pagestate.py @ c0a30a24

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 c0a30a24 was c21e87b, checked in by Jae Cho <jhjcho@…>, 13 years ago
updated datatloader name call
Property mode set to `100644`
File size: 66.9 KB

Rev	Line
[c77d859]	1
	2
[5062bbf]	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
[11a7e11]	13	import time
	14	import os
	15	import sys
[6f023e8]	16	import copy
[11a7e11]	17	import logging
[df7ed14]	18	import numpy
[c77d859]	19
[35b556d]	20	import xml.dom.minidom
[11a7e11]	21	from xml.dom.minidom import parse
	22	from lxml import etree
	23
[c21e87b]	24	import sans.dataloader
	25	from sans.dataloader.readers.cansas_reader import Reader as CansasReader
	26	from sans.dataloader.readers.cansas_reader import get_content, write_node
	27	from sans.dataloader.data_info import Data2D, Detector
[61cada5]	28
[11a7e11]	29	#Information to read/write state as xml
[61cada5]	30	FITTING_NODE_NAME = 'fitting_plug_in'
	31	CANSAS_NS = "cansas1d/1.0"
	32
[26f3dd5]	33	list_of_data_attributes = [["is_data", "is_data", "bool"],
[61cada5]	34	["group_id", "data_group_id", "string"],
	35	["data_name", "data_name", "string"],
	36	["data_id", "data_id", "string"],
	37	["name", "name", "string"],
[26f3dd5]	38	["data_name", "data_name", "string"]]
[e3d1423]	39	list_of_state_attributes = [["engine_type", "engine_type", "string"],
	40	["qmin", "qmin", "float"],
[61cada5]	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"],
[0b12abb5]	47	["formfactorcombobox", "formfactorcombobox", "float"],
	48	["structurecombobox", "structurecombobox", "float"],
[c0ff8cc]	49	["multi_factor","multi_factor","float"],
[26f3dd5]	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"],
[5cc7001]	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
[11a7e11]	65	list_of_model_attributes = [["values", "values"],
	66	["weights", "weights"]]
	67
[2296316]	68	list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]]
	69
[fb59ed9]	70	list_of_state_parameters = [["parameters", "parameters"] ,
	71	["str_parameters", "str_parameters"] ,
[61cada5]	72	["orientation_parameters", "orientation_params"],
	73	["dispersity_parameters", "orientation_params_disp"],
	74	["fixed_param", "fixed_param"],
	75	["fittable_param","fittable_param"]]
[df7ed14]	76	list_of_data_2d_attr = [["xmin", "xmin","float"],
	77	["xmax","xmax","float"],
	78	["ymin","ymin","float"],
	79	["ymax","ymax","float"],
	80	["_xaxis","_xaxis", "string"],
	81	["_xunit", "_xunit", "string"],
	82	["_yaxis","_yaxis","string"],
	83	["_yunit","_yunit","string"],
	84	["_zaxis","_zaxis","string"],
	85	["_zunit","_zunit","string"]]
	86	list_of_data2d_values = [["qx_data","qx_data","float"],
	87	["qy_data","qy_data","float"],
	88	["dqx_data","dqx_data","float"],
	89	["dqy_data","dqy_data","float"],
	90	["data","data","float"],
	91	["q_data","q_data","float"],
	92	["err_data","err_data","float"],
	93	["mask","mask","bool"]]
[61cada5]	94
[0b12abb5]	95	def parse_entry_helper( node, item):
	96	"""
	97	Create a numpy list from value extrated from the node
	98
	99	:param node: node from each the value is stored
	100	:param item: list name of three strings.the two first are name of data
	101	attribute and the third one is the type of the value of that
	102	attribute. type can be string, float, bool, etc.
	103
	104	: return: numpy array
	105	"""
	106	if node is not None:
	107	if item[2] == "string":
	108	return str(node.get(item[0]).strip())
	109	elif item[2] == "bool":
	110	try:
[e3d1423]	111	return node.get(item[0]).strip() == "True"
	112
[0b12abb5]	113	except:
	114	return None
	115	else:
	116	try:
	117	return float(node.get(item[0]))
	118	except:
	119	return None
	120
	121
[cfc0913]	122	class PageState(object):
[c77d859]	123	"""
[5062bbf]	124	Contains information to reconstruct a page of the fitpanel.
[c77d859]	125	"""
[61cada5]	126	def __init__(self, parent=None, model=None, data=None):
[c77d859]	127
	128	"""
[5062bbf]	129	Initialize the current state
	130
	131	:param model: a selected model within a page
	132	:param data:
	133
[c77d859]	134	"""
[61cada5]	135	self.file = None
[11a7e11]	136	#Time of state creation
	137	self.timestamp = time.time()
[c77d859]	138	## Data member to store the dispersion object created
	139	self._disp_obj_dict = {}
[61cada5]	140	#------------------------
[c77d859]	141	#Data used for fitting
	142	self.data = data
[2296316]	143	# model data
	144	self.theory_data = None
	145	#Is 2D
	146	self.is_2D = False
	147	self.images = None
	148
[61cada5]	149	#save additional information on data that dataloader.reader does not read
	150	self.is_data = None
	151	self.data_name = ""
[c0ff8cc]	152
[61cada5]	153	if self.data is not None:
	154	self.data_name = self.data.name
	155	self.data_id = None
	156	if self.data is not None and hasattr(self.data, "id"):
	157	self.data_id = self.data.id
	158	self.data_group_id = None
	159	if self.data is not None and hasattr(self.data, "group_id"):
	160	self.data_group_id = self.data.group_id
[0b12abb5]	161
[61cada5]	162	## reset True change the state of exsiting button
	163	self.reset = False
	164
[c99a6c5]	165	#engine type
	166	self.engine_type = None
[c77d859]	167	# flag to allow data2D plot
[cfc0913]	168	self.enable2D = False
[c77d859]	169	# model on which the fit would be performed
	170	self.model = model
[dce84c0]	171	#list of process done to model
	172	self.process = []
[c77d859]	173	#fit page manager
	174	self.manager = None
	175	#Store the parent of this panel parent
	176	# For this application fitpanel is the parent
	177	self.parent = parent
	178	# Event_owner is the owner of model event
	179	self.event_owner = None
[c9a4377]	180	##page name
[cfc0913]	181	self.page_name = ""
[c77d859]	182	# Contains link between model ,all its parameters, and panel organization
[61cada5]	183	self.parameters = []
[fb59ed9]	184	# String parameter list that can not be fitted
	185	self.str_parameters = []
[c77d859]	186	# Contains list of parameters that cannot be fitted and reference to
	187	#panel objects
[61cada5]	188	self.fixed_param = []
[c77d859]	189	# Contains list of parameters with dispersity and reference to
	190	#panel objects
[61cada5]	191	self.fittable_param = []
[60132ef]	192	## orientation parameters
[61cada5]	193	self.orientation_params = []
[fc6ea43]	194	## orientation parmaters for gaussian dispersity
[61cada5]	195	self.orientation_params_disp = []
[3370922]	196	## smearer info
[61cada5]	197	self.smearer = None
[7609f1a]	198	self.smear_type = None
	199	self.dq_l = None
	200	self.dq_r = None
	201
[c77d859]	202	#list of dispersion paramaters
[cfc0913]	203	self.disp_list =[]
[61cada5]	204	if self.model is not None:
[71f0373]	205	self.disp_list = self.model.getDispParamList()
[2296316]	206
[61cada5]	207	self.disp_cb_dict = {}
[2296316]	208	self.values = {}
	209	self.weights = {}
[dad49a0]	210
[c77d859]	211	#contains link between a model and selected parameters to fit
[61cada5]	212	self.param_toFit = []
[a074145]	213	##dictionary of model type and model class
[cfc0913]	214	self.model_list_box = None
[a074145]	215	## save the state of the context menu
[61cada5]	216	self.saved_states = {}
[240b9966]	217	## save selection of combobox
[3b9e023]	218	self.formfactorcombobox = None
	219	self.structurecombobox = None
[c0ff8cc]	220
[240b9966]	221	## radio box to select type of model
	222	self.shape_rbutton = False
	223	self.shape_indep_rbutton = False
	224	self.struct_rbutton = False
	225	self.plugin_rbutton = False
[b787e68c]	226	## the indice of the current selection
	227	self.disp_box = 0
[c77d859]	228	## Qrange
[cfc0913]	229	## Q range
[61cada5]	230	self.qmin = 0.001
	231	self.qmax = 0.1
[0b12abb5]	232	#reset data range
	233	self.qmax_x = None
	234	self.qmin_x = None
	235
[cfc0913]	236	self.npts = None
[61cada5]	237	self.name = ""
[4523b68]	238	self.multi_factor = None
[cfc0913]	239	## enable smearering state
	240	self.enable_smearer = False
[fc6ea43]	241	self.disable_smearer = True
[7609f1a]	242	self.pinhole_smearer = False
	243	self.slit_smearer = False
[cfc0913]	244	## disperity selection
[61cada5]	245	self.enable_disp = False
	246	self.disable_disp = True
[11a7e11]	247
[cfc0913]	248	## state of selected all check button
	249	self.cb1 = False
[0aeabc6]	250	## store value of chisqr
[61cada5]	251	self.tcChi = None
[240b9966]	252
[6f023e8]	253	def clone(self):
[61cada5]	254	"""
[5062bbf]	255	Create a new copy of the current object
[61cada5]	256	"""
	257	model = None
	258	if self.model is not None:
[6f023e8]	259	model = self.model.clone()
[bb70474]	260	model.name = self.model.name
[61cada5]	261	obj = PageState(self.parent, model=model)
	262	obj.file = copy.deepcopy(self.file)
[6f023e8]	263	obj.data = copy.deepcopy(self.data)
[61cada5]	264	if self.data is not None:
	265	self.data_name = self.data.name
	266	obj.data_name = self.data_name
	267	obj.is_data = self.is_data
[dcf29d7]	268	obj.model_list_box = copy.deepcopy(self.model_list_box)
[c99a6c5]	269	obj.engine_type = copy.deepcopy(self.engine_type)
[240b9966]	270
[61cada5]	271	obj.formfactorcombobox = self.formfactorcombobox
	272	obj.structurecombobox = self.structurecombobox
[240b9966]	273
	274	obj.shape_rbutton = self.shape_rbutton
	275	obj.shape_indep_rbutton = self.shape_indep_rbutton
	276	obj.struct_rbutton = self.struct_rbutton
	277	obj.plugin_rbutton = self.plugin_rbutton
	278
[dcf29d7]	279	obj.manager = self.manager
	280	obj.event_owner = self.event_owner
[71f0373]	281	obj.disp_list = copy.deepcopy(self.disp_list)
[fc6ea43]	282
[c477b31]	283	obj.enable2D = copy.deepcopy(self.enable2D)
[cfc0913]	284	obj.parameters = copy.deepcopy(self.parameters)
[fb59ed9]	285	obj.str_parameters = copy.deepcopy(self.str_parameters)
[cfc0913]	286	obj.fixed_param = copy.deepcopy(self.fixed_param)
	287	obj.fittable_param = copy.deepcopy(self.fittable_param)
[60132ef]	288	obj.orientation_params = copy.deepcopy(self.orientation_params)
[fc6ea43]	289	obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp)
[b787e68c]	290	obj.enable_disp = copy.deepcopy(self.enable_disp)
[fc6ea43]	291	obj.disable_disp = copy.deepcopy(self.disable_disp)
[0aeabc6]	292	obj.tcChi = self.tcChi
	293
[c477b31]	294	if len(self._disp_obj_dict)>0:
	295	for k , v in self._disp_obj_dict.iteritems():
	296	obj._disp_obj_dict[k]= v
[dad49a0]	297	if len(self.disp_cb_dict)>0:
	298	for k , v in self.disp_cb_dict.iteritems():
	299	obj.disp_cb_dict[k]= v
[2296316]	300	if len(self.values)>0:
	301	for k , v in self.values.iteritems():
	302	obj.values[k] = v
	303	if len(self.weights)>0:
	304	for k , v in self.weights.iteritems():
	305	obj.weights[k] = v
[b787e68c]	306	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
[fc6ea43]	307	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
[7609f1a]	308	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
	309	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
	310	obj.smear_type = copy.deepcopy(self.smear_type)
	311	obj.dq_l = copy.deepcopy(self.dq_l)
	312	obj.dq_r = copy.deepcopy(self.dq_r)
	313
[b787e68c]	314	obj.disp_box = copy.deepcopy(self.disp_box)
	315	obj.qmin = copy.deepcopy(self.qmin)
	316	obj.qmax = copy.deepcopy(self.qmax)
[c0ff8cc]	317	obj.multi_factor = self.multi_factor
[b787e68c]	318	obj.npts = copy.deepcopy(self.npts )
	319	obj.cb1 = copy.deepcopy(self.cb1)
[3370922]	320	obj.smearer = copy.deepcopy(self.smearer)
	321
[a074145]	322	for name, state in self.saved_states.iteritems():
	323	copy_name = copy.deepcopy(name)
	324	copy_state = state.clone()
	325	obj.saved_states[copy_name]= copy_state
[6f023e8]	326	return obj
[61cada5]	327
	328	def _repr_helper(self, list, rep):
	329	"""
[5062bbf]	330	Helper method to print a state
[61cada5]	331	"""
	332	for item in list:
[240b9966]	333	rep += "parameter name: %s \n"%str(item[1])
	334	rep += "value: %s\n"%str(item[2])
	335	rep += "selected: %s\n"%str(item[0])
	336	rep += "error displayed : %s \n"%str(item[4][0])
	337	rep += "error value:%s \n"%str(item[4][1])
	338	rep += "minimum displayed : %s \n"%str(item[5][0])
	339	rep += "minimum value : %s \n"%str(item[5][1])
	340	rep += "maximum displayed : %s \n"%str(item[6][0])
	341	rep += "maximum value : %s \n"%str(item[6][1])
	342	rep += "parameter unit: %s\n\n"%str(item[7])
	343	return rep
[c0ff8cc]	344
[61cada5]	345	def __repr__(self):
[11a7e11]	346	"""
[5062bbf]	347	output string for printing
[11a7e11]	348	"""
	349	rep = "\nState name: %s\n"%self.file
	350	t = time.localtime(self.timestamp)
[2296316]	351	time_str = time.strftime("%b %d %H;%M of %Y", t)
[c0ff8cc]	352
[11a7e11]	353	rep += "State created on : %s\n"%time_str
	354	rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox
	355	rep += "State structure factor combobox selection: %s\n"%self.structurecombobox
	356	rep += "is data : %s\n"%self.is_data
	357	rep += "data's name : %s\n"%self.data_name
	358	rep += "data's id : %s\n"%self.data_id
	359	rep += "model type (form factor) selected: %s\n"%self.shape_rbutton
[c0ff8cc]	360	rep += "multi_factor : %s\n"% str(self.multi_factor)
[11a7e11]	361	rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton
	362	rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton
	363	rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton
	364	rep += "data : %s\n"% str(self.data)
	365	rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin),
	366	str(self.qmax),str(self.npts))
[0b12abb5]	367	rep += "Dispersion selection : %s\n"%str(self.disp_box)
	368	rep += "Smearing enable : %s\n"%str(self.enable_smearer)
	369	rep += "Smearing disable : %s\n"%str(self.disable_smearer)
	370	rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer)
	371	rep += "Slit smearer enable : %s\n"%str(self.slit_smearer)
	372	rep += "Dispersity enable : %s\n"%str(self.enable_disp)
	373	rep += "Dispersity disable : %s\n"%str(self.disable_disp)
	374	rep += "Slit smearer enable: %s\n"%str(self.slit_smearer)
	375	rep += "2D enable : %s\n"%str(self.enable2D)
	376	rep += "All parameters checkbox selected: %s\n"%(self.cb1)
	377	rep += "Value of Chisqr : %s\n"%str(self.tcChi)
	378	rep += "Smear object : %s\n"%str(self.smearer)
	379	rep += "Smear type : %s\n"%(self.smear_type)
	380	rep += "dq_l : %s\n"%self.dq_l
	381	rep += "dq_r : %s\n"%self.dq_r
	382
[11a7e11]	383	rep += "model : %s\n\n"% str(self.model)
[2296316]	384	temp_parameters = []
	385	temp_fittable_param = []
	386	if self.data.__class__.__name__ == "Data2D":
	387	self.is_2D = True
	388	else:
	389	self.is_2D = False
	390	if self.data is not None:
	391	if not self.is_2D:
	392	for item in self.parameters:
	393	if not item in self.orientation_params:
	394	temp_parameters.append(item)
	395	for item in self.fittable_param:
	396	if not item in self.orientation_params_disp:
	397	temp_fittable_param.append(item)
	398	else:
	399	temp_parameters = self.parameters
	400	temp_fittable_param = self.fittable_param
	401
	402	rep += "number parameters(self.parameters): %s\n"%len(temp_parameters)
	403	rep = self._repr_helper( list=temp_parameters, rep=rep)
	404	rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters)
	405	rep = self._repr_helper( list=self.str_parameters, rep=rep)
	406	rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param)
	407	rep = self._repr_helper( list=temp_fittable_param, rep=rep)
	408	"""
	409	if is_2D:
	410	rep += "number orientation parameters"
	411	rep += "(self.orientation_params): %s\n"%len(self.orientation_params)
	412	rep = self._repr_helper( list=self.orientation_params, rep=rep)
	413	rep += "number dispersity parameters"
	414	rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp)
	415	rep = self._repr_helper( list=self.orientation_params_disp, rep=rep)
	416	"""
[61cada5]	417	return rep
[2296316]	418
	419	def set_report_string(self):
	420	"""
	421	Get the values (strings) from __str__ for report
	422	"""
	423	# Dictionary of teh report strings
	424	repo_time = ""
	425	model_name = ""
	426	title = ""
	427	title_name = ""
	428	file_name = ""
	429	param_string = ""
	430	paramval_string = ""
	431	chi2_string = ""
[c0ff8cc]	432	multi_factor_string = ""
[2296316]	433	q_range = ""
	434	strings = self.__repr__()
	435	lines = strings.split('\n')
	436
	437	# get all string values from __str__()
	438	for line in lines:
	439	value = ""
	440	content = line.split(":")
	441	name = content[0]
	442	try:
	443	value = content[1]
	444	except:
	445	pass
	446	if name.count("State created on"):
	447	repo_time = "Created on " + value
	448	if name.count("parameter name"):
	449	val_name = value.split(".")
	450	if len(val_name) > 1:
	451	if val_name[1].count("width"):
	452	param_string += value + ','
	453	else:
	454	continue
	455	else:
	456	param_string += value + ','
	457	if name == "value":
	458	param_string += value + ','
	459	if name == "error value":
	460	param_string += value + ','
	461	if name == "parameter unit":
	462	param_string += value + ':'
	463	if name == "Value of Chisqr ":
	464	chi2 = ("Chi2/Npts = " + value)
	465	chi2_string = CENTRE % chi2
[c0ff8cc]	466	if name == "multi_factor ":
	467	muti_factor = ("muti_factor = " + value)
	468	muti_factor_string = CENTRE % muti_factor
[2296316]	469	if name == "Title":
	470	if len(value.strip()) == 0:
	471	continue
	472	title = value + " [" + repo_time + "]"
	473	title_name = HEADER % title
	474	if name == "data ":
	475	try:
	476	file = ("File name:" + content[2])
	477	file_name = CENTRE % file
	478	if len(title) == 0:
	479	title = content[2] + " [" + repo_time + "]"
	480	title_name = HEADER % title
	481	except:
	482	pass
	483	if name == "Plotting Range":
	484	try:
	485	q_range = content[1] + " = " + content[2] \
	486	+ " = " + content[3].split(",")[0]
	487	q_name = ("Q Range: " + q_range)
	488	q_range = CENTRE % q_name
	489	except:
	490	pass
	491	paramval = ""
	492	for lines in param_string.split(":"):
	493	line = lines.split(",")
	494	if len(lines) > 0:
	495	param = line[0]
	496	param += " = " + line[1]
	497	if len(line[2].split()) > 0 and not line[2].count("None"):
	498	param += " +- " + line[2]
	499	if len(line[3].split()) > 0 and not line[3].count("None"):
	500	param += " " + line[3]
	501	if not paramval.count(param):
	502	paramval += param + "\n"
	503	paramval_string += CENTRE % param + "\n"
	504
[f5bdb4a]	505	text_string = "\n\n\n" + title + "\n\n" + file + \
	506	"\n" + q_name + \
	507	"\n" + chi2 + \
	508	"\n\n" + paramval
	509
	510	title_name = self._check_html_format(title_name)
	511	file_name = self._check_html_format(file_name)
	512	title = self._check_html_format(title)
	513
[2296316]	514	html_string = title_name + "\n" + file_name + \
	515	"\n" + q_range + \
	516	"\n" + chi2_string + \
	517	"\n" + ELINE + \
	518	"\n" + paramval_string + \
	519	"\n" + ELINE + \
	520	"\n" + FEET_1 % title + \
	521	"\n" + FEET_2
[f5bdb4a]	522
[2296316]	523	return html_string, text_string, title
	524
[f5bdb4a]	525	def _check_html_format(self, name):
	526	"""
	527	Check string '%' for html format
	528	"""
	529	if name.count('%'):
	530	name = name.replace('%', '&#37')
	531
	532	return name
	533
	534
[2296316]	535	def report(self, figs=None, canvases=None):
	536	"""
	537	Invoke report dialog panel
	538
	539	: param figs: list of pylab figures [list]
	540	"""
	541	from report_dialog import ReportDialog
	542	# get the strings for report
	543	html_str, text_str, title = self.set_report_string()
	544	# Allow 2 figures to append
	545	if len(figs) == 1:
	546	add_str = FEET_3
	547	elif len(figs) == 2:
	548	add_str = ELINE
	549	add_str += FEET_2 % ("%s")
	550	add_str += ELINE
	551	add_str += FEET_3
	552	elif len(figs) > 2:
	553	add_str = ELINE
	554	add_str += FEET_2 % ("%s")
	555	add_str += ELINE
	556	add_str += FEET_2 % ("%s")
	557	add_str += ELINE
	558	add_str += FEET_3
	559	else:
	560	add_str = ""
[c0ff8cc]	561
[2296316]	562	# final report html strings
	563	report_str = html_str % ("%s") + add_str
	564
	565	# make plot image
	566	images = self.set_plot_state(figs, canvases)
	567	report_list = [report_str, text_str, images ]
	568	dialog = ReportDialog(report_list, None, -1, "")
	569	dialog.ShowModal()
[c0ff8cc]	570
	571
[61cada5]	572	def _toXML_helper(self, list, element, newdoc):
	573	"""
[5062bbf]	574	Helper method to create xml file for saving state
[61cada5]	575	"""
	576	for item in list:
	577	sub_element = newdoc.createElement('parameter')
	578	sub_element.setAttribute('name', str(item[1]))
	579	sub_element.setAttribute('value', str(item[2]))
	580	sub_element.setAttribute('selected_to_fit', str(item[0]))
	581	sub_element.setAttribute('error_displayed', str(item[4][0]))
	582	sub_element.setAttribute('error_value', str(item[4][1]))
	583	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
	584	sub_element.setAttribute('minimum_value', str(item[5][1]))
	585	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
	586	sub_element.setAttribute('maximum_value', str(item[6][1]))
	587	sub_element.setAttribute('unit', str(item[7]))
	588	element.appendChild(sub_element)
	589
	590	def toXML(self, file="fitting_state.fitv", doc=None, entry_node=None):
	591	"""
[5062bbf]	592	Writes the state of the InversionControl panel to file, as XML.
	593
	594	Compatible with standalone writing, or appending to an
	595	already existing XML document. In that case, the XML document
	596	is required. An optional entry node in the XML document may also be given.
	597
	598	:param file: file to write to
	599	:param doc: XML document object [optional]
	600	:param entry_node: XML node within the XML document at which we will append the data [optional]
	601
[61cada5]	602	"""
	603	from xml.dom.minidom import getDOMImplementation
[71f0373]	604
[61cada5]	605	# Check whether we have to write a standalone XML file
	606	if doc is None:
	607	impl = getDOMImplementation()
	608	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
	609	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
	610	top_element = newdoc.documentElement
	611	else:
	612	# We are appending to an existing document
	613	newdoc = doc
	614	top_element = newdoc.createElement(FITTING_NODE_NAME)
	615	if entry_node is None:
	616	newdoc.documentElement.appendChild(top_element)
	617	else:
	618	entry_node.appendChild(top_element)
	619
	620	attr = newdoc.createAttribute("version")
	621	attr.nodeValue = '1.0'
	622	top_element.setAttributeNode(attr)
[cfc0913]	623
[61cada5]	624	# File name
	625	element = newdoc.createElement("filename")
	626	if self.file is not None:
	627	element.appendChild(newdoc.createTextNode(str(self.file)))
	628	else:
	629	element.appendChild(newdoc.createTextNode(str(file)))
	630	top_element.appendChild(element)
[11a7e11]	631
	632	element = newdoc.createElement("timestamp")
	633	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	634	attr = newdoc.createAttribute("epoch")
	635	attr.nodeValue = str(self.timestamp)
	636	element.setAttributeNode(attr)
	637	top_element.appendChild(element)
[61cada5]	638	# Inputs
	639	inputs = newdoc.createElement("Attributes")
	640	top_element.appendChild(inputs)
	641
[0b12abb5]	642
[61cada5]	643	if self.data is not None and hasattr(self.data, "group_id"):
	644	self.data_group_id = self.data.group_id
	645	if self.data is not None and hasattr(self.data, "is_data"):
	646	self.is_data = self.data.is_data
	647	if self.data is not None:
	648	self.data_name = self.data.name
	649	if self.data is not None and hasattr(self.data, "id"):
	650	self.data_id = self.data.id
	651
[26f3dd5]	652	for item in list_of_data_attributes:
[0b12abb5]	653	element = newdoc.createElement(item[0])
[2296316]	654	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
[0b12abb5]	655	inputs.appendChild(element)
[26f3dd5]	656
	657	for item in list_of_state_attributes:
	658	element = newdoc.createElement(item[0])
[2296316]	659	exec "element.setAttribute(item[0], str(self.%s))" % (item[1])
[26f3dd5]	660	inputs.appendChild(element)
[c0ff8cc]	661
[2296316]	662	# For self.values ={ disp_param_name: [vals,...],...}
[c0ff8cc]	663	# and for self.weights ={ disp_param_name: [weights,...],...}
[11a7e11]	664	for item in list_of_model_attributes:
	665	element = newdoc.createElement(item[0])
[2296316]	666	exec "list = self.%s" % item[1]
	667	for key, value in list.iteritems():
	668	sub_element = newdoc.createElement(key)
	669	sub_element.setAttribute('name', str(key))
	670	for val in value:
	671	com = "sub_element.appendChild"
	672	com += "(newdoc.createTextNode(str(%s)))"
	673	exec com % val
	674
	675	element.appendChild(sub_element)
[11a7e11]	676	inputs.appendChild(element)
[2296316]	677
	678	# Create doc for the dictionary of self._disp_obj_dic
	679	for item in list_of_obj_dic:
	680	element = newdoc.createElement(item[0])
	681	exec "list = self.%s" % item[1]
	682	for key, val in list.iteritems():
	683	value = repr(val)
	684	sub_element = newdoc.createElement(key)
	685	sub_element.setAttribute('name', str(key))
	686	sub_element.setAttribute('value', str(value))
	687	element.appendChild(sub_element)
	688	inputs.appendChild(element)
	689
[61cada5]	690	for item in list_of_state_parameters:
	691	element = newdoc.createElement(item[0])
[2296316]	692	com = "self._toXML_helper(list=self.%s,"
	693	com += " element=element, newdoc=newdoc)"
	694	exec com % item[1]
[61cada5]	695	inputs.appendChild(element)
[c0ff8cc]	696
[61cada5]	697	# Save the file
	698	if doc is None:
	699	fd = open(file, 'w')
	700	fd.write(newdoc.toprettyxml())
	701	fd.close()
	702	return None
	703	else:
	704	return newdoc.toprettyxml()
	705
	706	def _fromXML_helper(self, node, list):
	707	"""
[5062bbf]	708	Helper function to write state to xml
[61cada5]	709	"""
	710	for item in node:
[0b12abb5]	711	try:
	712	name = item.get('name')
	713	except:
	714	name = None
	715	try:
	716	value = item.get('value')
	717	except:
	718	value = None
	719	try:
[3ad91de]	720	selected_to_fit = (item.get('selected_to_fit') == "True")
[0b12abb5]	721	except:
	722	selected_to_fit = None
	723	try:
[3ad91de]	724	error_displayed = (item.get('error_displayed') == "True")
[0b12abb5]	725	except:
	726	error_displayed = None
	727	try:
	728	error_value = item.get('error_value')
	729	except:
	730	error_value = None
	731	try:
[3ad91de]	732	minimum_displayed = (item.get('minimum_displayed')== "True")
[0b12abb5]	733	except:
	734	minimum_displayed = None
	735	try:
	736	minimum_value = item.get('minimum_value')
	737	except:
	738	minimum_value = None
	739	try:
[3ad91de]	740	maximum_displayed = (item.get('maximum_displayed') == "True")
[0b12abb5]	741	except:
	742	maximum_displayed = None
	743	try:
	744	maximum_value = item.get('maximum_value')
	745	except:
	746	maximum_value = None
	747	try:
	748	unit = item.get('unit')
	749	except:
	750	unit = None
[2296316]	751	list.append([selected_to_fit, name, value, "+/-",
	752	[error_displayed, error_value],
	753	[minimum_displayed,minimum_value],
	754	[maximum_displayed,maximum_value], unit])
[cfc0913]	755
[61cada5]	756	def fromXML(self, file=None, node=None):
	757	"""
[5062bbf]	758	Load fitting state from a file
	759
	760	:param file: .fitv file
	761	:param node: node of a XML document to read from
	762
[61cada5]	763	"""
	764	if file is not None:
[11a7e11]	765	msg = "PageState no longer supports non-CanSAS"
	766	msg += " format for fitting files"
	767	raise RuntimeError, msg
[61cada5]	768
[11a7e11]	769	if node.get('version')and node.get('version') == '1.0':
[61cada5]	770
	771	# Get file name
	772	entry = get_content('ns:filename', node)
	773	if entry is not None:
	774	self.file = entry.text.strip()
[11a7e11]	775
	776	# Get time stamp
	777	entry = get_content('ns:timestamp', node)
	778	if entry is not None and entry.get('epoch'):
	779	try:
	780	self.timestamp = float(entry.get('epoch'))
	781	except:
	782	msg = "PageState.fromXML: Could not"
	783	msg += " read timestamp\n %s" % sys.exc_value
	784	logging.error(msg)
	785
[61cada5]	786	# Parse fitting attributes
	787	entry = get_content('ns:Attributes', node)
[0b12abb5]	788	for item in list_of_data_attributes:
	789	node = get_content('ns:%s'%item[0], entry)
	790	try:
[2296316]	791	exec "self.%s = parse_entry_helper(node, item)" % item[0]
[0b12abb5]	792
	793	except:
	794	raise
[2296316]	795
[61cada5]	796	if entry is not None:
[0b12abb5]	797
[61cada5]	798	for item in list_of_state_attributes:
[2296316]	799	node = get_content('ns:%s' % item[0], entry)
[0b12abb5]	800	try:
[2296316]	801	exec "self.%s = parse_entry_helper(node, item)" % \
	802	str(item[0])
[0b12abb5]	803	except:
	804	raise
	805
[2296316]	806	for item in list_of_state_parameters:
	807	node = get_content("ns:%s" % item[0], entry)
	808	exec "self._fromXML_helper(node=node, list=self.%s)" % \
	809	item[1]
	810
	811	# Recover _disp_obj_dict from xml file
	812	self._disp_obj_dict = {}
	813	for item in list_of_obj_dic:
	814	# Get node
	815	node = get_content("ns:%s" % item[0], entry)
	816	for attr in node:
	817	name = attr.get('name')
	818	val = attr.get('value')
	819	value = val.split(" instance")[0]
	820	disp_name = value.split("<")[1]
[11a7e11]	821	try:
[2296316]	822	# Try to recover disp_model object from strings
	823	com = "from sans.models.dispersion_models "
	824	com += "import %s as disp"
	825	com_name = disp_name.split(".")[3]
	826	exec com % com_name
	827	disp_model = disp()
	828	exec "self.%s['%s'] = com_name" % (item[1], name)
[11a7e11]	829	except:
[2296316]	830	pass
	831
	832	# get self.values and self.weights dic. if exists
	833	for item in list_of_model_attributes:
	834	node = get_content("ns:%s" % item[0], entry)
	835	dic = {}
	836	list = []
	837	for par in node:
	838	name = par.get('name')
	839	values = par.text.split('\n')
	840	# Get lines only with numbers
	841	for line in values:
	842	try:
	843	val= float(line)
	844	list.append(val)
	845	except:
	846	# pass if line is empty (it happens)
	847	pass
	848	dic[name] = numpy.array(list)
	849	exec "self.%s = dic" % item[1]
	850
	851	def set_plot_state(self, figs, canvases):
	852	"""
	853	Build image state that wx.html understand
	854	by plotting, putting it into wx.FileSystem image object
	855
	856	"""
	857	images = []
	858	# some imports
	859	import wx
	860
	861	# Reset memory
	862	self.imgRAM = None
	863	wx.MemoryFSHandler()
	864
	865	# For no figures in the list, prepare empty plot
	866	if figs == None or len(figs) == 0:
	867	figs = [None]
	868
	869	# Loop over the list of figures
	870	# use wx.MemoryFSHandler
	871	self.imgRAM = wx.MemoryFSHandler()
	872	for fig in figs:
	873	if figs != None:
	874	#fig.set_facecolor('w')
	875	ind = figs.index(fig)
	876	canvas = canvases[ind]
[0b12abb5]	877
[2296316]	878	#bmp = wx.BitmapDataObject()
	879	#bmp.SetBitmap(canvas.bitmap)
	880	#store the image in wx.FileSystem Object
	881	wx.FileSystem.AddHandler(wx.MemoryFSHandler())
	882
	883	# index of the fig
	884	ind = figs.index(fig)
	885
	886	#AddFile, image can be retrieved with 'memory:filename'
	887	self.imgRAM.AddFile('img_fit%s.png' % ind ,
	888	canvas.bitmap, wx.BITMAP_TYPE_PNG)
	889
	890	#append figs
	891	images.append(fig)
	892
[c0ff8cc]	893	return images
[61cada5]	894
	895	class Reader(CansasReader):
	896	"""
[5062bbf]	897	Class to load a .fitv fitting file
[61cada5]	898	"""
	899	## File type
	900	type_name = "Fitting"
	901
	902	## Wildcards
[b35d3d1]	903	type = ["Fitting files (.fitv)\|.fitv"
	904	"SANSView file (.svs)\|.svs"]
[61cada5]	905	## List of allowed extensions
[b35d3d1]	906	ext=['.fitv', '.FITV', '.svs', 'SVS']
[61cada5]	907
	908	def __init__(self, call_back=None, cansas=True):
[df7ed14]	909	CansasReader.__init__(self)
[61cada5]	910	"""
[5062bbf]	911	Initialize the call-back method to be called
	912	after we load a file
	913
	914	:param call_back: call-back method
	915	:param cansas: True = files will be written/read in CanSAS format
	916	False = write CanSAS format
[61cada5]	917
	918	"""
	919	## Call back method to be executed after a file is read
	920	self.call_back = call_back
	921	## CanSAS format flag
	922	self.cansas = cansas
[75fbd17]	923	self.state = None
	924	def get_state(self):
	925	return self.state
[61cada5]	926
	927	def read(self, path):
	928	"""
[5062bbf]	929	Load a new P(r) inversion state from file
	930
	931	:param path: file path
	932
[61cada5]	933	"""
[e9b12eaf]	934	if self.cansas == True:
[61cada5]	935	return self._read_cansas(path)
[e9b12eaf]	936
	937	def _data2d_to_xml_doc(self, datainfo):
[61cada5]	938	"""
[5062bbf]	939	Create an XML document to contain the content of a Data2D
	940
	941	:param datainfo: Data2D object
	942
[61cada5]	943	"""
	944	if not issubclass(datainfo.__class__, Data2D):
	945	raise RuntimeError, "The cansas writer expects a Data2D instance"
	946
	947	doc = xml.dom.minidom.Document()
	948	main_node = doc.createElement("SASroot")
	949	main_node.setAttribute("version", self.version)
[df7ed14]	950	main_node.setAttribute("xmlns", "cansas1d/%s" % self.version)
	951	main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
	952	main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version)
	953
[61cada5]	954	doc.appendChild(main_node)
	955
	956	entry_node = doc.createElement("SASentry")
	957	main_node.appendChild(entry_node)
[df7ed14]	958
[61cada5]	959	write_node(doc, entry_node, "Title", datainfo.title)
[df7ed14]	960	if datainfo is not None:
	961	write_node(doc, entry_node, "data_class", datainfo.__class__.__name__)
[61cada5]	962	for item in datainfo.run:
	963	runname = {}
	964	if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1:
	965	runname = {'name': datainfo.run_name[item] }
	966	write_node(doc, entry_node, "Run", item, runname)
	967	# Data info
[df7ed14]	968	new_node = doc.createElement("SASdata")
	969	entry_node.appendChild(new_node)
[e9b12eaf]	970	for item in list_of_data_2d_attr:
	971	element = doc.createElement(item[0])
	972	exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1])
[df7ed14]	973	new_node.appendChild(element)
	974
[e9b12eaf]	975	for item in list_of_data2d_values:
[df7ed14]	976	root_node = doc.createElement(item[0])
	977	new_node.appendChild(root_node)
	978
[35b556d]	979	exec "temp_list = datainfo.%s"%item[1]
[df7ed14]	980
[35b556d]	981	if temp_list is None or len(temp_list)== 0:
[df7ed14]	982	element = doc.createElement(item[0])
[35b556d]	983	exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list
[df7ed14]	984	root_node.appendChild(element)
[35b556d]	985	else:
	986	for value in temp_list:
[df7ed14]	987	element = doc.createElement(item[0])
	988	exec "element.setAttribute(item[0], str(%s))"%value
	989	root_node.appendChild(element)
	990
[61cada5]	991	# Sample info
	992	sample = doc.createElement("SASsample")
	993	if datainfo.sample.name is not None:
	994	sample.setAttribute("name", str(datainfo.sample.name))
	995	entry_node.appendChild(sample)
	996	write_node(doc, sample, "ID", str(datainfo.sample.ID))
	997	write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit})
	998	write_node(doc, sample, "transmission", datainfo.sample.transmission)
	999	write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit})
	1000
	1001	for item in datainfo.sample.details:
	1002	write_node(doc, sample, "details", item)
	1003
	1004	pos = doc.createElement("position")
	1005	written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit})
	1006	written = written \| write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit})
	1007	written = written \| write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit})
	1008	if written == True:
	1009	sample.appendChild(pos)
	1010
	1011	ori = doc.createElement("orientation")
	1012	written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit})
	1013	written = written \| write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit})
	1014	written = written \| write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit})
	1015	if written == True:
	1016	sample.appendChild(ori)
	1017
	1018	# Instrument info
	1019	instr = doc.createElement("SASinstrument")
	1020	entry_node.appendChild(instr)
	1021
	1022	write_node(doc, instr, "name", datainfo.instrument)
	1023
	1024	# Source
	1025	source = doc.createElement("SASsource")
	1026	if datainfo.source.name is not None:
	1027	source.setAttribute("name", str(datainfo.source.name))
	1028	instr.appendChild(source)
	1029
	1030	write_node(doc, source, "radiation", datainfo.source.radiation)
	1031	write_node(doc, source, "beam_shape", datainfo.source.beam_shape)
	1032	size = doc.createElement("beam_size")
	1033	if datainfo.source.beam_size_name is not None:
	1034	size.setAttribute("name", str(datainfo.source.beam_size_name))
	1035	written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit})
	1036	written = written \| write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit})
	1037	written = written \| write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit})
	1038	if written == True:
	1039	source.appendChild(size)
	1040
	1041	write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit})
	1042	write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit})
	1043	write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit})
	1044	write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit})
	1045
	1046	# Collimation
	1047	for item in datainfo.collimation:
	1048	coll = doc.createElement("SAScollimation")
	1049	if item.name is not None:
	1050	coll.setAttribute("name", str(item.name))
	1051	instr.appendChild(coll)
	1052
	1053	write_node(doc, coll, "length", item.length, {"unit":item.length_unit})
	1054
	1055	for apert in item.aperture:
	1056	ap = doc.createElement("aperture")
	1057	if apert.name is not None:
	1058	ap.setAttribute("name", str(apert.name))
	1059	if apert.type is not None:
	1060	ap.setAttribute("type", str(apert.type))
	1061	coll.appendChild(ap)
	1062
	1063	write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit})
	1064
	1065	size = doc.createElement("size")
	1066	if apert.size_name is not None:
	1067	size.setAttribute("name", str(apert.size_name))
	1068	written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit})
	1069	written = written \| write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit})
	1070	written = written \| write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit})
	1071	if written == True:
	1072	ap.appendChild(size)
	1073
	1074	# Detectors
	1075	for item in datainfo.detector:
	1076	det = doc.createElement("SASdetector")
	1077	written = write_node(doc, det, "name", item.name)
	1078	written = written \| write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit})
	1079	written = written \| write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit})
	1080	if written == True:
	1081	instr.appendChild(det)
	1082
	1083	off = doc.createElement("offset")
	1084	written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit})
	1085	written = written \| write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit})
	1086	written = written \| write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit})
	1087	if written == True:
	1088	det.appendChild(off)
	1089
	1090	center = doc.createElement("beam_center")
	1091	written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit})
	1092	written = written \| write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit})
	1093	written = written \| write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit})
	1094	if written == True:
	1095	det.appendChild(center)
	1096
	1097	pix = doc.createElement("pixel_size")
	1098	written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit})
	1099	written = written \| write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit})
	1100	written = written \| write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit})
	1101	if written == True:
	1102	det.appendChild(pix)
	1103
	1104	ori = doc.createElement("orientation")
	1105	written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit})
	1106	written = written \| write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit})
	1107	written = written \| write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit})
	1108	if written == True:
	1109	det.appendChild(ori)
	1110
	1111	# Processes info
	1112	for item in datainfo.process:
	1113	node = doc.createElement("SASprocess")
	1114	entry_node.appendChild(node)
	1115
	1116	write_node(doc, node, "name", item.name)
	1117	write_node(doc, node, "date", item.date)
	1118	write_node(doc, node, "description", item.description)
	1119	for term in item.term:
	1120	value = term['value']
	1121	del term['value']
	1122	write_node(doc, node, "term", value, term)
	1123	for note in item.notes:
	1124	write_node(doc, node, "SASprocessnote", note)
	1125	# Return the document, and the SASentry node associated with
	1126	# the data we just wrote
	1127	return doc, entry_node
[e9b12eaf]	1128
[61cada5]	1129	def _parse_state(self, entry):
	1130	"""
[5062bbf]	1131	Read a fit result from an XML node
	1132
	1133	:param entry: XML node to read from
	1134
	1135	:return: PageState object
[61cada5]	1136	"""
	1137	# Create an empty state
[b35d3d1]	1138	state = None
[61cada5]	1139	# Locate the P(r) node
	1140	try:
	1141	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS})
[b35d3d1]	1142	if nodes !=[]:
	1143	# Create an empty state
	1144	state = PageState()
	1145	state.fromXML(node=nodes[0])
[61cada5]	1146	except:
	1147	logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value)
	1148
	1149	return state
	1150
[0b12abb5]	1151
[df7ed14]	1152
	1153	def _parse_entry(self, dom):
[e9b12eaf]	1154	"""
[5062bbf]	1155	Parse a SASentry
	1156
	1157	:param node: SASentry node
	1158
[df7ed14]	1159	:return: Data1D/Data2D object
[5062bbf]	1160
[e9b12eaf]	1161	"""
[df7ed14]	1162	node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS})
	1163	if not node or node[0].text.lstrip().rstrip() != "Data2D":
	1164	return CansasReader._parse_entry(self, dom)
	1165
	1166	#Parse 2D
[e9b12eaf]	1167	data_info = Data2D()
	1168
	1169	# Look up title
	1170	self._store_content('ns:Title', dom, 'title', data_info)
	1171
	1172	# Look up run number
	1173	nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS})
	1174	for item in nodes:
	1175	if item.text is not None:
	1176	value = item.text.strip()
	1177	if len(value) > 0:
	1178	data_info.run.append(value)
	1179	if item.get('name') is not None:
	1180	data_info.run_name[value] = item.get('name')
	1181
	1182	# Look up instrument name
	1183	self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info)
	1184
	1185	# Notes
	1186	note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS})
	1187	for note in note_list:
	1188	try:
	1189	if note.text is not None:
	1190	note_value = note.text.strip()
	1191	if len(note_value) > 0:
	1192	data_info.notes.append(note_value)
	1193	except:
	1194	err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value
	1195	self.errors.append(err_mess)
	1196	logging.error(err_mess)
	1197
	1198	# Sample info ###################
	1199	entry = get_content('ns:SASsample', dom)
	1200	if entry is not None:
	1201	data_info.sample.name = entry.get('name')
	1202
	1203	self._store_content('ns:SASsample/ns:ID',
	1204	dom, 'ID', data_info.sample)
	1205	self._store_float('ns:SASsample/ns:thickness',
	1206	dom, 'thickness', data_info.sample)
	1207	self._store_float('ns:SASsample/ns:transmission',
	1208	dom, 'transmission', data_info.sample)
	1209	self._store_float('ns:SASsample/ns:temperature',
	1210	dom, 'temperature', data_info.sample)
	1211
	1212	nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS})
	1213	for item in nodes:
	1214	try:
	1215	if item.text is not None:
	1216	detail_value = item.text.strip()
	1217	if len(detail_value) > 0:
	1218	data_info.sample.details.append(detail_value)
	1219	except:
	1220	err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value
	1221	self.errors.append(err_mess)
	1222	logging.error(err_mess)
	1223
	1224	# Position (as a vector)
	1225	self._store_float('ns:SASsample/ns:position/ns:x',
	1226	dom, 'position.x', data_info.sample)
	1227	self._store_float('ns:SASsample/ns:position/ns:y',
	1228	dom, 'position.y', data_info.sample)
	1229	self._store_float('ns:SASsample/ns:position/ns:z',
	1230	dom, 'position.z', data_info.sample)
	1231
	1232	# Orientation (as a vector)
	1233	self._store_float('ns:SASsample/ns:orientation/ns:roll',
	1234	dom, 'orientation.x', data_info.sample)
	1235	self._store_float('ns:SASsample/ns:orientation/ns:pitch',
	1236	dom, 'orientation.y', data_info.sample)
	1237	self._store_float('ns:SASsample/ns:orientation/ns:yaw',
	1238	dom, 'orientation.z', data_info.sample)
	1239
	1240	# Source info ###################
	1241	entry = get_content('ns:SASinstrument/ns:SASsource', dom)
	1242	if entry is not None:
	1243	data_info.source.name = entry.get('name')
	1244
	1245	self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation',
	1246	dom, 'radiation', data_info.source)
	1247	self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape',
	1248	dom, 'beam_shape', data_info.source)
	1249	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength',
	1250	dom, 'wavelength', data_info.source)
	1251	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min',
	1252	dom, 'wavelength_min', data_info.source)
	1253	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max',
	1254	dom, 'wavelength_max', data_info.source)
	1255	self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread',
	1256	dom, 'wavelength_spread', data_info.source)
	1257
	1258	# Beam size (as a vector)
	1259	entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom)
	1260	if entry is not None:
	1261	data_info.source.beam_size_name = entry.get('name')
	1262
	1263	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x',
	1264	dom, 'beam_size.x', data_info.source)
	1265	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y',
	1266	dom, 'beam_size.y', data_info.source)
	1267	self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z',
	1268	dom, 'beam_size.z', data_info.source)
	1269
	1270	# Collimation info ###################
	1271	nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS})
	1272	for item in nodes:
	1273	collim = Collimation()
	1274	if item.get('name') is not None:
	1275	collim.name = item.get('name')
	1276	self._store_float('ns:length', item, 'length', collim)
	1277
	1278	# Look for apertures
	1279	apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS})
	1280	for apert in apert_list:
	1281	aperture = Aperture()
	1282
	1283	# Get the name and type of the aperture
	1284	aperture.name = apert.get('name')
	1285	aperture.type = apert.get('type')
	1286
	1287	self._store_float('ns:distance', apert, 'distance', aperture)
	1288
	1289	entry = get_content('ns:size', apert)
	1290	if entry is not None:
	1291	aperture.size_name = entry.get('name')
	1292
	1293	self._store_float('ns:size/ns:x', apert, 'size.x', aperture)
	1294	self._store_float('ns:size/ns:y', apert, 'size.y', aperture)
	1295	self._store_float('ns:size/ns:z', apert, 'size.z', aperture)
	1296
	1297	collim.aperture.append(aperture)
	1298
	1299	data_info.collimation.append(collim)
	1300
	1301	# Detector info ######################
	1302	nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS})
	1303	for item in nodes:
	1304
	1305	detector = Detector()
	1306
	1307	self._store_content('ns:name', item, 'name', detector)
	1308	self._store_float('ns:SDD', item, 'distance', detector)
	1309
	1310	# Detector offset (as a vector)
	1311	self._store_float('ns:offset/ns:x', item, 'offset.x', detector)
	1312	self._store_float('ns:offset/ns:y', item, 'offset.y', detector)
	1313	self._store_float('ns:offset/ns:z', item, 'offset.z', detector)
	1314
	1315	# Detector orientation (as a vector)
	1316	self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector)
	1317	self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector)
	1318	self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector)
	1319
	1320	# Beam center (as a vector)
	1321	self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector)
	1322	self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector)
	1323	self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector)
	1324
	1325	# Pixel size (as a vector)
	1326	self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector)
	1327	self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector)
	1328	self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector)
	1329
	1330	self._store_float('ns:slit_length', item, 'slit_length', detector)
	1331
	1332	data_info.detector.append(detector)
	1333
	1334	# Processes info ######################
	1335	nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS})
	1336	for item in nodes:
	1337	process = Process()
	1338	self._store_content('ns:name', item, 'name', process)
	1339	self._store_content('ns:date', item, 'date', process)
	1340	self._store_content('ns:description', item, 'description', process)
	1341
	1342	term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS})
	1343	for term in term_list:
	1344	try:
	1345	term_attr = {}
	1346	for attr in term.keys():
	1347	term_attr[attr] = term.get(attr).strip()
	1348	if term.text is not None:
	1349	term_attr['value'] = term.text.strip()
	1350	process.term.append(term_attr)
	1351	except:
	1352	err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value
	1353	self.errors.append(err_mess)
	1354	logging.error(err_mess)
	1355
	1356	note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS})
	1357	for note in note_list:
	1358	if note.text is not None:
	1359	process.notes.append(note.text.strip())
	1360
	1361	data_info.process.append(process)
	1362
	1363
	1364	# Data info ######################
	1365	nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS})
	1366	if len(nodes)>1:
	1367	raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries"
[df7ed14]	1368
	1369	for entry in nodes:
	1370	for item in list_of_data_2d_attr:
	1371	#get node
	1372	node = get_content('ns:%s'%item[0], entry)
[0b12abb5]	1373	exec "data_info.%s = parse_entry_helper(node, item)"%(item[1])
[e9b12eaf]	1374
[df7ed14]	1375	for item in list_of_data2d_values:
	1376	field = get_content('ns:%s'%item[0], entry)
	1377	list = []
	1378	if field is not None:
[0b12abb5]	1379	list = [parse_entry_helper(node, item) for node in field]
[df7ed14]	1380	exec "data_info.%s = numpy.array(list)"%item[0]
[e9b12eaf]	1381
	1382	return data_info
	1383
[61cada5]	1384	def _read_cansas(self, path):
	1385	"""
[5062bbf]	1386	Load data and P(r) information from a CanSAS XML file.
	1387
	1388	:param path: file path
	1389
	1390	:return: Data1D object if a single SASentry was found,
	1391	or a list of Data1D objects if multiple entries were found,
	1392	or None of nothing was found
	1393
	1394	:raise RuntimeError: when the file can't be opened
	1395	:raise ValueError: when the length of the data vectors are inconsistent
	1396
[61cada5]	1397	"""
	1398	output = []
[b63dc6e]	1399	basename = os.path.basename(path)
	1400	root, extension = os.path.splitext(basename)
	1401	ext = extension.lower()
[61cada5]	1402	try:
	1403	if os.path.isfile(path):
[b63dc6e]	1404
[61cada5]	1405	#TODO: eventually remove the check for .xml once
	1406	# the P(r) writer/reader is truly complete.
[b63dc6e]	1407	if ext in self.ext or \
	1408	ext == '.xml':
[61cada5]	1409
	1410	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
	1411	# Check the format version number
	1412	# Specifying the namespace will take care of the file format version
	1413	root = tree.getroot()
[df7ed14]	1414	entry_list = root.xpath('ns:SASentry', namespaces={'ns': CANSAS_NS})
[b35d3d1]	1415	for entry in entry_list:
[e9b12eaf]	1416	try:
	1417	sas_entry = self._parse_entry(entry)
	1418	except:
[df7ed14]	1419	raise
[61cada5]	1420	fitstate = self._parse_state(entry)
[b35d3d1]	1421
	1422	#state could be None when .svs file is loaded
	1423	#in this case, skip appending to output
	1424	if fitstate != None:
	1425	sas_entry.meta_data['fitstate'] = fitstate
	1426	sas_entry.filename = fitstate.file
	1427	output.append(sas_entry)
[61cada5]	1428	else:
[b63dc6e]	1429	self.call_back(format=ext)
[61cada5]	1430	raise RuntimeError, "%s is not a file" % path
[b35d3d1]	1431
[61cada5]	1432	# Return output consistent with the loader's api
	1433	if len(output)==0:
[b63dc6e]	1434	self.call_back(state=None, datainfo=None,format=ext)
[61cada5]	1435	return None
	1436	else:
[b35d3d1]	1437	for ind in range(len(output)):
	1438	# Call back to post the new state
	1439	state = output[ind].meta_data['fitstate']
	1440	t = time.localtime(state.timestamp)
	1441	time_str = time.strftime("%b %d %H:%M", t)
	1442	# Check that no time stamp is already appended
	1443	max_char = state.file.find("[")
	1444	if max_char < 0:
	1445	max_char = len(state.file)
[ef16f59]	1446	original_fname = state.file[0:max_char]
	1447	state.file = original_fname +' [' + time_str + ']'
[b35d3d1]	1448
	1449
	1450	if state is not None and state.is_data is not None:
	1451	exec 'output[%d].is_data = state.is_data'% ind
	1452
	1453	output[ind].filename = state.file
	1454	state.data = output[ind]
	1455	state.data.name = output[ind].filename #state.data_name
	1456	state.data.id = state.data_id
	1457	if state.is_data is not None:
	1458	state.data.is_data = state.is_data
[ef16f59]	1459	if output[ind].run_name is not None and len(output[ind].run_name) != 0 :
	1460	name = output[ind].run_name
	1461	else:
	1462	name=original_fname
	1463	state.data.group_id = name
	1464	#store state in fitting
[90a7bbd]	1465	self.call_back(state=state, datainfo=output[ind],format=ext)
[75fbd17]	1466	self.state= state
[ef16f59]	1467	return output
[b35d3d1]	1468
[61cada5]	1469	except:
[4bee68d]	1470	self.call_back(format=ext)
	1471	#self.state= state
[61cada5]	1472	raise
	1473
	1474	def write(self, filename, datainfo=None, fitstate=None):
	1475	"""
[b35d3d1]	1476	Write the content of a Data1D as a CanSAS XML file only for standalone
[5062bbf]	1477
	1478	:param filename: name of the file to write
	1479	:param datainfo: Data1D object
	1480	:param fitstate: PageState object
	1481
[61cada5]	1482	"""
	1483	# Sanity check
	1484	if self.cansas == True:
	1485
	1486	# Add fitting information to the XML document
[ef16f59]	1487	doc = self.write_toXML(datainfo, fitstate)
[61cada5]	1488	# Write the XML document
	1489	fd = open(filename, 'w')
	1490	fd.write(doc.toprettyxml())
	1491	fd.close()
	1492	else:
	1493	fitstate.toXML(file=filename)
	1494
[b35d3d1]	1495	def write_toXML(self, datainfo=None, state=None):
	1496	"""
	1497	Write toXML, a helper for write() , could be used by guimanager._on_save()
	1498
	1499	: return: xml doc
	1500	"""
[3c44c66]	1501
[b35d3d1]	1502	if state.data is None:
[c21e87b]	1503	data = sans.dataloader.data_info.Data1D(x=[], y=[])
[b35d3d1]	1504	else:
	1505	#make sure title and data run is filled up.
[028a0e8]	1506	if state.data.title == None or state.data.title=='': state.data.title = state.data.name
	1507	if state.data.run_name == None or state.data.run_name=={}:
	1508	state.data.run = [str(state.data.name)]
	1509	state.data.run_name[0] = state.data.name
[b35d3d1]	1510
[c21e87b]	1511	if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D):
[028a0e8]	1512
[b35d3d1]	1513	data = state.data
	1514	doc, sasentry = self._to_xml_doc(data)
	1515	else:
	1516	data = state.data
	1517	doc, sasentry = self._data2d_to_xml_doc(data)
	1518
	1519
	1520	if state is not None:
	1521	state.toXML(doc=doc, file=data.name, entry_node=sasentry)
	1522
	1523	return doc
[2296316]	1524
	1525	# Simple html report templet
	1526	HEADER = "<html>\n"
	1527	HEADER += "<head>\n"
	1528	HEADER += "<meta http-equiv=Content-Type content='text/html; "
	1529	HEADER += "charset=windows-1252'> \n"
	1530	HEADER += "<meta name=Generator >\n"
	1531	HEADER += "</head>\n"
	1532	HEADER += "<body lang=EN-US>\n"
	1533	HEADER += "<div class=WordSection1>\n"
	1534	HEADER += "<p class=MsoNormal><b><span ><center>"
	1535	HEADER += "%s</center></span></center></b></p>"
	1536	HEADER += "<p class=MsoNormal> </p>"
	1537	PARA = "<p class=MsoNormal> %s \n"
	1538	PARA += "</p>"
	1539	CENTRE = "<p class=MsoNormal><center> %s \n"
	1540	CENTRE += "</center></p>"
	1541	FEET_1 = \
	1542	"""
	1543	<p class=MsoNormal> </p>
	1544	<p class=MsoNormal><b><span ><center> Graph</span></center></b></p>
	1545	<p class=MsoNormal> </p>
	1546	<center>
	1547	<br>Model Computation<br>
	1548	<br>Data: "%s"<br>
	1549	"""
	1550	FEET_2 = \
	1551	"""
	1552	<img src="%s" >
	1553	</img>
	1554	"""
	1555	FEET_3 = \
	1556	"""
	1557	</center>
	1558	</div>
	1559	</body>
	1560	</html>
	1561	"""
	1562	ELINE = "<p class=MsoNormal> </p>"
	1563
[3c44c66]	1564	if __name__ == "__main__":
	1565	state = PageState(parent=None)
	1566	#state.toXML()
	1567	"""
[5062bbf]	1568
[3c44c66]	1569	file = open("test_state", "w")
	1570	pickle.dump(state, file)
	1571	print pickle.dumps(state)
	1572	state.data_name = "hello---->"
	1573	pickle.dump(state, file)
	1574	file = open("test_state", "r")
	1575	new_state= pickle.load(file)
	1576	print "new state", new_state
	1577	new_state= pickle.load(file)
	1578	print "new state", new_state
	1579	#print "state", state
	1580	"""
	1581	import bsddb
	1582	import pickle
	1583	db= bsddb.btopen('file_state.db', 'c')
	1584	val = (pickle.dumps(state), "hello", "hi")
	1585	db['state1']= pickle.dumps(val)
	1586	print pickle.loads(db['state1'])
	1587	state.data_name = "hello---->22"
	1588	db['state2']= pickle.dumps(state)
	1589	state.data_name = "hello---->2"
	1590	db['state3']= pickle.dumps(state)
	1591	del db['state3']
	1592	state.data_name = "hello---->3"
	1593	db['state4']= pickle.dumps(state)
	1594	new_state = pickle.loads(db['state1'])
	1595	#print db.last()
	1596	db.set_location('state2')
	1597	state.data_name = "hello---->5"
	1598	db['aastate5']= pickle.dumps(state)
	1599	db.keys().sort()
	1600	print pickle.loads(db['state2'])
	1601
	1602	db.close()

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SasView

source: sasview/fittingview/src/sans/perspectives/fitting/pagestate.py @ c0a30a24

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