cansas_reader.py @ da9ac4e6

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 da9ac4e6 was a7a5886, checked in by Gervaise Alina <gervyh@…>, 14 years ago
working pylint
Property mode set to `100644`
File size: 40.1 KB

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[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
	172	if len(output)==0:
	173	return None
	174	elif len(output)==1:
	175	return output[0]
	176	else:
	177	return output
	178
	179	def _parse_entry(self, dom):
	180	"""
[0997158f]	181	Parse a SASentry
	182
	183	:param node: SASentry node
	184
	185	:return: Data1D object
[8780e9a]	186	"""
	187	x = numpy.zeros(0)
	188	y = numpy.zeros(0)
	189
	190	data_info = Data1D(x, y)
	191
[b0d0723]	192	# Look up title
[fe78c7b]	193	self._store_content('ns:Title', dom, 'title', data_info)
[b0d0723]	194
[579ba85]	195	# Look up run number
[b0d0723]	196	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
[579ba85]	197	for item in nodes:
[b0d0723]	198	if item.text is not None:
	199	value = item.text.strip()
	200	if len(value) > 0:
	201	data_info.run.append(value)
	202	if item.get('name') is not None:
	203	data_info.run_name[value] = item.get('name')
[579ba85]	204
[8780e9a]	205	# Look up instrument name
[a7a5886]	206	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument',
	207	data_info)
[8780e9a]	208
[b0d0723]	209	# Notes
	210	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
[8780e9a]	211	for note in note_list:
	212	try:
[b0d0723]	213	if note.text is not None:
	214	note_value = note.text.strip()
	215	if len(note_value) > 0:
	216	data_info.notes.append(note_value)
[8780e9a]	217	except:
[a7a5886]	218	err_mess = "cansas_reader.read: error processing"
	219	err_mess += " entry notes\n %s" % sys.exc_value
[fe78c7b]	220	self.errors.append(err_mess)
	221	logging.error(err_mess)
[8780e9a]	222
	223	# Sample info ###################
[b0d0723]	224	entry = get_content('ns:SASsample', dom)
	225	if entry is not None:
	226	data_info.sample.name = entry.get('name')
[579ba85]	227
[fe78c7b]	228	self._store_content('ns:SASsample/ns:ID',
[8780e9a]	229	dom, 'ID', data_info.sample)
[fe78c7b]	230	self._store_float('ns:SASsample/ns:thickness',
[8780e9a]	231	dom, 'thickness', data_info.sample)
[fe78c7b]	232	self._store_float('ns:SASsample/ns:transmission',
[8780e9a]	233	dom, 'transmission', data_info.sample)
[fe78c7b]	234	self._store_float('ns:SASsample/ns:temperature',
[8780e9a]	235	dom, 'temperature', data_info.sample)
[b0d0723]	236
[a7a5886]	237	nodes = dom.xpath('ns:SASsample/ns:details',
	238	namespaces={'ns': CANSAS_NS})
[8780e9a]	239	for item in nodes:
	240	try:
[b0d0723]	241	if item.text is not None:
	242	detail_value = item.text.strip()
	243	if len(detail_value) > 0:
	244	data_info.sample.details.append(detail_value)
[8780e9a]	245	except:
[a7a5886]	246	err_mess = "cansas_reader.read: error processing "
	247	err_mess += " sample details\n %s" % sys.exc_value
[fe78c7b]	248	self.errors.append(err_mess)
	249	logging.error(err_mess)
[8780e9a]	250
	251	# Position (as a vector)
[fe78c7b]	252	self._store_float('ns:SASsample/ns:position/ns:x',
[8780e9a]	253	dom, 'position.x', data_info.sample)
[fe78c7b]	254	self._store_float('ns:SASsample/ns:position/ns:y',
[8780e9a]	255	dom, 'position.y', data_info.sample)
[fe78c7b]	256	self._store_float('ns:SASsample/ns:position/ns:z',
[8780e9a]	257	dom, 'position.z', data_info.sample)
	258
	259	# Orientation (as a vector)
[fe78c7b]	260	self._store_float('ns:SASsample/ns:orientation/ns:roll',
[8780e9a]	261	dom, 'orientation.x', data_info.sample)
[fe78c7b]	262	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
[8780e9a]	263	dom, 'orientation.y', data_info.sample)
[fe78c7b]	264	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
[8780e9a]	265	dom, 'orientation.z', data_info.sample)
	266
	267	# Source info ###################
[b0d0723]	268	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
	269	if entry is not None:
	270	data_info.source.name = entry.get('name')
[4c00964]	271
[fe78c7b]	272	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
[8780e9a]	273	dom, 'radiation', data_info.source)
[fe78c7b]	274	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
[8780e9a]	275	dom, 'beam_shape', data_info.source)
[fe78c7b]	276	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
[8780e9a]	277	dom, 'wavelength', data_info.source)
[fe78c7b]	278	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
[8780e9a]	279	dom, 'wavelength_min', data_info.source)
[fe78c7b]	280	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
[8780e9a]	281	dom, 'wavelength_max', data_info.source)
[fe78c7b]	282	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
[8780e9a]	283	dom, 'wavelength_spread', data_info.source)
	284
[579ba85]	285	# Beam size (as a vector)
[b0d0723]	286	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
	287	if entry is not None:
	288	data_info.source.beam_size_name = entry.get('name')
[579ba85]	289
[fe78c7b]	290	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
[8780e9a]	291	dom, 'beam_size.x', data_info.source)
[fe78c7b]	292	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
[8780e9a]	293	dom, 'beam_size.y', data_info.source)
[fe78c7b]	294	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
[8780e9a]	295	dom, 'beam_size.z', data_info.source)
	296
	297	# Collimation info ###################
[a7a5886]	298	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
	299	namespaces={'ns': CANSAS_NS})
[8780e9a]	300	for item in nodes:
	301	collim = Collimation()
[b0d0723]	302	if item.get('name') is not None:
	303	collim.name = item.get('name')
[fe78c7b]	304	self._store_float('ns:length', item, 'length', collim)
[8780e9a]	305
	306	# Look for apertures
[b0d0723]	307	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
[8780e9a]	308	for apert in apert_list:
[d6513cd]	309	aperture = Aperture()
[4c00964]	310
	311	# Get the name and type of the aperture
[b0d0723]	312	aperture.name = apert.get('name')
	313	aperture.type = apert.get('type')
[4c00964]	314
[fe78c7b]	315	self._store_float('ns:distance', apert, 'distance', aperture)
[579ba85]	316
[b0d0723]	317	entry = get_content('ns:size', apert)
	318	if entry is not None:
	319	aperture.size_name = entry.get('name')
[579ba85]	320
[fe78c7b]	321	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
	322	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
	323	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
[8780e9a]	324
	325	collim.aperture.append(aperture)
	326
	327	data_info.collimation.append(collim)
	328
	329	# Detector info ######################
[a7a5886]	330	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
	331	namespaces={'ns': CANSAS_NS})
[8780e9a]	332	for item in nodes:
	333
	334	detector = Detector()
	335
[fe78c7b]	336	self._store_content('ns:name', item, 'name', detector)
	337	self._store_float('ns:SDD', item, 'distance', detector)
[8780e9a]	338
	339	# Detector offset (as a vector)
[fe78c7b]	340	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
	341	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
	342	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
[8780e9a]	343
	344	# Detector orientation (as a vector)
[a7a5886]	345	self._store_float('ns:orientation/ns:roll', item, 'orientation.x',
	346	detector)
	347	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y',
	348	detector)
	349	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z',
	350	detector)
[8780e9a]	351
	352	# Beam center (as a vector)
[a7a5886]	353	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x',
	354	detector)
	355	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y',
	356	detector)
	357	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z',
	358	detector)
[8780e9a]	359
	360	# Pixel size (as a vector)
[a7a5886]	361	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x',
	362	detector)
	363	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y',
	364	detector)
	365	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z',
	366	detector)
[8780e9a]	367
[fe78c7b]	368	self._store_float('ns:slit_length', item, 'slit_length', detector)
[8780e9a]	369
	370	data_info.detector.append(detector)
	371
	372	# Processes info ######################
[b0d0723]	373	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
[8780e9a]	374	for item in nodes:
	375	process = Process()
[fe78c7b]	376	self._store_content('ns:name', item, 'name', process)
	377	self._store_content('ns:date', item, 'date', process)
	378	self._store_content('ns:description', item, 'description', process)
[8780e9a]	379
[b0d0723]	380	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
[8780e9a]	381	for term in term_list:
	382	try:
[b0d0723]	383	term_attr = {}
	384	for attr in term.keys():
	385	term_attr[attr] = term.get(attr).strip()
	386	if term.text is not None:
	387	term_attr['value'] = term.text.strip()
[8780e9a]	388	process.term.append(term_attr)
	389	except:
[a7a5886]	390	err_mess = "cansas_reader.read: error processing "
	391	err_mess += " process term\n %s" % sys.exc_value
[fe78c7b]	392	self.errors.append(err_mess)
	393	logging.error(err_mess)
[8780e9a]	394
[a7a5886]	395	note_list = item.xpath('ns:SASprocessnote',
	396	namespaces={'ns': CANSAS_NS})
[8780e9a]	397	for note in note_list:
[b0d0723]	398	if note.text is not None:
	399	process.notes.append(note.text.strip())
[8780e9a]	400
	401	data_info.process.append(process)
	402
	403
	404	# Data info ######################
[b0d0723]	405	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
[a7a5886]	406	if len(nodes) > 1:
	407	msg = "CanSAS reader is not compatible with multiple"
	408	msg += " SASdata entries"
	409	raise RuntimeError, msg
[579ba85]	410
[b0d0723]	411	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
	412
[8780e9a]	413	x = numpy.zeros(0)
	414	y = numpy.zeros(0)
	415	dx = numpy.zeros(0)
	416	dy = numpy.zeros(0)
[d00f8ff]	417	dxw = numpy.zeros(0)
	418	dxl = numpy.zeros(0)
[8780e9a]	419
	420	for item in nodes:
[b0d0723]	421	_x, attr = get_float('ns:Q', item)
	422	_dx, attr_d = get_float('ns:Qdev', item)
	423	_dxl, attr_l = get_float('ns:dQl', item)
	424	_dxw, attr_w = get_float('ns:dQw', item)
[8780e9a]	425	if _dx == None:
	426	_dx = 0.0
[d00f8ff]	427	if _dxl == None:
	428	_dxl = 0.0
	429	if _dxw == None:
	430	_dxw = 0.0
[8780e9a]	431
[a7a5886]	432	if attr.has_key('unit') and \
	433	attr['unit'].lower() != data_info.x_unit.lower():
[e390933]	434	if has_converter==True:
	435	try:
	436	data_conv_q = Converter(attr['unit'])
	437	_x = data_conv_q(_x, units=data_info.x_unit)
	438	except:
[a7a5886]	439	msg = "CanSAS reader: could not convert "
	440	msg += "Q unit [%s]; "
	441	msg += "expecting [%s]\n %s" % (attr['unit'],
	442	data_info.x_unit, sys.exc_value)
	443	raise ValueError, msg
	444
[e390933]	445	else:
[a7a5886]	446	msg = "CanSAS reader: unrecognized Q unit [%s]; "
	447	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
	448	raise ValueError, msg
	449
[d00f8ff]	450	# Error in Q
[a7a5886]	451	if attr_d.has_key('unit') and \
	452	attr_d['unit'].lower() != data_info.x_unit.lower():
[e390933]	453	if has_converter==True:
	454	try:
	455	data_conv_q = Converter(attr_d['unit'])
	456	_dx = data_conv_q(_dx, units=data_info.x_unit)
	457	except:
[a7a5886]	458	msg = "CanSAS reader: could not convert dQ unit [%s];"
	459	msg += " expecting "
	460	msg += "[%s]\n %s" % (attr['unit'],
	461	data_info.x_unit, sys.exc_value)
	462	raise ValueError, msg
	463
[e390933]	464	else:
[a7a5886]	465	msg = "CanSAS reader: unrecognized dQ unit [%s]; "
	466	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
	467	raise ValueError, msg
	468
[d00f8ff]	469	# Slit length
[a7a5886]	470	if attr_l.has_key('unit') and \
	471	attr_l['unit'].lower() != data_info.x_unit.lower():
	472	if has_converter == True:
[d00f8ff]	473	try:
	474	data_conv_q = Converter(attr_l['unit'])
	475	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
	476	except:
[a7a5886]	477	msg = "CanSAS reader: could not convert dQl unit [%s];"
	478	msg += " expecting [%s]\n %s" % (attr['unit'],
	479	data_info.x_unit, sys.exc_value)
	480	raise ValueError, msg
	481
[d00f8ff]	482	else:
[a7a5886]	483	msg = "CanSAS reader: unrecognized dQl unit [%s];"
	484	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
	485	raise ValueError, msg
	486
[d00f8ff]	487	# Slit width
[a7a5886]	488	if attr_w.has_key('unit') and \
	489	attr_w['unit'].lower() != data_info.x_unit.lower():
	490	if has_converter == True:
[d00f8ff]	491	try:
	492	data_conv_q = Converter(attr_w['unit'])
	493	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
	494	except:
[a7a5886]	495	msg = "CanSAS reader: could not convert dQw unit [%s];"
	496	msg += " expecting [%s]\n %s" % (attr['unit'],
	497	data_info.x_unit, sys.exc_value)
	498	raise ValueError, msg
	499
[d00f8ff]	500	else:
[a7a5886]	501	msg = "CanSAS reader: unrecognized dQw unit [%s];"
	502	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
	503	raise ValueError, msg
[b0d0723]	504	_y, attr = get_float('ns:I', item)
	505	_dy, attr_d = get_float('ns:Idev', item)
[8780e9a]	506	if _dy == None:
	507	_dy = 0.0
[a7a5886]	508	if attr.has_key('unit') and \
	509	attr['unit'].lower() != data_info.y_unit.lower():
[e390933]	510	if has_converter==True:
	511	try:
	512	data_conv_i = Converter(attr['unit'])
	513	_y = data_conv_i(_y, units=data_info.y_unit)
	514	except:
[a7a5886]	515	msg = "CanSAS reader: could not convert I(q) unit [%s];"
	516	msg += " expecting [%s]\n %s" % (attr['unit'],
	517	data_info.y_unit, sys.exc_value)
	518	raise ValueError, msg
[e390933]	519	else:
[a7a5886]	520	msg = "CanSAS reader: unrecognized I(q) unit [%s];"
	521	msg += " expecting [%s]" % (attr['unit'], data_info.y_unit)
	522	raise ValueError, msg
	523
	524	if attr_d.has_key('unit') and \
	525	attr_d['unit'].lower() != data_info.y_unit.lower():
[e390933]	526	if has_converter==True:
	527	try:
	528	data_conv_i = Converter(attr_d['unit'])
	529	_dy = data_conv_i(_dy, units=data_info.y_unit)
	530	except:
[a7a5886]	531	msg = "CanSAS reader: could not convert dI(q) unit "
	532	msg += "[%s]; expecting [%s]\n %s" % (attr_d['unit'],
	533	data_info.y_unit, sys.exc_value)
	534	raise ValueError, msg
[e390933]	535	else:
[a7a5886]	536	msg = "CanSAS reader: unrecognized dI(q) unit [%s]; "
	537	msg += "expecting [%s]" % (attr_d['unit'], data_info.y_unit)
	538	raise ValueError, msg
[8780e9a]	539
	540	if _x is not None and _y is not None:
	541	x = numpy.append(x, _x)
[579ba85]	542	y = numpy.append(y, _y)
	543	dx = numpy.append(dx, _dx)
	544	dy = numpy.append(dy, _dy)
[d00f8ff]	545	dxl = numpy.append(dxl, _dxl)
	546	dxw = numpy.append(dxw, _dxw)
	547
[8780e9a]	548	data_info.x = x
	549	data_info.y = y
	550	data_info.dx = dx
	551	data_info.dy = dy
[d00f8ff]	552	data_info.dxl = dxl
	553	data_info.dxw = dxw
[d6513cd]	554
	555	data_conv_q = None
	556	data_conv_i = None
	557
[ca10d8e]	558	if has_converter == True and data_info.x_unit != '1/A':
	559	data_conv_q = Converter('1/A')
[d6513cd]	560	# Test it
	561	data_conv_q(1.0, output.Q_unit)
	562
[ca10d8e]	563	if has_converter == True and data_info.y_unit != '1/cm':
	564	data_conv_i = Converter('1/cm')
[d6513cd]	565	# Test it
[e390933]	566	data_conv_i(1.0, output.I_unit)
	567
[99d1af6]	568	if data_conv_q is not None:
[d6513cd]	569	data_info.xaxis("\\rm{Q}", data_info.x_unit)
[99d1af6]	570	else:
	571	data_info.xaxis("\\rm{Q}", 'A^{-1}')
	572	if data_conv_i is not None:
[0e2aa40]	573	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
[99d1af6]	574	else:
[0e2aa40]	575	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
[99d1af6]	576
[8780e9a]	577	return data_info
	578
[b3de3a45]	579	def _to_xml_doc(self, datainfo):
[4c00964]	580	"""
[0997158f]	581	Create an XML document to contain the content of a Data1D
	582
	583	:param datainfo: Data1D object
[4c00964]	584	"""
	585
[7d8094b]	586	if not issubclass(datainfo.__class__, Data1D):
[4c00964]	587	raise RuntimeError, "The cansas writer expects a Data1D instance"
	588
	589	doc = xml.dom.minidom.Document()
	590	main_node = doc.createElement("SASroot")
[fee780b]	591	main_node.setAttribute("version", self.version)
	592	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
[a7a5886]	593	main_node.setAttribute("xmlns:xsi",
	594	"http://www.w3.org/2001/XMLSchema-instance")
	595	main_node.setAttribute("xsi:schemaLocation",
	596	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
[fee780b]	597
[4c00964]	598	doc.appendChild(main_node)
	599
	600	entry_node = doc.createElement("SASentry")
	601	main_node.appendChild(entry_node)
	602
[579ba85]	603	write_node(doc, entry_node, "Title", datainfo.title)
	604	for item in datainfo.run:
	605	runname = {}
[a7a5886]	606	if datainfo.run_name.has_key(item) and \
	607	len(str(datainfo.run_name[item]))>1:
[579ba85]	608	runname = {'name': datainfo.run_name[item] }
	609	write_node(doc, entry_node, "Run", item, runname)
[4c00964]	610
	611	# Data info
	612	node = doc.createElement("SASdata")
	613	entry_node.appendChild(node)
	614
[579ba85]	615	for i in range(len(datainfo.x)):
	616	pt = doc.createElement("Idata")
	617	node.appendChild(pt)
	618	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
	619	if len(datainfo.y)>=i:
[a7a5886]	620	write_node(doc, pt, "I", datainfo.y[i],
	621	{'unit':datainfo.y_unit})
[5b396b3]	622	if datainfo.dx !=None and len(datainfo.dx)>=i:
[a7a5886]	623	write_node(doc, pt, "Qdev", datainfo.dx[i],
	624	{'unit':datainfo.x_unit})
[f31701c]	625	if datainfo.dy !=None and len(datainfo.dy)>=i:
[a7a5886]	626	write_node(doc, pt, "Idev", datainfo.dy[i],
	627	{'unit':datainfo.y_unit})
[579ba85]	628
	629
[4c00964]	630	# Sample info
	631	sample = doc.createElement("SASsample")
[579ba85]	632	if datainfo.sample.name is not None:
	633	sample.setAttribute("name", str(datainfo.sample.name))
[4c00964]	634	entry_node.appendChild(sample)
[579ba85]	635	write_node(doc, sample, "ID", str(datainfo.sample.ID))
[a7a5886]	636	write_node(doc, sample, "thickness", datainfo.sample.thickness,
	637	{"unit":datainfo.sample.thickness_unit})
[4c00964]	638	write_node(doc, sample, "transmission", datainfo.sample.transmission)
[a7a5886]	639	write_node(doc, sample, "temperature", datainfo.sample.temperature,
	640	{"unit":datainfo.sample.temperature_unit})
[4c00964]	641
	642	for item in datainfo.sample.details:
	643	write_node(doc, sample, "details", item)
	644
	645	pos = doc.createElement("position")
[a7a5886]	646	written = write_node(doc, pos, "x", datainfo.sample.position.x,
	647	{"unit":datainfo.sample.position_unit})
	648	written = written \| write_node(doc, pos, "y",
	649	datainfo.sample.position.y,
	650	{"unit":datainfo.sample.position_unit})
	651	written = written \| write_node(doc, pos, "z",
	652	datainfo.sample.position.z,
	653	{"unit":datainfo.sample.position_unit})
[4c00964]	654	if written == True:
	655	sample.appendChild(pos)
	656
	657	ori = doc.createElement("orientation")
[a7a5886]	658	written = write_node(doc, ori, "roll",
	659	datainfo.sample.orientation.x,
	660	{"unit":datainfo.sample.orientation_unit})
	661	written = written \| write_node(doc, ori, "pitch",
	662	datainfo.sample.orientation.y,
	663	{"unit":datainfo.sample.orientation_unit})
	664	written = written \| write_node(doc, ori, "yaw",
	665	datainfo.sample.orientation.z,
	666	{"unit":datainfo.sample.orientation_unit})
[4c00964]	667	if written == True:
	668	sample.appendChild(ori)
	669
	670	# Instrument info
	671	instr = doc.createElement("SASinstrument")
	672	entry_node.appendChild(instr)
	673
	674	write_node(doc, instr, "name", datainfo.instrument)
	675
	676	# Source
	677	source = doc.createElement("SASsource")
[579ba85]	678	if datainfo.source.name is not None:
	679	source.setAttribute("name", str(datainfo.source.name))
[4c00964]	680	instr.appendChild(source)
	681
	682	write_node(doc, source, "radiation", datainfo.source.radiation)
	683	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
[579ba85]	684	size = doc.createElement("beam_size")
	685	if datainfo.source.beam_size_name is not None:
	686	size.setAttribute("name", str(datainfo.source.beam_size_name))
[a7a5886]	687	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
	688	{"unit":datainfo.source.beam_size_unit})
	689	written = written \| write_node(doc, size, "y",
	690	datainfo.source.beam_size.y,
	691	{"unit":datainfo.source.beam_size_unit})
	692	written = written \| write_node(doc, size, "z",
	693	datainfo.source.beam_size.z,
	694	{"unit":datainfo.source.beam_size_unit})
[579ba85]	695	if written == True:
	696	source.appendChild(size)
	697
[a7a5886]	698	write_node(doc, source, "wavelength",
	699	datainfo.source.wavelength,
	700	{"unit":datainfo.source.wavelength_unit})
	701	write_node(doc, source, "wavelength_min",
	702	datainfo.source.wavelength_min,
	703	{"unit":datainfo.source.wavelength_min_unit})
	704	write_node(doc, source, "wavelength_max",
	705	datainfo.source.wavelength_max,
	706	{"unit":datainfo.source.wavelength_max_unit})
	707	write_node(doc, source, "wavelength_spread",
	708	datainfo.source.wavelength_spread,
	709	{"unit":datainfo.source.wavelength_spread_unit})
[4c00964]	710
	711	# Collimation
	712	for item in datainfo.collimation:
	713	coll = doc.createElement("SAScollimation")
[579ba85]	714	if item.name is not None:
	715	coll.setAttribute("name", str(item.name))
[4c00964]	716	instr.appendChild(coll)
	717
[a7a5886]	718	write_node(doc, coll, "length", item.length,
	719	{"unit":item.length_unit})
[4c00964]	720
	721	for apert in item.aperture:
[579ba85]	722	ap = doc.createElement("aperture")
	723	if apert.name is not None:
	724	ap.setAttribute("name", str(apert.name))
	725	if apert.type is not None:
	726	ap.setAttribute("type", str(apert.type))
	727	coll.appendChild(ap)
[4c00964]	728
[a7a5886]	729	write_node(doc, ap, "distance", apert.distance,
	730	{"unit":apert.distance_unit})
[4c00964]	731
	732	size = doc.createElement("size")
[579ba85]	733	if apert.size_name is not None:
	734	size.setAttribute("name", str(apert.size_name))
[a7a5886]	735	written = write_node(doc, size, "x", apert.size.x,
	736	{"unit":apert.size_unit})
	737	written = written \| write_node(doc, size, "y", apert.size.y,
	738	{"unit":apert.size_unit})
	739	written = written \| write_node(doc, size, "z", apert.size.z,
	740	{"unit":apert.size_unit})
[579ba85]	741	if written == True:
	742	ap.appendChild(size)
[4c00964]	743
	744	# Detectors
	745	for item in datainfo.detector:
	746	det = doc.createElement("SASdetector")
[579ba85]	747	written = write_node(doc, det, "name", item.name)
[a7a5886]	748	written = written \| write_node(doc, det, "SDD", item.distance,
	749	{"unit":item.distance_unit})
	750	written = written \| write_node(doc, det, "slit_length",
	751	item.slit_length,
	752	{"unit":item.slit_length_unit})
[579ba85]	753	if written == True:
	754	instr.appendChild(det)
[4c00964]	755
	756	off = doc.createElement("offset")
[a7a5886]	757	written = write_node(doc, off, "x", item.offset.x,
	758	{"unit":item.offset_unit})
	759	written = written \| write_node(doc, off, "y", item.offset.y,
	760	{"unit":item.offset_unit})
	761	written = written \| write_node(doc, off, "z", item.offset.z,
	762	{"unit":item.offset_unit})
[579ba85]	763	if written == True:
	764	det.appendChild(off)
[4c00964]	765
	766	center = doc.createElement("beam_center")
[a7a5886]	767	written = write_node(doc, center, "x", item.beam_center.x,
	768	{"unit":item.beam_center_unit})
	769	written = written \| write_node(doc, center, "y",
	770	item.beam_center.y,
	771	{"unit":item.beam_center_unit})
	772	written = written \| write_node(doc, center, "z",
	773	item.beam_center.z,
	774	{"unit":item.beam_center_unit})
[579ba85]	775	if written == True:
	776	det.appendChild(center)
	777
[4c00964]	778	pix = doc.createElement("pixel_size")
[a7a5886]	779	written = write_node(doc, pix, "x", item.pixel_size.x,
	780	{"unit":item.pixel_size_unit})
	781	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
	782	{"unit":item.pixel_size_unit})
	783	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
	784	{"unit":item.pixel_size_unit})
[579ba85]	785	if written == True:
	786	det.appendChild(pix)
	787
	788	ori = doc.createElement("orientation")
[a7a5886]	789	written = write_node(doc, ori, "roll", item.orientation.x,
	790	{"unit":item.orientation_unit})
	791	written = written \| write_node(doc, ori, "pitch",
	792	item.orientation.y,
	793	{"unit":item.orientation_unit})
	794	written = written \| write_node(doc, ori, "yaw",
	795	item.orientation.z,
	796	{"unit":item.orientation_unit})
[579ba85]	797	if written == True:
	798	det.appendChild(ori)
	799
[4c00964]	800
[579ba85]	801	# Processes info
[4c00964]	802	for item in datainfo.process:
	803	node = doc.createElement("SASprocess")
	804	entry_node.appendChild(node)
	805
[579ba85]	806	write_node(doc, node, "name", item.name)
	807	write_node(doc, node, "date", item.date)
	808	write_node(doc, node, "description", item.description)
	809	for term in item.term:
	810	value = term['value']
	811	del term['value']
	812	write_node(doc, node, "term", value, term)
	813	for note in item.notes:
	814	write_node(doc, node, "SASprocessnote", note)
[4c00964]	815
[b3de3a45]	816	# Return the document, and the SASentry node associated with
	817	# the data we just wrote
	818	return doc, entry_node
	819
	820	def write(self, filename, datainfo):
	821	"""
[0997158f]	822	Write the content of a Data1D as a CanSAS XML file
	823
	824	:param filename: name of the file to write
	825	:param datainfo: Data1D object
[b3de3a45]	826	"""
	827	# Create XML document
	828	doc, sasentry = self._to_xml_doc(datainfo)
[4c00964]	829	# Write the file
	830	fd = open(filename, 'w')
	831	fd.write(doc.toprettyxml())
	832	fd.close()
	833
[fe78c7b]	834	def _store_float(self, location, node, variable, storage, optional=True):
	835	"""
[0997158f]	836	Get the content of a xpath location and store
	837	the result. Check that the units are compatible
	838	with the destination. The value is expected to
	839	be a float.
	840
	841	The xpath location might or might not exist.
	842	If it does not exist, nothing is done
	843
	844	:param location: xpath location to fetch
	845	:param node: node to read the data from
	846	:param variable: name of the data member to store it in [string]
	847	:param storage: data object that has the 'variable' data member
[a7a5886]	848	:param optional: if True, no exception will be raised
	849	if unit conversion can't be done
[0997158f]	850
	851	:raise ValueError: raised when the units are not recognized
[fe78c7b]	852	"""
	853	entry = get_content(location, node)
	854	try:
	855	value = float(entry.text)
	856	except:
	857	value = None
	858
	859	if value is not None:
	860	# If the entry has units, check to see that they are
	861	# compatible with what we currently have in the data object
	862	units = entry.get('unit')
	863	if units is not None:
	864	toks = variable.split('.')
	865	exec "local_unit = storage.%s_unit" % toks[0]
	866	if units.lower()!=local_unit.lower():
	867	if has_converter==True:
	868	try:
	869	conv = Converter(units)
[a7a5886]	870	exec "storage.%s = %g" % (variable,
	871	conv(value, units=local_unit))
[fe78c7b]	872	except:
[a7a5886]	873	err_mess = "CanSAS reader: could not convert"
	874	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
[fe78c7b]	875	% (variable, units, local_unit, sys.exc_value)
	876	self.errors.append(err_mess)
	877	if optional:
	878	logging.info(err_mess)
	879	else:
	880	raise ValueError, err_mess
	881	else:
[a7a5886]	882	err_mess = "CanSAS reader: unrecognized %s unit [%s];"
	883	err_mess += " expecting [%s]" % (variable,
	884	units, local_unit)
[fe78c7b]	885	self.errors.append(err_mess)
	886	if optional:
	887	logging.info(err_mess)
	888	else:
	889	raise ValueError, err_mess
	890	else:
	891	exec "storage.%s = value" % variable
	892	else:
	893	exec "storage.%s = value" % variable
	894
	895	def _store_content(self, location, node, variable, storage):
	896	"""
[0997158f]	897	Get the content of a xpath location and store
	898	the result. The value is treated as a string.
	899
	900	The xpath location might or might not exist.
	901	If it does not exist, nothing is done
	902
	903	:param location: xpath location to fetch
	904	:param node: node to read the data from
	905	:param variable: name of the data member to store it in [string]
	906	:param storage: data object that has the 'variable' data member
	907
	908	:return: return a list of errors
[fe78c7b]	909	"""
	910	entry = get_content(location, node)
	911	if entry is not None and entry.text is not None:
	912	exec "storage.%s = entry.text.strip()" % variable
	913
	914
	915
[8780e9a]	916	if __name__ == "__main__":
	917	logging.basicConfig(level=logging.ERROR,
	918	format='%(asctime)s %(levelname)s %(message)s',
	919	filename='cansas_reader.log',
	920	filemode='w')
	921	reader = Reader()
	922	print reader.read("../test/cansas1d.xml")
[b0d0723]	923	#print reader.read("../test/latex_smeared.xml")
[8780e9a]	924
	925
	926

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ da9ac4e6

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