cansas_reader.py @ 8e36cdd

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 8e36cdd was b0d0723, checked in by Mathieu Doucet <doucetm@…>, 15 years ago
dataloader: ported cansas reader to lxml
Property mode set to `100644`
File size: 34.2 KB

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

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 8e36cdd

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