cansas_reader.py @ aefde77

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since aefde77 was 2b538cd, checked in by krzywon, 7 years ago
Modify documentation and add instance check for numpy arrays in HDF5 reader.
Property mode set to `100644`
File size: 61.3 KB

Rev	Line
[d26dea0]	1	import logging
	2	import os
	3	import sys
	4	import datetime
	5	import inspect
[574adc7]	6
	7	import numpy as np
[d26dea0]	8
[682c432]	9	# The following 2 imports ARE used. Do not remove either.
	10	import xml.dom.minidom
	11	from xml.dom.minidom import parseString
	12
[7477fb9]	13	from lxml import etree
	14
[574adc7]	15	from sas.sascalc.data_util.nxsunit import Converter
	16
	17	# For saving individual sections of data
	18	from ..data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \
	19	Collimation, TransmissionSpectrum, Detector, Process, Aperture, \
	20	combine_data_info_with_plottable as combine_data
	21	from ..loader_exceptions import FileContentsException, DefaultReaderException, \
	22	DataReaderException
	23	from . import xml_reader
	24	from .xml_reader import XMLreader
	25	from .cansas_constants import CansasConstants, CurrentLevel
	26
[463e7ffc]	27	logger = logging.getLogger(__name__)
[c155a16]	28
[d26dea0]	29	PREPROCESS = "xmlpreprocess"
	30	ENCODING = "encoding"
	31	RUN_NAME_DEFAULT = "None"
[250fec92]	32	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	33	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	34	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	35	"as much of the data as possible.\n\n"
[d26dea0]	36
	37	CONSTANTS = CansasConstants()
	38	CANSAS_FORMAT = CONSTANTS.format
	39	CANSAS_NS = CONSTANTS.names
	40	ALLOW_ALL = True
	41
	42	class Reader(XMLreader):
	43	cansas_version = "1.0"
	44	base_ns = "{cansas1d/1.0}"
[250fec92]	45	cansas_defaults = None
[d26dea0]	46	type_name = "canSAS"
[250fec92]	47	invalid = True
[654e8e0]	48	frm = ""
[af08e55]	49	# Log messages and errors
[250fec92]	50	logging = None
	51	errors = set()
[af08e55]	52	# Namespace hierarchy for current xml_file object
[250fec92]	53	names = None
	54	ns_list = None
[af08e55]	55	# Temporary storage location for loading multiple data sets in a single file
[250fec92]	56	current_data1d = None
	57	data = None
[af08e55]	58	# Wildcards
[d26dea0]	59	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
[af08e55]	60	# List of allowed extensions
[d26dea0]	61	ext = ['.xml', '.XML', '.svs', '.SVS']
[af08e55]	62	# Flag to bypass extension check
[d26dea0]	63	allow_all = True
	64
[250fec92]	65	def reset_state(self):
	66	"""
	67	Resets the class state to a base case when loading a new data file so previous
	68	data files do not appear a second time
	69	"""
	70	self.current_datainfo = None
	71	self.current_dataset = None
	72	self.current_data1d = None
	73	self.data = []
	74	self.process = Process()
	75	self.transspectrum = TransmissionSpectrum()
	76	self.aperture = Aperture()
	77	self.collimation = Collimation()
	78	self.detector = Detector()
	79	self.names = []
	80	self.cansas_defaults = {}
	81	self.output = []
	82	self.ns_list = None
[d26dea0]	83	self.logging = []
	84	self.encoding = None
	85
[250fec92]	86	def read(self, xml_file, schema_path="", invalid=True):
[bc570f4]	87	if schema_path != "" or invalid != True:
	88	# read has been called from self.get_file_contents because xml file doens't conform to schema
	89	_, self.extension = os.path.splitext(os.path.basename(xml_file))
	90	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
[250fec92]	91
[bc570f4]	92	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
	93	return super(XMLreader, self).read(xml_file)
	94
	95	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
[7477fb9]	96	# Reset everything since we're loading a new file
[250fec92]	97	self.reset_state()
	98	self.invalid = invalid
[bc570f4]	99	if xml_file is None:
	100	xml_file = self.f_open.name
[7477fb9]	101	# We don't sure f_open since lxml handles opnening/closing files
[bc570f4]	102	try:
[8dec7e7]	103	# Raises FileContentsException
	104	self.load_file_and_schema(xml_file, schema_path)
[7477fb9]	105	# Parse each SASentry
[7b07fbe]	106	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
	107	namespaces={
	108	'ns': self.cansas_defaults.get(
	109	"ns")
	110	})
	111	self.is_cansas(self.extension)
[bc570f4]	112	self.set_processing_instructions()
	113	for entry in entry_list:
	114	self._parse_entry(entry)
[c54c965]	115	self.data_cleanup()
[bc570f4]	116	except FileContentsException as fc_exc:
[7477fb9]	117	# File doesn't meet schema - try loading with a less strict schema
	118	base_name = xml_reader.__file__
	119	base_name = base_name.replace("\\", "/")
	120	base = base_name.split("/sas/")[0]
	121	if self.cansas_version == "1.1":
	122	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	123	else:
	124	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	125	self.set_schema(invalid_schema)
	126	if self.invalid:
[250fec92]	127	try:
[7477fb9]	128	# Load data with less strict schema
	129	self.read(xml_file, invalid_schema, False)
	130
	131	# File can still be read but doesn't match schema, so raise exception
	132	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
[250fec92]	133	invalid_xml = self.find_invalid_xml()
[527a190]	134	if invalid_xml != "":
[7b07fbe]	135	basename, _ = os.path.splitext(
	136	os.path.basename(self.f_open.name))
[cd57c7d4]	137	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
	138	raise DataReaderException(invalid_xml) # Handled by base class
[7477fb9]	139	except FileContentsException as fc_exc:
[0615d54]	140	msg = "CanSAS Reader could not load the file {}".format(xml_file)
[7477fb9]	141	if fc_exc.message is not None: # Propagate error messages from earlier
[0615d54]	142	msg = fc_exc.message
[dcb91cf]	143	if not self.extension in self.ext: # If the file has no associated loader
	144	raise DefaultReaderException(msg)
[7477fb9]	145	raise FileContentsException(msg)
	146	pass
	147	else:
	148	raise fc_exc
	149	except Exception as e: # Convert all other exceptions to FileContentsExceptions
[574adc7]	150	raise FileContentsException(str(e))
[7b07fbe]	151	finally:
	152	if not self.f_open.closed:
	153	self.f_open.close()
[7477fb9]	154
	155	def load_file_and_schema(self, xml_file, schema_path=""):
	156	base_name = xml_reader.__file__
	157	base_name = base_name.replace("\\", "/")
	158	base = base_name.split("/sas/")[0]
	159
	160	# Try and parse the XML file
	161	try:
	162	self.set_xml_file(xml_file)
	163	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
[dcb91cf]	164	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
[7477fb9]	165	raise FileContentsException(msg)
	166
	167	self.cansas_version = self.xmlroot.get("version", "1.0")
	168	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
	169
	170	if schema_path == "":
	171	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
	172	base, self.cansas_defaults.get("schema").replace("\\", "/")
	173	)
	174	self.set_schema(schema_path)
	175
	176	def is_cansas(self, ext="xml"):
[250fec92]	177	"""
[7477fb9]	178	Checks to see if the XML file is a CanSAS file
[250fec92]	179
[7477fb9]	180	:param ext: The file extension of the data file
	181	:raises FileContentsException: Raised if XML file isn't valid CanSAS
[250fec92]	182	"""
[7477fb9]	183	if self.validate_xml(): # Check file is valid XML
	184	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	185	value = self.xmlroot.get(name)
	186	# Check schema CanSAS version matches file CanSAS version
	187	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
	188	return True
	189	if ext == "svs":
	190	return True # Why is this required?
	191	# If we get to this point then file isn't valid CanSAS
[dcb91cf]	192	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
[7477fb9]	193	raise FileContentsException("The file is not valid CanSAS")
[250fec92]	194
[7477fb9]	195	def _parse_entry(self, dom, recurse=False):
[654e8e0]	196	if not self._is_call_local() and not recurse:
[1686a333]	197	self.reset_state()
[7b07fbe]	198	if not recurse:
[7477fb9]	199	self.current_datainfo = DataInfo()
[7b07fbe]	200	# Raises FileContentsException if file doesn't meet CanSAS schema
	201	self.invalid = False
	202	# Look for a SASentry
	203	self.data = []
[1686a333]	204	self.parent_class = "SASentry"
[7b07fbe]	205	self.names.append("SASentry")
	206	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
	207	self.current_datainfo.meta_data[
	208	PREPROCESS] = self.processing_instructions
	209	if self._is_call_local() and not recurse:
	210	basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
	211	self.current_datainfo.filename = basename + self.extension
[7477fb9]	212	# Create an empty dataset if no data has been passed to the reader
	213	if self.current_dataset is None:
[7b07fbe]	214	self._initialize_new_data_set(dom)
[7477fb9]	215	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
[250fec92]	216
[7477fb9]	217	# Loop through each child in the parent element
[250fec92]	218	for node in dom:
[5f26aa4]	219	attr = node.attrib
	220	name = attr.get("name", "")
	221	type = attr.get("type", "")
[250fec92]	222	# Get the element name and set the current names level
	223	tagname = node.tag.replace(self.base_ns, "")
	224	tagname_original = tagname
	225	# Skip this iteration when loading in save state information
[7b07fbe]	226	if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
[250fec92]	227	continue
	228	# Get where to store content
	229	self.names.append(tagname_original)
	230	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	231	# If the element is a child element, recurse
	232	if len(node.getchildren()) > 0:
	233	self.parent_class = tagname_original
	234	if tagname == 'SASdata':
[af08e55]	235	self._initialize_new_data_set(node)
	236	if isinstance(self.current_dataset, plottable_2D):
	237	x_bins = attr.get("x_bins", "")
	238	y_bins = attr.get("y_bins", "")
	239	if x_bins is not "" and y_bins is not "":
	240	self.current_dataset.shape = (x_bins, y_bins)
	241	else:
	242	self.current_dataset.shape = ()
[7477fb9]	243	# Recurse to access data within the group
	244	self._parse_entry(node, recurse=True)
[5f26aa4]	245	if tagname == "SASsample":
	246	self.current_datainfo.sample.name = name
	247	elif tagname == "beam_size":
	248	self.current_datainfo.source.beam_size_name = name
	249	elif tagname == "SAScollimation":
	250	self.collimation.name = name
	251	elif tagname == "aperture":
	252	self.aperture.name = name
	253	self.aperture.type = type
[7477fb9]	254	self._add_intermediate()
[250fec92]	255	else:
[7b07fbe]	256	# TODO: Clean this up to make it faster (fewer if/elifs)
[1905128]	257	if isinstance(self.current_dataset, plottable_2D):
	258	data_point = node.text
	259	unit = attr.get('unit', '')
	260	else:
	261	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	262
[af08e55]	263	# If this is a dataset, store the data appropriately
[250fec92]	264	if tagname == 'Run':
[5f26aa4]	265	self.current_datainfo.run_name[data_point] = name
[250fec92]	266	self.current_datainfo.run.append(data_point)
	267	elif tagname == 'Title':
	268	self.current_datainfo.title = data_point
	269	elif tagname == 'SASnote':
	270	self.current_datainfo.notes.append(data_point)
	271
[0b79323]	272	# I and Q points
[af08e55]	273	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[527a190]	274	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	275	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	276	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	277	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	278	elif tagname == 'Q':
[527a190]	279	self.current_dataset.xaxis("Q", unit)
[250fec92]	280	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	281	elif tagname == 'Qdev':
	282	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	283	elif tagname == 'dQw':
[590b5c2]	284	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
[250fec92]	285	elif tagname == 'dQl':
	286	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	287	elif tagname == 'Qmean':
	288	pass
	289	elif tagname == 'Shadowfactor':
	290	pass
[ad4632c]	291	elif tagname == 'Sesans':
	292	self.current_datainfo.isSesans = bool(data_point)
[527a190]	293	self.current_dataset.xaxis(attr.get('x_axis'),
	294	attr.get('x_unit'))
	295	self.current_dataset.yaxis(attr.get('y_axis'),
	296	attr.get('y_unit'))
[63d773c]	297	elif tagname == 'yacceptance':
	298	self.current_datainfo.sample.yacceptance = (data_point, unit)
[ad4632c]	299	elif tagname == 'zacceptance':
	300	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	301
[af08e55]	302	# I and Qx, Qy - 2D data
	303	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	304	self.current_dataset.yaxis("Intensity", unit)
[1905128]	305	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	306	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	307	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	308	elif tagname == 'Qx':
	309	self.current_dataset.xaxis("Qx", unit)
[1905128]	310	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	311	elif tagname == 'Qy':
	312	self.current_dataset.yaxis("Qy", unit)
[1905128]	313	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	314	elif tagname == 'Qxdev':
	315	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	316	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	317	elif tagname == 'Qydev':
	318	self.current_dataset.yaxis("Qydev", unit)
[1905128]	319	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	320	elif tagname == 'Mask':
[bcabf4e]	321	inter = [item == "1" for item in data_point.split(",")]
[1905128]	322	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	323
	324	# Sample Information
[250fec92]	325	elif tagname == 'ID' and self.parent_class == 'SASsample':
	326	self.current_datainfo.sample.ID = data_point
	327	elif tagname == 'Title' and self.parent_class == 'SASsample':
	328	self.current_datainfo.sample.name = data_point
	329	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	330	self.current_datainfo.sample.thickness = data_point
	331	self.current_datainfo.sample.thickness_unit = unit
	332	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	333	self.current_datainfo.sample.transmission = data_point
	334	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	335	self.current_datainfo.sample.temperature = data_point
	336	self.current_datainfo.sample.temperature_unit = unit
	337	elif tagname == 'details' and self.parent_class == 'SASsample':
	338	self.current_datainfo.sample.details.append(data_point)
	339	elif tagname == 'x' and self.parent_class == 'position':
	340	self.current_datainfo.sample.position.x = data_point
	341	self.current_datainfo.sample.position_unit = unit
	342	elif tagname == 'y' and self.parent_class == 'position':
	343	self.current_datainfo.sample.position.y = data_point
	344	self.current_datainfo.sample.position_unit = unit
	345	elif tagname == 'z' and self.parent_class == 'position':
	346	self.current_datainfo.sample.position.z = data_point
	347	self.current_datainfo.sample.position_unit = unit
	348	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	349	self.current_datainfo.sample.orientation.x = data_point
	350	self.current_datainfo.sample.orientation_unit = unit
	351	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	352	self.current_datainfo.sample.orientation.y = data_point
	353	self.current_datainfo.sample.orientation_unit = unit
	354	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	355	self.current_datainfo.sample.orientation.z = data_point
	356	self.current_datainfo.sample.orientation_unit = unit
	357
[af08e55]	358	# Instrumental Information
[250fec92]	359	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	360	self.current_datainfo.instrument = data_point
[7477fb9]	361
[af08e55]	362	# Detector Information
[250fec92]	363	elif tagname == 'name' and self.parent_class == 'SASdetector':
	364	self.detector.name = data_point
	365	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	366	self.detector.distance = data_point
	367	self.detector.distance_unit = unit
	368	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	369	self.detector.slit_length = data_point
	370	self.detector.slit_length_unit = unit
	371	elif tagname == 'x' and self.parent_class == 'offset':
	372	self.detector.offset.x = data_point
	373	self.detector.offset_unit = unit
	374	elif tagname == 'y' and self.parent_class == 'offset':
	375	self.detector.offset.y = data_point
	376	self.detector.offset_unit = unit
	377	elif tagname == 'z' and self.parent_class == 'offset':
	378	self.detector.offset.z = data_point
	379	self.detector.offset_unit = unit
	380	elif tagname == 'x' and self.parent_class == 'beam_center':
	381	self.detector.beam_center.x = data_point
	382	self.detector.beam_center_unit = unit
	383	elif tagname == 'y' and self.parent_class == 'beam_center':
	384	self.detector.beam_center.y = data_point
	385	self.detector.beam_center_unit = unit
	386	elif tagname == 'z' and self.parent_class == 'beam_center':
	387	self.detector.beam_center.z = data_point
	388	self.detector.beam_center_unit = unit
	389	elif tagname == 'x' and self.parent_class == 'pixel_size':
	390	self.detector.pixel_size.x = data_point
	391	self.detector.pixel_size_unit = unit
	392	elif tagname == 'y' and self.parent_class == 'pixel_size':
	393	self.detector.pixel_size.y = data_point
	394	self.detector.pixel_size_unit = unit
	395	elif tagname == 'z' and self.parent_class == 'pixel_size':
	396	self.detector.pixel_size.z = data_point
	397	self.detector.pixel_size_unit = unit
	398	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	399	self.detector.orientation.x = data_point
	400	self.detector.orientation_unit = unit
	401	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	402	self.detector.orientation.y = data_point
	403	self.detector.orientation_unit = unit
	404	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	405	self.detector.orientation.z = data_point
	406	self.detector.orientation_unit = unit
[7477fb9]	407
[af08e55]	408	# Collimation and Aperture
[250fec92]	409	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	410	self.collimation.length = data_point
	411	self.collimation.length_unit = unit
	412	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	413	self.collimation.name = data_point
	414	elif tagname == 'distance' and self.parent_class == 'aperture':
	415	self.aperture.distance = data_point
	416	self.aperture.distance_unit = unit
	417	elif tagname == 'x' and self.parent_class == 'size':
	418	self.aperture.size.x = data_point
	419	self.collimation.size_unit = unit
	420	elif tagname == 'y' and self.parent_class == 'size':
	421	self.aperture.size.y = data_point
	422	self.collimation.size_unit = unit
	423	elif tagname == 'z' and self.parent_class == 'size':
	424	self.aperture.size.z = data_point
	425	self.collimation.size_unit = unit
	426
[af08e55]	427	# Process Information
[250fec92]	428	elif tagname == 'name' and self.parent_class == 'SASprocess':
	429	self.process.name = data_point
	430	elif tagname == 'description' and self.parent_class == 'SASprocess':
	431	self.process.description = data_point
	432	elif tagname == 'date' and self.parent_class == 'SASprocess':
	433	try:
	434	self.process.date = datetime.datetime.fromtimestamp(data_point)
	435	except:
	436	self.process.date = data_point
	437	elif tagname == 'SASprocessnote':
	438	self.process.notes.append(data_point)
	439	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	440	unit = attr.get("unit", "")
[7477fb9]	441	dic = { "name": name, "value": data_point, "unit": unit }
[5f26aa4]	442	self.process.term.append(dic)
[250fec92]	443
[af08e55]	444	# Transmission Spectrum
[250fec92]	445	elif tagname == 'T' and self.parent_class == 'Tdata':
	446	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	447	self.transspectrum.transmission_unit = unit
	448	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	449	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	450	self.transspectrum.transmission_deviation_unit = unit
	451	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	452	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	453	self.transspectrum.wavelength_unit = unit
	454
[af08e55]	455	# Source Information
[250fec92]	456	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	457	self.current_datainfo.source.wavelength = data_point
	458	self.current_datainfo.source.wavelength_unit = unit
	459	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	460	self.current_datainfo.source.wavelength_min = data_point
	461	self.current_datainfo.source.wavelength_min_unit = unit
	462	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	463	self.current_datainfo.source.wavelength_max = data_point
	464	self.current_datainfo.source.wavelength_max_unit = unit
	465	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	466	self.current_datainfo.source.wavelength_spread = data_point
	467	self.current_datainfo.source.wavelength_spread_unit = unit
	468	elif tagname == 'x' and self.parent_class == 'beam_size':
	469	self.current_datainfo.source.beam_size.x = data_point
	470	self.current_datainfo.source.beam_size_unit = unit
	471	elif tagname == 'y' and self.parent_class == 'beam_size':
	472	self.current_datainfo.source.beam_size.y = data_point
	473	self.current_datainfo.source.beam_size_unit = unit
	474	elif tagname == 'z' and self.parent_class == 'pixel_size':
	475	self.current_datainfo.source.data_point.z = data_point
	476	self.current_datainfo.source.beam_size_unit = unit
	477	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	478	self.current_datainfo.source.radiation = data_point
	479	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	480	self.current_datainfo.source.beam_shape = data_point
	481
[af08e55]	482	# Everything else goes in meta_data
[250fec92]	483	else:
	484	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	485	self.current_datainfo.meta_data[new_key] = data_point
	486
	487	self.names.remove(tagname_original)
	488	length = 0
	489	if len(self.names) > 1:
	490	length = len(self.names) - 1
	491	self.parent_class = self.names[length]
[654e8e0]	492	if not self._is_call_local() and not recurse:
	493	self.frm = ""
[7477fb9]	494	self.current_datainfo.errors = set()
	495	for error in self.errors:
	496	self.current_datainfo.errors.add(error)
[c54c965]	497	self.data_cleanup()
	498	self.sort_one_d_data()
	499	self.sort_two_d_data()
	500	self.reset_data_list()
[7b07fbe]	501	return self.output[0], None
[c54c965]	502
[654e8e0]	503	def _is_call_local(self):
	504	if self.frm == "":
	505	inter = inspect.stack()
	506	self.frm = inter[2]
	507	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	508	mod_name = mod_name.replace(".py", "")
	509	mod = mod_name.split("sas/")
	510	mod_name = mod[1]
	511	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	512	return False
	513	return True
	514
[7477fb9]	515	def _add_intermediate(self):
[250fec92]	516	"""
	517	This method stores any intermediate objects within the final data set after fully reading the set.
	518	"""
	519	if self.parent_class == 'SASprocess':
	520	self.current_datainfo.process.append(self.process)
	521	self.process = Process()
	522	elif self.parent_class == 'SASdetector':
	523	self.current_datainfo.detector.append(self.detector)
	524	self.detector = Detector()
	525	elif self.parent_class == 'SAStransmission_spectrum':
	526	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	527	self.transspectrum = TransmissionSpectrum()
	528	elif self.parent_class == 'SAScollimation':
	529	self.current_datainfo.collimation.append(self.collimation)
	530	self.collimation = Collimation()
[5f26aa4]	531	elif self.parent_class == 'aperture':
[250fec92]	532	self.collimation.aperture.append(self.aperture)
	533	self.aperture = Aperture()
	534	elif self.parent_class == 'SASdata':
	535	self.data.append(self.current_dataset)
	536
	537	def _get_node_value(self, node, tagname):
	538	"""
	539	Get the value of a node and any applicable units
	540
	541	:param node: The XML node to get the value of
	542	:param tagname: The tagname of the node
	543	"""
	544	#Get the text from the node and convert all whitespace to spaces
	545	units = ''
	546	node_value = node.text
	547	if node_value is not None:
	548	node_value = ' '.join(node_value.split())
	549	else:
	550	node_value = ""
	551
	552	# If the value is a float, compile with units.
	553	if self.ns_list.ns_datatype == "float":
	554	# If an empty value is given, set as zero.
	555	if node_value is None or node_value.isspace() \
	556	or node_value.lower() == "nan":
	557	node_value = "0.0"
	558	#Convert the value to the base units
	559	node_value, units = self._unit_conversion(node, tagname, node_value)
	560
	561	# If the value is a timestamp, convert to a datetime object
	562	elif self.ns_list.ns_datatype == "timestamp":
	563	if node_value is None or node_value.isspace():
	564	pass
	565	else:
	566	try:
	567	node_value = \
	568	datetime.datetime.fromtimestamp(node_value)
	569	except ValueError:
	570	node_value = None
	571	return node_value, units
	572
	573	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	574	"""
	575	A unit converter method used to convert the data included in the file
	576	to the default units listed in data_info
	577
[250fec92]	578	:param node: XML node
	579	:param tagname: name of the node
[d26dea0]	580	:param node_value: The value of the current dom node
	581	"""
	582	attr = node.attrib
	583	value_unit = ''
	584	err_msg = None
[682c432]	585	default_unit = None
[5f26aa4]	586	if not isinstance(node_value, float):
	587	node_value = float(node_value)
	588	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	589	try:
[62160509]	590	unit = attr['unit']
[2b538cd]	591	# Split the units to retain backwards compatibility with
	592	# projects, analyses, and saved data from v4.1.0
[62160509]	593	unit_list = unit.split("\|")
	594	if len(unit_list) > 1:
	595	local_unit = unit_list[1]
	596	else:
	597	local_unit = unit
[250fec92]	598	unitname = self.ns_list.current_level.get("unit", "")
	599	if "SASdetector" in self.names:
	600	save_in = "detector"
	601	elif "aperture" in self.names:
	602	save_in = "aperture"
	603	elif "SAScollimation" in self.names:
	604	save_in = "collimation"
	605	elif "SAStransmission_spectrum" in self.names:
	606	save_in = "transspectrum"
	607	elif "SASdata" in self.names:
	608	x = np.zeros(1)
	609	y = np.zeros(1)
	610	self.current_data1d = Data1D(x, y)
	611	save_in = "current_data1d"
	612	elif "SASsource" in self.names:
	613	save_in = "current_datainfo.source"
	614	elif "SASsample" in self.names:
	615	save_in = "current_datainfo.sample"
	616	elif "SASprocess" in self.names:
	617	save_in = "process"
	618	else:
	619	save_in = "current_datainfo"
[e6e89c4]	620	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
[574adc7]	621	if (local_unit and default_unit
	622	and local_unit.lower() != default_unit.lower()
	623	and local_unit.lower() != "none"):
[9efdb29]	624	# Check local units - bad units raise KeyError
	625	#print("loading", tagname, node_value, local_unit, default_unit)
	626	data_conv_q = Converter(local_unit)
	627	value_unit = default_unit
	628	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	629	else:
	630	value_unit = local_unit
	631	except KeyError:
[527a190]	632	# Do not throw an error for loading Sesans data in cansas xml
	633	# This is a temporary fix.
	634	if local_unit != "A" and local_unit != 'pol':
	635	err_msg = "CanSAS reader: unexpected "
	636	err_msg += "\"{0}\" unit [{1}]; "
	637	err_msg = err_msg.format(tagname, local_unit)
	638	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	639	value_unit = local_unit
[574adc7]	640	except Exception:
[d26dea0]	641	err_msg = "CanSAS reader: unknown error converting "
	642	err_msg += "\"{0}\" unit [{1}]"
	643	err_msg = err_msg.format(tagname, local_unit)
	644	value_unit = local_unit
	645	elif 'unit' in attr:
	646	value_unit = attr['unit']
	647	if err_msg:
	648	self.errors.add(err_msg)
	649	return node_value, value_unit
	650
[0b79323]	651	def _initialize_new_data_set(self, node=None):
	652	if node is not None:
	653	for child in node:
	654	if child.tag.replace(self.base_ns, "") == "Idata":
	655	for i_child in child:
	656	if i_child.tag.replace(self.base_ns, "") == "Qx":
	657	self.current_dataset = plottable_2D()
	658	return
	659	self.current_dataset = plottable_1D(np.array(0), np.array(0))
	660
	661	## Writing Methods
[250fec92]	662	def write(self, filename, datainfo):
[d26dea0]	663	"""
[250fec92]	664	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	665
[250fec92]	666	:param filename: name of the file to write
	667	:param datainfo: Data1D object
	668	"""
	669	# Create XML document
	670	doc, _ = self._to_xml_doc(datainfo)
	671	# Write the file
[e6e89c4]	672	file_ref = open(filename, 'wb')
[235f514]	673	if self.encoding is None:
[250fec92]	674	self.encoding = "UTF-8"
	675	doc.write(file_ref, encoding=self.encoding,
	676	pretty_print=True, xml_declaration=True)
	677	file_ref.close()
[d26dea0]	678
[250fec92]	679	def _to_xml_doc(self, datainfo):
[d26dea0]	680	"""
[250fec92]	681	Create an XML document to contain the content of a Data1D
[d26dea0]	682
[250fec92]	683	:param datainfo: Data1D object
[d26dea0]	684	"""
[af08e55]	685	is_2d = False
[83c09af]	686	if issubclass(datainfo.__class__, Data2D):
	687	is_2d = True
[d26dea0]	688
[250fec92]	689	# Get PIs and create root element
	690	pi_string = self._get_pi_string()
	691	# Define namespaces and create SASroot object
	692	main_node = self._create_main_node()
	693	# Create ElementTree, append SASroot and apply processing instructions
	694	base_string = pi_string + self.to_string(main_node)
	695	base_element = self.create_element_from_string(base_string)
	696	doc = self.create_tree(base_element)
	697	# Create SASentry Element
	698	entry_node = self.create_element("SASentry")
	699	root = doc.getroot()
	700	root.append(entry_node)
[d26dea0]	701
[250fec92]	702	# Add Title to SASentry
	703	self.write_node(entry_node, "Title", datainfo.title)
	704	# Add Run to SASentry
	705	self._write_run_names(datainfo, entry_node)
	706	# Add Data info to SASEntry
[83c09af]	707	if is_2d:
	708	self._write_data_2d(datainfo, entry_node)
	709	else:
	710	self._write_data(datainfo, entry_node)
[250fec92]	711	# Transmission Spectrum Info
[8434365]	712	# TODO: fix the writer to linearize all data, including T_spectrum
	713	# self._write_trans_spectrum(datainfo, entry_node)
[250fec92]	714	# Sample info
	715	self._write_sample_info(datainfo, entry_node)
	716	# Instrument info
	717	instr = self._write_instrument(datainfo, entry_node)
	718	# Source
	719	self._write_source(datainfo, instr)
	720	# Collimation
	721	self._write_collimation(datainfo, instr)
	722	# Detectors
	723	self._write_detectors(datainfo, instr)
	724	# Processes info
	725	self._write_process_notes(datainfo, entry_node)
	726	# Note info
	727	self._write_notes(datainfo, entry_node)
	728	# Return the document, and the SASentry node associated with
	729	# the data we just wrote
	730	# If the calling function was not the cansas reader, return a minidom
	731	# object rather than an lxml object.
[654e8e0]	732	self.frm = inspect.stack()[1]
	733	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	734	return doc, entry_node
[d26dea0]	735
[250fec92]	736	def write_node(self, parent, name, value, attr=None):
	737	"""
	738	:param doc: document DOM
	739	:param parent: parent node
	740	:param name: tag of the element
	741	:param value: value of the child text node
	742	:param attr: attribute dictionary
[d26dea0]	743
[250fec92]	744	:return: True if something was appended, otherwise False
	745	"""
	746	if value is not None:
	747	parent = self.ebuilder(parent, name, value, attr)
	748	return True
	749	return False
[d26dea0]	750
	751	def _get_pi_string(self):
	752	"""
	753	Creates the processing instructions header for writing to file
	754	"""
	755	pis = self.return_processing_instructions()
	756	if len(pis) > 0:
	757	pi_tree = self.create_tree(pis[0])
	758	i = 1
	759	for i in range(1, len(pis) - 1):
	760	pi_tree = self.append(pis[i], pi_tree)
	761	pi_string = self.to_string(pi_tree)
	762	else:
	763	pi_string = ""
	764	return pi_string
	765
	766	def _create_main_node(self):
	767	"""
	768	Creates the primary xml header used when writing to file
	769	"""
	770	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	771	version = self.cansas_version
	772	n_s = CANSAS_NS.get(version).get("ns")
	773	if version == "1.1":
	774	url = "http://www.cansas.org/formats/1.1/"
	775	else:
	776	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	777	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	778	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	779	"version" : version}
	780	nsmap = {'xsi' : xsi, None: n_s}
	781
	782	main_node = self.create_element("{" + n_s + "}SASroot",
	783	attrib=attrib, nsmap=nsmap)
	784	return main_node
	785
	786	def _write_run_names(self, datainfo, entry_node):
	787	"""
	788	Writes the run names to the XML file
	789
	790	:param datainfo: The Data1D object the information is coming from
	791	:param entry_node: lxml node ElementTree object to be appended to
	792	"""
[235f514]	793	if datainfo.run is None or datainfo.run == []:
[d26dea0]	794	datainfo.run.append(RUN_NAME_DEFAULT)
	795	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	796	for item in datainfo.run:
	797	runname = {}
	798	if item in datainfo.run_name and \
	799	len(str(datainfo.run_name[item])) > 1:
	800	runname = {'name': datainfo.run_name[item]}
	801	self.write_node(entry_node, "Run", item, runname)
	802
	803	def _write_data(self, datainfo, entry_node):
	804	"""
[83c09af]	805	Writes 1D I and Q data to the XML file
[d26dea0]	806
	807	:param datainfo: The Data1D object the information is coming from
	808	:param entry_node: lxml node ElementTree object to be appended to
	809	"""
	810	node = self.create_element("SASdata")
	811	self.append(node, entry_node)
	812
	813	for i in range(len(datainfo.x)):
	814	point = self.create_element("Idata")
	815	node.append(point)
	816	self.write_node(point, "Q", datainfo.x[i],
[527a190]	817	{'unit': datainfo.x_unit})
[d26dea0]	818	if len(datainfo.y) >= i:
	819	self.write_node(point, "I", datainfo.y[i],
[527a190]	820	{'unit': datainfo.y_unit})
[5f26aa4]	821	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	822	self.write_node(point, "Idev", datainfo.dy[i],
[527a190]	823	{'unit': datainfo.y_unit})
[5f26aa4]	824	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	825	self.write_node(point, "Qdev", datainfo.dx[i],
[527a190]	826	{'unit': datainfo.x_unit})
[5f26aa4]	827	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	828	self.write_node(point, "dQw", datainfo.dxw[i],
[527a190]	829	{'unit': datainfo.x_unit})
[5f26aa4]	830	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	831	self.write_node(point, "dQl", datainfo.dxl[i],
[527a190]	832	{'unit': datainfo.x_unit})
[ad4632c]	833	if datainfo.isSesans:
[527a190]	834	sesans_attrib = {'x_axis': datainfo._xaxis,
	835	'y_axis': datainfo._yaxis,
	836	'x_unit': datainfo.x_unit,
	837	'y_unit': datainfo.y_unit}
	838	sesans = self.create_element("Sesans", attrib=sesans_attrib)
[ad4632c]	839	sesans.text = str(datainfo.isSesans)
[527a190]	840	entry_node.append(sesans)
[6a455cd3]	841	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
[63d773c]	842	{'unit': datainfo.sample.yacceptance[1]})
[527a190]	843	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
[ad4632c]	844	{'unit': datainfo.sample.zacceptance[1]})
	845
[d26dea0]	846
[83c09af]	847	def _write_data_2d(self, datainfo, entry_node):
	848	"""
	849	Writes 2D data to the XML file
	850
	851	:param datainfo: The Data2D object the information is coming from
	852	:param entry_node: lxml node ElementTree object to be appended to
	853	"""
[af08e55]	854	attr = {}
	855	if datainfo.data.shape:
[1905128]	856	attr["x_bins"] = str(len(datainfo.x_bins))
	857	attr["y_bins"] = str(len(datainfo.y_bins))
	858	node = self.create_element("SASdata", attr)
[83c09af]	859	self.append(node, entry_node)
	860
[1905128]	861	point = self.create_element("Idata")
	862	node.append(point)
[574adc7]	863	qx = ','.join(str(v) for v in datainfo.qx_data)
	864	qy = ','.join(str(v) for v in datainfo.qy_data)
	865	intensity = ','.join(str(v) for v in datainfo.data)
[1905128]	866
	867	self.write_node(point, "Qx", qx,
	868	{'unit': datainfo._xunit})
	869	self.write_node(point, "Qy", qy,
	870	{'unit': datainfo._yunit})
	871	self.write_node(point, "I", intensity,
	872	{'unit': datainfo._zunit})
	873	if datainfo.err_data is not None:
[574adc7]	874	err = ','.join(str(v) for v in datainfo.err_data)
[1905128]	875	self.write_node(point, "Idev", err,
[83c09af]	876	{'unit': datainfo._zunit})
[1905128]	877	if datainfo.dqy_data is not None:
[574adc7]	878	dqy = ','.join(str(v) for v in datainfo.dqy_data)
[1905128]	879	self.write_node(point, "Qydev", dqy,
	880	{'unit': datainfo._yunit})
	881	if datainfo.dqx_data is not None:
[574adc7]	882	dqx = ','.join(str(v) for v in datainfo.dqx_data)
[1905128]	883	self.write_node(point, "Qxdev", dqx,
	884	{'unit': datainfo._xunit})
	885	if datainfo.mask is not None:
[574adc7]	886	mask = ','.join("1" if v else "0" for v in datainfo.mask)
[1905128]	887	self.write_node(point, "Mask", mask)
[83c09af]	888
[d26dea0]	889	def _write_trans_spectrum(self, datainfo, entry_node):
	890	"""
	891	Writes the transmission spectrum data to the XML file
	892
	893	:param datainfo: The Data1D object the information is coming from
	894	:param entry_node: lxml node ElementTree object to be appended to
	895	"""
	896	for i in range(len(datainfo.trans_spectrum)):
	897	spectrum = datainfo.trans_spectrum[i]
	898	node = self.create_element("SAStransmission_spectrum",
	899	{"name" : spectrum.name})
	900	self.append(node, entry_node)
	901	if isinstance(spectrum.timestamp, datetime.datetime):
	902	node.setAttribute("timestamp", spectrum.timestamp)
	903	for i in range(len(spectrum.wavelength)):
	904	point = self.create_element("Tdata")
	905	node.append(point)
	906	self.write_node(point, "Lambda", spectrum.wavelength[i],
	907	{'unit': spectrum.wavelength_unit})
	908	self.write_node(point, "T", spectrum.transmission[i],
	909	{'unit': spectrum.transmission_unit})
[7432acb]	910	if spectrum.transmission_deviation is not None \
[d26dea0]	911	and len(spectrum.transmission_deviation) >= i:
	912	self.write_node(point, "Tdev",
	913	spectrum.transmission_deviation[i],
	914	{'unit':
	915	spectrum.transmission_deviation_unit})
	916
	917	def _write_sample_info(self, datainfo, entry_node):
	918	"""
	919	Writes the sample information to the XML file
	920
	921	:param datainfo: The Data1D object the information is coming from
	922	:param entry_node: lxml node ElementTree object to be appended to
	923	"""
	924	sample = self.create_element("SASsample")
	925	if datainfo.sample.name is not None:
	926	self.write_attribute(sample, "name",
	927	str(datainfo.sample.name))
	928	self.append(sample, entry_node)
	929	self.write_node(sample, "ID", str(datainfo.sample.ID))
	930	self.write_node(sample, "thickness", datainfo.sample.thickness,
	931	{"unit": datainfo.sample.thickness_unit})
	932	self.write_node(sample, "transmission", datainfo.sample.transmission)
	933	self.write_node(sample, "temperature", datainfo.sample.temperature,
	934	{"unit": datainfo.sample.temperature_unit})
	935
	936	pos = self.create_element("position")
	937	written = self.write_node(pos,
	938	"x",
	939	datainfo.sample.position.x,
	940	{"unit": datainfo.sample.position_unit})
	941	written = written \| self.write_node( \
	942	pos, "y", datainfo.sample.position.y,
	943	{"unit": datainfo.sample.position_unit})
	944	written = written \| self.write_node( \
	945	pos, "z", datainfo.sample.position.z,
	946	{"unit": datainfo.sample.position_unit})
	947	if written == True:
	948	self.append(pos, sample)
	949
	950	ori = self.create_element("orientation")
	951	written = self.write_node(ori, "roll",
	952	datainfo.sample.orientation.x,
	953	{"unit": datainfo.sample.orientation_unit})
	954	written = written \| self.write_node( \
	955	ori, "pitch", datainfo.sample.orientation.y,
	956	{"unit": datainfo.sample.orientation_unit})
	957	written = written \| self.write_node( \
	958	ori, "yaw", datainfo.sample.orientation.z,
	959	{"unit": datainfo.sample.orientation_unit})
	960	if written == True:
	961	self.append(ori, sample)
	962
	963	for item in datainfo.sample.details:
	964	self.write_node(sample, "details", item)
	965
	966	def _write_instrument(self, datainfo, entry_node):
	967	"""
	968	Writes the instrumental 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	instr = self.create_element("SASinstrument")
	974	self.append(instr, entry_node)
	975	self.write_node(instr, "name", datainfo.instrument)
	976	return instr
	977
	978	def _write_source(self, datainfo, instr):
	979	"""
	980	Writes the source information to the XML file
	981
	982	:param datainfo: The Data1D object the information is coming from
	983	:param instr: instrument node to be appended to
	984	"""
	985	source = self.create_element("SASsource")
	986	if datainfo.source.name is not None:
	987	self.write_attribute(source, "name",
	988	str(datainfo.source.name))
	989	self.append(source, instr)
[235f514]	990	if datainfo.source.radiation is None or datainfo.source.radiation == '':
[d26dea0]	991	datainfo.source.radiation = "neutron"
	992	self.write_node(source, "radiation", datainfo.source.radiation)
	993
	994	size = self.create_element("beam_size")
	995	if datainfo.source.beam_size_name is not None:
	996	self.write_attribute(size, "name",
	997	str(datainfo.source.beam_size_name))
	998	written = self.write_node( \
	999	size, "x", datainfo.source.beam_size.x,
	1000	{"unit": datainfo.source.beam_size_unit})
	1001	written = written \| self.write_node( \
	1002	size, "y", datainfo.source.beam_size.y,
	1003	{"unit": datainfo.source.beam_size_unit})
	1004	written = written \| self.write_node( \
	1005	size, "z", datainfo.source.beam_size.z,
	1006	{"unit": datainfo.source.beam_size_unit})
	1007	if written == True:
	1008	self.append(size, source)
	1009
	1010	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1011	self.write_node(source, "wavelength",
	1012	datainfo.source.wavelength,
	1013	{"unit": datainfo.source.wavelength_unit})
	1014	self.write_node(source, "wavelength_min",
	1015	datainfo.source.wavelength_min,
	1016	{"unit": datainfo.source.wavelength_min_unit})
	1017	self.write_node(source, "wavelength_max",
	1018	datainfo.source.wavelength_max,
	1019	{"unit": datainfo.source.wavelength_max_unit})
	1020	self.write_node(source, "wavelength_spread",
	1021	datainfo.source.wavelength_spread,
	1022	{"unit": datainfo.source.wavelength_spread_unit})
	1023
	1024	def _write_collimation(self, datainfo, instr):
	1025	"""
	1026	Writes the collimation information to the XML file
	1027
	1028	:param datainfo: The Data1D object the information is coming from
	1029	:param instr: lxml node ElementTree object to be appended to
	1030	"""
[235f514]	1031	if datainfo.collimation == [] or datainfo.collimation is None:
[d26dea0]	1032	coll = Collimation()
	1033	datainfo.collimation.append(coll)
	1034	for item in datainfo.collimation:
	1035	coll = self.create_element("SAScollimation")
	1036	if item.name is not None:
	1037	self.write_attribute(coll, "name", str(item.name))
	1038	self.append(coll, instr)
	1039
	1040	self.write_node(coll, "length", item.length,
	1041	{"unit": item.length_unit})
	1042
	1043	for aperture in item.aperture:
	1044	apert = self.create_element("aperture")
	1045	if aperture.name is not None:
	1046	self.write_attribute(apert, "name", str(aperture.name))
	1047	if aperture.type is not None:
	1048	self.write_attribute(apert, "type", str(aperture.type))
	1049	self.append(apert, coll)
	1050
	1051	size = self.create_element("size")
	1052	if aperture.size_name is not None:
	1053	self.write_attribute(size, "name",
	1054	str(aperture.size_name))
	1055	written = self.write_node(size, "x", aperture.size.x,
	1056	{"unit": aperture.size_unit})
	1057	written = written \| self.write_node( \
	1058	size, "y", aperture.size.y,
	1059	{"unit": aperture.size_unit})
	1060	written = written \| self.write_node( \
	1061	size, "z", aperture.size.z,
	1062	{"unit": aperture.size_unit})
	1063	if written == True:
	1064	self.append(size, apert)
	1065
	1066	self.write_node(apert, "distance", aperture.distance,
	1067	{"unit": aperture.distance_unit})
	1068
	1069	def _write_detectors(self, datainfo, instr):
	1070	"""
	1071	Writes the detector information to the XML file
	1072
	1073	:param datainfo: The Data1D object the information is coming from
	1074	:param inst: lxml instrument node to be appended to
	1075	"""
[235f514]	1076	if datainfo.detector is None or datainfo.detector == []:
[d26dea0]	1077	det = Detector()
	1078	det.name = ""
	1079	datainfo.detector.append(det)
	1080
	1081	for item in datainfo.detector:
	1082	det = self.create_element("SASdetector")
	1083	written = self.write_node(det, "name", item.name)
	1084	written = written \| self.write_node(det, "SDD", item.distance,
	1085	{"unit": item.distance_unit})
	1086	if written == True:
	1087	self.append(det, instr)
	1088
	1089	off = self.create_element("offset")
	1090	written = self.write_node(off, "x", item.offset.x,
	1091	{"unit": item.offset_unit})
	1092	written = written \| self.write_node(off, "y", item.offset.y,
	1093	{"unit": item.offset_unit})
	1094	written = written \| self.write_node(off, "z", item.offset.z,
	1095	{"unit": item.offset_unit})
	1096	if written == True:
	1097	self.append(off, det)
	1098
	1099	ori = self.create_element("orientation")
	1100	written = self.write_node(ori, "roll", item.orientation.x,
	1101	{"unit": item.orientation_unit})
	1102	written = written \| self.write_node(ori, "pitch",
	1103	item.orientation.y,
	1104	{"unit": item.orientation_unit})
	1105	written = written \| self.write_node(ori, "yaw",
	1106	item.orientation.z,
	1107	{"unit": item.orientation_unit})
	1108	if written == True:
	1109	self.append(ori, det)
	1110
	1111	center = self.create_element("beam_center")
	1112	written = self.write_node(center, "x", item.beam_center.x,
	1113	{"unit": item.beam_center_unit})
	1114	written = written \| self.write_node(center, "y",
	1115	item.beam_center.y,
	1116	{"unit": item.beam_center_unit})
	1117	written = written \| self.write_node(center, "z",
	1118	item.beam_center.z,
	1119	{"unit": item.beam_center_unit})
	1120	if written == True:
	1121	self.append(center, det)
	1122
	1123	pix = self.create_element("pixel_size")
	1124	written = self.write_node(pix, "x", item.pixel_size.x,
	1125	{"unit": item.pixel_size_unit})
	1126	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1127	{"unit": item.pixel_size_unit})
	1128	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1129	{"unit": item.pixel_size_unit})
	1130	if written == True:
	1131	self.append(pix, det)
[3a9801f]	1132	self.write_node(det, "slit_length", item.slit_length,
	1133	{"unit": item.slit_length_unit})
	1134
[d26dea0]	1135
	1136	def _write_process_notes(self, datainfo, entry_node):
	1137	"""
	1138	Writes the process notes to the XML file
	1139
	1140	:param datainfo: The Data1D object the information is coming from
	1141	:param entry_node: lxml node ElementTree object to be appended to
	1142
	1143	"""
	1144	for item in datainfo.process:
	1145	node = self.create_element("SASprocess")
	1146	self.append(node, entry_node)
	1147	self.write_node(node, "name", item.name)
	1148	self.write_node(node, "date", item.date)
	1149	self.write_node(node, "description", item.description)
	1150	for term in item.term:
[1686a333]	1151	if isinstance(term, list):
	1152	value = term['value']
	1153	del term['value']
[5f26aa4]	1154	elif isinstance(term, dict):
	1155	value = term.get("value")
	1156	del term['value']
[1686a333]	1157	else:
	1158	value = term
[d26dea0]	1159	self.write_node(node, "term", value, term)
	1160	for note in item.notes:
	1161	self.write_node(node, "SASprocessnote", note)
	1162	if len(item.notes) == 0:
	1163	self.write_node(node, "SASprocessnote", "")
	1164
	1165	def _write_notes(self, datainfo, entry_node):
	1166	"""
	1167	Writes the notes to the XML file and creates an empty note if none
	1168	exist
	1169
	1170	:param datainfo: The Data1D object the information is coming from
	1171	:param entry_node: lxml node ElementTree object to be appended to
	1172
	1173	"""
	1174	if len(datainfo.notes) == 0:
	1175	node = self.create_element("SASnote")
	1176	self.append(node, entry_node)
	1177	else:
	1178	for item in datainfo.notes:
	1179	node = self.create_element("SASnote")
	1180	self.write_text(node, item)
	1181	self.append(node, entry_node)
	1182
[654e8e0]	1183	def _check_origin(self, entry_node, doc):
[d26dea0]	1184	"""
	1185	Return the document, and the SASentry node associated with
	1186	the data we just wrote.
	1187	If the calling function was not the cansas reader, return a minidom
	1188	object rather than an lxml object.
	1189
	1190	:param entry_node: lxml node ElementTree object to be appended to
	1191	:param doc: entire xml tree
	1192	"""
[654e8e0]	1193	if not self.frm:
	1194	self.frm = inspect.stack()[1]
	1195	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1196	mod_name = mod_name.replace(".py", "")
	1197	mod = mod_name.split("sas/")
	1198	mod_name = mod[1]
[45d90b9]	1199	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1200	string = self.to_string(doc, pretty_print=False)
	1201	doc = parseString(string)
	1202	node_name = entry_node.tag
	1203	node_list = doc.getElementsByTagName(node_name)
	1204	entry_node = node_list.item(0)
[5ce7f17]	1205	return doc, entry_node
[d26dea0]	1206
	1207	# DO NOT REMOVE - used in saving and loading panel states.
	1208	def _store_float(self, location, node, variable, storage, optional=True):
	1209	"""
	1210	Get the content of a xpath location and store
	1211	the result. Check that the units are compatible
	1212	with the destination. The value is expected to
	1213	be a float.
	1214
	1215	The xpath location might or might not exist.
	1216	If it does not exist, nothing is done
	1217
	1218	:param location: xpath location to fetch
	1219	:param node: node to read the data from
	1220	:param variable: name of the data member to store it in [string]
	1221	:param storage: data object that has the 'variable' data member
	1222	:param optional: if True, no exception will be raised
	1223	if unit conversion can't be done
	1224
	1225	:raise ValueError: raised when the units are not recognized
	1226	"""
	1227	entry = get_content(location, node)
	1228	try:
	1229	value = float(entry.text)
[574adc7]	1230	except ValueError:
[d26dea0]	1231	value = None
	1232
	1233	if value is not None:
	1234	# If the entry has units, check to see that they are
	1235	# compatible with what we currently have in the data object
	1236	units = entry.get('unit')
	1237	if units is not None:
	1238	toks = variable.split('.')
[e6e89c4]	1239	local_unit = getattr(storage, toks[0]+"_unit")
[7432acb]	1240	if local_unit is not None and units.lower() != local_unit.lower():
[9efdb29]	1241	try:
	1242	conv = Converter(units)
	1243	setattrchain(storage, variable, conv(value, units=local_unit))
	1244	except Exception:
	1245	_, exc_value, _ = sys.exc_info()
	1246	err_mess = "CanSAS reader: could not convert"
	1247	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1248	% (variable, units, local_unit, exc_value)
[d26dea0]	1249	self.errors.add(err_mess)
	1250	if optional:
[c155a16]	1251	logger.info(err_mess)
[d26dea0]	1252	else:
[574adc7]	1253	raise ValueError(err_mess)
[d26dea0]	1254	else:
[e6e89c4]	1255	setattrchain(storage, variable, value)
[d26dea0]	1256	else:
[e6e89c4]	1257	setattrchain(storage, variable, value)
[d26dea0]	1258
	1259	# DO NOT REMOVE - used in saving and loading panel states.
	1260	def _store_content(self, location, node, variable, storage):
	1261	"""
	1262	Get the content of a xpath location and store
	1263	the result. The value is treated as a string.
	1264
	1265	The xpath location might or might not exist.
	1266	If it does not exist, nothing is done
	1267
	1268	:param location: xpath location to fetch
	1269	:param node: node to read the data from
	1270	:param variable: name of the data member to store it in [string]
	1271	:param storage: data object that has the 'variable' data member
	1272
	1273	:return: return a list of errors
	1274	"""
	1275	entry = get_content(location, node)
	1276	if entry is not None and entry.text is not None:
[9efdb29]	1277	setattrchain(storage, variable, entry.text.strip())
[250fec92]	1278
	1279	# DO NOT REMOVE Called by outside packages:
	1280	# sas.sasgui.perspectives.invariant.invariant_state
	1281	# sas.sasgui.perspectives.fitting.pagestate
	1282	def get_content(location, node):
	1283	"""
	1284	Get the first instance of the content of a xpath location.
	1285
	1286	:param location: xpath location
	1287	:param node: node to start at
	1288
	1289	:return: Element, or None
	1290	"""
	1291	nodes = node.xpath(location,
	1292	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1293	if len(nodes) > 0:
	1294	return nodes[0]
	1295	else:
	1296	return None
	1297
	1298	# DO NOT REMOVE Called by outside packages:
	1299	# sas.sasgui.perspectives.fitting.pagestate
	1300	def write_node(doc, parent, name, value, attr=None):
	1301	"""
	1302	:param doc: document DOM
	1303	:param parent: parent node
	1304	:param name: tag of the element
	1305	:param value: value of the child text node
	1306	:param attr: attribute dictionary
	1307
	1308	:return: True if something was appended, otherwise False
	1309	"""
	1310	if attr is None:
	1311	attr = {}
	1312	if value is not None:
	1313	node = doc.createElement(name)
	1314	node.appendChild(doc.createTextNode(str(value)))
	1315	for item in attr:
	1316	node.setAttribute(item, attr[item])
	1317	parent.appendChild(node)
	1318	return True
	1319	return False
[e6e89c4]	1320
	1321	def getattrchain(obj, chain, default=None):
	1322	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
	1323	for part in chain.split('.'):
	1324	if hasattr(obj, part):
	1325	obj = getattr(obj, part, None)
	1326	else:
	1327	return default
	1328	return obj
	1329
	1330	def setattrchain(obj, chain, value):
	1331	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
	1332	parts = list(chain.split('.'))
	1333	for part in parts[-1]:
	1334	obj = getattr(obj, part, None)
	1335	if obj is None:
	1336	raise ValueError("missing parent object "+part)
	1337	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ aefde77

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