cansas_reader.py @ cb44d66

ticket-1094-headless

Last change on this file since cb44d66 was 8c9e65c, checked in by GitHub <noreply@…>, 6 years ago
py37 support for sascalc. Refs #888 an #1233.
Property mode set to `100644`
File size: 61.0 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	"""
[61f329f0]	70	super(Reader, self).reset_state()
[250fec92]	71	self.data = []
	72	self.process = Process()
	73	self.transspectrum = TransmissionSpectrum()
	74	self.aperture = Aperture()
	75	self.collimation = Collimation()
	76	self.detector = Detector()
	77	self.names = []
	78	self.cansas_defaults = {}
	79	self.ns_list = None
[d26dea0]	80	self.logging = []
	81	self.encoding = None
	82
[250fec92]	83	def read(self, xml_file, schema_path="", invalid=True):
[2469df7]	84	if schema_path != "" or not invalid:
[bc570f4]	85	# read has been called from self.get_file_contents because xml file doens't conform to schema
	86	_, self.extension = os.path.splitext(os.path.basename(xml_file))
	87	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
[250fec92]	88
[bc570f4]	89	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
	90	return super(XMLreader, self).read(xml_file)
	91
	92	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
[7477fb9]	93	# Reset everything since we're loading a new file
[250fec92]	94	self.reset_state()
	95	self.invalid = invalid
[bc570f4]	96	if xml_file is None:
	97	xml_file = self.f_open.name
[7477fb9]	98	# We don't sure f_open since lxml handles opnening/closing files
[bc570f4]	99	try:
[8dec7e7]	100	# Raises FileContentsException
	101	self.load_file_and_schema(xml_file, schema_path)
[7477fb9]	102	# Parse each SASentry
[7b07fbe]	103	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
	104	namespaces={
	105	'ns': self.cansas_defaults.get(
	106	"ns")
	107	})
	108	self.is_cansas(self.extension)
[bc570f4]	109	self.set_processing_instructions()
	110	for entry in entry_list:
	111	self._parse_entry(entry)
[c54c965]	112	self.data_cleanup()
[bc570f4]	113	except FileContentsException as fc_exc:
[7477fb9]	114	# File doesn't meet schema - try loading with a less strict schema
	115	base_name = xml_reader.__file__
	116	base_name = base_name.replace("\\", "/")
	117	base = base_name.split("/sas/")[0]
	118	if self.cansas_version == "1.1":
	119	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	120	else:
	121	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	122	self.set_schema(invalid_schema)
	123	if self.invalid:
[250fec92]	124	try:
[7477fb9]	125	# Load data with less strict schema
	126	self.read(xml_file, invalid_schema, False)
	127
	128	# File can still be read but doesn't match schema, so raise exception
	129	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
[250fec92]	130	invalid_xml = self.find_invalid_xml()
[527a190]	131	if invalid_xml != "":
[7b07fbe]	132	basename, _ = os.path.splitext(
	133	os.path.basename(self.f_open.name))
[cd57c7d4]	134	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
	135	raise DataReaderException(invalid_xml) # Handled by base class
[7477fb9]	136	except FileContentsException as fc_exc:
[0615d54]	137	msg = "CanSAS Reader could not load the file {}".format(xml_file)
[7477fb9]	138	if fc_exc.message is not None: # Propagate error messages from earlier
[0615d54]	139	msg = fc_exc.message
[dcb91cf]	140	if not self.extension in self.ext: # If the file has no associated loader
	141	raise DefaultReaderException(msg)
[7477fb9]	142	raise FileContentsException(msg)
	143	pass
	144	else:
	145	raise fc_exc
	146	except Exception as e: # Convert all other exceptions to FileContentsExceptions
[574adc7]	147	raise FileContentsException(str(e))
[7b07fbe]	148	finally:
	149	if not self.f_open.closed:
	150	self.f_open.close()
[7477fb9]	151
	152	def load_file_and_schema(self, xml_file, schema_path=""):
	153	base_name = xml_reader.__file__
	154	base_name = base_name.replace("\\", "/")
	155	base = base_name.split("/sas/")[0]
	156
	157	# Try and parse the XML file
	158	try:
	159	self.set_xml_file(xml_file)
	160	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
[dcb91cf]	161	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
[7477fb9]	162	raise FileContentsException(msg)
	163
	164	self.cansas_version = self.xmlroot.get("version", "1.0")
	165	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
	166
	167	if schema_path == "":
	168	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
	169	base, self.cansas_defaults.get("schema").replace("\\", "/")
	170	)
	171	self.set_schema(schema_path)
	172
	173	def is_cansas(self, ext="xml"):
[250fec92]	174	"""
[7477fb9]	175	Checks to see if the XML file is a CanSAS file
[250fec92]	176
[7477fb9]	177	:param ext: The file extension of the data file
	178	:raises FileContentsException: Raised if XML file isn't valid CanSAS
[250fec92]	179	"""
[7477fb9]	180	if self.validate_xml(): # Check file is valid XML
	181	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	182	value = self.xmlroot.get(name)
	183	# Check schema CanSAS version matches file CanSAS version
	184	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
	185	return True
	186	if ext == "svs":
	187	return True # Why is this required?
	188	# If we get to this point then file isn't valid CanSAS
[dcb91cf]	189	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
[7477fb9]	190	raise FileContentsException("The file is not valid CanSAS")
[250fec92]	191
[7477fb9]	192	def _parse_entry(self, dom, recurse=False):
[654e8e0]	193	if not self._is_call_local() and not recurse:
[1686a333]	194	self.reset_state()
[7b07fbe]	195	if not recurse:
[7477fb9]	196	self.current_datainfo = DataInfo()
[7b07fbe]	197	# Raises FileContentsException if file doesn't meet CanSAS schema
	198	self.invalid = False
	199	# Look for a SASentry
	200	self.data = []
[1686a333]	201	self.parent_class = "SASentry"
[7b07fbe]	202	self.names.append("SASentry")
	203	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
	204	self.current_datainfo.meta_data[
	205	PREPROCESS] = self.processing_instructions
	206	if self._is_call_local() and not recurse:
	207	basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
	208	self.current_datainfo.filename = basename + self.extension
[7477fb9]	209	# Create an empty dataset if no data has been passed to the reader
	210	if self.current_dataset is None:
[7b07fbe]	211	self._initialize_new_data_set(dom)
[7477fb9]	212	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
[250fec92]	213
[7477fb9]	214	# Loop through each child in the parent element
[250fec92]	215	for node in dom:
[5f26aa4]	216	attr = node.attrib
	217	name = attr.get("name", "")
	218	type = attr.get("type", "")
[250fec92]	219	# Get the element name and set the current names level
	220	tagname = node.tag.replace(self.base_ns, "")
	221	tagname_original = tagname
	222	# Skip this iteration when loading in save state information
[7b07fbe]	223	if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
[250fec92]	224	continue
	225	# Get where to store content
	226	self.names.append(tagname_original)
	227	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	228	# If the element is a child element, recurse
	229	if len(node.getchildren()) > 0:
	230	self.parent_class = tagname_original
	231	if tagname == 'SASdata':
[af08e55]	232	self._initialize_new_data_set(node)
	233	if isinstance(self.current_dataset, plottable_2D):
	234	x_bins = attr.get("x_bins", "")
	235	y_bins = attr.get("y_bins", "")
	236	if x_bins is not "" and y_bins is not "":
	237	self.current_dataset.shape = (x_bins, y_bins)
	238	else:
	239	self.current_dataset.shape = ()
[7477fb9]	240	# Recurse to access data within the group
	241	self._parse_entry(node, recurse=True)
[5f26aa4]	242	if tagname == "SASsample":
	243	self.current_datainfo.sample.name = name
	244	elif tagname == "beam_size":
	245	self.current_datainfo.source.beam_size_name = name
	246	elif tagname == "SAScollimation":
	247	self.collimation.name = name
	248	elif tagname == "aperture":
	249	self.aperture.name = name
	250	self.aperture.type = type
[7477fb9]	251	self._add_intermediate()
[250fec92]	252	else:
[7b07fbe]	253	# TODO: Clean this up to make it faster (fewer if/elifs)
[1905128]	254	if isinstance(self.current_dataset, plottable_2D):
	255	data_point = node.text
	256	unit = attr.get('unit', '')
	257	else:
	258	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	259
[af08e55]	260	# If this is a dataset, store the data appropriately
[250fec92]	261	if tagname == 'Run':
[5f26aa4]	262	self.current_datainfo.run_name[data_point] = name
[250fec92]	263	self.current_datainfo.run.append(data_point)
	264	elif tagname == 'Title':
	265	self.current_datainfo.title = data_point
	266	elif tagname == 'SASnote':
	267	self.current_datainfo.notes.append(data_point)
	268
[0b79323]	269	# I and Q points
[af08e55]	270	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[527a190]	271	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	272	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	273	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	274	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	275	elif tagname == 'Q':
[527a190]	276	self.current_dataset.xaxis("Q", unit)
[250fec92]	277	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	278	elif tagname == 'Qdev':
	279	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	280	elif tagname == 'dQw':
[590b5c2]	281	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
[250fec92]	282	elif tagname == 'dQl':
	283	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	284	elif tagname == 'Qmean':
	285	pass
	286	elif tagname == 'Shadowfactor':
	287	pass
[ad4632c]	288	elif tagname == 'Sesans':
	289	self.current_datainfo.isSesans = bool(data_point)
[527a190]	290	self.current_dataset.xaxis(attr.get('x_axis'),
	291	attr.get('x_unit'))
	292	self.current_dataset.yaxis(attr.get('y_axis'),
	293	attr.get('y_unit'))
[63d773c]	294	elif tagname == 'yacceptance':
	295	self.current_datainfo.sample.yacceptance = (data_point, unit)
[ad4632c]	296	elif tagname == 'zacceptance':
	297	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	298
[af08e55]	299	# I and Qx, Qy - 2D data
	300	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	301	self.current_dataset.yaxis("Intensity", unit)
[1905128]	302	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	303	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	304	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	305	elif tagname == 'Qx':
	306	self.current_dataset.xaxis("Qx", unit)
[1905128]	307	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	308	elif tagname == 'Qy':
	309	self.current_dataset.yaxis("Qy", unit)
[1905128]	310	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	311	elif tagname == 'Qxdev':
	312	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	313	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	314	elif tagname == 'Qydev':
	315	self.current_dataset.yaxis("Qydev", unit)
[1905128]	316	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	317	elif tagname == 'Mask':
[bcabf4e]	318	inter = [item == "1" for item in data_point.split(",")]
[1905128]	319	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	320
	321	# Sample Information
[250fec92]	322	elif tagname == 'ID' and self.parent_class == 'SASsample':
	323	self.current_datainfo.sample.ID = data_point
	324	elif tagname == 'Title' and self.parent_class == 'SASsample':
	325	self.current_datainfo.sample.name = data_point
	326	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	327	self.current_datainfo.sample.thickness = data_point
	328	self.current_datainfo.sample.thickness_unit = unit
	329	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	330	self.current_datainfo.sample.transmission = data_point
	331	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	332	self.current_datainfo.sample.temperature = data_point
	333	self.current_datainfo.sample.temperature_unit = unit
	334	elif tagname == 'details' and self.parent_class == 'SASsample':
	335	self.current_datainfo.sample.details.append(data_point)
	336	elif tagname == 'x' and self.parent_class == 'position':
	337	self.current_datainfo.sample.position.x = data_point
	338	self.current_datainfo.sample.position_unit = unit
	339	elif tagname == 'y' and self.parent_class == 'position':
	340	self.current_datainfo.sample.position.y = data_point
	341	self.current_datainfo.sample.position_unit = unit
	342	elif tagname == 'z' and self.parent_class == 'position':
	343	self.current_datainfo.sample.position.z = data_point
	344	self.current_datainfo.sample.position_unit = unit
	345	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	346	self.current_datainfo.sample.orientation.x = data_point
	347	self.current_datainfo.sample.orientation_unit = unit
	348	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	349	self.current_datainfo.sample.orientation.y = data_point
	350	self.current_datainfo.sample.orientation_unit = unit
	351	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	352	self.current_datainfo.sample.orientation.z = data_point
	353	self.current_datainfo.sample.orientation_unit = unit
	354
[af08e55]	355	# Instrumental Information
[250fec92]	356	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	357	self.current_datainfo.instrument = data_point
[7477fb9]	358
[af08e55]	359	# Detector Information
[250fec92]	360	elif tagname == 'name' and self.parent_class == 'SASdetector':
	361	self.detector.name = data_point
	362	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	363	self.detector.distance = data_point
	364	self.detector.distance_unit = unit
	365	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	366	self.detector.slit_length = data_point
	367	self.detector.slit_length_unit = unit
	368	elif tagname == 'x' and self.parent_class == 'offset':
	369	self.detector.offset.x = data_point
	370	self.detector.offset_unit = unit
	371	elif tagname == 'y' and self.parent_class == 'offset':
	372	self.detector.offset.y = data_point
	373	self.detector.offset_unit = unit
	374	elif tagname == 'z' and self.parent_class == 'offset':
	375	self.detector.offset.z = data_point
	376	self.detector.offset_unit = unit
	377	elif tagname == 'x' and self.parent_class == 'beam_center':
	378	self.detector.beam_center.x = data_point
	379	self.detector.beam_center_unit = unit
	380	elif tagname == 'y' and self.parent_class == 'beam_center':
	381	self.detector.beam_center.y = data_point
	382	self.detector.beam_center_unit = unit
	383	elif tagname == 'z' and self.parent_class == 'beam_center':
	384	self.detector.beam_center.z = data_point
	385	self.detector.beam_center_unit = unit
	386	elif tagname == 'x' and self.parent_class == 'pixel_size':
	387	self.detector.pixel_size.x = data_point
	388	self.detector.pixel_size_unit = unit
	389	elif tagname == 'y' and self.parent_class == 'pixel_size':
	390	self.detector.pixel_size.y = data_point
	391	self.detector.pixel_size_unit = unit
	392	elif tagname == 'z' and self.parent_class == 'pixel_size':
	393	self.detector.pixel_size.z = data_point
	394	self.detector.pixel_size_unit = unit
	395	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	396	self.detector.orientation.x = data_point
	397	self.detector.orientation_unit = unit
	398	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	399	self.detector.orientation.y = data_point
	400	self.detector.orientation_unit = unit
	401	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	402	self.detector.orientation.z = data_point
	403	self.detector.orientation_unit = unit
[7477fb9]	404
[af08e55]	405	# Collimation and Aperture
[250fec92]	406	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	407	self.collimation.length = data_point
	408	self.collimation.length_unit = unit
	409	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	410	self.collimation.name = data_point
	411	elif tagname == 'distance' and self.parent_class == 'aperture':
	412	self.aperture.distance = data_point
	413	self.aperture.distance_unit = unit
	414	elif tagname == 'x' and self.parent_class == 'size':
	415	self.aperture.size.x = data_point
	416	self.collimation.size_unit = unit
	417	elif tagname == 'y' and self.parent_class == 'size':
	418	self.aperture.size.y = data_point
	419	self.collimation.size_unit = unit
	420	elif tagname == 'z' and self.parent_class == 'size':
	421	self.aperture.size.z = data_point
	422	self.collimation.size_unit = unit
	423
[af08e55]	424	# Process Information
[250fec92]	425	elif tagname == 'name' and self.parent_class == 'SASprocess':
	426	self.process.name = data_point
	427	elif tagname == 'description' and self.parent_class == 'SASprocess':
	428	self.process.description = data_point
	429	elif tagname == 'date' and self.parent_class == 'SASprocess':
	430	try:
	431	self.process.date = datetime.datetime.fromtimestamp(data_point)
	432	except:
	433	self.process.date = data_point
	434	elif tagname == 'SASprocessnote':
	435	self.process.notes.append(data_point)
	436	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	437	unit = attr.get("unit", "")
[7477fb9]	438	dic = { "name": name, "value": data_point, "unit": unit }
[5f26aa4]	439	self.process.term.append(dic)
[250fec92]	440
[af08e55]	441	# Transmission Spectrum
[250fec92]	442	elif tagname == 'T' and self.parent_class == 'Tdata':
	443	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	444	self.transspectrum.transmission_unit = unit
	445	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	446	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	447	self.transspectrum.transmission_deviation_unit = unit
	448	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	449	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	450	self.transspectrum.wavelength_unit = unit
	451
[af08e55]	452	# Source Information
[250fec92]	453	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	454	self.current_datainfo.source.wavelength = data_point
	455	self.current_datainfo.source.wavelength_unit = unit
	456	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	457	self.current_datainfo.source.wavelength_min = data_point
	458	self.current_datainfo.source.wavelength_min_unit = unit
	459	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	460	self.current_datainfo.source.wavelength_max = data_point
	461	self.current_datainfo.source.wavelength_max_unit = unit
	462	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	463	self.current_datainfo.source.wavelength_spread = data_point
	464	self.current_datainfo.source.wavelength_spread_unit = unit
	465	elif tagname == 'x' and self.parent_class == 'beam_size':
	466	self.current_datainfo.source.beam_size.x = data_point
	467	self.current_datainfo.source.beam_size_unit = unit
	468	elif tagname == 'y' and self.parent_class == 'beam_size':
	469	self.current_datainfo.source.beam_size.y = data_point
	470	self.current_datainfo.source.beam_size_unit = unit
	471	elif tagname == 'z' and self.parent_class == 'pixel_size':
	472	self.current_datainfo.source.data_point.z = data_point
	473	self.current_datainfo.source.beam_size_unit = unit
	474	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	475	self.current_datainfo.source.radiation = data_point
	476	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	477	self.current_datainfo.source.beam_shape = data_point
	478
[af08e55]	479	# Everything else goes in meta_data
[250fec92]	480	else:
	481	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	482	self.current_datainfo.meta_data[new_key] = data_point
	483
	484	self.names.remove(tagname_original)
	485	length = 0
	486	if len(self.names) > 1:
	487	length = len(self.names) - 1
	488	self.parent_class = self.names[length]
[654e8e0]	489	if not self._is_call_local() and not recurse:
	490	self.frm = ""
[7477fb9]	491	self.current_datainfo.errors = set()
	492	for error in self.errors:
	493	self.current_datainfo.errors.add(error)
[c54c965]	494	self.data_cleanup()
	495	self.sort_one_d_data()
	496	self.sort_two_d_data()
	497	self.reset_data_list()
[7b07fbe]	498	return self.output[0], None
[c54c965]	499
[654e8e0]	500	def _is_call_local(self):
	501	if self.frm == "":
	502	inter = inspect.stack()
	503	self.frm = inter[2]
	504	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	505	mod_name = mod_name.replace(".py", "")
	506	mod = mod_name.split("sas/")
	507	mod_name = mod[1]
	508	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	509	return False
	510	return True
	511
[7477fb9]	512	def _add_intermediate(self):
[250fec92]	513	"""
	514	This method stores any intermediate objects within the final data set after fully reading the set.
	515	"""
	516	if self.parent_class == 'SASprocess':
	517	self.current_datainfo.process.append(self.process)
	518	self.process = Process()
	519	elif self.parent_class == 'SASdetector':
	520	self.current_datainfo.detector.append(self.detector)
	521	self.detector = Detector()
	522	elif self.parent_class == 'SAStransmission_spectrum':
	523	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	524	self.transspectrum = TransmissionSpectrum()
	525	elif self.parent_class == 'SAScollimation':
	526	self.current_datainfo.collimation.append(self.collimation)
	527	self.collimation = Collimation()
[5f26aa4]	528	elif self.parent_class == 'aperture':
[250fec92]	529	self.collimation.aperture.append(self.aperture)
	530	self.aperture = Aperture()
	531	elif self.parent_class == 'SASdata':
	532	self.data.append(self.current_dataset)
	533
	534	def _get_node_value(self, node, tagname):
	535	"""
	536	Get the value of a node and any applicable units
	537
	538	:param node: The XML node to get the value of
	539	:param tagname: The tagname of the node
	540	"""
	541	#Get the text from the node and convert all whitespace to spaces
	542	units = ''
	543	node_value = node.text
	544	if node_value is not None:
	545	node_value = ' '.join(node_value.split())
	546	else:
	547	node_value = ""
	548
	549	# If the value is a float, compile with units.
	550	if self.ns_list.ns_datatype == "float":
	551	# If an empty value is given, set as zero.
	552	if node_value is None or node_value.isspace() \
	553	or node_value.lower() == "nan":
	554	node_value = "0.0"
	555	#Convert the value to the base units
	556	node_value, units = self._unit_conversion(node, tagname, node_value)
	557
	558	# If the value is a timestamp, convert to a datetime object
	559	elif self.ns_list.ns_datatype == "timestamp":
	560	if node_value is None or node_value.isspace():
	561	pass
	562	else:
	563	try:
	564	node_value = \
	565	datetime.datetime.fromtimestamp(node_value)
	566	except ValueError:
	567	node_value = None
	568	return node_value, units
	569
	570	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	571	"""
	572	A unit converter method used to convert the data included in the file
	573	to the default units listed in data_info
	574
[250fec92]	575	:param node: XML node
	576	:param tagname: name of the node
[d26dea0]	577	:param node_value: The value of the current dom node
	578	"""
	579	attr = node.attrib
	580	value_unit = ''
	581	err_msg = None
[682c432]	582	default_unit = None
[5f26aa4]	583	if not isinstance(node_value, float):
	584	node_value = float(node_value)
	585	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	586	try:
[62160509]	587	unit = attr['unit']
[2b538cd]	588	# Split the units to retain backwards compatibility with
	589	# projects, analyses, and saved data from v4.1.0
[62160509]	590	unit_list = unit.split("\|")
	591	if len(unit_list) > 1:
	592	local_unit = unit_list[1]
	593	else:
	594	local_unit = unit
[250fec92]	595	unitname = self.ns_list.current_level.get("unit", "")
	596	if "SASdetector" in self.names:
	597	save_in = "detector"
	598	elif "aperture" in self.names:
	599	save_in = "aperture"
	600	elif "SAScollimation" in self.names:
	601	save_in = "collimation"
	602	elif "SAStransmission_spectrum" in self.names:
	603	save_in = "transspectrum"
	604	elif "SASdata" in self.names:
	605	x = np.zeros(1)
	606	y = np.zeros(1)
	607	self.current_data1d = Data1D(x, y)
	608	save_in = "current_data1d"
	609	elif "SASsource" in self.names:
	610	save_in = "current_datainfo.source"
	611	elif "SASsample" in self.names:
	612	save_in = "current_datainfo.sample"
	613	elif "SASprocess" in self.names:
	614	save_in = "process"
	615	else:
	616	save_in = "current_datainfo"
[e6e89c4]	617	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
[574adc7]	618	if (local_unit and default_unit
	619	and local_unit.lower() != default_unit.lower()
	620	and local_unit.lower() != "none"):
[9efdb29]	621	# Check local units - bad units raise KeyError
	622	#print("loading", tagname, node_value, local_unit, default_unit)
	623	data_conv_q = Converter(local_unit)
	624	value_unit = default_unit
	625	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	626	else:
	627	value_unit = local_unit
	628	except KeyError:
[527a190]	629	# Do not throw an error for loading Sesans data in cansas xml
	630	# This is a temporary fix.
	631	if local_unit != "A" and local_unit != 'pol':
	632	err_msg = "CanSAS reader: unexpected "
	633	err_msg += "\"{0}\" unit [{1}]; "
	634	err_msg = err_msg.format(tagname, local_unit)
	635	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	636	value_unit = local_unit
[574adc7]	637	except Exception:
[d26dea0]	638	err_msg = "CanSAS reader: unknown error converting "
	639	err_msg += "\"{0}\" unit [{1}]"
	640	err_msg = err_msg.format(tagname, local_unit)
	641	value_unit = local_unit
	642	elif 'unit' in attr:
	643	value_unit = attr['unit']
	644	if err_msg:
	645	self.errors.add(err_msg)
	646	return node_value, value_unit
	647
[0b79323]	648	def _initialize_new_data_set(self, node=None):
	649	if node is not None:
	650	for child in node:
	651	if child.tag.replace(self.base_ns, "") == "Idata":
	652	for i_child in child:
	653	if i_child.tag.replace(self.base_ns, "") == "Qx":
	654	self.current_dataset = plottable_2D()
	655	return
	656	self.current_dataset = plottable_1D(np.array(0), np.array(0))
	657
	658	## Writing Methods
[250fec92]	659	def write(self, filename, datainfo):
[d26dea0]	660	"""
[250fec92]	661	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	662
[250fec92]	663	:param filename: name of the file to write
	664	:param datainfo: Data1D object
	665	"""
	666	# Create XML document
	667	doc, _ = self._to_xml_doc(datainfo)
	668	# Write the file
[e6e89c4]	669	file_ref = open(filename, 'wb')
[235f514]	670	if self.encoding is None:
[250fec92]	671	self.encoding = "UTF-8"
	672	doc.write(file_ref, encoding=self.encoding,
	673	pretty_print=True, xml_declaration=True)
	674	file_ref.close()
[d26dea0]	675
[250fec92]	676	def _to_xml_doc(self, datainfo):
[d26dea0]	677	"""
[250fec92]	678	Create an XML document to contain the content of a Data1D
[d26dea0]	679
[250fec92]	680	:param datainfo: Data1D object
[d26dea0]	681	"""
[af08e55]	682	is_2d = False
[83c09af]	683	if issubclass(datainfo.__class__, Data2D):
	684	is_2d = True
[d26dea0]	685
[250fec92]	686	# Get PIs and create root element
	687	pi_string = self._get_pi_string()
	688	# Define namespaces and create SASroot object
	689	main_node = self._create_main_node()
	690	# Create ElementTree, append SASroot and apply processing instructions
	691	base_string = pi_string + self.to_string(main_node)
	692	base_element = self.create_element_from_string(base_string)
	693	doc = self.create_tree(base_element)
	694	# Create SASentry Element
	695	entry_node = self.create_element("SASentry")
	696	root = doc.getroot()
	697	root.append(entry_node)
[d26dea0]	698
[250fec92]	699	# Add Title to SASentry
	700	self.write_node(entry_node, "Title", datainfo.title)
	701	# Add Run to SASentry
	702	self._write_run_names(datainfo, entry_node)
	703	# Add Data info to SASEntry
[83c09af]	704	if is_2d:
	705	self._write_data_2d(datainfo, entry_node)
	706	else:
	707	self._write_data(datainfo, entry_node)
[250fec92]	708	# Transmission Spectrum Info
[8434365]	709	# TODO: fix the writer to linearize all data, including T_spectrum
	710	# self._write_trans_spectrum(datainfo, entry_node)
[250fec92]	711	# Sample info
	712	self._write_sample_info(datainfo, entry_node)
	713	# Instrument info
	714	instr = self._write_instrument(datainfo, entry_node)
	715	# Source
	716	self._write_source(datainfo, instr)
	717	# Collimation
	718	self._write_collimation(datainfo, instr)
	719	# Detectors
	720	self._write_detectors(datainfo, instr)
	721	# Processes info
	722	self._write_process_notes(datainfo, entry_node)
	723	# Note info
	724	self._write_notes(datainfo, entry_node)
	725	# Return the document, and the SASentry node associated with
	726	# the data we just wrote
	727	# If the calling function was not the cansas reader, return a minidom
	728	# object rather than an lxml object.
[654e8e0]	729	self.frm = inspect.stack()[1]
	730	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	731	return doc, entry_node
[d26dea0]	732
[250fec92]	733	def write_node(self, parent, name, value, attr=None):
	734	"""
	735	:param doc: document DOM
	736	:param parent: parent node
	737	:param name: tag of the element
	738	:param value: value of the child text node
	739	:param attr: attribute dictionary
[d26dea0]	740
[250fec92]	741	:return: True if something was appended, otherwise False
	742	"""
	743	if value is not None:
	744	parent = self.ebuilder(parent, name, value, attr)
	745	return True
	746	return False
[d26dea0]	747
	748	def _get_pi_string(self):
	749	"""
	750	Creates the processing instructions header for writing to file
	751	"""
	752	pis = self.return_processing_instructions()
	753	if len(pis) > 0:
	754	pi_tree = self.create_tree(pis[0])
	755	i = 1
	756	for i in range(1, len(pis) - 1):
	757	pi_tree = self.append(pis[i], pi_tree)
	758	pi_string = self.to_string(pi_tree)
	759	else:
	760	pi_string = ""
	761	return pi_string
	762
	763	def _create_main_node(self):
	764	"""
	765	Creates the primary xml header used when writing to file
	766	"""
	767	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	768	version = self.cansas_version
	769	n_s = CANSAS_NS.get(version).get("ns")
	770	if version == "1.1":
	771	url = "http://www.cansas.org/formats/1.1/"
	772	else:
	773	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	774	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	775	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	776	"version" : version}
	777	nsmap = {'xsi' : xsi, None: n_s}
	778
	779	main_node = self.create_element("{" + n_s + "}SASroot",
	780	attrib=attrib, nsmap=nsmap)
	781	return main_node
	782
	783	def _write_run_names(self, datainfo, entry_node):
	784	"""
	785	Writes the run names to the XML file
	786
	787	:param datainfo: The Data1D object the information is coming from
	788	:param entry_node: lxml node ElementTree object to be appended to
	789	"""
[235f514]	790	if datainfo.run is None or datainfo.run == []:
[d26dea0]	791	datainfo.run.append(RUN_NAME_DEFAULT)
	792	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	793	for item in datainfo.run:
	794	runname = {}
	795	if item in datainfo.run_name and \
	796	len(str(datainfo.run_name[item])) > 1:
	797	runname = {'name': datainfo.run_name[item]}
	798	self.write_node(entry_node, "Run", item, runname)
	799
	800	def _write_data(self, datainfo, entry_node):
	801	"""
[83c09af]	802	Writes 1D I and Q data to the XML file
[d26dea0]	803
	804	:param datainfo: The Data1D object the information is coming from
	805	:param entry_node: lxml node ElementTree object to be appended to
	806	"""
	807	node = self.create_element("SASdata")
	808	self.append(node, entry_node)
	809
	810	for i in range(len(datainfo.x)):
	811	point = self.create_element("Idata")
	812	node.append(point)
	813	self.write_node(point, "Q", datainfo.x[i],
[058f6c3]	814	{'unit': datainfo._xunit})
[d26dea0]	815	if len(datainfo.y) >= i:
	816	self.write_node(point, "I", datainfo.y[i],
[058f6c3]	817	{'unit': datainfo._yunit})
[5f26aa4]	818	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	819	self.write_node(point, "Idev", datainfo.dy[i],
[058f6c3]	820	{'unit': datainfo._yunit})
[5f26aa4]	821	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	822	self.write_node(point, "Qdev", datainfo.dx[i],
[058f6c3]	823	{'unit': datainfo._xunit})
[5f26aa4]	824	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	825	self.write_node(point, "dQw", datainfo.dxw[i],
[058f6c3]	826	{'unit': datainfo._xunit})
[5f26aa4]	827	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	828	self.write_node(point, "dQl", datainfo.dxl[i],
[058f6c3]	829	{'unit': datainfo._xunit})
[ad4632c]	830	if datainfo.isSesans:
[527a190]	831	sesans_attrib = {'x_axis': datainfo._xaxis,
	832	'y_axis': datainfo._yaxis,
	833	'x_unit': datainfo.x_unit,
	834	'y_unit': datainfo.y_unit}
	835	sesans = self.create_element("Sesans", attrib=sesans_attrib)
[ad4632c]	836	sesans.text = str(datainfo.isSesans)
[527a190]	837	entry_node.append(sesans)
[6a455cd3]	838	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
[63d773c]	839	{'unit': datainfo.sample.yacceptance[1]})
[527a190]	840	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
[ad4632c]	841	{'unit': datainfo.sample.zacceptance[1]})
	842
[d26dea0]	843
[83c09af]	844	def _write_data_2d(self, datainfo, entry_node):
	845	"""
	846	Writes 2D data to the XML file
	847
	848	:param datainfo: The Data2D object the information is coming from
	849	:param entry_node: lxml node ElementTree object to be appended to
	850	"""
[af08e55]	851	attr = {}
	852	if datainfo.data.shape:
[1905128]	853	attr["x_bins"] = str(len(datainfo.x_bins))
	854	attr["y_bins"] = str(len(datainfo.y_bins))
	855	node = self.create_element("SASdata", attr)
[83c09af]	856	self.append(node, entry_node)
	857
[1905128]	858	point = self.create_element("Idata")
	859	node.append(point)
[574adc7]	860	qx = ','.join(str(v) for v in datainfo.qx_data)
	861	qy = ','.join(str(v) for v in datainfo.qy_data)
	862	intensity = ','.join(str(v) for v in datainfo.data)
[1905128]	863
	864	self.write_node(point, "Qx", qx,
	865	{'unit': datainfo._xunit})
	866	self.write_node(point, "Qy", qy,
	867	{'unit': datainfo._yunit})
	868	self.write_node(point, "I", intensity,
	869	{'unit': datainfo._zunit})
	870	if datainfo.err_data is not None:
[574adc7]	871	err = ','.join(str(v) for v in datainfo.err_data)
[1905128]	872	self.write_node(point, "Idev", err,
[83c09af]	873	{'unit': datainfo._zunit})
[1905128]	874	if datainfo.dqy_data is not None:
[574adc7]	875	dqy = ','.join(str(v) for v in datainfo.dqy_data)
[1905128]	876	self.write_node(point, "Qydev", dqy,
	877	{'unit': datainfo._yunit})
	878	if datainfo.dqx_data is not None:
[574adc7]	879	dqx = ','.join(str(v) for v in datainfo.dqx_data)
[1905128]	880	self.write_node(point, "Qxdev", dqx,
	881	{'unit': datainfo._xunit})
	882	if datainfo.mask is not None:
[574adc7]	883	mask = ','.join("1" if v else "0" for v in datainfo.mask)
[1905128]	884	self.write_node(point, "Mask", mask)
[83c09af]	885
[d26dea0]	886	def _write_trans_spectrum(self, datainfo, entry_node):
	887	"""
	888	Writes the transmission spectrum data to the XML file
	889
	890	:param datainfo: The Data1D object the information is coming from
	891	:param entry_node: lxml node ElementTree object to be appended to
	892	"""
	893	for i in range(len(datainfo.trans_spectrum)):
	894	spectrum = datainfo.trans_spectrum[i]
	895	node = self.create_element("SAStransmission_spectrum",
	896	{"name" : spectrum.name})
	897	self.append(node, entry_node)
	898	if isinstance(spectrum.timestamp, datetime.datetime):
	899	node.setAttribute("timestamp", spectrum.timestamp)
	900	for i in range(len(spectrum.wavelength)):
	901	point = self.create_element("Tdata")
	902	node.append(point)
	903	self.write_node(point, "Lambda", spectrum.wavelength[i],
	904	{'unit': spectrum.wavelength_unit})
	905	self.write_node(point, "T", spectrum.transmission[i],
	906	{'unit': spectrum.transmission_unit})
[7432acb]	907	if spectrum.transmission_deviation is not None \
[d26dea0]	908	and len(spectrum.transmission_deviation) >= i:
	909	self.write_node(point, "Tdev",
	910	spectrum.transmission_deviation[i],
	911	{'unit':
	912	spectrum.transmission_deviation_unit})
	913
	914	def _write_sample_info(self, datainfo, entry_node):
	915	"""
	916	Writes the sample information to the XML file
	917
	918	:param datainfo: The Data1D object the information is coming from
	919	:param entry_node: lxml node ElementTree object to be appended to
	920	"""
	921	sample = self.create_element("SASsample")
	922	if datainfo.sample.name is not None:
	923	self.write_attribute(sample, "name",
	924	str(datainfo.sample.name))
	925	self.append(sample, entry_node)
	926	self.write_node(sample, "ID", str(datainfo.sample.ID))
	927	self.write_node(sample, "thickness", datainfo.sample.thickness,
	928	{"unit": datainfo.sample.thickness_unit})
	929	self.write_node(sample, "transmission", datainfo.sample.transmission)
	930	self.write_node(sample, "temperature", datainfo.sample.temperature,
	931	{"unit": datainfo.sample.temperature_unit})
	932
	933	pos = self.create_element("position")
	934	written = self.write_node(pos,
	935	"x",
	936	datainfo.sample.position.x,
	937	{"unit": datainfo.sample.position_unit})
	938	written = written \| self.write_node( \
	939	pos, "y", datainfo.sample.position.y,
	940	{"unit": datainfo.sample.position_unit})
	941	written = written \| self.write_node( \
	942	pos, "z", datainfo.sample.position.z,
	943	{"unit": datainfo.sample.position_unit})
[2469df7]	944	if written:
[d26dea0]	945	self.append(pos, sample)
	946
	947	ori = self.create_element("orientation")
	948	written = self.write_node(ori, "roll",
	949	datainfo.sample.orientation.x,
	950	{"unit": datainfo.sample.orientation_unit})
	951	written = written \| self.write_node( \
	952	ori, "pitch", datainfo.sample.orientation.y,
	953	{"unit": datainfo.sample.orientation_unit})
	954	written = written \| self.write_node( \
	955	ori, "yaw", datainfo.sample.orientation.z,
	956	{"unit": datainfo.sample.orientation_unit})
[2469df7]	957	if written:
[d26dea0]	958	self.append(ori, sample)
	959
	960	for item in datainfo.sample.details:
	961	self.write_node(sample, "details", item)
	962
	963	def _write_instrument(self, datainfo, entry_node):
	964	"""
	965	Writes the instrumental information to the XML file
	966
	967	:param datainfo: The Data1D object the information is coming from
	968	:param entry_node: lxml node ElementTree object to be appended to
	969	"""
	970	instr = self.create_element("SASinstrument")
	971	self.append(instr, entry_node)
	972	self.write_node(instr, "name", datainfo.instrument)
	973	return instr
	974
	975	def _write_source(self, datainfo, instr):
	976	"""
	977	Writes the source information to the XML file
	978
	979	:param datainfo: The Data1D object the information is coming from
	980	:param instr: instrument node to be appended to
	981	"""
	982	source = self.create_element("SASsource")
	983	if datainfo.source.name is not None:
	984	self.write_attribute(source, "name",
	985	str(datainfo.source.name))
	986	self.append(source, instr)
[235f514]	987	if datainfo.source.radiation is None or datainfo.source.radiation == '':
[d26dea0]	988	datainfo.source.radiation = "neutron"
	989	self.write_node(source, "radiation", datainfo.source.radiation)
	990
	991	size = self.create_element("beam_size")
	992	if datainfo.source.beam_size_name is not None:
	993	self.write_attribute(size, "name",
	994	str(datainfo.source.beam_size_name))
	995	written = self.write_node( \
	996	size, "x", datainfo.source.beam_size.x,
	997	{"unit": datainfo.source.beam_size_unit})
	998	written = written \| self.write_node( \
	999	size, "y", datainfo.source.beam_size.y,
	1000	{"unit": datainfo.source.beam_size_unit})
	1001	written = written \| self.write_node( \
	1002	size, "z", datainfo.source.beam_size.z,
	1003	{"unit": datainfo.source.beam_size_unit})
[2469df7]	1004	if written:
[d26dea0]	1005	self.append(size, source)
	1006
	1007	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1008	self.write_node(source, "wavelength",
	1009	datainfo.source.wavelength,
	1010	{"unit": datainfo.source.wavelength_unit})
	1011	self.write_node(source, "wavelength_min",
	1012	datainfo.source.wavelength_min,
	1013	{"unit": datainfo.source.wavelength_min_unit})
	1014	self.write_node(source, "wavelength_max",
	1015	datainfo.source.wavelength_max,
	1016	{"unit": datainfo.source.wavelength_max_unit})
	1017	self.write_node(source, "wavelength_spread",
	1018	datainfo.source.wavelength_spread,
	1019	{"unit": datainfo.source.wavelength_spread_unit})
	1020
	1021	def _write_collimation(self, datainfo, instr):
	1022	"""
	1023	Writes the collimation information to the XML file
	1024
	1025	:param datainfo: The Data1D object the information is coming from
	1026	:param instr: lxml node ElementTree object to be appended to
	1027	"""
[235f514]	1028	if datainfo.collimation == [] or datainfo.collimation is None:
[d26dea0]	1029	coll = Collimation()
	1030	datainfo.collimation.append(coll)
	1031	for item in datainfo.collimation:
	1032	coll = self.create_element("SAScollimation")
	1033	if item.name is not None:
	1034	self.write_attribute(coll, "name", str(item.name))
	1035	self.append(coll, instr)
	1036
	1037	self.write_node(coll, "length", item.length,
	1038	{"unit": item.length_unit})
	1039
	1040	for aperture in item.aperture:
	1041	apert = self.create_element("aperture")
	1042	if aperture.name is not None:
	1043	self.write_attribute(apert, "name", str(aperture.name))
	1044	if aperture.type is not None:
	1045	self.write_attribute(apert, "type", str(aperture.type))
	1046	self.append(apert, coll)
	1047
	1048	size = self.create_element("size")
	1049	if aperture.size_name is not None:
	1050	self.write_attribute(size, "name",
	1051	str(aperture.size_name))
	1052	written = self.write_node(size, "x", aperture.size.x,
	1053	{"unit": aperture.size_unit})
	1054	written = written \| self.write_node( \
	1055	size, "y", aperture.size.y,
	1056	{"unit": aperture.size_unit})
	1057	written = written \| self.write_node( \
	1058	size, "z", aperture.size.z,
	1059	{"unit": aperture.size_unit})
[2469df7]	1060	if written:
[d26dea0]	1061	self.append(size, apert)
	1062
	1063	self.write_node(apert, "distance", aperture.distance,
	1064	{"unit": aperture.distance_unit})
	1065
	1066	def _write_detectors(self, datainfo, instr):
	1067	"""
	1068	Writes the detector information to the XML file
	1069
	1070	:param datainfo: The Data1D object the information is coming from
	1071	:param inst: lxml instrument node to be appended to
	1072	"""
[235f514]	1073	if datainfo.detector is None or datainfo.detector == []:
[d26dea0]	1074	det = Detector()
	1075	det.name = ""
	1076	datainfo.detector.append(det)
	1077
	1078	for item in datainfo.detector:
	1079	det = self.create_element("SASdetector")
	1080	written = self.write_node(det, "name", item.name)
	1081	written = written \| self.write_node(det, "SDD", item.distance,
	1082	{"unit": item.distance_unit})
[2469df7]	1083	if written:
[d26dea0]	1084	self.append(det, instr)
	1085
	1086	off = self.create_element("offset")
	1087	written = self.write_node(off, "x", item.offset.x,
	1088	{"unit": item.offset_unit})
	1089	written = written \| self.write_node(off, "y", item.offset.y,
	1090	{"unit": item.offset_unit})
	1091	written = written \| self.write_node(off, "z", item.offset.z,
	1092	{"unit": item.offset_unit})
[2469df7]	1093	if written:
[d26dea0]	1094	self.append(off, det)
	1095
	1096	ori = self.create_element("orientation")
	1097	written = self.write_node(ori, "roll", item.orientation.x,
	1098	{"unit": item.orientation_unit})
	1099	written = written \| self.write_node(ori, "pitch",
	1100	item.orientation.y,
	1101	{"unit": item.orientation_unit})
	1102	written = written \| self.write_node(ori, "yaw",
	1103	item.orientation.z,
	1104	{"unit": item.orientation_unit})
[2469df7]	1105	if written:
[d26dea0]	1106	self.append(ori, det)
	1107
	1108	center = self.create_element("beam_center")
	1109	written = self.write_node(center, "x", item.beam_center.x,
	1110	{"unit": item.beam_center_unit})
	1111	written = written \| self.write_node(center, "y",
	1112	item.beam_center.y,
	1113	{"unit": item.beam_center_unit})
	1114	written = written \| self.write_node(center, "z",
	1115	item.beam_center.z,
	1116	{"unit": item.beam_center_unit})
[2469df7]	1117	if written:
[d26dea0]	1118	self.append(center, det)
	1119
	1120	pix = self.create_element("pixel_size")
	1121	written = self.write_node(pix, "x", item.pixel_size.x,
	1122	{"unit": item.pixel_size_unit})
	1123	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1124	{"unit": item.pixel_size_unit})
	1125	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1126	{"unit": item.pixel_size_unit})
[2469df7]	1127	if written:
[d26dea0]	1128	self.append(pix, det)
[3a9801f]	1129	self.write_node(det, "slit_length", item.slit_length,
	1130	{"unit": item.slit_length_unit})
	1131
[d26dea0]	1132
	1133	def _write_process_notes(self, datainfo, entry_node):
	1134	"""
	1135	Writes the process notes to the XML file
	1136
	1137	:param datainfo: The Data1D object the information is coming from
	1138	:param entry_node: lxml node ElementTree object to be appended to
	1139
	1140	"""
	1141	for item in datainfo.process:
	1142	node = self.create_element("SASprocess")
	1143	self.append(node, entry_node)
	1144	self.write_node(node, "name", item.name)
	1145	self.write_node(node, "date", item.date)
	1146	self.write_node(node, "description", item.description)
	1147	for term in item.term:
[1686a333]	1148	if isinstance(term, list):
	1149	value = term['value']
	1150	del term['value']
[5f26aa4]	1151	elif isinstance(term, dict):
	1152	value = term.get("value")
	1153	del term['value']
[1686a333]	1154	else:
	1155	value = term
[d26dea0]	1156	self.write_node(node, "term", value, term)
	1157	for note in item.notes:
	1158	self.write_node(node, "SASprocessnote", note)
	1159	if len(item.notes) == 0:
	1160	self.write_node(node, "SASprocessnote", "")
	1161
	1162	def _write_notes(self, datainfo, entry_node):
	1163	"""
	1164	Writes the notes to the XML file and creates an empty note if none
	1165	exist
	1166
	1167	:param datainfo: The Data1D object the information is coming from
	1168	:param entry_node: lxml node ElementTree object to be appended to
	1169
	1170	"""
	1171	if len(datainfo.notes) == 0:
	1172	node = self.create_element("SASnote")
	1173	self.append(node, entry_node)
	1174	else:
	1175	for item in datainfo.notes:
	1176	node = self.create_element("SASnote")
	1177	self.write_text(node, item)
	1178	self.append(node, entry_node)
	1179
[654e8e0]	1180	def _check_origin(self, entry_node, doc):
[d26dea0]	1181	"""
	1182	Return the document, and the SASentry node associated with
	1183	the data we just wrote.
	1184	If the calling function was not the cansas reader, return a minidom
	1185	object rather than an lxml object.
	1186
	1187	:param entry_node: lxml node ElementTree object to be appended to
	1188	:param doc: entire xml tree
	1189	"""
[654e8e0]	1190	if not self.frm:
	1191	self.frm = inspect.stack()[1]
	1192	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1193	mod_name = mod_name.replace(".py", "")
	1194	mod = mod_name.split("sas/")
	1195	mod_name = mod[1]
[45d90b9]	1196	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1197	string = self.to_string(doc, pretty_print=False)
	1198	doc = parseString(string)
	1199	node_name = entry_node.tag
	1200	node_list = doc.getElementsByTagName(node_name)
	1201	entry_node = node_list.item(0)
[5ce7f17]	1202	return doc, entry_node
[d26dea0]	1203
	1204	# DO NOT REMOVE - used in saving and loading panel states.
	1205	def _store_float(self, location, node, variable, storage, optional=True):
	1206	"""
	1207	Get the content of a xpath location and store
	1208	the result. Check that the units are compatible
	1209	with the destination. The value is expected to
	1210	be a float.
	1211
	1212	The xpath location might or might not exist.
	1213	If it does not exist, nothing is done
	1214
	1215	:param location: xpath location to fetch
	1216	:param node: node to read the data from
	1217	:param variable: name of the data member to store it in [string]
	1218	:param storage: data object that has the 'variable' data member
	1219	:param optional: if True, no exception will be raised
	1220	if unit conversion can't be done
	1221
	1222	:raise ValueError: raised when the units are not recognized
	1223	"""
	1224	entry = get_content(location, node)
	1225	try:
	1226	value = float(entry.text)
[574adc7]	1227	except ValueError:
[d26dea0]	1228	value = None
	1229
	1230	if value is not None:
	1231	# If the entry has units, check to see that they are
	1232	# compatible with what we currently have in the data object
	1233	units = entry.get('unit')
	1234	if units is not None:
	1235	toks = variable.split('.')
[e6e89c4]	1236	local_unit = getattr(storage, toks[0]+"_unit")
[7432acb]	1237	if local_unit is not None and units.lower() != local_unit.lower():
[9efdb29]	1238	try:
	1239	conv = Converter(units)
	1240	setattrchain(storage, variable, conv(value, units=local_unit))
[e090ba90]	1241	except Exception as exc:
[9efdb29]	1242	err_mess = "CanSAS reader: could not convert"
	1243	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
[e090ba90]	1244	% (variable, units, local_unit, exc)
[d26dea0]	1245	self.errors.add(err_mess)
	1246	if optional:
[c155a16]	1247	logger.info(err_mess)
[d26dea0]	1248	else:
[574adc7]	1249	raise ValueError(err_mess)
[d26dea0]	1250	else:
[e6e89c4]	1251	setattrchain(storage, variable, value)
[d26dea0]	1252	else:
[e6e89c4]	1253	setattrchain(storage, variable, value)
[d26dea0]	1254
	1255	# DO NOT REMOVE - used in saving and loading panel states.
	1256	def _store_content(self, location, node, variable, storage):
	1257	"""
	1258	Get the content of a xpath location and store
	1259	the result. The value is treated as a string.
	1260
	1261	The xpath location might or might not exist.
	1262	If it does not exist, nothing is done
	1263
	1264	:param location: xpath location to fetch
	1265	:param node: node to read the data from
	1266	:param variable: name of the data member to store it in [string]
	1267	:param storage: data object that has the 'variable' data member
	1268
	1269	:return: return a list of errors
	1270	"""
	1271	entry = get_content(location, node)
	1272	if entry is not None and entry.text is not None:
[9efdb29]	1273	setattrchain(storage, variable, entry.text.strip())
[250fec92]	1274
	1275	# DO NOT REMOVE Called by outside packages:
	1276	# sas.sasgui.perspectives.invariant.invariant_state
	1277	# sas.sasgui.perspectives.fitting.pagestate
	1278	def get_content(location, node):
	1279	"""
	1280	Get the first instance of the content of a xpath location.
	1281
	1282	:param location: xpath location
	1283	:param node: node to start at
	1284
	1285	:return: Element, or None
	1286	"""
	1287	nodes = node.xpath(location,
	1288	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1289	if len(nodes) > 0:
	1290	return nodes[0]
	1291	else:
	1292	return None
	1293
	1294	# DO NOT REMOVE Called by outside packages:
	1295	# sas.sasgui.perspectives.fitting.pagestate
	1296	def write_node(doc, parent, name, value, attr=None):
	1297	"""
	1298	:param doc: document DOM
	1299	:param parent: parent node
	1300	:param name: tag of the element
	1301	:param value: value of the child text node
	1302	:param attr: attribute dictionary
	1303
	1304	:return: True if something was appended, otherwise False
	1305	"""
	1306	if attr is None:
	1307	attr = {}
	1308	if value is not None:
	1309	node = doc.createElement(name)
	1310	node.appendChild(doc.createTextNode(str(value)))
	1311	for item in attr:
	1312	node.setAttribute(item, attr[item])
	1313	parent.appendChild(node)
	1314	return True
	1315	return False
[e6e89c4]	1316
	1317	def getattrchain(obj, chain, default=None):
	1318	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
	1319	for part in chain.split('.'):
	1320	if hasattr(obj, part):
	1321	obj = getattr(obj, part, None)
	1322	else:
	1323	return default
	1324	return obj
	1325
	1326	def setattrchain(obj, chain, value):
	1327	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
	1328	parts = list(chain.split('.'))
	1329	for part in parts[-1]:
	1330	obj = getattr(obj, part, None)
	1331	if obj is None:
	1332	raise ValueError("missing parent object "+part)
	1333	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ cb44d66

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