""" ScipyFitting module contains FitArrange , ScipyFit, Parameter classes.All listed classes work together to perform a simple fit with scipy optimizer. """ import numpy from scipy import optimize from AbstractFitEngine import FitEngine, SansAssembly, FitAbort class fitresult(object): """ Storing fit result """ def __init__(self, model=None, paramList=None): self.calls = None self.fitness = None self.chisqr = None self.pvec = None self.cov = None self.info = None self.mesg = None self.success = None self.stderr = None self.parameters = None self.model = model self.paramList = paramList def set_model(self, model): """ """ self.model = model def set_fitness(self, fitness): """ """ self.fitness = fitness def __str__(self): """ """ if self.pvec == None and self.model is None and self.paramList is None: return "No results" n = len(self.model.parameterset) result_param = zip(xrange(n), self.model.parameterset) L = ["P%-3d %s......|.....%s"%(p[0], p[1], p[1].value)\ for p in result_param if p[1].name in self.paramList] L.append("=== goodness of fit: %s" % (str(self.fitness))) return "\n".join(L) def print_summary(self): """ """ print self class ScipyFit(FitEngine): """ ScipyFit performs the Fit.This class can be used as follow: #Do the fit SCIPY create an engine: engine = ScipyFit() Use data must be of type plottable Use a sans model Add data with a dictionnary of FitArrangeDict 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.In case of Scipyfit set_param is called in fit () automatically. engine.set_param( model,"M1", {'A':2,'B':4}) Add model with a dictionnary of FitArrangeDict{} 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) """ def __init__(self): """ Creates a dictionary (self.fitArrangeDict={})of FitArrange elements with Uid as keys """ self.fitArrangeDict = {} self.paramList = [] #def fit(self, *args, **kw): # return profile(self._fit, *args, **kw) def fit(self, q=None, handler=None, curr_thread=None): """ """ fitproblem = [] for id, fproblem in self.fitArrangeDict.iteritems(): if fproblem.get_to_fit() == 1: fitproblem.append(fproblem) if len(fitproblem) > 1 : msg = "Scipy can't fit more than a single fit problem at a time." raise RuntimeError, msg return elif len(fitproblem) == 0 : raise RuntimeError, "No Assembly scheduled for Scipy fitting." return listdata = [] model = fitproblem[0].get_model() listdata = fitproblem[0].get_data() # Concatenate dList set (contains one or more data)before fitting data = listdata self.curr_thread = curr_thread result = fitresult(model=model, paramList=self.paramList) if handler is not None: handler.set_result(result=result) #try: functor = SansAssembly(self.paramList, model, data, handler=handler, fitresult=result, curr_thread= self.curr_thread) out, cov_x, info, mesg, success = optimize.leastsq(functor, model.getParams(self.paramList), full_output=1, warning=True) chisqr = functor.chisq(out) if cov_x is not None and numpy.isfinite(cov_x).all(): stderr = numpy.sqrt(numpy.diag(cov_x)) else: stderr = None if not (numpy.isnan(out).any()) or ( cov_x !=None) : result.fitness = chisqr result.stderr = stderr result.pvec = out result.success = success #print result if q is not None: #print "went here" q.put(result) #print "get q scipy fit enfine",q.get() return q return result else: raise ValueError, "SVD did not converge" + str(success) def profile(fn, *args, **kw): import cProfile, pstats, os global call_result def call(): global call_result call_result = fn(*args, **kw) cProfile.runctx('call()', dict(call=call), {}, 'profile.out') stats = pstats.Stats('profile.out') #stats.sort_stats('time') stats.sort_stats('calls') stats.print_stats() os.unlink('profile.out') return call_result