cansas_reader.py @ ca10d8e

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 ca10d8e was ca10d8e, checked in by Gervaise Alina <gervyh@…>, 15 years ago
reverse code from version 1237 with modification on output axis unit
Property mode set to `100644`
File size: 34.7 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:
	155	raise ValueError, "CanSAS reader: could not convert %s unit [%s]; expecting [%s]\n %s" \
	156	% (variable, attr['unit'], local_unit, sys.exc_value)
	157	else:
	158	raise ValueError, "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \
	159	% (variable, attr['unit'], local_unit)
	160	else:
	161	exec "storage.%s = value" % variable
	162	else:
	163	exec "storage.%s = value" % variable
	164
[8780e9a]	165
	166	def _store_content(location, node, variable, storage):
	167	"""
	168	Get the content of a xpath location and store
	169	the result. The value is treated as a string.
	170
	171	The xpath location might or might not exist.
	172	If it does not exist, nothing is done
	173
	174	@param location: xpath location to fetch
	175	@param node: node to read the data from
	176	@param variable: name of the data member to store it in [string]
	177	@param storage: data object that has the 'variable' data member
	178	"""
	179	value, attr = get_content(location, node)
	180	if value is not None:
	181	exec "storage.%s = value" % variable
	182
	183
	184	class Reader:
	185	"""
	186	Class to load cansas 1D XML files
	187
	188	Dependencies:
	189	The CanSas reader requires PyXML 0.8.4 or later.
	190	"""
	191	## CanSAS version
	192	version = '1.0'
	193	## File type
	194	type = ["CanSAS 1D files (.xml)\|.xml"]
	195	## List of allowed extensions
	196	ext=['.xml', '.XML']
	197
	198	def read(self, path):
	199	"""
	200	Load data file
	201
	202	@param path: file path
	203	@return: Data1D object if a single SASentry was found,
	204	or a list of Data1D objects if multiple entries were found,
	205	or None of nothing was found
	206	@raise RuntimeError: when the file can't be opened
	207	@raise ValueError: when the length of the data vectors are inconsistent
	208	"""
	209	from xml.dom.minidom import parse
	210
	211	output = []
	212
	213	if os.path.isfile(path):
	214	basename = os.path.basename(path)
	215	root, extension = os.path.splitext(basename)
	216	if extension.lower() in self.ext:
	217
	218	dom = parse(path)
	219
	220	# Check the format version number
	221	nodes = xpath.Evaluate('SASroot', dom)
	222	if nodes[0].hasAttributes():
	223	for i in range(nodes[0].attributes.length):
	224	if nodes[0].attributes.item(i).nodeName=='version':
	225	if nodes[0].attributes.item(i).nodeValue != self.version:
	226	raise ValueError, "cansas_reader: unrecognized version number %s" % \
	227	nodes[0].attributes.item(i).nodeValue
	228
	229	entry_list = xpath.Evaluate('SASroot/SASentry', dom)
	230	for entry in entry_list:
	231	sas_entry = self._parse_entry(entry)
	232	sas_entry.filename = basename
	233	output.append(sas_entry)
	234
	235	else:
	236	raise RuntimeError, "%s is not a file" % path
	237
	238	# Return output consistent with the loader's api
	239	if len(output)==0:
	240	return None
	241	elif len(output)==1:
	242	return output[0]
	243	else:
	244	return output
	245
	246	def _parse_entry(self, dom):
	247	"""
	248	Parse a SASentry
	249
	250	@param node: SASentry node
	251	@return: Data1D object
	252	"""
	253	x = numpy.zeros(0)
	254	y = numpy.zeros(0)
	255
	256	data_info = Data1D(x, y)
	257
	258	# Look up title
	259	_store_content('Title', dom, 'title', data_info)
[579ba85]	260	# Look up run number
	261	nodes = xpath.Evaluate('Run', dom)
	262	for item in nodes:
	263	value, attr = get_node_text(item)
	264	if value is not None:
	265	data_info.run.append(value)
	266	if attr.has_key('name'):
	267	data_info.run_name[value] = attr['name']
	268
[8780e9a]	269	# Look up instrument name
[579ba85]	270	_store_content('SASinstrument/name', dom, 'instrument', data_info)
	271	#value, attr = get_content('SASinstrument', dom)
	272	#if attr.has_key('name'):
	273	# data_info.instrument = attr['name']
[8780e9a]	274
	275	note_list = xpath.Evaluate('SASnote', dom)
	276	for note in note_list:
	277	try:
	278	note_value, note_attr = get_node_text(note)
	279	if note_value is not None:
	280	data_info.notes.append(note_value)
	281	except:
	282	logging.error("cansas_reader.read: error processing entry notes\n %s" % sys.exc_value)
	283
	284
	285	# Sample info ###################
[579ba85]	286	value, attr = get_content('SASsample', dom)
	287	if attr.has_key('name'):
	288	data_info.sample.name = attr['name']
	289
[8780e9a]	290	_store_content('SASsample/ID',
	291	dom, 'ID', data_info.sample)
	292	_store_float('SASsample/thickness',
	293	dom, 'thickness', data_info.sample)
	294	_store_float('SASsample/transmission',
	295	dom, 'transmission', data_info.sample)
	296	_store_float('SASsample/temperature',
	297	dom, 'temperature', data_info.sample)
	298	nodes = xpath.Evaluate('SASsample/details', dom)
	299	for item in nodes:
	300	try:
	301	detail_value, detail_attr = get_node_text(item)
	302	if detail_value is not None:
	303	data_info.sample.details.append(detail_value)
	304	except:
	305	logging.error("cansas_reader.read: error processing sample details\n %s" % sys.exc_value)
	306
	307	# Position (as a vector)
	308	_store_float('SASsample/position/x',
	309	dom, 'position.x', data_info.sample)
	310	_store_float('SASsample/position/y',
	311	dom, 'position.y', data_info.sample)
	312	_store_float('SASsample/position/z',
	313	dom, 'position.z', data_info.sample)
	314
	315	# Orientation (as a vector)
	316	_store_float('SASsample/orientation/roll',
	317	dom, 'orientation.x', data_info.sample)
	318	_store_float('SASsample/orientation/pitch',
	319	dom, 'orientation.y', data_info.sample)
	320	_store_float('SASsample/orientation/yaw',
	321	dom, 'orientation.z', data_info.sample)
	322
	323	# Source info ###################
[4c00964]	324	value, attr = get_content('SASinstrument/SASsource', dom)
	325	if attr.has_key('name'):
	326	data_info.source.name = attr['name']
	327
[8780e9a]	328	_store_content('SASinstrument/SASsource/radiation',
	329	dom, 'radiation', data_info.source)
	330	_store_content('SASinstrument/SASsource/beam_shape',
	331	dom, 'beam_shape', data_info.source)
	332	_store_float('SASinstrument/SASsource/wavelength',
	333	dom, 'wavelength', data_info.source)
	334	_store_float('SASinstrument/SASsource/wavelength_min',
	335	dom, 'wavelength_min', data_info.source)
	336	_store_float('SASinstrument/SASsource/wavelength_max',
	337	dom, 'wavelength_max', data_info.source)
	338	_store_float('SASinstrument/SASsource/wavelength_spread',
	339	dom, 'wavelength_spread', data_info.source)
	340
[579ba85]	341	# Beam size (as a vector)
	342	value, attr = get_content('SASinstrument/SASsource/beam_size', dom)
	343	if attr.has_key('name'):
	344	data_info.source.beam_size_name = attr['name']
	345
[8780e9a]	346	_store_float('SASinstrument/SASsource/beam_size/x',
	347	dom, 'beam_size.x', data_info.source)
	348	_store_float('SASinstrument/SASsource/beam_size/y',
	349	dom, 'beam_size.y', data_info.source)
	350	_store_float('SASinstrument/SASsource/beam_size/z',
	351	dom, 'beam_size.z', data_info.source)
	352
	353	# Collimation info ###################
	354	nodes = xpath.Evaluate('SASinstrument/SAScollimation', dom)
	355	for item in nodes:
	356	collim = Collimation()
[4c00964]	357	value, attr = get_node_text(item)
	358	if attr.has_key('name'):
	359	collim.name = attr['name']
[8780e9a]	360	_store_float('length', item, 'length', collim)
	361
	362	# Look for apertures
	363	apert_list = xpath.Evaluate('aperture', item)
	364	for apert in apert_list:
[d6513cd]	365	aperture = Aperture()
[4c00964]	366
	367	# Get the name and type of the aperture
[579ba85]	368	ap_value, ap_attr = get_node_text(apert)
[4c00964]	369	if ap_attr.has_key('name'):
	370	aperture.name = ap_attr['name']
	371	if ap_attr.has_key('type'):
	372	aperture.type = ap_attr['type']
	373
[8780e9a]	374	_store_float('distance', apert, 'distance', aperture)
[579ba85]	375
	376	value, attr = get_content('size', apert)
	377	if attr.has_key('name'):
	378	aperture.size_name = attr['name']
	379
[8780e9a]	380	_store_float('size/x', apert, 'size.x', aperture)
	381	_store_float('size/y', apert, 'size.y', aperture)
	382	_store_float('size/z', apert, 'size.z', aperture)
	383
	384	collim.aperture.append(aperture)
	385
	386	data_info.collimation.append(collim)
	387
	388	# Detector info ######################
	389	nodes = xpath.Evaluate('SASinstrument/SASdetector', dom)
	390	for item in nodes:
	391
	392	detector = Detector()
	393
	394	_store_content('name', item, 'name', detector)
	395	_store_float('SDD', item, 'distance', detector)
	396
	397	# Detector offset (as a vector)
	398	_store_float('offset/x', item, 'offset.x', detector)
	399	_store_float('offset/y', item, 'offset.y', detector)
	400	_store_float('offset/z', item, 'offset.z', detector)
	401
	402	# Detector orientation (as a vector)
[579ba85]	403	_store_float('orientation/roll', item, 'orientation.x', detector)
	404	_store_float('orientation/pitch', item, 'orientation.y', detector)
	405	_store_float('orientation/yaw', item, 'orientation.z', detector)
[8780e9a]	406
	407	# Beam center (as a vector)
	408	_store_float('beam_center/x', item, 'beam_center.x', detector)
	409	_store_float('beam_center/y', item, 'beam_center.y', detector)
	410	_store_float('beam_center/z', item, 'beam_center.z', detector)
	411
	412	# Pixel size (as a vector)
	413	_store_float('pixel_size/x', item, 'pixel_size.x', detector)
	414	_store_float('pixel_size/y', item, 'pixel_size.y', detector)
	415	_store_float('pixel_size/z', item, 'pixel_size.z', detector)
	416
	417	_store_float('slit_length', item, 'slit_length', detector)
	418
	419	data_info.detector.append(detector)
	420
	421	# Processes info ######################
	422	nodes = xpath.Evaluate('SASprocess', dom)
	423	for item in nodes:
	424	process = Process()
	425	_store_content('name', item, 'name', process)
	426	_store_content('date', item, 'date', process)
	427	_store_content('description', item, 'description', process)
	428
	429	term_list = xpath.Evaluate('term', item)
	430	for term in term_list:
	431	try:
	432	term_value, term_attr = get_node_text(term)
	433	term_attr['value'] = term_value
	434	if term_value is not None:
	435	process.term.append(term_attr)
	436	except:
	437	logging.error("cansas_reader.read: error processing process term\n %s" % sys.exc_value)
	438
	439	note_list = xpath.Evaluate('SASprocessnote', item)
	440	for note in note_list:
	441	try:
	442	note_value, note_attr = get_node_text(note)
	443	if note_value is not None:
	444	process.notes.append(note_value)
	445	except:
	446	logging.error("cansas_reader.read: error processing process notes\n %s" % sys.exc_value)
	447
	448
	449	data_info.process.append(process)
	450
	451
	452	# Data info ######################
[579ba85]	453	nodes = xpath.Evaluate('SASdata', dom)
	454	if len(nodes)>1:
	455	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
	456
[8780e9a]	457	nodes = xpath.Evaluate('SASdata/Idata', dom)
	458	x = numpy.zeros(0)
	459	y = numpy.zeros(0)
	460	dx = numpy.zeros(0)
	461	dy = numpy.zeros(0)
[d00f8ff]	462	dxw = numpy.zeros(0)
	463	dxl = numpy.zeros(0)
[8780e9a]	464
	465	for item in nodes:
	466	_x, attr = get_float('Q', item)
[e390933]	467	_dx, attr_d = get_float('Qdev', item)
[d00f8ff]	468	_dxl, attr_l = get_float('dQl', item)
	469	_dxw, attr_w = get_float('dQw', item)
[8780e9a]	470	if _dx == None:
	471	_dx = 0.0
[d00f8ff]	472	if _dxl == None:
	473	_dxl = 0.0
	474	if _dxw == None:
	475	_dxw = 0.0
[8780e9a]	476
[e390933]	477	if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower():
	478	if has_converter==True:
	479	try:
	480	data_conv_q = Converter(attr['unit'])
	481	_x = data_conv_q(_x, units=data_info.x_unit)
	482	except:
	483	raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \
	484	% (attr['unit'], data_info.x_unit, sys.exc_value)
	485	else:
	486	raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \
	487	% (attr['unit'], data_info.x_unit)
[d00f8ff]	488	# Error in Q
[e390933]	489	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower():
	490	if has_converter==True:
	491	try:
	492	data_conv_q = Converter(attr_d['unit'])
	493	_dx = data_conv_q(_dx, units=data_info.x_unit)
	494	except:
	495	raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \
	496	% (attr['unit'], data_info.x_unit, sys.exc_value)
	497	else:
	498	raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \
	499	% (attr['unit'], data_info.x_unit)
[d00f8ff]	500	# Slit length
	501	if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower():
	502	if has_converter==True:
	503	try:
	504	data_conv_q = Converter(attr_l['unit'])
	505	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
	506	except:
	507	raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \
	508	% (attr['unit'], data_info.x_unit, sys.exc_value)
	509	else:
	510	raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \
	511	% (attr['unit'], data_info.x_unit)
	512	# Slit width
	513	if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower():
	514	if has_converter==True:
	515	try:
	516	data_conv_q = Converter(attr_w['unit'])
	517	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
	518	except:
	519	raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \
	520	% (attr['unit'], data_info.x_unit, sys.exc_value)
	521	else:
	522	raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \
	523	% (attr['unit'], data_info.x_unit)
[e390933]	524
[8780e9a]	525	_y, attr = get_float('I', item)
[e390933]	526	_dy, attr_d = get_float('Idev', item)
[8780e9a]	527	if _dy == None:
	528	_dy = 0.0
	529	if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower():
[e390933]	530	if has_converter==True:
	531	try:
	532	data_conv_i = Converter(attr['unit'])
	533	_y = data_conv_i(_y, units=data_info.y_unit)
	534	except:
	535	raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \
	536	% (attr['unit'], data_info.y_unit, sys.exc_value)
	537	else:
	538	raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \
	539	% (attr['unit'], data_info.y_unit)
	540	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower():
	541	if has_converter==True:
	542	try:
	543	data_conv_i = Converter(attr_d['unit'])
	544	_dy = data_conv_i(_dy, units=data_info.y_unit)
	545	except:
	546	raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \
	547	% (attr_d['unit'], data_info.y_unit, sys.exc_value)
	548	else:
	549	raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \
	550	% (attr_d['unit'], data_info.y_unit)
[8780e9a]	551
	552	if _x is not None and _y is not None:
	553	x = numpy.append(x, _x)
[579ba85]	554	y = numpy.append(y, _y)
	555	dx = numpy.append(dx, _dx)
	556	dy = numpy.append(dy, _dy)
[d00f8ff]	557	dxl = numpy.append(dxl, _dxl)
	558	dxw = numpy.append(dxw, _dxw)
	559
[8780e9a]	560
	561	data_info.x = x
	562	data_info.y = y
	563	data_info.dx = dx
	564	data_info.dy = dy
[d00f8ff]	565	data_info.dxl = dxl
	566	data_info.dxw = dxw
[d6513cd]	567
	568	data_conv_q = None
	569	data_conv_i = None
	570
[ca10d8e]	571	if has_converter == True and data_info.x_unit != '1/A':
	572	data_conv_q = Converter('1/A')
[d6513cd]	573	# Test it
	574	data_conv_q(1.0, output.Q_unit)
	575
[ca10d8e]	576	if has_converter == True and data_info.y_unit != '1/cm':
	577	data_conv_i = Converter('1/cm')
[d6513cd]	578	# Test it
[e390933]	579	data_conv_i(1.0, output.I_unit)
	580
[99d1af6]	581	if data_conv_q is not None:
[d6513cd]	582	data_info.xaxis("\\rm{Q}", data_info.x_unit)
[99d1af6]	583	else:
	584	data_info.xaxis("\\rm{Q}", 'A^{-1}')
	585	if data_conv_i is not None:
[d6513cd]	586	data_info.yaxis("\\{I(Q)}", data_info.y_unit)
[99d1af6]	587	else:
	588	data_info.yaxis("\\rm{I(Q)}","cm^{-1}")
	589
[8780e9a]	590	return data_info
	591
[4c00964]	592	def write(self, filename, datainfo):
	593	"""
	594	Write the content of a Data1D as a CanSAS XML file
	595
	596	@param filename: name of the file to write
	597	@param datainfo: Data1D object
	598	"""
	599
	600	if not datainfo.__class__ == Data1D:
	601	raise RuntimeError, "The cansas writer expects a Data1D instance"
	602
	603	doc = xml.dom.minidom.Document()
	604	main_node = doc.createElement("SASroot")
[fee780b]	605	main_node.setAttribute("version", self.version)
	606	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	607	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
	608	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
	609
[4c00964]	610	doc.appendChild(main_node)
	611
	612	entry_node = doc.createElement("SASentry")
	613	main_node.appendChild(entry_node)
	614
[579ba85]	615	write_node(doc, entry_node, "Title", datainfo.title)
	616
	617	for item in datainfo.run:
	618	runname = {}
	619	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
	620	runname = {'name': datainfo.run_name[item] }
	621	write_node(doc, entry_node, "Run", item, runname)
[4c00964]	622
	623	# Data info
	624	node = doc.createElement("SASdata")
	625	entry_node.appendChild(node)
	626
[579ba85]	627	for i in range(len(datainfo.x)):
	628	pt = doc.createElement("Idata")
	629	node.appendChild(pt)
	630	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
	631	if len(datainfo.y)>=i:
	632	write_node(doc, pt, "I", datainfo.y[i], {'unit':datainfo.y_unit})
	633	if len(datainfo.dx)>=i:
	634	write_node(doc, pt, "Qdev", datainfo.dx[i], {'unit':datainfo.x_unit})
	635	if len(datainfo.dy)>=i:
	636	write_node(doc, pt, "Idev", datainfo.dy[i], {'unit':datainfo.y_unit})
	637
	638
[4c00964]	639	# Sample info
	640	sample = doc.createElement("SASsample")
[579ba85]	641	if datainfo.sample.name is not None:
	642	sample.setAttribute("name", str(datainfo.sample.name))
[4c00964]	643	entry_node.appendChild(sample)
[579ba85]	644	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[4c00964]	645	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
	646	write_node(doc, sample, "transmission", datainfo.sample.transmission)
	647	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
	648
	649	for item in datainfo.sample.details:
	650	write_node(doc, sample, "details", item)
	651
	652	pos = doc.createElement("position")
[579ba85]	653	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
	654	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
	655	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
[4c00964]	656	if written == True:
	657	sample.appendChild(pos)
	658
	659	ori = doc.createElement("orientation")
[579ba85]	660	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
	661	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
	662	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
[4c00964]	663	if written == True:
	664	sample.appendChild(ori)
	665
	666	# Instrument info
	667	instr = doc.createElement("SASinstrument")
	668	entry_node.appendChild(instr)
	669
	670	write_node(doc, instr, "name", datainfo.instrument)
	671
	672	# Source
	673	source = doc.createElement("SASsource")
[579ba85]	674	if datainfo.source.name is not None:
	675	source.setAttribute("name", str(datainfo.source.name))
[4c00964]	676	instr.appendChild(source)
	677
	678	write_node(doc, source, "radiation", datainfo.source.radiation)
	679	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
[579ba85]	680	size = doc.createElement("beam_size")
	681	if datainfo.source.beam_size_name is not None:
	682	size.setAttribute("name", str(datainfo.source.beam_size_name))
	683	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
	684	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
	685	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
	686	if written == True:
	687	source.appendChild(size)
	688
[4c00964]	689	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
	690	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
	691	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
	692	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
	693
	694	# Collimation
	695	for item in datainfo.collimation:
	696	coll = doc.createElement("SAScollimation")
[579ba85]	697	if item.name is not None:
	698	coll.setAttribute("name", str(item.name))
[4c00964]	699	instr.appendChild(coll)
	700
	701	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
	702
	703	for apert in item.aperture:
[579ba85]	704	ap = doc.createElement("aperture")
	705	if apert.name is not None:
	706	ap.setAttribute("name", str(apert.name))
	707	if apert.type is not None:
	708	ap.setAttribute("type", str(apert.type))
	709	coll.appendChild(ap)
[4c00964]	710
	711	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
	712
	713	size = doc.createElement("size")
[579ba85]	714	if apert.size_name is not None:
	715	size.setAttribute("name", str(apert.size_name))
	716	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
	717	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
	718	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
	719	if written == True:
	720	ap.appendChild(size)
[4c00964]	721
	722	# Detectors
	723	for item in datainfo.detector:
	724	det = doc.createElement("SASdetector")
[579ba85]	725	written = write_node(doc, det, "name", item.name)
	726	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
	727	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
	728	if written == True:
	729	instr.appendChild(det)
[4c00964]	730
	731	off = doc.createElement("offset")
[579ba85]	732	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
	733	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
	734	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
	735	if written == True:
	736	det.appendChild(off)
[4c00964]	737
	738	center = doc.createElement("beam_center")
[579ba85]	739	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
	740	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
	741	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
	742	if written == True:
	743	det.appendChild(center)
	744
[4c00964]	745	pix = doc.createElement("pixel_size")
[579ba85]	746	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
	747	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
	748	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
	749	if written == True:
	750	det.appendChild(pix)
	751
	752	ori = doc.createElement("orientation")
	753	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
	754	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
	755	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
	756	if written == True:
	757	det.appendChild(ori)
	758
[4c00964]	759
[579ba85]	760	# Processes info
[4c00964]	761	for item in datainfo.process:
	762	node = doc.createElement("SASprocess")
	763	entry_node.appendChild(node)
	764
[579ba85]	765	write_node(doc, node, "name", item.name)
	766	write_node(doc, node, "date", item.date)
	767	write_node(doc, node, "description", item.description)
	768	for term in item.term:
	769	value = term['value']
	770	del term['value']
	771	write_node(doc, node, "term", value, term)
	772	for note in item.notes:
	773	write_node(doc, node, "SASprocessnote", note)
[4c00964]	774
	775
	776	# Write the file
	777	fd = open(filename, 'w')
	778	fd.write(doc.toprettyxml())
	779	fd.close()
	780
	781
[8780e9a]	782	if __name__ == "__main__":
	783	logging.basicConfig(level=logging.ERROR,
	784	format='%(asctime)s %(levelname)s %(message)s',
	785	filename='cansas_reader.log',
	786	filemode='w')
	787	reader = Reader()
	788	print reader.read("../test/cansas1d.xml")
	789
	790
	791

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ ca10d8e

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