pagestate.py @ d06ae30

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 d06ae30 was d06ae30, checked in by gonzalezm, 9 years ago
Bug fix for ticket 263 about Report results reporting errors also for fixed parameters
Property mode set to `100644`
File size: 73.6 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	import string
20
21	import xml.dom.minidom
22	from xml.dom.minidom import parseString
23	from lxml import etree
24
25	import sas.dataloader
26	from sas.dataloader.readers.cansas_reader import Reader as CansasReader
27	from sas.dataloader.readers.cansas_reader import get_content, write_node
28	from sas.dataloader.data_info import Data2D
29	from sas.dataloader.data_info import Collimation
30	from sas.dataloader.data_info import Detector
31	from sas.dataloader.data_info import Process
32	from sas.dataloader.data_info import Aperture
33	#Information to read/write state as xml
34	FITTING_NODE_NAME = 'fitting_plug_in'
35	CANSAS_NS = "cansas1d/1.0"
36
37	list_of_data_attributes = [["is_data", "is_data", "bool"],
38	["group_id", "data_group_id", "string"],
39	["data_name", "data_name", "string"],
40	["data_id", "data_id", "string"],
41	["name", "name", "string"],
42	["data_name", "data_name", "string"]]
43	list_of_state_attributes = [["engine_type", "engine_type", "string"],
44	["qmin", "qmin", "float"],
45	["qmax", "qmax", "float"],
46	["npts", "npts", "float"],
47	#["shape_rbutton", "shape_rbutton", "bool"],
48	#["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
49	#["plugin_rbutton", "plugin_rbutton", "bool"],
50	#["struct_rbutton", "struct_rbutton", "bool"],
51	["categorycombobox", "categorycombobox", "string"],
52	["formfactorcombobox", "formfactorcombobox", "string"],
53	["structurecombobox", "structurecombobox", "string"],
54	["multi_factor","multi_factor","float"],
55	["magnetic_on","magnetic_on", "bool"],
56	["enable_smearer","enable_smearer","bool"],
57	["disable_smearer","disable_smearer","bool"],
58	["pinhole_smearer","pinhole_smearer","bool"],
59	["slit_smearer","slit_smearer","bool"],
60	["enable_disp","enable_disp","bool"],
61	["disable_disp","disable_disp","bool"],
62	["dI_noweight","dI_noweight","bool"],
63	["dI_didata","dI_didata","bool"],
64	["dI_sqrdata","dI_sqrdata","bool"],
65	["dI_idata","dI_idata","bool"],
66	["enable2D","enable2D","bool"],
67	["cb1","cb1","bool"],
68	["tcChi","tcChi","float"],
69	["smearer", "smearer", "float"],
70	["smear_type","smear_type", "string"],
71	["dq_l", "dq_l", "string"],
72	["dq_r","dq_r", "string"],
73	["dx_max", "dx_max", "float"],
74	["dx_min","dx_min", "float"],
75	["dxl", "dxl", "float"],
76	["dxw","dxw", "float"]]
77
78	list_of_model_attributes = [["values", "values"],
79	["weights", "weights"]]
80
81	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
82
83	list_of_state_parameters = [["parameters", "parameters"],
84	["str_parameters", "str_parameters"],
85	["orientation_parameters", "orientation_params"],
86	["dispersity_parameters", "orientation_params_disp"],
87	["fixed_param", "fixed_param"],
88	["fittable_param", "fittable_param"]]
89	list_of_data_2d_attr = [["xmin", "xmin", "float"],
90	["xmax", "xmax", "float"],
91	["ymin", "ymin", "float"],
92	["ymax", "ymax", "float"],
93	["_xaxis", "_xaxis", "string"],
94	["_xunit", "_xunit", "string"],
95	["_yaxis", "_yaxis", "string"],
96	["_yunit", "_yunit", "string"],
97	["_zaxis", "_zaxis", "string"],
98	["_zunit", "_zunit", "string"]]
99	list_of_data2d_values = [["qx_data", "qx_data", "float"],
100	["qy_data", "qy_data", "float"],
101	["dqx_data", "dqx_data", "float"],
102	["dqy_data", "dqy_data", "float"],
103	["data", "data", "float"],
104	["q_data", "q_data", "float"],
105	["err_data", "err_data", "float"],
106	["mask", "mask", "bool"]]
107
108
109	def parse_entry_helper(node, item):
110	"""
111	Create a numpy list from value extrated from the node
112
113	:param node: node from each the value is stored
114	:param item: list name of three strings.the two first are name of data
115	attribute and the third one is the type of the value of that
116	attribute. type can be string, float, bool, etc.
117
118	: return: numpy array
119	"""
120	if node is not None:
121	if item[2] == "string":
122	return str(node.get(item[0]).strip())
123	elif item[2] == "bool":
124	try:
125	return node.get(item[0]).strip() == "True"
126
127	except:
128	return None
129	else:
130	try:
131	return float(node.get(item[0]))
132	except:
133	return None
134
135
136	class PageState(object):
137	"""
138	Contains information to reconstruct a page of the fitpanel.
139	"""
140	def __init__(self, parent=None, model=None, data=None):
141	"""
142	Initialize the current state
143
144	:param model: a selected model within a page
145	:param data:
146
147	"""
148	self.file = None
149	#Time of state creation
150	self.timestamp = time.time()
151	## Data member to store the dispersion object created
152	self._disp_obj_dict = {}
153	#------------------------
154	#Data used for fitting
155	self.data = data
156	# model data
157	self.theory_data = None
158	#Is 2D
159	self.is_2D = False
160	self.images = None
161
162	#save additional information on data that dataloader.reader does not read
163	self.is_data = None
164	self.data_name = ""
165
166	if self.data is not None:
167	self.data_name = self.data.name
168	self.data_id = None
169	if self.data is not None and hasattr(self.data, "id"):
170	self.data_id = self.data.id
171	self.data_group_id = None
172	if self.data is not None and hasattr(self.data, "group_id"):
173	self.data_group_id = self.data.group_id
174
175	## reset True change the state of exsiting button
176	self.reset = False
177
178	#engine type
179	self.engine_type = None
180	# flag to allow data2D plot
181	self.enable2D = False
182	# model on which the fit would be performed
183	self.model = model
184	self.m_name = None
185	#list of process done to model
186	self.process = []
187	#fit page manager
188	self.manager = None
189	#Store the parent of this panel parent
190	# For this application fitpanel is the parent
191	self.parent = parent
192	# Event_owner is the owner of model event
193	self.event_owner = None
194	##page name
195	self.page_name = ""
196	# Contains link between model, all its parameters, and panel organization
197	self.parameters = []
198	# String parameter list that can not be fitted
199	self.str_parameters = []
200	# Contains list of parameters that cannot be fitted and reference to
201	#panel objects
202	self.fixed_param = []
203	# Contains list of parameters with dispersity and reference to
204	#panel objects
205	self.fittable_param = []
206	## orientation parameters
207	self.orientation_params = []
208	## orientation parameters for gaussian dispersity
209	self.orientation_params_disp = []
210	## smearer info
211	self.smearer = None
212	self.smear_type = None
213	self.dq_l = None
214	self.dq_r = None
215	self.dx_max = None
216	self.dx_min = None
217	self.dxl = None
218	self.dxw = None
219	#list of dispersion parameters
220	self.disp_list = []
221	if self.model is not None:
222	self.disp_list = self.model.getDispParamList()
223
224	self.disp_cb_dict = {}
225	self.values = {}
226	self.weights = {}
227
228	#contains link between a model and selected parameters to fit
229	self.param_toFit = []
230	##dictionary of model type and model class
231	self.model_list_box = None
232	## save the state of the context menu
233	self.saved_states = {}
234	## save selection of combobox
235	self.formfactorcombobox = None
236	self.categorycombobox = None
237	self.structurecombobox = None
238
239	## radio box to select type of model
240	#self.shape_rbutton = False
241	#self.shape_indep_rbutton = False
242	#self.struct_rbutton = False
243	#self.plugin_rbutton = False
244	## the indice of the current selection
245	self.disp_box = 0
246	## Qrange
247	## Q range
248	self.qmin = 0.001
249	self.qmax = 0.1
250	#reset data range
251	self.qmax_x = None
252	self.qmin_x = None
253
254	self.npts = None
255	self.name = ""
256	self.multi_factor = None
257	self.magnetic_on = False
258	## enable smearering state
259	self.enable_smearer = False
260	self.disable_smearer = True
261	self.pinhole_smearer = False
262	self.slit_smearer = False
263	# weighting options
264	self.dI_noweight = False
265	self.dI_didata = True
266	self.dI_sqrdata = False
267	self.dI_idata = False
268	## disperity selection
269	self.enable_disp = False
270	self.disable_disp = True
271
272	## state of selected all check button
273	self.cb1 = False
274	## store value of chisqr
275	self.tcChi = None
276
277	def clone(self):
278	"""
279	Create a new copy of the current object
280	"""
281	model = None
282	if self.model is not None:
283	model = self.model.clone()
284	model.name = self.model.name
285	obj = PageState(self.parent, model=model)
286	obj.file = copy.deepcopy(self.file)
287	obj.data = copy.deepcopy(self.data)
288	if self.data is not None:
289	self.data_name = self.data.name
290	obj.data_name = self.data_name
291	obj.is_data = self.is_data
292	obj.model_list_box = copy.deepcopy(self.model_list_box)
293	obj.engine_type = copy.deepcopy(self.engine_type)
294
295	obj.categorycombobox = self.categorycombobox
296	obj.formfactorcombobox = self.formfactorcombobox
297	obj.structurecombobox = self.structurecombobox
298
299	#obj.shape_rbutton = self.shape_rbutton
300	#obj.shape_indep_rbutton = self.shape_indep_rbutton
301	#obj.struct_rbutton = self.struct_rbutton
302	#obj.plugin_rbutton = self.plugin_rbutton
303
304	obj.manager = self.manager
305	obj.event_owner = self.event_owner
306	obj.disp_list = copy.deepcopy(self.disp_list)
307
308	obj.enable2D = copy.deepcopy(self.enable2D)
309	obj.parameters = copy.deepcopy(self.parameters)
310	obj.str_parameters = copy.deepcopy(self.str_parameters)
311	obj.fixed_param = copy.deepcopy(self.fixed_param)
312	obj.fittable_param = copy.deepcopy(self.fittable_param)
313	obj.orientation_params = copy.deepcopy(self.orientation_params)
314	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
315	obj.enable_disp = copy.deepcopy(self.enable_disp)
316	obj.disable_disp = copy.deepcopy(self.disable_disp)
317	obj.tcChi = self.tcChi
318
319	if len(self._disp_obj_dict) > 0:
320	for k, v in self._disp_obj_dict.iteritems():
321	obj._disp_obj_dict[k] = v
322	if len(self.disp_cb_dict) > 0:
323	for k, v in self.disp_cb_dict.iteritems():
324	obj.disp_cb_dict[k] = v
325	if len(self.values) > 0:
326	for k, v in self.values.iteritems():
327	obj.values[k] = v
328	if len(self.weights) > 0:
329	for k, v in self.weights.iteritems():
330	obj.weights[k] = v
331	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
332	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
333	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
334	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
335	obj.smear_type = copy.deepcopy(self.smear_type)
336	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
337	obj.dI_didata = copy.deepcopy(self.dI_didata)
338	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
339	obj.dI_idata = copy.deepcopy(self.dI_idata)
340	obj.dq_l = copy.deepcopy(self.dq_l)
341	obj.dq_r = copy.deepcopy(self.dq_r)
342	obj.dx_max = copy.deepcopy(self.dx_max)
343	obj.dx_min = copy.deepcopy(self.dx_min)
344	obj.dxl = copy.deepcopy(self.dxl)
345	obj.dxw = copy.deepcopy(self.dxw)
346	obj.disp_box = copy.deepcopy(self.disp_box)
347	obj.qmin = copy.deepcopy(self.qmin)
348	obj.qmax = copy.deepcopy(self.qmax)
349	obj.multi_factor = self.multi_factor
350	obj.magnetic_on = self.magnetic_on
351	obj.npts = copy.deepcopy(self.npts)
352	obj.cb1 = copy.deepcopy(self.cb1)
353	obj.smearer = copy.deepcopy(self.smearer)
354
355	for name, state in self.saved_states.iteritems():
356	copy_name = copy.deepcopy(name)
357	copy_state = state.clone()
358	obj.saved_states[copy_name] = copy_state
359	return obj
360
361	def _repr_helper(self, list, rep):
362	"""
363	Helper method to print a state
364	"""
365	for item in list:
366	rep += "parameter name: %s \n" % str(item[1])
367	rep += "value: %s\n" % str(item[2])
368	rep += "selected: %s\n" % str(item[0])
369	rep += "error displayed : %s \n" % str(item[4][0])
370	rep += "error value:%s \n" % str(item[4][1])
371	rep += "minimum displayed : %s \n" % str(item[5][0])
372	rep += "minimum value : %s \n" % str(item[5][1])
373	rep += "maximum displayed : %s \n" % str(item[6][0])
374	rep += "maximum value : %s \n" % str(item[6][1])
375	rep += "parameter unit: %s\n\n" % str(item[7])
376	return rep
377
378	def __repr__(self):
379	"""
380	output string for printing
381	"""
382	rep = "\nState name: %s\n" % self.file
383	t = time.localtime(self.timestamp)
384	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
385
386	rep += "State created: %s\n" % time_str
387	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
388	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
389	rep += "is data : %s\n" % self.is_data
390	rep += "data's name : %s\n" % self.data_name
391	rep += "data's id : %s\n" % self.data_id
392	if self.model != None:
393	m_name = self.model.__class__.__name__
394	if m_name == 'Model':
395	m_name = self.m_name
396	rep += "model name : %s\n" % m_name
397	else:
398	rep += "model name : None\n"
399	#rep += "model type (form factor) selected: %s\n" % self.shape_rbutton
400	rep += "multi_factor : %s\n" % str(self.multi_factor)
401	rep += "magnetic_on : %s\n"% str(self.magnetic_on)
402	rep += "model type (Category) selected: %s\n" % self.categorycombobox
403	#rep += "model type (shape independent) selected: %s\n" % self.shape_indep_rbutton
404	#rep += "model type (structure factor) selected: %s\n" % self.struct_rbutton
405	#rep += "model type (plug-in ) selected: %s\n" % self.plugin_rbutton
406	rep += "data : %s\n" % str(self.data)
407	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
408	str(self.qmax), str(self.npts))
409	rep += "Dispersion selection : %s\n" % str(self.disp_box)
410	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
411	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
412	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
413	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
414	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
415	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
416	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
417
418	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
419	rep += "dI_didata : %s\n" % str(self.dI_didata)
420	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
421	rep += "dI_idata : %s\n" % str(self.dI_idata)
422
423	rep += "2D enable : %s\n" % str(self.enable2D)
424	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
425	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
426	rep += "Smear object : %s\n" % str(self.smearer)
427	rep += "Smear type : %s\n" % (self.smear_type)
428	rep += "dq_l : %s\n" % self.dq_l
429	rep += "dq_r : %s\n" % self.dq_r
430	rep += "dx_max : %s\n" % str(self.dx_max)
431	rep += "dx_min : %s\n" % str(self.dx_min)
432	rep += "dxl : %s\n" % str(self.dxl)
433	rep += "dxw : %s\n" % str(self.dxw)
434	rep += "model : %s\n\n" % str(self.model)
435	temp_parameters = []
436	temp_fittable_param = []
437	if self.data.__class__.__name__ == "Data2D":
438	self.is_2D = True
439	else:
440	self.is_2D = False
441	if self.data is not None:
442	if not self.is_2D:
443	for item in self.parameters:
444	if not item in self.orientation_params:
445	temp_parameters.append(item)
446	for item in self.fittable_param:
447	if not item in self.orientation_params_disp:
448	temp_fittable_param.append(item)
449	else:
450	temp_parameters = self.parameters
451	temp_fittable_param = self.fittable_param
452
453	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
454	rep = self._repr_helper(list=temp_parameters, rep=rep)
455	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
456	rep = self._repr_helper(list=self.str_parameters, rep=rep)
457	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
458	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
459	"""
460	if is_2D:
461	rep += "number orientation parameters"
462	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
463	rep = self._repr_helper( list=self.orientation_params, rep=rep)
464	rep += "number dispersity parameters"
465	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
466	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
467	"""
468	return rep
469
470	def set_report_string(self):
471	"""
472	Get the values (strings) from __str__ for report
473	"""
474	# Dictionary of the report strings
475	repo_time = ""
476	model_name = ""
477	title = ""
478	title_name = ""
479	file_name = ""
480	param_string = ""
481	paramval_string = ""
482	chi2_string = ""
483	multi_factor_string = ""
484	q_range = ""
485	strings = self.__repr__()
486	lines = strings.split('\n')
487
488	# get all string values from __str__()
489	for line in lines:
490	value = ""
491	content = line.split(":")
492	name = content[0]
493	try:
494	value = content[1]
495	except:
496	pass
497	if name.count("State created"):
498	repo_time = "" + value
499	if name.count("parameter name"):
500	val_name = value.split(".")
501	if len(val_name) > 1:
502	if val_name[1].count("width"):
503	param_string += value + ','
504	else:
505	continue
506	else:
507	param_string += value + ','
508	if name == "value":
509	param_string += value + ','
510	if name == "selected":
511	if value == u' False':
512	fixed_parameter = True
513	else:
514	fixed_parameter = False
515	if name == "error value":
516	if fixed_parameter:
517	param_string += '(fixed),'
518	else:
519	param_string += value + ','
520	if name == "parameter unit":
521	param_string += value + ':'
522	if name == "Value of Chisqr ":
523	chi2 = ("Chi2/Npts = " + value)
524	chi2_string = CENTRE % chi2
525	if name == "multi_factor ":
526	muti_factor = ("muti_factor = " + value)
527	muti_factor_string = CENTRE % muti_factor
528	if name == "magentic_on ":
529	magentic_on = ("magentic_on = " + value)
530	if string(value) == 'True':
531	magentic_on_string = CENTRE % magentic_on
532	if name == "Title":
533	if len(value.strip()) == 0:
534	continue
535	title = value + " [" + repo_time + "]"
536	title_name = HEADER % title
537	if name == "data ":
538	try:
539	file = ("File name:" + content[2])
540	file_name = CENTRE % file
541	if len(title) == 0:
542	title = content[2] + " [" + repo_time + "]"
543	title_name = HEADER % title
544	except:
545	pass
546	if name == "model name ":
547	try:
548	modelname = "Model name:" + content[1]
549	except:
550	modelname = "Model name:" + " NAN"
551	model_name = CENTRE % modelname
552
553	if name == "Plotting Range":
554	try:
555	q_range = content[1] + " = " + content[2] \
556	+ " = " + content[3].split(",")[0]
557	q_name = ("Q Range: " + q_range)
558	q_range = CENTRE % q_name
559	except:
560	pass
561	paramval = ""
562	for lines in param_string.split(":"):
563	line = lines.split(",")
564	if len(lines) > 0:
565	param = line[0]
566	param += " = " + line[1]
567	if len(line[2].split()) > 0 and not line[2].count("None"):
568	param += " +- " + line[2]
569	if len(line[3].split()) > 0 and not line[3].count("None"):
570	param += " " + line[3]
571	if not paramval.count(param):
572	paramval += param + "\n"
573	paramval_string += CENTRE % param + "\n"
574
575	text_string = "\n\n\n" + title + "\n\n" + file + \
576	"\n" + q_name + \
577	"\n" + chi2 + \
578	"\n\n" + paramval
579
580	title_name = self._check_html_format(title_name)
581	file_name = self._check_html_format(file_name)
582	title = self._check_html_format(title)
583
584	html_string = title_name + "\n" + file_name + \
585	"\n" + model_name + \
586	"\n" + q_range + \
587	"\n" + chi2_string + \
588	"\n" + ELINE + \
589	"\n" + paramval_string + \
590	"\n" + ELINE + \
591	"\n" + FEET_1 % title + \
592	"\n" + FEET_2
593
594	return html_string, text_string, title
595
596	def _check_html_format(self, name):
597	"""
598	Check string '%' for html format
599	"""
600	if name.count('%'):
601	name = name.replace('%', '&#37')
602
603	return name
604
605	def report(self, figs=None, canvases=None):
606	"""
607	Invoke report dialog panel
608
609	: param figs: list of pylab figures [list]
610	"""
611	from sas.perspectives.fitting.report_dialog import ReportDialog
612	# get the strings for report
613	html_str, text_str, title = self.set_report_string()
614	# Allow 2 figures to append
615	if len(figs) == 1:
616	add_str = FEET_3
617	elif len(figs) == 2:
618	add_str = ELINE
619	add_str += FEET_2 % ("%s")
620	add_str += ELINE
621	add_str += FEET_3
622	elif len(figs) > 2:
623	add_str = ELINE
624	add_str += FEET_2 % ("%s")
625	add_str += ELINE
626	add_str += FEET_2 % ("%s")
627	add_str += ELINE
628	add_str += FEET_3
629	else:
630	add_str = ""
631
632	# final report html strings
633	report_str = html_str % ("%s") + add_str
634
635	# make plot image
636	images = self.set_plot_state(figs, canvases)
637	report_list = [report_str, text_str, images]
638	dialog = ReportDialog(report_list, None, -1, "")
639	dialog.ShowModal()
640
641	def _toXML_helper(self, thelist, element, newdoc):
642	"""
643	Helper method to create xml file for saving state
644	"""
645	for item in thelist:
646	sub_element = newdoc.createElement('parameter')
647	sub_element.setAttribute('name', str(item[1]))
648	sub_element.setAttribute('value', str(item[2]))
649	sub_element.setAttribute('selected_to_fit', str(item[0]))
650	sub_element.setAttribute('error_displayed', str(item[4][0]))
651	sub_element.setAttribute('error_value', str(item[4][1]))
652	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
653	sub_element.setAttribute('minimum_value', str(item[5][1]))
654	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
655	sub_element.setAttribute('maximum_value', str(item[6][1]))
656	sub_element.setAttribute('unit', str(item[7]))
657	element.appendChild(sub_element)
658
659	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
660	"""
661	Writes the state of the InversionControl panel to file, as XML.
662
663	Compatible with standalone writing, or appending to an
664	already existing XML document. In that case, the XML document
665	is required. An optional entry node in the XML document may also be given.
666
667	:param file: file to write to
668	:param doc: XML document object [optional]
669	:param entry_node: XML node within the XML document at which we will append the data [optional]
670
671	"""
672	from xml.dom.minidom import getDOMImplementation
673
674	# Check whether we have to write a standalone XML file
675	if doc is None:
676	impl = getDOMImplementation()
677	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
678	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
679	top_element = newdoc.documentElement
680	else:
681	# We are appending to an existing document
682	newdoc = doc
683	try:
684	top_element = newdoc.createElement(FITTING_NODE_NAME)
685	except:
686	string = etree.tostring(doc, pretty_print=True)
687	newdoc = parseString(string)
688	top_element = newdoc.createElement(FITTING_NODE_NAME)
689	if entry_node is None:
690	newdoc.documentElement.appendChild(top_element)
691	else:
692	try:
693	entry_node.appendChild(top_element)
694	except:
695	node_name = entry_node.tag
696	node_list = newdoc.getElementsByTagName(node_name)
697	entry_node = node_list.item(0)
698	entry_node.appendChild(top_element)
699
700	attr = newdoc.createAttribute("version")
701	attr.nodeValue = '1.0'
702	top_element.setAttributeNode(attr)
703
704	# File name
705	element = newdoc.createElement("filename")
706	if self.file is not None:
707	element.appendChild(newdoc.createTextNode(str(self.file)))
708	else:
709	element.appendChild(newdoc.createTextNode(str(file)))
710	top_element.appendChild(element)
711
712	element = newdoc.createElement("timestamp")
713	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
714	attr = newdoc.createAttribute("epoch")
715	attr.nodeValue = str(self.timestamp)
716	element.setAttributeNode(attr)
717	top_element.appendChild(element)
718	# Inputs
719	inputs = newdoc.createElement("Attributes")
720	top_element.appendChild(inputs)
721
722	if self.data is not None and hasattr(self.data, "group_id"):
723	self.data_group_id = self.data.group_id
724	if self.data is not None and hasattr(self.data, "is_data"):
725	self.is_data = self.data.is_data
726	if self.data is not None:
727	self.data_name = self.data.name
728	if self.data is not None and hasattr(self.data, "id"):
729	self.data_id = self.data.id
730
731	for item in list_of_data_attributes:
732	element = newdoc.createElement(item[0])
733	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
734	inputs.appendChild(element)
735
736	for item in list_of_state_attributes:
737	element = newdoc.createElement(item[0])
738	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
739	inputs.appendChild(element)
740
741	# For self.values ={ disp_param_name: [vals,...],...}
742	# and for self.weights ={ disp_param_name: [weights,...],...}
743	list = {}
744	for item in list_of_model_attributes:
745	element = newdoc.createElement(item[0])
746	exec "list = self.%s" % item[1]
747	for key, value in list.iteritems():
748	sub_element = newdoc.createElement(key)
749	sub_element.setAttribute('name', str(key))
750	for val in value:
751	com = "sub_element.appendChild"
752	com += "(newdoc.createTextNode(str(%s)))"
753	exec com % val
754
755	element.appendChild(sub_element)
756	inputs.appendChild(element)
757
758	# Create doc for the dictionary of self._disp_obj_dic
759	for item in list_of_obj_dic:
760	element = newdoc.createElement(item[0])
761	exec "list = self.%s" % item[1]
762	for key, val in list.iteritems():
763	value = repr(val)
764	sub_element = newdoc.createElement(key)
765	sub_element.setAttribute('name', str(key))
766	sub_element.setAttribute('value', str(value))
767	element.appendChild(sub_element)
768	inputs.appendChild(element)
769
770	for item in list_of_state_parameters:
771	element = newdoc.createElement(item[0])
772	com = "self._toXML_helper(thelist=self.%s,"
773	com += " element=element, newdoc=newdoc)"
774	exec com % item[1]
775	inputs.appendChild(element)
776
777	# Save the file
778	if doc is None:
779	fd = open(file, 'w')
780	fd.write(newdoc.toprettyxml())
781	fd.close()
782	return None
783	else:
784	return newdoc
785
786	def _fromXML_helper(self, node, list):
787	"""
788	Helper function to write state to xml
789	"""
790	for item in node:
791	try:
792	name = item.get('name')
793	except:
794	name = None
795	try:
796	value = item.get('value')
797	except:
798	value = None
799	try:
800	selected_to_fit = (item.get('selected_to_fit') == "True")
801	except:
802	selected_to_fit = None
803	try:
804	error_displayed = (item.get('error_displayed') == "True")
805	except:
806	error_displayed = None
807	try:
808	error_value = item.get('error_value')
809	except:
810	error_value = None
811	try:
812	minimum_displayed = (item.get('minimum_displayed') == "True")
813	except:
814	minimum_displayed = None
815	try:
816	minimum_value = item.get('minimum_value')
817	except:
818	minimum_value = None
819	try:
820	maximum_displayed = (item.get('maximum_displayed') == "True")
821	except:
822	maximum_displayed = None
823	try:
824	maximum_value = item.get('maximum_value')
825	except:
826	maximum_value = None
827	try:
828	unit = item.get('unit')
829	except:
830	unit = None
831	list.append([selected_to_fit, name, value, "+/-",
832	[error_displayed, error_value],
833	[minimum_displayed, minimum_value],
834	[maximum_displayed, maximum_value], unit])
835
836	def fromXML(self, file=None, node=None):
837	"""
838	Load fitting state from a file
839
840	:param file: .fitv file
841	:param node: node of a XML document to read from
842
843	"""
844	if file is not None:
845	msg = "PageState no longer supports non-CanSAS"
846	msg += " format for fitting files"
847	raise RuntimeError, msg
848
849	if node.get('version')and node.get('version') == '1.0':
850
851	# Get file name
852	entry = get_content('ns:filename', node)
853	if entry is not None:
854	self.file = entry.text.strip()
855
856	# Get time stamp
857	entry = get_content('ns:timestamp', node)
858	if entry is not None and entry.get('epoch'):
859	try:
860	self.timestamp = float(entry.get('epoch'))
861	except:
862	msg = "PageState.fromXML: Could not"
863	msg += " read timestamp\n %s" % sys.exc_value
864	logging.error(msg)
865
866	# Parse fitting attributes
867	entry = get_content('ns:Attributes', node)
868	for item in list_of_data_attributes:
869	node = get_content('ns:%s' % item[0], entry)
870	try:
871	exec "self.%s = parse_entry_helper(node, item)" % item[0]
872
873	except:
874	raise
875
876	if entry is not None:
877
878	for item in list_of_state_attributes:
879	node = get_content('ns:%s' % item[0], entry)
880	try:
881	exec "self.%s = parse_entry_helper(node, item)" % \
882	str(item[0])
883	except:
884	raise
885
886	for item in list_of_state_parameters:
887	node = get_content("ns:%s" % item[0], entry)
888	exec "self._fromXML_helper(node=node, list=self.%s)" % \
889	item[1]
890
891	# Recover _disp_obj_dict from xml file
892	self._disp_obj_dict = {}
893	disp_model = None
894	for item in list_of_obj_dic:
895	# Get node
896	node = get_content("ns:%s" % item[0], entry)
897	for attr in node:
898	name = attr.get('name')
899	val = attr.get('value')
900	value = val.split(" instance")[0]
901	disp_name = value.split("<")[1]
902	try:
903	# Try to recover disp_model object from strings
904	com = "from sas.models.dispersion_models "
905	com += "import %s as disp"
906	com_name = disp_name.split(".")[3]
907	exec com % com_name
908	disp_model = disp()
909	exec "self.%s['%s'] = com_name" % (item[1], name)
910	except:
911	pass
912
913	# get self.values and self.weights dic. if exists
914	for item in list_of_model_attributes:
915	node = get_content("ns:%s" % item[0], entry)
916	dic = {}
917	list = []
918	for par in node:
919	name = par.get('name')
920	values = par.text.split('\n')
921	# Get lines only with numbers
922	for line in values:
923	try:
924	val = float(line)
925	list.append(val)
926	except:
927	# pass if line is empty (it happens)
928	pass
929	dic[name] = numpy.array(list)
930	exec "self.%s = dic" % item[1]
931
932	def set_plot_state(self, figs, canvases):
933	"""
934	Build image state that wx.html understand
935	by plotting, putting it into wx.FileSystem image object
936
937	"""
938	images = []
939	# some imports
940	import wx
941
942	# Reset memory
943	self.imgRAM = None
944	wx.MemoryFSHandler()
945
946	# For no figures in the list, prepare empty plot
947	if figs == None or len(figs) == 0:
948	figs = [None]
949
950	# Loop over the list of figures
951	# use wx.MemoryFSHandler
952	self.imgRAM = wx.MemoryFSHandler()
953	for fig in figs:
954	if figs != None:
955	ind = figs.index(fig)
956	canvas = canvases[ind]
957
958	#store the image in wx.FileSystem Object
959	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
960
961	# index of the fig
962	ind = figs.index(fig)
963
964	#AddFile, image can be retrieved with 'memory:filename'
965	self.imgRAM.AddFile('img_fit%s.png' % ind,
966	canvas.bitmap, wx.BITMAP_TYPE_PNG)
967
968	#append figs
969	images.append(fig)
970
971	return images
972
973
974	class Reader(CansasReader):
975	"""
976	Class to load a .fitv fitting file
977	"""
978	## File type
979	type_name = "Fitting"
980
981	## Wildcards
982	type = ["Fitting files (.fitv)\|.fitv"
983	"SASView file (.svs)\|.svs"]
984	## List of allowed extensions
985	ext = ['.fitv', '.FITV', '.svs', 'SVS']
986
987	def __init__(self, call_back=None, cansas=True):
988	CansasReader.__init__(self)
989	"""
990	Initialize the call-back method to be called
991	after we load a file
992
993	:param call_back: call-back method
994	:param cansas: True = files will be written/read in CanSAS format
995	False = write CanSAS format
996
997	"""
998	## Call back method to be executed after a file is read
999	self.call_back = call_back
1000	## CanSAS format flag
1001	self.cansas = cansas
1002	self.state = None
1003
1004	def get_state(self):
1005	return self.state
1006
1007	def read(self, path):
1008	"""
1009	Load a new P(r) inversion state from file
1010
1011	:param path: file path
1012
1013	"""
1014	if self.cansas == True:
1015	return self._read_cansas(path)
1016
1017	def _data2d_to_xml_doc(self, datainfo):
1018	"""
1019	Create an XML document to contain the content of a Data2D
1020
1021	:param datainfo: Data2D object
1022
1023	"""
1024	if not issubclass(datainfo.__class__, Data2D):
1025	raise RuntimeError, "The cansas writer expects a Data2D instance"
1026
1027	doc = xml.dom.minidom.Document()
1028	main_node = doc.createElement("SASroot")
1029	main_node.setAttribute("version", self.version)
1030	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
1031	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
1032	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
1033
1034	doc.appendChild(main_node)
1035
1036	entry_node = doc.createElement("SASentry")
1037	main_node.appendChild(entry_node)
1038
1039	write_node(doc, entry_node, "Title", datainfo.title)
1040	if datainfo is not None:
1041	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
1042	for item in datainfo.run:
1043	runname = {}
1044	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
1045	runname = {'name': datainfo.run_name[item] }
1046	write_node(doc, entry_node, "Run", item, runname)
1047	# Data info
1048	new_node = doc.createElement("SASdata")
1049	entry_node.appendChild(new_node)
1050	for item in list_of_data_2d_attr:
1051	element = doc.createElement(item[0])
1052	exec "element.setAttribute(item[0], str(datainfo.%s))" % (item[1])
1053	new_node.appendChild(element)
1054
1055	for item in list_of_data2d_values:
1056	root_node = doc.createElement(item[0])
1057	new_node.appendChild(root_node)
1058	temp_list = None
1059	exec "temp_list = datainfo.%s" % item[1]
1060
1061	if temp_list is None or len(temp_list)== 0:
1062	element = doc.createElement(item[0])
1063	exec "element.appendChild(doc.createTextNode(str(%s)))" % temp_list
1064	root_node.appendChild(element)
1065	else:
1066	for value in temp_list:
1067	element = doc.createElement(item[0])
1068	exec "element.setAttribute(item[0], str(%s))" % value
1069	root_node.appendChild(element)
1070
1071	# Sample info
1072	sample = doc.createElement("SASsample")
1073	if datainfo.sample.name is not None:
1074	sample.setAttribute("name", str(datainfo.sample.name))
1075	entry_node.appendChild(sample)
1076	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1077	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1078	{"unit": datainfo.sample.thickness_unit})
1079	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1080	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1081	{"unit": datainfo.sample.temperature_unit})
1082
1083	for item in datainfo.sample.details:
1084	write_node(doc, sample, "details", item)
1085
1086	pos = doc.createElement("position")
1087	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1088	{"unit": datainfo.sample.position_unit})
1089	written = written \| write_node(doc, pos, "y",
1090	datainfo.sample.position.y,
1091	{"unit": datainfo.sample.position_unit})
1092	written = written \| write_node(doc, pos, "z",
1093	datainfo.sample.position.z,
1094	{"unit": datainfo.sample.position_unit})
1095	if written == True:
1096	sample.appendChild(pos)
1097
1098	ori = doc.createElement("orientation")
1099	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1100	{"unit": datainfo.sample.orientation_unit})
1101	written = written \| write_node(doc, ori, "pitch",
1102	datainfo.sample.orientation.y,
1103	{"unit": datainfo.sample.orientation_unit})
1104	written = written \| write_node(doc, ori, "yaw",
1105	datainfo.sample.orientation.z,
1106	{"unit": datainfo.sample.orientation_unit})
1107	if written == True:
1108	sample.appendChild(ori)
1109
1110	# Instrument info
1111	instr = doc.createElement("SASinstrument")
1112	entry_node.appendChild(instr)
1113
1114	write_node(doc, instr, "name", datainfo.instrument)
1115
1116	# Source
1117	source = doc.createElement("SASsource")
1118	if datainfo.source.name is not None:
1119	source.setAttribute("name", str(datainfo.source.name))
1120	instr.appendChild(source)
1121
1122	write_node(doc, source, "radiation", datainfo.source.radiation)
1123	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1124	size = doc.createElement("beam_size")
1125	if datainfo.source.beam_size_name is not None:
1126	size.setAttribute("name", str(datainfo.source.beam_size_name))
1127	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1128	{"unit": datainfo.source.beam_size_unit})
1129	written = written \| write_node(doc, size, "y",
1130	datainfo.source.beam_size.y,
1131	{"unit": datainfo.source.beam_size_unit})
1132	written = written \| write_node(doc, size, "z",
1133	datainfo.source.beam_size.z,
1134	{"unit": datainfo.source.beam_size_unit})
1135	if written == True:
1136	source.appendChild(size)
1137
1138	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1139	{"unit": datainfo.source.wavelength_unit})
1140	write_node(doc, source, "wavelength_min",
1141	datainfo.source.wavelength_min,
1142	{"unit": datainfo.source.wavelength_min_unit})
1143	write_node(doc, source, "wavelength_max",
1144	datainfo.source.wavelength_max,
1145	{"unit": datainfo.source.wavelength_max_unit})
1146	write_node(doc, source, "wavelength_spread",
1147	datainfo.source.wavelength_spread,
1148	{"unit": datainfo.source.wavelength_spread_unit})
1149
1150	# Collimation
1151	for item in datainfo.collimation:
1152	coll = doc.createElement("SAScollimation")
1153	if item.name is not None:
1154	coll.setAttribute("name", str(item.name))
1155	instr.appendChild(coll)
1156
1157	write_node(doc, coll, "length", item.length,
1158	{"unit": item.length_unit})
1159
1160	for apert in item.aperture:
1161	ap = doc.createElement("aperture")
1162	if apert.name is not None:
1163	ap.setAttribute("name", str(apert.name))
1164	if apert.type is not None:
1165	ap.setAttribute("type", str(apert.type))
1166	coll.appendChild(ap)
1167
1168	write_node(doc, ap, "distance", apert.distance,
1169	{"unit": apert.distance_unit})
1170
1171	size = doc.createElement("size")
1172	if apert.size_name is not None:
1173	size.setAttribute("name", str(apert.size_name))
1174	written = write_node(doc, size, "x", apert.size.x,
1175	{"unit": apert.size_unit})
1176	written = written \| write_node(doc, size, "y", apert.size.y,
1177	{"unit": apert.size_unit})
1178	written = written \| write_node(doc, size, "z", apert.size.z,
1179	{"unit": apert.size_unit})
1180	if written == True:
1181	ap.appendChild(size)
1182
1183	# Detectors
1184	for item in datainfo.detector:
1185	det = doc.createElement("SASdetector")
1186	written = write_node(doc, det, "name", item.name)
1187	written = written \| write_node(doc, det, "SDD", item.distance,
1188	{"unit": item.distance_unit})
1189	written = written \| write_node(doc, det, "slit_length",
1190	item.slit_length,
1191	{"unit": item.slit_length_unit})
1192	if written == True:
1193	instr.appendChild(det)
1194
1195	off = doc.createElement("offset")
1196	written = write_node(doc, off, "x", item.offset.x,
1197	{"unit": item.offset_unit})
1198	written = written \| write_node(doc, off, "y", item.offset.y,
1199	{"unit": item.offset_unit})
1200	written = written \| write_node(doc, off, "z", item.offset.z,
1201	{"unit": item.offset_unit})
1202	if written == True:
1203	det.appendChild(off)
1204
1205	center = doc.createElement("beam_center")
1206	written = write_node(doc, center, "x", item.beam_center.x,
1207	{"unit": item.beam_center_unit})
1208	written = written \| write_node(doc, center, "y",
1209	item.beam_center.y,
1210	{"unit": item.beam_center_unit})
1211	written = written \| write_node(doc, center, "z",
1212	item.beam_center.z,
1213	{"unit": item.beam_center_unit})
1214	if written == True:
1215	det.appendChild(center)
1216
1217	pix = doc.createElement("pixel_size")
1218	written = write_node(doc, pix, "x", item.pixel_size.x,
1219	{"unit": item.pixel_size_unit})
1220	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1221	{"unit": item.pixel_size_unit})
1222	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1223	{"unit": item.pixel_size_unit})
1224	if written == True:
1225	det.appendChild(pix)
1226
1227	ori = doc.createElement("orientation")
1228	written = write_node(doc, ori, "roll", item.orientation.x,
1229	{"unit": item.orientation_unit})
1230	written = written \| write_node(doc, ori, "pitch",
1231	item.orientation.y,
1232	{"unit": item.orientation_unit})
1233	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1234	{"unit": item.orientation_unit})
1235	if written == True:
1236	det.appendChild(ori)
1237
1238	# Processes info
1239	for item in datainfo.process:
1240	node = doc.createElement("SASprocess")
1241	entry_node.appendChild(node)
1242
1243	write_node(doc, node, "name", item.name)
1244	write_node(doc, node, "date", item.date)
1245	write_node(doc, node, "description", item.description)
1246	for term in item.term:
1247	value = term['value']
1248	del term['value']
1249	write_node(doc, node, "term", value, term)
1250	for note in item.notes:
1251	write_node(doc, node, "SASprocessnote", note)
1252	# Return the document, and the SASentry node associated with
1253	# the data we just wrote
1254	return doc, entry_node
1255
1256	def _parse_state(self, entry):
1257	"""
1258	Read a fit result from an XML node
1259
1260	:param entry: XML node to read from
1261
1262	:return: PageState object
1263	"""
1264	# Create an empty state
1265	state = None
1266	# Locate the P(r) node
1267	try:
1268	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1269	namespaces={'ns': CANSAS_NS})
1270	if nodes != []:
1271	# Create an empty state
1272	state = PageState()
1273	state.fromXML(node=nodes[0])
1274
1275	except:
1276	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1277
1278	return state
1279
1280	def _parse_save_state_entry(self, dom):
1281	"""
1282	Parse a SASentry
1283
1284	:param node: SASentry node
1285
1286	:return: Data1D/Data2D object
1287
1288	"""
1289	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1290	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1291	return_value, _ = self._parse_entry(dom)
1292	numpy.trim_zeros(return_value.x)
1293	numpy.trim_zeros(return_value.y)
1294	numpy.trim_zeros(return_value.dy)
1295	size_dx = return_value.dx.size
1296	size_dxl = return_value.dxl.size
1297	size_dxw = return_value.dxw.size
1298	if size_dxl == 0 and size_dxw == 0:
1299	return_value.dxl = None
1300	return_value.dxw = None
1301	numpy.trim_zeros(return_value.dx)
1302	elif size_dx == 0:
1303	return_value.dx = None
1304	size_dx = size_dxl
1305	numpy.trim_zeros(return_value.dxl)
1306	numpy.trim_zeros(return_value.dxw)
1307
1308	return return_value, _
1309
1310	#Parse 2D
1311	data_info = Data2D()
1312
1313	# Look up title
1314	self._store_content('ns:Title', dom, 'title', data_info)
1315
1316	# Look up run number
1317	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1318	for item in nodes:
1319	if item.text is not None:
1320	value = item.text.strip()
1321	if len(value) > 0:
1322	data_info.run.append(value)
1323	if item.get('name') is not None:
1324	data_info.run_name[value] = item.get('name')
1325
1326	# Look up instrument name
1327	self._store_content('ns:SASinstrument/ns:name', dom,
1328	'instrument', data_info)
1329
1330	# Notes
1331	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1332	for note in note_list:
1333	try:
1334	if note.text is not None:
1335	note_value = note.text.strip()
1336	if len(note_value) > 0:
1337	data_info.notes.append(note_value)
1338	except:
1339	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1340	self.errors.append(err_mess)
1341	logging.error(err_mess)
1342
1343	# Sample info ###################
1344	entry = get_content('ns:SASsample', dom)
1345	if entry is not None:
1346	data_info.sample.name = entry.get('name')
1347
1348	self._store_content('ns:SASsample/ns:ID',
1349	dom, 'ID', data_info.sample)
1350	self._store_float('ns:SASsample/ns:thickness',
1351	dom, 'thickness', data_info.sample)
1352	self._store_float('ns:SASsample/ns:transmission',
1353	dom, 'transmission', data_info.sample)
1354	self._store_float('ns:SASsample/ns:temperature',
1355	dom, 'temperature', data_info.sample)
1356
1357	nodes = dom.xpath('ns:SASsample/ns:details',
1358	namespaces={'ns': CANSAS_NS})
1359	for item in nodes:
1360	try:
1361	if item.text is not None:
1362	detail_value = item.text.strip()
1363	if len(detail_value) > 0:
1364	data_info.sample.details.append(detail_value)
1365	except:
1366	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1367	self.errors.append(err_mess)
1368	logging.error(err_mess)
1369
1370	# Position (as a vector)
1371	self._store_float('ns:SASsample/ns:position/ns:x',
1372	dom, 'position.x', data_info.sample)
1373	self._store_float('ns:SASsample/ns:position/ns:y',
1374	dom, 'position.y', data_info.sample)
1375	self._store_float('ns:SASsample/ns:position/ns:z',
1376	dom, 'position.z', data_info.sample)
1377
1378	# Orientation (as a vector)
1379	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1380	dom, 'orientation.x', data_info.sample)
1381	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1382	dom, 'orientation.y', data_info.sample)
1383	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1384	dom, 'orientation.z', data_info.sample)
1385
1386	# Source info ###################
1387	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1388	if entry is not None:
1389	data_info.source.name = entry.get('name')
1390
1391	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1392	dom, 'radiation', data_info.source)
1393	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1394	dom, 'beam_shape', data_info.source)
1395	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1396	dom, 'wavelength', data_info.source)
1397	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1398	dom, 'wavelength_min', data_info.source)
1399	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1400	dom, 'wavelength_max', data_info.source)
1401	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1402	dom, 'wavelength_spread', data_info.source)
1403
1404	# Beam size (as a vector)
1405	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1406	if entry is not None:
1407	data_info.source.beam_size_name = entry.get('name')
1408
1409	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1410	dom, 'beam_size.x', data_info.source)
1411	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1412	dom, 'beam_size.y', data_info.source)
1413	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1414	dom, 'beam_size.z', data_info.source)
1415
1416	# Collimation info ###################
1417	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1418	namespaces={'ns': CANSAS_NS})
1419	for item in nodes:
1420	collim = Collimation()
1421	if item.get('name') is not None:
1422	collim.name = item.get('name')
1423	self._store_float('ns:length', item, 'length', collim)
1424
1425	# Look for apertures
1426	apert_list = item.xpath('ns:aperture',
1427	namespaces={'ns': CANSAS_NS})
1428	for apert in apert_list:
1429	aperture = Aperture()
1430
1431	# Get the name and type of the aperture
1432	aperture.name = apert.get('name')
1433	aperture.type = apert.get('type')
1434
1435	self._store_float('ns:distance', apert, 'distance', aperture)
1436
1437	entry = get_content('ns:size', apert)
1438	if entry is not None:
1439	aperture.size_name = entry.get('name')
1440
1441	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1442	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1443	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1444
1445	collim.aperture.append(aperture)
1446
1447	data_info.collimation.append(collim)
1448
1449	# Detector info ######################
1450	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1451	namespaces={'ns': CANSAS_NS})
1452	for item in nodes:
1453
1454	detector = Detector()
1455
1456	self._store_content('ns:name', item, 'name', detector)
1457	self._store_float('ns:SDD', item, 'distance', detector)
1458
1459	# Detector offset (as a vector)
1460	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1461	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1462	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1463
1464	# Detector orientation (as a vector)
1465	self._store_float('ns:orientation/ns:roll', item,
1466	'orientation.x', detector)
1467	self._store_float('ns:orientation/ns:pitch', item,
1468	'orientation.y', detector)
1469	self._store_float('ns:orientation/ns:yaw', item,
1470	'orientation.z', detector)
1471
1472	# Beam center (as a vector)
1473	self._store_float('ns:beam_center/ns:x', item,
1474	'beam_center.x', detector)
1475	self._store_float('ns:beam_center/ns:y', item,
1476	'beam_center.y', detector)
1477	self._store_float('ns:beam_center/ns:z', item,
1478	'beam_center.z', detector)
1479
1480	# Pixel size (as a vector)
1481	self._store_float('ns:pixel_size/ns:x', item,
1482	'pixel_size.x', detector)
1483	self._store_float('ns:pixel_size/ns:y', item,
1484	'pixel_size.y', detector)
1485	self._store_float('ns:pixel_size/ns:z', item,
1486	'pixel_size.z', detector)
1487
1488	self._store_float('ns:slit_length', item, 'slit_length', detector)
1489
1490	data_info.detector.append(detector)
1491
1492	# Processes info ######################
1493	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1494	for item in nodes:
1495	process = Process()
1496	self._store_content('ns:name', item, 'name', process)
1497	self._store_content('ns:date', item, 'date', process)
1498	self._store_content('ns:description', item, 'description', process)
1499
1500	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1501	for term in term_list:
1502	try:
1503	term_attr = {}
1504	for attr in term.keys():
1505	term_attr[attr] = term.get(attr).strip()
1506	if term.text is not None:
1507	term_attr['value'] = term.text.strip()
1508	process.term.append(term_attr)
1509	except:
1510	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1511	self.errors.append(err_mess)
1512	logging.error(err_mess)
1513
1514	note_list = item.xpath('ns:SASprocessnote',
1515	namespaces={'ns': CANSAS_NS})
1516	for note in note_list:
1517	if note.text is not None:
1518	process.notes.append(note.text.strip())
1519
1520	data_info.process.append(process)
1521
1522	# Data info ######################
1523	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1524	if len(nodes) > 1:
1525	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1526
1527	for entry in nodes:
1528	for item in list_of_data_2d_attr:
1529	#get node
1530	node = get_content('ns:%s' % item[0], entry)
1531	exec "data_info.%s = parse_entry_helper(node, item)" % item[1]
1532
1533	for item in list_of_data2d_values:
1534	field = get_content('ns:%s' % item[0], entry)
1535	list = []
1536	if field is not None:
1537	list = [parse_entry_helper(node, item) for node in field]
1538	if len(list) < 2:
1539	exec "data_info.%s = None" % item[0]
1540	else:
1541	exec "data_info.%s = numpy.array(list)" % item[0]
1542
1543	return data_info
1544
1545	def _read_cansas(self, path):
1546	"""
1547	Load data and P(r) information from a CanSAS XML file.
1548
1549	:param path: file path
1550
1551	:return: Data1D object if a single SASentry was found,
1552	or a list of Data1D objects if multiple entries were found,
1553	or None of nothing was found
1554
1555	:raise RuntimeError: when the file can't be opened
1556	:raise ValueError: when the length of the data vectors are inconsistent
1557
1558	"""
1559	output = []
1560	basename = os.path.basename(path)
1561	root, extension = os.path.splitext(basename)
1562	ext = extension.lower()
1563	try:
1564	if os.path.isfile(path):
1565
1566	#TODO: eventually remove the check for .xml once
1567	# the P(r) writer/reader is truly complete.
1568	if ext in self.ext or \
1569	ext == '.xml':
1570
1571	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1572	# Check the format version number
1573	# Specifying the namespace will take care of the file format version
1574	root = tree.getroot()
1575	entry_list = root.xpath('ns:SASentry',
1576	namespaces={'ns': CANSAS_NS})
1577	for entry in entry_list:
1578	try:
1579	sas_entry, _ = self._parse_save_state_entry(entry)
1580	except:
1581	raise
1582	fitstate = self._parse_state(entry)
1583
1584	#state could be None when .svs file is loaded
1585	#in this case, skip appending to output
1586	if fitstate != None:
1587	sas_entry.meta_data['fitstate'] = fitstate
1588	sas_entry.filename = fitstate.file
1589	output.append(sas_entry)
1590	else:
1591	self.call_back(format=ext)
1592	raise RuntimeError, "%s is not a file" % path
1593
1594	# Return output consistent with the loader's api
1595	if len(output) == 0:
1596	self.call_back(state=None, datainfo=None, format=ext)
1597	return None
1598	else:
1599	for ind in range(len(output)):
1600	# Call back to post the new state
1601	state = output[ind].meta_data['fitstate']
1602	t = time.localtime(state.timestamp)
1603	time_str = time.strftime("%b %d %H:%M", t)
1604	# Check that no time stamp is already appended
1605	max_char = state.file.find("[")
1606	if max_char < 0:
1607	max_char = len(state.file)
1608	original_fname = state.file[0:max_char]
1609	state.file = original_fname + ' [' + time_str + ']'
1610
1611	if state is not None and state.is_data is not None:
1612	exec 'output[%d].is_data = state.is_data' % ind
1613
1614	output[ind].filename = state.file
1615	state.data = output[ind]
1616	state.data.name = output[ind].filename # state.data_name
1617	state.data.id = state.data_id
1618	if state.is_data is not None:
1619	state.data.is_data = state.is_data
1620	if output[ind].run_name is not None\
1621	and len(output[ind].run_name) != 0:
1622	name = output[ind].run_name
1623	else:
1624	name = original_fname
1625	state.data.group_id = name
1626	#store state in fitting
1627	self.call_back(state=state,
1628	datainfo=output[ind], format=ext)
1629	self.state = state
1630	return output
1631
1632	except:
1633	self.call_back(format=ext)
1634	#self.state= state
1635	raise
1636
1637	def write(self, filename, datainfo=None, fitstate=None):
1638	"""
1639	Write the content of a Data1D as a CanSAS XML file only for standalone
1640
1641	:param filename: name of the file to write
1642	:param datainfo: Data1D object
1643	:param fitstate: PageState object
1644
1645	"""
1646	# Sanity check
1647	if self.cansas == True:
1648	# Add fitting information to the XML document
1649	doc = self.write_toXML(datainfo, fitstate)
1650	# Write the XML document
1651	else:
1652	doc = fitstate.toXML(file=filename)
1653
1654	# Save the document no matter the type
1655	fd = open(filename, 'w')
1656	fd.write(doc.toprettyxml())
1657	fd.close()
1658
1659	def write_toXML(self, datainfo=None, state=None):
1660	"""
1661	Write toXML, a helper for write(),
1662	could be used by guimanager._on_save()
1663
1664	: return: xml doc
1665	"""
1666
1667	if state.data is None:
1668	data = sas.dataloader.data_info.Data1D(x=[], y=[])
1669	return None
1670	elif not state.data.is_data:
1671	return None
1672	else:
1673	#make sure title and data run is filled up.
1674	if state.data.title == None or state.data.title == '':
1675	state.data.title = state.data.name
1676	if state.data.run_name == None or state.data.run_name == {}:
1677	state.data.run = [str(state.data.name)]
1678	state.data.run_name[0] = state.data.name
1679
1680	if issubclass(state.data.__class__,
1681	sas.dataloader.data_info.Data1D):
1682	data = state.data
1683	doc, sasentry = self._to_xml_doc(data)
1684	else:
1685	data = state.data
1686	doc, sasentry = self._data2d_to_xml_doc(data)
1687
1688	if state is not None:
1689	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1690
1691	return doc
1692
1693	# Simple html report templet
1694	HEADER = "<html>\n"
1695	HEADER += "<head>\n"
1696	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1697	HEADER += "charset=windows-1252'> \n"
1698	HEADER += "<meta name=Generator >\n"
1699	HEADER += "</head>\n"
1700	HEADER += "<body lang=EN-US>\n"
1701	HEADER += "<div class=WordSection1>\n"
1702	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1703	HEADER += "%s</font></center></span></center></b></p>"
1704	HEADER += "<p class=MsoNormal> </p>"
1705	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1706	PARA += "</font></p>"
1707	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1708	CENTRE += "</font></center></p>"
1709	FEET_1 = \
1710	"""
1711	<p class=MsoNormal> </p>
1712	<br>
1713	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1714	</font></span></center></b></p>
1715	<p class=MsoNormal> </p>
1716	<center>
1717	<br><font size='4' >Model Computation</font>
1718	<br><font size='4' >Data: "%s"</font><br>
1719	"""
1720	FEET_2 = \
1721	"""
1722	<img src="%s" >
1723	</img>
1724	"""
1725	FEET_3 = \
1726	"""
1727	</center>
1728	</div>
1729	</body>
1730	</html>
1731	"""
1732	ELINE = "<p class=MsoNormal> </p>"
1733
1734	if __name__ == "__main__":
1735	state = PageState(parent=None)
1736	#state.toXML()
1737	"""
1738
1739	file = open("test_state", "w")
1740	pickle.dump(state, file)
1741	print pickle.dumps(state)
1742	state.data_name = "hello---->"
1743	pickle.dump(state, file)
1744	file = open("test_state", "r")
1745	new_state= pickle.load(file)
1746	print "new state", new_state
1747	new_state= pickle.load(file)
1748	print "new state", new_state
1749	#print "state", state
1750	"""
1751	import bsddb
1752	import pickle
1753	db = bsddb.btopen('file_state.db', 'c')
1754	val = (pickle.dumps(state), "hello", "hi")
1755	db['state1'] = pickle.dumps(val)
1756	print pickle.loads(db['state1'])
1757	state.data_name = "hello---->22"
1758	db['state2'] = pickle.dumps(state)
1759	state.data_name = "hello---->2"
1760	db['state3'] = pickle.dumps(state)
1761	del db['state3']
1762	state.data_name = "hello---->3"
1763	db['state4'] = pickle.dumps(state)
1764	new_state = pickle.loads(db['state1'])
1765	#print db.last()
1766	db.set_location('state2')
1767	state.data_name = "hello---->5"
1768	db['aastate5'] = pickle.dumps(state)
1769	db.keys().sort()
1770	print pickle.loads(db['state2'])
1771
1772	db.close()

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SasView

source: sasview/src/sas/perspectives/fitting/pagestate.py @ d06ae30

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