pagestate.py @ a805118

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 a805118 was a805118, checked in by Jae Cho <jhjcho@…>, 11 years ago
bug fix for saveproject
Property mode set to `100644`
File size: 71.2 KB

Line
1	"""
2	Class that holds a fit page state
3	"""
4	################################################################################
5	#This software was developed by the University of Tennessee as part of the
6	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
7	#project funded by the US National Science Foundation.
8	#
9	#See the license text in license.txt
10	#
11	#copyright 2009, University of Tennessee
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
28	from sans.dataloader.data_info import Collimation
29	from sans.dataloader.data_info import Detector
30	from sans.dataloader.data_info import Process
31	from sans.dataloader.data_info import Aperture
32	#Information to read/write state as xml
33	FITTING_NODE_NAME = 'fitting_plug_in'
34	CANSAS_NS = "cansas1d/1.0"
35
36	list_of_data_attributes = [["is_data", "is_data", "bool"],
37	["group_id", "data_group_id", "string"],
38	["data_name", "data_name", "string"],
39	["data_id", "data_id", "string"],
40	["name", "name", "string"],
41	["data_name", "data_name", "string"]]
42	list_of_state_attributes = [["engine_type", "engine_type", "string"],
43	["qmin", "qmin", "float"],
44	["qmax", "qmax", "float"],
45	["npts", "npts", "float"],
46	#["shape_rbutton", "shape_rbutton", "bool"],
47	#["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
48	#["plugin_rbutton", "plugin_rbutton", "bool"],
49	#["struct_rbutton", "struct_rbutton", "bool"],
50	["categorycombobox", "categorycombobox", "string"],
51	["formfactorcombobox", "formfactorcombobox", "string"],
52	["structurecombobox", "structurecombobox", "string"],
53	["multi_factor","multi_factor","float"],
54	["magnetic_on","magnetic_on", "bool"],
55	["enable_smearer","enable_smearer","bool"],
56	["disable_smearer","disable_smearer","bool"],
57	["pinhole_smearer","pinhole_smearer","bool"],
58	["slit_smearer","slit_smearer","bool"],
59	["enable_disp","enable_disp","bool"],
60	["disable_disp","disable_disp","bool"],
61	["dI_noweight","dI_noweight","bool"],
62	["dI_didata","dI_didata","bool"],
63	["dI_sqrdata","dI_sqrdata","bool"],
64	["dI_idata","dI_idata","bool"],
65	["enable2D","enable2D","bool"],
66	["cb1","cb1","bool"],
67	["tcChi","tcChi","float"],
68	["smearer", "smearer", "float"],
69	["smear_type","smear_type", "string"],
70	["dq_l", "dq_l", "string"],
71	["dq_r","dq_r", "string"]]
72
73	list_of_model_attributes = [["values", "values"],
74	["weights", "weights"]]
75
76	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
77
78	list_of_state_parameters = [["parameters", "parameters"],
79	["str_parameters", "str_parameters"],
80	["orientation_parameters", "orientation_params"],
81	["dispersity_parameters", "orientation_params_disp"],
82	["fixed_param", "fixed_param"],
83	["fittable_param", "fittable_param"]]
84	list_of_data_2d_attr = [["xmin", "xmin", "float"],
85	["xmax", "xmax", "float"],
86	["ymin", "ymin", "float"],
87	["ymax", "ymax", "float"],
88	["_xaxis", "_xaxis", "string"],
89	["_xunit", "_xunit", "string"],
90	["_yaxis", "_yaxis", "string"],
91	["_yunit", "_yunit", "string"],
92	["_zaxis", "_zaxis", "string"],
93	["_zunit", "_zunit", "string"]]
94	list_of_data2d_values = [["qx_data", "qx_data", "float"],
95	["qy_data", "qy_data", "float"],
96	["dqx_data", "dqx_data", "float"],
97	["dqy_data", "dqy_data", "float"],
98	["data", "data", "float"],
99	["q_data", "q_data", "float"],
100	["err_data", "err_data", "float"],
101	["mask", "mask", "bool"]]
102
103
104	def parse_entry_helper(node, item):
105	"""
106	Create a numpy list from value extrated from the node
107
108	:param node: node from each the value is stored
109	:param item: list name of three strings.the two first are name of data
110	attribute and the third one is the type of the value of that
111	attribute. type can be string, float, bool, etc.
112
113	: return: numpy array
114	"""
115	if node is not None:
116	if item[2] == "string":
117	return str(node.get(item[0]).strip())
118	elif item[2] == "bool":
119	try:
120	return node.get(item[0]).strip() == "True"
121
122	except:
123	return None
124	else:
125	try:
126	return float(node.get(item[0]))
127	except:
128	return None
129
130
131	class PageState(object):
132	"""
133	Contains information to reconstruct a page of the fitpanel.
134	"""
135	def __init__(self, parent=None, model=None, data=None):
136	"""
137	Initialize the current state
138
139	:param model: a selected model within a page
140	:param data:
141
142	"""
143	self.file = None
144	#Time of state creation
145	self.timestamp = time.time()
146	## Data member to store the dispersion object created
147	self._disp_obj_dict = {}
148	#------------------------
149	#Data used for fitting
150	self.data = data
151	# model data
152	self.theory_data = None
153	#Is 2D
154	self.is_2D = False
155	self.images = None
156
157	#save additional information on data that dataloader.reader does not read
158	self.is_data = None
159	self.data_name = ""
160
161	if self.data is not None:
162	self.data_name = self.data.name
163	self.data_id = None
164	if self.data is not None and hasattr(self.data, "id"):
165	self.data_id = self.data.id
166	self.data_group_id = None
167	if self.data is not None and hasattr(self.data, "group_id"):
168	self.data_group_id = self.data.group_id
169
170	## reset True change the state of exsiting button
171	self.reset = False
172
173	#engine type
174	self.engine_type = None
175	# flag to allow data2D plot
176	self.enable2D = False
177	# model on which the fit would be performed
178	self.model = model
179	self.m_name = None
180	#list of process done to model
181	self.process = []
182	#fit page manager
183	self.manager = None
184	#Store the parent of this panel parent
185	# For this application fitpanel is the parent
186	self.parent = parent
187	# Event_owner is the owner of model event
188	self.event_owner = None
189	##page name
190	self.page_name = ""
191	# Contains link between model ,all its parameters, and panel organization
192	self.parameters = []
193	# String parameter list that can not be fitted
194	self.str_parameters = []
195	# Contains list of parameters that cannot be fitted and reference to
196	#panel objects
197	self.fixed_param = []
198	# Contains list of parameters with dispersity and reference to
199	#panel objects
200	self.fittable_param = []
201	## orientation parameters
202	self.orientation_params = []
203	## orientation parmaters for gaussian dispersity
204	self.orientation_params_disp = []
205	## smearer info
206	self.smearer = None
207	self.smear_type = None
208	self.dq_l = None
209	self.dq_r = None
210
211	#list of dispersion paramaters
212	self.disp_list = []
213	if self.model is not None:
214	self.disp_list = self.model.getDispParamList()
215
216	self.disp_cb_dict = {}
217	self.values = {}
218	self.weights = {}
219
220	#contains link between a model and selected parameters to fit
221	self.param_toFit = []
222	##dictionary of model type and model class
223	self.model_list_box = None
224	## save the state of the context menu
225	self.saved_states = {}
226	## save selection of combobox
227	self.formfactorcombobox = None
228	self.categorycombobox = None
229	self.structurecombobox = None
230
231	## radio box to select type of model
232	#self.shape_rbutton = False
233	#self.shape_indep_rbutton = False
234	#self.struct_rbutton = False
235	#self.plugin_rbutton = False
236	## the indice of the current selection
237	self.disp_box = 0
238	## Qrange
239	## Q range
240	self.qmin = 0.001
241	self.qmax = 0.1
242	#reset data range
243	self.qmax_x = None
244	self.qmin_x = None
245
246	self.npts = None
247	self.name = ""
248	self.multi_factor = None
249	self.magnetic_on = False
250	## enable smearering state
251	self.enable_smearer = False
252	self.disable_smearer = True
253	self.pinhole_smearer = False
254	self.slit_smearer = False
255	# weighting options
256	self.dI_noweight = False
257	self.dI_didata = True
258	self.dI_sqrdata = False
259	self.dI_idata = False
260	## disperity selection
261	self.enable_disp = False
262	self.disable_disp = True
263
264	## state of selected all check button
265	self.cb1 = False
266	## store value of chisqr
267	self.tcChi = None
268
269	def clone(self):
270	"""
271	Create a new copy of the current object
272	"""
273	model = None
274	if self.model is not None:
275	model = self.model.clone()
276	model.name = self.model.name
277	obj = PageState(self.parent, model=model)
278	obj.file = copy.deepcopy(self.file)
279	obj.data = copy.deepcopy(self.data)
280	if self.data is not None:
281	self.data_name = self.data.name
282	obj.data_name = self.data_name
283	obj.is_data = self.is_data
284	obj.model_list_box = copy.deepcopy(self.model_list_box)
285	obj.engine_type = copy.deepcopy(self.engine_type)
286
287	obj.categorycombobox = self.categorycombobox
288	obj.formfactorcombobox = self.formfactorcombobox
289	obj.structurecombobox = self.structurecombobox
290
291	#obj.shape_rbutton = self.shape_rbutton
292	#obj.shape_indep_rbutton = self.shape_indep_rbutton
293	#obj.struct_rbutton = self.struct_rbutton
294	#obj.plugin_rbutton = self.plugin_rbutton
295
296	obj.manager = self.manager
297	obj.event_owner = self.event_owner
298	obj.disp_list = copy.deepcopy(self.disp_list)
299
300	obj.enable2D = copy.deepcopy(self.enable2D)
301	obj.parameters = copy.deepcopy(self.parameters)
302	obj.str_parameters = copy.deepcopy(self.str_parameters)
303	obj.fixed_param = copy.deepcopy(self.fixed_param)
304	obj.fittable_param = copy.deepcopy(self.fittable_param)
305	obj.orientation_params = copy.deepcopy(self.orientation_params)
306	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
307	obj.enable_disp = copy.deepcopy(self.enable_disp)
308	obj.disable_disp = copy.deepcopy(self.disable_disp)
309	obj.tcChi = self.tcChi
310
311	if len(self._disp_obj_dict) > 0:
312	for k, v in self._disp_obj_dict.iteritems():
313	obj._disp_obj_dict[k] = v
314	if len(self.disp_cb_dict) > 0:
315	for k, v in self.disp_cb_dict.iteritems():
316	obj.disp_cb_dict[k] = v
317	if len(self.values) > 0:
318	for k, v in self.values.iteritems():
319	obj.values[k] = v
320	if len(self.weights) > 0:
321	for k, v in self.weights.iteritems():
322	obj.weights[k] = v
323	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
324	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
325	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
326	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
327	obj.smear_type = copy.deepcopy(self.smear_type)
328	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
329	obj.dI_didata = copy.deepcopy(self.dI_didata)
330	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
331	obj.dI_idata = copy.deepcopy(self.dI_idata)
332	obj.dq_l = copy.deepcopy(self.dq_l)
333	obj.dq_r = copy.deepcopy(self.dq_r)
334
335	obj.disp_box = copy.deepcopy(self.disp_box)
336	obj.qmin = copy.deepcopy(self.qmin)
337	obj.qmax = copy.deepcopy(self.qmax)
338	obj.multi_factor = self.multi_factor
339	obj.magnetic_on = self.magnetic_on
340	obj.npts = copy.deepcopy(self.npts)
341	obj.cb1 = copy.deepcopy(self.cb1)
342	obj.smearer = copy.deepcopy(self.smearer)
343
344	for name, state in self.saved_states.iteritems():
345	copy_name = copy.deepcopy(name)
346	copy_state = state.clone()
347	obj.saved_states[copy_name] = copy_state
348	return obj
349
350	def _repr_helper(self, list, rep):
351	"""
352	Helper method to print a state
353	"""
354	for item in list:
355	rep += "parameter name: %s \n" % str(item[1])
356	rep += "value: %s\n" % str(item[2])
357	rep += "selected: %s\n" % str(item[0])
358	rep += "error displayed : %s \n" % str(item[4][0])
359	rep += "error value:%s \n" % str(item[4][1])
360	rep += "minimum displayed : %s \n" % str(item[5][0])
361	rep += "minimum value : %s \n" % str(item[5][1])
362	rep += "maximum displayed : %s \n" % str(item[6][0])
363	rep += "maximum value : %s \n" % str(item[6][1])
364	rep += "parameter unit: %s\n\n" % str(item[7])
365	return rep
366
367	def __repr__(self):
368	"""
369	output string for printing
370	"""
371	rep = "\nState name: %s\n" % self.file
372	t = time.localtime(self.timestamp)
373	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
374
375	rep += "State created: %s\n" % time_str
376	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
377	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
378	rep += "is data : %s\n" % self.is_data
379	rep += "data's name : %s\n" % self.data_name
380	rep += "data's id : %s\n" % self.data_id
381	if self.model != None:
382	m_name = self.model.__class__.__name__
383	if m_name == 'Model':
384	m_name = self.m_name
385	rep += "model name : %s\n" % m_name
386	else:
387	rep += "model name : None\n"
388	#rep += "model type (form factor) selected: %s\n" % self.shape_rbutton
389	rep += "multi_factor : %s\n" % str(self.multi_factor)
390	rep += "magnetic_on : %s\n"% str(self.magnetic_on)
391	rep += "model type (Category) selected: %s\n" % self.categorycombobox
392	#rep += "model type (shape independent) selected: %s\n" % self.shape_indep_rbutton
393	#rep += "model type (structure factor) selected: %s\n" % self.struct_rbutton
394	#rep += "model type (plug-in ) selected: %s\n" % self.plugin_rbutton
395	rep += "data : %s\n" % str(self.data)
396	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
397	str(self.qmax), str(self.npts))
398	rep += "Dispersion selection : %s\n" % str(self.disp_box)
399	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
400	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
401	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
402	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
403	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
404	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
405	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
406
407	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
408	rep += "dI_didata : %s\n" % str(self.dI_didata)
409	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
410	rep += "dI_idata : %s\n" % str(self.dI_idata)
411
412	rep += "2D enable : %s\n" % str(self.enable2D)
413	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
414	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
415	rep += "Smear object : %s\n" % str(self.smearer)
416	rep += "Smear type : %s\n" % (self.smear_type)
417	rep += "dq_l : %s\n" % self.dq_l
418	rep += "dq_r : %s\n" % self.dq_r
419
420	rep += "model : %s\n\n" % str(self.model)
421	temp_parameters = []
422	temp_fittable_param = []
423	if self.data.__class__.__name__ == "Data2D":
424	self.is_2D = True
425	else:
426	self.is_2D = False
427	if self.data is not None:
428	if not self.is_2D:
429	for item in self.parameters:
430	if not item in self.orientation_params:
431	temp_parameters.append(item)
432	for item in self.fittable_param:
433	if not item in self.orientation_params_disp:
434	temp_fittable_param.append(item)
435	else:
436	temp_parameters = self.parameters
437	temp_fittable_param = self.fittable_param
438
439	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
440	rep = self._repr_helper(list=temp_parameters, rep=rep)
441	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
442	rep = self._repr_helper(list=self.str_parameters, rep=rep)
443	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
444	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
445	"""
446	if is_2D:
447	rep += "number orientation parameters"
448	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
449	rep = self._repr_helper( list=self.orientation_params, rep=rep)
450	rep += "number dispersity parameters"
451	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
452	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
453	"""
454	return rep
455
456	def set_report_string(self):
457	"""
458	Get the values (strings) from __str__ for report
459	"""
460	# Dictionary of teh report strings
461	repo_time = ""
462	model_name = ""
463	title = ""
464	title_name = ""
465	file_name = ""
466	param_string = ""
467	paramval_string = ""
468	chi2_string = ""
469	multi_factor_string = ""
470	q_range = ""
471	strings = self.__repr__()
472	lines = strings.split('\n')
473
474	# get all string values from __str__()
475	for line in lines:
476	value = ""
477	content = line.split(":")
478	name = content[0]
479	try:
480	value = content[1]
481	except:
482	pass
483	if name.count("State created"):
484	repo_time = "" + value
485	if name.count("parameter name"):
486	val_name = value.split(".")
487	if len(val_name) > 1:
488	if val_name[1].count("width"):
489	param_string += value + ','
490	else:
491	continue
492	else:
493	param_string += value + ','
494	if name == "value":
495	param_string += value + ','
496	if name == "error value":
497	param_string += value + ','
498	if name == "parameter unit":
499	param_string += value + ':'
500	if name == "Value of Chisqr ":
501	chi2 = ("Chi2/Npts = " + value)
502	chi2_string = CENTRE % chi2
503	if name == "multi_factor ":
504	muti_factor = ("muti_factor = " + value)
505	muti_factor_string = CENTRE % muti_factor
506	if name == "magentic_on ":
507	magentic_on = ("magentic_on = " + value)
508	if string(value) == 'True':
509	magentic_on_string = CENTRE % magentic_on
510	if name == "Title":
511	if len(value.strip()) == 0:
512	continue
513	title = value + " [" + repo_time + "]"
514	title_name = HEADER % title
515	if name == "data ":
516	try:
517	file = ("File name:" + content[2])
518	file_name = CENTRE % file
519	if len(title) == 0:
520	title = content[2] + " [" + repo_time + "]"
521	title_name = HEADER % title
522	except:
523	pass
524	if name == "model name ":
525	try:
526	modelname = "Model name:" + content[1]
527	except:
528	modelname = "Model name:" + " NAN"
529	model_name = CENTRE % modelname
530
531	if name == "Plotting Range":
532	try:
533	q_range = content[1] + " = " + content[2] \
534	+ " = " + content[3].split(",")[0]
535	q_name = ("Q Range: " + q_range)
536	q_range = CENTRE % q_name
537	except:
538	pass
539	paramval = ""
540	for lines in param_string.split(":"):
541	line = lines.split(",")
542	if len(lines) > 0:
543	param = line[0]
544	param += " = " + line[1]
545	if len(line[2].split()) > 0 and not line[2].count("None"):
546	param += " +- " + line[2]
547	if len(line[3].split()) > 0 and not line[3].count("None"):
548	param += " " + line[3]
549	if not paramval.count(param):
550	paramval += param + "\n"
551	paramval_string += CENTRE % param + "\n"
552
553	text_string = "\n\n\n" + title + "\n\n" + file + \
554	"\n" + q_name + \
555	"\n" + chi2 + \
556	"\n\n" + paramval
557
558	title_name = self._check_html_format(title_name)
559	file_name = self._check_html_format(file_name)
560	title = self._check_html_format(title)
561
562	html_string = title_name + "\n" + file_name + \
563	"\n" + model_name + \
564	"\n" + q_range + \
565	"\n" + chi2_string + \
566	"\n" + ELINE + \
567	"\n" + paramval_string + \
568	"\n" + ELINE + \
569	"\n" + FEET_1 % title + \
570	"\n" + FEET_2
571
572	return html_string, text_string, title
573
574	def _check_html_format(self, name):
575	"""
576	Check string '%' for html format
577	"""
578	if name.count('%'):
579	name = name.replace('%', '&#37')
580
581	return name
582
583	def report(self, figs=None, canvases=None):
584	"""
585	Invoke report dialog panel
586
587	: param figs: list of pylab figures [list]
588	"""
589	from report_dialog import ReportDialog
590	# get the strings for report
591	html_str, text_str, title = self.set_report_string()
592	# Allow 2 figures to append
593	if len(figs) == 1:
594	add_str = FEET_3
595	elif len(figs) == 2:
596	add_str = ELINE
597	add_str += FEET_2 % ("%s")
598	add_str += ELINE
599	add_str += FEET_3
600	elif len(figs) > 2:
601	add_str = ELINE
602	add_str += FEET_2 % ("%s")
603	add_str += ELINE
604	add_str += FEET_2 % ("%s")
605	add_str += ELINE
606	add_str += FEET_3
607	else:
608	add_str = ""
609
610	# final report html strings
611	report_str = html_str % ("%s") + add_str
612
613	# make plot image
614	images = self.set_plot_state(figs, canvases)
615	report_list = [report_str, text_str, images]
616	dialog = ReportDialog(report_list, None, -1, "")
617	dialog.ShowModal()
618
619	def _toXML_helper(self, list, element, newdoc):
620	"""
621	Helper method to create xml file for saving state
622	"""
623	for item in list:
624	sub_element = newdoc.createElement('parameter')
625	sub_element.setAttribute('name', str(item[1]))
626	sub_element.setAttribute('value', str(item[2]))
627	sub_element.setAttribute('selected_to_fit', str(item[0]))
628	sub_element.setAttribute('error_displayed', str(item[4][0]))
629	sub_element.setAttribute('error_value', str(item[4][1]))
630	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
631	sub_element.setAttribute('minimum_value', str(item[5][1]))
632	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
633	sub_element.setAttribute('maximum_value', str(item[6][1]))
634	sub_element.setAttribute('unit', str(item[7]))
635	element.appendChild(sub_element)
636
637	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
638	"""
639	Writes the state of the InversionControl panel to file, as XML.
640
641	Compatible with standalone writing, or appending to an
642	already existing XML document. In that case, the XML document
643	is required. An optional entry node in the XML document may also be given.
644
645	:param file: file to write to
646	:param doc: XML document object [optional]
647	:param entry_node: XML node within the XML document at which we will append the data [optional]
648
649	"""
650	from xml.dom.minidom import getDOMImplementation
651
652	# Check whether we have to write a standalone XML file
653	if doc is None:
654	impl = getDOMImplementation()
655	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
656	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
657	top_element = newdoc.documentElement
658	else:
659	# We are appending to an existing document
660	newdoc = doc
661	top_element = newdoc.createElement(FITTING_NODE_NAME)
662	if entry_node is None:
663	newdoc.documentElement.appendChild(top_element)
664	else:
665	entry_node.appendChild(top_element)
666
667	attr = newdoc.createAttribute("version")
668	attr.nodeValue = '1.0'
669	top_element.setAttributeNode(attr)
670
671	# File name
672	element = newdoc.createElement("filename")
673	if self.file is not None:
674	element.appendChild(newdoc.createTextNode(str(self.file)))
675	else:
676	element.appendChild(newdoc.createTextNode(str(file)))
677	top_element.appendChild(element)
678
679	element = newdoc.createElement("timestamp")
680	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
681	attr = newdoc.createAttribute("epoch")
682	attr.nodeValue = str(self.timestamp)
683	element.setAttributeNode(attr)
684	top_element.appendChild(element)
685	# Inputs
686	inputs = newdoc.createElement("Attributes")
687	top_element.appendChild(inputs)
688
689	if self.data is not None and hasattr(self.data, "group_id"):
690	self.data_group_id = self.data.group_id
691	if self.data is not None and hasattr(self.data, "is_data"):
692	self.is_data = self.data.is_data
693	if self.data is not None:
694	self.data_name = self.data.name
695	if self.data is not None and hasattr(self.data, "id"):
696	self.data_id = self.data.id
697
698	for item in list_of_data_attributes:
699	element = newdoc.createElement(item[0])
700	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
701	inputs.appendChild(element)
702
703	for item in list_of_state_attributes:
704	element = newdoc.createElement(item[0])
705	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
706	inputs.appendChild(element)
707
708	# For self.values ={ disp_param_name: [vals,...],...}
709	# and for self.weights ={ disp_param_name: [weights,...],...}
710	list = {}
711	for item in list_of_model_attributes:
712	element = newdoc.createElement(item[0])
713	exec "list = self.%s" % item[1]
714	for key, value in list.iteritems():
715	sub_element = newdoc.createElement(key)
716	sub_element.setAttribute('name', str(key))
717	for val in value:
718	com = "sub_element.appendChild"
719	com += "(newdoc.createTextNode(str(%s)))"
720	exec com % val
721
722	element.appendChild(sub_element)
723	inputs.appendChild(element)
724
725	# Create doc for the dictionary of self._disp_obj_dic
726	for item in list_of_obj_dic:
727	element = newdoc.createElement(item[0])
728	exec "list = self.%s" % item[1]
729	for key, val in list.iteritems():
730	value = repr(val)
731	sub_element = newdoc.createElement(key)
732	sub_element.setAttribute('name', str(key))
733	sub_element.setAttribute('value', str(value))
734	element.appendChild(sub_element)
735	inputs.appendChild(element)
736
737	for item in list_of_state_parameters:
738	element = newdoc.createElement(item[0])
739	com = "self._toXML_helper(list=self.%s,"
740	com += " element=element, newdoc=newdoc)"
741	exec com % item[1]
742	inputs.appendChild(element)
743
744	# Save the file
745	if doc is None:
746	fd = open(file, 'w')
747	fd.write(newdoc.toprettyxml())
748	fd.close()
749	return None
750	else:
751	return newdoc.toprettyxml()
752
753	def _fromXML_helper(self, node, list):
754	"""
755	Helper function to write state to xml
756	"""
757	for item in node:
758	try:
759	name = item.get('name')
760	except:
761	name = None
762	try:
763	value = item.get('value')
764	except:
765	value = None
766	try:
767	selected_to_fit = (item.get('selected_to_fit') == "True")
768	except:
769	selected_to_fit = None
770	try:
771	error_displayed = (item.get('error_displayed') == "True")
772	except:
773	error_displayed = None
774	try:
775	error_value = item.get('error_value')
776	except:
777	error_value = None
778	try:
779	minimum_displayed = (item.get('minimum_displayed') == "True")
780	except:
781	minimum_displayed = None
782	try:
783	minimum_value = item.get('minimum_value')
784	except:
785	minimum_value = None
786	try:
787	maximum_displayed = (item.get('maximum_displayed') == "True")
788	except:
789	maximum_displayed = None
790	try:
791	maximum_value = item.get('maximum_value')
792	except:
793	maximum_value = None
794	try:
795	unit = item.get('unit')
796	except:
797	unit = None
798	list.append([selected_to_fit, name, value, "+/-",
799	[error_displayed, error_value],
800	[minimum_displayed, minimum_value],
801	[maximum_displayed, maximum_value], unit])
802
803	def fromXML(self, file=None, node=None):
804	"""
805	Load fitting state from a file
806
807	:param file: .fitv file
808	:param node: node of a XML document to read from
809
810	"""
811	if file is not None:
812	msg = "PageState no longer supports non-CanSAS"
813	msg += " format for fitting files"
814	raise RuntimeError, msg
815
816	if node.get('version')and node.get('version') == '1.0':
817
818	# Get file name
819	entry = get_content('ns:filename', node)
820	if entry is not None:
821	self.file = entry.text.strip()
822
823	# Get time stamp
824	entry = get_content('ns:timestamp', node)
825	if entry is not None and entry.get('epoch'):
826	try:
827	self.timestamp = float(entry.get('epoch'))
828	except:
829	msg = "PageState.fromXML: Could not"
830	msg += " read timestamp\n %s" % sys.exc_value
831	logging.error(msg)
832
833	# Parse fitting attributes
834	entry = get_content('ns:Attributes', node)
835	for item in list_of_data_attributes:
836	node = get_content('ns:%s' % item[0], entry)
837	try:
838	exec "self.%s = parse_entry_helper(node, item)" % item[0]
839
840	except:
841	raise
842
843	if entry is not None:
844
845	for item in list_of_state_attributes:
846	node = get_content('ns:%s' % item[0], entry)
847	try:
848	exec "self.%s = parse_entry_helper(node, item)" % \
849	str(item[0])
850	except:
851	raise
852
853	for item in list_of_state_parameters:
854	node = get_content("ns:%s" % item[0], entry)
855	exec "self._fromXML_helper(node=node, list=self.%s)" % \
856	item[1]
857
858	# Recover _disp_obj_dict from xml file
859	self._disp_obj_dict = {}
860	disp_model = None
861	for item in list_of_obj_dic:
862	# Get node
863	node = get_content("ns:%s" % item[0], entry)
864	for attr in node:
865	name = attr.get('name')
866	val = attr.get('value')
867	value = val.split(" instance")[0]
868	disp_name = value.split("<")[1]
869	try:
870	# Try to recover disp_model object from strings
871	com = "from sans.models.dispersion_models "
872	com += "import %s as disp"
873	com_name = disp_name.split(".")[3]
874	exec com % com_name
875	disp_model = disp()
876	exec "self.%s['%s'] = com_name" % (item[1], name)
877	except:
878	pass
879
880	# get self.values and self.weights dic. if exists
881	for item in list_of_model_attributes:
882	node = get_content("ns:%s" % item[0], entry)
883	dic = {}
884	list = []
885	for par in node:
886	name = par.get('name')
887	values = par.text.split('\n')
888	# Get lines only with numbers
889	for line in values:
890	try:
891	val = float(line)
892	list.append(val)
893	except:
894	# pass if line is empty (it happens)
895	pass
896	dic[name] = numpy.array(list)
897	exec "self.%s = dic" % item[1]
898
899	def set_plot_state(self, figs, canvases):
900	"""
901	Build image state that wx.html understand
902	by plotting, putting it into wx.FileSystem image object
903
904	"""
905	images = []
906	# some imports
907	import wx
908
909	# Reset memory
910	self.imgRAM = None
911	wx.MemoryFSHandler()
912
913	# For no figures in the list, prepare empty plot
914	if figs == None or len(figs) == 0:
915	figs = [None]
916
917	# Loop over the list of figures
918	# use wx.MemoryFSHandler
919	self.imgRAM = wx.MemoryFSHandler()
920	for fig in figs:
921	if figs != None:
922	ind = figs.index(fig)
923	canvas = canvases[ind]
924
925	#store the image in wx.FileSystem Object
926	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
927
928	# index of the fig
929	ind = figs.index(fig)
930
931	#AddFile, image can be retrieved with 'memory:filename'
932	self.imgRAM.AddFile('img_fit%s.png' % ind,
933	canvas.bitmap, wx.BITMAP_TYPE_PNG)
934
935	#append figs
936	images.append(fig)
937
938	return images
939
940
941	class Reader(CansasReader):
942	"""
943	Class to load a .fitv fitting file
944	"""
945	## File type
946	type_name = "Fitting"
947
948	## Wildcards
949	type = ["Fitting files (.fitv)\|.fitv"
950	"SANSView file (.svs)\|.svs"]
951	## List of allowed extensions
952	ext = ['.fitv', '.FITV', '.svs', 'SVS']
953
954	def __init__(self, call_back=None, cansas=True):
955	CansasReader.__init__(self)
956	"""
957	Initialize the call-back method to be called
958	after we load a file
959
960	:param call_back: call-back method
961	:param cansas: True = files will be written/read in CanSAS format
962	False = write CanSAS format
963
964	"""
965	## Call back method to be executed after a file is read
966	self.call_back = call_back
967	## CanSAS format flag
968	self.cansas = cansas
969	self.state = None
970
971	def get_state(self):
972	return self.state
973
974	def read(self, path):
975	"""
976	Load a new P(r) inversion state from file
977
978	:param path: file path
979
980	"""
981	if self.cansas == True:
982	return self._read_cansas(path)
983
984	def _data2d_to_xml_doc(self, datainfo):
985	"""
986	Create an XML document to contain the content of a Data2D
987
988	:param datainfo: Data2D object
989
990	"""
991	if not issubclass(datainfo.__class__, Data2D):
992	raise RuntimeError, "The cansas writer expects a Data2D instance"
993
994	doc = xml.dom.minidom.Document()
995	main_node = doc.createElement("SASroot")
996	main_node.setAttribute("version", self.version)
997	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
998	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
999	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
1000
1001	doc.appendChild(main_node)
1002
1003	entry_node = doc.createElement("SASentry")
1004	main_node.appendChild(entry_node)
1005
1006	write_node(doc, entry_node, "Title", datainfo.title)
1007	if datainfo is not None:
1008	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
1009	for item in datainfo.run:
1010	runname = {}
1011	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
1012	runname = {'name': datainfo.run_name[item] }
1013	write_node(doc, entry_node, "Run", item, runname)
1014	# Data info
1015	new_node = doc.createElement("SASdata")
1016	entry_node.appendChild(new_node)
1017	for item in list_of_data_2d_attr:
1018	element = doc.createElement(item[0])
1019	exec "element.setAttribute(item[0], str(datainfo.%s))" % (item[1])
1020	new_node.appendChild(element)
1021
1022	for item in list_of_data2d_values:
1023	root_node = doc.createElement(item[0])
1024	new_node.appendChild(root_node)
1025	temp_list = None
1026	exec "temp_list = datainfo.%s" % item[1]
1027
1028	if temp_list is None or len(temp_list)== 0:
1029	element = doc.createElement(item[0])
1030	exec "element.appendChild(doc.createTextNode(str(%s)))" % temp_list
1031	root_node.appendChild(element)
1032	else:
1033	for value in temp_list:
1034	element = doc.createElement(item[0])
1035	exec "element.setAttribute(item[0], str(%s))" % value
1036	root_node.appendChild(element)
1037
1038	# Sample info
1039	sample = doc.createElement("SASsample")
1040	if datainfo.sample.name is not None:
1041	sample.setAttribute("name", str(datainfo.sample.name))
1042	entry_node.appendChild(sample)
1043	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1044	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1045	{"unit": datainfo.sample.thickness_unit})
1046	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1047	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1048	{"unit": datainfo.sample.temperature_unit})
1049
1050	for item in datainfo.sample.details:
1051	write_node(doc, sample, "details", item)
1052
1053	pos = doc.createElement("position")
1054	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1055	{"unit": datainfo.sample.position_unit})
1056	written = written \| write_node(doc, pos, "y",
1057	datainfo.sample.position.y,
1058	{"unit": datainfo.sample.position_unit})
1059	written = written \| write_node(doc, pos, "z",
1060	datainfo.sample.position.z,
1061	{"unit": datainfo.sample.position_unit})
1062	if written == True:
1063	sample.appendChild(pos)
1064
1065	ori = doc.createElement("orientation")
1066	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1067	{"unit": datainfo.sample.orientation_unit})
1068	written = written \| write_node(doc, ori, "pitch",
1069	datainfo.sample.orientation.y,
1070	{"unit": datainfo.sample.orientation_unit})
1071	written = written \| write_node(doc, ori, "yaw",
1072	datainfo.sample.orientation.z,
1073	{"unit": datainfo.sample.orientation_unit})
1074	if written == True:
1075	sample.appendChild(ori)
1076
1077	# Instrument info
1078	instr = doc.createElement("SASinstrument")
1079	entry_node.appendChild(instr)
1080
1081	write_node(doc, instr, "name", datainfo.instrument)
1082
1083	# Source
1084	source = doc.createElement("SASsource")
1085	if datainfo.source.name is not None:
1086	source.setAttribute("name", str(datainfo.source.name))
1087	instr.appendChild(source)
1088
1089	write_node(doc, source, "radiation", datainfo.source.radiation)
1090	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1091	size = doc.createElement("beam_size")
1092	if datainfo.source.beam_size_name is not None:
1093	size.setAttribute("name", str(datainfo.source.beam_size_name))
1094	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1095	{"unit": datainfo.source.beam_size_unit})
1096	written = written \| write_node(doc, size, "y",
1097	datainfo.source.beam_size.y,
1098	{"unit": datainfo.source.beam_size_unit})
1099	written = written \| write_node(doc, size, "z",
1100	datainfo.source.beam_size.z,
1101	{"unit": datainfo.source.beam_size_unit})
1102	if written == True:
1103	source.appendChild(size)
1104
1105	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1106	{"unit": datainfo.source.wavelength_unit})
1107	write_node(doc, source, "wavelength_min",
1108	datainfo.source.wavelength_min,
1109	{"unit": datainfo.source.wavelength_min_unit})
1110	write_node(doc, source, "wavelength_max",
1111	datainfo.source.wavelength_max,
1112	{"unit": datainfo.source.wavelength_max_unit})
1113	write_node(doc, source, "wavelength_spread",
1114	datainfo.source.wavelength_spread,
1115	{"unit": datainfo.source.wavelength_spread_unit})
1116
1117	# Collimation
1118	for item in datainfo.collimation:
1119	coll = doc.createElement("SAScollimation")
1120	if item.name is not None:
1121	coll.setAttribute("name", str(item.name))
1122	instr.appendChild(coll)
1123
1124	write_node(doc, coll, "length", item.length,
1125	{"unit": item.length_unit})
1126
1127	for apert in item.aperture:
1128	ap = doc.createElement("aperture")
1129	if apert.name is not None:
1130	ap.setAttribute("name", str(apert.name))
1131	if apert.type is not None:
1132	ap.setAttribute("type", str(apert.type))
1133	coll.appendChild(ap)
1134
1135	write_node(doc, ap, "distance", apert.distance,
1136	{"unit": apert.distance_unit})
1137
1138	size = doc.createElement("size")
1139	if apert.size_name is not None:
1140	size.setAttribute("name", str(apert.size_name))
1141	written = write_node(doc, size, "x", apert.size.x,
1142	{"unit": apert.size_unit})
1143	written = written \| write_node(doc, size, "y", apert.size.y,
1144	{"unit": apert.size_unit})
1145	written = written \| write_node(doc, size, "z", apert.size.z,
1146	{"unit": apert.size_unit})
1147	if written == True:
1148	ap.appendChild(size)
1149
1150	# Detectors
1151	for item in datainfo.detector:
1152	det = doc.createElement("SASdetector")
1153	written = write_node(doc, det, "name", item.name)
1154	written = written \| write_node(doc, det, "SDD", item.distance,
1155	{"unit": item.distance_unit})
1156	written = written \| write_node(doc, det, "slit_length",
1157	item.slit_length,
1158	{"unit": item.slit_length_unit})
1159	if written == True:
1160	instr.appendChild(det)
1161
1162	off = doc.createElement("offset")
1163	written = write_node(doc, off, "x", item.offset.x,
1164	{"unit": item.offset_unit})
1165	written = written \| write_node(doc, off, "y", item.offset.y,
1166	{"unit": item.offset_unit})
1167	written = written \| write_node(doc, off, "z", item.offset.z,
1168	{"unit": item.offset_unit})
1169	if written == True:
1170	det.appendChild(off)
1171
1172	center = doc.createElement("beam_center")
1173	written = write_node(doc, center, "x", item.beam_center.x,
1174	{"unit": item.beam_center_unit})
1175	written = written \| write_node(doc, center, "y",
1176	item.beam_center.y,
1177	{"unit": item.beam_center_unit})
1178	written = written \| write_node(doc, center, "z",
1179	item.beam_center.z,
1180	{"unit": item.beam_center_unit})
1181	if written == True:
1182	det.appendChild(center)
1183
1184	pix = doc.createElement("pixel_size")
1185	written = write_node(doc, pix, "x", item.pixel_size.x,
1186	{"unit": item.pixel_size_unit})
1187	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1188	{"unit": item.pixel_size_unit})
1189	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1190	{"unit": item.pixel_size_unit})
1191	if written == True:
1192	det.appendChild(pix)
1193
1194	ori = doc.createElement("orientation")
1195	written = write_node(doc, ori, "roll", item.orientation.x,
1196	{"unit": item.orientation_unit})
1197	written = written \| write_node(doc, ori, "pitch",
1198	item.orientation.y,
1199	{"unit": item.orientation_unit})
1200	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1201	{"unit": item.orientation_unit})
1202	if written == True:
1203	det.appendChild(ori)
1204
1205	# Processes info
1206	for item in datainfo.process:
1207	node = doc.createElement("SASprocess")
1208	entry_node.appendChild(node)
1209
1210	write_node(doc, node, "name", item.name)
1211	write_node(doc, node, "date", item.date)
1212	write_node(doc, node, "description", item.description)
1213	for term in item.term:
1214	value = term['value']
1215	del term['value']
1216	write_node(doc, node, "term", value, term)
1217	for note in item.notes:
1218	write_node(doc, node, "SASprocessnote", note)
1219	# Return the document, and the SASentry node associated with
1220	# the data we just wrote
1221	return doc, entry_node
1222
1223	def _parse_state(self, entry):
1224	"""
1225	Read a fit result from an XML node
1226
1227	:param entry: XML node to read from
1228
1229	:return: PageState object
1230	"""
1231	# Create an empty state
1232	state = None
1233	# Locate the P(r) node
1234	try:
1235	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1236	namespaces={'ns': CANSAS_NS})
1237	if nodes != []:
1238	# Create an empty state
1239	state = PageState()
1240	state.fromXML(node=nodes[0])
1241	except:
1242	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1243
1244	return state
1245
1246	def _parse_entry(self, dom):
1247	"""
1248	Parse a SASentry
1249
1250	:param node: SASentry node
1251
1252	:return: Data1D/Data2D object
1253
1254	"""
1255	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1256	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1257	return CansasReader._parse_entry(self, dom)
1258
1259	#Parse 2D
1260	data_info = Data2D()
1261
1262	# Look up title
1263	self._store_content('ns:Title', dom, 'title', data_info)
1264
1265	# Look up run number
1266	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1267	for item in nodes:
1268	if item.text is not None:
1269	value = item.text.strip()
1270	if len(value) > 0:
1271	data_info.run.append(value)
1272	if item.get('name') is not None:
1273	data_info.run_name[value] = item.get('name')
1274
1275	# Look up instrument name
1276	self._store_content('ns:SASinstrument/ns:name', dom,
1277	'instrument', data_info)
1278
1279	# Notes
1280	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1281	for note in note_list:
1282	try:
1283	if note.text is not None:
1284	note_value = note.text.strip()
1285	if len(note_value) > 0:
1286	data_info.notes.append(note_value)
1287	except:
1288	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1289	self.errors.append(err_mess)
1290	logging.error(err_mess)
1291
1292	# Sample info ###################
1293	entry = get_content('ns:SASsample', dom)
1294	if entry is not None:
1295	data_info.sample.name = entry.get('name')
1296
1297	self._store_content('ns:SASsample/ns:ID',
1298	dom, 'ID', data_info.sample)
1299	self._store_float('ns:SASsample/ns:thickness',
1300	dom, 'thickness', data_info.sample)
1301	self._store_float('ns:SASsample/ns:transmission',
1302	dom, 'transmission', data_info.sample)
1303	self._store_float('ns:SASsample/ns:temperature',
1304	dom, 'temperature', data_info.sample)
1305
1306	nodes = dom.xpath('ns:SASsample/ns:details',
1307	namespaces={'ns': CANSAS_NS})
1308	for item in nodes:
1309	try:
1310	if item.text is not None:
1311	detail_value = item.text.strip()
1312	if len(detail_value) > 0:
1313	data_info.sample.details.append(detail_value)
1314	except:
1315	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1316	self.errors.append(err_mess)
1317	logging.error(err_mess)
1318
1319	# Position (as a vector)
1320	self._store_float('ns:SASsample/ns:position/ns:x',
1321	dom, 'position.x', data_info.sample)
1322	self._store_float('ns:SASsample/ns:position/ns:y',
1323	dom, 'position.y', data_info.sample)
1324	self._store_float('ns:SASsample/ns:position/ns:z',
1325	dom, 'position.z', data_info.sample)
1326
1327	# Orientation (as a vector)
1328	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1329	dom, 'orientation.x', data_info.sample)
1330	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1331	dom, 'orientation.y', data_info.sample)
1332	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1333	dom, 'orientation.z', data_info.sample)
1334
1335	# Source info ###################
1336	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1337	if entry is not None:
1338	data_info.source.name = entry.get('name')
1339
1340	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1341	dom, 'radiation', data_info.source)
1342	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1343	dom, 'beam_shape', data_info.source)
1344	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1345	dom, 'wavelength', data_info.source)
1346	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1347	dom, 'wavelength_min', data_info.source)
1348	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1349	dom, 'wavelength_max', data_info.source)
1350	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1351	dom, 'wavelength_spread', data_info.source)
1352
1353	# Beam size (as a vector)
1354	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1355	if entry is not None:
1356	data_info.source.beam_size_name = entry.get('name')
1357
1358	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1359	dom, 'beam_size.x', data_info.source)
1360	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1361	dom, 'beam_size.y', data_info.source)
1362	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1363	dom, 'beam_size.z', data_info.source)
1364
1365	# Collimation info ###################
1366	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1367	namespaces={'ns': CANSAS_NS})
1368	for item in nodes:
1369	collim = Collimation()
1370	if item.get('name') is not None:
1371	collim.name = item.get('name')
1372	self._store_float('ns:length', item, 'length', collim)
1373
1374	# Look for apertures
1375	apert_list = item.xpath('ns:aperture',
1376	namespaces={'ns': CANSAS_NS})
1377	for apert in apert_list:
1378	aperture = Aperture()
1379
1380	# Get the name and type of the aperture
1381	aperture.name = apert.get('name')
1382	aperture.type = apert.get('type')
1383
1384	self._store_float('ns:distance', apert, 'distance', aperture)
1385
1386	entry = get_content('ns:size', apert)
1387	if entry is not None:
1388	aperture.size_name = entry.get('name')
1389
1390	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1391	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1392	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1393
1394	collim.aperture.append(aperture)
1395
1396	data_info.collimation.append(collim)
1397
1398	# Detector info ######################
1399	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1400	namespaces={'ns': CANSAS_NS})
1401	for item in nodes:
1402
1403	detector = Detector()
1404
1405	self._store_content('ns:name', item, 'name', detector)
1406	self._store_float('ns:SDD', item, 'distance', detector)
1407
1408	# Detector offset (as a vector)
1409	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1410	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1411	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1412
1413	# Detector orientation (as a vector)
1414	self._store_float('ns:orientation/ns:roll', item,
1415	'orientation.x', detector)
1416	self._store_float('ns:orientation/ns:pitch', item,
1417	'orientation.y', detector)
1418	self._store_float('ns:orientation/ns:yaw', item,
1419	'orientation.z', detector)
1420
1421	# Beam center (as a vector)
1422	self._store_float('ns:beam_center/ns:x', item,
1423	'beam_center.x', detector)
1424	self._store_float('ns:beam_center/ns:y', item,
1425	'beam_center.y', detector)
1426	self._store_float('ns:beam_center/ns:z', item,
1427	'beam_center.z', detector)
1428
1429	# Pixel size (as a vector)
1430	self._store_float('ns:pixel_size/ns:x', item,
1431	'pixel_size.x', detector)
1432	self._store_float('ns:pixel_size/ns:y', item,
1433	'pixel_size.y', detector)
1434	self._store_float('ns:pixel_size/ns:z', item,
1435	'pixel_size.z', detector)
1436
1437	self._store_float('ns:slit_length', item, 'slit_length', detector)
1438
1439	data_info.detector.append(detector)
1440
1441	# Processes info ######################
1442	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1443	for item in nodes:
1444	process = Process()
1445	self._store_content('ns:name', item, 'name', process)
1446	self._store_content('ns:date', item, 'date', process)
1447	self._store_content('ns:description', item, 'description', process)
1448
1449	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1450	for term in term_list:
1451	try:
1452	term_attr = {}
1453	for attr in term.keys():
1454	term_attr[attr] = term.get(attr).strip()
1455	if term.text is not None:
1456	term_attr['value'] = term.text.strip()
1457	process.term.append(term_attr)
1458	except:
1459	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1460	self.errors.append(err_mess)
1461	logging.error(err_mess)
1462
1463	note_list = item.xpath('ns:SASprocessnote',
1464	namespaces={'ns': CANSAS_NS})
1465	for note in note_list:
1466	if note.text is not None:
1467	process.notes.append(note.text.strip())
1468
1469	data_info.process.append(process)
1470
1471	# Data info ######################
1472	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1473	if len(nodes) > 1:
1474	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1475
1476	for entry in nodes:
1477	for item in list_of_data_2d_attr:
1478	#get node
1479	node = get_content('ns:%s' % item[0], entry)
1480	exec "data_info.%s = parse_entry_helper(node, item)" % item[1]
1481
1482	for item in list_of_data2d_values:
1483	field = get_content('ns:%s' % item[0], entry)
1484	list = []
1485	if field is not None:
1486	list = [parse_entry_helper(node, item) for node in field]
1487	exec "data_info.%s = numpy.array(list)" % item[0]
1488
1489	return data_info
1490
1491	def _read_cansas(self, path):
1492	"""
1493	Load data and P(r) information from a CanSAS XML file.
1494
1495	:param path: file path
1496
1497	:return: Data1D object if a single SASentry was found,
1498	or a list of Data1D objects if multiple entries were found,
1499	or None of nothing was found
1500
1501	:raise RuntimeError: when the file can't be opened
1502	:raise ValueError: when the length of the data vectors are inconsistent
1503
1504	"""
1505	output = []
1506	basename = os.path.basename(path)
1507	root, extension = os.path.splitext(basename)
1508	ext = extension.lower()
1509	try:
1510	if os.path.isfile(path):
1511
1512	#TODO: eventually remove the check for .xml once
1513	# the P(r) writer/reader is truly complete.
1514	if ext in self.ext or \
1515	ext == '.xml':
1516
1517	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1518	# Check the format version number
1519	# Specifying the namespace will take care of the file format version
1520	root = tree.getroot()
1521	entry_list = root.xpath('ns:SASentry',
1522	namespaces={'ns': CANSAS_NS})
1523	for entry in entry_list:
1524	try:
1525	sas_entry = self._parse_entry(entry)
1526	except:
1527	raise
1528	fitstate = self._parse_state(entry)
1529
1530	#state could be None when .svs file is loaded
1531	#in this case, skip appending to output
1532	if fitstate != None:
1533	sas_entry.meta_data['fitstate'] = fitstate
1534	sas_entry.filename = fitstate.file
1535	output.append(sas_entry)
1536	else:
1537	self.call_back(format=ext)
1538	raise RuntimeError, "%s is not a file" % path
1539
1540	# Return output consistent with the loader's api
1541	if len(output) == 0:
1542	self.call_back(state=None, datainfo=None, format=ext)
1543	return None
1544	else:
1545	for ind in range(len(output)):
1546	# Call back to post the new state
1547	state = output[ind].meta_data['fitstate']
1548	t = time.localtime(state.timestamp)
1549	time_str = time.strftime("%b %d %H:%M", t)
1550	# Check that no time stamp is already appended
1551	max_char = state.file.find("[")
1552	if max_char < 0:
1553	max_char = len(state.file)
1554	original_fname = state.file[0:max_char]
1555	state.file = original_fname + ' [' + time_str + ']'
1556
1557	if state is not None and state.is_data is not None:
1558	exec 'output[%d].is_data = state.is_data' % ind
1559
1560	output[ind].filename = state.file
1561	state.data = output[ind]
1562	state.data.name = output[ind].filename # state.data_name
1563	state.data.id = state.data_id
1564	if state.is_data is not None:
1565	state.data.is_data = state.is_data
1566	if output[ind].run_name is not None\
1567	and len(output[ind].run_name) != 0:
1568	name = output[ind].run_name
1569	else:
1570	name = original_fname
1571	state.data.group_id = name
1572	#store state in fitting
1573	self.call_back(state=state,
1574	datainfo=output[ind], format=ext)
1575	self.state = state
1576	return output
1577
1578	except:
1579	self.call_back(format=ext)
1580	#self.state= state
1581	raise
1582
1583	def write(self, filename, datainfo=None, fitstate=None):
1584	"""
1585	Write the content of a Data1D as a CanSAS XML file only for standalone
1586
1587	:param filename: name of the file to write
1588	:param datainfo: Data1D object
1589	:param fitstate: PageState object
1590
1591	"""
1592	# Sanity check
1593	if self.cansas == True:
1594
1595	# Add fitting information to the XML document
1596	doc = self.write_toXML(datainfo, fitstate)
1597	# Write the XML document
1598	fd = open(filename, 'w')
1599	fd.write(doc.toprettyxml())
1600	fd.close()
1601	else:
1602	fitstate.toXML(file=filename)
1603
1604	def write_toXML(self, datainfo=None, state=None):
1605	"""
1606	Write toXML, a helper for write(),
1607	could be used by guimanager._on_save()
1608
1609	: return: xml doc
1610	"""
1611
1612	if state.data is None:
1613	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1614	return None
1615	else:
1616	#make sure title and data run is filled up.
1617	if state.data.title == None or state.data.title == '':
1618	state.data.title = state.data.name
1619	if state.data.run_name == None or state.data.run_name == {}:
1620	state.data.run = [str(state.data.name)]
1621	state.data.run_name[0] = state.data.name
1622
1623	if issubclass(state.data.__class__,
1624	sans.dataloader.data_info.Data1D):
1625	data = state.data
1626	doc, sasentry = self._to_xml_doc(data)
1627	else:
1628	data = state.data
1629	doc, sasentry = self._data2d_to_xml_doc(data)
1630
1631	if state is not None:
1632	state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1633
1634	return doc
1635
1636	# Simple html report templet
1637	HEADER = "<html>\n"
1638	HEADER += "<head>\n"
1639	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1640	HEADER += "charset=windows-1252'> \n"
1641	HEADER += "<meta name=Generator >\n"
1642	HEADER += "</head>\n"
1643	HEADER += "<body lang=EN-US>\n"
1644	HEADER += "<div class=WordSection1>\n"
1645	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1646	HEADER += "%s</font></center></span></center></b></p>"
1647	HEADER += "<p class=MsoNormal> </p>"
1648	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1649	PARA += "</font></p>"
1650	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1651	CENTRE += "</font></center></p>"
1652	FEET_1 = \
1653	"""
1654	<p class=MsoNormal> </p>
1655	<br>
1656	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1657	</font></span></center></b></p>
1658	<p class=MsoNormal> </p>
1659	<center>
1660	<br><font size='4' >Model Computation</font>
1661	<br><font size='4' >Data: "%s"</font><br>
1662	"""
1663	FEET_2 = \
1664	"""
1665	<img src="%s" >
1666	</img>
1667	"""
1668	FEET_3 = \
1669	"""
1670	</center>
1671	</div>
1672	</body>
1673	</html>
1674	"""
1675	ELINE = "<p class=MsoNormal> </p>"
1676
1677	if __name__ == "__main__":
1678	state = PageState(parent=None)
1679	#state.toXML()
1680	"""
1681
1682	file = open("test_state", "w")
1683	pickle.dump(state, file)
1684	print pickle.dumps(state)
1685	state.data_name = "hello---->"
1686	pickle.dump(state, file)
1687	file = open("test_state", "r")
1688	new_state= pickle.load(file)
1689	print "new state", new_state
1690	new_state= pickle.load(file)
1691	print "new state", new_state
1692	#print "state", state
1693	"""
1694	import bsddb
1695	import pickle
1696	db = bsddb.btopen('file_state.db', 'c')
1697	val = (pickle.dumps(state), "hello", "hi")
1698	db['state1'] = pickle.dumps(val)
1699	print pickle.loads(db['state1'])
1700	state.data_name = "hello---->22"
1701	db['state2'] = pickle.dumps(state)
1702	state.data_name = "hello---->2"
1703	db['state3'] = pickle.dumps(state)
1704	del db['state3']
1705	state.data_name = "hello---->3"
1706	db['state4'] = pickle.dumps(state)
1707	new_state = pickle.loads(db['state1'])
1708	#print db.last()
1709	db.set_location('state2')
1710	state.data_name = "hello---->5"
1711	db['aastate5'] = pickle.dumps(state)
1712	db.keys().sort()
1713	print pickle.loads(db['state2'])
1714
1715	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ a805118

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