pagestate.py @ ab0b93f

ESS_GUIESS_GUI_DocsESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_iss959ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalcmagnetic_scattrelease-4.2.2ticket-1009ticket-1094-headlessticket-1242-2d-resolutionticket-1243ticket-1249ticket885unittest-saveload

Last change on this file since ab0b93f was 277257f, checked in by Paul Kienzle <pkienzle@…>, 7 years ago
clean up plugin-model handling code; preserve active parameter values when plugin is updated
Property mode set to `100644`
File size: 54.6 KB

Rev	Line
[959eb01]	1	"""
[ba8d326]	2	Class that holds a fit page state
[959eb01]	3	"""
	4	# TODO: Refactor code so we don't need to use getattr/setattr
	5	################################################################################
	6	# This software was developed by the University of Tennessee as part of the
	7	# Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
	8	# project funded by the US National Science Foundation.
	9	#
	10	# See the license text in license.txt
	11	#
	12	# copyright 2009, University of Tennessee
	13	################################################################################
	14	import time
	15	import os
	16	import sys
	17	import copy
	18	import logging
	19	import numpy as np
	20	import traceback
	21
	22	import xml.dom.minidom
	23	from xml.dom.minidom import parseString
[00f7ff1]	24	from xml.dom.minidom import getDOMImplementation
[959eb01]	25	from lxml import etree
	26
	27	from sasmodels import convert
	28	import sasmodels.weights
	29
[00f7ff1]	30	from sas.sasview import __version__ as SASVIEW_VERSION
	31
[959eb01]	32	import sas.sascalc.dataloader
	33	from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader
	34	from sas.sascalc.dataloader.readers.cansas_reader import get_content, write_node
	35	from sas.sascalc.dataloader.data_info import Data2D, Collimation, Detector
	36	from sas.sascalc.dataloader.data_info import Process, Aperture
	37
	38	logger = logging.getLogger(__name__)
	39
	40	# Information to read/write state as xml
	41	FITTING_NODE_NAME = 'fitting_plug_in'
[ba8d326]	42	CANSAS_NS = {"ns": "cansas1d/1.0"}
[959eb01]	43
	44	CUSTOM_MODEL = 'Plugin Models'
	45	CUSTOM_MODEL_OLD = 'Customized Models'
	46
	47	LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"],
	48	["group_id", "data_group_id", "string"],
	49	["data_name", "data_name", "string"],
	50	["data_id", "data_id", "string"],
	51	["name", "name", "string"],
	52	["data_name", "data_name", "string"]]
	53	LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"],
	54	["qmax", "qmax", "float"],
	55	["npts", "npts", "float"],
	56	["categorycombobox", "categorycombobox", "string"],
	57	["formfactorcombobox", "formfactorcombobox",
	58	"string"],
	59	["structurecombobox", "structurecombobox",
	60	"string"],
	61	["multi_factor", "multi_factor", "float"],
	62	["magnetic_on", "magnetic_on", "bool"],
	63	["enable_smearer", "enable_smearer", "bool"],
	64	["disable_smearer", "disable_smearer", "bool"],
	65	["pinhole_smearer", "pinhole_smearer", "bool"],
	66	["slit_smearer", "slit_smearer", "bool"],
	67	["enable_disp", "enable_disp", "bool"],
	68	["disable_disp", "disable_disp", "bool"],
	69	["dI_noweight", "dI_noweight", "bool"],
	70	["dI_didata", "dI_didata", "bool"],
	71	["dI_sqrdata", "dI_sqrdata", "bool"],
	72	["dI_idata", "dI_idata", "bool"],
	73	["enable2D", "enable2D", "bool"],
	74	["cb1", "cb1", "bool"],
	75	["tcChi", "tcChi", "float"],
	76	["dq_l", "dq_l", "float"],
	77	["dq_r", "dq_r", "float"],
	78	["dx_percent", "dx_percent", "float"],
	79	["dxl", "dxl", "float"],
	80	["dxw", "dxw", "float"]]
	81
	82	LIST_OF_MODEL_ATTRIBUTES = [["values", "values"],
	83	["weights", "weights"]]
	84
[ba8d326]	85	DISPERSION_LIST = [["disp_obj_dict", "disp_obj_dict", "string"]]
[959eb01]	86
	87	LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"],
	88	["str_parameters", "str_parameters"],
	89	["orientation_parameters", "orientation_params"],
	90	["dispersity_parameters",
	91	"orientation_params_disp"],
	92	["fixed_param", "fixed_param"],
	93	["fittable_param", "fittable_param"]]
	94	LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"],
	95	["xmax", "xmax", "float"],
	96	["ymin", "ymin", "float"],
	97	["ymax", "ymax", "float"],
	98	["_xaxis", "_xaxis", "string"],
	99	["_xunit", "_xunit", "string"],
	100	["_yaxis", "_yaxis", "string"],
	101	["_yunit", "_yunit", "string"],
	102	["_zaxis", "_zaxis", "string"],
	103	["_zunit", "_zunit", "string"]]
	104	LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"],
	105	["qy_data", "qy_data", "float"],
	106	["dqx_data", "dqx_data", "float"],
	107	["dqy_data", "dqy_data", "float"],
	108	["data", "data", "float"],
	109	["q_data", "q_data", "float"],
	110	["err_data", "err_data", "float"],
	111	["mask", "mask", "bool"]]
	112
	113
	114	def parse_entry_helper(node, item):
	115	"""
	116	Create a numpy list from value extrated from the node
	117
	118	:param node: node from each the value is stored
	119	:param item: list name of three strings.the two first are name of data
	120	attribute and the third one is the type of the value of that
	121	attribute. type can be string, float, bool, etc.
	122
	123	: return: numpy array
	124	"""
	125	if node is not None:
	126	if item[2] == "string":
	127	return str(node.get(item[0]).strip())
	128	elif item[2] == "bool":
	129	try:
	130	return node.get(item[0]).strip() == "True"
	131	except Exception:
	132	return None
	133	else:
	134	try:
	135	return float(node.get(item[0]))
	136	except Exception:
	137	return None
	138
	139
	140	class PageState(object):
	141	"""
	142	Contains information to reconstruct a page of the fitpanel.
	143	"""
[00f7ff1]	144	def __init__(self, model=None, data=None):
[959eb01]	145	"""
	146	Initialize the current state
	147
	148	:param model: a selected model within a page
	149	:param data:
	150
	151	"""
	152	self.file = None
	153	# Time of state creation
	154	self.timestamp = time.time()
	155	# Data member to store the dispersion object created
[ba8d326]	156	self.disp_obj_dict = {}
[959eb01]	157	# ------------------------
	158	# Data used for fitting
	159	self.data = data
	160	# model data
	161	self.theory_data = None
	162	# Is 2D
	163	self.is_2D = False
	164	self.images = None
	165
	166	# save additional information on data that dataloader.reader
	167	# does not read
	168	self.is_data = None
	169	self.data_name = ""
	170
	171	if self.data is not None:
	172	self.data_name = self.data.name
	173	self.data_id = None
	174	if self.data is not None and hasattr(self.data, "id"):
	175	self.data_id = self.data.id
	176	self.data_group_id = None
	177	if self.data is not None and hasattr(self.data, "group_id"):
	178	self.data_group_id = self.data.group_id
	179
	180	# reset True change the state of existing button
	181	self.reset = False
	182
	183	# flag to allow data2D plot
	184	self.enable2D = False
	185	# model on which the fit would be performed
	186	self.model = model
	187	self.m_name = None
	188	# list of process done to model
	189	self.process = []
	190	# fit page manager
	191	self.manager = None
	192	# Event_owner is the owner of model event
	193	self.event_owner = None
	194	# page name
	195	self.page_name = ""
	196	# Contains link between model, its parameters, and panel organization
	197	self.parameters = []
	198	# String parameter list that can not be fitted
	199	self.str_parameters = []
	200	# Contains list of parameters that cannot be fitted and reference to
	201	# panel objects
	202	self.fixed_param = []
	203	# Contains list of parameters with dispersity and reference to
	204	# panel objects
	205	self.fittable_param = []
	206	# orientation parameters
	207	self.orientation_params = []
	208	# orientation parameters for gaussian dispersity
	209	self.orientation_params_disp = []
	210	self.dq_l = None
	211	self.dq_r = None
	212	self.dx_percent = None
	213	self.dx_old = False
	214	self.dxl = None
	215	self.dxw = None
	216	# list of dispersion parameters
	217	self.disp_list = []
	218	if self.model is not None:
	219	self.disp_list = self.model.getDispParamList()
	220
	221	self.disp_cb_dict = {}
	222	self.values = {}
	223	self.weights = {}
	224
	225	# contains link between a model and selected parameters to fit
	226	self.param_toFit = []
	227	# save the state of the context menu
	228	self.saved_states = {}
	229	# save selection of combobox
	230	self.formfactorcombobox = None
	231	self.categorycombobox = None
	232	self.structurecombobox = None
	233
	234	# radio box to select type of model
	235	# self.shape_rbutton = False
	236	# self.shape_indep_rbutton = False
	237	# self.struct_rbutton = False
	238	# self.plugin_rbutton = False
	239	# the indice of the current selection
	240	self.disp_box = 0
	241	# Qrange
	242	# Q range
	243	self.qmin = 0.001
	244	self.qmax = 0.1
	245	# reset data range
	246	self.qmax_x = None
	247	self.qmin_x = None
	248
	249	self.npts = None
	250	self.name = ""
	251	self.multi_factor = None
	252	self.magnetic_on = False
	253	# enable smearering state
	254	self.enable_smearer = False
	255	self.disable_smearer = True
	256	self.pinhole_smearer = False
	257	self.slit_smearer = False
	258	# weighting options
	259	self.dI_noweight = False
	260	self.dI_didata = True
	261	self.dI_sqrdata = False
	262	self.dI_idata = False
	263	# disperity selection
	264	self.enable_disp = False
	265	self.disable_disp = True
	266
	267	# state of selected all check button
	268	self.cb1 = False
	269	# store value of chisqr
	270	self.tcChi = None
[ba8d326]	271	self.version = (1, 0, 0)
[959eb01]	272
	273	def clone(self):
	274	"""
	275	Create a new copy of the current object
	276	"""
	277	model = None
	278	if self.model is not None:
	279	model = self.model.clone()
	280	model.name = self.model.name
[00f7ff1]	281	obj = PageState(model=model)
[959eb01]	282	obj.file = copy.deepcopy(self.file)
	283	obj.data = copy.deepcopy(self.data)
	284	if self.data is not None:
	285	self.data_name = self.data.name
	286	obj.data_name = self.data_name
	287	obj.is_data = self.is_data
	288
	289	obj.categorycombobox = self.categorycombobox
	290	obj.formfactorcombobox = self.formfactorcombobox
	291	obj.structurecombobox = self.structurecombobox
	292
	293	# obj.shape_rbutton = self.shape_rbutton
	294	# obj.shape_indep_rbutton = self.shape_indep_rbutton
	295	# obj.struct_rbutton = self.struct_rbutton
	296	# obj.plugin_rbutton = self.plugin_rbutton
	297
	298	obj.manager = self.manager
	299	obj.event_owner = self.event_owner
	300	obj.disp_list = copy.deepcopy(self.disp_list)
	301
	302	obj.enable2D = copy.deepcopy(self.enable2D)
	303	obj.parameters = copy.deepcopy(self.parameters)
	304	obj.str_parameters = copy.deepcopy(self.str_parameters)
	305	obj.fixed_param = copy.deepcopy(self.fixed_param)
	306	obj.fittable_param = copy.deepcopy(self.fittable_param)
	307	obj.orientation_params = copy.deepcopy(self.orientation_params)
	308	obj.orientation_params_disp = \
	309	copy.deepcopy(self.orientation_params_disp)
	310	obj.enable_disp = copy.deepcopy(self.enable_disp)
	311	obj.disable_disp = copy.deepcopy(self.disable_disp)
	312	obj.tcChi = self.tcChi
	313
[ba8d326]	314	if len(self.disp_obj_dict) > 0:
	315	for k, v in self.disp_obj_dict.iteritems():
	316	obj.disp_obj_dict[k] = v
[959eb01]	317	if len(self.disp_cb_dict) > 0:
	318	for k, v in self.disp_cb_dict.iteritems():
	319	obj.disp_cb_dict[k] = v
	320	if len(self.values) > 0:
	321	for k, v in self.values.iteritems():
	322	obj.values[k] = v
	323	if len(self.weights) > 0:
	324	for k, v in self.weights.iteritems():
	325	obj.weights[k] = v
	326	obj.enable_smearer = copy.deepcopy(self.enable_smearer)
	327	obj.disable_smearer = copy.deepcopy(self.disable_smearer)
	328	obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer)
	329	obj.slit_smearer = copy.deepcopy(self.slit_smearer)
	330	obj.dI_noweight = copy.deepcopy(self.dI_noweight)
	331	obj.dI_didata = copy.deepcopy(self.dI_didata)
	332	obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata)
	333	obj.dI_idata = copy.deepcopy(self.dI_idata)
	334	obj.dq_l = copy.deepcopy(self.dq_l)
	335	obj.dq_r = copy.deepcopy(self.dq_r)
	336	obj.dx_percent = copy.deepcopy(self.dx_percent)
	337	obj.dx_old = copy.deepcopy(self.dx_old)
	338	obj.dxl = copy.deepcopy(self.dxl)
	339	obj.dxw = copy.deepcopy(self.dxw)
	340	obj.disp_box = copy.deepcopy(self.disp_box)
	341	obj.qmin = copy.deepcopy(self.qmin)
	342	obj.qmax = copy.deepcopy(self.qmax)
	343	obj.multi_factor = self.multi_factor
	344	obj.magnetic_on = self.magnetic_on
	345	obj.npts = copy.deepcopy(self.npts)
	346	obj.cb1 = copy.deepcopy(self.cb1)
	347	obj.version = copy.deepcopy(self.version)
	348
	349	for name, state in self.saved_states.iteritems():
	350	copy_name = copy.deepcopy(name)
	351	copy_state = state.clone()
	352	obj.saved_states[copy_name] = copy_state
	353	return obj
	354
	355	def _old_first_model(self):
	356	"""
	357	Handle save states from 4.0.1 and before where the first item in the
	358	selection boxes of category, formfactor and structurefactor were not
	359	saved.
	360	:return: None
	361	"""
	362	if self.categorycombobox == CUSTOM_MODEL_OLD:
	363	self.categorycombobox = CUSTOM_MODEL
	364	if self.formfactorcombobox == '':
	365	FIRST_FORM = {
	366	'Shapes' : 'BCCrystalModel',
	367	'Uncategorized' : 'LineModel',
	368	'StructureFactor' : 'HardsphereStructure',
	369	'Ellipsoid' : 'core_shell_ellipsoid',
	370	'Lamellae' : 'lamellar',
	371	'Paracrystal' : 'bcc_paracrystal',
	372	'Parallelepiped' : 'core_shell_parallelepiped',
	373	'Shape Independent' : 'be_polyelectrolyte',
	374	'Sphere' : 'adsorbed_layer',
	375	'Structure Factor' : 'hardsphere',
	376	CUSTOM_MODEL : ''
	377	}
	378	if self.categorycombobox == '':
	379	if len(self.parameters) == 3:
	380	self.categorycombobox = "Shape-Independent"
	381	self.formfactorcombobox = 'PowerLawAbsModel'
	382	elif len(self.parameters) == 9:
	383	self.categorycombobox = 'Cylinder'
	384	self.formfactorcombobox = 'barbell'
	385	else:
	386	msg = "Save state does not have enough information to load"
	387	msg += " the all of the data."
	388	logger.warning(msg=msg)
	389	else:
	390	self.formfactorcombobox = FIRST_FORM[self.categorycombobox]
	391
	392	@staticmethod
	393	def param_remap_to_sasmodels_convert(params, is_string=False):
	394	"""
	395	Remaps the parameters for sasmodels conversion
	396
	397	:param params: list of parameters (likely self.parameters)
	398	:return: remapped dictionary of parameters
	399	"""
	400	p = dict()
	401	for fittable, name, value, _, uncert, lower, upper, units in params:
	402	if not value:
	403	value = np.nan
	404	if not uncert or uncert[1] == '' or uncert[1] == 'None':
	405	uncert[0] = False
	406	uncert[1] = np.nan
	407	if not upper or upper[1] == '' or upper[1] == 'None':
	408	upper[0] = False
	409	upper[1] = np.nan
	410	if not lower or lower[1] == '' or lower[1] == 'None':
	411	lower[0] = False
	412	lower[1] = np.nan
	413	if is_string:
	414	p[name] = str(value)
	415	else:
	416	p[name] = float(value)
	417	p[name + ".fittable"] = bool(fittable)
	418	p[name + ".std"] = float(uncert[1])
	419	p[name + ".upper"] = float(upper[1])
	420	p[name + ".lower"] = float(lower[1])
	421	p[name + ".units"] = units
	422	return p
	423
	424	@staticmethod
	425	def param_remap_from_sasmodels_convert(params):
	426	"""
	427	Converts {name : value} map back to [] param list
	428	:param params: parameter map returned from sasmodels
	429	:return: None
	430	"""
	431	p_map = []
	432	for name, info in params.iteritems():
	433	if ".fittable" in name or ".std" in name or ".upper" in name or \
	434	".lower" in name or ".units" in name:
	435	pass
	436	else:
	437	fittable = params.get(name + ".fittable", True)
	438	std = params.get(name + ".std", '0.0')
	439	upper = params.get(name + ".upper", 'inf')
	440	lower = params.get(name + ".lower", '-inf')
	441	units = params.get(name + ".units")
	442	if std is not None and std is not np.nan:
	443	std = [True, str(std)]
	444	else:
	445	std = [False, '']
	446	if lower is not None and lower is not np.nan:
	447	lower = [True, str(lower)]
	448	else:
	449	lower = [True, '-inf']
	450	if upper is not None and upper is not np.nan:
	451	upper = [True, str(upper)]
	452	else:
	453	upper = [True, 'inf']
	454	param_list = [bool(fittable), str(name), str(info),
	455	"+/-", std, lower, upper, str(units)]
	456	p_map.append(param_list)
	457	return p_map
	458
	459	def _convert_to_sasmodels(self):
	460	"""
	461	Convert parameters to a form usable by sasmodels converter
	462
	463	:return: None
	464	"""
	465	# Create conversion dictionary to send to sasmodels
	466	self._old_first_model()
	467	p = self.param_remap_to_sasmodels_convert(self.parameters)
	468	structurefactor, params = convert.convert_model(self.structurecombobox,
	469	p, False, self.version)
	470	formfactor, params = convert.convert_model(self.formfactorcombobox,
	471	params, False, self.version)
	472	if len(self.str_parameters) > 0:
	473	str_pars = self.param_remap_to_sasmodels_convert(
	474	self.str_parameters, True)
	475	formfactor, str_params = convert.convert_model(
	476	self.formfactorcombobox, str_pars, False, self.version)
	477	for key, value in str_params.iteritems():
	478	params[key] = value
	479
	480	if self.formfactorcombobox == 'SphericalSLDModel':
	481	self.multi_factor += 1
	482	self.formfactorcombobox = formfactor
	483	self.structurecombobox = structurefactor
	484	self.parameters = []
	485	self.parameters = self.param_remap_from_sasmodels_convert(params)
	486
	487	def _repr_helper(self, list, rep):
	488	"""
	489	Helper method to print a state
	490	"""
	491	for item in list:
	492	rep += "parameter name: %s \n" % str(item[1])
	493	rep += "value: %s\n" % str(item[2])
	494	rep += "selected: %s\n" % str(item[0])
	495	rep += "error displayed : %s \n" % str(item[4][0])
	496	rep += "error value:%s \n" % str(item[4][1])
	497	rep += "minimum displayed : %s \n" % str(item[5][0])
	498	rep += "minimum value : %s \n" % str(item[5][1])
	499	rep += "maximum displayed : %s \n" % str(item[6][0])
	500	rep += "maximum value : %s \n" % str(item[6][1])
	501	rep += "parameter unit: %s\n\n" % str(item[7])
	502	return rep
	503
	504	def __repr__(self):
	505	"""
	506	output string for printing
	507	"""
	508	rep = "\nState name: %s\n" % self.file
	509	t = time.localtime(self.timestamp)
[78312f7]	510	time_str = time.strftime("%b %d %Y %H:%M:%S ", t)
[959eb01]	511
	512	rep += "State created: %s\n" % time_str
	513	rep += "State form factor combobox selection: %s\n" % \
	514	self.formfactorcombobox
	515	rep += "State structure factor combobox selection: %s\n" % \
	516	self.structurecombobox
	517	rep += "is data : %s\n" % self.is_data
	518	rep += "data's name : %s\n" % self.data_name
	519	rep += "data's id : %s\n" % self.data_id
	520	if self.model is not None:
	521	m_name = self.model.__class__.__name__
	522	if m_name == 'Model':
	523	m_name = self.m_name
	524	rep += "model name : %s\n" % m_name
	525	else:
	526	rep += "model name : None\n"
	527	rep += "multi_factor : %s\n" % str(self.multi_factor)
	528	rep += "magnetic_on : %s\n" % str(self.magnetic_on)
	529	rep += "model type (Category) selected: %s\n" % self.categorycombobox
	530	rep += "data : %s\n" % str(self.data)
	531	rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % \
	532	(str(self.qmin), str(self.qmax), str(self.npts))
	533	rep += "Dispersion selection : %s\n" % str(self.disp_box)
	534	rep += "Smearing enable : %s\n" % str(self.enable_smearer)
	535	rep += "Smearing disable : %s\n" % str(self.disable_smearer)
	536	rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer)
	537	rep += "Slit smearer enable : %s\n" % str(self.slit_smearer)
	538	rep += "Dispersity enable : %s\n" % str(self.enable_disp)
	539	rep += "Dispersity disable : %s\n" % str(self.disable_disp)
	540	rep += "Slit smearer enable: %s\n" % str(self.slit_smearer)
	541
	542	rep += "dI_noweight : %s\n" % str(self.dI_noweight)
	543	rep += "dI_didata : %s\n" % str(self.dI_didata)
	544	rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata)
	545	rep += "dI_idata : %s\n" % str(self.dI_idata)
	546
	547	rep += "2D enable : %s\n" % str(self.enable2D)
	548	rep += "All parameters checkbox selected: %s\n" % self.cb1
	549	rep += "Value of Chisqr : %s\n" % str(self.tcChi)
	550	rep += "dq_l : %s\n" % self.dq_l
	551	rep += "dq_r : %s\n" % self.dq_r
	552	rep += "dx_percent : %s\n" % str(self.dx_percent)
	553	rep += "dxl : %s\n" % str(self.dxl)
	554	rep += "dxw : %s\n" % str(self.dxw)
	555	rep += "model : %s\n\n" % str(self.model)
	556	temp_parameters = []
	557	temp_fittable_param = []
	558	if self.data.__class__.__name__ == "Data2D":
	559	self.is_2D = True
	560	else:
	561	self.is_2D = False
	562	if self.data is not None:
	563	if not self.is_2D:
	564	for item in self.parameters:
	565	if item not in self.orientation_params:
	566	temp_parameters.append(item)
	567	for item in self.fittable_param:
	568	if item not in self.orientation_params_disp:
	569	temp_fittable_param.append(item)
	570	else:
	571	temp_parameters = self.parameters
	572	temp_fittable_param = self.fittable_param
	573
	574	rep += "number parameters(self.parameters): %s\n" % \
	575	len(temp_parameters)
	576	rep = self._repr_helper(list=temp_parameters, rep=rep)
	577	rep += "number str_parameters(self.str_parameters): %s\n" % \
	578	len(self.str_parameters)
	579	rep = self._repr_helper(list=self.str_parameters, rep=rep)
	580	rep += "number fittable_param(self.fittable_param): %s\n" % \
	581	len(temp_fittable_param)
	582	rep = self._repr_helper(list=temp_fittable_param, rep=rep)
	583	return rep
	584
[78312f7]	585	def _get_report_string(self):
[959eb01]	586	"""
	587	Get the values (strings) from __str__ for report
	588	"""
	589	# Dictionary of the report strings
	590	repo_time = ""
	591	model_name = ""
	592	title = ""
	593	title_name = ""
	594	file_name = ""
	595	param_string = ""
	596	paramval_string = ""
	597	chi2_string = ""
	598	q_range = ""
	599	strings = self.__repr__()
[78312f7]	600	fixed_parameter = False
[959eb01]	601	lines = strings.split('\n')
	602	# get all string values from __str__()
	603	for line in lines:
[78312f7]	604	# Skip lines which are not key: value pairs, which includes
	605	# blank lines and freeform notes in SASNotes fields.
	606	if not ':' in line:
	607	#msg = "Report string expected 'name: value' but got %r" % line
	608	#logger.error(msg)
	609	continue
	610
	611	name, value = [s.strip() for s in line.split(":", 1)]
	612	if name == "State created":
	613	repo_time = value
	614	elif name == "parameter name":
[959eb01]	615	val_name = value.split(".")
	616	if len(val_name) > 1:
	617	if val_name[1].count("width"):
	618	param_string += value + ','
	619	else:
	620	continue
	621	else:
	622	param_string += value + ','
[78312f7]	623	elif name == "value":
[959eb01]	624	param_string += value + ','
[78312f7]	625	elif name == "selected":
	626	# remember if it is fixed when reporting error value
	627	fixed_parameter = (value == u'False')
	628	elif name == "error value":
[959eb01]	629	if fixed_parameter:
	630	param_string += '(fixed),'
	631	else:
	632	param_string += value + ','
[78312f7]	633	elif name == "parameter unit":
[959eb01]	634	param_string += value + ':'
[78312f7]	635	elif name == "Value of Chisqr":
[959eb01]	636	chi2 = ("Chi2/Npts = " + value)
	637	chi2_string = CENTRE % chi2
[78312f7]	638	elif name == "Title":
[959eb01]	639	if len(value.strip()) == 0:
	640	continue
	641	title = value + " [" + repo_time + "]"
	642	title_name = HEADER % title
[78312f7]	643	elif name == "data":
[959eb01]	644	try:
[78312f7]	645	# parsing "data : File: filename [mmm dd hh:mm]"
	646	name = value.split(':', 1)[1].strip()
	647	file_value = "File name:" + name
[959eb01]	648	file_name = CENTRE % file_value
	649	if len(title) == 0:
[78312f7]	650	title = name + " [" + repo_time + "]"
[959eb01]	651	title_name = HEADER % title
	652	except Exception:
	653	msg = "While parsing 'data: ...'\n"
	654	logger.error(msg + traceback.format_exc())
[78312f7]	655	elif name == "model name":
[959eb01]	656	try:
[78312f7]	657	modelname = "Model name:" + value
	658	except Exception:
[959eb01]	659	modelname = "Model name:" + " NAN"
	660	model_name = CENTRE % modelname
	661
[78312f7]	662	elif name == "Plotting Range":
[959eb01]	663	try:
[78312f7]	664	parts = value.split(':')
	665	q_range = parts[0] + " = " + parts[1] \
	666	+ " = " + parts[2].split(",")[0]
[959eb01]	667	q_name = ("Q Range: " + q_range)
	668	q_range = CENTRE % q_name
	669	except Exception:
	670	msg = "While parsing 'Plotting Range: ...'\n"
	671	logger.error(msg + traceback.format_exc())
[78312f7]	672
[959eb01]	673	paramval = ""
	674	for lines in param_string.split(":"):
	675	line = lines.split(",")
	676	if len(lines) > 0:
	677	param = line[0]
	678	param += " = " + line[1]
	679	if len(line[2].split()) > 0 and not line[2].count("None"):
	680	param += " +- " + line[2]
	681	if len(line[3].split()) > 0 and not line[3].count("None"):
	682	param += " " + line[3]
	683	if not paramval.count(param):
	684	paramval += param + "\n"
	685	paramval_string += CENTRE % param + "\n"
	686
	687	text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % \
	688	(title, file, q_name, chi2, paramval)
	689
	690	title_name = self._check_html_format(title_name)
	691	file_name = self._check_html_format(file_name)
	692	title = self._check_html_format(title)
	693
	694	html_string = title_name + "\n" + file_name + \
	695	"\n" + model_name + \
	696	"\n" + q_range + \
	697	"\n" + chi2_string + \
	698	"\n" + ELINE + \
	699	"\n" + paramval_string + \
	700	"\n" + ELINE + \
[78312f7]	701	"\n" + FEET_1 % title
[959eb01]	702
	703	return html_string, text_string, title
	704
	705	def _check_html_format(self, name):
	706	"""
	707	Check string '%' for html format
	708	"""
	709	if name.count('%'):
	710	name = name.replace('%', '&#37')
	711
	712	return name
	713
[78312f7]	714	def report(self, fig_urls):
[959eb01]	715	"""
	716	Invoke report dialog panel
	717
	718	: param figs: list of pylab figures [list]
	719	"""
	720	# get the strings for report
[78312f7]	721	html_str, text_str, title = self._get_report_string()
[959eb01]	722	# Allow 2 figures to append
[78312f7]	723	image_links = [FEET_2%fig for fig in fig_urls]
[959eb01]	724
	725	# final report html strings
[78312f7]	726	report_str = html_str + ELINE.join(image_links)
[959eb01]	727
[78312f7]	728	return report_str, text_str
[959eb01]	729
	730	def _to_xml_helper(self, thelist, element, newdoc):
	731	"""
	732	Helper method to create xml file for saving state
	733	"""
	734	for item in thelist:
	735	sub_element = newdoc.createElement('parameter')
	736	sub_element.setAttribute('name', str(item[1]))
	737	sub_element.setAttribute('value', str(item[2]))
	738	sub_element.setAttribute('selected_to_fit', str(item[0]))
	739	sub_element.setAttribute('error_displayed', str(item[4][0]))
	740	sub_element.setAttribute('error_value', str(item[4][1]))
	741	sub_element.setAttribute('minimum_displayed', str(item[5][0]))
	742	sub_element.setAttribute('minimum_value', str(item[5][1]))
	743	sub_element.setAttribute('maximum_displayed', str(item[6][0]))
	744	sub_element.setAttribute('maximum_value', str(item[6][1]))
	745	sub_element.setAttribute('unit', str(item[7]))
	746	element.appendChild(sub_element)
	747
	748	def to_xml(self, file="fitting_state.fitv", doc=None,
	749	entry_node=None, batch_fit_state=None):
	750	"""
	751	Writes the state of the fit panel to file, as XML.
	752
	753	Compatible with standalone writing, or appending to an
	754	already existing XML document. In that case, the XML document is
	755	required. An optional entry node in the XML document may also be given.
	756
	757	:param file: file to write to
	758	:param doc: XML document object [optional]
	759	:param entry_node: XML node within the XML document at which we
	760	will append the data [optional]
	761	:param batch_fit_state: simultaneous fit state
	762	"""
	763	# Check whether we have to write a standalone XML file
	764	if doc is None:
	765	impl = getDOMImplementation()
	766	doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0")
	767	newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type)
	768	top_element = newdoc.documentElement
	769	else:
	770	# We are appending to an existing document
	771	newdoc = doc
	772	try:
	773	top_element = newdoc.createElement(FITTING_NODE_NAME)
[78312f7]	774	except Exception:
[959eb01]	775	string = etree.tostring(doc, pretty_print=True)
	776	newdoc = parseString(string)
	777	top_element = newdoc.createElement(FITTING_NODE_NAME)
	778	if entry_node is None:
	779	newdoc.documentElement.appendChild(top_element)
	780	else:
	781	try:
	782	entry_node.appendChild(top_element)
[78312f7]	783	except Exception:
[959eb01]	784	node_name = entry_node.tag
	785	node_list = newdoc.getElementsByTagName(node_name)
	786	entry_node = node_list.item(0)
	787	entry_node.appendChild(top_element)
	788
	789	attr = newdoc.createAttribute("version")
[00f7ff1]	790	attr.nodeValue = SASVIEW_VERSION
[959eb01]	791	# attr.nodeValue = '1.0'
	792	top_element.setAttributeNode(attr)
	793
	794	# File name
	795	element = newdoc.createElement("filename")
	796	if self.file is not None:
	797	element.appendChild(newdoc.createTextNode(str(self.file)))
	798	else:
	799	element.appendChild(newdoc.createTextNode(str(file)))
	800	top_element.appendChild(element)
	801
	802	element = newdoc.createElement("timestamp")
	803	element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp)))
	804	attr = newdoc.createAttribute("epoch")
	805	attr.nodeValue = str(self.timestamp)
	806	element.setAttributeNode(attr)
	807	top_element.appendChild(element)
	808
	809	# Inputs
	810	inputs = newdoc.createElement("Attributes")
	811	top_element.appendChild(inputs)
	812
	813	if self.data is not None and hasattr(self.data, "group_id"):
	814	self.data_group_id = self.data.group_id
	815	if self.data is not None and hasattr(self.data, "is_data"):
	816	self.is_data = self.data.is_data
	817	if self.data is not None:
	818	self.data_name = self.data.name
	819	if self.data is not None and hasattr(self.data, "id"):
	820	self.data_id = self.data.id
	821
	822	for item in LIST_OF_DATA_ATTRIBUTES:
	823	element = newdoc.createElement(item[0])
	824	element.setAttribute(item[0], str(getattr(self, item[1])))
	825	inputs.appendChild(element)
	826
	827	for item in LIST_OF_STATE_ATTRIBUTES:
	828	element = newdoc.createElement(item[0])
	829	element.setAttribute(item[0], str(getattr(self, item[1])))
	830	inputs.appendChild(element)
	831
	832	# For self.values ={ disp_param_name: [vals,...],...}
	833	# and for self.weights ={ disp_param_name: [weights,...],...}
	834	for item in LIST_OF_MODEL_ATTRIBUTES:
	835	element = newdoc.createElement(item[0])
	836	value_list = getattr(self, item[1])
	837	for key, value in value_list.iteritems():
	838	sub_element = newdoc.createElement(key)
	839	sub_element.setAttribute('name', str(key))
	840	for val in value:
	841	sub_element.appendChild(newdoc.createTextNode(str(val)))
	842
	843	element.appendChild(sub_element)
	844	inputs.appendChild(element)
	845
[ba8d326]	846	# Create doc for the dictionary of self.disp_obj_dic
[959eb01]	847	for tagname, varname, tagtype in DISPERSION_LIST:
	848	element = newdoc.createElement(tagname)
	849	value_list = getattr(self, varname)
	850	for key, value in value_list.iteritems():
	851	sub_element = newdoc.createElement(key)
	852	sub_element.setAttribute('name', str(key))
	853	sub_element.setAttribute('value', str(value))
	854	element.appendChild(sub_element)
	855	inputs.appendChild(element)
	856
	857	for item in LIST_OF_STATE_PARAMETERS:
	858	element = newdoc.createElement(item[0])
	859	self._to_xml_helper(thelist=getattr(self, item[1]),
	860	element=element, newdoc=newdoc)
	861	inputs.appendChild(element)
	862
	863	# Combined and Simultaneous Fit Parameters
	864	if batch_fit_state is not None:
	865	batch_combo = newdoc.createElement('simultaneous_fit')
	866	top_element.appendChild(batch_combo)
	867
	868	# Simultaneous Fit Number For Linking Later
	869	element = newdoc.createElement('sim_fit_number')
	870	element.setAttribute('fit_number', str(batch_fit_state.fit_page_no))
	871	batch_combo.appendChild(element)
	872
	873	# Save constraints
	874	constraints = newdoc.createElement('constraints')
	875	batch_combo.appendChild(constraints)
	876	for constraint in batch_fit_state.constraints_list:
	877	if constraint.model_cbox.GetValue() != "":
	878	# model_cbox, param_cbox, egal_txt, constraint,
	879	# btRemove, sizer
	880	doc_cons = newdoc.createElement('constraint')
	881	doc_cons.setAttribute('model_cbox',
	882	str(constraint.model_cbox.GetValue()))
	883	doc_cons.setAttribute('param_cbox',
	884	str(constraint.param_cbox.GetValue()))
	885	doc_cons.setAttribute('egal_txt',
	886	str(constraint.egal_txt.GetLabel()))
	887	doc_cons.setAttribute('constraint',
	888	str(constraint.constraint.GetValue()))
	889	constraints.appendChild(doc_cons)
	890
	891	# Save all models
	892	models = newdoc.createElement('model_list')
	893	batch_combo.appendChild(models)
	894	for model in batch_fit_state.model_list:
	895	doc_model = newdoc.createElement('model_list_item')
	896	doc_model.setAttribute('checked', str(model[0].GetValue()))
	897	keys = model[1].keys()
	898	doc_model.setAttribute('name', str(keys[0]))
	899	values = model[1].get(keys[0])
	900	doc_model.setAttribute('fit_number', str(model[2]))
	901	doc_model.setAttribute('fit_page_source', str(model[3]))
	902	doc_model.setAttribute('model_name', str(values.model.id))
	903	models.appendChild(doc_model)
	904
	905	# Select All Checkbox
	906	element = newdoc.createElement('select_all')
	907	if batch_fit_state.select_all:
	908	element.setAttribute('checked', 'True')
	909	else:
	910	element.setAttribute('checked', 'False')
	911	batch_combo.appendChild(element)
	912
	913	# Save the file
	914	if doc is None:
	915	fd = open(file, 'w')
	916	fd.write(newdoc.toprettyxml())
	917	fd.close()
	918	return None
	919	else:
	920	return newdoc
	921
	922	def _from_xml_helper(self, node, list):
	923	"""
	924	Helper function to write state to xml
	925	"""
	926	for item in node:
[ba8d326]	927	name = item.get('name')
	928	value = item.get('value')
	929	selected_to_fit = (item.get('selected_to_fit') == "True")
	930	error_displayed = (item.get('error_displayed') == "True")
	931	error_value = item.get('error_value')
	932	minimum_displayed = (item.get('minimum_displayed') == "True")
	933	minimum_value = item.get('minimum_value')
	934	maximum_displayed = (item.get('maximum_displayed') == "True")
	935	maximum_value = item.get('maximum_value')
	936	unit = item.get('unit')
[959eb01]	937	list.append([selected_to_fit, name, value, "+/-",
	938	[error_displayed, error_value],
	939	[minimum_displayed, minimum_value],
	940	[maximum_displayed, maximum_value], unit])
	941
	942	def from_xml(self, file=None, node=None):
	943	"""
	944	Load fitting state from a file
	945
	946	:param file: .fitv file
	947	:param node: node of a XML document to read from
	948	"""
	949	if file is not None:
	950	msg = "PageState no longer supports non-CanSAS"
	951	msg += " format for fitting files"
	952	raise RuntimeError, msg
	953
	954	if node.get('version'):
	955	# Get the version for model conversion purposes
	956	self.version = tuple(int(e) for e in
	957	str.split(node.get('version'), "."))
	958	# The tuple must be at least 3 items long
	959	while len(self.version) < 3:
	960	ver_list = list(self.version)
	961	ver_list.append(0)
	962	self.version = tuple(ver_list)
	963
	964	# Get file name
	965	entry = get_content('ns:filename', node)
[277257f]	966	if entry is not None and entry.text:
[959eb01]	967	self.file = entry.text.strip()
[277257f]	968	else:
	969	self.file = ''
[959eb01]	970
	971	# Get time stamp
	972	entry = get_content('ns:timestamp', node)
	973	if entry is not None and entry.get('epoch'):
	974	try:
	975	self.timestamp = float(entry.get('epoch'))
[78312f7]	976	except Exception:
[959eb01]	977	msg = "PageState.fromXML: Could not"
	978	msg += " read timestamp\n %s" % sys.exc_value
	979	logger.error(msg)
	980
	981	if entry is not None:
	982	# Parse fitting attributes
	983	entry = get_content('ns:Attributes', node)
	984	for item in LIST_OF_DATA_ATTRIBUTES:
	985	node = get_content('ns:%s' % item[0], entry)
	986	setattr(self, item[0], parse_entry_helper(node, item))
	987
	988	dx_old_node = get_content('ns:%s' % 'dx_min', entry)
	989	for item in LIST_OF_STATE_ATTRIBUTES:
	990	if item[0] == "dx_percent" and dx_old_node is not None:
	991	dxmin = ["dx_min", "dx_min", "float"]
	992	setattr(self, item[0], parse_entry_helper(dx_old_node,
	993	dxmin))
	994	self.dx_old = True
	995	else:
	996	node = get_content('ns:%s' % item[0], entry)
	997	setattr(self, item[0], parse_entry_helper(node, item))
	998
	999	for item in LIST_OF_STATE_PARAMETERS:
	1000	node = get_content("ns:%s" % item[0], entry)
	1001	self._from_xml_helper(node=node,
	1002	list=getattr(self, item[1]))
	1003
[ba8d326]	1004	# Recover disp_obj_dict from xml file
	1005	self.disp_obj_dict = {}
[959eb01]	1006	for tagname, varname, tagtype in DISPERSION_LIST:
	1007	node = get_content("ns:%s" % tagname, entry)
	1008	for attr in node:
	1009	parameter = str(attr.get('name'))
	1010	value = attr.get('value')
	1011	if value.startswith("<"):
	1012	try:
	1013	# <path.to.NamedDistribution object/instance...>
	1014	cls_name = value[1:].split()[0].split('.')[-1]
	1015	cls = getattr(sasmodels.weights, cls_name)
	1016	value = cls.type
	1017	except Exception:
	1018	base = "unable to load distribution %r for %s"
[ba8d326]	1019	logger.error(base, value, parameter)
[959eb01]	1020	continue
[ba8d326]	1021	disp_obj_dict = getattr(self, varname)
	1022	disp_obj_dict[parameter] = value
[959eb01]	1023
	1024	# get self.values and self.weights dic. if exists
	1025	for tagname, varname in LIST_OF_MODEL_ATTRIBUTES:
	1026	node = get_content("ns:%s" % tagname, entry)
	1027	dic = {}
	1028	value_list = []
	1029	for par in node:
	1030	name = par.get('name')
	1031	values = par.text.split()
	1032	# Get lines only with numbers
	1033	for line in values:
	1034	try:
	1035	val = float(line)
	1036	value_list.append(val)
	1037	except Exception:
	1038	# pass if line is empty (it happens)
	1039	msg = ("Error reading %r from %s %s\n"
	1040	% (line, tagname, name))
	1041	logger.error(msg + traceback.format_exc())
	1042	dic[name] = np.array(value_list)
	1043	setattr(self, varname, dic)
	1044
[ba8d326]	1045	class SimFitPageState(object):
[00f7ff1]	1046	"""
	1047	State of the simultaneous fit page for saving purposes
	1048	"""
	1049
	1050	def __init__(self):
	1051	# Sim Fit Page Number
	1052	self.fit_page_no = None
	1053	# Select all data
	1054	self.select_all = False
	1055	# Data sets sent to fit page
	1056	self.model_list = []
	1057	# Data sets to be fit
	1058	self.model_to_fit = []
	1059	# Number of constraints
	1060	self.no_constraint = 0
	1061	# Dictionary of constraints
	1062	self.constraint_dict = {}
	1063	# List of constraints
	1064	self.constraints_list = []
[959eb01]	1065
[ba8d326]	1066	def __repr__(self):
	1067	# TODO: should use __str__, not __repr__ (similarly for PageState)
	1068	# TODO: could use a nicer representation
	1069	repr = """\
	1070	fit page number : %(fit_page_no)s
	1071	select all : %(select_all)s
	1072	model_list : %(model_list)s
	1073	model to fit : %(model_to_fit)s
	1074	number of construsts : %(no_constraint)s
	1075	constraint dict : %(constraint_dict)s
	1076	constraints list : %(constraints_list)s
	1077	"""%self.__dict__
	1078	return repr
	1079
[959eb01]	1080	class Reader(CansasReader):
	1081	"""
	1082	Class to load a .fitv fitting file
	1083	"""
	1084	# File type
	1085	type_name = "Fitting"
	1086
	1087	# Wildcards
	1088	type = ["Fitting files (.fitv)\|.fitv"
	1089	"SASView file (.svs)\|.svs"]
	1090	# List of allowed extensions
	1091	ext = ['.fitv', '.FITV', '.svs', 'SVS']
	1092
	1093	def __init__(self, call_back=None, cansas=True):
	1094	CansasReader.__init__(self)
	1095	"""
	1096	Initialize the call-back method to be called
	1097	after we load a file
	1098
	1099	:param call_back: call-back method
	1100	:param cansas: True = files will be written/read in CanSAS format
	1101	False = write CanSAS format
	1102
	1103	"""
	1104	# Call back method to be executed after a file is read
	1105	self.call_back = call_back
	1106	# CanSAS format flag
	1107	self.cansas = cansas
	1108	self.state = None
	1109	# batch fitting params for saving
	1110	self.batchfit_params = []
	1111
	1112	def get_state(self):
	1113	return self.state
	1114
	1115	def read(self, path):
	1116	"""
	1117	Load a new P(r) inversion state from file
	1118
	1119	:param path: file path
	1120
	1121	"""
	1122	if self.cansas:
	1123	return self._read_cansas(path)
	1124
	1125	def _parse_state(self, entry):
	1126	"""
	1127	Read a fit result from an XML node
	1128
	1129	:param entry: XML node to read from
	1130	:return: PageState object
	1131	"""
	1132	# Create an empty state
	1133	state = None
	1134	# Locate the P(r) node
	1135	try:
	1136	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
[ba8d326]	1137	namespaces=CANSAS_NS)
[959eb01]	1138	if nodes:
	1139	# Create an empty state
	1140	state = PageState()
	1141	state.from_xml(node=nodes[0])
	1142
[ba8d326]	1143	except Exception:
[959eb01]	1144	logger.info("XML document does not contain fitting information.\n"
[ba8d326]	1145	+ traceback.format_exc())
[959eb01]	1146
	1147	return state
	1148
	1149	def _parse_simfit_state(self, entry):
	1150	"""
	1151	Parses the saved data for a simultaneous fit
	1152	:param entry: XML object to read from
	1153	:return: XML object for a simultaneous fit or None
	1154	"""
	1155	nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME,
[ba8d326]	1156	namespaces=CANSAS_NS)
[959eb01]	1157	if nodes:
	1158	simfitstate = nodes[0].xpath('ns:simultaneous_fit',
[ba8d326]	1159	namespaces=CANSAS_NS)
[959eb01]	1160	if simfitstate:
	1161	sim_fit_state = SimFitPageState()
	1162	simfitstate_0 = simfitstate[0]
	1163	all = simfitstate_0.xpath('ns:select_all',
[ba8d326]	1164	namespaces=CANSAS_NS)
[959eb01]	1165	atts = all[0].attrib
	1166	checked = atts.get('checked')
	1167	sim_fit_state.select_all = bool(checked)
	1168	model_list = simfitstate_0.xpath('ns:model_list',
[ba8d326]	1169	namespaces=CANSAS_NS)
[959eb01]	1170	model_list_items = model_list[0].xpath('ns:model_list_item',
[ba8d326]	1171	namespaces=CANSAS_NS)
[959eb01]	1172	for model in model_list_items:
	1173	attrs = model.attrib
	1174	sim_fit_state.model_list.append(attrs)
	1175
	1176	constraints = simfitstate_0.xpath('ns:constraints',
[ba8d326]	1177	namespaces=CANSAS_NS)
[959eb01]	1178	constraint_list = constraints[0].xpath('ns:constraint',
[ba8d326]	1179	namespaces=CANSAS_NS)
[959eb01]	1180	for constraint in constraint_list:
	1181	attrs = constraint.attrib
	1182	sim_fit_state.constraints_list.append(attrs)
	1183
	1184	return sim_fit_state
	1185	else:
	1186	return None
	1187
	1188	def _parse_save_state_entry(self, dom):
	1189	"""
	1190	Parse a SASentry
	1191
	1192	:param node: SASentry node
	1193
	1194	:return: Data1D/Data2D object
	1195
	1196	"""
[ba8d326]	1197	node = dom.xpath('ns:data_class', namespaces=CANSAS_NS)
[959eb01]	1198	return_value, _ = self._parse_entry(dom)
	1199	return return_value, _
	1200
	1201	def _read_cansas(self, path):
	1202	"""
	1203	Load data and fitting information from a CanSAS XML file.
	1204
	1205	:param path: file path
	1206	:return: Data1D object if a single SASentry was found,
	1207	or a list of Data1D objects if multiple entries were found,
	1208	or None of nothing was found
	1209	:raise RuntimeError: when the file can't be opened
	1210	:raise ValueError: when the length of the data vectors are inconsistent
	1211	"""
	1212	output = []
	1213	simfitstate = None
	1214	basename = os.path.basename(path)
	1215	root, extension = os.path.splitext(basename)
	1216	ext = extension.lower()
	1217	try:
	1218	if os.path.isfile(path):
	1219	if ext in self.ext or ext == '.xml':
	1220	tree = etree.parse(path, parser=etree.ETCompatXMLParser())
	1221	# Check the format version number
	1222	# Specifying the namespace will take care of the file
	1223	# format version
	1224	root = tree.getroot()
	1225	entry_list = root.xpath('ns:SASentry',
[ba8d326]	1226	namespaces=CANSAS_NS)
[959eb01]	1227	for entry in entry_list:
	1228	try:
	1229	sas_entry, _ = self._parse_save_state_entry(entry)
	1230	except:
	1231	raise
	1232	fitstate = self._parse_state(entry)
	1233
	1234	# state could be None when .svs file is loaded
	1235	# in this case, skip appending to output
	1236	if fitstate is not None:
	1237	sas_entry.meta_data['fitstate'] = fitstate
	1238	sas_entry.filename = fitstate.file
	1239	output.append(sas_entry)
	1240
	1241	else:
	1242	self.call_back(format=ext)
	1243	raise RuntimeError, "%s is not a file" % path
	1244
	1245	# Return output consistent with the loader's api
	1246	if len(output) == 0:
	1247	self.call_back(state=None, datainfo=None, format=ext)
	1248	return None
	1249	else:
[ba8d326]	1250	for data in output:
[959eb01]	1251	# Call back to post the new state
[ba8d326]	1252	state = data.meta_data['fitstate']
[959eb01]	1253	t = time.localtime(state.timestamp)
	1254	time_str = time.strftime("%b %d %H:%M", t)
	1255	# Check that no time stamp is already appended
	1256	max_char = state.file.find("[")
	1257	if max_char < 0:
	1258	max_char = len(state.file)
	1259	original_fname = state.file[0:max_char]
	1260	state.file = original_fname + ' [' + time_str + ']'
	1261
	1262	if state is not None and state.is_data is not None:
[ba8d326]	1263	data.is_data = state.is_data
[959eb01]	1264
[ba8d326]	1265	data.filename = state.file
	1266	state.data = data
	1267	state.data.name = data.filename # state.data_name
[959eb01]	1268	state.data.id = state.data_id
	1269	if state.is_data is not None:
	1270	state.data.is_data = state.is_data
[ba8d326]	1271	if data.run_name is not None and len(data.run_name) != 0:
	1272	if isinstance(data.run_name, dict):
	1273	# Note: key order in dict is not guaranteed, so sort
	1274	name = data.run_name.keys()[0]
[959eb01]	1275	else:
[ba8d326]	1276	name = data.run_name
[959eb01]	1277	else:
	1278	name = original_fname
	1279	state.data.group_id = name
	1280	state.version = fitstate.version
	1281	# store state in fitting
[ba8d326]	1282	self.call_back(state=state, datainfo=data, format=ext)
[959eb01]	1283	self.state = state
	1284	simfitstate = self._parse_simfit_state(entry)
	1285	if simfitstate is not None:
	1286	self.call_back(state=simfitstate)
	1287
	1288	return output
	1289	except:
	1290	self.call_back(format=ext)
	1291	raise
	1292
	1293	def write(self, filename, datainfo=None, fitstate=None):
	1294	"""
	1295	Write the content of a Data1D as a CanSAS XML file only for standalone
	1296
	1297	:param filename: name of the file to write
	1298	:param datainfo: Data1D object
	1299	:param fitstate: PageState object
	1300
	1301	"""
	1302	# Sanity check
	1303	if self.cansas:
	1304	# Add fitting information to the XML document
	1305	doc = self.write_toXML(datainfo, fitstate)
	1306	# Write the XML document
	1307	else:
	1308	doc = fitstate.to_xml(file=filename)
	1309
	1310	# Save the document no matter the type
	1311	fd = open(filename, 'w')
	1312	fd.write(doc.toprettyxml())
	1313	fd.close()
	1314
	1315	def write_toXML(self, datainfo=None, state=None, batchfit=None):
	1316	"""
	1317	Write toXML, a helper for write(),
	1318	could be used by guimanager._on_save()
	1319
	1320	: return: xml doc
	1321	"""
	1322
	1323	self.batchfit_params = batchfit
	1324	if state.data is None or not state.data.is_data:
	1325	return None
	1326	# make sure title and data run are filled.
	1327	if state.data.title is None or state.data.title == '':
	1328	state.data.title = state.data.name
	1329	if state.data.run_name is None or state.data.run_name == {}:
	1330	state.data.run = [str(state.data.name)]
	1331	state.data.run_name[0] = state.data.name
	1332
	1333	data = state.data
	1334	doc, sasentry = self._to_xml_doc(data)
	1335
	1336	if state is not None:
	1337	doc = state.to_xml(doc=doc, file=data.filename, entry_node=sasentry,
	1338	batch_fit_state=self.batchfit_params)
	1339
	1340	return doc
	1341
[78312f7]	1342	# Simple html report template
[959eb01]	1343	HEADER = "<html>\n"
	1344	HEADER += "<head>\n"
	1345	HEADER += "<meta http-equiv=Content-Type content='text/html; "
	1346	HEADER += "charset=windows-1252'> \n"
	1347	HEADER += "<meta name=Generator >\n"
	1348	HEADER += "</head>\n"
	1349	HEADER += "<body lang=EN-US>\n"
	1350	HEADER += "<div class=WordSection1>\n"
	1351	HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >"
	1352	HEADER += "%s</font></center></span></center></b></p>"
	1353	HEADER += "<p class=MsoNormal> </p>"
	1354	PARA = "<p class=MsoNormal><font size='4' > %s \n"
	1355	PARA += "</font></p>"
	1356	CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n"
	1357	CENTRE += "</font></center></p>"
	1358	FEET_1 = \
	1359	"""
	1360	<p class=MsoNormal> </p>
	1361	<br>
	1362	<p class=MsoNormal><b><span ><center> <font size='4' > Graph
	1363	</font></span></center></b></p>
	1364	<p class=MsoNormal> </p>
	1365	<center>
	1366	<br><font size='4' >Model Computation</font>
	1367	<br><font size='4' >Data: "%s"</font><br>
	1368	"""
	1369	FEET_2 = \
[78312f7]	1370	"""<img src="%s" ></img>
[959eb01]	1371	"""
	1372	FEET_3 = \
[78312f7]	1373	"""</center>
[959eb01]	1374	</div>
	1375	</body>
	1376	</html>
	1377	"""
[78312f7]	1378	ELINE = """<p class=MsoNormal> </p>
	1379	"""

Note: See TracBrowser for help on using the repository browser.

SasView

source: sasview/src/sas/sascalc/fit/pagestate.py @ ab0b93f

Download in other formats: