cansas_reader.py @ 97dea6c

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 97dea6c was 0997158f, checked in by Gervaise Alina <gervyh@…>, 15 years ago
working on documentation
Property mode set to `100644`
File size: 36.0 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 least one non-empty value
18	#TODO: Writing only allows one SASentry per file. Would be best to allow multiple entries.
19	#TODO: Store error list
20	#TODO: Allow for additional meta data for each section
21	#TODO: Notes need to be implemented. They can be any XML structure in version 1.0
22	# Process notes have the same problem.
23	#TODO: Unit conversion is not complete (temperature units are missing)
24
25
26	import logging
27	import numpy
28	import os, sys
29	from DataLoader.data_info import Data1D, Collimation, Detector, Process, Aperture
30	from lxml import etree
31	import xml.dom.minidom
32
33	has_converter = True
34	try:
35	from data_util.nxsunit import Converter
36	except:
37	has_converter = False
38
39	CANSAS_NS = "cansas1d/1.0"
40
41	def write_node(doc, parent, name, value, attr={}):
42	"""
43	:param doc: document DOM
44	:param parent: parent node
45	:param name: tag of the element
46	:param value: value of the child text node
47	:param attr: attribute dictionary
48
49	:return: True if something was appended, otherwise False
50	"""
51	if value is not None:
52	node = doc.createElement(name)
53	node.appendChild(doc.createTextNode(str(value)))
54	for item in attr:
55	node.setAttribute(item, attr[item])
56	parent.appendChild(node)
57	return True
58	return False
59
60	def get_content(location, node):
61	"""
62	Get the first instance of the content of a xpath location.
63
64	:param location: xpath location
65	:param node: node to start at
66
67	:return: Element, or None
68	"""
69	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
70
71	if len(nodes)>0:
72	return nodes[0]
73	else:
74	return None
75
76	def get_float(location, node):
77	"""
78	Get the content of a node as a float
79
80	:param location: xpath location
81	:param node: node to start at
82	"""
83	nodes = node.xpath(location, namespaces={'ns': CANSAS_NS})
84
85	value = None
86	attr = {}
87
88	if len(nodes)>0:
89	try:
90	value = float(nodes[0].text)
91	except:
92	# Could not pass, skip and return None
93	logging.error("cansas_reader.get_float: could not convert '%s' to float" % nodes[0].text)
94
95	if nodes[0].get('unit') is not None:
96	attr['unit'] = nodes[0].get('unit')
97
98	return value, attr
99
100
101
102	class Reader:
103	"""
104	Class to load cansas 1D XML files
105
106	:Dependencies:
107	The CanSas reader requires PyXML 0.8.4 or later.
108	"""
109	## CanSAS version
110	version = '1.0'
111	## File type
112	type_name = "CanSAS 1D"
113	## Wildcards
114	type = ["CanSAS 1D files (.xml)\|.xml"]
115	## List of allowed extensions
116	ext=['.xml', '.XML']
117
118	def __init__(self):
119	## List of errors
120	self.errors = []
121
122	def read(self, path):
123	"""
124	Load data file
125
126	:param path: file path
127
128	:return: Data1D object if a single SASentry was found,
129	or a list of Data1D objects if multiple entries were found,
130	or None of nothing was found
131
132	:raise RuntimeError: when the file can't be opened
133	:raise ValueError: when the length of the data vectors are inconsistent
134	"""
135	output = []
136
137	if os.path.isfile(path):
138	basename = os.path.basename(path)
139	root, extension = os.path.splitext(basename)
140	if extension.lower() in self.ext:
141
142	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
143	# Check the format version number
144	# Specifying the namespace will take care of the file format version
145	root = tree.getroot()
146
147	entry_list = root.xpath('/ns:SASroot/ns:SASentry', namespaces={'ns': CANSAS_NS})
148
149	for entry in entry_list:
150	self.errors = []
151	sas_entry = self._parse_entry(entry)
152	sas_entry.filename = basename
153
154	# Store loading process information
155	sas_entry.errors = self.errors
156	sas_entry.meta_data['loader'] = self.type_name
157	output.append(sas_entry)
158
159	else:
160	raise RuntimeError, "%s is not a file" % path
161
162	# Return output consistent with the loader's api
163	if len(output)==0:
164	return None
165	elif len(output)==1:
166	return output[0]
167	else:
168	return output
169
170	def _parse_entry(self, dom):
171	"""
172	Parse a SASentry
173
174	:param node: SASentry node
175
176	:return: Data1D object
177	"""
178	x = numpy.zeros(0)
179	y = numpy.zeros(0)
180
181	data_info = Data1D(x, y)
182
183	# Look up title
184	self._store_content('ns:Title', dom, 'title', data_info)
185
186	# Look up run number
187	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
188	for item in nodes:
189	if item.text is not None:
190	value = item.text.strip()
191	if len(value) > 0:
192	data_info.run.append(value)
193	if item.get('name') is not None:
194	data_info.run_name[value] = item.get('name')
195
196	# Look up instrument name
197	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
198
199	# Notes
200	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
201	for note in note_list:
202	try:
203	if note.text is not None:
204	note_value = note.text.strip()
205	if len(note_value) > 0:
206	data_info.notes.append(note_value)
207	except:
208	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
209	self.errors.append(err_mess)
210	logging.error(err_mess)
211
212	# Sample info ###################
213	entry = get_content('ns:SASsample', dom)
214	if entry is not None:
215	data_info.sample.name = entry.get('name')
216
217	self._store_content('ns:SASsample/ns:ID',
218	dom, 'ID', data_info.sample)
219	self._store_float('ns:SASsample/ns:thickness',
220	dom, 'thickness', data_info.sample)
221	self._store_float('ns:SASsample/ns:transmission',
222	dom, 'transmission', data_info.sample)
223	self._store_float('ns:SASsample/ns:temperature',
224	dom, 'temperature', data_info.sample)
225
226	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
227	for item in nodes:
228	try:
229	if item.text is not None:
230	detail_value = item.text.strip()
231	if len(detail_value) > 0:
232	data_info.sample.details.append(detail_value)
233	except:
234	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
235	self.errors.append(err_mess)
236	logging.error(err_mess)
237
238	# Position (as a vector)
239	self._store_float('ns:SASsample/ns:position/ns:x',
240	dom, 'position.x', data_info.sample)
241	self._store_float('ns:SASsample/ns:position/ns:y',
242	dom, 'position.y', data_info.sample)
243	self._store_float('ns:SASsample/ns:position/ns:z',
244	dom, 'position.z', data_info.sample)
245
246	# Orientation (as a vector)
247	self._store_float('ns:SASsample/ns:orientation/ns:roll',
248	dom, 'orientation.x', data_info.sample)
249	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
250	dom, 'orientation.y', data_info.sample)
251	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
252	dom, 'orientation.z', data_info.sample)
253
254	# Source info ###################
255	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
256	if entry is not None:
257	data_info.source.name = entry.get('name')
258
259	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
260	dom, 'radiation', data_info.source)
261	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
262	dom, 'beam_shape', data_info.source)
263	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
264	dom, 'wavelength', data_info.source)
265	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
266	dom, 'wavelength_min', data_info.source)
267	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
268	dom, 'wavelength_max', data_info.source)
269	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
270	dom, 'wavelength_spread', data_info.source)
271
272	# Beam size (as a vector)
273	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
274	if entry is not None:
275	data_info.source.beam_size_name = entry.get('name')
276
277	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
278	dom, 'beam_size.x', data_info.source)
279	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
280	dom, 'beam_size.y', data_info.source)
281	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
282	dom, 'beam_size.z', data_info.source)
283
284	# Collimation info ###################
285	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
286	for item in nodes:
287	collim = Collimation()
288	if item.get('name') is not None:
289	collim.name = item.get('name')
290	self._store_float('ns:length', item, 'length', collim)
291
292	# Look for apertures
293	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
294	for apert in apert_list:
295	aperture = Aperture()
296
297	# Get the name and type of the aperture
298	aperture.name = apert.get('name')
299	aperture.type = apert.get('type')
300
301	self._store_float('ns:distance', apert, 'distance', aperture)
302
303	entry = get_content('ns:size', apert)
304	if entry is not None:
305	aperture.size_name = entry.get('name')
306
307	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
308	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
309	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
310
311	collim.aperture.append(aperture)
312
313	data_info.collimation.append(collim)
314
315	# Detector info ######################
316	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
317	for item in nodes:
318
319	detector = Detector()
320
321	self._store_content('ns:name', item, 'name', detector)
322	self._store_float('ns:SDD', item, 'distance', detector)
323
324	# Detector offset (as a vector)
325	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
326	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
327	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
328
329	# Detector orientation (as a vector)
330	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
331	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
332	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
333
334	# Beam center (as a vector)
335	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
336	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
337	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
338
339	# Pixel size (as a vector)
340	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
341	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
342	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
343
344	self._store_float('ns:slit_length', item, 'slit_length', detector)
345
346	data_info.detector.append(detector)
347
348	# Processes info ######################
349	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
350	for item in nodes:
351	process = Process()
352	self._store_content('ns:name', item, 'name', process)
353	self._store_content('ns:date', item, 'date', process)
354	self._store_content('ns:description', item, 'description', process)
355
356	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
357	for term in term_list:
358	try:
359	term_attr = {}
360	for attr in term.keys():
361	term_attr[attr] = term.get(attr).strip()
362	if term.text is not None:
363	term_attr['value'] = term.text.strip()
364	process.term.append(term_attr)
365	except:
366	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
367	self.errors.append(err_mess)
368	logging.error(err_mess)
369
370	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
371	for note in note_list:
372	if note.text is not None:
373	process.notes.append(note.text.strip())
374
375	data_info.process.append(process)
376
377
378	# Data info ######################
379	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
380	if len(nodes)>1:
381	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
382
383	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': CANSAS_NS})
384
385	x = numpy.zeros(0)
386	y = numpy.zeros(0)
387	dx = numpy.zeros(0)
388	dy = numpy.zeros(0)
389	dxw = numpy.zeros(0)
390	dxl = numpy.zeros(0)
391
392	for item in nodes:
393	_x, attr = get_float('ns:Q', item)
394	_dx, attr_d = get_float('ns:Qdev', item)
395	_dxl, attr_l = get_float('ns:dQl', item)
396	_dxw, attr_w = get_float('ns:dQw', item)
397	if _dx == None:
398	_dx = 0.0
399	if _dxl == None:
400	_dxl = 0.0
401	if _dxw == None:
402	_dxw = 0.0
403
404	if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower():
405	if has_converter==True:
406	try:
407	data_conv_q = Converter(attr['unit'])
408	_x = data_conv_q(_x, units=data_info.x_unit)
409	except:
410	raise ValueError, "CanSAS reader: could not convert Q unit [%s]; expecting [%s]\n %s" \
411	% (attr['unit'], data_info.x_unit, sys.exc_value)
412	else:
413	raise ValueError, "CanSAS reader: unrecognized Q unit [%s]; expecting [%s]" \
414	% (attr['unit'], data_info.x_unit)
415	# Error in Q
416	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.x_unit.lower():
417	if has_converter==True:
418	try:
419	data_conv_q = Converter(attr_d['unit'])
420	_dx = data_conv_q(_dx, units=data_info.x_unit)
421	except:
422	raise ValueError, "CanSAS reader: could not convert dQ unit [%s]; expecting [%s]\n %s" \
423	% (attr['unit'], data_info.x_unit, sys.exc_value)
424	else:
425	raise ValueError, "CanSAS reader: unrecognized dQ unit [%s]; expecting [%s]" \
426	% (attr['unit'], data_info.x_unit)
427	# Slit length
428	if attr_l.has_key('unit') and attr_l['unit'].lower() != data_info.x_unit.lower():
429	if has_converter==True:
430	try:
431	data_conv_q = Converter(attr_l['unit'])
432	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
433	except:
434	raise ValueError, "CanSAS reader: could not convert dQl unit [%s]; expecting [%s]\n %s" \
435	% (attr['unit'], data_info.x_unit, sys.exc_value)
436	else:
437	raise ValueError, "CanSAS reader: unrecognized dQl unit [%s]; expecting [%s]" \
438	% (attr['unit'], data_info.x_unit)
439	# Slit width
440	if attr_w.has_key('unit') and attr_w['unit'].lower() != data_info.x_unit.lower():
441	if has_converter==True:
442	try:
443	data_conv_q = Converter(attr_w['unit'])
444	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
445	except:
446	raise ValueError, "CanSAS reader: could not convert dQw unit [%s]; expecting [%s]\n %s" \
447	% (attr['unit'], data_info.x_unit, sys.exc_value)
448	else:
449	raise ValueError, "CanSAS reader: unrecognized dQw unit [%s]; expecting [%s]" \
450	% (attr['unit'], data_info.x_unit)
451
452	_y, attr = get_float('ns:I', item)
453	_dy, attr_d = get_float('ns:Idev', item)
454	if _dy == None:
455	_dy = 0.0
456	if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower():
457	if has_converter==True:
458	try:
459	data_conv_i = Converter(attr['unit'])
460	_y = data_conv_i(_y, units=data_info.y_unit)
461	except:
462	raise ValueError, "CanSAS reader: could not convert I(q) unit [%s]; expecting [%s]\n %s" \
463	% (attr['unit'], data_info.y_unit, sys.exc_value)
464	else:
465	raise ValueError, "CanSAS reader: unrecognized I(q) unit [%s]; expecting [%s]" \
466	% (attr['unit'], data_info.y_unit)
467	if attr_d.has_key('unit') and attr_d['unit'].lower() != data_info.y_unit.lower():
468	if has_converter==True:
469	try:
470	data_conv_i = Converter(attr_d['unit'])
471	_dy = data_conv_i(_dy, units=data_info.y_unit)
472	except:
473	raise ValueError, "CanSAS reader: could not convert dI(q) unit [%s]; expecting [%s]\n %s" \
474	% (attr_d['unit'], data_info.y_unit, sys.exc_value)
475	else:
476	raise ValueError, "CanSAS reader: unrecognized dI(q) unit [%s]; expecting [%s]" \
477	% (attr_d['unit'], data_info.y_unit)
478
479	if _x is not None and _y is not None:
480	x = numpy.append(x, _x)
481	y = numpy.append(y, _y)
482	dx = numpy.append(dx, _dx)
483	dy = numpy.append(dy, _dy)
484	dxl = numpy.append(dxl, _dxl)
485	dxw = numpy.append(dxw, _dxw)
486
487
488	data_info.x = x
489	data_info.y = y
490	data_info.dx = dx
491	data_info.dy = dy
492	data_info.dxl = dxl
493	data_info.dxw = dxw
494
495	data_conv_q = None
496	data_conv_i = None
497
498	if has_converter == True and data_info.x_unit != '1/A':
499	data_conv_q = Converter('1/A')
500	# Test it
501	data_conv_q(1.0, output.Q_unit)
502
503	if has_converter == True and data_info.y_unit != '1/cm':
504	data_conv_i = Converter('1/cm')
505	# Test it
506	data_conv_i(1.0, output.I_unit)
507
508	if data_conv_q is not None:
509	data_info.xaxis("\\rm{Q}", data_info.x_unit)
510	else:
511	data_info.xaxis("\\rm{Q}", 'A^{-1}')
512	if data_conv_i is not None:
513	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
514	else:
515	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
516
517	return data_info
518
519	def _to_xml_doc(self, datainfo):
520	"""
521	Create an XML document to contain the content of a Data1D
522
523	:param datainfo: Data1D object
524	"""
525
526	if not issubclass(datainfo.__class__, Data1D):
527	raise RuntimeError, "The cansas writer expects a Data1D instance"
528
529	doc = xml.dom.minidom.Document()
530	main_node = doc.createElement("SASroot")
531	main_node.setAttribute("version", self.version)
532	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
533	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
534	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
535
536	doc.appendChild(main_node)
537
538	entry_node = doc.createElement("SASentry")
539	main_node.appendChild(entry_node)
540
541	write_node(doc, entry_node, "Title", datainfo.title)
542
543	for item in datainfo.run:
544	runname = {}
545	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
546	runname = {'name': datainfo.run_name[item] }
547	write_node(doc, entry_node, "Run", item, runname)
548
549	# Data info
550	node = doc.createElement("SASdata")
551	entry_node.appendChild(node)
552
553	for i in range(len(datainfo.x)):
554	pt = doc.createElement("Idata")
555	node.appendChild(pt)
556	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
557	if len(datainfo.y)>=i:
558	write_node(doc, pt, "I", datainfo.y[i], {'unit':datainfo.y_unit})
559	if datainfo.dx !=None and len(datainfo.dx)>=i:
560	write_node(doc, pt, "Qdev", datainfo.dx[i], {'unit':datainfo.x_unit})
561	if datainfo.dy !=None and len(datainfo.dy)>=i:
562	write_node(doc, pt, "Idev", datainfo.dy[i], {'unit':datainfo.y_unit})
563
564
565	# Sample info
566	sample = doc.createElement("SASsample")
567	if datainfo.sample.name is not None:
568	sample.setAttribute("name", str(datainfo.sample.name))
569	entry_node.appendChild(sample)
570	write_node(doc, sample, "ID", str(datainfo.sample.ID))
571	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
572	write_node(doc, sample, "transmission", datainfo.sample.transmission)
573	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
574
575	for item in datainfo.sample.details:
576	write_node(doc, sample, "details", item)
577
578	pos = doc.createElement("position")
579	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
580	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
581	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
582	if written == True:
583	sample.appendChild(pos)
584
585	ori = doc.createElement("orientation")
586	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
587	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
588	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
589	if written == True:
590	sample.appendChild(ori)
591
592	# Instrument info
593	instr = doc.createElement("SASinstrument")
594	entry_node.appendChild(instr)
595
596	write_node(doc, instr, "name", datainfo.instrument)
597
598	# Source
599	source = doc.createElement("SASsource")
600	if datainfo.source.name is not None:
601	source.setAttribute("name", str(datainfo.source.name))
602	instr.appendChild(source)
603
604	write_node(doc, source, "radiation", datainfo.source.radiation)
605	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
606	size = doc.createElement("beam_size")
607	if datainfo.source.beam_size_name is not None:
608	size.setAttribute("name", str(datainfo.source.beam_size_name))
609	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
610	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
611	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
612	if written == True:
613	source.appendChild(size)
614
615	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
616	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
617	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
618	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
619
620	# Collimation
621	for item in datainfo.collimation:
622	coll = doc.createElement("SAScollimation")
623	if item.name is not None:
624	coll.setAttribute("name", str(item.name))
625	instr.appendChild(coll)
626
627	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
628
629	for apert in item.aperture:
630	ap = doc.createElement("aperture")
631	if apert.name is not None:
632	ap.setAttribute("name", str(apert.name))
633	if apert.type is not None:
634	ap.setAttribute("type", str(apert.type))
635	coll.appendChild(ap)
636
637	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
638
639	size = doc.createElement("size")
640	if apert.size_name is not None:
641	size.setAttribute("name", str(apert.size_name))
642	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
643	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
644	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
645	if written == True:
646	ap.appendChild(size)
647
648	# Detectors
649	for item in datainfo.detector:
650	det = doc.createElement("SASdetector")
651	written = write_node(doc, det, "name", item.name)
652	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
653	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
654	if written == True:
655	instr.appendChild(det)
656
657	off = doc.createElement("offset")
658	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
659	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
660	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
661	if written == True:
662	det.appendChild(off)
663
664	center = doc.createElement("beam_center")
665	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
666	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
667	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
668	if written == True:
669	det.appendChild(center)
670
671	pix = doc.createElement("pixel_size")
672	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
673	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
674	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
675	if written == True:
676	det.appendChild(pix)
677
678	ori = doc.createElement("orientation")
679	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
680	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
681	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
682	if written == True:
683	det.appendChild(ori)
684
685
686	# Processes info
687	for item in datainfo.process:
688	node = doc.createElement("SASprocess")
689	entry_node.appendChild(node)
690
691	write_node(doc, node, "name", item.name)
692	write_node(doc, node, "date", item.date)
693	write_node(doc, node, "description", item.description)
694	for term in item.term:
695	value = term['value']
696	del term['value']
697	write_node(doc, node, "term", value, term)
698	for note in item.notes:
699	write_node(doc, node, "SASprocessnote", note)
700
701	# Return the document, and the SASentry node associated with
702	# the data we just wrote
703	return doc, entry_node
704
705	def write(self, filename, datainfo):
706	"""
707	Write the content of a Data1D as a CanSAS XML file
708
709	:param filename: name of the file to write
710	:param datainfo: Data1D object
711	"""
712	# Create XML document
713	doc, sasentry = self._to_xml_doc(datainfo)
714	# Write the file
715	fd = open(filename, 'w')
716	fd.write(doc.toprettyxml())
717	fd.close()
718
719	def _store_float(self, location, node, variable, storage, optional=True):
720	"""
721	Get the content of a xpath location and store
722	the result. Check that the units are compatible
723	with the destination. The value is expected to
724	be a float.
725
726	The xpath location might or might not exist.
727	If it does not exist, nothing is done
728
729	:param location: xpath location to fetch
730	:param node: node to read the data from
731	:param variable: name of the data member to store it in [string]
732	:param storage: data object that has the 'variable' data member
733	:param optional: if True, no exception will be raised if unit conversion can't be done
734
735	:raise ValueError: raised when the units are not recognized
736	"""
737	entry = get_content(location, node)
738	try:
739	value = float(entry.text)
740	except:
741	value = None
742
743	if value is not None:
744	# If the entry has units, check to see that they are
745	# compatible with what we currently have in the data object
746	units = entry.get('unit')
747	if units is not None:
748	toks = variable.split('.')
749	exec "local_unit = storage.%s_unit" % toks[0]
750	if units.lower()!=local_unit.lower():
751	if has_converter==True:
752	try:
753	conv = Converter(units)
754	exec "storage.%s = %g" % (variable, conv(value, units=local_unit))
755	except:
756	err_mess = "CanSAS reader: could not convert %s unit [%s]; expecting [%s]\n %s" \
757	% (variable, units, local_unit, sys.exc_value)
758	self.errors.append(err_mess)
759	if optional:
760	logging.info(err_mess)
761	else:
762	raise ValueError, err_mess
763	else:
764	err_mess = "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \
765	% (variable, units, local_unit)
766	self.errors.append(err_mess)
767	if optional:
768	logging.info(err_mess)
769	else:
770	raise ValueError, err_mess
771	else:
772	exec "storage.%s = value" % variable
773	else:
774	exec "storage.%s = value" % variable
775
776	def _store_content(self, location, node, variable, storage):
777	"""
778	Get the content of a xpath location and store
779	the result. The value is treated as a string.
780
781	The xpath location might or might not exist.
782	If it does not exist, nothing is done
783
784	:param location: xpath location to fetch
785	:param node: node to read the data from
786	:param variable: name of the data member to store it in [string]
787	:param storage: data object that has the 'variable' data member
788
789	:return: return a list of errors
790	"""
791	entry = get_content(location, node)
792	if entry is not None and entry.text is not None:
793	exec "storage.%s = entry.text.strip()" % variable
794
795
796
797	if __name__ == "__main__":
798	logging.basicConfig(level=logging.ERROR,
799	format='%(asctime)s %(levelname)s %(message)s',
800	filename='cansas_reader.log',
801	filemode='w')
802	reader = Reader()
803	print reader.read("../test/cansas1d.xml")
804	#print reader.read("../test/latex_smeared.xml")
805
806
807

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SasView

source: sasview/DataLoader/readers/cansas_reader.py @ 97dea6c

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