pagestate.py @ a706353b

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 a706353b was 4523b68, checked in by Jae Cho <jhjcho@…>, 14 years ago
added coremultishellmodel/multifunctional model
Property mode set to `100644`
File size: 54.3 KB

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2
3	################################################################################
4	#This software was developed by the University of Tennessee as part of the
5	#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
6	#project funded by the US National Science Foundation.
7	#
8	#See the license text in license.txt
9	#
10	#copyright 2009, University of Tennessee
11	################################################################################
12
13	import time
14	import os
15	import sys
16	import copy
17	import logging
18	import numpy
19
20	import xml.dom.minidom
21	from xml.dom.minidom import parse
22	from lxml import etree
23
24	import DataLoader
25	from DataLoader.readers.cansas_reader import Reader as CansasReader
26	from DataLoader.readers.cansas_reader import get_content, write_node
27	from DataLoader.data_info import Data2D, Detector
28
29	#Information to read/write state as xml
30	FITTING_NODE_NAME = 'fitting_plug_in'
31	CANSAS_NS = "cansas1d/1.0"
32
33	list_of_data_attributes = [["is_data", "is_data", "bool"],
34	["group_id", "data_group_id", "string"],
35	["data_name", "data_name", "string"],
36	["data_id", "data_id", "string"],
37	["name", "name", "string"],
38	["data_name", "data_name", "string"]]
39	list_of_state_attributes = [["engine_type", "engine_type", "string"],
40	["qmin", "qmin", "float"],
41	["qmax", "qmax", "float"],
42	["npts", "npts", "float"],
43	["shape_rbutton", "shape_rbutton", "bool"],
44	["shape_indep_rbutton", "shape_indep_rbutton", "bool"],
45	["plugin_rbutton", "plugin_rbutton","bool"],
46	["struct_rbutton", "struct_rbutton", "bool"],
47	["formfactorcombobox", "formfactorcombobox", "float"],
48	["structurecombobox", "structurecombobox", "float"],
49	["disp_box", "disp_box", "float"],
50	["enable_smearer","enable_smearer","bool"],
51	["disable_smearer","disable_smearer","bool"],
52	["pinhole_smearer","pinhole_smearer","bool"],
53	["slit_smearer","slit_smearer","bool"],
54	["enable_disp","enable_disp","bool"],
55	["disable_disp","disable_disp","bool"],
56	["slit_smearer","slit_smearer","bool"],
57	["enable2D","enable2D","bool"],
58	["cb1","cb1","bool"],
59	["tcChi","tcChi","float"],
60	["smearer", "smearer", "float"],
61	["smear_type","smear_type", "string"],
62	["dq_l", "dq_l", "string"],
63	["dq_r","dq_r", "string"]]
64
65	list_of_model_attributes = [["values", "values"],
66	["weights", "weights"]]
67
68	list_of_state_parameters = [["parameters", "parameters"] ,
69	["orientation_parameters", "orientation_params"],
70	["dispersity_parameters", "orientation_params_disp"],
71	["fixed_param", "fixed_param"],
72	["fittable_param","fittable_param"]]
73	list_of_data_2d_attr = [["xmin", "xmin","float"],
74	["xmax","xmax","float"],
75	["ymin","ymin","float"],
76	["ymax","ymax","float"],
77	["_xaxis","_xaxis", "string"],
78	["_xunit", "_xunit", "string"],
79	["_yaxis","_yaxis","string"],
80	["_yunit","_yunit","string"],
81	["_zaxis","_zaxis","string"],
82	["_zunit","_zunit","string"]]
83	list_of_data2d_values = [["qx_data","qx_data","float"],
84	["qy_data","qy_data","float"],
85	["dqx_data","dqx_data","float"],
86	["dqy_data","dqy_data","float"],
87	["data","data","float"],
88	["q_data","q_data","float"],
89	["err_data","err_data","float"],
90	["mask","mask","bool"]]
91
92	def parse_entry_helper( node, item):
93	"""
94	Create a numpy list from value extrated from the node
95
96	:param node: node from each the value is stored
97	:param item: list name of three strings.the two first are name of data
98	attribute and the third one is the type of the value of that
99	attribute. type can be string, float, bool, etc.
100
101	: return: numpy array
102	"""
103	if node is not None:
104	if item[2] == "string":
105	return str(node.get(item[0]).strip())
106	elif item[2] == "bool":
107	try:
108	return node.get(item[0]).strip() == "True"
109
110	except:
111	return None
112	else:
113	try:
114	return float(node.get(item[0]))
115	except:
116	return None
117
118
119	class PageState(object):
120	"""
121	Contains information to reconstruct a page of the fitpanel.
122	"""
123	def __init__(self, parent=None, model=None, data=None):
124
125	"""
126	Initialize the current state
127
128	:param model: a selected model within a page
129	:param data:
130
131	"""
132	self.file = None
133	#Time of state creation
134	self.timestamp = time.time()
135	## Data member to store the dispersion object created
136	self._disp_obj_dict = {}
137	#------------------------
138	#Data used for fitting
139	self.data = data
140	#save additional information on data that dataloader.reader does not read
141	self.is_data = None
142	self.data_name = ""
143
144	if self.data is not None:
145	self.data_name = self.data.name
146	self.data_id = None
147	if self.data is not None and hasattr(self.data, "id"):
148	self.data_id = self.data.id
149	self.data_group_id = None
150	if self.data is not None and hasattr(self.data, "group_id"):
151	self.data_group_id = self.data.group_id
152
153	## reset True change the state of exsiting button
154	self.reset = False
155
156	#engine type
157	self.engine_type = None
158	# flag to allow data2D plot
159	self.enable2D = False
160	# model on which the fit would be performed
161	self.model = model
162
163	#fit page manager
164	self.manager = None
165	#Store the parent of this panel parent
166	# For this application fitpanel is the parent
167	self.parent = parent
168	# Event_owner is the owner of model event
169	self.event_owner = None
170	##page name
171	self.page_name = ""
172	# Contains link between model ,all its parameters, and panel organization
173	self.parameters = []
174	# Contains list of parameters that cannot be fitted and reference to
175	#panel objects
176	self.fixed_param = []
177	# Contains list of parameters with dispersity and reference to
178	#panel objects
179	self.fittable_param = []
180	## orientation parameters
181	self.orientation_params = []
182	## orientation parmaters for gaussian dispersity
183	self.orientation_params_disp = []
184	## smearer info
185	self.smearer = None
186	self.smear_type = None
187	self.dq_l = None
188	self.dq_r = None
189
190	#list of dispersion paramaters
191	self.disp_list =[]
192	if self.model is not None:
193	self.disp_list = self.model.getDispParamList()
194	self._disp_obj_dict = {}
195	self.disp_cb_dict = {}
196	self.values = []
197	self.weights = []
198
199	#contains link between a model and selected parameters to fit
200	self.param_toFit = []
201	##dictionary of model type and model class
202	self.model_list_box = None
203	## save the state of the context menu
204	self.saved_states = {}
205	## save selection of combobox
206	self.formfactorcombobox = None
207	self.structurecombobox = None
208	## radio box to select type of model
209	self.shape_rbutton = False
210	self.shape_indep_rbutton = False
211	self.struct_rbutton = False
212	self.plugin_rbutton = False
213	## the indice of the current selection
214	self.disp_box = 0
215	## Qrange
216	## Q range
217	self.qmin = 0.001
218	self.qmax = 0.1
219	#reset data range
220	self.qmax_x = None
221	self.qmin_x = None
222
223	self.npts = None
224	self.name = ""
225	self.multi_factor = None
226	## enable smearering state
227	self.enable_smearer = False
228	self.disable_smearer = True
229	self.pinhole_smearer = False
230	self.slit_smearer = False
231	## disperity selection
232	self.enable_disp = False
233	self.disable_disp = True
234
235	## state of selected all check button
236	self.cb1 = False
237	## store value of chisqr
238	self.tcChi = None
239
240	def clone(self):
241	"""
242	Create a new copy of the current object
243	"""
244	model = None
245	if self.model is not None:
246	model = self.model.clone()
247	model.name = self.model.name
248	obj = PageState(self.parent, model=model)
249	obj.file = copy.deepcopy(self.file)
250	obj.data = copy.deepcopy(self.data)
251	if self.data is not None:
252	self.data_name = self.data.name
253	obj.data_name = self.data_name
254	obj.is_data = self.is_data
255	obj.model_list_box = copy.deepcopy(self.model_list_box)
256	obj.engine_type = copy.deepcopy(self.engine_type)
257
258	obj.formfactorcombobox = self.formfactorcombobox
259	obj.structurecombobox = self.structurecombobox
260
261	obj.shape_rbutton = self.shape_rbutton
262	obj.shape_indep_rbutton = self.shape_indep_rbutton
263	obj.struct_rbutton = self.struct_rbutton
264	obj.plugin_rbutton = self.plugin_rbutton
265
266	obj.manager = self.manager
267	obj.event_owner = self.event_owner
268	obj.disp_list = copy.deepcopy(self.disp_list)
269
270	obj.enable2D = copy.deepcopy(self.enable2D)
271	obj.parameters = copy.deepcopy(self.parameters)
272	obj.fixed_param = copy.deepcopy(self.fixed_param)
273	obj.fittable_param = copy.deepcopy(self.fittable_param)
274	obj.orientation_params = copy.deepcopy(self.orientation_params)
275	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
276	obj.enable_disp = copy.deepcopy(self.enable_disp)
277	obj.disable_disp = copy.deepcopy(self.disable_disp)
278	obj.tcChi = self.tcChi
279
280	if len(self._disp_obj_dict)>0:
281	for k , v in self._disp_obj_dict.iteritems():
282	obj._disp_obj_dict[k]= v
283	if len(self.disp_cb_dict)>0:
284	for k , v in self.disp_cb_dict.iteritems():
285	obj.disp_cb_dict[k]= v
286
287	obj.values = copy.deepcopy(self.values)
288	obj.weights = copy.deepcopy(self.weights)
289	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
290	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
291	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
292	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
293	obj.smear_type = copy.deepcopy(self.smear_type)
294	obj.dq_l = copy.deepcopy(self.dq_l)
295	obj.dq_r = copy.deepcopy(self.dq_r)
296
297	obj.disp_box = copy.deepcopy(self.disp_box)
298	obj.qmin = copy.deepcopy(self.qmin)
299	obj.qmax = copy.deepcopy(self.qmax)
300	obj.multi_factor = copy.deepcopy(self.multi_factor)
301	obj.npts = copy.deepcopy(self.npts )
302	obj.cb1 = copy.deepcopy(self.cb1)
303	obj.smearer = copy.deepcopy(self.smearer)
304
305	for name, state in self.saved_states.iteritems():
306	copy_name = copy.deepcopy(name)
307	copy_state = state.clone()
308	obj.saved_states[copy_name]= copy_state
309	return obj
310
311	def _repr_helper(self, list, rep):
312	"""
313	Helper method to print a state
314	"""
315	for item in list:
316	rep += "parameter name: %s \n"%str(item[1])
317	rep += "value: %s\n"%str(item[2])
318	rep += "selected: %s\n"%str(item[0])
319	rep += "error displayed : %s \n"%str(item[4][0])
320	rep += "error value:%s \n"%str(item[4][1])
321	rep += "minimum displayed : %s \n"%str(item[5][0])
322	rep += "minimum value : %s \n"%str(item[5][1])
323	rep += "maximum displayed : %s \n"%str(item[6][0])
324	rep += "maximum value : %s \n"%str(item[6][1])
325	rep += "parameter unit: %s\n\n"%str(item[7])
326	return rep
327
328	def __repr__(self):
329	"""
330	output string for printing
331	"""
332	rep = "\nState name: %s\n"%self.file
333	t = time.localtime(self.timestamp)
334	time_str = time.strftime("%b %d %H:%M", t)
335	rep += "State created on : %s\n"%time_str
336	rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox
337	rep += "State structure factor combobox selection: %s\n"%self.structurecombobox
338	rep += "is data : %s\n"%self.is_data
339	rep += "data's name : %s\n"%self.data_name
340	rep += "data's id : %s\n"%self.data_id
341	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
342	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
343	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
344	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
345	rep += "data : %s\n"% str(self.data)
346	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
347	str(self.qmax),str(self.npts))
348	rep += "Dispersion selection : %s\n"%str(self.disp_box)
349	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
350	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
351	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
352	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
353	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
354	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
355	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
356	rep += "2D enable : %s\n"%str(self.enable2D)
357	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
358	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
359	rep += "Smear object : %s\n"%str(self.smearer)
360	rep += "Smear type : %s\n"%(self.smear_type)
361	rep += "dq_l : %s\n"%self.dq_l
362	rep += "dq_r : %s\n"%self.dq_r
363
364	rep += "model : %s\n\n"% str(self.model)
365	rep += "number parameters(self.parameters): %s\n"%len(self.parameters)
366	rep = self._repr_helper( list=self.parameters, rep=rep)
367	rep += "number orientation parameters"
368	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
369	rep = self._repr_helper( list=self.orientation_params, rep=rep)
370	rep += "number dispersity parameters"
371	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
372	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
373
374	return rep
375
376	def _toXML_helper(self, list, element, newdoc):
377	"""
378	Helper method to create xml file for saving state
379	"""
380	for item in list:
381	sub_element = newdoc.createElement('parameter')
382	sub_element.setAttribute('name', str(item[1]))
383	sub_element.setAttribute('value', str(item[2]))
384	sub_element.setAttribute('selected_to_fit', str(item[0]))
385	sub_element.setAttribute('error_displayed', str(item[4][0]))
386	sub_element.setAttribute('error_value', str(item[4][1]))
387	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
388	sub_element.setAttribute('minimum_value', str(item[5][1]))
389	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
390	sub_element.setAttribute('maximum_value', str(item[6][1]))
391	sub_element.setAttribute('unit', str(item[7]))
392	element.appendChild(sub_element)
393
394	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
395	"""
396	Writes the state of the InversionControl panel to file, as XML.
397
398	Compatible with standalone writing, or appending to an
399	already existing XML document. In that case, the XML document
400	is required. An optional entry node in the XML document may also be given.
401
402	:param file: file to write to
403	:param doc: XML document object [optional]
404	:param entry_node: XML node within the XML document at which we will append the data [optional]
405
406	"""
407	from xml.dom.minidom import getDOMImplementation
408
409	# Check whether we have to write a standalone XML file
410	if doc is None:
411	impl = getDOMImplementation()
412	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
413	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
414	top_element = newdoc.documentElement
415	else:
416	# We are appending to an existing document
417	newdoc = doc
418	top_element = newdoc.createElement(FITTING_NODE_NAME)
419	if entry_node is None:
420	newdoc.documentElement.appendChild(top_element)
421	else:
422	entry_node.appendChild(top_element)
423
424	attr = newdoc.createAttribute("version")
425	attr.nodeValue = '1.0'
426	top_element.setAttributeNode(attr)
427
428	# File name
429	element = newdoc.createElement("filename")
430	if self.file is not None:
431	element.appendChild(newdoc.createTextNode(str(self.file)))
432	else:
433	element.appendChild(newdoc.createTextNode(str(file)))
434	top_element.appendChild(element)
435
436	element = newdoc.createElement("timestamp")
437	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
438	attr = newdoc.createAttribute("epoch")
439	attr.nodeValue = str(self.timestamp)
440	element.setAttributeNode(attr)
441	top_element.appendChild(element)
442	# Inputs
443	inputs = newdoc.createElement("Attributes")
444	top_element.appendChild(inputs)
445
446
447	if self.data is not None and hasattr(self.data, "group_id"):
448	self.data_group_id = self.data.group_id
449	if self.data is not None and hasattr(self.data, "is_data"):
450	self.is_data = self.data.is_data
451	if self.data is not None:
452	self.data_name = self.data.name
453	if self.data is not None and hasattr(self.data, "id"):
454	self.data_id = self.data.id
455
456	for item in list_of_data_attributes:
457	element = newdoc.createElement(item[0])
458	exec "element.setAttribute(item[0], str(self.%s))"%(item[1])
459	inputs.appendChild(element)
460
461	for item in list_of_state_attributes:
462	element = newdoc.createElement(item[0])
463	exec "element.setAttribute(item[0], str(self.%s))"%(item[1])
464	inputs.appendChild(element)
465
466	for item in list_of_model_attributes:
467	element = newdoc.createElement(item[0])
468	exec "list = self.%s"%item[1]
469	for value in list:
470	exec "element.appendChild(newdoc.createTextNode(str(%s)))"%value
471	inputs.appendChild(element)
472
473	for item in list_of_state_parameters:
474	element = newdoc.createElement(item[0])
475	exec "self._toXML_helper(list=self.%s, element=element, newdoc=newdoc)"%item[1]
476	inputs.appendChild(element)
477
478	# Save the file
479	if doc is None:
480	fd = open(file, 'w')
481	fd.write(newdoc.toprettyxml())
482	fd.close()
483	return None
484	else:
485	return newdoc.toprettyxml()
486
487	def _fromXML_helper(self, node, list):
488	"""
489	Helper function to write state to xml
490	"""
491	for item in node:
492	try:
493	name = item.get('name')
494	except:
495	name = None
496	try:
497	value = item.get('value')
498	except:
499	value = None
500	try:
501	selected_to_fit = (item.get('selected_to_fit') == "True")
502	except:
503	selected_to_fit = None
504	try:
505	error_displayed = (item.get('error_displayed') == "True")
506	except:
507	error_displayed = None
508	try:
509	error_value = item.get('error_value')
510	except:
511	error_value = None
512	try:
513	minimum_displayed = (item.get('minimum_displayed')== "True")
514	except:
515	minimum_displayed = None
516	try:
517	minimum_value = item.get('minimum_value')
518	except:
519	minimum_value = None
520	try:
521	maximum_displayed = (item.get('maximum_displayed') == "True")
522	except:
523	maximum_displayed = None
524	try:
525	maximum_value = item.get('maximum_value')
526	except:
527	maximum_value = None
528	try:
529	unit = item.get('unit')
530	except:
531	unit = None
532	list.append([selected_to_fit, name, value, "+/-",[error_displayed, error_value],
533	[minimum_displayed,minimum_value],[maximum_displayed,maximum_value], unit])
534
535	def fromXML(self, file=None, node=None):
536	"""
537	Load fitting state from a file
538
539	:param file: .fitv file
540	:param node: node of a XML document to read from
541
542	"""
543	if file is not None:
544	msg = "PageState no longer supports non-CanSAS"
545	msg += " format for fitting files"
546	raise RuntimeError, msg
547
548	if node.get('version')and node.get('version') == '1.0':
549
550	# Get file name
551	entry = get_content('ns:filename', node)
552	if entry is not None:
553	self.file = entry.text.strip()
554
555	# Get time stamp
556	entry = get_content('ns:timestamp', node)
557	if entry is not None and entry.get('epoch'):
558	try:
559	self.timestamp = float(entry.get('epoch'))
560	except:
561	msg = "PageState.fromXML: Could not"
562	msg += " read timestamp\n %s" % sys.exc_value
563	logging.error(msg)
564
565	# Parse fitting attributes
566	entry = get_content('ns:Attributes', node)
567	for item in list_of_data_attributes:
568	node = get_content('ns:%s'%item[0], entry)
569	try:
570	exec "self.%s = parse_entry_helper(node, item)"%item[0]
571
572	except:
573	raise
574
575	if entry is not None:
576
577	for item in list_of_state_attributes:
578	node = get_content('ns:%s'%item[0], entry)
579	try:
580	exec "self.%s = parse_entry_helper(node, item)"%str(item[0])
581	except:
582	raise
583
584	for item in list_of_model_attributes:
585	node = get_content("ns:%s"%item[0], entry)
586	list = []
587	for value in node:
588	try:
589	list.append(float(value))
590	except:
591	list.append(None)
592	exec "self.%s = list"%item[1]
593
594	for item in list_of_state_parameters:
595	node = get_content("ns:%s"%item[0], entry)
596	exec "self._fromXML_helper(node=node, list=self.%s)"%item[1]
597
598
599	class Reader(CansasReader):
600	"""
601	Class to load a .fitv fitting file
602	"""
603	## File type
604	type_name = "Fitting"
605
606	## Wildcards
607	type = ["Fitting files (.fitv)\|.fitv"
608	"SANSView file (.svs)\|.svs"]
609	## List of allowed extensions
610	ext=['.fitv', '.FITV', '.svs', 'SVS']
611
612	def __init__(self, call_back=None, cansas=True):
613	CansasReader.__init__(self)
614	"""
615	Initialize the call-back method to be called
616	after we load a file
617
618	:param call_back: call-back method
619	:param cansas: True = files will be written/read in CanSAS format
620	False = write CanSAS format
621
622	"""
623	## Call back method to be executed after a file is read
624	self.call_back = call_back
625	## CanSAS format flag
626	self.cansas = cansas
627
628	def read(self, path):
629	"""
630	Load a new P(r) inversion state from file
631
632	:param path: file path
633
634	"""
635	if self.cansas == True:
636	return self._read_cansas(path)
637
638	def _data2d_to_xml_doc(self, datainfo):
639	"""
640	Create an XML document to contain the content of a Data2D
641
642	:param datainfo: Data2D object
643
644	"""
645	if not issubclass(datainfo.__class__, Data2D):
646	raise RuntimeError, "The cansas writer expects a Data2D instance"
647
648	doc = xml.dom.minidom.Document()
649	main_node = doc.createElement("SASroot")
650	main_node.setAttribute("version", self.version)
651	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
652	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
653	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
654
655	doc.appendChild(main_node)
656
657	entry_node = doc.createElement("SASentry")
658	main_node.appendChild(entry_node)
659
660	write_node(doc, entry_node, "Title", datainfo.title)
661	if datainfo is not None:
662	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
663	for item in datainfo.run:
664	runname = {}
665	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
666	runname = {'name': datainfo.run_name[item] }
667	write_node(doc, entry_node, "Run", item, runname)
668	# Data info
669	new_node = doc.createElement("SASdata")
670	entry_node.appendChild(new_node)
671	for item in list_of_data_2d_attr:
672	element = doc.createElement(item[0])
673	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
674	new_node.appendChild(element)
675
676	for item in list_of_data2d_values:
677	root_node = doc.createElement(item[0])
678	new_node.appendChild(root_node)
679
680	exec "temp_list = datainfo.%s"%item[1]
681
682	if temp_list is None or len(temp_list)== 0:
683	element = doc.createElement(item[0])
684	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
685	root_node.appendChild(element)
686	else:
687	for value in temp_list:
688	element = doc.createElement(item[0])
689	exec "element.setAttribute(item[0], str(%s))"%value
690	root_node.appendChild(element)
691
692	# Sample info
693	sample = doc.createElement("SASsample")
694	if datainfo.sample.name is not None:
695	sample.setAttribute("name", str(datainfo.sample.name))
696	entry_node.appendChild(sample)
697	write_node(doc, sample, "ID", str(datainfo.sample.ID))
698	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
699	write_node(doc, sample, "transmission", datainfo.sample.transmission)
700	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
701
702	for item in datainfo.sample.details:
703	write_node(doc, sample, "details", item)
704
705	pos = doc.createElement("position")
706	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
707	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
708	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
709	if written == True:
710	sample.appendChild(pos)
711
712	ori = doc.createElement("orientation")
713	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
714	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
715	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
716	if written == True:
717	sample.appendChild(ori)
718
719	# Instrument info
720	instr = doc.createElement("SASinstrument")
721	entry_node.appendChild(instr)
722
723	write_node(doc, instr, "name", datainfo.instrument)
724
725	# Source
726	source = doc.createElement("SASsource")
727	if datainfo.source.name is not None:
728	source.setAttribute("name", str(datainfo.source.name))
729	instr.appendChild(source)
730
731	write_node(doc, source, "radiation", datainfo.source.radiation)
732	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
733	size = doc.createElement("beam_size")
734	if datainfo.source.beam_size_name is not None:
735	size.setAttribute("name", str(datainfo.source.beam_size_name))
736	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
737	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
738	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
739	if written == True:
740	source.appendChild(size)
741
742	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
743	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
744	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
745	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
746
747	# Collimation
748	for item in datainfo.collimation:
749	coll = doc.createElement("SAScollimation")
750	if item.name is not None:
751	coll.setAttribute("name", str(item.name))
752	instr.appendChild(coll)
753
754	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
755
756	for apert in item.aperture:
757	ap = doc.createElement("aperture")
758	if apert.name is not None:
759	ap.setAttribute("name", str(apert.name))
760	if apert.type is not None:
761	ap.setAttribute("type", str(apert.type))
762	coll.appendChild(ap)
763
764	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
765
766	size = doc.createElement("size")
767	if apert.size_name is not None:
768	size.setAttribute("name", str(apert.size_name))
769	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
770	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
771	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
772	if written == True:
773	ap.appendChild(size)
774
775	# Detectors
776	for item in datainfo.detector:
777	det = doc.createElement("SASdetector")
778	written = write_node(doc, det, "name", item.name)
779	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
780	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
781	if written == True:
782	instr.appendChild(det)
783
784	off = doc.createElement("offset")
785	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
786	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
787	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
788	if written == True:
789	det.appendChild(off)
790
791	center = doc.createElement("beam_center")
792	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
793	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
794	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
795	if written == True:
796	det.appendChild(center)
797
798	pix = doc.createElement("pixel_size")
799	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
800	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
801	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
802	if written == True:
803	det.appendChild(pix)
804
805	ori = doc.createElement("orientation")
806	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
807	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
808	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
809	if written == True:
810	det.appendChild(ori)
811
812	# Processes info
813	for item in datainfo.process:
814	node = doc.createElement("SASprocess")
815	entry_node.appendChild(node)
816
817	write_node(doc, node, "name", item.name)
818	write_node(doc, node, "date", item.date)
819	write_node(doc, node, "description", item.description)
820	for term in item.term:
821	value = term['value']
822	del term['value']
823	write_node(doc, node, "term", value, term)
824	for note in item.notes:
825	write_node(doc, node, "SASprocessnote", note)
826	# Return the document, and the SASentry node associated with
827	# the data we just wrote
828	return doc, entry_node
829
830	def _parse_state(self, entry):
831	"""
832	Read a fit result from an XML node
833
834	:param entry: XML node to read from
835
836	:return: PageState object
837	"""
838	# Create an empty state
839	state = None
840	# Locate the P(r) node
841	try:
842	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
843	if nodes !=[]:
844	# Create an empty state
845	state = PageState()
846	state.fromXML(node=nodes[0])
847	except:
848	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
849
850	return state
851
852
853
854	def _parse_entry(self, dom):
855	"""
856	Parse a SASentry
857
858	:param node: SASentry node
859
860	:return: Data1D/Data2D object
861
862	"""
863	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
864	if not node or node[0].text.lstrip().rstrip() != "Data2D":
865	return CansasReader._parse_entry(self, dom)
866
867	#Parse 2D
868	data_info = Data2D()
869
870	# Look up title
871	self._store_content('ns:Title', dom, 'title', data_info)
872
873	# Look up run number
874	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
875	for item in nodes:
876	if item.text is not None:
877	value = item.text.strip()
878	if len(value) > 0:
879	data_info.run.append(value)
880	if item.get('name') is not None:
881	data_info.run_name[value] = item.get('name')
882
883	# Look up instrument name
884	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
885
886	# Notes
887	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
888	for note in note_list:
889	try:
890	if note.text is not None:
891	note_value = note.text.strip()
892	if len(note_value) > 0:
893	data_info.notes.append(note_value)
894	except:
895	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
896	self.errors.append(err_mess)
897	logging.error(err_mess)
898
899	# Sample info ###################
900	entry = get_content('ns:SASsample', dom)
901	if entry is not None:
902	data_info.sample.name = entry.get('name')
903
904	self._store_content('ns:SASsample/ns:ID',
905	dom, 'ID', data_info.sample)
906	self._store_float('ns:SASsample/ns:thickness',
907	dom, 'thickness', data_info.sample)
908	self._store_float('ns:SASsample/ns:transmission',
909	dom, 'transmission', data_info.sample)
910	self._store_float('ns:SASsample/ns:temperature',
911	dom, 'temperature', data_info.sample)
912
913	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
914	for item in nodes:
915	try:
916	if item.text is not None:
917	detail_value = item.text.strip()
918	if len(detail_value) > 0:
919	data_info.sample.details.append(detail_value)
920	except:
921	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
922	self.errors.append(err_mess)
923	logging.error(err_mess)
924
925	# Position (as a vector)
926	self._store_float('ns:SASsample/ns:position/ns:x',
927	dom, 'position.x', data_info.sample)
928	self._store_float('ns:SASsample/ns:position/ns:y',
929	dom, 'position.y', data_info.sample)
930	self._store_float('ns:SASsample/ns:position/ns:z',
931	dom, 'position.z', data_info.sample)
932
933	# Orientation (as a vector)
934	self._store_float('ns:SASsample/ns:orientation/ns:roll',
935	dom, 'orientation.x', data_info.sample)
936	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
937	dom, 'orientation.y', data_info.sample)
938	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
939	dom, 'orientation.z', data_info.sample)
940
941	# Source info ###################
942	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
943	if entry is not None:
944	data_info.source.name = entry.get('name')
945
946	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
947	dom, 'radiation', data_info.source)
948	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
949	dom, 'beam_shape', data_info.source)
950	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
951	dom, 'wavelength', data_info.source)
952	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
953	dom, 'wavelength_min', data_info.source)
954	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
955	dom, 'wavelength_max', data_info.source)
956	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
957	dom, 'wavelength_spread', data_info.source)
958
959	# Beam size (as a vector)
960	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
961	if entry is not None:
962	data_info.source.beam_size_name = entry.get('name')
963
964	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
965	dom, 'beam_size.x', data_info.source)
966	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
967	dom, 'beam_size.y', data_info.source)
968	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
969	dom, 'beam_size.z', data_info.source)
970
971	# Collimation info ###################
972	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
973	for item in nodes:
974	collim = Collimation()
975	if item.get('name') is not None:
976	collim.name = item.get('name')
977	self._store_float('ns:length', item, 'length', collim)
978
979	# Look for apertures
980	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
981	for apert in apert_list:
982	aperture = Aperture()
983
984	# Get the name and type of the aperture
985	aperture.name = apert.get('name')
986	aperture.type = apert.get('type')
987
988	self._store_float('ns:distance', apert, 'distance', aperture)
989
990	entry = get_content('ns:size', apert)
991	if entry is not None:
992	aperture.size_name = entry.get('name')
993
994	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
995	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
996	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
997
998	collim.aperture.append(aperture)
999
1000	data_info.collimation.append(collim)
1001
1002	# Detector info ######################
1003	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
1004	for item in nodes:
1005
1006	detector = Detector()
1007
1008	self._store_content('ns:name', item, 'name', detector)
1009	self._store_float('ns:SDD', item, 'distance', detector)
1010
1011	# Detector offset (as a vector)
1012	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
1013	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
1014	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
1015
1016	# Detector orientation (as a vector)
1017	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
1018	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
1019	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
1020
1021	# Beam center (as a vector)
1022	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
1023	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
1024	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
1025
1026	# Pixel size (as a vector)
1027	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
1028	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
1029	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
1030
1031	self._store_float('ns:slit_length', item, 'slit_length', detector)
1032
1033	data_info.detector.append(detector)
1034
1035	# Processes info ######################
1036	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
1037	for item in nodes:
1038	process = Process()
1039	self._store_content('ns:name', item, 'name', process)
1040	self._store_content('ns:date', item, 'date', process)
1041	self._store_content('ns:description', item, 'description', process)
1042
1043	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
1044	for term in term_list:
1045	try:
1046	term_attr = {}
1047	for attr in term.keys():
1048	term_attr[attr] = term.get(attr).strip()
1049	if term.text is not None:
1050	term_attr['value'] = term.text.strip()
1051	process.term.append(term_attr)
1052	except:
1053	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
1054	self.errors.append(err_mess)
1055	logging.error(err_mess)
1056
1057	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
1058	for note in note_list:
1059	if note.text is not None:
1060	process.notes.append(note.text.strip())
1061
1062	data_info.process.append(process)
1063
1064
1065	# Data info ######################
1066	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
1067	if len(nodes)>1:
1068	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
1069
1070	for entry in nodes:
1071	for item in list_of_data_2d_attr:
1072	#get node
1073	node = get_content('ns:%s'%item[0], entry)
1074	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
1075
1076	for item in list_of_data2d_values:
1077	field = get_content('ns:%s'%item[0], entry)
1078	list = []
1079	if field is not None:
1080	list = [parse_entry_helper(node, item) for node in field]
1081	exec "data_info.%s = numpy.array(list)"%item[0]
1082
1083	return data_info
1084
1085	def _read_cansas(self, path):
1086	"""
1087	Load data and P(r) information from a CanSAS XML file.
1088
1089	:param path: file path
1090
1091	:return: Data1D object if a single SASentry was found,
1092	or a list of Data1D objects if multiple entries were found,
1093	or None of nothing was found
1094
1095	:raise RuntimeError: when the file can't be opened
1096	:raise ValueError: when the length of the data vectors are inconsistent
1097
1098	"""
1099	output = []
1100	basename = os.path.basename(path)
1101	root, extension = os.path.splitext(basename)
1102	ext = extension.lower()
1103	try:
1104	if os.path.isfile(path):
1105
1106	#TODO: eventually remove the check for .xml once
1107	# the P(r) writer/reader is truly complete.
1108	if ext in self.ext or \
1109	ext == '.xml':
1110
1111	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
1112	# Check the format version number
1113	# Specifying the namespace will take care of the file format version
1114	root = tree.getroot()
1115	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
1116	for entry in entry_list:
1117	try:
1118	sas_entry = self._parse_entry(entry)
1119	except:
1120	raise
1121	fitstate = self._parse_state(entry)
1122
1123	#state could be None when .svs file is loaded
1124	#in this case, skip appending to output
1125	if fitstate != None:
1126	sas_entry.meta_data['fitstate'] = fitstate
1127	sas_entry.filename = fitstate.file
1128	output.append(sas_entry)
1129	else:
1130	self.call_back(format=ext)
1131	raise RuntimeError, "%s is not a file" % path
1132
1133	# Return output consistent with the loader's api
1134	if len(output)==0:
1135	self.call_back(state=None, datainfo=None,format=ext)
1136	return None
1137	else:
1138	for ind in range(len(output)):
1139	# Call back to post the new state
1140	state = output[ind].meta_data['fitstate']
1141	t = time.localtime(state.timestamp)
1142	time_str = time.strftime("%b %d %H:%M", t)
1143	# Check that no time stamp is already appended
1144	max_char = state.file.find("[")
1145	if max_char < 0:
1146	max_char = len(state.file)
1147	original_fname = state.file[0:max_char]
1148	state.file = original_fname +' [' + time_str + ']'
1149
1150
1151	if state is not None and state.is_data is not None:
1152	exec 'output[%d].is_data = state.is_data'% ind
1153
1154	output[ind].filename = state.file
1155	state.data = output[ind]
1156	state.data.name = output[ind].filename #state.data_name
1157	state.data.id = state.data_id
1158	if state.is_data is not None:
1159	state.data.is_data = state.is_data
1160	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
1161	name = output[ind].run_name
1162	else:
1163	name=original_fname
1164	state.data.group_id = name
1165	#store state in fitting
1166	self.call_back(state=state, datainfo=output[ind],format=ext)
1167	return output
1168
1169	except:
1170	self.call_back(format=ext)
1171	raise
1172
1173	def write(self, filename, datainfo=None, fitstate=None):
1174	"""
1175	Write the content of a Data1D as a CanSAS XML file only for standalone
1176
1177	:param filename: name of the file to write
1178	:param datainfo: Data1D object
1179	:param fitstate: PageState object
1180
1181	"""
1182	# Sanity check
1183	if self.cansas == True:
1184
1185	# Add fitting information to the XML document
1186	doc = self.write_toXML(datainfo, fitstate)
1187	# Write the XML document
1188	fd = open(filename, 'w')
1189	fd.write(doc.toprettyxml())
1190	fd.close()
1191	else:
1192	fitstate.toXML(file=filename)
1193
1194	def write_toXML(self, datainfo=None, state=None):
1195	"""
1196	Write toXML, a helper for write() , could be used by guimanager._on_save()
1197
1198	: return: xml doc
1199	"""
1200
1201	if state.data is None:
1202	data = DataLoader.data_info.Data1D(x=[], y=[])
1203	else:
1204	#make sure title and data run is filled up.
1205	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
1206	if state.data.run_name == None or state.data.run_name=={}:
1207	state.data.run = [str(state.data.name)]
1208	state.data.run_name[0] = state.data.name
1209
1210	if issubclass(state.data.__class__, DataLoader.data_info.Data1D):
1211
1212	data = state.data
1213	doc, sasentry = self._to_xml_doc(data)
1214	else:
1215	data = state.data
1216	doc, sasentry = self._data2d_to_xml_doc(data)
1217
1218
1219	if state is not None:
1220	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
1221
1222	return doc
1223
1224	if __name__ == "__main__":
1225	state = PageState(parent=None)
1226	#state.toXML()
1227	"""
1228
1229	file = open("test_state", "w")
1230	pickle.dump(state, file)
1231	print pickle.dumps(state)
1232	state.data_name = "hello---->"
1233	pickle.dump(state, file)
1234	file = open("test_state", "r")
1235	new_state= pickle.load(file)
1236	print "new state", new_state
1237	new_state= pickle.load(file)
1238	print "new state", new_state
1239	#print "state", state
1240	"""
1241	import bsddb
1242	import pickle
1243	db= bsddb.btopen('file_state.db', 'c')
1244	val = (pickle.dumps(state), "hello", "hi")
1245	db['state1']= pickle.dumps(val)
1246	print pickle.loads(db['state1'])
1247	state.data_name = "hello---->22"
1248	db['state2']= pickle.dumps(state)
1249	state.data_name = "hello---->2"
1250	db['state3']= pickle.dumps(state)
1251	del db['state3']
1252	state.data_name = "hello---->3"
1253	db['state4']= pickle.dumps(state)
1254	new_state = pickle.loads(db['state1'])
1255	#print db.last()
1256	db.set_location('state2')
1257	state.data_name = "hello---->5"
1258	db['aastate5']= pickle.dumps(state)
1259	db.keys().sort()
1260	print pickle.loads(db['state2'])
1261
1262	db.close()

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SasView

source: sasview/sansview/perspectives/fitting/pagestate.py @ a706353b

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