source: sasview/park_integration/ScipyFitting.py @ 12eac73

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Last change on this file since 12eac73 was fd6b789, checked in by Gervaise Alina <gervyh@…>, 15 years ago

refactor fit engine set_model can receive sans.model or park.model has a parameter;set_del has a new parameters constraints

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1"""
2    @organization: ScipyFitting module contains FitArrange , ScipyFit,
3    Parameter classes.All listed classes work together to perform a
4    simple fit with scipy optimizer.
5"""
6
7import numpy 
8from scipy import optimize
9
10from AbstractFitEngine import FitEngine, SansAssembly,FitAbort
11
12class fitresult:
13    """
14        Storing fit result
15    """
16    calls     = None
17    fitness   = None
18    chisqr    = None
19    pvec      = None
20    cov       = None
21    info      = None
22    mesg      = None
23    success   = None
24    stderr    = None
25    parameters= None
26   
27
28class ScipyFit(FitEngine):
29    """
30        ScipyFit performs the Fit.This class can be used as follow:
31        #Do the fit SCIPY
32        create an engine: engine = ScipyFit()
33        Use data must be of type plottable
34        Use a sans model
35       
36        Add data with a dictionnary of FitArrangeDict where Uid is a key and data
37        is saved in FitArrange object.
38        engine.set_data(data,Uid)
39       
40        Set model parameter "M1"= model.name add {model.parameter.name:value}.
41        @note: Set_param() if used must always preceded set_model()
42             for the fit to be performed.In case of Scipyfit set_param is called in
43             fit () automatically.
44        engine.set_param( model,"M1", {'A':2,'B':4})
45       
46        Add model with a dictionnary of FitArrangeDict{} where Uid is a key and model
47        is save in FitArrange object.
48        engine.set_model(model,Uid)
49       
50        engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]]
51        chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax)
52    """
53    def __init__(self):
54        """
55            Creates a dictionary (self.fitArrangeDict={})of FitArrange elements
56            with Uid as keys
57        """
58        self.fitArrangeDict={}
59        self.paramList=[]
60    #def fit(self, *args, **kw):
61    #    return profile(self._fit, *args, **kw)
62
63    def fit(self ,q=None,handler=None,curr_thread= None):
64       
65        fitproblem=[]
66        for id ,fproblem in self.fitArrangeDict.iteritems():
67            if fproblem.get_to_fit()==1:
68                fitproblem.append(fproblem)
69        if len(fitproblem)>1 : 
70            raise RuntimeError, "Scipy can't fit more than a single fit problem at a time."
71            return
72        elif len(fitproblem)==0 : 
73            raise RuntimeError, "No Assembly scheduled for Scipy fitting."
74            return
75   
76        listdata=[]
77        model = fitproblem[0].get_model()
78        listdata = fitproblem[0].get_data()
79        # Concatenate dList set (contains one or more data)before fitting
80        #data=self._concatenateData( listdata)
81        data=listdata
82        self.curr_thread= curr_thread
83
84        #try:
85        functor= SansAssembly(self.paramList,model,data, curr_thread= self.curr_thread)
86        out, cov_x, info, mesg, success = optimize.leastsq(functor,model.getParams(self.paramList), full_output=1, warning=True)
87       
88        chisqr = functor.chisq(out)
89       
90        if cov_x is not None and numpy.isfinite(cov_x).all():
91            stderr = numpy.sqrt(numpy.diag(cov_x))
92        else:
93            stderr=None
94        if not (numpy.isnan(out).any()) or ( cov_x !=None) :
95                result = fitresult()
96                result.fitness = chisqr
97                result.stderr  = stderr
98                result.pvec = out
99                result.success = success
100                if q !=None:
101                    print "went here"
102                    q.put(result)
103                    print "get q scipy fit enfine",q.get()
104                    return q
105                return result
106        else: 
107            raise ValueError, "SVD did not converge"+str(success)
108        #except FitAbort:
109            ## fit engine is stop
110        #    return None
111       
112        #except:
113        #    raise
114       
115
116
117def profile(fn, *args, **kw):
118    import cProfile, pstats, os
119    global call_result
120    def call():
121        global call_result
122        call_result = fn(*args, **kw)
123    cProfile.runctx('call()', dict(call=call), {}, 'profile.out')
124    stats = pstats.Stats('profile.out')
125    #stats.sort_stats('time')
126    stats.sort_stats('calls')
127    stats.print_stats()
128    os.unlink('profile.out')
129    return call_result
130
131     
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