invariant_state.py @ c4ae1c2

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 c4ae1c2 was 4d29952, checked in by Gervaise Alina <gervyh@…>, 13 years ago
remove reference to theory1D
Property mode set to `100644`
File size: 32.8 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.gui_style import GUIFRAME_ID
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 = Data1D(x=[], y=[], dy=None)
91	self.theory_lowQ.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
92	self.theory_highQ = Data1D(x=[], y=[], dy=None)
93	self.theory_highQ.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
94	#self.is_time_machine = False
95	self.saved_state = list
96	self.state_list = state_list
97	self.bookmark_list = bookmark_list
98	self.input_list = input_list
99	self.output_list = output_list
100
101	self.compute_num = 0
102	self.state_num = 0
103	self.timestamp = ('00:00:00', '00/00/0000')
104	self.container = None
105	#plot image
106	self.wximbmp = None
107	# report_html strings
108	import sans.perspectives.invariant as invariant
109	path = invariant.get_data_path(media='media')
110	path_report_html = os.path.join(path,"report_template.html")
111	html_template = open(path_report_html,"r")
112	self.template_str = html_template.read()
113	self.report_str = self.template_str
114	#self.report_str_save = None
115	html_template.close()
116
117	def __str__(self):
118	"""
119	Pretty print
120
121	: return: string representing the state
122	"""
123	# Input string
124	compute_num = self.saved_state['compute_num']
125	compute_state = self.state_list[str(compute_num)]
126	my_time, date = self.timestamp
127	file_name = self.file
128
129	state_num = int(self.saved_state['state_num'])
130	state = "\n[Invariant computation for %s: " % file_name
131	state += "performed at %s on %s] \n" % (my_time, date)
132	state += "State No.: %d \n" % state_num
133	state += "\n=== Inputs ===\n"
134
135	# text ctl general inputs ( excluding extrapolation text ctl)
136	for key, value in self.input_list.iteritems():
137	if value == '':
138	continue
139	key_split = key.split('_')
140	max_ind = len(key_split)-1
141	if key_split[max_ind] == 'tcl':
142	name = ""
143	if key_split[1] == 'low' or key_split[1] == 'high':
144	continue
145	for ind in range(0, max_ind):
146	name += " %s" % key_split[ind]
147	state += "%s: %s\n" % (name.lstrip(" "), value)
148
149	# other input parameters
150	extra_lo = compute_state['enable_low_cbox']
151	if compute_state['enable_low_cbox']:
152	if compute_state['guinier']:
153	extra_lo = 'Guinier'
154	else:
155	extra_lo = 'Power law'
156	extra_hi = compute_state['enable_high_cbox']
157	if compute_state['enable_high_cbox']:
158	extra_hi = 'Power law'
159	state += "\nExtrapolation: High=%s; Low=%s\n" %(extra_hi, extra_lo)
160	low_off = False
161	high_off = False
162	for key, value in self.input_list.iteritems():
163	key_split = key.split('_')
164	max_ind = len(key_split) - 1
165	if key_split[max_ind] == 'tcl':
166	name = ""
167	# check each buttons whether or not ON or OFF
168	if key_split[1] == 'low' or key_split[1] == 'high':
169	if not compute_state['enable_low_cbox'] and \
170	key_split[max_ind-1] == 'low':
171	low_off = True
172	continue
173	elif not compute_state['enable_high_cbox'] and \
174	key_split[max_ind-1] == 'high':
175	high_off = True
176	continue
177	elif extra_lo == 'Guinier' and key_split[0] == 'power' and \
178	key_split[max_ind-1] == 'low':
179	continue
180	for ind in range(0, max_ind):
181	name += " %s" % key_split[ind]
182	name = name.lstrip(" ")
183	if name == "power low" :
184	if compute_state['fix_enable_low']:
185	name += ' (Fixed)'
186	else:
187	name += ' (Fitted)'
188	if name == "power high" :
189	if compute_state['fix_enable_high']:
190	name += ' (Fixed)'
191	else:
192	name += ' (Fitted)'
193	state += "%s: %s\n" % (name, value)
194	# Outputs
195	state += "\n=== Outputs ==="
196	for item in output_list:
197	item_split = item[0].split('_')
198	# Exclude the extrapolation that turned off
199	if len(item_split) > 1:
200	if low_off and item_split[1] == 'low':
201	continue
202	if high_off and item_split[1] == 'high':
203	continue
204	max_ind = len(item_split) - 1
205	value = None
206	try:
207	# Q* outputs
208	exec "value = self.container.%s\n" % item[0]
209	except:
210	# other outputs than Q*
211	name = item[0] + "_tcl"
212	if name in self.saved_state.keys():
213	exec "value = self.saved_state['%s']" % name
214
215	# Exclude the outputs w/''
216	if value == '':
217	continue
218	# Error outputs
219	if item_split[max_ind] == 'err':
220	state += "+- %s " % format_number(value)
221	# Percentage outputs
222	elif item_split[max_ind] == 'percent':
223	try:
224	value = float(value) * 100
225	except:
226	pass
227	state += "(%s %s)" % (format_number(value), '%')
228	# Outputs
229	else:
230	state += "\n%s: %s " % (item[1],
231	format_number(value, high=True))
232	# Include warning msg
233	if self.container is not None:
234	state += "\n\nNote:\n" + self.container.warning_msg
235	return state
236
237	def clone_state(self):
238	"""
239	deepcopy the state
240	"""
241	return copy.deepcopy(self.saved_state)
242
243	def toXML(self, file="inv_state.inv", doc=None, entry_node=None):
244	"""
245	Writes the state of the InversionControl panel to file, as XML.
246
247	Compatible with standalone writing, or appending to an
248	already existing XML document. In that case, the XML document
249	is required. An optional entry node in the XML document
250	may also be given.
251
252	: param file: file to write to
253	: param doc: XML document object [optional]
254	: param entry_node: XML node within the XML document at which
255	we will append the data [optional]
256	"""
257	from xml.dom.minidom import getDOMImplementation
258	import time
259	timestamp = time.time()
260	# Check whether we have to write a standalone XML file
261	if doc is None:
262	impl = getDOMImplementation()
263
264	doc_type = impl.createDocumentType(INVNODE_NAME, "1.0", "1.0")
265
266	newdoc = impl.createDocument(None, INVNODE_NAME, doc_type)
267	top_element = newdoc.documentElement
268	else:
269	# We are appending to an existing document
270	newdoc = doc
271	top_element = newdoc.createElement(INVNODE_NAME)
272	if entry_node is None:
273	newdoc.documentElement.appendChild(top_element)
274	else:
275	entry_node.appendChild(top_element)
276
277	attr = newdoc.createAttribute("version")
278	attr.nodeValue = '1.0'
279	top_element.setAttributeNode(attr)
280
281	# File name
282	element = newdoc.createElement("filename")
283	if self.file != None and self.file != '':
284	element.appendChild(newdoc.createTextNode(str(self.file)))
285	else:
286	element.appendChild(newdoc.createTextNode(str(file)))
287	top_element.appendChild(element)
288
289	element = newdoc.createElement("timestamp")
290	element.appendChild(newdoc.createTextNode(time.ctime(timestamp)))
291	attr = newdoc.createAttribute("epoch")
292	attr.nodeValue = str(timestamp)
293	element.setAttributeNode(attr)
294	top_element.appendChild(element)
295
296	# Current state
297	state = newdoc.createElement("state")
298	top_element.appendChild(state)
299
300	for name,value in self.saved_state.iteritems():
301	element = newdoc.createElement(str(name))
302	element.appendChild(newdoc.createTextNode(str(value)))
303	state.appendChild(element)
304
305	# State history list
306	history = newdoc.createElement("history")
307	top_element.appendChild(history)
308
309	for name, value in self.state_list.iteritems():
310	history_element = newdoc.createElement('state_' + str(name))
311	for state_name,state_value in value.iteritems():
312	state_element = newdoc.createElement(str(state_name))
313	child = newdoc.createTextNode(str(state_value))
314	state_element.appendChild(child)
315	history_element.appendChild(state_element)
316	#history_element.appendChild(state_list_element)
317	history.appendChild(history_element)
318
319	# Bookmarks bookmark_list[self.bookmark_num] = [\
320	#my_time,date,state,comp_state]
321	bookmark = newdoc.createElement("bookmark")
322	top_element.appendChild(bookmark)
323	item_list = ['time','date','state','comp_state']
324	for name, value_list in self.bookmark_list.iteritems():
325	element = newdoc.createElement('mark_'+ str(name))
326	_,date,state,comp_state = value_list
327	time_element = newdoc.createElement('time')
328	time_element.appendChild(newdoc.createTextNode(str(value_list[0])))
329	date_element = newdoc.createElement('date')
330	date_element.appendChild(newdoc.createTextNode(str(value_list[1])))
331	state_list_element = newdoc.createElement('state')
332	comp_state_list_element = newdoc.createElement('comp_state')
333	for state_name, state_value in value_list[2].iteritems():
334	state_element = newdoc.createElement(str(state_name))
335	child = newdoc.createTextNode(str(state_value))
336	state_element.appendChild(child)
337	state_list_element.appendChild(state_element)
338	for comp_name, comp_value in value_list[3].iteritems():
339	comp_element = newdoc.createElement(str(comp_name))
340	comp_element.appendChild(newdoc.createTextNode(str(comp_value)))
341	comp_state_list_element.appendChild(comp_element)
342	element.appendChild(time_element)
343	element.appendChild(date_element)
344	element.appendChild(state_list_element)
345	element.appendChild(comp_state_list_element)
346	bookmark.appendChild(element)
347
348	# Save the file
349	if doc is None:
350	fd = open('test000', 'w')
351	fd.write(newdoc.toprettyxml())
352	fd.close()
353	return None
354	else:
355	return newdoc.toprettyxml()
356
357	def fromXML(self, file=None, node=None):
358	"""
359	Load invariant states from a file
360
361	: param file: .inv file
362	: param node: node of a XML document to read from
363	"""
364	if file is not None:
365	msg = "InvariantSate no longer supports non-CanSAS"
366	msg += " format for invariant files"
367	raise RuntimeError, msg
368
369	if node.get('version')\
370	and node.get('version') == '1.0':
371
372	# Get file name
373	entry = get_content('ns:filename', node)
374	if entry is not None:
375	file_name = entry.text.strip()
376
377	# Get time stamp
378	entry = get_content('ns:timestamp', node)
379	if entry is not None and entry.get('epoch'):
380	try:
381	timestamp = (entry.get('epoch'))
382	except:
383	msg = "InvariantSate.fromXML: Could not read"
384	msg += " timestamp\n %s" % sys.exc_value
385	logging.error(msg)
386
387	# Parse bookmarks
388	entry_bookmark = get_content('ns:bookmark', node)
389
390	for ind in range(1, len(entry_bookmark) + 1):
391	temp_state = {}
392	temp_bookmark = {}
393	entry = get_content('ns:mark_%s' % ind, entry_bookmark)
394
395	if entry is not None:
396	my_time = get_content('ns:time', entry)
397	val_time = str(my_time.text.strip())
398	date = get_content('ns:date', entry)
399	val_date = str(date.text.strip())
400	state_entry = get_content('ns:state', entry)
401	for item in list:
402
403	input_field = get_content('ns:%s' % item, state_entry)
404	val = str(input_field.text.strip())
405	if input_field is not None:
406	try:
407	exec "temp_state['%s'] = %s" % (item, val)
408	except:
409	exec "temp_state['%s'] = '%s'" % (item, val)
410	comp_entry = get_content('ns:comp_state', entry)
411
412	for item in list:
413	input_field = get_content('ns:%s' % item, comp_entry)
414	val = str(input_field.text.strip())
415	if input_field is not None:
416	try:
417	exec "temp_bookmark['%s'] = %s" % (item, val)
418	except:
419	exec "temp_bookmark['%s'] = '%s'" % (item, val)
420	try:
421	cmd = "self.bookmark_list[%s] = [val_time,"
422	cmd += "val_date,temp_state,temp_bookmark]"
423	exec cmd % ind
424	except:
425	raise "missing components of bookmarks..."
426	# Parse histories
427	entry_history = get_content('ns:history', node)
428
429	for ind in range(0, len(entry_history)):
430	temp_state = {}
431	entry = get_content('ns:state_%s' % ind, entry_history)
432
433	if entry is not None:
434	for item in list:
435	input_field = get_content('ns:%s' % item, entry )
436	val = str(input_field.text.strip())
437
438	if input_field is not None:
439	try:
440	exec "temp_state['%s'] = %s" % (item, val)
441	except:
442	exec "temp_state['%s'] = '%s'" % (item, val)
443	finally:
444	exec "self.state_list['%s'] = temp_state" % ind
445	# Parse current state (ie, saved_state)
446	entry = get_content('ns:state', node)
447	if entry is not None:
448	for item in list:
449	input_field = get_content('ns:%s' % item, entry)
450	val = str(input_field.text.strip())
451	if input_field is not None:
452	self.set_saved_state(name=item, value=val)
453	self.file = file_name
454
455	def set_report_string(self):
456	"""
457	Get the values (strings) from __str__ for report
458	"""
459	strings = self.__str__()
460
461	# default string values
462	for num in range (1, 19):
463	exec "s_%s = 'NA'" % str(num)
464	lines = strings.split('\n')
465	# get all string values from __str__()
466	for line in range(0, len(lines)):
467	if line == 1:
468	s_1 = lines[1]
469	elif line == 2:
470	s_2 = lines[2]
471	else:
472	item = lines[line].split(':')
473	item[0] = item[0].strip()
474	if item[0] == "scale":
475	s_3 = item[1]
476	elif item[0] == "porod constant":
477	s_4 = item[1]
478	elif item[0] == "background":
479	s_5 = item[1]
480	elif item[0] == "contrast":
481	s_6 = item[1]
482	elif item[0] == "Extrapolation":
483	extra = item[1].split(";")
484	bool_0 = extra[0].split("=")
485	bool_1 = extra[1].split("=")
486	s_8 = " " + bool_0[0] + "Q region = " + bool_0[1]
487	s_7 = " " + bool_1[0] + "Q region = " + bool_1[1]
488	elif item[0] == "npts low":
489	s_9 = item[1]
490	elif item[0] == "npts high":
491	s_10 = item[1]
492	elif item[0] == "volume fraction":
493	val=item[1].split("+-")[0].strip()
494	error = item[1].split("+-")[1].strip()
495	s_17 = val + " ± " + error
496	elif item[0] == "specific surface":
497	val = item[1].split("+-")[0].strip()
498	error = item[1].split("+-")[1].strip()
499	s_18 = val + " ± " + error
500	elif item[0].split("(")[0].strip() == "power low":
501	s_11 = item[0]+" ="+item[1]
502	elif item[0].split("(")[0].strip() == "power high":
503	s_12 = item[0]+" ="+item[1]
504	elif item[0].split("[")[0].strip() == "Q* from low Q extrapolation":
505	#looks messy but this way the symbols +_ and % work on html
506	val = item[1].split("+-")[0].strip()
507	error = item[1].split("+-")[1].strip()
508	err = error.split("%")[0].strip()
509	percent = error.split("%")[1].strip()
510	s_13 = val + " ± " + err + "&#37" + percent
511	elif item[0].split("[")[0].strip() == "Q* from data":
512	val = item[1].split("+-")[0].strip()
513	error = item[1].split("+-")[1].strip()
514	err = error.split("%")[0].strip()
515	percent = error.split("%")[1].strip()
516	s_14 = val + " ± " + err + "&#37" + percent
517	elif item[0].split("[")[0].strip() == "Q* from high Q extrapolation":
518	val = item[1].split("+-")[0].strip()
519	error = item[1].split("+-")[1].strip()
520	err = error.split("%")[0].strip()
521	percent = error.split("%")[1].strip()
522	s_15 = val + " ± " + err + "&#37" + percent
523	elif item[0].split("[")[0].strip() == "total Q*":
524	val = item[1].split("+-")[0].strip()
525	error = item[1].split("+-")[1].strip()
526	s_16 = val + " ± " + error
527	else:
528	continue
529
530	s_1 = self._check_html_format(s_1)
531	file_name = self._check_html_format(self.file)
532
533	# make plot image
534	self.set_plot_state(extra_high=bool_0[1],extra_low=bool_1[1])
535	# get ready for report with setting all the html strings
536	self.report_str = str(self.template_str) % (s_1, s_2,
537	s_3, s_4, s_5, s_6, s_7, s_8,
538	s_9, s_10, s_11, s_12, s_13, s_14, s_15,
539	s_16, s_17, s_18, file_name, "%s")
540
541	def _check_html_format(self, name):
542	"""
543	Check string '%' for html format
544	"""
545	if name.count('%'):
546	name = name.replace('%', '&#37')
547
548	return name
549
550	def set_saved_state(self, name, value):
551	"""
552	Set the state list
553
554	: param name: name of the state component
555	: param value: value of the state component
556	"""
557	rb_list = [['power_law_low','guinier'],
558	['fit_enable_low','fix_enable_low'],
559	['fit_enable_high','fix_enable_high']]
560
561	try:
562	if value == None or value.lstrip().rstrip() == '':
563	exec "self.%s = '%s'" % (name, value)
564	exec "self.saved_state['%s'] = '%s'" % (name, value)
565	else:
566	exec 'self.%s = %s' % (name, value)
567	exec "self.saved_state['%s'] = %s" % (name, value)
568	# set the count part of radio button clicked
569	# False for the saved_state
570	for title, content in rb_list:
571	if name == title:
572	name = content
573	value = False
574	elif name == content:
575	name = title
576	value = False
577	exec "self.saved_state['%s'] = '%s'" % (name, value)
578	self.state_num = self.saved_state['state_num']
579	except:
580	pass
581
582	def set_plot_state(self, extra_high=False, extra_low=False):
583	"""
584	Build image state that wx.html understand
585	by plotting, putting it into wx.FileSystem image object
586
587	: extrap_high,extra_low: low/high extrapolations
588	are possible extra-plots
589	"""
590	# some imports
591	import wx
592	import matplotlib.pyplot as plt
593	from matplotlib.backends.backend_agg import FigureCanvasAgg
594
595	#we use simple plot, not plotpanel
596	#make matlab figure
597	fig = plt.figure()
598	fig.set_facecolor('w')
599	graph = fig.add_subplot(111)
600
601	#data plot
602	graph.errorbar(self.data.x, self.data.y, yerr=self.data.dy, fmt='o')
603	#low Q extrapolation fit plot
604	if not extra_low == 'False':
605	graph.plot(self.theory_lowQ.x,self.theory_lowQ.y)
606	#high Q extrapolation fit plot
607	if not extra_high == 'False':
608	graph.plot(self.theory_highQ.x,self.theory_highQ.y)
609	graph.set_xscale("log", nonposx='clip')
610	graph.set_yscale("log", nonposy='clip')
611	graph.set_xlabel('$\\rm{Q}(\\AA^{-1})$', fontsize = 12)
612	graph.set_ylabel('$\\rm{Intensity}(cm^{-1})$', fontsize = 12)
613	canvas = FigureCanvasAgg(fig)
614	#actually make image
615	canvas.draw()
616
617	#make python.Image object
618	#size
619	w, h = canvas.get_width_height()
620	#convert to wx.Image
621	wximg = wx.EmptyImage(w,h)
622	#wxim.SetData(img.convert('RGB').tostring() )
623	wximg.SetData(canvas.tostring_rgb())
624	#get the dynamic image for the htmlwindow
625	wximgbmp = wx.BitmapFromImage(wximg)
626	#store the image in wx.FileSystem Object
627	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
628	# use wx.MemoryFSHandler
629	self.imgRAM = wx.MemoryFSHandler()
630	#AddFile, image can be retrieved with 'memory:filename'
631	self.imgRAM.AddFile('img_inv.png', wximgbmp, wx.BITMAP_TYPE_PNG)
632
633	self.wximgbmp = 'memory:img_inv.png'
634	self.image = fig
635
636	class Reader(CansasReader):
637	"""
638	Class to load a .inv invariant file
639	"""
640	## File type
641	type_name = "Invariant"
642
643	## Wildcards
644	type = ["Invariant file (.inv)\|.inv",
645	"SANSView file (.svs)\|.svs"]
646	## List of allowed extensions
647	ext = ['.inv', '.INV', '.svs', 'SVS']
648
649	def __init__(self, call_back, cansas=True):
650	"""
651	Initialize the call-back method to be called
652	after we load a file
653
654	: param call_back: call-back method
655	: param cansas: True = files will be written/read in CanSAS format
656	False = write CanSAS format
657	"""
658	## Call back method to be executed after a file is read
659	self.call_back = call_back
660	## CanSAS format flag
661	self.cansas = cansas
662	self.state = None
663
664	def read(self, path):
665	"""
666	Load a new invariant state from file
667
668	: param path: file path
669	: return: None
670	"""
671	if self.cansas == True:
672	return self._read_cansas(path)
673	else:
674	return self._read_standalone(path)
675
676	def _read_standalone(self, path):
677	"""
678	Load a new invariant state from file.
679	The invariant node is assumed to be the top element.
680
681	: param path: file path
682	: return: None
683	"""
684	# Read the new state from file
685	state = InvariantState()
686
687	state.fromXML(file=path)
688
689	# Call back to post the new state
690	self.call_back(state)
691	return None
692
693	def _parse_state(self, entry):
694	"""
695	Read an invariant result from an XML node
696
697	: param entry: XML node to read from
698	: return: InvariantState object
699	"""
700	state = None
701	# Locate the invariant node
702	try:
703	nodes = entry.xpath('ns:%s' % INVNODE_NAME,
704	namespaces={'ns': CANSAS_NS})
705	# Create an empty state
706	if nodes != []:
707	state = InvariantState()
708	state.fromXML(node=nodes[0])
709	except:
710	msg = "XML document does not contain invariant"
711	msg += " information.\n %s" % sys.exc_value
712	logging.info(msg)
713	return state
714
715	def _read_cansas(self, path):
716	"""
717	Load data and invariant information from a CanSAS XML file.
718
719	: param path: file path
720	: return: Data1D object if a single SASentry was found,
721	or a list of Data1D objects if multiple entries were found,
722	or None of nothing was found
723	: raise RuntimeError: when the file can't be opened
724	: raise ValueError: when the length of the data vectors are inconsistent
725	"""
726	output = []
727	if os.path.isfile(path):
728	basename = os.path.basename(path)
729	root, extension = os.path.splitext(basename)
730
731	if extension.lower() in self.ext or \
732	extension.lower() == '.xml':
733	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
734
735	# Check the format version number
736	# Specifying the namespace will take care of
737	# the file format version
738	root = tree.getroot()
739
740	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
741	namespaces={'ns': CANSAS_NS})
742
743	for entry in entry_list:
744
745	sas_entry = self._parse_entry(entry)
746	invstate = self._parse_state(entry)
747
748	#invstate could be None when .svs file is loaded
749	#in this case, skip appending to output
750	if invstate != None:
751	sas_entry.meta_data['invstate'] = invstate
752	sas_entry.filename = invstate.file
753	output.append(sas_entry)
754	else:
755	raise RuntimeError, "%s is not a file" % path
756
757	# Return output consistent with the loader's api
758	if len(output) == 0:
759	return None
760	elif len(output) == 1:
761	# Call back to post the new state
762	self.state = output[0].meta_data['invstate']
763	self.call_back(state=output[0].meta_data['invstate'],
764	datainfo = output[0])
765	return output[0]
766	else:
767	return output
768
769	def get_state(self):
770	return self.state
771
772	def write(self, filename, datainfo=None, invstate=None):
773	"""
774	Write the content of a Data1D as a CanSAS XML file
775
776	: param filename: name of the file to write
777	: param datainfo: Data1D object
778	: param invstate: InvariantState object
779	"""
780	# Sanity check
781	if self.cansas == True:
782	doc = self.write_toXML(datainfo,invstate)
783	# Write the XML document
784	fd = open(filename, 'w')
785	fd.write(doc.toprettyxml())
786	fd.close()
787	else:
788	invstate.toXML(file=filename)
789
790	def write_toXML(self, datainfo=None, state=None):
791	"""
792	Write toXML, a helper for write()
793
794	: return: xml doc
795	"""
796	if datainfo is None:
797	datainfo = sans.dataloader.data_info.Data1D(x=[], y=[])
798	elif not issubclass(datainfo.__class__, sans.dataloader.data_info.Data1D):
799	msg = "The cansas writer expects a Data1D"
800	msg += " instance: %s" % str(datainfo.__class__.__name__)
801	raise RuntimeError, msg
802	#make sure title and data run is filled up.
803	if datainfo.title == None or datainfo.title == '':
804	datainfo.title = datainfo.name
805	if datainfo.run_name == None or datainfo.run_name == {}:
806	datainfo.run = [str(datainfo.name)]
807	datainfo.run_name[0] = datainfo.name
808	# Create basic XML document
809	doc, sasentry = self._to_xml_doc(datainfo)
810	# Add the invariant information to the XML document
811	if state is not None:
812	state.toXML(datainfo.name,doc=doc, entry_node=sasentry)
813	return doc
814

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SasView

source: sasview/invariantview/src/sans/perspectives/invariant/invariant_state.py @ c4ae1c2

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