pagestate.py @ 90662e6

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 90662e6 was acf8e4a5, checked in by Paul Kienzle <pkienzle@…>, 10 years ago
reference BumpsFit? directly and remove fit engine selection layer
Property mode set to `100644`
File size: 70.0 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" + title + "\n\n" + file + \
548	"\n" + q_name + \
549	"\n" + chi2 + \
550	"\n\n" + paramval
551
552	title_name = self._check_html_format(title_name)
553	file_name = self._check_html_format(file_name)
554	title = self._check_html_format(title)
555
556	html_string = title_name + "\n" + file_name + \
557	"\n" + model_name + \
558	"\n" + q_range + \
559	"\n" + chi2_string + \
560	"\n" + ELINE + \
561	"\n" + paramval_string + \
562	"\n" + ELINE + \
563	"\n" + FEET_1 % title + \
564	"\n" + FEET_2
565
566	return html_string, text_string, title
567
568	def _check_html_format(self, name):
569	"""
570	Check string '%' for html format
571	"""
572	if name.count('%'):
573	name = name.replace('%', '&#37')
574
575	return name
576
577	def report(self, figs=None, canvases=None):
578	"""
579	Invoke report dialog panel
580
581	: param figs: list of pylab figures [list]
582	"""
583	from sas.perspectives.fitting.report_dialog import ReportDialog
584	# get the strings for report
585	html_str, text_str, title = self.set_report_string()
586	# Allow 2 figures to append
587	if len(figs) == 1:
588	add_str = FEET_3
589	elif len(figs) == 2:
590	add_str = ELINE
591	add_str += FEET_2 % ("%s")
592	add_str += ELINE
593	add_str += FEET_3
594	elif len(figs) > 2:
595	add_str = ELINE
596	add_str += FEET_2 % ("%s")
597	add_str += ELINE
598	add_str += FEET_2 % ("%s")
599	add_str += ELINE
600	add_str += FEET_3
601	else:
602	add_str = ""
603
604	# final report html strings
605	report_str = html_str % ("%s") + add_str
606
607	# make plot image
608	images = self.set_plot_state(figs, canvases)
609	report_list = [report_str, text_str, images]
610	dialog = ReportDialog(report_list, None, -1, "")
611	dialog.Show()
612
613	def _toXML_helper(self, thelist, element, newdoc):
614	"""
615	Helper method to create xml file for saving state
616	"""
617	for item in thelist:
618	sub_element = newdoc.createElement('parameter')
619	sub_element.setAttribute('name', str(item[1]))
620	sub_element.setAttribute('value', str(item[2]))
621	sub_element.setAttribute('selected_to_fit', str(item[0]))
622	sub_element.setAttribute('error_displayed', str(item[4][0]))
623	sub_element.setAttribute('error_value', str(item[4][1]))
624	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
625	sub_element.setAttribute('minimum_value', str(item[5][1]))
626	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
627	sub_element.setAttribute('maximum_value', str(item[6][1]))
628	sub_element.setAttribute('unit', str(item[7]))
629	element.appendChild(sub_element)
630
631	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
632	"""
633	Writes the state of the InversionControl panel to file, as XML.
634
635	Compatible with standalone writing, or appending to an
636	already existing XML document. In that case, the XML document
637	is required. An optional entry node in the XML document may also be given.
638
639	:param file: file to write to
640	:param doc: XML document object [optional]
641	:param entry_node: XML node within the XML document at which we will append the data [optional]
642
643	"""
644	from xml.dom.minidom import getDOMImplementation
645
646	# Check whether we have to write a standalone XML file
647	if doc is None:
648	impl = getDOMImplementation()
649	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
650	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
651	top_element = newdoc.documentElement
652	else:
653	# We are appending to an existing document
654	newdoc = doc
655	try:
656	top_element = newdoc.createElement(FITTING_NODE_NAME)
657	except:
658	string = etree.tostring(doc, pretty_print=True)
659	newdoc = parseString(string)
660	top_element = newdoc.createElement(FITTING_NODE_NAME)
661	if entry_node is None:
662	newdoc.documentElement.appendChild(top_element)
663	else:
664	try:
665	entry_node.appendChild(top_element)
666	except:
667	node_name = entry_node.tag
668	node_list = newdoc.getElementsByTagName(node_name)
669	entry_node = node_list.item(0)
670	entry_node.appendChild(top_element)
671
672	attr = newdoc.createAttribute("version")
673	attr.nodeValue = '1.0'
674	top_element.setAttributeNode(attr)
675
676	# File name
677	element = newdoc.createElement("filename")
678	if self.file is not None:
679	element.appendChild(newdoc.createTextNode(str(self.file)))
680	else:
681	element.appendChild(newdoc.createTextNode(str(file)))
682	top_element.appendChild(element)
683
684	element = newdoc.createElement("timestamp")
685	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
686	attr = newdoc.createAttribute("epoch")
687	attr.nodeValue = str(self.timestamp)
688	element.setAttributeNode(attr)
689	top_element.appendChild(element)
690	# Inputs
691	inputs = newdoc.createElement("Attributes")
692	top_element.appendChild(inputs)
693
694	if self.data is not None and hasattr(self.data, "group_id"):
695	self.data_group_id = self.data.group_id
696	if self.data is not None and hasattr(self.data, "is_data"):
697	self.is_data = self.data.is_data
698	if self.data is not None:
699	self.data_name = self.data.name
700	if self.data is not None and hasattr(self.data, "id"):
701	self.data_id = self.data.id
702
703	for item in LIST_OF_DATA_ATTRIBUTES:
704	element = newdoc.createElement(item[0])
705	element.setAttribute(item[0], str(getattr(self, item[1])))
706	inputs.appendChild(element)
707
708	for item in LIST_OF_STATE_ATTRIBUTES:
709	element = newdoc.createElement(item[0])
710	element.setAttribute(item[0], str(getattr(self, item[1])))
711	inputs.appendChild(element)
712
713	# For self.values ={ disp_param_name: [vals,...],...}
714	# and for self.weights ={ disp_param_name: [weights,...],...}
715	value_list = {}
716	for item in LIST_OF_MODEL_ATTRIBUTES:
717	element = newdoc.createElement(item[0])
718	value_list = getattr(self, item[1])
719	for key, value in value_list.iteritems():
720	sub_element = newdoc.createElement(key)
721	sub_element.setAttribute('name', str(key))
722	for val in value:
723	sub_element.appendChild(newdoc.createTextNode(str(val)))
724
725	element.appendChild(sub_element)
726	inputs.appendChild(element)
727
728	# Create doc for the dictionary of self._disp_obj_dic
729	for item in DISPERSION_LIST:
730	element = newdoc.createElement(item[0])
731	value_list = getattr(self, item[1])
732	for key, val in value_list.iteritems():
733	value = repr(val)
734	sub_element = newdoc.createElement(key)
735	sub_element.setAttribute('name', str(key))
736	sub_element.setAttribute('value', str(value))
737	element.appendChild(sub_element)
738	inputs.appendChild(element)
739
740	for item in LIST_OF_STATE_PARAMETERS:
741	element = newdoc.createElement(item[0])
742	self._toXML_helper(thelist=getattr(self, item[1]), element=element, newdoc=newdoc)
743	inputs.appendChild(element)
744
745	# Save the file
746	if doc is None:
747	fd = open(file, 'w')
748	fd.write(newdoc.toprettyxml())
749	fd.close()
750	return None
751	else:
752	return newdoc
753
754	def _fromXML_helper(self, node, list):
755	"""
756	Helper function to write state to xml
757	"""
758	for item in node:
759	try:
760	name = item.get('name')
761	except:
762	name = None
763	try:
764	value = item.get('value')
765	except:
766	value = None
767	try:
768	selected_to_fit = (item.get('selected_to_fit') == "True")
769	except:
770	selected_to_fit = None
771	try:
772	error_displayed = (item.get('error_displayed') == "True")
773	except:
774	error_displayed = None
775	try:
776	error_value = item.get('error_value')
777	except:
778	error_value = None
779	try:
780	minimum_displayed = (item.get('minimum_displayed') == "True")
781	except:
782	minimum_displayed = None
783	try:
784	minimum_value = item.get('minimum_value')
785	except:
786	minimum_value = None
787	try:
788	maximum_displayed = (item.get('maximum_displayed') == "True")
789	except:
790	maximum_displayed = None
791	try:
792	maximum_value = item.get('maximum_value')
793	except:
794	maximum_value = None
795	try:
796	unit = item.get('unit')
797	except:
798	unit = None
799	list.append([selected_to_fit, name, value, "+/-",
800	[error_displayed, error_value],
801	[minimum_displayed, minimum_value],
802	[maximum_displayed, maximum_value], unit])
803
804	def fromXML(self, file=None, node=None):
805	"""
806	Load fitting state from a file
807
808	:param file: .fitv file
809	:param node: node of a XML document to read from
810
811	"""
812	if file is not None:
813	msg = "PageState no longer supports non-CanSAS"
814	msg += " format for fitting files"
815	raise RuntimeError, msg
816
817	if node.get('version')and node.get('version') == '1.0':
818
819	# Get file name
820	entry = get_content('ns:filename', node)
821	if entry is not None:
822	self.file = entry.text.strip()
823
824	# Get time stamp
825	entry = get_content('ns:timestamp', node)
826	if entry is not None and entry.get('epoch'):
827	try:
828	self.timestamp = float(entry.get('epoch'))
829	except:
830	msg = "PageState.fromXML: Could not"
831	msg += " read timestamp\n %s" % sys.exc_value
832	logging.error(msg)
833
834	# Parse fitting attributes
835	entry = get_content('ns:Attributes', node)
836	for item in LIST_OF_DATA_ATTRIBUTES:
837	node = get_content('ns:%s' % item[0], entry)
838	setattr(self, item[0], parse_entry_helper(node, item))
839
840	if entry is not None:
841	for item in LIST_OF_STATE_ATTRIBUTES:
842	node = get_content('ns:%s' % item[0], entry)
843	setattr(self, item[0], parse_entry_helper(node, item))
844
845	for item in LIST_OF_STATE_PARAMETERS:
846	node = get_content("ns:%s" % item[0], entry)
847	self._fromXML_helper(node=node, list=getattr(self, item[1]))
848
849	# Recover _disp_obj_dict from xml file
850	self._disp_obj_dict = {}
851	for item in DISPERSION_LIST:
852	# Get node
853	node = get_content("ns:%s" % item[0], entry)
854	for attr in node:
855	name = str(attr.get('name'))
856	val = attr.get('value')
857	value = val.split(" instance")[0]
858	disp_name = value.split("<")[1]
859	try:
860	# Try to recover disp_model object from strings
861	com = "from sas.models.dispersion_models "
862	com += "import %s as disp"
863	com_name = disp_name.split(".")[3]
864	exec com % com_name
865	disp_model = disp()
866	attribute = getattr(self, item[1])
867	attribute[name] = com_name
868	except:
869	logging.error(sys.exc_value)
870
871	# get self.values and self.weights dic. if exists
872	for item in LIST_OF_MODEL_ATTRIBUTES:
873	node = get_content("ns:%s" % item[0], entry)
874	dic = {}
875	value_list = []
876	for par in node:
877	name = par.get('name')
878	values = par.text.split('\n')
879	# Get lines only with numbers
880	for line in values:
881	try:
882	val = float(line)
883	value_list.append(val)
884	except:
885	# pass if line is empty (it happens)
886	logging.error(sys.exc_value)
887	dic[name] = numpy.array(value_list)
888	setattr(self, item[1], dic)
889
890	def set_plot_state(self, figs, canvases):
891	"""
892	Build image state that wx.html understand
893	by plotting, putting it into wx.FileSystem image object
894
895	"""
896	images = []
897	# some imports
898	import wx
899
900	# Reset memory
901	self.imgRAM = None
902	wx.MemoryFSHandler()
903
904	# For no figures in the list, prepare empty plot
905	if figs == None or len(figs) == 0:
906	figs = [None]
907
908	# Loop over the list of figures
909	# use wx.MemoryFSHandler
910	self.imgRAM = wx.MemoryFSHandler()
911	for fig in figs:
912	if figs != None:
913	ind = figs.index(fig)
914	canvas = canvases[ind]
915
916	#store the image in wx.FileSystem Object
917	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
918
919	# index of the fig
920	ind = figs.index(fig)
921
922	#AddFile, image can be retrieved with 'memory:filename'
923	self.imgRAM.AddFile('img_fit%s.png' % ind,
924	canvas.bitmap, wx.BITMAP_TYPE_PNG)
925
926	#append figs
927	images.append(fig)
928
929	return images
930
931
932	class Reader(CansasReader):
933	"""
934	Class to load a .fitv fitting file
935	"""
936	## File type
937	type_name = "Fitting"
938
939	## Wildcards
940	type = ["Fitting files (.fitv)\|.fitv"
941	"SASView file (.svs)\|.svs"]
942	## List of allowed extensions
943	ext = ['.fitv', '.FITV', '.svs', 'SVS']
944
945	def __init__(self, call_back=None, cansas=True):
946	CansasReader.__init__(self)
947	"""
948	Initialize the call-back method to be called
949	after we load a file
950
951	:param call_back: call-back method
952	:param cansas: True = files will be written/read in CanSAS format
953	False = write CanSAS format
954
955	"""
956	## Call back method to be executed after a file is read
957	self.call_back = call_back
958	## CanSAS format flag
959	self.cansas = cansas
960	self.state = None
961
962	def get_state(self):
963	return self.state
964
965	def read(self, path):
966	"""
967	Load a new P(r) inversion state from file
968
969	:param path: file path
970
971	"""
972	if self.cansas == True:
973	return self._read_cansas(path)
974
975	def _data2d_to_xml_doc(self, datainfo):
976	"""
977	Create an XML document to contain the content of a Data2D
978
979	:param datainfo: Data2D object
980
981	"""
982	if not issubclass(datainfo.__class__, Data2D):
983	raise RuntimeError, "The cansas writer expects a Data2D instance"
984
985	doc = xml.dom.minidom.Document()
986	main_node = doc.createElement("SASroot")
987	main_node.setAttribute("version", self.version)
988	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
989	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
990	main_node.setAttribute("xsi:schemaLocation",
991	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
992
993	doc.appendChild(main_node)
994
995	entry_node = doc.createElement("SASentry")
996	main_node.appendChild(entry_node)
997
998	write_node(doc, entry_node, "Title", datainfo.title)
999	if datainfo is not None:
1000	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
1001	for item in datainfo.run:
1002	runname = {}
1003	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item])) > 1:
1004	runname = {'name': datainfo.run_name[item]}
1005	write_node(doc, entry_node, "Run", item, runname)
1006	# Data info
1007	new_node = doc.createElement("SASdata")
1008	entry_node.appendChild(new_node)
1009	for item in LIST_OF_DATA_2D_ATTR:
1010	element = doc.createElement(item[0])
1011	element.setAttribute(item[0], str(getattr(datainfo, item[1])))
1012	new_node.appendChild(element)
1013
1014	for item in LIST_OF_DATA_2D_VALUES:
1015	root_node = doc.createElement(item[0])
1016	new_node.appendChild(root_node)
1017	temp_list = None
1018	temp_list = getattr(datainfo, item[1])
1019
1020	if temp_list is None or len(temp_list) == 0:
1021	element = doc.createElement(item[0])
1022	element.appendChild(doc.createTextNode(str(temp_list)))
1023	root_node.appendChild(element)
1024	else:
1025	for value in temp_list:
1026	element = doc.createElement(item[0])
1027	element.setAttribute(item[0], str(value))
1028	root_node.appendChild(element)
1029
1030	# Sample info
1031	sample = doc.createElement("SASsample")
1032	if datainfo.sample.name is not None:
1033	sample.setAttribute("name", str(datainfo.sample.name))
1034	entry_node.appendChild(sample)
1035	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1036	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1037	{"unit": datainfo.sample.thickness_unit})
1038	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1039	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1040	{"unit": datainfo.sample.temperature_unit})
1041
1042	for item in datainfo.sample.details:
1043	write_node(doc, sample, "details", item)
1044
1045	pos = doc.createElement("position")
1046	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1047	{"unit": datainfo.sample.position_unit})
1048	written = written \| write_node(doc, pos, "y",
1049	datainfo.sample.position.y,
1050	{"unit": datainfo.sample.position_unit})
1051	written = written \| write_node(doc, pos, "z",
1052	datainfo.sample.position.z,
1053	{"unit": datainfo.sample.position_unit})
1054	if written == True:
1055	sample.appendChild(pos)
1056
1057	ori = doc.createElement("orientation")
1058	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1059	{"unit": datainfo.sample.orientation_unit})
1060	written = written \| write_node(doc, ori, "pitch",
1061	datainfo.sample.orientation.y,
1062	{"unit": datainfo.sample.orientation_unit})
1063	written = written \| write_node(doc, ori, "yaw",
1064	datainfo.sample.orientation.z,
1065	{"unit": datainfo.sample.orientation_unit})
1066	if written == True:
1067	sample.appendChild(ori)
1068
1069	# Instrument info
1070	instr = doc.createElement("SASinstrument")
1071	entry_node.appendChild(instr)
1072
1073	write_node(doc, instr, "name", datainfo.instrument)
1074
1075	# Source
1076	source = doc.createElement("SASsource")
1077	if datainfo.source.name is not None:
1078	source.setAttribute("name", str(datainfo.source.name))
1079	instr.appendChild(source)
1080
1081	write_node(doc, source, "radiation", datainfo.source.radiation)
1082	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1083	size = doc.createElement("beam_size")
1084	if datainfo.source.beam_size_name is not None:
1085	size.setAttribute("name", str(datainfo.source.beam_size_name))
1086	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1087	{"unit": datainfo.source.beam_size_unit})
1088	written = written \| write_node(doc, size, "y",
1089	datainfo.source.beam_size.y,
1090	{"unit": datainfo.source.beam_size_unit})
1091	written = written \| write_node(doc, size, "z",
1092	datainfo.source.beam_size.z,
1093	{"unit": datainfo.source.beam_size_unit})
1094	if written == True:
1095	source.appendChild(size)
1096
1097	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1098	{"unit": datainfo.source.wavelength_unit})
1099	write_node(doc, source, "wavelength_min",
1100	datainfo.source.wavelength_min,
1101	{"unit": datainfo.source.wavelength_min_unit})
1102	write_node(doc, source, "wavelength_max",
1103	datainfo.source.wavelength_max,
1104	{"unit": datainfo.source.wavelength_max_unit})
1105	write_node(doc, source, "wavelength_spread",
1106	datainfo.source.wavelength_spread,
1107	{"unit": datainfo.source.wavelength_spread_unit})
1108
1109	# Collimation
1110	for item in datainfo.collimation:
1111	coll = doc.createElement("SAScollimation")
1112	if item.name is not None:
1113	coll.setAttribute("name", str(item.name))
1114	instr.appendChild(coll)
1115
1116	write_node(doc, coll, "length", item.length,
1117	{"unit": item.length_unit})
1118
1119	for apert in item.aperture:
1120	ap = doc.createElement("aperture")
1121	if apert.name is not None:
1122	ap.setAttribute("name", str(apert.name))
1123	if apert.type is not None:
1124	ap.setAttribute("type", str(apert.type))
1125	coll.appendChild(ap)
1126
1127	write_node(doc, ap, "distance", apert.distance,
1128	{"unit": apert.distance_unit})
1129
1130	size = doc.createElement("size")
1131	if apert.size_name is not None:
1132	size.setAttribute("name", str(apert.size_name))
1133	written = write_node(doc, size, "x", apert.size.x,
1134	{"unit": apert.size_unit})
1135	written = written \| write_node(doc, size, "y", apert.size.y,
1136	{"unit": apert.size_unit})
1137	written = written \| write_node(doc, size, "z", apert.size.z,
1138	{"unit": apert.size_unit})
1139	if written == True:
1140	ap.appendChild(size)
1141
1142	# Detectors
1143	for item in datainfo.detector:
1144	det = doc.createElement("SASdetector")
1145	written = write_node(doc, det, "name", item.name)
1146	written = written \| write_node(doc, det, "SDD", item.distance,
1147	{"unit": item.distance_unit})
1148	written = written \| write_node(doc, det, "slit_length",
1149	item.slit_length,
1150	{"unit": item.slit_length_unit})
1151	if written == True:
1152	instr.appendChild(det)
1153
1154	off = doc.createElement("offset")
1155	written = write_node(doc, off, "x", item.offset.x,
1156	{"unit": item.offset_unit})
1157	written = written \| write_node(doc, off, "y", item.offset.y,
1158	{"unit": item.offset_unit})
1159	written = written \| write_node(doc, off, "z", item.offset.z,
1160	{"unit": item.offset_unit})
1161	if written == True:
1162	det.appendChild(off)
1163
1164	center = doc.createElement("beam_center")
1165	written = write_node(doc, center, "x", item.beam_center.x,
1166	{"unit": item.beam_center_unit})
1167	written = written \| write_node(doc, center, "y",
1168	item.beam_center.y,
1169	{"unit": item.beam_center_unit})
1170	written = written \| write_node(doc, center, "z",
1171	item.beam_center.z,
1172	{"unit": item.beam_center_unit})
1173	if written == True:
1174	det.appendChild(center)
1175
1176	pix = doc.createElement("pixel_size")
1177	written = write_node(doc, pix, "x", item.pixel_size.x,
1178	{"unit": item.pixel_size_unit})
1179	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1180	{"unit": item.pixel_size_unit})
1181	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1182	{"unit": item.pixel_size_unit})
1183	if written == True:
1184	det.appendChild(pix)
1185
1186	ori = doc.createElement("orientation")
1187	written = write_node(doc, ori, "roll", item.orientation.x,
1188	{"unit": item.orientation_unit})
1189	written = written \| write_node(doc, ori, "pitch",
1190	item.orientation.y,
1191	{"unit": item.orientation_unit})
1192	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1193	{"unit": item.orientation_unit})
1194	if written == True:
1195	det.appendChild(ori)
1196
1197	# Processes info
1198	for item in datainfo.process:
1199	node = doc.createElement("SASprocess")
1200	entry_node.appendChild(node)
1201
1202	write_node(doc, node, "name", item.name)
1203	write_node(doc, node, "date", item.date)
1204	write_node(doc, node, "description", item.description)
1205	for term in item.term:
1206	value = term['value']
1207	del term['value']
1208	write_node(doc, node, "term", value, term)
1209	for note in item.notes:
1210	write_node(doc, node, "SASprocessnote", note)
1211	# Return the document, and the SASentry node associated with
1212	# the data we just wrote
1213	return doc, entry_node
1214
1215	def _parse_state(self, entry):
1216	"""
1217	Read a fit result from an XML node
1218
1219	:param entry: XML node to read from
1220
1221	:return: PageState object
1222	"""
1223	# Create an empty state
1224	state = None
1225	# Locate the P(r) node
1226	try:
1227	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1228	namespaces={'ns': CANSAS_NS})
1229	if nodes != []:
1230	# Create an empty state
1231	state = PageState()
1232	state.fromXML(node=nodes[0])
1233
1234	except:
1235	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1236
1237	return state
1238
1239	def _parse_save_state_entry(self, dom):
1240	"""
1241	Parse a SASentry
1242
1243	:param node: SASentry node
1244
1245	:return: Data1D/Data2D object
1246
1247	"""
1248	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1249	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1250	return_value, _ = self._parse_entry(dom)
1251	numpy.trim_zeros(return_value.x)
1252	numpy.trim_zeros(return_value.y)
1253	numpy.trim_zeros(return_value.dy)
1254	size_dx = return_value.dx.size
1255	size_dxl = return_value.dxl.size
1256	size_dxw = return_value.dxw.size
1257	if size_dxl == 0 and size_dxw == 0:
1258	return_value.dxl = None
1259	return_value.dxw = None
1260	numpy.trim_zeros(return_value.dx)
1261	elif size_dx == 0:
1262	return_value.dx = None
1263	size_dx = size_dxl
1264	numpy.trim_zeros(return_value.dxl)
1265	numpy.trim_zeros(return_value.dxw)
1266
1267	return return_value, _
1268
1269	#Parse 2D
1270	data_info = Data2D()
1271
1272	# Look up title
1273	self._store_content('ns:Title', dom, 'title', data_info)
1274
1275	# Look up run number
1276	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1277	for item in nodes:
1278	if item.text is not None:
1279	value = item.text.strip()
1280	if len(value) > 0:
1281	data_info.run.append(value)
1282	if item.get('name') is not None:
1283	data_info.run_name[value] = item.get('name')
1284
1285	# Look up instrument name
1286	self._store_content('ns:SASinstrument/ns:name', dom,
1287	'instrument', data_info)
1288
1289	# Notes
1290	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1291	for note in note_list:
1292	try:
1293	if note.text is not None:
1294	note_value = note.text.strip()
1295	if len(note_value) > 0:
1296	data_info.notes.append(note_value)
1297	except:
1298	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1299	self.errors.append(err_mess)
1300	logging.error(err_mess)
1301
1302	# Sample info ###################
1303	entry = get_content('ns:SASsample', dom)
1304	if entry is not None:
1305	data_info.sample.name = entry.get('name')
1306
1307	self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample)
1308	self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample)
1309	self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample)
1310	self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample)
1311
1312	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1313	for item in nodes:
1314	try:
1315	if item.text is not None:
1316	detail_value = item.text.strip()
1317	if len(detail_value) > 0:
1318	data_info.sample.details.append(detail_value)
1319	except:
1320	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1321	self.errors.append(err_mess)
1322	logging.error(err_mess)
1323
1324	# Position (as a vector)
1325	self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample)
1326	self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample)
1327	self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample)
1328
1329	# Orientation (as a vector)
1330	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1331	dom, 'orientation.x', data_info.sample)
1332	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1333	dom, 'orientation.y', data_info.sample)
1334	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1335	dom, 'orientation.z', data_info.sample)
1336
1337	# Source info ###################
1338	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1339	if entry is not None:
1340	data_info.source.name = entry.get('name')
1341
1342	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1343	dom, 'radiation', data_info.source)
1344	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1345	dom, 'beam_shape', data_info.source)
1346	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1347	dom, 'wavelength', data_info.source)
1348	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1349	dom, 'wavelength_min', data_info.source)
1350	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1351	dom, 'wavelength_max', data_info.source)
1352	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1353	dom, 'wavelength_spread', data_info.source)
1354
1355	# Beam size (as a vector)
1356	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1357	if entry is not None:
1358	data_info.source.beam_size_name = entry.get('name')
1359
1360	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1361	dom, 'beam_size.x', data_info.source)
1362	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1363	dom, 'beam_size.y', data_info.source)
1364	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1365	dom, 'beam_size.z', data_info.source)
1366
1367	# Collimation info ###################
1368	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1369	namespaces={'ns': CANSAS_NS})
1370	for item in nodes:
1371	collim = Collimation()
1372	if item.get('name') is not None:
1373	collim.name = item.get('name')
1374	self._store_float('ns:length', item, 'length', collim)
1375
1376	# Look for apertures
1377	apert_list = item.xpath('ns:aperture',
1378	namespaces={'ns': CANSAS_NS})
1379	for apert in apert_list:
1380	aperture = Aperture()
1381
1382	# Get the name and type of the aperture
1383	aperture.name = apert.get('name')
1384	aperture.type = apert.get('type')
1385
1386	self._store_float('ns:distance', apert, 'distance', aperture)
1387
1388	entry = get_content('ns:size', apert)
1389	if entry is not None:
1390	aperture.size_name = entry.get('name')
1391
1392	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1393	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1394	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1395
1396	collim.aperture.append(aperture)
1397
1398	data_info.collimation.append(collim)
1399
1400	# Detector info ######################
1401	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1402	namespaces={'ns': CANSAS_NS})
1403	for item in nodes:
1404
1405	detector = Detector()
1406
1407	self._store_content('ns:name', item, 'name', detector)
1408	self._store_float('ns:SDD', item, 'distance', detector)
1409
1410	# Detector offset (as a vector)
1411	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1412	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1413	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1414
1415	# Detector orientation (as a vector)
1416	self._store_float('ns:orientation/ns:roll', item,
1417	'orientation.x', detector)
1418	self._store_float('ns:orientation/ns:pitch', item,
1419	'orientation.y', detector)
1420	self._store_float('ns:orientation/ns:yaw', item,
1421	'orientation.z', detector)
1422
1423	# Beam center (as a vector)
1424	self._store_float('ns:beam_center/ns:x', item,
1425	'beam_center.x', detector)
1426	self._store_float('ns:beam_center/ns:y', item,
1427	'beam_center.y', detector)
1428	self._store_float('ns:beam_center/ns:z', item,
1429	'beam_center.z', detector)
1430
1431	# Pixel size (as a vector)
1432	self._store_float('ns:pixel_size/ns:x', item,
1433	'pixel_size.x', detector)
1434	self._store_float('ns:pixel_size/ns:y', item,
1435	'pixel_size.y', detector)
1436	self._store_float('ns:pixel_size/ns:z', item,
1437	'pixel_size.z', detector)
1438
1439	self._store_float('ns:slit_length', item, 'slit_length', detector)
1440
1441	data_info.detector.append(detector)
1442
1443	# Processes info ######################
1444	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1445	for item in nodes:
1446	process = Process()
1447	self._store_content('ns:name', item, 'name', process)
1448	self._store_content('ns:date', item, 'date', process)
1449	self._store_content('ns:description', item, 'description', process)
1450
1451	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1452	for term in term_list:
1453	try:
1454	term_attr = {}
1455	for attr in term.keys():
1456	term_attr[attr] = term.get(attr).strip()
1457	if term.text is not None:
1458	term_attr['value'] = term.text.strip()
1459	process.term.append(term_attr)
1460	except:
1461	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1462	self.errors.append(err_mess)
1463	logging.error(err_mess)
1464
1465	note_list = item.xpath('ns:SASprocessnote',
1466	namespaces={'ns': CANSAS_NS})
1467	for note in note_list:
1468	if note.text is not None:
1469	process.notes.append(note.text.strip())
1470
1471	data_info.process.append(process)
1472
1473	# Data info ######################
1474	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1475	if len(nodes) > 1:
1476	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1477
1478	for entry in nodes:
1479	for item in LIST_OF_DATA_2D_ATTR:
1480	#get node
1481	node = get_content('ns:%s' % item[0], entry)
1482	setattr(data_info, item[1], parse_entry_helper(node, item))
1483
1484	for item in LIST_OF_DATA_2D_VALUES:
1485	field = get_content('ns:%s' % item[0], entry)
1486	value_list = []
1487	if field is not None:
1488	value_list = [parse_entry_helper(node, item) for node in field]
1489	if len(value_list) < 2:
1490	setattr(data_info, item[0], None)
1491	else:
1492	setattr(data_info, item[0], numpy.array(value_list))
1493
1494	return data_info
1495
1496	def _read_cansas(self, path):
1497	"""
1498	Load data and P(r) information from a CanSAS XML file.
1499
1500	:param path: file path
1501
1502	:return: Data1D object if a single SASentry was found,
1503	or a list of Data1D objects if multiple entries were found,
1504	or None of nothing was found
1505
1506	:raise RuntimeError: when the file can't be opened
1507	:raise ValueError: when the length of the data vectors are inconsistent
1508
1509	"""
1510	output = []
1511	basename = os.path.basename(path)
1512	root, extension = os.path.splitext(basename)
1513	ext = extension.lower()
1514	try:
1515	if os.path.isfile(path):
1516
1517	#TODO: eventually remove the check for .xml once
1518	# the P(r) writer/reader is truly complete.
1519	if ext in self.ext or \
1520	ext == '.xml':
1521
1522	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1523	# Check the format version number
1524	# Specifying the namespace will take care of the file format version
1525	root = tree.getroot()
1526	entry_list = root.xpath('ns:SASentry',
1527	namespaces={'ns': CANSAS_NS})
1528	for entry in entry_list:
1529	try:
1530	sas_entry, _ = self._parse_save_state_entry(entry)
1531	except:
1532	raise
1533	fitstate = self._parse_state(entry)
1534
1535	#state could be None when .svs file is loaded
1536	#in this case, skip appending to output
1537	if fitstate != None:
1538	sas_entry.meta_data['fitstate'] = fitstate
1539	sas_entry.filename = fitstate.file
1540	output.append(sas_entry)
1541	else:
1542	self.call_back(format=ext)
1543	raise RuntimeError, "%s is not a file" % path
1544
1545	# Return output consistent with the loader's api
1546	if len(output) == 0:
1547	self.call_back(state=None, datainfo=None, format=ext)
1548	return None
1549	else:
1550	for ind in range(len(output)):
1551	# Call back to post the new state
1552	state = output[ind].meta_data['fitstate']
1553	t = time.localtime(state.timestamp)
1554	time_str = time.strftime("%b %d %H:%M", t)
1555	# Check that no time stamp is already appended
1556	max_char = state.file.find("[")
1557	if max_char < 0:
1558	max_char = len(state.file)
1559	original_fname = state.file[0:max_char]
1560	state.file = original_fname + ' [' + time_str + ']'
1561
1562	if state is not None and state.is_data is not None:
1563	output[ind].is_data = state.is_data
1564
1565	output[ind].filename = state.file
1566	state.data = output[ind]
1567	state.data.name = output[ind].filename # state.data_name
1568	state.data.id = state.data_id
1569	if state.is_data is not None:
1570	state.data.is_data = state.is_data
1571	if output[ind].run_name is not None\
1572	and len(output[ind].run_name) != 0:
1573	name = output[ind].run_name
1574	else:
1575	name = original_fname
1576	state.data.group_id = name
1577	#store state in fitting
1578	self.call_back(state=state,
1579	datainfo=output[ind], format=ext)
1580	self.state = state
1581	return output
1582	except:
1583	self.call_back(format=ext)
1584	raise
1585
1586	def write(self, filename, datainfo=None, fitstate=None):
1587	"""
1588	Write the content of a Data1D as a CanSAS XML file only for standalone
1589
1590	:param filename: name of the file to write
1591	:param datainfo: Data1D object
1592	:param fitstate: PageState object
1593
1594	"""
1595	# Sanity check
1596	if self.cansas == True:
1597	# Add fitting information to the XML document
1598	doc = self.write_toXML(datainfo, fitstate)
1599	# Write the XML document
1600	else:
1601	doc = fitstate.toXML(file=filename)
1602
1603	# Save the document no matter the type
1604	fd = open(filename, 'w')
1605	fd.write(doc.toprettyxml())
1606	fd.close()
1607
1608	def write_toXML(self, datainfo=None, state=None):
1609	"""
1610	Write toXML, a helper for write(),
1611	could be used by guimanager._on_save()
1612
1613	: return: xml doc
1614	"""
1615
1616	if state.data is None:
1617	data = sas.dataloader.data_info.Data1D(x=[], y=[])
1618	return None
1619	elif not state.data.is_data:
1620	return None
1621	else:
1622	#make sure title and data run is filled up.
1623	if state.data.title == None or state.data.title == '':
1624	state.data.title = state.data.name
1625	if state.data.run_name == None or state.data.run_name == {}:
1626	state.data.run = [str(state.data.name)]
1627	state.data.run_name[0] = state.data.name
1628
1629	if issubclass(state.data.__class__,
1630	sas.dataloader.data_info.Data1D):
1631	data = state.data
1632	doc, sasentry = self._to_xml_doc(data)
1633	else:
1634	data = state.data
1635	doc, sasentry = self._data2d_to_xml_doc(data)
1636
1637	if state is not None:
1638	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1639
1640	return doc
1641
1642	# Simple html report templet
1643	HEADER = "<html>\n"
1644	HEADER += "<head>\n"
1645	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1646	HEADER += "charset=windows-1252'> \n"
1647	HEADER += "<meta name=Generator >\n"
1648	HEADER += "</head>\n"
1649	HEADER += "<body lang=EN-US>\n"
1650	HEADER += "<div class=WordSection1>\n"
1651	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1652	HEADER += "%s</font></center></span></center></b></p>"
1653	HEADER += "<p class=MsoNormal> </p>"
1654	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1655	PARA += "</font></p>"
1656	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1657	CENTRE += "</font></center></p>"
1658	FEET_1 = \
1659	"""
1660	<p class=MsoNormal> </p>
1661	<br>
1662	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1663	</font></span></center></b></p>
1664	<p class=MsoNormal> </p>
1665	<center>
1666	<br><font size='4' >Model Computation</font>
1667	<br><font size='4' >Data: "%s"</font><br>
1668	"""
1669	FEET_2 = \
1670	"""
1671	<img src="%s" >
1672	</img>
1673	"""
1674	FEET_3 = \
1675	"""
1676	</center>
1677	</div>
1678	</body>
1679	</html>
1680	"""
1681	ELINE = "<p class=MsoNormal> </p>"
1682
1683	if __name__ == "__main__":
1684	state = PageState(parent=None)
1685	#state.toXML()
1686	"""
1687
1688	file = open("test_state", "w")
1689	pickle.dump(state, file)
1690	print pickle.dumps(state)
1691	state.data_name = "hello---->"
1692	pickle.dump(state, file)
1693	file = open("test_state", "r")
1694	new_state= pickle.load(file)
1695	print "new state", new_state
1696	new_state= pickle.load(file)
1697	print "new state", new_state
1698	#print "state", state
1699	"""
1700	import bsddb
1701	import pickle
1702	db = bsddb.btopen('file_state.db', 'c')
1703	val = (pickle.dumps(state), "hello", "hi")
1704	db['state1'] = pickle.dumps(val)
1705	print pickle.loads(db['state1'])
1706	state.data_name = "hello---->22"
1707	db['state2'] = pickle.dumps(state)
1708	state.data_name = "hello---->2"
1709	db['state3'] = pickle.dumps(state)
1710	del db['state3']
1711	state.data_name = "hello---->3"
1712	db['state4'] = pickle.dumps(state)
1713	new_state = pickle.loads(db['state1'])
1714	#print db.last()
1715	db.set_location('state2')
1716	state.data_name = "hello---->5"
1717	db['aastate5'] = pickle.dumps(state)
1718	db.keys().sort()
1719	print pickle.loads(db['state2'])
1720
1721	db.close()

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SasView

source: sasview/src/sas/perspectives/fitting/pagestate.py @ 90662e6

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