pagestate.py @ 8f5b34a

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 8f5b34a was 0483fd48, checked in by Jae Cho <jhjcho@…>, 13 years ago
removed file:// for img
Property mode set to `100644`
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2
3	################################################################################
4	#This software was developed by the University of Tennessee as part of the
5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
6	#project funded by the US National Science Foundation.
7	#
8	#See the license text in license.txt
9	#
10	#copyright 2009, University of Tennessee
11	################################################################################
12
13	import time
14	import os
15	import sys
16	import copy
17	import logging
18	import numpy
19
20	import xml.dom.minidom
21	from xml.dom.minidom import parse
22	from lxml import etree
23
24	import sans.dataloader
25	from sans.dataloader.readers.cansas_reader import Reader as CansasReader
26	from sans.dataloader.readers.cansas_reader import get_content, write_node
27	from sans.dataloader.data_info import Data2D, Detector
28
29	#Information to read/write state as xml
30	FITTING_NODE_NAME = 'fitting_plug_in'
31	CANSAS_NS = "cansas1d/1.0"
32
33	list_of_data_attributes = [["is_data", "is_data", "bool"],
34	["group_id", "data_group_id", "string"],
35	["data_name", "data_name", "string"],
36	["data_id", "data_id", "string"],
37	["name", "name", "string"],
38	["data_name", "data_name", "string"]]
39	list_of_state_attributes = [["engine_type", "engine_type", "string"],
40	["qmin", "qmin", "float"],
41	["qmax", "qmax", "float"],
42	["npts", "npts", "float"],
43	["shape_rbutton", "shape_rbutton", "bool"],
44	["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
45	["plugin_rbutton", "plugin_rbutton","bool"],
46	["struct_rbutton", "struct_rbutton", "bool"],
47	["formfactorcombobox", "formfactorcombobox", "float"],
48	["structurecombobox", "structurecombobox", "float"],
49	["multi_factor","multi_factor","float"],
50	["enable_smearer","enable_smearer","bool"],
51	["disable_smearer","disable_smearer","bool"],
52	["pinhole_smearer","pinhole_smearer","bool"],
53	["slit_smearer","slit_smearer","bool"],
54	["enable_disp","enable_disp","bool"],
55	["disable_disp","disable_disp","bool"],
56	["dI_noweight","dI_noweight","bool"],
57	["dI_didata","dI_didata","bool"],
58	["dI_sqrdata","dI_sqrdata","bool"],
59	["dI_idata","dI_idata","bool"],
60	["enable2D","enable2D","bool"],
61	["cb1","cb1","bool"],
62	["tcChi","tcChi","float"],
63	["smearer", "smearer", "float"],
64	["smear_type","smear_type", "string"],
65	["dq_l", "dq_l", "string"],
66	["dq_r","dq_r", "string"]]
67
68	list_of_model_attributes = [["values", "values"],
69	["weights", "weights"]]
70
71	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
72
73	list_of_state_parameters = [["parameters", "parameters"] ,
74	["str_parameters", "str_parameters"] ,
75	["orientation_parameters", "orientation_params"],
76	["dispersity_parameters", "orientation_params_disp"],
77	["fixed_param", "fixed_param"],
78	["fittable_param","fittable_param"]]
79	list_of_data_2d_attr = [["xmin", "xmin","float"],
80	["xmax","xmax","float"],
81	["ymin","ymin","float"],
82	["ymax","ymax","float"],
83	["_xaxis","_xaxis", "string"],
84	["_xunit", "_xunit", "string"],
85	["_yaxis","_yaxis","string"],
86	["_yunit","_yunit","string"],
87	["_zaxis","_zaxis","string"],
88	["_zunit","_zunit","string"]]
89	list_of_data2d_values = [["qx_data","qx_data","float"],
90	["qy_data","qy_data","float"],
91	["dqx_data","dqx_data","float"],
92	["dqy_data","dqy_data","float"],
93	["data","data","float"],
94	["q_data","q_data","float"],
95	["err_data","err_data","float"],
96	["mask","mask","bool"]]
97
98	def parse_entry_helper( node, item):
99	"""
100	Create a numpy list from value extrated from the node
101
102	:param node: node from each the value is stored
103	:param item: list name of three strings.the two first are name of data
104	attribute and the third one is the type of the value of that
105	attribute. type can be string, float, bool, etc.
106
107	: return: numpy array
108	"""
109	if node is not None:
110	if item[2] == "string":
111	return str(node.get(item[0]).strip())
112	elif item[2] == "bool":
113	try:
114	return node.get(item[0]).strip() == "True"
115
116	except:
117	return None
118	else:
119	try:
120	return float(node.get(item[0]))
121	except:
122	return None
123
124
125	class PageState(object):
126	"""
127	Contains information to reconstruct a page of the fitpanel.
128	"""
129	def __init__(self, parent=None, model=None, data=None):
130
131	"""
132	Initialize the current state
133
134	:param model: a selected model within a page
135	:param data:
136
137	"""
138	self.file = None
139	#Time of state creation
140	self.timestamp = time.time()
141	## Data member to store the dispersion object created
142	self._disp_obj_dict = {}
143	#------------------------
144	#Data used for fitting
145	self.data = data
146	# model data
147	self.theory_data = None
148	#Is 2D
149	self.is_2D = False
150	self.images = None
151
152	#save additional information on data that dataloader.reader does not read
153	self.is_data = None
154	self.data_name = ""
155
156	if self.data is not None:
157	self.data_name = self.data.name
158	self.data_id = None
159	if self.data is not None and hasattr(self.data, "id"):
160	self.data_id = self.data.id
161	self.data_group_id = None
162	if self.data is not None and hasattr(self.data, "group_id"):
163	self.data_group_id = self.data.group_id
164
165	## reset True change the state of exsiting button
166	self.reset = False
167
168	#engine type
169	self.engine_type = None
170	# flag to allow data2D plot
171	self.enable2D = False
172	# model on which the fit would be performed
173	self.model = model
174	#list of process done to model
175	self.process = []
176	#fit page manager
177	self.manager = None
178	#Store the parent of this panel parent
179	# For this application fitpanel is the parent
180	self.parent = parent
181	# Event_owner is the owner of model event
182	self.event_owner = None
183	##page name
184	self.page_name = ""
185	# Contains link between model ,all its parameters, and panel organization
186	self.parameters = []
187	# String parameter list that can not be fitted
188	self.str_parameters = []
189	# Contains list of parameters that cannot be fitted and reference to
190	#panel objects
191	self.fixed_param = []
192	# Contains list of parameters with dispersity and reference to
193	#panel objects
194	self.fittable_param = []
195	## orientation parameters
196	self.orientation_params = []
197	## orientation parmaters for gaussian dispersity
198	self.orientation_params_disp = []
199	## smearer info
200	self.smearer = None
201	self.smear_type = None
202	self.dq_l = None
203	self.dq_r = None
204
205	#list of dispersion paramaters
206	self.disp_list =[]
207	if self.model is not None:
208	self.disp_list = self.model.getDispParamList()
209
210	self.disp_cb_dict = {}
211	self.values = {}
212	self.weights = {}
213
214	#contains link between a model and selected parameters to fit
215	self.param_toFit = []
216	##dictionary of model type and model class
217	self.model_list_box = None
218	## save the state of the context menu
219	self.saved_states = {}
220	## save selection of combobox
221	self.formfactorcombobox = None
222	self.structurecombobox = None
223
224	## radio box to select type of model
225	self.shape_rbutton = False
226	self.shape_indep_rbutton = False
227	self.struct_rbutton = False
228	self.plugin_rbutton = False
229	## the indice of the current selection
230	self.disp_box = 0
231	## Qrange
232	## Q range
233	self.qmin = 0.001
234	self.qmax = 0.1
235	#reset data range
236	self.qmax_x = None
237	self.qmin_x = None
238
239	self.npts = None
240	self.name = ""
241	self.multi_factor = None
242	## enable smearering state
243	self.enable_smearer = False
244	self.disable_smearer = True
245	self.pinhole_smearer = False
246	self.slit_smearer = False
247	# weighting options
248	self.dI_noweight = False
249	self.dI_didata = True
250	self.dI_sqrdata = False
251	self.dI_idata = False
252	## disperity selection
253	self.enable_disp = False
254	self.disable_disp = True
255
256	## state of selected all check button
257	self.cb1 = False
258	## store value of chisqr
259	self.tcChi = None
260
261	def clone(self):
262	"""
263	Create a new copy of the current object
264	"""
265	model = None
266	if self.model is not None:
267	model = self.model.clone()
268	model.name = self.model.name
269	obj = PageState(self.parent, model=model)
270	obj.file = copy.deepcopy(self.file)
271	obj.data = copy.deepcopy(self.data)
272	if self.data is not None:
273	self.data_name = self.data.name
274	obj.data_name = self.data_name
275	obj.is_data = self.is_data
276	obj.model_list_box = copy.deepcopy(self.model_list_box)
277	obj.engine_type = copy.deepcopy(self.engine_type)
278
279	obj.formfactorcombobox = self.formfactorcombobox
280	obj.structurecombobox = self.structurecombobox
281
282	obj.shape_rbutton = self.shape_rbutton
283	obj.shape_indep_rbutton = self.shape_indep_rbutton
284	obj.struct_rbutton = self.struct_rbutton
285	obj.plugin_rbutton = self.plugin_rbutton
286
287	obj.manager = self.manager
288	obj.event_owner = self.event_owner
289	obj.disp_list = copy.deepcopy(self.disp_list)
290
291	obj.enable2D = copy.deepcopy(self.enable2D)
292	obj.parameters = copy.deepcopy(self.parameters)
293	obj.str_parameters = copy.deepcopy(self.str_parameters)
294	obj.fixed_param = copy.deepcopy(self.fixed_param)
295	obj.fittable_param = copy.deepcopy(self.fittable_param)
296	obj.orientation_params = copy.deepcopy(self.orientation_params)
297	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
298	obj.enable_disp = copy.deepcopy(self.enable_disp)
299	obj.disable_disp = copy.deepcopy(self.disable_disp)
300	obj.tcChi = self.tcChi
301
302	if len(self._disp_obj_dict)>0:
303	for k , v in self._disp_obj_dict.iteritems():
304	obj._disp_obj_dict[k]= v
305	if len(self.disp_cb_dict)>0:
306	for k , v in self.disp_cb_dict.iteritems():
307	obj.disp_cb_dict[k]= v
308	if len(self.values)>0:
309	for k , v in self.values.iteritems():
310	obj.values[k] = v
311	if len(self.weights)>0:
312	for k , v in self.weights.iteritems():
313	obj.weights[k] = v
314	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
315	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
316	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
317	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
318	obj.smear_type = copy.deepcopy(self.smear_type)
319	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
320	obj.dI_didata = copy.deepcopy(self.dI_didata)
321	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
322	obj.dI_idata = copy.deepcopy(self.dI_idata)
323	obj.dq_l = copy.deepcopy(self.dq_l)
324	obj.dq_r = copy.deepcopy(self.dq_r)
325
326	obj.disp_box = copy.deepcopy(self.disp_box)
327	obj.qmin = copy.deepcopy(self.qmin)
328	obj.qmax = copy.deepcopy(self.qmax)
329	obj.multi_factor = self.multi_factor
330	obj.npts = copy.deepcopy(self.npts )
331	obj.cb1 = copy.deepcopy(self.cb1)
332	obj.smearer = copy.deepcopy(self.smearer)
333
334	for name, state in self.saved_states.iteritems():
335	copy_name = copy.deepcopy(name)
336	copy_state = state.clone()
337	obj.saved_states[copy_name]= copy_state
338	return obj
339
340	def _repr_helper(self, list, rep):
341	"""
342	Helper method to print a state
343	"""
344	for item in list:
345	rep += "parameter name: %s \n"%str(item[1])
346	rep += "value: %s\n"%str(item[2])
347	rep += "selected: %s\n"%str(item[0])
348	rep += "error displayed : %s \n"%str(item[4][0])
349	rep += "error value:%s \n"%str(item[4][1])
350	rep += "minimum displayed : %s \n"%str(item[5][0])
351	rep += "minimum value : %s \n"%str(item[5][1])
352	rep += "maximum displayed : %s \n"%str(item[6][0])
353	rep += "maximum value : %s \n"%str(item[6][1])
354	rep += "parameter unit: %s\n\n"%str(item[7])
355	return rep
356
357	def __repr__(self):
358	"""
359	output string for printing
360	"""
361	rep = "\nState name: %s\n"%self.file
362	t = time.localtime(self.timestamp)
363	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
364
365	rep += "State created: %s\n"%time_str
366	rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox
367	rep += "State structure factor combobox selection: %s\n"%self.structurecombobox
368	rep += "is data : %s\n"%self.is_data
369	rep += "data's name : %s\n"%self.data_name
370	rep += "data's id : %s\n"%self.data_id
371	if self.model != None:
372	rep += "model name : %s\n"% self.model.__class__.__name__
373	else:
374	rep += "model name : None\n"
375	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
376	rep += "multi_factor : %s\n"% str(self.multi_factor)
377	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
378	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
379	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
380	rep += "data : %s\n"% str(self.data)
381	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
382	str(self.qmax),str(self.npts))
383	rep += "Dispersion selection : %s\n"%str(self.disp_box)
384	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
385	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
386	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
387	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
388	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
389	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
390	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
391
392	rep += "dI_noweight : %s\n"%str(self.dI_noweight)
393	rep += "dI_didata : %s\n"%str(self.dI_didata)
394	rep += "dI_sqrdata : %s\n"%str(self.dI_sqrdata)
395	rep += "dI_idata : %s\n"%str(self.dI_idata)
396
397
398	rep += "2D enable : %s\n"%str(self.enable2D)
399	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
400	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
401	rep += "Smear object : %s\n"%str(self.smearer)
402	rep += "Smear type : %s\n"%(self.smear_type)
403	rep += "dq_l : %s\n"%self.dq_l
404	rep += "dq_r : %s\n"%self.dq_r
405
406	rep += "model : %s\n\n"% str(self.model)
407	temp_parameters = []
408	temp_fittable_param = []
409	if self.data.__class__.__name__ == "Data2D":
410	self.is_2D = True
411	else:
412	self.is_2D = False
413	if self.data is not None:
414	if not self.is_2D:
415	for item in self.parameters:
416	if not item in self.orientation_params:
417	temp_parameters.append(item)
418	for item in self.fittable_param:
419	if not item in self.orientation_params_disp:
420	temp_fittable_param.append(item)
421	else:
422	temp_parameters = self.parameters
423	temp_fittable_param = self.fittable_param
424
425	rep += "number parameters(self.parameters): %s\n"%len(temp_parameters)
426	rep = self._repr_helper( list=temp_parameters, rep=rep)
427	rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters)
428	rep = self._repr_helper( list=self.str_parameters, rep=rep)
429	rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param)
430	rep = self._repr_helper( list=temp_fittable_param, rep=rep)
431	"""
432	if is_2D:
433	rep += "number orientation parameters"
434	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
435	rep = self._repr_helper( list=self.orientation_params, rep=rep)
436	rep += "number dispersity parameters"
437	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
438	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
439	"""
440	return rep
441
442	def set_report_string(self):
443	"""
444	Get the values (strings) from __str__ for report
445	"""
446	# Dictionary of teh report strings
447	repo_time = ""
448	model_name = ""
449	title = ""
450	title_name = ""
451	file_name = ""
452	param_string = ""
453	paramval_string = ""
454	chi2_string = ""
455	multi_factor_string = ""
456	q_range = ""
457	strings = self.__repr__()
458	lines = strings.split('\n')
459
460	# get all string values from __str__()
461	for line in lines:
462	value = ""
463	content = line.split(":")
464	name = content[0]
465	try:
466	value = content[1]
467	except:
468	pass
469	if name.count("State created"):
470	repo_time = "" + value
471	if name.count("parameter name"):
472	val_name = value.split(".")
473	if len(val_name) > 1:
474	if val_name[1].count("width"):
475	param_string += value + ','
476	else:
477	continue
478	else:
479	param_string += value + ','
480	if name == "value":
481	param_string += value + ','
482	if name == "error value":
483	param_string += value + ','
484	if name == "parameter unit":
485	param_string += value + ':'
486	if name == "Value of Chisqr ":
487	chi2 = ("Chi2/Npts = " + value)
488	chi2_string = CENTRE % chi2
489	if name == "multi_factor ":
490	muti_factor = ("muti_factor = " + value)
491	muti_factor_string = CENTRE % muti_factor
492	if name == "Title":
493	if len(value.strip()) == 0:
494	continue
495	title = value + " [" + repo_time + "]"
496	title_name = HEADER % title
497	if name == "data ":
498	try:
499	file = ("File name:" + content[2])
500	file_name = CENTRE % file
501	if len(title) == 0:
502	title = content[2] + " [" + repo_time + "]"
503	title_name = HEADER % title
504	except:
505	pass
506	if name == "model name ":
507	try:
508	modelname = "Model name:" + content[1]
509	except:
510	modelname = "Model name:" + " NAN"
511	model_name = CENTRE % modelname
512
513	if name == "Plotting Range":
514	try:
515	q_range = content[1] + " = " + content[2] \
516	+ " = " + content[3].split(",")[0]
517	q_name = ("Q Range: " + q_range)
518	q_range = CENTRE % q_name
519	except:
520	pass
521	paramval = ""
522	for lines in param_string.split(":"):
523	line = lines.split(",")
524	if len(lines) > 0:
525	param = line[0]
526	param += " = " + line[1]
527	if len(line[2].split()) > 0 and not line[2].count("None"):
528	param += " +- " + line[2]
529	if len(line[3].split()) > 0 and not line[3].count("None"):
530	param += " " + line[3]
531	if not paramval.count(param):
532	paramval += param + "\n"
533	paramval_string += CENTRE % param + "\n"
534
535	text_string = "\n\n\n" + title + "\n\n" + file + \
536	"\n" + q_name + \
537	"\n" + chi2 + \
538	"\n\n" + paramval
539
540	title_name = self._check_html_format(title_name)
541	file_name = self._check_html_format(file_name)
542	title = self._check_html_format(title)
543
544	html_string = title_name + "\n" + file_name + \
545	"\n" + model_name +\
546	"\n" + q_range + \
547	"\n" + chi2_string + \
548	"\n" + ELINE + \
549	"\n" + paramval_string + \
550	"\n" + ELINE + \
551	"\n" + FEET_1 % title + \
552	"\n" + FEET_2
553
554	return html_string, text_string, title
555
556	def _check_html_format(self, name):
557	"""
558	Check string '%' for html format
559	"""
560	if name.count('%'):
561	name = name.replace('%', '&#37')
562
563	return name
564
565
566	def report(self, figs=None, canvases=None):
567	"""
568	Invoke report dialog panel
569
570	: param figs: list of pylab figures [list]
571	"""
572	from report_dialog import ReportDialog
573	# get the strings for report
574	html_str, text_str, title = self.set_report_string()
575	# Allow 2 figures to append
576	if len(figs) == 1:
577	add_str = FEET_3
578	elif len(figs) == 2:
579	add_str = ELINE
580	add_str += FEET_2 % ("%s")
581	add_str += ELINE
582	add_str += FEET_3
583	elif len(figs) > 2:
584	add_str = ELINE
585	add_str += FEET_2 % ("%s")
586	add_str += ELINE
587	add_str += FEET_2 % ("%s")
588	add_str += ELINE
589	add_str += FEET_3
590	else:
591	add_str = ""
592
593	# final report html strings
594	report_str = html_str % ("%s") + add_str
595
596	# make plot image
597	images = self.set_plot_state(figs, canvases)
598	report_list = [report_str, text_str, images ]
599	dialog = ReportDialog(report_list, None, -1, "")
600	dialog.ShowModal()
601
602
603	def _toXML_helper(self, list, element, newdoc):
604	"""
605	Helper method to create xml file for saving state
606	"""
607	for item in list:
608	sub_element = newdoc.createElement('parameter')
609	sub_element.setAttribute('name', str(item[1]))
610	sub_element.setAttribute('value', str(item[2]))
611	sub_element.setAttribute('selected_to_fit', str(item[0]))
612	sub_element.setAttribute('error_displayed', str(item[4][0]))
613	sub_element.setAttribute('error_value', str(item[4][1]))
614	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
615	sub_element.setAttribute('minimum_value', str(item[5][1]))
616	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
617	sub_element.setAttribute('maximum_value', str(item[6][1]))
618	sub_element.setAttribute('unit', str(item[7]))
619	element.appendChild(sub_element)
620
621	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
622	"""
623	Writes the state of the InversionControl panel to file, as XML.
624
625	Compatible with standalone writing, or appending to an
626	already existing XML document. In that case, the XML document
627	is required. An optional entry node in the XML document may also be given.
628
629	:param file: file to write to
630	:param doc: XML document object [optional]
631	:param entry_node: XML node within the XML document at which we will append the data [optional]
632
633	"""
634	from xml.dom.minidom import getDOMImplementation
635
636	# Check whether we have to write a standalone XML file
637	if doc is None:
638	impl = getDOMImplementation()
639	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
640	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
641	top_element = newdoc.documentElement
642	else:
643	# We are appending to an existing document
644	newdoc = doc
645	top_element = newdoc.createElement(FITTING_NODE_NAME)
646	if entry_node is None:
647	newdoc.documentElement.appendChild(top_element)
648	else:
649	entry_node.appendChild(top_element)
650
651	attr = newdoc.createAttribute("version")
652	attr.nodeValue = '1.0'
653	top_element.setAttributeNode(attr)
654
655	# File name
656	element = newdoc.createElement("filename")
657	if self.file is not None:
658	element.appendChild(newdoc.createTextNode(str(self.file)))
659	else:
660	element.appendChild(newdoc.createTextNode(str(file)))
661	top_element.appendChild(element)
662
663	element = newdoc.createElement("timestamp")
664	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
665	attr = newdoc.createAttribute("epoch")
666	attr.nodeValue = str(self.timestamp)
667	element.setAttributeNode(attr)
668	top_element.appendChild(element)
669	# Inputs
670	inputs = newdoc.createElement("Attributes")
671	top_element.appendChild(inputs)
672
673
674	if self.data is not None and hasattr(self.data, "group_id"):
675	self.data_group_id = self.data.group_id
676	if self.data is not None and hasattr(self.data, "is_data"):
677	self.is_data = self.data.is_data
678	if self.data is not None:
679	self.data_name = self.data.name
680	if self.data is not None and hasattr(self.data, "id"):
681	self.data_id = self.data.id
682
683	for item in list_of_data_attributes:
684	element = newdoc.createElement(item[0])
685	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
686	inputs.appendChild(element)
687
688	for item in list_of_state_attributes:
689	element = newdoc.createElement(item[0])
690	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
691	inputs.appendChild(element)
692
693	# For self.values ={ disp_param_name: [vals,...],...}
694	# and for self.weights ={ disp_param_name: [weights,...],...}
695	for item in list_of_model_attributes:
696	element = newdoc.createElement(item[0])
697	exec "list = self.%s" % item[1]
698	for key, value in list.iteritems():
699	sub_element = newdoc.createElement(key)
700	sub_element.setAttribute('name', str(key))
701	for val in value:
702	com = "sub_element.appendChild"
703	com += "(newdoc.createTextNode(str(%s)))"
704	exec com % val
705
706	element.appendChild(sub_element)
707	inputs.appendChild(element)
708
709	# Create doc for the dictionary of self._disp_obj_dic
710	for item in list_of_obj_dic:
711	element = newdoc.createElement(item[0])
712	exec "list = self.%s" % item[1]
713	for key, val in list.iteritems():
714	value = repr(val)
715	sub_element = newdoc.createElement(key)
716	sub_element.setAttribute('name', str(key))
717	sub_element.setAttribute('value', str(value))
718	element.appendChild(sub_element)
719	inputs.appendChild(element)
720
721	for item in list_of_state_parameters:
722	element = newdoc.createElement(item[0])
723	com = "self._toXML_helper(list=self.%s,"
724	com += " element=element, newdoc=newdoc)"
725	exec com % item[1]
726	inputs.appendChild(element)
727
728	# Save the file
729	if doc is None:
730	fd = open(file, 'w')
731	fd.write(newdoc.toprettyxml())
732	fd.close()
733	return None
734	else:
735	return newdoc.toprettyxml()
736
737	def _fromXML_helper(self, node, list):
738	"""
739	Helper function to write state to xml
740	"""
741	for item in node:
742	try:
743	name = item.get('name')
744	except:
745	name = None
746	try:
747	value = item.get('value')
748	except:
749	value = None
750	try:
751	selected_to_fit = (item.get('selected_to_fit') == "True")
752	except:
753	selected_to_fit = None
754	try:
755	error_displayed = (item.get('error_displayed') == "True")
756	except:
757	error_displayed = None
758	try:
759	error_value = item.get('error_value')
760	except:
761	error_value = None
762	try:
763	minimum_displayed = (item.get('minimum_displayed')== "True")
764	except:
765	minimum_displayed = None
766	try:
767	minimum_value = item.get('minimum_value')
768	except:
769	minimum_value = None
770	try:
771	maximum_displayed = (item.get('maximum_displayed') == "True")
772	except:
773	maximum_displayed = None
774	try:
775	maximum_value = item.get('maximum_value')
776	except:
777	maximum_value = None
778	try:
779	unit = item.get('unit')
780	except:
781	unit = None
782	list.append([selected_to_fit, name, value, "+/-",
783	[error_displayed, error_value],
784	[minimum_displayed,minimum_value],
785	[maximum_displayed,maximum_value], unit])
786
787	def fromXML(self, file=None, node=None):
788	"""
789	Load fitting state from a file
790
791	:param file: .fitv file
792	:param node: node of a XML document to read from
793
794	"""
795	if file is not None:
796	msg = "PageState no longer supports non-CanSAS"
797	msg += " format for fitting files"
798	raise RuntimeError, msg
799
800	if node.get('version')and node.get('version') == '1.0':
801
802	# Get file name
803	entry = get_content('ns:filename', node)
804	if entry is not None:
805	self.file = entry.text.strip()
806
807	# Get time stamp
808	entry = get_content('ns:timestamp', node)
809	if entry is not None and entry.get('epoch'):
810	try:
811	self.timestamp = float(entry.get('epoch'))
812	except:
813	msg = "PageState.fromXML: Could not"
814	msg += " read timestamp\n %s" % sys.exc_value
815	logging.error(msg)
816
817	# Parse fitting attributes
818	entry = get_content('ns:Attributes', node)
819	for item in list_of_data_attributes:
820	node = get_content('ns:%s'%item[0], entry)
821	try:
822	exec "self.%s = parse_entry_helper(node, item)" % item[0]
823
824	except:
825	raise
826
827	if entry is not None:
828
829	for item in list_of_state_attributes:
830	node = get_content('ns:%s' % item[0], entry)
831	try:
832	exec "self.%s = parse_entry_helper(node, item)" % \
833	str(item[0])
834	except:
835	raise
836
837	for item in list_of_state_parameters:
838	node = get_content("ns:%s" % item[0], entry)
839	exec "self._fromXML_helper(node=node, list=self.%s)" % \
840	item[1]
841
842	# Recover _disp_obj_dict from xml file
843	self._disp_obj_dict = {}
844	for item in list_of_obj_dic:
845	# Get node
846	node = get_content("ns:%s" % item[0], entry)
847	for attr in node:
848	name = attr.get('name')
849	val = attr.get('value')
850	value = val.split(" instance")[0]
851	disp_name = value.split("<")[1]
852	try:
853	# Try to recover disp_model object from strings
854	com = "from sans.models.dispersion_models "
855	com += "import %s as disp"
856	com_name = disp_name.split(".")[3]
857	exec com % com_name
858	disp_model = disp()
859	exec "self.%s['%s'] = com_name" % (item[1], name)
860	except:
861	pass
862
863	# get self.values and self.weights dic. if exists
864	for item in list_of_model_attributes:
865	node = get_content("ns:%s" % item[0], entry)
866	dic = {}
867	list = []
868	for par in node:
869	name = par.get('name')
870	values = par.text.split('\n')
871	# Get lines only with numbers
872	for line in values:
873	try:
874	val= float(line)
875	list.append(val)
876	except:
877	# pass if line is empty (it happens)
878	pass
879	dic[name] = numpy.array(list)
880	exec "self.%s = dic" % item[1]
881
882	def set_plot_state(self, figs, canvases):
883	"""
884	Build image state that wx.html understand
885	by plotting, putting it into wx.FileSystem image object
886
887	"""
888	images = []
889	# some imports
890	import wx
891
892	# Reset memory
893	self.imgRAM = None
894	wx.MemoryFSHandler()
895
896	# For no figures in the list, prepare empty plot
897	if figs == None or len(figs) == 0:
898	figs = [None]
899
900	# Loop over the list of figures
901	# use wx.MemoryFSHandler
902	self.imgRAM = wx.MemoryFSHandler()
903	for fig in figs:
904	if figs != None:
905	#fig.set_facecolor('w')
906	ind = figs.index(fig)
907	canvas = canvases[ind]
908
909	#bmp = wx.BitmapDataObject()
910	#bmp.SetBitmap(canvas.bitmap)
911	#store the image in wx.FileSystem Object
912	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
913
914	# index of the fig
915	ind = figs.index(fig)
916
917	#AddFile, image can be retrieved with 'memory:filename'
918	self.imgRAM.AddFile('img_fit%s.png' % ind ,
919	canvas.bitmap, wx.BITMAP_TYPE_PNG)
920
921	#append figs
922	images.append(fig)
923
924	return images
925
926	class Reader(CansasReader):
927	"""
928	Class to load a .fitv fitting file
929	"""
930	## File type
931	type_name = "Fitting"
932
933	## Wildcards
934	type = ["Fitting files (.fitv)\|.fitv"
935	"SANSView file (.svs)\|.svs"]
936	## List of allowed extensions
937	ext=['.fitv', '.FITV', '.svs', 'SVS']
938
939	def __init__(self, call_back=None, cansas=True):
940	CansasReader.__init__(self)
941	"""
942	Initialize the call-back method to be called
943	after we load a file
944
945	:param call_back: call-back method
946	:param cansas: True = files will be written/read in CanSAS format
947	False = write CanSAS format
948
949	"""
950	## Call back method to be executed after a file is read
951	self.call_back = call_back
952	## CanSAS format flag
953	self.cansas = cansas
954	self.state = None
955	def get_state(self):
956	return self.state
957
958	def read(self, path):
959	"""
960	Load a new P(r) inversion state from file
961
962	:param path: file path
963
964	"""
965	if self.cansas == True:
966	return self._read_cansas(path)
967
968	def _data2d_to_xml_doc(self, datainfo):
969	"""
970	Create an XML document to contain the content of a Data2D
971
972	:param datainfo: Data2D object
973
974	"""
975	if not issubclass(datainfo.__class__, Data2D):
976	raise RuntimeError, "The cansas writer expects a Data2D instance"
977
978	doc = xml.dom.minidom.Document()
979	main_node = doc.createElement("SASroot")
980	main_node.setAttribute("version", self.version)
981	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
982	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
983	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
984
985	doc.appendChild(main_node)
986
987	entry_node = doc.createElement("SASentry")
988	main_node.appendChild(entry_node)
989
990	write_node(doc, entry_node, "Title", datainfo.title)
991	if datainfo is not None:
992	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
993	for item in datainfo.run:
994	runname = {}
995	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
996	runname = {'name': datainfo.run_name[item] }
997	write_node(doc, entry_node, "Run", item, runname)
998	# Data info
999	new_node = doc.createElement("SASdata")
1000	entry_node.appendChild(new_node)
1001	for item in list_of_data_2d_attr:
1002	element = doc.createElement(item[0])
1003	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
1004	new_node.appendChild(element)
1005
1006	for item in list_of_data2d_values:
1007	root_node = doc.createElement(item[0])
1008	new_node.appendChild(root_node)
1009
1010	exec "temp_list = datainfo.%s"%item[1]
1011
1012	if temp_list is None or len(temp_list)== 0:
1013	element = doc.createElement(item[0])
1014	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
1015	root_node.appendChild(element)
1016	else:
1017	for value in temp_list:
1018	element = doc.createElement(item[0])
1019	exec "element.setAttribute(item[0], str(%s))"%value
1020	root_node.appendChild(element)
1021
1022	# Sample info
1023	sample = doc.createElement("SASsample")
1024	if datainfo.sample.name is not None:
1025	sample.setAttribute("name", str(datainfo.sample.name))
1026	entry_node.appendChild(sample)
1027	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1028	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
1029	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1030	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
1031
1032	for item in datainfo.sample.details:
1033	write_node(doc, sample, "details", item)
1034
1035	pos = doc.createElement("position")
1036	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
1037	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
1038	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
1039	if written == True:
1040	sample.appendChild(pos)
1041
1042	ori = doc.createElement("orientation")
1043	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
1044	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1045	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1046	if written == True:
1047	sample.appendChild(ori)
1048
1049	# Instrument info
1050	instr = doc.createElement("SASinstrument")
1051	entry_node.appendChild(instr)
1052
1053	write_node(doc, instr, "name", datainfo.instrument)
1054
1055	# Source
1056	source = doc.createElement("SASsource")
1057	if datainfo.source.name is not None:
1058	source.setAttribute("name", str(datainfo.source.name))
1059	instr.appendChild(source)
1060
1061	write_node(doc, source, "radiation", datainfo.source.radiation)
1062	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1063	size = doc.createElement("beam_size")
1064	if datainfo.source.beam_size_name is not None:
1065	size.setAttribute("name", str(datainfo.source.beam_size_name))
1066	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1067	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1068	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1069	if written == True:
1070	source.appendChild(size)
1071
1072	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1073	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1074	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1075	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1076
1077	# Collimation
1078	for item in datainfo.collimation:
1079	coll = doc.createElement("SAScollimation")
1080	if item.name is not None:
1081	coll.setAttribute("name", str(item.name))
1082	instr.appendChild(coll)
1083
1084	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1085
1086	for apert in item.aperture:
1087	ap = doc.createElement("aperture")
1088	if apert.name is not None:
1089	ap.setAttribute("name", str(apert.name))
1090	if apert.type is not None:
1091	ap.setAttribute("type", str(apert.type))
1092	coll.appendChild(ap)
1093
1094	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1095
1096	size = doc.createElement("size")
1097	if apert.size_name is not None:
1098	size.setAttribute("name", str(apert.size_name))
1099	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1100	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1101	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1102	if written == True:
1103	ap.appendChild(size)
1104
1105	# Detectors
1106	for item in datainfo.detector:
1107	det = doc.createElement("SASdetector")
1108	written = write_node(doc, det, "name", item.name)
1109	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1110	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1111	if written == True:
1112	instr.appendChild(det)
1113
1114	off = doc.createElement("offset")
1115	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1116	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1117	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1118	if written == True:
1119	det.appendChild(off)
1120
1121	center = doc.createElement("beam_center")
1122	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1123	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1124	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1125	if written == True:
1126	det.appendChild(center)
1127
1128	pix = doc.createElement("pixel_size")
1129	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1130	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1131	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1132	if written == True:
1133	det.appendChild(pix)
1134
1135	ori = doc.createElement("orientation")
1136	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1137	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1138	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1139	if written == True:
1140	det.appendChild(ori)
1141
1142	# Processes info
1143	for item in datainfo.process:
1144	node = doc.createElement("SASprocess")
1145	entry_node.appendChild(node)
1146
1147	write_node(doc, node, "name", item.name)
1148	write_node(doc, node, "date", item.date)
1149	write_node(doc, node, "description", item.description)
1150	for term in item.term:
1151	value = term['value']
1152	del term['value']
1153	write_node(doc, node, "term", value, term)
1154	for note in item.notes:
1155	write_node(doc, node, "SASprocessnote", note)
1156	# Return the document, and the SASentry node associated with
1157	# the data we just wrote
1158	return doc, entry_node
1159
1160	def _parse_state(self, entry):
1161	"""
1162	Read a fit result from an XML node
1163
1164	:param entry: XML node to read from
1165
1166	:return: PageState object
1167	"""
1168	# Create an empty state
1169	state = None
1170	# Locate the P(r) node
1171	try:
1172	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
1173	if nodes !=[]:
1174	# Create an empty state
1175	state = PageState()
1176	state.fromXML(node=nodes[0])
1177	except:
1178	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1179
1180	return state
1181
1182
1183
1184	def _parse_entry(self, dom):
1185	"""
1186	Parse a SASentry
1187
1188	:param node: SASentry node
1189
1190	:return: Data1D/Data2D object
1191
1192	"""
1193	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1194	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1195	return CansasReader._parse_entry(self, dom)
1196
1197	#Parse 2D
1198	data_info = Data2D()
1199
1200	# Look up title
1201	self._store_content('ns:Title', dom, 'title', data_info)
1202
1203	# Look up run number
1204	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1205	for item in nodes:
1206	if item.text is not None:
1207	value = item.text.strip()
1208	if len(value) > 0:
1209	data_info.run.append(value)
1210	if item.get('name') is not None:
1211	data_info.run_name[value] = item.get('name')
1212
1213	# Look up instrument name
1214	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1215
1216	# Notes
1217	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1218	for note in note_list:
1219	try:
1220	if note.text is not None:
1221	note_value = note.text.strip()
1222	if len(note_value) > 0:
1223	data_info.notes.append(note_value)
1224	except:
1225	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1226	self.errors.append(err_mess)
1227	logging.error(err_mess)
1228
1229	# Sample info ###################
1230	entry = get_content('ns:SASsample', dom)
1231	if entry is not None:
1232	data_info.sample.name = entry.get('name')
1233
1234	self._store_content('ns:SASsample/ns:ID',
1235	dom, 'ID', data_info.sample)
1236	self._store_float('ns:SASsample/ns:thickness',
1237	dom, 'thickness', data_info.sample)
1238	self._store_float('ns:SASsample/ns:transmission',
1239	dom, 'transmission', data_info.sample)
1240	self._store_float('ns:SASsample/ns:temperature',
1241	dom, 'temperature', data_info.sample)
1242
1243	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1244	for item in nodes:
1245	try:
1246	if item.text is not None:
1247	detail_value = item.text.strip()
1248	if len(detail_value) > 0:
1249	data_info.sample.details.append(detail_value)
1250	except:
1251	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1252	self.errors.append(err_mess)
1253	logging.error(err_mess)
1254
1255	# Position (as a vector)
1256	self._store_float('ns:SASsample/ns:position/ns:x',
1257	dom, 'position.x', data_info.sample)
1258	self._store_float('ns:SASsample/ns:position/ns:y',
1259	dom, 'position.y', data_info.sample)
1260	self._store_float('ns:SASsample/ns:position/ns:z',
1261	dom, 'position.z', data_info.sample)
1262
1263	# Orientation (as a vector)
1264	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1265	dom, 'orientation.x', data_info.sample)
1266	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1267	dom, 'orientation.y', data_info.sample)
1268	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1269	dom, 'orientation.z', data_info.sample)
1270
1271	# Source info ###################
1272	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1273	if entry is not None:
1274	data_info.source.name = entry.get('name')
1275
1276	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1277	dom, 'radiation', data_info.source)
1278	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1279	dom, 'beam_shape', data_info.source)
1280	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1281	dom, 'wavelength', data_info.source)
1282	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1283	dom, 'wavelength_min', data_info.source)
1284	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1285	dom, 'wavelength_max', data_info.source)
1286	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1287	dom, 'wavelength_spread', data_info.source)
1288
1289	# Beam size (as a vector)
1290	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1291	if entry is not None:
1292	data_info.source.beam_size_name = entry.get('name')
1293
1294	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1295	dom, 'beam_size.x', data_info.source)
1296	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1297	dom, 'beam_size.y', data_info.source)
1298	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1299	dom, 'beam_size.z', data_info.source)
1300
1301	# Collimation info ###################
1302	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
1303	for item in nodes:
1304	collim = Collimation()
1305	if item.get('name') is not None:
1306	collim.name = item.get('name')
1307	self._store_float('ns:length', item, 'length', collim)
1308
1309	# Look for apertures
1310	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
1311	for apert in apert_list:
1312	aperture = Aperture()
1313
1314	# Get the name and type of the aperture
1315	aperture.name = apert.get('name')
1316	aperture.type = apert.get('type')
1317
1318	self._store_float('ns:distance', apert, 'distance', aperture)
1319
1320	entry = get_content('ns:size', apert)
1321	if entry is not None:
1322	aperture.size_name = entry.get('name')
1323
1324	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1325	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1326	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1327
1328	collim.aperture.append(aperture)
1329
1330	data_info.collimation.append(collim)
1331
1332	# Detector info ######################
1333	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1334	for item in nodes:
1335
1336	detector = Detector()
1337
1338	self._store_content('ns:name', item, 'name', detector)
1339	self._store_float('ns:SDD', item, 'distance', detector)
1340
1341	# Detector offset (as a vector)
1342	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1343	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1344	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1345
1346	# Detector orientation (as a vector)
1347	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1348	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1349	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1350
1351	# Beam center (as a vector)
1352	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1353	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1354	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1355
1356	# Pixel size (as a vector)
1357	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1358	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1359	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1360
1361	self._store_float('ns:slit_length', item, 'slit_length', detector)
1362
1363	data_info.detector.append(detector)
1364
1365	# Processes info ######################
1366	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1367	for item in nodes:
1368	process = Process()
1369	self._store_content('ns:name', item, 'name', process)
1370	self._store_content('ns:date', item, 'date', process)
1371	self._store_content('ns:description', item, 'description', process)
1372
1373	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1374	for term in term_list:
1375	try:
1376	term_attr = {}
1377	for attr in term.keys():
1378	term_attr[attr] = term.get(attr).strip()
1379	if term.text is not None:
1380	term_attr['value'] = term.text.strip()
1381	process.term.append(term_attr)
1382	except:
1383	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1384	self.errors.append(err_mess)
1385	logging.error(err_mess)
1386
1387	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1388	for note in note_list:
1389	if note.text is not None:
1390	process.notes.append(note.text.strip())
1391
1392	data_info.process.append(process)
1393
1394
1395	# Data info ######################
1396	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1397	if len(nodes)>1:
1398	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1399
1400	for entry in nodes:
1401	for item in list_of_data_2d_attr:
1402	#get node
1403	node = get_content('ns:%s'%item[0], entry)
1404	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1405
1406	for item in list_of_data2d_values:
1407	field = get_content('ns:%s'%item[0], entry)
1408	list = []
1409	if field is not None:
1410	list = [parse_entry_helper(node, item) for node in field]
1411	exec "data_info.%s = numpy.array(list)"%item[0]
1412
1413	return data_info
1414
1415	def _read_cansas(self, path):
1416	"""
1417	Load data and P(r) information from a CanSAS XML file.
1418
1419	:param path: file path
1420
1421	:return: Data1D object if a single SASentry was found,
1422	or a list of Data1D objects if multiple entries were found,
1423	or None of nothing was found
1424
1425	:raise RuntimeError: when the file can't be opened
1426	:raise ValueError: when the length of the data vectors are inconsistent
1427
1428	"""
1429	output = []
1430	basename = os.path.basename(path)
1431	root, extension = os.path.splitext(basename)
1432	ext = extension.lower()
1433	try:
1434	if os.path.isfile(path):
1435
1436	#TODO: eventually remove the check for .xml once
1437	# the P(r) writer/reader is truly complete.
1438	if ext in self.ext or \
1439	ext == '.xml':
1440
1441	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1442	# Check the format version number
1443	# Specifying the namespace will take care of the file format version
1444	root = tree.getroot()
1445	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1446	for entry in entry_list:
1447	try:
1448	sas_entry = self._parse_entry(entry)
1449	except:
1450	raise
1451	fitstate = self._parse_state(entry)
1452
1453	#state could be None when .svs file is loaded
1454	#in this case, skip appending to output
1455	if fitstate != None:
1456	sas_entry.meta_data['fitstate'] = fitstate
1457	sas_entry.filename = fitstate.file
1458	output.append(sas_entry)
1459	else:
1460	self.call_back(format=ext)
1461	raise RuntimeError, "%s is not a file" % path
1462
1463	# Return output consistent with the loader's api
1464	if len(output)==0:
1465	self.call_back(state=None, datainfo=None,format=ext)
1466	return None
1467	else:
1468	for ind in range(len(output)):
1469	# Call back to post the new state
1470	state = output[ind].meta_data['fitstate']
1471	t = time.localtime(state.timestamp)
1472	time_str = time.strftime("%b %d %H:%M", t)
1473	# Check that no time stamp is already appended
1474	max_char = state.file.find("[")
1475	if max_char < 0:
1476	max_char = len(state.file)
1477	original_fname = state.file[0:max_char]
1478	state.file = original_fname +' [' + time_str + ']'
1479
1480
1481	if state is not None and state.is_data is not None:
1482	exec 'output[%d].is_data = state.is_data'% ind
1483
1484	output[ind].filename = state.file
1485	state.data = output[ind]
1486	state.data.name = output[ind].filename #state.data_name
1487	state.data.id = state.data_id
1488	if state.is_data is not None:
1489	state.data.is_data = state.is_data
1490	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1491	name = output[ind].run_name
1492	else:
1493	name=original_fname
1494	state.data.group_id = name
1495	#store state in fitting
1496	self.call_back(state=state, datainfo=output[ind],format=ext)
1497	self.state= state
1498	return output
1499
1500	except:
1501	self.call_back(format=ext)
1502	#self.state= state
1503	raise
1504
1505	def write(self, filename, datainfo=None, fitstate=None):
1506	"""
1507	Write the content of a Data1D as a CanSAS XML file only for standalone
1508
1509	:param filename: name of the file to write
1510	:param datainfo: Data1D object
1511	:param fitstate: PageState object
1512
1513	"""
1514	# Sanity check
1515	if self.cansas == True:
1516
1517	# Add fitting information to the XML document
1518	doc = self.write_toXML(datainfo, fitstate)
1519	# Write the XML document
1520	fd = open(filename, 'w')
1521	fd.write(doc.toprettyxml())
1522	fd.close()
1523	else:
1524	fitstate.toXML(file=filename)
1525
1526	def write_toXML(self, datainfo=None, state=None):
1527	"""
1528	Write toXML, a helper for write() , could be used by guimanager._on_save()
1529
1530	: return: xml doc
1531	"""
1532
1533	if state.data is None:
1534	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1535	else:
1536	#make sure title and data run is filled up.
1537	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1538	if state.data.run_name == None or state.data.run_name=={}:
1539	state.data.run = [str(state.data.name)]
1540	state.data.run_name[0] = state.data.name
1541
1542	if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D):
1543
1544	data = state.data
1545	doc, sasentry = self._to_xml_doc(data)
1546	else:
1547	data = state.data
1548	doc, sasentry = self._data2d_to_xml_doc(data)
1549
1550
1551	if state is not None:
1552	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1553
1554	return doc
1555
1556	# Simple html report templet
1557	HEADER = "<html>\n"
1558	HEADER += "<head>\n"
1559	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1560	HEADER += "charset=windows-1252'> \n"
1561	HEADER += "<meta name=Generator >\n"
1562	HEADER += "</head>\n"
1563	HEADER += "<body lang=EN-US>\n"
1564	HEADER += "<div class=WordSection1>\n"
1565	HEADER += "<p class=MsoNormal><b><span ><center>"
1566	HEADER += "%s</center></span></center></b></p>"
1567	HEADER += "<p class=MsoNormal> </p>"
1568	PARA = "<p class=MsoNormal> %s \n"
1569	PARA += "</p>"
1570	CENTRE = "<p class=MsoNormal><center> %s \n"
1571	CENTRE += "</center></p>"
1572	FEET_1 = \
1573	"""
1574	<p class=MsoNormal> </p>
1575	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
1576	<p class=MsoNormal> </p>
1577	<center>
1578	<br>Model Computation<br>
1579	<br>Data: "%s"<br>
1580	"""
1581	FEET_2 = \
1582	"""
1583	<img src="%s" >
1584	</img>
1585	"""
1586	FEET_3 = \
1587	"""
1588	</center>
1589	</div>
1590	</body>
1591	</html>
1592	"""
1593	ELINE = "<p class=MsoNormal> </p>"
1594
1595	if __name__ == "__main__":
1596	state = PageState(parent=None)
1597	#state.toXML()
1598	"""
1599
1600	file = open("test_state", "w")
1601	pickle.dump(state, file)
1602	print pickle.dumps(state)
1603	state.data_name = "hello---->"
1604	pickle.dump(state, file)
1605	file = open("test_state", "r")
1606	new_state= pickle.load(file)
1607	print "new state", new_state
1608	new_state= pickle.load(file)
1609	print "new state", new_state
1610	#print "state", state
1611	"""
1612	import bsddb
1613	import pickle
1614	db= bsddb.btopen('file_state.db', 'c')
1615	val = (pickle.dumps(state), "hello", "hi")
1616	db['state1']= pickle.dumps(val)
1617	print pickle.loads(db['state1'])
1618	state.data_name = "hello---->22"
1619	db['state2']= pickle.dumps(state)
1620	state.data_name = "hello---->2"
1621	db['state3']= pickle.dumps(state)
1622	del db['state3']
1623	state.data_name = "hello---->3"
1624	db['state4']= pickle.dumps(state)
1625	new_state = pickle.loads(db['state1'])
1626	#print db.last()
1627	db.set_location('state2')
1628	state.data_name = "hello---->5"
1629	db['aastate5']= pickle.dumps(state)
1630	db.keys().sort()
1631	print pickle.loads(db['state2'])
1632
1633	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ 8f5b34a

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