cansas_reader.py @ dcf29d7

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 dcf29d7 was 0e2aa40, checked in by Jae Cho <jhjcho@…>, 15 years ago
Made the letter of units in plots consistent for all
Property mode set to `100644`
File size: 35.1 KB

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

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ dcf29d7

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