state_reader.py @ bc7bc839

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 bc7bc839 was 5c4b674, checked in by Gervaise Alina <gervyh@…>, 14 years ago
working on data panel
Property mode set to `100644`
File size: 71.0 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
18	# least one non-empty value
19	#TODO: Writing only allows one SASentry per file.
20	# Would be best to allow multiple entries.
21	#TODO: Store error list
22	#TODO: Allow for additional meta data for each section
23	#TODO: Notes need to be implemented. They can be any XML
24	# structure in version 1.0
25	# Process notes have the same problem.
26	#TODO: Unit conversion is not complete (temperature units are missing)
27
28
29	import logging
30	import numpy
31	import os
32	import sys
33	from sans.guiframe.dataFitting import Data1D
34	from sans.guiframe.dataFitting import Data2D
35	from DataLoader.data_info import Collimation
36	from DataLoader.data_info import Detector
37	from DataLoader.data_info import Process
38	from DataLoader.data_info import Aperture
39	from lxml import etree
40	import xml.dom.minidom
41
42	has_converter = True
43	try:
44	from data_util.nxsunit import Converter
45	except:
46	has_converter = False
47
48	STATE_NS = "State/1.0"
49
50	def write_node(doc, parent, name, value, attr={}):
51	"""
52	:param doc: document DOM
53	:param parent: parent node
54	:param name: tag of the element
55	:param value: value of the child text node
56	:param attr: attribute dictionary
57
58	:return: True if something was appended, otherwise False
59	"""
60	if value is not None:
61	node = doc.createElement(name)
62	node.appendChild(doc.createTextNode(str(value)))
63	for item in attr:
64	node.setAttribute(item, attr[item])
65	parent.appendChild(node)
66	return True
67	return False
68
69	def get_content(location, node):
70	"""
71	Get the first instance of the content of a xpath location.
72
73	:param location: xpath location
74	:param node: node to start at
75
76	:return: Element, or None
77	"""
78	nodes = node.xpath(location, namespaces={'ns': STATE_NODE})
79
80	if len(nodes)>0:
81	return nodes[0]
82	else:
83	return None
84
85	def get_float(location, node):
86	"""
87	Get the content of a node as a float
88
89	:param location: xpath location
90	:param node: node to start at
91	"""
92	nodes = node.xpath(location, namespaces={'ns': STATE_NODE})
93
94	value = None
95	attr = {}
96	if len(nodes) > 0:
97	try:
98	value = float(nodes[0].text)
99	except:
100	# Could not pass, skip and return None
101	msg = "state_reader.get_float: could not "
102	msg += " convert '%s' to float" % nodes[0].text
103	logging.error(msg)
104	if nodes[0].get('unit') is not None:
105	attr['unit'] = nodes[0].get('unit')
106	return value, attr
107
108
109	class Reader1D:
110	"""
111	read state of a plugin and available data
112
113	:Dependencies:
114	The CanSas reader requires PyXML 0.8.4 or later.
115	"""
116	## CanSAS version
117	version = '1.0'
118	## File type
119	type_name = "CanSAS 1D"
120	## Wildcards
121	type = []
122
123	## List of allowed extensions
124	ext = []
125
126	def __init__(self):
127	## List of errors
128	self.errors = []
129
130	def read(self, path):
131	"""
132	Load data file
133
134	:param path: file path
135
136	:return: Data1D object if a single SASentry was found,
137	or a list of Data1D objects if multiple entries were found,
138	or None of nothing was found
139
140	:raise RuntimeError: when the file can't be opened
141	:raise ValueError: when the length of the data vectors are inconsistent
142	"""
143	output = []
144	if os.path.isfile(path):
145	basename = os.path.basename(path)
146	root, extension = os.path.splitext(basename)
147	if extension.lower() in self.ext:
148
149	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
150	# Check the format version number
151	# Specifying the namespace will take care of the file
152	# format version
153	root = tree.getroot()
154
155	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
156	namespaces={'ns': STATE_NODE})
157
158	for entry in entry_list:
159	self.errors = []
160	sas_entry = self._parse_entry(entry)
161	sas_entry.filename = basename
162
163	# Store loading process information
164	sas_entry.errors = self.errors
165	sas_entry.meta_data['loader'] = self.type_name
166	output.append(sas_entry)
167
168	else:
169	raise RuntimeError, "%s is not a file" % path
170	# Return output consistent with the loader's api
171	if len(output) == 0:
172	#cannot return none when it cannot read
173	#return None
174	raise RuntimeError, "%s cannot be read \n" % path
175	elif len(output) == 1:
176	return output[0]
177	else:
178	return output
179
180	def _parse_entry(self, dom):
181	"""
182	Parse a SASentry
183
184	:param node: SASentry node
185
186	:return: Data1D object
187	"""
188	x = numpy.zeros(0)
189	y = numpy.zeros(0)
190
191	data_info = Data1D(x, y)
192
193	# Look up title
194	self._store_content('ns:Title', dom, 'title', data_info)
195
196	# Look up run number
197	nodes = dom.xpath('ns:Run', namespaces={'ns': STATE_NODE})
198	for item in nodes:
199	if item.text is not None:
200	value = item.text.strip()
201	if len(value) > 0:
202	data_info.run.append(value)
203	if item.get('name') is not None:
204	data_info.run_name[value] = item.get('name')
205
206	# Look up instrument name
207	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument',
208	data_info)
209
210	# Notes
211	note_list = dom.xpath('ns:SASnote', namespaces={'ns': STATE_NODE})
212	for note in note_list:
213	try:
214	if note.text is not None:
215	note_value = note.text.strip()
216	if len(note_value) > 0:
217	data_info.notes.append(note_value)
218	except:
219	err_mess = "state_reader.read: error processing"
220	err_mess += " entry notes\n %s" % sys.exc_value
221	self.errors.append(err_mess)
222	logging.error(err_mess)
223
224	# Sample info ###################
225	entry = get_content('ns:SASsample', dom)
226	if entry is not None:
227	data_info.sample.name = entry.get('name')
228
229	self._store_content('ns:SASsample/ns:ID',
230	dom, 'ID', data_info.sample)
231	self._store_float('ns:SASsample/ns:thickness',
232	dom, 'thickness', data_info.sample)
233	self._store_float('ns:SASsample/ns:transmission',
234	dom, 'transmission', data_info.sample)
235	self._store_float('ns:SASsample/ns:temperature',
236	dom, 'temperature', data_info.sample)
237
238	nodes = dom.xpath('ns:SASsample/ns:details',
239	namespaces={'ns': STATE_NODE})
240	for item in nodes:
241	try:
242	if item.text is not None:
243	detail_value = item.text.strip()
244	if len(detail_value) > 0:
245	data_info.sample.details.append(detail_value)
246	except:
247	err_mess = "state_reader.read: error processing "
248	err_mess += " sample details\n %s" % sys.exc_value
249	self.errors.append(err_mess)
250	logging.error(err_mess)
251
252	# Position (as a vector)
253	self._store_float('ns:SASsample/ns:position/ns:x',
254	dom, 'position.x', data_info.sample)
255	self._store_float('ns:SASsample/ns:position/ns:y',
256	dom, 'position.y', data_info.sample)
257	self._store_float('ns:SASsample/ns:position/ns:z',
258	dom, 'position.z', data_info.sample)
259
260	# Orientation (as a vector)
261	self._store_float('ns:SASsample/ns:orientation/ns:roll',
262	dom, 'orientation.x', data_info.sample)
263	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
264	dom, 'orientation.y', data_info.sample)
265	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
266	dom, 'orientation.z', data_info.sample)
267
268	# Source info ###################
269	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
270	if entry is not None:
271	data_info.source.name = entry.get('name')
272
273	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
274	dom, 'radiation', data_info.source)
275	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
276	dom, 'beam_shape', data_info.source)
277	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
278	dom, 'wavelength', data_info.source)
279	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
280	dom, 'wavelength_min', data_info.source)
281	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
282	dom, 'wavelength_max', data_info.source)
283	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
284	dom, 'wavelength_spread', data_info.source)
285
286	# Beam size (as a vector)
287	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
288	if entry is not None:
289	data_info.source.beam_size_name = entry.get('name')
290
291	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
292	dom, 'beam_size.x', data_info.source)
293	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
294	dom, 'beam_size.y', data_info.source)
295	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
296	dom, 'beam_size.z', data_info.source)
297
298	# Collimation info ###################
299	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
300	namespaces={'ns': STATE_NODE})
301	for item in nodes:
302	collim = Collimation()
303	if item.get('name') is not None:
304	collim.name = item.get('name')
305	self._store_float('ns:length', item, 'length', collim)
306
307	# Look for apertures
308	apert_list = item.xpath('ns:aperture', namespaces={'ns': STATE_NODE})
309	for apert in apert_list:
310	aperture = Aperture()
311
312	# Get the name and type of the aperture
313	aperture.name = apert.get('name')
314	aperture.type = apert.get('type')
315
316	self._store_float('ns:distance', apert, 'distance', aperture)
317
318	entry = get_content('ns:size', apert)
319	if entry is not None:
320	aperture.size_name = entry.get('name')
321
322	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
323	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
324	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
325
326	collim.aperture.append(aperture)
327
328	data_info.collimation.append(collim)
329
330	# Detector info ######################
331	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
332	namespaces={'ns': STATE_NODE})
333	for item in nodes:
334
335	detector = Detector()
336
337	self._store_content('ns:name', item, 'name', detector)
338	self._store_float('ns:SDD', item, 'distance', detector)
339
340	# Detector offset (as a vector)
341	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
342	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
343	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
344
345	# Detector orientation (as a vector)
346	self._store_float('ns:orientation/ns:roll', item, 'orientation.x',
347	detector)
348	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y',
349	detector)
350	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z',
351	detector)
352
353	# Beam center (as a vector)
354	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x',
355	detector)
356	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y',
357	detector)
358	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z',
359	detector)
360
361	# Pixel size (as a vector)
362	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x',
363	detector)
364	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y',
365	detector)
366	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z',
367	detector)
368
369	self._store_float('ns:slit_length', item, 'slit_length', detector)
370
371	data_info.detector.append(detector)
372
373	# Processes info ######################
374	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': STATE_NODE})
375	for item in nodes:
376	process = Process()
377	self._store_content('ns:name', item, 'name', process)
378	self._store_content('ns:date', item, 'date', process)
379	self._store_content('ns:description', item, 'description', process)
380
381	term_list = item.xpath('ns:term', namespaces={'ns': STATE_NODE})
382	for term in term_list:
383	try:
384	term_attr = {}
385	for attr in term.keys():
386	term_attr[attr] = term.get(attr).strip()
387	if term.text is not None:
388	term_attr['value'] = term.text.strip()
389	process.term.append(term_attr)
390	except:
391	err_mess = "state_reader.read: error processing "
392	err_mess += " process term\n %s" % sys.exc_value
393	self.errors.append(err_mess)
394	logging.error(err_mess)
395
396	note_list = item.xpath('ns:SASprocessnote',
397	namespaces={'ns': STATE_NODE})
398	for note in note_list:
399	if note.text is not None:
400	process.notes.append(note.text.strip())
401
402	data_info.process.append(process)
403
404
405	# Data info ######################
406	nodes = dom.xpath('ns:SASdata', namespaces={'ns': STATE_NODE})
407	if len(nodes) > 1:
408	msg = "CanSAS reader is not compatible with multiple"
409	msg += " SASdata entries"
410	raise RuntimeError, msg
411
412	nodes = dom.xpath('ns:SASdata/ns:Idata', namespaces={'ns': STATE_NODE})
413
414	x = numpy.zeros(0)
415	y = numpy.zeros(0)
416	dx = numpy.zeros(0)
417	dy = numpy.zeros(0)
418	dxw = numpy.zeros(0)
419	dxl = numpy.zeros(0)
420
421	for item in nodes:
422	_x, attr = get_float('ns:Q', item)
423	_dx, attr_d = get_float('ns:Qdev', item)
424	_dxl, attr_l = get_float('ns:dQl', item)
425	_dxw, attr_w = get_float('ns:dQw', item)
426	if _dx == None:
427	_dx = 0.0
428	if _dxl == None:
429	_dxl = 0.0
430	if _dxw == None:
431	_dxw = 0.0
432
433	if attr.has_key('unit') and \
434	attr['unit'].lower() != data_info.x_unit.lower():
435	if has_converter==True:
436	try:
437	data_conv_q = Converter(attr['unit'])
438	_x = data_conv_q(_x, units=data_info.x_unit)
439	except:
440	msg = "CanSAS reader: could not convert "
441	msg += "Q unit [%s]; "
442	msg += "expecting [%s]\n %s" % (attr['unit'],
443	data_info.x_unit, sys.exc_value)
444	raise ValueError, msg
445
446	else:
447	msg = "CanSAS reader: unrecognized Q unit [%s]; "
448	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
449	raise ValueError, msg
450
451	# Error in Q
452	if attr_d.has_key('unit') and \
453	attr_d['unit'].lower() != data_info.x_unit.lower():
454	if has_converter==True:
455	try:
456	data_conv_q = Converter(attr_d['unit'])
457	_dx = data_conv_q(_dx, units=data_info.x_unit)
458	except:
459	msg = "CanSAS reader: could not convert dQ unit [%s];"
460	msg += " expecting "
461	msg += "[%s]\n %s" % (attr['unit'],
462	data_info.x_unit, sys.exc_value)
463	raise ValueError, msg
464
465	else:
466	msg = "CanSAS reader: unrecognized dQ unit [%s]; "
467	msg += "expecting [%s]" % (attr['unit'], data_info.x_unit)
468	raise ValueError, msg
469
470	# Slit length
471	if attr_l.has_key('unit') and \
472	attr_l['unit'].lower() != data_info.x_unit.lower():
473	if has_converter == True:
474	try:
475	data_conv_q = Converter(attr_l['unit'])
476	_dxl = data_conv_q(_dxl, units=data_info.x_unit)
477	except:
478	msg = "CanSAS reader: could not convert dQl unit [%s];"
479	msg += " expecting [%s]\n %s" % (attr['unit'],
480	data_info.x_unit, sys.exc_value)
481	raise ValueError, msg
482
483	else:
484	msg = "CanSAS reader: unrecognized dQl unit [%s];"
485	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
486	raise ValueError, msg
487
488	# Slit width
489	if attr_w.has_key('unit') and \
490	attr_w['unit'].lower() != data_info.x_unit.lower():
491	if has_converter == True:
492	try:
493	data_conv_q = Converter(attr_w['unit'])
494	_dxw = data_conv_q(_dxw, units=data_info.x_unit)
495	except:
496	msg = "CanSAS reader: could not convert dQw unit [%s];"
497	msg += " expecting [%s]\n %s" % (attr['unit'],
498	data_info.x_unit, sys.exc_value)
499	raise ValueError, msg
500
501	else:
502	msg = "CanSAS reader: unrecognized dQw unit [%s];"
503	msg += " expecting [%s]" % (attr['unit'], data_info.x_unit)
504	raise ValueError, msg
505	_y, attr = get_float('ns:I', item)
506	_dy, attr_d = get_float('ns:Idev', item)
507	if _dy == None:
508	_dy = 0.0
509	if attr.has_key('unit') and \
510	attr['unit'].lower() != data_info.y_unit.lower():
511	if has_converter==True:
512	try:
513	data_conv_i = Converter(attr['unit'])
514	_y = data_conv_i(_y, units=data_info.y_unit)
515	except:
516	msg = "CanSAS reader: could not convert I(q) unit [%s];"
517	msg += " expecting [%s]\n %s" % (attr['unit'],
518	data_info.y_unit, sys.exc_value)
519	raise ValueError, msg
520	else:
521	msg = "CanSAS reader: unrecognized I(q) unit [%s];"
522	msg += " expecting [%s]" % (attr['unit'], data_info.y_unit)
523	raise ValueError, msg
524
525	if attr_d.has_key('unit') and \
526	attr_d['unit'].lower() != data_info.y_unit.lower():
527	if has_converter==True:
528	try:
529	data_conv_i = Converter(attr_d['unit'])
530	_dy = data_conv_i(_dy, units=data_info.y_unit)
531	except:
532	msg = "CanSAS reader: could not convert dI(q) unit "
533	msg += "[%s]; expecting [%s]\n %s" % (attr_d['unit'],
534	data_info.y_unit, sys.exc_value)
535	raise ValueError, msg
536	else:
537	msg = "CanSAS reader: unrecognized dI(q) unit [%s]; "
538	msg += "expecting [%s]" % (attr_d['unit'], data_info.y_unit)
539	raise ValueError, msg
540
541	if _x is not None and _y is not None:
542	x = numpy.append(x, _x)
543	y = numpy.append(y, _y)
544	dx = numpy.append(dx, _dx)
545	dy = numpy.append(dy, _dy)
546	dxl = numpy.append(dxl, _dxl)
547	dxw = numpy.append(dxw, _dxw)
548
549	data_info.x = x
550	data_info.y = y
551	data_info.dx = dx
552	data_info.dy = dy
553	data_info.dxl = dxl
554	data_info.dxw = dxw
555
556	data_conv_q = None
557	data_conv_i = None
558
559	if has_converter == True and data_info.x_unit != '1/A':
560	data_conv_q = Converter('1/A')
561	# Test it
562	data_conv_q(1.0, output.Q_unit)
563
564	if has_converter == True and data_info.y_unit != '1/cm':
565	data_conv_i = Converter('1/cm')
566	# Test it
567	data_conv_i(1.0, output.I_unit)
568
569	if data_conv_q is not None:
570	data_info.xaxis("\\rm{Q}", data_info.x_unit)
571	else:
572	data_info.xaxis("\\rm{Q}", 'A^{-1}')
573	if data_conv_i is not None:
574	data_info.yaxis("\\rm{Intensity}", data_info.y_unit)
575	else:
576	data_info.yaxis("\\rm{Intensity}","cm^{-1}")
577
578	return data_info
579
580	def _to_xml_doc(self, datainfo):
581	"""
582	Create an XML document to contain the content of a Data1D
583
584	:param datainfo: Data1D object
585	"""
586
587	if not issubclass(datainfo.__class__, Data1D):
588	raise RuntimeError, "The cansas writer expects a Data1D instance"
589
590	doc = xml.dom.minidom.Document()
591	main_node = doc.createElement("SASroot")
592	main_node.setAttribute("version", self.version)
593	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
594	main_node.setAttribute("xmlns:xsi",
595	"http://www.w3.org/2001/XMLSchema-instance")
596	main_node.setAttribute("xsi:schemaLocation",
597	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
598
599	doc.appendChild(main_node)
600
601	entry_node = doc.createElement("SASentry")
602	main_node.appendChild(entry_node)
603
604	write_node(doc, entry_node, "Title", datainfo.title)
605	for item in datainfo.run:
606	runname = {}
607	if datainfo.run_name.has_key(item) and \
608	len(str(datainfo.run_name[item]))>1:
609	runname = {'name': datainfo.run_name[item] }
610	write_node(doc, entry_node, "Run", item, runname)
611
612	# Data info
613	node = doc.createElement("SASdata")
614	entry_node.appendChild(node)
615
616	for i in range(len(datainfo.x)):
617	pt = doc.createElement("Idata")
618	node.appendChild(pt)
619	write_node(doc, pt, "Q", datainfo.x[i], {'unit':datainfo.x_unit})
620	if len(datainfo.y)>=i:
621	write_node(doc, pt, "I", datainfo.y[i],
622	{'unit':datainfo.y_unit})
623	if datainfo.dx != None and len(datainfo.dx) >= i:
624	write_node(doc, pt, "Qdev", datainfo.dx[i],
625	{'unit':datainfo.x_unit})
626	if datainfo.dxl != None and len(datainfo.dxl) >= i:
627	write_node(doc, pt, "dQl", datainfo.dxl[i],
628	{'unit':datainfo.x_unit})
629	if datainfo.dxw != None and len(datainfo.dxw) >= i:
630	write_node(doc, pt, "dQw", datainfo.dxw[i],
631	{'unit':datainfo.x_unit})
632	if datainfo.dy != None and len(datainfo.dy) >= i:
633	write_node(doc, pt, "Idev", datainfo.dy[i],
634	{'unit':datainfo.y_unit})
635	#data gui info
636	gui_info = doc.createElement("DataInfoGui")
637
638	write_node(doc, gui_info, "group_id", 'group_id')
639	for item in datainfo.group_id:
640	write_node(doc, gui_info, "group_id", str(item))
641	write_node(doc, gui_info, "name", datainfo.name)
642	write_node(doc, gui_info, "id", datainfo.id)
643	write_node(doc, gui_info, "group_id", datainfo.groud_id)
644	write_node(doc, gui_info, "name", datainfo.name)
645	write_node(doc, gui_info, "is_data", datainfo.is_data)
646	write_node(doc, gui_info, "xtransform", datainfo.xtransform)
647	write_node(doc, gui_info, "scale", datainfo.scale)
648	write_node(doc, gui_info, "ytransform", datainfo.ytransform)
649	write_node(doc, gui_info, "path", datainfo.path)
650	node.appendChild(gui_info)
651	# Sample info
652	sample = doc.createElement("SASsample")
653	if datainfo.sample.name is not None:
654	sample.setAttribute("name", str(datainfo.sample.name))
655	entry_node.appendChild(sample)
656	write_node(doc, sample, "ID", str(datainfo.sample.ID))
657	write_node(doc, sample, "thickness", datainfo.sample.thickness,
658	{"unit":datainfo.sample.thickness_unit})
659	write_node(doc, sample, "transmission", datainfo.sample.transmission)
660	write_node(doc, sample, "temperature", datainfo.sample.temperature,
661	{"unit":datainfo.sample.temperature_unit})
662
663	for item in datainfo.sample.details:
664	write_node(doc, sample, "details", item)
665
666	pos = doc.createElement("position")
667	written = write_node(doc, pos, "x", datainfo.sample.position.x,
668	{"unit":datainfo.sample.position_unit})
669	written = written \| write_node(doc, pos, "y",
670	datainfo.sample.position.y,
671	{"unit":datainfo.sample.position_unit})
672	written = written \| write_node(doc, pos, "z",
673	datainfo.sample.position.z,
674	{"unit":datainfo.sample.position_unit})
675	if written == True:
676	sample.appendChild(pos)
677
678	ori = doc.createElement("orientation")
679	written = write_node(doc, ori, "roll",
680	datainfo.sample.orientation.x,
681	{"unit":datainfo.sample.orientation_unit})
682	written = written \| write_node(doc, ori, "pitch",
683	datainfo.sample.orientation.y,
684	{"unit":datainfo.sample.orientation_unit})
685	written = written \| write_node(doc, ori, "yaw",
686	datainfo.sample.orientation.z,
687	{"unit":datainfo.sample.orientation_unit})
688	if written == True:
689	sample.appendChild(ori)
690
691	# Instrument info
692	instr = doc.createElement("SASinstrument")
693	entry_node.appendChild(instr)
694
695	write_node(doc, instr, "name", datainfo.instrument)
696
697	# Source
698	source = doc.createElement("SASsource")
699	if datainfo.source.name is not None:
700	source.setAttribute("name", str(datainfo.source.name))
701	instr.appendChild(source)
702
703	write_node(doc, source, "radiation", datainfo.source.radiation)
704	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
705	size = doc.createElement("beam_size")
706	if datainfo.source.beam_size_name is not None:
707	size.setAttribute("name", str(datainfo.source.beam_size_name))
708	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
709	{"unit":datainfo.source.beam_size_unit})
710	written = written \| write_node(doc, size, "y",
711	datainfo.source.beam_size.y,
712	{"unit":datainfo.source.beam_size_unit})
713	written = written \| write_node(doc, size, "z",
714	datainfo.source.beam_size.z,
715	{"unit":datainfo.source.beam_size_unit})
716	if written == True:
717	source.appendChild(size)
718
719	write_node(doc, source, "wavelength",
720	datainfo.source.wavelength,
721	{"unit":datainfo.source.wavelength_unit})
722	write_node(doc, source, "wavelength_min",
723	datainfo.source.wavelength_min,
724	{"unit":datainfo.source.wavelength_min_unit})
725	write_node(doc, source, "wavelength_max",
726	datainfo.source.wavelength_max,
727	{"unit":datainfo.source.wavelength_max_unit})
728	write_node(doc, source, "wavelength_spread",
729	datainfo.source.wavelength_spread,
730	{"unit":datainfo.source.wavelength_spread_unit})
731
732	# Collimation
733	for item in datainfo.collimation:
734	coll = doc.createElement("SAScollimation")
735	if item.name is not None:
736	coll.setAttribute("name", str(item.name))
737	instr.appendChild(coll)
738
739	write_node(doc, coll, "length", item.length,
740	{"unit":item.length_unit})
741
742	for apert in item.aperture:
743	ap = doc.createElement("aperture")
744	if apert.name is not None:
745	ap.setAttribute("name", str(apert.name))
746	if apert.type is not None:
747	ap.setAttribute("type", str(apert.type))
748	coll.appendChild(ap)
749
750	write_node(doc, ap, "distance", apert.distance,
751	{"unit":apert.distance_unit})
752
753	size = doc.createElement("size")
754	if apert.size_name is not None:
755	size.setAttribute("name", str(apert.size_name))
756	written = write_node(doc, size, "x", apert.size.x,
757	{"unit":apert.size_unit})
758	written = written \| write_node(doc, size, "y", apert.size.y,
759	{"unit":apert.size_unit})
760	written = written \| write_node(doc, size, "z", apert.size.z,
761	{"unit":apert.size_unit})
762	if written == True:
763	ap.appendChild(size)
764
765	# Detectors
766	for item in datainfo.detector:
767	det = doc.createElement("SASdetector")
768	written = write_node(doc, det, "name", item.name)
769	written = written \| write_node(doc, det, "SDD", item.distance,
770	{"unit":item.distance_unit})
771	written = written \| write_node(doc, det, "slit_length",
772	item.slit_length,
773	{"unit":item.slit_length_unit})
774	if written == True:
775	instr.appendChild(det)
776
777	off = doc.createElement("offset")
778	written = write_node(doc, off, "x", item.offset.x,
779	{"unit":item.offset_unit})
780	written = written \| write_node(doc, off, "y", item.offset.y,
781	{"unit":item.offset_unit})
782	written = written \| write_node(doc, off, "z", item.offset.z,
783	{"unit":item.offset_unit})
784	if written == True:
785	det.appendChild(off)
786
787	center = doc.createElement("beam_center")
788	written = write_node(doc, center, "x", item.beam_center.x,
789	{"unit":item.beam_center_unit})
790	written = written \| write_node(doc, center, "y",
791	item.beam_center.y,
792	{"unit":item.beam_center_unit})
793	written = written \| write_node(doc, center, "z",
794	item.beam_center.z,
795	{"unit":item.beam_center_unit})
796	if written == True:
797	det.appendChild(center)
798
799	pix = doc.createElement("pixel_size")
800	written = write_node(doc, pix, "x", item.pixel_size.x,
801	{"unit":item.pixel_size_unit})
802	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
803	{"unit":item.pixel_size_unit})
804	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
805	{"unit":item.pixel_size_unit})
806	if written == True:
807	det.appendChild(pix)
808
809	ori = doc.createElement("orientation")
810	written = write_node(doc, ori, "roll", item.orientation.x,
811	{"unit":item.orientation_unit})
812	written = written \| write_node(doc, ori, "pitch",
813	item.orientation.y,
814	{"unit":item.orientation_unit})
815	written = written \| write_node(doc, ori, "yaw",
816	item.orientation.z,
817	{"unit":item.orientation_unit})
818	if written == True:
819	det.appendChild(ori)
820
821
822	# Processes info
823	for item in datainfo.process:
824	node = doc.createElement("SASprocess")
825	entry_node.appendChild(node)
826
827	write_node(doc, node, "name", item.name)
828	write_node(doc, node, "date", item.date)
829	write_node(doc, node, "description", item.description)
830	for term in item.term:
831	value = term['value']
832	del term['value']
833	write_node(doc, node, "term", value, term)
834	for note in item.notes:
835	write_node(doc, node, "SASprocessnote", note)
836
837	# Return the document, and the SASentry node associated with
838	# the data we just wrote
839	return doc, entry_node
840
841	def write(self, filename, datainfo):
842	"""
843	Write the content of a Data1D as a CanSAS XML file
844
845	:param filename: name of the file to write
846	:param datainfo: Data1D object
847	"""
848	# Create XML document
849	doc, sasentry = self._to_xml_doc(datainfo)
850	# Write the file
851	fd = open(filename, 'w')
852	fd.write(doc.toprettyxml())
853	fd.close()
854
855	def _store_float(self, location, node, variable, storage, optional=True):
856	"""
857	Get the content of a xpath location and store
858	the result. Check that the units are compatible
859	with the destination. The value is expected to
860	be a float.
861
862	The xpath location might or might not exist.
863	If it does not exist, nothing is done
864
865	:param location: xpath location to fetch
866	:param node: node to read the data from
867	:param variable: name of the data member to store it in [string]
868	:param storage: data object that has the 'variable' data member
869	:param optional: if True, no exception will be raised
870	if unit conversion can't be done
871
872	:raise ValueError: raised when the units are not recognized
873	"""
874	entry = get_content(location, node)
875	try:
876	value = float(entry.text)
877	except:
878	value = None
879
880	if value is not None:
881	# If the entry has units, check to see that they are
882	# compatible with what we currently have in the data object
883	units = entry.get('unit')
884	if units is not None:
885	toks = variable.split('.')
886	exec "local_unit = storage.%s_unit" % toks[0]
887	if units.lower()!=local_unit.lower():
888	if has_converter==True:
889	try:
890	conv = Converter(units)
891	exec "storage.%s = %g" % (variable,
892	conv(value, units=local_unit))
893	except:
894	err_mess = "CanSAS reader: could not convert"
895	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
896	% (variable, units, local_unit, sys.exc_value)
897	self.errors.append(err_mess)
898	if optional:
899	logging.info(err_mess)
900	else:
901	raise ValueError, err_mess
902	else:
903	err_mess = "CanSAS reader: unrecognized %s unit [%s];"
904	err_mess += " expecting [%s]" % (variable,
905	units, local_unit)
906	self.errors.append(err_mess)
907	if optional:
908	logging.info(err_mess)
909	else:
910	raise ValueError, err_mess
911	else:
912	exec "storage.%s = value" % variable
913	else:
914	exec "storage.%s = value" % variable
915
916	def _store_content(self, location, node, variable, storage):
917	"""
918	Get the content of a xpath location and store
919	the result. The value is treated as a string.
920
921	The xpath location might or might not exist.
922	If it does not exist, nothing is done
923
924	:param location: xpath location to fetch
925	:param node: node to read the data from
926	:param variable: name of the data member to store it in [string]
927	:param storage: data object that has the 'variable' data member
928
929	:return: return a list of errors
930	"""
931	entry = get_content(location, node)
932	if entry is not None and entry.text is not None:
933	exec "storage.%s = entry.text.strip()" % variable
934
935
936
937	class Reader2D:
938	"""
939	Class to load a basic guiframe state
940	"""
941	## File type
942	type_name = "Fitting"
943
944	## Wildcards
945	type = ["Fitting files (.fitv)\|.fitv"
946	"SANSView file (.svs)\|.svs"]
947	## List of allowed extensions
948	ext=['.fitv', '.FITV', '.svs', 'SVS']
949
950	def __init__(self):
951	CansasReader.__init__(self)
952	"""
953	Initialize the call-back method to be called
954	after we load a file
955
956	:param call_back: call-back method
957	:param cansas: True = files will be written/read in CanSAS format
958	False = write CanSAS format
959
960	"""
961	## Call back method to be executed after a file is read
962	#self.call_back = call_back
963	## CanSAS format flag
964	self.cansas = cansas
965	self.state = None
966
967	def read(self, path):
968	"""
969	Load a new P(r) inversion state from file
970
971	:param path: file path
972
973	"""
974	if self.cansas == True:
975	return self._read_cansas(path)
976
977	def _to_xml_doc(self, datainfo):
978	"""
979	Create an XML document to contain the content of a Data2D
980
981	:param datainfo: Data2D object
982
983	"""
984	if not issubclass(datainfo.__class__, Data2D):
985	raise RuntimeError, "The cansas writer expects a Data2D instance"
986
987	doc = xml.dom.minidom.Document()
988	main_node = doc.createElement("SASroot")
989	main_node.setAttribute("version", self.version)
990	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
991	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
992	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
993
994	doc.appendChild(main_node)
995
996	entry_node = doc.createElement("SASentry")
997	main_node.appendChild(entry_node)
998
999	write_node(doc, entry_node, "Title", datainfo.title)
1000	if datainfo is not None:
1001	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
1002	for item in datainfo.run:
1003	runname = {}
1004	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
1005	runname = {'name': datainfo.run_name[item] }
1006	write_node(doc, entry_node, "Run", item, runname)
1007	# Data info
1008	new_node = doc.createElement("SASdata")
1009	entry_node.appendChild(new_node)
1010	for item in list_of_data_2d_attr:
1011	element = doc.createElement(item[0])
1012	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
1013	new_node.appendChild(element)
1014
1015	for item in list_of_data2d_values:
1016	root_node = doc.createElement(item[0])
1017	new_node.appendChild(root_node)
1018
1019	exec "temp_list = datainfo.%s"%item[1]
1020
1021	if temp_list is None or len(temp_list)== 0:
1022	element = doc.createElement(item[0])
1023	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
1024	root_node.appendChild(element)
1025	else:
1026	for value in temp_list:
1027	element = doc.createElement(item[0])
1028	exec "element.setAttribute(item[0], str(%s))"%value
1029	root_node.appendChild(element)
1030
1031	# Sample info
1032	sample = doc.createElement("SASsample")
1033	if datainfo.sample.name is not None:
1034	sample.setAttribute("name", str(datainfo.sample.name))
1035	entry_node.appendChild(sample)
1036	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1037	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
1038	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1039	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
1040
1041	for item in datainfo.sample.details:
1042	write_node(doc, sample, "details", item)
1043
1044	pos = doc.createElement("position")
1045	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
1046	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
1047	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
1048	if written == True:
1049	sample.appendChild(pos)
1050
1051	ori = doc.createElement("orientation")
1052	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
1053	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1054	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1055	if written == True:
1056	sample.appendChild(ori)
1057
1058	# Instrument info
1059	instr = doc.createElement("SASinstrument")
1060	entry_node.appendChild(instr)
1061
1062	write_node(doc, instr, "name", datainfo.instrument)
1063
1064	# Source
1065	source = doc.createElement("SASsource")
1066	if datainfo.source.name is not None:
1067	source.setAttribute("name", str(datainfo.source.name))
1068	instr.appendChild(source)
1069
1070	write_node(doc, source, "radiation", datainfo.source.radiation)
1071	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1072	size = doc.createElement("beam_size")
1073	if datainfo.source.beam_size_name is not None:
1074	size.setAttribute("name", str(datainfo.source.beam_size_name))
1075	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1076	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1077	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1078	if written == True:
1079	source.appendChild(size)
1080
1081	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1082	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1083	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1084	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1085
1086	# Collimation
1087	for item in datainfo.collimation:
1088	coll = doc.createElement("SAScollimation")
1089	if item.name is not None:
1090	coll.setAttribute("name", str(item.name))
1091	instr.appendChild(coll)
1092
1093	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1094
1095	for apert in item.aperture:
1096	ap = doc.createElement("aperture")
1097	if apert.name is not None:
1098	ap.setAttribute("name", str(apert.name))
1099	if apert.type is not None:
1100	ap.setAttribute("type", str(apert.type))
1101	coll.appendChild(ap)
1102
1103	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1104
1105	size = doc.createElement("size")
1106	if apert.size_name is not None:
1107	size.setAttribute("name", str(apert.size_name))
1108	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1109	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1110	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1111	if written == True:
1112	ap.appendChild(size)
1113
1114	# Detectors
1115	for item in datainfo.detector:
1116	det = doc.createElement("SASdetector")
1117	written = write_node(doc, det, "name", item.name)
1118	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1119	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1120	if written == True:
1121	instr.appendChild(det)
1122
1123	off = doc.createElement("offset")
1124	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1125	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1126	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1127	if written == True:
1128	det.appendChild(off)
1129
1130	center = doc.createElement("beam_center")
1131	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1132	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1133	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1134	if written == True:
1135	det.appendChild(center)
1136
1137	pix = doc.createElement("pixel_size")
1138	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1139	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1140	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1141	if written == True:
1142	det.appendChild(pix)
1143
1144	ori = doc.createElement("orientation")
1145	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1146	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1147	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1148	if written == True:
1149	det.appendChild(ori)
1150
1151	# Processes info
1152	for item in datainfo.process:
1153	node = doc.createElement("SASprocess")
1154	entry_node.appendChild(node)
1155
1156	write_node(doc, node, "name", item.name)
1157	write_node(doc, node, "date", item.date)
1158	write_node(doc, node, "description", item.description)
1159	for term in item.term:
1160	value = term['value']
1161	del term['value']
1162	write_node(doc, node, "term", value, term)
1163	for note in item.notes:
1164	write_node(doc, node, "SASprocessnote", note)
1165	# Return the document, and the SASentry node associated with
1166	# the data we just wrote
1167	return doc, entry_node
1168
1169	def _parse_state(self, entry, NODE_NAME= 'state'):
1170	"""
1171	Read a fit result from an XML node
1172
1173	:param entry: XML node to read from
1174
1175	:return: PageState object
1176	"""
1177	# Create an empty state
1178	state = None
1179	# Locate the P(r) node
1180	try:
1181	nodes = entry.xpath('ns:%s' % NODE_NAME, namespaces={'ns': STATE_NODE})
1182	if nodes !=[]:
1183	# Create an empty state
1184	state = PageState()
1185	state.fromXML(node=nodes[0])
1186	except:
1187	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1188
1189	return state
1190
1191
1192
1193	def _parse_entry(self, dom):
1194	"""
1195	Parse a SASentry
1196
1197	:param node: SASentry node
1198
1199	:return: Data1D/Data2D object
1200
1201	"""
1202	node = dom.xpath('ns:data_class', namespaces={'ns': STATE_NODE})
1203	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1204	return CansasReader._parse_entry(self, dom)
1205
1206	#Parse 2D
1207	data_info = Data2D()
1208
1209	# Look up title
1210	self._store_content('ns:Title', dom, 'title', data_info)
1211
1212	# Look up run number
1213	nodes = dom.xpath('ns:Run', namespaces={'ns': STATE_NODE})
1214	for item in nodes:
1215	if item.text is not None:
1216	value = item.text.strip()
1217	if len(value) > 0:
1218	data_info.run.append(value)
1219	if item.get('name') is not None:
1220	data_info.run_name[value] = item.get('name')
1221
1222	# Look up instrument name
1223	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1224
1225	# Notes
1226	note_list = dom.xpath('ns:SASnote', namespaces={'ns': STATE_NODE})
1227	for note in note_list:
1228	try:
1229	if note.text is not None:
1230	note_value = note.text.strip()
1231	if len(note_value) > 0:
1232	data_info.notes.append(note_value)
1233	except:
1234	err_mess = "state_reader.read: error processing entry notes\n %s" % sys.exc_value
1235	self.errors.append(err_mess)
1236	logging.error(err_mess)
1237
1238	# Sample info ###################
1239	entry = get_content('ns:SASsample', dom)
1240	if entry is not None:
1241	data_info.sample.name = entry.get('name')
1242
1243	self._store_content('ns:SASsample/ns:ID',
1244	dom, 'ID', data_info.sample)
1245	self._store_float('ns:SASsample/ns:thickness',
1246	dom, 'thickness', data_info.sample)
1247	self._store_float('ns:SASsample/ns:transmission',
1248	dom, 'transmission', data_info.sample)
1249	self._store_float('ns:SASsample/ns:temperature',
1250	dom, 'temperature', data_info.sample)
1251
1252	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': STATE_NODE})
1253	for item in nodes:
1254	try:
1255	if item.text is not None:
1256	detail_value = item.text.strip()
1257	if len(detail_value) > 0:
1258	data_info.sample.details.append(detail_value)
1259	except:
1260	err_mess = "state_reader.read: error processing sample details\n %s" % sys.exc_value
1261	self.errors.append(err_mess)
1262	logging.error(err_mess)
1263
1264	# Position (as a vector)
1265	self._store_float('ns:SASsample/ns:position/ns:x',
1266	dom, 'position.x', data_info.sample)
1267	self._store_float('ns:SASsample/ns:position/ns:y',
1268	dom, 'position.y', data_info.sample)
1269	self._store_float('ns:SASsample/ns:position/ns:z',
1270	dom, 'position.z', data_info.sample)
1271
1272	# Orientation (as a vector)
1273	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1274	dom, 'orientation.x', data_info.sample)
1275	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1276	dom, 'orientation.y', data_info.sample)
1277	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1278	dom, 'orientation.z', data_info.sample)
1279
1280	# Source info ###################
1281	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1282	if entry is not None:
1283	data_info.source.name = entry.get('name')
1284
1285	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1286	dom, 'radiation', data_info.source)
1287	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1288	dom, 'beam_shape', data_info.source)
1289	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1290	dom, 'wavelength', data_info.source)
1291	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1292	dom, 'wavelength_min', data_info.source)
1293	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1294	dom, 'wavelength_max', data_info.source)
1295	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1296	dom, 'wavelength_spread', data_info.source)
1297
1298	# Beam size (as a vector)
1299	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1300	if entry is not None:
1301	data_info.source.beam_size_name = entry.get('name')
1302
1303	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1304	dom, 'beam_size.x', data_info.source)
1305	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1306	dom, 'beam_size.y', data_info.source)
1307	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1308	dom, 'beam_size.z', data_info.source)
1309
1310	# Collimation info ###################
1311	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': STATE_NODE})
1312	for item in nodes:
1313	collim = Collimation()
1314	if item.get('name') is not None:
1315	collim.name = item.get('name')
1316	self._store_float('ns:length', item, 'length', collim)
1317
1318	# Look for apertures
1319	apert_list = item.xpath('ns:aperture', namespaces={'ns': STATE_NODE})
1320	for apert in apert_list:
1321	aperture = Aperture()
1322
1323	# Get the name and type of the aperture
1324	aperture.name = apert.get('name')
1325	aperture.type = apert.get('type')
1326
1327	self._store_float('ns:distance', apert, 'distance', aperture)
1328
1329	entry = get_content('ns:size', apert)
1330	if entry is not None:
1331	aperture.size_name = entry.get('name')
1332
1333	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1334	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1335	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1336
1337	collim.aperture.append(aperture)
1338
1339	data_info.collimation.append(collim)
1340
1341	# Detector info ######################
1342	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': STATE_NODE})
1343	for item in nodes:
1344
1345	detector = Detector()
1346
1347	self._store_content('ns:name', item, 'name', detector)
1348	self._store_float('ns:SDD', item, 'distance', detector)
1349
1350	# Detector offset (as a vector)
1351	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1352	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1353	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1354
1355	# Detector orientation (as a vector)
1356	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1357	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1358	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1359
1360	# Beam center (as a vector)
1361	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1362	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1363	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1364
1365	# Pixel size (as a vector)
1366	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1367	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1368	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1369
1370	self._store_float('ns:slit_length', item, 'slit_length', detector)
1371
1372	data_info.detector.append(detector)
1373
1374	# Processes info ######################
1375	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': STATE_NODE})
1376	for item in nodes:
1377	process = Process()
1378	self._store_content('ns:name', item, 'name', process)
1379	self._store_content('ns:date', item, 'date', process)
1380	self._store_content('ns:description', item, 'description', process)
1381
1382	term_list = item.xpath('ns:term', namespaces={'ns': STATE_NODE})
1383	for term in term_list:
1384	try:
1385	term_attr = {}
1386	for attr in term.keys():
1387	term_attr[attr] = term.get(attr).strip()
1388	if term.text is not None:
1389	term_attr['value'] = term.text.strip()
1390	process.term.append(term_attr)
1391	except:
1392	err_mess = "state_reader.read: error processing process term\n %s" % sys.exc_value
1393	self.errors.append(err_mess)
1394	logging.error(err_mess)
1395
1396	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': STATE_NODE})
1397	for note in note_list:
1398	if note.text is not None:
1399	process.notes.append(note.text.strip())
1400
1401	data_info.process.append(process)
1402
1403
1404	# Data info ######################
1405	nodes = dom.xpath('ns:SASdata', namespaces={'ns': STATE_NODE})
1406	if len(nodes)>1:
1407	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1408
1409	for entry in nodes:
1410	for item in list_of_data_2d_attr:
1411	#get node
1412	node = get_content('ns:%s'%item[0], entry)
1413	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1414
1415	for item in list_of_data2d_values:
1416	field = get_content('ns:%s'%item[0], entry)
1417	list = []
1418	if field is not None:
1419	list = [parse_entry_helper(node, item) for node in field]
1420	exec "data_info.%s = numpy.array(list)"%item[0]
1421
1422	return data_info
1423
1424	def _read_cansas(self, path):
1425	"""
1426	Load data and P(r) information from a CanSAS XML file.
1427
1428	:param path: file path
1429
1430	:return: Data1D object if a single SASentry was found,
1431	or a list of Data1D objects if multiple entries were found,
1432	or None of nothing was found
1433
1434	:raise RuntimeError: when the file can't be opened
1435	:raise ValueError: when the length of the data vectors are inconsistent
1436
1437	"""
1438	output = []
1439	basename = os.path.basename(path)
1440	root, extension = os.path.splitext(basename)
1441	ext = extension.lower()
1442	try:
1443	if os.path.isfile(path):
1444
1445	#TODO: eventually remove the check for .xml once
1446	# the P(r) writer/reader is truly complete.
1447	if ext in self.ext or \
1448	ext == '.xml':
1449
1450	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1451	# Check the format version number
1452	# Specifying the namespace will take care of the file format version
1453	root = tree.getroot()
1454	entry_list = root.xpath('ns:SASentry', namespaces={'ns': STATE_NODE})
1455	for entry in entry_list:
1456	try:
1457	sas_entry = self._parse_entry(entry)
1458	except:
1459	raise
1460	fitstate = self._parse_state(entry)
1461
1462	#state could be None when .svs file is loaded
1463	#in this case, skip appending to output
1464	if fitstate != None:
1465	sas_entry.meta_data['fitstate'] = fitstate
1466	sas_entry.filename = fitstate.file
1467	output.append(sas_entry)
1468	else:
1469	self.call_back(format=ext)
1470	raise RuntimeError, "%s is not a file" % path
1471
1472	# Return output consistent with the loader's api
1473	if len(output)==0:
1474	self.call_back(state=None, datainfo=None,format=ext)
1475	return None
1476	else:
1477	for ind in range(len(output)):
1478	# Call back to post the new state
1479	state = output[ind].meta_data['fitstate']
1480	t = time.localtime(state.timestamp)
1481	time_str = time.strftime("%b %d %H:%M", t)
1482	# Check that no time stamp is already appended
1483	max_char = state.file.find("[")
1484	if max_char < 0:
1485	max_char = len(state.file)
1486	original_fname = state.file[0:max_char]
1487	state.file = original_fname +' [' + time_str + ']'
1488
1489
1490	if state is not None and state.is_data is not None:
1491	exec 'output[%d].is_data = state.is_data'% ind
1492
1493	output[ind].filename = state.file
1494	state.data = output[ind]
1495	state.data.name = output[ind].filename #state.data_name
1496	state.data.id = state.data_id
1497	if state.is_data is not None:
1498	state.data.is_data = state.is_data
1499	if output[ind].run_name is not None and\
1500	len(output[ind].run_name) != 0 :
1501	name = output[ind].run_name
1502	else:
1503	name=original_fname
1504	state.data.group_id = name
1505	#store state in fitting
1506	self.call_back(state=state, datainfo=output[ind],format=ext)
1507	self.state= state
1508	return output
1509
1510	except:
1511	#self.call_back(format=ext)
1512	self.state= state
1513	raise
1514
1515	def write(self, filename, datainfo=None, fitstate=None):
1516	"""
1517	Write the content of a Data1D as a CanSAS XML file only for standalone
1518
1519	:param filename: name of the file to write
1520	:param datainfo: Data1D object
1521	:param fitstate: PageState object
1522
1523	"""
1524	# Sanity check
1525	if self.cansas == True:
1526
1527	# Add fitting information to the XML document
1528	doc = self.write_toXML(datainfo, fitstate)
1529	# Write the XML document
1530	fd = open(filename, 'w')
1531	fd.write(doc.toprettyxml())
1532	fd.close()
1533	else:
1534	fitstate.toXML(file=filename)
1535
1536	def write_toXML(self, datainfo=None, state=None):
1537	"""
1538	Write toXML, a helper for write() , could be used by guimanager._on_save()
1539
1540	: return: xml doc
1541	"""
1542
1543	if state.data is None:
1544	data = Data2D()
1545	else:
1546	#make sure title and data run is filled up.
1547	if state.data.title == None or state.data.title=='':
1548	state.data.title = state.data.name
1549	if state.data.run_name == None or state.data.run_name=={}:
1550	state.data.run = [str(state.data.name)]
1551	state.data.run_name[0] = state.data.name
1552	doc, sasentry = self._to_xml_doc(data)
1553
1554
1555	if state is not None:
1556	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1557
1558	return doc
1559
1560	if __name__ == "__main__":
1561	state = PageState(parent=None)
1562	#state.toXML()
1563	"""
1564
1565	file = open("test_state", "w")
1566	pickle.dump(state, file)
1567	print pickle.dumps(state)
1568	state.data_name = "hello---->"
1569	pickle.dump(state, file)
1570	file = open("test_state", "r")
1571	new_state= pickle.load(file)
1572	print "new state", new_state
1573	new_state= pickle.load(file)
1574	print "new state", new_state
1575	#print "state", state
1576	"""
1577	import bsddb
1578	import pickle
1579	db= bsddb.btopen('file_state.db', 'c')
1580	val = (pickle.dumps(state), "hello", "hi")
1581	db['state1']= pickle.dumps(val)
1582	print pickle.loads(db['state1'])
1583	state.data_name = "hello---->22"
1584	db['state2']= pickle.dumps(state)
1585	state.data_name = "hello---->2"
1586	db['state3']= pickle.dumps(state)
1587	del db['state3']
1588	state.data_name = "hello---->3"
1589	db['state4']= pickle.dumps(state)
1590	new_state = pickle.loads(db['state1'])
1591	#print db.last()
1592	db.set_location('state2')
1593	state.data_name = "hello---->5"
1594	db['aastate5']= pickle.dumps(state)
1595	db.keys().sort()
1596	print pickle.loads(db['state2'])
1597
1598	db.close()
1599
1600	logging.basicConfig(level=logging.ERROR,
1601	format='%(asctime)s %(levelname)s %(message)s',
1602	filename='state_reader.log',
1603	filemode='w')
1604	reader = Reader()
1605	print reader.read("../test/cansas1d.xml")
1606	#print reader.read("../test/latex_smeared.xml")
1607
1608
1609

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SasView

source: sasview/guiframe/state_reader.py @ bc7bc839

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