pagestate.py @ c7e12b6

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 c7e12b6 was 93f0a862, checked in by Jae Cho <jhjcho@…>, 13 years ago
fixed model_name on report for customized models
Property mode set to `100644`
File size: 68.3 KB

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1
2
3	################################################################################
4	#This software was developed by the University of Tennessee as part of the
5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
6	#project funded by the US National Science Foundation.
7	#
8	#See the license text in license.txt
9	#
10	#copyright 2009, University of Tennessee
11	################################################################################
12
13	import time
14	import os
15	import sys
16	import copy
17	import logging
18	import numpy
19
20	import xml.dom.minidom
21	from xml.dom.minidom import parse
22	from lxml import etree
23
24	import sans.dataloader
25	from sans.dataloader.readers.cansas_reader import Reader as CansasReader
26	from sans.dataloader.readers.cansas_reader import get_content, write_node
27	from sans.dataloader.data_info import Data2D, Detector
28
29	#Information to read/write state as xml
30	FITTING_NODE_NAME = 'fitting_plug_in'
31	CANSAS_NS = "cansas1d/1.0"
32
33	list_of_data_attributes = [["is_data", "is_data", "bool"],
34	["group_id", "data_group_id", "string"],
35	["data_name", "data_name", "string"],
36	["data_id", "data_id", "string"],
37	["name", "name", "string"],
38	["data_name", "data_name", "string"]]
39	list_of_state_attributes = [["engine_type", "engine_type", "string"],
40	["qmin", "qmin", "float"],
41	["qmax", "qmax", "float"],
42	["npts", "npts", "float"],
43	["shape_rbutton", "shape_rbutton", "bool"],
44	["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
45	["plugin_rbutton", "plugin_rbutton","bool"],
46	["struct_rbutton", "struct_rbutton", "bool"],
47	["formfactorcombobox", "formfactorcombobox", "string"],
48	["structurecombobox", "structurecombobox", "string"],
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	self.m_name = None
175	#list of process done to model
176	self.process = []
177	#fit page manager
178	self.manager = None
179	#Store the parent of this panel parent
180	# For this application fitpanel is the parent
181	self.parent = parent
182	# Event_owner is the owner of model event
183	self.event_owner = None
184	##page name
185	self.page_name = ""
186	# Contains link between model ,all its parameters, and panel organization
187	self.parameters = []
188	# String parameter list that can not be fitted
189	self.str_parameters = []
190	# Contains list of parameters that cannot be fitted and reference to
191	#panel objects
192	self.fixed_param = []
193	# Contains list of parameters with dispersity and reference to
194	#panel objects
195	self.fittable_param = []
196	## orientation parameters
197	self.orientation_params = []
198	## orientation parmaters for gaussian dispersity
199	self.orientation_params_disp = []
200	## smearer info
201	self.smearer = None
202	self.smear_type = None
203	self.dq_l = None
204	self.dq_r = None
205
206	#list of dispersion paramaters
207	self.disp_list =[]
208	if self.model is not None:
209	self.disp_list = self.model.getDispParamList()
210
211	self.disp_cb_dict = {}
212	self.values = {}
213	self.weights = {}
214
215	#contains link between a model and selected parameters to fit
216	self.param_toFit = []
217	##dictionary of model type and model class
218	self.model_list_box = None
219	## save the state of the context menu
220	self.saved_states = {}
221	## save selection of combobox
222	self.formfactorcombobox = None
223	self.structurecombobox = None
224
225	## radio box to select type of model
226	self.shape_rbutton = False
227	self.shape_indep_rbutton = False
228	self.struct_rbutton = False
229	self.plugin_rbutton = False
230	## the indice of the current selection
231	self.disp_box = 0
232	## Qrange
233	## Q range
234	self.qmin = 0.001
235	self.qmax = 0.1
236	#reset data range
237	self.qmax_x = None
238	self.qmin_x = None
239
240	self.npts = None
241	self.name = ""
242	self.multi_factor = None
243	## enable smearering state
244	self.enable_smearer = False
245	self.disable_smearer = True
246	self.pinhole_smearer = False
247	self.slit_smearer = False
248	# weighting options
249	self.dI_noweight = False
250	self.dI_didata = True
251	self.dI_sqrdata = False
252	self.dI_idata = False
253	## disperity selection
254	self.enable_disp = False
255	self.disable_disp = True
256
257	## state of selected all check button
258	self.cb1 = False
259	## store value of chisqr
260	self.tcChi = None
261
262	def clone(self):
263	"""
264	Create a new copy of the current object
265	"""
266	model = None
267	if self.model is not None:
268	model = self.model.clone()
269	model.name = self.model.name
270	obj = PageState(self.parent, model=model)
271	obj.file = copy.deepcopy(self.file)
272	obj.data = copy.deepcopy(self.data)
273	if self.data is not None:
274	self.data_name = self.data.name
275	obj.data_name = self.data_name
276	obj.is_data = self.is_data
277	obj.model_list_box = copy.deepcopy(self.model_list_box)
278	obj.engine_type = copy.deepcopy(self.engine_type)
279
280	obj.formfactorcombobox = self.formfactorcombobox
281	obj.structurecombobox = self.structurecombobox
282
283	obj.shape_rbutton = self.shape_rbutton
284	obj.shape_indep_rbutton = self.shape_indep_rbutton
285	obj.struct_rbutton = self.struct_rbutton
286	obj.plugin_rbutton = self.plugin_rbutton
287
288	obj.manager = self.manager
289	obj.event_owner = self.event_owner
290	obj.disp_list = copy.deepcopy(self.disp_list)
291
292	obj.enable2D = copy.deepcopy(self.enable2D)
293	obj.parameters = copy.deepcopy(self.parameters)
294	obj.str_parameters = copy.deepcopy(self.str_parameters)
295	obj.fixed_param = copy.deepcopy(self.fixed_param)
296	obj.fittable_param = copy.deepcopy(self.fittable_param)
297	obj.orientation_params = copy.deepcopy(self.orientation_params)
298	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
299	obj.enable_disp = copy.deepcopy(self.enable_disp)
300	obj.disable_disp = copy.deepcopy(self.disable_disp)
301	obj.tcChi = self.tcChi
302
303	if len(self._disp_obj_dict)>0:
304	for k , v in self._disp_obj_dict.iteritems():
305	obj._disp_obj_dict[k]= v
306	if len(self.disp_cb_dict)>0:
307	for k , v in self.disp_cb_dict.iteritems():
308	obj.disp_cb_dict[k]= v
309	if len(self.values)>0:
310	for k , v in self.values.iteritems():
311	obj.values[k] = v
312	if len(self.weights)>0:
313	for k , v in self.weights.iteritems():
314	obj.weights[k] = v
315	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
316	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
317	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
318	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
319	obj.smear_type = copy.deepcopy(self.smear_type)
320	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
321	obj.dI_didata = copy.deepcopy(self.dI_didata)
322	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
323	obj.dI_idata = copy.deepcopy(self.dI_idata)
324	obj.dq_l = copy.deepcopy(self.dq_l)
325	obj.dq_r = copy.deepcopy(self.dq_r)
326
327	obj.disp_box = copy.deepcopy(self.disp_box)
328	obj.qmin = copy.deepcopy(self.qmin)
329	obj.qmax = copy.deepcopy(self.qmax)
330	obj.multi_factor = self.multi_factor
331	obj.npts = copy.deepcopy(self.npts )
332	obj.cb1 = copy.deepcopy(self.cb1)
333	obj.smearer = copy.deepcopy(self.smearer)
334
335	for name, state in self.saved_states.iteritems():
336	copy_name = copy.deepcopy(name)
337	copy_state = state.clone()
338	obj.saved_states[copy_name]= copy_state
339	return obj
340
341	def _repr_helper(self, list, rep):
342	"""
343	Helper method to print a state
344	"""
345	for item in list:
346	rep += "parameter name: %s \n"%str(item[1])
347	rep += "value: %s\n"%str(item[2])
348	rep += "selected: %s\n"%str(item[0])
349	rep += "error displayed : %s \n"%str(item[4][0])
350	rep += "error value:%s \n"%str(item[4][1])
351	rep += "minimum displayed : %s \n"%str(item[5][0])
352	rep += "minimum value : %s \n"%str(item[5][1])
353	rep += "maximum displayed : %s \n"%str(item[6][0])
354	rep += "maximum value : %s \n"%str(item[6][1])
355	rep += "parameter unit: %s\n\n"%str(item[7])
356	return rep
357
358	def __repr__(self):
359	"""
360	output string for printing
361	"""
362	rep = "\nState name: %s\n"%self.file
363	t = time.localtime(self.timestamp)
364	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
365
366	rep += "State created: %s\n"%time_str
367	rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox
368	rep += "State structure factor combobox selection: %s\n"%self.structurecombobox
369	rep += "is data : %s\n"%self.is_data
370	rep += "data's name : %s\n"%self.data_name
371	rep += "data's id : %s\n"%self.data_id
372	if self.model != None:
373	m_name = self.model.__class__.__name__
374	if m_name == 'Model':
375	m_name = self.m_name
376	rep += "model name : %s\n"% m_name
377	else:
378	rep += "model name : None\n"
379	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
380	rep += "multi_factor : %s\n"% str(self.multi_factor)
381	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
382	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
383	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
384	rep += "data : %s\n"% str(self.data)
385	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
386	str(self.qmax),str(self.npts))
387	rep += "Dispersion selection : %s\n"%str(self.disp_box)
388	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
389	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
390	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
391	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
392	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
393	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
394	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
395
396	rep += "dI_noweight : %s\n"%str(self.dI_noweight)
397	rep += "dI_didata : %s\n"%str(self.dI_didata)
398	rep += "dI_sqrdata : %s\n"%str(self.dI_sqrdata)
399	rep += "dI_idata : %s\n"%str(self.dI_idata)
400
401
402	rep += "2D enable : %s\n"%str(self.enable2D)
403	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
404	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
405	rep += "Smear object : %s\n"%str(self.smearer)
406	rep += "Smear type : %s\n"%(self.smear_type)
407	rep += "dq_l : %s\n"%self.dq_l
408	rep += "dq_r : %s\n"%self.dq_r
409
410	rep += "model : %s\n\n"% str(self.model)
411	temp_parameters = []
412	temp_fittable_param = []
413	if self.data.__class__.__name__ == "Data2D":
414	self.is_2D = True
415	else:
416	self.is_2D = False
417	if self.data is not None:
418	if not self.is_2D:
419	for item in self.parameters:
420	if not item in self.orientation_params:
421	temp_parameters.append(item)
422	for item in self.fittable_param:
423	if not item in self.orientation_params_disp:
424	temp_fittable_param.append(item)
425	else:
426	temp_parameters = self.parameters
427	temp_fittable_param = self.fittable_param
428
429	rep += "number parameters(self.parameters): %s\n"%len(temp_parameters)
430	rep = self._repr_helper( list=temp_parameters, rep=rep)
431	rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters)
432	rep = self._repr_helper( list=self.str_parameters, rep=rep)
433	rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param)
434	rep = self._repr_helper( list=temp_fittable_param, rep=rep)
435	"""
436	if is_2D:
437	rep += "number orientation parameters"
438	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
439	rep = self._repr_helper( list=self.orientation_params, rep=rep)
440	rep += "number dispersity parameters"
441	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
442	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
443	"""
444	return rep
445
446	def set_report_string(self):
447	"""
448	Get the values (strings) from __str__ for report
449	"""
450	# Dictionary of teh report strings
451	repo_time = ""
452	model_name = ""
453	title = ""
454	title_name = ""
455	file_name = ""
456	param_string = ""
457	paramval_string = ""
458	chi2_string = ""
459	multi_factor_string = ""
460	q_range = ""
461	strings = self.__repr__()
462	lines = strings.split('\n')
463
464	# get all string values from __str__()
465	for line in lines:
466	value = ""
467	content = line.split(":")
468	name = content[0]
469	try:
470	value = content[1]
471	except:
472	pass
473	if name.count("State created"):
474	repo_time = "" + value
475	if name.count("parameter name"):
476	val_name = value.split(".")
477	if len(val_name) > 1:
478	if val_name[1].count("width"):
479	param_string += value + ','
480	else:
481	continue
482	else:
483	param_string += value + ','
484	if name == "value":
485	param_string += value + ','
486	if name == "error value":
487	param_string += value + ','
488	if name == "parameter unit":
489	param_string += value + ':'
490	if name == "Value of Chisqr ":
491	chi2 = ("Chi2/Npts = " + value)
492	chi2_string = CENTRE % chi2
493	if name == "multi_factor ":
494	muti_factor = ("muti_factor = " + value)
495	muti_factor_string = CENTRE % muti_factor
496	if name == "Title":
497	if len(value.strip()) == 0:
498	continue
499	title = value + " [" + repo_time + "]"
500	title_name = HEADER % title
501	if name == "data ":
502	try:
503	file = ("File name:" + content[2])
504	file_name = CENTRE % file
505	if len(title) == 0:
506	title = content[2] + " [" + repo_time + "]"
507	title_name = HEADER % title
508	except:
509	pass
510	if name == "model name ":
511	try:
512	modelname = "Model name:" + content[1]
513	except:
514	modelname = "Model name:" + " NAN"
515	model_name = CENTRE % modelname
516
517	if name == "Plotting Range":
518	try:
519	q_range = content[1] + " = " + content[2] \
520	+ " = " + content[3].split(",")[0]
521	q_name = ("Q Range: " + q_range)
522	q_range = CENTRE % q_name
523	except:
524	pass
525	paramval = ""
526	for lines in param_string.split(":"):
527	line = lines.split(",")
528	if len(lines) > 0:
529	param = line[0]
530	param += " = " + line[1]
531	if len(line[2].split()) > 0 and not line[2].count("None"):
532	param += " +- " + line[2]
533	if len(line[3].split()) > 0 and not line[3].count("None"):
534	param += " " + line[3]
535	if not paramval.count(param):
536	paramval += param + "\n"
537	paramval_string += CENTRE % param + "\n"
538
539	text_string = "\n\n\n" + title + "\n\n" + file + \
540	"\n" + q_name + \
541	"\n" + chi2 + \
542	"\n\n" + paramval
543
544	title_name = self._check_html_format(title_name)
545	file_name = self._check_html_format(file_name)
546	title = self._check_html_format(title)
547
548	html_string = title_name + "\n" + file_name + \
549	"\n" + model_name +\
550	"\n" + q_range + \
551	"\n" + chi2_string + \
552	"\n" + ELINE + \
553	"\n" + paramval_string + \
554	"\n" + ELINE + \
555	"\n" + FEET_1 % title + \
556	"\n" + FEET_2
557
558	return html_string, text_string, title
559
560	def _check_html_format(self, name):
561	"""
562	Check string '%' for html format
563	"""
564	if name.count('%'):
565	name = name.replace('%', '&#37')
566
567	return name
568
569
570	def report(self, figs=None, canvases=None):
571	"""
572	Invoke report dialog panel
573
574	: param figs: list of pylab figures [list]
575	"""
576	from report_dialog import ReportDialog
577	# get the strings for report
578	html_str, text_str, title = self.set_report_string()
579	# Allow 2 figures to append
580	if len(figs) == 1:
581	add_str = FEET_3
582	elif len(figs) == 2:
583	add_str = ELINE
584	add_str += FEET_2 % ("%s")
585	add_str += ELINE
586	add_str += FEET_3
587	elif len(figs) > 2:
588	add_str = ELINE
589	add_str += FEET_2 % ("%s")
590	add_str += ELINE
591	add_str += FEET_2 % ("%s")
592	add_str += ELINE
593	add_str += FEET_3
594	else:
595	add_str = ""
596
597	# final report html strings
598	report_str = html_str % ("%s") + add_str
599
600	# make plot image
601	images = self.set_plot_state(figs, canvases)
602	report_list = [report_str, text_str, images ]
603	dialog = ReportDialog(report_list, None, -1, "")
604	dialog.ShowModal()
605
606
607	def _toXML_helper(self, list, element, newdoc):
608	"""
609	Helper method to create xml file for saving state
610	"""
611	for item in list:
612	sub_element = newdoc.createElement('parameter')
613	sub_element.setAttribute('name', str(item[1]))
614	sub_element.setAttribute('value', str(item[2]))
615	sub_element.setAttribute('selected_to_fit', str(item[0]))
616	sub_element.setAttribute('error_displayed', str(item[4][0]))
617	sub_element.setAttribute('error_value', str(item[4][1]))
618	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
619	sub_element.setAttribute('minimum_value', str(item[5][1]))
620	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
621	sub_element.setAttribute('maximum_value', str(item[6][1]))
622	sub_element.setAttribute('unit', str(item[7]))
623	element.appendChild(sub_element)
624
625	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
626	"""
627	Writes the state of the InversionControl panel to file, as XML.
628
629	Compatible with standalone writing, or appending to an
630	already existing XML document. In that case, the XML document
631	is required. An optional entry node in the XML document may also be given.
632
633	:param file: file to write to
634	:param doc: XML document object [optional]
635	:param entry_node: XML node within the XML document at which we will append the data [optional]
636
637	"""
638	from xml.dom.minidom import getDOMImplementation
639
640	# Check whether we have to write a standalone XML file
641	if doc is None:
642	impl = getDOMImplementation()
643	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
644	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
645	top_element = newdoc.documentElement
646	else:
647	# We are appending to an existing document
648	newdoc = doc
649	top_element = newdoc.createElement(FITTING_NODE_NAME)
650	if entry_node is None:
651	newdoc.documentElement.appendChild(top_element)
652	else:
653	entry_node.appendChild(top_element)
654
655	attr = newdoc.createAttribute("version")
656	attr.nodeValue = '1.0'
657	top_element.setAttributeNode(attr)
658
659	# File name
660	element = newdoc.createElement("filename")
661	if self.file is not None:
662	element.appendChild(newdoc.createTextNode(str(self.file)))
663	else:
664	element.appendChild(newdoc.createTextNode(str(file)))
665	top_element.appendChild(element)
666
667	element = newdoc.createElement("timestamp")
668	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
669	attr = newdoc.createAttribute("epoch")
670	attr.nodeValue = str(self.timestamp)
671	element.setAttributeNode(attr)
672	top_element.appendChild(element)
673	# Inputs
674	inputs = newdoc.createElement("Attributes")
675	top_element.appendChild(inputs)
676
677
678	if self.data is not None and hasattr(self.data, "group_id"):
679	self.data_group_id = self.data.group_id
680	if self.data is not None and hasattr(self.data, "is_data"):
681	self.is_data = self.data.is_data
682	if self.data is not None:
683	self.data_name = self.data.name
684	if self.data is not None and hasattr(self.data, "id"):
685	self.data_id = self.data.id
686
687	for item in list_of_data_attributes:
688	element = newdoc.createElement(item[0])
689	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
690	inputs.appendChild(element)
691
692	for item in list_of_state_attributes:
693	element = newdoc.createElement(item[0])
694	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
695	inputs.appendChild(element)
696
697	# For self.values ={ disp_param_name: [vals,...],...}
698	# and for self.weights ={ disp_param_name: [weights,...],...}
699	for item in list_of_model_attributes:
700	element = newdoc.createElement(item[0])
701	exec "list = self.%s" % item[1]
702	for key, value in list.iteritems():
703	sub_element = newdoc.createElement(key)
704	sub_element.setAttribute('name', str(key))
705	for val in value:
706	com = "sub_element.appendChild"
707	com += "(newdoc.createTextNode(str(%s)))"
708	exec com % val
709
710	element.appendChild(sub_element)
711	inputs.appendChild(element)
712
713	# Create doc for the dictionary of self._disp_obj_dic
714	for item in list_of_obj_dic:
715	element = newdoc.createElement(item[0])
716	exec "list = self.%s" % item[1]
717	for key, val in list.iteritems():
718	value = repr(val)
719	sub_element = newdoc.createElement(key)
720	sub_element.setAttribute('name', str(key))
721	sub_element.setAttribute('value', str(value))
722	element.appendChild(sub_element)
723	inputs.appendChild(element)
724
725	for item in list_of_state_parameters:
726	element = newdoc.createElement(item[0])
727	com = "self._toXML_helper(list=self.%s,"
728	com += " element=element, newdoc=newdoc)"
729	exec com % item[1]
730	inputs.appendChild(element)
731
732	# Save the file
733	if doc is None:
734	fd = open(file, 'w')
735	fd.write(newdoc.toprettyxml())
736	fd.close()
737	return None
738	else:
739	return newdoc.toprettyxml()
740
741	def _fromXML_helper(self, node, list):
742	"""
743	Helper function to write state to xml
744	"""
745	for item in node:
746	try:
747	name = item.get('name')
748	except:
749	name = None
750	try:
751	value = item.get('value')
752	except:
753	value = None
754	try:
755	selected_to_fit = (item.get('selected_to_fit') == "True")
756	except:
757	selected_to_fit = None
758	try:
759	error_displayed = (item.get('error_displayed') == "True")
760	except:
761	error_displayed = None
762	try:
763	error_value = item.get('error_value')
764	except:
765	error_value = None
766	try:
767	minimum_displayed = (item.get('minimum_displayed')== "True")
768	except:
769	minimum_displayed = None
770	try:
771	minimum_value = item.get('minimum_value')
772	except:
773	minimum_value = None
774	try:
775	maximum_displayed = (item.get('maximum_displayed') == "True")
776	except:
777	maximum_displayed = None
778	try:
779	maximum_value = item.get('maximum_value')
780	except:
781	maximum_value = None
782	try:
783	unit = item.get('unit')
784	except:
785	unit = None
786	list.append([selected_to_fit, name, value, "+/-",
787	[error_displayed, error_value],
788	[minimum_displayed,minimum_value],
789	[maximum_displayed,maximum_value], unit])
790
791	def fromXML(self, file=None, node=None):
792	"""
793	Load fitting state from a file
794
795	:param file: .fitv file
796	:param node: node of a XML document to read from
797
798	"""
799	if file is not None:
800	msg = "PageState no longer supports non-CanSAS"
801	msg += " format for fitting files"
802	raise RuntimeError, msg
803
804	if node.get('version')and node.get('version') == '1.0':
805
806	# Get file name
807	entry = get_content('ns:filename', node)
808	if entry is not None:
809	self.file = entry.text.strip()
810
811	# Get time stamp
812	entry = get_content('ns:timestamp', node)
813	if entry is not None and entry.get('epoch'):
814	try:
815	self.timestamp = float(entry.get('epoch'))
816	except:
817	msg = "PageState.fromXML: Could not"
818	msg += " read timestamp\n %s" % sys.exc_value
819	logging.error(msg)
820
821	# Parse fitting attributes
822	entry = get_content('ns:Attributes', node)
823	for item in list_of_data_attributes:
824	node = get_content('ns:%s'%item[0], entry)
825	try:
826	exec "self.%s = parse_entry_helper(node, item)" % item[0]
827
828	except:
829	raise
830
831	if entry is not None:
832
833	for item in list_of_state_attributes:
834	node = get_content('ns:%s' % item[0], entry)
835	try:
836	exec "self.%s = parse_entry_helper(node, item)" % \
837	str(item[0])
838	except:
839	raise
840
841	for item in list_of_state_parameters:
842	node = get_content("ns:%s" % item[0], entry)
843	exec "self._fromXML_helper(node=node, list=self.%s)" % \
844	item[1]
845
846	# Recover _disp_obj_dict from xml file
847	self._disp_obj_dict = {}
848	for item in list_of_obj_dic:
849	# Get node
850	node = get_content("ns:%s" % item[0], entry)
851	for attr in node:
852	name = attr.get('name')
853	val = attr.get('value')
854	value = val.split(" instance")[0]
855	disp_name = value.split("<")[1]
856	try:
857	# Try to recover disp_model object from strings
858	com = "from sans.models.dispersion_models "
859	com += "import %s as disp"
860	com_name = disp_name.split(".")[3]
861	exec com % com_name
862	disp_model = disp()
863	exec "self.%s['%s'] = com_name" % (item[1], name)
864	except:
865	pass
866
867	# get self.values and self.weights dic. if exists
868	for item in list_of_model_attributes:
869	node = get_content("ns:%s" % item[0], entry)
870	dic = {}
871	list = []
872	for par in node:
873	name = par.get('name')
874	values = par.text.split('\n')
875	# Get lines only with numbers
876	for line in values:
877	try:
878	val= float(line)
879	list.append(val)
880	except:
881	# pass if line is empty (it happens)
882	pass
883	dic[name] = numpy.array(list)
884	exec "self.%s = dic" % item[1]
885
886	def set_plot_state(self, figs, canvases):
887	"""
888	Build image state that wx.html understand
889	by plotting, putting it into wx.FileSystem image object
890
891	"""
892	images = []
893	# some imports
894	import wx
895
896	# Reset memory
897	self.imgRAM = None
898	wx.MemoryFSHandler()
899
900	# For no figures in the list, prepare empty plot
901	if figs == None or len(figs) == 0:
902	figs = [None]
903
904	# Loop over the list of figures
905	# use wx.MemoryFSHandler
906	self.imgRAM = wx.MemoryFSHandler()
907	for fig in figs:
908	if figs != None:
909	#fig.set_facecolor('w')
910	ind = figs.index(fig)
911	canvas = canvases[ind]
912
913	#bmp = wx.BitmapDataObject()
914	#bmp.SetBitmap(canvas.bitmap)
915	#store the image in wx.FileSystem Object
916	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
917
918	# index of the fig
919	ind = figs.index(fig)
920
921	#AddFile, image can be retrieved with 'memory:filename'
922	self.imgRAM.AddFile('img_fit%s.png' % ind ,
923	canvas.bitmap, wx.BITMAP_TYPE_PNG)
924
925	#append figs
926	images.append(fig)
927
928	return images
929
930	class Reader(CansasReader):
931	"""
932	Class to load a .fitv fitting file
933	"""
934	## File type
935	type_name = "Fitting"
936
937	## Wildcards
938	type = ["Fitting files (.fitv)\|.fitv"
939	"SANSView file (.svs)\|.svs"]
940	## List of allowed extensions
941	ext=['.fitv', '.FITV', '.svs', 'SVS']
942
943	def __init__(self, call_back=None, cansas=True):
944	CansasReader.__init__(self)
945	"""
946	Initialize the call-back method to be called
947	after we load a file
948
949	:param call_back: call-back method
950	:param cansas: True = files will be written/read in CanSAS format
951	False = write CanSAS format
952
953	"""
954	## Call back method to be executed after a file is read
955	self.call_back = call_back
956	## CanSAS format flag
957	self.cansas = cansas
958	self.state = None
959	def get_state(self):
960	return self.state
961
962	def read(self, path):
963	"""
964	Load a new P(r) inversion state from file
965
966	:param path: file path
967
968	"""
969	if self.cansas == True:
970	return self._read_cansas(path)
971
972	def _data2d_to_xml_doc(self, datainfo):
973	"""
974	Create an XML document to contain the content of a Data2D
975
976	:param datainfo: Data2D object
977
978	"""
979	if not issubclass(datainfo.__class__, Data2D):
980	raise RuntimeError, "The cansas writer expects a Data2D instance"
981
982	doc = xml.dom.minidom.Document()
983	main_node = doc.createElement("SASroot")
984	main_node.setAttribute("version", self.version)
985	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
986	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
987	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
988
989	doc.appendChild(main_node)
990
991	entry_node = doc.createElement("SASentry")
992	main_node.appendChild(entry_node)
993
994	write_node(doc, entry_node, "Title", datainfo.title)
995	if datainfo is not None:
996	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
997	for item in datainfo.run:
998	runname = {}
999	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
1000	runname = {'name': datainfo.run_name[item] }
1001	write_node(doc, entry_node, "Run", item, runname)
1002	# Data info
1003	new_node = doc.createElement("SASdata")
1004	entry_node.appendChild(new_node)
1005	for item in list_of_data_2d_attr:
1006	element = doc.createElement(item[0])
1007	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
1008	new_node.appendChild(element)
1009
1010	for item in list_of_data2d_values:
1011	root_node = doc.createElement(item[0])
1012	new_node.appendChild(root_node)
1013
1014	exec "temp_list = datainfo.%s"%item[1]
1015
1016	if temp_list is None or len(temp_list)== 0:
1017	element = doc.createElement(item[0])
1018	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
1019	root_node.appendChild(element)
1020	else:
1021	for value in temp_list:
1022	element = doc.createElement(item[0])
1023	exec "element.setAttribute(item[0], str(%s))"%value
1024	root_node.appendChild(element)
1025
1026	# Sample info
1027	sample = doc.createElement("SASsample")
1028	if datainfo.sample.name is not None:
1029	sample.setAttribute("name", str(datainfo.sample.name))
1030	entry_node.appendChild(sample)
1031	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1032	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
1033	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1034	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
1035
1036	for item in datainfo.sample.details:
1037	write_node(doc, sample, "details", item)
1038
1039	pos = doc.createElement("position")
1040	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
1041	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
1042	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
1043	if written == True:
1044	sample.appendChild(pos)
1045
1046	ori = doc.createElement("orientation")
1047	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
1048	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
1049	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
1050	if written == True:
1051	sample.appendChild(ori)
1052
1053	# Instrument info
1054	instr = doc.createElement("SASinstrument")
1055	entry_node.appendChild(instr)
1056
1057	write_node(doc, instr, "name", datainfo.instrument)
1058
1059	# Source
1060	source = doc.createElement("SASsource")
1061	if datainfo.source.name is not None:
1062	source.setAttribute("name", str(datainfo.source.name))
1063	instr.appendChild(source)
1064
1065	write_node(doc, source, "radiation", datainfo.source.radiation)
1066	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1067	size = doc.createElement("beam_size")
1068	if datainfo.source.beam_size_name is not None:
1069	size.setAttribute("name", str(datainfo.source.beam_size_name))
1070	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
1071	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
1072	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
1073	if written == True:
1074	source.appendChild(size)
1075
1076	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
1077	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
1078	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
1079	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
1080
1081	# Collimation
1082	for item in datainfo.collimation:
1083	coll = doc.createElement("SAScollimation")
1084	if item.name is not None:
1085	coll.setAttribute("name", str(item.name))
1086	instr.appendChild(coll)
1087
1088	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
1089
1090	for apert in item.aperture:
1091	ap = doc.createElement("aperture")
1092	if apert.name is not None:
1093	ap.setAttribute("name", str(apert.name))
1094	if apert.type is not None:
1095	ap.setAttribute("type", str(apert.type))
1096	coll.appendChild(ap)
1097
1098	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
1099
1100	size = doc.createElement("size")
1101	if apert.size_name is not None:
1102	size.setAttribute("name", str(apert.size_name))
1103	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
1104	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
1105	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
1106	if written == True:
1107	ap.appendChild(size)
1108
1109	# Detectors
1110	for item in datainfo.detector:
1111	det = doc.createElement("SASdetector")
1112	written = write_node(doc, det, "name", item.name)
1113	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
1114	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
1115	if written == True:
1116	instr.appendChild(det)
1117
1118	off = doc.createElement("offset")
1119	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
1120	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
1121	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
1122	if written == True:
1123	det.appendChild(off)
1124
1125	center = doc.createElement("beam_center")
1126	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
1127	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
1128	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
1129	if written == True:
1130	det.appendChild(center)
1131
1132	pix = doc.createElement("pixel_size")
1133	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
1134	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
1135	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
1136	if written == True:
1137	det.appendChild(pix)
1138
1139	ori = doc.createElement("orientation")
1140	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
1141	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
1142	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
1143	if written == True:
1144	det.appendChild(ori)
1145
1146	# Processes info
1147	for item in datainfo.process:
1148	node = doc.createElement("SASprocess")
1149	entry_node.appendChild(node)
1150
1151	write_node(doc, node, "name", item.name)
1152	write_node(doc, node, "date", item.date)
1153	write_node(doc, node, "description", item.description)
1154	for term in item.term:
1155	value = term['value']
1156	del term['value']
1157	write_node(doc, node, "term", value, term)
1158	for note in item.notes:
1159	write_node(doc, node, "SASprocessnote", note)
1160	# Return the document, and the SASentry node associated with
1161	# the data we just wrote
1162	return doc, entry_node
1163
1164	def _parse_state(self, entry):
1165	"""
1166	Read a fit result from an XML node
1167
1168	:param entry: XML node to read from
1169
1170	:return: PageState object
1171	"""
1172	# Create an empty state
1173	state = None
1174	# Locate the P(r) node
1175	try:
1176	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
1177	if nodes !=[]:
1178	# Create an empty state
1179	state = PageState()
1180	state.fromXML(node=nodes[0])
1181	except:
1182	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1183
1184	return state
1185
1186
1187
1188	def _parse_entry(self, dom):
1189	"""
1190	Parse a SASentry
1191
1192	:param node: SASentry node
1193
1194	:return: Data1D/Data2D object
1195
1196	"""
1197	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1198	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1199	return CansasReader._parse_entry(self, dom)
1200
1201	#Parse 2D
1202	data_info = Data2D()
1203
1204	# Look up title
1205	self._store_content('ns:Title', dom, 'title', data_info)
1206
1207	# Look up run number
1208	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1209	for item in nodes:
1210	if item.text is not None:
1211	value = item.text.strip()
1212	if len(value) > 0:
1213	data_info.run.append(value)
1214	if item.get('name') is not None:
1215	data_info.run_name[value] = item.get('name')
1216
1217	# Look up instrument name
1218	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
1219
1220	# Notes
1221	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1222	for note in note_list:
1223	try:
1224	if note.text is not None:
1225	note_value = note.text.strip()
1226	if len(note_value) > 0:
1227	data_info.notes.append(note_value)
1228	except:
1229	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1230	self.errors.append(err_mess)
1231	logging.error(err_mess)
1232
1233	# Sample info ###################
1234	entry = get_content('ns:SASsample', dom)
1235	if entry is not None:
1236	data_info.sample.name = entry.get('name')
1237
1238	self._store_content('ns:SASsample/ns:ID',
1239	dom, 'ID', data_info.sample)
1240	self._store_float('ns:SASsample/ns:thickness',
1241	dom, 'thickness', data_info.sample)
1242	self._store_float('ns:SASsample/ns:transmission',
1243	dom, 'transmission', data_info.sample)
1244	self._store_float('ns:SASsample/ns:temperature',
1245	dom, 'temperature', data_info.sample)
1246
1247	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1248	for item in nodes:
1249	try:
1250	if item.text is not None:
1251	detail_value = item.text.strip()
1252	if len(detail_value) > 0:
1253	data_info.sample.details.append(detail_value)
1254	except:
1255	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1256	self.errors.append(err_mess)
1257	logging.error(err_mess)
1258
1259	# Position (as a vector)
1260	self._store_float('ns:SASsample/ns:position/ns:x',
1261	dom, 'position.x', data_info.sample)
1262	self._store_float('ns:SASsample/ns:position/ns:y',
1263	dom, 'position.y', data_info.sample)
1264	self._store_float('ns:SASsample/ns:position/ns:z',
1265	dom, 'position.z', data_info.sample)
1266
1267	# Orientation (as a vector)
1268	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1269	dom, 'orientation.x', data_info.sample)
1270	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1271	dom, 'orientation.y', data_info.sample)
1272	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1273	dom, 'orientation.z', data_info.sample)
1274
1275	# Source info ###################
1276	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1277	if entry is not None:
1278	data_info.source.name = entry.get('name')
1279
1280	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1281	dom, 'radiation', data_info.source)
1282	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1283	dom, 'beam_shape', data_info.source)
1284	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1285	dom, 'wavelength', data_info.source)
1286	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1287	dom, 'wavelength_min', data_info.source)
1288	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1289	dom, 'wavelength_max', data_info.source)
1290	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1291	dom, 'wavelength_spread', data_info.source)
1292
1293	# Beam size (as a vector)
1294	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1295	if entry is not None:
1296	data_info.source.beam_size_name = entry.get('name')
1297
1298	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1299	dom, 'beam_size.x', data_info.source)
1300	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1301	dom, 'beam_size.y', data_info.source)
1302	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1303	dom, 'beam_size.z', data_info.source)
1304
1305	# Collimation info ###################
1306	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
1307	for item in nodes:
1308	collim = Collimation()
1309	if item.get('name') is not None:
1310	collim.name = item.get('name')
1311	self._store_float('ns:length', item, 'length', collim)
1312
1313	# Look for apertures
1314	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
1315	for apert in apert_list:
1316	aperture = Aperture()
1317
1318	# Get the name and type of the aperture
1319	aperture.name = apert.get('name')
1320	aperture.type = apert.get('type')
1321
1322	self._store_float('ns:distance', apert, 'distance', aperture)
1323
1324	entry = get_content('ns:size', apert)
1325	if entry is not None:
1326	aperture.size_name = entry.get('name')
1327
1328	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1329	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1330	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1331
1332	collim.aperture.append(aperture)
1333
1334	data_info.collimation.append(collim)
1335
1336	# Detector info ######################
1337	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1338	for item in nodes:
1339
1340	detector = Detector()
1341
1342	self._store_content('ns:name', item, 'name', detector)
1343	self._store_float('ns:SDD', item, 'distance', detector)
1344
1345	# Detector offset (as a vector)
1346	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1347	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1348	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1349
1350	# Detector orientation (as a vector)
1351	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1352	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1353	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1354
1355	# Beam center (as a vector)
1356	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1357	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1358	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1359
1360	# Pixel size (as a vector)
1361	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1362	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1363	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1364
1365	self._store_float('ns:slit_length', item, 'slit_length', detector)
1366
1367	data_info.detector.append(detector)
1368
1369	# Processes info ######################
1370	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1371	for item in nodes:
1372	process = Process()
1373	self._store_content('ns:name', item, 'name', process)
1374	self._store_content('ns:date', item, 'date', process)
1375	self._store_content('ns:description', item, 'description', process)
1376
1377	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1378	for term in term_list:
1379	try:
1380	term_attr = {}
1381	for attr in term.keys():
1382	term_attr[attr] = term.get(attr).strip()
1383	if term.text is not None:
1384	term_attr['value'] = term.text.strip()
1385	process.term.append(term_attr)
1386	except:
1387	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1388	self.errors.append(err_mess)
1389	logging.error(err_mess)
1390
1391	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1392	for note in note_list:
1393	if note.text is not None:
1394	process.notes.append(note.text.strip())
1395
1396	data_info.process.append(process)
1397
1398
1399	# Data info ######################
1400	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1401	if len(nodes)>1:
1402	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1403
1404	for entry in nodes:
1405	for item in list_of_data_2d_attr:
1406	#get node
1407	node = get_content('ns:%s'%item[0], entry)
1408	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1409
1410	for item in list_of_data2d_values:
1411	field = get_content('ns:%s'%item[0], entry)
1412	list = []
1413	if field is not None:
1414	list = [parse_entry_helper(node, item) for node in field]
1415	exec "data_info.%s = numpy.array(list)"%item[0]
1416
1417	return data_info
1418
1419	def _read_cansas(self, path):
1420	"""
1421	Load data and P(r) information from a CanSAS XML file.
1422
1423	:param path: file path
1424
1425	:return: Data1D object if a single SASentry was found,
1426	or a list of Data1D objects if multiple entries were found,
1427	or None of nothing was found
1428
1429	:raise RuntimeError: when the file can't be opened
1430	:raise ValueError: when the length of the data vectors are inconsistent
1431
1432	"""
1433	output = []
1434	basename = os.path.basename(path)
1435	root, extension = os.path.splitext(basename)
1436	ext = extension.lower()
1437	try:
1438	if os.path.isfile(path):
1439
1440	#TODO: eventually remove the check for .xml once
1441	# the P(r) writer/reader is truly complete.
1442	if ext in self.ext or \
1443	ext == '.xml':
1444
1445	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1446	# Check the format version number
1447	# Specifying the namespace will take care of the file format version
1448	root = tree.getroot()
1449	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1450	for entry in entry_list:
1451	try:
1452	sas_entry = self._parse_entry(entry)
1453	except:
1454	raise
1455	fitstate = self._parse_state(entry)
1456
1457	#state could be None when .svs file is loaded
1458	#in this case, skip appending to output
1459	if fitstate != None:
1460	sas_entry.meta_data['fitstate'] = fitstate
1461	sas_entry.filename = fitstate.file
1462	output.append(sas_entry)
1463	else:
1464	self.call_back(format=ext)
1465	raise RuntimeError, "%s is not a file" % path
1466
1467	# Return output consistent with the loader's api
1468	if len(output)==0:
1469	self.call_back(state=None, datainfo=None,format=ext)
1470	return None
1471	else:
1472	for ind in range(len(output)):
1473	# Call back to post the new state
1474	state = output[ind].meta_data['fitstate']
1475	t = time.localtime(state.timestamp)
1476	time_str = time.strftime("%b %d %H:%M", t)
1477	# Check that no time stamp is already appended
1478	max_char = state.file.find("[")
1479	if max_char < 0:
1480	max_char = len(state.file)
1481	original_fname = state.file[0:max_char]
1482	state.file = original_fname +' [' + time_str + ']'
1483
1484
1485	if state is not None and state.is_data is not None:
1486	exec 'output[%d].is_data = state.is_data'% ind
1487
1488	output[ind].filename = state.file
1489	state.data = output[ind]
1490	state.data.name = output[ind].filename #state.data_name
1491	state.data.id = state.data_id
1492	if state.is_data is not None:
1493	state.data.is_data = state.is_data
1494	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1495	name = output[ind].run_name
1496	else:
1497	name=original_fname
1498	state.data.group_id = name
1499	#store state in fitting
1500	self.call_back(state=state, datainfo=output[ind],format=ext)
1501	self.state= state
1502	return output
1503
1504	except:
1505	self.call_back(format=ext)
1506	#self.state= state
1507	raise
1508
1509	def write(self, filename, datainfo=None, fitstate=None):
1510	"""
1511	Write the content of a Data1D as a CanSAS XML file only for standalone
1512
1513	:param filename: name of the file to write
1514	:param datainfo: Data1D object
1515	:param fitstate: PageState object
1516
1517	"""
1518	# Sanity check
1519	if self.cansas == True:
1520
1521	# Add fitting information to the XML document
1522	doc = self.write_toXML(datainfo, fitstate)
1523	# Write the XML document
1524	fd = open(filename, 'w')
1525	fd.write(doc.toprettyxml())
1526	fd.close()
1527	else:
1528	fitstate.toXML(file=filename)
1529
1530	def write_toXML(self, datainfo=None, state=None):
1531	"""
1532	Write toXML, a helper for write() , could be used by guimanager._on_save()
1533
1534	: return: xml doc
1535	"""
1536
1537	if state.data is None:
1538	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1539	else:
1540	#make sure title and data run is filled up.
1541	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1542	if state.data.run_name == None or state.data.run_name=={}:
1543	state.data.run = [str(state.data.name)]
1544	state.data.run_name[0] = state.data.name
1545
1546	if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D):
1547
1548	data = state.data
1549	doc, sasentry = self._to_xml_doc(data)
1550	else:
1551	data = state.data
1552	doc, sasentry = self._data2d_to_xml_doc(data)
1553
1554
1555	if state is not None:
1556	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1557
1558	return doc
1559
1560	# Simple html report templet
1561	HEADER = "<html>\n"
1562	HEADER += "<head>\n"
1563	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1564	HEADER += "charset=windows-1252'> \n"
1565	HEADER += "<meta name=Generator >\n"
1566	HEADER += "</head>\n"
1567	HEADER += "<body lang=EN-US>\n"
1568	HEADER += "<div class=WordSection1>\n"
1569	HEADER += "<p class=MsoNormal><b><span ><center>"
1570	HEADER += "%s</center></span></center></b></p>"
1571	HEADER += "<p class=MsoNormal> </p>"
1572	PARA = "<p class=MsoNormal> %s \n"
1573	PARA += "</p>"
1574	CENTRE = "<p class=MsoNormal><center> %s \n"
1575	CENTRE += "</center></p>"
1576	FEET_1 = \
1577	"""
1578	<p class=MsoNormal> </p>
1579	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
1580	<p class=MsoNormal> </p>
1581	<center>
1582	<br>Model Computation<br>
1583	<br>Data: "%s"<br>
1584	"""
1585	FEET_2 = \
1586	"""
1587	<img src="%s" >
1588	</img>
1589	"""
1590	FEET_3 = \
1591	"""
1592	</center>
1593	</div>
1594	</body>
1595	</html>
1596	"""
1597	ELINE = "<p class=MsoNormal> </p>"
1598
1599	if __name__ == "__main__":
1600	state = PageState(parent=None)
1601	#state.toXML()
1602	"""
1603
1604	file = open("test_state", "w")
1605	pickle.dump(state, file)
1606	print pickle.dumps(state)
1607	state.data_name = "hello---->"
1608	pickle.dump(state, file)
1609	file = open("test_state", "r")
1610	new_state= pickle.load(file)
1611	print "new state", new_state
1612	new_state= pickle.load(file)
1613	print "new state", new_state
1614	#print "state", state
1615	"""
1616	import bsddb
1617	import pickle
1618	db= bsddb.btopen('file_state.db', 'c')
1619	val = (pickle.dumps(state), "hello", "hi")
1620	db['state1']= pickle.dumps(val)
1621	print pickle.loads(db['state1'])
1622	state.data_name = "hello---->22"
1623	db['state2']= pickle.dumps(state)
1624	state.data_name = "hello---->2"
1625	db['state3']= pickle.dumps(state)
1626	del db['state3']
1627	state.data_name = "hello---->3"
1628	db['state4']= pickle.dumps(state)
1629	new_state = pickle.loads(db['state1'])
1630	#print db.last()
1631	db.set_location('state2')
1632	state.data_name = "hello---->5"
1633	db['aastate5']= pickle.dumps(state)
1634	db.keys().sort()
1635	print pickle.loads(db['state2'])
1636
1637	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ c7e12b6

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