cansas_reader.py @ 32e8c78

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalccostrafo411magnetic_scattrelease-4.1.1release-4.1.2release-4.2.2release_4.0.1ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since 32e8c78 was fe78c7b, checked in by Mathieu Doucet <doucetm@…>, 15 years ago
DataLoader?: exception no longer raised when units are wrong for an entry; the entry is not loaded and an error is logged instead. Loader info is now stored.
Property mode set to `100644`
File size: 35.9 KB

Rev	Line
[8780e9a]	1	"""
	2	This software was developed by the University of Tennessee as part of the
	3	Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	4	project funded by the US National Science Foundation.
	5
	6	See the license text in license.txt
	7
[b0d0723]	8	copyright 2008, 2009, University of Tennessee
[8780e9a]	9	"""
[579ba85]	10	# Known issue: reader not compatible with multiple SASdata entries
	11	# within a single SASentry. Will raise a runtime error.
[8780e9a]	12
[4c00964]	13	#TODO: check that all vectors are written only if they have at least one non-empty value
[579ba85]	14	#TODO: Writing only allows one SASentry per file. Would be best to allow multiple entries.
[8780e9a]	15	#TODO: Store error list
	16	#TODO: Allow for additional meta data for each section
	17	#TODO: Notes need to be implemented. They can be any XML structure in version 1.0
	18	# Process notes have the same problem.
[e390933]	19	#TODO: Unit conversion is not complete (temperature units are missing)
[8780e9a]	20
	21
	22	import logging
	23	import numpy
	24	import os, sys
[d6513cd]	25	from DataLoader.data_info import Data1D, Collimation, Detector, Process, Aperture
[b0d0723]	26	from lxml import etree
	27	import xml.dom.minidom
[8780e9a]	28
[b39c817]	29	has_converter = True
	30	try:
	31	from data_util.nxsunit import Converter
	32	except:
	33	has_converter = False
	34
[b0d0723]	35	CANSAS_NS = "cansas1d/1.0"
	36
[4c00964]	37	def write_node(doc, parent, name, value, attr={}):
	38	"""
	39	@param doc: document DOM
	40	@param parent: parent node
	41	@param name: tag of the element
	42	@param value: value of the child text node
	43	@param attr: attribute dictionary
	44	@return: True if something was appended, otherwise False
	45	"""
	46	if value is not None:
	47	node = doc.createElement(name)
	48	node.appendChild(doc.createTextNode(str(value)))
	49	for item in attr:
	50	node.setAttribute(item, attr[item])
	51	parent.appendChild(node)
	52	return True
	53	return False
	54
[8780e9a]	55	def get_content(location, node):
	56	"""
	57	Get the first instance of the content of a xpath location
	58
	59	@param location: xpath location
	60	@param node: node to start at
[b0d0723]	61	@return: Element, or None
[8780e9a]	62	"""
[b0d0723]	63	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
	64
[8780e9a]	65	if len(nodes)>0:
[b0d0723]	66	return nodes[0]
	67	else:
	68	return None
[8780e9a]	69
	70	def get_float(location, node):
	71	"""
[b0d0723]	72	Get the content of a node as a float
[8780e9a]	73
	74	@param location: xpath location
	75	@param node: node to start at
	76	"""
[b0d0723]	77	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
	78
[8780e9a]	79	value = None
	80	attr = {}
[b0d0723]	81
	82	if len(nodes)>0:
[8780e9a]	83	try:
[b0d0723]	84	value = float(nodes[0].text)
[8780e9a]	85	except:
	86	# Could not pass, skip and return None
[b0d0723]	87	logging.error("cansas_reader.get_float: could not convert '%s' to float" % nodes[0].text)
[8780e9a]	88
[b0d0723]	89	if nodes[0].get('unit') is not None:
	90	attr['unit'] = nodes[0].get('unit')
	91
[8780e9a]	92	return value, attr
	93
[b39c817]	94
[8780e9a]	95
	96	class Reader:
	97	"""
	98	Class to load cansas 1D XML files
	99
	100	Dependencies:
	101	The CanSas reader requires PyXML 0.8.4 or later.
	102	"""
	103	## CanSAS version
	104	version = '1.0'
	105	## File type
[28caa03]	106	type_name = "CanSAS 1D"
	107	## Wildcards
[8780e9a]	108	type = ["CanSAS 1D files (.xml)\|.xml"]
	109	## List of allowed extensions
	110	ext=['.xml', '.XML']
	111
[fe78c7b]	112	def __init__(self):
	113	## List of errors
	114	self.errors = []
	115
[8780e9a]	116	def read(self, path):
	117	"""
	118	Load data file
	119
	120	@param path: file path
	121	@return: Data1D object if a single SASentry was found,
	122	or a list of Data1D objects if multiple entries were found,
	123	or None of nothing was found
	124	@raise RuntimeError: when the file can't be opened
	125	@raise ValueError: when the length of the data vectors are inconsistent
	126	"""
	127	output = []
	128
	129	if os.path.isfile(path):
	130	basename = os.path.basename(path)
	131	root, extension = os.path.splitext(basename)
	132	if extension.lower() in self.ext:
	133
[b0d0723]	134	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
[8780e9a]	135	# Check the format version number
[b0d0723]	136	# Specifying the namespace will take care of the file format version
	137	root = tree.getroot()
	138
	139	entry_list = root.xpath('/ns:SASroot/ns:SASentry', namespaces={'ns': CANSAS_NS})
[8780e9a]	140
	141	for entry in entry_list:
[fe78c7b]	142	self.errors = []
[8780e9a]	143	sas_entry = self._parse_entry(entry)
	144	sas_entry.filename = basename
[fe78c7b]	145
	146	# Store loading process information
	147	sas_entry.errors = self.errors
	148	sas_entry.meta_data['loader'] = self.type_name
[8780e9a]	149	output.append(sas_entry)
	150
	151	else:
	152	raise RuntimeError, "%s is not a file" % path
	153
	154	# Return output consistent with the loader's api
	155	if len(output)==0:
	156	return None
	157	elif len(output)==1:
	158	return output[0]
	159	else:
	160	return output
	161
	162	def _parse_entry(self, dom):
	163	"""
	164	Parse a SASentry
	165
	166	@param node: SASentry node
	167	@return: Data1D object
	168	"""
	169	x = numpy.zeros(0)
	170	y = numpy.zeros(0)
	171
	172	data_info = Data1D(x, y)
	173
[b0d0723]	174	# Look up title
[fe78c7b]	175	self._store_content('ns:Title', dom, 'title', data_info)
[b0d0723]	176
[579ba85]	177	# Look up run number
[b0d0723]	178	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
[579ba85]	179	for item in nodes:
[b0d0723]	180	if item.text is not None:
	181	value = item.text.strip()
	182	if len(value) > 0:
	183	data_info.run.append(value)
	184	if item.get('name') is not None:
	185	data_info.run_name[value] = item.get('name')
[579ba85]	186
[8780e9a]	187	# Look up instrument name
[fe78c7b]	188	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
[8780e9a]	189
[b0d0723]	190	# Notes
	191	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
[8780e9a]	192	for note in note_list:
	193	try:
[b0d0723]	194	if note.text is not None:
	195	note_value = note.text.strip()
	196	if len(note_value) > 0:
	197	data_info.notes.append(note_value)
[8780e9a]	198	except:
[fe78c7b]	199	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
	200	self.errors.append(err_mess)
	201	logging.error(err_mess)
[8780e9a]	202
	203	# Sample info ###################
[b0d0723]	204	entry = get_content('ns:SASsample', dom)
	205	if entry is not None:
	206	data_info.sample.name = entry.get('name')
[579ba85]	207
[fe78c7b]	208	self._store_content('ns:SASsample/ns:ID',
[8780e9a]	209	dom, 'ID', data_info.sample)
[fe78c7b]	210	self._store_float('ns:SASsample/ns:thickness',
[8780e9a]	211	dom, 'thickness', data_info.sample)
[fe78c7b]	212	self._store_float('ns:SASsample/ns:transmission',
[8780e9a]	213	dom, 'transmission', data_info.sample)
[fe78c7b]	214	self._store_float('ns:SASsample/ns:temperature',
[8780e9a]	215	dom, 'temperature', data_info.sample)
[b0d0723]	216
	217	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
[8780e9a]	218	for item in nodes:
	219	try:
[b0d0723]	220	if item.text is not None:
	221	detail_value = item.text.strip()
	222	if len(detail_value) > 0:
	223	data_info.sample.details.append(detail_value)
[8780e9a]	224	except:
[fe78c7b]	225	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
	226	self.errors.append(err_mess)
	227	logging.error(err_mess)
[8780e9a]	228
	229	# Position (as a vector)
[fe78c7b]	230	self._store_float('ns:SASsample/ns:position/ns:x',
[8780e9a]	231	dom, 'position.x', data_info.sample)
[fe78c7b]	232	self._store_float('ns:SASsample/ns:position/ns:y',
[8780e9a]	233	dom, 'position.y', data_info.sample)
[fe78c7b]	234	self._store_float('ns:SASsample/ns:position/ns:z',
[8780e9a]	235	dom, 'position.z', data_info.sample)
	236
	237	# Orientation (as a vector)
[fe78c7b]	238	self._store_float('ns:SASsample/ns:orientation/ns:roll',
[8780e9a]	239	dom, 'orientation.x', data_info.sample)
[fe78c7b]	240	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
[8780e9a]	241	dom, 'orientation.y', data_info.sample)
[fe78c7b]	242	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
[8780e9a]	243	dom, 'orientation.z', data_info.sample)
	244
	245	# Source info ###################
[b0d0723]	246	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
	247	if entry is not None:
	248	data_info.source.name = entry.get('name')
[4c00964]	249
[fe78c7b]	250	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
[8780e9a]	251	dom, 'radiation', data_info.source)
[fe78c7b]	252	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
[8780e9a]	253	dom, 'beam_shape', data_info.source)
[fe78c7b]	254	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
[8780e9a]	255	dom, 'wavelength', data_info.source)
[fe78c7b]	256	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
[8780e9a]	257	dom, 'wavelength_min', data_info.source)
[fe78c7b]	258	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
[8780e9a]	259	dom, 'wavelength_max', data_info.source)
[fe78c7b]	260	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
[8780e9a]	261	dom, 'wavelength_spread', data_info.source)
	262
[579ba85]	263	# Beam size (as a vector)
[b0d0723]	264	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
	265	if entry is not None:
	266	data_info.source.beam_size_name = entry.get('name')
[579ba85]	267
[fe78c7b]	268	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
[8780e9a]	269	dom, 'beam_size.x', data_info.source)
[fe78c7b]	270	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
[8780e9a]	271	dom, 'beam_size.y', data_info.source)
[fe78c7b]	272	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
[8780e9a]	273	dom, 'beam_size.z', data_info.source)
	274
	275	# Collimation info ###################
[b0d0723]	276	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
[8780e9a]	277	for item in nodes:
	278	collim = Collimation()
[b0d0723]	279	if item.get('name') is not None:
	280	collim.name = item.get('name')
[fe78c7b]	281	self._store_float('ns:length', item, 'length', collim)
[8780e9a]	282
	283	# Look for apertures
[b0d0723]	284	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
[8780e9a]	285	for apert in apert_list:
[d6513cd]	286	aperture = Aperture()
[4c00964]	287
	288	# Get the name and type of the aperture
[b0d0723]	289	aperture.name = apert.get('name')
	290	aperture.type = apert.get('type')
[4c00964]	291
[fe78c7b]	292	self._store_float('ns:distance', apert, 'distance', aperture)
[579ba85]	293
[b0d0723]	294	entry = get_content('ns:size', apert)
	295	if entry is not None:
	296	aperture.size_name = entry.get('name')
[579ba85]	297
[fe78c7b]	298	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
	299	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
	300	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
[8780e9a]	301
	302	collim.aperture.append(aperture)
	303
	304	data_info.collimation.append(collim)
	305
	306	# Detector info ######################
[b0d0723]	307	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
[8780e9a]	308	for item in nodes:
	309
	310	detector = Detector()
	311
[fe78c7b]	312	self._store_content('ns:name', item, 'name', detector)
	313	self._store_float('ns:SDD', item, 'distance', detector)
[8780e9a]	314
	315	# Detector offset (as a vector)
[fe78c7b]	316	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
	317	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
	318	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
[8780e9a]	319
	320	# Detector orientation (as a vector)
[fe78c7b]	321	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
	322	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
	323	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
[8780e9a]	324
	325	# Beam center (as a vector)
[fe78c7b]	326	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
	327	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
	328	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
[8780e9a]	329
	330	# Pixel size (as a vector)
[fe78c7b]	331	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
	332	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
	333	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
[8780e9a]	334
[fe78c7b]	335	self._store_float('ns:slit_length', item, 'slit_length', detector)
[8780e9a]	336
	337	data_info.detector.append(detector)
	338
	339	# Processes info ######################
[b0d0723]	340	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
[8780e9a]	341	for item in nodes:
	342	process = Process()
[fe78c7b]	343	self._store_content('ns:name', item, 'name', process)
	344	self._store_content('ns:date', item, 'date', process)
	345	self._store_content('ns:description', item, 'description', process)
[8780e9a]	346
[b0d0723]	347	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
[8780e9a]	348	for term in term_list:
	349	try:
[b0d0723]	350	term_attr = {}
	351	for attr in term.keys():
	352	term_attr[attr] = term.get(attr).strip()
	353	if term.text is not None:
	354	term_attr['value'] = term.text.strip()
[8780e9a]	355	process.term.append(term_attr)
	356	except:
[fe78c7b]	357	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
	358	self.errors.append(err_mess)
	359	logging.error(err_mess)
[8780e9a]	360
[b0d0723]	361	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
[8780e9a]	362	for note in note_list:
[b0d0723]	363	if note.text is not None:
	364	process.notes.append(note.text.strip())
[8780e9a]	365
	366	data_info.process.append(process)
	367
	368
	369	# Data info ######################
[b0d0723]	370	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
[579ba85]	371	if len(nodes)>1:
	372	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
	373
[b0d0723]	374	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
	375
[8780e9a]	376	x = numpy.zeros(0)
	377	y = numpy.zeros(0)
	378	dx = numpy.zeros(0)
	379	dy = numpy.zeros(0)
[d00f8ff]	380	dxw = numpy.zeros(0)
	381	dxl = numpy.zeros(0)
[8780e9a]	382
	383	for item in nodes:
[b0d0723]	384	_x, attr = get_float('ns:Q', item)
	385	_dx, attr_d = get_float('ns:Qdev', item)
	386	_dxl, attr_l = get_float('ns:dQl', item)
	387	_dxw, attr_w = get_float('ns:dQw', item)
[8780e9a]	388	if _dx == None:
	389	_dx = 0.0
[d00f8ff]	390	if _dxl == None:
	391	_dxl = 0.0
	392	if _dxw == None:
	393	_dxw = 0.0
[8780e9a]	394
[e390933]	395	if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower():
	396	if has_converter==True:
	397	try:
	398	data_conv_q = Converter(attr['unit'])
	399	_x = data_conv_q(_x, units=data_info.x_unit)
	400	except:
	401	raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \
	402	% (attr['unit'], data_info.x_unit, sys.exc_value)
	403	else:
	404	raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \
	405	% (attr['unit'], data_info.x_unit)
[d00f8ff]	406	# Error in Q
[e390933]	407	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower():
	408	if has_converter==True:
	409	try:
	410	data_conv_q = Converter(attr_d['unit'])
	411	_dx = data_conv_q(_dx, units=data_info.x_unit)
	412	except:
	413	raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \
	414	% (attr['unit'], data_info.x_unit, sys.exc_value)
	415	else:
	416	raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \
	417	% (attr['unit'], data_info.x_unit)
[d00f8ff]	418	# Slit length
	419	if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower():
	420	if has_converter==True:
	421	try:
	422	data_conv_q = Converter(attr_l['unit'])
	423	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
	424	except:
	425	raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \
	426	% (attr['unit'], data_info.x_unit, sys.exc_value)
	427	else:
	428	raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \
	429	% (attr['unit'], data_info.x_unit)
	430	# Slit width
	431	if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower():
	432	if has_converter==True:
	433	try:
	434	data_conv_q = Converter(attr_w['unit'])
	435	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
	436	except:
	437	raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \
	438	% (attr['unit'], data_info.x_unit, sys.exc_value)
	439	else:
	440	raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \
	441	% (attr['unit'], data_info.x_unit)
[e390933]	442
[b0d0723]	443	_y, attr = get_float('ns:I', item)
	444	_dy, attr_d = get_float('ns:Idev', item)
[8780e9a]	445	if _dy == None:
	446	_dy = 0.0
	447	if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower():
[e390933]	448	if has_converter==True:
	449	try:
	450	data_conv_i = Converter(attr['unit'])
	451	_y = data_conv_i(_y, units=data_info.y_unit)
	452	except:
	453	raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \
	454	% (attr['unit'], data_info.y_unit, sys.exc_value)
	455	else:
	456	raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \
	457	% (attr['unit'], data_info.y_unit)
	458	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower():
	459	if has_converter==True:
	460	try:
	461	data_conv_i = Converter(attr_d['unit'])
	462	_dy = data_conv_i(_dy, units=data_info.y_unit)
	463	except:
	464	raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \
	465	% (attr_d['unit'], data_info.y_unit, sys.exc_value)
	466	else:
	467	raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \
	468	% (attr_d['unit'], data_info.y_unit)
[8780e9a]	469
	470	if _x is not None and _y is not None:
	471	x = numpy.append(x, _x)
[579ba85]	472	y = numpy.append(y, _y)
	473	dx = numpy.append(dx, _dx)
	474	dy = numpy.append(dy, _dy)
[d00f8ff]	475	dxl = numpy.append(dxl, _dxl)
	476	dxw = numpy.append(dxw, _dxw)
	477
[8780e9a]	478
	479	data_info.x = x
	480	data_info.y = y
	481	data_info.dx = dx
	482	data_info.dy = dy
[d00f8ff]	483	data_info.dxl = dxl
	484	data_info.dxw = dxw
[d6513cd]	485
	486	data_conv_q = None
	487	data_conv_i = None
	488
[ca10d8e]	489	if has_converter == True and data_info.x_unit != '1/A':
	490	data_conv_q = Converter('1/A')
[d6513cd]	491	# Test it
	492	data_conv_q(1.0, output.Q_unit)
	493
[ca10d8e]	494	if has_converter == True and data_info.y_unit != '1/cm':
	495	data_conv_i = Converter('1/cm')
[d6513cd]	496	# Test it
[e390933]	497	data_conv_i(1.0, output.I_unit)
	498
[99d1af6]	499	if data_conv_q is not None:
[d6513cd]	500	data_info.xaxis("\\rm{Q}", data_info.x_unit)
[99d1af6]	501	else:
	502	data_info.xaxis("\\rm{Q}", 'A^{-1}')
	503	if data_conv_i is not None:
[0e2aa40]	504	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
[99d1af6]	505	else:
[0e2aa40]	506	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
[99d1af6]	507
[8780e9a]	508	return data_info
	509
[b3de3a45]	510	def _to_xml_doc(self, datainfo):
[4c00964]	511	"""
[b3de3a45]	512	Create an XML document to contain the content of a Data1D
[4c00964]	513
	514	@param datainfo: Data1D object
	515	"""
	516
[7d8094b]	517	if not issubclass(datainfo.__class__, Data1D):
[4c00964]	518	raise RuntimeError, "The cansas writer expects a Data1D instance"
	519
	520	doc = xml.dom.minidom.Document()
	521	main_node = doc.createElement("SASroot")
[fee780b]	522	main_node.setAttribute("version", self.version)
	523	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	524	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
	525	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
	526
[4c00964]	527	doc.appendChild(main_node)
	528
	529	entry_node = doc.createElement("SASentry")
	530	main_node.appendChild(entry_node)
	531
[579ba85]	532	write_node(doc, entry_node, "Title", datainfo.title)
	533
	534	for item in datainfo.run:
	535	runname = {}
	536	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
	537	runname = {'name': datainfo.run_name[item] }
	538	write_node(doc, entry_node, "Run", item, runname)
[4c00964]	539
	540	# Data info
	541	node = doc.createElement("SASdata")
	542	entry_node.appendChild(node)
	543
[579ba85]	544	for i in range(len(datainfo.x)):
	545	pt = doc.createElement("Idata")
	546	node.appendChild(pt)
	547	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
	548	if len(datainfo.y)>=i:
	549	write_node(doc, pt, "I", datainfo.y[i], {'unit':datainfo.y_unit})
[5b396b3]	550	if datainfo.dx !=None and len(datainfo.dx)>=i:
[579ba85]	551	write_node(doc, pt, "Qdev", datainfo.dx[i], {'unit':datainfo.x_unit})
[f31701c]	552	if datainfo.dy !=None and len(datainfo.dy)>=i:
[579ba85]	553	write_node(doc, pt, "Idev", datainfo.dy[i], {'unit':datainfo.y_unit})
	554
	555
[4c00964]	556	# Sample info
	557	sample = doc.createElement("SASsample")
[579ba85]	558	if datainfo.sample.name is not None:
	559	sample.setAttribute("name", str(datainfo.sample.name))
[4c00964]	560	entry_node.appendChild(sample)
[579ba85]	561	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[4c00964]	562	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
	563	write_node(doc, sample, "transmission", datainfo.sample.transmission)
	564	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
	565
	566	for item in datainfo.sample.details:
	567	write_node(doc, sample, "details", item)
	568
	569	pos = doc.createElement("position")
[579ba85]	570	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
	571	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
	572	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
[4c00964]	573	if written == True:
	574	sample.appendChild(pos)
	575
	576	ori = doc.createElement("orientation")
[579ba85]	577	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
	578	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
	579	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
[4c00964]	580	if written == True:
	581	sample.appendChild(ori)
	582
	583	# Instrument info
	584	instr = doc.createElement("SASinstrument")
	585	entry_node.appendChild(instr)
	586
	587	write_node(doc, instr, "name", datainfo.instrument)
	588
	589	# Source
	590	source = doc.createElement("SASsource")
[579ba85]	591	if datainfo.source.name is not None:
	592	source.setAttribute("name", str(datainfo.source.name))
[4c00964]	593	instr.appendChild(source)
	594
	595	write_node(doc, source, "radiation", datainfo.source.radiation)
	596	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
[579ba85]	597	size = doc.createElement("beam_size")
	598	if datainfo.source.beam_size_name is not None:
	599	size.setAttribute("name", str(datainfo.source.beam_size_name))
	600	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
	601	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
	602	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
	603	if written == True:
	604	source.appendChild(size)
	605
[4c00964]	606	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
	607	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
	608	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
	609	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
	610
	611	# Collimation
	612	for item in datainfo.collimation:
	613	coll = doc.createElement("SAScollimation")
[579ba85]	614	if item.name is not None:
	615	coll.setAttribute("name", str(item.name))
[4c00964]	616	instr.appendChild(coll)
	617
	618	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
	619
	620	for apert in item.aperture:
[579ba85]	621	ap = doc.createElement("aperture")
	622	if apert.name is not None:
	623	ap.setAttribute("name", str(apert.name))
	624	if apert.type is not None:
	625	ap.setAttribute("type", str(apert.type))
	626	coll.appendChild(ap)
[4c00964]	627
	628	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
	629
	630	size = doc.createElement("size")
[579ba85]	631	if apert.size_name is not None:
	632	size.setAttribute("name", str(apert.size_name))
	633	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
	634	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
	635	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
	636	if written == True:
	637	ap.appendChild(size)
[4c00964]	638
	639	# Detectors
	640	for item in datainfo.detector:
	641	det = doc.createElement("SASdetector")
[579ba85]	642	written = write_node(doc, det, "name", item.name)
	643	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
	644	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
	645	if written == True:
	646	instr.appendChild(det)
[4c00964]	647
	648	off = doc.createElement("offset")
[579ba85]	649	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
	650	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
	651	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
	652	if written == True:
	653	det.appendChild(off)
[4c00964]	654
	655	center = doc.createElement("beam_center")
[579ba85]	656	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
	657	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
	658	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
	659	if written == True:
	660	det.appendChild(center)
	661
[4c00964]	662	pix = doc.createElement("pixel_size")
[579ba85]	663	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
	664	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
	665	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
	666	if written == True:
	667	det.appendChild(pix)
	668
	669	ori = doc.createElement("orientation")
	670	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
	671	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
	672	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
	673	if written == True:
	674	det.appendChild(ori)
	675
[4c00964]	676
[579ba85]	677	# Processes info
[4c00964]	678	for item in datainfo.process:
	679	node = doc.createElement("SASprocess")
	680	entry_node.appendChild(node)
	681
[579ba85]	682	write_node(doc, node, "name", item.name)
	683	write_node(doc, node, "date", item.date)
	684	write_node(doc, node, "description", item.description)
	685	for term in item.term:
	686	value = term['value']
	687	del term['value']
	688	write_node(doc, node, "term", value, term)
	689	for note in item.notes:
	690	write_node(doc, node, "SASprocessnote", note)
[4c00964]	691
[b3de3a45]	692	# Return the document, and the SASentry node associated with
	693	# the data we just wrote
	694	return doc, entry_node
	695
	696	def write(self, filename, datainfo):
	697	"""
	698	Write the content of a Data1D as a CanSAS XML file
	699
	700	@param filename: name of the file to write
	701	@param datainfo: Data1D object
	702	"""
	703	# Create XML document
	704	doc, sasentry = self._to_xml_doc(datainfo)
[4c00964]	705	# Write the file
	706	fd = open(filename, 'w')
	707	fd.write(doc.toprettyxml())
	708	fd.close()
	709
[fe78c7b]	710	def _store_float(self, location, node, variable, storage, optional=True):
	711	"""
	712	Get the content of a xpath location and store
	713	the result. Check that the units are compatible
	714	with the destination. The value is expected to
	715	be a float.
	716
	717	The xpath location might or might not exist.
	718	If it does not exist, nothing is done
	719
	720	@param location: xpath location to fetch
	721	@param node: node to read the data from
	722	@param variable: name of the data member to store it in [string]
	723	@param storage: data object that has the 'variable' data member
	724	@param optional: if True, no exception will be raised if unit conversion can't be done
	725
	726	@raise ValueError: raised when the units are not recognized
	727	"""
	728	entry = get_content(location, node)
	729	try:
	730	value = float(entry.text)
	731	except:
	732	value = None
	733
	734	if value is not None:
	735	# If the entry has units, check to see that they are
	736	# compatible with what we currently have in the data object
	737	units = entry.get('unit')
	738	if units is not None:
	739	toks = variable.split('.')
	740	exec "local_unit = storage.%s_unit" % toks[0]
	741	if units.lower()!=local_unit.lower():
	742	if has_converter==True:
	743	try:
	744	conv = Converter(units)
	745	exec "storage.%s = %g" % (variable, conv(value, units=local_unit))
	746	except:
	747	err_mess = "CanSAS reader: could not convert %s unit [%s]; expecting [%s]\n %s" \
	748	% (variable, units, local_unit, sys.exc_value)
	749	self.errors.append(err_mess)
	750	if optional:
	751	logging.info(err_mess)
	752	else:
	753	raise ValueError, err_mess
	754	else:
	755	err_mess = "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \
	756	% (variable, units, local_unit)
	757	self.errors.append(err_mess)
	758	if optional:
	759	logging.info(err_mess)
	760	else:
	761	raise ValueError, err_mess
	762	else:
	763	exec "storage.%s = value" % variable
	764	else:
	765	exec "storage.%s = value" % variable
	766
	767	def _store_content(self, location, node, variable, storage):
	768	"""
	769	Get the content of a xpath location and store
	770	the result. The value is treated as a string.
	771
	772	The xpath location might or might not exist.
	773	If it does not exist, nothing is done
	774
	775	@param location: xpath location to fetch
	776	@param node: node to read the data from
	777	@param variable: name of the data member to store it in [string]
	778	@param storage: data object that has the 'variable' data member
	779	@return: return a list of errors
	780	"""
	781	entry = get_content(location, node)
	782	if entry is not None and entry.text is not None:
	783	exec "storage.%s = entry.text.strip()" % variable
	784
	785
	786
[8780e9a]	787	if __name__ == "__main__":
	788	logging.basicConfig(level=logging.ERROR,
	789	format='%(asctime)s %(levelname)s %(message)s',
	790	filename='cansas_reader.log',
	791	filemode='w')
	792	reader = Reader()
	793	print reader.read("../test/cansas1d.xml")
[b0d0723]	794	#print reader.read("../test/latex_smeared.xml")
[8780e9a]	795
	796
	797

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 32e8c78

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