invariant_state.py @ 18c8c3d

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 18c8c3d was 51f14603, checked in by Peter Parker, 11 years ago
Refs #202 - Fix Sphinx build errors (not including park-1.2.1/). Most warnings remain.
Property mode set to `100644`
File size: 32.0 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 we will append the data [optional]
255	"""
256	from xml.dom.minidom import getDOMImplementation
257	import time
258	timestamp = time.time()
259	# Check whether we have to write a standalone XML file
260	if doc is None:
261	impl = getDOMImplementation()
262
263	doc_type = impl.createDocumentType(INVNODE_NAME, "1.0", "1.0")
264
265	newdoc = impl.createDocument(None, INVNODE_NAME, doc_type)
266	top_element = newdoc.documentElement
267	else:
268	# We are appending to an existing document
269	newdoc = doc
270	top_element = newdoc.createElement(INVNODE_NAME)
271	if entry_node is None:
272	newdoc.documentElement.appendChild(top_element)
273	else:
274	entry_node.appendChild(top_element)
275
276	attr = newdoc.createAttribute("version")
277	attr.nodeValue = '1.0'
278	top_element.setAttributeNode(attr)
279
280	# File name
281	element = newdoc.createElement("filename")
282	if self.file != None and self.file != '':
283	element.appendChild(newdoc.createTextNode(str(self.file)))
284	else:
285	element.appendChild(newdoc.createTextNode(str(file)))
286	top_element.appendChild(element)
287
288	element = newdoc.createElement("timestamp")
289	element.appendChild(newdoc.createTextNode(time.ctime(timestamp)))
290	attr = newdoc.createAttribute("epoch")
291	attr.nodeValue = str(timestamp)
292	element.setAttributeNode(attr)
293	top_element.appendChild(element)
294
295	# Current state
296	state = newdoc.createElement("state")
297	top_element.appendChild(state)
298
299	for name,value in self.saved_state.iteritems():
300	element = newdoc.createElement(str(name))
301	element.appendChild(newdoc.createTextNode(str(value)))
302	state.appendChild(element)
303
304	# State history list
305	history = newdoc.createElement("history")
306	top_element.appendChild(history)
307
308	for name, value in self.state_list.iteritems():
309	history_element = newdoc.createElement('state_' + str(name))
310	for state_name,state_value in value.iteritems():
311	state_element = newdoc.createElement(str(state_name))
312	child = newdoc.createTextNode(str(state_value))
313	state_element.appendChild(child)
314	history_element.appendChild(state_element)
315	#history_element.appendChild(state_list_element)
316	history.appendChild(history_element)
317
318	# Bookmarks bookmark_list[self.bookmark_num] = [\
319	#my_time,date,state,comp_state]
320	bookmark = newdoc.createElement("bookmark")
321	top_element.appendChild(bookmark)
322	item_list = ['time','date','state','comp_state']
323	for name, value_list in self.bookmark_list.iteritems():
324	element = newdoc.createElement('mark_'+ str(name))
325	_,date,state,comp_state = value_list
326	time_element = newdoc.createElement('time')
327	time_element.appendChild(newdoc.createTextNode(str(value_list[0])))
328	date_element = newdoc.createElement('date')
329	date_element.appendChild(newdoc.createTextNode(str(value_list[1])))
330	state_list_element = newdoc.createElement('state')
331	comp_state_list_element = newdoc.createElement('comp_state')
332	for state_name, state_value in value_list[2].iteritems():
333	state_element = newdoc.createElement(str(state_name))
334	child = newdoc.createTextNode(str(state_value))
335	state_element.appendChild(child)
336	state_list_element.appendChild(state_element)
337	for comp_name, comp_value in value_list[3].iteritems():
338	comp_element = newdoc.createElement(str(comp_name))
339	comp_element.appendChild(newdoc.createTextNode(str(comp_value)))
340	comp_state_list_element.appendChild(comp_element)
341	element.appendChild(time_element)
342	element.appendChild(date_element)
343	element.appendChild(state_list_element)
344	element.appendChild(comp_state_list_element)
345	bookmark.appendChild(element)
346
347	# Save the file
348	if doc is None:
349	fd = open('test000', 'w')
350	fd.write(newdoc.toprettyxml())
351	fd.close()
352	return None
353	else:
354	return newdoc.toprettyxml()
355
356	def fromXML(self, file=None, node=None):
357	"""
358	Load invariant states from a file
359
360	: param file: .inv file
361	: param node: node of a XML document to read from
362	"""
363	if file is not None:
364	msg = "InvariantSate no longer supports non-CanSAS"
365	msg += " format for invariant files"
366	raise RuntimeError, msg
367
368	if node.get('version')\
369	and node.get('version') == '1.0':
370
371	# Get file name
372	entry = get_content('ns:filename', node)
373	if entry is not None:
374	file_name = entry.text.strip()
375
376	# Get time stamp
377	entry = get_content('ns:timestamp', node)
378	if entry is not None and entry.get('epoch'):
379	try:
380	timestamp = (entry.get('epoch'))
381	except:
382	msg = "InvariantSate.fromXML: Could not read"
383	msg += " timestamp\n %s" % sys.exc_value
384	logging.error(msg)
385
386	# Parse bookmarks
387	entry_bookmark = get_content('ns:bookmark', node)
388
389	for ind in range(1, len(entry_bookmark) + 1):
390	temp_state = {}
391	temp_bookmark = {}
392	entry = get_content('ns:mark_%s' % ind, entry_bookmark)
393
394	if entry is not None:
395	my_time = get_content('ns:time', entry)
396	val_time = str(my_time.text.strip())
397	date = get_content('ns:date', entry)
398	val_date = str(date.text.strip())
399	state_entry = get_content('ns:state', entry)
400	for item in list:
401
402	input_field = get_content('ns:%s' % item, state_entry)
403	val = str(input_field.text.strip())
404	if input_field is not None:
405	try:
406	exec "temp_state['%s'] = %s" % (item, val)
407	except:
408	exec "temp_state['%s'] = '%s'" % (item, val)
409	comp_entry = get_content('ns:comp_state', entry)
410
411	for item in list:
412	input_field = get_content('ns:%s' % item, comp_entry)
413	val = str(input_field.text.strip())
414	if input_field is not None:
415	try:
416	exec "temp_bookmark['%s'] = %s" % (item, val)
417	except:
418	exec "temp_bookmark['%s'] = '%s'" % (item, val)
419	try:
420	cmd = "self.bookmark_list[%s] = [val_time,"
421	cmd += "val_date,temp_state,temp_bookmark]"
422	exec cmd % ind
423	except:
424	raise "missing components of bookmarks..."
425	# Parse histories
426	entry_history = get_content('ns:history', node)
427
428	for ind in range(0, len(entry_history)):
429	temp_state = {}
430	entry = get_content('ns:state_%s' % ind, entry_history)
431
432	if entry is not None:
433	for item in list:
434	input_field = get_content('ns:%s' % item, entry )
435	val = str(input_field.text.strip())
436
437	if input_field is not None:
438	try:
439	exec "temp_state['%s'] = %s" % (item, val)
440	except:
441	exec "temp_state['%s'] = '%s'" % (item, val)
442	finally:
443	exec "self.state_list['%s'] = temp_state" % ind
444	# Parse current state (ie, saved_state)
445	entry = get_content('ns:state', node)
446	if entry is not None:
447	for item in list:
448	input_field = get_content('ns:%s' % item, entry)
449	val = str(input_field.text.strip())
450	if input_field is not None:
451	self.set_saved_state(name=item, value=val)
452	self.file = file_name
453
454	def set_report_string(self):
455	"""
456	Get the values (strings) from __str__ for report
457	"""
458	strings = self.__str__()
459
460	# default string values
461	for num in range (1, 19):
462	exec "s_%s = 'NA'" % str(num)
463	lines = strings.split('\n')
464	# get all string values from __str__()
465	for line in range(0, len(lines)):
466	if line == 1:
467	s_1 = lines[1]
468	elif line == 2:
469	s_2 = lines[2]
470	else:
471	item = lines[line].split(':')
472	item[0] = item[0].strip()
473	if item[0] == "scale":
474	s_3 = item[1]
475	elif item[0] == "porod constant":
476	s_4 = item[1]
477	elif item[0] == "background":
478	s_5 = item[1]
479	elif item[0] == "contrast":
480	s_6 = item[1]
481	elif item[0] == "Extrapolation":
482	extra = item[1].split(";")
483	bool_0 = extra[0].split("=")
484	bool_1 = extra[1].split("=")
485	s_8 = " " + bool_0[0] + "Q region = " + bool_0[1]
486	s_7 = " " + bool_1[0] + "Q region = " + bool_1[1]
487	elif item[0] == "npts low":
488	s_9 = item[1]
489	elif item[0] == "npts high":
490	s_10 = item[1]
491	elif item[0] == "volume fraction":
492	val=item[1].split("+-")[0].strip()
493	error = item[1].split("+-")[1].strip()
494	s_17 = val + " ± " + error
495	elif item[0] == "specific surface":
496	val = item[1].split("+-")[0].strip()
497	error = item[1].split("+-")[1].strip()
498	s_18 = val + " ± " + error
499	elif item[0].split("(")[0].strip() == "power low":
500	s_11 = item[0]+" ="+item[1]
501	elif item[0].split("(")[0].strip() == "power high":
502	s_12 = item[0]+" ="+item[1]
503	elif item[0].split("[")[0].strip() == "Q* from low Q extrapolation":
504	#looks messy but this way the symbols +_ and % work on html
505	val = item[1].split("+-")[0].strip()
506	error = item[1].split("+-")[1].strip()
507	err = error.split("%")[0].strip()
508	percent = error.split("%")[1].strip()
509	s_13 = val + " ± " + err + "&#37" + percent
510	elif item[0].split("[")[0].strip() == "Q* from data":
511	val = item[1].split("+-")[0].strip()
512	error = item[1].split("+-")[1].strip()
513	err = error.split("%")[0].strip()
514	percent = error.split("%")[1].strip()
515	s_14 = val + " ± " + err + "&#37" + percent
516	elif item[0].split("[")[0].strip() == "Q* from high Q extrapolation":
517	val = item[1].split("+-")[0].strip()
518	error = item[1].split("+-")[1].strip()
519	err = error.split("%")[0].strip()
520	percent = error.split("%")[1].strip()
521	s_15 = val + " ± " + err + "&#37" + percent
522	elif item[0].split("[")[0].strip() == "total Q*":
523	val = item[1].split("+-")[0].strip()
524	error = item[1].split("+-")[1].strip()
525	s_16 = val + " ± " + error
526	else:
527	continue
528
529	s_1 = self._check_html_format(s_1)
530	file_name = self._check_html_format(self.file)
531
532	# make plot image
533	self.set_plot_state(extra_high=bool_0[1],extra_low=bool_1[1])
534	# get ready for report with setting all the html strings
535	self.report_str = str(self.template_str) % (s_1, s_2,
536	s_3, s_4, s_5, s_6, s_7, s_8,
537	s_9, s_10, s_11, s_12, s_13, s_14, s_15,
538	s_16, s_17, s_18, file_name, "%s")
539
540	def _check_html_format(self, name):
541	"""
542	Check string '%' for html format
543	"""
544	if name.count('%'):
545	name = name.replace('%', '&#37')
546
547	return name
548
549	def set_saved_state(self, name, value):
550	"""
551	Set the state list
552
553	: param name: name of the state component
554	: param value: value of the state component
555	"""
556	rb_list = [['power_law_low','guinier'],
557	['fit_enable_low','fix_enable_low'],
558	['fit_enable_high','fix_enable_high']]
559
560	try:
561	if value == None or value.lstrip().rstrip() == '':
562	exec "self.%s = '%s'" % (name, value)
563	exec "self.saved_state['%s'] = '%s'" % (name, value)
564	else:
565	exec 'self.%s = %s' % (name, value)
566	exec "self.saved_state['%s'] = %s" % (name, value)
567	# set the count part of radio button clicked
568	# False for the saved_state
569	for title, content in rb_list:
570	if name == title:
571	name = content
572	value = False
573	elif name == content:
574	name = title
575	value = False
576	exec "self.saved_state['%s'] = '%s'" % (name, value)
577	self.state_num = self.saved_state['state_num']
578	except:
579	pass
580
581	def set_plot_state(self, extra_high=False, extra_low=False):
582	"""
583	Build image state that wx.html understand
584	by plotting, putting it into wx.FileSystem image object
585
586	: extrap_high,extra_low: low/high extrapolations
587	are possible extra-plots
588	"""
589	# some imports
590	import wx
591	import matplotlib.pyplot as plt
592	from matplotlib.backends.backend_agg import FigureCanvasAgg
593
594	#we use simple plot, not plotpanel
595	#make matlab figure
596	fig = plt.figure()
597	fig.set_facecolor('w')
598	graph = fig.add_subplot(111)
599
600	#data plot
601	graph.errorbar(self.data.x, self.data.y, yerr=self.data.dy, fmt='o')
602	#low Q extrapolation fit plot
603	if not extra_low == 'False':
604	graph.plot(self.theory_lowQ.x,self.theory_lowQ.y)
605	#high Q extrapolation fit plot
606	if not extra_high == 'False':
607	graph.plot(self.theory_highQ.x,self.theory_highQ.y)
608	graph.set_xscale("log", nonposx='clip')
609	graph.set_yscale("log", nonposy='clip')
610	graph.set_xlabel('$\\rm{Q}(\\AA^{-1})$', fontsize = 12)
611	graph.set_ylabel('$\\rm{Intensity}(cm^{-1})$', fontsize = 12)
612	canvas = FigureCanvasAgg(fig)
613	#actually make image
614	canvas.draw()
615
616	#make python.Image object
617	#size
618	w, h = canvas.get_width_height()
619	#convert to wx.Image
620	wximg = wx.EmptyImage(w,h)
621	#wxim.SetData(img.convert('RGB').tostring() )
622	wximg.SetData(canvas.tostring_rgb())
623	#get the dynamic image for the htmlwindow
624	wximgbmp = wx.BitmapFromImage(wximg)
625	#store the image in wx.FileSystem Object
626	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
627	# use wx.MemoryFSHandler
628	self.imgRAM = wx.MemoryFSHandler()
629	#AddFile, image can be retrieved with 'memory:filename'
630	self.imgRAM.AddFile('img_inv.png', wximgbmp, wx.BITMAP_TYPE_PNG)
631
632	self.wximgbmp = 'memory:img_inv.png'
633	self.image = fig
634
635	class Reader(CansasReader):
636	"""
637	Class to load a .inv invariant file
638	"""
639	## File type
640	type_name = "Invariant"
641
642	## Wildcards
643	type = ["Invariant file (.inv)\|.inv",
644	"SANSView file (.svs)\|.svs"]
645	## List of allowed extensions
646	ext = ['.inv', '.INV', '.svs', 'SVS']
647
648	def __init__(self, call_back, cansas=True):
649	"""
650	Initialize the call-back method to be called
651	after we load a file
652
653	: param call_back: call-back method
654	: param cansas: True = files will be written/read in CanSAS format
655	False = write CanSAS format
656	"""
657	## Call back method to be executed after a file is read
658	self.call_back = call_back
659	## CanSAS format flag
660	self.cansas = cansas
661	self.state = None
662
663	def read(self, path):
664	"""
665	Load a new invariant state from file
666
667	: param path: file path
668	: return: None
669	"""
670	if self.cansas == True:
671	return self._read_cansas(path)
672	else:
673	return self._read_standalone(path)
674
675	def _read_standalone(self, path):
676	"""
677	Load a new invariant state from file.
678	The invariant node is assumed to be the top element.
679
680	: param path: file path
681	: return: None
682	"""
683	# Read the new state from file
684	state = InvariantState()
685
686	state.fromXML(file=path)
687
688	# Call back to post the new state
689	self.call_back(state)
690	return None
691
692	def _parse_state(self, entry):
693	"""
694	Read an invariant result from an XML node
695
696	: param entry: XML node to read from
697	: return: InvariantState object
698	"""
699	state = None
700	# Locate the invariant node
701	try:
702	nodes = entry.xpath('ns:%s' % INVNODE_NAME,
703	namespaces={'ns': CANSAS_NS})
704	# Create an empty state
705	if nodes != []:
706	state = InvariantState()
707	state.fromXML(node=nodes[0])
708	except:
709	msg = "XML document does not contain invariant"
710	msg += " information.\n %s" % sys.exc_value
711	logging.info(msg)
712	return state
713
714	def _read_cansas(self, path):
715	"""
716	Load data and invariant information from a CanSAS XML file.
717
718	: param path: file path
719	: return: Data1D object if a single SASentry was found,
720	or a list of Data1D objects if multiple entries were found,
721	or None of nothing was found
722	: raise RuntimeError: when the file can't be opened
723	: raise ValueError: when the length of the data vectors are inconsistent
724	"""
725	output = []
726	if os.path.isfile(path):
727	basename = os.path.basename(path)
728	root, extension = os.path.splitext(basename)
729
730	if extension.lower() in self.ext or \
731	extension.lower() == '.xml':
732	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
733
734	# Check the format version number
735	# Specifying the namespace will take care of
736	# the file format version
737	root = tree.getroot()
738
739	entry_list = root.xpath('/ns:SASroot/ns:SASentry',
740	namespaces={'ns': CANSAS_NS})
741
742	for entry in entry_list:
743
744	sas_entry = self._parse_entry(entry)
745	invstate = self._parse_state(entry)
746
747	#invstate could be None when .svs file is loaded
748	#in this case, skip appending to output
749	if invstate != None:
750	sas_entry.meta_data['invstate'] = invstate
751	sas_entry.filename = invstate.file
752	output.append(sas_entry)
753	else:
754	raise RuntimeError, "%s is not a file" % path
755
756	# Return output consistent with the loader's api
757	if len(output) == 0:
758	return None
759	elif len(output) == 1:
760	# Call back to post the new state
761	self.state = output[0].meta_data['invstate']
762	self.call_back(state=output[0].meta_data['invstate'],
763	datainfo = output[0])
764	return output[0]
765	else:
766	return output
767
768	def get_state(self):
769	return self.state
770
771	def write(self, filename, datainfo=None, invstate=None):
772	"""
773	Write the content of a Data1D as a CanSAS XML file
774
775	: param filename: name of the file to write
776	: param datainfo: Data1D object
777	: param invstate: InvariantState object
778	"""
779	# Sanity check
780	if self.cansas == True:
781	doc = self.write_toXML(datainfo,invstate)
782	# Write the XML document
783	fd = open(filename, 'w')
784	fd.write(doc.toprettyxml())
785	fd.close()
786	else:
787	invstate.toXML(file=filename)
788
789	def write_toXML(self, datainfo=None, state=None):
790	"""
791	Write toXML, a helper for write()
792
793	: return: xml doc
794	"""
795	if datainfo is None:
796	datainfo = sans.dataloader.data_info.Data1D(x=[], y=[])
797	elif not issubclass(datainfo.__class__, sans.dataloader.data_info.Data1D):
798	msg = "The cansas writer expects a Data1D"
799	msg += " instance: %s" % str(datainfo.__class__.__name__)
800	raise RuntimeError, msg
801	#make sure title and data run is filled up.
802	if datainfo.title == None or datainfo.title == '':
803	datainfo.title = datainfo.name
804	if datainfo.run_name == None or datainfo.run_name == {}:
805	datainfo.run = [str(datainfo.name)]
806	datainfo.run_name[0] = datainfo.name
807	# Create basic XML document
808	doc, sasentry = self._to_xml_doc(datainfo)
809	# Add the invariant information to the XML document
810	if state is not None:
811	state.toXML(datainfo.name,doc=doc, entry_node=sasentry)
812	return doc
813

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/src/sans/perspectives/invariant/invariant_state.py @ 18c8c3d

Download in other formats: