cansas_reader.py @ f00072f

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

Last change on this file since f00072f was e6e89c4, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
exec magic for dereferencing default units didn't work in python 3
Property mode set to `100644`
File size: 63.7 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	HAS_CONVERTER = True
	37
	38	CONSTANTS = CansasConstants()
	39	CANSAS_FORMAT = CONSTANTS.format
	40	CANSAS_NS = CONSTANTS.names
	41	ALLOW_ALL = True
	42
	43	class Reader(XMLreader):
	44	cansas_version = "1.0"
	45	base_ns = "{cansas1d/1.0}"
[250fec92]	46	cansas_defaults = None
[d26dea0]	47	type_name = "canSAS"
[250fec92]	48	invalid = True
[654e8e0]	49	frm = ""
[af08e55]	50	# Log messages and errors
[250fec92]	51	logging = None
	52	errors = set()
[af08e55]	53	# Namespace hierarchy for current xml_file object
[250fec92]	54	names = None
	55	ns_list = None
[af08e55]	56	# Temporary storage location for loading multiple data sets in a single file
[250fec92]	57	current_data1d = None
	58	data = None
[af08e55]	59	# Wildcards
[d26dea0]	60	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
[af08e55]	61	# List of allowed extensions
[d26dea0]	62	ext = ['.xml', '.XML', '.svs', '.SVS']
[af08e55]	63	# Flag to bypass extension check
[d26dea0]	64	allow_all = True
	65
[250fec92]	66	def reset_state(self):
	67	"""
	68	Resets the class state to a base case when loading a new data file so previous
	69	data files do not appear a second time
	70	"""
	71	self.current_datainfo = None
	72	self.current_dataset = None
	73	self.current_data1d = None
	74	self.data = []
	75	self.process = Process()
	76	self.transspectrum = TransmissionSpectrum()
	77	self.aperture = Aperture()
	78	self.collimation = Collimation()
	79	self.detector = Detector()
	80	self.names = []
	81	self.cansas_defaults = {}
	82	self.output = []
	83	self.ns_list = None
[d26dea0]	84	self.logging = []
	85	self.encoding = None
	86
[250fec92]	87	def read(self, xml_file, schema_path="", invalid=True):
[bc570f4]	88	if schema_path != "" or invalid != True:
	89	# read has been called from self.get_file_contents because xml file doens't conform to schema
	90	_, self.extension = os.path.splitext(os.path.basename(xml_file))
	91	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
[250fec92]	92
[bc570f4]	93	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
	94	return super(XMLreader, self).read(xml_file)
	95
	96	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
[7477fb9]	97	# Reset everything since we're loading a new file
[250fec92]	98	self.reset_state()
	99	self.invalid = invalid
[bc570f4]	100	if xml_file is None:
	101	xml_file = self.f_open.name
[7477fb9]	102	# We don't sure f_open since lxml handles opnening/closing files
[bc570f4]	103	if not self.f_open.closed:
	104	self.f_open.close()
[7477fb9]	105
[bc570f4]	106	basename, _ = os.path.splitext(os.path.basename(xml_file))
[8dec7e7]	107
[bc570f4]	108	try:
[8dec7e7]	109	# Raises FileContentsException
	110	self.load_file_and_schema(xml_file, schema_path)
	111	self.current_datainfo = DataInfo()
[7477fb9]	112	# Raises FileContentsException if file doesn't meet CanSAS schema
	113	self.is_cansas(self.extension)
	114	self.invalid = False # If we reach this point then file must be valid CanSAS
	115
	116	# Parse each SASentry
	117	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', namespaces={
	118	'ns': self.cansas_defaults.get("ns")
	119	})
	120	# Look for a SASentry
[bc570f4]	121	self.names.append("SASentry")
	122	self.set_processing_instructions()
	123
	124	for entry in entry_list:
	125	self.current_datainfo.filename = basename + self.extension
	126	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
[7477fb9]	127	self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions
[bc570f4]	128	self._parse_entry(entry)
[c54c965]	129	self.data_cleanup()
[bc570f4]	130	except FileContentsException as fc_exc:
[7477fb9]	131	# File doesn't meet schema - try loading with a less strict schema
	132	base_name = xml_reader.__file__
	133	base_name = base_name.replace("\\", "/")
	134	base = base_name.split("/sas/")[0]
	135	if self.cansas_version == "1.1":
	136	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	137	else:
	138	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	139	self.set_schema(invalid_schema)
	140	if self.invalid:
[250fec92]	141	try:
[7477fb9]	142	# Load data with less strict schema
	143	self.read(xml_file, invalid_schema, False)
	144
	145	# File can still be read but doesn't match schema, so raise exception
	146	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
[250fec92]	147	invalid_xml = self.find_invalid_xml()
[527a190]	148	if invalid_xml != "":
[cd57c7d4]	149	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
	150	raise DataReaderException(invalid_xml) # Handled by base class
[7477fb9]	151	except FileContentsException as fc_exc:
[0615d54]	152	msg = "CanSAS Reader could not load the file {}".format(xml_file)
[7477fb9]	153	if fc_exc.message is not None: # Propagate error messages from earlier
[0615d54]	154	msg = fc_exc.message
[dcb91cf]	155	if not self.extension in self.ext: # If the file has no associated loader
	156	raise DefaultReaderException(msg)
[7477fb9]	157	raise FileContentsException(msg)
	158	pass
	159	else:
	160	raise fc_exc
	161	except Exception as e: # Convert all other exceptions to FileContentsExceptions
[574adc7]	162	raise
	163	raise FileContentsException(str(e))
[250fec92]	164
[7477fb9]	165
	166	def load_file_and_schema(self, xml_file, schema_path=""):
	167	base_name = xml_reader.__file__
	168	base_name = base_name.replace("\\", "/")
	169	base = base_name.split("/sas/")[0]
	170
	171	# Try and parse the XML file
	172	try:
	173	self.set_xml_file(xml_file)
	174	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
[dcb91cf]	175	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
[7477fb9]	176	raise FileContentsException(msg)
	177
	178	self.cansas_version = self.xmlroot.get("version", "1.0")
	179	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
	180
	181	if schema_path == "":
	182	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
	183	base, self.cansas_defaults.get("schema").replace("\\", "/")
	184	)
	185	self.set_schema(schema_path)
	186
	187	def is_cansas(self, ext="xml"):
[250fec92]	188	"""
[7477fb9]	189	Checks to see if the XML file is a CanSAS file
[250fec92]	190
[7477fb9]	191	:param ext: The file extension of the data file
	192	:raises FileContentsException: Raised if XML file isn't valid CanSAS
[250fec92]	193	"""
[7477fb9]	194	if self.validate_xml(): # Check file is valid XML
	195	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	196	value = self.xmlroot.get(name)
	197	# Check schema CanSAS version matches file CanSAS version
	198	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
	199	return True
	200	if ext == "svs":
	201	return True # Why is this required?
	202	# If we get to this point then file isn't valid CanSAS
[dcb91cf]	203	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
[7477fb9]	204	raise FileContentsException("The file is not valid CanSAS")
[250fec92]	205
[7477fb9]	206	def _parse_entry(self, dom, recurse=False):
[654e8e0]	207	if not self._is_call_local() and not recurse:
[1686a333]	208	self.reset_state()
[7477fb9]	209	self.data = []
	210	self.current_datainfo = DataInfo()
[1686a333]	211	self.names.append("SASentry")
	212	self.parent_class = "SASentry"
[7477fb9]	213	# Create an empty dataset if no data has been passed to the reader
	214	if self.current_dataset is None:
	215	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
	216	np.empty(0), np.empty(0))
	217	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
[250fec92]	218
[7477fb9]	219	# Loop through each child in the parent element
[250fec92]	220	for node in dom:
[5f26aa4]	221	attr = node.attrib
	222	name = attr.get("name", "")
	223	type = attr.get("type", "")
[250fec92]	224	# Get the element name and set the current names level
	225	tagname = node.tag.replace(self.base_ns, "")
	226	tagname_original = tagname
	227	# Skip this iteration when loading in save state information
	228	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	229	continue
	230	# Get where to store content
	231	self.names.append(tagname_original)
	232	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	233	# If the element is a child element, recurse
	234	if len(node.getchildren()) > 0:
	235	self.parent_class = tagname_original
	236	if tagname == 'SASdata':
[af08e55]	237	self._initialize_new_data_set(node)
	238	if isinstance(self.current_dataset, plottable_2D):
	239	x_bins = attr.get("x_bins", "")
	240	y_bins = attr.get("y_bins", "")
	241	if x_bins is not "" and y_bins is not "":
	242	self.current_dataset.shape = (x_bins, y_bins)
	243	else:
	244	self.current_dataset.shape = ()
[7477fb9]	245	# Recurse to access data within the group
	246	self._parse_entry(node, recurse=True)
[5f26aa4]	247	if tagname == "SASsample":
	248	self.current_datainfo.sample.name = name
	249	elif tagname == "beam_size":
	250	self.current_datainfo.source.beam_size_name = name
	251	elif tagname == "SAScollimation":
	252	self.collimation.name = name
	253	elif tagname == "aperture":
	254	self.aperture.name = name
	255	self.aperture.type = type
[7477fb9]	256	self._add_intermediate()
[250fec92]	257	else:
[1905128]	258	if isinstance(self.current_dataset, plottable_2D):
	259	data_point = node.text
	260	unit = attr.get('unit', '')
	261	else:
	262	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	263
[af08e55]	264	# If this is a dataset, store the data appropriately
[250fec92]	265	if tagname == 'Run':
[5f26aa4]	266	self.current_datainfo.run_name[data_point] = name
[250fec92]	267	self.current_datainfo.run.append(data_point)
	268	elif tagname == 'Title':
	269	self.current_datainfo.title = data_point
	270	elif tagname == 'SASnote':
	271	self.current_datainfo.notes.append(data_point)
	272
[0b79323]	273	# I and Q points
[af08e55]	274	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[527a190]	275	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	276	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[af08e55]	277	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	278	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	279	elif tagname == 'Q':
[527a190]	280	self.current_dataset.xaxis("Q", unit)
[250fec92]	281	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	282	elif tagname == 'Qdev':
	283	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	284	elif tagname == 'dQw':
[590b5c2]	285	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
[250fec92]	286	elif tagname == 'dQl':
	287	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	288	elif tagname == 'Qmean':
	289	pass
	290	elif tagname == 'Shadowfactor':
	291	pass
[ad4632c]	292	elif tagname == 'Sesans':
	293	self.current_datainfo.isSesans = bool(data_point)
[527a190]	294	self.current_dataset.xaxis(attr.get('x_axis'),
	295	attr.get('x_unit'))
	296	self.current_dataset.yaxis(attr.get('y_axis'),
	297	attr.get('y_unit'))
[63d773c]	298	elif tagname == 'yacceptance':
	299	self.current_datainfo.sample.yacceptance = (data_point, unit)
[ad4632c]	300	elif tagname == 'zacceptance':
	301	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	302
[af08e55]	303	# I and Qx, Qy - 2D data
	304	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	305	self.current_dataset.yaxis("Intensity", unit)
[1905128]	306	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	307	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
[1905128]	308	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	309	elif tagname == 'Qx':
	310	self.current_dataset.xaxis("Qx", unit)
[1905128]	311	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	312	elif tagname == 'Qy':
	313	self.current_dataset.yaxis("Qy", unit)
[1905128]	314	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	315	elif tagname == 'Qxdev':
	316	self.current_dataset.xaxis("Qxdev", unit)
[1905128]	317	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	318	elif tagname == 'Qydev':
	319	self.current_dataset.yaxis("Qydev", unit)
[1905128]	320	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
[af08e55]	321	elif tagname == 'Mask':
[bcabf4e]	322	inter = [item == "1" for item in data_point.split(",")]
[1905128]	323	self.current_dataset.mask = np.asarray(inter, dtype=bool)
[af08e55]	324
	325	# Sample Information
[250fec92]	326	elif tagname == 'ID' and self.parent_class == 'SASsample':
	327	self.current_datainfo.sample.ID = data_point
	328	elif tagname == 'Title' and self.parent_class == 'SASsample':
	329	self.current_datainfo.sample.name = data_point
	330	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	331	self.current_datainfo.sample.thickness = data_point
	332	self.current_datainfo.sample.thickness_unit = unit
	333	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	334	self.current_datainfo.sample.transmission = data_point
	335	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	336	self.current_datainfo.sample.temperature = data_point
	337	self.current_datainfo.sample.temperature_unit = unit
	338	elif tagname == 'details' and self.parent_class == 'SASsample':
	339	self.current_datainfo.sample.details.append(data_point)
	340	elif tagname == 'x' and self.parent_class == 'position':
	341	self.current_datainfo.sample.position.x = data_point
	342	self.current_datainfo.sample.position_unit = unit
	343	elif tagname == 'y' and self.parent_class == 'position':
	344	self.current_datainfo.sample.position.y = data_point
	345	self.current_datainfo.sample.position_unit = unit
	346	elif tagname == 'z' and self.parent_class == 'position':
	347	self.current_datainfo.sample.position.z = data_point
	348	self.current_datainfo.sample.position_unit = unit
	349	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	350	self.current_datainfo.sample.orientation.x = data_point
	351	self.current_datainfo.sample.orientation_unit = unit
	352	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	353	self.current_datainfo.sample.orientation.y = data_point
	354	self.current_datainfo.sample.orientation_unit = unit
	355	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	356	self.current_datainfo.sample.orientation.z = data_point
	357	self.current_datainfo.sample.orientation_unit = unit
	358
[af08e55]	359	# Instrumental Information
[250fec92]	360	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	361	self.current_datainfo.instrument = data_point
[7477fb9]	362
[af08e55]	363	# Detector Information
[250fec92]	364	elif tagname == 'name' and self.parent_class == 'SASdetector':
	365	self.detector.name = data_point
	366	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	367	self.detector.distance = data_point
	368	self.detector.distance_unit = unit
	369	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	370	self.detector.slit_length = data_point
	371	self.detector.slit_length_unit = unit
	372	elif tagname == 'x' and self.parent_class == 'offset':
	373	self.detector.offset.x = data_point
	374	self.detector.offset_unit = unit
	375	elif tagname == 'y' and self.parent_class == 'offset':
	376	self.detector.offset.y = data_point
	377	self.detector.offset_unit = unit
	378	elif tagname == 'z' and self.parent_class == 'offset':
	379	self.detector.offset.z = data_point
	380	self.detector.offset_unit = unit
	381	elif tagname == 'x' and self.parent_class == 'beam_center':
	382	self.detector.beam_center.x = data_point
	383	self.detector.beam_center_unit = unit
	384	elif tagname == 'y' and self.parent_class == 'beam_center':
	385	self.detector.beam_center.y = data_point
	386	self.detector.beam_center_unit = unit
	387	elif tagname == 'z' and self.parent_class == 'beam_center':
	388	self.detector.beam_center.z = data_point
	389	self.detector.beam_center_unit = unit
	390	elif tagname == 'x' and self.parent_class == 'pixel_size':
	391	self.detector.pixel_size.x = data_point
	392	self.detector.pixel_size_unit = unit
	393	elif tagname == 'y' and self.parent_class == 'pixel_size':
	394	self.detector.pixel_size.y = data_point
	395	self.detector.pixel_size_unit = unit
	396	elif tagname == 'z' and self.parent_class == 'pixel_size':
	397	self.detector.pixel_size.z = data_point
	398	self.detector.pixel_size_unit = unit
	399	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	400	self.detector.orientation.x = data_point
	401	self.detector.orientation_unit = unit
	402	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	403	self.detector.orientation.y = data_point
	404	self.detector.orientation_unit = unit
	405	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	406	self.detector.orientation.z = data_point
	407	self.detector.orientation_unit = unit
[7477fb9]	408
[af08e55]	409	# Collimation and Aperture
[250fec92]	410	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	411	self.collimation.length = data_point
	412	self.collimation.length_unit = unit
	413	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	414	self.collimation.name = data_point
	415	elif tagname == 'distance' and self.parent_class == 'aperture':
	416	self.aperture.distance = data_point
	417	self.aperture.distance_unit = unit
	418	elif tagname == 'x' and self.parent_class == 'size':
	419	self.aperture.size.x = data_point
	420	self.collimation.size_unit = unit
	421	elif tagname == 'y' and self.parent_class == 'size':
	422	self.aperture.size.y = data_point
	423	self.collimation.size_unit = unit
	424	elif tagname == 'z' and self.parent_class == 'size':
	425	self.aperture.size.z = data_point
	426	self.collimation.size_unit = unit
	427
[af08e55]	428	# Process Information
[250fec92]	429	elif tagname == 'name' and self.parent_class == 'SASprocess':
	430	self.process.name = data_point
	431	elif tagname == 'description' and self.parent_class == 'SASprocess':
	432	self.process.description = data_point
	433	elif tagname == 'date' and self.parent_class == 'SASprocess':
	434	try:
	435	self.process.date = datetime.datetime.fromtimestamp(data_point)
	436	except:
	437	self.process.date = data_point
	438	elif tagname == 'SASprocessnote':
	439	self.process.notes.append(data_point)
	440	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	441	unit = attr.get("unit", "")
[7477fb9]	442	dic = { "name": name, "value": data_point, "unit": unit }
[5f26aa4]	443	self.process.term.append(dic)
[250fec92]	444
[af08e55]	445	# Transmission Spectrum
[250fec92]	446	elif tagname == 'T' and self.parent_class == 'Tdata':
	447	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	448	self.transspectrum.transmission_unit = unit
	449	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	450	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	451	self.transspectrum.transmission_deviation_unit = unit
	452	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	453	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	454	self.transspectrum.wavelength_unit = unit
	455
[af08e55]	456	# Source Information
[250fec92]	457	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	458	self.current_datainfo.source.wavelength = data_point
	459	self.current_datainfo.source.wavelength_unit = unit
	460	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	461	self.current_datainfo.source.wavelength_min = data_point
	462	self.current_datainfo.source.wavelength_min_unit = unit
	463	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	464	self.current_datainfo.source.wavelength_max = data_point
	465	self.current_datainfo.source.wavelength_max_unit = unit
	466	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	467	self.current_datainfo.source.wavelength_spread = data_point
	468	self.current_datainfo.source.wavelength_spread_unit = unit
	469	elif tagname == 'x' and self.parent_class == 'beam_size':
	470	self.current_datainfo.source.beam_size.x = data_point
	471	self.current_datainfo.source.beam_size_unit = unit
	472	elif tagname == 'y' and self.parent_class == 'beam_size':
	473	self.current_datainfo.source.beam_size.y = data_point
	474	self.current_datainfo.source.beam_size_unit = unit
	475	elif tagname == 'z' and self.parent_class == 'pixel_size':
	476	self.current_datainfo.source.data_point.z = data_point
	477	self.current_datainfo.source.beam_size_unit = unit
	478	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	479	self.current_datainfo.source.radiation = data_point
	480	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	481	self.current_datainfo.source.beam_shape = data_point
	482
[af08e55]	483	# Everything else goes in meta_data
[250fec92]	484	else:
	485	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	486	self.current_datainfo.meta_data[new_key] = data_point
	487
	488	self.names.remove(tagname_original)
	489	length = 0
	490	if len(self.names) > 1:
	491	length = len(self.names) - 1
	492	self.parent_class = self.names[length]
[654e8e0]	493	if not self._is_call_local() and not recurse:
	494	self.frm = ""
[7477fb9]	495	self.current_datainfo.errors = set()
	496	for error in self.errors:
	497	self.current_datainfo.errors.add(error)
[c54c965]	498	self.data_cleanup()
	499	self.sort_one_d_data()
	500	self.sort_two_d_data()
	501	self.reset_data_list()
[1686a333]	502	empty = None
	503	return self.output[0], empty
[250fec92]	504
[c54c965]	505	def data_cleanup(self):
	506	"""
	507	Clean up the data sets and refresh everything
	508	:return: None
	509	"""
	510	has_error_dx = self.current_dataset.dx is not None
[ae69c690]	511	has_error_dxl = self.current_dataset.dxl is not None
	512	has_error_dxw = self.current_dataset.dxw is not None
[c54c965]	513	has_error_dy = self.current_dataset.dy is not None
	514	self.remove_empty_q_values(has_error_dx=has_error_dx,
[ae69c690]	515	has_error_dxl=has_error_dxl,
	516	has_error_dxw=has_error_dxw,
[c54c965]	517	has_error_dy=has_error_dy)
	518	self.send_to_output() # Combine datasets with DataInfo
	519	self.current_datainfo = DataInfo() # Reset DataInfo
	520
[654e8e0]	521	def _is_call_local(self):
	522	if self.frm == "":
	523	inter = inspect.stack()
	524	self.frm = inter[2]
	525	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	526	mod_name = mod_name.replace(".py", "")
	527	mod = mod_name.split("sas/")
	528	mod_name = mod[1]
	529	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	530	return False
	531	return True
	532
[7477fb9]	533	def _add_intermediate(self):
[250fec92]	534	"""
	535	This method stores any intermediate objects within the final data set after fully reading the set.
	536	"""
	537	if self.parent_class == 'SASprocess':
	538	self.current_datainfo.process.append(self.process)
	539	self.process = Process()
	540	elif self.parent_class == 'SASdetector':
	541	self.current_datainfo.detector.append(self.detector)
	542	self.detector = Detector()
	543	elif self.parent_class == 'SAStransmission_spectrum':
	544	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	545	self.transspectrum = TransmissionSpectrum()
	546	elif self.parent_class == 'SAScollimation':
	547	self.current_datainfo.collimation.append(self.collimation)
	548	self.collimation = Collimation()
[5f26aa4]	549	elif self.parent_class == 'aperture':
[250fec92]	550	self.collimation.aperture.append(self.aperture)
	551	self.aperture = Aperture()
	552	elif self.parent_class == 'SASdata':
	553	self._check_for_empty_resolution()
	554	self.data.append(self.current_dataset)
	555
	556	def _get_node_value(self, node, tagname):
	557	"""
	558	Get the value of a node and any applicable units
	559
	560	:param node: The XML node to get the value of
	561	:param tagname: The tagname of the node
	562	"""
	563	#Get the text from the node and convert all whitespace to spaces
	564	units = ''
	565	node_value = node.text
	566	if node_value is not None:
	567	node_value = ' '.join(node_value.split())
	568	else:
	569	node_value = ""
	570
	571	# If the value is a float, compile with units.
	572	if self.ns_list.ns_datatype == "float":
	573	# If an empty value is given, set as zero.
	574	if node_value is None or node_value.isspace() \
	575	or node_value.lower() == "nan":
	576	node_value = "0.0"
	577	#Convert the value to the base units
	578	node_value, units = self._unit_conversion(node, tagname, node_value)
	579
	580	# If the value is a timestamp, convert to a datetime object
	581	elif self.ns_list.ns_datatype == "timestamp":
	582	if node_value is None or node_value.isspace():
	583	pass
	584	else:
	585	try:
	586	node_value = \
	587	datetime.datetime.fromtimestamp(node_value)
	588	except ValueError:
	589	node_value = None
	590	return node_value, units
	591
	592	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	593	"""
	594	A unit converter method used to convert the data included in the file
	595	to the default units listed in data_info
	596
[250fec92]	597	:param node: XML node
	598	:param tagname: name of the node
[d26dea0]	599	:param node_value: The value of the current dom node
	600	"""
	601	attr = node.attrib
	602	value_unit = ''
	603	err_msg = None
[682c432]	604	default_unit = None
[5f26aa4]	605	if not isinstance(node_value, float):
	606	node_value = float(node_value)
	607	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	608	try:
	609	local_unit = attr['unit']
[250fec92]	610	unitname = self.ns_list.current_level.get("unit", "")
	611	if "SASdetector" in self.names:
	612	save_in = "detector"
	613	elif "aperture" in self.names:
	614	save_in = "aperture"
	615	elif "SAScollimation" in self.names:
	616	save_in = "collimation"
	617	elif "SAStransmission_spectrum" in self.names:
	618	save_in = "transspectrum"
	619	elif "SASdata" in self.names:
	620	x = np.zeros(1)
	621	y = np.zeros(1)
	622	self.current_data1d = Data1D(x, y)
	623	save_in = "current_data1d"
	624	elif "SASsource" in self.names:
	625	save_in = "current_datainfo.source"
	626	elif "SASsample" in self.names:
	627	save_in = "current_datainfo.sample"
	628	elif "SASprocess" in self.names:
	629	save_in = "process"
	630	else:
	631	save_in = "current_datainfo"
[e6e89c4]	632	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
[574adc7]	633	if (local_unit and default_unit
	634	and local_unit.lower() != default_unit.lower()
	635	and local_unit.lower() != "none"):
	636	if HAS_CONVERTER:
[af08e55]	637	# Check local units - bad units raise KeyError
[e6e89c4]	638	#print("loading", tagname, node_value, local_unit, default_unit)
[d26dea0]	639	data_conv_q = Converter(local_unit)
	640	value_unit = default_unit
[682c432]	641	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	642	else:
	643	value_unit = local_unit
	644	err_msg = "Unit converter is not available.\n"
	645	else:
	646	value_unit = local_unit
	647	except KeyError:
[527a190]	648	# Do not throw an error for loading Sesans data in cansas xml
	649	# This is a temporary fix.
	650	if local_unit != "A" and local_unit != 'pol':
	651	err_msg = "CanSAS reader: unexpected "
	652	err_msg += "\"{0}\" unit [{1}]; "
	653	err_msg = err_msg.format(tagname, local_unit)
	654	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	655	value_unit = local_unit
[574adc7]	656	except Exception:
[d26dea0]	657	err_msg = "CanSAS reader: unknown error converting "
	658	err_msg += "\"{0}\" unit [{1}]"
	659	err_msg = err_msg.format(tagname, local_unit)
	660	value_unit = local_unit
	661	elif 'unit' in attr:
	662	value_unit = attr['unit']
	663	if err_msg:
	664	self.errors.add(err_msg)
	665	return node_value, value_unit
	666
[250fec92]	667	def _check_for_empty_resolution(self):
[d26dea0]	668	"""
[7477fb9]	669	a method to check all resolution data sets are the same size as I and q
	670	"""
	671	dql_exists = False
	672	dqw_exists = False
	673	dq_exists = False
	674	di_exists = False
	675	if self.current_dataset.dxl is not None:
	676	dql_exists = True
	677	if self.current_dataset.dxw is not None:
	678	dqw_exists = True
	679	if self.current_dataset.dx is not None:
	680	dq_exists = True
	681	if self.current_dataset.dy is not None:
	682	di_exists = True
	683	if dqw_exists and not dql_exists:
[ae69c690]	684	array_size = self.current_dataset.dxw.size
	685	self.current_dataset.dxl = np.zeros(array_size)
[7477fb9]	686	elif dql_exists and not dqw_exists:
[ae69c690]	687	array_size = self.current_dataset.dxl.size
	688	self.current_dataset.dxw = np.zeros(array_size)
[7477fb9]	689	elif not dql_exists and not dqw_exists and not dq_exists:
[ae69c690]	690	array_size = self.current_dataset.x.size
[7477fb9]	691	self.current_dataset.dx = np.append(self.current_dataset.dx,
	692	np.zeros([array_size]))
	693	if not di_exists:
[ae69c690]	694	array_size = self.current_dataset.y.size
[7477fb9]	695	self.current_dataset.dy = np.append(self.current_dataset.dy,
	696	np.zeros([array_size]))
[d26dea0]	697
[0b79323]	698	def _initialize_new_data_set(self, node=None):
	699	if node is not None:
	700	for child in node:
	701	if child.tag.replace(self.base_ns, "") == "Idata":
	702	for i_child in child:
	703	if i_child.tag.replace(self.base_ns, "") == "Qx":
	704	self.current_dataset = plottable_2D()
	705	return
	706	self.current_dataset = plottable_1D(np.array(0), np.array(0))
	707
	708	## Writing Methods
[250fec92]	709	def write(self, filename, datainfo):
[d26dea0]	710	"""
[250fec92]	711	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	712
[250fec92]	713	:param filename: name of the file to write
	714	:param datainfo: Data1D object
	715	"""
	716	# Create XML document
	717	doc, _ = self._to_xml_doc(datainfo)
	718	# Write the file
[e6e89c4]	719	file_ref = open(filename, 'wb')
[235f514]	720	if self.encoding is None:
[250fec92]	721	self.encoding = "UTF-8"
	722	doc.write(file_ref, encoding=self.encoding,
	723	pretty_print=True, xml_declaration=True)
	724	file_ref.close()
[d26dea0]	725
[250fec92]	726	def _to_xml_doc(self, datainfo):
[d26dea0]	727	"""
[250fec92]	728	Create an XML document to contain the content of a Data1D
[d26dea0]	729
[250fec92]	730	:param datainfo: Data1D object
[d26dea0]	731	"""
[af08e55]	732	is_2d = False
[83c09af]	733	if issubclass(datainfo.__class__, Data2D):
	734	is_2d = True
[d26dea0]	735
[250fec92]	736	# Get PIs and create root element
	737	pi_string = self._get_pi_string()
	738	# Define namespaces and create SASroot object
	739	main_node = self._create_main_node()
	740	# Create ElementTree, append SASroot and apply processing instructions
	741	base_string = pi_string + self.to_string(main_node)
	742	base_element = self.create_element_from_string(base_string)
	743	doc = self.create_tree(base_element)
	744	# Create SASentry Element
	745	entry_node = self.create_element("SASentry")
	746	root = doc.getroot()
	747	root.append(entry_node)
[d26dea0]	748
[250fec92]	749	# Add Title to SASentry
	750	self.write_node(entry_node, "Title", datainfo.title)
	751	# Add Run to SASentry
	752	self._write_run_names(datainfo, entry_node)
	753	# Add Data info to SASEntry
[83c09af]	754	if is_2d:
	755	self._write_data_2d(datainfo, entry_node)
	756	else:
	757	self._write_data(datainfo, entry_node)
[250fec92]	758	# Transmission Spectrum Info
[8434365]	759	# TODO: fix the writer to linearize all data, including T_spectrum
	760	# self._write_trans_spectrum(datainfo, entry_node)
[250fec92]	761	# Sample info
	762	self._write_sample_info(datainfo, entry_node)
	763	# Instrument info
	764	instr = self._write_instrument(datainfo, entry_node)
	765	# Source
	766	self._write_source(datainfo, instr)
	767	# Collimation
	768	self._write_collimation(datainfo, instr)
	769	# Detectors
	770	self._write_detectors(datainfo, instr)
	771	# Processes info
	772	self._write_process_notes(datainfo, entry_node)
	773	# Note info
	774	self._write_notes(datainfo, entry_node)
	775	# Return the document, and the SASentry node associated with
	776	# the data we just wrote
	777	# If the calling function was not the cansas reader, return a minidom
	778	# object rather than an lxml object.
[654e8e0]	779	self.frm = inspect.stack()[1]
	780	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	781	return doc, entry_node
[d26dea0]	782
[250fec92]	783	def write_node(self, parent, name, value, attr=None):
	784	"""
	785	:param doc: document DOM
	786	:param parent: parent node
	787	:param name: tag of the element
	788	:param value: value of the child text node
	789	:param attr: attribute dictionary
[d26dea0]	790
[250fec92]	791	:return: True if something was appended, otherwise False
	792	"""
	793	if value is not None:
	794	parent = self.ebuilder(parent, name, value, attr)
	795	return True
	796	return False
[d26dea0]	797
	798	def _get_pi_string(self):
	799	"""
	800	Creates the processing instructions header for writing to file
	801	"""
	802	pis = self.return_processing_instructions()
	803	if len(pis) > 0:
	804	pi_tree = self.create_tree(pis[0])
	805	i = 1
	806	for i in range(1, len(pis) - 1):
	807	pi_tree = self.append(pis[i], pi_tree)
	808	pi_string = self.to_string(pi_tree)
	809	else:
	810	pi_string = ""
	811	return pi_string
	812
	813	def _create_main_node(self):
	814	"""
	815	Creates the primary xml header used when writing to file
	816	"""
	817	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	818	version = self.cansas_version
	819	n_s = CANSAS_NS.get(version).get("ns")
	820	if version == "1.1":
	821	url = "http://www.cansas.org/formats/1.1/"
	822	else:
	823	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	824	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	825	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	826	"version" : version}
	827	nsmap = {'xsi' : xsi, None: n_s}
	828
	829	main_node = self.create_element("{" + n_s + "}SASroot",
	830	attrib=attrib, nsmap=nsmap)
	831	return main_node
	832
	833	def _write_run_names(self, datainfo, entry_node):
	834	"""
	835	Writes the run names to the XML file
	836
	837	:param datainfo: The Data1D object the information is coming from
	838	:param entry_node: lxml node ElementTree object to be appended to
	839	"""
[235f514]	840	if datainfo.run is None or datainfo.run == []:
[d26dea0]	841	datainfo.run.append(RUN_NAME_DEFAULT)
	842	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	843	for item in datainfo.run:
	844	runname = {}
	845	if item in datainfo.run_name and \
	846	len(str(datainfo.run_name[item])) > 1:
	847	runname = {'name': datainfo.run_name[item]}
	848	self.write_node(entry_node, "Run", item, runname)
	849
	850	def _write_data(self, datainfo, entry_node):
	851	"""
[83c09af]	852	Writes 1D I and Q data to the XML file
[d26dea0]	853
	854	:param datainfo: The Data1D object the information is coming from
	855	:param entry_node: lxml node ElementTree object to be appended to
	856	"""
	857	node = self.create_element("SASdata")
	858	self.append(node, entry_node)
	859
	860	for i in range(len(datainfo.x)):
	861	point = self.create_element("Idata")
	862	node.append(point)
	863	self.write_node(point, "Q", datainfo.x[i],
[527a190]	864	{'unit': datainfo.x_unit})
[d26dea0]	865	if len(datainfo.y) >= i:
	866	self.write_node(point, "I", datainfo.y[i],
[527a190]	867	{'unit': datainfo.y_unit})
[5f26aa4]	868	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	869	self.write_node(point, "Idev", datainfo.dy[i],
[527a190]	870	{'unit': datainfo.y_unit})
[5f26aa4]	871	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	872	self.write_node(point, "Qdev", datainfo.dx[i],
[527a190]	873	{'unit': datainfo.x_unit})
[5f26aa4]	874	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	875	self.write_node(point, "dQw", datainfo.dxw[i],
[527a190]	876	{'unit': datainfo.x_unit})
[5f26aa4]	877	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	878	self.write_node(point, "dQl", datainfo.dxl[i],
[527a190]	879	{'unit': datainfo.x_unit})
[ad4632c]	880	if datainfo.isSesans:
[527a190]	881	sesans_attrib = {'x_axis': datainfo._xaxis,
	882	'y_axis': datainfo._yaxis,
	883	'x_unit': datainfo.x_unit,
	884	'y_unit': datainfo.y_unit}
	885	sesans = self.create_element("Sesans", attrib=sesans_attrib)
[ad4632c]	886	sesans.text = str(datainfo.isSesans)
[527a190]	887	entry_node.append(sesans)
[6a455cd3]	888	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
[63d773c]	889	{'unit': datainfo.sample.yacceptance[1]})
[527a190]	890	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
[ad4632c]	891	{'unit': datainfo.sample.zacceptance[1]})
	892
[d26dea0]	893
[83c09af]	894	def _write_data_2d(self, datainfo, entry_node):
	895	"""
	896	Writes 2D data to the XML file
	897
	898	:param datainfo: The Data2D object the information is coming from
	899	:param entry_node: lxml node ElementTree object to be appended to
	900	"""
[af08e55]	901	attr = {}
	902	if datainfo.data.shape:
[1905128]	903	attr["x_bins"] = str(len(datainfo.x_bins))
	904	attr["y_bins"] = str(len(datainfo.y_bins))
	905	node = self.create_element("SASdata", attr)
[83c09af]	906	self.append(node, entry_node)
	907
[1905128]	908	point = self.create_element("Idata")
	909	node.append(point)
[574adc7]	910	qx = ','.join(str(v) for v in datainfo.qx_data)
	911	qy = ','.join(str(v) for v in datainfo.qy_data)
	912	intensity = ','.join(str(v) for v in datainfo.data)
[1905128]	913
	914	self.write_node(point, "Qx", qx,
	915	{'unit': datainfo._xunit})
	916	self.write_node(point, "Qy", qy,
	917	{'unit': datainfo._yunit})
	918	self.write_node(point, "I", intensity,
	919	{'unit': datainfo._zunit})
	920	if datainfo.err_data is not None:
[574adc7]	921	err = ','.join(str(v) for v in datainfo.err_data)
[1905128]	922	self.write_node(point, "Idev", err,
[83c09af]	923	{'unit': datainfo._zunit})
[1905128]	924	if datainfo.dqy_data is not None:
[574adc7]	925	dqy = ','.join(str(v) for v in datainfo.dqy_data)
[1905128]	926	self.write_node(point, "Qydev", dqy,
	927	{'unit': datainfo._yunit})
	928	if datainfo.dqx_data is not None:
[574adc7]	929	dqx = ','.join(str(v) for v in datainfo.dqx_data)
[1905128]	930	self.write_node(point, "Qxdev", dqx,
	931	{'unit': datainfo._xunit})
	932	if datainfo.mask is not None:
[574adc7]	933	mask = ','.join("1" if v else "0" for v in datainfo.mask)
[1905128]	934	self.write_node(point, "Mask", mask)
[83c09af]	935
[d26dea0]	936	def _write_trans_spectrum(self, datainfo, entry_node):
	937	"""
	938	Writes the transmission spectrum data to the XML file
	939
	940	:param datainfo: The Data1D object the information is coming from
	941	:param entry_node: lxml node ElementTree object to be appended to
	942	"""
	943	for i in range(len(datainfo.trans_spectrum)):
	944	spectrum = datainfo.trans_spectrum[i]
	945	node = self.create_element("SAStransmission_spectrum",
	946	{"name" : spectrum.name})
	947	self.append(node, entry_node)
	948	if isinstance(spectrum.timestamp, datetime.datetime):
	949	node.setAttribute("timestamp", spectrum.timestamp)
	950	for i in range(len(spectrum.wavelength)):
	951	point = self.create_element("Tdata")
	952	node.append(point)
	953	self.write_node(point, "Lambda", spectrum.wavelength[i],
	954	{'unit': spectrum.wavelength_unit})
	955	self.write_node(point, "T", spectrum.transmission[i],
	956	{'unit': spectrum.transmission_unit})
[7432acb]	957	if spectrum.transmission_deviation is not None \
[d26dea0]	958	and len(spectrum.transmission_deviation) >= i:
	959	self.write_node(point, "Tdev",
	960	spectrum.transmission_deviation[i],
	961	{'unit':
	962	spectrum.transmission_deviation_unit})
	963
	964	def _write_sample_info(self, datainfo, entry_node):
	965	"""
	966	Writes the sample information to the XML file
	967
	968	:param datainfo: The Data1D object the information is coming from
	969	:param entry_node: lxml node ElementTree object to be appended to
	970	"""
	971	sample = self.create_element("SASsample")
	972	if datainfo.sample.name is not None:
	973	self.write_attribute(sample, "name",
	974	str(datainfo.sample.name))
	975	self.append(sample, entry_node)
	976	self.write_node(sample, "ID", str(datainfo.sample.ID))
	977	self.write_node(sample, "thickness", datainfo.sample.thickness,
	978	{"unit": datainfo.sample.thickness_unit})
	979	self.write_node(sample, "transmission", datainfo.sample.transmission)
	980	self.write_node(sample, "temperature", datainfo.sample.temperature,
	981	{"unit": datainfo.sample.temperature_unit})
	982
	983	pos = self.create_element("position")
	984	written = self.write_node(pos,
	985	"x",
	986	datainfo.sample.position.x,
	987	{"unit": datainfo.sample.position_unit})
	988	written = written \| self.write_node( \
	989	pos, "y", datainfo.sample.position.y,
	990	{"unit": datainfo.sample.position_unit})
	991	written = written \| self.write_node( \
	992	pos, "z", datainfo.sample.position.z,
	993	{"unit": datainfo.sample.position_unit})
	994	if written == True:
	995	self.append(pos, sample)
	996
	997	ori = self.create_element("orientation")
	998	written = self.write_node(ori, "roll",
	999	datainfo.sample.orientation.x,
	1000	{"unit": datainfo.sample.orientation_unit})
	1001	written = written \| self.write_node( \
	1002	ori, "pitch", datainfo.sample.orientation.y,
	1003	{"unit": datainfo.sample.orientation_unit})
	1004	written = written \| self.write_node( \
	1005	ori, "yaw", datainfo.sample.orientation.z,
	1006	{"unit": datainfo.sample.orientation_unit})
	1007	if written == True:
	1008	self.append(ori, sample)
	1009
	1010	for item in datainfo.sample.details:
	1011	self.write_node(sample, "details", item)
	1012
	1013	def _write_instrument(self, datainfo, entry_node):
	1014	"""
	1015	Writes the instrumental information to the XML file
	1016
	1017	:param datainfo: The Data1D object the information is coming from
	1018	:param entry_node: lxml node ElementTree object to be appended to
	1019	"""
	1020	instr = self.create_element("SASinstrument")
	1021	self.append(instr, entry_node)
	1022	self.write_node(instr, "name", datainfo.instrument)
	1023	return instr
	1024
	1025	def _write_source(self, datainfo, instr):
	1026	"""
	1027	Writes the source information to the XML file
	1028
	1029	:param datainfo: The Data1D object the information is coming from
	1030	:param instr: instrument node to be appended to
	1031	"""
	1032	source = self.create_element("SASsource")
	1033	if datainfo.source.name is not None:
	1034	self.write_attribute(source, "name",
	1035	str(datainfo.source.name))
	1036	self.append(source, instr)
[235f514]	1037	if datainfo.source.radiation is None or datainfo.source.radiation == '':
[d26dea0]	1038	datainfo.source.radiation = "neutron"
	1039	self.write_node(source, "radiation", datainfo.source.radiation)
	1040
	1041	size = self.create_element("beam_size")
	1042	if datainfo.source.beam_size_name is not None:
	1043	self.write_attribute(size, "name",
	1044	str(datainfo.source.beam_size_name))
	1045	written = self.write_node( \
	1046	size, "x", datainfo.source.beam_size.x,
	1047	{"unit": datainfo.source.beam_size_unit})
	1048	written = written \| self.write_node( \
	1049	size, "y", datainfo.source.beam_size.y,
	1050	{"unit": datainfo.source.beam_size_unit})
	1051	written = written \| self.write_node( \
	1052	size, "z", datainfo.source.beam_size.z,
	1053	{"unit": datainfo.source.beam_size_unit})
	1054	if written == True:
	1055	self.append(size, source)
	1056
	1057	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1058	self.write_node(source, "wavelength",
	1059	datainfo.source.wavelength,
	1060	{"unit": datainfo.source.wavelength_unit})
	1061	self.write_node(source, "wavelength_min",
	1062	datainfo.source.wavelength_min,
	1063	{"unit": datainfo.source.wavelength_min_unit})
	1064	self.write_node(source, "wavelength_max",
	1065	datainfo.source.wavelength_max,
	1066	{"unit": datainfo.source.wavelength_max_unit})
	1067	self.write_node(source, "wavelength_spread",
	1068	datainfo.source.wavelength_spread,
	1069	{"unit": datainfo.source.wavelength_spread_unit})
	1070
	1071	def _write_collimation(self, datainfo, instr):
	1072	"""
	1073	Writes the collimation information to the XML file
	1074
	1075	:param datainfo: The Data1D object the information is coming from
	1076	:param instr: lxml node ElementTree object to be appended to
	1077	"""
[235f514]	1078	if datainfo.collimation == [] or datainfo.collimation is None:
[d26dea0]	1079	coll = Collimation()
	1080	datainfo.collimation.append(coll)
	1081	for item in datainfo.collimation:
	1082	coll = self.create_element("SAScollimation")
	1083	if item.name is not None:
	1084	self.write_attribute(coll, "name", str(item.name))
	1085	self.append(coll, instr)
	1086
	1087	self.write_node(coll, "length", item.length,
	1088	{"unit": item.length_unit})
	1089
	1090	for aperture in item.aperture:
	1091	apert = self.create_element("aperture")
	1092	if aperture.name is not None:
	1093	self.write_attribute(apert, "name", str(aperture.name))
	1094	if aperture.type is not None:
	1095	self.write_attribute(apert, "type", str(aperture.type))
	1096	self.append(apert, coll)
	1097
	1098	size = self.create_element("size")
	1099	if aperture.size_name is not None:
	1100	self.write_attribute(size, "name",
	1101	str(aperture.size_name))
	1102	written = self.write_node(size, "x", aperture.size.x,
	1103	{"unit": aperture.size_unit})
	1104	written = written \| self.write_node( \
	1105	size, "y", aperture.size.y,
	1106	{"unit": aperture.size_unit})
	1107	written = written \| self.write_node( \
	1108	size, "z", aperture.size.z,
	1109	{"unit": aperture.size_unit})
	1110	if written == True:
	1111	self.append(size, apert)
	1112
	1113	self.write_node(apert, "distance", aperture.distance,
	1114	{"unit": aperture.distance_unit})
	1115
	1116	def _write_detectors(self, datainfo, instr):
	1117	"""
	1118	Writes the detector information to the XML file
	1119
	1120	:param datainfo: The Data1D object the information is coming from
	1121	:param inst: lxml instrument node to be appended to
	1122	"""
[235f514]	1123	if datainfo.detector is None or datainfo.detector == []:
[d26dea0]	1124	det = Detector()
	1125	det.name = ""
	1126	datainfo.detector.append(det)
	1127
	1128	for item in datainfo.detector:
	1129	det = self.create_element("SASdetector")
	1130	written = self.write_node(det, "name", item.name)
	1131	written = written \| self.write_node(det, "SDD", item.distance,
	1132	{"unit": item.distance_unit})
	1133	if written == True:
	1134	self.append(det, instr)
	1135
	1136	off = self.create_element("offset")
	1137	written = self.write_node(off, "x", item.offset.x,
	1138	{"unit": item.offset_unit})
	1139	written = written \| self.write_node(off, "y", item.offset.y,
	1140	{"unit": item.offset_unit})
	1141	written = written \| self.write_node(off, "z", item.offset.z,
	1142	{"unit": item.offset_unit})
	1143	if written == True:
	1144	self.append(off, det)
	1145
	1146	ori = self.create_element("orientation")
	1147	written = self.write_node(ori, "roll", item.orientation.x,
	1148	{"unit": item.orientation_unit})
	1149	written = written \| self.write_node(ori, "pitch",
	1150	item.orientation.y,
	1151	{"unit": item.orientation_unit})
	1152	written = written \| self.write_node(ori, "yaw",
	1153	item.orientation.z,
	1154	{"unit": item.orientation_unit})
	1155	if written == True:
	1156	self.append(ori, det)
	1157
	1158	center = self.create_element("beam_center")
	1159	written = self.write_node(center, "x", item.beam_center.x,
	1160	{"unit": item.beam_center_unit})
	1161	written = written \| self.write_node(center, "y",
	1162	item.beam_center.y,
	1163	{"unit": item.beam_center_unit})
	1164	written = written \| self.write_node(center, "z",
	1165	item.beam_center.z,
	1166	{"unit": item.beam_center_unit})
	1167	if written == True:
	1168	self.append(center, det)
	1169
	1170	pix = self.create_element("pixel_size")
	1171	written = self.write_node(pix, "x", item.pixel_size.x,
	1172	{"unit": item.pixel_size_unit})
	1173	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1174	{"unit": item.pixel_size_unit})
	1175	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1176	{"unit": item.pixel_size_unit})
	1177	if written == True:
	1178	self.append(pix, det)
[3a9801f]	1179	self.write_node(det, "slit_length", item.slit_length,
	1180	{"unit": item.slit_length_unit})
	1181
[d26dea0]	1182
	1183	def _write_process_notes(self, datainfo, entry_node):
	1184	"""
	1185	Writes the process notes to the XML file
	1186
	1187	:param datainfo: The Data1D object the information is coming from
	1188	:param entry_node: lxml node ElementTree object to be appended to
	1189
	1190	"""
	1191	for item in datainfo.process:
	1192	node = self.create_element("SASprocess")
	1193	self.append(node, entry_node)
	1194	self.write_node(node, "name", item.name)
	1195	self.write_node(node, "date", item.date)
	1196	self.write_node(node, "description", item.description)
	1197	for term in item.term:
[1686a333]	1198	if isinstance(term, list):
	1199	value = term['value']
	1200	del term['value']
[5f26aa4]	1201	elif isinstance(term, dict):
	1202	value = term.get("value")
	1203	del term['value']
[1686a333]	1204	else:
	1205	value = term
[d26dea0]	1206	self.write_node(node, "term", value, term)
	1207	for note in item.notes:
	1208	self.write_node(node, "SASprocessnote", note)
	1209	if len(item.notes) == 0:
	1210	self.write_node(node, "SASprocessnote", "")
	1211
	1212	def _write_notes(self, datainfo, entry_node):
	1213	"""
	1214	Writes the notes to the XML file and creates an empty note if none
	1215	exist
	1216
	1217	:param datainfo: The Data1D object the information is coming from
	1218	:param entry_node: lxml node ElementTree object to be appended to
	1219
	1220	"""
	1221	if len(datainfo.notes) == 0:
	1222	node = self.create_element("SASnote")
	1223	self.append(node, entry_node)
	1224	else:
	1225	for item in datainfo.notes:
	1226	node = self.create_element("SASnote")
	1227	self.write_text(node, item)
	1228	self.append(node, entry_node)
	1229
[654e8e0]	1230	def _check_origin(self, entry_node, doc):
[d26dea0]	1231	"""
	1232	Return the document, and the SASentry node associated with
	1233	the data we just wrote.
	1234	If the calling function was not the cansas reader, return a minidom
	1235	object rather than an lxml object.
	1236
	1237	:param entry_node: lxml node ElementTree object to be appended to
	1238	:param doc: entire xml tree
	1239	"""
[654e8e0]	1240	if not self.frm:
	1241	self.frm = inspect.stack()[1]
	1242	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1243	mod_name = mod_name.replace(".py", "")
	1244	mod = mod_name.split("sas/")
	1245	mod_name = mod[1]
[45d90b9]	1246	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1247	string = self.to_string(doc, pretty_print=False)
	1248	doc = parseString(string)
	1249	node_name = entry_node.tag
	1250	node_list = doc.getElementsByTagName(node_name)
	1251	entry_node = node_list.item(0)
[5ce7f17]	1252	return doc, entry_node
[d26dea0]	1253
	1254	# DO NOT REMOVE - used in saving and loading panel states.
	1255	def _store_float(self, location, node, variable, storage, optional=True):
	1256	"""
	1257	Get the content of a xpath location and store
	1258	the result. Check that the units are compatible
	1259	with the destination. The value is expected to
	1260	be a float.
	1261
	1262	The xpath location might or might not exist.
	1263	If it does not exist, nothing is done
	1264
	1265	:param location: xpath location to fetch
	1266	:param node: node to read the data from
	1267	:param variable: name of the data member to store it in [string]
	1268	:param storage: data object that has the 'variable' data member
	1269	:param optional: if True, no exception will be raised
	1270	if unit conversion can't be done
	1271
	1272	:raise ValueError: raised when the units are not recognized
	1273	"""
	1274	entry = get_content(location, node)
	1275	try:
	1276	value = float(entry.text)
[574adc7]	1277	except ValueError:
[d26dea0]	1278	value = None
	1279
	1280	if value is not None:
	1281	# If the entry has units, check to see that they are
	1282	# compatible with what we currently have in the data object
	1283	units = entry.get('unit')
	1284	if units is not None:
	1285	toks = variable.split('.')
[e6e89c4]	1286	# TODO: why split() when accessing unit, but not when setting value?
	1287	local_unit = getattr(storage, toks[0]+"_unit")
[7432acb]	1288	if local_unit is not None and units.lower() != local_unit.lower():
[d26dea0]	1289	if HAS_CONVERTER == True:
	1290	try:
	1291	conv = Converter(units)
[e6e89c4]	1292	setattrchain(storage, variable, conv(value, units=local_unit))
[574adc7]	1293	except Exception:
[d26dea0]	1294	_, exc_value, _ = sys.exc_info()
	1295	err_mess = "CanSAS reader: could not convert"
	1296	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1297	% (variable, units, local_unit, exc_value)
	1298	self.errors.add(err_mess)
	1299	if optional:
[c155a16]	1300	logger.info(err_mess)
[d26dea0]	1301	else:
[574adc7]	1302	raise ValueError(err_mess)
[d26dea0]	1303	else:
	1304	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1305	% (variable, units)
	1306	err_mess += " expecting [%s]" % local_unit
	1307	self.errors.add(err_mess)
	1308	if optional:
[c155a16]	1309	logger.info(err_mess)
[d26dea0]	1310	else:
[574adc7]	1311	raise ValueError(err_mess)
[d26dea0]	1312	else:
[e6e89c4]	1313	setattrchain(storage, variable, value)
[d26dea0]	1314	else:
[e6e89c4]	1315	setattrchain(storage, variable, value)
[d26dea0]	1316
	1317	# DO NOT REMOVE - used in saving and loading panel states.
	1318	def _store_content(self, location, node, variable, storage):
	1319	"""
	1320	Get the content of a xpath location and store
	1321	the result. The value is treated as a string.
	1322
	1323	The xpath location might or might not exist.
	1324	If it does not exist, nothing is done
	1325
	1326	:param location: xpath location to fetch
	1327	:param node: node to read the data from
	1328	:param variable: name of the data member to store it in [string]
	1329	:param storage: data object that has the 'variable' data member
	1330
	1331	:return: return a list of errors
	1332	"""
	1333	entry = get_content(location, node)
	1334	if entry is not None and entry.text is not None:
[574adc7]	1335	exec("storage.%s = entry.text.strip()" % variable)
[250fec92]	1336
	1337	# DO NOT REMOVE Called by outside packages:
	1338	# sas.sasgui.perspectives.invariant.invariant_state
	1339	# sas.sasgui.perspectives.fitting.pagestate
	1340	def get_content(location, node):
	1341	"""
	1342	Get the first instance of the content of a xpath location.
	1343
	1344	:param location: xpath location
	1345	:param node: node to start at
	1346
	1347	:return: Element, or None
	1348	"""
	1349	nodes = node.xpath(location,
	1350	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1351	if len(nodes) > 0:
	1352	return nodes[0]
	1353	else:
	1354	return None
	1355
	1356	# DO NOT REMOVE Called by outside packages:
	1357	# sas.sasgui.perspectives.fitting.pagestate
	1358	def write_node(doc, parent, name, value, attr=None):
	1359	"""
	1360	:param doc: document DOM
	1361	:param parent: parent node
	1362	:param name: tag of the element
	1363	:param value: value of the child text node
	1364	:param attr: attribute dictionary
	1365
	1366	:return: True if something was appended, otherwise False
	1367	"""
	1368	if attr is None:
	1369	attr = {}
	1370	if value is not None:
	1371	node = doc.createElement(name)
	1372	node.appendChild(doc.createTextNode(str(value)))
	1373	for item in attr:
	1374	node.setAttribute(item, attr[item])
	1375	parent.appendChild(node)
	1376	return True
	1377	return False
[e6e89c4]	1378
	1379	def getattrchain(obj, chain, default=None):
	1380	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
	1381	for part in chain.split('.'):
	1382	if hasattr(obj, part):
	1383	obj = getattr(obj, part, None)
	1384	else:
	1385	return default
	1386	return obj
	1387
	1388	def setattrchain(obj, chain, value):
	1389	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
	1390	parts = list(chain.split('.'))
	1391	for part in parts[-1]:
	1392	obj = getattr(obj, part, None)
	1393	if obj is None:
	1394	raise ValueError("missing parent object "+part)
	1395	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ f00072f

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