cansas_reader.py @ 5d2b35a

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 5d2b35a was 121c224, checked in by Jae Cho <jhjcho@…>, 14 years ago
final fixes for dQ=0 and Q=0 points
Property mode set to `100644`
File size: 41.1 KB

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2
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
14	# Known issue: reader not compatible with multiple SASdata entries
15	# within a single SASentry. Will raise a runtime error.
16
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.
21	#TODO: Store error list
22	#TODO: Allow for additional meta data for each section
23	#TODO: Notes need to be implemented. They can be any XML
24	# structure in version 1.0
25	# Process notes have the same problem.
26	#TODO: Unit conversion is not complete (temperature units are missing)
27
28
29	import logging
30	import numpy
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
38	from lxml import etree
39	import xml.dom.minidom
40	_ZERO = 1e-16
41	has_converter = True
42	try:
43	from data_util.nxsunit import Converter
44	except:
45	has_converter = False
46
47	CANSAS_NS = "cansas1d/1.0"
48
49	def write_node(doc, parent, name, value, attr={}):
50	"""
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
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
68	def get_content(location, node):
69	"""
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
76	"""
77	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
78
79	if len(nodes)>0:
80	return nodes[0]
81	else:
82	return None
83
84	def get_float(location, node):
85	"""
86	Get the content of a node as a float
87
88	:param location: xpath location
89	:param node: node to start at
90	"""
91	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
92
93	value = None
94	attr = {}
95	if len(nodes) > 0:
96	try:
97	value = float(nodes[0].text)
98	except:
99	# Could not pass, skip and return None
100	msg = "cansas_reader.get_float: could not "
101	msg += " convert '%s' to float" % nodes[0].text
102	logging.error(msg)
103	if nodes[0].get('unit') is not None:
104	attr['unit'] = nodes[0].get('unit')
105	return value, attr
106
107
108	class Reader:
109	"""
110	Class to load cansas 1D XML files
111
112	:Dependencies:
113	The CanSas reader requires PyXML 0.8.4 or later.
114	"""
115	## CanSAS version
116	version = '1.0'
117	## File type
118	type_name = "CanSAS 1D"
119	## Wildcards
120	type = ["CanSAS 1D files (.xml)\|.xml",
121	"CanSAS 1D AVE files (.AVEx)\|.AVEx",
122	"CanSAS 1D AVE files (.ABSx)\|.ABSx"]
123
124	## List of allowed extensions
125	ext = ['.xml', '.XML','.avex', '.AVEx', '.absx', 'ABSx']
126
127	def __init__(self):
128	## List of errors
129	self.errors = []
130
131	def read(self, path):
132	"""
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
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
150	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
151	# Check the format version number
152	# Specifying the namespace will take care of the file
153	# format version
154	root = tree.getroot()
155
156	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
157	namespaces={'ns': CANSAS_NS})
158
159	for entry in entry_list:
160	self.errors = []
161	sas_entry = self._parse_entry(entry)
162	sas_entry.filename = basename
163
164	# Store loading process information
165	sas_entry.errors = self.errors
166	sas_entry.meta_data['loader'] = self.type_name
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	#cannot return none when it cannot read
174	#return None
175	raise RuntimeError, "%s cannot be read \n" % path
176	elif len(output) == 1:
177	return output[0]
178	else:
179	return output
180
181	def _parse_entry(self, dom):
182	"""
183	Parse a SASentry
184
185	:param node: SASentry node
186
187	:return: Data1D object
188	"""
189	x = numpy.zeros(0)
190	y = numpy.zeros(0)
191
192	data_info = Data1D(x, y)
193
194	# Look up title
195	self._store_content('ns:Title', dom, 'title', data_info)
196
197	# Look up run number
198	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
199	for item in nodes:
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')
206
207	# Look up instrument name
208	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument',
209	data_info)
210
211	# Notes
212	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
213	for note in note_list:
214	try:
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)
219	except:
220	err_mess = "cansas_reader.read: error processing"
221	err_mess += " entry notes\n %s" % sys.exc_value
222	self.errors.append(err_mess)
223	logging.error(err_mess)
224
225	# Sample info ###################
226	entry = get_content('ns:SASsample', dom)
227	if entry is not None:
228	data_info.sample.name = entry.get('name')
229
230	self._store_content('ns:SASsample/ns:ID',
231	dom, 'ID', data_info.sample)
232	self._store_float('ns:SASsample/ns:thickness',
233	dom, 'thickness', data_info.sample)
234	self._store_float('ns:SASsample/ns:transmission',
235	dom, 'transmission', data_info.sample)
236	self._store_float('ns:SASsample/ns:temperature',
237	dom, 'temperature', data_info.sample)
238
239	nodes = dom.xpath('ns:SASsample/ns:details',
240	namespaces={'ns': CANSAS_NS})
241	for item in nodes:
242	try:
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)
247	except:
248	err_mess = "cansas_reader.read: error processing "
249	err_mess += " sample details\n %s" % sys.exc_value
250	self.errors.append(err_mess)
251	logging.error(err_mess)
252
253	# Position (as a vector)
254	self._store_float('ns:SASsample/ns:position/ns:x',
255	dom, 'position.x', data_info.sample)
256	self._store_float('ns:SASsample/ns:position/ns:y',
257	dom, 'position.y', data_info.sample)
258	self._store_float('ns:SASsample/ns:position/ns:z',
259	dom, 'position.z', data_info.sample)
260
261	# Orientation (as a vector)
262	self._store_float('ns:SASsample/ns:orientation/ns:roll',
263	dom, 'orientation.x', data_info.sample)
264	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
265	dom, 'orientation.y', data_info.sample)
266	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
267	dom, 'orientation.z', data_info.sample)
268
269	# Source info ###################
270	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
271	if entry is not None:
272	data_info.source.name = entry.get('name')
273
274	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
275	dom, 'radiation', data_info.source)
276	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
277	dom, 'beam_shape', data_info.source)
278	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
279	dom, 'wavelength', data_info.source)
280	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
281	dom, 'wavelength_min', data_info.source)
282	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
283	dom, 'wavelength_max', data_info.source)
284	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
285	dom, 'wavelength_spread', data_info.source)
286
287	# Beam size (as a vector)
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')
291
292	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
293	dom, 'beam_size.x', data_info.source)
294	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
295	dom, 'beam_size.y', data_info.source)
296	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
297	dom, 'beam_size.z', data_info.source)
298
299	# Collimation info ###################
300	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
301	namespaces={'ns': CANSAS_NS})
302	for item in nodes:
303	collim = Collimation()
304	if item.get('name') is not None:
305	collim.name = item.get('name')
306	self._store_float('ns:length', item, 'length', collim)
307
308	# Look for apertures
309	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
310	for apert in apert_list:
311	aperture = Aperture()
312
313	# Get the name and type of the aperture
314	aperture.name = apert.get('name')
315	aperture.type = apert.get('type')
316
317	self._store_float('ns:distance', apert, 'distance', aperture)
318
319	entry = get_content('ns:size', apert)
320	if entry is not None:
321	aperture.size_name = entry.get('name')
322
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)
326
327	collim.aperture.append(aperture)
328
329	data_info.collimation.append(collim)
330
331	# Detector info ######################
332	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
333	namespaces={'ns': CANSAS_NS})
334	for item in nodes:
335
336	detector = Detector()
337
338	self._store_content('ns:name', item, 'name', detector)
339	self._store_float('ns:SDD', item, 'distance', detector)
340
341	# Detector offset (as a vector)
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)
345
346	# Detector orientation (as a vector)
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)
353
354	# Beam center (as a vector)
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)
361
362	# Pixel size (as a vector)
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)
369
370	self._store_float('ns:slit_length', item, 'slit_length', detector)
371
372	data_info.detector.append(detector)
373
374	# Processes info ######################
375	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
376	for item in nodes:
377	process = Process()
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)
381
382	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
383	for term in term_list:
384	try:
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()
390	process.term.append(term_attr)
391	except:
392	err_mess = "cansas_reader.read: error processing "
393	err_mess += " process term\n %s" % sys.exc_value
394	self.errors.append(err_mess)
395	logging.error(err_mess)
396
397	note_list = item.xpath('ns:SASprocessnote',
398	namespaces={'ns': CANSAS_NS})
399	for note in note_list:
400	if note.text is not None:
401	process.notes.append(note.text.strip())
402
403	data_info.process.append(process)
404
405
406	# Data info ######################
407	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
408	if len(nodes) > 1:
409	msg = "CanSAS reader is not compatible with multiple"
410	msg += " SASdata entries"
411	raise RuntimeError, msg
412
413	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
414
415	x = numpy.zeros(0)
416	y = numpy.zeros(0)
417	dx = numpy.zeros(0)
418	dy = numpy.zeros(0)
419	dxw = numpy.zeros(0)
420	dxl = numpy.zeros(0)
421
422	for item in nodes:
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)
427	if _dx == None:
428	_dx = 0.0
429	if _dxl == None:
430	_dxl = 0.0
431	if _dxw == None:
432	_dxw = 0.0
433
434	if attr.has_key('unit') and \
435	attr['unit'].lower() != data_info.x_unit.lower():
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:
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
447	else:
448	msg = "CanSAS reader: unrecognized Q unit [%s]; "
449	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
450	raise ValueError, msg
451
452	# Error in Q
453	if attr_d.has_key('unit') and \
454	attr_d['unit'].lower() != data_info.x_unit.lower():
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:
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
466	else:
467	msg = "CanSAS reader: unrecognized dQ unit [%s]; "
468	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
469	raise ValueError, msg
470
471	# Slit length
472	if attr_l.has_key('unit') and \
473	attr_l['unit'].lower() != data_info.x_unit.lower():
474	if has_converter == True:
475	try:
476	data_conv_q = Converter(attr_l['unit'])
477	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
478	except:
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
484	else:
485	msg = "CanSAS reader: unrecognized dQl unit [%s];"
486	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
487	raise ValueError, msg
488
489	# Slit width
490	if attr_w.has_key('unit') and \
491	attr_w['unit'].lower() != data_info.x_unit.lower():
492	if has_converter == True:
493	try:
494	data_conv_q = Converter(attr_w['unit'])
495	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
496	except:
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
502	else:
503	msg = "CanSAS reader: unrecognized dQw unit [%s];"
504	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
505	raise ValueError, msg
506	_y, attr = get_float('ns:I', item)
507	_dy, attr_d = get_float('ns:Idev', item)
508	if _dy == None:
509	_dy = 0.0
510	if attr.has_key('unit') and \
511	attr['unit'].lower() != data_info.y_unit.lower():
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:
517	if attr['unit'].lower() == 'count':
518	pass
519	else:
520	msg = "CanSAS reader: could not"
521	msg += " convert I(q) unit [%s];" % str(attr['unit'])
522	msg += " expecting [%s]\n" % str(data_info.y_unit)
523	msg += " %s" % str(sys.exc_value)
524	raise ValueError, msg
525	else:
526	msg = "CanSAS reader: unrecognized I(q) unit [%s];"
527	msg += " expecting [%s]" % (attr['unit'], data_info.y_unit)
528	raise ValueError, msg
529
530	if attr_d.has_key('unit') and \
531	attr_d['unit'].lower() != data_info.y_unit.lower():
532	if has_converter==True:
533	try:
534	data_conv_i = Converter(attr_d['unit'])
535	_dy = data_conv_i(_dy, units=data_info.y_unit)
536	except:
537	if attr_d['unit'].lower() == 'count':
538	pass
539	else:
540	msg = "CanSAS reader: could not convert dI(q) unit "
541	msg += "[%s]; expecting [%s]\n %s" % (attr_d['unit'],
542	data_info.y_unit, sys.exc_value)
543	raise ValueError, msg
544	else:
545	msg = "CanSAS reader: unrecognized dI(q) unit [%s]; "
546	msg += "expecting [%s]" % (attr_d['unit'], data_info.y_unit)
547	raise ValueError, msg
548
549	if _x is not None and _y is not None:
550	x = numpy.append(x, _x)
551	y = numpy.append(y, _y)
552	dx = numpy.append(dx, _dx)
553	dy = numpy.append(dy, _dy)
554	dxl = numpy.append(dxl, _dxl)
555	dxw = numpy.append(dxw, _dxw)
556	# Zeros in dx, dy
557	if not numpy.all(dx==0):
558	dx[dx==0] = _ZERO
559	if not numpy.all(dy==0):
560	dy[dy==0] = _ZERO
561
562	data_info.x = x[x!=0]
563	data_info.y = y[x!=0]
564	data_info.dx = dx[x!=0]
565
566	data_info.dy = dy[x!=0]
567	data_info.dxl = dxl[x!=0]
568	data_info.dxw = dxw[x!=0]
569
570	data_conv_q = None
571	data_conv_i = None
572
573	if has_converter == True and data_info.x_unit != '1/A':
574	data_conv_q = Converter('1/A')
575	# Test it
576	data_conv_q(1.0, output.Q_unit)
577
578	if has_converter == True and data_info.y_unit != '1/cm':
579	data_conv_i = Converter('1/cm')
580	# Test it
581	data_conv_i(1.0, output.I_unit)
582
583	if data_conv_q is not None:
584	data_info.xaxis("\\rm{Q}", data_info.x_unit)
585	else:
586	data_info.xaxis("\\rm{Q}", 'A^{-1}')
587	if data_conv_i is not None:
588	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
589	else:
590	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
591
592	return data_info
593
594	def _to_xml_doc(self, datainfo):
595	"""
596	Create an XML document to contain the content of a Data1D
597
598	:param datainfo: Data1D object
599	"""
600
601	if not issubclass(datainfo.__class__, Data1D):
602	raise RuntimeError, "The cansas writer expects a Data1D instance"
603
604	doc = xml.dom.minidom.Document()
605	main_node = doc.createElement("SASroot")
606	main_node.setAttribute("version", self.version)
607	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
608	main_node.setAttribute("xmlns:xsi",
609	"http://www.w3.org/2001/XMLSchema-instance")
610	main_node.setAttribute("xsi:schemaLocation",
611	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
612
613	doc.appendChild(main_node)
614
615	entry_node = doc.createElement("SASentry")
616	main_node.appendChild(entry_node)
617
618	write_node(doc, entry_node, "Title", datainfo.title)
619	for item in datainfo.run:
620	runname = {}
621	if datainfo.run_name.has_key(item) and \
622	len(str(datainfo.run_name[item]))>1:
623	runname = {'name': datainfo.run_name[item] }
624	write_node(doc, entry_node, "Run", item, runname)
625
626	# Data info
627	node = doc.createElement("SASdata")
628	entry_node.appendChild(node)
629
630	for i in range(len(datainfo.x)):
631	pt = doc.createElement("Idata")
632	node.appendChild(pt)
633	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
634	if len(datainfo.y)>=i:
635	write_node(doc, pt, "I", datainfo.y[i],
636	{'unit':datainfo.y_unit})
637	if datainfo.dx != None and len(datainfo.dx) >= i:
638	write_node(doc, pt, "Qdev", datainfo.dx[i],
639	{'unit':datainfo.x_unit})
640	if datainfo.dxl != None and len(datainfo.dxl) >= i:
641	write_node(doc, pt, "dQl", datainfo.dxl[i],
642	{'unit':datainfo.x_unit})
643	if datainfo.dxw != None and len(datainfo.dxw) >= i:
644	write_node(doc, pt, "dQw", datainfo.dxw[i],
645	{'unit':datainfo.x_unit})
646	if datainfo.dy != None and len(datainfo.dy) >= i:
647	write_node(doc, pt, "Idev", datainfo.dy[i],
648	{'unit':datainfo.y_unit})
649
650
651	# Sample info
652	sample = doc.createElement("SASsample")
653	if datainfo.sample.name is not None:
654	sample.setAttribute("name", str(datainfo.sample.name))
655	entry_node.appendChild(sample)
656	write_node(doc, sample, "ID", str(datainfo.sample.ID))
657	write_node(doc, sample, "thickness", datainfo.sample.thickness,
658	{"unit":datainfo.sample.thickness_unit})
659	write_node(doc, sample, "transmission", datainfo.sample.transmission)
660	write_node(doc, sample, "temperature", datainfo.sample.temperature,
661	{"unit":datainfo.sample.temperature_unit})
662
663	for item in datainfo.sample.details:
664	write_node(doc, sample, "details", item)
665
666	pos = doc.createElement("position")
667	written = write_node(doc, pos, "x", datainfo.sample.position.x,
668	{"unit":datainfo.sample.position_unit})
669	written = written \| write_node(doc, pos, "y",
670	datainfo.sample.position.y,
671	{"unit":datainfo.sample.position_unit})
672	written = written \| write_node(doc, pos, "z",
673	datainfo.sample.position.z,
674	{"unit":datainfo.sample.position_unit})
675	if written == True:
676	sample.appendChild(pos)
677
678	ori = doc.createElement("orientation")
679	written = write_node(doc, ori, "roll",
680	datainfo.sample.orientation.x,
681	{"unit":datainfo.sample.orientation_unit})
682	written = written \| write_node(doc, ori, "pitch",
683	datainfo.sample.orientation.y,
684	{"unit":datainfo.sample.orientation_unit})
685	written = written \| write_node(doc, ori, "yaw",
686	datainfo.sample.orientation.z,
687	{"unit":datainfo.sample.orientation_unit})
688	if written == True:
689	sample.appendChild(ori)
690
691	# Instrument info
692	instr = doc.createElement("SASinstrument")
693	entry_node.appendChild(instr)
694
695	write_node(doc, instr, "name", datainfo.instrument)
696
697	# Source
698	source = doc.createElement("SASsource")
699	if datainfo.source.name is not None:
700	source.setAttribute("name", str(datainfo.source.name))
701	instr.appendChild(source)
702
703	write_node(doc, source, "radiation", datainfo.source.radiation)
704	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
705	size = doc.createElement("beam_size")
706	if datainfo.source.beam_size_name is not None:
707	size.setAttribute("name", str(datainfo.source.beam_size_name))
708	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
709	{"unit":datainfo.source.beam_size_unit})
710	written = written \| write_node(doc, size, "y",
711	datainfo.source.beam_size.y,
712	{"unit":datainfo.source.beam_size_unit})
713	written = written \| write_node(doc, size, "z",
714	datainfo.source.beam_size.z,
715	{"unit":datainfo.source.beam_size_unit})
716	if written == True:
717	source.appendChild(size)
718
719	write_node(doc, source, "wavelength",
720	datainfo.source.wavelength,
721	{"unit":datainfo.source.wavelength_unit})
722	write_node(doc, source, "wavelength_min",
723	datainfo.source.wavelength_min,
724	{"unit":datainfo.source.wavelength_min_unit})
725	write_node(doc, source, "wavelength_max",
726	datainfo.source.wavelength_max,
727	{"unit":datainfo.source.wavelength_max_unit})
728	write_node(doc, source, "wavelength_spread",
729	datainfo.source.wavelength_spread,
730	{"unit":datainfo.source.wavelength_spread_unit})
731
732	# Collimation
733	for item in datainfo.collimation:
734	coll = doc.createElement("SAScollimation")
735	if item.name is not None:
736	coll.setAttribute("name", str(item.name))
737	instr.appendChild(coll)
738
739	write_node(doc, coll, "length", item.length,
740	{"unit":item.length_unit})
741
742	for apert in item.aperture:
743	ap = doc.createElement("aperture")
744	if apert.name is not None:
745	ap.setAttribute("name", str(apert.name))
746	if apert.type is not None:
747	ap.setAttribute("type", str(apert.type))
748	coll.appendChild(ap)
749
750	write_node(doc, ap, "distance", apert.distance,
751	{"unit":apert.distance_unit})
752
753	size = doc.createElement("size")
754	if apert.size_name is not None:
755	size.setAttribute("name", str(apert.size_name))
756	written = write_node(doc, size, "x", apert.size.x,
757	{"unit":apert.size_unit})
758	written = written \| write_node(doc, size, "y", apert.size.y,
759	{"unit":apert.size_unit})
760	written = written \| write_node(doc, size, "z", apert.size.z,
761	{"unit":apert.size_unit})
762	if written == True:
763	ap.appendChild(size)
764
765	# Detectors
766	for item in datainfo.detector:
767	det = doc.createElement("SASdetector")
768	written = write_node(doc, det, "name", item.name)
769	written = written \| write_node(doc, det, "SDD", item.distance,
770	{"unit":item.distance_unit})
771	written = written \| write_node(doc, det, "slit_length",
772	item.slit_length,
773	{"unit":item.slit_length_unit})
774	if written == True:
775	instr.appendChild(det)
776
777	off = doc.createElement("offset")
778	written = write_node(doc, off, "x", item.offset.x,
779	{"unit":item.offset_unit})
780	written = written \| write_node(doc, off, "y", item.offset.y,
781	{"unit":item.offset_unit})
782	written = written \| write_node(doc, off, "z", item.offset.z,
783	{"unit":item.offset_unit})
784	if written == True:
785	det.appendChild(off)
786
787	center = doc.createElement("beam_center")
788	written = write_node(doc, center, "x", item.beam_center.x,
789	{"unit":item.beam_center_unit})
790	written = written \| write_node(doc, center, "y",
791	item.beam_center.y,
792	{"unit":item.beam_center_unit})
793	written = written \| write_node(doc, center, "z",
794	item.beam_center.z,
795	{"unit":item.beam_center_unit})
796	if written == True:
797	det.appendChild(center)
798
799	pix = doc.createElement("pixel_size")
800	written = write_node(doc, pix, "x", item.pixel_size.x,
801	{"unit":item.pixel_size_unit})
802	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
803	{"unit":item.pixel_size_unit})
804	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
805	{"unit":item.pixel_size_unit})
806	if written == True:
807	det.appendChild(pix)
808
809	ori = doc.createElement("orientation")
810	written = write_node(doc, ori, "roll", item.orientation.x,
811	{"unit":item.orientation_unit})
812	written = written \| write_node(doc, ori, "pitch",
813	item.orientation.y,
814	{"unit":item.orientation_unit})
815	written = written \| write_node(doc, ori, "yaw",
816	item.orientation.z,
817	{"unit":item.orientation_unit})
818	if written == True:
819	det.appendChild(ori)
820
821
822	# Processes info
823	for item in datainfo.process:
824	node = doc.createElement("SASprocess")
825	entry_node.appendChild(node)
826
827	write_node(doc, node, "name", item.name)
828	write_node(doc, node, "date", item.date)
829	write_node(doc, node, "description", item.description)
830	for term in item.term:
831	value = term['value']
832	del term['value']
833	write_node(doc, node, "term", value, term)
834	for note in item.notes:
835	write_node(doc, node, "SASprocessnote", note)
836
837	# Return the document, and the SASentry node associated with
838	# the data we just wrote
839	return doc, entry_node
840
841	def write(self, filename, datainfo):
842	"""
843	Write the content of a Data1D as a CanSAS XML file
844
845	:param filename: name of the file to write
846	:param datainfo: Data1D object
847	"""
848	# Create XML document
849	doc, sasentry = self._to_xml_doc(datainfo)
850	# Write the file
851	fd = open(filename, 'w')
852	fd.write(doc.toprettyxml())
853	fd.close()
854
855	def _store_float(self, location, node, variable, storage, optional=True):
856	"""
857	Get the content of a xpath location and store
858	the result. Check that the units are compatible
859	with the destination. The value is expected to
860	be a float.
861
862	The xpath location might or might not exist.
863	If it does not exist, nothing is done
864
865	:param location: xpath location to fetch
866	:param node: node to read the data from
867	:param variable: name of the data member to store it in [string]
868	:param storage: data object that has the 'variable' data member
869	:param optional: if True, no exception will be raised
870	if unit conversion can't be done
871
872	:raise ValueError: raised when the units are not recognized
873	"""
874	entry = get_content(location, node)
875	try:
876	value = float(entry.text)
877	except:
878	value = None
879
880	if value is not None:
881	# If the entry has units, check to see that they are
882	# compatible with what we currently have in the data object
883	units = entry.get('unit')
884	if units is not None:
885	toks = variable.split('.')
886	exec "local_unit = storage.%s_unit" % toks[0]
887	if units.lower()!=local_unit.lower():
888	if has_converter==True:
889	try:
890	conv = Converter(units)
891	exec "storage.%s = %g" % (variable,
892	conv(value, units=local_unit))
893	except:
894	err_mess = "CanSAS reader: could not convert"
895	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
896	% (variable, units, local_unit, sys.exc_value)
897	self.errors.append(err_mess)
898	if optional:
899	logging.info(err_mess)
900	else:
901	raise ValueError, err_mess
902	else:
903	err_mess = "CanSAS reader: unrecognized %s unit [%s];"
904	err_mess += " expecting [%s]" % (variable,
905	units, local_unit)
906	self.errors.append(err_mess)
907	if optional:
908	logging.info(err_mess)
909	else:
910	raise ValueError, err_mess
911	else:
912	exec "storage.%s = value" % variable
913	else:
914	exec "storage.%s = value" % variable
915
916	def _store_content(self, location, node, variable, storage):
917	"""
918	Get the content of a xpath location and store
919	the result. The value is treated as a string.
920
921	The xpath location might or might not exist.
922	If it does not exist, nothing is done
923
924	:param location: xpath location to fetch
925	:param node: node to read the data from
926	:param variable: name of the data member to store it in [string]
927	:param storage: data object that has the 'variable' data member
928
929	:return: return a list of errors
930	"""
931	entry = get_content(location, node)
932	if entry is not None and entry.text is not None:
933	exec "storage.%s = entry.text.strip()" % variable
934
935
936
937	if __name__ == "__main__":
938	logging.basicConfig(level=logging.ERROR,
939	format='%(asctime)s %(levelname)s %(message)s',
940	filename='cansas_reader.log',
941	filemode='w')
942	reader = Reader()
943	print reader.read("../test/cansas1d.xml")
944	#print reader.read("../test/latex_smeared.xml")
945
946
947

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 5d2b35a

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