cansas_reader.py @ 3b0f8cc

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 3b0f8cc was dcb91cf, checked in by lewis, 7 years ago
Make suggested changes
Property mode set to `100644`
File size: 63.4 KB

Rev	Line
[d26dea0]	1	import logging
[250fec92]	2	import numpy as np
[d26dea0]	3	import os
	4	import sys
	5	import datetime
	6	import inspect
	7	# For saving individual sections of data
[83c09af]	8	from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \
[af08e55]	9	plottable_1D, plottable_2D
[83c09af]	10	from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \
	11	Detector, Process, Aperture
	12	from sas.sascalc.dataloader.data_info import \
	13	combine_data_info_with_plottable as combine_data
[b699768]	14	import sas.sascalc.dataloader.readers.xml_reader as xml_reader
	15	from sas.sascalc.dataloader.readers.xml_reader import XMLreader
[250fec92]	16	from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel
[3ece5dd]	17	from sas.sascalc.dataloader.loader_exceptions import FileContentsException, \
	18	DefaultReaderException, DataReaderException
[d26dea0]	19
[682c432]	20	# The following 2 imports ARE used. Do not remove either.
	21	import xml.dom.minidom
	22	from xml.dom.minidom import parseString
	23
[7477fb9]	24	from lxml import etree
	25
[463e7ffc]	26	logger = logging.getLogger(__name__)
[c155a16]	27
[d26dea0]	28	PREPROCESS = "xmlpreprocess"
	29	ENCODING = "encoding"
	30	RUN_NAME_DEFAULT = "None"
[250fec92]	31	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
	32	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
	33	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
	34	"as much of the data as possible.\n\n"
[d26dea0]	35	HAS_CONVERTER = True
	36	try:
[b699768]	37	from sas.sascalc.data_util.nxsunit import Converter
[d26dea0]	38	except ImportError:
	39	HAS_CONVERTER = False
	40
	41	CONSTANTS = CansasConstants()
	42	CANSAS_FORMAT = CONSTANTS.format
	43	CANSAS_NS = CONSTANTS.names
	44	ALLOW_ALL = True
	45
	46	class Reader(XMLreader):
	47	cansas_version = "1.0"
	48	base_ns = "{cansas1d/1.0}"
[250fec92]	49	cansas_defaults = None
[d26dea0]	50	type_name = "canSAS"
[250fec92]	51	invalid = True
[654e8e0]	52	frm = ""
[af08e55]	53	# Log messages and errors
[250fec92]	54	logging = None
	55	errors = set()
[af08e55]	56	# Namespace hierarchy for current xml_file object
[250fec92]	57	names = None
	58	ns_list = None
[af08e55]	59	# Temporary storage location for loading multiple data sets in a single file
[250fec92]	60	current_data1d = None
	61	data = None
[af08e55]	62	# Wildcards
[d26dea0]	63	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
[af08e55]	64	# List of allowed extensions
[d26dea0]	65	ext = ['.xml', '.XML', '.svs', '.SVS']
[af08e55]	66	# Flag to bypass extension check
[d26dea0]	67	allow_all = True
	68
[250fec92]	69	def reset_state(self):
	70	"""
	71	Resets the class state to a base case when loading a new data file so previous
	72	data files do not appear a second time
	73	"""
	74	self.current_datainfo = None
	75	self.current_dataset = None
	76	self.current_data1d = None
	77	self.data = []
	78	self.process = Process()
	79	self.transspectrum = TransmissionSpectrum()
	80	self.aperture = Aperture()
	81	self.collimation = Collimation()
	82	self.detector = Detector()
	83	self.names = []
	84	self.cansas_defaults = {}
	85	self.output = []
	86	self.ns_list = None
[d26dea0]	87	self.logging = []
	88	self.encoding = None
	89
[250fec92]	90	def read(self, xml_file, schema_path="", invalid=True):
[bc570f4]	91	if schema_path != "" or invalid != True:
	92	# read has been called from self.get_file_contents because xml file doens't conform to schema
	93	_, self.extension = os.path.splitext(os.path.basename(xml_file))
	94	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
	95
	96	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
	97	return super(XMLreader, self).read(xml_file)
	98
	99	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
[7477fb9]	100	# Reset everything since we're loading a new file
[250fec92]	101	self.reset_state()
	102	self.invalid = invalid
[bc570f4]	103	if xml_file is None:
	104	xml_file = self.f_open.name
[7477fb9]	105	# We don't sure f_open since lxml handles opnening/closing files
[bc570f4]	106	if not self.f_open.closed:
	107	self.f_open.close()
[7477fb9]	108
[bc570f4]	109	basename, _ = os.path.splitext(os.path.basename(xml_file))
[8dec7e7]	110
[bc570f4]	111	try:
[8dec7e7]	112	# Raises FileContentsException
	113	self.load_file_and_schema(xml_file, schema_path)
	114	self.current_datainfo = DataInfo()
[7477fb9]	115	# Raises FileContentsException if file doesn't meet CanSAS schema
	116	self.is_cansas(self.extension)
	117	self.invalid = False # If we reach this point then file must be valid CanSAS
	118
	119	# Parse each SASentry
	120	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', namespaces={
	121	'ns': self.cansas_defaults.get("ns")
	122	})
	123	# Look for a SASentry
[bc570f4]	124	self.names.append("SASentry")
	125	self.set_processing_instructions()
	126
	127	for entry in entry_list:
	128	self.current_datainfo.filename = basename + self.extension
	129	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
[7477fb9]	130	self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions
[bc570f4]	131	self._parse_entry(entry)
[248ff73]	132	has_error_dx = self.current_dataset.dx is not None
	133	has_error_dy = self.current_dataset.dy is not None
	134	self.remove_empty_q_values(has_error_dx=has_error_dx,
	135	has_error_dy=has_error_dy)
	136	self.send_to_output() # Combine datasets with DataInfo
	137	self.current_datainfo = DataInfo() # Reset DataInfo
[bc570f4]	138	except FileContentsException as fc_exc:
[7477fb9]	139	# File doesn't meet schema - try loading with a less strict schema
	140	base_name = xml_reader.__file__
	141	base_name = base_name.replace("\\", "/")
	142	base = base_name.split("/sas/")[0]
	143	if self.cansas_version == "1.1":
	144	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
	145	else:
	146	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
	147	self.set_schema(invalid_schema)
	148	if self.invalid:
	149	try:
	150	# Load data with less strict schema
	151	self.read(xml_file, invalid_schema, False)
	152
	153	# File can still be read but doesn't match schema, so raise exception
	154	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
[250fec92]	155	invalid_xml = self.find_invalid_xml()
[bc570f4]	156	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
[7477fb9]	157	raise DataReaderException(invalid_xml) # Handled by base class
	158	except FileContentsException as fc_exc:
[0615d54]	159	msg = "CanSAS Reader could not load the file {}".format(xml_file)
[7477fb9]	160	if fc_exc.message is not None: # Propagate error messages from earlier
[0615d54]	161	msg = fc_exc.message
[dcb91cf]	162	if not self.extension in self.ext: # If the file has no associated loader
	163	raise DefaultReaderException(msg)
[7477fb9]	164	raise FileContentsException(msg)
	165	pass
	166	else:
	167	raise fc_exc
	168	except Exception as e: # Convert all other exceptions to FileContentsExceptions
	169	raise FileContentsException(e.message)
[250fec92]	170
[7477fb9]	171
	172	def load_file_and_schema(self, xml_file, schema_path=""):
	173	base_name = xml_reader.__file__
	174	base_name = base_name.replace("\\", "/")
	175	base = base_name.split("/sas/")[0]
	176
	177	# Try and parse the XML file
	178	try:
	179	self.set_xml_file(xml_file)
	180	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
[dcb91cf]	181	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
[7477fb9]	182	raise FileContentsException(msg)
	183
	184	self.cansas_version = self.xmlroot.get("version", "1.0")
	185	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
	186
	187	if schema_path == "":
	188	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
	189	base, self.cansas_defaults.get("schema").replace("\\", "/")
	190	)
	191	self.set_schema(schema_path)
	192
	193	def is_cansas(self, ext="xml"):
[250fec92]	194	"""
[7477fb9]	195	Checks to see if the XML file is a CanSAS file
[250fec92]	196
[7477fb9]	197	:param ext: The file extension of the data file
	198	:raises FileContentsException: Raised if XML file isn't valid CanSAS
[250fec92]	199	"""
[7477fb9]	200	if self.validate_xml(): # Check file is valid XML
	201	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
	202	value = self.xmlroot.get(name)
	203	# Check schema CanSAS version matches file CanSAS version
	204	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
	205	return True
	206	if ext == "svs":
	207	return True # Why is this required?
	208	# If we get to this point then file isn't valid CanSAS
[dcb91cf]	209	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
[7477fb9]	210	raise FileContentsException("The file is not valid CanSAS")
[250fec92]	211
[7477fb9]	212	def _parse_entry(self, dom, recurse=False):
[654e8e0]	213	if not self._is_call_local() and not recurse:
[1686a333]	214	self.reset_state()
[7477fb9]	215	self.data = []
	216	self.current_datainfo = DataInfo()
[1686a333]	217	self.names.append("SASentry")
	218	self.parent_class = "SASentry"
[7477fb9]	219	# Create an empty dataset if no data has been passed to the reader
	220	if self.current_dataset is None:
	221	self.current_dataset = plottable_1D(np.empty(0), np.empty(0),
	222	np.empty(0), np.empty(0))
	223	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
[250fec92]	224
[7477fb9]	225	# Loop through each child in the parent element
[250fec92]	226	for node in dom:
[5f26aa4]	227	attr = node.attrib
	228	name = attr.get("name", "")
	229	type = attr.get("type", "")
[250fec92]	230	# Get the element name and set the current names level
	231	tagname = node.tag.replace(self.base_ns, "")
	232	tagname_original = tagname
	233	# Skip this iteration when loading in save state information
	234	if tagname == "fitting_plug_in" or tagname == "pr_inversion" or tagname == "invariant":
	235	continue
	236	# Get where to store content
	237	self.names.append(tagname_original)
	238	self.ns_list = CONSTANTS.iterate_namespace(self.names)
	239	# If the element is a child element, recurse
	240	if len(node.getchildren()) > 0:
	241	self.parent_class = tagname_original
	242	if tagname == 'SASdata':
[0b79323]	243	self._initialize_new_data_set(node)
	244	if isinstance(self.current_dataset, plottable_2D):
	245	x_bins = attr.get("x_bins", "")
	246	y_bins = attr.get("y_bins", "")
	247	if x_bins is not "" and y_bins is not "":
	248	self.current_dataset.shape = (x_bins, y_bins)
	249	else:
	250	self.current_dataset.shape = ()
[7477fb9]	251	# Recurse to access data within the group
	252	self._parse_entry(node, recurse=True)
[5f26aa4]	253	if tagname == "SASsample":
	254	self.current_datainfo.sample.name = name
	255	elif tagname == "beam_size":
	256	self.current_datainfo.source.beam_size_name = name
	257	elif tagname == "SAScollimation":
	258	self.collimation.name = name
	259	elif tagname == "aperture":
	260	self.aperture.name = name
	261	self.aperture.type = type
[7477fb9]	262	self._add_intermediate()
[250fec92]	263	else:
[0b79323]	264	if isinstance(self.current_dataset, plottable_2D):
	265	data_point = node.text
	266	unit = attr.get('unit', '')
	267	else:
	268	data_point, unit = self._get_node_value(node, tagname)
[250fec92]	269
[af08e55]	270	# If this is a dataset, store the data appropriately
[250fec92]	271	if tagname == 'Run':
[5f26aa4]	272	self.current_datainfo.run_name[data_point] = name
[250fec92]	273	self.current_datainfo.run.append(data_point)
	274	elif tagname == 'Title':
	275	self.current_datainfo.title = data_point
	276	elif tagname == 'SASnote':
	277	self.current_datainfo.notes.append(data_point)
[0b79323]	278
	279	# I and Q points
	280	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
[c221349]	281	unit_list = unit.split("\|")
[ad4632c]	282	if len(unit_list) > 1:
[c221349]	283	self.current_dataset.yaxis(unit_list[0].strip(),
	284	unit_list[1].strip())
[ad4632c]	285	else:
	286	self.current_dataset.yaxis("Intensity", unit)
[250fec92]	287	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
[0b79323]	288	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
[250fec92]	289	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
	290	elif tagname == 'Q':
[c221349]	291	unit_list = unit.split("\|")
[ad4632c]	292	if len(unit_list) > 1:
[c221349]	293	self.current_dataset.xaxis(unit_list[0].strip(),
	294	unit_list[1].strip())
[ad4632c]	295	else:
	296	self.current_dataset.xaxis("Q", unit)
[250fec92]	297	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
	298	elif tagname == 'Qdev':
	299	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
	300	elif tagname == 'dQw':
[248ff73]	301	if self.current_dataset.dqw is None: self.current_dataset.dqw = np.empty(0)
[250fec92]	302	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
	303	elif tagname == 'dQl':
[248ff73]	304	if self.current_dataset.dxl is None: self.current_dataset.dxl = np.empty(0)
[250fec92]	305	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
[1686a333]	306	elif tagname == 'Qmean':
	307	pass
	308	elif tagname == 'Shadowfactor':
	309	pass
[ad4632c]	310	elif tagname == 'Sesans':
	311	self.current_datainfo.isSesans = bool(data_point)
[63d773c]	312	elif tagname == 'yacceptance':
	313	self.current_datainfo.sample.yacceptance = (data_point, unit)
[ad4632c]	314	elif tagname == 'zacceptance':
	315	self.current_datainfo.sample.zacceptance = (data_point, unit)
[250fec92]	316
[0b79323]	317	# I and Qx, Qy - 2D data
	318	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
	319	self.current_dataset.yaxis("Intensity", unit)
	320	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
	321	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
	322	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
	323	elif tagname == 'Qx':
	324	self.current_dataset.xaxis("Qx", unit)
	325	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
	326	elif tagname == 'Qy':
	327	self.current_dataset.yaxis("Qy", unit)
	328	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
	329	elif tagname == 'Qxdev':
	330	self.current_dataset.xaxis("Qxdev", unit)
	331	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
	332	elif tagname == 'Qydev':
	333	self.current_dataset.yaxis("Qydev", unit)
	334	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
	335	elif tagname == 'Mask':
	336	inter = [item == "1" for item in data_point.split(",")]
	337	self.current_dataset.mask = np.asarray(inter, dtype=bool)
	338
[af08e55]	339	# Sample Information
[250fec92]	340	elif tagname == 'ID' and self.parent_class == 'SASsample':
	341	self.current_datainfo.sample.ID = data_point
	342	elif tagname == 'Title' and self.parent_class == 'SASsample':
	343	self.current_datainfo.sample.name = data_point
	344	elif tagname == 'thickness' and self.parent_class == 'SASsample':
	345	self.current_datainfo.sample.thickness = data_point
	346	self.current_datainfo.sample.thickness_unit = unit
	347	elif tagname == 'transmission' and self.parent_class == 'SASsample':
	348	self.current_datainfo.sample.transmission = data_point
	349	elif tagname == 'temperature' and self.parent_class == 'SASsample':
	350	self.current_datainfo.sample.temperature = data_point
	351	self.current_datainfo.sample.temperature_unit = unit
	352	elif tagname == 'details' and self.parent_class == 'SASsample':
	353	self.current_datainfo.sample.details.append(data_point)
	354	elif tagname == 'x' and self.parent_class == 'position':
	355	self.current_datainfo.sample.position.x = data_point
	356	self.current_datainfo.sample.position_unit = unit
	357	elif tagname == 'y' and self.parent_class == 'position':
	358	self.current_datainfo.sample.position.y = data_point
	359	self.current_datainfo.sample.position_unit = unit
	360	elif tagname == 'z' and self.parent_class == 'position':
	361	self.current_datainfo.sample.position.z = data_point
	362	self.current_datainfo.sample.position_unit = unit
	363	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	364	self.current_datainfo.sample.orientation.x = data_point
	365	self.current_datainfo.sample.orientation_unit = unit
	366	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	367	self.current_datainfo.sample.orientation.y = data_point
	368	self.current_datainfo.sample.orientation_unit = unit
	369	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
	370	self.current_datainfo.sample.orientation.z = data_point
	371	self.current_datainfo.sample.orientation_unit = unit
	372
[af08e55]	373	# Instrumental Information
[250fec92]	374	elif tagname == 'name' and self.parent_class == 'SASinstrument':
	375	self.current_datainfo.instrument = data_point
[7477fb9]	376
[af08e55]	377	# Detector Information
[250fec92]	378	elif tagname == 'name' and self.parent_class == 'SASdetector':
	379	self.detector.name = data_point
	380	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
	381	self.detector.distance = data_point
	382	self.detector.distance_unit = unit
	383	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
	384	self.detector.slit_length = data_point
	385	self.detector.slit_length_unit = unit
	386	elif tagname == 'x' and self.parent_class == 'offset':
	387	self.detector.offset.x = data_point
	388	self.detector.offset_unit = unit
	389	elif tagname == 'y' and self.parent_class == 'offset':
	390	self.detector.offset.y = data_point
	391	self.detector.offset_unit = unit
	392	elif tagname == 'z' and self.parent_class == 'offset':
	393	self.detector.offset.z = data_point
	394	self.detector.offset_unit = unit
	395	elif tagname == 'x' and self.parent_class == 'beam_center':
	396	self.detector.beam_center.x = data_point
	397	self.detector.beam_center_unit = unit
	398	elif tagname == 'y' and self.parent_class == 'beam_center':
	399	self.detector.beam_center.y = data_point
	400	self.detector.beam_center_unit = unit
	401	elif tagname == 'z' and self.parent_class == 'beam_center':
	402	self.detector.beam_center.z = data_point
	403	self.detector.beam_center_unit = unit
	404	elif tagname == 'x' and self.parent_class == 'pixel_size':
	405	self.detector.pixel_size.x = data_point
	406	self.detector.pixel_size_unit = unit
	407	elif tagname == 'y' and self.parent_class == 'pixel_size':
	408	self.detector.pixel_size.y = data_point
	409	self.detector.pixel_size_unit = unit
	410	elif tagname == 'z' and self.parent_class == 'pixel_size':
	411	self.detector.pixel_size.z = data_point
	412	self.detector.pixel_size_unit = unit
	413	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	414	self.detector.orientation.x = data_point
	415	self.detector.orientation_unit = unit
	416	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	417	self.detector.orientation.y = data_point
	418	self.detector.orientation_unit = unit
	419	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
	420	self.detector.orientation.z = data_point
	421	self.detector.orientation_unit = unit
[7477fb9]	422
[af08e55]	423	# Collimation and Aperture
[250fec92]	424	elif tagname == 'length' and self.parent_class == 'SAScollimation':
	425	self.collimation.length = data_point
	426	self.collimation.length_unit = unit
	427	elif tagname == 'name' and self.parent_class == 'SAScollimation':
	428	self.collimation.name = data_point
	429	elif tagname == 'distance' and self.parent_class == 'aperture':
	430	self.aperture.distance = data_point
	431	self.aperture.distance_unit = unit
	432	elif tagname == 'x' and self.parent_class == 'size':
	433	self.aperture.size.x = data_point
	434	self.collimation.size_unit = unit
	435	elif tagname == 'y' and self.parent_class == 'size':
	436	self.aperture.size.y = data_point
	437	self.collimation.size_unit = unit
	438	elif tagname == 'z' and self.parent_class == 'size':
	439	self.aperture.size.z = data_point
	440	self.collimation.size_unit = unit
	441
[af08e55]	442	# Process Information
[250fec92]	443	elif tagname == 'name' and self.parent_class == 'SASprocess':
	444	self.process.name = data_point
	445	elif tagname == 'description' and self.parent_class == 'SASprocess':
	446	self.process.description = data_point
	447	elif tagname == 'date' and self.parent_class == 'SASprocess':
	448	try:
	449	self.process.date = datetime.datetime.fromtimestamp(data_point)
	450	except:
	451	self.process.date = data_point
	452	elif tagname == 'SASprocessnote':
	453	self.process.notes.append(data_point)
	454	elif tagname == 'term' and self.parent_class == 'SASprocess':
[5f26aa4]	455	unit = attr.get("unit", "")
[7477fb9]	456	dic = { "name": name, "value": data_point, "unit": unit }
[5f26aa4]	457	self.process.term.append(dic)
[250fec92]	458
[af08e55]	459	# Transmission Spectrum
[250fec92]	460	elif tagname == 'T' and self.parent_class == 'Tdata':
	461	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
	462	self.transspectrum.transmission_unit = unit
	463	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
	464	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
	465	self.transspectrum.transmission_deviation_unit = unit
	466	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
	467	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
	468	self.transspectrum.wavelength_unit = unit
	469
[af08e55]	470	# Source Information
[250fec92]	471	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
	472	self.current_datainfo.source.wavelength = data_point
	473	self.current_datainfo.source.wavelength_unit = unit
	474	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
	475	self.current_datainfo.source.wavelength_min = data_point
	476	self.current_datainfo.source.wavelength_min_unit = unit
	477	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
	478	self.current_datainfo.source.wavelength_max = data_point
	479	self.current_datainfo.source.wavelength_max_unit = unit
	480	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
	481	self.current_datainfo.source.wavelength_spread = data_point
	482	self.current_datainfo.source.wavelength_spread_unit = unit
	483	elif tagname == 'x' and self.parent_class == 'beam_size':
	484	self.current_datainfo.source.beam_size.x = data_point
	485	self.current_datainfo.source.beam_size_unit = unit
	486	elif tagname == 'y' and self.parent_class == 'beam_size':
	487	self.current_datainfo.source.beam_size.y = data_point
	488	self.current_datainfo.source.beam_size_unit = unit
	489	elif tagname == 'z' and self.parent_class == 'pixel_size':
	490	self.current_datainfo.source.data_point.z = data_point
	491	self.current_datainfo.source.beam_size_unit = unit
	492	elif tagname == 'radiation' and self.parent_class == 'SASsource':
	493	self.current_datainfo.source.radiation = data_point
	494	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
	495	self.current_datainfo.source.beam_shape = data_point
	496
[af08e55]	497	# Everything else goes in meta_data
[250fec92]	498	else:
	499	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
	500	self.current_datainfo.meta_data[new_key] = data_point
	501
	502	self.names.remove(tagname_original)
	503	length = 0
	504	if len(self.names) > 1:
	505	length = len(self.names) - 1
	506	self.parent_class = self.names[length]
[654e8e0]	507	if not self._is_call_local() and not recurse:
	508	self.frm = ""
[7477fb9]	509	self.current_datainfo.errors = set()
	510	for error in self.errors:
	511	self.current_datainfo.errors.add(error)
	512	self.errors.clear()
	513	self.send_to_output()
[1686a333]	514	empty = None
	515	return self.output[0], empty
[250fec92]	516
[654e8e0]	517	def _is_call_local(self):
	518	if self.frm == "":
	519	inter = inspect.stack()
	520	self.frm = inter[2]
	521	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[1686a333]	522	mod_name = mod_name.replace(".py", "")
	523	mod = mod_name.split("sas/")
	524	mod_name = mod[1]
	525	if mod_name != "sascalc/dataloader/readers/cansas_reader":
	526	return False
	527	return True
	528
[7477fb9]	529	def _add_intermediate(self):
[250fec92]	530	"""
	531	This method stores any intermediate objects within the final data set after fully reading the set.
	532	"""
	533	if self.parent_class == 'SASprocess':
	534	self.current_datainfo.process.append(self.process)
	535	self.process = Process()
	536	elif self.parent_class == 'SASdetector':
	537	self.current_datainfo.detector.append(self.detector)
	538	self.detector = Detector()
	539	elif self.parent_class == 'SAStransmission_spectrum':
	540	self.current_datainfo.trans_spectrum.append(self.transspectrum)
	541	self.transspectrum = TransmissionSpectrum()
	542	elif self.parent_class == 'SAScollimation':
	543	self.current_datainfo.collimation.append(self.collimation)
	544	self.collimation = Collimation()
[5f26aa4]	545	elif self.parent_class == 'aperture':
[250fec92]	546	self.collimation.aperture.append(self.aperture)
	547	self.aperture = Aperture()
	548	elif self.parent_class == 'SASdata':
	549	self._check_for_empty_resolution()
	550	self.data.append(self.current_dataset)
	551
	552	def _get_node_value(self, node, tagname):
	553	"""
	554	Get the value of a node and any applicable units
	555
	556	:param node: The XML node to get the value of
	557	:param tagname: The tagname of the node
	558	"""
	559	#Get the text from the node and convert all whitespace to spaces
	560	units = ''
	561	node_value = node.text
	562	if node_value is not None:
	563	node_value = ' '.join(node_value.split())
	564	else:
	565	node_value = ""
	566
	567	# If the value is a float, compile with units.
	568	if self.ns_list.ns_datatype == "float":
	569	# If an empty value is given, set as zero.
	570	if node_value is None or node_value.isspace() \
	571	or node_value.lower() == "nan":
	572	node_value = "0.0"
	573	#Convert the value to the base units
	574	node_value, units = self._unit_conversion(node, tagname, node_value)
	575
	576	# If the value is a timestamp, convert to a datetime object
	577	elif self.ns_list.ns_datatype == "timestamp":
	578	if node_value is None or node_value.isspace():
	579	pass
	580	else:
	581	try:
	582	node_value = \
	583	datetime.datetime.fromtimestamp(node_value)
	584	except ValueError:
	585	node_value = None
	586	return node_value, units
	587
	588	def _unit_conversion(self, node, tagname, node_value):
[d26dea0]	589	"""
	590	A unit converter method used to convert the data included in the file
	591	to the default units listed in data_info
	592
[250fec92]	593	:param node: XML node
	594	:param tagname: name of the node
[d26dea0]	595	:param node_value: The value of the current dom node
	596	"""
	597	attr = node.attrib
	598	value_unit = ''
	599	err_msg = None
[682c432]	600	default_unit = None
[5f26aa4]	601	if not isinstance(node_value, float):
	602	node_value = float(node_value)
	603	if 'unit' in attr and attr.get('unit') is not None:
[d26dea0]	604	try:
	605	local_unit = attr['unit']
[250fec92]	606	unitname = self.ns_list.current_level.get("unit", "")
	607	if "SASdetector" in self.names:
	608	save_in = "detector"
	609	elif "aperture" in self.names:
	610	save_in = "aperture"
	611	elif "SAScollimation" in self.names:
	612	save_in = "collimation"
	613	elif "SAStransmission_spectrum" in self.names:
	614	save_in = "transspectrum"
	615	elif "SASdata" in self.names:
	616	x = np.zeros(1)
	617	y = np.zeros(1)
	618	self.current_data1d = Data1D(x, y)
	619	save_in = "current_data1d"
	620	elif "SASsource" in self.names:
	621	save_in = "current_datainfo.source"
	622	elif "SASsample" in self.names:
	623	save_in = "current_datainfo.sample"
	624	elif "SASprocess" in self.names:
	625	save_in = "process"
	626	else:
	627	save_in = "current_datainfo"
	628	exec "default_unit = self.{0}.{1}".format(save_in, unitname)
	629	if local_unit and default_unit and local_unit.lower() != default_unit.lower() \
[d26dea0]	630	and local_unit.lower() != "none":
	631	if HAS_CONVERTER == True:
[af08e55]	632	# Check local units - bad units raise KeyError
[d26dea0]	633	data_conv_q = Converter(local_unit)
	634	value_unit = default_unit
[682c432]	635	node_value = data_conv_q(node_value, units=default_unit)
[d26dea0]	636	else:
	637	value_unit = local_unit
	638	err_msg = "Unit converter is not available.\n"
	639	else:
	640	value_unit = local_unit
	641	except KeyError:
	642	err_msg = "CanSAS reader: unexpected "
	643	err_msg += "\"{0}\" unit [{1}]; "
	644	err_msg = err_msg.format(tagname, local_unit)
[682c432]	645	err_msg += "expecting [{0}]".format(default_unit)
[d26dea0]	646	value_unit = local_unit
	647	except:
	648	err_msg = "CanSAS reader: unknown error converting "
	649	err_msg += "\"{0}\" unit [{1}]"
	650	err_msg = err_msg.format(tagname, local_unit)
	651	value_unit = local_unit
	652	elif 'unit' in attr:
	653	value_unit = attr['unit']
	654	if err_msg:
	655	self.errors.add(err_msg)
	656	return node_value, value_unit
	657
[250fec92]	658	def _check_for_empty_resolution(self):
[d26dea0]	659	"""
[7477fb9]	660	a method to check all resolution data sets are the same size as I and q
	661	"""
	662	dql_exists = False
	663	dqw_exists = False
	664	dq_exists = False
	665	di_exists = False
	666	if self.current_dataset.dxl is not None:
	667	dql_exists = True
	668	if self.current_dataset.dxw is not None:
	669	dqw_exists = True
	670	if self.current_dataset.dx is not None:
	671	dq_exists = True
	672	if self.current_dataset.dy is not None:
	673	di_exists = True
	674	if dqw_exists and not dql_exists:
	675	array_size = self.current_dataset.dxw.size - 1
	676	self.current_dataset.dxl = np.append(self.current_dataset.dxl,
	677	np.zeros([array_size]))
	678	elif dql_exists and not dqw_exists:
	679	array_size = self.current_dataset.dxl.size - 1
	680	self.current_dataset.dxw = np.append(self.current_dataset.dxw,
	681	np.zeros([array_size]))
	682	elif not dql_exists and not dqw_exists and not dq_exists:
	683	array_size = self.current_dataset.x.size - 1
	684	self.current_dataset.dx = np.append(self.current_dataset.dx,
	685	np.zeros([array_size]))
	686	if not di_exists:
	687	array_size = self.current_dataset.y.size - 1
	688	self.current_dataset.dy = np.append(self.current_dataset.dy,
	689	np.zeros([array_size]))
[d26dea0]	690
[0b79323]	691	def _initialize_new_data_set(self, node=None):
	692	if node is not None:
	693	for child in node:
	694	if child.tag.replace(self.base_ns, "") == "Idata":
	695	for i_child in child:
	696	if i_child.tag.replace(self.base_ns, "") == "Qx":
	697	self.current_dataset = plottable_2D()
	698	return
	699	self.current_dataset = plottable_1D(np.array(0), np.array(0))
	700
	701	## Writing Methods
[250fec92]	702	def write(self, filename, datainfo):
[d26dea0]	703	"""
[250fec92]	704	Write the content of a Data1D as a CanSAS XML file
[d26dea0]	705
[250fec92]	706	:param filename: name of the file to write
	707	:param datainfo: Data1D object
	708	"""
	709	# Create XML document
	710	doc, _ = self._to_xml_doc(datainfo)
	711	# Write the file
	712	file_ref = open(filename, 'w')
[235f514]	713	if self.encoding is None:
[250fec92]	714	self.encoding = "UTF-8"
	715	doc.write(file_ref, encoding=self.encoding,
	716	pretty_print=True, xml_declaration=True)
	717	file_ref.close()
[d26dea0]	718
[250fec92]	719	def _to_xml_doc(self, datainfo):
[d26dea0]	720	"""
[250fec92]	721	Create an XML document to contain the content of a Data1D
[d26dea0]	722
[250fec92]	723	:param datainfo: Data1D object
[d26dea0]	724	"""
[af08e55]	725	is_2d = False
[83c09af]	726	if issubclass(datainfo.__class__, Data2D):
	727	is_2d = True
[d26dea0]	728
[250fec92]	729	# Get PIs and create root element
	730	pi_string = self._get_pi_string()
	731	# Define namespaces and create SASroot object
	732	main_node = self._create_main_node()
	733	# Create ElementTree, append SASroot and apply processing instructions
	734	base_string = pi_string + self.to_string(main_node)
	735	base_element = self.create_element_from_string(base_string)
	736	doc = self.create_tree(base_element)
	737	# Create SASentry Element
	738	entry_node = self.create_element("SASentry")
	739	root = doc.getroot()
	740	root.append(entry_node)
[d26dea0]	741
[250fec92]	742	# Add Title to SASentry
	743	self.write_node(entry_node, "Title", datainfo.title)
	744	# Add Run to SASentry
	745	self._write_run_names(datainfo, entry_node)
	746	# Add Data info to SASEntry
[83c09af]	747	if is_2d:
	748	self._write_data_2d(datainfo, entry_node)
	749	else:
	750	self._write_data(datainfo, entry_node)
[250fec92]	751	# Transmission Spectrum Info
[8434365]	752	# TODO: fix the writer to linearize all data, including T_spectrum
	753	# self._write_trans_spectrum(datainfo, entry_node)
[250fec92]	754	# Sample info
	755	self._write_sample_info(datainfo, entry_node)
	756	# Instrument info
	757	instr = self._write_instrument(datainfo, entry_node)
	758	# Source
	759	self._write_source(datainfo, instr)
	760	# Collimation
	761	self._write_collimation(datainfo, instr)
	762	# Detectors
	763	self._write_detectors(datainfo, instr)
	764	# Processes info
	765	self._write_process_notes(datainfo, entry_node)
	766	# Note info
	767	self._write_notes(datainfo, entry_node)
	768	# Return the document, and the SASentry node associated with
	769	# the data we just wrote
	770	# If the calling function was not the cansas reader, return a minidom
	771	# object rather than an lxml object.
[654e8e0]	772	self.frm = inspect.stack()[1]
	773	doc, entry_node = self._check_origin(entry_node, doc)
[250fec92]	774	return doc, entry_node
[d26dea0]	775
[250fec92]	776	def write_node(self, parent, name, value, attr=None):
	777	"""
	778	:param doc: document DOM
	779	:param parent: parent node
	780	:param name: tag of the element
	781	:param value: value of the child text node
	782	:param attr: attribute dictionary
[d26dea0]	783
[250fec92]	784	:return: True if something was appended, otherwise False
	785	"""
	786	if value is not None:
	787	parent = self.ebuilder(parent, name, value, attr)
	788	return True
	789	return False
[d26dea0]	790
	791	def _get_pi_string(self):
	792	"""
	793	Creates the processing instructions header for writing to file
	794	"""
	795	pis = self.return_processing_instructions()
	796	if len(pis) > 0:
	797	pi_tree = self.create_tree(pis[0])
	798	i = 1
	799	for i in range(1, len(pis) - 1):
	800	pi_tree = self.append(pis[i], pi_tree)
	801	pi_string = self.to_string(pi_tree)
	802	else:
	803	pi_string = ""
	804	return pi_string
	805
	806	def _create_main_node(self):
	807	"""
	808	Creates the primary xml header used when writing to file
	809	"""
	810	xsi = "http://www.w3.org/2001/XMLSchema-instance"
	811	version = self.cansas_version
	812	n_s = CANSAS_NS.get(version).get("ns")
	813	if version == "1.1":
	814	url = "http://www.cansas.org/formats/1.1/"
	815	else:
	816	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
	817	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
	818	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
	819	"version" : version}
	820	nsmap = {'xsi' : xsi, None: n_s}
	821
	822	main_node = self.create_element("{" + n_s + "}SASroot",
	823	attrib=attrib, nsmap=nsmap)
	824	return main_node
	825
	826	def _write_run_names(self, datainfo, entry_node):
	827	"""
	828	Writes the run names to the XML file
	829
	830	:param datainfo: The Data1D object the information is coming from
	831	:param entry_node: lxml node ElementTree object to be appended to
	832	"""
[235f514]	833	if datainfo.run is None or datainfo.run == []:
[d26dea0]	834	datainfo.run.append(RUN_NAME_DEFAULT)
	835	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
	836	for item in datainfo.run:
	837	runname = {}
	838	if item in datainfo.run_name and \
	839	len(str(datainfo.run_name[item])) > 1:
	840	runname = {'name': datainfo.run_name[item]}
	841	self.write_node(entry_node, "Run", item, runname)
	842
	843	def _write_data(self, datainfo, entry_node):
	844	"""
[83c09af]	845	Writes 1D I and Q data to the XML file
[d26dea0]	846
	847	:param datainfo: The Data1D object the information is coming from
	848	:param entry_node: lxml node ElementTree object to be appended to
	849	"""
	850	node = self.create_element("SASdata")
	851	self.append(node, entry_node)
	852
	853	for i in range(len(datainfo.x)):
	854	point = self.create_element("Idata")
	855	node.append(point)
	856	self.write_node(point, "Q", datainfo.x[i],
[ad4632c]	857	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[d26dea0]	858	if len(datainfo.y) >= i:
	859	self.write_node(point, "I", datainfo.y[i],
[ad4632c]	860	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	861	if datainfo.dy is not None and len(datainfo.dy) > i:
[d26dea0]	862	self.write_node(point, "Idev", datainfo.dy[i],
[ad4632c]	863	{'unit': datainfo._yaxis + " \| " + datainfo._yunit})
[5f26aa4]	864	if datainfo.dx is not None and len(datainfo.dx) > i:
[d26dea0]	865	self.write_node(point, "Qdev", datainfo.dx[i],
[ad4632c]	866	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	867	if datainfo.dxw is not None and len(datainfo.dxw) > i:
[d26dea0]	868	self.write_node(point, "dQw", datainfo.dxw[i],
[ad4632c]	869	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
[5f26aa4]	870	if datainfo.dxl is not None and len(datainfo.dxl) > i:
[d26dea0]	871	self.write_node(point, "dQl", datainfo.dxl[i],
[ad4632c]	872	{'unit': datainfo._xaxis + " \| " + datainfo._xunit})
	873	if datainfo.isSesans:
	874	sesans = self.create_element("Sesans")
	875	sesans.text = str(datainfo.isSesans)
	876	node.append(sesans)
[63d773c]	877	self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0],
	878	{'unit': datainfo.sample.yacceptance[1]})
[ad4632c]	879	self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0],
	880	{'unit': datainfo.sample.zacceptance[1]})
	881
[d26dea0]	882
[83c09af]	883	def _write_data_2d(self, datainfo, entry_node):
	884	"""
	885	Writes 2D data to the XML file
	886
	887	:param datainfo: The Data2D object the information is coming from
	888	:param entry_node: lxml node ElementTree object to be appended to
	889	"""
[af08e55]	890	attr = {}
	891	if datainfo.data.shape:
[1905128]	892	attr["x_bins"] = str(len(datainfo.x_bins))
	893	attr["y_bins"] = str(len(datainfo.y_bins))
	894	node = self.create_element("SASdata", attr)
[83c09af]	895	self.append(node, entry_node)
	896
[1905128]	897	point = self.create_element("Idata")
	898	node.append(point)
	899	qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))])
	900	qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))])
	901	intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))])
	902
	903	self.write_node(point, "Qx", qx,
	904	{'unit': datainfo._xunit})
	905	self.write_node(point, "Qy", qy,
	906	{'unit': datainfo._yunit})
	907	self.write_node(point, "I", intensity,
	908	{'unit': datainfo._zunit})
	909	if datainfo.err_data is not None:
[5e6df0e]	910	err = ','.join([str(datainfo.err_data[i]) for i in
	911	xrange(len(datainfo.err_data))])
[1905128]	912	self.write_node(point, "Idev", err,
[83c09af]	913	{'unit': datainfo._zunit})
[1905128]	914	if datainfo.dqy_data is not None:
[5e6df0e]	915	dqy = ','.join([str(datainfo.dqy_data[i]) for i in
	916	xrange(len(datainfo.dqy_data))])
[1905128]	917	self.write_node(point, "Qydev", dqy,
	918	{'unit': datainfo._yunit})
	919	if datainfo.dqx_data is not None:
[5e6df0e]	920	dqx = ','.join([str(datainfo.dqx_data[i]) for i in
	921	xrange(len(datainfo.dqx_data))])
[1905128]	922	self.write_node(point, "Qxdev", dqx,
	923	{'unit': datainfo._xunit})
	924	if datainfo.mask is not None:
[5e6df0e]	925	mask = ','.join(
[bcabf4e]	926	["1" if datainfo.mask[i] else "0"
	927	for i in xrange(len(datainfo.mask))])
[1905128]	928	self.write_node(point, "Mask", mask)
[83c09af]	929
[d26dea0]	930	def _write_trans_spectrum(self, datainfo, entry_node):
	931	"""
	932	Writes the transmission spectrum data to the XML file
	933
	934	:param datainfo: The Data1D object the information is coming from
	935	:param entry_node: lxml node ElementTree object to be appended to
	936	"""
	937	for i in range(len(datainfo.trans_spectrum)):
	938	spectrum = datainfo.trans_spectrum[i]
	939	node = self.create_element("SAStransmission_spectrum",
	940	{"name" : spectrum.name})
	941	self.append(node, entry_node)
	942	if isinstance(spectrum.timestamp, datetime.datetime):
	943	node.setAttribute("timestamp", spectrum.timestamp)
	944	for i in range(len(spectrum.wavelength)):
	945	point = self.create_element("Tdata")
	946	node.append(point)
	947	self.write_node(point, "Lambda", spectrum.wavelength[i],
	948	{'unit': spectrum.wavelength_unit})
	949	self.write_node(point, "T", spectrum.transmission[i],
	950	{'unit': spectrum.transmission_unit})
[7432acb]	951	if spectrum.transmission_deviation is not None \
[d26dea0]	952	and len(spectrum.transmission_deviation) >= i:
	953	self.write_node(point, "Tdev",
	954	spectrum.transmission_deviation[i],
	955	{'unit':
	956	spectrum.transmission_deviation_unit})
	957
	958	def _write_sample_info(self, datainfo, entry_node):
	959	"""
	960	Writes the sample information to the XML file
	961
	962	:param datainfo: The Data1D object the information is coming from
	963	:param entry_node: lxml node ElementTree object to be appended to
	964	"""
	965	sample = self.create_element("SASsample")
	966	if datainfo.sample.name is not None:
	967	self.write_attribute(sample, "name",
	968	str(datainfo.sample.name))
	969	self.append(sample, entry_node)
	970	self.write_node(sample, "ID", str(datainfo.sample.ID))
	971	self.write_node(sample, "thickness", datainfo.sample.thickness,
	972	{"unit": datainfo.sample.thickness_unit})
	973	self.write_node(sample, "transmission", datainfo.sample.transmission)
	974	self.write_node(sample, "temperature", datainfo.sample.temperature,
	975	{"unit": datainfo.sample.temperature_unit})
	976
	977	pos = self.create_element("position")
	978	written = self.write_node(pos,
	979	"x",
	980	datainfo.sample.position.x,
	981	{"unit": datainfo.sample.position_unit})
	982	written = written \| self.write_node( \
	983	pos, "y", datainfo.sample.position.y,
	984	{"unit": datainfo.sample.position_unit})
	985	written = written \| self.write_node( \
	986	pos, "z", datainfo.sample.position.z,
	987	{"unit": datainfo.sample.position_unit})
	988	if written == True:
	989	self.append(pos, sample)
	990
	991	ori = self.create_element("orientation")
	992	written = self.write_node(ori, "roll",
	993	datainfo.sample.orientation.x,
	994	{"unit": datainfo.sample.orientation_unit})
	995	written = written \| self.write_node( \
	996	ori, "pitch", datainfo.sample.orientation.y,
	997	{"unit": datainfo.sample.orientation_unit})
	998	written = written \| self.write_node( \
	999	ori, "yaw", datainfo.sample.orientation.z,
	1000	{"unit": datainfo.sample.orientation_unit})
	1001	if written == True:
	1002	self.append(ori, sample)
	1003
	1004	for item in datainfo.sample.details:
	1005	self.write_node(sample, "details", item)
	1006
	1007	def _write_instrument(self, datainfo, entry_node):
	1008	"""
	1009	Writes the instrumental information to the XML file
	1010
	1011	:param datainfo: The Data1D object the information is coming from
	1012	:param entry_node: lxml node ElementTree object to be appended to
	1013	"""
	1014	instr = self.create_element("SASinstrument")
	1015	self.append(instr, entry_node)
	1016	self.write_node(instr, "name", datainfo.instrument)
	1017	return instr
	1018
	1019	def _write_source(self, datainfo, instr):
	1020	"""
	1021	Writes the source information to the XML file
	1022
	1023	:param datainfo: The Data1D object the information is coming from
	1024	:param instr: instrument node to be appended to
	1025	"""
	1026	source = self.create_element("SASsource")
	1027	if datainfo.source.name is not None:
	1028	self.write_attribute(source, "name",
	1029	str(datainfo.source.name))
	1030	self.append(source, instr)
[235f514]	1031	if datainfo.source.radiation is None or datainfo.source.radiation == '':
[d26dea0]	1032	datainfo.source.radiation = "neutron"
	1033	self.write_node(source, "radiation", datainfo.source.radiation)
	1034
	1035	size = self.create_element("beam_size")
	1036	if datainfo.source.beam_size_name is not None:
	1037	self.write_attribute(size, "name",
	1038	str(datainfo.source.beam_size_name))
	1039	written = self.write_node( \
	1040	size, "x", datainfo.source.beam_size.x,
	1041	{"unit": datainfo.source.beam_size_unit})
	1042	written = written \| self.write_node( \
	1043	size, "y", datainfo.source.beam_size.y,
	1044	{"unit": datainfo.source.beam_size_unit})
	1045	written = written \| self.write_node( \
	1046	size, "z", datainfo.source.beam_size.z,
	1047	{"unit": datainfo.source.beam_size_unit})
	1048	if written == True:
	1049	self.append(size, source)
	1050
	1051	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
	1052	self.write_node(source, "wavelength",
	1053	datainfo.source.wavelength,
	1054	{"unit": datainfo.source.wavelength_unit})
	1055	self.write_node(source, "wavelength_min",
	1056	datainfo.source.wavelength_min,
	1057	{"unit": datainfo.source.wavelength_min_unit})
	1058	self.write_node(source, "wavelength_max",
	1059	datainfo.source.wavelength_max,
	1060	{"unit": datainfo.source.wavelength_max_unit})
	1061	self.write_node(source, "wavelength_spread",
	1062	datainfo.source.wavelength_spread,
	1063	{"unit": datainfo.source.wavelength_spread_unit})
	1064
	1065	def _write_collimation(self, datainfo, instr):
	1066	"""
	1067	Writes the collimation information to the XML file
	1068
	1069	:param datainfo: The Data1D object the information is coming from
	1070	:param instr: lxml node ElementTree object to be appended to
	1071	"""
[235f514]	1072	if datainfo.collimation == [] or datainfo.collimation is None:
[d26dea0]	1073	coll = Collimation()
	1074	datainfo.collimation.append(coll)
	1075	for item in datainfo.collimation:
	1076	coll = self.create_element("SAScollimation")
	1077	if item.name is not None:
	1078	self.write_attribute(coll, "name", str(item.name))
	1079	self.append(coll, instr)
	1080
	1081	self.write_node(coll, "length", item.length,
	1082	{"unit": item.length_unit})
	1083
	1084	for aperture in item.aperture:
	1085	apert = self.create_element("aperture")
	1086	if aperture.name is not None:
	1087	self.write_attribute(apert, "name", str(aperture.name))
	1088	if aperture.type is not None:
	1089	self.write_attribute(apert, "type", str(aperture.type))
	1090	self.append(apert, coll)
	1091
	1092	size = self.create_element("size")
	1093	if aperture.size_name is not None:
	1094	self.write_attribute(size, "name",
	1095	str(aperture.size_name))
	1096	written = self.write_node(size, "x", aperture.size.x,
	1097	{"unit": aperture.size_unit})
	1098	written = written \| self.write_node( \
	1099	size, "y", aperture.size.y,
	1100	{"unit": aperture.size_unit})
	1101	written = written \| self.write_node( \
	1102	size, "z", aperture.size.z,
	1103	{"unit": aperture.size_unit})
	1104	if written == True:
	1105	self.append(size, apert)
	1106
	1107	self.write_node(apert, "distance", aperture.distance,
	1108	{"unit": aperture.distance_unit})
	1109
	1110	def _write_detectors(self, datainfo, instr):
	1111	"""
	1112	Writes the detector information to the XML file
	1113
	1114	:param datainfo: The Data1D object the information is coming from
	1115	:param inst: lxml instrument node to be appended to
	1116	"""
[235f514]	1117	if datainfo.detector is None or datainfo.detector == []:
[d26dea0]	1118	det = Detector()
	1119	det.name = ""
	1120	datainfo.detector.append(det)
	1121
	1122	for item in datainfo.detector:
	1123	det = self.create_element("SASdetector")
	1124	written = self.write_node(det, "name", item.name)
	1125	written = written \| self.write_node(det, "SDD", item.distance,
	1126	{"unit": item.distance_unit})
	1127	if written == True:
	1128	self.append(det, instr)
	1129
	1130	off = self.create_element("offset")
	1131	written = self.write_node(off, "x", item.offset.x,
	1132	{"unit": item.offset_unit})
	1133	written = written \| self.write_node(off, "y", item.offset.y,
	1134	{"unit": item.offset_unit})
	1135	written = written \| self.write_node(off, "z", item.offset.z,
	1136	{"unit": item.offset_unit})
	1137	if written == True:
	1138	self.append(off, det)
	1139
	1140	ori = self.create_element("orientation")
	1141	written = self.write_node(ori, "roll", item.orientation.x,
	1142	{"unit": item.orientation_unit})
	1143	written = written \| self.write_node(ori, "pitch",
	1144	item.orientation.y,
	1145	{"unit": item.orientation_unit})
	1146	written = written \| self.write_node(ori, "yaw",
	1147	item.orientation.z,
	1148	{"unit": item.orientation_unit})
	1149	if written == True:
	1150	self.append(ori, det)
	1151
	1152	center = self.create_element("beam_center")
	1153	written = self.write_node(center, "x", item.beam_center.x,
	1154	{"unit": item.beam_center_unit})
	1155	written = written \| self.write_node(center, "y",
	1156	item.beam_center.y,
	1157	{"unit": item.beam_center_unit})
	1158	written = written \| self.write_node(center, "z",
	1159	item.beam_center.z,
	1160	{"unit": item.beam_center_unit})
	1161	if written == True:
	1162	self.append(center, det)
	1163
	1164	pix = self.create_element("pixel_size")
	1165	written = self.write_node(pix, "x", item.pixel_size.x,
	1166	{"unit": item.pixel_size_unit})
	1167	written = written \| self.write_node(pix, "y", item.pixel_size.y,
	1168	{"unit": item.pixel_size_unit})
	1169	written = written \| self.write_node(pix, "z", item.pixel_size.z,
	1170	{"unit": item.pixel_size_unit})
	1171	if written == True:
	1172	self.append(pix, det)
[3a9801f]	1173	self.write_node(det, "slit_length", item.slit_length,
	1174	{"unit": item.slit_length_unit})
	1175
[d26dea0]	1176
	1177	def _write_process_notes(self, datainfo, entry_node):
	1178	"""
	1179	Writes the process notes to the XML file
	1180
	1181	:param datainfo: The Data1D object the information is coming from
	1182	:param entry_node: lxml node ElementTree object to be appended to
	1183
	1184	"""
	1185	for item in datainfo.process:
	1186	node = self.create_element("SASprocess")
	1187	self.append(node, entry_node)
	1188	self.write_node(node, "name", item.name)
	1189	self.write_node(node, "date", item.date)
	1190	self.write_node(node, "description", item.description)
	1191	for term in item.term:
[1686a333]	1192	if isinstance(term, list):
	1193	value = term['value']
	1194	del term['value']
[5f26aa4]	1195	elif isinstance(term, dict):
	1196	value = term.get("value")
	1197	del term['value']
[1686a333]	1198	else:
	1199	value = term
[d26dea0]	1200	self.write_node(node, "term", value, term)
	1201	for note in item.notes:
	1202	self.write_node(node, "SASprocessnote", note)
	1203	if len(item.notes) == 0:
	1204	self.write_node(node, "SASprocessnote", "")
	1205
	1206	def _write_notes(self, datainfo, entry_node):
	1207	"""
	1208	Writes the notes to the XML file and creates an empty note if none
	1209	exist
	1210
	1211	:param datainfo: The Data1D object the information is coming from
	1212	:param entry_node: lxml node ElementTree object to be appended to
	1213
	1214	"""
	1215	if len(datainfo.notes) == 0:
	1216	node = self.create_element("SASnote")
	1217	self.append(node, entry_node)
	1218	else:
	1219	for item in datainfo.notes:
	1220	node = self.create_element("SASnote")
	1221	self.write_text(node, item)
	1222	self.append(node, entry_node)
	1223
[654e8e0]	1224	def _check_origin(self, entry_node, doc):
[d26dea0]	1225	"""
	1226	Return the document, and the SASentry node associated with
	1227	the data we just wrote.
	1228	If the calling function was not the cansas reader, return a minidom
	1229	object rather than an lxml object.
	1230
	1231	:param entry_node: lxml node ElementTree object to be appended to
	1232	:param doc: entire xml tree
	1233	"""
[654e8e0]	1234	if not self.frm:
	1235	self.frm = inspect.stack()[1]
	1236	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
[d26dea0]	1237	mod_name = mod_name.replace(".py", "")
	1238	mod = mod_name.split("sas/")
	1239	mod_name = mod[1]
[45d90b9]	1240	if mod_name != "sascalc/dataloader/readers/cansas_reader":
[d26dea0]	1241	string = self.to_string(doc, pretty_print=False)
	1242	doc = parseString(string)
	1243	node_name = entry_node.tag
	1244	node_list = doc.getElementsByTagName(node_name)
	1245	entry_node = node_list.item(0)
[5ce7f17]	1246	return doc, entry_node
[d26dea0]	1247
	1248	# DO NOT REMOVE - used in saving and loading panel states.
	1249	def _store_float(self, location, node, variable, storage, optional=True):
	1250	"""
	1251	Get the content of a xpath location and store
	1252	the result. Check that the units are compatible
	1253	with the destination. The value is expected to
	1254	be a float.
	1255
	1256	The xpath location might or might not exist.
	1257	If it does not exist, nothing is done
	1258
	1259	:param location: xpath location to fetch
	1260	:param node: node to read the data from
	1261	:param variable: name of the data member to store it in [string]
	1262	:param storage: data object that has the 'variable' data member
	1263	:param optional: if True, no exception will be raised
	1264	if unit conversion can't be done
	1265
	1266	:raise ValueError: raised when the units are not recognized
	1267	"""
	1268	entry = get_content(location, node)
	1269	try:
	1270	value = float(entry.text)
	1271	except:
	1272	value = None
	1273
	1274	if value is not None:
	1275	# If the entry has units, check to see that they are
	1276	# compatible with what we currently have in the data object
	1277	units = entry.get('unit')
	1278	if units is not None:
	1279	toks = variable.split('.')
	1280	local_unit = None
	1281	exec "local_unit = storage.%s_unit" % toks[0]
[7432acb]	1282	if local_unit is not None and units.lower() != local_unit.lower():
[d26dea0]	1283	if HAS_CONVERTER == True:
	1284	try:
	1285	conv = Converter(units)
	1286	exec "storage.%s = %g" % \
	1287	(variable, conv(value, units=local_unit))
	1288	except:
	1289	_, exc_value, _ = sys.exc_info()
	1290	err_mess = "CanSAS reader: could not convert"
	1291	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
	1292	% (variable, units, local_unit, exc_value)
	1293	self.errors.add(err_mess)
	1294	if optional:
[c155a16]	1295	logger.info(err_mess)
[d26dea0]	1296	else:
	1297	raise ValueError, err_mess
	1298	else:
	1299	err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
	1300	% (variable, units)
	1301	err_mess += " expecting [%s]" % local_unit
	1302	self.errors.add(err_mess)
	1303	if optional:
[c155a16]	1304	logger.info(err_mess)
[d26dea0]	1305	else:
	1306	raise ValueError, err_mess
	1307	else:
	1308	exec "storage.%s = value" % variable
	1309	else:
	1310	exec "storage.%s = value" % variable
	1311
	1312	# DO NOT REMOVE - used in saving and loading panel states.
	1313	def _store_content(self, location, node, variable, storage):
	1314	"""
	1315	Get the content of a xpath location and store
	1316	the result. The value is treated as a string.
	1317
	1318	The xpath location might or might not exist.
	1319	If it does not exist, nothing is done
	1320
	1321	:param location: xpath location to fetch
	1322	:param node: node to read the data from
	1323	:param variable: name of the data member to store it in [string]
	1324	:param storage: data object that has the 'variable' data member
	1325
	1326	:return: return a list of errors
	1327	"""
	1328	entry = get_content(location, node)
	1329	if entry is not None and entry.text is not None:
	1330	exec "storage.%s = entry.text.strip()" % variable
[250fec92]	1331
	1332	# DO NOT REMOVE Called by outside packages:
	1333	# sas.sasgui.perspectives.invariant.invariant_state
	1334	# sas.sasgui.perspectives.fitting.pagestate
	1335	def get_content(location, node):
	1336	"""
	1337	Get the first instance of the content of a xpath location.
	1338
	1339	:param location: xpath location
	1340	:param node: node to start at
	1341
	1342	:return: Element, or None
	1343	"""
	1344	nodes = node.xpath(location,
	1345	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
	1346	if len(nodes) > 0:
	1347	return nodes[0]
	1348	else:
	1349	return None
	1350
	1351	# DO NOT REMOVE Called by outside packages:
	1352	# sas.sasgui.perspectives.fitting.pagestate
	1353	def write_node(doc, parent, name, value, attr=None):
	1354	"""
	1355	:param doc: document DOM
	1356	:param parent: parent node
	1357	:param name: tag of the element
	1358	:param value: value of the child text node
	1359	:param attr: attribute dictionary
	1360
	1361	:return: True if something was appended, otherwise False
	1362	"""
	1363	if attr is None:
	1364	attr = {}
	1365	if value is not None:
	1366	node = doc.createElement(name)
	1367	node.appendChild(doc.createTextNode(str(value)))
	1368	for item in attr:
	1369	node.setAttribute(item, attr[item])
	1370	parent.appendChild(node)
	1371	return True
	1372	return False

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 3b0f8cc

Download in other formats: