pagestate.py @ 22ce7e2

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 22ce7e2 was 8e671c39, checked in by Jae Cho <jhjcho@…>, 13 years ago
fixed minor bug in report due to the recent changes in gui
Property mode set to `100644`
File size: 67.7 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 sans.dataloader
25	from sans.dataloader.readers.cansas_reader import Reader as CansasReader
26	from sans.dataloader.readers.cansas_reader import get_content, write_node
27	from sans.dataloader.data_info import Data2D, Detector
28
29	#Information to read/write state as xml
30	FITTING_NODE_NAME = 'fitting_plug_in'
31	CANSAS_NS = "cansas1d/1.0"
32
33	list_of_data_attributes = [["is_data", "is_data", "bool"],
34	["group_id", "data_group_id", "string"],
35	["data_name", "data_name", "string"],
36	["data_id", "data_id", "string"],
37	["name", "name", "string"],
38	["data_name", "data_name", "string"]]
39	list_of_state_attributes = [["engine_type", "engine_type", "string"],
40	["qmin", "qmin", "float"],
41	["qmax", "qmax", "float"],
42	["npts", "npts", "float"],
43	["shape_rbutton", "shape_rbutton", "bool"],
44	["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
45	["plugin_rbutton", "plugin_rbutton","bool"],
46	["struct_rbutton", "struct_rbutton", "bool"],
47	["formfactorcombobox", "formfactorcombobox", "float"],
48	["structurecombobox", "structurecombobox", "float"],
49	["multi_factor","multi_factor","float"],
50	["enable_smearer","enable_smearer","bool"],
51	["disable_smearer","disable_smearer","bool"],
52	["pinhole_smearer","pinhole_smearer","bool"],
53	["slit_smearer","slit_smearer","bool"],
54	["enable_disp","enable_disp","bool"],
55	["disable_disp","disable_disp","bool"],
56	["dI_noweight","dI_noweight","bool"],
57	["dI_didata","dI_didata","bool"],
58	["dI_sqrdata","dI_sqrdata","bool"],
59	["dI_idata","dI_idata","bool"],
60	["enable2D","enable2D","bool"],
61	["cb1","cb1","bool"],
62	["tcChi","tcChi","float"],
63	["smearer", "smearer", "float"],
64	["smear_type","smear_type", "string"],
65	["dq_l", "dq_l", "string"],
66	["dq_r","dq_r", "string"]]
67
68	list_of_model_attributes = [["values", "values"],
69	["weights", "weights"]]
70
71	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
72
73	list_of_state_parameters = [["parameters", "parameters"] ,
74	["str_parameters", "str_parameters"] ,
75	["orientation_parameters", "orientation_params"],
76	["dispersity_parameters", "orientation_params_disp"],
77	["fixed_param", "fixed_param"],
78	["fittable_param","fittable_param"]]
79	list_of_data_2d_attr = [["xmin", "xmin","float"],
80	["xmax","xmax","float"],
81	["ymin","ymin","float"],
82	["ymax","ymax","float"],
83	["_xaxis","_xaxis", "string"],
84	["_xunit", "_xunit", "string"],
85	["_yaxis","_yaxis","string"],
86	["_yunit","_yunit","string"],
87	["_zaxis","_zaxis","string"],
88	["_zunit","_zunit","string"]]
89	list_of_data2d_values = [["qx_data","qx_data","float"],
90	["qy_data","qy_data","float"],
91	["dqx_data","dqx_data","float"],
92	["dqy_data","dqy_data","float"],
93	["data","data","float"],
94	["q_data","q_data","float"],
95	["err_data","err_data","float"],
96	["mask","mask","bool"]]
97
98	def parse_entry_helper( node, item):
99	"""
100	Create a numpy list from value extrated from the node
101
102	:param node: node from each the value is stored
103	:param item: list name of three strings.the two first are name of data
104	attribute and the third one is the type of the value of that
105	attribute. type can be string, float, bool, etc.
106
107	: return: numpy array
108	"""
109	if node is not None:
110	if item[2] == "string":
111	return str(node.get(item[0]).strip())
112	elif item[2] == "bool":
113	try:
114	return node.get(item[0]).strip() == "True"
115
116	except:
117	return None
118	else:
119	try:
120	return float(node.get(item[0]))
121	except:
122	return None
123
124
125	class PageState(object):
126	"""
127	Contains information to reconstruct a page of the fitpanel.
128	"""
129	def __init__(self, parent=None, model=None, data=None):
130
131	"""
132	Initialize the current state
133
134	:param model: a selected model within a page
135	:param data:
136
137	"""
138	self.file = None
139	#Time of state creation
140	self.timestamp = time.time()
141	## Data member to store the dispersion object created
142	self._disp_obj_dict = {}
143	#------------------------
144	#Data used for fitting
145	self.data = data
146	# model data
147	self.theory_data = None
148	#Is 2D
149	self.is_2D = False
150	self.images = None
151
152	#save additional information on data that dataloader.reader does not read
153	self.is_data = None
154	self.data_name = ""
155
156	if self.data is not None:
157	self.data_name = self.data.name
158	self.data_id = None
159	if self.data is not None and hasattr(self.data, "id"):
160	self.data_id = self.data.id
161	self.data_group_id = None
162	if self.data is not None and hasattr(self.data, "group_id"):
163	self.data_group_id = self.data.group_id
164
165	## reset True change the state of exsiting button
166	self.reset = False
167
168	#engine type
169	self.engine_type = None
170	# flag to allow data2D plot
171	self.enable2D = False
172	# model on which the fit would be performed
173	self.model = model
174	#list of process done to model
175	self.process = []
176	#fit page manager
177	self.manager = None
178	#Store the parent of this panel parent
179	# For this application fitpanel is the parent
180	self.parent = parent
181	# Event_owner is the owner of model event
182	self.event_owner = None
183	##page name
184	self.page_name = ""
185	# Contains link between model ,all its parameters, and panel organization
186	self.parameters = []
187	# String parameter list that can not be fitted
188	self.str_parameters = []
189	# Contains list of parameters that cannot be fitted and reference to
190	#panel objects
191	self.fixed_param = []
192	# Contains list of parameters with dispersity and reference to
193	#panel objects
194	self.fittable_param = []
195	## orientation parameters
196	self.orientation_params = []
197	## orientation parmaters for gaussian dispersity
198	self.orientation_params_disp = []
199	## smearer info
200	self.smearer = None
201	self.smear_type = None
202	self.dq_l = None
203	self.dq_r = None
204
205	#list of dispersion paramaters
206	self.disp_list =[]
207	if self.model is not None:
208	self.disp_list = self.model.getDispParamList()
209
210	self.disp_cb_dict = {}
211	self.values = {}
212	self.weights = {}
213
214	#contains link between a model and selected parameters to fit
215	self.param_toFit = []
216	##dictionary of model type and model class
217	self.model_list_box = None
218	## save the state of the context menu
219	self.saved_states = {}
220	## save selection of combobox
221	self.formfactorcombobox = None
222	self.structurecombobox = None
223
224	## radio box to select type of model
225	self.shape_rbutton = False
226	self.shape_indep_rbutton = False
227	self.struct_rbutton = False
228	self.plugin_rbutton = False
229	## the indice of the current selection
230	self.disp_box = 0
231	## Qrange
232	## Q range
233	self.qmin = 0.001
234	self.qmax = 0.1
235	#reset data range
236	self.qmax_x = None
237	self.qmin_x = None
238
239	self.npts = None
240	self.name = ""
241	self.multi_factor = None
242	## enable smearering state
243	self.enable_smearer = False
244	self.disable_smearer = True
245	self.pinhole_smearer = False
246	self.slit_smearer = False
247	# weighting options
248	self.dI_noweight = False
249	self.dI_didata = True
250	self.dI_sqrdata = False
251	self.dI_idata = False
252	## disperity selection
253	self.enable_disp = False
254	self.disable_disp = True
255
256	## state of selected all check button
257	self.cb1 = False
258	## store value of chisqr
259	self.tcChi = None
260
261	def clone(self):
262	"""
263	Create a new copy of the current object
264	"""
265	model = None
266	if self.model is not None:
267	model = self.model.clone()
268	model.name = self.model.name
269	obj = PageState(self.parent, model=model)
270	obj.file = copy.deepcopy(self.file)
271	obj.data = copy.deepcopy(self.data)
272	if self.data is not None:
273	self.data_name = self.data.name
274	obj.data_name = self.data_name
275	obj.is_data = self.is_data
276	obj.model_list_box = copy.deepcopy(self.model_list_box)
277	obj.engine_type = copy.deepcopy(self.engine_type)
278
279	obj.formfactorcombobox = self.formfactorcombobox
280	obj.structurecombobox = self.structurecombobox
281
282	obj.shape_rbutton = self.shape_rbutton
283	obj.shape_indep_rbutton = self.shape_indep_rbutton
284	obj.struct_rbutton = self.struct_rbutton
285	obj.plugin_rbutton = self.plugin_rbutton
286
287	obj.manager = self.manager
288	obj.event_owner = self.event_owner
289	obj.disp_list = copy.deepcopy(self.disp_list)
290
291	obj.enable2D = copy.deepcopy(self.enable2D)
292	obj.parameters = copy.deepcopy(self.parameters)
293	obj.str_parameters = copy.deepcopy(self.str_parameters)
294	obj.fixed_param = copy.deepcopy(self.fixed_param)
295	obj.fittable_param = copy.deepcopy(self.fittable_param)
296	obj.orientation_params = copy.deepcopy(self.orientation_params)
297	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
298	obj.enable_disp = copy.deepcopy(self.enable_disp)
299	obj.disable_disp = copy.deepcopy(self.disable_disp)
300	obj.tcChi = self.tcChi
301
302	if len(self._disp_obj_dict)>0:
303	for k , v in self._disp_obj_dict.iteritems():
304	obj._disp_obj_dict[k]= v
305	if len(self.disp_cb_dict)>0:
306	for k , v in self.disp_cb_dict.iteritems():
307	obj.disp_cb_dict[k]= v
308	if len(self.values)>0:
309	for k , v in self.values.iteritems():
310	obj.values[k] = v
311	if len(self.weights)>0:
312	for k , v in self.weights.iteritems():
313	obj.weights[k] = v
314	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
315	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
316	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
317	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
318	obj.smear_type = copy.deepcopy(self.smear_type)
319	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
320	obj.dI_didata = copy.deepcopy(self.dI_didata)
321	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
322	obj.dI_idata = copy.deepcopy(self.dI_idata)
323	obj.dq_l = copy.deepcopy(self.dq_l)
324	obj.dq_r = copy.deepcopy(self.dq_r)
325
326	obj.disp_box = copy.deepcopy(self.disp_box)
327	obj.qmin = copy.deepcopy(self.qmin)
328	obj.qmax = copy.deepcopy(self.qmax)
329	obj.multi_factor = self.multi_factor
330	obj.npts = copy.deepcopy(self.npts )
331	obj.cb1 = copy.deepcopy(self.cb1)
332	obj.smearer = copy.deepcopy(self.smearer)
333
334	for name, state in self.saved_states.iteritems():
335	copy_name = copy.deepcopy(name)
336	copy_state = state.clone()
337	obj.saved_states[copy_name]= copy_state
338	return obj
339
340	def _repr_helper(self, list, rep):
341	"""
342	Helper method to print a state
343	"""
344	for item in list:
345	rep += "parameter name: %s \n"%str(item[1])
346	rep += "value: %s\n"%str(item[2])
347	rep += "selected: %s\n"%str(item[0])
348	rep += "error displayed : %s \n"%str(item[4][0])
349	rep += "error value:%s \n"%str(item[4][1])
350	rep += "minimum displayed : %s \n"%str(item[5][0])
351	rep += "minimum value : %s \n"%str(item[5][1])
352	rep += "maximum displayed : %s \n"%str(item[6][0])
353	rep += "maximum value : %s \n"%str(item[6][1])
354	rep += "parameter unit: %s\n\n"%str(item[7])
355	return rep
356
357	def __repr__(self):
358	"""
359	output string for printing
360	"""
361	rep = "\nState name: %s\n"%self.file
362	t = time.localtime(self.timestamp)
363	time_str = time.strftime("%b %d %H;%M of %Y", t)
364
365	rep += "State created on : %s\n"%time_str
366	rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox
367	rep += "State structure factor combobox selection: %s\n"%self.structurecombobox
368	rep += "is data : %s\n"%self.is_data
369	rep += "data's name : %s\n"%self.data_name
370	rep += "data's id : %s\n"%self.data_id
371	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
372	rep += "multi_factor : %s\n"% str(self.multi_factor)
373	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
374	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
375	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
376	rep += "data : %s\n"% str(self.data)
377	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
378	str(self.qmax),str(self.npts))
379	rep += "Dispersion selection : %s\n"%str(self.disp_box)
380	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
381	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
382	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
383	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
384	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
385	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
386	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
387
388	rep += "dI_noweight : %s\n"%str(self.dI_noweight)
389	rep += "dI_didata : %s\n"%str(self.dI_didata)
390	rep += "dI_sqrdata : %s\n"%str(self.dI_sqrdata)
391	rep += "dI_idata : %s\n"%str(self.dI_idata)
392
393
394	rep += "2D enable : %s\n"%str(self.enable2D)
395	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
396	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
397	rep += "Smear object : %s\n"%str(self.smearer)
398	rep += "Smear type : %s\n"%(self.smear_type)
399	rep += "dq_l : %s\n"%self.dq_l
400	rep += "dq_r : %s\n"%self.dq_r
401
402	rep += "model : %s\n\n"% str(self.model)
403	temp_parameters = []
404	temp_fittable_param = []
405	if self.data.__class__.__name__ == "Data2D":
406	self.is_2D = True
407	else:
408	self.is_2D = False
409	if self.data is not None:
410	if not self.is_2D:
411	for item in self.parameters:
412	if not item in self.orientation_params:
413	temp_parameters.append(item)
414	for item in self.fittable_param:
415	if not item in self.orientation_params_disp:
416	temp_fittable_param.append(item)
417	else:
418	temp_parameters = self.parameters
419	temp_fittable_param = self.fittable_param
420
421	rep += "number parameters(self.parameters): %s\n"%len(temp_parameters)
422	rep = self._repr_helper( list=temp_parameters, rep=rep)
423	rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters)
424	rep = self._repr_helper( list=self.str_parameters, rep=rep)
425	rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param)
426	rep = self._repr_helper( list=temp_fittable_param, rep=rep)
427	"""
428	if is_2D:
429	rep += "number orientation parameters"
430	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
431	rep = self._repr_helper( list=self.orientation_params, rep=rep)
432	rep += "number dispersity parameters"
433	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
434	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
435	"""
436	return rep
437
438	def set_report_string(self):
439	"""
440	Get the values (strings) from __str__ for report
441	"""
442	# Dictionary of teh report strings
443	repo_time = ""
444	model_name = ""
445	title = ""
446	title_name = ""
447	file_name = ""
448	param_string = ""
449	paramval_string = ""
450	chi2_string = ""
451	multi_factor_string = ""
452	q_range = ""
453	strings = self.__repr__()
454	lines = strings.split('\n')
455
456	# get all string values from __str__()
457	for line in lines:
458	value = ""
459	content = line.split(":")
460	name = content[0]
461	try:
462	value = content[1]
463	except:
464	pass
465	if name.count("State created on"):
466	repo_time = "Created on " + value
467	if name.count("parameter name"):
468	val_name = value.split(".")
469	if len(val_name) > 1:
470	if val_name[1].count("width"):
471	param_string += value + ','
472	else:
473	continue
474	else:
475	param_string += value + ','
476	if name == "value":
477	param_string += value + ','
478	if name == "error value":
479	param_string += value + ','
480	if name == "parameter unit":
481	param_string += value + ':'
482	if name == "Value of Chisqr ":
483	chi2 = ("Chi2/Npts = " + value)
484	chi2_string = CENTRE % chi2
485	if name == "multi_factor ":
486	muti_factor = ("muti_factor = " + value)
487	muti_factor_string = CENTRE % muti_factor
488	if name == "Title":
489	if len(value.strip()) == 0:
490	continue
491	title = value + " [" + repo_time + "]"
492	title_name = HEADER % title
493	if name == "data ":
494	try:
495	file = ("File name:" + content[2])
496	file_name = CENTRE % file
497	if len(title) == 0:
498	title = content[2] + " [" + repo_time + "]"
499	title_name = HEADER % title
500	except:
501	pass
502	if name == "Plotting Range":
503	try:
504	q_range = content[1] + " = " + content[2] \
505	+ " = " + content[3].split(",")[0]
506	q_name = ("Q Range: " + q_range)
507	q_range = CENTRE % q_name
508	except:
509	pass
510	paramval = ""
511	paramval_string += "<table> <tr>"
512	for lines in param_string.split(":"):
513	line = lines.split(",")
514	if len(lines) > 0:
515	param = line[0]
516	param += " = " + line[1]
517	if len(line[2].split()) > 0 and not line[2].count("None"):
518	param += " +- " + line[2]
519	if len(line[3].split()) > 0 and not line[3].count("None"):
520	param += " " + line[3]
521	if not paramval.count(param):
522	paramval += param + "\n"
523	paramval_string += CENTRE % param + "\n"
524	paramval_string += '</tr>'
525	paramval_string += '</table>'
526	text_string = "\n\n\n" + title + "\n\n" + file + \
527	"\n" + q_name + \
528	"\n" + chi2 + \
529	"\n\n" + paramval
530
531	title_name = self._check_html_format(title_name)
532	file_name = self._check_html_format(file_name)
533	title = self._check_html_format(title)
534
535	html_string = title_name + "\n" + file_name + \
536	"\n" + q_range + \
537	"\n" + chi2_string + \
538	"\n" + ELINE + \
539	"\n" + paramval_string + \
540	"\n" + ELINE + \
541	"\n" + FEET_1 % title + \
542	"\n" + FEET_2
543
544	return html_string, text_string, title
545
546	def _check_html_format(self, name):
547	"""
548	Check string '%' for html format
549	"""
550	if name.count('%'):
551	name = name.replace('%', '&#37')
552
553	return name
554
555
556	def report(self, figs=None, canvases=None):
557	"""
558	Invoke report dialog panel
559
560	: param figs: list of pylab figures [list]
561	"""
562	from report_dialog import ReportDialog
563	# get the strings for report
564	html_str, text_str, title = self.set_report_string()
565	# Allow 2 figures to append
566	if len(figs) == 1:
567	add_str = FEET_3
568	elif len(figs) == 2:
569	add_str = ELINE
570	add_str += FEET_2 % ("%s")
571	add_str += ELINE
572	add_str += FEET_3
573	elif len(figs) > 2:
574	add_str = ELINE
575	add_str += FEET_2 % ("%s")
576	add_str += ELINE
577	add_str += FEET_2 % ("%s")
578	add_str += ELINE
579	add_str += FEET_3
580	else:
581	add_str = ""
582
583	# final report html strings
584	report_str = html_str % ("%s") + add_str
585
586	# make plot image
587	images = self.set_plot_state(figs, canvases)
588	report_list = [report_str, text_str, images ]
589	dialog = ReportDialog(report_list, None, -1, "")
590	dialog.ShowModal()
591
592
593	def _toXML_helper(self, list, element, newdoc):
594	"""
595	Helper method to create xml file for saving state
596	"""
597	for item in list:
598	sub_element = newdoc.createElement('parameter')
599	sub_element.setAttribute('name', str(item[1]))
600	sub_element.setAttribute('value', str(item[2]))
601	sub_element.setAttribute('selected_to_fit', str(item[0]))
602	sub_element.setAttribute('error_displayed', str(item[4][0]))
603	sub_element.setAttribute('error_value', str(item[4][1]))
604	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
605	sub_element.setAttribute('minimum_value', str(item[5][1]))
606	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
607	sub_element.setAttribute('maximum_value', str(item[6][1]))
608	sub_element.setAttribute('unit', str(item[7]))
609	element.appendChild(sub_element)
610
611	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
612	"""
613	Writes the state of the InversionControl panel to file, as XML.
614
615	Compatible with standalone writing, or appending to an
616	already existing XML document. In that case, the XML document
617	is required. An optional entry node in the XML document may also be given.
618
619	:param file: file to write to
620	:param doc: XML document object [optional]
621	:param entry_node: XML node within the XML document at which we will append the data [optional]
622
623	"""
624	from xml.dom.minidom import getDOMImplementation
625
626	# Check whether we have to write a standalone XML file
627	if doc is None:
628	impl = getDOMImplementation()
629	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
630	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
631	top_element = newdoc.documentElement
632	else:
633	# We are appending to an existing document
634	newdoc = doc
635	top_element = newdoc.createElement(FITTING_NODE_NAME)
636	if entry_node is None:
637	newdoc.documentElement.appendChild(top_element)
638	else:
639	entry_node.appendChild(top_element)
640
641	attr = newdoc.createAttribute("version")
642	attr.nodeValue = '1.0'
643	top_element.setAttributeNode(attr)
644
645	# File name
646	element = newdoc.createElement("filename")
647	if self.file is not None:
648	element.appendChild(newdoc.createTextNode(str(self.file)))
649	else:
650	element.appendChild(newdoc.createTextNode(str(file)))
651	top_element.appendChild(element)
652
653	element = newdoc.createElement("timestamp")
654	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
655	attr = newdoc.createAttribute("epoch")
656	attr.nodeValue = str(self.timestamp)
657	element.setAttributeNode(attr)
658	top_element.appendChild(element)
659	# Inputs
660	inputs = newdoc.createElement("Attributes")
661	top_element.appendChild(inputs)
662
663
664	if self.data is not None and hasattr(self.data, "group_id"):
665	self.data_group_id = self.data.group_id
666	if self.data is not None and hasattr(self.data, "is_data"):
667	self.is_data = self.data.is_data
668	if self.data is not None:
669	self.data_name = self.data.name
670	if self.data is not None and hasattr(self.data, "id"):
671	self.data_id = self.data.id
672
673	for item in list_of_data_attributes:
674	element = newdoc.createElement(item[0])
675	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
676	inputs.appendChild(element)
677
678	for item in list_of_state_attributes:
679	element = newdoc.createElement(item[0])
680	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
681	inputs.appendChild(element)
682
683	# For self.values ={ disp_param_name: [vals,...],...}
684	# and for self.weights ={ disp_param_name: [weights,...],...}
685	for item in list_of_model_attributes:
686	element = newdoc.createElement(item[0])
687	exec "list = self.%s" % item[1]
688	for key, value in list.iteritems():
689	sub_element = newdoc.createElement(key)
690	sub_element.setAttribute('name', str(key))
691	for val in value:
692	com = "sub_element.appendChild"
693	com += "(newdoc.createTextNode(str(%s)))"
694	exec com % val
695
696	element.appendChild(sub_element)
697	inputs.appendChild(element)
698
699	# Create doc for the dictionary of self._disp_obj_dic
700	for item in list_of_obj_dic:
701	element = newdoc.createElement(item[0])
702	exec "list = self.%s" % item[1]
703	for key, val in list.iteritems():
704	value = repr(val)
705	sub_element = newdoc.createElement(key)
706	sub_element.setAttribute('name', str(key))
707	sub_element.setAttribute('value', str(value))
708	element.appendChild(sub_element)
709	inputs.appendChild(element)
710
711	for item in list_of_state_parameters:
712	element = newdoc.createElement(item[0])
713	com = "self._toXML_helper(list=self.%s,"
714	com += " element=element, newdoc=newdoc)"
715	exec com % item[1]
716	inputs.appendChild(element)
717
718	# Save the file
719	if doc is None:
720	fd = open(file, 'w')
721	fd.write(newdoc.toprettyxml())
722	fd.close()
723	return None
724	else:
725	return newdoc.toprettyxml()
726
727	def _fromXML_helper(self, node, list):
728	"""
729	Helper function to write state to xml
730	"""
731	for item in node:
732	try:
733	name = item.get('name')
734	except:
735	name = None
736	try:
737	value = item.get('value')
738	except:
739	value = None
740	try:
741	selected_to_fit = (item.get('selected_to_fit') == "True")
742	except:
743	selected_to_fit = None
744	try:
745	error_displayed = (item.get('error_displayed') == "True")
746	except:
747	error_displayed = None
748	try:
749	error_value = item.get('error_value')
750	except:
751	error_value = None
752	try:
753	minimum_displayed = (item.get('minimum_displayed')== "True")
754	except:
755	minimum_displayed = None
756	try:
757	minimum_value = item.get('minimum_value')
758	except:
759	minimum_value = None
760	try:
761	maximum_displayed = (item.get('maximum_displayed') == "True")
762	except:
763	maximum_displayed = None
764	try:
765	maximum_value = item.get('maximum_value')
766	except:
767	maximum_value = None
768	try:
769	unit = item.get('unit')
770	except:
771	unit = None
772	list.append([selected_to_fit, name, value, "+/-",
773	[error_displayed, error_value],
774	[minimum_displayed,minimum_value],
775	[maximum_displayed,maximum_value], unit])
776
777	def fromXML(self, file=None, node=None):
778	"""
779	Load fitting state from a file
780
781	:param file: .fitv file
782	:param node: node of a XML document to read from
783
784	"""
785	if file is not None:
786	msg = "PageState no longer supports non-CanSAS"
787	msg += " format for fitting files"
788	raise RuntimeError, msg
789
790	if node.get('version')and node.get('version') == '1.0':
791
792	# Get file name
793	entry = get_content('ns:filename', node)
794	if entry is not None:
795	self.file = entry.text.strip()
796
797	# Get time stamp
798	entry = get_content('ns:timestamp', node)
799	if entry is not None and entry.get('epoch'):
800	try:
801	self.timestamp = float(entry.get('epoch'))
802	except:
803	msg = "PageState.fromXML: Could not"
804	msg += " read timestamp\n %s" % sys.exc_value
805	logging.error(msg)
806
807	# Parse fitting attributes
808	entry = get_content('ns:Attributes', node)
809	for item in list_of_data_attributes:
810	node = get_content('ns:%s'%item[0], entry)
811	try:
812	exec "self.%s = parse_entry_helper(node, item)" % item[0]
813
814	except:
815	raise
816
817	if entry is not None:
818
819	for item in list_of_state_attributes:
820	node = get_content('ns:%s' % item[0], entry)
821	try:
822	exec "self.%s = parse_entry_helper(node, item)" % \
823	str(item[0])
824	except:
825	raise
826
827	for item in list_of_state_parameters:
828	node = get_content("ns:%s" % item[0], entry)
829	exec "self._fromXML_helper(node=node, list=self.%s)" % \
830	item[1]
831
832	# Recover _disp_obj_dict from xml file
833	self._disp_obj_dict = {}
834	for item in list_of_obj_dic:
835	# Get node
836	node = get_content("ns:%s" % item[0], entry)
837	for attr in node:
838	name = attr.get('name')
839	val = attr.get('value')
840	value = val.split(" instance")[0]
841	disp_name = value.split("<")[1]
842	try:
843	# Try to recover disp_model object from strings
844	com = "from sans.models.dispersion_models "
845	com += "import %s as disp"
846	com_name = disp_name.split(".")[3]
847	exec com % com_name
848	disp_model = disp()
849	exec "self.%s['%s'] = com_name" % (item[1], name)
850	except:
851	pass
852
853	# get self.values and self.weights dic. if exists
854	for item in list_of_model_attributes:
855	node = get_content("ns:%s" % item[0], entry)
856	dic = {}
857	list = []
858	for par in node:
859	name = par.get('name')
860	values = par.text.split('\n')
861	# Get lines only with numbers
862	for line in values:
863	try:
864	val= float(line)
865	list.append(val)
866	except:
867	# pass if line is empty (it happens)
868	pass
869	dic[name] = numpy.array(list)
870	exec "self.%s = dic" % item[1]
871
872	def set_plot_state(self, figs, canvases):
873	"""
874	Build image state that wx.html understand
875	by plotting, putting it into wx.FileSystem image object
876
877	"""
878	images = []
879	# some imports
880	import wx
881
882	# Reset memory
883	self.imgRAM = None
884	wx.MemoryFSHandler()
885
886	# For no figures in the list, prepare empty plot
887	if figs == None or len(figs) == 0:
888	figs = [None]
889
890	# Loop over the list of figures
891	# use wx.MemoryFSHandler
892	self.imgRAM = wx.MemoryFSHandler()
893	for fig in figs:
894	if figs != None:
895	#fig.set_facecolor('w')
896	ind = figs.index(fig)
897	canvas = canvases[ind]
898
899	#bmp = wx.BitmapDataObject()
900	#bmp.SetBitmap(canvas.bitmap)
901	#store the image in wx.FileSystem Object
902	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
903
904	# index of the fig
905	ind = figs.index(fig)
906
907	#AddFile, image can be retrieved with 'memory:filename'
908	self.imgRAM.AddFile('img_fit%s.png' % ind ,
909	canvas.bitmap, wx.BITMAP_TYPE_PNG)
910
911	#append figs
912	images.append(fig)
913
914	return images
915
916	class Reader(CansasReader):
917	"""
918	Class to load a .fitv fitting file
919	"""
920	## File type
921	type_name = "Fitting"
922
923	## Wildcards
924	type = ["Fitting files (.fitv)\|.fitv"
925	"SANSView file (.svs)\|.svs"]
926	## List of allowed extensions
927	ext=['.fitv', '.FITV', '.svs', 'SVS']
928
929	def __init__(self, call_back=None, cansas=True):
930	CansasReader.__init__(self)
931	"""
932	Initialize the call-back method to be called
933	after we load a file
934
935	:param call_back: call-back method
936	:param cansas: True = files will be written/read in CanSAS format
937	False = write CanSAS format
938
939	"""
940	## Call back method to be executed after a file is read
941	self.call_back = call_back
942	## CanSAS format flag
943	self.cansas = cansas
944	self.state = None
945	def get_state(self):
946	return self.state
947
948	def read(self, path):
949	"""
950	Load a new P(r) inversion state from file
951
952	:param path: file path
953
954	"""
955	if self.cansas == True:
956	return self._read_cansas(path)
957
958	def _data2d_to_xml_doc(self, datainfo):
959	"""
960	Create an XML document to contain the content of a Data2D
961
962	:param datainfo: Data2D object
963
964	"""
965	if not issubclass(datainfo.__class__, Data2D):
966	raise RuntimeError, "The cansas writer expects a Data2D instance"
967
968	doc = xml.dom.minidom.Document()
969	main_node = doc.createElement("SASroot")
970	main_node.setAttribute("version", self.version)
971	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
972	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
973	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
974
975	doc.appendChild(main_node)
976
977	entry_node = doc.createElement("SASentry")
978	main_node.appendChild(entry_node)
979
980	write_node(doc, entry_node, "Title", datainfo.title)
981	if datainfo is not None:
982	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
983	for item in datainfo.run:
984	runname = {}
985	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
986	runname = {'name': datainfo.run_name[item] }
987	write_node(doc, entry_node, "Run", item, runname)
988	# Data info
989	new_node = doc.createElement("SASdata")
990	entry_node.appendChild(new_node)
991	for item in list_of_data_2d_attr:
992	element = doc.createElement(item[0])
993	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
994	new_node.appendChild(element)
995
996	for item in list_of_data2d_values:
997	root_node = doc.createElement(item[0])
998	new_node.appendChild(root_node)
999
1000	exec "temp_list = datainfo.%s"%item[1]
1001
1002	if temp_list is None or len(temp_list)== 0:
1003	element = doc.createElement(item[0])
1004	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
1005	root_node.appendChild(element)
1006	else:
1007	for value in temp_list:
1008	element = doc.createElement(item[0])
1009	exec "element.setAttribute(item[0], str(%s))"%value
1010	root_node.appendChild(element)
1011
1012	# Sample info
1013	sample = doc.createElement("SASsample")
1014	if datainfo.sample.name is not None:
1015	sample.setAttribute("name", str(datainfo.sample.name))
1016	entry_node.appendChild(sample)
1017	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1018	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
1019	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1020	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
1021
1022	for item in datainfo.sample.details:
1023	write_node(doc, sample, "details", item)
1024
1025	pos = doc.createElement("position")
1026	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
1027	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
1028	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
1029	if written == True:
1030	sample.appendChild(pos)
1031
1032	ori = doc.createElement("orientation")
1033	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
1034	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1035	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1036	if written == True:
1037	sample.appendChild(ori)
1038
1039	# Instrument info
1040	instr = doc.createElement("SASinstrument")
1041	entry_node.appendChild(instr)
1042
1043	write_node(doc, instr, "name", datainfo.instrument)
1044
1045	# Source
1046	source = doc.createElement("SASsource")
1047	if datainfo.source.name is not None:
1048	source.setAttribute("name", str(datainfo.source.name))
1049	instr.appendChild(source)
1050
1051	write_node(doc, source, "radiation", datainfo.source.radiation)
1052	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1053	size = doc.createElement("beam_size")
1054	if datainfo.source.beam_size_name is not None:
1055	size.setAttribute("name", str(datainfo.source.beam_size_name))
1056	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1057	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1058	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1059	if written == True:
1060	source.appendChild(size)
1061
1062	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1063	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1064	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1065	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1066
1067	# Collimation
1068	for item in datainfo.collimation:
1069	coll = doc.createElement("SAScollimation")
1070	if item.name is not None:
1071	coll.setAttribute("name", str(item.name))
1072	instr.appendChild(coll)
1073
1074	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1075
1076	for apert in item.aperture:
1077	ap = doc.createElement("aperture")
1078	if apert.name is not None:
1079	ap.setAttribute("name", str(apert.name))
1080	if apert.type is not None:
1081	ap.setAttribute("type", str(apert.type))
1082	coll.appendChild(ap)
1083
1084	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1085
1086	size = doc.createElement("size")
1087	if apert.size_name is not None:
1088	size.setAttribute("name", str(apert.size_name))
1089	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1090	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1091	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1092	if written == True:
1093	ap.appendChild(size)
1094
1095	# Detectors
1096	for item in datainfo.detector:
1097	det = doc.createElement("SASdetector")
1098	written = write_node(doc, det, "name", item.name)
1099	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1100	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1101	if written == True:
1102	instr.appendChild(det)
1103
1104	off = doc.createElement("offset")
1105	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1106	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1107	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1108	if written == True:
1109	det.appendChild(off)
1110
1111	center = doc.createElement("beam_center")
1112	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1113	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1114	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1115	if written == True:
1116	det.appendChild(center)
1117
1118	pix = doc.createElement("pixel_size")
1119	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1120	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1121	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1122	if written == True:
1123	det.appendChild(pix)
1124
1125	ori = doc.createElement("orientation")
1126	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1127	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1128	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1129	if written == True:
1130	det.appendChild(ori)
1131
1132	# Processes info
1133	for item in datainfo.process:
1134	node = doc.createElement("SASprocess")
1135	entry_node.appendChild(node)
1136
1137	write_node(doc, node, "name", item.name)
1138	write_node(doc, node, "date", item.date)
1139	write_node(doc, node, "description", item.description)
1140	for term in item.term:
1141	value = term['value']
1142	del term['value']
1143	write_node(doc, node, "term", value, term)
1144	for note in item.notes:
1145	write_node(doc, node, "SASprocessnote", note)
1146	# Return the document, and the SASentry node associated with
1147	# the data we just wrote
1148	return doc, entry_node
1149
1150	def _parse_state(self, entry):
1151	"""
1152	Read a fit result from an XML node
1153
1154	:param entry: XML node to read from
1155
1156	:return: PageState object
1157	"""
1158	# Create an empty state
1159	state = None
1160	# Locate the P(r) node
1161	try:
1162	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
1163	if nodes !=[]:
1164	# Create an empty state
1165	state = PageState()
1166	state.fromXML(node=nodes[0])
1167	except:
1168	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1169
1170	return state
1171
1172
1173
1174	def _parse_entry(self, dom):
1175	"""
1176	Parse a SASentry
1177
1178	:param node: SASentry node
1179
1180	:return: Data1D/Data2D object
1181
1182	"""
1183	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1184	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1185	return CansasReader._parse_entry(self, dom)
1186
1187	#Parse 2D
1188	data_info = Data2D()
1189
1190	# Look up title
1191	self._store_content('ns:Title', dom, 'title', data_info)
1192
1193	# Look up run number
1194	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1195	for item in nodes:
1196	if item.text is not None:
1197	value = item.text.strip()
1198	if len(value) > 0:
1199	data_info.run.append(value)
1200	if item.get('name') is not None:
1201	data_info.run_name[value] = item.get('name')
1202
1203	# Look up instrument name
1204	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1205
1206	# Notes
1207	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1208	for note in note_list:
1209	try:
1210	if note.text is not None:
1211	note_value = note.text.strip()
1212	if len(note_value) > 0:
1213	data_info.notes.append(note_value)
1214	except:
1215	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1216	self.errors.append(err_mess)
1217	logging.error(err_mess)
1218
1219	# Sample info ###################
1220	entry = get_content('ns:SASsample', dom)
1221	if entry is not None:
1222	data_info.sample.name = entry.get('name')
1223
1224	self._store_content('ns:SASsample/ns:ID',
1225	dom, 'ID', data_info.sample)
1226	self._store_float('ns:SASsample/ns:thickness',
1227	dom, 'thickness', data_info.sample)
1228	self._store_float('ns:SASsample/ns:transmission',
1229	dom, 'transmission', data_info.sample)
1230	self._store_float('ns:SASsample/ns:temperature',
1231	dom, 'temperature', data_info.sample)
1232
1233	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1234	for item in nodes:
1235	try:
1236	if item.text is not None:
1237	detail_value = item.text.strip()
1238	if len(detail_value) > 0:
1239	data_info.sample.details.append(detail_value)
1240	except:
1241	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1242	self.errors.append(err_mess)
1243	logging.error(err_mess)
1244
1245	# Position (as a vector)
1246	self._store_float('ns:SASsample/ns:position/ns:x',
1247	dom, 'position.x', data_info.sample)
1248	self._store_float('ns:SASsample/ns:position/ns:y',
1249	dom, 'position.y', data_info.sample)
1250	self._store_float('ns:SASsample/ns:position/ns:z',
1251	dom, 'position.z', data_info.sample)
1252
1253	# Orientation (as a vector)
1254	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1255	dom, 'orientation.x', data_info.sample)
1256	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1257	dom, 'orientation.y', data_info.sample)
1258	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1259	dom, 'orientation.z', data_info.sample)
1260
1261	# Source info ###################
1262	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1263	if entry is not None:
1264	data_info.source.name = entry.get('name')
1265
1266	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1267	dom, 'radiation', data_info.source)
1268	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1269	dom, 'beam_shape', data_info.source)
1270	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1271	dom, 'wavelength', data_info.source)
1272	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1273	dom, 'wavelength_min', data_info.source)
1274	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1275	dom, 'wavelength_max', data_info.source)
1276	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1277	dom, 'wavelength_spread', data_info.source)
1278
1279	# Beam size (as a vector)
1280	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1281	if entry is not None:
1282	data_info.source.beam_size_name = entry.get('name')
1283
1284	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1285	dom, 'beam_size.x', data_info.source)
1286	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1287	dom, 'beam_size.y', data_info.source)
1288	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1289	dom, 'beam_size.z', data_info.source)
1290
1291	# Collimation info ###################
1292	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
1293	for item in nodes:
1294	collim = Collimation()
1295	if item.get('name') is not None:
1296	collim.name = item.get('name')
1297	self._store_float('ns:length', item, 'length', collim)
1298
1299	# Look for apertures
1300	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
1301	for apert in apert_list:
1302	aperture = Aperture()
1303
1304	# Get the name and type of the aperture
1305	aperture.name = apert.get('name')
1306	aperture.type = apert.get('type')
1307
1308	self._store_float('ns:distance', apert, 'distance', aperture)
1309
1310	entry = get_content('ns:size', apert)
1311	if entry is not None:
1312	aperture.size_name = entry.get('name')
1313
1314	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1315	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1316	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1317
1318	collim.aperture.append(aperture)
1319
1320	data_info.collimation.append(collim)
1321
1322	# Detector info ######################
1323	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1324	for item in nodes:
1325
1326	detector = Detector()
1327
1328	self._store_content('ns:name', item, 'name', detector)
1329	self._store_float('ns:SDD', item, 'distance', detector)
1330
1331	# Detector offset (as a vector)
1332	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1333	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1334	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1335
1336	# Detector orientation (as a vector)
1337	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1338	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1339	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1340
1341	# Beam center (as a vector)
1342	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1343	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1344	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1345
1346	# Pixel size (as a vector)
1347	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1348	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1349	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1350
1351	self._store_float('ns:slit_length', item, 'slit_length', detector)
1352
1353	data_info.detector.append(detector)
1354
1355	# Processes info ######################
1356	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1357	for item in nodes:
1358	process = Process()
1359	self._store_content('ns:name', item, 'name', process)
1360	self._store_content('ns:date', item, 'date', process)
1361	self._store_content('ns:description', item, 'description', process)
1362
1363	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1364	for term in term_list:
1365	try:
1366	term_attr = {}
1367	for attr in term.keys():
1368	term_attr[attr] = term.get(attr).strip()
1369	if term.text is not None:
1370	term_attr['value'] = term.text.strip()
1371	process.term.append(term_attr)
1372	except:
1373	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1374	self.errors.append(err_mess)
1375	logging.error(err_mess)
1376
1377	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1378	for note in note_list:
1379	if note.text is not None:
1380	process.notes.append(note.text.strip())
1381
1382	data_info.process.append(process)
1383
1384
1385	# Data info ######################
1386	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1387	if len(nodes)>1:
1388	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1389
1390	for entry in nodes:
1391	for item in list_of_data_2d_attr:
1392	#get node
1393	node = get_content('ns:%s'%item[0], entry)
1394	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1395
1396	for item in list_of_data2d_values:
1397	field = get_content('ns:%s'%item[0], entry)
1398	list = []
1399	if field is not None:
1400	list = [parse_entry_helper(node, item) for node in field]
1401	exec "data_info.%s = numpy.array(list)"%item[0]
1402
1403	return data_info
1404
1405	def _read_cansas(self, path):
1406	"""
1407	Load data and P(r) information from a CanSAS XML file.
1408
1409	:param path: file path
1410
1411	:return: Data1D object if a single SASentry was found,
1412	or a list of Data1D objects if multiple entries were found,
1413	or None of nothing was found
1414
1415	:raise RuntimeError: when the file can't be opened
1416	:raise ValueError: when the length of the data vectors are inconsistent
1417
1418	"""
1419	output = []
1420	basename = os.path.basename(path)
1421	root, extension = os.path.splitext(basename)
1422	ext = extension.lower()
1423	try:
1424	if os.path.isfile(path):
1425
1426	#TODO: eventually remove the check for .xml once
1427	# the P(r) writer/reader is truly complete.
1428	if ext in self.ext or \
1429	ext == '.xml':
1430
1431	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1432	# Check the format version number
1433	# Specifying the namespace will take care of the file format version
1434	root = tree.getroot()
1435	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1436	for entry in entry_list:
1437	try:
1438	sas_entry = self._parse_entry(entry)
1439	except:
1440	raise
1441	fitstate = self._parse_state(entry)
1442
1443	#state could be None when .svs file is loaded
1444	#in this case, skip appending to output
1445	if fitstate != None:
1446	sas_entry.meta_data['fitstate'] = fitstate
1447	sas_entry.filename = fitstate.file
1448	output.append(sas_entry)
1449	else:
1450	self.call_back(format=ext)
1451	raise RuntimeError, "%s is not a file" % path
1452
1453	# Return output consistent with the loader's api
1454	if len(output)==0:
1455	self.call_back(state=None, datainfo=None,format=ext)
1456	return None
1457	else:
1458	for ind in range(len(output)):
1459	# Call back to post the new state
1460	state = output[ind].meta_data['fitstate']
1461	t = time.localtime(state.timestamp)
1462	time_str = time.strftime("%b %d %H:%M", t)
1463	# Check that no time stamp is already appended
1464	max_char = state.file.find("[")
1465	if max_char < 0:
1466	max_char = len(state.file)
1467	original_fname = state.file[0:max_char]
1468	state.file = original_fname +' [' + time_str + ']'
1469
1470
1471	if state is not None and state.is_data is not None:
1472	exec 'output[%d].is_data = state.is_data'% ind
1473
1474	output[ind].filename = state.file
1475	state.data = output[ind]
1476	state.data.name = output[ind].filename #state.data_name
1477	state.data.id = state.data_id
1478	if state.is_data is not None:
1479	state.data.is_data = state.is_data
1480	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1481	name = output[ind].run_name
1482	else:
1483	name=original_fname
1484	state.data.group_id = name
1485	#store state in fitting
1486	self.call_back(state=state, datainfo=output[ind],format=ext)
1487	self.state= state
1488	return output
1489
1490	except:
1491	self.call_back(format=ext)
1492	#self.state= state
1493	raise
1494
1495	def write(self, filename, datainfo=None, fitstate=None):
1496	"""
1497	Write the content of a Data1D as a CanSAS XML file only for standalone
1498
1499	:param filename: name of the file to write
1500	:param datainfo: Data1D object
1501	:param fitstate: PageState object
1502
1503	"""
1504	# Sanity check
1505	if self.cansas == True:
1506
1507	# Add fitting information to the XML document
1508	doc = self.write_toXML(datainfo, fitstate)
1509	# Write the XML document
1510	fd = open(filename, 'w')
1511	fd.write(doc.toprettyxml())
1512	fd.close()
1513	else:
1514	fitstate.toXML(file=filename)
1515
1516	def write_toXML(self, datainfo=None, state=None):
1517	"""
1518	Write toXML, a helper for write() , could be used by guimanager._on_save()
1519
1520	: return: xml doc
1521	"""
1522
1523	if state.data is None:
1524	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1525	else:
1526	#make sure title and data run is filled up.
1527	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1528	if state.data.run_name == None or state.data.run_name=={}:
1529	state.data.run = [str(state.data.name)]
1530	state.data.run_name[0] = state.data.name
1531
1532	if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D):
1533
1534	data = state.data
1535	doc, sasentry = self._to_xml_doc(data)
1536	else:
1537	data = state.data
1538	doc, sasentry = self._data2d_to_xml_doc(data)
1539
1540
1541	if state is not None:
1542	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1543
1544	return doc
1545
1546	# Simple html report templet
1547	HEADER = "<html>\n"
1548	HEADER += "<head>\n"
1549	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1550	HEADER += "charset=windows-1252'> \n"
1551	HEADER += "<meta name=Generator >\n"
1552	HEADER += "</head>\n"
1553	HEADER += "<body lang=EN-US>\n"
1554	HEADER += "<div class=WordSection1>\n"
1555	HEADER += "<p class=MsoNormal><b><span ><center>"
1556	HEADER += "%s</center></span></center></b></p>"
1557	HEADER += "<p class=MsoNormal> </p>"
1558	PARA = "<p class=MsoNormal> %s \n"
1559	PARA += "</p>"
1560	CENTRE = "<center> %s \n"
1561	CENTRE += "</center>"
1562	FEET_1 = \
1563	"""
1564	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
1565	<center>
1566	<br>Model Computation<br>
1567	<br>Data: "%s"<br>
1568	"""
1569	FEET_2 = \
1570	"""
1571	<img src="%s" >
1572	</img>
1573	"""
1574	FEET_3 = \
1575	"""
1576	</center>
1577	</div>
1578	</body>
1579	</html>
1580	"""
1581	ELINE = "<p class=MsoNormal> </p>"
1582
1583	if __name__ == "__main__":
1584	state = PageState(parent=None)
1585	#state.toXML()
1586	"""
1587
1588	file = open("test_state", "w")
1589	pickle.dump(state, file)
1590	print pickle.dumps(state)
1591	state.data_name = "hello---->"
1592	pickle.dump(state, file)
1593	file = open("test_state", "r")
1594	new_state= pickle.load(file)
1595	print "new state", new_state
1596	new_state= pickle.load(file)
1597	print "new state", new_state
1598	#print "state", state
1599	"""
1600	import bsddb
1601	import pickle
1602	db= bsddb.btopen('file_state.db', 'c')
1603	val = (pickle.dumps(state), "hello", "hi")
1604	db['state1']= pickle.dumps(val)
1605	print pickle.loads(db['state1'])
1606	state.data_name = "hello---->22"
1607	db['state2']= pickle.dumps(state)
1608	state.data_name = "hello---->2"
1609	db['state3']= pickle.dumps(state)
1610	del db['state3']
1611	state.data_name = "hello---->3"
1612	db['state4']= pickle.dumps(state)
1613	new_state = pickle.loads(db['state1'])
1614	#print db.last()
1615	db.set_location('state2')
1616	state.data_name = "hello---->5"
1617	db['aastate5']= pickle.dumps(state)
1618	db.keys().sort()
1619	print pickle.loads(db['state2'])
1620
1621	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ 22ce7e2

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