pagestate.py @ a342928

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 a342928 was 0e33a8d, checked in by Doucet, Mathieu <doucetm@…>, 9 years ago
Minor fixes to state loading
Property mode set to `100644`
File size: 69.9 KB

Line
1	"""
2	Class that holds a fit page state
3	"""
4	#TODO: Refactor code so we don't need to use getattr/setattr
5	################################################################################
6	#This software was developed by the University of Tennessee as part of the
7	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
8	#project funded by the US National Science Foundation.
9	#
10	#See the license text in license.txt
11	#
12	#copyright 2009, University of Tennessee
13	################################################################################
14	import time
15	import os
16	import sys
17	import copy
18	import logging
19	import numpy
20	import string
21
22	import xml.dom.minidom
23	from xml.dom.minidom import parseString
24	from lxml import etree
25
26	import sas.dataloader
27	from sas.dataloader.readers.cansas_reader import Reader as CansasReader
28	from sas.dataloader.readers.cansas_reader import get_content, write_node
29	from sas.dataloader.data_info import Data2D
30	from sas.dataloader.data_info import Collimation
31	from sas.dataloader.data_info import Detector
32	from sas.dataloader.data_info import Process
33	from sas.dataloader.data_info import Aperture
34	#Information to read/write state as xml
35	FITTING_NODE_NAME = 'fitting_plug_in'
36	CANSAS_NS = "cansas1d/1.0"
37
38	LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"],
39	["group_id", "data_group_id", "string"],
40	["data_name", "data_name", "string"],
41	["data_id", "data_id", "string"],
42	["name", "name", "string"],
43	["data_name", "data_name", "string"]]
44	LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"],
45	["qmax", "qmax", "float"],
46	["npts", "npts", "float"],
47	["categorycombobox", "categorycombobox", "string"],
48	["formfactorcombobox", "formfactorcombobox", "string"],
49	["structurecombobox", "structurecombobox", "string"],
50	["multi_factor", "multi_factor", "float"],
51	["magnetic_on", "magnetic_on", "bool"],
52	["enable_smearer", "enable_smearer", "bool"],
53	["disable_smearer", "disable_smearer", "bool"],
54	["pinhole_smearer", "pinhole_smearer", "bool"],
55	["slit_smearer", "slit_smearer", "bool"],
56	["enable_disp", "enable_disp", "bool"],
57	["disable_disp", "disable_disp", "bool"],
58	["dI_noweight", "dI_noweight", "bool"],
59	["dI_didata", "dI_didata", "bool"],
60	["dI_sqrdata", "dI_sqrdata", "bool"],
61	["dI_idata", "dI_idata", "bool"],
62	["enable2D", "enable2D", "bool"],
63	["cb1", "cb1", "bool"],
64	["tcChi", "tcChi", "float"],
65	["smearer", "smearer", "float"],
66	["smear_type", "smear_type", "string"],
67	["dq_l", "dq_l", "string"],
68	["dq_r", "dq_r", "string"],
69	["dx_max", "dx_max", "float"],
70	["dx_min", "dx_min", "float"],
71	["dxl", "dxl", "float"],
72	["dxw", "dxw", "float"]]
73
74	LIST_OF_MODEL_ATTRIBUTES = [["values", "values"],
75	["weights", "weights"]]
76
77	DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]]
78
79	LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"],
80	["str_parameters", "str_parameters"],
81	["orientation_parameters", "orientation_params"],
82	["dispersity_parameters", "orientation_params_disp"],
83	["fixed_param", "fixed_param"],
84	["fittable_param", "fittable_param"]]
85	LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"],
86	["xmax", "xmax", "float"],
87	["ymin", "ymin", "float"],
88	["ymax", "ymax", "float"],
89	["_xaxis", "_xaxis", "string"],
90	["_xunit", "_xunit", "string"],
91	["_yaxis", "_yaxis", "string"],
92	["_yunit", "_yunit", "string"],
93	["_zaxis", "_zaxis", "string"],
94	["_zunit", "_zunit", "string"]]
95	LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"],
96	["qy_data", "qy_data", "float"],
97	["dqx_data", "dqx_data", "float"],
98	["dqy_data", "dqy_data", "float"],
99	["data", "data", "float"],
100	["q_data", "q_data", "float"],
101	["err_data", "err_data", "float"],
102	["mask", "mask", "bool"]]
103
104
105	def parse_entry_helper(node, item):
106	"""
107	Create a numpy list from value extrated from the node
108
109	:param node: node from each the value is stored
110	:param item: list name of three strings.the two first are name of data
111	attribute and the third one is the type of the value of that
112	attribute. type can be string, float, bool, etc.
113
114	: return: numpy array
115	"""
116	if node is not None:
117	if item[2] == "string":
118	return str(node.get(item[0]).strip())
119	elif item[2] == "bool":
120	try:
121	return node.get(item[0]).strip() == "True"
122
123	except:
124	return None
125	else:
126	try:
127	return float(node.get(item[0]))
128	except:
129	return None
130
131
132	class PageState(object):
133	"""
134	Contains information to reconstruct a page of the fitpanel.
135	"""
136	def __init__(self, parent=None, model=None, data=None):
137	"""
138	Initialize the current state
139
140	:param model: a selected model within a page
141	:param data:
142
143	"""
144	self.file = None
145	#Time of state creation
146	self.timestamp = time.time()
147	## Data member to store the dispersion object created
148	self._disp_obj_dict = {}
149	#------------------------
150	#Data used for fitting
151	self.data = data
152	# model data
153	self.theory_data = None
154	#Is 2D
155	self.is_2D = False
156	self.images = None
157
158	#save additional information on data that dataloader.reader does not read
159	self.is_data = None
160	self.data_name = ""
161
162	if self.data is not None:
163	self.data_name = self.data.name
164	self.data_id = None
165	if self.data is not None and hasattr(self.data, "id"):
166	self.data_id = self.data.id
167	self.data_group_id = None
168	if self.data is not None and hasattr(self.data, "group_id"):
169	self.data_group_id = self.data.group_id
170
171	## reset True change the state of exsiting button
172	self.reset = False
173
174	# flag to allow data2D plot
175	self.enable2D = False
176	# model on which the fit would be performed
177	self.model = model
178	self.m_name = None
179	#list of process done to model
180	self.process = []
181	#fit page manager
182	self.manager = None
183	#Store the parent of this panel parent
184	# For this application fitpanel is the parent
185	self.parent = parent
186	# Event_owner is the owner of model event
187	self.event_owner = None
188	##page name
189	self.page_name = ""
190	# Contains link between model, all its parameters, and panel organization
191	self.parameters = []
192	# String parameter list that can not be fitted
193	self.str_parameters = []
194	# Contains list of parameters that cannot be fitted and reference to
195	#panel objects
196	self.fixed_param = []
197	# Contains list of parameters with dispersity and reference to
198	#panel objects
199	self.fittable_param = []
200	## orientation parameters
201	self.orientation_params = []
202	## orientation parameters for gaussian dispersity
203	self.orientation_params_disp = []
204	## smearer info
205	self.smearer = None
206	self.smear_type = None
207	self.dq_l = None
208	self.dq_r = None
209	self.dx_max = None
210	self.dx_min = None
211	self.dxl = None
212	self.dxw = None
213	#list of dispersion parameters
214	self.disp_list = []
215	if self.model is not None:
216	self.disp_list = self.model.getDispParamList()
217
218	self.disp_cb_dict = {}
219	self.values = {}
220	self.weights = {}
221
222	#contains link between a model and selected parameters to fit
223	self.param_toFit = []
224	##dictionary of model type and model class
225	self.model_list_box = None
226	## save the state of the context menu
227	self.saved_states = {}
228	## save selection of combobox
229	self.formfactorcombobox = None
230	self.categorycombobox = None
231	self.structurecombobox = None
232
233	## radio box to select type of model
234	#self.shape_rbutton = False
235	#self.shape_indep_rbutton = False
236	#self.struct_rbutton = False
237	#self.plugin_rbutton = False
238	## the indice of the current selection
239	self.disp_box = 0
240	## Qrange
241	## Q range
242	self.qmin = 0.001
243	self.qmax = 0.1
244	#reset data range
245	self.qmax_x = None
246	self.qmin_x = None
247
248	self.npts = None
249	self.name = ""
250	self.multi_factor = None
251	self.magnetic_on = False
252	## enable smearering state
253	self.enable_smearer = False
254	self.disable_smearer = True
255	self.pinhole_smearer = False
256	self.slit_smearer = False
257	# weighting options
258	self.dI_noweight = False
259	self.dI_didata = True
260	self.dI_sqrdata = False
261	self.dI_idata = False
262	## disperity selection
263	self.enable_disp = False
264	self.disable_disp = True
265
266	## state of selected all check button
267	self.cb1 = False
268	## store value of chisqr
269	self.tcChi = None
270
271	def clone(self):
272	"""
273	Create a new copy of the current object
274	"""
275	model = None
276	if self.model is not None:
277	model = self.model.clone()
278	model.name = self.model.name
279	obj = PageState(self.parent, model=model)
280	obj.file = copy.deepcopy(self.file)
281	obj.data = copy.deepcopy(self.data)
282	if self.data is not None:
283	self.data_name = self.data.name
284	obj.data_name = self.data_name
285	obj.is_data = self.is_data
286	obj.model_list_box = copy.deepcopy(self.model_list_box)
287
288	obj.categorycombobox = self.categorycombobox
289	obj.formfactorcombobox = self.formfactorcombobox
290	obj.structurecombobox = self.structurecombobox
291
292	#obj.shape_rbutton = self.shape_rbutton
293	#obj.shape_indep_rbutton = self.shape_indep_rbutton
294	#obj.struct_rbutton = self.struct_rbutton
295	#obj.plugin_rbutton = self.plugin_rbutton
296
297	obj.manager = self.manager
298	obj.event_owner = self.event_owner
299	obj.disp_list = copy.deepcopy(self.disp_list)
300
301	obj.enable2D = copy.deepcopy(self.enable2D)
302	obj.parameters = copy.deepcopy(self.parameters)
303	obj.str_parameters = copy.deepcopy(self.str_parameters)
304	obj.fixed_param = copy.deepcopy(self.fixed_param)
305	obj.fittable_param = copy.deepcopy(self.fittable_param)
306	obj.orientation_params = copy.deepcopy(self.orientation_params)
307	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
308	obj.enable_disp = copy.deepcopy(self.enable_disp)
309	obj.disable_disp = copy.deepcopy(self.disable_disp)
310	obj.tcChi = self.tcChi
311
312	if len(self._disp_obj_dict) > 0:
313	for k, v in self._disp_obj_dict.iteritems():
314	obj._disp_obj_dict[k] = v
315	if len(self.disp_cb_dict) > 0:
316	for k, v in self.disp_cb_dict.iteritems():
317	obj.disp_cb_dict[k] = v
318	if len(self.values) > 0:
319	for k, v in self.values.iteritems():
320	obj.values[k] = v
321	if len(self.weights) > 0:
322	for k, v in self.weights.iteritems():
323	obj.weights[k] = v
324	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
325	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
326	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
327	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
328	obj.smear_type = copy.deepcopy(self.smear_type)
329	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
330	obj.dI_didata = copy.deepcopy(self.dI_didata)
331	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
332	obj.dI_idata = copy.deepcopy(self.dI_idata)
333	obj.dq_l = copy.deepcopy(self.dq_l)
334	obj.dq_r = copy.deepcopy(self.dq_r)
335	obj.dx_max = copy.deepcopy(self.dx_max)
336	obj.dx_min = copy.deepcopy(self.dx_min)
337	obj.dxl = copy.deepcopy(self.dxl)
338	obj.dxw = copy.deepcopy(self.dxw)
339	obj.disp_box = copy.deepcopy(self.disp_box)
340	obj.qmin = copy.deepcopy(self.qmin)
341	obj.qmax = copy.deepcopy(self.qmax)
342	obj.multi_factor = self.multi_factor
343	obj.magnetic_on = self.magnetic_on
344	obj.npts = copy.deepcopy(self.npts)
345	obj.cb1 = copy.deepcopy(self.cb1)
346	obj.smearer = copy.deepcopy(self.smearer)
347
348	for name, state in self.saved_states.iteritems():
349	copy_name = copy.deepcopy(name)
350	copy_state = state.clone()
351	obj.saved_states[copy_name] = copy_state
352	return obj
353
354	def _repr_helper(self, list, rep):
355	"""
356	Helper method to print a state
357	"""
358	for item in list:
359	rep += "parameter name: %s \n" % str(item[1])
360	rep += "value: %s\n" % str(item[2])
361	rep += "selected: %s\n" % str(item[0])
362	rep += "error displayed : %s \n" % str(item[4][0])
363	rep += "error value:%s \n" % str(item[4][1])
364	rep += "minimum displayed : %s \n" % str(item[5][0])
365	rep += "minimum value : %s \n" % str(item[5][1])
366	rep += "maximum displayed : %s \n" % str(item[6][0])
367	rep += "maximum value : %s \n" % str(item[6][1])
368	rep += "parameter unit: %s\n\n" % str(item[7])
369	return rep
370
371	def __repr__(self):
372	"""
373	output string for printing
374	"""
375	rep = "\nState name: %s\n" % self.file
376	t = time.localtime(self.timestamp)
377	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
378
379	rep += "State created: %s\n" % time_str
380	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
381	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
382	rep += "is data : %s\n" % self.is_data
383	rep += "data's name : %s\n" % self.data_name
384	rep += "data's id : %s\n" % self.data_id
385	if self.model != None:
386	m_name = self.model.__class__.__name__
387	if m_name == 'Model':
388	m_name = self.m_name
389	rep += "model name : %s\n" % m_name
390	else:
391	rep += "model name : None\n"
392	rep += "multi_factor : %s\n" % str(self.multi_factor)
393	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
394	rep += "model type (Category) selected: %s\n" % self.categorycombobox
395	rep += "data : %s\n" % str(self.data)
396	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
397	str(self.qmax), str(self.npts))
398	rep += "Dispersion selection : %s\n" % str(self.disp_box)
399	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
400	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
401	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
402	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
403	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
404	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
405	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
406
407	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
408	rep += "dI_didata : %s\n" % str(self.dI_didata)
409	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
410	rep += "dI_idata : %s\n" % str(self.dI_idata)
411
412	rep += "2D enable : %s\n" % str(self.enable2D)
413	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
414	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
415	rep += "Smear object : %s\n" % str(self.smearer)
416	rep += "Smear type : %s\n" % (self.smear_type)
417	rep += "dq_l : %s\n" % self.dq_l
418	rep += "dq_r : %s\n" % self.dq_r
419	rep += "dx_max : %s\n" % str(self.dx_max)
420	rep += "dx_min : %s\n" % str(self.dx_min)
421	rep += "dxl : %s\n" % str(self.dxl)
422	rep += "dxw : %s\n" % str(self.dxw)
423	rep += "model : %s\n\n" % str(self.model)
424	temp_parameters = []
425	temp_fittable_param = []
426	if self.data.__class__.__name__ == "Data2D":
427	self.is_2D = True
428	else:
429	self.is_2D = False
430	if self.data is not None:
431	if not self.is_2D:
432	for item in self.parameters:
433	if not item in self.orientation_params:
434	temp_parameters.append(item)
435	for item in self.fittable_param:
436	if not item in self.orientation_params_disp:
437	temp_fittable_param.append(item)
438	else:
439	temp_parameters = self.parameters
440	temp_fittable_param = self.fittable_param
441
442	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
443	rep = self._repr_helper(list=temp_parameters, rep=rep)
444	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
445	rep = self._repr_helper(list=self.str_parameters, rep=rep)
446	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
447	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
448	return rep
449
450	def set_report_string(self):
451	"""
452	Get the values (strings) from __str__ for report
453	"""
454	# Dictionary of the report strings
455	repo_time = ""
456	model_name = ""
457	title = ""
458	title_name = ""
459	file_name = ""
460	param_string = ""
461	paramval_string = ""
462	chi2_string = ""
463	q_range = ""
464	strings = self.__repr__()
465	lines = strings.split('\n')
466
467	# get all string values from __str__()
468	for line in lines:
469	value = ""
470	content = line.split(":")
471	name = content[0]
472	try:
473	value = content[1]
474	except:
475	logging.error(sys.exc_value)
476	if name.count("State created"):
477	repo_time = "" + value
478	if name.count("parameter name"):
479	val_name = value.split(".")
480	if len(val_name) > 1:
481	if val_name[1].count("width"):
482	param_string += value + ','
483	else:
484	continue
485	else:
486	param_string += value + ','
487	if name == "value":
488	param_string += value + ','
489	if name == "selected":
490	if value == u' False':
491	fixed_parameter = True
492	else:
493	fixed_parameter = False
494	if name == "error value":
495	if fixed_parameter:
496	param_string += '(fixed),'
497	else:
498	param_string += value + ','
499	if name == "parameter unit":
500	param_string += value + ':'
501	if name == "Value of Chisqr ":
502	chi2 = ("Chi2/Npts = " + value)
503	chi2_string = CENTRE % chi2
504	if name == "Title":
505	if len(value.strip()) == 0:
506	continue
507	title = value + " [" + repo_time + "]"
508	title_name = HEADER % title
509	if name == "data ":
510	try:
511	file_value = ("File name:" + content[2])
512	file_name = CENTRE % file_value
513	if len(title) == 0:
514	title = content[2] + " [" + repo_time + "]"
515	title_name = HEADER % title
516	except:
517	logging.error(sys.exc_value)
518	if name == "model name ":
519	try:
520	modelname = "Model name:" + content[1]
521	except:
522	modelname = "Model name:" + " NAN"
523	model_name = CENTRE % modelname
524
525	if name == "Plotting Range":
526	try:
527	q_range = content[1] + " = " + content[2] \
528	+ " = " + content[3].split(",")[0]
529	q_name = ("Q Range: " + q_range)
530	q_range = CENTRE % q_name
531	except:
532	logging.error(sys.exc_value)
533	paramval = ""
534	for lines in param_string.split(":"):
535	line = lines.split(",")
536	if len(lines) > 0:
537	param = line[0]
538	param += " = " + line[1]
539	if len(line[2].split()) > 0 and not line[2].count("None"):
540	param += " +- " + line[2]
541	if len(line[3].split()) > 0 and not line[3].count("None"):
542	param += " " + line[3]
543	if not paramval.count(param):
544	paramval += param + "\n"
545	paramval_string += CENTRE % param + "\n"
546
547	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % (title, file, q_name, chi2, paramval)
548
549	title_name = self._check_html_format(title_name)
550	file_name = self._check_html_format(file_name)
551	title = self._check_html_format(title)
552
553	html_string = title_name + "\n" + file_name + \
554	"\n" + model_name + \
555	"\n" + q_range + \
556	"\n" + chi2_string + \
557	"\n" + ELINE + \
558	"\n" + paramval_string + \
559	"\n" + ELINE + \
560	"\n" + FEET_1 % title + \
561	"\n" + FEET_2
562
563	return html_string, text_string, title
564
565	def _check_html_format(self, name):
566	"""
567	Check string '%' for html format
568	"""
569	if name.count('%'):
570	name = name.replace('%', '&#37')
571
572	return name
573
574	def report(self, figs=None, canvases=None):
575	"""
576	Invoke report dialog panel
577
578	: param figs: list of pylab figures [list]
579	"""
580	from sas.perspectives.fitting.report_dialog import ReportDialog
581	# get the strings for report
582	html_str, text_str, title = self.set_report_string()
583	# Allow 2 figures to append
584	if len(figs) == 1:
585	add_str = FEET_3
586	elif len(figs) == 2:
587	add_str = ELINE
588	add_str += FEET_2 % ("%s")
589	add_str += ELINE
590	add_str += FEET_3
591	elif len(figs) > 2:
592	add_str = ELINE
593	add_str += FEET_2 % ("%s")
594	add_str += ELINE
595	add_str += FEET_2 % ("%s")
596	add_str += ELINE
597	add_str += FEET_3
598	else:
599	add_str = ""
600
601	# final report html strings
602	report_str = html_str % ("%s") + add_str
603
604	# make plot image
605	images = self.set_plot_state(figs, canvases)
606	report_list = [report_str, text_str, images]
607	dialog = ReportDialog(report_list, None, -1, "")
608	dialog.Show()
609
610	def _toXML_helper(self, thelist, element, newdoc):
611	"""
612	Helper method to create xml file for saving state
613	"""
614	for item in thelist:
615	sub_element = newdoc.createElement('parameter')
616	sub_element.setAttribute('name', str(item[1]))
617	sub_element.setAttribute('value', str(item[2]))
618	sub_element.setAttribute('selected_to_fit', str(item[0]))
619	sub_element.setAttribute('error_displayed', str(item[4][0]))
620	sub_element.setAttribute('error_value', str(item[4][1]))
621	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
622	sub_element.setAttribute('minimum_value', str(item[5][1]))
623	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
624	sub_element.setAttribute('maximum_value', str(item[6][1]))
625	sub_element.setAttribute('unit', str(item[7]))
626	element.appendChild(sub_element)
627
628	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
629	"""
630	Writes the state of the InversionControl panel to file, as XML.
631
632	Compatible with standalone writing, or appending to an
633	already existing XML document. In that case, the XML document
634	is required. An optional entry node in the XML document may also be given.
635
636	:param file: file to write to
637	:param doc: XML document object [optional]
638	:param entry_node: XML node within the XML document at which we will append the data [optional]
639
640	"""
641	from xml.dom.minidom import getDOMImplementation
642
643	# Check whether we have to write a standalone XML file
644	if doc is None:
645	impl = getDOMImplementation()
646	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
647	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
648	top_element = newdoc.documentElement
649	else:
650	# We are appending to an existing document
651	newdoc = doc
652	try:
653	top_element = newdoc.createElement(FITTING_NODE_NAME)
654	except:
655	string = etree.tostring(doc, pretty_print=True)
656	newdoc = parseString(string)
657	top_element = newdoc.createElement(FITTING_NODE_NAME)
658	if entry_node is None:
659	newdoc.documentElement.appendChild(top_element)
660	else:
661	try:
662	entry_node.appendChild(top_element)
663	except:
664	node_name = entry_node.tag
665	node_list = newdoc.getElementsByTagName(node_name)
666	entry_node = node_list.item(0)
667	entry_node.appendChild(top_element)
668
669	attr = newdoc.createAttribute("version")
670	attr.nodeValue = '1.0'
671	top_element.setAttributeNode(attr)
672
673	# File name
674	element = newdoc.createElement("filename")
675	if self.file is not None:
676	element.appendChild(newdoc.createTextNode(str(self.file)))
677	else:
678	element.appendChild(newdoc.createTextNode(str(file)))
679	top_element.appendChild(element)
680
681	element = newdoc.createElement("timestamp")
682	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
683	attr = newdoc.createAttribute("epoch")
684	attr.nodeValue = str(self.timestamp)
685	element.setAttributeNode(attr)
686	top_element.appendChild(element)
687	# Inputs
688	inputs = newdoc.createElement("Attributes")
689	top_element.appendChild(inputs)
690
691	if self.data is not None and hasattr(self.data, "group_id"):
692	self.data_group_id = self.data.group_id
693	if self.data is not None and hasattr(self.data, "is_data"):
694	self.is_data = self.data.is_data
695	if self.data is not None:
696	self.data_name = self.data.name
697	if self.data is not None and hasattr(self.data, "id"):
698	self.data_id = self.data.id
699
700	for item in LIST_OF_DATA_ATTRIBUTES:
701	element = newdoc.createElement(item[0])
702	element.setAttribute(item[0], str(getattr(self, item[1])))
703	inputs.appendChild(element)
704
705	for item in LIST_OF_STATE_ATTRIBUTES:
706	element = newdoc.createElement(item[0])
707	element.setAttribute(item[0], str(getattr(self, item[1])))
708	inputs.appendChild(element)
709
710	# For self.values ={ disp_param_name: [vals,...],...}
711	# and for self.weights ={ disp_param_name: [weights,...],...}
712	value_list = {}
713	for item in LIST_OF_MODEL_ATTRIBUTES:
714	element = newdoc.createElement(item[0])
715	value_list = getattr(self, item[1])
716	for key, value in value_list.iteritems():
717	sub_element = newdoc.createElement(key)
718	sub_element.setAttribute('name', str(key))
719	for val in value:
720	sub_element.appendChild(newdoc.createTextNode(str(val)))
721
722	element.appendChild(sub_element)
723	inputs.appendChild(element)
724
725	# Create doc for the dictionary of self._disp_obj_dic
726	for item in DISPERSION_LIST:
727	element = newdoc.createElement(item[0])
728	value_list = getattr(self, item[1])
729	for key, val in value_list.iteritems():
730	value = repr(val)
731	sub_element = newdoc.createElement(key)
732	sub_element.setAttribute('name', str(key))
733	sub_element.setAttribute('value', str(value))
734	element.appendChild(sub_element)
735	inputs.appendChild(element)
736
737	for item in LIST_OF_STATE_PARAMETERS:
738	element = newdoc.createElement(item[0])
739	self._toXML_helper(thelist=getattr(self, item[1]), element=element, newdoc=newdoc)
740	inputs.appendChild(element)
741
742	# Save the file
743	if doc is None:
744	fd = open(file, 'w')
745	fd.write(newdoc.toprettyxml())
746	fd.close()
747	return None
748	else:
749	return newdoc
750
751	def _fromXML_helper(self, node, list):
752	"""
753	Helper function to write state to xml
754	"""
755	for item in node:
756	try:
757	name = item.get('name')
758	except:
759	name = None
760	try:
761	value = item.get('value')
762	except:
763	value = None
764	try:
765	selected_to_fit = (item.get('selected_to_fit') == "True")
766	except:
767	selected_to_fit = None
768	try:
769	error_displayed = (item.get('error_displayed') == "True")
770	except:
771	error_displayed = None
772	try:
773	error_value = item.get('error_value')
774	except:
775	error_value = None
776	try:
777	minimum_displayed = (item.get('minimum_displayed') == "True")
778	except:
779	minimum_displayed = None
780	try:
781	minimum_value = item.get('minimum_value')
782	except:
783	minimum_value = None
784	try:
785	maximum_displayed = (item.get('maximum_displayed') == "True")
786	except:
787	maximum_displayed = None
788	try:
789	maximum_value = item.get('maximum_value')
790	except:
791	maximum_value = None
792	try:
793	unit = item.get('unit')
794	except:
795	unit = None
796	list.append([selected_to_fit, name, value, "+/-",
797	[error_displayed, error_value],
798	[minimum_displayed, minimum_value],
799	[maximum_displayed, maximum_value], unit])
800
801	def fromXML(self, file=None, node=None):
802	"""
803	Load fitting state from a file
804
805	:param file: .fitv file
806	:param node: node of a XML document to read from
807
808	"""
809	if file is not None:
810	msg = "PageState no longer supports non-CanSAS"
811	msg += " format for fitting files"
812	raise RuntimeError, msg
813
814	if node.get('version')and node.get('version') == '1.0':
815
816	# Get file name
817	entry = get_content('ns:filename', node)
818	if entry is not None:
819	self.file = entry.text.strip()
820
821	# Get time stamp
822	entry = get_content('ns:timestamp', node)
823	if entry is not None and entry.get('epoch'):
824	try:
825	self.timestamp = float(entry.get('epoch'))
826	except:
827	msg = "PageState.fromXML: Could not"
828	msg += " read timestamp\n %s" % sys.exc_value
829	logging.error(msg)
830
831	# Parse fitting attributes
832	entry = get_content('ns:Attributes', node)
833	for item in LIST_OF_DATA_ATTRIBUTES:
834	node = get_content('ns:%s' % item[0], entry)
835	setattr(self, item[0], parse_entry_helper(node, item))
836
837	if entry is not None:
838	for item in LIST_OF_STATE_ATTRIBUTES:
839	node = get_content('ns:%s' % item[0], entry)
840	setattr(self, item[0], parse_entry_helper(node, item))
841
842	for item in LIST_OF_STATE_PARAMETERS:
843	node = get_content("ns:%s" % item[0], entry)
844	self._fromXML_helper(node=node, list=getattr(self, item[1]))
845
846	# Recover _disp_obj_dict from xml file
847	self._disp_obj_dict = {}
848	for item in DISPERSION_LIST:
849	# Get node
850	node = get_content("ns:%s" % item[0], entry)
851	for attr in node:
852	name = str(attr.get('name'))
853	val = attr.get('value')
854	value = val.split(" instance")[0]
855	disp_name = value.split("<")[1]
856	try:
857	# Try to recover disp_model object from strings
858	com = "from sas.models.dispersion_models "
859	com += "import %s as disp"
860	com_name = disp_name.split(".")[3]
861	exec com % com_name
862	disp_model = disp()
863	attribute = getattr(self, item[1])
864	attribute[name] = com_name
865	except:
866	logging.error(sys.exc_value)
867
868	# get self.values and self.weights dic. if exists
869	for item in LIST_OF_MODEL_ATTRIBUTES:
870	node = get_content("ns:%s" % item[0], entry)
871	dic = {}
872	value_list = []
873	for par in node:
874	name = par.get('name')
875	values = par.text.split('\n')
876	# Get lines only with numbers
877	for line in values:
878	try:
879	val = float(line)
880	value_list.append(val)
881	except:
882	# pass if line is empty (it happens)
883	logging.error(sys.exc_value)
884	dic[name] = numpy.array(value_list)
885	setattr(self, item[1], dic)
886
887	def set_plot_state(self, figs, canvases):
888	"""
889	Build image state that wx.html understand
890	by plotting, putting it into wx.FileSystem image object
891
892	"""
893	images = []
894	# some imports
895	import wx
896
897	# Reset memory
898	self.imgRAM = None
899	wx.MemoryFSHandler()
900
901	# For no figures in the list, prepare empty plot
902	if figs == None or len(figs) == 0:
903	figs = [None]
904
905	# Loop over the list of figures
906	# use wx.MemoryFSHandler
907	self.imgRAM = wx.MemoryFSHandler()
908	for fig in figs:
909	if figs != None:
910	ind = figs.index(fig)
911	canvas = canvases[ind]
912
913	#store the image in wx.FileSystem Object
914	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
915
916	# index of the fig
917	ind = figs.index(fig)
918
919	#AddFile, image can be retrieved with 'memory:filename'
920	self.imgRAM.AddFile('img_fit%s.png' % ind,
921	canvas.bitmap, wx.BITMAP_TYPE_PNG)
922
923	#append figs
924	images.append(fig)
925
926	return images
927
928
929	class Reader(CansasReader):
930	"""
931	Class to load a .fitv fitting file
932	"""
933	## File type
934	type_name = "Fitting"
935
936	## Wildcards
937	type = ["Fitting files (.fitv)\|.fitv"
938	"SASView file (.svs)\|.svs"]
939	## List of allowed extensions
940	ext = ['.fitv', '.FITV', '.svs', 'SVS']
941
942	def __init__(self, call_back=None, cansas=True):
943	CansasReader.__init__(self)
944	"""
945	Initialize the call-back method to be called
946	after we load a file
947
948	:param call_back: call-back method
949	:param cansas: True = files will be written/read in CanSAS format
950	False = write CanSAS format
951
952	"""
953	## Call back method to be executed after a file is read
954	self.call_back = call_back
955	## CanSAS format flag
956	self.cansas = cansas
957	self.state = None
958
959	def get_state(self):
960	return self.state
961
962	def read(self, path):
963	"""
964	Load a new P(r) inversion state from file
965
966	:param path: file path
967
968	"""
969	if self.cansas == True:
970	return self._read_cansas(path)
971
972	def _data2d_to_xml_doc(self, datainfo):
973	"""
974	Create an XML document to contain the content of a Data2D
975
976	:param datainfo: Data2D object
977
978	"""
979	if not issubclass(datainfo.__class__, Data2D):
980	raise RuntimeError, "The cansas writer expects a Data2D instance"
981
982	doc = xml.dom.minidom.Document()
983	main_node = doc.createElement("SASroot")
984	main_node.setAttribute("version", self.version)
985	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
986	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
987	main_node.setAttribute("xsi:schemaLocation",
988	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
989
990	doc.appendChild(main_node)
991
992	entry_node = doc.createElement("SASentry")
993	main_node.appendChild(entry_node)
994
995	write_node(doc, entry_node, "Title", datainfo.title)
996	if datainfo is not None:
997	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
998	for item in datainfo.run:
999	runname = {}
1000	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item])) > 1:
1001	runname = {'name': datainfo.run_name[item]}
1002	write_node(doc, entry_node, "Run", item, runname)
1003	# Data info
1004	new_node = doc.createElement("SASdata")
1005	entry_node.appendChild(new_node)
1006	for item in LIST_OF_DATA_2D_ATTR:
1007	element = doc.createElement(item[0])
1008	element.setAttribute(item[0], str(getattr(datainfo, item[1])))
1009	new_node.appendChild(element)
1010
1011	for item in LIST_OF_DATA_2D_VALUES:
1012	root_node = doc.createElement(item[0])
1013	new_node.appendChild(root_node)
1014	temp_list = None
1015	temp_list = getattr(datainfo, item[1])
1016
1017	if temp_list is None or len(temp_list) == 0:
1018	element = doc.createElement(item[0])
1019	element.appendChild(doc.createTextNode(str(temp_list)))
1020	root_node.appendChild(element)
1021	else:
1022	for value in temp_list:
1023	element = doc.createElement(item[0])
1024	element.setAttribute(item[0], str(value))
1025	root_node.appendChild(element)
1026
1027	# Sample info
1028	sample = doc.createElement("SASsample")
1029	if datainfo.sample.name is not None:
1030	sample.setAttribute("name", str(datainfo.sample.name))
1031	entry_node.appendChild(sample)
1032	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1033	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1034	{"unit": datainfo.sample.thickness_unit})
1035	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1036	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1037	{"unit": datainfo.sample.temperature_unit})
1038
1039	for item in datainfo.sample.details:
1040	write_node(doc, sample, "details", item)
1041
1042	pos = doc.createElement("position")
1043	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1044	{"unit": datainfo.sample.position_unit})
1045	written = written \| write_node(doc, pos, "y",
1046	datainfo.sample.position.y,
1047	{"unit": datainfo.sample.position_unit})
1048	written = written \| write_node(doc, pos, "z",
1049	datainfo.sample.position.z,
1050	{"unit": datainfo.sample.position_unit})
1051	if written == True:
1052	sample.appendChild(pos)
1053
1054	ori = doc.createElement("orientation")
1055	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1056	{"unit": datainfo.sample.orientation_unit})
1057	written = written \| write_node(doc, ori, "pitch",
1058	datainfo.sample.orientation.y,
1059	{"unit": datainfo.sample.orientation_unit})
1060	written = written \| write_node(doc, ori, "yaw",
1061	datainfo.sample.orientation.z,
1062	{"unit": datainfo.sample.orientation_unit})
1063	if written == True:
1064	sample.appendChild(ori)
1065
1066	# Instrument info
1067	instr = doc.createElement("SASinstrument")
1068	entry_node.appendChild(instr)
1069
1070	write_node(doc, instr, "name", datainfo.instrument)
1071
1072	# Source
1073	source = doc.createElement("SASsource")
1074	if datainfo.source.name is not None:
1075	source.setAttribute("name", str(datainfo.source.name))
1076	instr.appendChild(source)
1077
1078	write_node(doc, source, "radiation", datainfo.source.radiation)
1079	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1080	size = doc.createElement("beam_size")
1081	if datainfo.source.beam_size_name is not None:
1082	size.setAttribute("name", str(datainfo.source.beam_size_name))
1083	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1084	{"unit": datainfo.source.beam_size_unit})
1085	written = written \| write_node(doc, size, "y",
1086	datainfo.source.beam_size.y,
1087	{"unit": datainfo.source.beam_size_unit})
1088	written = written \| write_node(doc, size, "z",
1089	datainfo.source.beam_size.z,
1090	{"unit": datainfo.source.beam_size_unit})
1091	if written == True:
1092	source.appendChild(size)
1093
1094	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1095	{"unit": datainfo.source.wavelength_unit})
1096	write_node(doc, source, "wavelength_min",
1097	datainfo.source.wavelength_min,
1098	{"unit": datainfo.source.wavelength_min_unit})
1099	write_node(doc, source, "wavelength_max",
1100	datainfo.source.wavelength_max,
1101	{"unit": datainfo.source.wavelength_max_unit})
1102	write_node(doc, source, "wavelength_spread",
1103	datainfo.source.wavelength_spread,
1104	{"unit": datainfo.source.wavelength_spread_unit})
1105
1106	# Collimation
1107	for item in datainfo.collimation:
1108	coll = doc.createElement("SAScollimation")
1109	if item.name is not None:
1110	coll.setAttribute("name", str(item.name))
1111	instr.appendChild(coll)
1112
1113	write_node(doc, coll, "length", item.length,
1114	{"unit": item.length_unit})
1115
1116	for apert in item.aperture:
1117	ap = doc.createElement("aperture")
1118	if apert.name is not None:
1119	ap.setAttribute("name", str(apert.name))
1120	if apert.type is not None:
1121	ap.setAttribute("type", str(apert.type))
1122	coll.appendChild(ap)
1123
1124	write_node(doc, ap, "distance", apert.distance,
1125	{"unit": apert.distance_unit})
1126
1127	size = doc.createElement("size")
1128	if apert.size_name is not None:
1129	size.setAttribute("name", str(apert.size_name))
1130	written = write_node(doc, size, "x", apert.size.x,
1131	{"unit": apert.size_unit})
1132	written = written \| write_node(doc, size, "y", apert.size.y,
1133	{"unit": apert.size_unit})
1134	written = written \| write_node(doc, size, "z", apert.size.z,
1135	{"unit": apert.size_unit})
1136	if written == True:
1137	ap.appendChild(size)
1138
1139	# Detectors
1140	for item in datainfo.detector:
1141	det = doc.createElement("SASdetector")
1142	written = write_node(doc, det, "name", item.name)
1143	written = written \| write_node(doc, det, "SDD", item.distance,
1144	{"unit": item.distance_unit})
1145	written = written \| write_node(doc, det, "slit_length",
1146	item.slit_length,
1147	{"unit": item.slit_length_unit})
1148	if written == True:
1149	instr.appendChild(det)
1150
1151	off = doc.createElement("offset")
1152	written = write_node(doc, off, "x", item.offset.x,
1153	{"unit": item.offset_unit})
1154	written = written \| write_node(doc, off, "y", item.offset.y,
1155	{"unit": item.offset_unit})
1156	written = written \| write_node(doc, off, "z", item.offset.z,
1157	{"unit": item.offset_unit})
1158	if written == True:
1159	det.appendChild(off)
1160
1161	center = doc.createElement("beam_center")
1162	written = write_node(doc, center, "x", item.beam_center.x,
1163	{"unit": item.beam_center_unit})
1164	written = written \| write_node(doc, center, "y",
1165	item.beam_center.y,
1166	{"unit": item.beam_center_unit})
1167	written = written \| write_node(doc, center, "z",
1168	item.beam_center.z,
1169	{"unit": item.beam_center_unit})
1170	if written == True:
1171	det.appendChild(center)
1172
1173	pix = doc.createElement("pixel_size")
1174	written = write_node(doc, pix, "x", item.pixel_size.x,
1175	{"unit": item.pixel_size_unit})
1176	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1177	{"unit": item.pixel_size_unit})
1178	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1179	{"unit": item.pixel_size_unit})
1180	if written == True:
1181	det.appendChild(pix)
1182
1183	ori = doc.createElement("orientation")
1184	written = write_node(doc, ori, "roll", item.orientation.x,
1185	{"unit": item.orientation_unit})
1186	written = written \| write_node(doc, ori, "pitch",
1187	item.orientation.y,
1188	{"unit": item.orientation_unit})
1189	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1190	{"unit": item.orientation_unit})
1191	if written == True:
1192	det.appendChild(ori)
1193
1194	# Processes info
1195	for item in datainfo.process:
1196	node = doc.createElement("SASprocess")
1197	entry_node.appendChild(node)
1198
1199	write_node(doc, node, "name", item.name)
1200	write_node(doc, node, "date", item.date)
1201	write_node(doc, node, "description", item.description)
1202	for term in item.term:
1203	value = term['value']
1204	del term['value']
1205	write_node(doc, node, "term", value, term)
1206	for note in item.notes:
1207	write_node(doc, node, "SASprocessnote", note)
1208	# Return the document, and the SASentry node associated with
1209	# the data we just wrote
1210	return doc, entry_node
1211
1212	def _parse_state(self, entry):
1213	"""
1214	Read a fit result from an XML node
1215
1216	:param entry: XML node to read from
1217
1218	:return: PageState object
1219	"""
1220	# Create an empty state
1221	state = None
1222	# Locate the P(r) node
1223	try:
1224	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1225	namespaces={'ns': CANSAS_NS})
1226	if nodes != []:
1227	# Create an empty state
1228	state = PageState()
1229	state.fromXML(node=nodes[0])
1230
1231	except:
1232	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1233
1234	return state
1235
1236	def _parse_save_state_entry(self, dom):
1237	"""
1238	Parse a SASentry
1239
1240	:param node: SASentry node
1241
1242	:return: Data1D/Data2D object
1243
1244	"""
1245	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1246	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1247	return_value, _ = self._parse_entry(dom)
1248	numpy.trim_zeros(return_value.x)
1249	numpy.trim_zeros(return_value.y)
1250	numpy.trim_zeros(return_value.dy)
1251	size_dx = return_value.dx.size
1252	size_dxl = return_value.dxl.size
1253	size_dxw = return_value.dxw.size
1254	if size_dxl == 0 and size_dxw == 0:
1255	return_value.dxl = None
1256	return_value.dxw = None
1257	numpy.trim_zeros(return_value.dx)
1258	elif size_dx == 0:
1259	return_value.dx = None
1260	size_dx = size_dxl
1261	numpy.trim_zeros(return_value.dxl)
1262	numpy.trim_zeros(return_value.dxw)
1263
1264	return return_value, _
1265
1266	#Parse 2D
1267	data_info = Data2D()
1268
1269	# Look up title
1270	self._store_content('ns:Title', dom, 'title', data_info)
1271
1272	# Look up run number
1273	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1274	for item in nodes:
1275	if item.text is not None:
1276	value = item.text.strip()
1277	if len(value) > 0:
1278	data_info.run.append(value)
1279	if item.get('name') is not None:
1280	data_info.run_name[value] = item.get('name')
1281
1282	# Look up instrument name
1283	self._store_content('ns:SASinstrument/ns:name', dom,
1284	'instrument', data_info)
1285
1286	# Notes
1287	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1288	for note in note_list:
1289	try:
1290	if note.text is not None:
1291	note_value = note.text.strip()
1292	if len(note_value) > 0:
1293	data_info.notes.append(note_value)
1294	except:
1295	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1296	self.errors.append(err_mess)
1297	logging.error(err_mess)
1298
1299	# Sample info ###################
1300	entry = get_content('ns:SASsample', dom)
1301	if entry is not None:
1302	data_info.sample.name = entry.get('name')
1303
1304	self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample)
1305	self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample)
1306	self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample)
1307	self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample)
1308
1309	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1310	for item in nodes:
1311	try:
1312	if item.text is not None:
1313	detail_value = item.text.strip()
1314	if len(detail_value) > 0:
1315	data_info.sample.details.append(detail_value)
1316	except:
1317	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1318	self.errors.append(err_mess)
1319	logging.error(err_mess)
1320
1321	# Position (as a vector)
1322	self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample)
1323	self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample)
1324	self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample)
1325
1326	# Orientation (as a vector)
1327	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1328	dom, 'orientation.x', data_info.sample)
1329	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1330	dom, 'orientation.y', data_info.sample)
1331	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1332	dom, 'orientation.z', data_info.sample)
1333
1334	# Source info ###################
1335	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1336	if entry is not None:
1337	data_info.source.name = entry.get('name')
1338
1339	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1340	dom, 'radiation', data_info.source)
1341	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1342	dom, 'beam_shape', data_info.source)
1343	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1344	dom, 'wavelength', data_info.source)
1345	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1346	dom, 'wavelength_min', data_info.source)
1347	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1348	dom, 'wavelength_max', data_info.source)
1349	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1350	dom, 'wavelength_spread', data_info.source)
1351
1352	# Beam size (as a vector)
1353	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1354	if entry is not None:
1355	data_info.source.beam_size_name = entry.get('name')
1356
1357	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1358	dom, 'beam_size.x', data_info.source)
1359	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1360	dom, 'beam_size.y', data_info.source)
1361	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1362	dom, 'beam_size.z', data_info.source)
1363
1364	# Collimation info ###################
1365	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1366	namespaces={'ns': CANSAS_NS})
1367	for item in nodes:
1368	collim = Collimation()
1369	if item.get('name') is not None:
1370	collim.name = item.get('name')
1371	self._store_float('ns:length', item, 'length', collim)
1372
1373	# Look for apertures
1374	apert_list = item.xpath('ns:aperture',
1375	namespaces={'ns': CANSAS_NS})
1376	for apert in apert_list:
1377	aperture = Aperture()
1378
1379	# Get the name and type of the aperture
1380	aperture.name = apert.get('name')
1381	aperture.type = apert.get('type')
1382
1383	self._store_float('ns:distance', apert, 'distance', aperture)
1384
1385	entry = get_content('ns:size', apert)
1386	if entry is not None:
1387	aperture.size_name = entry.get('name')
1388
1389	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1390	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1391	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1392
1393	collim.aperture.append(aperture)
1394
1395	data_info.collimation.append(collim)
1396
1397	# Detector info ######################
1398	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1399	namespaces={'ns': CANSAS_NS})
1400	for item in nodes:
1401
1402	detector = Detector()
1403
1404	self._store_content('ns:name', item, 'name', detector)
1405	self._store_float('ns:SDD', item, 'distance', detector)
1406
1407	# Detector offset (as a vector)
1408	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1409	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1410	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1411
1412	# Detector orientation (as a vector)
1413	self._store_float('ns:orientation/ns:roll', item,
1414	'orientation.x', detector)
1415	self._store_float('ns:orientation/ns:pitch', item,
1416	'orientation.y', detector)
1417	self._store_float('ns:orientation/ns:yaw', item,
1418	'orientation.z', detector)
1419
1420	# Beam center (as a vector)
1421	self._store_float('ns:beam_center/ns:x', item,
1422	'beam_center.x', detector)
1423	self._store_float('ns:beam_center/ns:y', item,
1424	'beam_center.y', detector)
1425	self._store_float('ns:beam_center/ns:z', item,
1426	'beam_center.z', detector)
1427
1428	# Pixel size (as a vector)
1429	self._store_float('ns:pixel_size/ns:x', item,
1430	'pixel_size.x', detector)
1431	self._store_float('ns:pixel_size/ns:y', item,
1432	'pixel_size.y', detector)
1433	self._store_float('ns:pixel_size/ns:z', item,
1434	'pixel_size.z', detector)
1435
1436	self._store_float('ns:slit_length', item, 'slit_length', detector)
1437
1438	data_info.detector.append(detector)
1439
1440	# Processes info ######################
1441	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1442	for item in nodes:
1443	process = Process()
1444	self._store_content('ns:name', item, 'name', process)
1445	self._store_content('ns:date', item, 'date', process)
1446	self._store_content('ns:description', item, 'description', process)
1447
1448	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1449	for term in term_list:
1450	try:
1451	term_attr = {}
1452	for attr in term.keys():
1453	term_attr[attr] = term.get(attr).strip()
1454	if term.text is not None:
1455	term_attr['value'] = term.text.strip()
1456	process.term.append(term_attr)
1457	except:
1458	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1459	self.errors.append(err_mess)
1460	logging.error(err_mess)
1461
1462	note_list = item.xpath('ns:SASprocessnote',
1463	namespaces={'ns': CANSAS_NS})
1464	for note in note_list:
1465	if note.text is not None:
1466	process.notes.append(note.text.strip())
1467
1468	data_info.process.append(process)
1469
1470	# Data info ######################
1471	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1472	if len(nodes) > 1:
1473	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1474
1475	for entry in nodes:
1476	for item in LIST_OF_DATA_2D_ATTR:
1477	#get node
1478	node = get_content('ns:%s' % item[0], entry)
1479	setattr(data_info, item[1], parse_entry_helper(node, item))
1480
1481	for item in LIST_OF_DATA_2D_VALUES:
1482	field = get_content('ns:%s' % item[0], entry)
1483	value_list = []
1484	if field is not None:
1485	value_list = [parse_entry_helper(node, item) for node in field]
1486	if len(value_list) < 2:
1487	setattr(data_info, item[0], None)
1488	else:
1489	setattr(data_info, item[0], numpy.array(value_list))
1490
1491	return data_info
1492
1493	def _read_cansas(self, path):
1494	"""
1495	Load data and P(r) information from a CanSAS XML file.
1496
1497	:param path: file path
1498
1499	:return: Data1D object if a single SASentry was found,
1500	or a list of Data1D objects if multiple entries were found,
1501	or None of nothing was found
1502
1503	:raise RuntimeError: when the file can't be opened
1504	:raise ValueError: when the length of the data vectors are inconsistent
1505
1506	"""
1507	output = []
1508	basename = os.path.basename(path)
1509	root, extension = os.path.splitext(basename)
1510	ext = extension.lower()
1511	try:
1512	if os.path.isfile(path):
1513
1514	#TODO: eventually remove the check for .xml once
1515	# the P(r) writer/reader is truly complete.
1516	if ext in self.ext or \
1517	ext == '.xml':
1518
1519	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1520	# Check the format version number
1521	# Specifying the namespace will take care of the file format version
1522	root = tree.getroot()
1523	entry_list = root.xpath('ns:SASentry',
1524	namespaces={'ns': CANSAS_NS})
1525	for entry in entry_list:
1526	try:
1527	sas_entry, _ = self._parse_save_state_entry(entry)
1528	except:
1529	raise
1530	fitstate = self._parse_state(entry)
1531
1532	#state could be None when .svs file is loaded
1533	#in this case, skip appending to output
1534	if fitstate != None:
1535	sas_entry.meta_data['fitstate'] = fitstate
1536	sas_entry.filename = fitstate.file
1537	output.append(sas_entry)
1538	else:
1539	self.call_back(format=ext)
1540	raise RuntimeError, "%s is not a file" % path
1541
1542	# Return output consistent with the loader's api
1543	if len(output) == 0:
1544	self.call_back(state=None, datainfo=None, format=ext)
1545	return None
1546	else:
1547	for ind in range(len(output)):
1548	# Call back to post the new state
1549	state = output[ind].meta_data['fitstate']
1550	t = time.localtime(state.timestamp)
1551	time_str = time.strftime("%b %d %H:%M", t)
1552	# Check that no time stamp is already appended
1553	max_char = state.file.find("[")
1554	if max_char < 0:
1555	max_char = len(state.file)
1556	original_fname = state.file[0:max_char]
1557	state.file = original_fname + ' [' + time_str + ']'
1558
1559	if state is not None and state.is_data is not None:
1560	output[ind].is_data = state.is_data
1561
1562	output[ind].filename = state.file
1563	state.data = output[ind]
1564	state.data.name = output[ind].filename # state.data_name
1565	state.data.id = state.data_id
1566	if state.is_data is not None:
1567	state.data.is_data = state.is_data
1568	if output[ind].run_name is not None\
1569	and len(output[ind].run_name) != 0:
1570	name = output[ind].run_name
1571	else:
1572	name = original_fname
1573	state.data.group_id = name
1574	#store state in fitting
1575	self.call_back(state=state,
1576	datainfo=output[ind], format=ext)
1577	self.state = state
1578	return output
1579	except:
1580	self.call_back(format=ext)
1581	raise
1582
1583	def write(self, filename, datainfo=None, fitstate=None):
1584	"""
1585	Write the content of a Data1D as a CanSAS XML file only for standalone
1586
1587	:param filename: name of the file to write
1588	:param datainfo: Data1D object
1589	:param fitstate: PageState object
1590
1591	"""
1592	# Sanity check
1593	if self.cansas == True:
1594	# Add fitting information to the XML document
1595	doc = self.write_toXML(datainfo, fitstate)
1596	# Write the XML document
1597	else:
1598	doc = fitstate.toXML(file=filename)
1599
1600	# Save the document no matter the type
1601	fd = open(filename, 'w')
1602	fd.write(doc.toprettyxml())
1603	fd.close()
1604
1605	def write_toXML(self, datainfo=None, state=None):
1606	"""
1607	Write toXML, a helper for write(),
1608	could be used by guimanager._on_save()
1609
1610	: return: xml doc
1611	"""
1612
1613	if state.data is None:
1614	data = sas.dataloader.data_info.Data1D(x=[], y=[])
1615	return None
1616	elif not state.data.is_data:
1617	return None
1618	else:
1619	#make sure title and data run is filled up.
1620	if state.data.title == None or state.data.title == '':
1621	state.data.title = state.data.name
1622	if state.data.run_name == None or state.data.run_name == {}:
1623	state.data.run = [str(state.data.name)]
1624	state.data.run_name[0] = state.data.name
1625
1626	if issubclass(state.data.__class__,
1627	sas.dataloader.data_info.Data1D):
1628	data = state.data
1629	doc, sasentry = self._to_xml_doc(data)
1630	else:
1631	data = state.data
1632	doc, sasentry = self._data2d_to_xml_doc(data)
1633
1634	if state is not None:
1635	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1636
1637	return doc
1638
1639	# Simple html report templet
1640	HEADER = "<html>\n"
1641	HEADER += "<head>\n"
1642	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1643	HEADER += "charset=windows-1252'> \n"
1644	HEADER += "<meta name=Generator >\n"
1645	HEADER += "</head>\n"
1646	HEADER += "<body lang=EN-US>\n"
1647	HEADER += "<div class=WordSection1>\n"
1648	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1649	HEADER += "%s</font></center></span></center></b></p>"
1650	HEADER += "<p class=MsoNormal> </p>"
1651	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1652	PARA += "</font></p>"
1653	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1654	CENTRE += "</font></center></p>"
1655	FEET_1 = \
1656	"""
1657	<p class=MsoNormal> </p>
1658	<br>
1659	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1660	</font></span></center></b></p>
1661	<p class=MsoNormal> </p>
1662	<center>
1663	<br><font size='4' >Model Computation</font>
1664	<br><font size='4' >Data: "%s"</font><br>
1665	"""
1666	FEET_2 = \
1667	"""
1668	<img src="%s" >
1669	</img>
1670	"""
1671	FEET_3 = \
1672	"""
1673	</center>
1674	</div>
1675	</body>
1676	</html>
1677	"""
1678	ELINE = "<p class=MsoNormal> </p>"
1679
1680	if __name__ == "__main__":
1681	state = PageState(parent=None)
1682	#state.toXML()
1683	"""
1684
1685	file = open("test_state", "w")
1686	pickle.dump(state, file)
1687	print pickle.dumps(state)
1688	state.data_name = "hello---->"
1689	pickle.dump(state, file)
1690	file = open("test_state", "r")
1691	new_state= pickle.load(file)
1692	print "new state", new_state
1693	new_state= pickle.load(file)
1694	print "new state", new_state
1695	#print "state", state
1696	"""
1697	import bsddb
1698	import pickle
1699	db = bsddb.btopen('file_state.db', 'c')
1700	val = (pickle.dumps(state), "hello", "hi")
1701	db['state1'] = pickle.dumps(val)
1702	print pickle.loads(db['state1'])
1703	state.data_name = "hello---->22"
1704	db['state2'] = pickle.dumps(state)
1705	state.data_name = "hello---->2"
1706	db['state3'] = pickle.dumps(state)
1707	del db['state3']
1708	state.data_name = "hello---->3"
1709	db['state4'] = pickle.dumps(state)
1710	new_state = pickle.loads(db['state1'])
1711	#print db.last()
1712	db.set_location('state2')
1713	state.data_name = "hello---->5"
1714	db['aastate5'] = pickle.dumps(state)
1715	db.keys().sort()
1716	print pickle.loads(db['state2'])
1717
1718	db.close()

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SasView

source: sasview/src/sas/perspectives/fitting/pagestate.py @ a342928

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