invariant_state.py @ 54547cc1

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 54547cc1 was a60b8b6, checked in by Jae Cho <jhjcho@…>, 13 years ago
updated dataloader calls
Property mode set to `100644`
File size: 32.7 KB

Line
1	"""
2	"""
3
4	#import time
5	import os
6	import sys
7	import logging
8	import copy
9	import sans.dataloader
10	#from xml.dom.minidom import parse
11	from lxml import etree
12	from sans.dataloader.readers.cansas_reader import Reader as CansasReader
13	from sans.dataloader.readers.cansas_reader import get_content
14	from sans.guiframe.utils import format_number
15	from sans.guiframe.dataFitting import Theory1D
16	from sans.guiframe.dataFitting import Data1D
17
18	INVNODE_NAME = 'invariant'
19	CANSAS_NS = "cansas1d/1.0"
20
21	# default state
22	list = {'file': 'None',
23	'compute_num':0,
24	'state_num':0,
25	'is_time_machine':False,
26	'background_tcl':0.0,
27	'scale_tcl':1.0,
28	'contrast_tcl':1.0,
29	'porod_constant_tcl':'',
30	'npts_low_tcl':10,
31	'npts_high_tcl':10,
32	'power_high_tcl':4.0,
33	'power_low_tcl': 4.0,
34	'enable_high_cbox':False,
35	'enable_low_cbox':False,
36	'guinier': True,
37	'power_law_high': False,
38	'power_law_low': False,
39	'fit_enable_high': False,
40	'fit_enable_low': False,
41	'fix_enable_high':True,
42	'fix_enable_low':True,
43	'volume_tcl':'',
44	'volume_err_tcl':'',
45	'surface_tcl':'',
46	'surface_err_tcl':''}
47	# list of states: This list will be filled as panel
48	# init and the number of states increases
49	state_list = {}
50	bookmark_list = {}
51	# list of input parameters (will be filled up on panel init) used by __str__
52	input_list = {'background_tcl':0,
53	'scale_tcl':0,
54	'contrast_tcl':0,
55	'porod_constant_tcl':'',
56	'npts_low_tcl':0,
57	'npts_high_tcl':0,
58	'power_high_tcl':0,
59	'power_low_tcl': 0}
60	# list of output parameters (order sensitive) used by __str__
61	output_list = [["qstar_low", "Q* from low Q extrapolation [1/(cm*A)]"],
62	["qstar_low_err", "dQ* from low Q extrapolation"],
63	["qstar_low_percent", "Q* percent from low Q extrapolation"],
64	["qstar", "Q* from data [1/(cm*A)]"],
65	["qstar_err", "dQ* from data"],
66	["qstar_percent", "Q* percent from data"],
67	["qstar_high", "Q* from high Q extrapolation [1/(cm*A)]"],
68	["qstar_high_err", "dQ* from high Q extrapolation"],
69	["qstar_high_percent", "Q* percent from low Q extrapolation"],
70	["qstar_total", "total Q* [1/(cm*A)]"],
71	["qstar_total_err", "total dQ*"],
72	["volume", "volume fraction"],
73	["volume_err", "volume fraction error"],
74	["surface", "specific surface"],
75	["surface_err", "specific surface error"]]
76
77
78
79	class InvariantState(object):
80	"""
81	Class to hold the state information of the InversionControl panel.
82	"""
83	def __init__(self):
84	"""
85	Default values
86	"""
87	# Input
88	self.file = None
89	self.data = Data1D(x=[], y=[], dx=None, dy=None)
90	self.theory_lowQ = Theory1D(x=[], y=[], dy=None)
91	self.theory_highQ = Theory1D(x=[], y=[], dy=None)
92	#self.is_time_machine = False
93	self.saved_state = list
94	self.state_list = state_list
95	self.bookmark_list = bookmark_list
96	self.input_list = input_list
97	self.output_list = output_list
98
99	self.compute_num = 0
100	self.state_num = 0
101	self.timestamp = ('00:00:00', '00/00/0000')
102	self.container = None
103	#plot image
104	self.wximbmp = None
105	# report_html strings
106	import sans.perspectives.invariant as invariant
107	path = invariant.get_data_path(media='media')
108	path_report_html = os.path.join(path,"report_template.html")
109	html_template = open(path_report_html,"r")
110	self.template_str = html_template.read()
111	self.report_str = self.template_str
112	#self.report_str_save = None
113	html_template.close()
114
115	def __str__(self):
116	"""
117	Pretty print
118
119	: return: string representing the state
120	"""
121	# Input string
122	compute_num = self.saved_state['compute_num']
123	compute_state = self.state_list[str(compute_num)]
124	my_time, date = self.timestamp
125	file_name = self.file
126
127	state_num = int(self.saved_state['state_num'])
128	state = "\n[Invariant computation for %s: " % file_name
129	state += "performed at %s on %s] \n" % (my_time, date)
130	state += "State No.: %d \n" % state_num
131	state += "\n=== Inputs ===\n"
132
133	# text ctl general inputs ( excluding extrapolation text ctl)
134	for key, value in self.input_list.iteritems():
135	if value == '':
136	continue
137	key_split = key.split('_')
138	max_ind = len(key_split)-1
139	if key_split[max_ind] == 'tcl':
140	name = ""
141	if key_split[1] == 'low' or key_split[1] == 'high':
142	continue
143	for ind in range(0, max_ind):
144	name += " %s" % key_split[ind]
145	state += "%s: %s\n" % (name.lstrip(" "), value)
146
147	# other input parameters
148	extra_lo = compute_state['enable_low_cbox']
149	if compute_state['enable_low_cbox']:
150	if compute_state['guinier']:
151	extra_lo = 'Guinier'
152	else:
153	extra_lo = 'Power law'
154	extra_hi = compute_state['enable_high_cbox']
155	if compute_state['enable_high_cbox']:
156	extra_hi = 'Power law'
157	state += "\nExtrapolation: High=%s; Low=%s\n" %(extra_hi, extra_lo)
158	low_off = False
159	high_off = False
160	for key, value in self.input_list.iteritems():
161	key_split = key.split('_')
162	max_ind = len(key_split) - 1
163	if key_split[max_ind] == 'tcl':
164	name = ""
165	# check each buttons whether or not ON or OFF
166	if key_split[1] == 'low' or key_split[1] == 'high':
167	if not compute_state['enable_low_cbox'] and \
168	key_split[max_ind-1] == 'low':
169	low_off = True
170	continue
171	elif not compute_state['enable_high_cbox'] and \
172	key_split[max_ind-1] == 'high':
173	high_off = True
174	continue
175	elif extra_lo == 'Guinier' and key_split[0] == 'power' and \
176	key_split[max_ind-1] == 'low':
177	continue
178	for ind in range(0, max_ind):
179	name += " %s" % key_split[ind]
180	name = name.lstrip(" ")
181	if name == "power low" :
182	if compute_state['fix_enable_low']:
183	name += ' (Fixed)'
184	else:
185	name += ' (Fitted)'
186	if name == "power high" :
187	if compute_state['fix_enable_high']:
188	name += ' (Fixed)'
189	else:
190	name += ' (Fitted)'
191	state += "%s: %s\n" % (name, value)
192	# Outputs
193	state += "\n=== Outputs ==="
194	for item in output_list:
195	item_split = item[0].split('_')
196	# Exclude the extrapolation that turned off
197	if len(item_split) > 1:
198	if low_off and item_split[1] == 'low':
199	continue
200	if high_off and item_split[1] == 'high':
201	continue
202	max_ind = len(item_split) - 1
203	value = None
204	try:
205	# Q* outputs
206	exec "value = self.container.%s\n" % item[0]
207	except:
208	# other outputs than Q*
209	name = item[0] + "_tcl"
210	if name in self.saved_state.keys():
211	exec "value = self.saved_state['%s']" % name
212
213	# Exclude the outputs w/''
214	if value == '':
215	continue
216	# Error outputs
217	if item_split[max_ind] == 'err':
218	state += "+- %s " % format_number(value)
219	# Percentage outputs
220	elif item_split[max_ind] == 'percent':
221	try:
222	value = float(value) * 100
223	except:
224	pass
225	state += "(%s %s)" % (format_number(value), '%')
226	# Outputs
227	else:
228	state += "\n%s: %s " % (item[1],
229	format_number(value, high=True))
230	# Include warning msg
231	if self.container is not None:
232	state += "\n\nNote:\n" + self.container.warning_msg
233	return state
234
235	def clone_state(self):
236	"""
237	deepcopy the state
238	"""
239	return copy.deepcopy(self.saved_state)
240
241	def toXML(self, file="inv_state.inv", doc=None, entry_node=None):
242	"""
243	Writes the state of the InversionControl panel to file, as XML.
244
245	Compatible with standalone writing, or appending to an
246	already existing XML document. In that case, the XML document
247	is required. An optional entry node in the XML document
248	may also be given.
249
250	: param file: file to write to
251	: param doc: XML document object [optional]
252	: param entry_node: XML node within the XML document at which
253	we will append the data [optional]
254	"""
255	from xml.dom.minidom import getDOMImplementation
256	import time
257	timestamp = time.time()
258	# Check whether we have to write a standalone XML file
259	if doc is None:
260	impl = getDOMImplementation()
261
262	doc_type = impl.createDocumentType(INVNODE_NAME, "1.0", "1.0")
263
264	newdoc = impl.createDocument(None, INVNODE_NAME, doc_type)
265	top_element = newdoc.documentElement
266	else:
267	# We are appending to an existing document
268	newdoc = doc
269	top_element = newdoc.createElement(INVNODE_NAME)
270	if entry_node is None:
271	newdoc.documentElement.appendChild(top_element)
272	else:
273	entry_node.appendChild(top_element)
274
275	attr = newdoc.createAttribute("version")
276	attr.nodeValue = '1.0'
277	top_element.setAttributeNode(attr)
278
279	# File name
280	element = newdoc.createElement("filename")
281	if self.file != None and self.file != '':
282	element.appendChild(newdoc.createTextNode(str(self.file)))
283	else:
284	element.appendChild(newdoc.createTextNode(str(file)))
285	top_element.appendChild(element)
286
287	element = newdoc.createElement("timestamp")
288	element.appendChild(newdoc.createTextNode(time.ctime(timestamp)))
289	attr = newdoc.createAttribute("epoch")
290	attr.nodeValue = str(timestamp)
291	element.setAttributeNode(attr)
292	top_element.appendChild(element)
293
294	# Current state
295	state = newdoc.createElement("state")
296	top_element.appendChild(state)
297
298	for name,value in self.saved_state.iteritems():
299	element = newdoc.createElement(str(name))
300	element.appendChild(newdoc.createTextNode(str(value)))
301	state.appendChild(element)
302
303	# State history list
304	history = newdoc.createElement("history")
305	top_element.appendChild(history)
306
307	for name, value in self.state_list.iteritems():
308	history_element = newdoc.createElement('state_' + str(name))
309	for state_name,state_value in value.iteritems():
310	state_element = newdoc.createElement(str(state_name))
311	child = newdoc.createTextNode(str(state_value))
312	state_element.appendChild(child)
313	history_element.appendChild(state_element)
314	#history_element.appendChild(state_list_element)
315	history.appendChild(history_element)
316
317	# Bookmarks bookmark_list[self.bookmark_num] = [\
318	#my_time,date,state,comp_state]
319	bookmark = newdoc.createElement("bookmark")
320	top_element.appendChild(bookmark)
321	item_list = ['time','date','state','comp_state']
322	for name, value_list in self.bookmark_list.iteritems():
323	element = newdoc.createElement('mark_'+ str(name))
324	_,date,state,comp_state = value_list
325	time_element = newdoc.createElement('time')
326	time_element.appendChild(newdoc.createTextNode(str(value_list[0])))
327	date_element = newdoc.createElement('date')
328	date_element.appendChild(newdoc.createTextNode(str(value_list[1])))
329	state_list_element = newdoc.createElement('state')
330	comp_state_list_element = newdoc.createElement('comp_state')
331	for state_name, state_value in value_list[2].iteritems():
332	state_element = newdoc.createElement(str(state_name))
333	child = newdoc.createTextNode(str(state_value))
334	state_element.appendChild(child)
335	state_list_element.appendChild(state_element)
336	for comp_name, comp_value in value_list[3].iteritems():
337	comp_element = newdoc.createElement(str(comp_name))
338	comp_element.appendChild(newdoc.createTextNode(str(comp_value)))
339	comp_state_list_element.appendChild(comp_element)
340	element.appendChild(time_element)
341	element.appendChild(date_element)
342	element.appendChild(state_list_element)
343	element.appendChild(comp_state_list_element)
344	bookmark.appendChild(element)
345
346	# Save the file
347	if doc is None:
348	fd = open('test000', 'w')
349	fd.write(newdoc.toprettyxml())
350	fd.close()
351	return None
352	else:
353	return newdoc.toprettyxml()
354
355	def fromXML(self, file=None, node=None):
356	"""
357	Load invariant states from a file
358
359	: param file: .inv file
360	: param node: node of a XML document to read from
361	"""
362	if file is not None:
363	msg = "InvariantSate no longer supports non-CanSAS"
364	msg += " format for invariant files"
365	raise RuntimeError, msg
366
367	if node.get('version')\
368	and node.get('version') == '1.0':
369
370	# Get file name
371	entry = get_content('ns:filename', node)
372	if entry is not None:
373	file_name = entry.text.strip()
374
375	# Get time stamp
376	entry = get_content('ns:timestamp', node)
377	if entry is not None and entry.get('epoch'):
378	try:
379	timestamp = (entry.get('epoch'))
380	except:
381	msg = "InvariantSate.fromXML: Could not read"
382	msg += " timestamp\n %s" % sys.exc_value
383	logging.error(msg)
384
385	# Parse bookmarks
386	entry_bookmark = get_content('ns:bookmark', node)
387
388	for ind in range(1, len(entry_bookmark) + 1):
389	temp_state = {}
390	temp_bookmark = {}
391	entry = get_content('ns:mark_%s' % ind, entry_bookmark)
392
393	if entry is not None:
394	my_time = get_content('ns:time', entry)
395	val_time = str(my_time.text.strip())
396	date = get_content('ns:date', entry)
397	val_date = str(date.text.strip())
398	state_entry = get_content('ns:state', entry)
399	for item in list:
400
401	input_field = get_content('ns:%s' % item, state_entry)
402	val = str(input_field.text.strip())
403	if input_field is not None:
404	try:
405	exec "temp_state['%s'] = %s" % (item, val)
406	except:
407	exec "temp_state['%s'] = '%s'" % (item, val)
408	comp_entry = get_content('ns:comp_state', entry)
409
410	for item in list:
411	input_field = get_content('ns:%s' % item, comp_entry)
412	val = str(input_field.text.strip())
413	if input_field is not None:
414	try:
415	exec "temp_bookmark['%s'] = %s" % (item, val)
416	except:
417	exec "temp_bookmark['%s'] = '%s'" % (item, val)
418	try:
419	cmd = "self.bookmark_list[%s] = [val_time,"
420	cmd += "val_date,temp_state,temp_bookmark]"
421	exec cmd % ind
422	except:
423	raise "missing components of bookmarks..."
424	# Parse histories
425	entry_history = get_content('ns:history', node)
426
427	for ind in range(0, len(entry_history)):
428	temp_state = {}
429	entry = get_content('ns:state_%s' % ind, entry_history)
430
431	if entry is not None:
432	for item in list:
433	input_field = get_content('ns:%s' % item, entry )
434	val = str(input_field.text.strip())
435
436	if input_field is not None:
437	try:
438	exec "temp_state['%s'] = %s" % (item, val)
439	except:
440	exec "temp_state['%s'] = '%s'" % (item, val)
441	finally:
442	exec "self.state_list['%s'] = temp_state" % ind
443	# Parse current state (ie, saved_state)
444	entry = get_content('ns:state', node)
445	if entry is not None:
446	for item in list:
447	input_field = get_content('ns:%s' % item, entry)
448	val = str(input_field.text.strip())
449	if input_field is not None:
450	self.set_saved_state(name=item, value=val)
451	self.file = file_name
452
453	def set_report_string(self):
454	"""
455	Get the values (strings) from __str__ for report
456	"""
457	strings = self.__str__()
458
459	# default string values
460	for num in range (1, 19):
461	exec "s_%s = 'NA'" % str(num)
462	lines = strings.split('\n')
463	# get all string values from __str__()
464	for line in range(0, len(lines)):
465	if line == 1:
466	s_1 = lines[1]
467	elif line == 2:
468	s_2 = lines[2]
469	else:
470	item = lines[line].split(':')
471	item[0] = item[0].strip()
472	if item[0] == "scale":
473	s_3 = item[1]
474	elif item[0] == "porod constant":
475	s_4 = item[1]
476	elif item[0] == "background":
477	s_5 = item[1]
478	elif item[0] == "contrast":
479	s_6 = item[1]
480	elif item[0] == "Extrapolation":
481	extra = item[1].split(";")
482	bool_0 = extra[0].split("=")
483	bool_1 = extra[1].split("=")
484	s_8 = " " + bool_0[0] + "Q region = " + bool_0[1]
485	s_7 = " " + bool_1[0] + "Q region = " + bool_1[1]
486	elif item[0] == "npts low":
487	s_9 = item[1]
488	elif item[0] == "npts high":
489	s_10 = item[1]
490	elif item[0] == "volume fraction":
491	val=item[1].split("+-")[0].strip()
492	error = item[1].split("+-")[1].strip()
493	s_17 = val + " ± " + error
494	elif item[0] == "specific surface":
495	val = item[1].split("+-")[0].strip()
496	error = item[1].split("+-")[1].strip()
497	s_18 = val + " ± " + error
498	elif item[0].split("(")[0].strip() == "power low":
499	s_11 = item[0]+" ="+item[1]
500	elif item[0].split("(")[0].strip() == "power high":
501	s_12 = item[0]+" ="+item[1]
502	elif item[0].split("[")[0].strip() == "Q* from low Q extrapolation":
503	#looks messy but this way the symbols +_ and % work on html
504	val = item[1].split("+-")[0].strip()
505	error = item[1].split("+-")[1].strip()
506	err = error.split("%")[0].strip()
507	percent = error.split("%")[1].strip()
508	s_13 = val + " ± " + err + "&#37" + percent
509	elif item[0].split("[")[0].strip() == "Q* from data":
510	val = item[1].split("+-")[0].strip()
511	error = item[1].split("+-")[1].strip()
512	err = error.split("%")[0].strip()
513	percent = error.split("%")[1].strip()
514	s_14 = val + " ± " + err + "&#37" + percent
515	elif item[0].split("[")[0].strip() == "Q* from high Q extrapolation":
516	val = item[1].split("+-")[0].strip()
517	error = item[1].split("+-")[1].strip()
518	err = error.split("%")[0].strip()
519	percent = error.split("%")[1].strip()
520	s_15 = val + " ± " + err + "&#37" + percent
521	elif item[0].split("[")[0].strip() == "total Q*":
522	val = item[1].split("+-")[0].strip()
523	error = item[1].split("+-")[1].strip()
524	s_16 = val + " ± " + error
525	else:
526	continue
527
528	s_1 = self._check_html_format(s_1)
529	file_name = self._check_html_format(self.file)
530
531	# make plot image
532	self.set_plot_state(extra_high=bool_0[1],extra_low=bool_1[1])
533	# get ready for report with setting all the html strings
534	self.report_str = str(self.template_str) % (s_1, s_2,
535	s_3, s_4, s_5, s_6, s_7, s_8,
536	s_9, s_10, s_11, s_12, s_13, s_14, s_15,
537	s_16, s_17, s_18, file_name, "%s")
538
539	def _check_html_format(self, name):
540	"""
541	Check string '%' for html format
542	"""
543	if name.count('%'):
544	name = name.replace('%', '&#37')
545
546	return name
547
548	def set_saved_state(self, name, value):
549	"""
550	Set the state list
551
552	: param name: name of the state component
553	: param value: value of the state component
554	"""
555	rb_list = [['power_law_low','guinier'],
556	['fit_enable_low','fix_enable_low'],
557	['fit_enable_high','fix_enable_high']]
558
559	try:
560	if value == None or value.lstrip().rstrip() == '':
561	exec "self.%s = '%s'" % (name, value)
562	exec "self.saved_state['%s'] = '%s'" % (name, value)
563	else:
564	exec 'self.%s = %s' % (name, value)
565	exec "self.saved_state['%s'] = %s" % (name, value)
566	# set the count part of radio button clicked
567	# False for the saved_state
568	for title, content in rb_list:
569	if name == title:
570	name = content
571	value = False
572	elif name == content:
573	name = title
574	value = False
575	exec "self.saved_state['%s'] = '%s'" % (name, value)
576	self.state_num = self.saved_state['state_num']
577	except:
578	pass
579
580	def set_plot_state(self, extra_high=False, extra_low=False):
581	"""
582	Build image state that wx.html understand
583	by plotting, putting it into wx.FileSystem image object
584
585	: extrap_high,extra_low: low/high extrapolations
586	are possible extra-plots
587	"""
588	# some imports
589	import wx
590	import matplotlib.pyplot as plt
591	from matplotlib.backends.backend_agg import FigureCanvasAgg
592
593	#we use simple plot, not plotpanel
594	#make matlab figure
595	fig = plt.figure()
596	fig.set_facecolor('w')
597	graph = fig.add_subplot(111)
598
599	#data plot
600	graph.errorbar(self.data.x, self.data.y, yerr=self.data.dy, fmt='o')
601	#low Q extrapolation fit plot
602	if not extra_low == 'False':
603	graph.plot(self.theory_lowQ.x,self.theory_lowQ.y)
604	#high Q extrapolation fit plot
605	if not extra_high == 'False':
606	graph.plot(self.theory_highQ.x,self.theory_highQ.y)
607	graph.set_xscale("log", nonposx='clip')
608	graph.set_yscale("log", nonposy='clip')
609	graph.set_xlabel('$\\rm{Q}(\\AA^{-1})$', fontsize = 12)
610	graph.set_ylabel('$\\rm{Intensity}(cm^{-1})$', fontsize = 12)
611	canvas = FigureCanvasAgg(fig)
612	#actually make image
613	canvas.draw()
614
615	#make python.Image object
616	#size
617	w, h = canvas.get_width_height()
618	#convert to wx.Image
619	wximg = wx.EmptyImage(w,h)
620	#wxim.SetData(img.convert('RGB').tostring() )
621	wximg.SetData(canvas.tostring_rgb())
622	#get the dynamic image for the htmlwindow
623	wximgbmp = wx.BitmapFromImage(wximg)
624	#store the image in wx.FileSystem Object
625	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
626	# use wx.MemoryFSHandler
627	self.imgRAM = wx.MemoryFSHandler()
628	#AddFile, image can be retrieved with 'memory:filename'
629	self.imgRAM.AddFile('img_inv.png', wximgbmp, wx.BITMAP_TYPE_PNG)
630
631	self.wximgbmp = 'memory:img_inv.png'
632	self.image = fig
633
634	class Reader(CansasReader):
635	"""
636	Class to load a .inv invariant file
637	"""
638	## File type
639	type_name = "Invariant"
640
641	## Wildcards
642	type = ["Invariant file (.inv)\|.inv",
643	"SANSView file (.svs)\|.svs"]
644	## List of allowed extensions
645	ext = ['.inv', '.INV', '.svs', 'SVS']
646
647	def __init__(self, call_back, cansas=True):
648	"""
649	Initialize the call-back method to be called
650	after we load a file
651
652	: param call_back: call-back method
653	: param cansas: True = files will be written/read in CanSAS format
654	False = write CanSAS format
655	"""
656	## Call back method to be executed after a file is read
657	self.call_back = call_back
658	## CanSAS format flag
659	self.cansas = cansas
660	self.state = None
661
662	def read(self, path):
663	"""
664	Load a new invariant state from file
665
666	: param path: file path
667	: return: None
668	"""
669	if self.cansas == True:
670	return self._read_cansas(path)
671	else:
672	return self._read_standalone(path)
673
674	def _read_standalone(self, path):
675	"""
676	Load a new invariant state from file.
677	The invariant node is assumed to be the top element.
678
679	: param path: file path
680	: return: None
681	"""
682	# Read the new state from file
683	state = InvariantState()
684
685	state.fromXML(file=path)
686
687	# Call back to post the new state
688	self.call_back(state)
689	return None
690
691	def _parse_state(self, entry):
692	"""
693	Read an invariant result from an XML node
694
695	: param entry: XML node to read from
696	: return: InvariantState object
697	"""
698	state = None
699	# Locate the invariant node
700	try:
701	nodes = entry.xpath('ns:%s' % INVNODE_NAME,
702	namespaces={'ns': CANSAS_NS})
703	# Create an empty state
704	if nodes != []:
705	state = InvariantState()
706	state.fromXML(node=nodes[0])
707	except:
708	msg = "XML document does not contain invariant"
709	msg += " information.\n %s" % sys.exc_value
710	logging.info(msg)
711	return state
712
713	def _read_cansas(self, path):
714	"""
715	Load data and invariant information from a CanSAS XML file.
716
717	: param path: file path
718	: return: Data1D object if a single SASentry was found,
719	or a list of Data1D objects if multiple entries were found,
720	or None of nothing was found
721	: raise RuntimeError: when the file can't be opened
722	: raise ValueError: when the length of the data vectors are inconsistent
723	"""
724	output = []
725	if os.path.isfile(path):
726	basename = os.path.basename(path)
727	root, extension = os.path.splitext(basename)
728
729	if extension.lower() in self.ext or \
730	extension.lower() == '.xml':
731	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
732
733	# Check the format version number
734	# Specifying the namespace will take care of
735	# the file format version
736	root = tree.getroot()
737
738	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
739	namespaces={'ns': CANSAS_NS})
740
741	for entry in entry_list:
742
743	sas_entry = self._parse_entry(entry)
744	invstate = self._parse_state(entry)
745
746	#invstate could be None when .svs file is loaded
747	#in this case, skip appending to output
748	if invstate != None:
749	sas_entry.meta_data['invstate'] = invstate
750	sas_entry.filename = invstate.file
751	output.append(sas_entry)
752	else:
753	raise RuntimeError, "%s is not a file" % path
754
755	# Return output consistent with the loader's api
756	if len(output) == 0:
757	return None
758	elif len(output) == 1:
759	# Call back to post the new state
760	self.state = output[0].meta_data['invstate']
761	self.call_back(state=output[0].meta_data['invstate'],
762	datainfo = output[0])
763	return output[0]
764	else:
765	return output
766
767	def get_state(self):
768	return self.state
769
770	def write(self, filename, datainfo=None, invstate=None):
771	"""
772	Write the content of a Data1D as a CanSAS XML file
773
774	: param filename: name of the file to write
775	: param datainfo: Data1D object
776	: param invstate: InvariantState object
777	"""
778	# Sanity check
779	if self.cansas == True:
780	doc = self.write_toXML(datainfo,invstate)
781	# Write the XML document
782	fd = open(filename, 'w')
783	fd.write(doc.toprettyxml())
784	fd.close()
785	else:
786	invstate.toXML(file=filename)
787
788	def write_toXML(self, datainfo=None, state=None):
789	"""
790	Write toXML, a helper for write()
791
792	: return: xml doc
793	"""
794	if datainfo is None:
795	datainfo = sans.dataloader.data_info.Data1D(x=[], y=[])
796	elif not issubclass(datainfo.__class__, sans.dataloader.data_info.Data1D):
797	msg = "The cansas writer expects a Data1D"
798	msg += " instance: %s" % str(datainfo.__class__.__name__)
799	raise RuntimeError, msg
800	#make sure title and data run is filled up.
801	if datainfo.title == None or datainfo.title == '':
802	datainfo.title = datainfo.name
803	if datainfo.run_name == None or datainfo.run_name == {}:
804	datainfo.run = [str(datainfo.name)]
805	datainfo.run_name[0] = datainfo.name
806	# Create basic XML document
807	doc, sasentry = self._to_xml_doc(datainfo)
808	# Add the invariant information to the XML document
809	if state is not None:
810	state.toXML(datainfo.name,doc=doc, entry_node=sasentry)
811	return doc
812

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SasView

source: sasview/invariantview/src/sans/perspectives/invariant/invariant_state.py @ 54547cc1

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