pagestate.py @ 397b4e7

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 397b4e7 was 3b148c3, checked in by Jae Cho <jhjcho@…>, 12 years ago
fixed a bug, 'saving as project' error when fitpage has no data set
Property mode set to `100644`
File size: 71.9 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	["dx_max", "dx_max", "float"],
73	["dx_min","dx_min", "float"],
74	["dxl", "dxl", "float"],
75	["dxw","dxw", "float"]]
76
77	list_of_model_attributes = [["values", "values"],
78	["weights", "weights"]]
79
80	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
81
82	list_of_state_parameters = [["parameters", "parameters"],
83	["str_parameters", "str_parameters"],
84	["orientation_parameters", "orientation_params"],
85	["dispersity_parameters", "orientation_params_disp"],
86	["fixed_param", "fixed_param"],
87	["fittable_param", "fittable_param"]]
88	list_of_data_2d_attr = [["xmin", "xmin", "float"],
89	["xmax", "xmax", "float"],
90	["ymin", "ymin", "float"],
91	["ymax", "ymax", "float"],
92	["_xaxis", "_xaxis", "string"],
93	["_xunit", "_xunit", "string"],
94	["_yaxis", "_yaxis", "string"],
95	["_yunit", "_yunit", "string"],
96	["_zaxis", "_zaxis", "string"],
97	["_zunit", "_zunit", "string"]]
98	list_of_data2d_values = [["qx_data", "qx_data", "float"],
99	["qy_data", "qy_data", "float"],
100	["dqx_data", "dqx_data", "float"],
101	["dqy_data", "dqy_data", "float"],
102	["data", "data", "float"],
103	["q_data", "q_data", "float"],
104	["err_data", "err_data", "float"],
105	["mask", "mask", "bool"]]
106
107
108	def parse_entry_helper(node, item):
109	"""
110	Create a numpy list from value extrated from the node
111
112	:param node: node from each the value is stored
113	:param item: list name of three strings.the two first are name of data
114	attribute and the third one is the type of the value of that
115	attribute. type can be string, float, bool, etc.
116
117	: return: numpy array
118	"""
119	if node is not None:
120	if item[2] == "string":
121	return str(node.get(item[0]).strip())
122	elif item[2] == "bool":
123	try:
124	return node.get(item[0]).strip() == "True"
125
126	except:
127	return None
128	else:
129	try:
130	return float(node.get(item[0]))
131	except:
132	return None
133
134
135	class PageState(object):
136	"""
137	Contains information to reconstruct a page of the fitpanel.
138	"""
139	def __init__(self, parent=None, model=None, data=None):
140	"""
141	Initialize the current state
142
143	:param model: a selected model within a page
144	:param data:
145
146	"""
147	self.file = None
148	#Time of state creation
149	self.timestamp = time.time()
150	## Data member to store the dispersion object created
151	self._disp_obj_dict = {}
152	#------------------------
153	#Data used for fitting
154	self.data = data
155	# model data
156	self.theory_data = None
157	#Is 2D
158	self.is_2D = False
159	self.images = None
160
161	#save additional information on data that dataloader.reader does not read
162	self.is_data = None
163	self.data_name = ""
164
165	if self.data is not None:
166	self.data_name = self.data.name
167	self.data_id = None
168	if self.data is not None and hasattr(self.data, "id"):
169	self.data_id = self.data.id
170	self.data_group_id = None
171	if self.data is not None and hasattr(self.data, "group_id"):
172	self.data_group_id = self.data.group_id
173
174	## reset True change the state of exsiting button
175	self.reset = False
176
177	#engine type
178	self.engine_type = None
179	# flag to allow data2D plot
180	self.enable2D = False
181	# model on which the fit would be performed
182	self.model = model
183	self.m_name = None
184	#list of process done to model
185	self.process = []
186	#fit page manager
187	self.manager = None
188	#Store the parent of this panel parent
189	# For this application fitpanel is the parent
190	self.parent = parent
191	# Event_owner is the owner of model event
192	self.event_owner = None
193	##page name
194	self.page_name = ""
195	# Contains link between model ,all its parameters, and panel organization
196	self.parameters = []
197	# String parameter list that can not be fitted
198	self.str_parameters = []
199	# Contains list of parameters that cannot be fitted and reference to
200	#panel objects
201	self.fixed_param = []
202	# Contains list of parameters with dispersity and reference to
203	#panel objects
204	self.fittable_param = []
205	## orientation parameters
206	self.orientation_params = []
207	## orientation parmaters for gaussian dispersity
208	self.orientation_params_disp = []
209	## smearer info
210	self.smearer = None
211	self.smear_type = None
212	self.dq_l = None
213	self.dq_r = None
214	self.dx_max = None
215	self.dx_min = None
216	self.dxl = None
217	self.dxw = None
218	#list of dispersion paramaters
219	self.disp_list = []
220	if self.model is not None:
221	self.disp_list = self.model.getDispParamList()
222
223	self.disp_cb_dict = {}
224	self.values = {}
225	self.weights = {}
226
227	#contains link between a model and selected parameters to fit
228	self.param_toFit = []
229	##dictionary of model type and model class
230	self.model_list_box = None
231	## save the state of the context menu
232	self.saved_states = {}
233	## save selection of combobox
234	self.formfactorcombobox = None
235	self.categorycombobox = None
236	self.structurecombobox = None
237
238	## radio box to select type of model
239	#self.shape_rbutton = False
240	#self.shape_indep_rbutton = False
241	#self.struct_rbutton = False
242	#self.plugin_rbutton = False
243	## the indice of the current selection
244	self.disp_box = 0
245	## Qrange
246	## Q range
247	self.qmin = 0.001
248	self.qmax = 0.1
249	#reset data range
250	self.qmax_x = None
251	self.qmin_x = None
252
253	self.npts = None
254	self.name = ""
255	self.multi_factor = None
256	self.magnetic_on = False
257	## enable smearering state
258	self.enable_smearer = False
259	self.disable_smearer = True
260	self.pinhole_smearer = False
261	self.slit_smearer = False
262	# weighting options
263	self.dI_noweight = False
264	self.dI_didata = True
265	self.dI_sqrdata = False
266	self.dI_idata = False
267	## disperity selection
268	self.enable_disp = False
269	self.disable_disp = True
270
271	## state of selected all check button
272	self.cb1 = False
273	## store value of chisqr
274	self.tcChi = None
275
276	def clone(self):
277	"""
278	Create a new copy of the current object
279	"""
280	model = None
281	if self.model is not None:
282	model = self.model.clone()
283	model.name = self.model.name
284	obj = PageState(self.parent, model=model)
285	obj.file = copy.deepcopy(self.file)
286	obj.data = copy.deepcopy(self.data)
287	if self.data is not None:
288	self.data_name = self.data.name
289	obj.data_name = self.data_name
290	obj.is_data = self.is_data
291	obj.model_list_box = copy.deepcopy(self.model_list_box)
292	obj.engine_type = copy.deepcopy(self.engine_type)
293
294	obj.categorycombobox = self.categorycombobox
295	obj.formfactorcombobox = self.formfactorcombobox
296	obj.structurecombobox = self.structurecombobox
297
298	#obj.shape_rbutton = self.shape_rbutton
299	#obj.shape_indep_rbutton = self.shape_indep_rbutton
300	#obj.struct_rbutton = self.struct_rbutton
301	#obj.plugin_rbutton = self.plugin_rbutton
302
303	obj.manager = self.manager
304	obj.event_owner = self.event_owner
305	obj.disp_list = copy.deepcopy(self.disp_list)
306
307	obj.enable2D = copy.deepcopy(self.enable2D)
308	obj.parameters = copy.deepcopy(self.parameters)
309	obj.str_parameters = copy.deepcopy(self.str_parameters)
310	obj.fixed_param = copy.deepcopy(self.fixed_param)
311	obj.fittable_param = copy.deepcopy(self.fittable_param)
312	obj.orientation_params = copy.deepcopy(self.orientation_params)
313	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
314	obj.enable_disp = copy.deepcopy(self.enable_disp)
315	obj.disable_disp = copy.deepcopy(self.disable_disp)
316	obj.tcChi = self.tcChi
317
318	if len(self._disp_obj_dict) > 0:
319	for k, v in self._disp_obj_dict.iteritems():
320	obj._disp_obj_dict[k] = v
321	if len(self.disp_cb_dict) > 0:
322	for k, v in self.disp_cb_dict.iteritems():
323	obj.disp_cb_dict[k] = v
324	if len(self.values) > 0:
325	for k, v in self.values.iteritems():
326	obj.values[k] = v
327	if len(self.weights) > 0:
328	for k, v in self.weights.iteritems():
329	obj.weights[k] = v
330	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
331	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
332	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
333	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
334	obj.smear_type = copy.deepcopy(self.smear_type)
335	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
336	obj.dI_didata = copy.deepcopy(self.dI_didata)
337	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
338	obj.dI_idata = copy.deepcopy(self.dI_idata)
339	obj.dq_l = copy.deepcopy(self.dq_l)
340	obj.dq_r = copy.deepcopy(self.dq_r)
341	obj.dx_max = copy.deepcopy(self.dx_max)
342	obj.dx_min = copy.deepcopy(self.dx_min)
343	obj.dxl = copy.deepcopy(self.dxl)
344	obj.dxw = copy.deepcopy(self.dxw)
345	obj.disp_box = copy.deepcopy(self.disp_box)
346	obj.qmin = copy.deepcopy(self.qmin)
347	obj.qmax = copy.deepcopy(self.qmax)
348	obj.multi_factor = self.multi_factor
349	obj.magnetic_on = self.magnetic_on
350	obj.npts = copy.deepcopy(self.npts)
351	obj.cb1 = copy.deepcopy(self.cb1)
352	obj.smearer = copy.deepcopy(self.smearer)
353
354	for name, state in self.saved_states.iteritems():
355	copy_name = copy.deepcopy(name)
356	copy_state = state.clone()
357	obj.saved_states[copy_name] = copy_state
358	return obj
359
360	def _repr_helper(self, list, rep):
361	"""
362	Helper method to print a state
363	"""
364	for item in list:
365	rep += "parameter name: %s \n" % str(item[1])
366	rep += "value: %s\n" % str(item[2])
367	rep += "selected: %s\n" % str(item[0])
368	rep += "error displayed : %s \n" % str(item[4][0])
369	rep += "error value:%s \n" % str(item[4][1])
370	rep += "minimum displayed : %s \n" % str(item[5][0])
371	rep += "minimum value : %s \n" % str(item[5][1])
372	rep += "maximum displayed : %s \n" % str(item[6][0])
373	rep += "maximum value : %s \n" % str(item[6][1])
374	rep += "parameter unit: %s\n\n" % str(item[7])
375	return rep
376
377	def __repr__(self):
378	"""
379	output string for printing
380	"""
381	rep = "\nState name: %s\n" % self.file
382	t = time.localtime(self.timestamp)
383	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
384
385	rep += "State created: %s\n" % time_str
386	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
387	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
388	rep += "is data : %s\n" % self.is_data
389	rep += "data's name : %s\n" % self.data_name
390	rep += "data's id : %s\n" % self.data_id
391	if self.model != None:
392	m_name = self.model.__class__.__name__
393	if m_name == 'Model':
394	m_name = self.m_name
395	rep += "model name : %s\n" % m_name
396	else:
397	rep += "model name : None\n"
398	#rep += "model type (form factor) selected: %s\n" % self.shape_rbutton
399	rep += "multi_factor : %s\n" % str(self.multi_factor)
400	rep += "magnetic_on : %s\n"% str(self.magnetic_on)
401	rep += "model type (Category) selected: %s\n" % self.categorycombobox
402	#rep += "model type (shape independent) selected: %s\n" % self.shape_indep_rbutton
403	#rep += "model type (structure factor) selected: %s\n" % self.struct_rbutton
404	#rep += "model type (plug-in ) selected: %s\n" % self.plugin_rbutton
405	rep += "data : %s\n" % str(self.data)
406	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
407	str(self.qmax), str(self.npts))
408	rep += "Dispersion selection : %s\n" % str(self.disp_box)
409	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
410	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
411	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
412	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
413	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
414	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
415	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
416
417	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
418	rep += "dI_didata : %s\n" % str(self.dI_didata)
419	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
420	rep += "dI_idata : %s\n" % str(self.dI_idata)
421
422	rep += "2D enable : %s\n" % str(self.enable2D)
423	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
424	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
425	rep += "Smear object : %s\n" % str(self.smearer)
426	rep += "Smear type : %s\n" % (self.smear_type)
427	rep += "dq_l : %s\n" % self.dq_l
428	rep += "dq_r : %s\n" % self.dq_r
429	rep += "dx_max : %s\n" % str(self.dx_max)
430	rep += "dx_min : %s\n" % str(self.dx_min)
431	rep += "dxl : %s\n" % str(self.dxl)
432	rep += "dxw : %s\n" % str(self.dxw)
433	rep += "model : %s\n\n" % str(self.model)
434	temp_parameters = []
435	temp_fittable_param = []
436	if self.data.__class__.__name__ == "Data2D":
437	self.is_2D = True
438	else:
439	self.is_2D = False
440	if self.data is not None:
441	if not self.is_2D:
442	for item in self.parameters:
443	if not item in self.orientation_params:
444	temp_parameters.append(item)
445	for item in self.fittable_param:
446	if not item in self.orientation_params_disp:
447	temp_fittable_param.append(item)
448	else:
449	temp_parameters = self.parameters
450	temp_fittable_param = self.fittable_param
451
452	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
453	rep = self._repr_helper(list=temp_parameters, rep=rep)
454	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
455	rep = self._repr_helper(list=self.str_parameters, rep=rep)
456	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
457	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
458	"""
459	if is_2D:
460	rep += "number orientation parameters"
461	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
462	rep = self._repr_helper( list=self.orientation_params, rep=rep)
463	rep += "number dispersity parameters"
464	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
465	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
466	"""
467	return rep
468
469	def set_report_string(self):
470	"""
471	Get the values (strings) from __str__ for report
472	"""
473	# Dictionary of teh report strings
474	repo_time = ""
475	model_name = ""
476	title = ""
477	title_name = ""
478	file_name = ""
479	param_string = ""
480	paramval_string = ""
481	chi2_string = ""
482	multi_factor_string = ""
483	q_range = ""
484	strings = self.__repr__()
485	lines = strings.split('\n')
486
487	# get all string values from __str__()
488	for line in lines:
489	value = ""
490	content = line.split(":")
491	name = content[0]
492	try:
493	value = content[1]
494	except:
495	pass
496	if name.count("State created"):
497	repo_time = "" + value
498	if name.count("parameter name"):
499	val_name = value.split(".")
500	if len(val_name) > 1:
501	if val_name[1].count("width"):
502	param_string += value + ','
503	else:
504	continue
505	else:
506	param_string += value + ','
507	if name == "value":
508	param_string += value + ','
509	if name == "error value":
510	param_string += value + ','
511	if name == "parameter unit":
512	param_string += value + ':'
513	if name == "Value of Chisqr ":
514	chi2 = ("Chi2/Npts = " + value)
515	chi2_string = CENTRE % chi2
516	if name == "multi_factor ":
517	muti_factor = ("muti_factor = " + value)
518	muti_factor_string = CENTRE % muti_factor
519	if name == "magentic_on ":
520	magentic_on = ("magentic_on = " + value)
521	if string(value) == 'True':
522	magentic_on_string = CENTRE % magentic_on
523	if name == "Title":
524	if len(value.strip()) == 0:
525	continue
526	title = value + " [" + repo_time + "]"
527	title_name = HEADER % title
528	if name == "data ":
529	try:
530	file = ("File name:" + content[2])
531	file_name = CENTRE % file
532	if len(title) == 0:
533	title = content[2] + " [" + repo_time + "]"
534	title_name = HEADER % title
535	except:
536	pass
537	if name == "model name ":
538	try:
539	modelname = "Model name:" + content[1]
540	except:
541	modelname = "Model name:" + " NAN"
542	model_name = CENTRE % modelname
543
544	if name == "Plotting Range":
545	try:
546	q_range = content[1] + " = " + content[2] \
547	+ " = " + content[3].split(",")[0]
548	q_name = ("Q Range: " + q_range)
549	q_range = CENTRE % q_name
550	except:
551	pass
552	paramval = ""
553	for lines in param_string.split(":"):
554	line = lines.split(",")
555	if len(lines) > 0:
556	param = line[0]
557	param += " = " + line[1]
558	if len(line[2].split()) > 0 and not line[2].count("None"):
559	param += " +- " + line[2]
560	if len(line[3].split()) > 0 and not line[3].count("None"):
561	param += " " + line[3]
562	if not paramval.count(param):
563	paramval += param + "\n"
564	paramval_string += CENTRE % param + "\n"
565
566	text_string = "\n\n\n" + title + "\n\n" + file + \
567	"\n" + q_name + \
568	"\n" + chi2 + \
569	"\n\n" + paramval
570
571	title_name = self._check_html_format(title_name)
572	file_name = self._check_html_format(file_name)
573	title = self._check_html_format(title)
574
575	html_string = title_name + "\n" + file_name + \
576	"\n" + model_name + \
577	"\n" + q_range + \
578	"\n" + chi2_string + \
579	"\n" + ELINE + \
580	"\n" + paramval_string + \
581	"\n" + ELINE + \
582	"\n" + FEET_1 % title + \
583	"\n" + FEET_2
584
585	return html_string, text_string, title
586
587	def _check_html_format(self, name):
588	"""
589	Check string '%' for html format
590	"""
591	if name.count('%'):
592	name = name.replace('%', '&#37')
593
594	return name
595
596	def report(self, figs=None, canvases=None):
597	"""
598	Invoke report dialog panel
599
600	: param figs: list of pylab figures [list]
601	"""
602	from report_dialog import ReportDialog
603	# get the strings for report
604	html_str, text_str, title = self.set_report_string()
605	# Allow 2 figures to append
606	if len(figs) == 1:
607	add_str = FEET_3
608	elif len(figs) == 2:
609	add_str = ELINE
610	add_str += FEET_2 % ("%s")
611	add_str += ELINE
612	add_str += FEET_3
613	elif len(figs) > 2:
614	add_str = ELINE
615	add_str += FEET_2 % ("%s")
616	add_str += ELINE
617	add_str += FEET_2 % ("%s")
618	add_str += ELINE
619	add_str += FEET_3
620	else:
621	add_str = ""
622
623	# final report html strings
624	report_str = html_str % ("%s") + add_str
625
626	# make plot image
627	images = self.set_plot_state(figs, canvases)
628	report_list = [report_str, text_str, images]
629	dialog = ReportDialog(report_list, None, -1, "")
630	dialog.ShowModal()
631
632	def _toXML_helper(self, list, element, newdoc):
633	"""
634	Helper method to create xml file for saving state
635	"""
636	for item in list:
637	sub_element = newdoc.createElement('parameter')
638	sub_element.setAttribute('name', str(item[1]))
639	sub_element.setAttribute('value', str(item[2]))
640	sub_element.setAttribute('selected_to_fit', str(item[0]))
641	sub_element.setAttribute('error_displayed', str(item[4][0]))
642	sub_element.setAttribute('error_value', str(item[4][1]))
643	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
644	sub_element.setAttribute('minimum_value', str(item[5][1]))
645	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
646	sub_element.setAttribute('maximum_value', str(item[6][1]))
647	sub_element.setAttribute('unit', str(item[7]))
648	element.appendChild(sub_element)
649
650	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
651	"""
652	Writes the state of the InversionControl panel to file, as XML.
653
654	Compatible with standalone writing, or appending to an
655	already existing XML document. In that case, the XML document
656	is required. An optional entry node in the XML document may also be given.
657
658	:param file: file to write to
659	:param doc: XML document object [optional]
660	:param entry_node: XML node within the XML document at which we will append the data [optional]
661
662	"""
663	from xml.dom.minidom import getDOMImplementation
664
665	# Check whether we have to write a standalone XML file
666	if doc is None:
667	impl = getDOMImplementation()
668	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
669	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
670	top_element = newdoc.documentElement
671	else:
672	# We are appending to an existing document
673	newdoc = doc
674	top_element = newdoc.createElement(FITTING_NODE_NAME)
675	if entry_node is None:
676	newdoc.documentElement.appendChild(top_element)
677	else:
678	entry_node.appendChild(top_element)
679
680	attr = newdoc.createAttribute("version")
681	attr.nodeValue = '1.0'
682	top_element.setAttributeNode(attr)
683
684	# File name
685	element = newdoc.createElement("filename")
686	if self.file is not None:
687	element.appendChild(newdoc.createTextNode(str(self.file)))
688	else:
689	element.appendChild(newdoc.createTextNode(str(file)))
690	top_element.appendChild(element)
691
692	element = newdoc.createElement("timestamp")
693	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
694	attr = newdoc.createAttribute("epoch")
695	attr.nodeValue = str(self.timestamp)
696	element.setAttributeNode(attr)
697	top_element.appendChild(element)
698	# Inputs
699	inputs = newdoc.createElement("Attributes")
700	top_element.appendChild(inputs)
701
702	if self.data is not None and hasattr(self.data, "group_id"):
703	self.data_group_id = self.data.group_id
704	if self.data is not None and hasattr(self.data, "is_data"):
705	self.is_data = self.data.is_data
706	if self.data is not None:
707	self.data_name = self.data.name
708	if self.data is not None and hasattr(self.data, "id"):
709	self.data_id = self.data.id
710
711	for item in list_of_data_attributes:
712	element = newdoc.createElement(item[0])
713	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
714	inputs.appendChild(element)
715
716	for item in list_of_state_attributes:
717	element = newdoc.createElement(item[0])
718	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
719	inputs.appendChild(element)
720
721	# For self.values ={ disp_param_name: [vals,...],...}
722	# and for self.weights ={ disp_param_name: [weights,...],...}
723	list = {}
724	for item in list_of_model_attributes:
725	element = newdoc.createElement(item[0])
726	exec "list = self.%s" % item[1]
727	for key, value in list.iteritems():
728	sub_element = newdoc.createElement(key)
729	sub_element.setAttribute('name', str(key))
730	for val in value:
731	com = "sub_element.appendChild"
732	com += "(newdoc.createTextNode(str(%s)))"
733	exec com % val
734
735	element.appendChild(sub_element)
736	inputs.appendChild(element)
737
738	# Create doc for the dictionary of self._disp_obj_dic
739	for item in list_of_obj_dic:
740	element = newdoc.createElement(item[0])
741	exec "list = self.%s" % item[1]
742	for key, val in list.iteritems():
743	value = repr(val)
744	sub_element = newdoc.createElement(key)
745	sub_element.setAttribute('name', str(key))
746	sub_element.setAttribute('value', str(value))
747	element.appendChild(sub_element)
748	inputs.appendChild(element)
749
750	for item in list_of_state_parameters:
751	element = newdoc.createElement(item[0])
752	com = "self._toXML_helper(list=self.%s,"
753	com += " element=element, newdoc=newdoc)"
754	exec com % item[1]
755	inputs.appendChild(element)
756
757	# Save the file
758	if doc is None:
759	fd = open(file, 'w')
760	fd.write(newdoc.toprettyxml())
761	fd.close()
762	return None
763	else:
764	return newdoc.toprettyxml()
765
766	def _fromXML_helper(self, node, list):
767	"""
768	Helper function to write state to xml
769	"""
770	for item in node:
771	try:
772	name = item.get('name')
773	except:
774	name = None
775	try:
776	value = item.get('value')
777	except:
778	value = None
779	try:
780	selected_to_fit = (item.get('selected_to_fit') == "True")
781	except:
782	selected_to_fit = None
783	try:
784	error_displayed = (item.get('error_displayed') == "True")
785	except:
786	error_displayed = None
787	try:
788	error_value = item.get('error_value')
789	except:
790	error_value = None
791	try:
792	minimum_displayed = (item.get('minimum_displayed') == "True")
793	except:
794	minimum_displayed = None
795	try:
796	minimum_value = item.get('minimum_value')
797	except:
798	minimum_value = None
799	try:
800	maximum_displayed = (item.get('maximum_displayed') == "True")
801	except:
802	maximum_displayed = None
803	try:
804	maximum_value = item.get('maximum_value')
805	except:
806	maximum_value = None
807	try:
808	unit = item.get('unit')
809	except:
810	unit = None
811	list.append([selected_to_fit, name, value, "+/-",
812	[error_displayed, error_value],
813	[minimum_displayed, minimum_value],
814	[maximum_displayed, maximum_value], unit])
815
816	def fromXML(self, file=None, node=None):
817	"""
818	Load fitting state from a file
819
820	:param file: .fitv file
821	:param node: node of a XML document to read from
822
823	"""
824	if file is not None:
825	msg = "PageState no longer supports non-CanSAS"
826	msg += " format for fitting files"
827	raise RuntimeError, msg
828
829	if node.get('version')and node.get('version') == '1.0':
830
831	# Get file name
832	entry = get_content('ns:filename', node)
833	if entry is not None:
834	self.file = entry.text.strip()
835
836	# Get time stamp
837	entry = get_content('ns:timestamp', node)
838	if entry is not None and entry.get('epoch'):
839	try:
840	self.timestamp = float(entry.get('epoch'))
841	except:
842	msg = "PageState.fromXML: Could not"
843	msg += " read timestamp\n %s" % sys.exc_value
844	logging.error(msg)
845
846	# Parse fitting attributes
847	entry = get_content('ns:Attributes', node)
848	for item in list_of_data_attributes:
849	node = get_content('ns:%s' % item[0], entry)
850	try:
851	exec "self.%s = parse_entry_helper(node, item)" % item[0]
852
853	except:
854	raise
855
856	if entry is not None:
857
858	for item in list_of_state_attributes:
859	node = get_content('ns:%s' % item[0], entry)
860	try:
861	exec "self.%s = parse_entry_helper(node, item)" % \
862	str(item[0])
863	except:
864	raise
865
866	for item in list_of_state_parameters:
867	node = get_content("ns:%s" % item[0], entry)
868	exec "self._fromXML_helper(node=node, list=self.%s)" % \
869	item[1]
870
871	# Recover _disp_obj_dict from xml file
872	self._disp_obj_dict = {}
873	disp_model = None
874	for item in list_of_obj_dic:
875	# Get node
876	node = get_content("ns:%s" % item[0], entry)
877	for attr in node:
878	name = attr.get('name')
879	val = attr.get('value')
880	value = val.split(" instance")[0]
881	disp_name = value.split("<")[1]
882	try:
883	# Try to recover disp_model object from strings
884	com = "from sans.models.dispersion_models "
885	com += "import %s as disp"
886	com_name = disp_name.split(".")[3]
887	exec com % com_name
888	disp_model = disp()
889	exec "self.%s['%s'] = com_name" % (item[1], name)
890	except:
891	pass
892
893	# get self.values and self.weights dic. if exists
894	for item in list_of_model_attributes:
895	node = get_content("ns:%s" % item[0], entry)
896	dic = {}
897	list = []
898	for par in node:
899	name = par.get('name')
900	values = par.text.split('\n')
901	# Get lines only with numbers
902	for line in values:
903	try:
904	val = float(line)
905	list.append(val)
906	except:
907	# pass if line is empty (it happens)
908	pass
909	dic[name] = numpy.array(list)
910	exec "self.%s = dic" % item[1]
911
912	def set_plot_state(self, figs, canvases):
913	"""
914	Build image state that wx.html understand
915	by plotting, putting it into wx.FileSystem image object
916
917	"""
918	images = []
919	# some imports
920	import wx
921
922	# Reset memory
923	self.imgRAM = None
924	wx.MemoryFSHandler()
925
926	# For no figures in the list, prepare empty plot
927	if figs == None or len(figs) == 0:
928	figs = [None]
929
930	# Loop over the list of figures
931	# use wx.MemoryFSHandler
932	self.imgRAM = wx.MemoryFSHandler()
933	for fig in figs:
934	if figs != None:
935	ind = figs.index(fig)
936	canvas = canvases[ind]
937
938	#store the image in wx.FileSystem Object
939	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
940
941	# index of the fig
942	ind = figs.index(fig)
943
944	#AddFile, image can be retrieved with 'memory:filename'
945	self.imgRAM.AddFile('img_fit%s.png' % ind,
946	canvas.bitmap, wx.BITMAP_TYPE_PNG)
947
948	#append figs
949	images.append(fig)
950
951	return images
952
953
954	class Reader(CansasReader):
955	"""
956	Class to load a .fitv fitting file
957	"""
958	## File type
959	type_name = "Fitting"
960
961	## Wildcards
962	type = ["Fitting files (.fitv)\|.fitv"
963	"SANSView file (.svs)\|.svs"]
964	## List of allowed extensions
965	ext = ['.fitv', '.FITV', '.svs', 'SVS']
966
967	def __init__(self, call_back=None, cansas=True):
968	CansasReader.__init__(self)
969	"""
970	Initialize the call-back method to be called
971	after we load a file
972
973	:param call_back: call-back method
974	:param cansas: True = files will be written/read in CanSAS format
975	False = write CanSAS format
976
977	"""
978	## Call back method to be executed after a file is read
979	self.call_back = call_back
980	## CanSAS format flag
981	self.cansas = cansas
982	self.state = None
983
984	def get_state(self):
985	return self.state
986
987	def read(self, path):
988	"""
989	Load a new P(r) inversion state from file
990
991	:param path: file path
992
993	"""
994	if self.cansas == True:
995	return self._read_cansas(path)
996
997	def _data2d_to_xml_doc(self, datainfo):
998	"""
999	Create an XML document to contain the content of a Data2D
1000
1001	:param datainfo: Data2D object
1002
1003	"""
1004	if not issubclass(datainfo.__class__, Data2D):
1005	raise RuntimeError, "The cansas writer expects a Data2D instance"
1006
1007	doc = xml.dom.minidom.Document()
1008	main_node = doc.createElement("SASroot")
1009	main_node.setAttribute("version", self.version)
1010	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
1011	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
1012	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
1013
1014	doc.appendChild(main_node)
1015
1016	entry_node = doc.createElement("SASentry")
1017	main_node.appendChild(entry_node)
1018
1019	write_node(doc, entry_node, "Title", datainfo.title)
1020	if datainfo is not None:
1021	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
1022	for item in datainfo.run:
1023	runname = {}
1024	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
1025	runname = {'name': datainfo.run_name[item] }
1026	write_node(doc, entry_node, "Run", item, runname)
1027	# Data info
1028	new_node = doc.createElement("SASdata")
1029	entry_node.appendChild(new_node)
1030	for item in list_of_data_2d_attr:
1031	element = doc.createElement(item[0])
1032	exec "element.setAttribute(item[0], str(datainfo.%s))" % (item[1])
1033	new_node.appendChild(element)
1034
1035	for item in list_of_data2d_values:
1036	root_node = doc.createElement(item[0])
1037	new_node.appendChild(root_node)
1038	temp_list = None
1039	exec "temp_list = datainfo.%s" % item[1]
1040
1041	if temp_list is None or len(temp_list)== 0:
1042	element = doc.createElement(item[0])
1043	exec "element.appendChild(doc.createTextNode(str(%s)))" % temp_list
1044	root_node.appendChild(element)
1045	else:
1046	for value in temp_list:
1047	element = doc.createElement(item[0])
1048	exec "element.setAttribute(item[0], str(%s))" % value
1049	root_node.appendChild(element)
1050
1051	# Sample info
1052	sample = doc.createElement("SASsample")
1053	if datainfo.sample.name is not None:
1054	sample.setAttribute("name", str(datainfo.sample.name))
1055	entry_node.appendChild(sample)
1056	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1057	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1058	{"unit": datainfo.sample.thickness_unit})
1059	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1060	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1061	{"unit": datainfo.sample.temperature_unit})
1062
1063	for item in datainfo.sample.details:
1064	write_node(doc, sample, "details", item)
1065
1066	pos = doc.createElement("position")
1067	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1068	{"unit": datainfo.sample.position_unit})
1069	written = written \| write_node(doc, pos, "y",
1070	datainfo.sample.position.y,
1071	{"unit": datainfo.sample.position_unit})
1072	written = written \| write_node(doc, pos, "z",
1073	datainfo.sample.position.z,
1074	{"unit": datainfo.sample.position_unit})
1075	if written == True:
1076	sample.appendChild(pos)
1077
1078	ori = doc.createElement("orientation")
1079	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1080	{"unit": datainfo.sample.orientation_unit})
1081	written = written \| write_node(doc, ori, "pitch",
1082	datainfo.sample.orientation.y,
1083	{"unit": datainfo.sample.orientation_unit})
1084	written = written \| write_node(doc, ori, "yaw",
1085	datainfo.sample.orientation.z,
1086	{"unit": datainfo.sample.orientation_unit})
1087	if written == True:
1088	sample.appendChild(ori)
1089
1090	# Instrument info
1091	instr = doc.createElement("SASinstrument")
1092	entry_node.appendChild(instr)
1093
1094	write_node(doc, instr, "name", datainfo.instrument)
1095
1096	# Source
1097	source = doc.createElement("SASsource")
1098	if datainfo.source.name is not None:
1099	source.setAttribute("name", str(datainfo.source.name))
1100	instr.appendChild(source)
1101
1102	write_node(doc, source, "radiation", datainfo.source.radiation)
1103	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1104	size = doc.createElement("beam_size")
1105	if datainfo.source.beam_size_name is not None:
1106	size.setAttribute("name", str(datainfo.source.beam_size_name))
1107	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1108	{"unit": datainfo.source.beam_size_unit})
1109	written = written \| write_node(doc, size, "y",
1110	datainfo.source.beam_size.y,
1111	{"unit": datainfo.source.beam_size_unit})
1112	written = written \| write_node(doc, size, "z",
1113	datainfo.source.beam_size.z,
1114	{"unit": datainfo.source.beam_size_unit})
1115	if written == True:
1116	source.appendChild(size)
1117
1118	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1119	{"unit": datainfo.source.wavelength_unit})
1120	write_node(doc, source, "wavelength_min",
1121	datainfo.source.wavelength_min,
1122	{"unit": datainfo.source.wavelength_min_unit})
1123	write_node(doc, source, "wavelength_max",
1124	datainfo.source.wavelength_max,
1125	{"unit": datainfo.source.wavelength_max_unit})
1126	write_node(doc, source, "wavelength_spread",
1127	datainfo.source.wavelength_spread,
1128	{"unit": datainfo.source.wavelength_spread_unit})
1129
1130	# Collimation
1131	for item in datainfo.collimation:
1132	coll = doc.createElement("SAScollimation")
1133	if item.name is not None:
1134	coll.setAttribute("name", str(item.name))
1135	instr.appendChild(coll)
1136
1137	write_node(doc, coll, "length", item.length,
1138	{"unit": item.length_unit})
1139
1140	for apert in item.aperture:
1141	ap = doc.createElement("aperture")
1142	if apert.name is not None:
1143	ap.setAttribute("name", str(apert.name))
1144	if apert.type is not None:
1145	ap.setAttribute("type", str(apert.type))
1146	coll.appendChild(ap)
1147
1148	write_node(doc, ap, "distance", apert.distance,
1149	{"unit": apert.distance_unit})
1150
1151	size = doc.createElement("size")
1152	if apert.size_name is not None:
1153	size.setAttribute("name", str(apert.size_name))
1154	written = write_node(doc, size, "x", apert.size.x,
1155	{"unit": apert.size_unit})
1156	written = written \| write_node(doc, size, "y", apert.size.y,
1157	{"unit": apert.size_unit})
1158	written = written \| write_node(doc, size, "z", apert.size.z,
1159	{"unit": apert.size_unit})
1160	if written == True:
1161	ap.appendChild(size)
1162
1163	# Detectors
1164	for item in datainfo.detector:
1165	det = doc.createElement("SASdetector")
1166	written = write_node(doc, det, "name", item.name)
1167	written = written \| write_node(doc, det, "SDD", item.distance,
1168	{"unit": item.distance_unit})
1169	written = written \| write_node(doc, det, "slit_length",
1170	item.slit_length,
1171	{"unit": item.slit_length_unit})
1172	if written == True:
1173	instr.appendChild(det)
1174
1175	off = doc.createElement("offset")
1176	written = write_node(doc, off, "x", item.offset.x,
1177	{"unit": item.offset_unit})
1178	written = written \| write_node(doc, off, "y", item.offset.y,
1179	{"unit": item.offset_unit})
1180	written = written \| write_node(doc, off, "z", item.offset.z,
1181	{"unit": item.offset_unit})
1182	if written == True:
1183	det.appendChild(off)
1184
1185	center = doc.createElement("beam_center")
1186	written = write_node(doc, center, "x", item.beam_center.x,
1187	{"unit": item.beam_center_unit})
1188	written = written \| write_node(doc, center, "y",
1189	item.beam_center.y,
1190	{"unit": item.beam_center_unit})
1191	written = written \| write_node(doc, center, "z",
1192	item.beam_center.z,
1193	{"unit": item.beam_center_unit})
1194	if written == True:
1195	det.appendChild(center)
1196
1197	pix = doc.createElement("pixel_size")
1198	written = write_node(doc, pix, "x", item.pixel_size.x,
1199	{"unit": item.pixel_size_unit})
1200	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1201	{"unit": item.pixel_size_unit})
1202	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1203	{"unit": item.pixel_size_unit})
1204	if written == True:
1205	det.appendChild(pix)
1206
1207	ori = doc.createElement("orientation")
1208	written = write_node(doc, ori, "roll", item.orientation.x,
1209	{"unit": item.orientation_unit})
1210	written = written \| write_node(doc, ori, "pitch",
1211	item.orientation.y,
1212	{"unit": item.orientation_unit})
1213	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1214	{"unit": item.orientation_unit})
1215	if written == True:
1216	det.appendChild(ori)
1217
1218	# Processes info
1219	for item in datainfo.process:
1220	node = doc.createElement("SASprocess")
1221	entry_node.appendChild(node)
1222
1223	write_node(doc, node, "name", item.name)
1224	write_node(doc, node, "date", item.date)
1225	write_node(doc, node, "description", item.description)
1226	for term in item.term:
1227	value = term['value']
1228	del term['value']
1229	write_node(doc, node, "term", value, term)
1230	for note in item.notes:
1231	write_node(doc, node, "SASprocessnote", note)
1232	# Return the document, and the SASentry node associated with
1233	# the data we just wrote
1234	return doc, entry_node
1235
1236	def _parse_state(self, entry):
1237	"""
1238	Read a fit result from an XML node
1239
1240	:param entry: XML node to read from
1241
1242	:return: PageState object
1243	"""
1244	# Create an empty state
1245	state = None
1246	# Locate the P(r) node
1247	try:
1248	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1249	namespaces={'ns': CANSAS_NS})
1250	if nodes != []:
1251	# Create an empty state
1252	state = PageState()
1253	state.fromXML(node=nodes[0])
1254	except:
1255	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1256
1257	return state
1258
1259	def _parse_entry(self, dom):
1260	"""
1261	Parse a SASentry
1262
1263	:param node: SASentry node
1264
1265	:return: Data1D/Data2D object
1266
1267	"""
1268	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1269	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1270	return CansasReader._parse_entry(self, dom)
1271
1272	#Parse 2D
1273	data_info = Data2D()
1274
1275	# Look up title
1276	self._store_content('ns:Title', dom, 'title', data_info)
1277
1278	# Look up run number
1279	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1280	for item in nodes:
1281	if item.text is not None:
1282	value = item.text.strip()
1283	if len(value) > 0:
1284	data_info.run.append(value)
1285	if item.get('name') is not None:
1286	data_info.run_name[value] = item.get('name')
1287
1288	# Look up instrument name
1289	self._store_content('ns:SASinstrument/ns:name', dom,
1290	'instrument', data_info)
1291
1292	# Notes
1293	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1294	for note in note_list:
1295	try:
1296	if note.text is not None:
1297	note_value = note.text.strip()
1298	if len(note_value) > 0:
1299	data_info.notes.append(note_value)
1300	except:
1301	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1302	self.errors.append(err_mess)
1303	logging.error(err_mess)
1304
1305	# Sample info ###################
1306	entry = get_content('ns:SASsample', dom)
1307	if entry is not None:
1308	data_info.sample.name = entry.get('name')
1309
1310	self._store_content('ns:SASsample/ns:ID',
1311	dom, 'ID', data_info.sample)
1312	self._store_float('ns:SASsample/ns:thickness',
1313	dom, 'thickness', data_info.sample)
1314	self._store_float('ns:SASsample/ns:transmission',
1315	dom, 'transmission', data_info.sample)
1316	self._store_float('ns:SASsample/ns:temperature',
1317	dom, 'temperature', data_info.sample)
1318
1319	nodes = dom.xpath('ns:SASsample/ns:details',
1320	namespaces={'ns': CANSAS_NS})
1321	for item in nodes:
1322	try:
1323	if item.text is not None:
1324	detail_value = item.text.strip()
1325	if len(detail_value) > 0:
1326	data_info.sample.details.append(detail_value)
1327	except:
1328	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1329	self.errors.append(err_mess)
1330	logging.error(err_mess)
1331
1332	# Position (as a vector)
1333	self._store_float('ns:SASsample/ns:position/ns:x',
1334	dom, 'position.x', data_info.sample)
1335	self._store_float('ns:SASsample/ns:position/ns:y',
1336	dom, 'position.y', data_info.sample)
1337	self._store_float('ns:SASsample/ns:position/ns:z',
1338	dom, 'position.z', data_info.sample)
1339
1340	# Orientation (as a vector)
1341	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1342	dom, 'orientation.x', data_info.sample)
1343	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1344	dom, 'orientation.y', data_info.sample)
1345	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1346	dom, 'orientation.z', data_info.sample)
1347
1348	# Source info ###################
1349	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1350	if entry is not None:
1351	data_info.source.name = entry.get('name')
1352
1353	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1354	dom, 'radiation', data_info.source)
1355	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1356	dom, 'beam_shape', data_info.source)
1357	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1358	dom, 'wavelength', data_info.source)
1359	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1360	dom, 'wavelength_min', data_info.source)
1361	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1362	dom, 'wavelength_max', data_info.source)
1363	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1364	dom, 'wavelength_spread', data_info.source)
1365
1366	# Beam size (as a vector)
1367	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1368	if entry is not None:
1369	data_info.source.beam_size_name = entry.get('name')
1370
1371	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1372	dom, 'beam_size.x', data_info.source)
1373	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1374	dom, 'beam_size.y', data_info.source)
1375	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1376	dom, 'beam_size.z', data_info.source)
1377
1378	# Collimation info ###################
1379	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1380	namespaces={'ns': CANSAS_NS})
1381	for item in nodes:
1382	collim = Collimation()
1383	if item.get('name') is not None:
1384	collim.name = item.get('name')
1385	self._store_float('ns:length', item, 'length', collim)
1386
1387	# Look for apertures
1388	apert_list = item.xpath('ns:aperture',
1389	namespaces={'ns': CANSAS_NS})
1390	for apert in apert_list:
1391	aperture = Aperture()
1392
1393	# Get the name and type of the aperture
1394	aperture.name = apert.get('name')
1395	aperture.type = apert.get('type')
1396
1397	self._store_float('ns:distance', apert, 'distance', aperture)
1398
1399	entry = get_content('ns:size', apert)
1400	if entry is not None:
1401	aperture.size_name = entry.get('name')
1402
1403	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1404	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1405	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1406
1407	collim.aperture.append(aperture)
1408
1409	data_info.collimation.append(collim)
1410
1411	# Detector info ######################
1412	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1413	namespaces={'ns': CANSAS_NS})
1414	for item in nodes:
1415
1416	detector = Detector()
1417
1418	self._store_content('ns:name', item, 'name', detector)
1419	self._store_float('ns:SDD', item, 'distance', detector)
1420
1421	# Detector offset (as a vector)
1422	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1423	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1424	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1425
1426	# Detector orientation (as a vector)
1427	self._store_float('ns:orientation/ns:roll', item,
1428	'orientation.x', detector)
1429	self._store_float('ns:orientation/ns:pitch', item,
1430	'orientation.y', detector)
1431	self._store_float('ns:orientation/ns:yaw', item,
1432	'orientation.z', detector)
1433
1434	# Beam center (as a vector)
1435	self._store_float('ns:beam_center/ns:x', item,
1436	'beam_center.x', detector)
1437	self._store_float('ns:beam_center/ns:y', item,
1438	'beam_center.y', detector)
1439	self._store_float('ns:beam_center/ns:z', item,
1440	'beam_center.z', detector)
1441
1442	# Pixel size (as a vector)
1443	self._store_float('ns:pixel_size/ns:x', item,
1444	'pixel_size.x', detector)
1445	self._store_float('ns:pixel_size/ns:y', item,
1446	'pixel_size.y', detector)
1447	self._store_float('ns:pixel_size/ns:z', item,
1448	'pixel_size.z', detector)
1449
1450	self._store_float('ns:slit_length', item, 'slit_length', detector)
1451
1452	data_info.detector.append(detector)
1453
1454	# Processes info ######################
1455	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1456	for item in nodes:
1457	process = Process()
1458	self._store_content('ns:name', item, 'name', process)
1459	self._store_content('ns:date', item, 'date', process)
1460	self._store_content('ns:description', item, 'description', process)
1461
1462	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1463	for term in term_list:
1464	try:
1465	term_attr = {}
1466	for attr in term.keys():
1467	term_attr[attr] = term.get(attr).strip()
1468	if term.text is not None:
1469	term_attr['value'] = term.text.strip()
1470	process.term.append(term_attr)
1471	except:
1472	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1473	self.errors.append(err_mess)
1474	logging.error(err_mess)
1475
1476	note_list = item.xpath('ns:SASprocessnote',
1477	namespaces={'ns': CANSAS_NS})
1478	for note in note_list:
1479	if note.text is not None:
1480	process.notes.append(note.text.strip())
1481
1482	data_info.process.append(process)
1483
1484	# Data info ######################
1485	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1486	if len(nodes) > 1:
1487	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1488
1489	for entry in nodes:
1490	for item in list_of_data_2d_attr:
1491	#get node
1492	node = get_content('ns:%s' % item[0], entry)
1493	exec "data_info.%s = parse_entry_helper(node, item)" % item[1]
1494
1495	for item in list_of_data2d_values:
1496	field = get_content('ns:%s' % item[0], entry)
1497	list = []
1498	if field is not None:
1499	list = [parse_entry_helper(node, item) for node in field]
1500	exec "data_info.%s = numpy.array(list)" % item[0]
1501
1502	return data_info
1503
1504	def _read_cansas(self, path):
1505	"""
1506	Load data and P(r) information from a CanSAS XML file.
1507
1508	:param path: file path
1509
1510	:return: Data1D object if a single SASentry was found,
1511	or a list of Data1D objects if multiple entries were found,
1512	or None of nothing was found
1513
1514	:raise RuntimeError: when the file can't be opened
1515	:raise ValueError: when the length of the data vectors are inconsistent
1516
1517	"""
1518	output = []
1519	basename = os.path.basename(path)
1520	root, extension = os.path.splitext(basename)
1521	ext = extension.lower()
1522	try:
1523	if os.path.isfile(path):
1524
1525	#TODO: eventually remove the check for .xml once
1526	# the P(r) writer/reader is truly complete.
1527	if ext in self.ext or \
1528	ext == '.xml':
1529
1530	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1531	# Check the format version number
1532	# Specifying the namespace will take care of the file format version
1533	root = tree.getroot()
1534	entry_list = root.xpath('ns:SASentry',
1535	namespaces={'ns': CANSAS_NS})
1536	for entry in entry_list:
1537	try:
1538	sas_entry = self._parse_entry(entry)
1539	except:
1540	raise
1541	fitstate = self._parse_state(entry)
1542
1543	#state could be None when .svs file is loaded
1544	#in this case, skip appending to output
1545	if fitstate != None:
1546	sas_entry.meta_data['fitstate'] = fitstate
1547	sas_entry.filename = fitstate.file
1548	output.append(sas_entry)
1549	else:
1550	self.call_back(format=ext)
1551	raise RuntimeError, "%s is not a file" % path
1552
1553	# Return output consistent with the loader's api
1554	if len(output) == 0:
1555	self.call_back(state=None, datainfo=None, format=ext)
1556	return None
1557	else:
1558	for ind in range(len(output)):
1559	# Call back to post the new state
1560	state = output[ind].meta_data['fitstate']
1561	t = time.localtime(state.timestamp)
1562	time_str = time.strftime("%b %d %H:%M", t)
1563	# Check that no time stamp is already appended
1564	max_char = state.file.find("[")
1565	if max_char < 0:
1566	max_char = len(state.file)
1567	original_fname = state.file[0:max_char]
1568	state.file = original_fname + ' [' + time_str + ']'
1569
1570	if state is not None and state.is_data is not None:
1571	exec 'output[%d].is_data = state.is_data' % ind
1572
1573	output[ind].filename = state.file
1574	state.data = output[ind]
1575	state.data.name = output[ind].filename # state.data_name
1576	state.data.id = state.data_id
1577	if state.is_data is not None:
1578	state.data.is_data = state.is_data
1579	if output[ind].run_name is not None\
1580	and len(output[ind].run_name) != 0:
1581	name = output[ind].run_name
1582	else:
1583	name = original_fname
1584	state.data.group_id = name
1585	#store state in fitting
1586	self.call_back(state=state,
1587	datainfo=output[ind], format=ext)
1588	self.state = state
1589	return output
1590
1591	except:
1592	self.call_back(format=ext)
1593	#self.state= state
1594	raise
1595
1596	def write(self, filename, datainfo=None, fitstate=None):
1597	"""
1598	Write the content of a Data1D as a CanSAS XML file only for standalone
1599
1600	:param filename: name of the file to write
1601	:param datainfo: Data1D object
1602	:param fitstate: PageState object
1603
1604	"""
1605	# Sanity check
1606	if self.cansas == True:
1607
1608	# Add fitting information to the XML document
1609	doc = self.write_toXML(datainfo, fitstate)
1610	# Write the XML document
1611	fd = open(filename, 'w')
1612	fd.write(doc.toprettyxml())
1613	fd.close()
1614	else:
1615	fitstate.toXML(file=filename)
1616
1617	def write_toXML(self, datainfo=None, state=None):
1618	"""
1619	Write toXML, a helper for write(),
1620	could be used by guimanager._on_save()
1621
1622	: return: xml doc
1623	"""
1624
1625	if state.data is None:
1626	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1627	return None
1628	elif not state.data.is_data:
1629	return None
1630	else:
1631	#make sure title and data run is filled up.
1632	if state.data.title == None or state.data.title == '':
1633	state.data.title = state.data.name
1634	if state.data.run_name == None or state.data.run_name == {}:
1635	state.data.run = [str(state.data.name)]
1636	state.data.run_name[0] = state.data.name
1637
1638	if issubclass(state.data.__class__,
1639	sans.dataloader.data_info.Data1D):
1640	data = state.data
1641	doc, sasentry = self._to_xml_doc(data)
1642	else:
1643	data = state.data
1644	doc, sasentry = self._data2d_to_xml_doc(data)
1645
1646	if state is not None:
1647	state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1648
1649	return doc
1650
1651	# Simple html report templet
1652	HEADER = "<html>\n"
1653	HEADER += "<head>\n"
1654	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1655	HEADER += "charset=windows-1252'> \n"
1656	HEADER += "<meta name=Generator >\n"
1657	HEADER += "</head>\n"
1658	HEADER += "<body lang=EN-US>\n"
1659	HEADER += "<div class=WordSection1>\n"
1660	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1661	HEADER += "%s</font></center></span></center></b></p>"
1662	HEADER += "<p class=MsoNormal> </p>"
1663	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1664	PARA += "</font></p>"
1665	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1666	CENTRE += "</font></center></p>"
1667	FEET_1 = \
1668	"""
1669	<p class=MsoNormal> </p>
1670	<br>
1671	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1672	</font></span></center></b></p>
1673	<p class=MsoNormal> </p>
1674	<center>
1675	<br><font size='4' >Model Computation</font>
1676	<br><font size='4' >Data: "%s"</font><br>
1677	"""
1678	FEET_2 = \
1679	"""
1680	<img src="%s" >
1681	</img>
1682	"""
1683	FEET_3 = \
1684	"""
1685	</center>
1686	</div>
1687	</body>
1688	</html>
1689	"""
1690	ELINE = "<p class=MsoNormal> </p>"
1691
1692	if __name__ == "__main__":
1693	state = PageState(parent=None)
1694	#state.toXML()
1695	"""
1696
1697	file = open("test_state", "w")
1698	pickle.dump(state, file)
1699	print pickle.dumps(state)
1700	state.data_name = "hello---->"
1701	pickle.dump(state, file)
1702	file = open("test_state", "r")
1703	new_state= pickle.load(file)
1704	print "new state", new_state
1705	new_state= pickle.load(file)
1706	print "new state", new_state
1707	#print "state", state
1708	"""
1709	import bsddb
1710	import pickle
1711	db = bsddb.btopen('file_state.db', 'c')
1712	val = (pickle.dumps(state), "hello", "hi")
1713	db['state1'] = pickle.dumps(val)
1714	print pickle.loads(db['state1'])
1715	state.data_name = "hello---->22"
1716	db['state2'] = pickle.dumps(state)
1717	state.data_name = "hello---->2"
1718	db['state3'] = pickle.dumps(state)
1719	del db['state3']
1720	state.data_name = "hello---->3"
1721	db['state4'] = pickle.dumps(state)
1722	new_state = pickle.loads(db['state1'])
1723	#print db.last()
1724	db.set_location('state2')
1725	state.data_name = "hello---->5"
1726	db['aastate5'] = pickle.dumps(state)
1727	db.keys().sort()
1728	print pickle.loads(db['state2'])
1729
1730	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ 397b4e7

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