation_unit})
	1157	if written == True:
	1158	self.append(ori, det)
	1159
	1160	center = self.create_element("beam_center")
	1161	written = self.write_node(center, "x", item.beam_center.x,
	1162	{"unit": item.beam_center_unit})
	1163	written = written \| self.write_node(center, "y",
	1164	item.beam_center.y,
	1165	{"unit": item.beam_center_unit})
	1166	written = written \| self.write_node(center, "z",
	1167	item.beam_center.z,
	1168	{"unit": item.beam_center_unit})
	1169	if written == True:
	1170	self.append(center, det)
	1171
	1172	pix = self.create_element("pixel_size")
	1173	written = self.write_node(pix, "x", item.pixel_size.x,
	1174	{"unit": item.pixel_size_unit})
	1175	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1176	{"unit": item.pixel_size_unit})
	1177	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1178	{"unit": item.pixel_size_unit})
	1179	written = written \| self.write_node(det, "slit_length",
	1180	item.slit_length,
	1181	{"unit": item.slit_length_unit})
	1182	if written == True:
	1183	self.append(pix, det)
	1184
	1185	def _write_process_notes(self, datainfo, entry_node):
	1186	"""
	1187	Writes the process notes to the XML file
	1188
	1189	:param datainfo: The Data1D object the information is coming from
	1190	:param entry_node: lxml node ElementTree object to be appended to
	1191
	1192	"""
	1193	for item in datainfo.process:
	1194	node = self.create_element("SASprocess")
	1195	self.append(node, entry_node)
	1196	self.write_node(node, "name", item.name)
	1197	self.write_node(node, "date", item.date)
	1198	self.write_node(node, "description", item.description)
	1199	for term in item.term:
[1686a333]	1200	if isinstance(term, list):
	1201	value = term['value']
	1202	del term['value']
[5f26aa4]	1203	elif isinstance(term, dict):
	1204	value = term.get("value")
	1205	del term['value']
[1686a333]	1206	else:
	1207	value = term
[d26dea0]	1208	self.write_node(node, "term", value, term)
	1209	for note in item.notes:
	1210	self.write_node(node, "SASprocessnote", note)
	1211	if len(item.notes) == 0:
	1212	self.write_node(node, "SASprocessnote", "")
	1213
	1214	def _write_notes(self, datainfo, entry_node):
	1215	"""
	1216	Writes the notes to the XML file and creates an empty note if none
	1217	exist
	1218
	1219	:param datainfo: The Data1D object the information is coming from
	1220	:param entry_node: lxml node ElementTree object to be appended to
	1221
	1222	"""
	1223	if len(datainfo.notes) == 0:
	1224	node = self.create_element("SASnote")
	1225	self.append(node, entry_node)
	1226	else:
	1227	for item in datainfo.notes:
	1228	node = self.create_element("SASnote")
	1229	self.write_text(node, item)
	1230	self.append(node, entry_node)
	1231
[654e8e0]	1232	def _check_origin(self, entry_node, doc):
[d26dea0]	1233	"""
	1234	Return the document, and the SASentry node associated with
	1235	the data we just wrote.
	1236	If the calling function was not the cansas reader, return a minidom
	1237	object rather than an lxml object.
	1238
	1239	:param entry_node: lxml node ElementTree object to be appended to
	1240	:param doc: entire xml tree
	1241	"""
[654e8e0]	1242	if not self.frm:
	1243	self.frm = inspect.stack()[1]
	1244	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1245	mod_name = mod_name.replace(".py", "")
	1246	mod = mod_name.split("sas/")
	1247	mod_name = mod[1]
[45d90b9]	1248	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1249	string = self.to_string(doc, pretty_print=False)
	1250	doc = parseString(string)
	1251	node_name = entry_node.tag
	1252	node_list = doc.getElementsByTagName(node_name)
	1253	entry_node = node_list.item(0)
[5ce7f17]	1254	return doc, entry_node
[d26dea0]	1255
	1256	# DO NOT REMOVE - used in saving and loading panel states.
	1257	def _store_float(self, location, node, variable, storage, optional=True):
	1258	"""
	1259	Get the content of a xpath location and store
	1260	the result. Check that the units are compatible
	1261	with the destination. The value is expected to
	1262	be a float.
	1263
	1264	The xpath location might or might not exist.
	1265	If it does not exist, nothing is done
	1266
	1267	:param location: xpath location to fetch
	1268	:param node: node to read the data from
	1269	:param variable: name of the data member to store it in [string]
	1270	:param storage: data object that has the 'variable' data member
	1271	:param optional: if True, no exception will be raised
	1272	if unit conversion can't be done
	1273
	1274	:raise ValueError: raised when the units are not recognized
	1275	"""
	1276	entry = get_content(location, node)
	1277	try:
	1278	value = float(entry.text)
	1279	except:
	1280	value = None
	1281
	1282	if value is not None:
	1283	# If the entry has units, check to see that they are
	1284	# compatible with what we currently have in the data object
	1285	units = entry.get('unit')
	1286	if units is not None:
	1287	toks = variable.split('.')
	1288	local_unit = None
	1289	exec "local_unit = storage.%s_unit" % toks[0]
	1290	if local_unit != None and units.lower() != local_unit.lower():
	1291	if HAS_CONVERTER == True:
	1292	try:
	1293	conv = Converter(units)
	1294	exec "storage.%s = %g" % \
	1295	(variable, conv(value, units=local_unit))
	1296	except:
	1297	_, exc_value, _ = sys.exc_info()
	1298	err_mess = "CanSAS reader: could not convert"
	1299	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1300	% (variable, units, local_unit, exc_value)
	1301	self.errors.add(err_mess)
	1302	if optional:
	1303	logging.info(err_mess)
	1304	else:
	1305	raise ValueError, err_mess
	1306	else:
	1307	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1308	% (variable, units)
	1309	err_mess += " expecting [%s]" % local_unit
	1310	self.errors.add(err_mess)
	1311	if optional:
	1312	logging.info(err_mess)
	1313	else:
	1314	raise ValueError, err_mess
	1315	else:
	1316	exec "storage.%s = value" % variable
	1317	else:
	1318	exec "storage.%s = value" % variable
	1319
	1320	# DO NOT REMOVE - used in saving and loading panel states.
	1321	def _store_content(self, location, node, variable, storage):
	1322	"""
	1323	Get the content of a xpath location and store
	1324	the result. The value is treated as a string.
	1325
	1326	The xpath location might or might not exist.
	1327	If it does not exist, nothing is done
	1328
	1329	:param location: xpath location to fetch
	1330	:param node: node to read the data from
	1331	:param variable: name of the data member to store it in [string]
	1332	:param storage: data object that has the 'variable' data member
	1333
	1334	:return: return a list of errors
	1335	"""
	1336	entry = get_content(location, node)
	1337	if entry is not None and entry.text is not None:
	1338	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1339
	1340
	1341	# DO NOT REMOVE Called by outside packages:
	1342	# sas.sasgui.perspectives.invariant.invariant_state
	1343	# sas.sasgui.perspectives.fitting.pagestate
	1344	def get_content(location, node):
	1345	"""
	1346	Get the first instance of the content of a xpath location.
	1347
	1348	:param location: xpath location
	1349	:param node: node to start at
	1350
	1351	:return: Element, or None
	1352	"""
	1353	nodes = node.xpath(location,
	1354	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1355	if len(nodes) > 0:
	1356	return nodes[0]
	1357	else:
	1358	return None
	1359
	1360	# DO NOT REMOVE Called by outside packages:
	1361	# sas.sasgui.perspectives.fitting.pagestate
	1362	def write_node(doc, parent, name, value, attr=None):
	1363	"""
	1364	:param doc: document DOM
	1365	:param parent: parent node
	1366	:param name: tag of the element
	1367	:param value: value of the child text node
	1368	:param attr: attribute dictionary
	1369
	1370	:return: True if something was appended, otherwise False
	1371	"""
	1372	if attr is None:
	1373	attr = {}
	1374	if value is not None:
	1375	node = doc.createElement(name)
	1376	node.appendChild(doc.createTextNode(str(value)))
	1377	for item in attr:
	1378	node.setAttribute(item, attr[item])
	1379	parent.appendChild(node)
	1380	return True
	1381	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 654e8e0

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