invariant_state.py @ 3cd5806

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 3cd5806 was 5dc6d84, checked in by Jae Cho <jhjcho@…>, 14 years ago
fixed a bug in importing time and extrapolation string on report
Property mode set to `100644`
File size: 32.1 KB

Line
1	"""
2	"""
3
4	#import time
5	import os
6	import sys
7	import logging
8	import copy
9	import DataLoader
10	#from xml.dom.minidom import parse
11	from lxml import etree
12	from DataLoader.readers.cansas_reader import Reader as CansasReader
13	from 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	exec "value = self.saved_state['%s']" % name
211
212	# Exclude the outputs w/''
213	if value == '':
214	continue
215	# Error outputs
216	if item_split[max_ind] == 'err':
217	state += "+- %s " % format_number(value)
218	# Percentage outputs
219	elif item_split[max_ind] == 'percent':
220	try:
221	value = float(value) * 100
222	except:
223	pass
224	state += "(%s %s)" % (format_number(value), '%')
225	# Outputs
226	else:
227	state += "\n%s: %s " % (item[1],
228	format_number(value, high=True))
229	# Include warning msg
230	state += "\n\nNote:\n" + self.container.warning_msg
231	return state
232
233	def clone_state(self):
234	"""
235	deepcopy the state
236	"""
237	return copy.deepcopy(self.saved_state)
238
239	def toXML(self, file="inv_state.inv", doc=None, entry_node=None):
240	"""
241	Writes the state of the InversionControl panel to file, as XML.
242
243	Compatible with standalone writing, or appending to an
244	already existing XML document. In that case, the XML document
245	is required. An optional entry node in the XML document
246	may also be given.
247
248	: param file: file to write to
249	: param doc: XML document object [optional]
250	: param entry_node: XML node within the XML document at which
251	we will append the data [optional]
252	"""
253	from xml.dom.minidom import getDOMImplementation
254	import time
255	timestamp = time.time()
256	# Check whether we have to write a standalone XML file
257	if doc is None:
258	impl = getDOMImplementation()
259
260	doc_type = impl.createDocumentType(INVNODE_NAME, "1.0", "1.0")
261
262	newdoc = impl.createDocument(None, INVNODE_NAME, doc_type)
263	top_element = newdoc.documentElement
264	else:
265	# We are appending to an existing document
266	newdoc = doc
267	top_element = newdoc.createElement(INVNODE_NAME)
268	if entry_node is None:
269	newdoc.documentElement.appendChild(top_element)
270	else:
271	entry_node.appendChild(top_element)
272
273	attr = newdoc.createAttribute("version")
274	attr.nodeValue = '1.0'
275	top_element.setAttributeNode(attr)
276
277	# File name
278	element = newdoc.createElement("filename")
279	if self.file != None and self.file != '':
280	element.appendChild(newdoc.createTextNode(str(self.file)))
281	else:
282	element.appendChild(newdoc.createTextNode(str(file)))
283	top_element.appendChild(element)
284
285	element = newdoc.createElement("timestamp")
286	element.appendChild(newdoc.createTextNode(time.ctime(timestamp)))
287	attr = newdoc.createAttribute("epoch")
288	attr.nodeValue = str(timestamp)
289	element.setAttributeNode(attr)
290	top_element.appendChild(element)
291
292	# Current state
293	state = newdoc.createElement("state")
294	top_element.appendChild(state)
295
296	for name,value in self.saved_state.iteritems():
297	element = newdoc.createElement(str(name))
298	element.appendChild(newdoc.createTextNode(str(value)))
299	state.appendChild(element)
300
301	# State history list
302	history = newdoc.createElement("history")
303	top_element.appendChild(history)
304
305	for name, value in self.state_list.iteritems():
306	history_element = newdoc.createElement('state_' + str(name))
307	for state_name,state_value in value.iteritems():
308	state_element = newdoc.createElement(str(state_name))
309	child = newdoc.createTextNode(str(state_value))
310	state_element.appendChild(child)
311	history_element.appendChild(state_element)
312	#history_element.appendChild(state_list_element)
313	history.appendChild(history_element)
314
315	# Bookmarks bookmark_list[self.bookmark_num] = [\
316	#my_time,date,state,comp_state]
317	bookmark = newdoc.createElement("bookmark")
318	top_element.appendChild(bookmark)
319	item_list = ['time','date','state','comp_state']
320	for name, value_list in self.bookmark_list.iteritems():
321	element = newdoc.createElement('mark_'+ str(name))
322	time,date,state,comp_state = value_list
323	time_element = newdoc.createElement('time')
324	time_element.appendChild(newdoc.createTextNode(str(value_list[0])))
325	date_element = newdoc.createElement('date')
326	date_element.appendChild(newdoc.createTextNode(str(value_list[1])))
327	state_list_element = newdoc.createElement('state')
328	comp_state_list_element = newdoc.createElement('comp_state')
329	for state_name, state_value in value_list[2].iteritems():
330	state_element = newdoc.createElement(str(state_name))
331	child = newdoc.createTextNode(str(state_value))
332	state_element.appendChild(child)
333	state_list_element.appendChild(state_element)
334	for comp_name, comp_value in value_list[3].iteritems():
335	comp_element = newdoc.createElement(str(comp_name))
336	comp_element.appendChild(newdoc.createTextNode(str(comp_value)))
337	comp_state_list_element.appendChild(comp_element)
338	element.appendChild(time_element)
339	element.appendChild(date_element)
340	element.appendChild(state_list_element)
341	element.appendChild(comp_state_list_element)
342	bookmark.appendChild(element)
343
344	# Save the file
345	if doc is None:
346	fd = open('test000', 'w')
347	fd.write(newdoc.toprettyxml())
348	fd.close()
349	return None
350	else:
351	return newdoc.toprettyxml()
352
353	def fromXML(self, file=None, node=None):
354	"""
355	Load invariant states from a file
356
357	: param file: .inv file
358	: param node: node of a XML document to read from
359	"""
360	if file is not None:
361	msg = "InvariantSate no longer supports non-CanSAS"
362	msg += " format for invariant files"
363	raise RuntimeError, msg
364
365	if node.get('version')\
366	and node.get('version') == '1.0':
367
368	# Get file name
369	entry = get_content('ns:filename', node)
370	if entry is not None:
371	file_name = entry.text.strip()
372
373	# Get time stamp
374	entry = get_content('ns:timestamp', node)
375	if entry is not None and entry.get('epoch'):
376	try:
377	timestamp = (entry.get('epoch'))
378	except:
379	msg = "InvariantSate.fromXML: Could not read"
380	msg += " timestamp\n %s" % sys.exc_value
381	logging.error(msg)
382
383	# Parse bookmarks
384	entry_bookmark = get_content('ns:bookmark', node)
385
386	for ind in range(1, len(entry_bookmark) + 1):
387	temp_state = {}
388	temp_bookmark = {}
389	entry = get_content('ns:mark_%s' % ind, entry_bookmark)
390
391	if entry is not None:
392	time = get_content('ns:time', entry)
393	val_time = str(time.text.strip())
394	date = get_content('ns:date', entry)
395	val_date = str(date.text.strip())
396	state_entry = get_content('ns:state', entry)
397	for item in list:
398
399	input_field = get_content('ns:%s' % item, state_entry)
400	val = str(input_field.text.strip())
401	if input_field is not None:
402	try:
403	exec "temp_state['%s'] = %s" % (item, val)
404	except:
405	exec "temp_state['%s'] = '%s'" % (item, val)
406	comp_entry = get_content('ns:comp_state', entry)
407
408	for item in list:
409	input_field = get_content('ns:%s' % item, comp_entry)
410	val = str(input_field.text.strip())
411	if input_field is not None:
412	try:
413	exec "temp_bookmark['%s'] = %s" % (item, val)
414	except:
415	exec "temp_bookmark['%s'] = '%s'" % (item, val)
416	try:
417	cmd = "self.bookmark_list[%s] = [val_time,"
418	cmd += "val_date,temp_state,temp_bookmark]"
419	exec cmd % ind
420	except:
421	raise "missing components of bookmarks..."
422	# Parse histories
423	entry_history = get_content('ns:history', node)
424
425	for ind in range(0, len(entry_history)):
426	temp_state = {}
427	entry = get_content('ns:state_%s' % ind, entry_history)
428
429	if entry is not None:
430	for item in list:
431	input_field = get_content('ns:%s' % item, entry )
432	val = str(input_field.text.strip())
433
434	if input_field is not None:
435	try:
436	exec "temp_state['%s'] = %s" % (item, val)
437	except:
438	exec "temp_state['%s'] = '%s'" % (item, val)
439	finally:
440	exec "self.state_list['%s'] = temp_state" % ind
441	# Parse current state (ie, saved_state)
442	entry = get_content('ns:state', node)
443	if entry is not None:
444	for item in list:
445	input_field = get_content('ns:%s' % item, entry)
446	val = str(input_field.text.strip())
447	if input_field is not None:
448	self.set_saved_state(name=item, value=val)
449	self.file = file_name
450
451	def set_report_string(self):
452	"""
453	Get the values (strings) from __str__ for report
454	"""
455	strings = self.__str__()
456
457	# default string values
458	for num in range (1, 19):
459	exec "s_%s = 'NA'" % str(num)
460	lines = strings.split('\n')
461	# get all string values from __str__()
462	for line in range(0, len(lines)):
463	if line == 1:
464	s_1 = lines[1]
465	elif line == 2:
466	s_2 = lines[2]
467	else:
468	item = lines[line].split(':')
469	item[0] = item[0].strip()
470	if item[0] == "scale":
471	s_3 = item[1]
472	elif item[0] == "porod constant":
473	s_4 = item[1]
474	elif item[0] == "background":
475	s_5 = item[1]
476	elif item[0] == "contrast":
477	s_6 = item[1]
478	elif item[0] == "Extrapolation":
479	extra = item[1].split(";")
480	bool_0 = extra[0].split("=")
481	bool_1 = extra[1].split("=")
482	s_8 = " " + bool_0[0] + "Q region = " + bool_0[1]
483	s_7 = " " + bool_1[0] + "Q region = " + bool_1[1]
484	elif item[0] == "npts low":
485	s_9 = item[1]
486	elif item[0] == "npts high":
487	s_10 = item[1]
488	elif item[0] == "volume fraction":
489	val=item[1].split("+-")[0].strip()
490	error = item[1].split("+-")[1].strip()
491	s_17 = val + " ± " + error
492	elif item[0] == "specific surface":
493	val = item[1].split("+-")[0].strip()
494	error = item[1].split("+-")[1].strip()
495	s_18 = val + " ± " + error
496	elif item[0].split("(")[0].strip() == "power low":
497	s_11 = item[0]+" ="+item[1]
498	elif item[0].split("(")[0].strip() == "power high":
499	s_12 = item[0]+" ="+item[1]
500	elif item[0].split("[")[0].strip() == "Q* from low Q extrapolation":
501	#looks messy but this way the symbols +_ and % work on html
502	val = item[1].split("+-")[0].strip()
503	error = item[1].split("+-")[1].strip()
504	err = error.split("%")[0].strip()
505	percent = error.split("%")[1].strip()
506	s_13 = val + " ± " + err + "&#37" + percent
507	elif item[0].split("[")[0].strip() == "Q* from data":
508	val = item[1].split("+-")[0].strip()
509	error = item[1].split("+-")[1].strip()
510	err = error.split("%")[0].strip()
511	percent = error.split("%")[1].strip()
512	s_14 = val + " ± " + err + "&#37" + percent
513	elif item[0].split("[")[0].strip() == "Q* from high Q extrapolation":
514	val = item[1].split("+-")[0].strip()
515	error = item[1].split("+-")[1].strip()
516	err = error.split("%")[0].strip()
517	percent = error.split("%")[1].strip()
518	s_15 = val + " ± " + err + "&#37" + percent
519	elif item[0].split("[")[0].strip() == "total Q*":
520	val = item[1].split("+-")[0].strip()
521	error = item[1].split("+-")[1].strip()
522	s_16 = val + " ± " + error
523	else:
524	continue
525
526	# make plot image
527	self.set_plot_state(extra_high=bool_0[1],extra_low=bool_1[1])
528	# get ready for report with setting all the html strings
529	self.report_str = str(self.template_str) % (s_1, s_2,
530	s_3, s_4, s_5, s_6, s_7, s_8,
531	s_9, s_10, s_11, s_12, s_13, s_14, s_15,
532	s_16, s_17, s_18, self.file, "%s")
533
534	def set_saved_state(self, name, value):
535	"""
536	Set the state list
537
538	: param name: name of the state component
539	: param value: value of the state component
540	"""
541	rb_list = [['power_law_low','guinier'],
542	['fit_enable_low','fix_enable_low'],
543	['fit_enable_high','fix_enable_high']]
544
545	try:
546	if value == None or value.lstrip().rstrip() == '':
547	exec "self.%s = '%s'" % (name, value)
548	exec "self.saved_state['%s'] = '%s'" % (name, value)
549	else:
550	exec 'self.%s = %s' % (name, value)
551	exec "self.saved_state['%s'] = %s" % (name, value)
552	# set the count part of radio button clicked
553	# False for the saved_state
554	for title, content in rb_list:
555	if name == title:
556	name = content
557	value = False
558	elif name == content:
559	name = title
560	value = False
561	exec "self.saved_state['%s'] = '%s'" % (name, value)
562	self.state_num = self.saved_state['state_num']
563	except:
564	pass
565
566	def set_plot_state(self, extra_high=False, extra_low=False):
567	"""
568	Build image state that wx.html understand
569	by plotting, putting it into wx.FileSystem image object
570
571	: extrap_high,extra_low: low/high extrapolations
572	are possible extra-plots
573	"""
574	# some imports
575	import wx
576	import matplotlib.pyplot as plt
577	from matplotlib.backends.backend_agg import FigureCanvasAgg
578
579	#we use simple plot, not plotpanel
580	#make matlab figure
581	fig = plt.figure()
582	fig.set_facecolor('w')
583	graph = fig.add_subplot(111)
584
585	#data plot
586	graph.errorbar(self.data.x, self.data.y, yerr=self.data.dy, fmt='o')
587	#low Q extrapolation fit plot
588	if not extra_low == 'False':
589	graph.plot(self.theory_lowQ.x,self.theory_lowQ.y)
590	#high Q extrapolation fit plot
591	if not extra_high == 'False':
592	graph.plot(self.theory_highQ.x,self.theory_highQ.y)
593	graph.set_xscale("log", nonposx='clip')
594	graph.set_yscale("log", nonposy='clip')
595	graph.set_xlabel('$\\rm{Q}(\\AA^{-1})$', fontsize = 12)
596	graph.set_ylabel('$\\rm{Intensity}(cm^{-1})$', fontsize = 12)
597	canvas = FigureCanvasAgg(fig)
598	#actually make image
599	canvas.draw()
600
601	#make python.Image object
602	#size
603	w, h = canvas.get_width_height()
604	#convert to wx.Image
605	wximg = wx.EmptyImage(w,h)
606	#wxim.SetData(img.convert('RGB').tostring() )
607	wximg.SetData(canvas.tostring_rgb())
608	#get the dynamic image for the htmlwindow
609	wximgbmp = wx.BitmapFromImage(wximg)
610	#store the image in wx.FileSystem Object
611	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
612	# use wx.MemoryFSHandler
613	self.imgRAM = wx.MemoryFSHandler()
614	#AddFile, image can be retrieved with 'memory:filename'
615	self.imgRAM.AddFile('img_inv.png', wximgbmp, wx.BITMAP_TYPE_PNG)
616
617	self.wximgbmp = 'memory:img_inv.png'
618	self.image = fig
619
620	class Reader(CansasReader):
621	"""
622	Class to load a .inv invariant file
623	"""
624	## File type
625	type_name = "Invariant"
626
627	## Wildcards
628	type = ["Invariant file (.inv)\|.inv",
629	"SANSView file (.svs)\|.svs"]
630	## List of allowed extensions
631	ext = ['.inv', '.INV', '.svs', 'SVS']
632
633	def __init__(self, call_back, cansas=True):
634	"""
635	Initialize the call-back method to be called
636	after we load a file
637
638	: param call_back: call-back method
639	: param cansas: True = files will be written/read in CanSAS format
640	False = write CanSAS format
641	"""
642	## Call back method to be executed after a file is read
643	self.call_back = call_back
644	## CanSAS format flag
645	self.cansas = cansas
646
647	def read(self, path):
648	"""
649	Load a new invariant state from file
650
651	: param path: file path
652	: return: None
653	"""
654	if self.cansas == True:
655	return self._read_cansas(path)
656	else:
657	return self._read_standalone(path)
658
659	def _read_standalone(self, path):
660	"""
661	Load a new invariant state from file.
662	The invariant node is assumed to be the top element.
663
664	: param path: file path
665	: return: None
666	"""
667	# Read the new state from file
668	state = InvariantState()
669
670	state.fromXML(file=path)
671
672	# Call back to post the new state
673	self.call_back(state)
674	return None
675
676	def _parse_state(self, entry):
677	"""
678	Read an invariant result from an XML node
679
680	: param entry: XML node to read from
681	: return: InvariantState object
682	"""
683	state = None
684	# Locate the invariant node
685	try:
686	nodes = entry.xpath('ns:%s' % INVNODE_NAME,
687	namespaces={'ns': CANSAS_NS})
688	# Create an empty state
689	if nodes != []:
690	state = InvariantState()
691	state.fromXML(node=nodes[0])
692	except:
693	msg = "XML document does not contain invariant"
694	msg += " information.\n %s" % sys.exc_value
695	logging.info(msg)
696	return state
697
698	def _read_cansas(self, path):
699	"""
700	Load data and invariant information from a CanSAS XML file.
701
702	: param path: file path
703	: return: Data1D object if a single SASentry was found,
704	or a list of Data1D objects if multiple entries were found,
705	or None of nothing was found
706	: raise RuntimeError: when the file can't be opened
707	: raise ValueError: when the length of the data vectors are inconsistent
708	"""
709	output = []
710	if os.path.isfile(path):
711	basename = os.path.basename(path)
712	root, extension = os.path.splitext(basename)
713
714	if extension.lower() in self.ext or \
715	extension.lower() == '.xml':
716	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
717
718	# Check the format version number
719	# Specifying the namespace will take care of
720	# the file format version
721	root = tree.getroot()
722
723	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
724	namespaces={'ns': CANSAS_NS})
725
726	for entry in entry_list:
727
728	sas_entry = self._parse_entry(entry)
729	invstate = self._parse_state(entry)
730
731	#invstate could be None when .svs file is loaded
732	#in this case, skip appending to output
733	if invstate != None:
734	sas_entry.meta_data['invstate'] = invstate
735	sas_entry.filename = invstate.file
736	output.append(sas_entry)
737	else:
738	raise RuntimeError, "%s is not a file" % path
739
740	# Return output consistent with the loader's api
741	if len(output) == 0:
742	return None
743	elif len(output) == 1:
744	# Call back to post the new state
745
746	self.call_back(state=output[0].meta_data['invstate'],
747	datainfo = output[0])
748	return output[0]
749	else:
750	return output
751
752
753	def write(self, filename, datainfo=None, invstate=None):
754	"""
755	Write the content of a Data1D as a CanSAS XML file
756
757	: param filename: name of the file to write
758	: param datainfo: Data1D object
759	: param invstate: InvariantState object
760	"""
761	# Sanity check
762	if self.cansas == True:
763	doc = self.write_toXML(datainfo,invstate)
764	# Write the XML document
765	fd = open(filename, 'w')
766	fd.write(doc.toprettyxml())
767	fd.close()
768	else:
769	invstate.toXML(file=filename)
770
771	def write_toXML(self, datainfo=None, state=None):
772	"""
773	Write toXML, a helper for write()
774
775	: return: xml doc
776	"""
777	if datainfo is None:
778	datainfo = DataLoader.data_info.Data1D(x=[], y=[])
779	elif not issubclass(datainfo.__class__, DataLoader.data_info.Data1D):
780	msg = "The cansas writer expects a Data1D"
781	msg += " instance: %s" % str(datainfo.__class__.__name__)
782	raise RuntimeError, msg
783	#make sure title and data run is filled up.
784	if datainfo.title == None or datainfo.title == '':
785	datainfo.title = datainfo.name
786	if datainfo.run_name == None or datainfo.run_name == {}:
787	datainfo.run = [str(datainfo.name)]
788	datainfo.run_name[0] = datainfo.name
789	# Create basic XML document
790	doc, sasentry = self._to_xml_doc(datainfo)
791	# Add the invariant information to the XML document
792	if state is not None:
793	state.toXML(datainfo.name,doc=doc, entry_node=sasentry)
794	return doc
795

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SasView

source: sasview/invariantview/perspectives/invariant/invariant_state.py @ 3cd5806

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