cansas_reader.py @ 8db3904

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 8db3904 was a01c743, checked in by Gervaise Alina <gervyh@…>, 14 years ago
raise an error when nothing can be read remove return none
Property mode set to `100644`
File size: 40.2 KB

Rev	Line
[8780e9a]	1
	2
[0997158f]	3	############################################################################
	4	#This software was developed by the University of Tennessee as part of the
	5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	6	#project funded by the US National Science Foundation.
	7	#If you use DANSE applications to do scientific research that leads to
	8	#publication, we ask that you acknowledge the use of the software with the
	9	#following sentence:
	10	#This work benefited from DANSE software developed under NSF award DMR-0520547.
	11	#copyright 2008,2009 University of Tennessee
	12	#############################################################################
	13
[579ba85]	14	# Known issue: reader not compatible with multiple SASdata entries
	15	# within a single SASentry. Will raise a runtime error.
[8780e9a]	16
[a7a5886]	17	#TODO: check that all vectors are written only if they have at
	18	# least one non-empty value
	19	#TODO: Writing only allows one SASentry per file.
	20	# Would be best to allow multiple entries.
[8780e9a]	21	#TODO: Store error list
	22	#TODO: Allow for additional meta data for each section
[a7a5886]	23	#TODO: Notes need to be implemented. They can be any XML
	24	# structure in version 1.0
[8780e9a]	25	# Process notes have the same problem.
[e390933]	26	#TODO: Unit conversion is not complete (temperature units are missing)
[8780e9a]	27
	28
	29	import logging
	30	import numpy
[a7a5886]	31	import os
	32	import sys
	33	from DataLoader.data_info import Data1D
	34	from DataLoader.data_info import Collimation
	35	from DataLoader.data_info import Detector
	36	from DataLoader.data_info import Process
	37	from DataLoader.data_info import Aperture
[b0d0723]	38	from lxml import etree
	39	import xml.dom.minidom
[8780e9a]	40
[b39c817]	41	has_converter = True
	42	try:
	43	from data_util.nxsunit import Converter
	44	except:
	45	has_converter = False
	46
[b0d0723]	47	CANSAS_NS = "cansas1d/1.0"
	48
[4c00964]	49	def write_node(doc, parent, name, value, attr={}):
	50	"""
[0997158f]	51	:param doc: document DOM
	52	:param parent: parent node
	53	:param name: tag of the element
	54	:param value: value of the child text node
	55	:param attr: attribute dictionary
	56
	57	:return: True if something was appended, otherwise False
[4c00964]	58	"""
	59	if value is not None:
	60	node = doc.createElement(name)
	61	node.appendChild(doc.createTextNode(str(value)))
	62	for item in attr:
	63	node.setAttribute(item, attr[item])
	64	parent.appendChild(node)
	65	return True
	66	return False
	67
[8780e9a]	68	def get_content(location, node):
	69	"""
[0997158f]	70	Get the first instance of the content of a xpath location.
	71
	72	:param location: xpath location
	73	:param node: node to start at
	74
	75	:return: Element, or None
[8780e9a]	76	"""
[b0d0723]	77	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
	78
[8780e9a]	79	if len(nodes)>0:
[b0d0723]	80	return nodes[0]
	81	else:
	82	return None
[8780e9a]	83
	84	def get_float(location, node):
	85	"""
[0997158f]	86	Get the content of a node as a float
	87
	88	:param location: xpath location
	89	:param node: node to start at
[8780e9a]	90	"""
[b0d0723]	91	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
	92
[8780e9a]	93	value = None
	94	attr = {}
[a7a5886]	95	if len(nodes) > 0:
[8780e9a]	96	try:
[b0d0723]	97	value = float(nodes[0].text)
[8780e9a]	98	except:
	99	# Could not pass, skip and return None
[a7a5886]	100	msg = "cansas_reader.get_float: could not "
	101	msg += " convert '%s' to float" % nodes[0].text
	102	logging.error(msg)
[b0d0723]	103	if nodes[0].get('unit') is not None:
	104	attr['unit'] = nodes[0].get('unit')
[8780e9a]	105	return value, attr
	106
[b39c817]	107
[8780e9a]	108	class Reader:
	109	"""
[0997158f]	110	Class to load cansas 1D XML files
	111
	112	:Dependencies:
	113	The CanSas reader requires PyXML 0.8.4 or later.
[8780e9a]	114	"""
	115	## CanSAS version
	116	version = '1.0'
	117	## File type
[28caa03]	118	type_name = "CanSAS 1D"
	119	## Wildcards
[7406040]	120	type = ["CanSAS 1D files (.xml)\|.xml",
	121	"CanSAS 1D AVE files (.AVEx)\|.AVEx",
	122	"CanSAS 1D AVE files (.ABSx)\|.ABSx"]
	123
[8780e9a]	124	## List of allowed extensions
[a7a5886]	125	ext = ['.xml', '.XML','.avex', '.AVEx', '.absx', 'ABSx']
[8780e9a]	126
[fe78c7b]	127	def __init__(self):
	128	## List of errors
	129	self.errors = []
	130
[8780e9a]	131	def read(self, path):
	132	"""
[0997158f]	133	Load data file
	134
	135	:param path: file path
	136
	137	:return: Data1D object if a single SASentry was found,
	138	or a list of Data1D objects if multiple entries were found,
	139	or None of nothing was found
	140
	141	:raise RuntimeError: when the file can't be opened
	142	:raise ValueError: when the length of the data vectors are inconsistent
[8780e9a]	143	"""
	144	output = []
	145	if os.path.isfile(path):
	146	basename = os.path.basename(path)
	147	root, extension = os.path.splitext(basename)
	148	if extension.lower() in self.ext:
	149
[b0d0723]	150	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
[8780e9a]	151	# Check the format version number
[a7a5886]	152	# Specifying the namespace will take care of the file
	153	# format version
[b0d0723]	154	root = tree.getroot()
	155
[a7a5886]	156	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
	157	namespaces={'ns': CANSAS_NS})
[8780e9a]	158
	159	for entry in entry_list:
[fe78c7b]	160	self.errors = []
[8780e9a]	161	sas_entry = self._parse_entry(entry)
	162	sas_entry.filename = basename
[fe78c7b]	163
	164	# Store loading process information
	165	sas_entry.errors = self.errors
	166	sas_entry.meta_data['loader'] = self.type_name
[8780e9a]	167	output.append(sas_entry)
	168
	169	else:
	170	raise RuntimeError, "%s is not a file" % path
	171	# Return output consistent with the loader's api
[a01c743]	172	if len(output) == 0:
	173	#cannot return none when it cannot read
	174	#return None
	175	raise RuntimeError, "%s cannot be read \n" % path
	176	elif len(output) == 1:
[8780e9a]	177	return output[0]
	178	else:
	179	return output
	180
	181	def _parse_entry(self, dom):
	182	"""
[0997158f]	183	Parse a SASentry
	184
	185	:param node: SASentry node
	186
	187	:return: Data1D object
[8780e9a]	188	"""
	189	x = numpy.zeros(0)
	190	y = numpy.zeros(0)
	191
	192	data_info = Data1D(x, y)
	193
[b0d0723]	194	# Look up title
[fe78c7b]	195	self._store_content('ns:Title', dom, 'title', data_info)
[b0d0723]	196
[579ba85]	197	# Look up run number
[b0d0723]	198	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
[579ba85]	199	for item in nodes:
[b0d0723]	200	if item.text is not None:
	201	value = item.text.strip()
	202	if len(value) > 0:
	203	data_info.run.append(value)
	204	if item.get('name') is not None:
	205	data_info.run_name[value] = item.get('name')
[579ba85]	206
[8780e9a]	207	# Look up instrument name
[a7a5886]	208	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument',
	209	data_info)
[8780e9a]	210
[b0d0723]	211	# Notes
	212	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
[8780e9a]	213	for note in note_list:
	214	try:
[b0d0723]	215	if note.text is not None:
	216	note_value = note.text.strip()
	217	if len(note_value) > 0:
	218	data_info.notes.append(note_value)
[8780e9a]	219	except:
[a7a5886]	220	err_mess = "cansas_reader.read: error processing"
	221	err_mess += " entry notes\n %s" % sys.exc_value
[fe78c7b]	222	self.errors.append(err_mess)
	223	logging.error(err_mess)
[8780e9a]	224
	225	# Sample info ###################
[b0d0723]	226	entry = get_content('ns:SASsample', dom)
	227	if entry is not None:
	228	data_info.sample.name = entry.get('name')
[579ba85]	229
[fe78c7b]	230	self._store_content('ns:SASsample/ns:ID',
[8780e9a]	231	dom, 'ID', data_info.sample)
[fe78c7b]	232	self._store_float('ns:SASsample/ns:thickness',
[8780e9a]	233	dom, 'thickness', data_info.sample)
[fe78c7b]	234	self._store_float('ns:SASsample/ns:transmission',
[8780e9a]	235	dom, 'transmission', data_info.sample)
[fe78c7b]	236	self._store_float('ns:SASsample/ns:temperature',
[8780e9a]	237	dom, 'temperature', data_info.sample)
[b0d0723]	238
[a7a5886]	239	nodes = dom.xpath('ns:SASsample/ns:details',
	240	namespaces={'ns': CANSAS_NS})
[8780e9a]	241	for item in nodes:
	242	try:
[b0d0723]	243	if item.text is not None:
	244	detail_value = item.text.strip()
	245	if len(detail_value) > 0:
	246	data_info.sample.details.append(detail_value)
[8780e9a]	247	except:
[a7a5886]	248	err_mess = "cansas_reader.read: error processing "
	249	err_mess += " sample details\n %s" % sys.exc_value
[fe78c7b]	250	self.errors.append(err_mess)
	251	logging.error(err_mess)
[8780e9a]	252
	253	# Position (as a vector)
[fe78c7b]	254	self._store_float('ns:SASsample/ns:position/ns:x',
[8780e9a]	255	dom, 'position.x', data_info.sample)
[fe78c7b]	256	self._store_float('ns:SASsample/ns:position/ns:y',
[8780e9a]	257	dom, 'position.y', data_info.sample)
[fe78c7b]	258	self._store_float('ns:SASsample/ns:position/ns:z',
[8780e9a]	259	dom, 'position.z', data_info.sample)
	260
	261	# Orientation (as a vector)
[fe78c7b]	262	self._store_float('ns:SASsample/ns:orientation/ns:roll',
[8780e9a]	263	dom, 'orientation.x', data_info.sample)
[fe78c7b]	264	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
[8780e9a]	265	dom, 'orientation.y', data_info.sample)
[fe78c7b]	266	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
[8780e9a]	267	dom, 'orientation.z', data_info.sample)
	268
	269	# Source info ###################
[b0d0723]	270	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
	271	if entry is not None:
	272	data_info.source.name = entry.get('name')
[4c00964]	273
[fe78c7b]	274	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
[8780e9a]	275	dom, 'radiation', data_info.source)
[fe78c7b]	276	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
[8780e9a]	277	dom, 'beam_shape', data_info.source)
[fe78c7b]	278	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
[8780e9a]	279	dom, 'wavelength', data_info.source)
[fe78c7b]	280	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
[8780e9a]	281	dom, 'wavelength_min', data_info.source)
[fe78c7b]	282	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
[8780e9a]	283	dom, 'wavelength_max', data_info.source)
[fe78c7b]	284	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
[8780e9a]	285	dom, 'wavelength_spread', data_info.source)
	286
[579ba85]	287	# Beam size (as a vector)
[b0d0723]	288	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
	289	if entry is not None:
	290	data_info.source.beam_size_name = entry.get('name')
[579ba85]	291
[fe78c7b]	292	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
[8780e9a]	293	dom, 'beam_size.x', data_info.source)
[fe78c7b]	294	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
[8780e9a]	295	dom, 'beam_size.y', data_info.source)
[fe78c7b]	296	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
[8780e9a]	297	dom, 'beam_size.z', data_info.source)
	298
	299	# Collimation info ###################
[a7a5886]	300	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
	301	namespaces={'ns': CANSAS_NS})
[8780e9a]	302	for item in nodes:
	303	collim = Collimation()
[b0d0723]	304	if item.get('name') is not None:
	305	collim.name = item.get('name')
[fe78c7b]	306	self._store_float('ns:length', item, 'length', collim)
[8780e9a]	307
	308	# Look for apertures
[b0d0723]	309	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
[8780e9a]	310	for apert in apert_list:
[d6513cd]	311	aperture = Aperture()
[4c00964]	312
	313	# Get the name and type of the aperture
[b0d0723]	314	aperture.name = apert.get('name')
	315	aperture.type = apert.get('type')
[4c00964]	316
[fe78c7b]	317	self._store_float('ns:distance', apert, 'distance', aperture)
[579ba85]	318
[b0d0723]	319	entry = get_content('ns:size', apert)
	320	if entry is not None:
	321	aperture.size_name = entry.get('name')
[579ba85]	322
[fe78c7b]	323	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
	324	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
	325	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
[8780e9a]	326
	327	collim.aperture.append(aperture)
	328
	329	data_info.collimation.append(collim)
	330
	331	# Detector info ######################
[a7a5886]	332	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
	333	namespaces={'ns': CANSAS_NS})
[8780e9a]	334	for item in nodes:
	335
	336	detector = Detector()
	337
[fe78c7b]	338	self._store_content('ns:name', item, 'name', detector)
	339	self._store_float('ns:SDD', item, 'distance', detector)
[8780e9a]	340
	341	# Detector offset (as a vector)
[fe78c7b]	342	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
	343	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
	344	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
[8780e9a]	345
	346	# Detector orientation (as a vector)
[a7a5886]	347	self._store_float('ns:orientation/ns:roll', item, 'orientation.x',
	348	detector)
	349	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y',
	350	detector)
	351	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z',
	352	detector)
[8780e9a]	353
	354	# Beam center (as a vector)
[a7a5886]	355	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x',
	356	detector)
	357	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y',
	358	detector)
	359	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z',
	360	detector)
[8780e9a]	361
	362	# Pixel size (as a vector)
[a7a5886]	363	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x',
	364	detector)
	365	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y',
	366	detector)
	367	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z',
	368	detector)
[8780e9a]	369
[fe78c7b]	370	self._store_float('ns:slit_length', item, 'slit_length', detector)
[8780e9a]	371
	372	data_info.detector.append(detector)
	373
	374	# Processes info ######################
[b0d0723]	375	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
[8780e9a]	376	for item in nodes:
	377	process = Process()
[fe78c7b]	378	self._store_content('ns:name', item, 'name', process)
	379	self._store_content('ns:date', item, 'date', process)
	380	self._store_content('ns:description', item, 'description', process)
[8780e9a]	381
[b0d0723]	382	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
[8780e9a]	383	for term in term_list:
	384	try:
[b0d0723]	385	term_attr = {}
	386	for attr in term.keys():
	387	term_attr[attr] = term.get(attr).strip()
	388	if term.text is not None:
	389	term_attr['value'] = term.text.strip()
[8780e9a]	390	process.term.append(term_attr)
	391	except:
[a7a5886]	392	err_mess = "cansas_reader.read: error processing "
	393	err_mess += " process term\n %s" % sys.exc_value
[fe78c7b]	394	self.errors.append(err_mess)
	395	logging.error(err_mess)
[8780e9a]	396
[a7a5886]	397	note_list = item.xpath('ns:SASprocessnote',
	398	namespaces={'ns': CANSAS_NS})
[8780e9a]	399	for note in note_list:
[b0d0723]	400	if note.text is not None:
	401	process.notes.append(note.text.strip())
[8780e9a]	402
	403	data_info.process.append(process)
	404
	405
	406	# Data info ######################
[b0d0723]	407	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
[a7a5886]	408	if len(nodes) > 1:
	409	msg = "CanSAS reader is not compatible with multiple"
	410	msg += " SASdata entries"
	411	raise RuntimeError, msg
[579ba85]	412
[b0d0723]	413	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
	414
[8780e9a]	415	x = numpy.zeros(0)
	416	y = numpy.zeros(0)
	417	dx = numpy.zeros(0)
	418	dy = numpy.zeros(0)
[d00f8ff]	419	dxw = numpy.zeros(0)
	420	dxl = numpy.zeros(0)
[8780e9a]	421
	422	for item in nodes:
[b0d0723]	423	_x, attr = get_float('ns:Q', item)
	424	_dx, attr_d = get_float('ns:Qdev', item)
	425	_dxl, attr_l = get_float('ns:dQl', item)
	426	_dxw, attr_w = get_float('ns:dQw', item)
[8780e9a]	427	if _dx == None:
	428	_dx = 0.0
[d00f8ff]	429	if _dxl == None:
	430	_dxl = 0.0
	431	if _dxw == None:
	432	_dxw = 0.0
[8780e9a]	433
[a7a5886]	434	if attr.has_key('unit') and \
	435	attr['unit'].lower() != data_info.x_unit.lower():
[e390933]	436	if has_converter==True:
	437	try:
	438	data_conv_q = Converter(attr['unit'])
	439	_x = data_conv_q(_x, units=data_info.x_unit)
	440	except:
[a7a5886]	441	msg = "CanSAS reader: could not convert "
	442	msg += "Q unit [%s]; "
	443	msg += "expecting [%s]\n %s" % (attr['unit'],
	444	data_info.x_unit, sys.exc_value)
	445	raise ValueError, msg
	446
[e390933]	447	else:
[a7a5886]	448	msg = "CanSAS reader: unrecognized Q unit [%s]; "
	449	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
	450	raise ValueError, msg
	451
[d00f8ff]	452	# Error in Q
[a7a5886]	453	if attr_d.has_key('unit') and \
	454	attr_d['unit'].lower() != data_info.x_unit.lower():
[e390933]	455	if has_converter==True:
	456	try:
	457	data_conv_q = Converter(attr_d['unit'])
	458	_dx = data_conv_q(_dx, units=data_info.x_unit)
	459	except:
[a7a5886]	460	msg = "CanSAS reader: could not convert dQ unit [%s];"
	461	msg += " expecting "
	462	msg += "[%s]\n %s" % (attr['unit'],
	463	data_info.x_unit, sys.exc_value)
	464	raise ValueError, msg
	465
[e390933]	466	else:
[a7a5886]	467	msg = "CanSAS reader: unrecognized dQ unit [%s]; "
	468	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
	469	raise ValueError, msg
	470
[d00f8ff]	471	# Slit length
[a7a5886]	472	if attr_l.has_key('unit') and \
	473	attr_l['unit'].lower() != data_info.x_unit.lower():
	474	if has_converter == True:
[d00f8ff]	475	try:
	476	data_conv_q = Converter(attr_l['unit'])
	477	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
	478	except:
[a7a5886]	479	msg = "CanSAS reader: could not convert dQl unit [%s];"
	480	msg += " expecting [%s]\n %s" % (attr['unit'],
	481	data_info.x_unit, sys.exc_value)
	482	raise ValueError, msg
	483
[d00f8ff]	484	else:
[a7a5886]	485	msg = "CanSAS reader: unrecognized dQl unit [%s];"
	486	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
	487	raise ValueError, msg
	488
[d00f8ff]	489	# Slit width
[a7a5886]	490	if attr_w.has_key('unit') and \
	491	attr_w['unit'].lower() != data_info.x_unit.lower():
	492	if has_converter == True:
[d00f8ff]	493	try:
	494	data_conv_q = Converter(attr_w['unit'])
	495	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
	496	except:
[a7a5886]	497	msg = "CanSAS reader: could not convert dQw unit [%s];"
	498	msg += " expecting [%s]\n %s" % (attr['unit'],
	499	data_info.x_unit, sys.exc_value)
	500	raise ValueError, msg
	501
[d00f8ff]	502	else:
[a7a5886]	503	msg = "CanSAS reader: unrecognized dQw unit [%s];"
	504	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
	505	raise ValueError, msg
[b0d0723]	506	_y, attr = get_float('ns:I', item)
	507	_dy, attr_d = get_float('ns:Idev', item)
[8780e9a]	508	if _dy == None:
	509	_dy = 0.0
[a7a5886]	510	if attr.has_key('unit') and \
	511	attr['unit'].lower() != data_info.y_unit.lower():
[e390933]	512	if has_converter==True:
	513	try:
	514	data_conv_i = Converter(attr['unit'])
	515	_y = data_conv_i(_y, units=data_info.y_unit)
	516	except:
[a7a5886]	517	msg = "CanSAS reader: could not convert I(q) unit [%s];"
	518	msg += " expecting [%s]\n %s" % (attr['unit'],
	519	data_info.y_unit, sys.exc_value)
	520	raise ValueError, msg
[e390933]	521	else:
[a7a5886]	522	msg = "CanSAS reader: unrecognized I(q) unit [%s];"
	523	msg += " expecting [%s]" % (attr['unit'], data_info.y_unit)
	524	raise ValueError, msg
	525
	526	if attr_d.has_key('unit') and \
	527	attr_d['unit'].lower() != data_info.y_unit.lower():
[e390933]	528	if has_converter==True:
	529	try:
	530	data_conv_i = Converter(attr_d['unit'])
	531	_dy = data_conv_i(_dy, units=data_info.y_unit)
	532	except:
[a7a5886]	533	msg = "CanSAS reader: could not convert dI(q) unit "
	534	msg += "[%s]; expecting [%s]\n %s" % (attr_d['unit'],
	535	data_info.y_unit, sys.exc_value)
	536	raise ValueError, msg
[e390933]	537	else:
[a7a5886]	538	msg = "CanSAS reader: unrecognized dI(q) unit [%s]; "
	539	msg += "expecting [%s]" % (attr_d['unit'], data_info.y_unit)
	540	raise ValueError, msg
[8780e9a]	541
	542	if _x is not None and _y is not None:
	543	x = numpy.append(x, _x)
[579ba85]	544	y = numpy.append(y, _y)
	545	dx = numpy.append(dx, _dx)
	546	dy = numpy.append(dy, _dy)
[d00f8ff]	547	dxl = numpy.append(dxl, _dxl)
	548	dxw = numpy.append(dxw, _dxw)
	549
[8780e9a]	550	data_info.x = x
	551	data_info.y = y
	552	data_info.dx = dx
	553	data_info.dy = dy
[d00f8ff]	554	data_info.dxl = dxl
	555	data_info.dxw = dxw
[d6513cd]	556
	557	data_conv_q = None
	558	data_conv_i = None
	559
[ca10d8e]	560	if has_converter == True and data_info.x_unit != '1/A':
	561	data_conv_q = Converter('1/A')
[d6513cd]	562	# Test it
	563	data_conv_q(1.0, output.Q_unit)
	564
[ca10d8e]	565	if has_converter == True and data_info.y_unit != '1/cm':
	566	data_conv_i = Converter('1/cm')
[d6513cd]	567	# Test it
[e390933]	568	data_conv_i(1.0, output.I_unit)
	569
[99d1af6]	570	if data_conv_q is not None:
[d6513cd]	571	data_info.xaxis("\\rm{Q}", data_info.x_unit)
[99d1af6]	572	else:
	573	data_info.xaxis("\\rm{Q}", 'A^{-1}')
	574	if data_conv_i is not None:
[0e2aa40]	575	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
[99d1af6]	576	else:
[0e2aa40]	577	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
[99d1af6]	578
[8780e9a]	579	return data_info
	580
[b3de3a45]	581	def _to_xml_doc(self, datainfo):
[4c00964]	582	"""
[0997158f]	583	Create an XML document to contain the content of a Data1D
	584
	585	:param datainfo: Data1D object
[4c00964]	586	"""
	587
[7d8094b]	588	if not issubclass(datainfo.__class__, Data1D):
[4c00964]	589	raise RuntimeError, "The cansas writer expects a Data1D instance"
	590
	591	doc = xml.dom.minidom.Document()
	592	main_node = doc.createElement("SASroot")
[fee780b]	593	main_node.setAttribute("version", self.version)
	594	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
[a7a5886]	595	main_node.setAttribute("xmlns:xsi",
	596	"http://www.w3.org/2001/XMLSchema-instance")
	597	main_node.setAttribute("xsi:schemaLocation",
	598	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
[fee780b]	599
[4c00964]	600	doc.appendChild(main_node)
	601
	602	entry_node = doc.createElement("SASentry")
	603	main_node.appendChild(entry_node)
	604
[579ba85]	605	write_node(doc, entry_node, "Title", datainfo.title)
	606	for item in datainfo.run:
	607	runname = {}
[a7a5886]	608	if datainfo.run_name.has_key(item) and \
	609	len(str(datainfo.run_name[item]))>1:
[579ba85]	610	runname = {'name': datainfo.run_name[item] }
	611	write_node(doc, entry_node, "Run", item, runname)
[4c00964]	612
	613	# Data info
	614	node = doc.createElement("SASdata")
	615	entry_node.appendChild(node)
	616
[579ba85]	617	for i in range(len(datainfo.x)):
	618	pt = doc.createElement("Idata")
	619	node.appendChild(pt)
	620	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
	621	if len(datainfo.y)>=i:
[a7a5886]	622	write_node(doc, pt, "I", datainfo.y[i],
	623	{'unit':datainfo.y_unit})
[5b396b3]	624	if datainfo.dx !=None and len(datainfo.dx)>=i:
[a7a5886]	625	write_node(doc, pt, "Qdev", datainfo.dx[i],
	626	{'unit':datainfo.x_unit})
[f31701c]	627	if datainfo.dy !=None and len(datainfo.dy)>=i:
[a7a5886]	628	write_node(doc, pt, "Idev", datainfo.dy[i],
	629	{'unit':datainfo.y_unit})
[579ba85]	630
	631
[4c00964]	632	# Sample info
	633	sample = doc.createElement("SASsample")
[579ba85]	634	if datainfo.sample.name is not None:
	635	sample.setAttribute("name", str(datainfo.sample.name))
[4c00964]	636	entry_node.appendChild(sample)
[579ba85]	637	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[a7a5886]	638	write_node(doc, sample, "thickness", datainfo.sample.thickness,
	639	{"unit":datainfo.sample.thickness_unit})
[4c00964]	640	write_node(doc, sample, "transmission", datainfo.sample.transmission)
[a7a5886]	641	write_node(doc, sample, "temperature", datainfo.sample.temperature,
	642	{"unit":datainfo.sample.temperature_unit})
[4c00964]	643
	644	for item in datainfo.sample.details:
	645	write_node(doc, sample, "details", item)
	646
	647	pos = doc.createElement("position")
[a7a5886]	648	written = write_node(doc, pos, "x", datainfo.sample.position.x,
	649	{"unit":datainfo.sample.position_unit})
	650	written = written \| write_node(doc, pos, "y",
	651	datainfo.sample.position.y,
	652	{"unit":datainfo.sample.position_unit})
	653	written = written \| write_node(doc, pos, "z",
	654	datainfo.sample.position.z,
	655	{"unit":datainfo.sample.position_unit})
[4c00964]	656	if written == True:
	657	sample.appendChild(pos)
	658
	659	ori = doc.createElement("orientation")
[a7a5886]	660	written = write_node(doc, ori, "roll",
	661	datainfo.sample.orientation.x,
	662	{"unit":datainfo.sample.orientation_unit})
	663	written = written \| write_node(doc, ori, "pitch",
	664	datainfo.sample.orientation.y,
	665	{"unit":datainfo.sample.orientation_unit})
	666	written = written \| write_node(doc, ori, "yaw",
	667	datainfo.sample.orientation.z,
	668	{"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))
[a7a5886]	689	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
	690	{"unit":datainfo.source.beam_size_unit})
	691	written = written \| write_node(doc, size, "y",
	692	datainfo.source.beam_size.y,
	693	{"unit":datainfo.source.beam_size_unit})
	694	written = written \| write_node(doc, size, "z",
	695	datainfo.source.beam_size.z,
	696	{"unit":datainfo.source.beam_size_unit})
[579ba85]	697	if written == True:
	698	source.appendChild(size)
	699
[a7a5886]	700	write_node(doc, source, "wavelength",
	701	datainfo.source.wavelength,
	702	{"unit":datainfo.source.wavelength_unit})
	703	write_node(doc, source, "wavelength_min",
	704	datainfo.source.wavelength_min,
	705	{"unit":datainfo.source.wavelength_min_unit})
	706	write_node(doc, source, "wavelength_max",
	707	datainfo.source.wavelength_max,
	708	{"unit":datainfo.source.wavelength_max_unit})
	709	write_node(doc, source, "wavelength_spread",
	710	datainfo.source.wavelength_spread,
	711	{"unit":datainfo.source.wavelength_spread_unit})
[4c00964]	712
	713	# Collimation
	714	for item in datainfo.collimation:
	715	coll = doc.createElement("SAScollimation")
[579ba85]	716	if item.name is not None:
	717	coll.setAttribute("name", str(item.name))
[4c00964]	718	instr.appendChild(coll)
	719
[a7a5886]	720	write_node(doc, coll, "length", item.length,
	721	{"unit":item.length_unit})
[4c00964]	722
	723	for apert in item.aperture:
[579ba85]	724	ap = doc.createElement("aperture")
	725	if apert.name is not None:
	726	ap.setAttribute("name", str(apert.name))
	727	if apert.type is not None:
	728	ap.setAttribute("type", str(apert.type))
	729	coll.appendChild(ap)
[4c00964]	730
[a7a5886]	731	write_node(doc, ap, "distance", apert.distance,
	732	{"unit":apert.distance_unit})
[4c00964]	733
	734	size = doc.createElement("size")
[579ba85]	735	if apert.size_name is not None:
	736	size.setAttribute("name", str(apert.size_name))
[a7a5886]	737	written = write_node(doc, size, "x", apert.size.x,
	738	{"unit":apert.size_unit})
	739	written = written \| write_node(doc, size, "y", apert.size.y,
	740	{"unit":apert.size_unit})
	741	written = written \| write_node(doc, size, "z", apert.size.z,
	742	{"unit":apert.size_unit})
[579ba85]	743	if written == True:
	744	ap.appendChild(size)
[4c00964]	745
	746	# Detectors
	747	for item in datainfo.detector:
	748	det = doc.createElement("SASdetector")
[579ba85]	749	written = write_node(doc, det, "name", item.name)
[a7a5886]	750	written = written \| write_node(doc, det, "SDD", item.distance,
	751	{"unit":item.distance_unit})
	752	written = written \| write_node(doc, det, "slit_length",
	753	item.slit_length,
	754	{"unit":item.slit_length_unit})
[579ba85]	755	if written == True:
	756	instr.appendChild(det)
[4c00964]	757
	758	off = doc.createElement("offset")
[a7a5886]	759	written = write_node(doc, off, "x", item.offset.x,
	760	{"unit":item.offset_unit})
	761	written = written \| write_node(doc, off, "y", item.offset.y,
	762	{"unit":item.offset_unit})
	763	written = written \| write_node(doc, off, "z", item.offset.z,
	764	{"unit":item.offset_unit})
[579ba85]	765	if written == True:
	766	det.appendChild(off)
[4c00964]	767
	768	center = doc.createElement("beam_center")
[a7a5886]	769	written = write_node(doc, center, "x", item.beam_center.x,
	770	{"unit":item.beam_center_unit})
	771	written = written \| write_node(doc, center, "y",
	772	item.beam_center.y,
	773	{"unit":item.beam_center_unit})
	774	written = written \| write_node(doc, center, "z",
	775	item.beam_center.z,
	776	{"unit":item.beam_center_unit})
[579ba85]	777	if written == True:
	778	det.appendChild(center)
	779
[4c00964]	780	pix = doc.createElement("pixel_size")
[a7a5886]	781	written = write_node(doc, pix, "x", item.pixel_size.x,
	782	{"unit":item.pixel_size_unit})
	783	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
	784	{"unit":item.pixel_size_unit})
	785	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
	786	{"unit":item.pixel_size_unit})
[579ba85]	787	if written == True:
	788	det.appendChild(pix)
	789
	790	ori = doc.createElement("orientation")
[a7a5886]	791	written = write_node(doc, ori, "roll", item.orientation.x,
	792	{"unit":item.orientation_unit})
	793	written = written \| write_node(doc, ori, "pitch",
	794	item.orientation.y,
	795	{"unit":item.orientation_unit})
	796	written = written \| write_node(doc, ori, "yaw",
	797	item.orientation.z,
	798	{"unit":item.orientation_unit})
[579ba85]	799	if written == True:
	800	det.appendChild(ori)
	801
[4c00964]	802
[579ba85]	803	# Processes info
[4c00964]	804	for item in datainfo.process:
	805	node = doc.createElement("SASprocess")
	806	entry_node.appendChild(node)
	807
[579ba85]	808	write_node(doc, node, "name", item.name)
	809	write_node(doc, node, "date", item.date)
	810	write_node(doc, node, "description", item.description)
	811	for term in item.term:
	812	value = term['value']
	813	del term['value']
	814	write_node(doc, node, "term", value, term)
	815	for note in item.notes:
	816	write_node(doc, node, "SASprocessnote", note)
[4c00964]	817
[b3de3a45]	818	# Return the document, and the SASentry node associated with
	819	# the data we just wrote
	820	return doc, entry_node
	821
	822	def write(self, filename, datainfo):
	823	"""
[0997158f]	824	Write the content of a Data1D as a CanSAS XML file
	825
	826	:param filename: name of the file to write
	827	:param datainfo: Data1D object
[b3de3a45]	828	"""
	829	# Create XML document
	830	doc, sasentry = self._to_xml_doc(datainfo)
[4c00964]	831	# Write the file
	832	fd = open(filename, 'w')
	833	fd.write(doc.toprettyxml())
	834	fd.close()
	835
[fe78c7b]	836	def _store_float(self, location, node, variable, storage, optional=True):
	837	"""
[0997158f]	838	Get the content of a xpath location and store
	839	the result. Check that the units are compatible
	840	with the destination. The value is expected to
	841	be a float.
	842
	843	The xpath location might or might not exist.
	844	If it does not exist, nothing is done
	845
	846	:param location: xpath location to fetch
	847	:param node: node to read the data from
	848	:param variable: name of the data member to store it in [string]
	849	:param storage: data object that has the 'variable' data member
[a7a5886]	850	:param optional: if True, no exception will be raised
	851	if unit conversion can't be done
[0997158f]	852
	853	:raise ValueError: raised when the units are not recognized
[fe78c7b]	854	"""
	855	entry = get_content(location, node)
	856	try:
	857	value = float(entry.text)
	858	except:
	859	value = None
	860
	861	if value is not None:
	862	# If the entry has units, check to see that they are
	863	# compatible with what we currently have in the data object
	864	units = entry.get('unit')
	865	if units is not None:
	866	toks = variable.split('.')
	867	exec "local_unit = storage.%s_unit" % toks[0]
	868	if units.lower()!=local_unit.lower():
	869	if has_converter==True:
	870	try:
	871	conv = Converter(units)
[a7a5886]	872	exec "storage.%s = %g" % (variable,
	873	conv(value, units=local_unit))
[fe78c7b]	874	except:
[a7a5886]	875	err_mess = "CanSAS reader: could not convert"
	876	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
[fe78c7b]	877	% (variable, units, local_unit, sys.exc_value)
	878	self.errors.append(err_mess)
	879	if optional:
	880	logging.info(err_mess)
	881	else:
	882	raise ValueError, err_mess
	883	else:
[a7a5886]	884	err_mess = "CanSAS reader: unrecognized %s unit [%s];"
	885	err_mess += " expecting [%s]" % (variable,
	886	units, local_unit)
[fe78c7b]	887	self.errors.append(err_mess)
	888	if optional:
	889	logging.info(err_mess)
	890	else:
	891	raise ValueError, err_mess
	892	else:
	893	exec "storage.%s = value" % variable
	894	else:
	895	exec "storage.%s = value" % variable
	896
	897	def _store_content(self, location, node, variable, storage):
	898	"""
[0997158f]	899	Get the content of a xpath location and store
	900	the result. The value is treated as a string.
	901
	902	The xpath location might or might not exist.
	903	If it does not exist, nothing is done
	904
	905	:param location: xpath location to fetch
	906	:param node: node to read the data from
	907	:param variable: name of the data member to store it in [string]
	908	:param storage: data object that has the 'variable' data member
	909
	910	:return: return a list of errors
[fe78c7b]	911	"""
	912	entry = get_content(location, node)
	913	if entry is not None and entry.text is not None:
	914	exec "storage.%s = entry.text.strip()" % variable
	915
	916
	917
[8780e9a]	918	if __name__ == "__main__":
	919	logging.basicConfig(level=logging.ERROR,
	920	format='%(asctime)s %(levelname)s %(message)s',
	921	filename='cansas_reader.log',
	922	filemode='w')
	923	reader = Reader()
	924	print reader.read("../test/cansas1d.xml")
[b0d0723]	925	#print reader.read("../test/latex_smeared.xml")
[8780e9a]	926
	927
	928

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 8db3904

Download in other formats: