pagestate.py @ a3f125f0

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 a3f125f0 was b1e609c, checked in by Doucet, Mathieu <doucetm@…>, 9 years ago
pylint fixes
Property mode set to `100644`
File size: 70.1 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 = [["engine_type", "engine_type", "string"],
45	["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	#engine type
176	self.engine_type = None
177	# flag to allow data2D plot
178	self.enable2D = False
179	# model on which the fit would be performed
180	self.model = model
181	self.m_name = None
182	#list of process done to model
183	self.process = []
184	#fit page manager
185	self.manager = None
186	#Store the parent of this panel parent
187	# For this application fitpanel is the parent
188	self.parent = parent
189	# Event_owner is the owner of model event
190	self.event_owner = None
191	##page name
192	self.page_name = ""
193	# Contains link between model, all its parameters, and panel organization
194	self.parameters = []
195	# String parameter list that can not be fitted
196	self.str_parameters = []
197	# Contains list of parameters that cannot be fitted and reference to
198	#panel objects
199	self.fixed_param = []
200	# Contains list of parameters with dispersity and reference to
201	#panel objects
202	self.fittable_param = []
203	## orientation parameters
204	self.orientation_params = []
205	## orientation parameters for gaussian dispersity
206	self.orientation_params_disp = []
207	## smearer info
208	self.smearer = None
209	self.smear_type = None
210	self.dq_l = None
211	self.dq_r = None
212	self.dx_max = None
213	self.dx_min = None
214	self.dxl = None
215	self.dxw = None
216	#list of dispersion parameters
217	self.disp_list = []
218	if self.model is not None:
219	self.disp_list = self.model.getDispParamList()
220
221	self.disp_cb_dict = {}
222	self.values = {}
223	self.weights = {}
224
225	#contains link between a model and selected parameters to fit
226	self.param_toFit = []
227	##dictionary of model type and model class
228	self.model_list_box = None
229	## save the state of the context menu
230	self.saved_states = {}
231	## save selection of combobox
232	self.formfactorcombobox = None
233	self.categorycombobox = None
234	self.structurecombobox = None
235
236	## radio box to select type of model
237	#self.shape_rbutton = False
238	#self.shape_indep_rbutton = False
239	#self.struct_rbutton = False
240	#self.plugin_rbutton = False
241	## the indice of the current selection
242	self.disp_box = 0
243	## Qrange
244	## Q range
245	self.qmin = 0.001
246	self.qmax = 0.1
247	#reset data range
248	self.qmax_x = None
249	self.qmin_x = None
250
251	self.npts = None
252	self.name = ""
253	self.multi_factor = None
254	self.magnetic_on = False
255	## enable smearering state
256	self.enable_smearer = False
257	self.disable_smearer = True
258	self.pinhole_smearer = False
259	self.slit_smearer = False
260	# weighting options
261	self.dI_noweight = False
262	self.dI_didata = True
263	self.dI_sqrdata = False
264	self.dI_idata = False
265	## disperity selection
266	self.enable_disp = False
267	self.disable_disp = True
268
269	## state of selected all check button
270	self.cb1 = False
271	## store value of chisqr
272	self.tcChi = None
273
274	def clone(self):
275	"""
276	Create a new copy of the current object
277	"""
278	model = None
279	if self.model is not None:
280	model = self.model.clone()
281	model.name = self.model.name
282	obj = PageState(self.parent, model=model)
283	obj.file = copy.deepcopy(self.file)
284	obj.data = copy.deepcopy(self.data)
285	if self.data is not None:
286	self.data_name = self.data.name
287	obj.data_name = self.data_name
288	obj.is_data = self.is_data
289	obj.model_list_box = copy.deepcopy(self.model_list_box)
290	obj.engine_type = copy.deepcopy(self.engine_type)
291
292	obj.categorycombobox = self.categorycombobox
293	obj.formfactorcombobox = self.formfactorcombobox
294	obj.structurecombobox = self.structurecombobox
295
296	#obj.shape_rbutton = self.shape_rbutton
297	#obj.shape_indep_rbutton = self.shape_indep_rbutton
298	#obj.struct_rbutton = self.struct_rbutton
299	#obj.plugin_rbutton = self.plugin_rbutton
300
301	obj.manager = self.manager
302	obj.event_owner = self.event_owner
303	obj.disp_list = copy.deepcopy(self.disp_list)
304
305	obj.enable2D = copy.deepcopy(self.enable2D)
306	obj.parameters = copy.deepcopy(self.parameters)
307	obj.str_parameters = copy.deepcopy(self.str_parameters)
308	obj.fixed_param = copy.deepcopy(self.fixed_param)
309	obj.fittable_param = copy.deepcopy(self.fittable_param)
310	obj.orientation_params = copy.deepcopy(self.orientation_params)
311	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
312	obj.enable_disp = copy.deepcopy(self.enable_disp)
313	obj.disable_disp = copy.deepcopy(self.disable_disp)
314	obj.tcChi = self.tcChi
315
316	if len(self._disp_obj_dict) > 0:
317	for k, v in self._disp_obj_dict.iteritems():
318	obj._disp_obj_dict[k] = v
319	if len(self.disp_cb_dict) > 0:
320	for k, v in self.disp_cb_dict.iteritems():
321	obj.disp_cb_dict[k] = v
322	if len(self.values) > 0:
323	for k, v in self.values.iteritems():
324	obj.values[k] = v
325	if len(self.weights) > 0:
326	for k, v in self.weights.iteritems():
327	obj.weights[k] = v
328	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
329	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
330	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
331	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
332	obj.smear_type = copy.deepcopy(self.smear_type)
333	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
334	obj.dI_didata = copy.deepcopy(self.dI_didata)
335	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
336	obj.dI_idata = copy.deepcopy(self.dI_idata)
337	obj.dq_l = copy.deepcopy(self.dq_l)
338	obj.dq_r = copy.deepcopy(self.dq_r)
339	obj.dx_max = copy.deepcopy(self.dx_max)
340	obj.dx_min = copy.deepcopy(self.dx_min)
341	obj.dxl = copy.deepcopy(self.dxl)
342	obj.dxw = copy.deepcopy(self.dxw)
343	obj.disp_box = copy.deepcopy(self.disp_box)
344	obj.qmin = copy.deepcopy(self.qmin)
345	obj.qmax = copy.deepcopy(self.qmax)
346	obj.multi_factor = self.multi_factor
347	obj.magnetic_on = self.magnetic_on
348	obj.npts = copy.deepcopy(self.npts)
349	obj.cb1 = copy.deepcopy(self.cb1)
350	obj.smearer = copy.deepcopy(self.smearer)
351
352	for name, state in self.saved_states.iteritems():
353	copy_name = copy.deepcopy(name)
354	copy_state = state.clone()
355	obj.saved_states[copy_name] = copy_state
356	return obj
357
358	def _repr_helper(self, list, rep):
359	"""
360	Helper method to print a state
361	"""
362	for item in list:
363	rep += "parameter name: %s \n" % str(item[1])
364	rep += "value: %s\n" % str(item[2])
365	rep += "selected: %s\n" % str(item[0])
366	rep += "error displayed : %s \n" % str(item[4][0])
367	rep += "error value:%s \n" % str(item[4][1])
368	rep += "minimum displayed : %s \n" % str(item[5][0])
369	rep += "minimum value : %s \n" % str(item[5][1])
370	rep += "maximum displayed : %s \n" % str(item[6][0])
371	rep += "maximum value : %s \n" % str(item[6][1])
372	rep += "parameter unit: %s\n\n" % str(item[7])
373	return rep
374
375	def __repr__(self):
376	"""
377	output string for printing
378	"""
379	rep = "\nState name: %s\n" % self.file
380	t = time.localtime(self.timestamp)
381	time_str = time.strftime("%b %d %Y %H;%M;%S ", t)
382
383	rep += "State created: %s\n" % time_str
384	rep += "State form factor combobox selection: %s\n" % self.formfactorcombobox
385	rep += "State structure factor combobox selection: %s\n" % self.structurecombobox
386	rep += "is data : %s\n" % self.is_data
387	rep += "data's name : %s\n" % self.data_name
388	rep += "data's id : %s\n" % self.data_id
389	if self.model != None:
390	m_name = self.model.__class__.__name__
391	if m_name == 'Model':
392	m_name = self.m_name
393	rep += "model name : %s\n" % m_name
394	else:
395	rep += "model name : None\n"
396	rep += "multi_factor : %s\n" % str(self.multi_factor)
397	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
398	rep += "model type (Category) selected: %s\n" % self.categorycombobox
399	rep += "data : %s\n" % str(self.data)
400	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % (str(self.qmin),
401	str(self.qmax), str(self.npts))
402	rep += "Dispersion selection : %s\n" % str(self.disp_box)
403	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
404	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
405	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
406	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
407	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
408	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
409	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
410
411	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
412	rep += "dI_didata : %s\n" % str(self.dI_didata)
413	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
414	rep += "dI_idata : %s\n" % str(self.dI_idata)
415
416	rep += "2D enable : %s\n" % str(self.enable2D)
417	rep += "All parameters checkbox selected: %s\n" % (self.cb1)
418	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
419	rep += "Smear object : %s\n" % str(self.smearer)
420	rep += "Smear type : %s\n" % (self.smear_type)
421	rep += "dq_l : %s\n" % self.dq_l
422	rep += "dq_r : %s\n" % self.dq_r
423	rep += "dx_max : %s\n" % str(self.dx_max)
424	rep += "dx_min : %s\n" % str(self.dx_min)
425	rep += "dxl : %s\n" % str(self.dxl)
426	rep += "dxw : %s\n" % str(self.dxw)
427	rep += "model : %s\n\n" % str(self.model)
428	temp_parameters = []
429	temp_fittable_param = []
430	if self.data.__class__.__name__ == "Data2D":
431	self.is_2D = True
432	else:
433	self.is_2D = False
434	if self.data is not None:
435	if not self.is_2D:
436	for item in self.parameters:
437	if not item in self.orientation_params:
438	temp_parameters.append(item)
439	for item in self.fittable_param:
440	if not item in self.orientation_params_disp:
441	temp_fittable_param.append(item)
442	else:
443	temp_parameters = self.parameters
444	temp_fittable_param = self.fittable_param
445
446	rep += "number parameters(self.parameters): %s\n" % len(temp_parameters)
447	rep = self._repr_helper(list=temp_parameters, rep=rep)
448	rep += "number str_parameters(self.str_parameters): %s\n" % len(self.str_parameters)
449	rep = self._repr_helper(list=self.str_parameters, rep=rep)
450	rep += "number fittable_param(self.fittable_param): %s\n" % len(temp_fittable_param)
451	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
452	return rep
453
454	def set_report_string(self):
455	"""
456	Get the values (strings) from __str__ for report
457	"""
458	# Dictionary of the report strings
459	repo_time = ""
460	model_name = ""
461	title = ""
462	title_name = ""
463	file_name = ""
464	param_string = ""
465	paramval_string = ""
466	chi2_string = ""
467	q_range = ""
468	strings = self.__repr__()
469	lines = strings.split('\n')
470
471	# get all string values from __str__()
472	for line in lines:
473	value = ""
474	content = line.split(":")
475	name = content[0]
476	try:
477	value = content[1]
478	except:
479	logging.error(sys.exc_value)
480	if name.count("State created"):
481	repo_time = "" + value
482	if name.count("parameter name"):
483	val_name = value.split(".")
484	if len(val_name) > 1:
485	if val_name[1].count("width"):
486	param_string += value + ','
487	else:
488	continue
489	else:
490	param_string += value + ','
491	if name == "value":
492	param_string += value + ','
493	if name == "selected":
494	if value == u' False':
495	fixed_parameter = True
496	else:
497	fixed_parameter = False
498	if name == "error value":
499	if fixed_parameter:
500	param_string += '(fixed),'
501	else:
502	param_string += value + ','
503	if name == "parameter unit":
504	param_string += value + ':'
505	if name == "Value of Chisqr ":
506	chi2 = ("Chi2/Npts = " + value)
507	chi2_string = CENTRE % chi2
508	if name == "Title":
509	if len(value.strip()) == 0:
510	continue
511	title = value + " [" + repo_time + "]"
512	title_name = HEADER % title
513	if name == "data ":
514	try:
515	file_value = ("File name:" + content[2])
516	file_name = CENTRE % file_value
517	if len(title) == 0:
518	title = content[2] + " [" + repo_time + "]"
519	title_name = HEADER % title
520	except:
521	logging.error(sys.exc_value)
522	if name == "model name ":
523	try:
524	modelname = "Model name:" + content[1]
525	except:
526	modelname = "Model name:" + " NAN"
527	model_name = CENTRE % modelname
528
529	if name == "Plotting Range":
530	try:
531	q_range = content[1] + " = " + content[2] \
532	+ " = " + content[3].split(",")[0]
533	q_name = ("Q Range: " + q_range)
534	q_range = CENTRE % q_name
535	except:
536	logging.error(sys.exc_value)
537	paramval = ""
538	for lines in param_string.split(":"):
539	line = lines.split(",")
540	if len(lines) > 0:
541	param = line[0]
542	param += " = " + line[1]
543	if len(line[2].split()) > 0 and not line[2].count("None"):
544	param += " +- " + line[2]
545	if len(line[3].split()) > 0 and not line[3].count("None"):
546	param += " " + line[3]
547	if not paramval.count(param):
548	paramval += param + "\n"
549	paramval_string += CENTRE % param + "\n"
550
551	text_string = "\n\n\n" + title + "\n\n" + file + \
552	"\n" + q_name + \
553	"\n" + chi2 + \
554	"\n\n" + paramval
555
556	title_name = self._check_html_format(title_name)
557	file_name = self._check_html_format(file_name)
558	title = self._check_html_format(title)
559
560	html_string = title_name + "\n" + file_name + \
561	"\n" + model_name + \
562	"\n" + q_range + \
563	"\n" + chi2_string + \
564	"\n" + ELINE + \
565	"\n" + paramval_string + \
566	"\n" + ELINE + \
567	"\n" + FEET_1 % title + \
568	"\n" + FEET_2
569
570	return html_string, text_string, title
571
572	def _check_html_format(self, name):
573	"""
574	Check string '%' for html format
575	"""
576	if name.count('%'):
577	name = name.replace('%', '&#37')
578
579	return name
580
581	def report(self, figs=None, canvases=None):
582	"""
583	Invoke report dialog panel
584
585	: param figs: list of pylab figures [list]
586	"""
587	from sas.perspectives.fitting.report_dialog import ReportDialog
588	# get the strings for report
589	html_str, text_str, title = self.set_report_string()
590	# Allow 2 figures to append
591	if len(figs) == 1:
592	add_str = FEET_3
593	elif len(figs) == 2:
594	add_str = ELINE
595	add_str += FEET_2 % ("%s")
596	add_str += ELINE
597	add_str += FEET_3
598	elif len(figs) > 2:
599	add_str = ELINE
600	add_str += FEET_2 % ("%s")
601	add_str += ELINE
602	add_str += FEET_2 % ("%s")
603	add_str += ELINE
604	add_str += FEET_3
605	else:
606	add_str = ""
607
608	# final report html strings
609	report_str = html_str % ("%s") + add_str
610
611	# make plot image
612	images = self.set_plot_state(figs, canvases)
613	report_list = [report_str, text_str, images]
614	dialog = ReportDialog(report_list, None, -1, "")
615	dialog.Show()
616
617	def _toXML_helper(self, thelist, element, newdoc):
618	"""
619	Helper method to create xml file for saving state
620	"""
621	for item in thelist:
622	sub_element = newdoc.createElement('parameter')
623	sub_element.setAttribute('name', str(item[1]))
624	sub_element.setAttribute('value', str(item[2]))
625	sub_element.setAttribute('selected_to_fit', str(item[0]))
626	sub_element.setAttribute('error_displayed', str(item[4][0]))
627	sub_element.setAttribute('error_value', str(item[4][1]))
628	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
629	sub_element.setAttribute('minimum_value', str(item[5][1]))
630	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
631	sub_element.setAttribute('maximum_value', str(item[6][1]))
632	sub_element.setAttribute('unit', str(item[7]))
633	element.appendChild(sub_element)
634
635	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
636	"""
637	Writes the state of the InversionControl panel to file, as XML.
638
639	Compatible with standalone writing, or appending to an
640	already existing XML document. In that case, the XML document
641	is required. An optional entry node in the XML document may also be given.
642
643	:param file: file to write to
644	:param doc: XML document object [optional]
645	:param entry_node: XML node within the XML document at which we will append the data [optional]
646
647	"""
648	from xml.dom.minidom import getDOMImplementation
649
650	# Check whether we have to write a standalone XML file
651	if doc is None:
652	impl = getDOMImplementation()
653	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
654	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
655	top_element = newdoc.documentElement
656	else:
657	# We are appending to an existing document
658	newdoc = doc
659	try:
660	top_element = newdoc.createElement(FITTING_NODE_NAME)
661	except:
662	string = etree.tostring(doc, pretty_print=True)
663	newdoc = parseString(string)
664	top_element = newdoc.createElement(FITTING_NODE_NAME)
665	if entry_node is None:
666	newdoc.documentElement.appendChild(top_element)
667	else:
668	try:
669	entry_node.appendChild(top_element)
670	except:
671	node_name = entry_node.tag
672	node_list = newdoc.getElementsByTagName(node_name)
673	entry_node = node_list.item(0)
674	entry_node.appendChild(top_element)
675
676	attr = newdoc.createAttribute("version")
677	attr.nodeValue = '1.0'
678	top_element.setAttributeNode(attr)
679
680	# File name
681	element = newdoc.createElement("filename")
682	if self.file is not None:
683	element.appendChild(newdoc.createTextNode(str(self.file)))
684	else:
685	element.appendChild(newdoc.createTextNode(str(file)))
686	top_element.appendChild(element)
687
688	element = newdoc.createElement("timestamp")
689	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
690	attr = newdoc.createAttribute("epoch")
691	attr.nodeValue = str(self.timestamp)
692	element.setAttributeNode(attr)
693	top_element.appendChild(element)
694	# Inputs
695	inputs = newdoc.createElement("Attributes")
696	top_element.appendChild(inputs)
697
698	if self.data is not None and hasattr(self.data, "group_id"):
699	self.data_group_id = self.data.group_id
700	if self.data is not None and hasattr(self.data, "is_data"):
701	self.is_data = self.data.is_data
702	if self.data is not None:
703	self.data_name = self.data.name
704	if self.data is not None and hasattr(self.data, "id"):
705	self.data_id = self.data.id
706
707	for item in LIST_OF_DATA_ATTRIBUTES:
708	element = newdoc.createElement(item[0])
709	element.setAttribute(item[0], str(getattr(self, item[1])))
710	inputs.appendChild(element)
711
712	for item in LIST_OF_STATE_ATTRIBUTES:
713	element = newdoc.createElement(item[0])
714	element.setAttribute(item[0], str(getattr(self, item[1])))
715	inputs.appendChild(element)
716
717	# For self.values ={ disp_param_name: [vals,...],...}
718	# and for self.weights ={ disp_param_name: [weights,...],...}
719	value_list = {}
720	for item in LIST_OF_MODEL_ATTRIBUTES:
721	element = newdoc.createElement(item[0])
722	value_list = getattr(self, item[1])
723	for key, value in value_list.iteritems():
724	sub_element = newdoc.createElement(key)
725	sub_element.setAttribute('name', str(key))
726	for val in value:
727	sub_element.appendChild(newdoc.createTextNode(str(val)))
728
729	element.appendChild(sub_element)
730	inputs.appendChild(element)
731
732	# Create doc for the dictionary of self._disp_obj_dic
733	for item in DISPERSION_LIST:
734	element = newdoc.createElement(item[0])
735	value_list = getattr(self, item[1])
736	for key, val in value_list.iteritems():
737	value = repr(val)
738	sub_element = newdoc.createElement(key)
739	sub_element.setAttribute('name', str(key))
740	sub_element.setAttribute('value', str(value))
741	element.appendChild(sub_element)
742	inputs.appendChild(element)
743
744	for item in LIST_OF_STATE_PARAMETERS:
745	element = newdoc.createElement(item[0])
746	self._toXML_helper(thelist=getattr(self, item[1]), element=element, newdoc=newdoc)
747	inputs.appendChild(element)
748
749	# Save the file
750	if doc is None:
751	fd = open(file, 'w')
752	fd.write(newdoc.toprettyxml())
753	fd.close()
754	return None
755	else:
756	return newdoc
757
758	def _fromXML_helper(self, node, list):
759	"""
760	Helper function to write state to xml
761	"""
762	for item in node:
763	try:
764	name = item.get('name')
765	except:
766	name = None
767	try:
768	value = item.get('value')
769	except:
770	value = None
771	try:
772	selected_to_fit = (item.get('selected_to_fit') == "True")
773	except:
774	selected_to_fit = None
775	try:
776	error_displayed = (item.get('error_displayed') == "True")
777	except:
778	error_displayed = None
779	try:
780	error_value = item.get('error_value')
781	except:
782	error_value = None
783	try:
784	minimum_displayed = (item.get('minimum_displayed') == "True")
785	except:
786	minimum_displayed = None
787	try:
788	minimum_value = item.get('minimum_value')
789	except:
790	minimum_value = None
791	try:
792	maximum_displayed = (item.get('maximum_displayed') == "True")
793	except:
794	maximum_displayed = None
795	try:
796	maximum_value = item.get('maximum_value')
797	except:
798	maximum_value = None
799	try:
800	unit = item.get('unit')
801	except:
802	unit = None
803	list.append([selected_to_fit, name, value, "+/-",
804	[error_displayed, error_value],
805	[minimum_displayed, minimum_value],
806	[maximum_displayed, maximum_value], unit])
807
808	def fromXML(self, file=None, node=None):
809	"""
810	Load fitting state from a file
811
812	:param file: .fitv file
813	:param node: node of a XML document to read from
814
815	"""
816	if file is not None:
817	msg = "PageState no longer supports non-CanSAS"
818	msg += " format for fitting files"
819	raise RuntimeError, msg
820
821	if node.get('version')and node.get('version') == '1.0':
822
823	# Get file name
824	entry = get_content('ns:filename', node)
825	if entry is not None:
826	self.file = entry.text.strip()
827
828	# Get time stamp
829	entry = get_content('ns:timestamp', node)
830	if entry is not None and entry.get('epoch'):
831	try:
832	self.timestamp = float(entry.get('epoch'))
833	except:
834	msg = "PageState.fromXML: Could not"
835	msg += " read timestamp\n %s" % sys.exc_value
836	logging.error(msg)
837
838	# Parse fitting attributes
839	entry = get_content('ns:Attributes', node)
840	for item in LIST_OF_DATA_ATTRIBUTES:
841	node = get_content('ns:%s' % item[0], entry)
842	setattr(self, item[0], parse_entry_helper(node, item))
843
844	if entry is not None:
845	for item in LIST_OF_STATE_ATTRIBUTES:
846	node = get_content('ns:%s' % item[0], entry)
847	setattr(self, item[0], parse_entry_helper(node, item))
848
849	for item in LIST_OF_STATE_PARAMETERS:
850	node = get_content("ns:%s" % item[0], entry)
851	self._fromXML_helper(node=node, list=getattr(self, item[1]))
852
853	# Recover _disp_obj_dict from xml file
854	self._disp_obj_dict = {}
855	for item in DISPERSION_LIST:
856	# Get node
857	node = get_content("ns:%s" % item[0], entry)
858	for attr in node:
859	name = str(attr.get('name'))
860	val = attr.get('value')
861	value = val.split(" instance")[0]
862	disp_name = value.split("<")[1]
863	try:
864	# Try to recover disp_model object from strings
865	com = "from sas.models.dispersion_models "
866	com += "import %s as disp"
867	com_name = disp_name.split(".")[3]
868	exec com % com_name
869	disp_model = disp()
870	attribute = getattr(self, item[1])
871	attribute[name] = com_name
872	except:
873	logging.error(sys.exc_value)
874
875	# get self.values and self.weights dic. if exists
876	for item in LIST_OF_MODEL_ATTRIBUTES:
877	node = get_content("ns:%s" % item[0], entry)
878	dic = {}
879	value_list = []
880	for par in node:
881	name = par.get('name')
882	values = par.text.split('\n')
883	# Get lines only with numbers
884	for line in values:
885	try:
886	val = float(line)
887	value_list.append(val)
888	except:
889	# pass if line is empty (it happens)
890	logging.error(sys.exc_value)
891	dic[name] = numpy.array(value_list)
892	setattr(self, item[1], dic)
893
894	def set_plot_state(self, figs, canvases):
895	"""
896	Build image state that wx.html understand
897	by plotting, putting it into wx.FileSystem image object
898
899	"""
900	images = []
901	# some imports
902	import wx
903
904	# Reset memory
905	self.imgRAM = None
906	wx.MemoryFSHandler()
907
908	# For no figures in the list, prepare empty plot
909	if figs == None or len(figs) == 0:
910	figs = [None]
911
912	# Loop over the list of figures
913	# use wx.MemoryFSHandler
914	self.imgRAM = wx.MemoryFSHandler()
915	for fig in figs:
916	if figs != None:
917	ind = figs.index(fig)
918	canvas = canvases[ind]
919
920	#store the image in wx.FileSystem Object
921	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
922
923	# index of the fig
924	ind = figs.index(fig)
925
926	#AddFile, image can be retrieved with 'memory:filename'
927	self.imgRAM.AddFile('img_fit%s.png' % ind,
928	canvas.bitmap, wx.BITMAP_TYPE_PNG)
929
930	#append figs
931	images.append(fig)
932
933	return images
934
935
936	class Reader(CansasReader):
937	"""
938	Class to load a .fitv fitting file
939	"""
940	## File type
941	type_name = "Fitting"
942
943	## Wildcards
944	type = ["Fitting files (.fitv)\|.fitv"
945	"SASView file (.svs)\|.svs"]
946	## List of allowed extensions
947	ext = ['.fitv', '.FITV', '.svs', 'SVS']
948
949	def __init__(self, call_back=None, cansas=True):
950	CansasReader.__init__(self)
951	"""
952	Initialize the call-back method to be called
953	after we load a file
954
955	:param call_back: call-back method
956	:param cansas: True = files will be written/read in CanSAS format
957	False = write CanSAS format
958
959	"""
960	## Call back method to be executed after a file is read
961	self.call_back = call_back
962	## CanSAS format flag
963	self.cansas = cansas
964	self.state = None
965
966	def get_state(self):
967	return self.state
968
969	def read(self, path):
970	"""
971	Load a new P(r) inversion state from file
972
973	:param path: file path
974
975	"""
976	if self.cansas == True:
977	return self._read_cansas(path)
978
979	def _data2d_to_xml_doc(self, datainfo):
980	"""
981	Create an XML document to contain the content of a Data2D
982
983	:param datainfo: Data2D object
984
985	"""
986	if not issubclass(datainfo.__class__, Data2D):
987	raise RuntimeError, "The cansas writer expects a Data2D instance"
988
989	doc = xml.dom.minidom.Document()
990	main_node = doc.createElement("SASroot")
991	main_node.setAttribute("version", self.version)
992	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
993	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
994	main_node.setAttribute("xsi:schemaLocation",
995	"cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
996
997	doc.appendChild(main_node)
998
999	entry_node = doc.createElement("SASentry")
1000	main_node.appendChild(entry_node)
1001
1002	write_node(doc, entry_node, "Title", datainfo.title)
1003	if datainfo is not None:
1004	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
1005	for item in datainfo.run:
1006	runname = {}
1007	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item])) > 1:
1008	runname = {'name': datainfo.run_name[item]}
1009	write_node(doc, entry_node, "Run", item, runname)
1010	# Data info
1011	new_node = doc.createElement("SASdata")
1012	entry_node.appendChild(new_node)
1013	for item in LIST_OF_DATA_2D_ATTR:
1014	element = doc.createElement(item[0])
1015	element.setAttribute(item[0], str(getattr(datainfo, item[1])))
1016	new_node.appendChild(element)
1017
1018	for item in LIST_OF_DATA_2D_VALUES:
1019	root_node = doc.createElement(item[0])
1020	new_node.appendChild(root_node)
1021	temp_list = None
1022	temp_list = getattr(datainfo, item[1])
1023
1024	if temp_list is None or len(temp_list) == 0:
1025	element = doc.createElement(item[0])
1026	element.appendChild(doc.createTextNode(str(temp_list)))
1027	root_node.appendChild(element)
1028	else:
1029	for value in temp_list:
1030	element = doc.createElement(item[0])
1031	element.setAttribute(item[0], str(value))
1032	root_node.appendChild(element)
1033
1034	# Sample info
1035	sample = doc.createElement("SASsample")
1036	if datainfo.sample.name is not None:
1037	sample.setAttribute("name", str(datainfo.sample.name))
1038	entry_node.appendChild(sample)
1039	write_node(doc, sample, "ID", str(datainfo.sample.ID))
1040	write_node(doc, sample, "thickness", datainfo.sample.thickness,
1041	{"unit": datainfo.sample.thickness_unit})
1042	write_node(doc, sample, "transmission", datainfo.sample.transmission)
1043	write_node(doc, sample, "temperature", datainfo.sample.temperature,
1044	{"unit": datainfo.sample.temperature_unit})
1045
1046	for item in datainfo.sample.details:
1047	write_node(doc, sample, "details", item)
1048
1049	pos = doc.createElement("position")
1050	written = write_node(doc, pos, "x", datainfo.sample.position.x,
1051	{"unit": datainfo.sample.position_unit})
1052	written = written \| write_node(doc, pos, "y",
1053	datainfo.sample.position.y,
1054	{"unit": datainfo.sample.position_unit})
1055	written = written \| write_node(doc, pos, "z",
1056	datainfo.sample.position.z,
1057	{"unit": datainfo.sample.position_unit})
1058	if written == True:
1059	sample.appendChild(pos)
1060
1061	ori = doc.createElement("orientation")
1062	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x,
1063	{"unit": datainfo.sample.orientation_unit})
1064	written = written \| write_node(doc, ori, "pitch",
1065	datainfo.sample.orientation.y,
1066	{"unit": datainfo.sample.orientation_unit})
1067	written = written \| write_node(doc, ori, "yaw",
1068	datainfo.sample.orientation.z,
1069	{"unit": datainfo.sample.orientation_unit})
1070	if written == True:
1071	sample.appendChild(ori)
1072
1073	# Instrument info
1074	instr = doc.createElement("SASinstrument")
1075	entry_node.appendChild(instr)
1076
1077	write_node(doc, instr, "name", datainfo.instrument)
1078
1079	# Source
1080	source = doc.createElement("SASsource")
1081	if datainfo.source.name is not None:
1082	source.setAttribute("name", str(datainfo.source.name))
1083	instr.appendChild(source)
1084
1085	write_node(doc, source, "radiation", datainfo.source.radiation)
1086	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
1087	size = doc.createElement("beam_size")
1088	if datainfo.source.beam_size_name is not None:
1089	size.setAttribute("name", str(datainfo.source.beam_size_name))
1090	written = write_node(doc, size, "x", datainfo.source.beam_size.x,
1091	{"unit": datainfo.source.beam_size_unit})
1092	written = written \| write_node(doc, size, "y",
1093	datainfo.source.beam_size.y,
1094	{"unit": datainfo.source.beam_size_unit})
1095	written = written \| write_node(doc, size, "z",
1096	datainfo.source.beam_size.z,
1097	{"unit": datainfo.source.beam_size_unit})
1098	if written == True:
1099	source.appendChild(size)
1100
1101	write_node(doc, source, "wavelength", datainfo.source.wavelength,
1102	{"unit": datainfo.source.wavelength_unit})
1103	write_node(doc, source, "wavelength_min",
1104	datainfo.source.wavelength_min,
1105	{"unit": datainfo.source.wavelength_min_unit})
1106	write_node(doc, source, "wavelength_max",
1107	datainfo.source.wavelength_max,
1108	{"unit": datainfo.source.wavelength_max_unit})
1109	write_node(doc, source, "wavelength_spread",
1110	datainfo.source.wavelength_spread,
1111	{"unit": datainfo.source.wavelength_spread_unit})
1112
1113	# Collimation
1114	for item in datainfo.collimation:
1115	coll = doc.createElement("SAScollimation")
1116	if item.name is not None:
1117	coll.setAttribute("name", str(item.name))
1118	instr.appendChild(coll)
1119
1120	write_node(doc, coll, "length", item.length,
1121	{"unit": item.length_unit})
1122
1123	for apert in item.aperture:
1124	ap = doc.createElement("aperture")
1125	if apert.name is not None:
1126	ap.setAttribute("name", str(apert.name))
1127	if apert.type is not None:
1128	ap.setAttribute("type", str(apert.type))
1129	coll.appendChild(ap)
1130
1131	write_node(doc, ap, "distance", apert.distance,
1132	{"unit": apert.distance_unit})
1133
1134	size = doc.createElement("size")
1135	if apert.size_name is not None:
1136	size.setAttribute("name", str(apert.size_name))
1137	written = write_node(doc, size, "x", apert.size.x,
1138	{"unit": apert.size_unit})
1139	written = written \| write_node(doc, size, "y", apert.size.y,
1140	{"unit": apert.size_unit})
1141	written = written \| write_node(doc, size, "z", apert.size.z,
1142	{"unit": apert.size_unit})
1143	if written == True:
1144	ap.appendChild(size)
1145
1146	# Detectors
1147	for item in datainfo.detector:
1148	det = doc.createElement("SASdetector")
1149	written = write_node(doc, det, "name", item.name)
1150	written = written \| write_node(doc, det, "SDD", item.distance,
1151	{"unit": item.distance_unit})
1152	written = written \| write_node(doc, det, "slit_length",
1153	item.slit_length,
1154	{"unit": item.slit_length_unit})
1155	if written == True:
1156	instr.appendChild(det)
1157
1158	off = doc.createElement("offset")
1159	written = write_node(doc, off, "x", item.offset.x,
1160	{"unit": item.offset_unit})
1161	written = written \| write_node(doc, off, "y", item.offset.y,
1162	{"unit": item.offset_unit})
1163	written = written \| write_node(doc, off, "z", item.offset.z,
1164	{"unit": item.offset_unit})
1165	if written == True:
1166	det.appendChild(off)
1167
1168	center = doc.createElement("beam_center")
1169	written = write_node(doc, center, "x", item.beam_center.x,
1170	{"unit": item.beam_center_unit})
1171	written = written \| write_node(doc, center, "y",
1172	item.beam_center.y,
1173	{"unit": item.beam_center_unit})
1174	written = written \| write_node(doc, center, "z",
1175	item.beam_center.z,
1176	{"unit": item.beam_center_unit})
1177	if written == True:
1178	det.appendChild(center)
1179
1180	pix = doc.createElement("pixel_size")
1181	written = write_node(doc, pix, "x", item.pixel_size.x,
1182	{"unit": item.pixel_size_unit})
1183	written = written \| write_node(doc, pix, "y", item.pixel_size.y,
1184	{"unit": item.pixel_size_unit})
1185	written = written \| write_node(doc, pix, "z", item.pixel_size.z,
1186	{"unit": item.pixel_size_unit})
1187	if written == True:
1188	det.appendChild(pix)
1189
1190	ori = doc.createElement("orientation")
1191	written = write_node(doc, ori, "roll", item.orientation.x,
1192	{"unit": item.orientation_unit})
1193	written = written \| write_node(doc, ori, "pitch",
1194	item.orientation.y,
1195	{"unit": item.orientation_unit})
1196	written = written \| write_node(doc, ori, "yaw", item.orientation.z,
1197	{"unit": item.orientation_unit})
1198	if written == True:
1199	det.appendChild(ori)
1200
1201	# Processes info
1202	for item in datainfo.process:
1203	node = doc.createElement("SASprocess")
1204	entry_node.appendChild(node)
1205
1206	write_node(doc, node, "name", item.name)
1207	write_node(doc, node, "date", item.date)
1208	write_node(doc, node, "description", item.description)
1209	for term in item.term:
1210	value = term['value']
1211	del term['value']
1212	write_node(doc, node, "term", value, term)
1213	for note in item.notes:
1214	write_node(doc, node, "SASprocessnote", note)
1215	# Return the document, and the SASentry node associated with
1216	# the data we just wrote
1217	return doc, entry_node
1218
1219	def _parse_state(self, entry):
1220	"""
1221	Read a fit result from an XML node
1222
1223	:param entry: XML node to read from
1224
1225	:return: PageState object
1226	"""
1227	# Create an empty state
1228	state = None
1229	# Locate the P(r) node
1230	try:
1231	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
1232	namespaces={'ns': CANSAS_NS})
1233	if nodes != []:
1234	# Create an empty state
1235	state = PageState()
1236	state.fromXML(node=nodes[0])
1237
1238	except:
1239	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
1240
1241	return state
1242
1243	def _parse_save_state_entry(self, dom):
1244	"""
1245	Parse a SASentry
1246
1247	:param node: SASentry node
1248
1249	:return: Data1D/Data2D object
1250
1251	"""
1252	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
1253	if not node or node[0].text.lstrip().rstrip() != "Data2D":
1254	return_value, _ = self._parse_entry(dom)
1255	numpy.trim_zeros(return_value.x)
1256	numpy.trim_zeros(return_value.y)
1257	numpy.trim_zeros(return_value.dy)
1258	size_dx = return_value.dx.size
1259	size_dxl = return_value.dxl.size
1260	size_dxw = return_value.dxw.size
1261	if size_dxl == 0 and size_dxw == 0:
1262	return_value.dxl = None
1263	return_value.dxw = None
1264	numpy.trim_zeros(return_value.dx)
1265	elif size_dx == 0:
1266	return_value.dx = None
1267	size_dx = size_dxl
1268	numpy.trim_zeros(return_value.dxl)
1269	numpy.trim_zeros(return_value.dxw)
1270
1271	return return_value, _
1272
1273	#Parse 2D
1274	data_info = Data2D()
1275
1276	# Look up title
1277	self._store_content('ns:Title', dom, 'title', data_info)
1278
1279	# Look up run number
1280	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
1281	for item in nodes:
1282	if item.text is not None:
1283	value = item.text.strip()
1284	if len(value) > 0:
1285	data_info.run.append(value)
1286	if item.get('name') is not None:
1287	data_info.run_name[value] = item.get('name')
1288
1289	# Look up instrument name
1290	self._store_content('ns:SASinstrument/ns:name', dom,
1291	'instrument', data_info)
1292
1293	# Notes
1294	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
1295	for note in note_list:
1296	try:
1297	if note.text is not None:
1298	note_value = note.text.strip()
1299	if len(note_value) > 0:
1300	data_info.notes.append(note_value)
1301	except:
1302	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
1303	self.errors.append(err_mess)
1304	logging.error(err_mess)
1305
1306	# Sample info ###################
1307	entry = get_content('ns:SASsample', dom)
1308	if entry is not None:
1309	data_info.sample.name = entry.get('name')
1310
1311	self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample)
1312	self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample)
1313	self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample)
1314	self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample)
1315
1316	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
1317	for item in nodes:
1318	try:
1319	if item.text is not None:
1320	detail_value = item.text.strip()
1321	if len(detail_value) > 0:
1322	data_info.sample.details.append(detail_value)
1323	except:
1324	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
1325	self.errors.append(err_mess)
1326	logging.error(err_mess)
1327
1328	# Position (as a vector)
1329	self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample)
1330	self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample)
1331	self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample)
1332
1333	# Orientation (as a vector)
1334	self._store_float('ns:SASsample/ns:orientation/ns:roll',
1335	dom, 'orientation.x', data_info.sample)
1336	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
1337	dom, 'orientation.y', data_info.sample)
1338	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
1339	dom, 'orientation.z', data_info.sample)
1340
1341	# Source info ###################
1342	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
1343	if entry is not None:
1344	data_info.source.name = entry.get('name')
1345
1346	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
1347	dom, 'radiation', data_info.source)
1348	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
1349	dom, 'beam_shape', data_info.source)
1350	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
1351	dom, 'wavelength', data_info.source)
1352	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
1353	dom, 'wavelength_min', data_info.source)
1354	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
1355	dom, 'wavelength_max', data_info.source)
1356	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
1357	dom, 'wavelength_spread', data_info.source)
1358
1359	# Beam size (as a vector)
1360	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
1361	if entry is not None:
1362	data_info.source.beam_size_name = entry.get('name')
1363
1364	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
1365	dom, 'beam_size.x', data_info.source)
1366	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
1367	dom, 'beam_size.y', data_info.source)
1368	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
1369	dom, 'beam_size.z', data_info.source)
1370
1371	# Collimation info ###################
1372	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation',
1373	namespaces={'ns': CANSAS_NS})
1374	for item in nodes:
1375	collim = Collimation()
1376	if item.get('name') is not None:
1377	collim.name = item.get('name')
1378	self._store_float('ns:length', item, 'length', collim)
1379
1380	# Look for apertures
1381	apert_list = item.xpath('ns:aperture',
1382	namespaces={'ns': CANSAS_NS})
1383	for apert in apert_list:
1384	aperture = Aperture()
1385
1386	# Get the name and type of the aperture
1387	aperture.name = apert.get('name')
1388	aperture.type = apert.get('type')
1389
1390	self._store_float('ns:distance', apert, 'distance', aperture)
1391
1392	entry = get_content('ns:size', apert)
1393	if entry is not None:
1394	aperture.size_name = entry.get('name')
1395
1396	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
1397	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
1398	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
1399
1400	collim.aperture.append(aperture)
1401
1402	data_info.collimation.append(collim)
1403
1404	# Detector info ######################
1405	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector',
1406	namespaces={'ns': CANSAS_NS})
1407	for item in nodes:
1408
1409	detector = Detector()
1410
1411	self._store_content('ns:name', item, 'name', detector)
1412	self._store_float('ns:SDD', item, 'distance', detector)
1413
1414	# Detector offset (as a vector)
1415	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1416	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1417	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1418
1419	# Detector orientation (as a vector)
1420	self._store_float('ns:orientation/ns:roll', item,
1421	'orientation.x', detector)
1422	self._store_float('ns:orientation/ns:pitch', item,
1423	'orientation.y', detector)
1424	self._store_float('ns:orientation/ns:yaw', item,
1425	'orientation.z', detector)
1426
1427	# Beam center (as a vector)
1428	self._store_float('ns:beam_center/ns:x', item,
1429	'beam_center.x', detector)
1430	self._store_float('ns:beam_center/ns:y', item,
1431	'beam_center.y', detector)
1432	self._store_float('ns:beam_center/ns:z', item,
1433	'beam_center.z', detector)
1434
1435	# Pixel size (as a vector)
1436	self._store_float('ns:pixel_size/ns:x', item,
1437	'pixel_size.x', detector)
1438	self._store_float('ns:pixel_size/ns:y', item,
1439	'pixel_size.y', detector)
1440	self._store_float('ns:pixel_size/ns:z', item,
1441	'pixel_size.z', detector)
1442
1443	self._store_float('ns:slit_length', item, 'slit_length', detector)
1444
1445	data_info.detector.append(detector)
1446
1447	# Processes info ######################
1448	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1449	for item in nodes:
1450	process = Process()
1451	self._store_content('ns:name', item, 'name', process)
1452	self._store_content('ns:date', item, 'date', process)
1453	self._store_content('ns:description', item, 'description', process)
1454
1455	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1456	for term in term_list:
1457	try:
1458	term_attr = {}
1459	for attr in term.keys():
1460	term_attr[attr] = term.get(attr).strip()
1461	if term.text is not None:
1462	term_attr['value'] = term.text.strip()
1463	process.term.append(term_attr)
1464	except:
1465	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1466	self.errors.append(err_mess)
1467	logging.error(err_mess)
1468
1469	note_list = item.xpath('ns:SASprocessnote',
1470	namespaces={'ns': CANSAS_NS})
1471	for note in note_list:
1472	if note.text is not None:
1473	process.notes.append(note.text.strip())
1474
1475	data_info.process.append(process)
1476
1477	# Data info ######################
1478	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1479	if len(nodes) > 1:
1480	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1481
1482	for entry in nodes:
1483	for item in LIST_OF_DATA_2D_ATTR:
1484	#get node
1485	node = get_content('ns:%s' % item[0], entry)
1486	setattr(data_info, item[1], parse_entry_helper(node, item))
1487
1488	for item in LIST_OF_DATA_2D_VALUES:
1489	field = get_content('ns:%s' % item[0], entry)
1490	value_list = []
1491	if field is not None:
1492	value_list = [parse_entry_helper(node, item) for node in field]
1493	if len(value_list) < 2:
1494	setattr(data_info, item[0], None)
1495	else:
1496	setattr(data_info, item[0], numpy.array(value_list))
1497
1498	return data_info
1499
1500	def _read_cansas(self, path):
1501	"""
1502	Load data and P(r) information from a CanSAS XML file.
1503
1504	:param path: file path
1505
1506	:return: Data1D object if a single SASentry was found,
1507	or a list of Data1D objects if multiple entries were found,
1508	or None of nothing was found
1509
1510	:raise RuntimeError: when the file can't be opened
1511	:raise ValueError: when the length of the data vectors are inconsistent
1512
1513	"""
1514	output = []
1515	basename = os.path.basename(path)
1516	root, extension = os.path.splitext(basename)
1517	ext = extension.lower()
1518	try:
1519	if os.path.isfile(path):
1520
1521	#TODO: eventually remove the check for .xml once
1522	# the P(r) writer/reader is truly complete.
1523	if ext in self.ext or \
1524	ext == '.xml':
1525
1526	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1527	# Check the format version number
1528	# Specifying the namespace will take care of the file format version
1529	root = tree.getroot()
1530	entry_list = root.xpath('ns:SASentry',
1531	namespaces={'ns': CANSAS_NS})
1532	for entry in entry_list:
1533	try:
1534	sas_entry, _ = self._parse_save_state_entry(entry)
1535	except:
1536	raise
1537	fitstate = self._parse_state(entry)
1538
1539	#state could be None when .svs file is loaded
1540	#in this case, skip appending to output
1541	if fitstate != None:
1542	sas_entry.meta_data['fitstate'] = fitstate
1543	sas_entry.filename = fitstate.file
1544	output.append(sas_entry)
1545	else:
1546	self.call_back(format=ext)
1547	raise RuntimeError, "%s is not a file" % path
1548
1549	# Return output consistent with the loader's api
1550	if len(output) == 0:
1551	self.call_back(state=None, datainfo=None, format=ext)
1552	return None
1553	else:
1554	for ind in range(len(output)):
1555	# Call back to post the new state
1556	state = output[ind].meta_data['fitstate']
1557	t = time.localtime(state.timestamp)
1558	time_str = time.strftime("%b %d %H:%M", t)
1559	# Check that no time stamp is already appended
1560	max_char = state.file.find("[")
1561	if max_char < 0:
1562	max_char = len(state.file)
1563	original_fname = state.file[0:max_char]
1564	state.file = original_fname + ' [' + time_str + ']'
1565
1566	if state is not None and state.is_data is not None:
1567	output[ind].is_data = state.is_data
1568
1569	output[ind].filename = state.file
1570	state.data = output[ind]
1571	state.data.name = output[ind].filename # state.data_name
1572	state.data.id = state.data_id
1573	if state.is_data is not None:
1574	state.data.is_data = state.is_data
1575	if output[ind].run_name is not None\
1576	and len(output[ind].run_name) != 0:
1577	name = output[ind].run_name
1578	else:
1579	name = original_fname
1580	state.data.group_id = name
1581	#store state in fitting
1582	self.call_back(state=state,
1583	datainfo=output[ind], format=ext)
1584	self.state = state
1585	return output
1586	except:
1587	self.call_back(format=ext)
1588	raise
1589
1590	def write(self, filename, datainfo=None, fitstate=None):
1591	"""
1592	Write the content of a Data1D as a CanSAS XML file only for standalone
1593
1594	:param filename: name of the file to write
1595	:param datainfo: Data1D object
1596	:param fitstate: PageState object
1597
1598	"""
1599	# Sanity check
1600	if self.cansas == True:
1601	# Add fitting information to the XML document
1602	doc = self.write_toXML(datainfo, fitstate)
1603	# Write the XML document
1604	else:
1605	doc = fitstate.toXML(file=filename)
1606
1607	# Save the document no matter the type
1608	fd = open(filename, 'w')
1609	fd.write(doc.toprettyxml())
1610	fd.close()
1611
1612	def write_toXML(self, datainfo=None, state=None):
1613	"""
1614	Write toXML, a helper for write(),
1615	could be used by guimanager._on_save()
1616
1617	: return: xml doc
1618	"""
1619
1620	if state.data is None:
1621	data = sas.dataloader.data_info.Data1D(x=[], y=[])
1622	return None
1623	elif not state.data.is_data:
1624	return None
1625	else:
1626	#make sure title and data run is filled up.
1627	if state.data.title == None or state.data.title == '':
1628	state.data.title = state.data.name
1629	if state.data.run_name == None or state.data.run_name == {}:
1630	state.data.run = [str(state.data.name)]
1631	state.data.run_name[0] = state.data.name
1632
1633	if issubclass(state.data.__class__,
1634	sas.dataloader.data_info.Data1D):
1635	data = state.data
1636	doc, sasentry = self._to_xml_doc(data)
1637	else:
1638	data = state.data
1639	doc, sasentry = self._data2d_to_xml_doc(data)
1640
1641	if state is not None:
1642	doc = state.toXML(doc=doc, file=data.filename, entry_node=sasentry)
1643
1644	return doc
1645
1646	# Simple html report templet
1647	HEADER = "<html>\n"
1648	HEADER += "<head>\n"
1649	HEADER += "<meta http-equiv=Content-Type content='text/html; "
1650	HEADER += "charset=windows-1252'> \n"
1651	HEADER += "<meta name=Generator >\n"
1652	HEADER += "</head>\n"
1653	HEADER += "<body lang=EN-US>\n"
1654	HEADER += "<div class=WordSection1>\n"
1655	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
1656	HEADER += "%s</font></center></span></center></b></p>"
1657	HEADER += "<p class=MsoNormal> </p>"
1658	PARA = "<p class=MsoNormal><font size='4' > %s \n"
1659	PARA += "</font></p>"
1660	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
1661	CENTRE += "</font></center></p>"
1662	FEET_1 = \
1663	"""
1664	<p class=MsoNormal> </p>
1665	<br>
1666	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
1667	</font></span></center></b></p>
1668	<p class=MsoNormal> </p>
1669	<center>
1670	<br><font size='4' >Model Computation</font>
1671	<br><font size='4' >Data: "%s"</font><br>
1672	"""
1673	FEET_2 = \
1674	"""
1675	<img src="%s" >
1676	</img>
1677	"""
1678	FEET_3 = \
1679	"""
1680	</center>
1681	</div>
1682	</body>
1683	</html>
1684	"""
1685	ELINE = "<p class=MsoNormal> </p>"
1686
1687	if __name__ == "__main__":
1688	state = PageState(parent=None)
1689	#state.toXML()
1690	"""
1691
1692	file = open("test_state", "w")
1693	pickle.dump(state, file)
1694	print pickle.dumps(state)
1695	state.data_name = "hello---->"
1696	pickle.dump(state, file)
1697	file = open("test_state", "r")
1698	new_state= pickle.load(file)
1699	print "new state", new_state
1700	new_state= pickle.load(file)
1701	print "new state", new_state
1702	#print "state", state
1703	"""
1704	import bsddb
1705	import pickle
1706	db = bsddb.btopen('file_state.db', 'c')
1707	val = (pickle.dumps(state), "hello", "hi")
1708	db['state1'] = pickle.dumps(val)
1709	print pickle.loads(db['state1'])
1710	state.data_name = "hello---->22"
1711	db['state2'] = pickle.dumps(state)
1712	state.data_name = "hello---->2"
1713	db['state3'] = pickle.dumps(state)
1714	del db['state3']
1715	state.data_name = "hello---->3"
1716	db['state4'] = pickle.dumps(state)
1717	new_state = pickle.loads(db['state1'])
1718	#print db.last()
1719	db.set_location('state2')
1720	state.data_name = "hello---->5"
1721	db['aastate5'] = pickle.dumps(state)
1722	db.keys().sort()
1723	print pickle.loads(db['state2'])
1724
1725	db.close()

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SasView

source: sasview/src/sas/perspectives/fitting/pagestate.py @ a3f125f0

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