pagestate.py @ b699768

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 b699768 was b699768, checked in by Piotr Rozyczko <piotr.rozyczko@…>, 8 years ago
Initial commit of the refactored SasCalc? module.
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 wx
18	import copy
19	import logging
20	import numpy
21	import string
22
23	import xml.dom.minidom
24	from xml.dom.minidom import parseString
25	from lxml import etree
26
27	import sas.sascalc.dataloader
28	from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader
29	from sas.sascalc.dataloader.readers.cansas_reader import get_content, write_node
30	from sas.sascalc.dataloader.data_info import Data2D
31	from sas.sascalc.dataloader.data_info import Collimation
32	from sas.sascalc.dataloader.data_info import Detector
33	from sas.sascalc.dataloader.data_info import Process
34	from sas.sascalc.dataloader.data_info import Aperture
35	#Information to read/write state as xml
36	FITTING_NODE_NAME = 'fitting_plug_in'
37	CANSAS_NS = "cansas1d/1.0"
38
39	LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"],
40	["group_id", "data_group_id", "string"],
41	["data_name", "data_name", "string"],
42	["data_id", "data_id", "string"],
43	["name", "name", "string"],
44	["data_name", "data_name", "string"]]
45	LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"],
46	["qmax", "qmax", "float"],
47	["npts", "npts", "float"],
48	["categorycombobox", "categorycombobox", "string"],
49	["formfactorcombobox", "formfactorcombobox", "string"],
50	["structurecombobox", "structurecombobox", "string"],
51	["multi_factor", "multi_factor", "float"],
52	["magnetic_on", "magnetic_on", "bool"],
53	["enable_smearer", "enable_smearer", "bool"],
54	["disable_smearer", "disable_smearer", "bool"],
55	["pinhole_smearer", "pinhole_smearer", "bool"],
56	["slit_smearer", "slit_smearer", "bool"],
57	["enable_disp", "enable_disp", "bool"],
58	["disable_disp", "disable_disp", "bool"],
59	["dI_noweight", "dI_noweight", "bool"],
60	["dI_didata", "dI_didata", "bool"],
61	["dI_sqrdata", "dI_sqrdata", "bool"],
62	["dI_idata", "dI_idata", "bool"],
63	["enable2D", "enable2D", "bool"],
64	["cb1", "cb1", "bool"],
65	["tcChi", "tcChi", "float"],
66	["smearer", "smearer", "float"],
67	["smear_type", "smear_type", "string"],
68	["dq_l", "dq_l", "string"],
69	["dq_r", "dq_r", "string"],
70	["dx_max", "dx_max", "float"],
71	["dx_min", "dx_min", "float"],
72	["dxl", "dxl", "float"],
73	["dxw", "dxw", "float"]]
74
75	LIST_OF_MODEL_ATTRIBUTES = [["values", "values"],
76	["weights", "weights"]]
77
78	DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]]
79
80	LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"],
81	["str_parameters", "str_parameters"],
82	["orientation_parameters", "orientation_params"],
83	["dispersity_parameters", "orientation_params_disp"],
84	["fixed_param", "fixed_param"],
85	["fittable_param", "fittable_param"]]
86	LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"],
87	["xmax", "xmax", "float"],
88	["ymin", "ymin", "float"],
89	["ymax", "ymax", "float"],
90	["_xaxis", "_xaxis", "string"],
91	["_xunit", "_xunit", "string"],
92	["_yaxis", "_yaxis", "string"],
93	["_yunit", "_yunit", "string"],
94	["_zaxis", "_zaxis", "string"],
95	["_zunit", "_zunit", "string"]]
96	LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"],
97	["qy_data", "qy_data", "float"],
98	["dqx_data", "dqx_data", "float"],
99	["dqy_data", "dqy_data", "float"],
100	["data", "data", "float"],
101	["q_data", "q_data", "float"],
102	["err_data", "err_data", "float"],
103	["mask", "mask", "bool"]]
104
105
106	def parse_entry_helper(node, item):
107	"""
108	Create a numpy list from value extrated from the node
109
110	:param node: node from each the value is stored
111	:param item: list name of three strings.the two first are name of data
112	attribute and the third one is the type of the value of that
113	attribute. type can be string, float, bool, etc.
114
115	: return: numpy array
116	"""
117	if node is not None:
118	if item[2] == "string":
119	return str(node.get(item[0]).strip())
120	elif item[2] == "bool":
121	try:
122	return node.get(item[0]).strip() == "True"
123
124	except:
125	return None
126	else:
127	try:
128	return float(node.get(item[0]))
129	except:
130	return None
131
132
133	class PageState(object):
134	"""
135	Contains information to reconstruct a page of the fitpanel.
136	"""
137	def __init__(self, parent=None, model=None, data=None):
138	"""
139	Initialize the current state
140
141	:param model: a selected model within a page
142	:param data:
143
144	"""
145	self.file = None
146	#Time of state creation
147	self.timestamp = time.time()
148	## Data member to store the dispersion object created
149	self._disp_obj_dict = {}
150	#------------------------
151	#Data used for fitting
152	self.data = data
153	# model data
154	self.theory_data = None
155	#Is 2D
156	self.is_2D = False
157	self.images = None
158
159	#save additional information on data that dataloader.reader does not read
160	self.is_data = None
161	self.data_name = ""
162
163	if self.data is not None:
164	self.data_name = self.data.name
165	self.data_id = None
166	if self.data is not None and hasattr(self.data, "id"):
167	self.data_id = self.data.id
168	self.data_group_id = None
169	if self.data is not None and hasattr(self.data, "group_id"):
170	self.data_group_id = self.data.group_id
171
172	## reset True change the state of exsiting button
173	self.reset = False
174
175	# flag to allow data2D plot
176	self.enable2D = False
177	# model on which the fit would be performed
178	self.model = model
179	self.m_name = None
180	#list of process done to model
181	self.process = []
182	#fit page manager
183	self.manager = None
184	#Store the parent of this panel parent
185	# For this application fitpanel is the parent
186	self.parent = parent
187	# Event_owner is the owner of model event
188	self.event_owner = None
189	##page name
190	self.page_name = ""
191	# Contains link between model, all its parameters, and panel organization
192	self.parameters = []
193	# String parameter list that can not be fitted
194	self.str_parameters = []
195	# Contains list of parameters that cannot be fitted and reference to
196	#panel objects
197	self.fixed_param = []
198	# Contains list of parameters with dispersity and reference to
199	#panel objects
200	self.fittable_param = []
201	## orientation parameters
202	self.orientation_params = []
203	## orientation parameters for gaussian dispersity
204	self.orientation_params_disp = []
205	## smearer info
206	self.smearer = None
207	self.smear_type = None
208	self.dq_l = None
209	self.dq_r = None
210	self.dx_max = None
211	self.dx_min = None
212	self.dxl = None
213	self.dxw = None
214	#list of dispersion parameters
215	self.disp_list = []
216	if self.model is not None:
217	self.disp_list = self.model.getDispParamList()
218
219	self.disp_cb_dict = {}
220	self.values = {}
221	self.weights = {}
222
223	#contains link between a model and selected parameters to fit
224	self.param_toFit = []
225	##dictionary of model type and model class
226	self.model_list_box = None
227	## save the state of the context menu
228	self.saved_states = {}
229	## save selection of combobox
230	self.formfactorcombobox = None
231	self.categorycombobox = None
232	self.structurecombobox = None
233
234	## radio box to select type of model
235	#self.shape_rbutton = False
236	#self.shape_indep_rbutton = False
237	#self.struct_rbutton = False
238	#self.plugin_rbutton = False
239	## the indice of the current selection
240	self.disp_box = 0
241	## Qrange
242	## Q range
243	self.qmin = 0.001
244	self.qmax = 0.1
245	#reset data range
246	self.qmax_x = None
247	self.qmin_x = None
248
249	self.npts = None
250	self.name = ""
251	self.multi_factor = None
252	self.magnetic_on = False
253	## enable smearering state
254	self.enable_smearer = False
255	self.disable_smearer = True
256	self.pinhole_smearer = False
257	self.slit_smearer = False
258	# weighting options
259	self.dI_noweight = False
260	self.dI_didata = True
261	self.dI_sqrdata = False
262	self.dI_idata = False
263	## disperity selection
264	self.enable_disp = False
265	self.disable_disp = True
266
267	## state of selected all check button
268	self.cb1 = False
269	## store value of chisqr
270	self.tcChi = None
271
272	def clone(self):
273	"""
274	Create a new copy of the current object
275	"""
276	model = None
277	if self.model is not None:
278	model = self.model.clone()
279	model.name = self.model.name
280	obj = PageState(self.parent, model=model)
281	obj.file = copy.deepcopy(self.file)
282	obj.data = copy.deepcopy(self.data)
283	if self.data is not None:
284	self.data_name = self.data.name
285	obj.data_name = self.data_name
286	obj.is_data = self.is_data
287	obj.model_list_box = copy.deepcopy(self.model_list_box)
288
289	obj.categorycombobox = self.categorycombobox
290	obj.formfactorcombobox = self.formfactorcombobox
291	obj.structurecombobox = self.structurecombobox
292
293	#obj.shape_rbutton = self.shape_rbutton
294	#obj.shape_indep_rbutton = self.shape_indep_rbutton
295	#obj.struct_rbutton = self.struct_rbutton
296	#obj.plugin_rbutton = self.plugin_rbutton
297
298	obj.manager = self.manager
299	obj.event_owner = self.event_owner
300	obj.disp_list = copy.deepcopy(self.disp_list)
301
302	obj.enable2D = copy.deepcopy(self.enable2D)
303	obj.parameters = copy.deepcopy(self.parameters)
304	obj.str_parameters = copy.deepcopy(self.str_parameters)
305	obj.fixed_param = copy.deepcopy(self.fixed_param)
306	obj.fittable_param = copy.deepcopy(self.fittable_param)
307	obj.orientation_params = copy.deepcopy(self.orientation_params)
308	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
309	obj.enable_disp = copy.deepcopy(self.enable_disp)
310	obj.disable_disp = copy.deepcopy(self.disable_disp)
311	obj.tcChi = self.tcChi
312
313	if len(self._disp_obj_dict) > 0:
314	for k, v in self._disp_obj_dict.iteritems():
315	obj._disp_obj_dict[k] = v
316	if len(self.disp_cb_dict) > 0:
317	for k, v in self.disp_cb_dict.iteritems():
318	obj.disp_cb_dict[k] = v
319	if len(self.values) > 0:
320	for k, v in self.values.iteritems():
321	obj.values[k] = v
322	if len(self.weights) > 0:
323	for k, v in self.weights.iteritems():
324	obj.weights[k] = v
325	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
326	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
327	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
328	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
329	obj.smear_type = copy.deepcopy(self.smear_type)
330	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
331	obj.dI_didata = copy.deepcopy(self.dI_didata)
332	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
333	obj.dI_idata = copy.deepcopy(self.dI_idata)
334	obj.dq_l = copy.deepcopy(self.dq_l)
335	obj.dq_r = copy.deepcopy(self.dq_r)
336	obj.dx_max = copy.deepcopy(self.dx_max)
337	obj.dx_min = copy.deepcopy(self.dx_min)
338	obj.dxl = copy.deepcopy(self.dxl)
339	obj.dxw = copy.deepcopy(self.dxw)
340	obj.disp_box = copy.deepcopy(self.disp_box)
341	obj.qmin = copy.deepcopy(self.qmin)
342	obj.qmax = copy.deepcopy(self.qmax)
343	obj.multi_factor = self.multi_factor
344	obj.magnetic_on = self.magnetic_on
345	obj.npts = copy.deepcopy(self.npts)
346	obj.cb1 = copy.deepcopy(self.cb1)
347	obj.smearer = copy.deepcopy(self.smearer)
348
349	for name, state in self.saved_states.iteritems():
350	copy_name = copy.deepcopy(name)
351	copy_state = state.clone()
352	obj.saved_states[copy_name] = copy_state
353	return obj
354
355	def _repr_helper(self, list, rep):
356	"""
357	Helper method to print a state
358	"""
359	for item in list:
360	rep += "parameter name: %s \n" % str(item[1])
361	rep += "value: %s\n" % str(item[2])
362	rep += "selected: %s\n" % str(item[0])
363	rep += "error displayed : %s \n" % str(item[4][0])
364	rep += "error value:%s \n" % str(item[4][1])
365	rep += "minimum displayed : %s \n" % str(item[5][0])
366	rep += "minimum value : %s \n" % str(item[5][1])
367	rep += "maximum displayed : %s \n" % str(item[6][0])
368	rep += "maximum value : %s \n" % str(item[6][1])
369	rep += "parameter unit: %s\n\n" % str(item[7])
370	return rep
371
372	def __repr__(self):
373	"""
374	output string for printing
375	"""
376	rep = "\nState name: %s\n" % self.file
377	t = time.localtime(self.timestamp)
378	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
379
380	rep += "State created: %s\n" % time_str
381	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
382	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
383	rep += "is data : %s\n" % self.is_data
384	rep += "data's name : %s\n" % self.data_name
385	rep += "data's id : %s\n" % self.data_id
386	if self.model != None:
387	m_name = self.model.__class__.__name__
388	if m_name == 'Model':
389	m_name = self.m_name
390	rep += "model name : %s\n" % m_name
391	else:
392	rep += "model name : None\n"
393	rep += "multi_factor : %s\n" % str(self.multi_factor)
394	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
395	rep += "model type (Category) selected: %s\n" % self.categorycombobox
396	rep += "data : %s\n" % str(self.data)
397	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
398	str(self.qmax), str(self.npts))
399	rep += "Dispersion selection : %s\n" % str(self.disp_box)
400	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
401	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
402	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
403	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
404	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
405	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
406	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
407
408	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
409	rep += "dI_didata : %s\n" % str(self.dI_didata)
410	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
411	rep += "dI_idata : %s\n" % str(self.dI_idata)
412
413	rep += "2D enable : %s\n" % str(self.enable2D)
414	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
415	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
416	rep += "Smear object : %s\n" % str(self.smearer)
417	rep += "Smear type : %s\n" % (self.smear_type)
418	rep += "dq_l : %s\n" % self.dq_l
419	rep += "dq_r : %s\n" % self.dq_r
420	rep += "dx_max : %s\n" % str(self.dx_max)
421	rep += "dx_min : %s\n" % str(self.dx_min)
422	rep += "dxl : %s\n" % str(self.dxl)
423	rep += "dxw : %s\n" % str(self.dxw)
424	rep += "model : %s\n\n" % str(self.model)
425	temp_parameters = []
426	temp_fittable_param = []
427	if self.data.__class__.__name__ == "Data2D":
428	self.is_2D = True
429	else:
430	self.is_2D = False
431	if self.data is not None:
432	if not self.is_2D:
433	for item in self.parameters:
434	if not item in self.orientation_params:
435	temp_parameters.append(item)
436	for item in self.fittable_param:
437	if not item in self.orientation_params_disp:
438	temp_fittable_param.append(item)
439	else:
440	temp_parameters = self.parameters
441	temp_fittable_param = self.fittable_param
442
443	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
444	rep = self._repr_helper(list=temp_parameters, rep=rep)
445	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
446	rep = self._repr_helper(list=self.str_parameters, rep=rep)
447	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
448	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
449	return rep
450
451	def set_report_string(self):
452	"""
453	Get the values (strings) from __str__ for report
454	"""
455	# Dictionary of the report strings
456	repo_time = ""
457	model_name = ""
458	title = ""
459	title_name = ""
460	file_name = ""
461	param_string = ""
462	paramval_string = ""
463	chi2_string = ""
464	q_range = ""
465	strings = self.__repr__()
466	lines = strings.split('\n')
467
468	# get all string values from __str__()
469	for line in lines:
470	value = ""
471	content = line.split(":")
472	name = content[0]
473	try:
474	value = content[1]
475	except:
476	logging.error(sys.exc_value)
477	if name.count("State created"):
478	repo_time = "" + value
479	if name.count("parameter name"):
480	val_name = value.split(".")
481	if len(val_name) > 1:
482	if val_name[1].count("width"):
483	param_string += value + ','
484	else:
485	continue
486	else:
487	param_string += value + ','
488	if name == "value":
489	param_string += value + ','
490	if name == "selected":
491	if value == u' False':
492	fixed_parameter = True
493	else:
494	fixed_parameter = False
495	if name == "error value":
496	if fixed_parameter:
497	param_string += '(fixed),'
498	else:
499	param_string += value + ','
500	if name == "parameter unit":
501	param_string += value + ':'
502	if name == "Value of Chisqr ":
503	chi2 = ("Chi2/Npts = " + value)
504	chi2_string = CENTRE % chi2
505	if name == "Title":
506	if len(value.strip()) == 0:
507	continue
508	title = value + " [" + repo_time + "]"
509	title_name = HEADER % title
510	if name == "data ":
511	try:
512	file_value = ("File name:" + content[2])
513	file_name = CENTRE % file_value
514	if len(title) == 0:
515	title = content[2] + " [" + repo_time + "]"
516	title_name = HEADER % title
517	except:
518	logging.error(sys.exc_value)
519	if name == "model name ":
520	try:
521	modelname = "Model name:" + content[1]
522	except:
523	modelname = "Model name:" + " NAN"
524	model_name = CENTRE % modelname
525
526	if name == "Plotting Range":
527	try:
528	q_range = content[1] + " = " + content[2] \
529	+ " = " + content[3].split(",")[0]
530	q_name = ("Q Range: " + q_range)
531	q_range = CENTRE % q_name
532	except:
533	logging.error(sys.exc_value)
534	paramval = ""
535	for lines in param_string.split(":"):
536	line = lines.split(",")
537	if len(lines) > 0:
538	param = line[0]
539	param += " = " + line[1]
540	if len(line[2].split()) > 0 and not line[2].count("None"):
541	param += " +- " + line[2]
542	if len(line[3].split()) > 0 and not line[3].count("None"):
543	param += " " + line[3]
544	if not paramval.count(param):
545	paramval += param + "\n"
546	paramval_string += CENTRE % param + "\n"
547
548	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % (title, file, q_name, chi2, paramval)
549
550	title_name = self._check_html_format(title_name)
551	file_name = self._check_html_format(file_name)
552	title = self._check_html_format(title)
553
554	html_string = title_name + "\n" + file_name + \
555	"\n" + model_name + \
556	"\n" + q_range + \
557	"\n" + chi2_string + \
558	"\n" + ELINE + \
559	"\n" + paramval_string + \
560	"\n" + ELINE + \
561	"\n" + FEET_1 % title + \
562	"\n" + FEET_2
563
564	return html_string, text_string, title
565
566	def _check_html_format(self, name):
567	"""
568	Check string '%' for html format
569	"""
570	if name.count('%'):
571	name = name.replace('%', '&#37')
572
573	return name
574
575	def report(self, figs=None, canvases=None):
576	"""
577	Invoke report dialog panel
578
579	: param figs: list of pylab figures [list]
580	"""
581	from sas.perspectives.fitting.report_dialog import ReportDialog
582	# get the strings for report
583	html_str, text_str, title = self.set_report_string()
584	# Allow 2 figures to append
585	if len(figs) == 1:
586	add_str = FEET_3
587	elif len(figs) == 2:
588	add_str = ELINE
589	add_str += FEET_2 % ("%s")
590	add_str += ELINE
591	add_str += FEET_3
592	elif len(figs) > 2:
593	add_str = ELINE
594	add_str += FEET_2 % ("%s")
595	add_str += ELINE
596	add_str += FEET_2 % ("%s")
597	add_str += ELINE
598	add_str += FEET_3
599	else:
600	add_str = ""
601
602	# final report html strings
603	report_str = html_str % ("%s") + add_str
604
605	# make plot image
606	images = self.set_plot_state(figs, canvases)
607	report_list = [report_str, text_str, images]
608	dialog = ReportDialog(report_list, None, wx.ID_ANY, "")
609	dialog.Show()
610
611	def _toXML_helper(self, thelist, element, newdoc):
612	"""
613	Helper method to create xml file for saving state
614	"""
615	for item in thelist:
616	sub_element = newdoc.createElement('parameter')
617	sub_element.setAttribute('name', str(item[1]))
618	sub_element.setAttribute('value', str(item[2]))
619	sub_element.setAttribute('selected_to_fit', str(item[0]))
620	sub_element.setAttribute('error_displayed', str(item[4][0]))
621	sub_element.setAttribute('error_value', str(item[4][1]))
622	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
623	sub_element.setAttribute('minimum_value', str(item[5][1]))
624	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
625	sub_element.setAttribute('maximum_value', str(item[6][1]))
626	sub_element.setAttribute('unit', str(item[7]))
627	element.appendChild(sub_element)
628
629	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
630	"""
631	Writes the state of the InversionControl panel to file, as XML.
632
633	Compatible with standalone writing, or appending to an
634	already existing XML document. In that case, the XML document
635	is required. An optional entry node in the XML document may also be given.
636
637	:param file: file to write to
638	:param doc: XML document object [optional]
639	:param entry_node: XML node within the XML document at which we will append the data [optional]
640
641	"""
642	from xml.dom.minidom import getDOMImplementation
643
644	# Check whether we have to write a standalone XML file
645	if doc is None:
646	impl = getDOMImplementation()
647	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
648	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
649	top_element = newdoc.documentElement
650	else:
651	# We are appending to an existing document
652	newdoc = doc
653	try:
654	top_element = newdoc.createElement(FITTING_NODE_NAME)
655	except:
656	string = etree.tostring(doc, pretty_print=True)
657	newdoc = parseString(string)
658	top_element = newdoc.createElement(FITTING_NODE_NAME)
659	if entry_node is None:
660	newdoc.documentElement.appendChild(top_element)
661	else:
662	try:
663	entry_node.appendChild(top_element)
664	except:
665	node_name = entry_node.tag
666	node_list = newdoc.getElementsByTagName(node_name)
667	entry_node = node_list.item(0)
668	entry_node.appendChild(top_element)
669
670	attr = newdoc.createAttribute("version")
671	attr.nodeValue = '1.0'
672	top_element.setAttributeNode(attr)
673
674	# File name
675	element = newdoc.createElement("filename")
676	if self.file is not None:
677	element.appendChild(newdoc.createTextNode(str(self.file)))
678	else:
679	element.appendChild(newdoc.createTextNode(str(file)))
680	top_element.appendChild(element)
681
682	element = newdoc.createElement("timestamp")
683	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
684	attr = newdoc.createAttribute("epoch")
685	attr.nodeValue = str(self.timestamp)
686	element.setAttributeNode(attr)
687	top_element.appendChild(element)
688	# Inputs
689	inputs = newdoc.createElement("Attributes")
690	top_element.appendChild(inputs)
691
692	if self.data is not None and hasattr(self.data, "group_id"):
693	self.data_group_id = self.data.group_id
694	if self.data is not None and hasattr(self.data, "is_data"):
695	self.is_data = self.data.is_data
696	if self.data is not None:
697	self.data_name = self.data.name
698	if self.data is not None and hasattr(self.data, "id"):
699	self.data_id = self.data.id
700
701	for item in LIST_OF_DATA_ATTRIBUTES:
702	element = newdoc.createElement(item[0])
703	element.setAttribute(item[0], str(getattr(self, item[1])))
704	inputs.appendChild(element)
705
706	for item in LIST_OF_STATE_ATTRIBUTES:
707	element = newdoc.createElement(item[0])
708	element.setAttribute(item[0], str(getattr(self, item[1])))
709	inputs.appendChild(element)
710
711	# For self.values ={ disp_param_name: [vals,...],...}
712	# and for self.weights ={ disp_param_name: [weights,...],...}
713	value_list = {}
714	for item in LIST_OF_MODEL_ATTRIBUTES:
715	element = newdoc.createElement(item[0])
716	value_list = getattr(self, item[1])
717	for key, value in value_list.iteritems():
718	sub_element = newdoc.createElement(key)
719	sub_element.setAttribute('name', str(key))
720	for val in value:
721	sub_element.appendChild(newdoc.createTextNode(str(val)))
722
723	element.appendChild(sub_element)
724	inputs.appendChild(element)
725
726	# Create doc for the dictionary of self._disp_obj_dic
727	for item in DISPERSION_LIST:
728	element = newdoc.createElement(item[0])
729	value_list = getattr(self, item[1])
730	for key, val in value_list.iteritems():
731	value = repr(val)
732	sub_element = newdoc.createElement(key)
733	sub_element.setAttribute('name', str(key))
734	sub_element.setAttribute('value', str(value))
735	element.appendChild(sub_element)
736	inputs.appendChild(element)
737
738	for item in LIST_OF_STATE_PARAMETERS:
739	element = newdoc.createElement(item[0])
740	self._toXML_helper(thelist=getattr(self, item[1]), element=element, newdoc=newdoc)
741	inputs.appendChild(element)
742
743	# Save the file
744	if doc is None:
745	fd = open(file, 'w')
746	fd.write(newdoc.toprettyxml())
747	fd.close()
748	return None
749	else:
750	return newdoc
751
752	def _fromXML_helper(self, node, list):
753	"""
754	Helper function to write state to xml
755	"""
756	for item in node:
757	try:
758	name = item.get('name')
759	except:
760	name = None
761	try:
762	value = item.get('value')
763	except:
764	value = None
765	try:
766	selected_to_fit = (item.get('selected_to_fit') == "True")
767	except:
768	selected_to_fit = None
769	try:
770	error_displayed = (item.get('error_displayed') == "True")
771	except:
772	error_displayed = None
773	try:
774	error_value = item.get('error_value')
775	except:
776	error_value = None
777	try:
778	minimum_displayed = (item.get('minimum_displayed') == "True")
779	except:
780	minimum_displayed = None
781	try:
782	minimum_value = item.get('minimum_value')
783	except:
784	minimum_value = None
785	try:
786	maximum_displayed = (item.get('maximum_displayed') == "True")
787	except:
788	maximum_displayed = None
789	try:
790	maximum_value = item.get('maximum_value')
791	except:
792	maximum_value = None
793	try:
794	unit = item.get('unit')
795	except:
796	unit = None
797	list.append([selected_to_fit, name, value, "+/-",
798	[error_displayed, error_value],
799	[minimum_displayed, minimum_value],
800	[maximum_displayed, maximum_value], unit])
801
802	def fromXML(self, file=None, node=None):
803	"""
804	Load fitting state from a file
805
806	:param file: .fitv file
807	:param node: node of a XML document to read from
808
809	"""
810	if file is not None:
811	msg = "PageState no longer supports non-CanSAS"
812	msg += " format for fitting files"
813	raise RuntimeError, msg
814
815	if node.get('version')and node.get('version') == '1.0':
816
817	# Get file name
818	entry = get_content('ns:filename', node)
819	if entry is not None:
820	self.file = entry.text.strip()
821
822	# Get time stamp
823	entry = get_content('ns:timestamp', node)
824	if entry is not None and entry.get('epoch'):
825	try:
826	self.timestamp = float(entry.get('epoch'))
827	except:
828	msg = "PageState.fromXML: Could not"
829	msg += " read timestamp\n %s" % sys.exc_value
830	logging.error(msg)
831
832	# Parse fitting attributes
833	entry = get_content('ns:Attributes', node)
834	for item in LIST_OF_DATA_ATTRIBUTES:
835	node = get_content('ns:%s' % item[0], entry)
836	setattr(self, item[0], parse_entry_helper(node, item))
837
838	if entry is not None:
839	for item in LIST_OF_STATE_ATTRIBUTES:
840	node = get_content('ns:%s' % item[0], entry)
841	setattr(self, item[0], parse_entry_helper(node, item))
842
843	for item in LIST_OF_STATE_PARAMETERS:
844	node = get_content("ns:%s" % item[0], entry)
845	self._fromXML_helper(node=node, list=getattr(self, item[1]))
846
847	# Recover _disp_obj_dict from xml file
848	self._disp_obj_dict = {}
849	for item in DISPERSION_LIST:
850	# Get node
851	node = get_content("ns:%s" % item[0], entry)
852	for attr in node:
853	name = str(attr.get('name'))
854	val = attr.get('value')
855	value = val.split(" instance")[0]
856	disp_name = value.split("<")[1]
857	try:
858	# Try to recover disp_model object from strings
859	com = "from sas.models.dispersion_models "
860	com += "import %s as disp"
861	com_name = disp_name.split(".")[3]
862	exec com % com_name
863	disp_model = disp()
864	attribute = getattr(self, item[1])
865	attribute[name] = com_name
866	except:
867	logging.error(sys.exc_value)
868
869	# get self.values and self.weights dic. if exists
870	for item in LIST_OF_MODEL_ATTRIBUTES:
871	node = get_content("ns:%s" % item[0], entry)
872	dic = {}
873	value_list = []
874	for par in node:
875	name = par.get('name')
876	values = par.text.split('\n')
877	# Get lines only with numbers
878	for line in values:
879	try:
880	val = float(line)
881	value_list.append(val)
882	except:
883	# pass if line is empty (it happens)
884	logging.error(sys.exc_value)
885	dic[name] = numpy.array(value_list)
886	setattr(self, item[1], dic)
887
888	def set_plot_state(self, figs, canvases):
889	"""
890	Build image state that wx.html understand
891	by plotting, putting it into wx.FileSystem image object
892
893	"""
894	images = []
895	# some imports
896	import wx
897
898	# Reset memory
899	self.imgRAM = None
900	wx.MemoryFSHandler()
901
902	# For no figures in the list, prepare empty plot
903	if figs == None or len(figs) == 0:
904	figs = [None]
905
906	# Loop over the list of figures
907	# use wx.MemoryFSHandler
908	self.imgRAM = wx.MemoryFSHandler()
909	for fig in figs:
910	if figs != None:
911	ind = figs.index(fig)
912	canvas = canvases[ind]
913
914	#store the image in wx.FileSystem Object
915	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
916
917	# index of the fig
918	ind = figs.index(fig)
919
920	#AddFile, image can be retrieved with 'memory:filename'
921	self.imgRAM.AddFile('img_fit%s.png' % ind,
922	canvas.bitmap, wx.BITMAP_TYPE_PNG)
923
924	#append figs
925	images.append(fig)
926
927	return images
928
929
930	class Reader(CansasReader):
931	"""
932	Class to load a .fitv fitting file
933	"""
934	## File type
935	type_name = "Fitting"
936
937	## Wildcards
938	type = ["Fitting files (.fitv)\|.fitv"
939	"SASView file (.svs)\|.svs"]
940	## List of allowed extensions
941	ext = ['.fitv', '.FITV', '.svs', 'SVS']
942
943	def __init__(self, call_back=None, cansas=True):
944	CansasReader.__init__(self)
945	"""
946	Initialize the call-back method to be called
947	after we load a file
948
949	:param call_back: call-back method
950	:param cansas: True = files will be written/read in CanSAS format
951	False = write CanSAS format
952
953	"""
954	## Call back method to be executed after a file is read
955	self.call_back = call_back
956	## CanSAS format flag
957	self.cansas = cansas
958	self.state = None
959
960	def get_state(self):
961	return self.state
962
963	def read(self, path):
964	"""
965	Load a new P(r) inversion state from file
966
967	:param path: file path
968
969	"""
970	if self.cansas == True:
971	return self._read_cansas(path)
972
973	def _data2d_to_xml_doc(self, datainfo):
974	"""
975	Create an XML document to contain the content of a Data2D
976
977	:param datainfo: Data2D object
978
979	"""
980	if not issubclass(datainfo.__class__, Data2D):
981	raise RuntimeError, "The cansas writer expects a Data2D instance"
982
983	doc = xml.dom.minidom.Document()
984	main_node = doc.createElement("SASroot")
985	main_node.setAttribute("version", self.version)
986	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
987	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
988	main_node.setAttribute("xsi:schemaLocation",
989	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
990
991	doc.appendChild(main_node)
992
993	entry_node = doc.createElement("SASentry")
994	main_node.appendChild(entry_node)
995
996	write_node(doc, entry_node, "Title", datainfo.title)
997	if datainfo is not None:
998	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
999	for item in datainfo.run:
1000	runname = {}
1001	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item])) > 1:
1002	runname = {'name': datainfo.run_name[item]}
1003	write_node(doc, entry_node, "Run", item, runname)
1004	# Data info
1005	new_node = doc.createElement("SASdata")
1006	entry_node.appendChild(new_node)
1007	for item in LIST_OF_DATA_2D_ATTR:
1008	element = doc.createElement(item[0])
1009	element.setAttribute(item[0], str(getattr(datainfo, item[1])))
1010	new_node.appendChild(element)
1011
1012	for item in LIST_OF_DATA_2D_VALUES:
1013	root_node = doc.createElement(item[0])
1014	new_node.appendChild(root_node)
1015	temp_list = None
1016	temp_list = getattr(datainfo, item[1])
1017
1018	if temp_list is None or len(temp_list) == 0:
1019	element = doc.createElement(item[0])
1020	element.appendChild(doc.createTextNode(str(temp_list)))
1021	root_node.appendChild(element)
1022	else:
1023	for value in temp_list:
1024	element = doc.createElement(item[0])
1025	element.setAttribute(item[0], str(value))
1026	root_node.appendChild(element)
1027
1028	# Sample info
1029	sample = doc.createElement("SASsample")
1030	if datainfo.sample.name is not None:
1031	sample.setAttribute("name", str(datainfo.sample.name))
1032	entry_node.appendChild(sample)
1033	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1034	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1035	{"unit": datainfo.sample.thickness_unit})
1036	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1037	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1038	{"unit": datainfo.sample.temperature_unit})
1039
1040	for item in datainfo.sample.details:
1041	write_node(doc, sample, "details", item)
1042
1043	pos = doc.createElement("position")
1044	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1045	{"unit": datainfo.sample.position_unit})
1046	written = written \| write_node(doc, pos, "y",
1047	datainfo.sample.position.y,
1048	{"unit": datainfo.sample.position_unit})
1049	written = written \| write_node(doc, pos, "z",
1050	datainfo.sample.position.z,
1051	{"unit": datainfo.sample.position_unit})
1052	if written == True:
1053	sample.appendChild(pos)
1054
1055	ori = doc.createElement("orientation")
1056	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1057	{"unit": datainfo.sample.orientation_unit})
1058	written = written \| write_node(doc, ori, "pitch",
1059	datainfo.sample.orientation.y,
1060	{"unit": datainfo.sample.orientation_unit})
1061	written = written \| write_node(doc, ori, "yaw",
1062	datainfo.sample.orientation.z,
1063	{"unit": datainfo.sample.orientation_unit})
1064	if written == True:
1065	sample.appendChild(ori)
1066
1067	# Instrument info
1068	instr = doc.createElement("SASinstrument")
1069	entry_node.appendChild(instr)
1070
1071	write_node(doc, instr, "name", datainfo.instrument)
1072
1073	# Source
1074	source = doc.createElement("SASsource")
1075	if datainfo.source.name is not None:
1076	source.setAttribute("name", str(datainfo.source.name))
1077	instr.appendChild(source)
1078
1079	write_node(doc, source, "radiation", datainfo.source.radiation)
1080	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1081	size = doc.createElement("beam_size")
1082	if datainfo.source.beam_size_name is not None:
1083	size.setAttribute("name", str(datainfo.source.beam_size_name))
1084	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1085	{"unit": datainfo.source.beam_size_unit})
1086	written = written \| write_node(doc, size, "y",
1087	datainfo.source.beam_size.y,
1088	{"unit": datainfo.source.beam_size_unit})
1089	written = written \| write_node(doc, size, "z",
1090	datainfo.source.beam_size.z,
1091	{"unit": datainfo.source.beam_size_unit})
1092	if written == True:
1093	source.appendChild(size)
1094
1095	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1096	{"unit": datainfo.source.wavelength_unit})
1097	write_node(doc, source, "wavelength_min",
1098	datainfo.source.wavelength_min,
1099	{"unit": datainfo.source.wavelength_min_unit})
1100	write_node(doc, source, "wavelength_max",
1101	datainfo.source.wavelength_max,
1102	{"unit": datainfo.source.wavelength_max_unit})
1103	write_node(doc, source, "wavelength_spread",
1104	datainfo.source.wavelength_spread,
1105	{"unit": datainfo.source.wavelength_spread_unit})
1106
1107	# Collimation
1108	for item in datainfo.collimation:
1109	coll = doc.createElement("SAScollimation")
1110	if item.name is not None:
1111	coll.setAttribute("name", str(item.name))
1112	instr.appendChild(coll)
1113
1114	write_node(doc, coll, "length", item.length,
1115	{"unit": item.length_unit})
1116
1117	for apert in item.aperture:
1118	ap = doc.createElement("aperture")
1119	if apert.name is not None:
1120	ap.setAttribute("name", str(apert.name))
1121	if apert.type is not None:
1122	ap.setAttribute("type", str(apert.type))
1123	coll.appendChild(ap)
1124
1125	write_node(doc, ap, "distance", apert.distance,
1126	{"unit": apert.distance_unit})
1127
1128	size = doc.createElement("size")
1129	if apert.size_name is not None:
1130	size.setAttribute("name", str(apert.size_name))
1131	written = write_node(doc, size, "x", apert.size.x,
1132	{"unit": apert.size_unit})
1133	written = written \| write_node(doc, size, "y", apert.size.y,
1134	{"unit": apert.size_unit})
1135	written = written \| write_node(doc, size, "z", apert.size.z,
1136	{"unit": apert.size_unit})
1137	if written == True:
1138	ap.appendChild(size)
1139
1140	# Detectors
1141	for item in datainfo.detector:
1142	det = doc.createElement("SASdetector")
1143	written = write_node(doc, det, "name", item.name)
1144	written = written \| write_node(doc, det, "SDD", item.distance,
1145	{"unit": item.distance_unit})
1146	written = written \| write_node(doc, det, "slit_length",
1147	item.slit_length,
1148	{"unit": item.slit_length_unit})
1149	if written == True:
1150	instr.appendChild(det)
1151
1152	off = doc.createElement("offset")
1153	written = write_node(doc, off, "x", item.offset.x,
1154	{"unit": item.offset_unit})
1155	written = written \| write_node(doc, off, "y", item.offset.y,
1156	{"unit": item.offset_unit})
1157	written = written \| write_node(doc, off, "z", item.offset.z,
1158	{"unit": item.offset_unit})
1159	if written == True:
1160	det.appendChild(off)
1161
1162	center = doc.createElement("beam_center")
1163	written = write_node(doc, center, "x", item.beam_center.x,
1164	{"unit": item.beam_center_unit})
1165	written = written \| write_node(doc, center, "y",
1166	item.beam_center.y,
1167	{"unit": item.beam_center_unit})
1168	written = written \| write_node(doc, center, "z",
1169	item.beam_center.z,
1170	{"unit": item.beam_center_unit})
1171	if written == True:
1172	det.appendChild(center)
1173
1174	pix = doc.createElement("pixel_size")
1175	written = write_node(doc, pix, "x", item.pixel_size.x,
1176	{"unit": item.pixel_size_unit})
1177	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1178	{"unit": item.pixel_size_unit})
1179	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1180	{"unit": item.pixel_size_unit})
1181	if written == True:
1182	det.appendChild(pix)
1183
1184	ori = doc.createElement("orientation")
1185	written = write_node(doc, ori, "roll", item.orientation.x,
1186	{"unit": item.orientation_unit})
1187	written = written \| write_node(doc, ori, "pitch",
1188	item.orientation.y,
1189	{"unit": item.orientation_unit})
1190	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1191	{"unit": item.orientation_unit})
1192	if written == True:
1193	det.appendChild(ori)
1194
1195	# Processes info
1196	for item in datainfo.process:
1197	node = doc.createElement("SASprocess")
1198	entry_node.appendChild(node)
1199
1200	write_node(doc, node, "name", item.name)
1201	write_node(doc, node, "date", item.date)
1202	write_node(doc, node, "description", item.description)
1203	for term in item.term:
1204	value = term['value']
1205	del term['value']
1206	write_node(doc, node, "term", value, term)
1207	for note in item.notes:
1208	write_node(doc, node, "SASprocessnote", note)
1209	# Return the document, and the SASentry node associated with
1210	# the data we just wrote
1211	return doc, entry_node
1212
1213	def _parse_state(self, entry):
1214	"""
1215	Read a fit result from an XML node
1216
1217	:param entry: XML node to read from
1218
1219	:return: PageState object
1220	"""
1221	# Create an empty state
1222	state = None
1223	# Locate the P(r) node
1224	try:
1225	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1226	namespaces={'ns': CANSAS_NS})
1227	if nodes != []:
1228	# Create an empty state
1229	state = PageState()
1230	state.fromXML(node=nodes[0])
1231
1232	except:
1233	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1234
1235	return state
1236
1237	def _parse_save_state_entry(self, dom):
1238	"""
1239	Parse a SASentry
1240
1241	:param node: SASentry node
1242
1243	:return: Data1D/Data2D object
1244
1245	"""
1246	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1247	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1248	return_value, _ = self._parse_entry(dom)
1249	numpy.trim_zeros(return_value.x)
1250	numpy.trim_zeros(return_value.y)
1251	numpy.trim_zeros(return_value.dy)
1252	size_dx = return_value.dx.size
1253	size_dxl = return_value.dxl.size
1254	size_dxw = return_value.dxw.size
1255	if size_dxl == 0 and size_dxw == 0:
1256	return_value.dxl = None
1257	return_value.dxw = None
1258	numpy.trim_zeros(return_value.dx)
1259	elif size_dx == 0:
1260	return_value.dx = None
1261	size_dx = size_dxl
1262	numpy.trim_zeros(return_value.dxl)
1263	numpy.trim_zeros(return_value.dxw)
1264
1265	return return_value, _
1266
1267	#Parse 2D
1268	data_info = Data2D()
1269
1270	# Look up title
1271	self._store_content('ns:Title', dom, 'title', data_info)
1272
1273	# Look up run number
1274	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1275	for item in nodes:
1276	if item.text is not None:
1277	value = item.text.strip()
1278	if len(value) > 0:
1279	data_info.run.append(value)
1280	if item.get('name') is not None:
1281	data_info.run_name[value] = item.get('name')
1282
1283	# Look up instrument name
1284	self._store_content('ns:SASinstrument/ns:name', dom,
1285	'instrument', data_info)
1286
1287	# Notes
1288	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1289	for note in note_list:
1290	try:
1291	if note.text is not None:
1292	note_value = note.text.strip()
1293	if len(note_value) > 0:
1294	data_info.notes.append(note_value)
1295	except:
1296	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1297	self.errors.append(err_mess)
1298	logging.error(err_mess)
1299
1300	# Sample info ###################
1301	entry = get_content('ns:SASsample', dom)
1302	if entry is not None:
1303	data_info.sample.name = entry.get('name')
1304
1305	self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample)
1306	self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample)
1307	self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample)
1308	self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample)
1309
1310	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1311	for item in nodes:
1312	try:
1313	if item.text is not None:
1314	detail_value = item.text.strip()
1315	if len(detail_value) > 0:
1316	data_info.sample.details.append(detail_value)
1317	except:
1318	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1319	self.errors.append(err_mess)
1320	logging.error(err_mess)
1321
1322	# Position (as a vector)
1323	self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample)
1324	self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample)
1325	self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample)
1326
1327	# Orientation (as a vector)
1328	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1329	dom, 'orientation.x', data_info.sample)
1330	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1331	dom, 'orientation.y', data_info.sample)
1332	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1333	dom, 'orientation.z', data_info.sample)
1334
1335	# Source info ###################
1336	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1337	if entry is not None:
1338	data_info.source.name = entry.get('name')
1339
1340	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1341	dom, 'radiation', data_info.source)
1342	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1343	dom, 'beam_shape', data_info.source)
1344	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1345	dom, 'wavelength', data_info.source)
1346	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1347	dom, 'wavelength_min', data_info.source)
1348	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1349	dom, 'wavelength_max', data_info.source)
1350	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1351	dom, 'wavelength_spread', data_info.source)
1352
1353	# Beam size (as a vector)
1354	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1355	if entry is not None:
1356	data_info.source.beam_size_name = entry.get('name')
1357
1358	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1359	dom, 'beam_size.x', data_info.source)
1360	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1361	dom, 'beam_size.y', data_info.source)
1362	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1363	dom, 'beam_size.z', data_info.source)
1364
1365	# Collimation info ###################
1366	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1367	namespaces={'ns': CANSAS_NS})
1368	for item in nodes:
1369	collim = Collimation()
1370	if item.get('name') is not None:
1371	collim.name = item.get('name')
1372	self._store_float('ns:length', item, 'length', collim)
1373
1374	# Look for apertures
1375	apert_list = item.xpath('ns:aperture',
1376	namespaces={'ns': CANSAS_NS})
1377	for apert in apert_list:
1378	aperture = Aperture()
1379
1380	# Get the name and type of the aperture
1381	aperture.name = apert.get('name')
1382	aperture.type = apert.get('type')
1383
1384	self._store_float('ns:distance', apert, 'distance', aperture)
1385
1386	entry = get_content('ns:size', apert)
1387	if entry is not None:
1388	aperture.size_name = entry.get('name')
1389
1390	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1391	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1392	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1393
1394	collim.aperture.append(aperture)
1395
1396	data_info.collimation.append(collim)
1397
1398	# Detector info ######################
1399	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1400	namespaces={'ns': CANSAS_NS})
1401	for item in nodes:
1402
1403	detector = Detector()
1404
1405	self._store_content('ns:name', item, 'name', detector)
1406	self._store_float('ns:SDD', item, 'distance', detector)
1407
1408	# Detector offset (as a vector)
1409	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1410	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1411	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1412
1413	# Detector orientation (as a vector)
1414	self._store_float('ns:orientation/ns:roll', item,
1415	'orientation.x', detector)
1416	self._store_float('ns:orientation/ns:pitch', item,
1417	'orientation.y', detector)
1418	self._store_float('ns:orientation/ns:yaw', item,
1419	'orientation.z', detector)
1420
1421	# Beam center (as a vector)
1422	self._store_float('ns:beam_center/ns:x', item,
1423	'beam_center.x', detector)
1424	self._store_float('ns:beam_center/ns:y', item,
1425	'beam_center.y', detector)
1426	self._store_float('ns:beam_center/ns:z', item,
1427	'beam_center.z', detector)
1428
1429	# Pixel size (as a vector)
1430	self._store_float('ns:pixel_size/ns:x', item,
1431	'pixel_size.x', detector)
1432	self._store_float('ns:pixel_size/ns:y', item,
1433	'pixel_size.y', detector)
1434	self._store_float('ns:pixel_size/ns:z', item,
1435	'pixel_size.z', detector)
1436
1437	self._store_float('ns:slit_length', item, 'slit_length', detector)
1438
1439	data_info.detector.append(detector)
1440
1441	# Processes info ######################
1442	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1443	for item in nodes:
1444	process = Process()
1445	self._store_content('ns:name', item, 'name', process)
1446	self._store_content('ns:date', item, 'date', process)
1447	self._store_content('ns:description', item, 'description', process)
1448
1449	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1450	for term in term_list:
1451	try:
1452	term_attr = {}
1453	for attr in term.keys():
1454	term_attr[attr] = term.get(attr).strip()
1455	if term.text is not None:
1456	term_attr['value'] = term.text.strip()
1457	process.term.append(term_attr)
1458	except:
1459	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1460	self.errors.append(err_mess)
1461	logging.error(err_mess)
1462
1463	note_list = item.xpath('ns:SASprocessnote',
1464	namespaces={'ns': CANSAS_NS})
1465	for note in note_list:
1466	if note.text is not None:
1467	process.notes.append(note.text.strip())
1468
1469	data_info.process.append(process)
1470
1471	# Data info ######################
1472	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1473	if len(nodes) > 1:
1474	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1475
1476	for entry in nodes:
1477	for item in LIST_OF_DATA_2D_ATTR:
1478	#get node
1479	node = get_content('ns:%s' % item[0], entry)
1480	setattr(data_info, item[1], parse_entry_helper(node, item))
1481
1482	for item in LIST_OF_DATA_2D_VALUES:
1483	field = get_content('ns:%s' % item[0], entry)
1484	value_list = []
1485	if field is not None:
1486	value_list = [parse_entry_helper(node, item) for node in field]
1487	if len(value_list) < 2:
1488	setattr(data_info, item[0], None)
1489	else:
1490	setattr(data_info, item[0], numpy.array(value_list))
1491
1492	return data_info
1493
1494	def _read_cansas(self, path):
1495	"""
1496	Load data and P(r) information from a CanSAS XML file.
1497
1498	:param path: file path
1499
1500	:return: Data1D object if a single SASentry was found,
1501	or a list of Data1D objects if multiple entries were found,
1502	or None of nothing was found
1503
1504	:raise RuntimeError: when the file can't be opened
1505	:raise ValueError: when the length of the data vectors are inconsistent
1506
1507	"""
1508	output = []
1509	basename = os.path.basename(path)
1510	root, extension = os.path.splitext(basename)
1511	ext = extension.lower()
1512	try:
1513	if os.path.isfile(path):
1514
1515	#TODO: eventually remove the check for .xml once
1516	# the P(r) writer/reader is truly complete.
1517	if ext in self.ext or \
1518	ext == '.xml':
1519
1520	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1521	# Check the format version number
1522	# Specifying the namespace will take care of the file format version
1523	root = tree.getroot()
1524	entry_list = root.xpath('ns:SASentry',
1525	namespaces={'ns': CANSAS_NS})
1526	for entry in entry_list:
1527	try:
1528	sas_entry, _ = self._parse_save_state_entry(entry)
1529	except:
1530	raise
1531	fitstate = self._parse_state(entry)
1532
1533	#state could be None when .svs file is loaded
1534	#in this case, skip appending to output
1535	if fitstate != None:
1536	sas_entry.meta_data['fitstate'] = fitstate
1537	sas_entry.filename = fitstate.file
1538	output.append(sas_entry)
1539	else:
1540	self.call_back(format=ext)
1541	raise RuntimeError, "%s is not a file" % path
1542
1543	# Return output consistent with the loader's api
1544	if len(output) == 0:
1545	self.call_back(state=None, datainfo=None, format=ext)
1546	return None
1547	else:
1548	for ind in range(len(output)):
1549	# Call back to post the new state
1550	state = output[ind].meta_data['fitstate']
1551	t = time.localtime(state.timestamp)
1552	time_str = time.strftime("%b %d %H:%M", t)
1553	# Check that no time stamp is already appended
1554	max_char = state.file.find("[")
1555	if max_char < 0:
1556	max_char = len(state.file)
1557	original_fname = state.file[0:max_char]
1558	state.file = original_fname + ' [' + time_str + ']'
1559
1560	if state is not None and state.is_data is not None:
1561	output[ind].is_data = state.is_data
1562
1563	output[ind].filename = state.file
1564	state.data = output[ind]
1565	state.data.name = output[ind].filename # state.data_name
1566	state.data.id = state.data_id
1567	if state.is_data is not None:
1568	state.data.is_data = state.is_data
1569	if output[ind].run_name is not None\
1570	and len(output[ind].run_name) != 0:
1571	name = output[ind].run_name
1572	else:
1573	name = original_fname
1574	state.data.group_id = name
1575	#store state in fitting
1576	self.call_back(state=state,
1577	datainfo=output[ind], format=ext)
1578	self.state = state
1579	return output
1580	except:
1581	self.call_back(format=ext)
1582	raise
1583
1584	def write(self, filename, datainfo=None, fitstate=None):
1585	"""
1586	Write the content of a Data1D as a CanSAS XML file only for standalone
1587
1588	:param filename: name of the file to write
1589	:param datainfo: Data1D object
1590	:param fitstate: PageState object
1591
1592	"""
1593	# Sanity check
1594	if self.cansas == True:
1595	# Add fitting information to the XML document
1596	doc = self.write_toXML(datainfo, fitstate)
1597	# Write the XML document
1598	else:
1599	doc = fitstate.toXML(file=filename)
1600
1601	# Save the document no matter the type
1602	fd = open(filename, 'w')
1603	fd.write(doc.toprettyxml())
1604	fd.close()
1605
1606	def write_toXML(self, datainfo=None, state=None):
1607	"""
1608	Write toXML, a helper for write(),
1609	could be used by guimanager._on_save()
1610
1611	: return: xml doc
1612	"""
1613
1614	if state.data is None:
1615	data = sas.dataloader.data_info.Data1D(x=[], y=[])
1616	return None
1617	elif not state.data.is_data:
1618	return None
1619	else:
1620	#make sure title and data run is filled up.
1621	if state.data.title == None or state.data.title == '':
1622	state.data.title = state.data.name
1623	if state.data.run_name == None or state.data.run_name == {}:
1624	state.data.run = [str(state.data.name)]
1625	state.data.run_name[0] = state.data.name
1626
1627	if issubclass(state.data.__class__,
1628	sas.dataloader.data_info.Data1D):
1629	data = state.data
1630	doc, sasentry = self._to_xml_doc(data)
1631	else:
1632	data = state.data
1633	doc, sasentry = self._data2d_to_xml_doc(data)
1634
1635	if state is not None:
1636	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1637
1638	return doc
1639
1640	# Simple html report templet
1641	HEADER = "<html>\n"
1642	HEADER += "<head>\n"
1643	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1644	HEADER += "charset=windows-1252'> \n"
1645	HEADER += "<meta name=Generator >\n"
1646	HEADER += "</head>\n"
1647	HEADER += "<body lang=EN-US>\n"
1648	HEADER += "<div class=WordSection1>\n"
1649	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1650	HEADER += "%s</font></center></span></center></b></p>"
1651	HEADER += "<p class=MsoNormal> </p>"
1652	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1653	PARA += "</font></p>"
1654	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1655	CENTRE += "</font></center></p>"
1656	FEET_1 = \
1657	"""
1658	<p class=MsoNormal> </p>
1659	<br>
1660	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1661	</font></span></center></b></p>
1662	<p class=MsoNormal> </p>
1663	<center>
1664	<br><font size='4' >Model Computation</font>
1665	<br><font size='4' >Data: "%s"</font><br>
1666	"""
1667	FEET_2 = \
1668	"""
1669	<img src="%s" >
1670	</img>
1671	"""
1672	FEET_3 = \
1673	"""
1674	</center>
1675	</div>
1676	</body>
1677	</html>
1678	"""
1679	ELINE = "<p class=MsoNormal> </p>"
1680
1681	if __name__ == "__main__":
1682	state = PageState(parent=None)
1683	#state.toXML()
1684	"""
1685
1686	file = open("test_state", "w")
1687	pickle.dump(state, file)
1688	print pickle.dumps(state)
1689	state.data_name = "hello---->"
1690	pickle.dump(state, file)
1691	file = open("test_state", "r")
1692	new_state= pickle.load(file)
1693	print "new state", new_state
1694	new_state= pickle.load(file)
1695	print "new state", new_state
1696	#print "state", state
1697	"""
1698	import bsddb
1699	import pickle
1700	db = bsddb.btopen('file_state.db', 'c')
1701	val = (pickle.dumps(state), "hello", "hi")
1702	db['state1'] = pickle.dumps(val)
1703	print pickle.loads(db['state1'])
1704	state.data_name = "hello---->22"
1705	db['state2'] = pickle.dumps(state)
1706	state.data_name = "hello---->2"
1707	db['state3'] = pickle.dumps(state)
1708	del db['state3']
1709	state.data_name = "hello---->3"
1710	db['state4'] = pickle.dumps(state)
1711	new_state = pickle.loads(db['state1'])
1712	#print db.last()
1713	db.set_location('state2')
1714	state.data_name = "hello---->5"
1715	db['aastate5'] = pickle.dumps(state)
1716	db.keys().sort()
1717	print pickle.loads(db['state2'])
1718
1719	db.close()

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SasView

source: sasview/src/sas/perspectives/fitting/pagestate.py @ b699768

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