cansas_reader.py @ 4a7ad5f

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 4a7ad5f 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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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
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	return None
174	elif len(output)==1:
175	return output[0]
176	else:
177	return output
178
179	def _parse_entry(self, dom):
180	"""
181	Parse a SASentry
182
183	:param node: SASentry node
184
185	:return: Data1D object
186	"""
187	x = numpy.zeros(0)
188	y = numpy.zeros(0)
189
190	data_info = Data1D(x, y)
191
192	# Look up title
193	self._store_content('ns:Title', dom, 'title', data_info)
194
195	# Look up run number
196	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
197	for item in nodes:
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')
204
205	# Look up instrument name
206	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument',
207	data_info)
208
209	# Notes
210	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
211	for note in note_list:
212	try:
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)
217	except:
218	err_mess = "cansas_reader.read: error processing"
219	err_mess += " entry notes\n %s" % sys.exc_value
220	self.errors.append(err_mess)
221	logging.error(err_mess)
222
223	# Sample info ###################
224	entry = get_content('ns:SASsample', dom)
225	if entry is not None:
226	data_info.sample.name = entry.get('name')
227
228	self._store_content('ns:SASsample/ns:ID',
229	dom, 'ID', data_info.sample)
230	self._store_float('ns:SASsample/ns:thickness',
231	dom, 'thickness', data_info.sample)
232	self._store_float('ns:SASsample/ns:transmission',
233	dom, 'transmission', data_info.sample)
234	self._store_float('ns:SASsample/ns:temperature',
235	dom, 'temperature', data_info.sample)
236
237	nodes = dom.xpath('ns:SASsample/ns:details',
238	namespaces={'ns': CANSAS_NS})
239	for item in nodes:
240	try:
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)
245	except:
246	err_mess = "cansas_reader.read: error processing "
247	err_mess += " sample details\n %s" % sys.exc_value
248	self.errors.append(err_mess)
249	logging.error(err_mess)
250
251	# Position (as a vector)
252	self._store_float('ns:SASsample/ns:position/ns:x',
253	dom, 'position.x', data_info.sample)
254	self._store_float('ns:SASsample/ns:position/ns:y',
255	dom, 'position.y', data_info.sample)
256	self._store_float('ns:SASsample/ns:position/ns:z',
257	dom, 'position.z', data_info.sample)
258
259	# Orientation (as a vector)
260	self._store_float('ns:SASsample/ns:orientation/ns:roll',
261	dom, 'orientation.x', data_info.sample)
262	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
263	dom, 'orientation.y', data_info.sample)
264	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
265	dom, 'orientation.z', data_info.sample)
266
267	# Source info ###################
268	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
269	if entry is not None:
270	data_info.source.name = entry.get('name')
271
272	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
273	dom, 'radiation', data_info.source)
274	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
275	dom, 'beam_shape', data_info.source)
276	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
277	dom, 'wavelength', data_info.source)
278	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
279	dom, 'wavelength_min', data_info.source)
280	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
281	dom, 'wavelength_max', data_info.source)
282	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
283	dom, 'wavelength_spread', data_info.source)
284
285	# Beam size (as a vector)
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')
289
290	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
291	dom, 'beam_size.x', data_info.source)
292	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
293	dom, 'beam_size.y', data_info.source)
294	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
295	dom, 'beam_size.z', data_info.source)
296
297	# Collimation info ###################
298	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
299	namespaces={'ns': CANSAS_NS})
300	for item in nodes:
301	collim = Collimation()
302	if item.get('name') is not None:
303	collim.name = item.get('name')
304	self._store_float('ns:length', item, 'length', collim)
305
306	# Look for apertures
307	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
308	for apert in apert_list:
309	aperture = Aperture()
310
311	# Get the name and type of the aperture
312	aperture.name = apert.get('name')
313	aperture.type = apert.get('type')
314
315	self._store_float('ns:distance', apert, 'distance', aperture)
316
317	entry = get_content('ns:size', apert)
318	if entry is not None:
319	aperture.size_name = entry.get('name')
320
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)
324
325	collim.aperture.append(aperture)
326
327	data_info.collimation.append(collim)
328
329	# Detector info ######################
330	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
331	namespaces={'ns': CANSAS_NS})
332	for item in nodes:
333
334	detector = Detector()
335
336	self._store_content('ns:name', item, 'name', detector)
337	self._store_float('ns:SDD', item, 'distance', detector)
338
339	# Detector offset (as a vector)
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)
343
344	# Detector orientation (as a vector)
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)
351
352	# Beam center (as a vector)
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)
359
360	# Pixel size (as a vector)
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)
367
368	self._store_float('ns:slit_length', item, 'slit_length', detector)
369
370	data_info.detector.append(detector)
371
372	# Processes info ######################
373	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
374	for item in nodes:
375	process = Process()
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)
379
380	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
381	for term in term_list:
382	try:
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()
388	process.term.append(term_attr)
389	except:
390	err_mess = "cansas_reader.read: error processing "
391	err_mess += " process term\n %s" % sys.exc_value
392	self.errors.append(err_mess)
393	logging.error(err_mess)
394
395	note_list = item.xpath('ns:SASprocessnote',
396	namespaces={'ns': CANSAS_NS})
397	for note in note_list:
398	if note.text is not None:
399	process.notes.append(note.text.strip())
400
401	data_info.process.append(process)
402
403
404	# Data info ######################
405	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
406	if len(nodes) > 1:
407	msg = "CanSAS reader is not compatible with multiple"
408	msg += " SASdata entries"
409	raise RuntimeError, msg
410
411	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
412
413	x = numpy.zeros(0)
414	y = numpy.zeros(0)
415	dx = numpy.zeros(0)
416	dy = numpy.zeros(0)
417	dxw = numpy.zeros(0)
418	dxl = numpy.zeros(0)
419
420	for item in nodes:
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)
425	if _dx == None:
426	_dx = 0.0
427	if _dxl == None:
428	_dxl = 0.0
429	if _dxw == None:
430	_dxw = 0.0
431
432	if attr.has_key('unit') and \
433	attr['unit'].lower() != data_info.x_unit.lower():
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:
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
445	else:
446	msg = "CanSAS reader: unrecognized Q unit [%s]; "
447	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
448	raise ValueError, msg
449
450	# Error in Q
451	if attr_d.has_key('unit') and \
452	attr_d['unit'].lower() != data_info.x_unit.lower():
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:
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
464	else:
465	msg = "CanSAS reader: unrecognized dQ unit [%s]; "
466	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
467	raise ValueError, msg
468
469	# Slit length
470	if attr_l.has_key('unit') and \
471	attr_l['unit'].lower() != data_info.x_unit.lower():
472	if has_converter == True:
473	try:
474	data_conv_q = Converter(attr_l['unit'])
475	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
476	except:
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
482	else:
483	msg = "CanSAS reader: unrecognized dQl unit [%s];"
484	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
485	raise ValueError, msg
486
487	# Slit width
488	if attr_w.has_key('unit') and \
489	attr_w['unit'].lower() != data_info.x_unit.lower():
490	if has_converter == True:
491	try:
492	data_conv_q = Converter(attr_w['unit'])
493	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
494	except:
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
500	else:
501	msg = "CanSAS reader: unrecognized dQw unit [%s];"
502	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
503	raise ValueError, msg
504	_y, attr = get_float('ns:I', item)
505	_dy, attr_d = get_float('ns:Idev', item)
506	if _dy == None:
507	_dy = 0.0
508	if attr.has_key('unit') and \
509	attr['unit'].lower() != data_info.y_unit.lower():
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:
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
519	else:
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():
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:
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
535	else:
536	msg = "CanSAS reader: unrecognized dI(q) unit [%s]; "
537	msg += "expecting [%s]" % (attr_d['unit'], data_info.y_unit)
538	raise ValueError, msg
539
540	if _x is not None and _y is not None:
541	x = numpy.append(x, _x)
542	y = numpy.append(y, _y)
543	dx = numpy.append(dx, _dx)
544	dy = numpy.append(dy, _dy)
545	dxl = numpy.append(dxl, _dxl)
546	dxw = numpy.append(dxw, _dxw)
547
548	data_info.x = x
549	data_info.y = y
550	data_info.dx = dx
551	data_info.dy = dy
552	data_info.dxl = dxl
553	data_info.dxw = dxw
554
555	data_conv_q = None
556	data_conv_i = None
557
558	if has_converter == True and data_info.x_unit != '1/A':
559	data_conv_q = Converter('1/A')
560	# Test it
561	data_conv_q(1.0, output.Q_unit)
562
563	if has_converter == True and data_info.y_unit != '1/cm':
564	data_conv_i = Converter('1/cm')
565	# Test it
566	data_conv_i(1.0, output.I_unit)
567
568	if data_conv_q is not None:
569	data_info.xaxis("\\rm{Q}", data_info.x_unit)
570	else:
571	data_info.xaxis("\\rm{Q}", 'A^{-1}')
572	if data_conv_i is not None:
573	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
574	else:
575	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
576
577	return data_info
578
579	def _to_xml_doc(self, datainfo):
580	"""
581	Create an XML document to contain the content of a Data1D
582
583	:param datainfo: Data1D object
584	"""
585
586	if not issubclass(datainfo.__class__, Data1D):
587	raise RuntimeError, "The cansas writer expects a Data1D instance"
588
589	doc = xml.dom.minidom.Document()
590	main_node = doc.createElement("SASroot")
591	main_node.setAttribute("version", self.version)
592	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
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)
597
598	doc.appendChild(main_node)
599
600	entry_node = doc.createElement("SASentry")
601	main_node.appendChild(entry_node)
602
603	write_node(doc, entry_node, "Title", datainfo.title)
604	for item in datainfo.run:
605	runname = {}
606	if datainfo.run_name.has_key(item) and \
607	len(str(datainfo.run_name[item]))>1:
608	runname = {'name': datainfo.run_name[item] }
609	write_node(doc, entry_node, "Run", item, runname)
610
611	# Data info
612	node = doc.createElement("SASdata")
613	entry_node.appendChild(node)
614
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:
620	write_node(doc, pt, "I", datainfo.y[i],
621	{'unit':datainfo.y_unit})
622	if datainfo.dx !=None and len(datainfo.dx)>=i:
623	write_node(doc, pt, "Qdev", datainfo.dx[i],
624	{'unit':datainfo.x_unit})
625	if datainfo.dy !=None and len(datainfo.dy)>=i:
626	write_node(doc, pt, "Idev", datainfo.dy[i],
627	{'unit':datainfo.y_unit})
628
629
630	# Sample info
631	sample = doc.createElement("SASsample")
632	if datainfo.sample.name is not None:
633	sample.setAttribute("name", str(datainfo.sample.name))
634	entry_node.appendChild(sample)
635	write_node(doc, sample, "ID", str(datainfo.sample.ID))
636	write_node(doc, sample, "thickness", datainfo.sample.thickness,
637	{"unit":datainfo.sample.thickness_unit})
638	write_node(doc, sample, "transmission", datainfo.sample.transmission)
639	write_node(doc, sample, "temperature", datainfo.sample.temperature,
640	{"unit":datainfo.sample.temperature_unit})
641
642	for item in datainfo.sample.details:
643	write_node(doc, sample, "details", item)
644
645	pos = doc.createElement("position")
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})
654	if written == True:
655	sample.appendChild(pos)
656
657	ori = doc.createElement("orientation")
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})
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")
678	if datainfo.source.name is not None:
679	source.setAttribute("name", str(datainfo.source.name))
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)
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))
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})
695	if written == True:
696	source.appendChild(size)
697
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})
710
711	# Collimation
712	for item in datainfo.collimation:
713	coll = doc.createElement("SAScollimation")
714	if item.name is not None:
715	coll.setAttribute("name", str(item.name))
716	instr.appendChild(coll)
717
718	write_node(doc, coll, "length", item.length,
719	{"unit":item.length_unit})
720
721	for apert in item.aperture:
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)
728
729	write_node(doc, ap, "distance", apert.distance,
730	{"unit":apert.distance_unit})
731
732	size = doc.createElement("size")
733	if apert.size_name is not None:
734	size.setAttribute("name", str(apert.size_name))
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})
741	if written == True:
742	ap.appendChild(size)
743
744	# Detectors
745	for item in datainfo.detector:
746	det = doc.createElement("SASdetector")
747	written = write_node(doc, det, "name", item.name)
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})
753	if written == True:
754	instr.appendChild(det)
755
756	off = doc.createElement("offset")
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})
763	if written == True:
764	det.appendChild(off)
765
766	center = doc.createElement("beam_center")
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})
775	if written == True:
776	det.appendChild(center)
777
778	pix = doc.createElement("pixel_size")
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})
785	if written == True:
786	det.appendChild(pix)
787
788	ori = doc.createElement("orientation")
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})
797	if written == True:
798	det.appendChild(ori)
799
800
801	# Processes info
802	for item in datainfo.process:
803	node = doc.createElement("SASprocess")
804	entry_node.appendChild(node)
805
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)
815
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	"""
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
826	"""
827	# Create XML document
828	doc, sasentry = self._to_xml_doc(datainfo)
829	# Write the file
830	fd = open(filename, 'w')
831	fd.write(doc.toprettyxml())
832	fd.close()
833
834	def _store_float(self, location, node, variable, storage, optional=True):
835	"""
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
848	:param optional: if True, no exception will be raised
849	if unit conversion can't be done
850
851	:raise ValueError: raised when the units are not recognized
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)
870	exec "storage.%s = %g" % (variable,
871	conv(value, units=local_unit))
872	except:
873	err_mess = "CanSAS reader: could not convert"
874	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
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:
882	err_mess = "CanSAS reader: unrecognized %s unit [%s];"
883	err_mess += " expecting [%s]" % (variable,
884	units, local_unit)
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	"""
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
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
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")
923	#print reader.read("../test/latex_smeared.xml")
924
925
926

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 4a7ad5f

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