pagestate.py @ ca2bdae

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 ca2bdae was 55bb249c, checked in by Jae Cho <jhjcho@…>, 13 years ago
added custom weighting for single fit
Property mode set to `100644`
File size: 67.7 KB

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1
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 %H;%M of %Y", t)
364
365	rep += "State created on : %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	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
372	rep += "multi_factor : %s\n"% str(self.multi_factor)
373	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
374	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
375	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
376	rep += "data : %s\n"% str(self.data)
377	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
378	str(self.qmax),str(self.npts))
379	rep += "Dispersion selection : %s\n"%str(self.disp_box)
380	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
381	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
382	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
383	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
384	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
385	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
386	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
387
388	rep += "dI_noweight : %s\n"%str(self.dI_noweight)
389	rep += "dI_didata : %s\n"%str(self.dI_didata)
390	rep += "dI_sqrdata : %s\n"%str(self.dI_sqrdata)
391	rep += "dI_idata : %s\n"%str(self.dI_idata)
392
393
394	rep += "2D enable : %s\n"%str(self.enable2D)
395	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
396	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
397	rep += "Smear object : %s\n"%str(self.smearer)
398	rep += "Smear type : %s\n"%(self.smear_type)
399	rep += "dq_l : %s\n"%self.dq_l
400	rep += "dq_r : %s\n"%self.dq_r
401
402	rep += "model : %s\n\n"% str(self.model)
403	temp_parameters = []
404	temp_fittable_param = []
405	if self.data.__class__.__name__ == "Data2D":
406	self.is_2D = True
407	else:
408	self.is_2D = False
409	if self.data is not None:
410	if not self.is_2D:
411	for item in self.parameters:
412	if not item in self.orientation_params:
413	temp_parameters.append(item)
414	for item in self.fittable_param:
415	if not item in self.orientation_params_disp:
416	temp_fittable_param.append(item)
417	else:
418	temp_parameters = self.parameters
419	temp_fittable_param = self.fittable_param
420
421	rep += "number parameters(self.parameters): %s\n"%len(temp_parameters)
422	rep = self._repr_helper( list=temp_parameters, rep=rep)
423	rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters)
424	rep = self._repr_helper( list=self.str_parameters, rep=rep)
425	rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param)
426	rep = self._repr_helper( list=temp_fittable_param, rep=rep)
427	"""
428	if is_2D:
429	rep += "number orientation parameters"
430	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
431	rep = self._repr_helper( list=self.orientation_params, rep=rep)
432	rep += "number dispersity parameters"
433	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
434	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
435	"""
436	return rep
437
438	def set_report_string(self):
439	"""
440	Get the values (strings) from __str__ for report
441	"""
442	# Dictionary of teh report strings
443	repo_time = ""
444	model_name = ""
445	title = ""
446	title_name = ""
447	file_name = ""
448	param_string = ""
449	paramval_string = ""
450	chi2_string = ""
451	multi_factor_string = ""
452	q_range = ""
453	strings = self.__repr__()
454	lines = strings.split('\n')
455
456	# get all string values from __str__()
457	for line in lines:
458	value = ""
459	content = line.split(":")
460	name = content[0]
461	try:
462	value = content[1]
463	except:
464	pass
465	if name.count("State created on"):
466	repo_time = "Created on " + value
467	if name.count("parameter name"):
468	val_name = value.split(".")
469	if len(val_name) > 1:
470	if val_name[1].count("width"):
471	param_string += value + ','
472	else:
473	continue
474	else:
475	param_string += value + ','
476	if name == "value":
477	param_string += value + ','
478	if name == "error value":
479	param_string += value + ','
480	if name == "parameter unit":
481	param_string += value + ':'
482	if name == "Value of Chisqr ":
483	chi2 = ("Chi2/Npts = " + value)
484	chi2_string = CENTRE % chi2
485	if name == "multi_factor ":
486	muti_factor = ("muti_factor = " + value)
487	muti_factor_string = CENTRE % muti_factor
488	if name == "Title":
489	if len(value.strip()) == 0:
490	continue
491	title = value + " [" + repo_time + "]"
492	title_name = HEADER % title
493	if name == "data ":
494	try:
495	file = ("File name:" + content[2])
496	file_name = CENTRE % file
497	if len(title) == 0:
498	title = content[2] + " [" + repo_time + "]"
499	title_name = HEADER % title
500	except:
501	pass
502	if name == "Plotting Range":
503	try:
504	q_range = content[1] + " = " + content[2] \
505	+ " = " + content[3].split(",")[0]
506	q_name = ("Q Range: " + q_range)
507	q_range = CENTRE % q_name
508	except:
509	pass
510	paramval = ""
511	for lines in param_string.split(":"):
512	line = lines.split(",")
513	if len(lines) > 0:
514	param = line[0]
515	param += " = " + line[1]
516	if len(line[2].split()) > 0 and not line[2].count("None"):
517	param += " +- " + line[2]
518	if len(line[3].split()) > 0 and not line[3].count("None"):
519	param += " " + line[3]
520	if not paramval.count(param):
521	paramval += param + "\n"
522	paramval_string += CENTRE % param + "\n"
523
524	text_string = "\n\n\n" + title + "\n\n" + file + \
525	"\n" + q_name + \
526	"\n" + chi2 + \
527	"\n\n" + paramval
528
529	title_name = self._check_html_format(title_name)
530	file_name = self._check_html_format(file_name)
531	title = self._check_html_format(title)
532
533	html_string = title_name + "\n" + file_name + \
534	"\n" + q_range + \
535	"\n" + chi2_string + \
536	"\n" + ELINE + \
537	"\n" + paramval_string + \
538	"\n" + ELINE + \
539	"\n" + FEET_1 % title + \
540	"\n" + FEET_2
541
542	return html_string, text_string, title
543
544	def _check_html_format(self, name):
545	"""
546	Check string '%' for html format
547	"""
548	if name.count('%'):
549	name = name.replace('%', '&#37')
550
551	return name
552
553
554	def report(self, figs=None, canvases=None):
555	"""
556	Invoke report dialog panel
557
558	: param figs: list of pylab figures [list]
559	"""
560	from report_dialog import ReportDialog
561	# get the strings for report
562	html_str, text_str, title = self.set_report_string()
563	# Allow 2 figures to append
564	if len(figs) == 1:
565	add_str = FEET_3
566	elif len(figs) == 2:
567	add_str = ELINE
568	add_str += FEET_2 % ("%s")
569	add_str += ELINE
570	add_str += FEET_3
571	elif len(figs) > 2:
572	add_str = ELINE
573	add_str += FEET_2 % ("%s")
574	add_str += ELINE
575	add_str += FEET_2 % ("%s")
576	add_str += ELINE
577	add_str += FEET_3
578	else:
579	add_str = ""
580
581	# final report html strings
582	report_str = html_str % ("%s") + add_str
583
584	# make plot image
585	images = self.set_plot_state(figs, canvases)
586	report_list = [report_str, text_str, images ]
587	dialog = ReportDialog(report_list, None, -1, "")
588	dialog.ShowModal()
589
590
591	def _toXML_helper(self, list, element, newdoc):
592	"""
593	Helper method to create xml file for saving state
594	"""
595	for item in list:
596	sub_element = newdoc.createElement('parameter')
597	sub_element.setAttribute('name', str(item[1]))
598	sub_element.setAttribute('value', str(item[2]))
599	sub_element.setAttribute('selected_to_fit', str(item[0]))
600	sub_element.setAttribute('error_displayed', str(item[4][0]))
601	sub_element.setAttribute('error_value', str(item[4][1]))
602	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
603	sub_element.setAttribute('minimum_value', str(item[5][1]))
604	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
605	sub_element.setAttribute('maximum_value', str(item[6][1]))
606	sub_element.setAttribute('unit', str(item[7]))
607	element.appendChild(sub_element)
608
609	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
610	"""
611	Writes the state of the InversionControl panel to file, as XML.
612
613	Compatible with standalone writing, or appending to an
614	already existing XML document. In that case, the XML document
615	is required. An optional entry node in the XML document may also be given.
616
617	:param file: file to write to
618	:param doc: XML document object [optional]
619	:param entry_node: XML node within the XML document at which we will append the data [optional]
620
621	"""
622	from xml.dom.minidom import getDOMImplementation
623
624	# Check whether we have to write a standalone XML file
625	if doc is None:
626	impl = getDOMImplementation()
627	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
628	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
629	top_element = newdoc.documentElement
630	else:
631	# We are appending to an existing document
632	newdoc = doc
633	top_element = newdoc.createElement(FITTING_NODE_NAME)
634	if entry_node is None:
635	newdoc.documentElement.appendChild(top_element)
636	else:
637	entry_node.appendChild(top_element)
638
639	attr = newdoc.createAttribute("version")
640	attr.nodeValue = '1.0'
641	top_element.setAttributeNode(attr)
642
643	# File name
644	element = newdoc.createElement("filename")
645	if self.file is not None:
646	element.appendChild(newdoc.createTextNode(str(self.file)))
647	else:
648	element.appendChild(newdoc.createTextNode(str(file)))
649	top_element.appendChild(element)
650
651	element = newdoc.createElement("timestamp")
652	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
653	attr = newdoc.createAttribute("epoch")
654	attr.nodeValue = str(self.timestamp)
655	element.setAttributeNode(attr)
656	top_element.appendChild(element)
657	# Inputs
658	inputs = newdoc.createElement("Attributes")
659	top_element.appendChild(inputs)
660
661
662	if self.data is not None and hasattr(self.data, "group_id"):
663	self.data_group_id = self.data.group_id
664	if self.data is not None and hasattr(self.data, "is_data"):
665	self.is_data = self.data.is_data
666	if self.data is not None:
667	self.data_name = self.data.name
668	if self.data is not None and hasattr(self.data, "id"):
669	self.data_id = self.data.id
670
671	for item in list_of_data_attributes:
672	element = newdoc.createElement(item[0])
673	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
674	inputs.appendChild(element)
675
676	for item in list_of_state_attributes:
677	element = newdoc.createElement(item[0])
678	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
679	inputs.appendChild(element)
680
681	# For self.values ={ disp_param_name: [vals,...],...}
682	# and for self.weights ={ disp_param_name: [weights,...],...}
683	for item in list_of_model_attributes:
684	element = newdoc.createElement(item[0])
685	exec "list = self.%s" % item[1]
686	for key, value in list.iteritems():
687	sub_element = newdoc.createElement(key)
688	sub_element.setAttribute('name', str(key))
689	for val in value:
690	com = "sub_element.appendChild"
691	com += "(newdoc.createTextNode(str(%s)))"
692	exec com % val
693
694	element.appendChild(sub_element)
695	inputs.appendChild(element)
696
697	# Create doc for the dictionary of self._disp_obj_dic
698	for item in list_of_obj_dic:
699	element = newdoc.createElement(item[0])
700	exec "list = self.%s" % item[1]
701	for key, val in list.iteritems():
702	value = repr(val)
703	sub_element = newdoc.createElement(key)
704	sub_element.setAttribute('name', str(key))
705	sub_element.setAttribute('value', str(value))
706	element.appendChild(sub_element)
707	inputs.appendChild(element)
708
709	for item in list_of_state_parameters:
710	element = newdoc.createElement(item[0])
711	com = "self._toXML_helper(list=self.%s,"
712	com += " element=element, newdoc=newdoc)"
713	exec com % item[1]
714	inputs.appendChild(element)
715
716	# Save the file
717	if doc is None:
718	fd = open(file, 'w')
719	fd.write(newdoc.toprettyxml())
720	fd.close()
721	return None
722	else:
723	return newdoc.toprettyxml()
724
725	def _fromXML_helper(self, node, list):
726	"""
727	Helper function to write state to xml
728	"""
729	for item in node:
730	try:
731	name = item.get('name')
732	except:
733	name = None
734	try:
735	value = item.get('value')
736	except:
737	value = None
738	try:
739	selected_to_fit = (item.get('selected_to_fit') == "True")
740	except:
741	selected_to_fit = None
742	try:
743	error_displayed = (item.get('error_displayed') == "True")
744	except:
745	error_displayed = None
746	try:
747	error_value = item.get('error_value')
748	except:
749	error_value = None
750	try:
751	minimum_displayed = (item.get('minimum_displayed')== "True")
752	except:
753	minimum_displayed = None
754	try:
755	minimum_value = item.get('minimum_value')
756	except:
757	minimum_value = None
758	try:
759	maximum_displayed = (item.get('maximum_displayed') == "True")
760	except:
761	maximum_displayed = None
762	try:
763	maximum_value = item.get('maximum_value')
764	except:
765	maximum_value = None
766	try:
767	unit = item.get('unit')
768	except:
769	unit = None
770	list.append([selected_to_fit, name, value, "+/-",
771	[error_displayed, error_value],
772	[minimum_displayed,minimum_value],
773	[maximum_displayed,maximum_value], unit])
774
775	def fromXML(self, file=None, node=None):
776	"""
777	Load fitting state from a file
778
779	:param file: .fitv file
780	:param node: node of a XML document to read from
781
782	"""
783	if file is not None:
784	msg = "PageState no longer supports non-CanSAS"
785	msg += " format for fitting files"
786	raise RuntimeError, msg
787
788	if node.get('version')and node.get('version') == '1.0':
789
790	# Get file name
791	entry = get_content('ns:filename', node)
792	if entry is not None:
793	self.file = entry.text.strip()
794
795	# Get time stamp
796	entry = get_content('ns:timestamp', node)
797	if entry is not None and entry.get('epoch'):
798	try:
799	self.timestamp = float(entry.get('epoch'))
800	except:
801	msg = "PageState.fromXML: Could not"
802	msg += " read timestamp\n %s" % sys.exc_value
803	logging.error(msg)
804
805	# Parse fitting attributes
806	entry = get_content('ns:Attributes', node)
807	for item in list_of_data_attributes:
808	node = get_content('ns:%s'%item[0], entry)
809	try:
810	exec "self.%s = parse_entry_helper(node, item)" % item[0]
811
812	except:
813	raise
814
815	if entry is not None:
816
817	for item in list_of_state_attributes:
818	node = get_content('ns:%s' % item[0], entry)
819	try:
820	exec "self.%s = parse_entry_helper(node, item)" % \
821	str(item[0])
822	except:
823	raise
824
825	for item in list_of_state_parameters:
826	node = get_content("ns:%s" % item[0], entry)
827	exec "self._fromXML_helper(node=node, list=self.%s)" % \
828	item[1]
829
830	# Recover _disp_obj_dict from xml file
831	self._disp_obj_dict = {}
832	for item in list_of_obj_dic:
833	# Get node
834	node = get_content("ns:%s" % item[0], entry)
835	for attr in node:
836	name = attr.get('name')
837	val = attr.get('value')
838	value = val.split(" instance")[0]
839	disp_name = value.split("<")[1]
840	try:
841	# Try to recover disp_model object from strings
842	com = "from sans.models.dispersion_models "
843	com += "import %s as disp"
844	com_name = disp_name.split(".")[3]
845	exec com % com_name
846	disp_model = disp()
847	exec "self.%s['%s'] = com_name" % (item[1], name)
848	except:
849	pass
850
851	# get self.values and self.weights dic. if exists
852	for item in list_of_model_attributes:
853	node = get_content("ns:%s" % item[0], entry)
854	dic = {}
855	list = []
856	for par in node:
857	name = par.get('name')
858	values = par.text.split('\n')
859	# Get lines only with numbers
860	for line in values:
861	try:
862	val= float(line)
863	list.append(val)
864	except:
865	# pass if line is empty (it happens)
866	pass
867	dic[name] = numpy.array(list)
868	exec "self.%s = dic" % item[1]
869
870	def set_plot_state(self, figs, canvases):
871	"""
872	Build image state that wx.html understand
873	by plotting, putting it into wx.FileSystem image object
874
875	"""
876	images = []
877	# some imports
878	import wx
879
880	# Reset memory
881	self.imgRAM = None
882	wx.MemoryFSHandler()
883
884	# For no figures in the list, prepare empty plot
885	if figs == None or len(figs) == 0:
886	figs = [None]
887
888	# Loop over the list of figures
889	# use wx.MemoryFSHandler
890	self.imgRAM = wx.MemoryFSHandler()
891	for fig in figs:
892	if figs != None:
893	#fig.set_facecolor('w')
894	ind = figs.index(fig)
895	canvas = canvases[ind]
896
897	#bmp = wx.BitmapDataObject()
898	#bmp.SetBitmap(canvas.bitmap)
899	#store the image in wx.FileSystem Object
900	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
901
902	# index of the fig
903	ind = figs.index(fig)
904
905	#AddFile, image can be retrieved with 'memory:filename'
906	self.imgRAM.AddFile('img_fit%s.png' % ind ,
907	canvas.bitmap, wx.BITMAP_TYPE_PNG)
908
909	#append figs
910	images.append(fig)
911
912	return images
913
914	class Reader(CansasReader):
915	"""
916	Class to load a .fitv fitting file
917	"""
918	## File type
919	type_name = "Fitting"
920
921	## Wildcards
922	type = ["Fitting files (.fitv)\|.fitv"
923	"SANSView file (.svs)\|.svs"]
924	## List of allowed extensions
925	ext=['.fitv', '.FITV', '.svs', 'SVS']
926
927	def __init__(self, call_back=None, cansas=True):
928	CansasReader.__init__(self)
929	"""
930	Initialize the call-back method to be called
931	after we load a file
932
933	:param call_back: call-back method
934	:param cansas: True = files will be written/read in CanSAS format
935	False = write CanSAS format
936
937	"""
938	## Call back method to be executed after a file is read
939	self.call_back = call_back
940	## CanSAS format flag
941	self.cansas = cansas
942	self.state = None
943	def get_state(self):
944	return self.state
945
946	def read(self, path):
947	"""
948	Load a new P(r) inversion state from file
949
950	:param path: file path
951
952	"""
953	if self.cansas == True:
954	return self._read_cansas(path)
955
956	def _data2d_to_xml_doc(self, datainfo):
957	"""
958	Create an XML document to contain the content of a Data2D
959
960	:param datainfo: Data2D object
961
962	"""
963	if not issubclass(datainfo.__class__, Data2D):
964	raise RuntimeError, "The cansas writer expects a Data2D instance"
965
966	doc = xml.dom.minidom.Document()
967	main_node = doc.createElement("SASroot")
968	main_node.setAttribute("version", self.version)
969	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
970	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
971	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
972
973	doc.appendChild(main_node)
974
975	entry_node = doc.createElement("SASentry")
976	main_node.appendChild(entry_node)
977
978	write_node(doc, entry_node, "Title", datainfo.title)
979	if datainfo is not None:
980	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
981	for item in datainfo.run:
982	runname = {}
983	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
984	runname = {'name': datainfo.run_name[item] }
985	write_node(doc, entry_node, "Run", item, runname)
986	# Data info
987	new_node = doc.createElement("SASdata")
988	entry_node.appendChild(new_node)
989	for item in list_of_data_2d_attr:
990	element = doc.createElement(item[0])
991	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
992	new_node.appendChild(element)
993
994	for item in list_of_data2d_values:
995	root_node = doc.createElement(item[0])
996	new_node.appendChild(root_node)
997
998	exec "temp_list = datainfo.%s"%item[1]
999
1000	if temp_list is None or len(temp_list)== 0:
1001	element = doc.createElement(item[0])
1002	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
1003	root_node.appendChild(element)
1004	else:
1005	for value in temp_list:
1006	element = doc.createElement(item[0])
1007	exec "element.setAttribute(item[0], str(%s))"%value
1008	root_node.appendChild(element)
1009
1010	# Sample info
1011	sample = doc.createElement("SASsample")
1012	if datainfo.sample.name is not None:
1013	sample.setAttribute("name", str(datainfo.sample.name))
1014	entry_node.appendChild(sample)
1015	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1016	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
1017	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1018	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
1019
1020	for item in datainfo.sample.details:
1021	write_node(doc, sample, "details", item)
1022
1023	pos = doc.createElement("position")
1024	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
1025	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
1026	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
1027	if written == True:
1028	sample.appendChild(pos)
1029
1030	ori = doc.createElement("orientation")
1031	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
1032	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1033	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1034	if written == True:
1035	sample.appendChild(ori)
1036
1037	# Instrument info
1038	instr = doc.createElement("SASinstrument")
1039	entry_node.appendChild(instr)
1040
1041	write_node(doc, instr, "name", datainfo.instrument)
1042
1043	# Source
1044	source = doc.createElement("SASsource")
1045	if datainfo.source.name is not None:
1046	source.setAttribute("name", str(datainfo.source.name))
1047	instr.appendChild(source)
1048
1049	write_node(doc, source, "radiation", datainfo.source.radiation)
1050	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1051	size = doc.createElement("beam_size")
1052	if datainfo.source.beam_size_name is not None:
1053	size.setAttribute("name", str(datainfo.source.beam_size_name))
1054	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1055	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1056	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1057	if written == True:
1058	source.appendChild(size)
1059
1060	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1061	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1062	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1063	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1064
1065	# Collimation
1066	for item in datainfo.collimation:
1067	coll = doc.createElement("SAScollimation")
1068	if item.name is not None:
1069	coll.setAttribute("name", str(item.name))
1070	instr.appendChild(coll)
1071
1072	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1073
1074	for apert in item.aperture:
1075	ap = doc.createElement("aperture")
1076	if apert.name is not None:
1077	ap.setAttribute("name", str(apert.name))
1078	if apert.type is not None:
1079	ap.setAttribute("type", str(apert.type))
1080	coll.appendChild(ap)
1081
1082	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1083
1084	size = doc.createElement("size")
1085	if apert.size_name is not None:
1086	size.setAttribute("name", str(apert.size_name))
1087	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1088	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1089	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1090	if written == True:
1091	ap.appendChild(size)
1092
1093	# Detectors
1094	for item in datainfo.detector:
1095	det = doc.createElement("SASdetector")
1096	written = write_node(doc, det, "name", item.name)
1097	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1098	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1099	if written == True:
1100	instr.appendChild(det)
1101
1102	off = doc.createElement("offset")
1103	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1104	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1105	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1106	if written == True:
1107	det.appendChild(off)
1108
1109	center = doc.createElement("beam_center")
1110	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1111	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1112	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1113	if written == True:
1114	det.appendChild(center)
1115
1116	pix = doc.createElement("pixel_size")
1117	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1118	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1119	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1120	if written == True:
1121	det.appendChild(pix)
1122
1123	ori = doc.createElement("orientation")
1124	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1125	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1126	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1127	if written == True:
1128	det.appendChild(ori)
1129
1130	# Processes info
1131	for item in datainfo.process:
1132	node = doc.createElement("SASprocess")
1133	entry_node.appendChild(node)
1134
1135	write_node(doc, node, "name", item.name)
1136	write_node(doc, node, "date", item.date)
1137	write_node(doc, node, "description", item.description)
1138	for term in item.term:
1139	value = term['value']
1140	del term['value']
1141	write_node(doc, node, "term", value, term)
1142	for note in item.notes:
1143	write_node(doc, node, "SASprocessnote", note)
1144	# Return the document, and the SASentry node associated with
1145	# the data we just wrote
1146	return doc, entry_node
1147
1148	def _parse_state(self, entry):
1149	"""
1150	Read a fit result from an XML node
1151
1152	:param entry: XML node to read from
1153
1154	:return: PageState object
1155	"""
1156	# Create an empty state
1157	state = None
1158	# Locate the P(r) node
1159	try:
1160	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
1161	if nodes !=[]:
1162	# Create an empty state
1163	state = PageState()
1164	state.fromXML(node=nodes[0])
1165	except:
1166	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1167
1168	return state
1169
1170
1171
1172	def _parse_entry(self, dom):
1173	"""
1174	Parse a SASentry
1175
1176	:param node: SASentry node
1177
1178	:return: Data1D/Data2D object
1179
1180	"""
1181	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1182	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1183	return CansasReader._parse_entry(self, dom)
1184
1185	#Parse 2D
1186	data_info = Data2D()
1187
1188	# Look up title
1189	self._store_content('ns:Title', dom, 'title', data_info)
1190
1191	# Look up run number
1192	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1193	for item in nodes:
1194	if item.text is not None:
1195	value = item.text.strip()
1196	if len(value) > 0:
1197	data_info.run.append(value)
1198	if item.get('name') is not None:
1199	data_info.run_name[value] = item.get('name')
1200
1201	# Look up instrument name
1202	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1203
1204	# Notes
1205	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1206	for note in note_list:
1207	try:
1208	if note.text is not None:
1209	note_value = note.text.strip()
1210	if len(note_value) > 0:
1211	data_info.notes.append(note_value)
1212	except:
1213	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1214	self.errors.append(err_mess)
1215	logging.error(err_mess)
1216
1217	# Sample info ###################
1218	entry = get_content('ns:SASsample', dom)
1219	if entry is not None:
1220	data_info.sample.name = entry.get('name')
1221
1222	self._store_content('ns:SASsample/ns:ID',
1223	dom, 'ID', data_info.sample)
1224	self._store_float('ns:SASsample/ns:thickness',
1225	dom, 'thickness', data_info.sample)
1226	self._store_float('ns:SASsample/ns:transmission',
1227	dom, 'transmission', data_info.sample)
1228	self._store_float('ns:SASsample/ns:temperature',
1229	dom, 'temperature', data_info.sample)
1230
1231	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1232	for item in nodes:
1233	try:
1234	if item.text is not None:
1235	detail_value = item.text.strip()
1236	if len(detail_value) > 0:
1237	data_info.sample.details.append(detail_value)
1238	except:
1239	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1240	self.errors.append(err_mess)
1241	logging.error(err_mess)
1242
1243	# Position (as a vector)
1244	self._store_float('ns:SASsample/ns:position/ns:x',
1245	dom, 'position.x', data_info.sample)
1246	self._store_float('ns:SASsample/ns:position/ns:y',
1247	dom, 'position.y', data_info.sample)
1248	self._store_float('ns:SASsample/ns:position/ns:z',
1249	dom, 'position.z', data_info.sample)
1250
1251	# Orientation (as a vector)
1252	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1253	dom, 'orientation.x', data_info.sample)
1254	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1255	dom, 'orientation.y', data_info.sample)
1256	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1257	dom, 'orientation.z', data_info.sample)
1258
1259	# Source info ###################
1260	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1261	if entry is not None:
1262	data_info.source.name = entry.get('name')
1263
1264	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1265	dom, 'radiation', data_info.source)
1266	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1267	dom, 'beam_shape', data_info.source)
1268	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1269	dom, 'wavelength', data_info.source)
1270	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1271	dom, 'wavelength_min', data_info.source)
1272	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1273	dom, 'wavelength_max', data_info.source)
1274	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1275	dom, 'wavelength_spread', data_info.source)
1276
1277	# Beam size (as a vector)
1278	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1279	if entry is not None:
1280	data_info.source.beam_size_name = entry.get('name')
1281
1282	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1283	dom, 'beam_size.x', data_info.source)
1284	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1285	dom, 'beam_size.y', data_info.source)
1286	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1287	dom, 'beam_size.z', data_info.source)
1288
1289	# Collimation info ###################
1290	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
1291	for item in nodes:
1292	collim = Collimation()
1293	if item.get('name') is not None:
1294	collim.name = item.get('name')
1295	self._store_float('ns:length', item, 'length', collim)
1296
1297	# Look for apertures
1298	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
1299	for apert in apert_list:
1300	aperture = Aperture()
1301
1302	# Get the name and type of the aperture
1303	aperture.name = apert.get('name')
1304	aperture.type = apert.get('type')
1305
1306	self._store_float('ns:distance', apert, 'distance', aperture)
1307
1308	entry = get_content('ns:size', apert)
1309	if entry is not None:
1310	aperture.size_name = entry.get('name')
1311
1312	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1313	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1314	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1315
1316	collim.aperture.append(aperture)
1317
1318	data_info.collimation.append(collim)
1319
1320	# Detector info ######################
1321	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1322	for item in nodes:
1323
1324	detector = Detector()
1325
1326	self._store_content('ns:name', item, 'name', detector)
1327	self._store_float('ns:SDD', item, 'distance', detector)
1328
1329	# Detector offset (as a vector)
1330	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1331	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1332	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1333
1334	# Detector orientation (as a vector)
1335	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1336	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1337	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1338
1339	# Beam center (as a vector)
1340	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1341	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1342	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1343
1344	# Pixel size (as a vector)
1345	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1346	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1347	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1348
1349	self._store_float('ns:slit_length', item, 'slit_length', detector)
1350
1351	data_info.detector.append(detector)
1352
1353	# Processes info ######################
1354	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1355	for item in nodes:
1356	process = Process()
1357	self._store_content('ns:name', item, 'name', process)
1358	self._store_content('ns:date', item, 'date', process)
1359	self._store_content('ns:description', item, 'description', process)
1360
1361	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1362	for term in term_list:
1363	try:
1364	term_attr = {}
1365	for attr in term.keys():
1366	term_attr[attr] = term.get(attr).strip()
1367	if term.text is not None:
1368	term_attr['value'] = term.text.strip()
1369	process.term.append(term_attr)
1370	except:
1371	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1372	self.errors.append(err_mess)
1373	logging.error(err_mess)
1374
1375	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1376	for note in note_list:
1377	if note.text is not None:
1378	process.notes.append(note.text.strip())
1379
1380	data_info.process.append(process)
1381
1382
1383	# Data info ######################
1384	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1385	if len(nodes)>1:
1386	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1387
1388	for entry in nodes:
1389	for item in list_of_data_2d_attr:
1390	#get node
1391	node = get_content('ns:%s'%item[0], entry)
1392	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1393
1394	for item in list_of_data2d_values:
1395	field = get_content('ns:%s'%item[0], entry)
1396	list = []
1397	if field is not None:
1398	list = [parse_entry_helper(node, item) for node in field]
1399	exec "data_info.%s = numpy.array(list)"%item[0]
1400
1401	return data_info
1402
1403	def _read_cansas(self, path):
1404	"""
1405	Load data and P(r) information from a CanSAS XML file.
1406
1407	:param path: file path
1408
1409	:return: Data1D object if a single SASentry was found,
1410	or a list of Data1D objects if multiple entries were found,
1411	or None of nothing was found
1412
1413	:raise RuntimeError: when the file can't be opened
1414	:raise ValueError: when the length of the data vectors are inconsistent
1415
1416	"""
1417	output = []
1418	basename = os.path.basename(path)
1419	root, extension = os.path.splitext(basename)
1420	ext = extension.lower()
1421	try:
1422	if os.path.isfile(path):
1423
1424	#TODO: eventually remove the check for .xml once
1425	# the P(r) writer/reader is truly complete.
1426	if ext in self.ext or \
1427	ext == '.xml':
1428
1429	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1430	# Check the format version number
1431	# Specifying the namespace will take care of the file format version
1432	root = tree.getroot()
1433	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1434	for entry in entry_list:
1435	try:
1436	sas_entry = self._parse_entry(entry)
1437	except:
1438	raise
1439	fitstate = self._parse_state(entry)
1440
1441	#state could be None when .svs file is loaded
1442	#in this case, skip appending to output
1443	if fitstate != None:
1444	sas_entry.meta_data['fitstate'] = fitstate
1445	sas_entry.filename = fitstate.file
1446	output.append(sas_entry)
1447	else:
1448	self.call_back(format=ext)
1449	raise RuntimeError, "%s is not a file" % path
1450
1451	# Return output consistent with the loader's api
1452	if len(output)==0:
1453	self.call_back(state=None, datainfo=None,format=ext)
1454	return None
1455	else:
1456	for ind in range(len(output)):
1457	# Call back to post the new state
1458	state = output[ind].meta_data['fitstate']
1459	t = time.localtime(state.timestamp)
1460	time_str = time.strftime("%b %d %H:%M", t)
1461	# Check that no time stamp is already appended
1462	max_char = state.file.find("[")
1463	if max_char < 0:
1464	max_char = len(state.file)
1465	original_fname = state.file[0:max_char]
1466	state.file = original_fname +' [' + time_str + ']'
1467
1468
1469	if state is not None and state.is_data is not None:
1470	exec 'output[%d].is_data = state.is_data'% ind
1471
1472	output[ind].filename = state.file
1473	state.data = output[ind]
1474	state.data.name = output[ind].filename #state.data_name
1475	state.data.id = state.data_id
1476	if state.is_data is not None:
1477	state.data.is_data = state.is_data
1478	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1479	name = output[ind].run_name
1480	else:
1481	name=original_fname
1482	state.data.group_id = name
1483	#store state in fitting
1484	self.call_back(state=state, datainfo=output[ind],format=ext)
1485	self.state= state
1486	return output
1487
1488	except:
1489	self.call_back(format=ext)
1490	#self.state= state
1491	raise
1492
1493	def write(self, filename, datainfo=None, fitstate=None):
1494	"""
1495	Write the content of a Data1D as a CanSAS XML file only for standalone
1496
1497	:param filename: name of the file to write
1498	:param datainfo: Data1D object
1499	:param fitstate: PageState object
1500
1501	"""
1502	# Sanity check
1503	if self.cansas == True:
1504
1505	# Add fitting information to the XML document
1506	doc = self.write_toXML(datainfo, fitstate)
1507	# Write the XML document
1508	fd = open(filename, 'w')
1509	fd.write(doc.toprettyxml())
1510	fd.close()
1511	else:
1512	fitstate.toXML(file=filename)
1513
1514	def write_toXML(self, datainfo=None, state=None):
1515	"""
1516	Write toXML, a helper for write() , could be used by guimanager._on_save()
1517
1518	: return: xml doc
1519	"""
1520
1521	if state.data is None:
1522	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1523	else:
1524	#make sure title and data run is filled up.
1525	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1526	if state.data.run_name == None or state.data.run_name=={}:
1527	state.data.run = [str(state.data.name)]
1528	state.data.run_name[0] = state.data.name
1529
1530	if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D):
1531
1532	data = state.data
1533	doc, sasentry = self._to_xml_doc(data)
1534	else:
1535	data = state.data
1536	doc, sasentry = self._data2d_to_xml_doc(data)
1537
1538
1539	if state is not None:
1540	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1541
1542	return doc
1543
1544	# Simple html report templet
1545	HEADER = "<html>\n"
1546	HEADER += "<head>\n"
1547	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1548	HEADER += "charset=windows-1252'> \n"
1549	HEADER += "<meta name=Generator >\n"
1550	HEADER += "</head>\n"
1551	HEADER += "<body lang=EN-US>\n"
1552	HEADER += "<div class=WordSection1>\n"
1553	HEADER += "<p class=MsoNormal><b><span ><center>"
1554	HEADER += "%s</center></span></center></b></p>"
1555	HEADER += "<p class=MsoNormal> </p>"
1556	PARA = "<p class=MsoNormal> %s \n"
1557	PARA += "</p>"
1558	CENTRE = "<p class=MsoNormal><center> %s \n"
1559	CENTRE += "</center></p>"
1560	FEET_1 = \
1561	"""
1562	<p class=MsoNormal> </p>
1563	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
1564	<p class=MsoNormal> </p>
1565	<center>
1566	<br>Model Computation<br>
1567	<br>Data: "%s"<br>
1568	"""
1569	FEET_2 = \
1570	"""
1571	<img src="%s" >
1572	</img>
1573	"""
1574	FEET_3 = \
1575	"""
1576	</center>
1577	</div>
1578	</body>
1579	</html>
1580	"""
1581	ELINE = "<p class=MsoNormal> </p>"
1582
1583	if __name__ == "__main__":
1584	state = PageState(parent=None)
1585	#state.toXML()
1586	"""
1587
1588	file = open("test_state", "w")
1589	pickle.dump(state, file)
1590	print pickle.dumps(state)
1591	state.data_name = "hello---->"
1592	pickle.dump(state, file)
1593	file = open("test_state", "r")
1594	new_state= pickle.load(file)
1595	print "new state", new_state
1596	new_state= pickle.load(file)
1597	print "new state", new_state
1598	#print "state", state
1599	"""
1600	import bsddb
1601	import pickle
1602	db= bsddb.btopen('file_state.db', 'c')
1603	val = (pickle.dumps(state), "hello", "hi")
1604	db['state1']= pickle.dumps(val)
1605	print pickle.loads(db['state1'])
1606	state.data_name = "hello---->22"
1607	db['state2']= pickle.dumps(state)
1608	state.data_name = "hello---->2"
1609	db['state3']= pickle.dumps(state)
1610	del db['state3']
1611	state.data_name = "hello---->3"
1612	db['state4']= pickle.dumps(state)
1613	new_state = pickle.loads(db['state1'])
1614	#print db.last()
1615	db.set_location('state2')
1616	state.data_name = "hello---->5"
1617	db['aastate5']= pickle.dumps(state)
1618	db.keys().sort()
1619	print pickle.loads(db['state2'])
1620
1621	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ ca2bdae

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