cansas_reader.py @ 07f8d9a

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 07f8d9a was 28caa03, checked in by Mathieu Doucet <doucetm@…>, 16 years ago
Improved hierarchical reader structure, put back reader plugin, minor fixes.
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
[28caa03]	198	type_name = "CanSAS 1D"
	199	## Wildcards
[8780e9a]	200	type = ["CanSAS 1D files (.xml)\|.xml"]
	201	## List of allowed extensions
	202	ext=['.xml', '.XML']
	203
	204	def read(self, path):
	205	"""
	206	Load data file
	207
	208	@param path: file path
	209	@return: Data1D object if a single SASentry was found,
	210	or a list of Data1D objects if multiple entries were found,
	211	or None of nothing was found
	212	@raise RuntimeError: when the file can't be opened
	213	@raise ValueError: when the length of the data vectors are inconsistent
	214	"""
	215	from xml.dom.minidom import parse
	216
	217	output = []
	218
	219	if os.path.isfile(path):
	220	basename = os.path.basename(path)
	221	root, extension = os.path.splitext(basename)
	222	if extension.lower() in self.ext:
	223
	224	dom = parse(path)
	225
	226	# Check the format version number
	227	nodes = xpath.Evaluate('SASroot', dom)
	228	if nodes[0].hasAttributes():
	229	for i in range(nodes[0].attributes.length):
	230	if nodes[0].attributes.item(i).nodeName=='version':
	231	if nodes[0].attributes.item(i).nodeValue != self.version:
	232	raise ValueError, "cansas_reader: unrecognized version number %s" % \
	233	nodes[0].attributes.item(i).nodeValue
	234
	235	entry_list = xpath.Evaluate('SASroot/SASentry', dom)
	236	for entry in entry_list:
	237	sas_entry = self._parse_entry(entry)
	238	sas_entry.filename = basename
	239	output.append(sas_entry)
	240
	241	else:
	242	raise RuntimeError, "%s is not a file" % path
	243
	244	# Return output consistent with the loader's api
	245	if len(output)==0:
	246	return None
	247	elif len(output)==1:
	248	return output[0]
	249	else:
	250	return output
	251
	252	def _parse_entry(self, dom):
	253	"""
	254	Parse a SASentry
	255
	256	@param node: SASentry node
	257	@return: Data1D object
	258	"""
	259	x = numpy.zeros(0)
	260	y = numpy.zeros(0)
	261
	262	data_info = Data1D(x, y)
	263
	264	# Look up title
	265	_store_content('Title', dom, 'title', data_info)
[579ba85]	266	# Look up run number
	267	nodes = xpath.Evaluate('Run', dom)
	268	for item in nodes:
	269	value, attr = get_node_text(item)
	270	if value is not None:
	271	data_info.run.append(value)
	272	if attr.has_key('name'):
	273	data_info.run_name[value] = attr['name']
	274
[8780e9a]	275	# Look up instrument name
[579ba85]	276	_store_content('SASinstrument/name', dom, 'instrument', data_info)
	277	#value, attr = get_content('SASinstrument', dom)
	278	#if attr.has_key('name'):
	279	# data_info.instrument = attr['name']
[8780e9a]	280
	281	note_list = xpath.Evaluate('SASnote', dom)
	282	for note in note_list:
	283	try:
	284	note_value, note_attr = get_node_text(note)
	285	if note_value is not None:
	286	data_info.notes.append(note_value)
	287	except:
	288	logging.error("cansas_reader.read: error processing entry notes\n %s" % sys.exc_value)
	289
	290
	291	# Sample info ###################
[579ba85]	292	value, attr = get_content('SASsample', dom)
	293	if attr.has_key('name'):
	294	data_info.sample.name = attr['name']
	295
[8780e9a]	296	_store_content('SASsample/ID',
	297	dom, 'ID', data_info.sample)
	298	_store_float('SASsample/thickness',
	299	dom, 'thickness', data_info.sample)
	300	_store_float('SASsample/transmission',
	301	dom, 'transmission', data_info.sample)
	302	_store_float('SASsample/temperature',
	303	dom, 'temperature', data_info.sample)
	304	nodes = xpath.Evaluate('SASsample/details', dom)
	305	for item in nodes:
	306	try:
	307	detail_value, detail_attr = get_node_text(item)
	308	if detail_value is not None:
	309	data_info.sample.details.append(detail_value)
	310	except:
	311	logging.error("cansas_reader.read: error processing sample details\n %s" % sys.exc_value)
	312
	313	# Position (as a vector)
	314	_store_float('SASsample/position/x',
	315	dom, 'position.x', data_info.sample)
	316	_store_float('SASsample/position/y',
	317	dom, 'position.y', data_info.sample)
	318	_store_float('SASsample/position/z',
	319	dom, 'position.z', data_info.sample)
	320
	321	# Orientation (as a vector)
	322	_store_float('SASsample/orientation/roll',
	323	dom, 'orientation.x', data_info.sample)
	324	_store_float('SASsample/orientation/pitch',
	325	dom, 'orientation.y', data_info.sample)
	326	_store_float('SASsample/orientation/yaw',
	327	dom, 'orientation.z', data_info.sample)
	328
	329	# Source info ###################
[4c00964]	330	value, attr = get_content('SASinstrument/SASsource', dom)
	331	if attr.has_key('name'):
	332	data_info.source.name = attr['name']
	333
[8780e9a]	334	_store_content('SASinstrument/SASsource/radiation',
	335	dom, 'radiation', data_info.source)
	336	_store_content('SASinstrument/SASsource/beam_shape',
	337	dom, 'beam_shape', data_info.source)
	338	_store_float('SASinstrument/SASsource/wavelength',
	339	dom, 'wavelength', data_info.source)
	340	_store_float('SASinstrument/SASsource/wavelength_min',
	341	dom, 'wavelength_min', data_info.source)
	342	_store_float('SASinstrument/SASsource/wavelength_max',
	343	dom, 'wavelength_max', data_info.source)
	344	_store_float('SASinstrument/SASsource/wavelength_spread',
	345	dom, 'wavelength_spread', data_info.source)
	346
[579ba85]	347	# Beam size (as a vector)
	348	value, attr = get_content('SASinstrument/SASsource/beam_size', dom)
	349	if attr.has_key('name'):
	350	data_info.source.beam_size_name = attr['name']
	351
[8780e9a]	352	_store_float('SASinstrument/SASsource/beam_size/x',
	353	dom, 'beam_size.x', data_info.source)
	354	_store_float('SASinstrument/SASsource/beam_size/y',
	355	dom, 'beam_size.y', data_info.source)
	356	_store_float('SASinstrument/SASsource/beam_size/z',
	357	dom, 'beam_size.z', data_info.source)
	358
	359	# Collimation info ###################
	360	nodes = xpath.Evaluate('SASinstrument/SAScollimation', dom)
	361	for item in nodes:
	362	collim = Collimation()
[4c00964]	363	value, attr = get_node_text(item)
	364	if attr.has_key('name'):
	365	collim.name = attr['name']
[8780e9a]	366	_store_float('length', item, 'length', collim)
	367
	368	# Look for apertures
	369	apert_list = xpath.Evaluate('aperture', item)
	370	for apert in apert_list:
[d6513cd]	371	aperture = Aperture()
[4c00964]	372
	373	# Get the name and type of the aperture
[579ba85]	374	ap_value, ap_attr = get_node_text(apert)
[4c00964]	375	if ap_attr.has_key('name'):
	376	aperture.name = ap_attr['name']
	377	if ap_attr.has_key('type'):
	378	aperture.type = ap_attr['type']
	379
[8780e9a]	380	_store_float('distance', apert, 'distance', aperture)
[579ba85]	381
	382	value, attr = get_content('size', apert)
	383	if attr.has_key('name'):
	384	aperture.size_name = attr['name']
	385
[8780e9a]	386	_store_float('size/x', apert, 'size.x', aperture)
	387	_store_float('size/y', apert, 'size.y', aperture)
	388	_store_float('size/z', apert, 'size.z', aperture)
	389
	390	collim.aperture.append(aperture)
	391
	392	data_info.collimation.append(collim)
	393
	394	# Detector info ######################
	395	nodes = xpath.Evaluate('SASinstrument/SASdetector', dom)
	396	for item in nodes:
	397
	398	detector = Detector()
	399
	400	_store_content('name', item, 'name', detector)
	401	_store_float('SDD', item, 'distance', detector)
	402
	403	# Detector offset (as a vector)
	404	_store_float('offset/x', item, 'offset.x', detector)
	405	_store_float('offset/y', item, 'offset.y', detector)
	406	_store_float('offset/z', item, 'offset.z', detector)
	407
	408	# Detector orientation (as a vector)
[579ba85]	409	_store_float('orientation/roll', item, 'orientation.x', detector)
	410	_store_float('orientation/pitch', item, 'orientation.y', detector)
	411	_store_float('orientation/yaw', item, 'orientation.z', detector)
[8780e9a]	412
	413	# Beam center (as a vector)
	414	_store_float('beam_center/x', item, 'beam_center.x', detector)
	415	_store_float('beam_center/y', item, 'beam_center.y', detector)
	416	_store_float('beam_center/z', item, 'beam_center.z', detector)
	417
	418	# Pixel size (as a vector)
	419	_store_float('pixel_size/x', item, 'pixel_size.x', detector)
	420	_store_float('pixel_size/y', item, 'pixel_size.y', detector)
	421	_store_float('pixel_size/z', item, 'pixel_size.z', detector)
	422
	423	_store_float('slit_length', item, 'slit_length', detector)
	424
	425	data_info.detector.append(detector)
	426
	427	# Processes info ######################
	428	nodes = xpath.Evaluate('SASprocess', dom)
	429	for item in nodes:
	430	process = Process()
	431	_store_content('name', item, 'name', process)
	432	_store_content('date', item, 'date', process)
	433	_store_content('description', item, 'description', process)
	434
	435	term_list = xpath.Evaluate('term', item)
	436	for term in term_list:
	437	try:
	438	term_value, term_attr = get_node_text(term)
	439	term_attr['value'] = term_value
	440	if term_value is not None:
	441	process.term.append(term_attr)
	442	except:
	443	logging.error("cansas_reader.read: error processing process term\n %s" % sys.exc_value)
	444
	445	note_list = xpath.Evaluate('SASprocessnote', item)
	446	for note in note_list:
	447	try:
	448	note_value, note_attr = get_node_text(note)
	449	if note_value is not None:
	450	process.notes.append(note_value)
	451	except:
	452	logging.error("cansas_reader.read: error processing process notes\n %s" % sys.exc_value)
	453
	454
	455	data_info.process.append(process)
	456
	457
	458	# Data info ######################
[579ba85]	459	nodes = xpath.Evaluate('SASdata', dom)
	460	if len(nodes)>1:
	461	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
	462
[8780e9a]	463	nodes = xpath.Evaluate('SASdata/Idata', dom)
	464	x = numpy.zeros(0)
	465	y = numpy.zeros(0)
	466	dx = numpy.zeros(0)
	467	dy = numpy.zeros(0)
[d00f8ff]	468	dxw = numpy.zeros(0)
	469	dxl = numpy.zeros(0)
[8780e9a]	470
	471	for item in nodes:
	472	_x, attr = get_float('Q', item)
[e390933]	473	_dx, attr_d = get_float('Qdev', item)
[d00f8ff]	474	_dxl, attr_l = get_float('dQl', item)
	475	_dxw, attr_w = get_float('dQw', item)
[8780e9a]	476	if _dx == None:
	477	_dx = 0.0
[d00f8ff]	478	if _dxl == None:
	479	_dxl = 0.0
	480	if _dxw == None:
	481	_dxw = 0.0
[8780e9a]	482
[e390933]	483	if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower():
	484	if has_converter==True:
	485	try:
	486	data_conv_q = Converter(attr['unit'])
	487	_x = data_conv_q(_x, units=data_info.x_unit)
	488	except:
	489	raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \
	490	% (attr['unit'], data_info.x_unit, sys.exc_value)
	491	else:
	492	raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \
	493	% (attr['unit'], data_info.x_unit)
[d00f8ff]	494	# Error in Q
[e390933]	495	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower():
	496	if has_converter==True:
	497	try:
	498	data_conv_q = Converter(attr_d['unit'])
	499	_dx = data_conv_q(_dx, units=data_info.x_unit)
	500	except:
	501	raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \
	502	% (attr['unit'], data_info.x_unit, sys.exc_value)
	503	else:
	504	raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \
	505	% (attr['unit'], data_info.x_unit)
[d00f8ff]	506	# Slit length
	507	if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower():
	508	if has_converter==True:
	509	try:
	510	data_conv_q = Converter(attr_l['unit'])
	511	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
	512	except:
	513	raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \
	514	% (attr['unit'], data_info.x_unit, sys.exc_value)
	515	else:
	516	raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \
	517	% (attr['unit'], data_info.x_unit)
	518	# Slit width
	519	if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower():
	520	if has_converter==True:
	521	try:
	522	data_conv_q = Converter(attr_w['unit'])
	523	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
	524	except:
	525	raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \
	526	% (attr['unit'], data_info.x_unit, sys.exc_value)
	527	else:
	528	raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \
	529	% (attr['unit'], data_info.x_unit)
[e390933]	530
[8780e9a]	531	_y, attr = get_float('I', item)
[e390933]	532	_dy, attr_d = get_float('Idev', item)
[8780e9a]	533	if _dy == None:
	534	_dy = 0.0
	535	if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower():
[e390933]	536	if has_converter==True:
	537	try:
	538	data_conv_i = Converter(attr['unit'])
	539	_y = data_conv_i(_y, units=data_info.y_unit)
	540	except:
	541	raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \
	542	% (attr['unit'], data_info.y_unit, sys.exc_value)
	543	else:
	544	raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \
	545	% (attr['unit'], data_info.y_unit)
	546	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower():
	547	if has_converter==True:
	548	try:
	549	data_conv_i = Converter(attr_d['unit'])
	550	_dy = data_conv_i(_dy, units=data_info.y_unit)
	551	except:
	552	raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \
	553	% (attr_d['unit'], data_info.y_unit, sys.exc_value)
	554	else:
	555	raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \
	556	% (attr_d['unit'], data_info.y_unit)
[8780e9a]	557
	558	if _x is not None and _y is not None:
	559	x = numpy.append(x, _x)
[579ba85]	560	y = numpy.append(y, _y)
	561	dx = numpy.append(dx, _dx)
	562	dy = numpy.append(dy, _dy)
[d00f8ff]	563	dxl = numpy.append(dxl, _dxl)
	564	dxw = numpy.append(dxw, _dxw)
	565
[8780e9a]	566
	567	data_info.x = x
	568	data_info.y = y
	569	data_info.dx = dx
	570	data_info.dy = dy
[d00f8ff]	571	data_info.dxl = dxl
	572	data_info.dxw = dxw
[d6513cd]	573
	574	data_conv_q = None
	575	data_conv_i = None
	576
[ca10d8e]	577	if has_converter == True and data_info.x_unit != '1/A':
	578	data_conv_q = Converter('1/A')
[d6513cd]	579	# Test it
	580	data_conv_q(1.0, output.Q_unit)
	581
[ca10d8e]	582	if has_converter == True and data_info.y_unit != '1/cm':
	583	data_conv_i = Converter('1/cm')
[d6513cd]	584	# Test it
[e390933]	585	data_conv_i(1.0, output.I_unit)
	586
[99d1af6]	587	if data_conv_q is not None:
[d6513cd]	588	data_info.xaxis("\\rm{Q}", data_info.x_unit)
[99d1af6]	589	else:
	590	data_info.xaxis("\\rm{Q}", 'A^{-1}')
	591	if data_conv_i is not None:
[0e2aa40]	592	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
[99d1af6]	593	else:
[0e2aa40]	594	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
[99d1af6]	595
[8780e9a]	596	return data_info
	597
[4c00964]	598	def write(self, filename, datainfo):
	599	"""
	600	Write the content of a Data1D as a CanSAS XML file
	601
	602	@param filename: name of the file to write
	603	@param datainfo: Data1D object
	604	"""
	605
	606	if not datainfo.__class__ == Data1D:
	607	raise RuntimeError, "The cansas writer expects a Data1D instance"
	608
	609	doc = xml.dom.minidom.Document()
	610	main_node = doc.createElement("SASroot")
[fee780b]	611	main_node.setAttribute("version", self.version)
	612	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	613	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
	614	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
	615
[4c00964]	616	doc.appendChild(main_node)
	617
	618	entry_node = doc.createElement("SASentry")
	619	main_node.appendChild(entry_node)
	620
[579ba85]	621	write_node(doc, entry_node, "Title", datainfo.title)
	622
	623	for item in datainfo.run:
	624	runname = {}
	625	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
	626	runname = {'name': datainfo.run_name[item] }
	627	write_node(doc, entry_node, "Run", item, runname)
[4c00964]	628
	629	# Data info
	630	node = doc.createElement("SASdata")
	631	entry_node.appendChild(node)
	632
[579ba85]	633	for i in range(len(datainfo.x)):
	634	pt = doc.createElement("Idata")
	635	node.appendChild(pt)
	636	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
	637	if len(datainfo.y)>=i:
	638	write_node(doc, pt, "I", datainfo.y[i], {'unit':datainfo.y_unit})
[5b396b3]	639	if datainfo.dx !=None and len(datainfo.dx)>=i:
[579ba85]	640	write_node(doc, pt, "Qdev", datainfo.dx[i], {'unit':datainfo.x_unit})
[72b524b]	641	if datainfo.dx !=None and len(datainfo.dy)>=i:
[579ba85]	642	write_node(doc, pt, "Idev", datainfo.dy[i], {'unit':datainfo.y_unit})
	643
	644
[4c00964]	645	# Sample info
	646	sample = doc.createElement("SASsample")
[579ba85]	647	if datainfo.sample.name is not None:
	648	sample.setAttribute("name", str(datainfo.sample.name))
[4c00964]	649	entry_node.appendChild(sample)
[579ba85]	650	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[4c00964]	651	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
	652	write_node(doc, sample, "transmission", datainfo.sample.transmission)
	653	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
	654
	655	for item in datainfo.sample.details:
	656	write_node(doc, sample, "details", item)
	657
	658	pos = doc.createElement("position")
[579ba85]	659	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
	660	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
	661	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
[4c00964]	662	if written == True:
	663	sample.appendChild(pos)
	664
	665	ori = doc.createElement("orientation")
[579ba85]	666	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
	667	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
	668	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
[4c00964]	669	if written == True:
	670	sample.appendChild(ori)
	671
	672	# Instrument info
	673	instr = doc.createElement("SASinstrument")
	674	entry_node.appendChild(instr)
	675
	676	write_node(doc, instr, "name", datainfo.instrument)
	677
	678	# Source
	679	source = doc.createElement("SASsource")
[579ba85]	680	if datainfo.source.name is not None:
	681	source.setAttribute("name", str(datainfo.source.name))
[4c00964]	682	instr.appendChild(source)
	683
	684	write_node(doc, source, "radiation", datainfo.source.radiation)
	685	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
[579ba85]	686	size = doc.createElement("beam_size")
	687	if datainfo.source.beam_size_name is not None:
	688	size.setAttribute("name", str(datainfo.source.beam_size_name))
	689	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
	690	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
	691	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
	692	if written == True:
	693	source.appendChild(size)
	694
[4c00964]	695	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
	696	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
	697	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
	698	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
	699
	700	# Collimation
	701	for item in datainfo.collimation:
	702	coll = doc.createElement("SAScollimation")
[579ba85]	703	if item.name is not None:
	704	coll.setAttribute("name", str(item.name))
[4c00964]	705	instr.appendChild(coll)
	706
	707	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
	708
	709	for apert in item.aperture:
[579ba85]	710	ap = doc.createElement("aperture")
	711	if apert.name is not None:
	712	ap.setAttribute("name", str(apert.name))
	713	if apert.type is not None:
	714	ap.setAttribute("type", str(apert.type))
	715	coll.appendChild(ap)
[4c00964]	716
	717	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
	718
	719	size = doc.createElement("size")
[579ba85]	720	if apert.size_name is not None:
	721	size.setAttribute("name", str(apert.size_name))
	722	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
	723	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
	724	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
	725	if written == True:
	726	ap.appendChild(size)
[4c00964]	727
	728	# Detectors
	729	for item in datainfo.detector:
	730	det = doc.createElement("SASdetector")
[579ba85]	731	written = write_node(doc, det, "name", item.name)
	732	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
	733	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
	734	if written == True:
	735	instr.appendChild(det)
[4c00964]	736
	737	off = doc.createElement("offset")
[579ba85]	738	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
	739	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
	740	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
	741	if written == True:
	742	det.appendChild(off)
[4c00964]	743
	744	center = doc.createElement("beam_center")
[579ba85]	745	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
	746	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
	747	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
	748	if written == True:
	749	det.appendChild(center)
	750
[4c00964]	751	pix = doc.createElement("pixel_size")
[579ba85]	752	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
	753	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
	754	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
	755	if written == True:
	756	det.appendChild(pix)
	757
	758	ori = doc.createElement("orientation")
	759	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
	760	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
	761	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
	762	if written == True:
	763	det.appendChild(ori)
	764
[4c00964]	765
[579ba85]	766	# Processes info
[4c00964]	767	for item in datainfo.process:
	768	node = doc.createElement("SASprocess")
	769	entry_node.appendChild(node)
	770
[579ba85]	771	write_node(doc, node, "name", item.name)
	772	write_node(doc, node, "date", item.date)
	773	write_node(doc, node, "description", item.description)
	774	for term in item.term:
	775	value = term['value']
	776	del term['value']
	777	write_node(doc, node, "term", value, term)
	778	for note in item.notes:
	779	write_node(doc, node, "SASprocessnote", note)
[4c00964]	780
	781
	782	# Write the file
	783	fd = open(filename, 'w')
	784	fd.write(doc.toprettyxml())
	785	fd.close()
	786
	787
[8780e9a]	788	if __name__ == "__main__":
	789	logging.basicConfig(level=logging.ERROR,
	790	format='%(asctime)s %(levelname)s %(message)s',
	791	filename='cansas_reader.log',
	792	filemode='w')
	793	reader = Reader()
	794	print reader.read("../test/cansas1d.xml")
	795
	796
	797

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 07f8d9a

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