""" ParkFitting module contains SansParameter,Model,Data FitArrange, ParkFit,Parameter classes.All listed classes work together to perform a simple fit with park optimizer. """ #import time #import numpy import park from park import fit, fitresult from park import assembly from park.fitmc import FitSimplex, FitMC #from Loader import Load from AbstractFitEngine import FitEngine class ParkFit(FitEngine): """ ParkFit performs the Fit.This class can be used as follow: #Do the fit Park create an engine: engine = ParkFit() Use data must be of type plottable Use a sans model Add data with a dictionnary of FitArrangeList where Uid is a key and data is saved in FitArrange object. engine.set_data(data,Uid) Set model parameter "M1"= model.name add {model.parameter.name:value}. :note: Set_param() if used must always preceded set_model() for the fit to be performed. engine.set_param( model,"M1", {'A':2,'B':4}) Add model with a dictionnary of FitArrangeList{} where Uid is a key and model is save in FitArrange object. engine.set_model(model,Uid) engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]] chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax) :note: {model.parameter.name:value} is ignored in fit function since the user should make sure to call set_param himself. """ def __init__(self): """ Creates a dictionary (self.fitArrangeList={})of FitArrange elements with Uid as keys """ self.fitArrangeDict = {} self.paramList = [] def createAssembly(self): """ Extract sansmodel and sansdata from self.FitArrangelist ={Uid:FitArrange} Create parkmodel and park data ,form a list couple of parkmodel and parkdata create an assembly self.problem= park.Assembly([(parkmodel,parkdata)]) """ mylist = [] listmodel = [] i = 0 fitproblems = [] for id,fproblem in self.fitArrangeDict.iteritems(): if fproblem.get_to_fit() == 1: fitproblems.append(fproblem) if len(fitproblems) == 0: raise RuntimeError, "No Assembly scheduled for Park fitting." return for item in fitproblems: parkmodel = item.get_model() for p in parkmodel.parameterset: ## does not allow status change for constraint parameters if p.status != 'computed': if p._getname()in item.pars: ## make parameters selected for fit will be between boundaries p.set(p.range) else: p.status = 'fixed' i += 1 Ldata = item.get_data() #parkdata=self._concatenateData(Ldata) parkdata = Ldata fitness = (parkmodel, parkdata) mylist.append(fitness) self.problem = park.Assembly(mylist) def fit(self, q=None, handler=None, curr_thread=None): """ Performs fit with park.fit module.It can perform fit with one model and a set of data, more than two fit of one model and sets of data or fit with more than two model associated with their set of data and constraints :param pars: Dictionary of parameter names for the model and their values. :param qmin: The minimum value of data's range to be fit :param qmax: The maximum value of data's range to be fit :note: all parameter are ignored most of the time.Are just there to keep ScipyFit and ParkFit interface the same. :return: result.fitness Value of the goodness of fit metric :return: result.pvec list of parameter with the best value found during fitting :return: result.cov Covariance matrix """ self.createAssembly() localfit = FitSimplex() localfit.ftol = 1e-8 # See `park.fitresult.FitHandler` for details. fitter = FitMC(localfit=localfit, start_points=1) if handler == None: handler = fitresult.ConsoleUpdate(improvement_delta=0.1) result = fit.fit(self.problem, fitter=fitter, handler=handler) self.problem.all_results(result) if result != None: if q != None: q.put(result) return q return result else: raise ValueError, "SVD did not converge"