invariant_state.py @ 1805b87

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 1805b87 was 78a205a, checked in by Mathieu Doucet <doucetm@…>, 10 years ago
pylint fixes
Property mode set to `100644`
File size: 30.5 KB

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

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SasView

source: sasview/src/sas/perspectives/invariant/invariant_state.py @ 1805b87

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