pagestate.py @ c31fd9f

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 c31fd9f was f5bdb4a, checked in by Jae Cho <jhjcho@…>, 14 years ago
fixed html string format problem because of '%" symbol
Property mode set to `100644`
File size: 66.9 KB

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2
3	################################################################################
4	#This software was developed by the University of Tennessee as part of the
5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
6	#project funded by the US National Science Foundation.
7	#
8	#See the license text in license.txt
9	#
10	#copyright 2009, University of Tennessee
11	################################################################################
12
13	import time
14	import os
15	import sys
16	import copy
17	import logging
18	import numpy
19
20	import xml.dom.minidom
21	from xml.dom.minidom import parse
22	from lxml import etree
23
24	import 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	text_string = "\n\n\n" + title + "\n\n" + file + \
506	"\n" + q_name + \
507	"\n" + chi2 + \
508	"\n\n" + paramval
509
510	title_name = self._check_html_format(title_name)
511	file_name = self._check_html_format(file_name)
512	title = self._check_html_format(title)
513
514	html_string = title_name + "\n" + file_name + \
515	"\n" + q_range + \
516	"\n" + chi2_string + \
517	"\n" + ELINE + \
518	"\n" + paramval_string + \
519	"\n" + ELINE + \
520	"\n" + FEET_1 % title + \
521	"\n" + FEET_2
522
523	return html_string, text_string, title
524
525	def _check_html_format(self, name):
526	"""
527	Check string '%' for html format
528	"""
529	if name.count('%'):
530	name = name.replace('%', '&#37')
531
532	return name
533
534
535	def report(self, figs=None, canvases=None):
536	"""
537	Invoke report dialog panel
538
539	: param figs: list of pylab figures [list]
540	"""
541	from report_dialog import ReportDialog
542	# get the strings for report
543	html_str, text_str, title = self.set_report_string()
544	# Allow 2 figures to append
545	if len(figs) == 1:
546	add_str = FEET_3
547	elif len(figs) == 2:
548	add_str = ELINE
549	add_str += FEET_2 % ("%s")
550	add_str += ELINE
551	add_str += FEET_3
552	elif len(figs) > 2:
553	add_str = ELINE
554	add_str += FEET_2 % ("%s")
555	add_str += ELINE
556	add_str += FEET_2 % ("%s")
557	add_str += ELINE
558	add_str += FEET_3
559	else:
560	add_str = ""
561
562	# final report html strings
563	report_str = html_str % ("%s") + add_str
564
565	# make plot image
566	images = self.set_plot_state(figs, canvases)
567	report_list = [report_str, text_str, images ]
568	dialog = ReportDialog(report_list, None, -1, "")
569	dialog.ShowModal()
570
571
572	def _toXML_helper(self, list, element, newdoc):
573	"""
574	Helper method to create xml file for saving state
575	"""
576	for item in list:
577	sub_element = newdoc.createElement('parameter')
578	sub_element.setAttribute('name', str(item[1]))
579	sub_element.setAttribute('value', str(item[2]))
580	sub_element.setAttribute('selected_to_fit', str(item[0]))
581	sub_element.setAttribute('error_displayed', str(item[4][0]))
582	sub_element.setAttribute('error_value', str(item[4][1]))
583	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
584	sub_element.setAttribute('minimum_value', str(item[5][1]))
585	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
586	sub_element.setAttribute('maximum_value', str(item[6][1]))
587	sub_element.setAttribute('unit', str(item[7]))
588	element.appendChild(sub_element)
589
590	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
591	"""
592	Writes the state of the InversionControl panel to file, as XML.
593
594	Compatible with standalone writing, or appending to an
595	already existing XML document. In that case, the XML document
596	is required. An optional entry node in the XML document may also be given.
597
598	:param file: file to write to
599	:param doc: XML document object [optional]
600	:param entry_node: XML node within the XML document at which we will append the data [optional]
601
602	"""
603	from xml.dom.minidom import getDOMImplementation
604
605	# Check whether we have to write a standalone XML file
606	if doc is None:
607	impl = getDOMImplementation()
608	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
609	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
610	top_element = newdoc.documentElement
611	else:
612	# We are appending to an existing document
613	newdoc = doc
614	top_element = newdoc.createElement(FITTING_NODE_NAME)
615	if entry_node is None:
616	newdoc.documentElement.appendChild(top_element)
617	else:
618	entry_node.appendChild(top_element)
619
620	attr = newdoc.createAttribute("version")
621	attr.nodeValue = '1.0'
622	top_element.setAttributeNode(attr)
623
624	# File name
625	element = newdoc.createElement("filename")
626	if self.file is not None:
627	element.appendChild(newdoc.createTextNode(str(self.file)))
628	else:
629	element.appendChild(newdoc.createTextNode(str(file)))
630	top_element.appendChild(element)
631
632	element = newdoc.createElement("timestamp")
633	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
634	attr = newdoc.createAttribute("epoch")
635	attr.nodeValue = str(self.timestamp)
636	element.setAttributeNode(attr)
637	top_element.appendChild(element)
638	# Inputs
639	inputs = newdoc.createElement("Attributes")
640	top_element.appendChild(inputs)
641
642
643	if self.data is not None and hasattr(self.data, "group_id"):
644	self.data_group_id = self.data.group_id
645	if self.data is not None and hasattr(self.data, "is_data"):
646	self.is_data = self.data.is_data
647	if self.data is not None:
648	self.data_name = self.data.name
649	if self.data is not None and hasattr(self.data, "id"):
650	self.data_id = self.data.id
651
652	for item in list_of_data_attributes:
653	element = newdoc.createElement(item[0])
654	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
655	inputs.appendChild(element)
656
657	for item in list_of_state_attributes:
658	element = newdoc.createElement(item[0])
659	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
660	inputs.appendChild(element)
661
662	# For self.values ={ disp_param_name: [vals,...],...}
663	# and for self.weights ={ disp_param_name: [weights,...],...}
664	for item in list_of_model_attributes:
665	element = newdoc.createElement(item[0])
666	exec "list = self.%s" % item[1]
667	for key, value in list.iteritems():
668	sub_element = newdoc.createElement(key)
669	sub_element.setAttribute('name', str(key))
670	for val in value:
671	com = "sub_element.appendChild"
672	com += "(newdoc.createTextNode(str(%s)))"
673	exec com % val
674
675	element.appendChild(sub_element)
676	inputs.appendChild(element)
677
678	# Create doc for the dictionary of self._disp_obj_dic
679	for item in list_of_obj_dic:
680	element = newdoc.createElement(item[0])
681	exec "list = self.%s" % item[1]
682	for key, val in list.iteritems():
683	value = repr(val)
684	sub_element = newdoc.createElement(key)
685	sub_element.setAttribute('name', str(key))
686	sub_element.setAttribute('value', str(value))
687	element.appendChild(sub_element)
688	inputs.appendChild(element)
689
690	for item in list_of_state_parameters:
691	element = newdoc.createElement(item[0])
692	com = "self._toXML_helper(list=self.%s,"
693	com += " element=element, newdoc=newdoc)"
694	exec com % item[1]
695	inputs.appendChild(element)
696
697	# Save the file
698	if doc is None:
699	fd = open(file, 'w')
700	fd.write(newdoc.toprettyxml())
701	fd.close()
702	return None
703	else:
704	return newdoc.toprettyxml()
705
706	def _fromXML_helper(self, node, list):
707	"""
708	Helper function to write state to xml
709	"""
710	for item in node:
711	try:
712	name = item.get('name')
713	except:
714	name = None
715	try:
716	value = item.get('value')
717	except:
718	value = None
719	try:
720	selected_to_fit = (item.get('selected_to_fit') == "True")
721	except:
722	selected_to_fit = None
723	try:
724	error_displayed = (item.get('error_displayed') == "True")
725	except:
726	error_displayed = None
727	try:
728	error_value = item.get('error_value')
729	except:
730	error_value = None
731	try:
732	minimum_displayed = (item.get('minimum_displayed')== "True")
733	except:
734	minimum_displayed = None
735	try:
736	minimum_value = item.get('minimum_value')
737	except:
738	minimum_value = None
739	try:
740	maximum_displayed = (item.get('maximum_displayed') == "True")
741	except:
742	maximum_displayed = None
743	try:
744	maximum_value = item.get('maximum_value')
745	except:
746	maximum_value = None
747	try:
748	unit = item.get('unit')
749	except:
750	unit = None
751	list.append([selected_to_fit, name, value, "+/-",
752	[error_displayed, error_value],
753	[minimum_displayed,minimum_value],
754	[maximum_displayed,maximum_value], unit])
755
756	def fromXML(self, file=None, node=None):
757	"""
758	Load fitting state from a file
759
760	:param file: .fitv file
761	:param node: node of a XML document to read from
762
763	"""
764	if file is not None:
765	msg = "PageState no longer supports non-CanSAS"
766	msg += " format for fitting files"
767	raise RuntimeError, msg
768
769	if node.get('version')and node.get('version') == '1.0':
770
771	# Get file name
772	entry = get_content('ns:filename', node)
773	if entry is not None:
774	self.file = entry.text.strip()
775
776	# Get time stamp
777	entry = get_content('ns:timestamp', node)
778	if entry is not None and entry.get('epoch'):
779	try:
780	self.timestamp = float(entry.get('epoch'))
781	except:
782	msg = "PageState.fromXML: Could not"
783	msg += " read timestamp\n %s" % sys.exc_value
784	logging.error(msg)
785
786	# Parse fitting attributes
787	entry = get_content('ns:Attributes', node)
788	for item in list_of_data_attributes:
789	node = get_content('ns:%s'%item[0], entry)
790	try:
791	exec "self.%s = parse_entry_helper(node, item)" % item[0]
792
793	except:
794	raise
795
796	if entry is not None:
797
798	for item in list_of_state_attributes:
799	node = get_content('ns:%s' % item[0], entry)
800	try:
801	exec "self.%s = parse_entry_helper(node, item)" % \
802	str(item[0])
803	except:
804	raise
805
806	for item in list_of_state_parameters:
807	node = get_content("ns:%s" % item[0], entry)
808	exec "self._fromXML_helper(node=node, list=self.%s)" % \
809	item[1]
810
811	# Recover _disp_obj_dict from xml file
812	self._disp_obj_dict = {}
813	for item in list_of_obj_dic:
814	# Get node
815	node = get_content("ns:%s" % item[0], entry)
816	for attr in node:
817	name = attr.get('name')
818	val = attr.get('value')
819	value = val.split(" instance")[0]
820	disp_name = value.split("<")[1]
821	try:
822	# Try to recover disp_model object from strings
823	com = "from sans.models.dispersion_models "
824	com += "import %s as disp"
825	com_name = disp_name.split(".")[3]
826	exec com % com_name
827	disp_model = disp()
828	exec "self.%s['%s'] = com_name" % (item[1], name)
829	except:
830	pass
831
832	# get self.values and self.weights dic. if exists
833	for item in list_of_model_attributes:
834	node = get_content("ns:%s" % item[0], entry)
835	dic = {}
836	list = []
837	for par in node:
838	name = par.get('name')
839	values = par.text.split('\n')
840	# Get lines only with numbers
841	for line in values:
842	try:
843	val= float(line)
844	list.append(val)
845	except:
846	# pass if line is empty (it happens)
847	pass
848	dic[name] = numpy.array(list)
849	exec "self.%s = dic" % item[1]
850
851	def set_plot_state(self, figs, canvases):
852	"""
853	Build image state that wx.html understand
854	by plotting, putting it into wx.FileSystem image object
855
856	"""
857	images = []
858	# some imports
859	import wx
860
861	# Reset memory
862	self.imgRAM = None
863	wx.MemoryFSHandler()
864
865	# For no figures in the list, prepare empty plot
866	if figs == None or len(figs) == 0:
867	figs = [None]
868
869	# Loop over the list of figures
870	# use wx.MemoryFSHandler
871	self.imgRAM = wx.MemoryFSHandler()
872	for fig in figs:
873	if figs != None:
874	#fig.set_facecolor('w')
875	ind = figs.index(fig)
876	canvas = canvases[ind]
877
878	#bmp = wx.BitmapDataObject()
879	#bmp.SetBitmap(canvas.bitmap)
880	#store the image in wx.FileSystem Object
881	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
882
883	# index of the fig
884	ind = figs.index(fig)
885
886	#AddFile, image can be retrieved with 'memory:filename'
887	self.imgRAM.AddFile('img_fit%s.png' % ind ,
888	canvas.bitmap, wx.BITMAP_TYPE_PNG)
889
890	#append figs
891	images.append(fig)
892
893	return images
894
895	class Reader(CansasReader):
896	"""
897	Class to load a .fitv fitting file
898	"""
899	## File type
900	type_name = "Fitting"
901
902	## Wildcards
903	type = ["Fitting files (.fitv)\|.fitv"
904	"SANSView file (.svs)\|.svs"]
905	## List of allowed extensions
906	ext=['.fitv', '.FITV', '.svs', 'SVS']
907
908	def __init__(self, call_back=None, cansas=True):
909	CansasReader.__init__(self)
910	"""
911	Initialize the call-back method to be called
912	after we load a file
913
914	:param call_back: call-back method
915	:param cansas: True = files will be written/read in CanSAS format
916	False = write CanSAS format
917
918	"""
919	## Call back method to be executed after a file is read
920	self.call_back = call_back
921	## CanSAS format flag
922	self.cansas = cansas
923	self.state = None
924	def get_state(self):
925	return self.state
926
927	def read(self, path):
928	"""
929	Load a new P(r) inversion state from file
930
931	:param path: file path
932
933	"""
934	if self.cansas == True:
935	return self._read_cansas(path)
936
937	def _data2d_to_xml_doc(self, datainfo):
938	"""
939	Create an XML document to contain the content of a Data2D
940
941	:param datainfo: Data2D object
942
943	"""
944	if not issubclass(datainfo.__class__, Data2D):
945	raise RuntimeError, "The cansas writer expects a Data2D instance"
946
947	doc = xml.dom.minidom.Document()
948	main_node = doc.createElement("SASroot")
949	main_node.setAttribute("version", self.version)
950	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
951	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
952	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
953
954	doc.appendChild(main_node)
955
956	entry_node = doc.createElement("SASentry")
957	main_node.appendChild(entry_node)
958
959	write_node(doc, entry_node, "Title", datainfo.title)
960	if datainfo is not None:
961	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
962	for item in datainfo.run:
963	runname = {}
964	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
965	runname = {'name': datainfo.run_name[item] }
966	write_node(doc, entry_node, "Run", item, runname)
967	# Data info
968	new_node = doc.createElement("SASdata")
969	entry_node.appendChild(new_node)
970	for item in list_of_data_2d_attr:
971	element = doc.createElement(item[0])
972	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
973	new_node.appendChild(element)
974
975	for item in list_of_data2d_values:
976	root_node = doc.createElement(item[0])
977	new_node.appendChild(root_node)
978
979	exec "temp_list = datainfo.%s"%item[1]
980
981	if temp_list is None or len(temp_list)== 0:
982	element = doc.createElement(item[0])
983	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
984	root_node.appendChild(element)
985	else:
986	for value in temp_list:
987	element = doc.createElement(item[0])
988	exec "element.setAttribute(item[0], str(%s))"%value
989	root_node.appendChild(element)
990
991	# Sample info
992	sample = doc.createElement("SASsample")
993	if datainfo.sample.name is not None:
994	sample.setAttribute("name", str(datainfo.sample.name))
995	entry_node.appendChild(sample)
996	write_node(doc, sample, "ID", str(datainfo.sample.ID))
997	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
998	write_node(doc, sample, "transmission", datainfo.sample.transmission)
999	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
1000
1001	for item in datainfo.sample.details:
1002	write_node(doc, sample, "details", item)
1003
1004	pos = doc.createElement("position")
1005	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
1006	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
1007	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
1008	if written == True:
1009	sample.appendChild(pos)
1010
1011	ori = doc.createElement("orientation")
1012	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
1013	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1014	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1015	if written == True:
1016	sample.appendChild(ori)
1017
1018	# Instrument info
1019	instr = doc.createElement("SASinstrument")
1020	entry_node.appendChild(instr)
1021
1022	write_node(doc, instr, "name", datainfo.instrument)
1023
1024	# Source
1025	source = doc.createElement("SASsource")
1026	if datainfo.source.name is not None:
1027	source.setAttribute("name", str(datainfo.source.name))
1028	instr.appendChild(source)
1029
1030	write_node(doc, source, "radiation", datainfo.source.radiation)
1031	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1032	size = doc.createElement("beam_size")
1033	if datainfo.source.beam_size_name is not None:
1034	size.setAttribute("name", str(datainfo.source.beam_size_name))
1035	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1036	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1037	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1038	if written == True:
1039	source.appendChild(size)
1040
1041	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1042	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1043	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1044	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1045
1046	# Collimation
1047	for item in datainfo.collimation:
1048	coll = doc.createElement("SAScollimation")
1049	if item.name is not None:
1050	coll.setAttribute("name", str(item.name))
1051	instr.appendChild(coll)
1052
1053	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1054
1055	for apert in item.aperture:
1056	ap = doc.createElement("aperture")
1057	if apert.name is not None:
1058	ap.setAttribute("name", str(apert.name))
1059	if apert.type is not None:
1060	ap.setAttribute("type", str(apert.type))
1061	coll.appendChild(ap)
1062
1063	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1064
1065	size = doc.createElement("size")
1066	if apert.size_name is not None:
1067	size.setAttribute("name", str(apert.size_name))
1068	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1069	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1070	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1071	if written == True:
1072	ap.appendChild(size)
1073
1074	# Detectors
1075	for item in datainfo.detector:
1076	det = doc.createElement("SASdetector")
1077	written = write_node(doc, det, "name", item.name)
1078	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1079	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1080	if written == True:
1081	instr.appendChild(det)
1082
1083	off = doc.createElement("offset")
1084	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1085	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1086	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1087	if written == True:
1088	det.appendChild(off)
1089
1090	center = doc.createElement("beam_center")
1091	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1092	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1093	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1094	if written == True:
1095	det.appendChild(center)
1096
1097	pix = doc.createElement("pixel_size")
1098	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1099	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1100	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1101	if written == True:
1102	det.appendChild(pix)
1103
1104	ori = doc.createElement("orientation")
1105	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1106	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1107	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1108	if written == True:
1109	det.appendChild(ori)
1110
1111	# Processes info
1112	for item in datainfo.process:
1113	node = doc.createElement("SASprocess")
1114	entry_node.appendChild(node)
1115
1116	write_node(doc, node, "name", item.name)
1117	write_node(doc, node, "date", item.date)
1118	write_node(doc, node, "description", item.description)
1119	for term in item.term:
1120	value = term['value']
1121	del term['value']
1122	write_node(doc, node, "term", value, term)
1123	for note in item.notes:
1124	write_node(doc, node, "SASprocessnote", note)
1125	# Return the document, and the SASentry node associated with
1126	# the data we just wrote
1127	return doc, entry_node
1128
1129	def _parse_state(self, entry):
1130	"""
1131	Read a fit result from an XML node
1132
1133	:param entry: XML node to read from
1134
1135	:return: PageState object
1136	"""
1137	# Create an empty state
1138	state = None
1139	# Locate the P(r) node
1140	try:
1141	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
1142	if nodes !=[]:
1143	# Create an empty state
1144	state = PageState()
1145	state.fromXML(node=nodes[0])
1146	except:
1147	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1148
1149	return state
1150
1151
1152
1153	def _parse_entry(self, dom):
1154	"""
1155	Parse a SASentry
1156
1157	:param node: SASentry node
1158
1159	:return: Data1D/Data2D object
1160
1161	"""
1162	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1163	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1164	return CansasReader._parse_entry(self, dom)
1165
1166	#Parse 2D
1167	data_info = Data2D()
1168
1169	# Look up title
1170	self._store_content('ns:Title', dom, 'title', data_info)
1171
1172	# Look up run number
1173	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1174	for item in nodes:
1175	if item.text is not None:
1176	value = item.text.strip()
1177	if len(value) > 0:
1178	data_info.run.append(value)
1179	if item.get('name') is not None:
1180	data_info.run_name[value] = item.get('name')
1181
1182	# Look up instrument name
1183	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1184
1185	# Notes
1186	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1187	for note in note_list:
1188	try:
1189	if note.text is not None:
1190	note_value = note.text.strip()
1191	if len(note_value) > 0:
1192	data_info.notes.append(note_value)
1193	except:
1194	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1195	self.errors.append(err_mess)
1196	logging.error(err_mess)
1197
1198	# Sample info ###################
1199	entry = get_content('ns:SASsample', dom)
1200	if entry is not None:
1201	data_info.sample.name = entry.get('name')
1202
1203	self._store_content('ns:SASsample/ns:ID',
1204	dom, 'ID', data_info.sample)
1205	self._store_float('ns:SASsample/ns:thickness',
1206	dom, 'thickness', data_info.sample)
1207	self._store_float('ns:SASsample/ns:transmission',
1208	dom, 'transmission', data_info.sample)
1209	self._store_float('ns:SASsample/ns:temperature',
1210	dom, 'temperature', data_info.sample)
1211
1212	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1213	for item in nodes:
1214	try:
1215	if item.text is not None:
1216	detail_value = item.text.strip()
1217	if len(detail_value) > 0:
1218	data_info.sample.details.append(detail_value)
1219	except:
1220	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1221	self.errors.append(err_mess)
1222	logging.error(err_mess)
1223
1224	# Position (as a vector)
1225	self._store_float('ns:SASsample/ns:position/ns:x',
1226	dom, 'position.x', data_info.sample)
1227	self._store_float('ns:SASsample/ns:position/ns:y',
1228	dom, 'position.y', data_info.sample)
1229	self._store_float('ns:SASsample/ns:position/ns:z',
1230	dom, 'position.z', data_info.sample)
1231
1232	# Orientation (as a vector)
1233	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1234	dom, 'orientation.x', data_info.sample)
1235	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1236	dom, 'orientation.y', data_info.sample)
1237	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1238	dom, 'orientation.z', data_info.sample)
1239
1240	# Source info ###################
1241	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1242	if entry is not None:
1243	data_info.source.name = entry.get('name')
1244
1245	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1246	dom, 'radiation', data_info.source)
1247	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1248	dom, 'beam_shape', data_info.source)
1249	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1250	dom, 'wavelength', data_info.source)
1251	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1252	dom, 'wavelength_min', data_info.source)
1253	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1254	dom, 'wavelength_max', data_info.source)
1255	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1256	dom, 'wavelength_spread', data_info.source)
1257
1258	# Beam size (as a vector)
1259	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1260	if entry is not None:
1261	data_info.source.beam_size_name = entry.get('name')
1262
1263	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1264	dom, 'beam_size.x', data_info.source)
1265	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1266	dom, 'beam_size.y', data_info.source)
1267	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1268	dom, 'beam_size.z', data_info.source)
1269
1270	# Collimation info ###################
1271	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
1272	for item in nodes:
1273	collim = Collimation()
1274	if item.get('name') is not None:
1275	collim.name = item.get('name')
1276	self._store_float('ns:length', item, 'length', collim)
1277
1278	# Look for apertures
1279	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
1280	for apert in apert_list:
1281	aperture = Aperture()
1282
1283	# Get the name and type of the aperture
1284	aperture.name = apert.get('name')
1285	aperture.type = apert.get('type')
1286
1287	self._store_float('ns:distance', apert, 'distance', aperture)
1288
1289	entry = get_content('ns:size', apert)
1290	if entry is not None:
1291	aperture.size_name = entry.get('name')
1292
1293	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1294	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1295	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1296
1297	collim.aperture.append(aperture)
1298
1299	data_info.collimation.append(collim)
1300
1301	# Detector info ######################
1302	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1303	for item in nodes:
1304
1305	detector = Detector()
1306
1307	self._store_content('ns:name', item, 'name', detector)
1308	self._store_float('ns:SDD', item, 'distance', detector)
1309
1310	# Detector offset (as a vector)
1311	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1312	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1313	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1314
1315	# Detector orientation (as a vector)
1316	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1317	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1318	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1319
1320	# Beam center (as a vector)
1321	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1322	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1323	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1324
1325	# Pixel size (as a vector)
1326	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1327	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1328	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1329
1330	self._store_float('ns:slit_length', item, 'slit_length', detector)
1331
1332	data_info.detector.append(detector)
1333
1334	# Processes info ######################
1335	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1336	for item in nodes:
1337	process = Process()
1338	self._store_content('ns:name', item, 'name', process)
1339	self._store_content('ns:date', item, 'date', process)
1340	self._store_content('ns:description', item, 'description', process)
1341
1342	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1343	for term in term_list:
1344	try:
1345	term_attr = {}
1346	for attr in term.keys():
1347	term_attr[attr] = term.get(attr).strip()
1348	if term.text is not None:
1349	term_attr['value'] = term.text.strip()
1350	process.term.append(term_attr)
1351	except:
1352	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1353	self.errors.append(err_mess)
1354	logging.error(err_mess)
1355
1356	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1357	for note in note_list:
1358	if note.text is not None:
1359	process.notes.append(note.text.strip())
1360
1361	data_info.process.append(process)
1362
1363
1364	# Data info ######################
1365	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1366	if len(nodes)>1:
1367	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1368
1369	for entry in nodes:
1370	for item in list_of_data_2d_attr:
1371	#get node
1372	node = get_content('ns:%s'%item[0], entry)
1373	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1374
1375	for item in list_of_data2d_values:
1376	field = get_content('ns:%s'%item[0], entry)
1377	list = []
1378	if field is not None:
1379	list = [parse_entry_helper(node, item) for node in field]
1380	exec "data_info.%s = numpy.array(list)"%item[0]
1381
1382	return data_info
1383
1384	def _read_cansas(self, path):
1385	"""
1386	Load data and P(r) information from a CanSAS XML file.
1387
1388	:param path: file path
1389
1390	:return: Data1D object if a single SASentry was found,
1391	or a list of Data1D objects if multiple entries were found,
1392	or None of nothing was found
1393
1394	:raise RuntimeError: when the file can't be opened
1395	:raise ValueError: when the length of the data vectors are inconsistent
1396
1397	"""
1398	output = []
1399	basename = os.path.basename(path)
1400	root, extension = os.path.splitext(basename)
1401	ext = extension.lower()
1402	try:
1403	if os.path.isfile(path):
1404
1405	#TODO: eventually remove the check for .xml once
1406	# the P(r) writer/reader is truly complete.
1407	if ext in self.ext or \
1408	ext == '.xml':
1409
1410	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1411	# Check the format version number
1412	# Specifying the namespace will take care of the file format version
1413	root = tree.getroot()
1414	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1415	for entry in entry_list:
1416	try:
1417	sas_entry = self._parse_entry(entry)
1418	except:
1419	raise
1420	fitstate = self._parse_state(entry)
1421
1422	#state could be None when .svs file is loaded
1423	#in this case, skip appending to output
1424	if fitstate != None:
1425	sas_entry.meta_data['fitstate'] = fitstate
1426	sas_entry.filename = fitstate.file
1427	output.append(sas_entry)
1428	else:
1429	self.call_back(format=ext)
1430	raise RuntimeError, "%s is not a file" % path
1431
1432	# Return output consistent with the loader's api
1433	if len(output)==0:
1434	self.call_back(state=None, datainfo=None,format=ext)
1435	return None
1436	else:
1437	for ind in range(len(output)):
1438	# Call back to post the new state
1439	state = output[ind].meta_data['fitstate']
1440	t = time.localtime(state.timestamp)
1441	time_str = time.strftime("%b %d %H:%M", t)
1442	# Check that no time stamp is already appended
1443	max_char = state.file.find("[")
1444	if max_char < 0:
1445	max_char = len(state.file)
1446	original_fname = state.file[0:max_char]
1447	state.file = original_fname +' [' + time_str + ']'
1448
1449
1450	if state is not None and state.is_data is not None:
1451	exec 'output[%d].is_data = state.is_data'% ind
1452
1453	output[ind].filename = state.file
1454	state.data = output[ind]
1455	state.data.name = output[ind].filename #state.data_name
1456	state.data.id = state.data_id
1457	if state.is_data is not None:
1458	state.data.is_data = state.is_data
1459	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1460	name = output[ind].run_name
1461	else:
1462	name=original_fname
1463	state.data.group_id = name
1464	#store state in fitting
1465	self.call_back(state=state, datainfo=output[ind],format=ext)
1466	self.state= state
1467	return output
1468
1469	except:
1470	self.call_back(format=ext)
1471	#self.state= state
1472	raise
1473
1474	def write(self, filename, datainfo=None, fitstate=None):
1475	"""
1476	Write the content of a Data1D as a CanSAS XML file only for standalone
1477
1478	:param filename: name of the file to write
1479	:param datainfo: Data1D object
1480	:param fitstate: PageState object
1481
1482	"""
1483	# Sanity check
1484	if self.cansas == True:
1485
1486	# Add fitting information to the XML document
1487	doc = self.write_toXML(datainfo, fitstate)
1488	# Write the XML document
1489	fd = open(filename, 'w')
1490	fd.write(doc.toprettyxml())
1491	fd.close()
1492	else:
1493	fitstate.toXML(file=filename)
1494
1495	def write_toXML(self, datainfo=None, state=None):
1496	"""
1497	Write toXML, a helper for write() , could be used by guimanager._on_save()
1498
1499	: return: xml doc
1500	"""
1501
1502	if state.data is None:
1503	data = DataLoader.data_info.Data1D(x=[], y=[])
1504	else:
1505	#make sure title and data run is filled up.
1506	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1507	if state.data.run_name == None or state.data.run_name=={}:
1508	state.data.run = [str(state.data.name)]
1509	state.data.run_name[0] = state.data.name
1510
1511	if issubclass(state.data.__class__, DataLoader.data_info.Data1D):
1512
1513	data = state.data
1514	doc, sasentry = self._to_xml_doc(data)
1515	else:
1516	data = state.data
1517	doc, sasentry = self._data2d_to_xml_doc(data)
1518
1519
1520	if state is not None:
1521	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1522
1523	return doc
1524
1525	# Simple html report templet
1526	HEADER = "<html>\n"
1527	HEADER += "<head>\n"
1528	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1529	HEADER += "charset=windows-1252'> \n"
1530	HEADER += "<meta name=Generator >\n"
1531	HEADER += "</head>\n"
1532	HEADER += "<body lang=EN-US>\n"
1533	HEADER += "<div class=WordSection1>\n"
1534	HEADER += "<p class=MsoNormal><b><span ><center>"
1535	HEADER += "%s</center></span></center></b></p>"
1536	HEADER += "<p class=MsoNormal> </p>"
1537	PARA = "<p class=MsoNormal> %s \n"
1538	PARA += "</p>"
1539	CENTRE = "<p class=MsoNormal><center> %s \n"
1540	CENTRE += "</center></p>"
1541	FEET_1 = \
1542	"""
1543	<p class=MsoNormal> </p>
1544	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
1545	<p class=MsoNormal> </p>
1546	<center>
1547	<br>Model Computation<br>
1548	<br>Data: "%s"<br>
1549	"""
1550	FEET_2 = \
1551	"""
1552	<img src="%s" >
1553	</img>
1554	"""
1555	FEET_3 = \
1556	"""
1557	</center>
1558	</div>
1559	</body>
1560	</html>
1561	"""
1562	ELINE = "<p class=MsoNormal> </p>"
1563
1564	if __name__ == "__main__":
1565	state = PageState(parent=None)
1566	#state.toXML()
1567	"""
1568
1569	file = open("test_state", "w")
1570	pickle.dump(state, file)
1571	print pickle.dumps(state)
1572	state.data_name = "hello---->"
1573	pickle.dump(state, file)
1574	file = open("test_state", "r")
1575	new_state= pickle.load(file)
1576	print "new state", new_state
1577	new_state= pickle.load(file)
1578	print "new state", new_state
1579	#print "state", state
1580	"""
1581	import bsddb
1582	import pickle
1583	db= bsddb.btopen('file_state.db', 'c')
1584	val = (pickle.dumps(state), "hello", "hi")
1585	db['state1']= pickle.dumps(val)
1586	print pickle.loads(db['state1'])
1587	state.data_name = "hello---->22"
1588	db['state2']= pickle.dumps(state)
1589	state.data_name = "hello---->2"
1590	db['state3']= pickle.dumps(state)
1591	del db['state3']
1592	state.data_name = "hello---->3"
1593	db['state4']= pickle.dumps(state)
1594	new_state = pickle.loads(db['state1'])
1595	#print db.last()
1596	db.set_location('state2')
1597	state.data_name = "hello---->5"
1598	db['aastate5']= pickle.dumps(state)
1599	db.keys().sort()
1600	print pickle.loads(db['state2'])
1601
1602	db.close()

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SasView

source: sasview/sansview/perspectives/fitting/pagestate.py @ c31fd9f

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