cansas_reader.py @ d6bc9901

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

Last change on this file since d6bc9901 was ae69c690, checked in by krzywon, 7 years ago
Ensure dxl and dxw and the same length as each other and as x.
Property mode set to `100644`
File size: 63.5 KB

Rev	Line
[d26dea0]	1	import logging
[250fec92]	2	import numpy as np
[d26dea0]	3	import os
	4	import sys
	5	import datetime
	6	import inspect
	7	# For saving individual sections of data
[83c09af]	8	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
[af08e55]	9	plottable_1D, plottable_2D
[83c09af]	10	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
	11	Detector, Process, Aperture
	12	from sas.sascalc.dataloader.data_info import \
	13	combine_data_info_with_plottable as combine_data
[b699768]	14	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	15	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
[250fec92]	16	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
[3ece5dd]	17	from sas.sascalc.dataloader.loader_exceptions import FileContentsException, \
	18	DefaultReaderException, DataReaderException
[d26dea0]	19
[682c432]	20	# The following 2 imports ARE used. Do not remove either.
	21	import xml.dom.minidom
	22	from xml.dom.minidom import parseString
	23
[7477fb9]	24	from lxml import etree
	25
[463e7ffc]	26	logger = logging.getLogger(__name__)
[c155a16]	27
[d26dea0]	28	PREPROCESS = "xmlpreprocess"
	29	ENCODING = "encoding"
	30	RUN_NAME_DEFAULT = "None"
[250fec92]	31	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	32	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	33	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	34	"as much of the data as possible.\n\n"
[d26dea0]	35	HAS_CONVERTER = True
	36	try:
[b699768]	37	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	38	except ImportError:
	39	HAS_CONVERTER = False
	40
	41	CONSTANTS = CansasConstants()
	42	CANSAS_FORMAT = CONSTANTS.format
	43	CANSAS_NS = CONSTANTS.names
	44	ALLOW_ALL = True
	45
	46	class Reader(XMLreader):
	47	cansas_version = "1.0"
	48	base_ns = "{cansas1d/1.0}"
[250fec92]	49	cansas_defaults = None
[d26dea0]	50	type_name = "canSAS"
[250fec92]	51	invalid = True
[654e8e0]	52	frm = ""
[af08e55]	53	# Log messages and errors
[250fec92]	54	logging = None
	55	errors = set()
[af08e55]	56	# Namespace hierarchy for current xml_file object
[250fec92]	57	names = None
	58	ns_list = None
[af08e55]	59	# Temporary storage location for loading multiple data sets in a single file
[250fec92]	60	current_data1d = None
	61	data = None
[af08e55]	62	# Wildcards
[d26dea0]	63	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
[af08e55]	64	# List of allowed extensions
[d26dea0]	65	ext = ['.xml', '.XML', '.svs', '.SVS']
[af08e55]	66	# Flag to bypass extension check
[d26dea0]	67	allow_all = True
	68
[250fec92]	69	def reset_state(self):
	70	"""
	71	Resets the class state to a base case when loading a new data file so previous
	72	data files do not appear a second time
	73	"""
	74	self.current_datainfo = None
	75	self.current_dataset = None
	76	self.current_data1d = None
	77	self.data = []
	78	self.process = Process()
	79	self.transspectrum = TransmissionSpectrum()
	80	self.aperture = Aperture()
	81	self.collimation = Collimation()
	82	self.detector = Detector()
	83	self.names = []
	84	self.cansas_defaults = {}
	85	self.output = []
	86	self.ns_list = None
[d26dea0]	87	self.logging = []
	88	self.encoding = None
	89
[250fec92]	90	def read(self, xml_file, schema_path="", invalid=True):
[bc570f4]	91	if schema_path != "" or invalid != True:
	92	# read has been called from self.get_file_contents because xml file doens't conform to schema
	93	_, self.extension = os.path.splitext(os.path.basename(xml_file))
	94	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
[250fec92]	95
[bc570f4]	96	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
	97	return super(XMLreader, self).read(xml_file)
	98
	99	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
[7477fb9]	100	# Reset everything since we're loading a new file
[250fec92]	101	self.reset_state()
	102	self.invalid = invalid
[bc570f4]	103	if xml_file is None:
	104	xml_file = self.f_open.name
[7477fb9]	105	# We don't sure f_open since lxml handles opnening/closing files
[bc570f4]	106	if not self.f_open.closed:
	107	self.f_open.close()
[7477fb9]	108
[bc570f4]	109	basename, _ = os.path.splitext(os.path.basename(xml_file))
[8dec7e7]	110
[bc570f4]	111	try:
[8dec7e7]	112	# Raises FileContentsException
	113	self.load_file_and_schema(xml_file, schema_path)
	114	self.current_datainfo = DataInfo()
[7477fb9]	115	# Raises FileContentsException if file doesn't meet CanSAS schema
	116	self.is_cansas(self.extension)
	117	self.invalid = False # If we reach this point then file must be valid CanSAS
	118
	119	# Parse each SASentry
	120	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', namespaces={
	121	'ns': self.cansas_defaults.get("ns")
	122	})
	123	# Look for a SASentry
[bc570f4]	124	self.names.append("SASentry")
	125	self.set_processing_instructions()
	126
	127	for entry in entry_list:
	128	self.current_datainfo.filename = basename + self.extension
	129	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
[7477fb9]	130	self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions
[bc570f4]	131	self._parse_entry(entry)
[c54c965]	132	self.data_cleanup()
[bc570f4]	133	except FileContentsException as fc_exc:
[7477fb9]	134	# File doesn't meet schema - try loading with a less strict schema
	135	base_name = xml_reader.__file__
	136	base_name = base_name.replace("\\", "/")
	137	base = base_name.split("/sas/")[0]
	138	if self.cansas_version == "1.1":
	139	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	140	else:
	141	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	142	self.set_schema(invalid_schema)
	143	if self.invalid:
[250fec92]	144	try:
[7477fb9]	145	# Load data with less strict schema
	146	self.read(xml_file, invalid_schema, False)
	147
	148	# File can still be read but doesn't match schema, so raise exception
	149	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
[250fec92]	150	invalid_xml = self.find_invalid_xml()
[527a190]	151	if invalid_xml != "":
[cd57c7d4]	152	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
	153	raise DataReaderException(invalid_xml) # Handled by base class
[7477fb9]	154	except FileContentsException as fc_exc:
[0615d54]	155	msg = "CanSAS Reader could not load the file {}".format(xml_file)
[7477fb9]	156	if fc_exc.message is not None: # Propagate error messages from earlier
[0615d54]	157	msg = fc_exc.message
[dcb91cf]	158	if not self.extension in self.ext: # If the file has no associated loader
	159	raise DefaultReaderException(msg)
[7477fb9]	160	raise FileContentsException(msg)
	161	pass
	162	else:
	163	raise fc_exc
	164	except Exception as e: # Convert all other exceptions to FileContentsExceptions
	165	raise FileContentsException(e.message)
[250fec92]	166
[7477fb9]	167
	168	def load_file_and_schema(self, xml_file, schema_path=""):
	169	base_name = xml_reader.__file__
	170	base_name = base_name.replace("\\", "/")
	171	base = base_name.split("/sas/")[0]
	172
	173	# Try and parse the XML file
	174	try:
	175	self.set_xml_file(xml_file)
	176	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
[dcb91cf]	177	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
[7477fb9]	178	raise FileContentsException(msg)
	179
	180	self.cansas_version = self.xmlroot.get("version", "1.0")
	181	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
	182
	183	if schema_path == "":
	184	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
	185	base, self.cansas_defaults.get("schema").replace("\\", "/")
	186	)
	187	self.set_schema(schema_path)
	188
	189	def is_cansas(self, ext="xml"):
[250fec92]	190	"""
[7477fb9]	191	Checks to see if the XML file is a CanSAS file
[250fec92]	192
[7477fb9]	193	:param ext: The file extension of the data file
	194	:raises FileContentsException: Raised if XML file isn't valid CanSAS
[250fec92]	195	"""
[7477fb9]	196	if self.validate_xml(): # Check file is valid XML
	197	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	198	value = self.xmlroot.get(name)
	199	# Check schema CanSAS version matches file CanSAS version
	200	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
	201	return True
	202	if ext == "svs":
	203	return True # Why is this required?
	204	# If we get to this point then file isn't valid CanSAS
[dcb91cf]	205	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
[7477fb9]	206	raise FileContentsException("The file is not valid CanSAS")
[250fec92]	207
[7477fb9]	208	def _parse_entry(self, dom, recurse=False):
[654e8e0]	209	if not self._is_call_local() and not recurse:
[1686a333]	210	self.reset_state()
[7477fb9]	211	self.data = []
	212	self.current_datainfo = DataInfo()
[1686a333]	213	self.names.append("SASentry")
	214	self.parent_class = "SASentry"
[7477fb9]	215	# Create an empty dataset if no data has been passed to the reader
	216	if self.current_dataset is None:
	217	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
	218	np.empty(0), np.empty(0))
	219	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
[250fec92]	220
[7477fb9]	221	# Loop through each child in the parent element
[250fec92]	222	for node in dom:
[5f26aa4]	223	attr = node.attrib
	224	name = attr.get("name", "")
	225	type = attr.get("type", "")
[250fec92]	226	# Get the element name and set the current names level
	227	tagname = node.tag.replace(self.base_ns, "")
	228	tagname_original = tagname
	229	# Skip this iteration when loading in save state information
	230	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	231	continue
	232	# Get where to store content
	233	self.names.append(tagname_original)
	234	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	235	# If the element is a child element, recurse
	236	if len(node.getchildren()) > 0:
	237	self.parent_class = tagname_original
	238	if tagname == 'SASdata':
[af08e55]	239	self._initialize_new_data_set(node)
	240	if isinstance(self.current_dataset, plottable_2D):
	241	x_bins = attr.get("x_bins", "")
	242	y_bins = attr.get("y_bins", "")
	243	if x_bins is not "" and y_bins is not "":
	244	self.current_dataset.shape = (x_bins, y_bins)
	245	else:
	246	self.current_dataset.shape = ()
[7477fb9]	247	# Recurse to access data within the group
	248	self._parse_entry(node, recurse=True)
[5f26aa4]	249	if tagname == "SASsample":
	250	self.current_datainfo.sample.name = name
	251	elif tagname == "beam_size":
	252	self.current_datainfo.source.beam_size_name = name
	253	elif tagname == "SAScollimation":
	254	self.collimation.name = name
	255	elif tagname == "aperture":
	256	self.aperture.name = name
	257	self.aperture.type = type
[7477fb9]	258	self._add_intermediate()
[250fec92]	259	else:
[1905128]	260	if isinstance(self.current_dataset, plottable_2D):
	261	data_point = node.text
	262	unit = attr.get('unit', '')
	263	else:
	264	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	265
[af08e55]	266	# If this is a dataset, store the data appropriately
[250fec92]	267	if tagname == 'Run':
[5f26aa4]	268	self.current_datainfo.run_name[data_point] = name
[250fec92]	269	self.current_datainfo.run.append(data_point)
	270	elif tagname == 'Title':
	271	self.current_datainfo.title = data_point
	272	elif tagname == 'SASnote':
	273	self.current_datainfo.notes.append(data_point)
	274
[0b79323]	275	# I and Q points
[af08e55]	276	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[527a190]	277	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	278	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	279	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	280	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	281	elif tagname == 'Q':
[527a190]	282	self.current_dataset.xaxis("Q", unit)
[250fec92]	283	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	284	elif tagname == 'Qdev':
	285	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	286	elif tagname == 'dQw':
[590b5c2]	287	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
[250fec92]	288	elif tagname == 'dQl':
	289	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	290	elif tagname == 'Qmean':
	291	pass
	292	elif tagname == 'Shadowfactor':
	293	pass
[ad4632c]	294	elif tagname == 'Sesans':
	295	self.current_datainfo.isSesans = bool(data_point)
[527a190]	296	self.current_dataset.xaxis(attr.get('x_axis'),
	297	attr.get('x_unit'))
	298	self.current_dataset.yaxis(attr.get('y_axis'),
	299	attr.get('y_unit'))
[63d773c]	300	elif tagname == 'yacceptance':
	301	self.current_datainfo.sample.yacceptance = (data_point, unit)
[ad4632c]	302	elif tagname == 'zacceptance':
	303	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	304
[af08e55]	305	# I and Qx, Qy - 2D data
	306	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	307	self.current_dataset.yaxis("Intensity", unit)
[1905128]	308	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	309	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	310	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	311	elif tagname == 'Qx':
	312	self.current_dataset.xaxis("Qx", unit)
[1905128]	313	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	314	elif tagname == 'Qy':
	315	self.current_dataset.yaxis("Qy", unit)
[1905128]	316	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	317	elif tagname == 'Qxdev':
	318	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	319	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	320	elif tagname == 'Qydev':
	321	self.current_dataset.yaxis("Qydev", unit)
[1905128]	322	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	323	elif tagname == 'Mask':
[bcabf4e]	324	inter = [item == "1" for item in data_point.split(",")]
[1905128]	325	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	326
	327	# Sample Information
[250fec92]	328	elif tagname == 'ID' and self.parent_class == 'SASsample':
	329	self.current_datainfo.sample.ID = data_point
	330	elif tagname == 'Title' and self.parent_class == 'SASsample':
	331	self.current_datainfo.sample.name = data_point
	332	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	333	self.current_datainfo.sample.thickness = data_point
	334	self.current_datainfo.sample.thickness_unit = unit
	335	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	336	self.current_datainfo.sample.transmission = data_point
	337	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	338	self.current_datainfo.sample.temperature = data_point
	339	self.current_datainfo.sample.temperature_unit = unit
	340	elif tagname == 'details' and self.parent_class == 'SASsample':
	341	self.current_datainfo.sample.details.append(data_point)
	342	elif tagname == 'x' and self.parent_class == 'position':
	343	self.current_datainfo.sample.position.x = data_point
	344	self.current_datainfo.sample.position_unit = unit
	345	elif tagname == 'y' and self.parent_class == 'position':
	346	self.current_datainfo.sample.position.y = data_point
	347	self.current_datainfo.sample.position_unit = unit
	348	elif tagname == 'z' and self.parent_class == 'position':
	349	self.current_datainfo.sample.position.z = data_point
	350	self.current_datainfo.sample.position_unit = unit
	351	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	352	self.current_datainfo.sample.orientation.x = data_point
	353	self.current_datainfo.sample.orientation_unit = unit
	354	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	355	self.current_datainfo.sample.orientation.y = data_point
	356	self.current_datainfo.sample.orientation_unit = unit
	357	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	358	self.current_datainfo.sample.orientation.z = data_point
	359	self.current_datainfo.sample.orientation_unit = unit
	360
[af08e55]	361	# Instrumental Information
[250fec92]	362	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	363	self.current_datainfo.instrument = data_point
[7477fb9]	364
[af08e55]	365	# Detector Information
[250fec92]	366	elif tagname == 'name' and self.parent_class == 'SASdetector':
	367	self.detector.name = data_point
	368	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	369	self.detector.distance = data_point
	370	self.detector.distance_unit = unit
	371	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	372	self.detector.slit_length = data_point
	373	self.detector.slit_length_unit = unit
	374	elif tagname == 'x' and self.parent_class == 'offset':
	375	self.detector.offset.x = data_point
	376	self.detector.offset_unit = unit
	377	elif tagname == 'y' and self.parent_class == 'offset':
	378	self.detector.offset.y = data_point
	379	self.detector.offset_unit = unit
	380	elif tagname == 'z' and self.parent_class == 'offset':
	381	self.detector.offset.z = data_point
	382	self.detector.offset_unit = unit
	383	elif tagname == 'x' and self.parent_class == 'beam_center':
	384	self.detector.beam_center.x = data_point
	385	self.detector.beam_center_unit = unit
	386	elif tagname == 'y' and self.parent_class == 'beam_center':
	387	self.detector.beam_center.y = data_point
	388	self.detector.beam_center_unit = unit
	389	elif tagname == 'z' and self.parent_class == 'beam_center':
	390	self.detector.beam_center.z = data_point
	391	self.detector.beam_center_unit = unit
	392	elif tagname == 'x' and self.parent_class == 'pixel_size':
	393	self.detector.pixel_size.x = data_point
	394	self.detector.pixel_size_unit = unit
	395	elif tagname == 'y' and self.parent_class == 'pixel_size':
	396	self.detector.pixel_size.y = data_point
	397	self.detector.pixel_size_unit = unit
	398	elif tagname == 'z' and self.parent_class == 'pixel_size':
	399	self.detector.pixel_size.z = data_point
	400	self.detector.pixel_size_unit = unit
	401	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	402	self.detector.orientation.x = data_point
	403	self.detector.orientation_unit = unit
	404	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	405	self.detector.orientation.y = data_point
	406	self.detector.orientation_unit = unit
	407	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	408	self.detector.orientation.z = data_point
	409	self.detector.orientation_unit = unit
[7477fb9]	410
[af08e55]	411	# Collimation and Aperture
[250fec92]	412	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	413	self.collimation.length = data_point
	414	self.collimation.length_unit = unit
	415	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	416	self.collimation.name = data_point
	417	elif tagname == 'distance' and self.parent_class == 'aperture':
	418	self.aperture.distance = data_point
	419	self.aperture.distance_unit = unit
	420	elif tagname == 'x' and self.parent_class == 'size':
	421	self.aperture.size.x = data_point
	422	self.collimation.size_unit = unit
	423	elif tagname == 'y' and self.parent_class == 'size':
	424	self.aperture.size.y = data_point
	425	self.collimation.size_unit = unit
	426	elif tagname == 'z' and self.parent_class == 'size':
	427	self.aperture.size.z = data_point
	428	self.collimation.size_unit = unit
	429
[af08e55]	430	# Process Information
[250fec92]	431	elif tagname == 'name' and self.parent_class == 'SASprocess':
	432	self.process.name = data_point
	433	elif tagname == 'description' and self.parent_class == 'SASprocess':
	434	self.process.description = data_point
	435	elif tagname == 'date' and self.parent_class == 'SASprocess':
	436	try:
	437	self.process.date = datetime.datetime.fromtimestamp(data_point)
	438	except:
	439	self.process.date = data_point
	440	elif tagname == 'SASprocessnote':
	441	self.process.notes.append(data_point)
	442	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	443	unit = attr.get("unit", "")
[7477fb9]	444	dic = { "name": name, "value": data_point, "unit": unit }
[5f26aa4]	445	self.process.term.append(dic)
[250fec92]	446
[af08e55]	447	# Transmission Spectrum
[250fec92]	448	elif tagname == 'T' and self.parent_class == 'Tdata':
	449	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	450	self.transspectrum.transmission_unit = unit
	451	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	452	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	453	self.transspectrum.transmission_deviation_unit = unit
	454	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	455	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	456	self.transspectrum.wavelength_unit = unit
	457
[af08e55]	458	# Source Information
[250fec92]	459	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	460	self.current_datainfo.source.wavelength = data_point
	461	self.current_datainfo.source.wavelength_unit = unit
	462	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	463	self.current_datainfo.source.wavelength_min = data_point
	464	self.current_datainfo.source.wavelength_min_unit = unit
	465	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	466	self.current_datainfo.source.wavelength_max = data_point
	467	self.current_datainfo.source.wavelength_max_unit = unit
	468	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	469	self.current_datainfo.source.wavelength_spread = data_point
	470	self.current_datainfo.source.wavelength_spread_unit = unit
	471	elif tagname == 'x' and self.parent_class == 'beam_size':
	472	self.current_datainfo.source.beam_size.x = data_point
	473	self.current_datainfo.source.beam_size_unit = unit
	474	elif tagname == 'y' and self.parent_class == 'beam_size':
	475	self.current_datainfo.source.beam_size.y = data_point
	476	self.current_datainfo.source.beam_size_unit = unit
	477	elif tagname == 'z' and self.parent_class == 'pixel_size':
	478	self.current_datainfo.source.data_point.z = data_point
	479	self.current_datainfo.source.beam_size_unit = unit
	480	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	481	self.current_datainfo.source.radiation = data_point
	482	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	483	self.current_datainfo.source.beam_shape = data_point
	484
[af08e55]	485	# Everything else goes in meta_data
[250fec92]	486	else:
	487	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	488	self.current_datainfo.meta_data[new_key] = data_point
	489
	490	self.names.remove(tagname_original)
	491	length = 0
	492	if len(self.names) > 1:
	493	length = len(self.names) - 1
	494	self.parent_class = self.names[length]
[654e8e0]	495	if not self._is_call_local() and not recurse:
	496	self.frm = ""
[7477fb9]	497	self.current_datainfo.errors = set()
	498	for error in self.errors:
	499	self.current_datainfo.errors.add(error)
[c54c965]	500	self.data_cleanup()
	501	self.sort_one_d_data()
	502	self.sort_two_d_data()
	503	self.reset_data_list()
[1686a333]	504	empty = None
	505	return self.output[0], empty
[250fec92]	506
[c54c965]	507	def data_cleanup(self):
	508	"""
	509	Clean up the data sets and refresh everything
	510	:return: None
	511	"""
	512	has_error_dx = self.current_dataset.dx is not None
[ae69c690]	513	has_error_dxl = self.current_dataset.dxl is not None
	514	has_error_dxw = self.current_dataset.dxw is not None
[c54c965]	515	has_error_dy = self.current_dataset.dy is not None
	516	self.remove_empty_q_values(has_error_dx=has_error_dx,
[ae69c690]	517	has_error_dxl=has_error_dxl,
	518	has_error_dxw=has_error_dxw,
[c54c965]	519	has_error_dy=has_error_dy)
	520	self.send_to_output() # Combine datasets with DataInfo
	521	self.current_datainfo = DataInfo() # Reset DataInfo
	522
[654e8e0]	523	def _is_call_local(self):
	524	if self.frm == "":
	525	inter = inspect.stack()
	526	self.frm = inter[2]
	527	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	528	mod_name = mod_name.replace(".py", "")
	529	mod = mod_name.split("sas/")
	530	mod_name = mod[1]
	531	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	532	return False
	533	return True
	534
[7477fb9]	535	def _add_intermediate(self):
[250fec92]	536	"""
	537	This method stores any intermediate objects within the final data set after fully reading the set.
	538	"""
	539	if self.parent_class == 'SASprocess':
	540	self.current_datainfo.process.append(self.process)
	541	self.process = Process()
	542	elif self.parent_class == 'SASdetector':
	543	self.current_datainfo.detector.append(self.detector)
	544	self.detector = Detector()
	545	elif self.parent_class == 'SAStransmission_spectrum':
	546	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	547	self.transspectrum = TransmissionSpectrum()
	548	elif self.parent_class == 'SAScollimation':
	549	self.current_datainfo.collimation.append(self.collimation)
	550	self.collimation = Collimation()
[5f26aa4]	551	elif self.parent_class == 'aperture':
[250fec92]	552	self.collimation.aperture.append(self.aperture)
	553	self.aperture = Aperture()
	554	elif self.parent_class == 'SASdata':
	555	self._check_for_empty_resolution()
	556	self.data.append(self.current_dataset)
	557
	558	def _get_node_value(self, node, tagname):
	559	"""
	560	Get the value of a node and any applicable units
	561
	562	:param node: The XML node to get the value of
	563	:param tagname: The tagname of the node
	564	"""
	565	#Get the text from the node and convert all whitespace to spaces
	566	units = ''
	567	node_value = node.text
	568	if node_value is not None:
	569	node_value = ' '.join(node_value.split())
	570	else:
	571	node_value = ""
	572
	573	# If the value is a float, compile with units.
	574	if self.ns_list.ns_datatype == "float":
	575	# If an empty value is given, set as zero.
	576	if node_value is None or node_value.isspace() \
	577	or node_value.lower() == "nan":
	578	node_value = "0.0"
	579	#Convert the value to the base units
	580	node_value, units = self._unit_conversion(node, tagname, node_value)
	581
	582	# If the value is a timestamp, convert to a datetime object
	583	elif self.ns_list.ns_datatype == "timestamp":
	584	if node_value is None or node_value.isspace():
	585	pass
	586	else:
	587	try:
	588	node_value = \
	589	datetime.datetime.fromtimestamp(node_value)
	590	except ValueError:
	591	node_value = None
	592	return node_value, units
	593
	594	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	595	"""
	596	A unit converter method used to convert the data included in the file
	597	to the default units listed in data_info
	598
[250fec92]	599	:param node: XML node
	600	:param tagname: name of the node
[d26dea0]	601	:param node_value: The value of the current dom node
	602	"""
	603	attr = node.attrib
	604	value_unit = ''
	605	err_msg = None
[682c432]	606	default_unit = None
[5f26aa4]	607	if not isinstance(node_value, float):
	608	node_value = float(node_value)
	609	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	610	try:
	611	local_unit = attr['unit']
[250fec92]	612	unitname = self.ns_list.current_level.get("unit", "")
	613	if "SASdetector" in self.names:
	614	save_in = "detector"
	615	elif "aperture" in self.names:
	616	save_in = "aperture"
	617	elif "SAScollimation" in self.names:
	618	save_in = "collimation"
	619	elif "SAStransmission_spectrum" in self.names:
	620	save_in = "transspectrum"
	621	elif "SASdata" in self.names:
	622	x = np.zeros(1)
	623	y = np.zeros(1)
	624	self.current_data1d = Data1D(x, y)
	625	save_in = "current_data1d"
	626	elif "SASsource" in self.names:
	627	save_in = "current_datainfo.source"
	628	elif "SASsample" in self.names:
	629	save_in = "current_datainfo.sample"
	630	elif "SASprocess" in self.names:
	631	save_in = "process"
	632	else:
	633	save_in = "current_datainfo"
	634	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	635	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	636	and local_unit.lower() != "none":
	637	if HAS_CONVERTER == True:
[af08e55]	638	# Check local units - bad units raise KeyError
[d26dea0]	639	data_conv_q = Converter(local_unit)
	640	value_unit = default_unit
[682c432]	641	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	642	else:
	643	value_unit = local_unit
	644	err_msg = "Unit converter is not available.\n"
	645	else:
	646	value_unit = local_unit
	647	except KeyError:
[527a190]	648	# Do not throw an error for loading Sesans data in cansas xml
	649	# This is a temporary fix.
	650	if local_unit != "A" and local_unit != 'pol':
	651	err_msg = "CanSAS reader: unexpected "
	652	err_msg += "\"{0}\" unit [{1}]; "
	653	err_msg = err_msg.format(tagname, local_unit)
	654	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	655	value_unit = local_unit
	656	except:
	657	err_msg = "CanSAS reader: unknown error converting "
	658	err_msg += "\"{0}\" unit [{1}]"
	659	err_msg = err_msg.format(tagname, local_unit)
	660	value_unit = local_unit
	661	elif 'unit' in attr:
	662	value_unit = attr['unit']
	663	if err_msg:
	664	self.errors.add(err_msg)
	665	return node_value, value_unit
	666
[250fec92]	667	def _check_for_empty_resolution(self):
[d26dea0]	668	"""
[7477fb9]	669	a method to check all resolution data sets are the same size as I and q
	670	"""
	671	dql_exists = False
	672	dqw_exists = False
	673	dq_exists = False
	674	di_exists = False
	675	if self.current_dataset.dxl is not None:
	676	dql_exists = True
	677	if self.current_dataset.dxw is not None:
	678	dqw_exists = True
	679	if self.current_dataset.dx is not None:
	680	dq_exists = True
	681	if self.current_dataset.dy is not None:
	682	di_exists = True
	683	if dqw_exists and not dql_exists:
[ae69c690]	684	array_size = self.current_dataset.dxw.size
	685	self.current_dataset.dxl = np.zeros(array_size)
[7477fb9]	686	elif dql_exists and not dqw_exists:
[ae69c690]	687	array_size = self.current_dataset.dxl.size
	688	self.current_dataset.dxw = np.zeros(array_size)
[7477fb9]	689	elif not dql_exists and not dqw_exists and not dq_exists:
[ae69c690]	690	array_size = self.current_dataset.x.size
[7477fb9]	691	self.current_dataset.dx = np.append(self.current_dataset.dx,
	692	np.zeros([array_size]))
	693	if not di_exists:
[ae69c690]	694	array_size = self.current_dataset.y.size
[7477fb9]	695	self.current_dataset.dy = np.append(self.current_dataset.dy,
	696	np.zeros([array_size]))
[d26dea0]	697
[0b79323]	698	def _initialize_new_data_set(self, node=None):
	699	if node is not None:
	700	for child in node:
	701	if child.tag.replace(self.base_ns, "") == "Idata":
	702	for i_child in child:
	703	if i_child.tag.replace(self.base_ns, "") == "Qx":
	704	self.current_dataset = plottable_2D()
	705	return
	706	self.current_dataset = plottable_1D(np.array(0), np.array(0))
	707
	708	## Writing Methods
[250fec92]	709	def write(self, filename, datainfo):
[d26dea0]	710	"""
[250fec92]	711	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	712
[250fec92]	713	:param filename: name of the file to write
	714	:param datainfo: Data1D object
	715	"""
	716	# Create XML document
	717	doc, _ = self._to_xml_doc(datainfo)
	718	# Write the file
	719	file_ref = open(filename, 'w')
[235f514]	720	if self.encoding is None:
[250fec92]	721	self.encoding = "UTF-8"
	722	doc.write(file_ref, encoding=self.encoding,
	723	pretty_print=True, xml_declaration=True)
	724	file_ref.close()
[d26dea0]	725
[250fec92]	726	def _to_xml_doc(self, datainfo):
[d26dea0]	727	"""
[250fec92]	728	Create an XML document to contain the content of a Data1D
[d26dea0]	729
[250fec92]	730	:param datainfo: Data1D object
[d26dea0]	731	"""
[af08e55]	732	is_2d = False
[83c09af]	733	if issubclass(datainfo.__class__, Data2D):
	734	is_2d = True
[d26dea0]	735
[250fec92]	736	# Get PIs and create root element
	737	pi_string = self._get_pi_string()
	738	# Define namespaces and create SASroot object
	739	main_node = self._create_main_node()
	740	# Create ElementTree, append SASroot and apply processing instructions
	741	base_string = pi_string + self.to_string(main_node)
	742	base_element = self.create_element_from_string(base_string)
	743	doc = self.create_tree(base_element)
	744	# Create SASentry Element
	745	entry_node = self.create_element("SASentry")
	746	root = doc.getroot()
	747	root.append(entry_node)
[d26dea0]	748
[250fec92]	749	# Add Title to SASentry
	750	self.write_node(entry_node, "Title", datainfo.title)
	751	# Add Run to SASentry
	752	self._write_run_names(datainfo, entry_node)
	753	# Add Data info to SASEntry
[83c09af]	754	if is_2d:
	755	self._write_data_2d(datainfo, entry_node)
	756	else:
	757	self._write_data(datainfo, entry_node)
[250fec92]	758	# Transmission Spectrum Info
[8434365]	759	# TODO: fix the writer to linearize all data, including T_spectrum
	760	# self._write_trans_spectrum(datainfo, entry_node)
[250fec92]	761	# Sample info
	762	self._write_sample_info(datainfo, entry_node)
	763	# Instrument info
	764	instr = self._write_instrument(datainfo, entry_node)
	765	# Source
	766	self._write_source(datainfo, instr)
	767	# Collimation
	768	self._write_collimation(datainfo, instr)
	769	# Detectors
	770	self._write_detectors(datainfo, instr)
	771	# Processes info
	772	self._write_process_notes(datainfo, entry_node)
	773	# Note info
	774	self._write_notes(datainfo, entry_node)
	775	# Return the document, and the SASentry node associated with
	776	# the data we just wrote
	777	# If the calling function was not the cansas reader, return a minidom
	778	# object rather than an lxml object.
[654e8e0]	779	self.frm = inspect.stack()[1]
	780	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	781	return doc, entry_node
[d26dea0]	782
[250fec92]	783	def write_node(self, parent, name, value, attr=None):
	784	"""
	785	:param doc: document DOM
	786	:param parent: parent node
	787	:param name: tag of the element
	788	:param value: value of the child text node
	789	:param attr: attribute dictionary
[d26dea0]	790
[250fec92]	791	:return: True if something was appended, otherwise False
	792	"""
	793	if value is not None:
	794	parent = self.ebuilder(parent, name, value, attr)
	795	return True
	796	return False
[d26dea0]	797
	798	def _get_pi_string(self):
	799	"""
	800	Creates the processing instructions header for writing to file
	801	"""
	802	pis = self.return_processing_instructions()
	803	if len(pis) > 0:
	804	pi_tree = self.create_tree(pis[0])
	805	i = 1
	806	for i in range(1, len(pis) - 1):
	807	pi_tree = self.append(pis[i], pi_tree)
	808	pi_string = self.to_string(pi_tree)
	809	else:
	810	pi_string = ""
	811	return pi_string
	812
	813	def _create_main_node(self):
	814	"""
	815	Creates the primary xml header used when writing to file
	816	"""
	817	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	818	version = self.cansas_version
	819	n_s = CANSAS_NS.get(version).get("ns")
	820	if version == "1.1":
	821	url = "http://www.cansas.org/formats/1.1/"
	822	else:
	823	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	824	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	825	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	826	"version" : version}
	827	nsmap = {'xsi' : xsi, None: n_s}
	828
	829	main_node = self.create_element("{" + n_s + "}SASroot",
	830	attrib=attrib, nsmap=nsmap)
	831	return main_node
	832
	833	def _write_run_names(self, datainfo, entry_node):
	834	"""
	835	Writes the run names to the XML file
	836
	837	:param datainfo: The Data1D object the information is coming from
	838	:param entry_node: lxml node ElementTree object to be appended to
	839	"""
[235f514]	840	if datainfo.run is None or datainfo.run == []:
[d26dea0]	841	datainfo.run.append(RUN_NAME_DEFAULT)
	842	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	843	for item in datainfo.run:
	844	runname = {}
	845	if item in datainfo.run_name and \
	846	len(str(datainfo.run_name[item])) > 1:
	847	runname = {'name': datainfo.run_name[item]}
	848	self.write_node(entry_node, "Run", item, runname)
	849
	850	def _write_data(self, datainfo, entry_node):
	851	"""
[83c09af]	852	Writes 1D I and Q data to the XML file
[d26dea0]	853
	854	:param datainfo: The Data1D object the information is coming from
	855	:param entry_node: lxml node ElementTree object to be appended to
	856	"""
	857	node = self.create_element("SASdata")
	858	self.append(node, entry_node)
	859
	860	for i in range(len(datainfo.x)):
	861	point = self.create_element("Idata")
	862	node.append(point)
	863	self.write_node(point, "Q", datainfo.x[i],
[527a190]	864	{'unit': datainfo.x_unit})
[d26dea0]	865	if len(datainfo.y) >= i:
	866	self.write_node(point, "I", datainfo.y[i],
[527a190]	867	{'unit': datainfo.y_unit})
[5f26aa4]	868	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	869	self.write_node(point, "Idev", datainfo.dy[i],
[527a190]	870	{'unit': datainfo.y_unit})
[5f26aa4]	871	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	872	self.write_node(point, "Qdev", datainfo.dx[i],
[527a190]	873	{'unit': datainfo.x_unit})
[5f26aa4]	874	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	875	self.write_node(point, "dQw", datainfo.dxw[i],
[527a190]	876	{'unit': datainfo.x_unit})
[5f26aa4]	877	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	878	self.write_node(point, "dQl", datainfo.dxl[i],
[527a190]	879	{'unit': datainfo.x_unit})
[ad4632c]	880	if datainfo.isSesans:
[527a190]	881	sesans_attrib = {'x_axis': datainfo._xaxis,
	882	'y_axis': datainfo._yaxis,
	883	'x_unit': datainfo.x_unit,
	884	'y_unit': datainfo.y_unit}
	885	sesans = self.create_element("Sesans", attrib=sesans_attrib)
[ad4632c]	886	sesans.text = str(datainfo.isSesans)
[527a190]	887	entry_node.append(sesans)
[6a455cd3]	888	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
[63d773c]	889	{'unit': datainfo.sample.yacceptance[1]})
[527a190]	890	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
[ad4632c]	891	{'unit': datainfo.sample.zacceptance[1]})
	892
[d26dea0]	893
[83c09af]	894	def _write_data_2d(self, datainfo, entry_node):
	895	"""
	896	Writes 2D data to the XML file
	897
	898	:param datainfo: The Data2D object the information is coming from
	899	:param entry_node: lxml node ElementTree object to be appended to
	900	"""
[af08e55]	901	attr = {}
	902	if datainfo.data.shape:
[1905128]	903	attr["x_bins"] = str(len(datainfo.x_bins))
	904	attr["y_bins"] = str(len(datainfo.y_bins))
	905	node = self.create_element("SASdata", attr)
[83c09af]	906	self.append(node, entry_node)
	907
[1905128]	908	point = self.create_element("Idata")
	909	node.append(point)
	910	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
	911	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
	912	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
	913
	914	self.write_node(point, "Qx", qx,
	915	{'unit': datainfo._xunit})
	916	self.write_node(point, "Qy", qy,
	917	{'unit': datainfo._yunit})
	918	self.write_node(point, "I", intensity,
	919	{'unit': datainfo._zunit})
	920	if datainfo.err_data is not None:
[5e6df0e]	921	err = ','.join([str(datainfo.err_data[i]) for i in
	922	xrange(len(datainfo.err_data))])
[1905128]	923	self.write_node(point, "Idev", err,
[83c09af]	924	{'unit': datainfo._zunit})
[1905128]	925	if datainfo.dqy_data is not None:
[5e6df0e]	926	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
	927	xrange(len(datainfo.dqy_data))])
[1905128]	928	self.write_node(point, "Qydev", dqy,
	929	{'unit': datainfo._yunit})
	930	if datainfo.dqx_data is not None:
[5e6df0e]	931	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
	932	xrange(len(datainfo.dqx_data))])
[1905128]	933	self.write_node(point, "Qxdev", dqx,
	934	{'unit': datainfo._xunit})
	935	if datainfo.mask is not None:
[5e6df0e]	936	mask = ','.join(
[bcabf4e]	937	["1" if datainfo.mask[i] else "0"
	938	for i in xrange(len(datainfo.mask))])
[1905128]	939	self.write_node(point, "Mask", mask)
[83c09af]	940
[d26dea0]	941	def _write_trans_spectrum(self, datainfo, entry_node):
	942	"""
	943	Writes the transmission spectrum data to the XML file
	944
	945	:param datainfo: The Data1D object the information is coming from
	946	:param entry_node: lxml node ElementTree object to be appended to
	947	"""
	948	for i in range(len(datainfo.trans_spectrum)):
	949	spectrum = datainfo.trans_spectrum[i]
	950	node = self.create_element("SAStransmission_spectrum",
	951	{"name" : spectrum.name})
	952	self.append(node, entry_node)
	953	if isinstance(spectrum.timestamp, datetime.datetime):
	954	node.setAttribute("timestamp", spectrum.timestamp)
	955	for i in range(len(spectrum.wavelength)):
	956	point = self.create_element("Tdata")
	957	node.append(point)
	958	self.write_node(point, "Lambda", spectrum.wavelength[i],
	959	{'unit': spectrum.wavelength_unit})
	960	self.write_node(point, "T", spectrum.transmission[i],
	961	{'unit': spectrum.transmission_unit})
[7432acb]	962	if spectrum.transmission_deviation is not None \
[d26dea0]	963	and len(spectrum.transmission_deviation) >= i:
	964	self.write_node(point, "Tdev",
	965	spectrum.transmission_deviation[i],
	966	{'unit':
	967	spectrum.transmission_deviation_unit})
	968
	969	def _write_sample_info(self, datainfo, entry_node):
	970	"""
	971	Writes the sample information to the XML file
	972
	973	:param datainfo: The Data1D object the information is coming from
	974	:param entry_node: lxml node ElementTree object to be appended to
	975	"""
	976	sample = self.create_element("SASsample")
	977	if datainfo.sample.name is not None:
	978	self.write_attribute(sample, "name",
	979	str(datainfo.sample.name))
	980	self.append(sample, entry_node)
	981	self.write_node(sample, "ID", str(datainfo.sample.ID))
	982	self.write_node(sample, "thickness", datainfo.sample.thickness,
	983	{"unit": datainfo.sample.thickness_unit})
	984	self.write_node(sample, "transmission", datainfo.sample.transmission)
	985	self.write_node(sample, "temperature", datainfo.sample.temperature,
	986	{"unit": datainfo.sample.temperature_unit})
	987
	988	pos = self.create_element("position")
	989	written = self.write_node(pos,
	990	"x",
	991	datainfo.sample.position.x,
	992	{"unit": datainfo.sample.position_unit})
	993	written = written \| self.write_node( \
	994	pos, "y", datainfo.sample.position.y,
	995	{"unit": datainfo.sample.position_unit})
	996	written = written \| self.write_node( \
	997	pos, "z", datainfo.sample.position.z,
	998	{"unit": datainfo.sample.position_unit})
	999	if written == True:
	1000	self.append(pos, sample)
	1001
	1002	ori = self.create_element("orientation")
	1003	written = self.write_node(ori, "roll",
	1004	datainfo.sample.orientation.x,
	1005	{"unit": datainfo.sample.orientation_unit})
	1006	written = written \| self.write_node( \
	1007	ori, "pitch", datainfo.sample.orientation.y,
	1008	{"unit": datainfo.sample.orientation_unit})
	1009	written = written \| self.write_node( \
	1010	ori, "yaw", datainfo.sample.orientation.z,
	1011	{"unit": datainfo.sample.orientation_unit})
	1012	if written == True:
	1013	self.append(ori, sample)
	1014
	1015	for item in datainfo.sample.details:
	1016	self.write_node(sample, "details", item)
	1017
	1018	def _write_instrument(self, datainfo, entry_node):
	1019	"""
	1020	Writes the instrumental information to the XML file
	1021
	1022	:param datainfo: The Data1D object the information is coming from
	1023	:param entry_node: lxml node ElementTree object to be appended to
	1024	"""
	1025	instr = self.create_element("SASinstrument")
	1026	self.append(instr, entry_node)
	1027	self.write_node(instr, "name", datainfo.instrument)
	1028	return instr
	1029
	1030	def _write_source(self, datainfo, instr):
	1031	"""
	1032	Writes the source information to the XML file
	1033
	1034	:param datainfo: The Data1D object the information is coming from
	1035	:param instr: instrument node to be appended to
	1036	"""
	1037	source = self.create_element("SASsource")
	1038	if datainfo.source.name is not None:
	1039	self.write_attribute(source, "name",
	1040	str(datainfo.source.name))
	1041	self.append(source, instr)
[235f514]	1042	if datainfo.source.radiation is None or datainfo.source.radiation == '':
[d26dea0]	1043	datainfo.source.radiation = "neutron"
	1044	self.write_node(source, "radiation", datainfo.source.radiation)
	1045
	1046	size = self.create_element("beam_size")
	1047	if datainfo.source.beam_size_name is not None:
	1048	self.write_attribute(size, "name",
	1049	str(datainfo.source.beam_size_name))
	1050	written = self.write_node( \
	1051	size, "x", datainfo.source.beam_size.x,
	1052	{"unit": datainfo.source.beam_size_unit})
	1053	written = written \| self.write_node( \
	1054	size, "y", datainfo.source.beam_size.y,
	1055	{"unit": datainfo.source.beam_size_unit})
	1056	written = written \| self.write_node( \
	1057	size, "z", datainfo.source.beam_size.z,
	1058	{"unit": datainfo.source.beam_size_unit})
	1059	if written == True:
	1060	self.append(size, source)
	1061
	1062	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1063	self.write_node(source, "wavelength",
	1064	datainfo.source.wavelength,
	1065	{"unit": datainfo.source.wavelength_unit})
	1066	self.write_node(source, "wavelength_min",
	1067	datainfo.source.wavelength_min,
	1068	{"unit": datainfo.source.wavelength_min_unit})
	1069	self.write_node(source, "wavelength_max",
	1070	datainfo.source.wavelength_max,
	1071	{"unit": datainfo.source.wavelength_max_unit})
	1072	self.write_node(source, "wavelength_spread",
	1073	datainfo.source.wavelength_spread,
	1074	{"unit": datainfo.source.wavelength_spread_unit})
	1075
	1076	def _write_collimation(self, datainfo, instr):
	1077	"""
	1078	Writes the collimation information to the XML file
	1079
	1080	:param datainfo: The Data1D object the information is coming from
	1081	:param instr: lxml node ElementTree object to be appended to
	1082	"""
[235f514]	1083	if datainfo.collimation == [] or datainfo.collimation is None:
[d26dea0]	1084	coll = Collimation()
	1085	datainfo.collimation.append(coll)
	1086	for item in datainfo.collimation:
	1087	coll = self.create_element("SAScollimation")
	1088	if item.name is not None:
	1089	self.write_attribute(coll, "name", str(item.name))
	1090	self.append(coll, instr)
	1091
	1092	self.write_node(coll, "length", item.length,
	1093	{"unit": item.length_unit})
	1094
	1095	for aperture in item.aperture:
	1096	apert = self.create_element("aperture")
	1097	if aperture.name is not None:
	1098	self.write_attribute(apert, "name", str(aperture.name))
	1099	if aperture.type is not None:
	1100	self.write_attribute(apert, "type", str(aperture.type))
	1101	self.append(apert, coll)
	1102
	1103	size = self.create_element("size")
	1104	if aperture.size_name is not None:
	1105	self.write_attribute(size, "name",
	1106	str(aperture.size_name))
	1107	written = self.write_node(size, "x", aperture.size.x,
	1108	{"unit": aperture.size_unit})
	1109	written = written \| self.write_node( \
	1110	size, "y", aperture.size.y,
	1111	{"unit": aperture.size_unit})
	1112	written = written \| self.write_node( \
	1113	size, "z", aperture.size.z,
	1114	{"unit": aperture.size_unit})
	1115	if written == True:
	1116	self.append(size, apert)
	1117
	1118	self.write_node(apert, "distance", aperture.distance,
	1119	{"unit": aperture.distance_unit})
	1120
	1121	def _write_detectors(self, datainfo, instr):
	1122	"""
	1123	Writes the detector information to the XML file
	1124
	1125	:param datainfo: The Data1D object the information is coming from
	1126	:param inst: lxml instrument node to be appended to
	1127	"""
[235f514]	1128	if datainfo.detector is None or datainfo.detector == []:
[d26dea0]	1129	det = Detector()
	1130	det.name = ""
	1131	datainfo.detector.append(det)
	1132
	1133	for item in datainfo.detector:
	1134	det = self.create_element("SASdetector")
	1135	written = self.write_node(det, "name", item.name)
	1136	written = written \| self.write_node(det, "SDD", item.distance,
	1137	{"unit": item.distance_unit})
	1138	if written == True:
	1139	self.append(det, instr)
	1140
	1141	off = self.create_element("offset")
	1142	written = self.write_node(off, "x", item.offset.x,
	1143	{"unit": item.offset_unit})
	1144	written = written \| self.write_node(off, "y", item.offset.y,
	1145	{"unit": item.offset_unit})
	1146	written = written \| self.write_node(off, "z", item.offset.z,
	1147	{"unit": item.offset_unit})
	1148	if written == True:
	1149	self.append(off, det)
	1150
	1151	ori = self.create_element("orientation")
	1152	written = self.write_node(ori, "roll", item.orientation.x,
	1153	{"unit": item.orientation_unit})
	1154	written = written \| self.write_node(ori, "pitch",
	1155	item.orientation.y,
	1156	{"unit": item.orientation_unit})
	1157	written = written \| self.write_node(ori, "yaw",
	1158	item.orientation.z,
	1159	{"unit": item.orientation_unit})
	1160	if written == True:
	1161	self.append(ori, det)
	1162
	1163	center = self.create_element("beam_center")
	1164	written = self.write_node(center, "x", item.beam_center.x,
	1165	{"unit": item.beam_center_unit})
	1166	written = written \| self.write_node(center, "y",
	1167	item.beam_center.y,
	1168	{"unit": item.beam_center_unit})
	1169	written = written \| self.write_node(center, "z",
	1170	item.beam_center.z,
	1171	{"unit": item.beam_center_unit})
	1172	if written == True:
	1173	self.append(center, det)
	1174
	1175	pix = self.create_element("pixel_size")
	1176	written = self.write_node(pix, "x", item.pixel_size.x,
	1177	{"unit": item.pixel_size_unit})
	1178	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1179	{"unit": item.pixel_size_unit})
	1180	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1181	{"unit": item.pixel_size_unit})
	1182	if written == True:
	1183	self.append(pix, det)
[3a9801f]	1184	self.write_node(det, "slit_length", item.slit_length,
	1185	{"unit": item.slit_length_unit})
	1186
[d26dea0]	1187
	1188	def _write_process_notes(self, datainfo, entry_node):
	1189	"""
	1190	Writes the process notes to the XML file
	1191
	1192	:param datainfo: The Data1D object the information is coming from
	1193	:param entry_node: lxml node ElementTree object to be appended to
	1194
	1195	"""
	1196	for item in datainfo.process:
	1197	node = self.create_element("SASprocess")
	1198	self.append(node, entry_node)
	1199	self.write_node(node, "name", item.name)
	1200	self.write_node(node, "date", item.date)
	1201	self.write_node(node, "description", item.description)
	1202	for term in item.term:
[1686a333]	1203	if isinstance(term, list):
	1204	value = term['value']
	1205	del term['value']
[5f26aa4]	1206	elif isinstance(term, dict):
	1207	value = term.get("value")
	1208	del term['value']
[1686a333]	1209	else:
	1210	value = term
[d26dea0]	1211	self.write_node(node, "term", value, term)
	1212	for note in item.notes:
	1213	self.write_node(node, "SASprocessnote", note)
	1214	if len(item.notes) == 0:
	1215	self.write_node(node, "SASprocessnote", "")
	1216
	1217	def _write_notes(self, datainfo, entry_node):
	1218	"""
	1219	Writes the notes to the XML file and creates an empty note if none
	1220	exist
	1221
	1222	:param datainfo: The Data1D object the information is coming from
	1223	:param entry_node: lxml node ElementTree object to be appended to
	1224
	1225	"""
	1226	if len(datainfo.notes) == 0:
	1227	node = self.create_element("SASnote")
	1228	self.append(node, entry_node)
	1229	else:
	1230	for item in datainfo.notes:
	1231	node = self.create_element("SASnote")
	1232	self.write_text(node, item)
	1233	self.append(node, entry_node)
	1234
[654e8e0]	1235	def _check_origin(self, entry_node, doc):
[d26dea0]	1236	"""
	1237	Return the document, and the SASentry node associated with
	1238	the data we just wrote.
	1239	If the calling function was not the cansas reader, return a minidom
	1240	object rather than an lxml object.
	1241
	1242	:param entry_node: lxml node ElementTree object to be appended to
	1243	:param doc: entire xml tree
	1244	"""
[654e8e0]	1245	if not self.frm:
	1246	self.frm = inspect.stack()[1]
	1247	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1248	mod_name = mod_name.replace(".py", "")
	1249	mod = mod_name.split("sas/")
	1250	mod_name = mod[1]
[45d90b9]	1251	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1252	string = self.to_string(doc, pretty_print=False)
	1253	doc = parseString(string)
	1254	node_name = entry_node.tag
	1255	node_list = doc.getElementsByTagName(node_name)
	1256	entry_node = node_list.item(0)
[5ce7f17]	1257	return doc, entry_node
[d26dea0]	1258
	1259	# DO NOT REMOVE - used in saving and loading panel states.
	1260	def _store_float(self, location, node, variable, storage, optional=True):
	1261	"""
	1262	Get the content of a xpath location and store
	1263	the result. Check that the units are compatible
	1264	with the destination. The value is expected to
	1265	be a float.
	1266
	1267	The xpath location might or might not exist.
	1268	If it does not exist, nothing is done
	1269
	1270	:param location: xpath location to fetch
	1271	:param node: node to read the data from
	1272	:param variable: name of the data member to store it in [string]
	1273	:param storage: data object that has the 'variable' data member
	1274	:param optional: if True, no exception will be raised
	1275	if unit conversion can't be done
	1276
	1277	:raise ValueError: raised when the units are not recognized
	1278	"""
	1279	entry = get_content(location, node)
	1280	try:
	1281	value = float(entry.text)
	1282	except:
	1283	value = None
	1284
	1285	if value is not None:
	1286	# If the entry has units, check to see that they are
	1287	# compatible with what we currently have in the data object
	1288	units = entry.get('unit')
	1289	if units is not None:
	1290	toks = variable.split('.')
	1291	local_unit = None
	1292	exec "local_unit = storage.%s_unit" % toks[0]
[7432acb]	1293	if local_unit is not None and units.lower() != local_unit.lower():
[d26dea0]	1294	if HAS_CONVERTER == True:
	1295	try:
	1296	conv = Converter(units)
	1297	exec "storage.%s = %g" % \
	1298	(variable, conv(value, units=local_unit))
	1299	except:
	1300	_, exc_value, _ = sys.exc_info()
	1301	err_mess = "CanSAS reader: could not convert"
	1302	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1303	% (variable, units, local_unit, exc_value)
	1304	self.errors.add(err_mess)
	1305	if optional:
[c155a16]	1306	logger.info(err_mess)
[d26dea0]	1307	else:
	1308	raise ValueError, err_mess
	1309	else:
	1310	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1311	% (variable, units)
	1312	err_mess += " expecting [%s]" % local_unit
	1313	self.errors.add(err_mess)
	1314	if optional:
[c155a16]	1315	logger.info(err_mess)
[d26dea0]	1316	else:
	1317	raise ValueError, err_mess
	1318	else:
	1319	exec "storage.%s = value" % variable
	1320	else:
	1321	exec "storage.%s = value" % variable
	1322
	1323	# DO NOT REMOVE - used in saving and loading panel states.
	1324	def _store_content(self, location, node, variable, storage):
	1325	"""
	1326	Get the content of a xpath location and store
	1327	the result. The value is treated as a string.
	1328
	1329	The xpath location might or might not exist.
	1330	If it does not exist, nothing is done
	1331
	1332	:param location: xpath location to fetch
	1333	:param node: node to read the data from
	1334	:param variable: name of the data member to store it in [string]
	1335	:param storage: data object that has the 'variable' data member
	1336
	1337	:return: return a list of errors
	1338	"""
	1339	entry = get_content(location, node)
	1340	if entry is not None and entry.text is not None:
	1341	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1342
	1343	# DO NOT REMOVE Called by outside packages:
	1344	# sas.sasgui.perspectives.invariant.invariant_state
	1345	# sas.sasgui.perspectives.fitting.pagestate
	1346	def get_content(location, node):
	1347	"""
	1348	Get the first instance of the content of a xpath location.
	1349
	1350	:param location: xpath location
	1351	:param node: node to start at
	1352
	1353	:return: Element, or None
	1354	"""
	1355	nodes = node.xpath(location,
	1356	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1357	if len(nodes) > 0:
	1358	return nodes[0]
	1359	else:
	1360	return None
	1361
	1362	# DO NOT REMOVE Called by outside packages:
	1363	# sas.sasgui.perspectives.fitting.pagestate
	1364	def write_node(doc, parent, name, value, attr=None):
	1365	"""
	1366	:param doc: document DOM
	1367	:param parent: parent node
	1368	:param name: tag of the element
	1369	:param value: value of the child text node
	1370	:param attr: attribute dictionary
	1371
	1372	:return: True if something was appended, otherwise False
	1373	"""
	1374	if attr is None:
	1375	attr = {}
	1376	if value is not None:
	1377	node = doc.createElement(name)
	1378	node.appendChild(doc.createTextNode(str(value)))
	1379	for item in attr:
	1380	node.setAttribute(item, attr[item])
	1381	parent.appendChild(node)
	1382	return True
	1383	return False

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ d6bc9901

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