cansas_reader.py @ de1da34

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 de1da34 was 72b524b, checked in by Gervaise Alina <gervyh@…>, 16 years ago
add error handling for dy==None when writing file
Property mode set to `100644`
File size: 34.8 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	raise ValueError, "CanSAS reader: could not convert %s unit [%s]; expecting [%s]\n %s" \
156	% (variable, attr['unit'], local_unit, sys.exc_value)
157	else:
158	raise ValueError, "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \
159	% (variable, attr['unit'], local_unit)
160	else:
161	exec "storage.%s = value" % variable
162	else:
163	exec "storage.%s = value" % variable
164
165
166	def _store_content(location, node, variable, storage):
167	"""
168	Get the content of a xpath location and store
169	the result. The value is treated as a string.
170
171	The xpath location might or might not exist.
172	If it does not exist, nothing is done
173
174	@param location: xpath location to fetch
175	@param node: node to read the data from
176	@param variable: name of the data member to store it in [string]
177	@param storage: data object that has the 'variable' data member
178	"""
179	value, attr = get_content(location, node)
180	if value is not None:
181	exec "storage.%s = value" % variable
182
183
184	class Reader:
185	"""
186	Class to load cansas 1D XML files
187
188	Dependencies:
189	The CanSas reader requires PyXML 0.8.4 or later.
190	"""
191	## CanSAS version
192	version = '1.0'
193	## File type
194	type = ["CanSAS 1D files (.xml)\|.xml"]
195	## List of allowed extensions
196	ext=['.xml', '.XML']
197
198	def read(self, path):
199	"""
200	Load data file
201
202	@param path: file path
203	@return: Data1D object if a single SASentry was found,
204	or a list of Data1D objects if multiple entries were found,
205	or None of nothing was found
206	@raise RuntimeError: when the file can't be opened
207	@raise ValueError: when the length of the data vectors are inconsistent
208	"""
209	from xml.dom.minidom import parse
210
211	output = []
212
213	if os.path.isfile(path):
214	basename = os.path.basename(path)
215	root, extension = os.path.splitext(basename)
216	if extension.lower() in self.ext:
217
218	dom = parse(path)
219
220	# Check the format version number
221	nodes = xpath.Evaluate('SASroot', dom)
222	if nodes[0].hasAttributes():
223	for i in range(nodes[0].attributes.length):
224	if nodes[0].attributes.item(i).nodeName=='version':
225	if nodes[0].attributes.item(i).nodeValue != self.version:
226	raise ValueError, "cansas_reader: unrecognized version number %s" % \
227	nodes[0].attributes.item(i).nodeValue
228
229	entry_list = xpath.Evaluate('SASroot/SASentry', dom)
230	for entry in entry_list:
231	sas_entry = self._parse_entry(entry)
232	sas_entry.filename = basename
233	output.append(sas_entry)
234
235	else:
236	raise RuntimeError, "%s is not a file" % path
237
238	# Return output consistent with the loader's api
239	if len(output)==0:
240	return None
241	elif len(output)==1:
242	return output[0]
243	else:
244	return output
245
246	def _parse_entry(self, dom):
247	"""
248	Parse a SASentry
249
250	@param node: SASentry node
251	@return: Data1D object
252	"""
253	x = numpy.zeros(0)
254	y = numpy.zeros(0)
255
256	data_info = Data1D(x, y)
257
258	# Look up title
259	_store_content('Title', dom, 'title', data_info)
260	# Look up run number
261	nodes = xpath.Evaluate('Run', dom)
262	for item in nodes:
263	value, attr = get_node_text(item)
264	if value is not None:
265	data_info.run.append(value)
266	if attr.has_key('name'):
267	data_info.run_name[value] = attr['name']
268
269	# Look up instrument name
270	_store_content('SASinstrument/name', dom, 'instrument', data_info)
271	#value, attr = get_content('SASinstrument', dom)
272	#if attr.has_key('name'):
273	# data_info.instrument = attr['name']
274
275	note_list = xpath.Evaluate('SASnote', dom)
276	for note in note_list:
277	try:
278	note_value, note_attr = get_node_text(note)
279	if note_value is not None:
280	data_info.notes.append(note_value)
281	except:
282	logging.error("cansas_reader.read: error processing entry notes\n %s" % sys.exc_value)
283
284
285	# Sample info ###################
286	value, attr = get_content('SASsample', dom)
287	if attr.has_key('name'):
288	data_info.sample.name = attr['name']
289
290	_store_content('SASsample/ID',
291	dom, 'ID', data_info.sample)
292	_store_float('SASsample/thickness',
293	dom, 'thickness', data_info.sample)
294	_store_float('SASsample/transmission',
295	dom, 'transmission', data_info.sample)
296	_store_float('SASsample/temperature',
297	dom, 'temperature', data_info.sample)
298	nodes = xpath.Evaluate('SASsample/details', dom)
299	for item in nodes:
300	try:
301	detail_value, detail_attr = get_node_text(item)
302	if detail_value is not None:
303	data_info.sample.details.append(detail_value)
304	except:
305	logging.error("cansas_reader.read: error processing sample details\n %s" % sys.exc_value)
306
307	# Position (as a vector)
308	_store_float('SASsample/position/x',
309	dom, 'position.x', data_info.sample)
310	_store_float('SASsample/position/y',
311	dom, 'position.y', data_info.sample)
312	_store_float('SASsample/position/z',
313	dom, 'position.z', data_info.sample)
314
315	# Orientation (as a vector)
316	_store_float('SASsample/orientation/roll',
317	dom, 'orientation.x', data_info.sample)
318	_store_float('SASsample/orientation/pitch',
319	dom, 'orientation.y', data_info.sample)
320	_store_float('SASsample/orientation/yaw',
321	dom, 'orientation.z', data_info.sample)
322
323	# Source info ###################
324	value, attr = get_content('SASinstrument/SASsource', dom)
325	if attr.has_key('name'):
326	data_info.source.name = attr['name']
327
328	_store_content('SASinstrument/SASsource/radiation',
329	dom, 'radiation', data_info.source)
330	_store_content('SASinstrument/SASsource/beam_shape',
331	dom, 'beam_shape', data_info.source)
332	_store_float('SASinstrument/SASsource/wavelength',
333	dom, 'wavelength', data_info.source)
334	_store_float('SASinstrument/SASsource/wavelength_min',
335	dom, 'wavelength_min', data_info.source)
336	_store_float('SASinstrument/SASsource/wavelength_max',
337	dom, 'wavelength_max', data_info.source)
338	_store_float('SASinstrument/SASsource/wavelength_spread',
339	dom, 'wavelength_spread', data_info.source)
340
341	# Beam size (as a vector)
342	value, attr = get_content('SASinstrument/SASsource/beam_size', dom)
343	if attr.has_key('name'):
344	data_info.source.beam_size_name = attr['name']
345
346	_store_float('SASinstrument/SASsource/beam_size/x',
347	dom, 'beam_size.x', data_info.source)
348	_store_float('SASinstrument/SASsource/beam_size/y',
349	dom, 'beam_size.y', data_info.source)
350	_store_float('SASinstrument/SASsource/beam_size/z',
351	dom, 'beam_size.z', data_info.source)
352
353	# Collimation info ###################
354	nodes = xpath.Evaluate('SASinstrument/SAScollimation', dom)
355	for item in nodes:
356	collim = Collimation()
357	value, attr = get_node_text(item)
358	if attr.has_key('name'):
359	collim.name = attr['name']
360	_store_float('length', item, 'length', collim)
361
362	# Look for apertures
363	apert_list = xpath.Evaluate('aperture', item)
364	for apert in apert_list:
365	aperture = Aperture()
366
367	# Get the name and type of the aperture
368	ap_value, ap_attr = get_node_text(apert)
369	if ap_attr.has_key('name'):
370	aperture.name = ap_attr['name']
371	if ap_attr.has_key('type'):
372	aperture.type = ap_attr['type']
373
374	_store_float('distance', apert, 'distance', aperture)
375
376	value, attr = get_content('size', apert)
377	if attr.has_key('name'):
378	aperture.size_name = attr['name']
379
380	_store_float('size/x', apert, 'size.x', aperture)
381	_store_float('size/y', apert, 'size.y', aperture)
382	_store_float('size/z', apert, 'size.z', aperture)
383
384	collim.aperture.append(aperture)
385
386	data_info.collimation.append(collim)
387
388	# Detector info ######################
389	nodes = xpath.Evaluate('SASinstrument/SASdetector', dom)
390	for item in nodes:
391
392	detector = Detector()
393
394	_store_content('name', item, 'name', detector)
395	_store_float('SDD', item, 'distance', detector)
396
397	# Detector offset (as a vector)
398	_store_float('offset/x', item, 'offset.x', detector)
399	_store_float('offset/y', item, 'offset.y', detector)
400	_store_float('offset/z', item, 'offset.z', detector)
401
402	# Detector orientation (as a vector)
403	_store_float('orientation/roll', item, 'orientation.x', detector)
404	_store_float('orientation/pitch', item, 'orientation.y', detector)
405	_store_float('orientation/yaw', item, 'orientation.z', detector)
406
407	# Beam center (as a vector)
408	_store_float('beam_center/x', item, 'beam_center.x', detector)
409	_store_float('beam_center/y', item, 'beam_center.y', detector)
410	_store_float('beam_center/z', item, 'beam_center.z', detector)
411
412	# Pixel size (as a vector)
413	_store_float('pixel_size/x', item, 'pixel_size.x', detector)
414	_store_float('pixel_size/y', item, 'pixel_size.y', detector)
415	_store_float('pixel_size/z', item, 'pixel_size.z', detector)
416
417	_store_float('slit_length', item, 'slit_length', detector)
418
419	data_info.detector.append(detector)
420
421	# Processes info ######################
422	nodes = xpath.Evaluate('SASprocess', dom)
423	for item in nodes:
424	process = Process()
425	_store_content('name', item, 'name', process)
426	_store_content('date', item, 'date', process)
427	_store_content('description', item, 'description', process)
428
429	term_list = xpath.Evaluate('term', item)
430	for term in term_list:
431	try:
432	term_value, term_attr = get_node_text(term)
433	term_attr['value'] = term_value
434	if term_value is not None:
435	process.term.append(term_attr)
436	except:
437	logging.error("cansas_reader.read: error processing process term\n %s" % sys.exc_value)
438
439	note_list = xpath.Evaluate('SASprocessnote', item)
440	for note in note_list:
441	try:
442	note_value, note_attr = get_node_text(note)
443	if note_value is not None:
444	process.notes.append(note_value)
445	except:
446	logging.error("cansas_reader.read: error processing process notes\n %s" % sys.exc_value)
447
448
449	data_info.process.append(process)
450
451
452	# Data info ######################
453	nodes = xpath.Evaluate('SASdata', dom)
454	if len(nodes)>1:
455	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
456
457	nodes = xpath.Evaluate('SASdata/Idata', dom)
458	x = numpy.zeros(0)
459	y = numpy.zeros(0)
460	dx = numpy.zeros(0)
461	dy = numpy.zeros(0)
462	dxw = numpy.zeros(0)
463	dxl = numpy.zeros(0)
464
465	for item in nodes:
466	_x, attr = get_float('Q', item)
467	_dx, attr_d = get_float('Qdev', item)
468	_dxl, attr_l = get_float('dQl', item)
469	_dxw, attr_w = get_float('dQw', item)
470	if _dx == None:
471	_dx = 0.0
472	if _dxl == None:
473	_dxl = 0.0
474	if _dxw == None:
475	_dxw = 0.0
476
477	if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower():
478	if has_converter==True:
479	try:
480	data_conv_q = Converter(attr['unit'])
481	_x = data_conv_q(_x, units=data_info.x_unit)
482	except:
483	raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \
484	% (attr['unit'], data_info.x_unit, sys.exc_value)
485	else:
486	raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \
487	% (attr['unit'], data_info.x_unit)
488	# Error in Q
489	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower():
490	if has_converter==True:
491	try:
492	data_conv_q = Converter(attr_d['unit'])
493	_dx = data_conv_q(_dx, units=data_info.x_unit)
494	except:
495	raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \
496	% (attr['unit'], data_info.x_unit, sys.exc_value)
497	else:
498	raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \
499	% (attr['unit'], data_info.x_unit)
500	# Slit length
501	if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower():
502	if has_converter==True:
503	try:
504	data_conv_q = Converter(attr_l['unit'])
505	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
506	except:
507	raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \
508	% (attr['unit'], data_info.x_unit, sys.exc_value)
509	else:
510	raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \
511	% (attr['unit'], data_info.x_unit)
512	# Slit width
513	if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower():
514	if has_converter==True:
515	try:
516	data_conv_q = Converter(attr_w['unit'])
517	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
518	except:
519	raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \
520	% (attr['unit'], data_info.x_unit, sys.exc_value)
521	else:
522	raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \
523	% (attr['unit'], data_info.x_unit)
524
525	_y, attr = get_float('I', item)
526	_dy, attr_d = get_float('Idev', item)
527	if _dy == None:
528	_dy = 0.0
529	if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower():
530	if has_converter==True:
531	try:
532	data_conv_i = Converter(attr['unit'])
533	_y = data_conv_i(_y, units=data_info.y_unit)
534	except:
535	raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \
536	% (attr['unit'], data_info.y_unit, sys.exc_value)
537	else:
538	raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \
539	% (attr['unit'], data_info.y_unit)
540	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower():
541	if has_converter==True:
542	try:
543	data_conv_i = Converter(attr_d['unit'])
544	_dy = data_conv_i(_dy, units=data_info.y_unit)
545	except:
546	raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \
547	% (attr_d['unit'], data_info.y_unit, sys.exc_value)
548	else:
549	raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \
550	% (attr_d['unit'], data_info.y_unit)
551
552	if _x is not None and _y is not None:
553	x = numpy.append(x, _x)
554	y = numpy.append(y, _y)
555	dx = numpy.append(dx, _dx)
556	dy = numpy.append(dy, _dy)
557	dxl = numpy.append(dxl, _dxl)
558	dxw = numpy.append(dxw, _dxw)
559
560
561	data_info.x = x
562	data_info.y = y
563	data_info.dx = dx
564	data_info.dy = dy
565	data_info.dxl = dxl
566	data_info.dxw = dxw
567
568	data_conv_q = None
569	data_conv_i = None
570
571	if has_converter == True and data_info.x_unit != '1/A':
572	data_conv_q = Converter('1/A')
573	# Test it
574	data_conv_q(1.0, output.Q_unit)
575
576	if has_converter == True and data_info.y_unit != '1/cm':
577	data_conv_i = Converter('1/cm')
578	# Test it
579	data_conv_i(1.0, output.I_unit)
580
581	if data_conv_q is not None:
582	data_info.xaxis("\\rm{Q}", data_info.x_unit)
583	else:
584	data_info.xaxis("\\rm{Q}", 'A^{-1}')
585	if data_conv_i is not None:
586	data_info.yaxis("\\{I(Q)}", data_info.y_unit)
587	else:
588	data_info.yaxis("\\rm{I(Q)}","cm^{-1}")
589
590	return data_info
591
592	def write(self, filename, datainfo):
593	"""
594	Write the content of a Data1D as a CanSAS XML file
595
596	@param filename: name of the file to write
597	@param datainfo: Data1D object
598	"""
599
600	if not datainfo.__class__ == Data1D:
601	raise RuntimeError, "The cansas writer expects a Data1D instance"
602
603	doc = xml.dom.minidom.Document()
604	main_node = doc.createElement("SASroot")
605	main_node.setAttribute("version", self.version)
606	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
607	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
608	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
609
610	doc.appendChild(main_node)
611
612	entry_node = doc.createElement("SASentry")
613	main_node.appendChild(entry_node)
614
615	write_node(doc, entry_node, "Title", datainfo.title)
616
617	for item in datainfo.run:
618	runname = {}
619	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
620	runname = {'name': datainfo.run_name[item] }
621	write_node(doc, entry_node, "Run", item, runname)
622
623	# Data info
624	node = doc.createElement("SASdata")
625	entry_node.appendChild(node)
626
627	for i in range(len(datainfo.x)):
628	pt = doc.createElement("Idata")
629	node.appendChild(pt)
630	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
631	if len(datainfo.y)>=i:
632	write_node(doc, pt, "I", datainfo.y[i], {'unit':datainfo.y_unit})
633	if datainfo.dx !=None and len(datainfo.dx)>=i:
634	write_node(doc, pt, "Qdev", datainfo.dx[i], {'unit':datainfo.x_unit})
635	if datainfo.dx !=None and len(datainfo.dy)>=i:
636	write_node(doc, pt, "Idev", datainfo.dy[i], {'unit':datainfo.y_unit})
637
638
639	# Sample info
640	sample = doc.createElement("SASsample")
641	if datainfo.sample.name is not None:
642	sample.setAttribute("name", str(datainfo.sample.name))
643	entry_node.appendChild(sample)
644	write_node(doc, sample, "ID", str(datainfo.sample.ID))
645	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
646	write_node(doc, sample, "transmission", datainfo.sample.transmission)
647	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
648
649	for item in datainfo.sample.details:
650	write_node(doc, sample, "details", item)
651
652	pos = doc.createElement("position")
653	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
654	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
655	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
656	if written == True:
657	sample.appendChild(pos)
658
659	ori = doc.createElement("orientation")
660	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
661	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
662	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
663	if written == True:
664	sample.appendChild(ori)
665
666	# Instrument info
667	instr = doc.createElement("SASinstrument")
668	entry_node.appendChild(instr)
669
670	write_node(doc, instr, "name", datainfo.instrument)
671
672	# Source
673	source = doc.createElement("SASsource")
674	if datainfo.source.name is not None:
675	source.setAttribute("name", str(datainfo.source.name))
676	instr.appendChild(source)
677
678	write_node(doc, source, "radiation", datainfo.source.radiation)
679	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
680	size = doc.createElement("beam_size")
681	if datainfo.source.beam_size_name is not None:
682	size.setAttribute("name", str(datainfo.source.beam_size_name))
683	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
684	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
685	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
686	if written == True:
687	source.appendChild(size)
688
689	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
690	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
691	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
692	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
693
694	# Collimation
695	for item in datainfo.collimation:
696	coll = doc.createElement("SAScollimation")
697	if item.name is not None:
698	coll.setAttribute("name", str(item.name))
699	instr.appendChild(coll)
700
701	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
702
703	for apert in item.aperture:
704	ap = doc.createElement("aperture")
705	if apert.name is not None:
706	ap.setAttribute("name", str(apert.name))
707	if apert.type is not None:
708	ap.setAttribute("type", str(apert.type))
709	coll.appendChild(ap)
710
711	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
712
713	size = doc.createElement("size")
714	if apert.size_name is not None:
715	size.setAttribute("name", str(apert.size_name))
716	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
717	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
718	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
719	if written == True:
720	ap.appendChild(size)
721
722	# Detectors
723	for item in datainfo.detector:
724	det = doc.createElement("SASdetector")
725	written = write_node(doc, det, "name", item.name)
726	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
727	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
728	if written == True:
729	instr.appendChild(det)
730
731	off = doc.createElement("offset")
732	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
733	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
734	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
735	if written == True:
736	det.appendChild(off)
737
738	center = doc.createElement("beam_center")
739	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
740	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
741	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
742	if written == True:
743	det.appendChild(center)
744
745	pix = doc.createElement("pixel_size")
746	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
747	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
748	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
749	if written == True:
750	det.appendChild(pix)
751
752	ori = doc.createElement("orientation")
753	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
754	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
755	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
756	if written == True:
757	det.appendChild(ori)
758
759
760	# Processes info
761	for item in datainfo.process:
762	node = doc.createElement("SASprocess")
763	entry_node.appendChild(node)
764
765	write_node(doc, node, "name", item.name)
766	write_node(doc, node, "date", item.date)
767	write_node(doc, node, "description", item.description)
768	for term in item.term:
769	value = term['value']
770	del term['value']
771	write_node(doc, node, "term", value, term)
772	for note in item.notes:
773	write_node(doc, node, "SASprocessnote", note)
774
775
776	# Write the file
777	fd = open(filename, 'w')
778	fd.write(doc.toprettyxml())
779	fd.close()
780
781
782	if __name__ == "__main__":
783	logging.basicConfig(level=logging.ERROR,
784	format='%(asctime)s %(levelname)s %(message)s',
785	filename='cansas_reader.log',
786	filemode='w')
787	reader = Reader()
788	print reader.read("../test/cansas1d.xml")
789
790
791

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ de1da34

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