pagestate.py @ f7d0b74

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 f7d0b74 was c0ff8cc, checked in by Jae Cho <jhjcho@…>, 14 years ago
fixed problem in saving w/multifunctional models
Property mode set to `100644`
File size: 66.5 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 DataLoader
25	from DataLoader.readers.cansas_reader import Reader as CansasReader
26	from DataLoader.readers.cansas_reader import get_content, write_node
27	from 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	["slit_smearer","slit_smearer","bool"],
57	["enable2D","enable2D","bool"],
58	["cb1","cb1","bool"],
59	["tcChi","tcChi","float"],
60	["smearer", "smearer", "float"],
61	["smear_type","smear_type", "string"],
62	["dq_l", "dq_l", "string"],
63	["dq_r","dq_r", "string"]]
64
65	list_of_model_attributes = [["values", "values"],
66	["weights", "weights"]]
67
68	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
69
70	list_of_state_parameters = [["parameters", "parameters"] ,
71	["str_parameters", "str_parameters"] ,
72	["orientation_parameters", "orientation_params"],
73	["dispersity_parameters", "orientation_params_disp"],
74	["fixed_param", "fixed_param"],
75	["fittable_param","fittable_param"]]
76	list_of_data_2d_attr = [["xmin", "xmin","float"],
77	["xmax","xmax","float"],
78	["ymin","ymin","float"],
79	["ymax","ymax","float"],
80	["_xaxis","_xaxis", "string"],
81	["_xunit", "_xunit", "string"],
82	["_yaxis","_yaxis","string"],
83	["_yunit","_yunit","string"],
84	["_zaxis","_zaxis","string"],
85	["_zunit","_zunit","string"]]
86	list_of_data2d_values = [["qx_data","qx_data","float"],
87	["qy_data","qy_data","float"],
88	["dqx_data","dqx_data","float"],
89	["dqy_data","dqy_data","float"],
90	["data","data","float"],
91	["q_data","q_data","float"],
92	["err_data","err_data","float"],
93	["mask","mask","bool"]]
94
95	def parse_entry_helper( node, item):
96	"""
97	Create a numpy list from value extrated from the node
98
99	:param node: node from each the value is stored
100	:param item: list name of three strings.the two first are name of data
101	attribute and the third one is the type of the value of that
102	attribute. type can be string, float, bool, etc.
103
104	: return: numpy array
105	"""
106	if node is not None:
107	if item[2] == "string":
108	return str(node.get(item[0]).strip())
109	elif item[2] == "bool":
110	try:
111	return node.get(item[0]).strip() == "True"
112
113	except:
114	return None
115	else:
116	try:
117	return float(node.get(item[0]))
118	except:
119	return None
120
121
122	class PageState(object):
123	"""
124	Contains information to reconstruct a page of the fitpanel.
125	"""
126	def __init__(self, parent=None, model=None, data=None):
127
128	"""
129	Initialize the current state
130
131	:param model: a selected model within a page
132	:param data:
133
134	"""
135	self.file = None
136	#Time of state creation
137	self.timestamp = time.time()
138	## Data member to store the dispersion object created
139	self._disp_obj_dict = {}
140	#------------------------
141	#Data used for fitting
142	self.data = data
143	# model data
144	self.theory_data = None
145	#Is 2D
146	self.is_2D = False
147	self.images = None
148
149	#save additional information on data that dataloader.reader does not read
150	self.is_data = None
151	self.data_name = ""
152
153	if self.data is not None:
154	self.data_name = self.data.name
155	self.data_id = None
156	if self.data is not None and hasattr(self.data, "id"):
157	self.data_id = self.data.id
158	self.data_group_id = None
159	if self.data is not None and hasattr(self.data, "group_id"):
160	self.data_group_id = self.data.group_id
161
162	## reset True change the state of exsiting button
163	self.reset = False
164
165	#engine type
166	self.engine_type = None
167	# flag to allow data2D plot
168	self.enable2D = False
169	# model on which the fit would be performed
170	self.model = model
171	#list of process done to model
172	self.process = []
173	#fit page manager
174	self.manager = None
175	#Store the parent of this panel parent
176	# For this application fitpanel is the parent
177	self.parent = parent
178	# Event_owner is the owner of model event
179	self.event_owner = None
180	##page name
181	self.page_name = ""
182	# Contains link between model ,all its parameters, and panel organization
183	self.parameters = []
184	# String parameter list that can not be fitted
185	self.str_parameters = []
186	# Contains list of parameters that cannot be fitted and reference to
187	#panel objects
188	self.fixed_param = []
189	# Contains list of parameters with dispersity and reference to
190	#panel objects
191	self.fittable_param = []
192	## orientation parameters
193	self.orientation_params = []
194	## orientation parmaters for gaussian dispersity
195	self.orientation_params_disp = []
196	## smearer info
197	self.smearer = None
198	self.smear_type = None
199	self.dq_l = None
200	self.dq_r = None
201
202	#list of dispersion paramaters
203	self.disp_list =[]
204	if self.model is not None:
205	self.disp_list = self.model.getDispParamList()
206
207	self.disp_cb_dict = {}
208	self.values = {}
209	self.weights = {}
210
211	#contains link between a model and selected parameters to fit
212	self.param_toFit = []
213	##dictionary of model type and model class
214	self.model_list_box = None
215	## save the state of the context menu
216	self.saved_states = {}
217	## save selection of combobox
218	self.formfactorcombobox = None
219	self.structurecombobox = None
220
221	## radio box to select type of model
222	self.shape_rbutton = False
223	self.shape_indep_rbutton = False
224	self.struct_rbutton = False
225	self.plugin_rbutton = False
226	## the indice of the current selection
227	self.disp_box = 0
228	## Qrange
229	## Q range
230	self.qmin = 0.001
231	self.qmax = 0.1
232	#reset data range
233	self.qmax_x = None
234	self.qmin_x = None
235
236	self.npts = None
237	self.name = ""
238	self.multi_factor = None
239	## enable smearering state
240	self.enable_smearer = False
241	self.disable_smearer = True
242	self.pinhole_smearer = False
243	self.slit_smearer = False
244	## disperity selection
245	self.enable_disp = False
246	self.disable_disp = True
247
248	## state of selected all check button
249	self.cb1 = False
250	## store value of chisqr
251	self.tcChi = None
252
253	def clone(self):
254	"""
255	Create a new copy of the current object
256	"""
257	model = None
258	if self.model is not None:
259	model = self.model.clone()
260	model.name = self.model.name
261	obj = PageState(self.parent, model=model)
262	obj.file = copy.deepcopy(self.file)
263	obj.data = copy.deepcopy(self.data)
264	if self.data is not None:
265	self.data_name = self.data.name
266	obj.data_name = self.data_name
267	obj.is_data = self.is_data
268	obj.model_list_box = copy.deepcopy(self.model_list_box)
269	obj.engine_type = copy.deepcopy(self.engine_type)
270
271	obj.formfactorcombobox = self.formfactorcombobox
272	obj.structurecombobox = self.structurecombobox
273
274	obj.shape_rbutton = self.shape_rbutton
275	obj.shape_indep_rbutton = self.shape_indep_rbutton
276	obj.struct_rbutton = self.struct_rbutton
277	obj.plugin_rbutton = self.plugin_rbutton
278
279	obj.manager = self.manager
280	obj.event_owner = self.event_owner
281	obj.disp_list = copy.deepcopy(self.disp_list)
282
283	obj.enable2D = copy.deepcopy(self.enable2D)
284	obj.parameters = copy.deepcopy(self.parameters)
285	obj.str_parameters = copy.deepcopy(self.str_parameters)
286	obj.fixed_param = copy.deepcopy(self.fixed_param)
287	obj.fittable_param = copy.deepcopy(self.fittable_param)
288	obj.orientation_params = copy.deepcopy(self.orientation_params)
289	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
290	obj.enable_disp = copy.deepcopy(self.enable_disp)
291	obj.disable_disp = copy.deepcopy(self.disable_disp)
292	obj.tcChi = self.tcChi
293
294	if len(self._disp_obj_dict)>0:
295	for k , v in self._disp_obj_dict.iteritems():
296	obj._disp_obj_dict[k]= v
297	if len(self.disp_cb_dict)>0:
298	for k , v in self.disp_cb_dict.iteritems():
299	obj.disp_cb_dict[k]= v
300	if len(self.values)>0:
301	for k , v in self.values.iteritems():
302	obj.values[k] = v
303	if len(self.weights)>0:
304	for k , v in self.weights.iteritems():
305	obj.weights[k] = v
306	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
307	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
308	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
309	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
310	obj.smear_type = copy.deepcopy(self.smear_type)
311	obj.dq_l = copy.deepcopy(self.dq_l)
312	obj.dq_r = copy.deepcopy(self.dq_r)
313
314	obj.disp_box = copy.deepcopy(self.disp_box)
315	obj.qmin = copy.deepcopy(self.qmin)
316	obj.qmax = copy.deepcopy(self.qmax)
317	obj.multi_factor = self.multi_factor
318	obj.npts = copy.deepcopy(self.npts )
319	obj.cb1 = copy.deepcopy(self.cb1)
320	obj.smearer = copy.deepcopy(self.smearer)
321
322	for name, state in self.saved_states.iteritems():
323	copy_name = copy.deepcopy(name)
324	copy_state = state.clone()
325	obj.saved_states[copy_name]= copy_state
326	return obj
327
328	def _repr_helper(self, list, rep):
329	"""
330	Helper method to print a state
331	"""
332	for item in list:
333	rep += "parameter name: %s \n"%str(item[1])
334	rep += "value: %s\n"%str(item[2])
335	rep += "selected: %s\n"%str(item[0])
336	rep += "error displayed : %s \n"%str(item[4][0])
337	rep += "error value:%s \n"%str(item[4][1])
338	rep += "minimum displayed : %s \n"%str(item[5][0])
339	rep += "minimum value : %s \n"%str(item[5][1])
340	rep += "maximum displayed : %s \n"%str(item[6][0])
341	rep += "maximum value : %s \n"%str(item[6][1])
342	rep += "parameter unit: %s\n\n"%str(item[7])
343	return rep
344
345	def __repr__(self):
346	"""
347	output string for printing
348	"""
349	rep = "\nState name: %s\n"%self.file
350	t = time.localtime(self.timestamp)
351	time_str = time.strftime("%b %d %H;%M of %Y", t)
352
353	rep += "State created on : %s\n"%time_str
354	rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox
355	rep += "State structure factor combobox selection: %s\n"%self.structurecombobox
356	rep += "is data : %s\n"%self.is_data
357	rep += "data's name : %s\n"%self.data_name
358	rep += "data's id : %s\n"%self.data_id
359	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
360	rep += "multi_factor : %s\n"% str(self.multi_factor)
361	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
362	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
363	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
364	rep += "data : %s\n"% str(self.data)
365	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
366	str(self.qmax),str(self.npts))
367	rep += "Dispersion selection : %s\n"%str(self.disp_box)
368	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
369	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
370	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
371	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
372	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
373	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
374	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
375	rep += "2D enable : %s\n"%str(self.enable2D)
376	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
377	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
378	rep += "Smear object : %s\n"%str(self.smearer)
379	rep += "Smear type : %s\n"%(self.smear_type)
380	rep += "dq_l : %s\n"%self.dq_l
381	rep += "dq_r : %s\n"%self.dq_r
382
383	rep += "model : %s\n\n"% str(self.model)
384	temp_parameters = []
385	temp_fittable_param = []
386	if self.data.__class__.__name__ == "Data2D":
387	self.is_2D = True
388	else:
389	self.is_2D = False
390	if self.data is not None:
391	if not self.is_2D:
392	for item in self.parameters:
393	if not item in self.orientation_params:
394	temp_parameters.append(item)
395	for item in self.fittable_param:
396	if not item in self.orientation_params_disp:
397	temp_fittable_param.append(item)
398	else:
399	temp_parameters = self.parameters
400	temp_fittable_param = self.fittable_param
401
402	rep += "number parameters(self.parameters): %s\n"%len(temp_parameters)
403	rep = self._repr_helper( list=temp_parameters, rep=rep)
404	rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters)
405	rep = self._repr_helper( list=self.str_parameters, rep=rep)
406	rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param)
407	rep = self._repr_helper( list=temp_fittable_param, rep=rep)
408	"""
409	if is_2D:
410	rep += "number orientation parameters"
411	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
412	rep = self._repr_helper( list=self.orientation_params, rep=rep)
413	rep += "number dispersity parameters"
414	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
415	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
416	"""
417	return rep
418
419	def set_report_string(self):
420	"""
421	Get the values (strings) from __str__ for report
422	"""
423	# Dictionary of teh report strings
424	repo_time = ""
425	model_name = ""
426	title = ""
427	title_name = ""
428	file_name = ""
429	param_string = ""
430	paramval_string = ""
431	chi2_string = ""
432	multi_factor_string = ""
433	q_range = ""
434	strings = self.__repr__()
435	lines = strings.split('\n')
436
437	# get all string values from __str__()
438	for line in lines:
439	value = ""
440	content = line.split(":")
441	name = content[0]
442	try:
443	value = content[1]
444	except:
445	pass
446	if name.count("State created on"):
447	repo_time = "Created on " + value
448	if name.count("parameter name"):
449	val_name = value.split(".")
450	if len(val_name) > 1:
451	if val_name[1].count("width"):
452	param_string += value + ','
453	else:
454	continue
455	else:
456	param_string += value + ','
457	if name == "value":
458	param_string += value + ','
459	if name == "error value":
460	param_string += value + ','
461	if name == "parameter unit":
462	param_string += value + ':'
463	if name == "Value of Chisqr ":
464	chi2 = ("Chi2/Npts = " + value)
465	chi2_string = CENTRE % chi2
466	if name == "multi_factor ":
467	muti_factor = ("muti_factor = " + value)
468	muti_factor_string = CENTRE % muti_factor
469	if name == "Title":
470	if len(value.strip()) == 0:
471	continue
472	title = value + " [" + repo_time + "]"
473	title_name = HEADER % title
474	if name == "data ":
475	try:
476	file = ("File name:" + content[2])
477	file_name = CENTRE % file
478	if len(title) == 0:
479	title = content[2] + " [" + repo_time + "]"
480	title_name = HEADER % title
481	except:
482	pass
483	if name == "Plotting Range":
484	try:
485	q_range = content[1] + " = " + content[2] \
486	+ " = " + content[3].split(",")[0]
487	q_name = ("Q Range: " + q_range)
488	q_range = CENTRE % q_name
489	except:
490	pass
491	paramval = ""
492	for lines in param_string.split(":"):
493	line = lines.split(",")
494	if len(lines) > 0:
495	param = line[0]
496	param += " = " + line[1]
497	if len(line[2].split()) > 0 and not line[2].count("None"):
498	param += " +- " + line[2]
499	if len(line[3].split()) > 0 and not line[3].count("None"):
500	param += " " + line[3]
501	if not paramval.count(param):
502	paramval += param + "\n"
503	paramval_string += CENTRE % param + "\n"
504
505	html_string = title_name + "\n" + file_name + \
506	"\n" + q_range + \
507	"\n" + chi2_string + \
508	"\n" + ELINE + \
509	"\n" + paramval_string + \
510	"\n" + ELINE + \
511	"\n" + FEET_1 % title + \
512	"\n" + FEET_2
513
514	text_string = "\n\n\n" + title + "\n\n" + file + \
515	"\n" + q_name + \
516	"\n" + chi2 + \
517	"\n\n" + paramval
518
519	return html_string, text_string, title
520
521	def report(self, figs=None, canvases=None):
522	"""
523	Invoke report dialog panel
524
525	: param figs: list of pylab figures [list]
526	"""
527	from report_dialog import ReportDialog
528	# get the strings for report
529	html_str, text_str, title = self.set_report_string()
530	# Allow 2 figures to append
531	if len(figs) == 1:
532	add_str = FEET_3
533	elif len(figs) == 2:
534	add_str = ELINE
535	add_str += FEET_2 % ("%s")
536	add_str += ELINE
537	add_str += FEET_3
538	elif len(figs) > 2:
539	add_str = ELINE
540	add_str += FEET_2 % ("%s")
541	add_str += ELINE
542	add_str += FEET_2 % ("%s")
543	add_str += ELINE
544	add_str += FEET_3
545	else:
546	add_str = ""
547
548	# final report html strings
549	report_str = html_str % ("%s") + add_str
550
551	# make plot image
552	images = self.set_plot_state(figs, canvases)
553	report_list = [report_str, text_str, images ]
554	dialog = ReportDialog(report_list, None, -1, "")
555	dialog.ShowModal()
556
557
558	def _toXML_helper(self, list, element, newdoc):
559	"""
560	Helper method to create xml file for saving state
561	"""
562	for item in list:
563	sub_element = newdoc.createElement('parameter')
564	sub_element.setAttribute('name', str(item[1]))
565	sub_element.setAttribute('value', str(item[2]))
566	sub_element.setAttribute('selected_to_fit', str(item[0]))
567	sub_element.setAttribute('error_displayed', str(item[4][0]))
568	sub_element.setAttribute('error_value', str(item[4][1]))
569	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
570	sub_element.setAttribute('minimum_value', str(item[5][1]))
571	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
572	sub_element.setAttribute('maximum_value', str(item[6][1]))
573	sub_element.setAttribute('unit', str(item[7]))
574	element.appendChild(sub_element)
575
576	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
577	"""
578	Writes the state of the InversionControl panel to file, as XML.
579
580	Compatible with standalone writing, or appending to an
581	already existing XML document. In that case, the XML document
582	is required. An optional entry node in the XML document may also be given.
583
584	:param file: file to write to
585	:param doc: XML document object [optional]
586	:param entry_node: XML node within the XML document at which we will append the data [optional]
587
588	"""
589	from xml.dom.minidom import getDOMImplementation
590
591	# Check whether we have to write a standalone XML file
592	if doc is None:
593	impl = getDOMImplementation()
594	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
595	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
596	top_element = newdoc.documentElement
597	else:
598	# We are appending to an existing document
599	newdoc = doc
600	top_element = newdoc.createElement(FITTING_NODE_NAME)
601	if entry_node is None:
602	newdoc.documentElement.appendChild(top_element)
603	else:
604	entry_node.appendChild(top_element)
605
606	attr = newdoc.createAttribute("version")
607	attr.nodeValue = '1.0'
608	top_element.setAttributeNode(attr)
609
610	# File name
611	element = newdoc.createElement("filename")
612	if self.file is not None:
613	element.appendChild(newdoc.createTextNode(str(self.file)))
614	else:
615	element.appendChild(newdoc.createTextNode(str(file)))
616	top_element.appendChild(element)
617
618	element = newdoc.createElement("timestamp")
619	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
620	attr = newdoc.createAttribute("epoch")
621	attr.nodeValue = str(self.timestamp)
622	element.setAttributeNode(attr)
623	top_element.appendChild(element)
624	# Inputs
625	inputs = newdoc.createElement("Attributes")
626	top_element.appendChild(inputs)
627
628
629	if self.data is not None and hasattr(self.data, "group_id"):
630	self.data_group_id = self.data.group_id
631	if self.data is not None and hasattr(self.data, "is_data"):
632	self.is_data = self.data.is_data
633	if self.data is not None:
634	self.data_name = self.data.name
635	if self.data is not None and hasattr(self.data, "id"):
636	self.data_id = self.data.id
637
638	for item in list_of_data_attributes:
639	element = newdoc.createElement(item[0])
640	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
641	inputs.appendChild(element)
642
643	for item in list_of_state_attributes:
644	element = newdoc.createElement(item[0])
645	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
646	inputs.appendChild(element)
647
648	# For self.values ={ disp_param_name: [vals,...],...}
649	# and for self.weights ={ disp_param_name: [weights,...],...}
650	for item in list_of_model_attributes:
651	element = newdoc.createElement(item[0])
652	exec "list = self.%s" % item[1]
653	for key, value in list.iteritems():
654	sub_element = newdoc.createElement(key)
655	sub_element.setAttribute('name', str(key))
656	for val in value:
657	com = "sub_element.appendChild"
658	com += "(newdoc.createTextNode(str(%s)))"
659	exec com % val
660
661	element.appendChild(sub_element)
662	inputs.appendChild(element)
663
664	# Create doc for the dictionary of self._disp_obj_dic
665	for item in list_of_obj_dic:
666	element = newdoc.createElement(item[0])
667	exec "list = self.%s" % item[1]
668	for key, val in list.iteritems():
669	value = repr(val)
670	sub_element = newdoc.createElement(key)
671	sub_element.setAttribute('name', str(key))
672	sub_element.setAttribute('value', str(value))
673	element.appendChild(sub_element)
674	inputs.appendChild(element)
675
676	for item in list_of_state_parameters:
677	element = newdoc.createElement(item[0])
678	com = "self._toXML_helper(list=self.%s,"
679	com += " element=element, newdoc=newdoc)"
680	exec com % item[1]
681	inputs.appendChild(element)
682
683	# Save the file
684	if doc is None:
685	fd = open(file, 'w')
686	fd.write(newdoc.toprettyxml())
687	fd.close()
688	return None
689	else:
690	return newdoc.toprettyxml()
691
692	def _fromXML_helper(self, node, list):
693	"""
694	Helper function to write state to xml
695	"""
696	for item in node:
697	try:
698	name = item.get('name')
699	except:
700	name = None
701	try:
702	value = item.get('value')
703	except:
704	value = None
705	try:
706	selected_to_fit = (item.get('selected_to_fit') == "True")
707	except:
708	selected_to_fit = None
709	try:
710	error_displayed = (item.get('error_displayed') == "True")
711	except:
712	error_displayed = None
713	try:
714	error_value = item.get('error_value')
715	except:
716	error_value = None
717	try:
718	minimum_displayed = (item.get('minimum_displayed')== "True")
719	except:
720	minimum_displayed = None
721	try:
722	minimum_value = item.get('minimum_value')
723	except:
724	minimum_value = None
725	try:
726	maximum_displayed = (item.get('maximum_displayed') == "True")
727	except:
728	maximum_displayed = None
729	try:
730	maximum_value = item.get('maximum_value')
731	except:
732	maximum_value = None
733	try:
734	unit = item.get('unit')
735	except:
736	unit = None
737	list.append([selected_to_fit, name, value, "+/-",
738	[error_displayed, error_value],
739	[minimum_displayed,minimum_value],
740	[maximum_displayed,maximum_value], unit])
741
742	def fromXML(self, file=None, node=None):
743	"""
744	Load fitting state from a file
745
746	:param file: .fitv file
747	:param node: node of a XML document to read from
748
749	"""
750	if file is not None:
751	msg = "PageState no longer supports non-CanSAS"
752	msg += " format for fitting files"
753	raise RuntimeError, msg
754
755	if node.get('version')and node.get('version') == '1.0':
756
757	# Get file name
758	entry = get_content('ns:filename', node)
759	if entry is not None:
760	self.file = entry.text.strip()
761
762	# Get time stamp
763	entry = get_content('ns:timestamp', node)
764	if entry is not None and entry.get('epoch'):
765	try:
766	self.timestamp = float(entry.get('epoch'))
767	except:
768	msg = "PageState.fromXML: Could not"
769	msg += " read timestamp\n %s" % sys.exc_value
770	logging.error(msg)
771
772	# Parse fitting attributes
773	entry = get_content('ns:Attributes', node)
774	for item in list_of_data_attributes:
775	node = get_content('ns:%s'%item[0], entry)
776	try:
777	exec "self.%s = parse_entry_helper(node, item)" % item[0]
778
779	except:
780	raise
781
782	if entry is not None:
783
784	for item in list_of_state_attributes:
785	node = get_content('ns:%s' % item[0], entry)
786	try:
787	exec "self.%s = parse_entry_helper(node, item)" % \
788	str(item[0])
789	except:
790	raise
791
792	for item in list_of_state_parameters:
793	node = get_content("ns:%s" % item[0], entry)
794	exec "self._fromXML_helper(node=node, list=self.%s)" % \
795	item[1]
796
797	# Recover _disp_obj_dict from xml file
798	self._disp_obj_dict = {}
799	for item in list_of_obj_dic:
800	# Get node
801	node = get_content("ns:%s" % item[0], entry)
802	for attr in node:
803	name = attr.get('name')
804	val = attr.get('value')
805	value = val.split(" instance")[0]
806	disp_name = value.split("<")[1]
807	try:
808	# Try to recover disp_model object from strings
809	com = "from sans.models.dispersion_models "
810	com += "import %s as disp"
811	com_name = disp_name.split(".")[3]
812	exec com % com_name
813	disp_model = disp()
814	exec "self.%s['%s'] = com_name" % (item[1], name)
815	except:
816	pass
817
818	# get self.values and self.weights dic. if exists
819	for item in list_of_model_attributes:
820	node = get_content("ns:%s" % item[0], entry)
821	dic = {}
822	list = []
823	for par in node:
824	name = par.get('name')
825	values = par.text.split('\n')
826	# Get lines only with numbers
827	for line in values:
828	try:
829	val= float(line)
830	list.append(val)
831	except:
832	# pass if line is empty (it happens)
833	pass
834	dic[name] = numpy.array(list)
835	exec "self.%s = dic" % item[1]
836
837	def set_plot_state(self, figs, canvases):
838	"""
839	Build image state that wx.html understand
840	by plotting, putting it into wx.FileSystem image object
841
842	"""
843	images = []
844	# some imports
845	import wx
846
847	# Reset memory
848	self.imgRAM = None
849	wx.MemoryFSHandler()
850
851	# For no figures in the list, prepare empty plot
852	if figs == None or len(figs) == 0:
853	figs = [None]
854
855	# Loop over the list of figures
856	# use wx.MemoryFSHandler
857	self.imgRAM = wx.MemoryFSHandler()
858	for fig in figs:
859	if figs != None:
860	#fig.set_facecolor('w')
861	ind = figs.index(fig)
862	canvas = canvases[ind]
863
864	#bmp = wx.BitmapDataObject()
865	#bmp.SetBitmap(canvas.bitmap)
866	#store the image in wx.FileSystem Object
867	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
868
869	# index of the fig
870	ind = figs.index(fig)
871
872	#AddFile, image can be retrieved with 'memory:filename'
873	self.imgRAM.AddFile('img_fit%s.png' % ind ,
874	canvas.bitmap, wx.BITMAP_TYPE_PNG)
875
876	#append figs
877	images.append(fig)
878
879	return images
880
881	class Reader(CansasReader):
882	"""
883	Class to load a .fitv fitting file
884	"""
885	## File type
886	type_name = "Fitting"
887
888	## Wildcards
889	type = ["Fitting files (.fitv)\|.fitv"
890	"SANSView file (.svs)\|.svs"]
891	## List of allowed extensions
892	ext=['.fitv', '.FITV', '.svs', 'SVS']
893
894	def __init__(self, call_back=None, cansas=True):
895	CansasReader.__init__(self)
896	"""
897	Initialize the call-back method to be called
898	after we load a file
899
900	:param call_back: call-back method
901	:param cansas: True = files will be written/read in CanSAS format
902	False = write CanSAS format
903
904	"""
905	## Call back method to be executed after a file is read
906	self.call_back = call_back
907	## CanSAS format flag
908	self.cansas = cansas
909	self.state = None
910	def get_state(self):
911	return self.state
912
913	def read(self, path):
914	"""
915	Load a new P(r) inversion state from file
916
917	:param path: file path
918
919	"""
920	if self.cansas == True:
921	return self._read_cansas(path)
922
923	def _data2d_to_xml_doc(self, datainfo):
924	"""
925	Create an XML document to contain the content of a Data2D
926
927	:param datainfo: Data2D object
928
929	"""
930	if not issubclass(datainfo.__class__, Data2D):
931	raise RuntimeError, "The cansas writer expects a Data2D instance"
932
933	doc = xml.dom.minidom.Document()
934	main_node = doc.createElement("SASroot")
935	main_node.setAttribute("version", self.version)
936	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
937	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
938	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
939
940	doc.appendChild(main_node)
941
942	entry_node = doc.createElement("SASentry")
943	main_node.appendChild(entry_node)
944
945	write_node(doc, entry_node, "Title", datainfo.title)
946	if datainfo is not None:
947	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
948	for item in datainfo.run:
949	runname = {}
950	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
951	runname = {'name': datainfo.run_name[item] }
952	write_node(doc, entry_node, "Run", item, runname)
953	# Data info
954	new_node = doc.createElement("SASdata")
955	entry_node.appendChild(new_node)
956	for item in list_of_data_2d_attr:
957	element = doc.createElement(item[0])
958	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
959	new_node.appendChild(element)
960
961	for item in list_of_data2d_values:
962	root_node = doc.createElement(item[0])
963	new_node.appendChild(root_node)
964
965	exec "temp_list = datainfo.%s"%item[1]
966
967	if temp_list is None or len(temp_list)== 0:
968	element = doc.createElement(item[0])
969	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
970	root_node.appendChild(element)
971	else:
972	for value in temp_list:
973	element = doc.createElement(item[0])
974	exec "element.setAttribute(item[0], str(%s))"%value
975	root_node.appendChild(element)
976
977	# Sample info
978	sample = doc.createElement("SASsample")
979	if datainfo.sample.name is not None:
980	sample.setAttribute("name", str(datainfo.sample.name))
981	entry_node.appendChild(sample)
982	write_node(doc, sample, "ID", str(datainfo.sample.ID))
983	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
984	write_node(doc, sample, "transmission", datainfo.sample.transmission)
985	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
986
987	for item in datainfo.sample.details:
988	write_node(doc, sample, "details", item)
989
990	pos = doc.createElement("position")
991	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
992	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
993	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
994	if written == True:
995	sample.appendChild(pos)
996
997	ori = doc.createElement("orientation")
998	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
999	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1000	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1001	if written == True:
1002	sample.appendChild(ori)
1003
1004	# Instrument info
1005	instr = doc.createElement("SASinstrument")
1006	entry_node.appendChild(instr)
1007
1008	write_node(doc, instr, "name", datainfo.instrument)
1009
1010	# Source
1011	source = doc.createElement("SASsource")
1012	if datainfo.source.name is not None:
1013	source.setAttribute("name", str(datainfo.source.name))
1014	instr.appendChild(source)
1015
1016	write_node(doc, source, "radiation", datainfo.source.radiation)
1017	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1018	size = doc.createElement("beam_size")
1019	if datainfo.source.beam_size_name is not None:
1020	size.setAttribute("name", str(datainfo.source.beam_size_name))
1021	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1022	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1023	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1024	if written == True:
1025	source.appendChild(size)
1026
1027	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1028	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1029	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1030	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1031
1032	# Collimation
1033	for item in datainfo.collimation:
1034	coll = doc.createElement("SAScollimation")
1035	if item.name is not None:
1036	coll.setAttribute("name", str(item.name))
1037	instr.appendChild(coll)
1038
1039	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1040
1041	for apert in item.aperture:
1042	ap = doc.createElement("aperture")
1043	if apert.name is not None:
1044	ap.setAttribute("name", str(apert.name))
1045	if apert.type is not None:
1046	ap.setAttribute("type", str(apert.type))
1047	coll.appendChild(ap)
1048
1049	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1050
1051	size = doc.createElement("size")
1052	if apert.size_name is not None:
1053	size.setAttribute("name", str(apert.size_name))
1054	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1055	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1056	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1057	if written == True:
1058	ap.appendChild(size)
1059
1060	# Detectors
1061	for item in datainfo.detector:
1062	det = doc.createElement("SASdetector")
1063	written = write_node(doc, det, "name", item.name)
1064	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1065	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1066	if written == True:
1067	instr.appendChild(det)
1068
1069	off = doc.createElement("offset")
1070	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1071	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1072	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1073	if written == True:
1074	det.appendChild(off)
1075
1076	center = doc.createElement("beam_center")
1077	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1078	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1079	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1080	if written == True:
1081	det.appendChild(center)
1082
1083	pix = doc.createElement("pixel_size")
1084	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1085	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1086	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1087	if written == True:
1088	det.appendChild(pix)
1089
1090	ori = doc.createElement("orientation")
1091	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1092	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1093	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1094	if written == True:
1095	det.appendChild(ori)
1096
1097	# Processes info
1098	for item in datainfo.process:
1099	node = doc.createElement("SASprocess")
1100	entry_node.appendChild(node)
1101
1102	write_node(doc, node, "name", item.name)
1103	write_node(doc, node, "date", item.date)
1104	write_node(doc, node, "description", item.description)
1105	for term in item.term:
1106	value = term['value']
1107	del term['value']
1108	write_node(doc, node, "term", value, term)
1109	for note in item.notes:
1110	write_node(doc, node, "SASprocessnote", note)
1111	# Return the document, and the SASentry node associated with
1112	# the data we just wrote
1113	return doc, entry_node
1114
1115	def _parse_state(self, entry):
1116	"""
1117	Read a fit result from an XML node
1118
1119	:param entry: XML node to read from
1120
1121	:return: PageState object
1122	"""
1123	# Create an empty state
1124	state = None
1125	# Locate the P(r) node
1126	try:
1127	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
1128	if nodes !=[]:
1129	# Create an empty state
1130	state = PageState()
1131	state.fromXML(node=nodes[0])
1132	except:
1133	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1134
1135	return state
1136
1137
1138
1139	def _parse_entry(self, dom):
1140	"""
1141	Parse a SASentry
1142
1143	:param node: SASentry node
1144
1145	:return: Data1D/Data2D object
1146
1147	"""
1148	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1149	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1150	return CansasReader._parse_entry(self, dom)
1151
1152	#Parse 2D
1153	data_info = Data2D()
1154
1155	# Look up title
1156	self._store_content('ns:Title', dom, 'title', data_info)
1157
1158	# Look up run number
1159	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1160	for item in nodes:
1161	if item.text is not None:
1162	value = item.text.strip()
1163	if len(value) > 0:
1164	data_info.run.append(value)
1165	if item.get('name') is not None:
1166	data_info.run_name[value] = item.get('name')
1167
1168	# Look up instrument name
1169	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1170
1171	# Notes
1172	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1173	for note in note_list:
1174	try:
1175	if note.text is not None:
1176	note_value = note.text.strip()
1177	if len(note_value) > 0:
1178	data_info.notes.append(note_value)
1179	except:
1180	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1181	self.errors.append(err_mess)
1182	logging.error(err_mess)
1183
1184	# Sample info ###################
1185	entry = get_content('ns:SASsample', dom)
1186	if entry is not None:
1187	data_info.sample.name = entry.get('name')
1188
1189	self._store_content('ns:SASsample/ns:ID',
1190	dom, 'ID', data_info.sample)
1191	self._store_float('ns:SASsample/ns:thickness',
1192	dom, 'thickness', data_info.sample)
1193	self._store_float('ns:SASsample/ns:transmission',
1194	dom, 'transmission', data_info.sample)
1195	self._store_float('ns:SASsample/ns:temperature',
1196	dom, 'temperature', data_info.sample)
1197
1198	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1199	for item in nodes:
1200	try:
1201	if item.text is not None:
1202	detail_value = item.text.strip()
1203	if len(detail_value) > 0:
1204	data_info.sample.details.append(detail_value)
1205	except:
1206	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1207	self.errors.append(err_mess)
1208	logging.error(err_mess)
1209
1210	# Position (as a vector)
1211	self._store_float('ns:SASsample/ns:position/ns:x',
1212	dom, 'position.x', data_info.sample)
1213	self._store_float('ns:SASsample/ns:position/ns:y',
1214	dom, 'position.y', data_info.sample)
1215	self._store_float('ns:SASsample/ns:position/ns:z',
1216	dom, 'position.z', data_info.sample)
1217
1218	# Orientation (as a vector)
1219	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1220	dom, 'orientation.x', data_info.sample)
1221	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1222	dom, 'orientation.y', data_info.sample)
1223	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1224	dom, 'orientation.z', data_info.sample)
1225
1226	# Source info ###################
1227	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1228	if entry is not None:
1229	data_info.source.name = entry.get('name')
1230
1231	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1232	dom, 'radiation', data_info.source)
1233	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1234	dom, 'beam_shape', data_info.source)
1235	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1236	dom, 'wavelength', data_info.source)
1237	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1238	dom, 'wavelength_min', data_info.source)
1239	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1240	dom, 'wavelength_max', data_info.source)
1241	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1242	dom, 'wavelength_spread', data_info.source)
1243
1244	# Beam size (as a vector)
1245	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1246	if entry is not None:
1247	data_info.source.beam_size_name = entry.get('name')
1248
1249	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1250	dom, 'beam_size.x', data_info.source)
1251	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1252	dom, 'beam_size.y', data_info.source)
1253	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1254	dom, 'beam_size.z', data_info.source)
1255
1256	# Collimation info ###################
1257	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
1258	for item in nodes:
1259	collim = Collimation()
1260	if item.get('name') is not None:
1261	collim.name = item.get('name')
1262	self._store_float('ns:length', item, 'length', collim)
1263
1264	# Look for apertures
1265	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
1266	for apert in apert_list:
1267	aperture = Aperture()
1268
1269	# Get the name and type of the aperture
1270	aperture.name = apert.get('name')
1271	aperture.type = apert.get('type')
1272
1273	self._store_float('ns:distance', apert, 'distance', aperture)
1274
1275	entry = get_content('ns:size', apert)
1276	if entry is not None:
1277	aperture.size_name = entry.get('name')
1278
1279	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1280	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1281	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1282
1283	collim.aperture.append(aperture)
1284
1285	data_info.collimation.append(collim)
1286
1287	# Detector info ######################
1288	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1289	for item in nodes:
1290
1291	detector = Detector()
1292
1293	self._store_content('ns:name', item, 'name', detector)
1294	self._store_float('ns:SDD', item, 'distance', detector)
1295
1296	# Detector offset (as a vector)
1297	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1298	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1299	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1300
1301	# Detector orientation (as a vector)
1302	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1303	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1304	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1305
1306	# Beam center (as a vector)
1307	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1308	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1309	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1310
1311	# Pixel size (as a vector)
1312	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1313	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1314	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1315
1316	self._store_float('ns:slit_length', item, 'slit_length', detector)
1317
1318	data_info.detector.append(detector)
1319
1320	# Processes info ######################
1321	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1322	for item in nodes:
1323	process = Process()
1324	self._store_content('ns:name', item, 'name', process)
1325	self._store_content('ns:date', item, 'date', process)
1326	self._store_content('ns:description', item, 'description', process)
1327
1328	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1329	for term in term_list:
1330	try:
1331	term_attr = {}
1332	for attr in term.keys():
1333	term_attr[attr] = term.get(attr).strip()
1334	if term.text is not None:
1335	term_attr['value'] = term.text.strip()
1336	process.term.append(term_attr)
1337	except:
1338	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1339	self.errors.append(err_mess)
1340	logging.error(err_mess)
1341
1342	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1343	for note in note_list:
1344	if note.text is not None:
1345	process.notes.append(note.text.strip())
1346
1347	data_info.process.append(process)
1348
1349
1350	# Data info ######################
1351	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1352	if len(nodes)>1:
1353	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1354
1355	for entry in nodes:
1356	for item in list_of_data_2d_attr:
1357	#get node
1358	node = get_content('ns:%s'%item[0], entry)
1359	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1360
1361	for item in list_of_data2d_values:
1362	field = get_content('ns:%s'%item[0], entry)
1363	list = []
1364	if field is not None:
1365	list = [parse_entry_helper(node, item) for node in field]
1366	exec "data_info.%s = numpy.array(list)"%item[0]
1367
1368	return data_info
1369
1370	def _read_cansas(self, path):
1371	"""
1372	Load data and P(r) information from a CanSAS XML file.
1373
1374	:param path: file path
1375
1376	:return: Data1D object if a single SASentry was found,
1377	or a list of Data1D objects if multiple entries were found,
1378	or None of nothing was found
1379
1380	:raise RuntimeError: when the file can't be opened
1381	:raise ValueError: when the length of the data vectors are inconsistent
1382
1383	"""
1384	output = []
1385	basename = os.path.basename(path)
1386	root, extension = os.path.splitext(basename)
1387	ext = extension.lower()
1388	try:
1389	if os.path.isfile(path):
1390
1391	#TODO: eventually remove the check for .xml once
1392	# the P(r) writer/reader is truly complete.
1393	if ext in self.ext or \
1394	ext == '.xml':
1395
1396	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1397	# Check the format version number
1398	# Specifying the namespace will take care of the file format version
1399	root = tree.getroot()
1400	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1401	for entry in entry_list:
1402	try:
1403	sas_entry = self._parse_entry(entry)
1404	except:
1405	raise
1406	fitstate = self._parse_state(entry)
1407
1408	#state could be None when .svs file is loaded
1409	#in this case, skip appending to output
1410	if fitstate != None:
1411	sas_entry.meta_data['fitstate'] = fitstate
1412	sas_entry.filename = fitstate.file
1413	output.append(sas_entry)
1414	else:
1415	self.call_back(format=ext)
1416	raise RuntimeError, "%s is not a file" % path
1417
1418	# Return output consistent with the loader's api
1419	if len(output)==0:
1420	self.call_back(state=None, datainfo=None,format=ext)
1421	return None
1422	else:
1423	for ind in range(len(output)):
1424	# Call back to post the new state
1425	state = output[ind].meta_data['fitstate']
1426	t = time.localtime(state.timestamp)
1427	time_str = time.strftime("%b %d %H:%M", t)
1428	# Check that no time stamp is already appended
1429	max_char = state.file.find("[")
1430	if max_char < 0:
1431	max_char = len(state.file)
1432	original_fname = state.file[0:max_char]
1433	state.file = original_fname +' [' + time_str + ']'
1434
1435
1436	if state is not None and state.is_data is not None:
1437	exec 'output[%d].is_data = state.is_data'% ind
1438
1439	output[ind].filename = state.file
1440	state.data = output[ind]
1441	state.data.name = output[ind].filename #state.data_name
1442	state.data.id = state.data_id
1443	if state.is_data is not None:
1444	state.data.is_data = state.is_data
1445	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1446	name = output[ind].run_name
1447	else:
1448	name=original_fname
1449	state.data.group_id = name
1450	#store state in fitting
1451	self.call_back(state=state, datainfo=output[ind],format=ext)
1452	self.state= state
1453	return output
1454
1455	except:
1456	#self.call_back(format=ext)
1457	self.state= state
1458	raise
1459
1460	def write(self, filename, datainfo=None, fitstate=None):
1461	"""
1462	Write the content of a Data1D as a CanSAS XML file only for standalone
1463
1464	:param filename: name of the file to write
1465	:param datainfo: Data1D object
1466	:param fitstate: PageState object
1467
1468	"""
1469	# Sanity check
1470	if self.cansas == True:
1471
1472	# Add fitting information to the XML document
1473	doc = self.write_toXML(datainfo, fitstate)
1474	# Write the XML document
1475	fd = open(filename, 'w')
1476	fd.write(doc.toprettyxml())
1477	fd.close()
1478	else:
1479	fitstate.toXML(file=filename)
1480
1481	def write_toXML(self, datainfo=None, state=None):
1482	"""
1483	Write toXML, a helper for write() , could be used by guimanager._on_save()
1484
1485	: return: xml doc
1486	"""
1487
1488	if state.data is None:
1489	data = DataLoader.data_info.Data1D(x=[], y=[])
1490	else:
1491	#make sure title and data run is filled up.
1492	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1493	if state.data.run_name == None or state.data.run_name=={}:
1494	state.data.run = [str(state.data.name)]
1495	state.data.run_name[0] = state.data.name
1496
1497	if issubclass(state.data.__class__, DataLoader.data_info.Data1D):
1498
1499	data = state.data
1500	doc, sasentry = self._to_xml_doc(data)
1501	else:
1502	data = state.data
1503	doc, sasentry = self._data2d_to_xml_doc(data)
1504
1505
1506	if state is not None:
1507	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1508
1509	return doc
1510
1511	# Simple html report templet
1512	HEADER = "<html>\n"
1513	HEADER += "<head>\n"
1514	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1515	HEADER += "charset=windows-1252'> \n"
1516	HEADER += "<meta name=Generator >\n"
1517	HEADER += "</head>\n"
1518	HEADER += "<body lang=EN-US>\n"
1519	HEADER += "<div class=WordSection1>\n"
1520	HEADER += "<p class=MsoNormal><b><span ><center>"
1521	HEADER += "%s</center></span></center></b></p>"
1522	HEADER += "<p class=MsoNormal> </p>"
1523	PARA = "<p class=MsoNormal> %s \n"
1524	PARA += "</p>"
1525	CENTRE = "<p class=MsoNormal><center> %s \n"
1526	CENTRE += "</center></p>"
1527	FEET_1 = \
1528	"""
1529	<p class=MsoNormal> </p>
1530	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
1531	<p class=MsoNormal> </p>
1532	<center>
1533	<br>Model Computation<br>
1534	<br>Data: "%s"<br>
1535	"""
1536	FEET_2 = \
1537	"""
1538	<img src="%s" >
1539	</img>
1540	"""
1541	FEET_3 = \
1542	"""
1543	</center>
1544	</div>
1545	</body>
1546	</html>
1547	"""
1548	ELINE = "<p class=MsoNormal> </p>"
1549
1550	if __name__ == "__main__":
1551	state = PageState(parent=None)
1552	#state.toXML()
1553	"""
1554
1555	file = open("test_state", "w")
1556	pickle.dump(state, file)
1557	print pickle.dumps(state)
1558	state.data_name = "hello---->"
1559	pickle.dump(state, file)
1560	file = open("test_state", "r")
1561	new_state= pickle.load(file)
1562	print "new state", new_state
1563	new_state= pickle.load(file)
1564	print "new state", new_state
1565	#print "state", state
1566	"""
1567	import bsddb
1568	import pickle
1569	db= bsddb.btopen('file_state.db', 'c')
1570	val = (pickle.dumps(state), "hello", "hi")
1571	db['state1']= pickle.dumps(val)
1572	print pickle.loads(db['state1'])
1573	state.data_name = "hello---->22"
1574	db['state2']= pickle.dumps(state)
1575	state.data_name = "hello---->2"
1576	db['state3']= pickle.dumps(state)
1577	del db['state3']
1578	state.data_name = "hello---->3"
1579	db['state4']= pickle.dumps(state)
1580	new_state = pickle.loads(db['state1'])
1581	#print db.last()
1582	db.set_location('state2')
1583	state.data_name = "hello---->5"
1584	db['aastate5']= pickle.dumps(state)
1585	db.keys().sort()
1586	print pickle.loads(db['state2'])
1587
1588	db.close()

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SasView

source: sasview/sansview/perspectives/fitting/pagestate.py @ f7d0b74

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