pagestate.py @ 56acb5d

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 56acb5d was f32d144, checked in by Mathieu Doucet <doucetm@…>, 13 years ago
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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, Detector
28
29	#Information to read/write state as xml
30	FITTING_NODE_NAME = 'fitting_plug_in'
31	CANSAS_NS = "cansas1d/1.0"
32
33	list_of_data_attributes = [["is_data", "is_data", "bool"],
34	["group_id", "data_group_id", "string"],
35	["data_name", "data_name", "string"],
36	["data_id", "data_id", "string"],
37	["name", "name", "string"],
38	["data_name", "data_name", "string"]]
39	list_of_state_attributes = [["engine_type", "engine_type", "string"],
40	["qmin", "qmin", "float"],
41	["qmax", "qmax", "float"],
42	["npts", "npts", "float"],
43	["shape_rbutton", "shape_rbutton", "bool"],
44	["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
45	["plugin_rbutton", "plugin_rbutton", "bool"],
46	["struct_rbutton", "struct_rbutton", "bool"],
47	["formfactorcombobox", "formfactorcombobox", "string"],
48	["structurecombobox", "structurecombobox", "string"],
49	["multi_factor","multi_factor","float"],
50	["enable_smearer","enable_smearer","bool"],
51	["disable_smearer","disable_smearer","bool"],
52	["pinhole_smearer","pinhole_smearer","bool"],
53	["slit_smearer","slit_smearer","bool"],
54	["enable_disp","enable_disp","bool"],
55	["disable_disp","disable_disp","bool"],
56	["dI_noweight","dI_noweight","bool"],
57	["dI_didata","dI_didata","bool"],
58	["dI_sqrdata","dI_sqrdata","bool"],
59	["dI_idata","dI_idata","bool"],
60	["enable2D","enable2D","bool"],
61	["cb1","cb1","bool"],
62	["tcChi","tcChi","float"],
63	["smearer", "smearer", "float"],
64	["smear_type","smear_type", "string"],
65	["dq_l", "dq_l", "string"],
66	["dq_r","dq_r", "string"]]
67
68	list_of_model_attributes = [["values", "values"],
69	["weights", "weights"]]
70
71	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
72
73	list_of_state_parameters = [["parameters", "parameters"],
74	["str_parameters", "str_parameters"],
75	["orientation_parameters", "orientation_params"],
76	["dispersity_parameters", "orientation_params_disp"],
77	["fixed_param", "fixed_param"],
78	["fittable_param", "fittable_param"]]
79	list_of_data_2d_attr = [["xmin", "xmin", "float"],
80	["xmax", "xmax", "float"],
81	["ymin", "ymin", "float"],
82	["ymax", "ymax", "float"],
83	["_xaxis", "_xaxis", "string"],
84	["_xunit", "_xunit", "string"],
85	["_yaxis", "_yaxis", "string"],
86	["_yunit", "_yunit", "string"],
87	["_zaxis", "_zaxis", "string"],
88	["_zunit", "_zunit", "string"]]
89	list_of_data2d_values = [["qx_data", "qx_data", "float"],
90	["qy_data", "qy_data", "float"],
91	["dqx_data", "dqx_data", "float"],
92	["dqy_data", "dqy_data", "float"],
93	["data", "data", "float"],
94	["q_data", "q_data", "float"],
95	["err_data", "err_data", "float"],
96	["mask", "mask", "bool"]]
97
98
99	def parse_entry_helper(node, item):
100	"""
101	Create a numpy list from value extrated from the node
102
103	:param node: node from each the value is stored
104	:param item: list name of three strings.the two first are name of data
105	attribute and the third one is the type of the value of that
106	attribute. type can be string, float, bool, etc.
107
108	: return: numpy array
109	"""
110	if node is not None:
111	if item[2] == "string":
112	return str(node.get(item[0]).strip())
113	elif item[2] == "bool":
114	try:
115	return node.get(item[0]).strip() == "True"
116
117	except:
118	return None
119	else:
120	try:
121	return float(node.get(item[0]))
122	except:
123	return None
124
125
126	class PageState(object):
127	"""
128	Contains information to reconstruct a page of the fitpanel.
129	"""
130	def __init__(self, parent=None, model=None, data=None):
131	"""
132	Initialize the current state
133
134	:param model: a selected model within a page
135	:param data:
136
137	"""
138	self.file = None
139	#Time of state creation
140	self.timestamp = time.time()
141	## Data member to store the dispersion object created
142	self._disp_obj_dict = {}
143	#------------------------
144	#Data used for fitting
145	self.data = data
146	# model data
147	self.theory_data = None
148	#Is 2D
149	self.is_2D = False
150	self.images = None
151
152	#save additional information on data that dataloader.reader does not read
153	self.is_data = None
154	self.data_name = ""
155
156	if self.data is not None:
157	self.data_name = self.data.name
158	self.data_id = None
159	if self.data is not None and hasattr(self.data, "id"):
160	self.data_id = self.data.id
161	self.data_group_id = None
162	if self.data is not None and hasattr(self.data, "group_id"):
163	self.data_group_id = self.data.group_id
164
165	## reset True change the state of exsiting button
166	self.reset = False
167
168	#engine type
169	self.engine_type = None
170	# flag to allow data2D plot
171	self.enable2D = False
172	# model on which the fit would be performed
173	self.model = model
174	self.m_name = None
175	#list of process done to model
176	self.process = []
177	#fit page manager
178	self.manager = None
179	#Store the parent of this panel parent
180	# For this application fitpanel is the parent
181	self.parent = parent
182	# Event_owner is the owner of model event
183	self.event_owner = None
184	##page name
185	self.page_name = ""
186	# Contains link between model ,all its parameters, and panel organization
187	self.parameters = []
188	# String parameter list that can not be fitted
189	self.str_parameters = []
190	# Contains list of parameters that cannot be fitted and reference to
191	#panel objects
192	self.fixed_param = []
193	# Contains list of parameters with dispersity and reference to
194	#panel objects
195	self.fittable_param = []
196	## orientation parameters
197	self.orientation_params = []
198	## orientation parmaters for gaussian dispersity
199	self.orientation_params_disp = []
200	## smearer info
201	self.smearer = None
202	self.smear_type = None
203	self.dq_l = None
204	self.dq_r = None
205
206	#list of dispersion paramaters
207	self.disp_list = []
208	if self.model is not None:
209	self.disp_list = self.model.getDispParamList()
210
211	self.disp_cb_dict = {}
212	self.values = {}
213	self.weights = {}
214
215	#contains link between a model and selected parameters to fit
216	self.param_toFit = []
217	##dictionary of model type and model class
218	self.model_list_box = None
219	## save the state of the context menu
220	self.saved_states = {}
221	## save selection of combobox
222	self.formfactorcombobox = None
223	self.structurecombobox = None
224
225	## radio box to select type of model
226	self.shape_rbutton = False
227	self.shape_indep_rbutton = False
228	self.struct_rbutton = False
229	self.plugin_rbutton = False
230	## the indice of the current selection
231	self.disp_box = 0
232	## Qrange
233	## Q range
234	self.qmin = 0.001
235	self.qmax = 0.1
236	#reset data range
237	self.qmax_x = None
238	self.qmin_x = None
239
240	self.npts = None
241	self.name = ""
242	self.multi_factor = None
243	## enable smearering state
244	self.enable_smearer = False
245	self.disable_smearer = True
246	self.pinhole_smearer = False
247	self.slit_smearer = False
248	# weighting options
249	self.dI_noweight = False
250	self.dI_didata = True
251	self.dI_sqrdata = False
252	self.dI_idata = False
253	## disperity selection
254	self.enable_disp = False
255	self.disable_disp = True
256
257	## state of selected all check button
258	self.cb1 = False
259	## store value of chisqr
260	self.tcChi = None
261
262	def clone(self):
263	"""
264	Create a new copy of the current object
265	"""
266	model = None
267	if self.model is not None:
268	model = self.model.clone()
269	model.name = self.model.name
270	obj = PageState(self.parent, model=model)
271	obj.file = copy.deepcopy(self.file)
272	obj.data = copy.deepcopy(self.data)
273	if self.data is not None:
274	self.data_name = self.data.name
275	obj.data_name = self.data_name
276	obj.is_data = self.is_data
277	obj.model_list_box = copy.deepcopy(self.model_list_box)
278	obj.engine_type = copy.deepcopy(self.engine_type)
279
280	obj.formfactorcombobox = self.formfactorcombobox
281	obj.structurecombobox = self.structurecombobox
282
283	obj.shape_rbutton = self.shape_rbutton
284	obj.shape_indep_rbutton = self.shape_indep_rbutton
285	obj.struct_rbutton = self.struct_rbutton
286	obj.plugin_rbutton = self.plugin_rbutton
287
288	obj.manager = self.manager
289	obj.event_owner = self.event_owner
290	obj.disp_list = copy.deepcopy(self.disp_list)
291
292	obj.enable2D = copy.deepcopy(self.enable2D)
293	obj.parameters = copy.deepcopy(self.parameters)
294	obj.str_parameters = copy.deepcopy(self.str_parameters)
295	obj.fixed_param = copy.deepcopy(self.fixed_param)
296	obj.fittable_param = copy.deepcopy(self.fittable_param)
297	obj.orientation_params = copy.deepcopy(self.orientation_params)
298	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
299	obj.enable_disp = copy.deepcopy(self.enable_disp)
300	obj.disable_disp = copy.deepcopy(self.disable_disp)
301	obj.tcChi = self.tcChi
302
303	if len(self._disp_obj_dict) > 0:
304	for k, v in self._disp_obj_dict.iteritems():
305	obj._disp_obj_dict[k] = v
306	if len(self.disp_cb_dict) > 0:
307	for k, v in self.disp_cb_dict.iteritems():
308	obj.disp_cb_dict[k] = v
309	if len(self.values) > 0:
310	for k, v in self.values.iteritems():
311	obj.values[k] = v
312	if len(self.weights) > 0:
313	for k, v in self.weights.iteritems():
314	obj.weights[k] = v
315	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
316	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
317	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
318	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
319	obj.smear_type = copy.deepcopy(self.smear_type)
320	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
321	obj.dI_didata = copy.deepcopy(self.dI_didata)
322	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
323	obj.dI_idata = copy.deepcopy(self.dI_idata)
324	obj.dq_l = copy.deepcopy(self.dq_l)
325	obj.dq_r = copy.deepcopy(self.dq_r)
326
327	obj.disp_box = copy.deepcopy(self.disp_box)
328	obj.qmin = copy.deepcopy(self.qmin)
329	obj.qmax = copy.deepcopy(self.qmax)
330	obj.multi_factor = self.multi_factor
331	obj.npts = copy.deepcopy(self.npts)
332	obj.cb1 = copy.deepcopy(self.cb1)
333	obj.smearer = copy.deepcopy(self.smearer)
334
335	for name, state in self.saved_states.iteritems():
336	copy_name = copy.deepcopy(name)
337	copy_state = state.clone()
338	obj.saved_states[copy_name] = copy_state
339	return obj
340
341	def _repr_helper(self, list, rep):
342	"""
343	Helper method to print a state
344	"""
345	for item in list:
346	rep += "parameter name: %s \n" % str(item[1])
347	rep += "value: %s\n" % str(item[2])
348	rep += "selected: %s\n" % str(item[0])
349	rep += "error displayed : %s \n" % str(item[4][0])
350	rep += "error value:%s \n" % str(item[4][1])
351	rep += "minimum displayed : %s \n" % str(item[5][0])
352	rep += "minimum value : %s \n" % str(item[5][1])
353	rep += "maximum displayed : %s \n" % str(item[6][0])
354	rep += "maximum value : %s \n" % str(item[6][1])
355	rep += "parameter unit: %s\n\n" % str(item[7])
356	return rep
357
358	def __repr__(self):
359	"""
360	output string for printing
361	"""
362	rep = "\nState name: %s\n" % self.file
363	t = time.localtime(self.timestamp)
364	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
365
366	rep += "State created: %s\n" % time_str
367	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
368	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
369	rep += "is data : %s\n" % self.is_data
370	rep += "data's name : %s\n" % self.data_name
371	rep += "data's id : %s\n" % self.data_id
372	if self.model != None:
373	m_name = self.model.__class__.__name__
374	if m_name == 'Model':
375	m_name = self.m_name
376	rep += "model name : %s\n" % m_name
377	else:
378	rep += "model name : None\n"
379	rep += "model type (form factor) selected: %s\n" % self.shape_rbutton
380	rep += "multi_factor : %s\n" % str(self.multi_factor)
381	rep += "model type (shape independent) selected: %s\n" % self.shape_indep_rbutton
382	rep += "model type (structure factor) selected: %s\n" % self.struct_rbutton
383	rep += "model type (plug-in ) selected: %s\n" % self.plugin_rbutton
384	rep += "data : %s\n" % str(self.data)
385	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
386	str(self.qmax), str(self.npts))
387	rep += "Dispersion selection : %s\n" % str(self.disp_box)
388	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
389	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
390	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
391	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
392	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
393	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
394	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
395
396	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
397	rep += "dI_didata : %s\n" % str(self.dI_didata)
398	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
399	rep += "dI_idata : %s\n" % str(self.dI_idata)
400
401	rep += "2D enable : %s\n" % str(self.enable2D)
402	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
403	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
404	rep += "Smear object : %s\n" % str(self.smearer)
405	rep += "Smear type : %s\n" % (self.smear_type)
406	rep += "dq_l : %s\n" % self.dq_l
407	rep += "dq_r : %s\n" % self.dq_r
408
409	rep += "model : %s\n\n" % str(self.model)
410	temp_parameters = []
411	temp_fittable_param = []
412	if self.data.__class__.__name__ == "Data2D":
413	self.is_2D = True
414	else:
415	self.is_2D = False
416	if self.data is not None:
417	if not self.is_2D:
418	for item in self.parameters:
419	if not item in self.orientation_params:
420	temp_parameters.append(item)
421	for item in self.fittable_param:
422	if not item in self.orientation_params_disp:
423	temp_fittable_param.append(item)
424	else:
425	temp_parameters = self.parameters
426	temp_fittable_param = self.fittable_param
427
428	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
429	rep = self._repr_helper(list=temp_parameters, rep=rep)
430	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
431	rep = self._repr_helper(list=self.str_parameters, rep=rep)
432	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
433	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
434	"""
435	if is_2D:
436	rep += "number orientation parameters"
437	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
438	rep = self._repr_helper( list=self.orientation_params, rep=rep)
439	rep += "number dispersity parameters"
440	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
441	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
442	"""
443	return rep
444
445	def set_report_string(self):
446	"""
447	Get the values (strings) from __str__ for report
448	"""
449	# Dictionary of teh report strings
450	repo_time = ""
451	model_name = ""
452	title = ""
453	title_name = ""
454	file_name = ""
455	param_string = ""
456	paramval_string = ""
457	chi2_string = ""
458	multi_factor_string = ""
459	q_range = ""
460	strings = self.__repr__()
461	lines = strings.split('\n')
462
463	# get all string values from __str__()
464	for line in lines:
465	value = ""
466	content = line.split(":")
467	name = content[0]
468	try:
469	value = content[1]
470	except:
471	pass
472	if name.count("State created"):
473	repo_time = "" + value
474	if name.count("parameter name"):
475	val_name = value.split(".")
476	if len(val_name) > 1:
477	if val_name[1].count("width"):
478	param_string += value + ','
479	else:
480	continue
481	else:
482	param_string += value + ','
483	if name == "value":
484	param_string += value + ','
485	if name == "error value":
486	param_string += value + ','
487	if name == "parameter unit":
488	param_string += value + ':'
489	if name == "Value of Chisqr ":
490	chi2 = ("Chi2/Npts = " + value)
491	chi2_string = CENTRE % chi2
492	if name == "multi_factor ":
493	muti_factor = ("muti_factor = " + value)
494	muti_factor_string = CENTRE % muti_factor
495	if name == "Title":
496	if len(value.strip()) == 0:
497	continue
498	title = value + " [" + repo_time + "]"
499	title_name = HEADER % title
500	if name == "data ":
501	try:
502	file = ("File name:" + content[2])
503	file_name = CENTRE % file
504	if len(title) == 0:
505	title = content[2] + " [" + repo_time + "]"
506	title_name = HEADER % title
507	except:
508	pass
509	if name == "model name ":
510	try:
511	modelname = "Model name:" + content[1]
512	except:
513	modelname = "Model name:" + " NAN"
514	model_name = CENTRE % modelname
515
516	if name == "Plotting Range":
517	try:
518	q_range = content[1] + " = " + content[2] \
519	+ " = " + content[3].split(",")[0]
520	q_name = ("Q Range: " + q_range)
521	q_range = CENTRE % q_name
522	except:
523	pass
524	paramval = ""
525	for lines in param_string.split(":"):
526	line = lines.split(",")
527	if len(lines) > 0:
528	param = line[0]
529	param += " = " + line[1]
530	if len(line[2].split()) > 0 and not line[2].count("None"):
531	param += " +- " + line[2]
532	if len(line[3].split()) > 0 and not line[3].count("None"):
533	param += " " + line[3]
534	if not paramval.count(param):
535	paramval += param + "\n"
536	paramval_string += CENTRE % param + "\n"
537
538	text_string = "\n\n\n" + title + "\n\n" + file + \
539	"\n" + q_name + \
540	"\n" + chi2 + \
541	"\n\n" + paramval
542
543	title_name = self._check_html_format(title_name)
544	file_name = self._check_html_format(file_name)
545	title = self._check_html_format(title)
546
547	html_string = title_name + "\n" + file_name + \
548	"\n" + model_name + \
549	"\n" + q_range + \
550	"\n" + chi2_string + \
551	"\n" + ELINE + \
552	"\n" + paramval_string + \
553	"\n" + ELINE + \
554	"\n" + FEET_1 % title + \
555	"\n" + FEET_2
556
557	return html_string, text_string, title
558
559	def _check_html_format(self, name):
560	"""
561	Check string '%' for html format
562	"""
563	if name.count('%'):
564	name = name.replace('%', '&#37')
565
566	return name
567
568	def report(self, figs=None, canvases=None):
569	"""
570	Invoke report dialog panel
571
572	: param figs: list of pylab figures [list]
573	"""
574	from report_dialog import ReportDialog
575	# get the strings for report
576	html_str, text_str, title = self.set_report_string()
577	# Allow 2 figures to append
578	if len(figs) == 1:
579	add_str = FEET_3
580	elif len(figs) == 2:
581	add_str = ELINE
582	add_str += FEET_2 % ("%s")
583	add_str += ELINE
584	add_str += FEET_3
585	elif len(figs) > 2:
586	add_str = ELINE
587	add_str += FEET_2 % ("%s")
588	add_str += ELINE
589	add_str += FEET_2 % ("%s")
590	add_str += ELINE
591	add_str += FEET_3
592	else:
593	add_str = ""
594
595	# final report html strings
596	report_str = html_str % ("%s") + add_str
597
598	# make plot image
599	images = self.set_plot_state(figs, canvases)
600	report_list = [report_str, text_str, images]
601	dialog = ReportDialog(report_list, None, -1, "")
602	dialog.ShowModal()
603
604	def _toXML_helper(self, list, element, newdoc):
605	"""
606	Helper method to create xml file for saving state
607	"""
608	for item in list:
609	sub_element = newdoc.createElement('parameter')
610	sub_element.setAttribute('name', str(item[1]))
611	sub_element.setAttribute('value', str(item[2]))
612	sub_element.setAttribute('selected_to_fit', str(item[0]))
613	sub_element.setAttribute('error_displayed', str(item[4][0]))
614	sub_element.setAttribute('error_value', str(item[4][1]))
615	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
616	sub_element.setAttribute('minimum_value', str(item[5][1]))
617	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
618	sub_element.setAttribute('maximum_value', str(item[6][1]))
619	sub_element.setAttribute('unit', str(item[7]))
620	element.appendChild(sub_element)
621
622	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
623	"""
624	Writes the state of the InversionControl panel to file, as XML.
625
626	Compatible with standalone writing, or appending to an
627	already existing XML document. In that case, the XML document
628	is required. An optional entry node in the XML document may also be given.
629
630	:param file: file to write to
631	:param doc: XML document object [optional]
632	:param entry_node: XML node within the XML document at which we will append the data [optional]
633
634	"""
635	from xml.dom.minidom import getDOMImplementation
636
637	# Check whether we have to write a standalone XML file
638	if doc is None:
639	impl = getDOMImplementation()
640	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
641	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
642	top_element = newdoc.documentElement
643	else:
644	# We are appending to an existing document
645	newdoc = doc
646	top_element = newdoc.createElement(FITTING_NODE_NAME)
647	if entry_node is None:
648	newdoc.documentElement.appendChild(top_element)
649	else:
650	entry_node.appendChild(top_element)
651
652	attr = newdoc.createAttribute("version")
653	attr.nodeValue = '1.0'
654	top_element.setAttributeNode(attr)
655
656	# File name
657	element = newdoc.createElement("filename")
658	if self.file is not None:
659	element.appendChild(newdoc.createTextNode(str(self.file)))
660	else:
661	element.appendChild(newdoc.createTextNode(str(file)))
662	top_element.appendChild(element)
663
664	element = newdoc.createElement("timestamp")
665	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
666	attr = newdoc.createAttribute("epoch")
667	attr.nodeValue = str(self.timestamp)
668	element.setAttributeNode(attr)
669	top_element.appendChild(element)
670	# Inputs
671	inputs = newdoc.createElement("Attributes")
672	top_element.appendChild(inputs)
673
674	if self.data is not None and hasattr(self.data, "group_id"):
675	self.data_group_id = self.data.group_id
676	if self.data is not None and hasattr(self.data, "is_data"):
677	self.is_data = self.data.is_data
678	if self.data is not None:
679	self.data_name = self.data.name
680	if self.data is not None and hasattr(self.data, "id"):
681	self.data_id = self.data.id
682
683	for item in list_of_data_attributes:
684	element = newdoc.createElement(item[0])
685	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
686	inputs.appendChild(element)
687
688	for item in list_of_state_attributes:
689	element = newdoc.createElement(item[0])
690	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
691	inputs.appendChild(element)
692
693	# For self.values ={ disp_param_name: [vals,...],...}
694	# and for self.weights ={ disp_param_name: [weights,...],...}
695	for item in list_of_model_attributes:
696	element = newdoc.createElement(item[0])
697	exec "list = self.%s" % item[1]
698	for key, value in list.iteritems():
699	sub_element = newdoc.createElement(key)
700	sub_element.setAttribute('name', str(key))
701	for val in value:
702	com = "sub_element.appendChild"
703	com += "(newdoc.createTextNode(str(%s)))"
704	exec com % val
705
706	element.appendChild(sub_element)
707	inputs.appendChild(element)
708
709	# Create doc for the dictionary of self._disp_obj_dic
710	for item in list_of_obj_dic:
711	element = newdoc.createElement(item[0])
712	exec "list = self.%s" % item[1]
713	for key, val in list.iteritems():
714	value = repr(val)
715	sub_element = newdoc.createElement(key)
716	sub_element.setAttribute('name', str(key))
717	sub_element.setAttribute('value', str(value))
718	element.appendChild(sub_element)
719	inputs.appendChild(element)
720
721	for item in list_of_state_parameters:
722	element = newdoc.createElement(item[0])
723	com = "self._toXML_helper(list=self.%s,"
724	com += " element=element, newdoc=newdoc)"
725	exec com % item[1]
726	inputs.appendChild(element)
727
728	# Save the file
729	if doc is None:
730	fd = open(file, 'w')
731	fd.write(newdoc.toprettyxml())
732	fd.close()
733	return None
734	else:
735	return newdoc.toprettyxml()
736
737	def _fromXML_helper(self, node, list):
738	"""
739	Helper function to write state to xml
740	"""
741	for item in node:
742	try:
743	name = item.get('name')
744	except:
745	name = None
746	try:
747	value = item.get('value')
748	except:
749	value = None
750	try:
751	selected_to_fit = (item.get('selected_to_fit') == "True")
752	except:
753	selected_to_fit = None
754	try:
755	error_displayed = (item.get('error_displayed') == "True")
756	except:
757	error_displayed = None
758	try:
759	error_value = item.get('error_value')
760	except:
761	error_value = None
762	try:
763	minimum_displayed = (item.get('minimum_displayed') == "True")
764	except:
765	minimum_displayed = None
766	try:
767	minimum_value = item.get('minimum_value')
768	except:
769	minimum_value = None
770	try:
771	maximum_displayed = (item.get('maximum_displayed') == "True")
772	except:
773	maximum_displayed = None
774	try:
775	maximum_value = item.get('maximum_value')
776	except:
777	maximum_value = None
778	try:
779	unit = item.get('unit')
780	except:
781	unit = None
782	list.append([selected_to_fit, name, value, "+/-",
783	[error_displayed, error_value],
784	[minimum_displayed, minimum_value],
785	[maximum_displayed, maximum_value], unit])
786
787	def fromXML(self, file=None, node=None):
788	"""
789	Load fitting state from a file
790
791	:param file: .fitv file
792	:param node: node of a XML document to read from
793
794	"""
795	if file is not None:
796	msg = "PageState no longer supports non-CanSAS"
797	msg += " format for fitting files"
798	raise RuntimeError, msg
799
800	if node.get('version')and node.get('version') == '1.0':
801
802	# Get file name
803	entry = get_content('ns:filename', node)
804	if entry is not None:
805	self.file = entry.text.strip()
806
807	# Get time stamp
808	entry = get_content('ns:timestamp', node)
809	if entry is not None and entry.get('epoch'):
810	try:
811	self.timestamp = float(entry.get('epoch'))
812	except:
813	msg = "PageState.fromXML: Could not"
814	msg += " read timestamp\n %s" % sys.exc_value
815	logging.error(msg)
816
817	# Parse fitting attributes
818	entry = get_content('ns:Attributes', node)
819	for item in list_of_data_attributes:
820	node = get_content('ns:%s' % item[0], entry)
821	try:
822	exec "self.%s = parse_entry_helper(node, item)" % item[0]
823
824	except:
825	raise
826
827	if entry is not None:
828
829	for item in list_of_state_attributes:
830	node = get_content('ns:%s' % item[0], entry)
831	try:
832	exec "self.%s = parse_entry_helper(node, item)" % \
833	str(item[0])
834	except:
835	raise
836
837	for item in list_of_state_parameters:
838	node = get_content("ns:%s" % item[0], entry)
839	exec "self._fromXML_helper(node=node, list=self.%s)" % \
840	item[1]
841
842	# Recover _disp_obj_dict from xml file
843	self._disp_obj_dict = {}
844	for item in list_of_obj_dic:
845	# Get node
846	node = get_content("ns:%s" % item[0], entry)
847	for attr in node:
848	name = attr.get('name')
849	val = attr.get('value')
850	value = val.split(" instance")[0]
851	disp_name = value.split("<")[1]
852	try:
853	# Try to recover disp_model object from strings
854	com = "from sans.models.dispersion_models "
855	com += "import %s as disp"
856	com_name = disp_name.split(".")[3]
857	exec com % com_name
858	disp_model = disp()
859	exec "self.%s['%s'] = com_name" % (item[1], name)
860	except:
861	pass
862
863	# get self.values and self.weights dic. if exists
864	for item in list_of_model_attributes:
865	node = get_content("ns:%s" % item[0], entry)
866	dic = {}
867	list = []
868	for par in node:
869	name = par.get('name')
870	values = par.text.split('\n')
871	# Get lines only with numbers
872	for line in values:
873	try:
874	val = float(line)
875	list.append(val)
876	except:
877	# pass if line is empty (it happens)
878	pass
879	dic[name] = numpy.array(list)
880	exec "self.%s = dic" % item[1]
881
882	def set_plot_state(self, figs, canvases):
883	"""
884	Build image state that wx.html understand
885	by plotting, putting it into wx.FileSystem image object
886
887	"""
888	images = []
889	# some imports
890	import wx
891
892	# Reset memory
893	self.imgRAM = None
894	wx.MemoryFSHandler()
895
896	# For no figures in the list, prepare empty plot
897	if figs == None or len(figs) == 0:
898	figs = [None]
899
900	# Loop over the list of figures
901	# use wx.MemoryFSHandler
902	self.imgRAM = wx.MemoryFSHandler()
903	for fig in figs:
904	if figs != None:
905	ind = figs.index(fig)
906	canvas = canvases[ind]
907
908	#store the image in wx.FileSystem Object
909	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
910
911	# index of the fig
912	ind = figs.index(fig)
913
914	#AddFile, image can be retrieved with 'memory:filename'
915	self.imgRAM.AddFile('img_fit%s.png' % ind,
916	canvas.bitmap, wx.BITMAP_TYPE_PNG)
917
918	#append figs
919	images.append(fig)
920
921	return images
922
923
924	class Reader(CansasReader):
925	"""
926	Class to load a .fitv fitting file
927	"""
928	## File type
929	type_name = "Fitting"
930
931	## Wildcards
932	type = ["Fitting files (.fitv)\|.fitv"
933	"SANSView file (.svs)\|.svs"]
934	## List of allowed extensions
935	ext = ['.fitv', '.FITV', '.svs', 'SVS']
936
937	def __init__(self, call_back=None, cansas=True):
938	CansasReader.__init__(self)
939	"""
940	Initialize the call-back method to be called
941	after we load a file
942
943	:param call_back: call-back method
944	:param cansas: True = files will be written/read in CanSAS format
945	False = write CanSAS format
946
947	"""
948	## Call back method to be executed after a file is read
949	self.call_back = call_back
950	## CanSAS format flag
951	self.cansas = cansas
952	self.state = None
953
954	def get_state(self):
955	return self.state
956
957	def read(self, path):
958	"""
959	Load a new P(r) inversion state from file
960
961	:param path: file path
962
963	"""
964	if self.cansas == True:
965	return self._read_cansas(path)
966
967	def _data2d_to_xml_doc(self, datainfo):
968	"""
969	Create an XML document to contain the content of a Data2D
970
971	:param datainfo: Data2D object
972
973	"""
974	if not issubclass(datainfo.__class__, Data2D):
975	raise RuntimeError, "The cansas writer expects a Data2D instance"
976
977	doc = xml.dom.minidom.Document()
978	main_node = doc.createElement("SASroot")
979	main_node.setAttribute("version", self.version)
980	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
981	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
982	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
983
984	doc.appendChild(main_node)
985
986	entry_node = doc.createElement("SASentry")
987	main_node.appendChild(entry_node)
988
989	write_node(doc, entry_node, "Title", datainfo.title)
990	if datainfo is not None:
991	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
992	for item in datainfo.run:
993	runname = {}
994	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
995	runname = {'name': datainfo.run_name[item] }
996	write_node(doc, entry_node, "Run", item, runname)
997	# Data info
998	new_node = doc.createElement("SASdata")
999	entry_node.appendChild(new_node)
1000	for item in list_of_data_2d_attr:
1001	element = doc.createElement(item[0])
1002	exec "element.setAttribute(item[0], str(datainfo.%s))" % (item[1])
1003	new_node.appendChild(element)
1004
1005	for item in list_of_data2d_values:
1006	root_node = doc.createElement(item[0])
1007	new_node.appendChild(root_node)
1008
1009	exec "temp_list = datainfo.%s" % item[1]
1010
1011	if temp_list is None or len(temp_list)== 0:
1012	element = doc.createElement(item[0])
1013	exec "element.appendChild(doc.createTextNode(str(%s)))" % temp_list
1014	root_node.appendChild(element)
1015	else:
1016	for value in temp_list:
1017	element = doc.createElement(item[0])
1018	exec "element.setAttribute(item[0], str(%s))" % value
1019	root_node.appendChild(element)
1020
1021	# Sample info
1022	sample = doc.createElement("SASsample")
1023	if datainfo.sample.name is not None:
1024	sample.setAttribute("name", str(datainfo.sample.name))
1025	entry_node.appendChild(sample)
1026	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1027	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1028	{"unit": datainfo.sample.thickness_unit})
1029	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1030	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1031	{"unit": datainfo.sample.temperature_unit})
1032
1033	for item in datainfo.sample.details:
1034	write_node(doc, sample, "details", item)
1035
1036	pos = doc.createElement("position")
1037	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1038	{"unit": datainfo.sample.position_unit})
1039	written = written \| write_node(doc, pos, "y",
1040	datainfo.sample.position.y,
1041	{"unit": datainfo.sample.position_unit})
1042	written = written \| write_node(doc, pos, "z",
1043	datainfo.sample.position.z,
1044	{"unit": datainfo.sample.position_unit})
1045	if written == True:
1046	sample.appendChild(pos)
1047
1048	ori = doc.createElement("orientation")
1049	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1050	{"unit": datainfo.sample.orientation_unit})
1051	written = written \| write_node(doc, ori, "pitch",
1052	datainfo.sample.orientation.y,
1053	{"unit": datainfo.sample.orientation_unit})
1054	written = written \| write_node(doc, ori, "yaw",
1055	datainfo.sample.orientation.z,
1056	{"unit": datainfo.sample.orientation_unit})
1057	if written == True:
1058	sample.appendChild(ori)
1059
1060	# Instrument info
1061	instr = doc.createElement("SASinstrument")
1062	entry_node.appendChild(instr)
1063
1064	write_node(doc, instr, "name", datainfo.instrument)
1065
1066	# Source
1067	source = doc.createElement("SASsource")
1068	if datainfo.source.name is not None:
1069	source.setAttribute("name", str(datainfo.source.name))
1070	instr.appendChild(source)
1071
1072	write_node(doc, source, "radiation", datainfo.source.radiation)
1073	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1074	size = doc.createElement("beam_size")
1075	if datainfo.source.beam_size_name is not None:
1076	size.setAttribute("name", str(datainfo.source.beam_size_name))
1077	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1078	{"unit": datainfo.source.beam_size_unit})
1079	written = written \| write_node(doc, size, "y",
1080	datainfo.source.beam_size.y,
1081	{"unit": datainfo.source.beam_size_unit})
1082	written = written \| write_node(doc, size, "z",
1083	datainfo.source.beam_size.z,
1084	{"unit": datainfo.source.beam_size_unit})
1085	if written == True:
1086	source.appendChild(size)
1087
1088	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1089	{"unit": datainfo.source.wavelength_unit})
1090	write_node(doc, source, "wavelength_min",
1091	datainfo.source.wavelength_min,
1092	{"unit": datainfo.source.wavelength_min_unit})
1093	write_node(doc, source, "wavelength_max",
1094	datainfo.source.wavelength_max,
1095	{"unit": datainfo.source.wavelength_max_unit})
1096	write_node(doc, source, "wavelength_spread",
1097	datainfo.source.wavelength_spread,
1098	{"unit": datainfo.source.wavelength_spread_unit})
1099
1100	# Collimation
1101	for item in datainfo.collimation:
1102	coll = doc.createElement("SAScollimation")
1103	if item.name is not None:
1104	coll.setAttribute("name", str(item.name))
1105	instr.appendChild(coll)
1106
1107	write_node(doc, coll, "length", item.length,
1108	{"unit": item.length_unit})
1109
1110	for apert in item.aperture:
1111	ap = doc.createElement("aperture")
1112	if apert.name is not None:
1113	ap.setAttribute("name", str(apert.name))
1114	if apert.type is not None:
1115	ap.setAttribute("type", str(apert.type))
1116	coll.appendChild(ap)
1117
1118	write_node(doc, ap, "distance", apert.distance,
1119	{"unit": apert.distance_unit})
1120
1121	size = doc.createElement("size")
1122	if apert.size_name is not None:
1123	size.setAttribute("name", str(apert.size_name))
1124	written = write_node(doc, size, "x", apert.size.x,
1125	{"unit": apert.size_unit})
1126	written = written \| write_node(doc, size, "y", apert.size.y,
1127	{"unit": apert.size_unit})
1128	written = written \| write_node(doc, size, "z", apert.size.z,
1129	{"unit": apert.size_unit})
1130	if written == True:
1131	ap.appendChild(size)
1132
1133	# Detectors
1134	for item in datainfo.detector:
1135	det = doc.createElement("SASdetector")
1136	written = write_node(doc, det, "name", item.name)
1137	written = written \| write_node(doc, det, "SDD", item.distance,
1138	{"unit": item.distance_unit})
1139	written = written \| write_node(doc, det, "slit_length",
1140	item.slit_length,
1141	{"unit": item.slit_length_unit})
1142	if written == True:
1143	instr.appendChild(det)
1144
1145	off = doc.createElement("offset")
1146	written = write_node(doc, off, "x", item.offset.x,
1147	{"unit": item.offset_unit})
1148	written = written \| write_node(doc, off, "y", item.offset.y,
1149	{"unit": item.offset_unit})
1150	written = written \| write_node(doc, off, "z", item.offset.z,
1151	{"unit": item.offset_unit})
1152	if written == True:
1153	det.appendChild(off)
1154
1155	center = doc.createElement("beam_center")
1156	written = write_node(doc, center, "x", item.beam_center.x,
1157	{"unit": item.beam_center_unit})
1158	written = written \| write_node(doc, center, "y",
1159	item.beam_center.y,
1160	{"unit": item.beam_center_unit})
1161	written = written \| write_node(doc, center, "z",
1162	item.beam_center.z,
1163	{"unit": item.beam_center_unit})
1164	if written == True:
1165	det.appendChild(center)
1166
1167	pix = doc.createElement("pixel_size")
1168	written = write_node(doc, pix, "x", item.pixel_size.x,
1169	{"unit": item.pixel_size_unit})
1170	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1171	{"unit": item.pixel_size_unit})
1172	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1173	{"unit": item.pixel_size_unit})
1174	if written == True:
1175	det.appendChild(pix)
1176
1177	ori = doc.createElement("orientation")
1178	written = write_node(doc, ori, "roll", item.orientation.x,
1179	{"unit": item.orientation_unit})
1180	written = written \| write_node(doc, ori, "pitch",
1181	item.orientation.y,
1182	{"unit": item.orientation_unit})
1183	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1184	{"unit": item.orientation_unit})
1185	if written == True:
1186	det.appendChild(ori)
1187
1188	# Processes info
1189	for item in datainfo.process:
1190	node = doc.createElement("SASprocess")
1191	entry_node.appendChild(node)
1192
1193	write_node(doc, node, "name", item.name)
1194	write_node(doc, node, "date", item.date)
1195	write_node(doc, node, "description", item.description)
1196	for term in item.term:
1197	value = term['value']
1198	del term['value']
1199	write_node(doc, node, "term", value, term)
1200	for note in item.notes:
1201	write_node(doc, node, "SASprocessnote", note)
1202	# Return the document, and the SASentry node associated with
1203	# the data we just wrote
1204	return doc, entry_node
1205
1206	def _parse_state(self, entry):
1207	"""
1208	Read a fit result from an XML node
1209
1210	:param entry: XML node to read from
1211
1212	:return: PageState object
1213	"""
1214	# Create an empty state
1215	state = None
1216	# Locate the P(r) node
1217	try:
1218	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1219	namespaces={'ns': CANSAS_NS})
1220	if nodes != []:
1221	# Create an empty state
1222	state = PageState()
1223	state.fromXML(node=nodes[0])
1224	except:
1225	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1226
1227	return state
1228
1229	def _parse_entry(self, dom):
1230	"""
1231	Parse a SASentry
1232
1233	:param node: SASentry node
1234
1235	:return: Data1D/Data2D object
1236
1237	"""
1238	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1239	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1240	return CansasReader._parse_entry(self, dom)
1241
1242	#Parse 2D
1243	data_info = Data2D()
1244
1245	# Look up title
1246	self._store_content('ns:Title', dom, 'title', data_info)
1247
1248	# Look up run number
1249	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1250	for item in nodes:
1251	if item.text is not None:
1252	value = item.text.strip()
1253	if len(value) > 0:
1254	data_info.run.append(value)
1255	if item.get('name') is not None:
1256	data_info.run_name[value] = item.get('name')
1257
1258	# Look up instrument name
1259	self._store_content('ns:SASinstrument/ns:name', dom,
1260	'instrument', data_info)
1261
1262	# Notes
1263	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1264	for note in note_list:
1265	try:
1266	if note.text is not None:
1267	note_value = note.text.strip()
1268	if len(note_value) > 0:
1269	data_info.notes.append(note_value)
1270	except:
1271	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1272	self.errors.append(err_mess)
1273	logging.error(err_mess)
1274
1275	# Sample info ###################
1276	entry = get_content('ns:SASsample', dom)
1277	if entry is not None:
1278	data_info.sample.name = entry.get('name')
1279
1280	self._store_content('ns:SASsample/ns:ID',
1281	dom, 'ID', data_info.sample)
1282	self._store_float('ns:SASsample/ns:thickness',
1283	dom, 'thickness', data_info.sample)
1284	self._store_float('ns:SASsample/ns:transmission',
1285	dom, 'transmission', data_info.sample)
1286	self._store_float('ns:SASsample/ns:temperature',
1287	dom, 'temperature', data_info.sample)
1288
1289	nodes = dom.xpath('ns:SASsample/ns:details',
1290	namespaces={'ns': CANSAS_NS})
1291	for item in nodes:
1292	try:
1293	if item.text is not None:
1294	detail_value = item.text.strip()
1295	if len(detail_value) > 0:
1296	data_info.sample.details.append(detail_value)
1297	except:
1298	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1299	self.errors.append(err_mess)
1300	logging.error(err_mess)
1301
1302	# Position (as a vector)
1303	self._store_float('ns:SASsample/ns:position/ns:x',
1304	dom, 'position.x', data_info.sample)
1305	self._store_float('ns:SASsample/ns:position/ns:y',
1306	dom, 'position.y', data_info.sample)
1307	self._store_float('ns:SASsample/ns:position/ns:z',
1308	dom, 'position.z', data_info.sample)
1309
1310	# Orientation (as a vector)
1311	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1312	dom, 'orientation.x', data_info.sample)
1313	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1314	dom, 'orientation.y', data_info.sample)
1315	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1316	dom, 'orientation.z', data_info.sample)
1317
1318	# Source info ###################
1319	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1320	if entry is not None:
1321	data_info.source.name = entry.get('name')
1322
1323	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1324	dom, 'radiation', data_info.source)
1325	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1326	dom, 'beam_shape', data_info.source)
1327	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1328	dom, 'wavelength', data_info.source)
1329	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1330	dom, 'wavelength_min', data_info.source)
1331	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1332	dom, 'wavelength_max', data_info.source)
1333	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1334	dom, 'wavelength_spread', data_info.source)
1335
1336	# Beam size (as a vector)
1337	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1338	if entry is not None:
1339	data_info.source.beam_size_name = entry.get('name')
1340
1341	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1342	dom, 'beam_size.x', data_info.source)
1343	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1344	dom, 'beam_size.y', data_info.source)
1345	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1346	dom, 'beam_size.z', data_info.source)
1347
1348	# Collimation info ###################
1349	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1350	namespaces={'ns': CANSAS_NS})
1351	for item in nodes:
1352	collim = Collimation()
1353	if item.get('name') is not None:
1354	collim.name = item.get('name')
1355	self._store_float('ns:length', item, 'length', collim)
1356
1357	# Look for apertures
1358	apert_list = item.xpath('ns:aperture',
1359	namespaces={'ns': CANSAS_NS})
1360	for apert in apert_list:
1361	aperture = Aperture()
1362
1363	# Get the name and type of the aperture
1364	aperture.name = apert.get('name')
1365	aperture.type = apert.get('type')
1366
1367	self._store_float('ns:distance', apert, 'distance', aperture)
1368
1369	entry = get_content('ns:size', apert)
1370	if entry is not None:
1371	aperture.size_name = entry.get('name')
1372
1373	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1374	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1375	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1376
1377	collim.aperture.append(aperture)
1378
1379	data_info.collimation.append(collim)
1380
1381	# Detector info ######################
1382	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1383	namespaces={'ns': CANSAS_NS})
1384	for item in nodes:
1385
1386	detector = Detector()
1387
1388	self._store_content('ns:name', item, 'name', detector)
1389	self._store_float('ns:SDD', item, 'distance', detector)
1390
1391	# Detector offset (as a vector)
1392	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1393	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1394	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1395
1396	# Detector orientation (as a vector)
1397	self._store_float('ns:orientation/ns:roll', item,
1398	'orientation.x', detector)
1399	self._store_float('ns:orientation/ns:pitch', item,
1400	'orientation.y', detector)
1401	self._store_float('ns:orientation/ns:yaw', item,
1402	'orientation.z', detector)
1403
1404	# Beam center (as a vector)
1405	self._store_float('ns:beam_center/ns:x', item,
1406	'beam_center.x', detector)
1407	self._store_float('ns:beam_center/ns:y', item,
1408	'beam_center.y', detector)
1409	self._store_float('ns:beam_center/ns:z', item,
1410	'beam_center.z', detector)
1411
1412	# Pixel size (as a vector)
1413	self._store_float('ns:pixel_size/ns:x', item,
1414	'pixel_size.x', detector)
1415	self._store_float('ns:pixel_size/ns:y', item,
1416	'pixel_size.y', detector)
1417	self._store_float('ns:pixel_size/ns:z', item,
1418	'pixel_size.z', detector)
1419
1420	self._store_float('ns:slit_length', item, 'slit_length', detector)
1421
1422	data_info.detector.append(detector)
1423
1424	# Processes info ######################
1425	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1426	for item in nodes:
1427	process = Process()
1428	self._store_content('ns:name', item, 'name', process)
1429	self._store_content('ns:date', item, 'date', process)
1430	self._store_content('ns:description', item, 'description', process)
1431
1432	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1433	for term in term_list:
1434	try:
1435	term_attr = {}
1436	for attr in term.keys():
1437	term_attr[attr] = term.get(attr).strip()
1438	if term.text is not None:
1439	term_attr['value'] = term.text.strip()
1440	process.term.append(term_attr)
1441	except:
1442	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1443	self.errors.append(err_mess)
1444	logging.error(err_mess)
1445
1446	note_list = item.xpath('ns:SASprocessnote',
1447	namespaces={'ns': CANSAS_NS})
1448	for note in note_list:
1449	if note.text is not None:
1450	process.notes.append(note.text.strip())
1451
1452	data_info.process.append(process)
1453
1454	# Data info ######################
1455	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1456	if len(nodes) > 1:
1457	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1458
1459	for entry in nodes:
1460	for item in list_of_data_2d_attr:
1461	#get node
1462	node = get_content('ns:%s' % item[0], entry)
1463	exec "data_info.%s = parse_entry_helper(node, item)" % item[1]
1464
1465	for item in list_of_data2d_values:
1466	field = get_content('ns:%s' % item[0], entry)
1467	list = []
1468	if field is not None:
1469	list = [parse_entry_helper(node, item) for node in field]
1470	exec "data_info.%s = numpy.array(list)" % item[0]
1471
1472	return data_info
1473
1474	def _read_cansas(self, path):
1475	"""
1476	Load data and P(r) information from a CanSAS XML file.
1477
1478	:param path: file path
1479
1480	:return: Data1D object if a single SASentry was found,
1481	or a list of Data1D objects if multiple entries were found,
1482	or None of nothing was found
1483
1484	:raise RuntimeError: when the file can't be opened
1485	:raise ValueError: when the length of the data vectors are inconsistent
1486
1487	"""
1488	output = []
1489	basename = os.path.basename(path)
1490	root, extension = os.path.splitext(basename)
1491	ext = extension.lower()
1492	try:
1493	if os.path.isfile(path):
1494
1495	#TODO: eventually remove the check for .xml once
1496	# the P(r) writer/reader is truly complete.
1497	if ext in self.ext or \
1498	ext == '.xml':
1499
1500	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1501	# Check the format version number
1502	# Specifying the namespace will take care of the file format version
1503	root = tree.getroot()
1504	entry_list = root.xpath('ns:SASentry',
1505	namespaces={'ns': CANSAS_NS})
1506	for entry in entry_list:
1507	try:
1508	sas_entry = self._parse_entry(entry)
1509	except:
1510	raise
1511	fitstate = self._parse_state(entry)
1512
1513	#state could be None when .svs file is loaded
1514	#in this case, skip appending to output
1515	if fitstate != None:
1516	sas_entry.meta_data['fitstate'] = fitstate
1517	sas_entry.filename = fitstate.file
1518	output.append(sas_entry)
1519	else:
1520	self.call_back(format=ext)
1521	raise RuntimeError, "%s is not a file" % path
1522
1523	# Return output consistent with the loader's api
1524	if len(output) == 0:
1525	self.call_back(state=None, datainfo=None, format=ext)
1526	return None
1527	else:
1528	for ind in range(len(output)):
1529	# Call back to post the new state
1530	state = output[ind].meta_data['fitstate']
1531	t = time.localtime(state.timestamp)
1532	time_str = time.strftime("%b %d %H:%M", t)
1533	# Check that no time stamp is already appended
1534	max_char = state.file.find("[")
1535	if max_char < 0:
1536	max_char = len(state.file)
1537	original_fname = state.file[0:max_char]
1538	state.file = original_fname + ' [' + time_str + ']'
1539
1540	if state is not None and state.is_data is not None:
1541	exec 'output[%d].is_data = state.is_data' % ind
1542
1543	output[ind].filename = state.file
1544	state.data = output[ind]
1545	state.data.name = output[ind].filename # state.data_name
1546	state.data.id = state.data_id
1547	if state.is_data is not None:
1548	state.data.is_data = state.is_data
1549	if output[ind].run_name is not None\
1550	and len(output[ind].run_name) != 0:
1551	name = output[ind].run_name
1552	else:
1553	name = original_fname
1554	state.data.group_id = name
1555	#store state in fitting
1556	self.call_back(state=state,
1557	datainfo=output[ind], format=ext)
1558	self.state = state
1559	return output
1560
1561	except:
1562	self.call_back(format=ext)
1563	#self.state= state
1564	raise
1565
1566	def write(self, filename, datainfo=None, fitstate=None):
1567	"""
1568	Write the content of a Data1D as a CanSAS XML file only for standalone
1569
1570	:param filename: name of the file to write
1571	:param datainfo: Data1D object
1572	:param fitstate: PageState object
1573
1574	"""
1575	# Sanity check
1576	if self.cansas == True:
1577
1578	# Add fitting information to the XML document
1579	doc = self.write_toXML(datainfo, fitstate)
1580	# Write the XML document
1581	fd = open(filename, 'w')
1582	fd.write(doc.toprettyxml())
1583	fd.close()
1584	else:
1585	fitstate.toXML(file=filename)
1586
1587	def write_toXML(self, datainfo=None, state=None):
1588	"""
1589	Write toXML, a helper for write(),
1590	could be used by guimanager._on_save()
1591
1592	: return: xml doc
1593	"""
1594
1595	if state.data is None:
1596	data = sans.dataloader.data_info.Data1D(x=[], y=[])
1597	else:
1598	#make sure title and data run is filled up.
1599	if state.data.title == None or state.data.title == '':
1600	state.data.title = state.data.name
1601	if state.data.run_name == None or state.data.run_name == {}:
1602	state.data.run = [str(state.data.name)]
1603	state.data.run_name[0] = state.data.name
1604
1605	if issubclass(state.data.__class__,
1606	sans.dataloader.data_info.Data1D):
1607	data = state.data
1608	doc, sasentry = self._to_xml_doc(data)
1609	else:
1610	data = state.data
1611	doc, sasentry = self._data2d_to_xml_doc(data)
1612
1613	if state is not None:
1614	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1615
1616	return doc
1617
1618	# Simple html report templet
1619	HEADER = "<html>\n"
1620	HEADER += "<head>\n"
1621	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1622	HEADER += "charset=windows-1252'> \n"
1623	HEADER += "<meta name=Generator >\n"
1624	HEADER += "</head>\n"
1625	HEADER += "<body lang=EN-US>\n"
1626	HEADER += "<div class=WordSection1>\n"
1627	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1628	HEADER += "%s</font></center></span></center></b></p>"
1629	HEADER += "<p class=MsoNormal> </p>"
1630	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1631	PARA += "</font></p>"
1632	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1633	CENTRE += "</font></center></p>"
1634	FEET_1 = \
1635	"""
1636	<p class=MsoNormal> </p>
1637	<br>
1638	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1639	</font></span></center></b></p>
1640	<p class=MsoNormal> </p>
1641	<center>
1642	<br><font size='4' >Model Computation</font>
1643	<br><font size='4' >Data: "%s"</font><br>
1644	"""
1645	FEET_2 = \
1646	"""
1647	<img src="%s" >
1648	</img>
1649	"""
1650	FEET_3 = \
1651	"""
1652	</center>
1653	</div>
1654	</body>
1655	</html>
1656	"""
1657	ELINE = "<p class=MsoNormal> </p>"
1658
1659	if __name__ == "__main__":
1660	state = PageState(parent=None)
1661	#state.toXML()
1662	"""
1663
1664	file = open("test_state", "w")
1665	pickle.dump(state, file)
1666	print pickle.dumps(state)
1667	state.data_name = "hello---->"
1668	pickle.dump(state, file)
1669	file = open("test_state", "r")
1670	new_state= pickle.load(file)
1671	print "new state", new_state
1672	new_state= pickle.load(file)
1673	print "new state", new_state
1674	#print "state", state
1675	"""
1676	import bsddb
1677	import pickle
1678	db = bsddb.btopen('file_state.db', 'c')
1679	val = (pickle.dumps(state), "hello", "hi")
1680	db['state1'] = pickle.dumps(val)
1681	print pickle.loads(db['state1'])
1682	state.data_name = "hello---->22"
1683	db['state2'] = pickle.dumps(state)
1684	state.data_name = "hello---->2"
1685	db['state3'] = pickle.dumps(state)
1686	del db['state3']
1687	state.data_name = "hello---->3"
1688	db['state4'] = pickle.dumps(state)
1689	new_state = pickle.loads(db['state1'])
1690	#print db.last()
1691	db.set_location('state2')
1692	state.data_name = "hello---->5"
1693	db['aastate5'] = pickle.dumps(state)
1694	db.keys().sort()
1695	print pickle.loads(db['state2'])
1696
1697	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ 56acb5d

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