cansas_reader.py @ 0a5c8f5

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 0a5c8f5 was 0a5c8f5, checked in by Jae Cho <jhjcho@…>, 12 years ago
accept non standard extension for xml
Property mode set to `100644`
File size: 41.3 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 sans.dataloader.data_info import Data1D
34	from sans.dataloader.data_info import Collimation
35	from sans.dataloader.data_info import Detector
36	from sans.dataloader.data_info import Process
37	from sans.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	allow_all = True
49
50	def write_node(doc, parent, name, value, attr={}):
51	"""
52	:param doc: document DOM
53	:param parent: parent node
54	:param name: tag of the element
55	:param value: value of the child text node
56	:param attr: attribute dictionary
57
58	:return: True if something was appended, otherwise False
59	"""
60	if value is not None:
61	node = doc.createElement(name)
62	node.appendChild(doc.createTextNode(str(value)))
63	for item in attr:
64	node.setAttribute(item, attr[item])
65	parent.appendChild(node)
66	return True
67	return False
68
69	def get_content(location, node):
70	"""
71	Get the first instance of the content of a xpath location.
72
73	:param location: xpath location
74	:param node: node to start at
75
76	:return: Element, or None
77	"""
78	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
79
80	if len(nodes)>0:
81	return nodes[0]
82	else:
83	return None
84
85	def get_float(location, node):
86	"""
87	Get the content of a node as a float
88
89	:param location: xpath location
90	:param node: node to start at
91	"""
92	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
93
94	value = None
95	attr = {}
96	if len(nodes) > 0:
97	try:
98	value = float(nodes[0].text)
99	except:
100	# Could not pass, skip and return None
101	msg = "cansas_reader.get_float: could not "
102	msg += " convert '%s' to float" % nodes[0].text
103	logging.error(msg)
104	if nodes[0].get('unit') is not None:
105	attr['unit'] = nodes[0].get('unit')
106	return value, attr
107
108
109	class Reader:
110	"""
111	Class to load cansas 1D XML files
112
113	:Dependencies:
114	The CanSas reader requires PyXML 0.8.4 or later.
115	"""
116	## CanSAS version
117	version = '1.0'
118	## File type
119	type_name = "CanSAS 1D"
120	## Wildcards
121	type = ["CanSAS 1D files (.xml)\|.xml",
122	"CanSAS 1D AVE files (.AVEx)\|.AVEx",
123	"CanSAS 1D AVE files (.ABSx)\|.ABSx"]
124
125	## List of allowed extensions
126	ext = ['.xml', '.XML','.avex', '.AVEx', '.absx', 'ABSx']
127
128	def __init__(self):
129	## List of errors
130	self.errors = []
131
132	def read(self, path):
133	"""
134	Load data file
135
136	:param path: file path
137
138	:return: Data1D object if a single SASentry was found,
139	or a list of Data1D objects if multiple entries were found,
140	or None of nothing was found
141
142	:raise RuntimeError: when the file can't be opened
143	:raise ValueError: when the length of the data vectors are inconsistent
144	"""
145	output = []
146	if os.path.isfile(path):
147	basename = os.path.basename(path)
148	root, extension = os.path.splitext(basename)
149	if allow_all or extension.lower() in self.ext:
150	try:
151	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
152	# Check the format version number
153	# Specifying the namespace will take care of the file
154	# format version
155	root = tree.getroot()
156
157	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
158	namespaces={'ns': CANSAS_NS})
159
160	for entry in entry_list:
161	self.errors = []
162	sas_entry = self._parse_entry(entry)
163	sas_entry.filename = basename
164
165	# Store loading process information
166	sas_entry.errors = self.errors
167	sas_entry.meta_data['loader'] = self.type_name
168	output.append(sas_entry)
169	except:
170	raise RuntimeError, "%s cannot be read \n" % path
171	else:
172	raise RuntimeError, "%s is not a file" % path
173	# Return output consistent with the loader's api
174	if len(output) == 0:
175	#cannot return none when it cannot read
176	#return None
177	raise RuntimeError, "%s cannot be read \n" % path
178	elif len(output) == 1:
179	return output[0]
180	else:
181	return output
182
183	def _parse_entry(self, dom):
184	"""
185	Parse a SASentry
186
187	:param node: SASentry node
188
189	:return: Data1D object
190	"""
191	x = numpy.zeros(0)
192	y = numpy.zeros(0)
193
194	data_info = Data1D(x, y)
195
196	# Look up title
197	self._store_content('ns:Title', dom, 'title', data_info)
198
199	# Look up run number
200	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
201	for item in nodes:
202	if item.text is not None:
203	value = item.text.strip()
204	if len(value) > 0:
205	data_info.run.append(value)
206	if item.get('name') is not None:
207	data_info.run_name[value] = item.get('name')
208
209	# Look up instrument name
210	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument',
211	data_info)
212
213	# Notes
214	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
215	for note in note_list:
216	try:
217	if note.text is not None:
218	note_value = note.text.strip()
219	if len(note_value) > 0:
220	data_info.notes.append(note_value)
221	except:
222	err_mess = "cansas_reader.read: error processing"
223	err_mess += " entry notes\n %s" % sys.exc_value
224	self.errors.append(err_mess)
225	logging.error(err_mess)
226
227	# Sample info ###################
228	entry = get_content('ns:SASsample', dom)
229	if entry is not None:
230	data_info.sample.name = entry.get('name')
231
232	self._store_content('ns:SASsample/ns:ID',
233	dom, 'ID', data_info.sample)
234	self._store_float('ns:SASsample/ns:thickness',
235	dom, 'thickness', data_info.sample)
236	self._store_float('ns:SASsample/ns:transmission',
237	dom, 'transmission', data_info.sample)
238	self._store_float('ns:SASsample/ns:temperature',
239	dom, 'temperature', data_info.sample)
240
241	nodes = dom.xpath('ns:SASsample/ns:details',
242	namespaces={'ns': CANSAS_NS})
243	for item in nodes:
244	try:
245	if item.text is not None:
246	detail_value = item.text.strip()
247	if len(detail_value) > 0:
248	data_info.sample.details.append(detail_value)
249	except:
250	err_mess = "cansas_reader.read: error processing "
251	err_mess += " sample details\n %s" % sys.exc_value
252	self.errors.append(err_mess)
253	logging.error(err_mess)
254
255	# Position (as a vector)
256	self._store_float('ns:SASsample/ns:position/ns:x',
257	dom, 'position.x', data_info.sample)
258	self._store_float('ns:SASsample/ns:position/ns:y',
259	dom, 'position.y', data_info.sample)
260	self._store_float('ns:SASsample/ns:position/ns:z',
261	dom, 'position.z', data_info.sample)
262
263	# Orientation (as a vector)
264	self._store_float('ns:SASsample/ns:orientation/ns:roll',
265	dom, 'orientation.x', data_info.sample)
266	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
267	dom, 'orientation.y', data_info.sample)
268	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
269	dom, 'orientation.z', data_info.sample)
270
271	# Source info ###################
272	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
273	if entry is not None:
274	data_info.source.name = entry.get('name')
275
276	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
277	dom, 'radiation', data_info.source)
278	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
279	dom, 'beam_shape', data_info.source)
280	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
281	dom, 'wavelength', data_info.source)
282	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
283	dom, 'wavelength_min', data_info.source)
284	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
285	dom, 'wavelength_max', data_info.source)
286	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
287	dom, 'wavelength_spread', data_info.source)
288
289	# Beam size (as a vector)
290	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
291	if entry is not None:
292	data_info.source.beam_size_name = entry.get('name')
293
294	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
295	dom, 'beam_size.x', data_info.source)
296	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
297	dom, 'beam_size.y', data_info.source)
298	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
299	dom, 'beam_size.z', data_info.source)
300
301	# Collimation info ###################
302	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
303	namespaces={'ns': CANSAS_NS})
304	for item in nodes:
305	collim = Collimation()
306	if item.get('name') is not None:
307	collim.name = item.get('name')
308	self._store_float('ns:length', item, 'length', collim)
309
310	# Look for apertures
311	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
312	for apert in apert_list:
313	aperture = Aperture()
314
315	# Get the name and type of the aperture
316	aperture.name = apert.get('name')
317	aperture.type = apert.get('type')
318
319	self._store_float('ns:distance', apert, 'distance', aperture)
320
321	entry = get_content('ns:size', apert)
322	if entry is not None:
323	aperture.size_name = entry.get('name')
324
325	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
326	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
327	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
328
329	collim.aperture.append(aperture)
330
331	data_info.collimation.append(collim)
332
333	# Detector info ######################
334	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
335	namespaces={'ns': CANSAS_NS})
336	for item in nodes:
337
338	detector = Detector()
339
340	self._store_content('ns:name', item, 'name', detector)
341	self._store_float('ns:SDD', item, 'distance', detector)
342
343	# Detector offset (as a vector)
344	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
345	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
346	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
347
348	# Detector orientation (as a vector)
349	self._store_float('ns:orientation/ns:roll', item, 'orientation.x',
350	detector)
351	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y',
352	detector)
353	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z',
354	detector)
355
356	# Beam center (as a vector)
357	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x',
358	detector)
359	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y',
360	detector)
361	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z',
362	detector)
363
364	# Pixel size (as a vector)
365	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x',
366	detector)
367	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y',
368	detector)
369	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z',
370	detector)
371
372	self._store_float('ns:slit_length', item, 'slit_length', detector)
373
374	data_info.detector.append(detector)
375
376	# Processes info ######################
377	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
378	for item in nodes:
379	process = Process()
380	self._store_content('ns:name', item, 'name', process)
381	self._store_content('ns:date', item, 'date', process)
382	self._store_content('ns:description', item, 'description', process)
383
384	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
385	for term in term_list:
386	try:
387	term_attr = {}
388	for attr in term.keys():
389	term_attr[attr] = term.get(attr).strip()
390	if term.text is not None:
391	term_attr['value'] = term.text.strip()
392	process.term.append(term_attr)
393	except:
394	err_mess = "cansas_reader.read: error processing "
395	err_mess += " process term\n %s" % sys.exc_value
396	self.errors.append(err_mess)
397	logging.error(err_mess)
398
399	note_list = item.xpath('ns:SASprocessnote',
400	namespaces={'ns': CANSAS_NS})
401	for note in note_list:
402	if note.text is not None:
403	process.notes.append(note.text.strip())
404
405	data_info.process.append(process)
406
407
408	# Data info ######################
409	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
410	if len(nodes) > 1:
411	msg = "CanSAS reader is not compatible with multiple"
412	msg += " SASdata entries"
413	raise RuntimeError, msg
414
415	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
416
417	x = numpy.zeros(0)
418	y = numpy.zeros(0)
419	dx = numpy.zeros(0)
420	dy = numpy.zeros(0)
421	dxw = numpy.zeros(0)
422	dxl = numpy.zeros(0)
423
424	for item in nodes:
425	_x, attr = get_float('ns:Q', item)
426	_dx, attr_d = get_float('ns:Qdev', item)
427	_dxl, attr_l = get_float('ns:dQl', item)
428	_dxw, attr_w = get_float('ns:dQw', item)
429	if _dx == None:
430	_dx = 0.0
431	if _dxl == None:
432	_dxl = 0.0
433	if _dxw == None:
434	_dxw = 0.0
435
436	if attr.has_key('unit') and \
437	attr['unit'].lower() != data_info.x_unit.lower():
438	if has_converter==True:
439	try:
440	data_conv_q = Converter(attr['unit'])
441	_x = data_conv_q(_x, units=data_info.x_unit)
442	except:
443	msg = "CanSAS reader: could not convert "
444	msg += "Q unit [%s]; "
445	msg += "expecting [%s]\n %s" % (attr['unit'],
446	data_info.x_unit, sys.exc_value)
447	raise ValueError, msg
448
449	else:
450	msg = "CanSAS reader: unrecognized Q unit [%s]; "
451	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
452	raise ValueError, msg
453
454	# Error in Q
455	if attr_d.has_key('unit') and \
456	attr_d['unit'].lower() != data_info.x_unit.lower():
457	if has_converter==True:
458	try:
459	data_conv_q = Converter(attr_d['unit'])
460	_dx = data_conv_q(_dx, units=data_info.x_unit)
461	except:
462	msg = "CanSAS reader: could not convert dQ unit [%s];"
463	msg += " expecting "
464	msg += "[%s]\n %s" % (attr['unit'],
465	data_info.x_unit, sys.exc_value)
466	raise ValueError, msg
467
468	else:
469	msg = "CanSAS reader: unrecognized dQ unit [%s]; "
470	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
471	raise ValueError, msg
472
473	# Slit length
474	if attr_l.has_key('unit') and \
475	attr_l['unit'].lower() != data_info.x_unit.lower():
476	if has_converter == True:
477	try:
478	data_conv_q = Converter(attr_l['unit'])
479	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
480	except:
481	msg = "CanSAS reader: could not convert dQl unit [%s];"
482	msg += " expecting [%s]\n %s" % (attr['unit'],
483	data_info.x_unit, sys.exc_value)
484	raise ValueError, msg
485
486	else:
487	msg = "CanSAS reader: unrecognized dQl unit [%s];"
488	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
489	raise ValueError, msg
490
491	# Slit width
492	if attr_w.has_key('unit') and \
493	attr_w['unit'].lower() != data_info.x_unit.lower():
494	if has_converter == True:
495	try:
496	data_conv_q = Converter(attr_w['unit'])
497	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
498	except:
499	msg = "CanSAS reader: could not convert dQw unit [%s];"
500	msg += " expecting [%s]\n %s" % (attr['unit'],
501	data_info.x_unit, sys.exc_value)
502	raise ValueError, msg
503
504	else:
505	msg = "CanSAS reader: unrecognized dQw unit [%s];"
506	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
507	raise ValueError, msg
508	_y, attr = get_float('ns:I', item)
509	_dy, attr_d = get_float('ns:Idev', item)
510	if _dy == None:
511	_dy = 0.0
512	if attr.has_key('unit') and \
513	attr['unit'].lower() != data_info.y_unit.lower():
514	if has_converter==True:
515	try:
516	data_conv_i = Converter(attr['unit'])
517	_y = data_conv_i(_y, units=data_info.y_unit)
518	except:
519	if attr['unit'].lower() == 'count':
520	pass
521	else:
522	msg = "CanSAS reader: could not"
523	msg += " convert I(q) unit [%s];" % str(attr['unit'])
524	msg += " expecting [%s]\n" % str(data_info.y_unit)
525	msg += " %s" % str(sys.exc_value)
526	raise ValueError, msg
527	else:
528	msg = "CanSAS reader: unrecognized I(q) unit [%s];"
529	msg += " expecting [%s]" % (attr['unit'], data_info.y_unit)
530	raise ValueError, msg
531
532	if attr_d.has_key('unit') and \
533	attr_d['unit'].lower() != data_info.y_unit.lower():
534	if has_converter==True:
535	try:
536	data_conv_i = Converter(attr_d['unit'])
537	_dy = data_conv_i(_dy, units=data_info.y_unit)
538	except:
539	if attr_d['unit'].lower() == 'count':
540	pass
541	else:
542	msg = "CanSAS reader: could not convert dI(q) unit "
543	msg += "[%s]; expecting [%s]\n %s" % (attr_d['unit'],
544	data_info.y_unit, sys.exc_value)
545	raise ValueError, msg
546	else:
547	msg = "CanSAS reader: unrecognized dI(q) unit [%s]; "
548	msg += "expecting [%s]" % (attr_d['unit'], data_info.y_unit)
549	raise ValueError, msg
550
551	if _x is not None and _y is not None:
552	x = numpy.append(x, _x)
553	y = numpy.append(y, _y)
554	dx = numpy.append(dx, _dx)
555	dy = numpy.append(dy, _dy)
556	dxl = numpy.append(dxl, _dxl)
557	dxw = numpy.append(dxw, _dxw)
558	# Zeros in dx, dy
559	if not numpy.all(dx==0):
560	dx[dx==0] = _ZERO
561	if not numpy.all(dy==0):
562	dy[dy==0] = _ZERO
563
564	data_info.x = x[x!=0]
565	data_info.y = y[x!=0]
566	data_info.dx = dx[x!=0]
567
568	data_info.dy = dy[x!=0]
569	data_info.dxl = dxl[x!=0]
570	data_info.dxw = dxw[x!=0]
571
572	data_conv_q = None
573	data_conv_i = None
574
575	if has_converter == True and data_info.x_unit != '1/A':
576	data_conv_q = Converter('1/A')
577	# Test it
578	data_conv_q(1.0, output.Q_unit)
579
580	if has_converter == True and data_info.y_unit != '1/cm':
581	data_conv_i = Converter('1/cm')
582	# Test it
583	data_conv_i(1.0, output.I_unit)
584
585	if data_conv_q is not None:
586	data_info.xaxis("\\rm{Q}", data_info.x_unit)
587	else:
588	data_info.xaxis("\\rm{Q}", 'A^{-1}')
589	if data_conv_i is not None:
590	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
591	else:
592	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
593
594	return data_info
595
596	def _to_xml_doc(self, datainfo):
597	"""
598	Create an XML document to contain the content of a Data1D
599
600	:param datainfo: Data1D object
601	"""
602
603	if not issubclass(datainfo.__class__, Data1D):
604	raise RuntimeError, "The cansas writer expects a Data1D instance"
605
606	doc = xml.dom.minidom.Document()
607	main_node = doc.createElement("SASroot")
608	main_node.setAttribute("version", self.version)
609	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
610	main_node.setAttribute("xmlns:xsi",
611	"http://www.w3.org/2001/XMLSchema-instance")
612	main_node.setAttribute("xsi:schemaLocation",
613	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
614
615	doc.appendChild(main_node)
616
617	entry_node = doc.createElement("SASentry")
618	main_node.appendChild(entry_node)
619
620	write_node(doc, entry_node, "Title", datainfo.title)
621	for item in datainfo.run:
622	runname = {}
623	if datainfo.run_name.has_key(item) and \
624	len(str(datainfo.run_name[item]))>1:
625	runname = {'name': datainfo.run_name[item] }
626	write_node(doc, entry_node, "Run", item, runname)
627
628	# Data info
629	node = doc.createElement("SASdata")
630	entry_node.appendChild(node)
631
632	for i in range(len(datainfo.x)):
633	pt = doc.createElement("Idata")
634	node.appendChild(pt)
635	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
636	if len(datainfo.y)>=i:
637	write_node(doc, pt, "I", datainfo.y[i],
638	{'unit':datainfo.y_unit})
639	if datainfo.dx != None and len(datainfo.dx) >= i:
640	write_node(doc, pt, "Qdev", datainfo.dx[i],
641	{'unit':datainfo.x_unit})
642	if datainfo.dxl != None and len(datainfo.dxl) >= i:
643	write_node(doc, pt, "dQl", datainfo.dxl[i],
644	{'unit':datainfo.x_unit})
645	if datainfo.dxw != None and len(datainfo.dxw) >= i:
646	write_node(doc, pt, "dQw", datainfo.dxw[i],
647	{'unit':datainfo.x_unit})
648	if datainfo.dy != None and len(datainfo.dy) >= i:
649	write_node(doc, pt, "Idev", datainfo.dy[i],
650	{'unit':datainfo.y_unit})
651
652
653	# Sample info
654	sample = doc.createElement("SASsample")
655	if datainfo.sample.name is not None:
656	sample.setAttribute("name", str(datainfo.sample.name))
657	entry_node.appendChild(sample)
658	write_node(doc, sample, "ID", str(datainfo.sample.ID))
659	write_node(doc, sample, "thickness", datainfo.sample.thickness,
660	{"unit":datainfo.sample.thickness_unit})
661	write_node(doc, sample, "transmission", datainfo.sample.transmission)
662	write_node(doc, sample, "temperature", datainfo.sample.temperature,
663	{"unit":datainfo.sample.temperature_unit})
664
665	for item in datainfo.sample.details:
666	write_node(doc, sample, "details", item)
667
668	pos = doc.createElement("position")
669	written = write_node(doc, pos, "x", datainfo.sample.position.x,
670	{"unit":datainfo.sample.position_unit})
671	written = written \| write_node(doc, pos, "y",
672	datainfo.sample.position.y,
673	{"unit":datainfo.sample.position_unit})
674	written = written \| write_node(doc, pos, "z",
675	datainfo.sample.position.z,
676	{"unit":datainfo.sample.position_unit})
677	if written == True:
678	sample.appendChild(pos)
679
680	ori = doc.createElement("orientation")
681	written = write_node(doc, ori, "roll",
682	datainfo.sample.orientation.x,
683	{"unit":datainfo.sample.orientation_unit})
684	written = written \| write_node(doc, ori, "pitch",
685	datainfo.sample.orientation.y,
686	{"unit":datainfo.sample.orientation_unit})
687	written = written \| write_node(doc, ori, "yaw",
688	datainfo.sample.orientation.z,
689	{"unit":datainfo.sample.orientation_unit})
690	if written == True:
691	sample.appendChild(ori)
692
693	# Instrument info
694	instr = doc.createElement("SASinstrument")
695	entry_node.appendChild(instr)
696
697	write_node(doc, instr, "name", datainfo.instrument)
698
699	# Source
700	source = doc.createElement("SASsource")
701	if datainfo.source.name is not None:
702	source.setAttribute("name", str(datainfo.source.name))
703	instr.appendChild(source)
704
705	write_node(doc, source, "radiation", datainfo.source.radiation)
706	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
707	size = doc.createElement("beam_size")
708	if datainfo.source.beam_size_name is not None:
709	size.setAttribute("name", str(datainfo.source.beam_size_name))
710	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
711	{"unit":datainfo.source.beam_size_unit})
712	written = written \| write_node(doc, size, "y",
713	datainfo.source.beam_size.y,
714	{"unit":datainfo.source.beam_size_unit})
715	written = written \| write_node(doc, size, "z",
716	datainfo.source.beam_size.z,
717	{"unit":datainfo.source.beam_size_unit})
718	if written == True:
719	source.appendChild(size)
720
721	write_node(doc, source, "wavelength",
722	datainfo.source.wavelength,
723	{"unit":datainfo.source.wavelength_unit})
724	write_node(doc, source, "wavelength_min",
725	datainfo.source.wavelength_min,
726	{"unit":datainfo.source.wavelength_min_unit})
727	write_node(doc, source, "wavelength_max",
728	datainfo.source.wavelength_max,
729	{"unit":datainfo.source.wavelength_max_unit})
730	write_node(doc, source, "wavelength_spread",
731	datainfo.source.wavelength_spread,
732	{"unit":datainfo.source.wavelength_spread_unit})
733
734	# Collimation
735	for item in datainfo.collimation:
736	coll = doc.createElement("SAScollimation")
737	if item.name is not None:
738	coll.setAttribute("name", str(item.name))
739	instr.appendChild(coll)
740
741	write_node(doc, coll, "length", item.length,
742	{"unit":item.length_unit})
743
744	for apert in item.aperture:
745	ap = doc.createElement("aperture")
746	if apert.name is not None:
747	ap.setAttribute("name", str(apert.name))
748	if apert.type is not None:
749	ap.setAttribute("type", str(apert.type))
750	coll.appendChild(ap)
751
752	write_node(doc, ap, "distance", apert.distance,
753	{"unit":apert.distance_unit})
754
755	size = doc.createElement("size")
756	if apert.size_name is not None:
757	size.setAttribute("name", str(apert.size_name))
758	written = write_node(doc, size, "x", apert.size.x,
759	{"unit":apert.size_unit})
760	written = written \| write_node(doc, size, "y", apert.size.y,
761	{"unit":apert.size_unit})
762	written = written \| write_node(doc, size, "z", apert.size.z,
763	{"unit":apert.size_unit})
764	if written == True:
765	ap.appendChild(size)
766
767	# Detectors
768	for item in datainfo.detector:
769	det = doc.createElement("SASdetector")
770	written = write_node(doc, det, "name", item.name)
771	written = written \| write_node(doc, det, "SDD", item.distance,
772	{"unit":item.distance_unit})
773	written = written \| write_node(doc, det, "slit_length",
774	item.slit_length,
775	{"unit":item.slit_length_unit})
776	if written == True:
777	instr.appendChild(det)
778
779	off = doc.createElement("offset")
780	written = write_node(doc, off, "x", item.offset.x,
781	{"unit":item.offset_unit})
782	written = written \| write_node(doc, off, "y", item.offset.y,
783	{"unit":item.offset_unit})
784	written = written \| write_node(doc, off, "z", item.offset.z,
785	{"unit":item.offset_unit})
786	if written == True:
787	det.appendChild(off)
788
789	center = doc.createElement("beam_center")
790	written = write_node(doc, center, "x", item.beam_center.x,
791	{"unit":item.beam_center_unit})
792	written = written \| write_node(doc, center, "y",
793	item.beam_center.y,
794	{"unit":item.beam_center_unit})
795	written = written \| write_node(doc, center, "z",
796	item.beam_center.z,
797	{"unit":item.beam_center_unit})
798	if written == True:
799	det.appendChild(center)
800
801	pix = doc.createElement("pixel_size")
802	written = write_node(doc, pix, "x", item.pixel_size.x,
803	{"unit":item.pixel_size_unit})
804	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
805	{"unit":item.pixel_size_unit})
806	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
807	{"unit":item.pixel_size_unit})
808	if written == True:
809	det.appendChild(pix)
810
811	ori = doc.createElement("orientation")
812	written = write_node(doc, ori, "roll", item.orientation.x,
813	{"unit":item.orientation_unit})
814	written = written \| write_node(doc, ori, "pitch",
815	item.orientation.y,
816	{"unit":item.orientation_unit})
817	written = written \| write_node(doc, ori, "yaw",
818	item.orientation.z,
819	{"unit":item.orientation_unit})
820	if written == True:
821	det.appendChild(ori)
822
823
824	# Processes info
825	for item in datainfo.process:
826	node = doc.createElement("SASprocess")
827	entry_node.appendChild(node)
828
829	write_node(doc, node, "name", item.name)
830	write_node(doc, node, "date", item.date)
831	write_node(doc, node, "description", item.description)
832	for term in item.term:
833	value = term['value']
834	del term['value']
835	write_node(doc, node, "term", value, term)
836	for note in item.notes:
837	write_node(doc, node, "SASprocessnote", note)
838
839	# Return the document, and the SASentry node associated with
840	# the data we just wrote
841	return doc, entry_node
842
843	def write(self, filename, datainfo):
844	"""
845	Write the content of a Data1D as a CanSAS XML file
846
847	:param filename: name of the file to write
848	:param datainfo: Data1D object
849	"""
850	# Create XML document
851	doc, sasentry = self._to_xml_doc(datainfo)
852	# Write the file
853	fd = open(filename, 'w')
854	fd.write(doc.toprettyxml())
855	fd.close()
856
857	def _store_float(self, location, node, variable, storage, optional=True):
858	"""
859	Get the content of a xpath location and store
860	the result. Check that the units are compatible
861	with the destination. The value is expected to
862	be a float.
863
864	The xpath location might or might not exist.
865	If it does not exist, nothing is done
866
867	:param location: xpath location to fetch
868	:param node: node to read the data from
869	:param variable: name of the data member to store it in [string]
870	:param storage: data object that has the 'variable' data member
871	:param optional: if True, no exception will be raised
872	if unit conversion can't be done
873
874	:raise ValueError: raised when the units are not recognized
875	"""
876	entry = get_content(location, node)
877	try:
878	value = float(entry.text)
879	except:
880	value = None
881
882	if value is not None:
883	# If the entry has units, check to see that they are
884	# compatible with what we currently have in the data object
885	units = entry.get('unit')
886	if units is not None:
887	toks = variable.split('.')
888	exec "local_unit = storage.%s_unit" % toks[0]
889	if units.lower()!=local_unit.lower():
890	if has_converter==True:
891	try:
892	conv = Converter(units)
893	exec "storage.%s = %g" % (variable,
894	conv(value, units=local_unit))
895	except:
896	err_mess = "CanSAS reader: could not convert"
897	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
898	% (variable, units, local_unit, sys.exc_value)
899	self.errors.append(err_mess)
900	if optional:
901	logging.info(err_mess)
902	else:
903	raise ValueError, err_mess
904	else:
905	err_mess = "CanSAS reader: unrecognized %s unit [%s];"
906	err_mess += " expecting [%s]" % (variable,
907	units, local_unit)
908	self.errors.append(err_mess)
909	if optional:
910	logging.info(err_mess)
911	else:
912	raise ValueError, err_mess
913	else:
914	exec "storage.%s = value" % variable
915	else:
916	exec "storage.%s = value" % variable
917
918	def _store_content(self, location, node, variable, storage):
919	"""
920	Get the content of a xpath location and store
921	the result. The value is treated as a string.
922
923	The xpath location might or might not exist.
924	If it does not exist, nothing is done
925
926	:param location: xpath location to fetch
927	:param node: node to read the data from
928	:param variable: name of the data member to store it in [string]
929	:param storage: data object that has the 'variable' data member
930
931	:return: return a list of errors
932	"""
933	entry = get_content(location, node)
934	if entry is not None and entry.text is not None:
935	exec "storage.%s = entry.text.strip()" % variable
936
937
938
939	if __name__ == "__main__":
940	logging.basicConfig(level=logging.ERROR,
941	format='%(asctime)s %(levelname)s %(message)s',
942	filename='cansas_reader.log',
943	filemode='w')
944	reader = Reader()
945	print reader.read("../test/cansas1d.xml")
946	#print reader.read("../test/latex_smeared.xml")
947
948
949

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SasView

source: sasview/sansdataloader/src/sans/dataloader/readers/cansas_reader.py @ 0a5c8f5

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