cansas_reader.py @ 00c3aac

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 00c3aac was d3966c2, checked in by Jae Cho <jhjcho@…>, 15 years ago
made it more flexible
Property mode set to `100644`
File size: 35.1 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
	8	copyright 2008, University of Tennessee
	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
[8780e9a]	26	from xml import xpath
[4c00964]	27	import xml.dom.minidom
	28
[8780e9a]	29
[b39c817]	30	has_converter = True
	31	try:
	32	from data_util.nxsunit import Converter
	33	except:
	34	has_converter = False
	35
[4c00964]	36	def write_node(doc, parent, name, value, attr={}):
	37	"""
	38	@param doc: document DOM
	39	@param parent: parent node
	40	@param name: tag of the element
	41	@param value: value of the child text node
	42	@param attr: attribute dictionary
	43	@return: True if something was appended, otherwise False
	44	"""
	45	if value is not None:
	46	node = doc.createElement(name)
	47	node.appendChild(doc.createTextNode(str(value)))
	48	for item in attr:
	49	node.setAttribute(item, attr[item])
	50	parent.appendChild(node)
	51	return True
	52	return False
	53
[8780e9a]	54	def get_node_text(node):
	55	"""
	56	Get the text context of a node
	57
	58	@param node: node to read from
	59	@return: content, attribute list
	60	"""
	61	content = None
	62	attr = {}
	63	for item in node.childNodes:
	64	if item.nodeName.find('text')>=0 \
	65	and len(item.nodeValue.strip())>0:
	66	content = item.nodeValue.strip()
	67	break
	68
	69	if node.hasAttributes():
	70	for i in range(node.attributes.length):
	71	attr[node.attributes.item(i).nodeName] \
	72	= node.attributes.item(i).nodeValue
	73
	74	return content, attr
	75
	76	def get_content(location, node):
	77	"""
	78	Get the first instance of the content of a xpath location
	79
	80	@param location: xpath location
	81	@param node: node to start at
	82	"""
	83	value = None
	84	attr = {}
	85	nodes = xpath.Evaluate(location, node)
	86	if len(nodes)>0:
	87	try:
	88	# Skip comments and empty lines
	89	for item in nodes[0].childNodes:
	90	if item.nodeName.find('text')>=0 \
	91	and len(item.nodeValue.strip())>0:
	92	value = item.nodeValue.strip()
	93	break
	94
[d6513cd]	95	if nodes[0].hasAttributes():
	96	for i in range(nodes[0].attributes.length):
	97	attr[nodes[0].attributes.item(i).nodeName] \
	98	= nodes[0].attributes.item(i).nodeValue
[8780e9a]	99	except:
	100	# problem reading the node. Skip it and return that
	101	# nothing was found
	102	logging.error("cansas_reader.get_content: %s\n %s" % (location, sys.exc_value))
	103
	104	return value, attr
	105
	106	def get_float(location, node):
	107	"""
	108	Get the content of a node as a float
	109
	110	@param location: xpath location
	111	@param node: node to start at
	112	"""
	113	value = None
	114	attr = {}
	115	content, attr = get_content(location, node)
	116	if content is not None:
	117	try:
[b39c817]	118	value = float(content)
[8780e9a]	119	except:
	120	# Could not pass, skip and return None
	121	logging.error("cansas_reader.get_float: could not convert '%s' to float" % content)
	122
	123	return value, attr
	124
	125	def _store_float(location, node, variable, storage):
	126	"""
	127	Get the content of a xpath location and store
	128	the result. Check that the units are compatible
	129	with the destination. The value is expected to
	130	be a float.
	131
	132	The xpath location might or might not exist.
	133	If it does not exist, nothing is done
	134
	135	@param location: xpath location to fetch
	136	@param node: node to read the data from
	137	@param variable: name of the data member to store it in [string]
	138	@param storage: data object that has the 'variable' data member
	139
	140	@raise ValueError: raised when the units are not recognized
	141	"""
	142	value, attr = get_float(location, node)
	143	if value is not None:
	144	# If the entry has units, check to see that they are
	145	# compatible with what we currently have in the data object
	146	if attr.has_key('unit'):
	147	toks = variable.split('.')
[e390933]	148	exec "local_unit = storage.%s_unit" % toks[0]
	149	if attr['unit'].lower()!=local_unit.lower():
[b39c817]	150	if has_converter==True:
	151	try:
	152	conv = Converter(attr['unit'])
	153	exec "storage.%s = %g" % (variable, conv(value, units=local_unit))
	154	except:
[d3966c2]	155	#Below three lines were added for the unit = 1/A. local unit is defined in 'mm'. Need to check!!!
	156	if variable == 'slit_length' and attr['unit'] !=local_unit:
	157	pass
	158	else:
	159	raise ValueError, "CanSAS reader: could not convert %s unit [%s]; expecting [%s]\n %s" \
	160	% (variable, attr['unit'], local_unit, sys.exc_value)
[b39c817]	161	else:
	162	raise ValueError, "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \
	163	% (variable, attr['unit'], local_unit)
	164	else:
	165	exec "storage.%s = value" % variable
	166	else:
	167	exec "storage.%s = value" % variable
	168
[8780e9a]	169
	170	def _store_content(location, node, variable, storage):
	171	"""
	172	Get the content of a xpath location and store
	173	the result. The value is treated as a string.
	174
	175	The xpath location might or might not exist.
	176	If it does not exist, nothing is done
	177
	178	@param location: xpath location to fetch
	179	@param node: node to read the data from
	180	@param variable: name of the data member to store it in [string]
	181	@param storage: data object that has the 'variable' data member
	182	"""
	183	value, attr = get_content(location, node)
	184	if value is not None:
	185	exec "storage.%s = value" % variable
	186
	187
	188	class Reader:
	189	"""
	190	Class to load cansas 1D XML files
	191
	192	Dependencies:
	193	The CanSas reader requires PyXML 0.8.4 or later.
	194	"""
	195	## CanSAS version
	196	version = '1.0'
	197	## File type
	198	type = ["CanSAS 1D files (.xml)\|.xml"]
	199	## List of allowed extensions
	200	ext=['.xml', '.XML']
	201
	202	def read(self, path):
	203	"""
	204	Load data file
	205
	206	@param path: file path
	207	@return: Data1D object if a single SASentry was found,
	208	or a list of Data1D objects if multiple entries were found,
	209	or None of nothing was found
	210	@raise RuntimeError: when the file can't be opened
	211	@raise ValueError: when the length of the data vectors are inconsistent
	212	"""
	213	from xml.dom.minidom import parse
	214
	215	output = []
	216
	217	if os.path.isfile(path):
	218	basename = os.path.basename(path)
	219	root, extension = os.path.splitext(basename)
	220	if extension.lower() in self.ext:
	221
	222	dom = parse(path)
	223
	224	# Check the format version number
	225	nodes = xpath.Evaluate('SASroot', dom)
	226	if nodes[0].hasAttributes():
	227	for i in range(nodes[0].attributes.length):
	228	if nodes[0].attributes.item(i).nodeName=='version':
	229	if nodes[0].attributes.item(i).nodeValue != self.version:
	230	raise ValueError, "cansas_reader: unrecognized version number %s" % \
	231	nodes[0].attributes.item(i).nodeValue
	232
	233	entry_list = xpath.Evaluate('SASroot/SASentry', dom)
	234	for entry in entry_list:
	235	sas_entry = self._parse_entry(entry)
	236	sas_entry.filename = basename
	237	output.append(sas_entry)
	238
	239	else:
	240	raise RuntimeError, "%s is not a file" % path
	241
	242	# Return output consistent with the loader's api
	243	if len(output)==0:
	244	return None
	245	elif len(output)==1:
	246	return output[0]
	247	else:
	248	return output
	249
	250	def _parse_entry(self, dom):
	251	"""
	252	Parse a SASentry
	253
	254	@param node: SASentry node
	255	@return: Data1D object
	256	"""
	257	x = numpy.zeros(0)
	258	y = numpy.zeros(0)
	259
	260	data_info = Data1D(x, y)
	261
	262	# Look up title
	263	_store_content('Title', dom, 'title', data_info)
[579ba85]	264	# Look up run number
	265	nodes = xpath.Evaluate('Run', dom)
	266	for item in nodes:
	267	value, attr = get_node_text(item)
	268	if value is not None:
	269	data_info.run.append(value)
	270	if attr.has_key('name'):
	271	data_info.run_name[value] = attr['name']
	272
[8780e9a]	273	# Look up instrument name
[579ba85]	274	_store_content('SASinstrument/name', dom, 'instrument', data_info)
	275	#value, attr = get_content('SASinstrument', dom)
	276	#if attr.has_key('name'):
	277	# data_info.instrument = attr['name']
[8780e9a]	278
	279	note_list = xpath.Evaluate('SASnote', dom)
	280	for note in note_list:
	281	try:
	282	note_value, note_attr = get_node_text(note)
	283	if note_value is not None:
	284	data_info.notes.append(note_value)
	285	except:
	286	logging.error("cansas_reader.read: error processing entry notes\n %s" % sys.exc_value)
	287
	288
	289	# Sample info ###################
[579ba85]	290	value, attr = get_content('SASsample', dom)
	291	if attr.has_key('name'):
	292	data_info.sample.name = attr['name']
	293
[8780e9a]	294	_store_content('SASsample/ID',
	295	dom, 'ID', data_info.sample)
	296	_store_float('SASsample/thickness',
	297	dom, 'thickness', data_info.sample)
	298	_store_float('SASsample/transmission',
	299	dom, 'transmission', data_info.sample)
	300	_store_float('SASsample/temperature',
	301	dom, 'temperature', data_info.sample)
	302	nodes = xpath.Evaluate('SASsample/details', dom)
	303	for item in nodes:
	304	try:
	305	detail_value, detail_attr = get_node_text(item)
	306	if detail_value is not None:
	307	data_info.sample.details.append(detail_value)
	308	except:
	309	logging.error("cansas_reader.read: error processing sample details\n %s" % sys.exc_value)
	310
	311	# Position (as a vector)
	312	_store_float('SASsample/position/x',
	313	dom, 'position.x', data_info.sample)
	314	_store_float('SASsample/position/y',
	315	dom, 'position.y', data_info.sample)
	316	_store_float('SASsample/position/z',
	317	dom, 'position.z', data_info.sample)
	318
	319	# Orientation (as a vector)
	320	_store_float('SASsample/orientation/roll',
	321	dom, 'orientation.x', data_info.sample)
	322	_store_float('SASsample/orientation/pitch',
	323	dom, 'orientation.y', data_info.sample)
	324	_store_float('SASsample/orientation/yaw',
	325	dom, 'orientation.z', data_info.sample)
	326
	327	# Source info ###################
[4c00964]	328	value, attr = get_content('SASinstrument/SASsource', dom)
	329	if attr.has_key('name'):
	330	data_info.source.name = attr['name']
	331
[8780e9a]	332	_store_content('SASinstrument/SASsource/radiation',
	333	dom, 'radiation', data_info.source)
	334	_store_content('SASinstrument/SASsource/beam_shape',
	335	dom, 'beam_shape', data_info.source)
	336	_store_float('SASinstrument/SASsource/wavelength',
	337	dom, 'wavelength', data_info.source)
	338	_store_float('SASinstrument/SASsource/wavelength_min',
	339	dom, 'wavelength_min', data_info.source)
	340	_store_float('SASinstrument/SASsource/wavelength_max',
	341	dom, 'wavelength_max', data_info.source)
	342	_store_float('SASinstrument/SASsource/wavelength_spread',
	343	dom, 'wavelength_spread', data_info.source)
	344
[579ba85]	345	# Beam size (as a vector)
	346	value, attr = get_content('SASinstrument/SASsource/beam_size', dom)
	347	if attr.has_key('name'):
	348	data_info.source.beam_size_name = attr['name']
	349
[8780e9a]	350	_store_float('SASinstrument/SASsource/beam_size/x',
	351	dom, 'beam_size.x', data_info.source)
	352	_store_float('SASinstrument/SASsource/beam_size/y',
	353	dom, 'beam_size.y', data_info.source)
	354	_store_float('SASinstrument/SASsource/beam_size/z',
	355	dom, 'beam_size.z', data_info.source)
	356
	357	# Collimation info ###################
	358	nodes = xpath.Evaluate('SASinstrument/SAScollimation', dom)
	359	for item in nodes:
	360	collim = Collimation()
[4c00964]	361	value, attr = get_node_text(item)
	362	if attr.has_key('name'):
	363	collim.name = attr['name']
[8780e9a]	364	_store_float('length', item, 'length', collim)
	365
	366	# Look for apertures
	367	apert_list = xpath.Evaluate('aperture', item)
	368	for apert in apert_list:
[d6513cd]	369	aperture = Aperture()
[4c00964]	370
	371	# Get the name and type of the aperture
[579ba85]	372	ap_value, ap_attr = get_node_text(apert)
[4c00964]	373	if ap_attr.has_key('name'):
	374	aperture.name = ap_attr['name']
	375	if ap_attr.has_key('type'):
	376	aperture.type = ap_attr['type']
	377
[8780e9a]	378	_store_float('distance', apert, 'distance', aperture)
[579ba85]	379
	380	value, attr = get_content('size', apert)
	381	if attr.has_key('name'):
	382	aperture.size_name = attr['name']
	383
[8780e9a]	384	_store_float('size/x', apert, 'size.x', aperture)
	385	_store_float('size/y', apert, 'size.y', aperture)
	386	_store_float('size/z', apert, 'size.z', aperture)
	387
	388	collim.aperture.append(aperture)
	389
	390	data_info.collimation.append(collim)
	391
	392	# Detector info ######################
	393	nodes = xpath.Evaluate('SASinstrument/SASdetector', dom)
	394	for item in nodes:
	395
	396	detector = Detector()
	397
	398	_store_content('name', item, 'name', detector)
	399	_store_float('SDD', item, 'distance', detector)
	400
	401	# Detector offset (as a vector)
	402	_store_float('offset/x', item, 'offset.x', detector)
	403	_store_float('offset/y', item, 'offset.y', detector)
	404	_store_float('offset/z', item, 'offset.z', detector)
	405
	406	# Detector orientation (as a vector)
[579ba85]	407	_store_float('orientation/roll', item, 'orientation.x', detector)
	408	_store_float('orientation/pitch', item, 'orientation.y', detector)
	409	_store_float('orientation/yaw', item, 'orientation.z', detector)
[8780e9a]	410
	411	# Beam center (as a vector)
	412	_store_float('beam_center/x', item, 'beam_center.x', detector)
	413	_store_float('beam_center/y', item, 'beam_center.y', detector)
	414	_store_float('beam_center/z', item, 'beam_center.z', detector)
	415
	416	# Pixel size (as a vector)
	417	_store_float('pixel_size/x', item, 'pixel_size.x', detector)
	418	_store_float('pixel_size/y', item, 'pixel_size.y', detector)
	419	_store_float('pixel_size/z', item, 'pixel_size.z', detector)
	420
	421	_store_float('slit_length', item, 'slit_length', detector)
	422
	423	data_info.detector.append(detector)
	424
	425	# Processes info ######################
	426	nodes = xpath.Evaluate('SASprocess', dom)
	427	for item in nodes:
	428	process = Process()
	429	_store_content('name', item, 'name', process)
	430	_store_content('date', item, 'date', process)
	431	_store_content('description', item, 'description', process)
	432
	433	term_list = xpath.Evaluate('term', item)
	434	for term in term_list:
	435	try:
	436	term_value, term_attr = get_node_text(term)
	437	term_attr['value'] = term_value
	438	if term_value is not None:
	439	process.term.append(term_attr)
	440	except:
	441	logging.error("cansas_reader.read: error processing process term\n %s" % sys.exc_value)
	442
	443	note_list = xpath.Evaluate('SASprocessnote', item)
	444	for note in note_list:
	445	try:
	446	note_value, note_attr = get_node_text(note)
	447	if note_value is not None:
	448	process.notes.append(note_value)
	449	except:
	450	logging.error("cansas_reader.read: error processing process notes\n %s" % sys.exc_value)
	451
	452
	453	data_info.process.append(process)
	454
	455
	456	# Data info ######################
[579ba85]	457	nodes = xpath.Evaluate('SASdata', dom)
	458	if len(nodes)>1:
	459	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
	460
[8780e9a]	461	nodes = xpath.Evaluate('SASdata/Idata', dom)
	462	x = numpy.zeros(0)
	463	y = numpy.zeros(0)
	464	dx = numpy.zeros(0)
	465	dy = numpy.zeros(0)
[d00f8ff]	466	dxw = numpy.zeros(0)
	467	dxl = numpy.zeros(0)
[8780e9a]	468
	469	for item in nodes:
	470	_x, attr = get_float('Q', item)
[e390933]	471	_dx, attr_d = get_float('Qdev', item)
[d00f8ff]	472	_dxl, attr_l = get_float('dQl', item)
	473	_dxw, attr_w = get_float('dQw', item)
[8780e9a]	474	if _dx == None:
	475	_dx = 0.0
[d00f8ff]	476	if _dxl == None:
	477	_dxl = 0.0
	478	if _dxw == None:
	479	_dxw = 0.0
[8780e9a]	480
[e390933]	481	if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower():
	482	if has_converter==True:
	483	try:
	484	data_conv_q = Converter(attr['unit'])
	485	_x = data_conv_q(_x, units=data_info.x_unit)
	486	except:
	487	raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \
	488	% (attr['unit'], data_info.x_unit, sys.exc_value)
	489	else:
	490	raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \
	491	% (attr['unit'], data_info.x_unit)
[d00f8ff]	492	# Error in Q
[e390933]	493	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower():
	494	if has_converter==True:
	495	try:
	496	data_conv_q = Converter(attr_d['unit'])
	497	_dx = data_conv_q(_dx, units=data_info.x_unit)
	498	except:
	499	raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \
	500	% (attr['unit'], data_info.x_unit, sys.exc_value)
	501	else:
	502	raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \
	503	% (attr['unit'], data_info.x_unit)
[d00f8ff]	504	# Slit length
	505	if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower():
	506	if has_converter==True:
	507	try:
	508	data_conv_q = Converter(attr_l['unit'])
	509	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
	510	except:
	511	raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \
	512	% (attr['unit'], data_info.x_unit, sys.exc_value)
	513	else:
	514	raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \
	515	% (attr['unit'], data_info.x_unit)
	516	# Slit width
	517	if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower():
	518	if has_converter==True:
	519	try:
	520	data_conv_q = Converter(attr_w['unit'])
	521	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
	522	except:
	523	raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \
	524	% (attr['unit'], data_info.x_unit, sys.exc_value)
	525	else:
	526	raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \
	527	% (attr['unit'], data_info.x_unit)
[e390933]	528
[8780e9a]	529	_y, attr = get_float('I', item)
[e390933]	530	_dy, attr_d = get_float('Idev', item)
[8780e9a]	531	if _dy == None:
	532	_dy = 0.0
	533	if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower():
[e390933]	534	if has_converter==True:
	535	try:
	536	data_conv_i = Converter(attr['unit'])
	537	_y = data_conv_i(_y, units=data_info.y_unit)
	538	except:
	539	raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \
	540	% (attr['unit'], data_info.y_unit, sys.exc_value)
	541	else:
	542	raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \
	543	% (attr['unit'], data_info.y_unit)
	544	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower():
	545	if has_converter==True:
	546	try:
	547	data_conv_i = Converter(attr_d['unit'])
	548	_dy = data_conv_i(_dy, units=data_info.y_unit)
	549	except:
	550	raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \
	551	% (attr_d['unit'], data_info.y_unit, sys.exc_value)
	552	else:
	553	raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \
	554	% (attr_d['unit'], data_info.y_unit)
[8780e9a]	555
	556	if _x is not None and _y is not None:
	557	x = numpy.append(x, _x)
[579ba85]	558	y = numpy.append(y, _y)
	559	dx = numpy.append(dx, _dx)
	560	dy = numpy.append(dy, _dy)
[d00f8ff]	561	dxl = numpy.append(dxl, _dxl)
	562	dxw = numpy.append(dxw, _dxw)
	563
[8780e9a]	564
	565	data_info.x = x
	566	data_info.y = y
	567	data_info.dx = dx
	568	data_info.dy = dy
[d00f8ff]	569	data_info.dxl = dxl
	570	data_info.dxw = dxw
[d6513cd]	571
	572	data_conv_q = None
	573	data_conv_i = None
	574
[ca10d8e]	575	if has_converter == True and data_info.x_unit != '1/A':
	576	data_conv_q = Converter('1/A')
[d6513cd]	577	# Test it
	578	data_conv_q(1.0, output.Q_unit)
	579
[ca10d8e]	580	if has_converter == True and data_info.y_unit != '1/cm':
	581	data_conv_i = Converter('1/cm')
[d6513cd]	582	# Test it
[e390933]	583	data_conv_i(1.0, output.I_unit)
	584
[99d1af6]	585	if data_conv_q is not None:
[d6513cd]	586	data_info.xaxis("\\rm{Q}", data_info.x_unit)
[99d1af6]	587	else:
	588	data_info.xaxis("\\rm{Q}", 'A^{-1}')
	589	if data_conv_i is not None:
[d6513cd]	590	data_info.yaxis("\\{I(Q)}", data_info.y_unit)
[99d1af6]	591	else:
	592	data_info.yaxis("\\rm{I(Q)}","cm^{-1}")
	593
[8780e9a]	594	return data_info
	595
[4c00964]	596	def write(self, filename, datainfo):
	597	"""
	598	Write the content of a Data1D as a CanSAS XML file
	599
	600	@param filename: name of the file to write
	601	@param datainfo: Data1D object
	602	"""
	603
	604	if not datainfo.__class__ == Data1D:
	605	raise RuntimeError, "The cansas writer expects a Data1D instance"
	606
	607	doc = xml.dom.minidom.Document()
	608	main_node = doc.createElement("SASroot")
[fee780b]	609	main_node.setAttribute("version", self.version)
	610	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	611	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
	612	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
	613
[4c00964]	614	doc.appendChild(main_node)
	615
	616	entry_node = doc.createElement("SASentry")
	617	main_node.appendChild(entry_node)
	618
[579ba85]	619	write_node(doc, entry_node, "Title", datainfo.title)
	620
	621	for item in datainfo.run:
	622	runname = {}
	623	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
	624	runname = {'name': datainfo.run_name[item] }
	625	write_node(doc, entry_node, "Run", item, runname)
[4c00964]	626
	627	# Data info
	628	node = doc.createElement("SASdata")
	629	entry_node.appendChild(node)
	630
[579ba85]	631	for i in range(len(datainfo.x)):
	632	pt = doc.createElement("Idata")
	633	node.appendChild(pt)
	634	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
	635	if len(datainfo.y)>=i:
	636	write_node(doc, pt, "I", datainfo.y[i], {'unit':datainfo.y_unit})
[5b396b3]	637	if datainfo.dx !=None and len(datainfo.dx)>=i:
[579ba85]	638	write_node(doc, pt, "Qdev", datainfo.dx[i], {'unit':datainfo.x_unit})
[72b524b]	639	if datainfo.dx !=None and len(datainfo.dy)>=i:
[579ba85]	640	write_node(doc, pt, "Idev", datainfo.dy[i], {'unit':datainfo.y_unit})
	641
	642
[4c00964]	643	# Sample info
	644	sample = doc.createElement("SASsample")
[579ba85]	645	if datainfo.sample.name is not None:
	646	sample.setAttribute("name", str(datainfo.sample.name))
[4c00964]	647	entry_node.appendChild(sample)
[579ba85]	648	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[4c00964]	649	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
	650	write_node(doc, sample, "transmission", datainfo.sample.transmission)
	651	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
	652
	653	for item in datainfo.sample.details:
	654	write_node(doc, sample, "details", item)
	655
	656	pos = doc.createElement("position")
[579ba85]	657	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
	658	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
	659	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
[4c00964]	660	if written == True:
	661	sample.appendChild(pos)
	662
	663	ori = doc.createElement("orientation")
[579ba85]	664	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
	665	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
	666	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
[4c00964]	667	if written == True:
	668	sample.appendChild(ori)
	669
	670	# Instrument info
	671	instr = doc.createElement("SASinstrument")
	672	entry_node.appendChild(instr)
	673
	674	write_node(doc, instr, "name", datainfo.instrument)
	675
	676	# Source
	677	source = doc.createElement("SASsource")
[579ba85]	678	if datainfo.source.name is not None:
	679	source.setAttribute("name", str(datainfo.source.name))
[4c00964]	680	instr.appendChild(source)
	681
	682	write_node(doc, source, "radiation", datainfo.source.radiation)
	683	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
[579ba85]	684	size = doc.createElement("beam_size")
	685	if datainfo.source.beam_size_name is not None:
	686	size.setAttribute("name", str(datainfo.source.beam_size_name))
	687	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
	688	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
	689	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
	690	if written == True:
	691	source.appendChild(size)
	692
[4c00964]	693	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
	694	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
	695	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
	696	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
	697
	698	# Collimation
	699	for item in datainfo.collimation:
	700	coll = doc.createElement("SAScollimation")
[579ba85]	701	if item.name is not None:
	702	coll.setAttribute("name", str(item.name))
[4c00964]	703	instr.appendChild(coll)
	704
	705	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
	706
	707	for apert in item.aperture:
[579ba85]	708	ap = doc.createElement("aperture")
	709	if apert.name is not None:
	710	ap.setAttribute("name", str(apert.name))
	711	if apert.type is not None:
	712	ap.setAttribute("type", str(apert.type))
	713	coll.appendChild(ap)
[4c00964]	714
	715	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
	716
	717	size = doc.createElement("size")
[579ba85]	718	if apert.size_name is not None:
	719	size.setAttribute("name", str(apert.size_name))
	720	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
	721	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
	722	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
	723	if written == True:
	724	ap.appendChild(size)
[4c00964]	725
	726	# Detectors
	727	for item in datainfo.detector:
	728	det = doc.createElement("SASdetector")
[579ba85]	729	written = write_node(doc, det, "name", item.name)
	730	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
	731	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
	732	if written == True:
	733	instr.appendChild(det)
[4c00964]	734
	735	off = doc.createElement("offset")
[579ba85]	736	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
	737	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
	738	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
	739	if written == True:
	740	det.appendChild(off)
[4c00964]	741
	742	center = doc.createElement("beam_center")
[579ba85]	743	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
	744	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
	745	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
	746	if written == True:
	747	det.appendChild(center)
	748
[4c00964]	749	pix = doc.createElement("pixel_size")
[579ba85]	750	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
	751	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
	752	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
	753	if written == True:
	754	det.appendChild(pix)
	755
	756	ori = doc.createElement("orientation")
	757	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
	758	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
	759	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
	760	if written == True:
	761	det.appendChild(ori)
	762
[4c00964]	763
[579ba85]	764	# Processes info
[4c00964]	765	for item in datainfo.process:
	766	node = doc.createElement("SASprocess")
	767	entry_node.appendChild(node)
	768
[579ba85]	769	write_node(doc, node, "name", item.name)
	770	write_node(doc, node, "date", item.date)
	771	write_node(doc, node, "description", item.description)
	772	for term in item.term:
	773	value = term['value']
	774	del term['value']
	775	write_node(doc, node, "term", value, term)
	776	for note in item.notes:
	777	write_node(doc, node, "SASprocessnote", note)
[4c00964]	778
	779
	780	# Write the file
	781	fd = open(filename, 'w')
	782	fd.write(doc.toprettyxml())
	783	fd.close()
	784
	785
[8780e9a]	786	if __name__ == "__main__":
	787	logging.basicConfig(level=logging.ERROR,
	788	format='%(asctime)s %(levelname)s %(message)s',
	789	filename='cansas_reader.log',
	790	filemode='w')
	791	reader = Reader()
	792	print reader.read("../test/cansas1d.xml")
	793
	794
	795

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 00c3aac

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