Python symfit.parameters函数代码示例

def fourier_series(x, f, n=0):
    """
    Returns a symbolic fourier series of order `n`.

    :param n: Order of the fourier series.
    :param x: Independent variable
    :param f: Frequency of the fourier series
    """
    # Make the parameter objects for all the terms
    a0, *cos_a = parameters(','.join(['a{}'.format(i) for i in range(0, n + 1)]))
    sin_b = parameters(','.join(['b{}'.format(i) for i in range(1, n + 1)]))
    # Construct the series
    series = a0 + sum(ai * cos(i * f * x) + bi * sin(i * f * x)
                     for i, (ai, bi) in enumerate(zip(cos_a, sin_b), start=1))
    return series

    def test_known_solution(self):
        p, c1 = parameters('p, c1')
        y, t = variables('y, t')
        p.value = 3.0

        model_dict = {
            D(y, t): - p * y,
        }

        # Lets say we know the exact solution to this problem
        sol = Model({y: exp(- p * t)})

        # Generate some data
        tdata = np.linspace(0, 3, 10001)
        ydata = sol(t=tdata, p=3.22)[0]
        ydata += np.random.normal(0, 0.005, ydata.shape)

        ode_model = ODEModel(model_dict, initial={t: 0.0, y: ydata[0]})
        fit = Fit(ode_model, t=tdata, y=ydata)
        ode_result = fit.execute()

        c1.value = ydata[0]
        fit = Fit(sol, t=tdata, y=ydata)
        fit_result = fit.execute()

        self.assertAlmostEqual(ode_result.value(p) / fit_result.value(p), 1, 2)
        self.assertAlmostEqual(ode_result.r_squared / fit_result.r_squared, 1, 4)
        self.assertAlmostEqual(ode_result.stdev(p) / fit_result.stdev(p), 1, 3)

    def test_simple_kinetics(self):
        """
        Simple kinetics data to test fitting
        """
        tdata = np.array([10, 26, 44, 70, 120])
        adata = 10e-4 * np.array([44, 34, 27, 20, 14])
        a, b, t = variables('a, b, t')
        k, a0 = parameters('k, a0')
        k.value = 0.01
        # a0.value, a0.min, a0.max = 54 * 10e-4, 40e-4, 60e-4
        a0 = 54 * 10e-4

        model_dict = {
            D(a, t): - k * a**2,
            D(b, t): k * a**2,
        }

        ode_model = ODEModel(model_dict, initial={t: 0.0, a: a0, b: 0.0})

        # Analytical solution
        model = GradientModel({a: 1 / (k * t + 1 / a0)})
        fit = Fit(model, t=tdata, a=adata)
        fit_result = fit.execute()

        fit = Fit(ode_model, t=tdata, a=adata, b=None, minimizer=MINPACK)
        ode_result = fit.execute()
        self.assertAlmostEqual(ode_result.value(k) / fit_result.value(k), 1.0, 4)
        self.assertAlmostEqual(ode_result.stdev(k) / fit_result.stdev(k), 1.0, 4)
        self.assertAlmostEqual(ode_result.r_squared / fit_result.r_squared, 1, 4)

        fit = Fit(ode_model, t=tdata, a=adata, b=None)
        ode_result = fit.execute()
        self.assertAlmostEqual(ode_result.value(k) / fit_result.value(k), 1.0, 4)
        self.assertAlmostEqual(ode_result.stdev(k) / fit_result.stdev(k), 1.0, 4)
        self.assertAlmostEqual(ode_result.r_squared / fit_result.r_squared, 1, 4)

    def test_taylor_model(self):
        a, b = parameters('a, b')
        x, y, z = variables('x, y, z')

        model = Model({y: a * x + b})
        appr = TaylorModel(model)
        self.assertEqual(set([a, b]), set(appr.params))
        appr.p0 = {a: 2.0, b: 5.0}
        self.assertEqual(set(appr.p0.keys()), set(appr.params_0[p] for p in appr.params))
        self.assertTrue(LinearLeastSquares.is_linear(appr))

        model = Model({z: a * x**2 + b * y**2})
        appr = TaylorModel(model)
        appr.p0 = {a: 2, b: 5}
        model = Model({z: a * x**2 + b * y**2})
        appr_2 = TaylorModel(model)
        appr_2.p0 = {a: 1, b: 1}
        self.assertTrue(appr == appr_2)

        model = Model({y: a * sympy.exp(x * b)})
        appr = TaylorModel(model)
        appr.p0 = {a: 2.0, b: 5.0}
        self.assertTrue(LinearLeastSquares.is_linear(appr))

        model = Model({y: sympy.sin(a * x)})
        appr = TaylorModel(model)
        appr.p0 = {a: 0.0}
        self.assertTrue(LinearLeastSquares.is_linear(appr))

    def test_data_for_constraint(self):
        """
        Test the signature handling when constraints are at play. Constraints
        should take seperate data, but still kwargs that are not found in either
        the model nor the constraints should raise an error.
        """
        A, mu, sig = parameters('A, mu, sig')
        x, y, Y = variables('x, y, Y')

        model = Model({y: A * Gaussian(x, mu=mu, sig=sig)})
        constraint = Model.as_constraint(Y, model, constraint_type=Eq)

        np.random.seed(2)
        xdata = np.random.normal(1.2, 2, 10)
        ydata, xedges = np.histogram(xdata, bins=int(np.sqrt(len(xdata))),
                                     density=True)

        # Allowed
        fit = Fit(model, x=xdata, y=ydata, Y=2, constraints=[constraint])
        fit = Fit(model, x=xdata, y=ydata)
        fit = Fit(model, x=xdata, objective=LogLikelihood)

        # Not allowed
        with self.assertRaises(TypeError):
            fit = Fit(model, x=xdata, y=ydata, Y=2)
        with self.assertRaises(TypeError):
            fit = Fit(model, x=xdata, y=ydata, Y=2, Z=3, constraints=[constraint])

    def test_straight_line_analytical(self):
        """
        Test symfit against a straight line, for which the parameters and their
        uncertainties are known analytically. Assuming equal weights.
        """
        data = [[0, 1], [1, 0], [3, 2], [5, 4]]
        xdata, ydata = (np.array(i, dtype='float64') for i in zip(*data))
        # x = np.arange(0, 100, 0.1)
        # np.random.seed(10)
        # y = 3.0*x + 105.0 + np.random.normal(size=x.shape)

        dx = xdata - xdata.mean()
        dy = ydata - ydata.mean()
        mean_squared_x = np.mean(xdata**2) - np.mean(xdata)**2
        mean_xy = np.mean(xdata * ydata) - np.mean(xdata)*np.mean(ydata)
        a = mean_xy/mean_squared_x
        b = ydata.mean() - a * xdata.mean()
        self.assertAlmostEqual(a, 0.694915, 6) # values from Mathematica
        self.assertAlmostEqual(b, 0.186441, 6)

        S = np.sum((ydata - (a*xdata + b))**2)
        var_a_exact = S/(len(xdata) * (len(xdata) - 2) * mean_squared_x)
        var_b_exact = var_a_exact*np.mean(xdata**2)
        a_exact = a
        b_exact = b

        # We will now compare these exact results with values from symfit, numerically
        a, b = parameters('a, b')
        x, y = variables('x, y')
        model = {y: a*x + b}
        fit = NumericalLeastSquares(model, x=xdata, y=ydata)#, absolute_sigma=False)
        fit_result = fit.execute()

        popt, pcov = curve_fit(lambda z, c, d: c * z + d, xdata, ydata,
                               jac=lambda z, c, d: np.transpose([xdata, np.ones_like(xdata)]))
#                               jac=lambda p, x, y, func: np.transpose([x, np.ones_like(x)]))
                                # Dfun=lambda p, x, y, func: print(p, func, x, y))

        # curve_fit
        self.assertAlmostEqual(a_exact, popt[0], 4)
        self.assertAlmostEqual(b_exact, popt[1], 4)
        self.assertAlmostEqual(var_a_exact, pcov[0][0], 6)
        self.assertAlmostEqual(var_b_exact, pcov[1][1], 6)

        self.assertAlmostEqual(a_exact, fit_result.value(a), 4)
        self.assertAlmostEqual(b_exact, fit_result.value(b), 4)
        self.assertAlmostEqual(var_a_exact, fit_result.variance(a), 6)
        self.assertAlmostEqual(var_b_exact, fit_result.variance(b), 6)

        # Do the fit with the LinearLeastSquares object
        fit = LinearLeastSquares(model, x=xdata, y=ydata)
        fit_result = fit.execute()
        self.assertAlmostEqual(a_exact, fit_result.value(a), 4)
        self.assertAlmostEqual(b_exact, fit_result.value(b), 4)
        self.assertAlmostEqual(var_a_exact, fit_result.variance(a), 6)
        self.assertAlmostEqual(var_b_exact, fit_result.variance(b), 6)

        # Lets also make sure the entire covariance matrix is the same
        for cov1, cov2 in zip(fit_result.params.covariance_matrix.flatten(), pcov.flatten()):
            self.assertAlmostEqual(cov1, cov2)

    def test_likelihood_fitting_gaussian(self):
        """
        Fit using the likelihood method.
        """
        mu, sig = parameters('mu, sig')
        sig.min = 0.01
        sig.value = 3.0
        mu.value = 50.
        x = Variable()
        pdf = Gaussian(x, mu, sig)

        np.random.seed(10)
        xdata = np.random.normal(51., 3.5, 10000)

        # Expected parameter values
        mean = np.mean(xdata)
        stdev = np.std(xdata)
        mean_stdev = stdev/np.sqrt(len(xdata))

        fit = Fit(pdf, xdata, objective=LogLikelihood)
        fit_result = fit.execute()

        self.assertAlmostEqual(fit_result.value(mu) / mean, 1, 6)
        self.assertAlmostEqual(fit_result.stdev(mu) / mean_stdev, 1, 3)
        self.assertAlmostEqual(fit_result.value(sig) / np.std(xdata), 1, 6)

    def test_vector_fitting(self):
        """
        Tests fitting to a 3 component vector valued function, without bounds
        or guesses.
        """
        a, b, c = parameters('a, b, c')
        a_i, b_i, c_i = variables('a_i, b_i, c_i')

        model = {a_i: a, b_i: b, c_i: c}

        xdata = np.array([
            [10.1, 9., 10.5, 11.2, 9.5, 9.6, 10.],
            [102.1, 101., 100.4, 100.8, 99.2, 100., 100.8],
            [71.6, 73.2, 69.5, 70.2, 70.8, 70.6, 70.1],
        ])

        fit = NumericalLeastSquares(
            model=model,
            a_i=xdata[0],
            b_i=xdata[1],
            c_i=xdata[2],
        )
        fit_result = fit.execute()

        self.assertAlmostEqual(fit_result.value(a), 9.985691, 6)
        self.assertAlmostEqual(fit_result.value(b), 1.006143e+02, 4)
        self.assertAlmostEqual(fit_result.value(c), 7.085713e+01, 5)

    def test_pickle(self):
        """
        Make sure models can be pickled are preserved when pickling
        """
        a, b = parameters('a, b')
        x, y = variables('x, y')
        exact_model = Model({y: a * x ** b})
        constraint = Model.as_constraint(Eq(a, b), exact_model)
        num_model = CallableNumericalModel(
            {y: a * x ** b}, independent_vars=[x], params=[a, b]
        )
        connected_num_model = CallableNumericalModel(
            {y: a * x ** b}, connectivity_mapping={y: {x, a, b}}
        )
        # Test if lsoda args and kwargs are pickled too
        ode_model = ODEModel({D(y, x): a * x + b}, {x: 0.0}, 3, 4, some_kwarg=True)

        models = [exact_model, constraint, num_model, ode_model,
                  connected_num_model]
        for model in models:
            new_model = pickle.loads(pickle.dumps(model))
            # Compare signatures
            self.assertEqual(model.__signature__, new_model.__signature__)
            # Trigger the cached vars because we compare `__dict__` s
            model.vars
            new_model.vars
            # Explicitly make sure the connectivity mapping is identical.
            self.assertEqual(model.connectivity_mapping,
                             new_model.connectivity_mapping)
            if not isinstance(model, ODEModel):
                model.function_dict
                model.vars_as_functions
                new_model.function_dict
                new_model.vars_as_functions
            self.assertEqual(model.__dict__, new_model.__dict__)

    def test_vector_none_fitting(self):
        """
        Fit to a 3 component vector valued function with one variables data set
        to None, without bounds or guesses.
        """
        a, b, c = parameters('a, b, c')
        a_i, b_i, c_i = variables('a_i, b_i, c_i')

        model = {a_i: a, b_i: b, c_i: c}

        xdata = np.array([
            [10.1, 9., 10.5, 11.2, 9.5, 9.6, 10.],
            [102.1, 101., 100.4, 100.8, 99.2, 100., 100.8],
            [71.6, 73.2, 69.5, 70.2, 70.8, 70.6, 70.1],
        ])

        fit_none = NumericalLeastSquares(
            model=model,
            a_i=xdata[0],
            b_i=xdata[1],
            c_i=None,
        )
        fit = NumericalLeastSquares(
            model=model,
            a_i=xdata[0],
            b_i=xdata[1],
            c_i=xdata[2],
        )
        fit_none_result = fit_none.execute()
        fit_result = fit.execute()

        self.assertAlmostEqual(fit_none_result.value(a), fit_result.value(a), 4)
        self.assertAlmostEqual(fit_none_result.value(b), fit_result.value(b), 4)
        # the parameter without data should be unchanged.
        self.assertAlmostEqual(fit_none_result.value(c), 1.0)

    def test_global_fitting(self):
        """
        In case of shared parameters between the components of the model, `Fit`
        should automatically use `ConstrainedLeastSquares`.
        :return:
        """
        x_1, x_2, y_1, y_2 = variables('x_1, x_2, y_1, y_2')
        y0, a_1, a_2, b_1, b_2 = parameters('y0, a_1, a_2, b_1, b_2')

        # The following vector valued function links all the equations together
        # as stated in the intro.
        model = Model({
            y_1: a_1 * x_1**2 + b_1 * x_1 + y0,
            y_2: a_2 * x_2**2 + b_2 * x_2 + y0,
        })
        self.assertTrue(model.shared_parameters)

        # Generate data from this model
        xdata1 = np.linspace(0, 10)
        xdata2 = xdata1[::2] # Only every other point.

        ydata1, ydata2 = model(x_1=xdata1, x_2=xdata2, a_1=101.3, b_1=0.5, a_2=56.3, b_2=1.1111, y0=10.8)
        # Add some noise to make it appear like real data
        np.random.seed(1)
        ydata1 += np.random.normal(0, 2, size=ydata1.shape)
        ydata2 += np.random.normal(0, 2, size=ydata2.shape)

        xdata = [xdata1, xdata2]
        ydata = [ydata1, ydata2]

        # Guesses
        a_1.value = 100
        a_2.value = 50
        b_1.value = 1
        b_2.value = 1
        y0.value = 10

        fit = Fit(
            model, x_1=xdata[0], x_2=xdata[1], y_1=ydata[0], y_2=ydata[1]
        )
        self.assertIsInstance(fit.fit, ConstrainedNumericalLeastSquares)

        # The next model does not share parameters, but is still a vector
        model = Model({
            y_1: a_1 * x_1**2 + b_1 * x_1,
            y_2: a_2 * x_2**2 + b_2 * x_2,
        })
        fit = Fit(
            model, x_1=xdata[0], x_2=xdata[1], y_1=ydata[0], y_2=ydata[1]
        )
        self.assertFalse(model.shared_parameters)
        self.assertIsInstance(fit.fit, NumericalLeastSquares)

        # Scalar model, so it should use NumericalLeastSquares.
        model = Model({
            y_1: a_1 * x_1**2 + b_1 * x_1,
        })
        fit = Fit(model, x_1=xdata[0], y_1=ydata[0])
        self.assertFalse(model.shared_parameters)
        self.assertIsInstance(fit.fit, NumericalLeastSquares)

    def test_single_eval(self):
        """
        Eval an ODEModel at a single value rather than a vector.
        """
        x, y, t = variables('x, y, t')
        k, = parameters('k') # C is the integration constant.

        # The harmonic oscillator as a system, >1st order is not supported yet.
        harmonic_dict = {
            D(x, t): - k * y,
            D(y, t): k * x,
        }

        # Make a second model to prevent caching of integration results.
        # This also means harmonic_dict should NOT be a Model object.
        harmonic_model_array = ODEModel(harmonic_dict, initial={t: 0.0, x: 1.0, y: 0.0})
        harmonic_model_points = ODEModel(harmonic_dict, initial={t: 0.0, x: 1.0, y: 0.0})
        tdata = np.linspace(0, 100, 101)
        X, Y = harmonic_model_array(t=tdata, k=0.1)
        # Shuffle the data to prevent using the result at time t to calculate
        # t+dt
        random_order = np.random.permutation(len(tdata))
        for idx in random_order:
            t = tdata[idx]
            X_val = X[idx]
            Y_val = Y[idx]
            X_point, Y_point = harmonic_model_points(t=t, k=0.1)
            self.assertAlmostEqual(X_point[0], X_val)
            self.assertAlmostEqual(Y_point[0], Y_val)

    def test_simple_kinetics(self):
        """
        Simple kinetics data to test fitting
        """
        tdata = np.array([10, 26, 44, 70, 120])
        adata = 10e-4 * np.array([44, 34, 27, 20, 14])
        a, b, t = variables('a, b, t')
        k, a0 = parameters('k, a0')
        k.value = 0.01
        # a0.value, a0.min, a0.max = 54 * 10e-4, 40e-4, 60e-4
        a0 = 54 * 10e-4

        model_dict = {
            D(a, t): - k * a**2,
            D(b, t): k * a**2,
        }

        ode_model = ODEModel(model_dict, initial={t: 0.0, a: a0, b: 0.0})

        # Generate some data
        tvec = np.linspace(0, 500, 1000)

        fit = NumericalLeastSquares(ode_model, t=tdata, a=adata, b=None)
        fit_result = fit.execute()
        # print(fit_result)
        self.assertAlmostEqual(fit_result.value(k), 4.302875e-01, 4)
        self.assertAlmostEqual(fit_result.stdev(k), 6.447068e-03, 4)

        fit = Fit(ode_model, t=tdata, a=adata, b=None)
        fit_result = fit.execute()
        # print(fit_result)
        self.assertAlmostEqual(fit_result.value(k), 4.302875e-01, 4)
        self.assertTrue(np.isnan(fit_result.stdev(k)))

    def test_full_eval_range(self):
        """
        Test if ODEModels can be evaluated at t < t_initial.

        A bit of a no news is good news test.
        """
        tdata = np.array([0, 10, 26, 44, 70, 120])
        adata = 10e-4 * np.array([54, 44, 34, 27, 20, 14])
        a, b, t = variables('a, b, t')
        k, a0 = parameters('k, a0')
        k.value = 0.01
        t0 = tdata[2]
        a0 = adata[2]
        b0 = 0.02729855 # Obtained from evaluating from t=0.

        model_dict = {
            D(a, t): - k * a**2,
            D(b, t): k * a**2,
        }

        ode_model = ODEModel(model_dict, initial={t: t0, a: a0, b: b0})

        fit = Fit(ode_model, t=tdata, a=adata, b=None)
        ode_result = fit.execute()
        self.assertGreater(ode_result.r_squared, 0.95, 4)

        # Now start from a timepoint that is not in the t-array such that it
        # triggers another pathway to be taken in integrating it.
        # Again, no news is good news.
        ode_model = ODEModel(model_dict, initial={t: t0 + 1e-5, a: a0, b: b0})

        fit = Fit(ode_model, t=tdata, a=adata, b=None)
        ode_result = fit.execute()
        self.assertGreater(ode_result.r_squared, 0.95, 4)

    def test_vector_fitting_guess(self):
        """
        Tests fitting to a 3 component vector valued function, with guesses.
        """
        a, b, c = parameters('a, b, c')
        a.value = 10
        b.value = 100
        a_i, b_i, c_i = variables('a_i, b_i, c_i')

        model = {a_i: a, b_i: b, c_i: c}

        xdata = np.array([
            [10.1, 9., 10.5, 11.2, 9.5, 9.6, 10.],
            [102.1, 101., 100.4, 100.8, 99.2, 100., 100.8],
            [71.6, 73.2, 69.5, 70.2, 70.8, 70.6, 70.1],
        ])

        fit = NumericalLeastSquares(
            model=model,
            a_i=xdata[0],
            b_i=xdata[1],
            c_i=xdata[2],
        )
        fit_result = fit.execute()

        self.assertAlmostEqual(fit_result.value(a), np.mean(xdata[0]), 4)
        self.assertAlmostEqual(fit_result.value(b), np.mean(xdata[1]), 4)
        self.assertAlmostEqual(fit_result.value(c), np.mean(xdata[2]), 4)