def test_odr_model_default_meta(self): def func(b, x): return b[0] + b[1] * x p = Model(func) p.set_meta(name='Sample Model Meta', ref='ODRPACK') assert_equal(p.meta, {'name': 'Sample Model Meta', 'ref': 'ODRPACK'})
def chi2_iterative(k, k_nn, Foward=True): """ Esta funcion agarra un eje X (k), un eje Y (k_nn) y busca los parametros para ajustar la mejor recta, buscando el regimen lineal de la curva. Esto lo hace sacando puntos de la curva, ajustando la curva resultante, y luego comparando los parametros de los distintos ajustes, seleccionando el de menor chi2. Si Foward=True entonces la funcion va a ir sacando puntos del final para encontrar kmax. Si Foward=False, la funcion va a sacar puntos del principio para calcular kmin. El punto va a estar dado por k[index]. Returns: m, b, chi2_stat, index m: pendiente de la recta resultante b: ordenada de la recta resultante chi2: estadistico de chi2 de la recta resultante index: indice del elemento donde empieza/termina el regimen lineal. . . """ chi2_list = [] m_list = [] b_list = [] if Foward == True: for j in range(0, len(k) - 3): k_nn_temp = k_nn[:len(k_nn) - j] k_temp = k[:len(k) - j] linear_model = Model(linear) data = RealData(k_temp, k_nn_temp) odr = ODR(data, linear_model, beta0=[0., 1.]) out = odr.run() chi2_list.append(out.res_var) m_list.append(out.beta[0]) b_list.append(out.beta[1]) else: for j in range(0, len(k) - 3): k_nn_temp = k_nn[j:] k_temp = k[j:] linear_model = Model(linear) data = RealData(k_temp, k_nn_temp) odr = ODR(data, linear_model, beta0=[0., 1.]) out = odr.run() chi2_list.append(out.res_var) m_list.append(out.beta[0]) b_list.append(out.beta[1]) #index = ClosestToOne(chi2_list) index = chi2_list.index(min(chi2_list)) m = m_list[index] b = b_list[index] chi2 = chi2_list[index] return m, b, chi2, index
def test_explicit(self): explicit_mod = Model( self.explicit_fcn, fjacb=self.explicit_fjb, fjacd=self.explicit_fjd, meta=dict(name='Sample Explicit Model', ref='ODRPACK UG, pg. 39'), ) explicit_dat = Data([0.,0.,5.,7.,7.5,10.,16.,26.,30.,34.,34.5,100.], [1265.,1263.6,1258.,1254.,1253.,1249.8,1237.,1218.,1220.6, 1213.8,1215.5,1212.]) explicit_odr = ODR(explicit_dat, explicit_mod, beta0=[1500.0, -50.0, -0.1], ifixx=[0,0,1,1,1,1,1,1,1,1,1,0]) explicit_odr.set_job(deriv=2) explicit_odr.set_iprint(init=0, iter=0, final=0) out = explicit_odr.run() assert_array_almost_equal( out.beta, np.array([1.2646548050648876e+03, -5.4018409956678255e+01, -8.7849712165253724e-02]), ) assert_array_almost_equal( out.sd_beta, np.array([1.0349270280543437, 1.583997785262061, 0.0063321988657267]), ) assert_array_almost_equal( out.cov_beta, np.array([[4.4949592379003039e-01, -3.7421976890364739e-01, -8.0978217468468912e-04], [-3.7421976890364739e-01, 1.0529686462751804e+00, -1.9453521827942002e-03], [-8.0978217468468912e-04, -1.9453521827942002e-03, 1.6827336938454476e-05]]), )
def test_output_file_overwrite(self): """ Verify fix for gh-1892 """ def func(b, x): return b[0] + b[1] * x p = Model(func) data = Data(np.arange(10), 12 * np.arange(10)) tmp_dir = tempfile.mkdtemp() error_file_path = os.path.join(tmp_dir, "error.dat") report_file_path = os.path.join(tmp_dir, "report.dat") try: ODR(data, p, beta0=[0.1, 13], errfile=error_file_path, rptfile=report_file_path).run() ODR(data, p, beta0=[0.1, 13], errfile=error_file_path, rptfile=report_file_path, overwrite=True).run() finally: # remove output files for clean up shutil.rmtree(tmp_dir)
def orthoregress(x, y): """Perform an Orthogonal Distance Regression on the given data, using the same interface as the standard scipy.stats.linregress function. Adapted from https://gist.github.com/robintw/d94eb527c44966fbc8b9#file-orthoregress-py Arguments: x: x data y: y data Returns: [slope, intercept, residual] Uses standard ordinary least squares to estimate the starting parameters then uses the scipy.odr interface to the ODRPACK Fortran code to do the orthogonal distance calculations. """ def f(p, x): """Basic linear regression 'model' for use with ODR""" return (p[0] * x) + p[1] linreg = stats.linregress(x, y) mod = Model(f) dat = Data(x, y) od = ODR(dat, mod, beta0=linreg[0:2]) out = od.run() return list(out.beta) + [out.res_var]
def fit_slope(X, Y, eX=None, eY=None): """Will fit a Y vs X with errors using the scipy ODR functionalities and a linear fitting function Args: X: Y: input arrays eX: eY: input uncertaintites [None] Returns: odr output """ # First filtering the Nan good = ~np.isnan(X) if eX is None: eX_good = None else: eX_good = eX[good] if eY is None: eY_good = None else: eY_good = eY[good] linear = Model(linear_fit) odr_data = RealData(X[good], Y[good], sx=eX_good, sy=eY_good) odr_run = ODR(odr_data, linear, beta0=[2., 1.]) return odr_run.run()
def do_the_fit(obs, **kwargs): global print_output, beta0 func = kwargs.get('function') yerr = kwargs.get('yerr') length = len(yerr) xerr = kwargs.get('xerr') if length == len(obs): assert 'x_constants' in kwargs data = RealData(kwargs.get('x_constants'), obs, sy=yerr) fit_type = 2 elif length == len(obs) // 2: data = RealData(obs[:length], obs[length:], sx=xerr, sy=yerr) fit_type = 0 else: raise Exception('x and y do not fit together.') model = Model(func) odr = ODR(data, model, beta0, partol=np.finfo(np.float64).eps) odr.set_job(fit_type=fit_type, deriv=1) output = odr.run() if print_output and not silent: print(*output.stopreason) print('chisquare/d.o.f.:', output.res_var) print_output = 0 beta0 = output.beta return output.beta[kwargs.get('n')]
def meanResiduals(pts): f = lambda B, x: B[0] * x + B[1] model = Model(f) data = RealData(list(p.x() for p in pts), list(p.y() for p in pts)) odr = ODR(data, model, beta0=[0., 1.]) out = odr.run() return out.sum_square / len(pts)
def __init__(self, recebe_x, recebe_y, recebe_x_erro, recebe_y_erro): #construtor da classe super().__init__( recebe_x, recebe_y, recebe_x_erro, recebe_y_erro) #chama o construtor da classe Fit_curve self.model = Model( self.funcao) #cria uma classe model com a função racional
def regress_odr(x, y, sx, sy, beta0=[0., 1.]): """Return an ODR linear fit """ linear = Model(my_linear) mydata = RealData(x.ravel(), y.ravel(), sx=sx.ravel(), sy=sy.ravel()) myodr = ODR(mydata, linear, beta0=beta0) return myodr.run()
def voltage_current_regression(): # read data from datafile df = pd.read_table(os.path.join(os.path.dirname(__file__), DATA_PATH, '1_a_soneloid.dat'), delim_whitespace=True, names=['current', 'voltage_min', 'voltage_max'], decimal=',', comment='#') # add columns for voltage mean and error df['voltage_mean'] = 0.5 * (df['voltage_min'] + df['voltage_max']) df['voltage_error'] = df['voltage_max'] - df['voltage_min'] # Create a model for fitting. linear_model = Model(regression_func) x = np.array(df['current']) y = np.array(df['voltage_mean']) sy = np.array(df['voltage_error']) data = RealData(x, y, sy=sy) odr = ODR(data, linear_model, beta0=[0., 1.]) out = odr.run() return out
def find_c13(self): ''' Find the c13 parameter by fitting a curve to the measured group velocities using the scipy ODR library. Since c13 is par tof the equation for the curve, the c13 value corresponding to the best fit curve is the result of the inversion. ''' self.c13_max = np.sqrt( self.c33 * (self.c11)) #The most physically reasonable maximum for c13 self.c13_min = np.sqrt(self.c33 * (self.c11 - 2 * self.c66) + self.c66**2) - self.c66 self.c13_0 = self.c13_min * 1.2 model = Model(self.forward_model, estimate=[self.c13_0, self.theta0, self.c11, self.c33]) data = RealData(self.group_angles, self.group_vels, sy=self.group_vel_err) fit = ODR(data, model, beta0=[self.c13_0, self.theta0, self.c11, self.c33], ifixb=[1, 1, 1, 1]) output = fit.run() best_fit = output.beta errors = output.sd_beta self.c13 = best_fit[0] self.c13_err = errors[0] self.theta0 = best_fit[1]
def graph(a,toc): #a:odr with xerrors or curvefit without? toc: number of the figure plt.figure(toc,figsize=(15,10)) for tickLabel in plt.gca().get_xticklabels()+plt.gca().get_yticklabels(): tickLabel.set_fontsize(15) plt.title("Number of coincidence counts in the peak of $Na^{22}$ wrt angle",fontsize=17) plt.xlabel(r'Angle $\theta$ (°)',fontsize=17) plt.ylabel('# coincidence events',fontsize=17) plt.scatter(Ld,res,label='\n Data with parameters'+\ ' \n $16$ $cm$ source-detectors'+\ ' \n $150$ $s/points$') if a==False: par, par_va = curve_fit(simplegaussian, Ld, res, p0=[70000, 180, 10,1000],sigma=err_res,absolute_sigma=True) chi2=round(sum(((res - simplegaussian(Ld,*par) )/ err_res) ** 2)/(len(Ld)-3),2) plt.plot(Lc,simplegaussian(Lc, *par),color='gold',label='Fit with '+r'$A\exp\{\frac{-(\theta-\mu)^2}{2\sigma^2}\}+Cst$'+\ ' \n $A =$%s'%int(par[0])+' $ \pm$ %s'%int(np.sqrt(np.diag(par_va)[0]))+' #'+\ ' \n $\mu =$ %s'%round(par[1],1)+' $\pm$ %s'%round(np.sqrt(np.diag(par_va)[1]),1)+'°'+\ ' \n $\sigma =$ %s'%round(par[2],1)+ '$\pm$ %s'%round(np.sqrt(np.diag(par_va)[2]),1)+'°'+\ ' \n $Cst=$ %s'%int(par[3])+' $\pm$ %s'%int(np.sqrt(np.diag(par_va)[3]))+' #'+\ ' \n $\chi^2/dof = $ %s'%chi2) plt.errorbar(Ld, res, err_res,fmt='.',label=r'$y=\sqrt{counts}$ '+\ '\n $x=0°$', color='black',ecolor='lightgray', elinewidth=3, capsize=0) else: data = RealData(Ld,res,err_resx,err_res) model = Model(simplegaussianl) odr = ODR(data, model, [73021, 183, 11,1208]) odr.set_job(fit_type=2) output = odr.run() xn = Lc yn = simplegaussianl(output.beta, xn) #pl.hold(True) #plot(Ld,res,'ro') #print(x,y) plt.plot(xn,yn,'k-',label=' ODR leastsq fit'+\ ' \n $\chi^2/dof = $ %s'%round(output.sum_square/(len(Ld)-3),2)+'\n') odr.set_job(fit_type=0) output = odr.run() par,par_va=output.beta,output.cov_beta yn = simplegaussianl(output.beta, xn) plt.plot(xn,yn,color='gold',label='ODR fit '+r'$A\exp\{\frac{-(\theta-\mu)^2}{2\sigma^2}\}+Cst$'+\ ' \n $A =$%s'%int(par[0])+' $ \pm$ %s'%int(np.sqrt(np.diag(par_va)[0]))+' #'+\ ' \n $\mu =$ %s'%round(par[1],1)+' $\pm$ %s'%round(np.sqrt(np.diag(par_va)[1]),1)+'°'+\ ' \n $\sigma =$ %s'%round(par[2],1)+ '$\pm$ %s'%round(np.sqrt(np.diag(par_va)[2]),1)+'°'+\ ' \n $Cst=$ %s'%int(par[3])+' $\pm$ %s'%int(np.sqrt(np.diag(par_va)[3]))+' #'+\ ' \n Sum of squares/dof $= $ %s'%round(output.sum_square/(len(Ld)-3),2)) plt.legend(loc=0) plt.errorbar(Ld, res, err_res,err_resx,label=r'$y=\sqrt{counts}$ '+\ '\n $x=$%s'%errx+'°',fmt='.', color='black',ecolor='lightgray', elinewidth=3, capsize=0) plt.gca().set_xlim(140,220) plt.legend(bbox_to_anchor=(0.68, 0.58), loc=1, borderaxespad=0.,prop={'size':14}) plt.yscale('log') plt.ylim(1e2,1e5)
def ortho_regress(x, y): linreg = linregress(x, y) mod = Model(f) dat = Data(x, y) od = ODR(dat, mod, beta0=linreg[0:2]) out = od.run() #print(list(out.beta)) #return list(out.beta) + [np.nan, np.nan, np.nan] return(list(out.beta))
def test_empty_data(self): beta0 = [0.02, 0.0] linear = Model(self.empty_data_func) empty_dat = Data([], []) assert_warns(OdrWarning, ODR, empty_dat, linear, beta0=beta0) empty_dat = RealData([], []) assert_warns(OdrWarning, ODR, empty_dat, linear, beta0=beta0)
def fit(self, x, y): # Initial estimate of betas linreg = linregress(x, y) linear = Model(self.model) mydata = Data(x, y) myodr = ODR(mydata, linear, beta0=linreg[0:2]) myoutput = myodr.run() self.betas = myoutput.beta
def orthogonal_distance_regression(func, data, err, beta0=None): """Fit the function using scipy.odr and return fit output.""" if not beta0: beta0 = _start_values(data) model = Model(func) rdata = _real_data(data, err) fit = ODR(rdata, model, beta0=beta0) output = fit.run() print(output.beta) return output
def sigma(X, Y, X_err, Y_err): linear_model = Model(Linear) data = RealData(X, Y, sx=X_err, sy=Y_err) odr = ODR(data, linear_model, beta0=[0., 1.]) out = odr.run() m = out.beta[0] b = out.beta[1] recta = [(I[i] - (V[i] * m + b)) for i in range(len(I))] return len(recta), f.dispersion(recta)
def orthoregress(x, y, xerr, yerr): linreg = linregress(x, y) mod = Model(f) dat = RealData(x, y, sx=xerr, sy=yerr) od = ODR(dat, mod, beta0=linreg[0:2]) out = od.run() return list(out.beta)
def test_lorentz(self): l_sy = np.array([.29] * 18) l_sx = np.array([ .000972971, .000948268, .000707632, .000706679, .000706074, .000703918, .000698955, .000456856, .000455207, .000662717, .000654619, .000652694, .000000859202, .00106589, .00106378, .00125483, .00140818, .00241839 ]) l_dat = RealData( [ 3.9094, 3.85945, 3.84976, 3.84716, 3.84551, 3.83964, 3.82608, 3.78847, 3.78163, 3.72558, 3.70274, 3.6973, 3.67373, 3.65982, 3.6562, 3.62498, 3.55525, 3.41886 ], [ 652, 910.5, 984, 1000, 1007.5, 1053, 1160.5, 1409.5, 1430, 1122, 957.5, 920, 777.5, 709.5, 698, 578.5, 418.5, 275.5 ], sx=l_sx, sy=l_sy, ) l_mod = Model(self.lorentz, meta=dict(name='Lorentz Peak')) l_odr = ODR(l_dat, l_mod, beta0=(1000., .1, 3.8)) out = l_odr.run() assert_array_almost_equal( out.beta, np.array([ 1.4306780846149925e+03, 1.3390509034538309e-01, 3.7798193600109009e+00 ]), ) assert_array_almost_equal( out.sd_beta, np.array([ 7.3621186811330963e-01, 3.5068899941471650e-04, 2.4451209281408992e-04 ]), ) assert_array_almost_equal( out.cov_beta, np.array([[ 2.4714409064597873e-01, -6.9067261911110836e-05, -3.1236953270424990e-05 ], [ -6.9067261911110836e-05, 5.6077531517333009e-08, 3.6133261832722601e-08 ], [ -3.1236953270424990e-05, 3.6133261832722601e-08, 2.7261220025171730e-08 ]]), )
def orth_regression(obs, model): linear = Model(f) mydata = RealData(obs, model) myodr = ODR(mydata, linear, beta0=[1., 0.]) myoutput = myodr.run() params = myoutput.beta gradient = params[0] y_intercept = params[1] res_var = myoutput.res_var return np.around(gradient, 2), np.around(y_intercept, 2), np.around(res_var, 2)
def run(self): fit_data = RealData(self.data['ref_spd'].values.flatten(), self.data['target_spd'].values.flatten()) p, res = lstsq(np.nan_to_num(fit_data.x[:, np.newaxis] ** [1, 0]), np.nan_to_num(np.asarray(fit_data.y) [:, np.newaxis]))[0:2] self._model = ODR(fit_data, Model(OrthogonalLeastSquares.linear_func), beta0=[p[0][0], p[1][0]]) self.out = self._model.run() self.params = {'slope': self.out.beta[0], 'offset': self.out.beta[1]} self.params['r2'] = self.get_r2() self.params['Num data points'] = self.num_data_pts # print("Model output:", self.out.pprint()) self.show_params()
def ODR_fitting(xdata, ydata, fitfunction, beta, fix): bpl_all = Model(fitfunction) data_all = RealData(xdata, ydata, sx=np.cov([xdata, ydata])[0][1], sy=np.cov([xdata, ydata])[0][1]) odr_all = ODR(data_all, bpl_all, beta0=beta, ifixb=fix) odr_all.set_job(fit_type=0) output_all = odr_all.run() #output_all.pprint() return (output_all.beta, output_all.sd_beta)
def test_ifixx(self): x1 = [-2.01, -0.99, -0.001, 1.02, 1.98] x2 = [3.98, 1.01, 0.001, 0.998, 4.01] fix = np.vstack((np.zeros_like(x1, dtype=int), np.ones_like(x2, dtype=int))) data = Data(np.vstack((x1, x2)), y=1, fix=fix) model = Model(lambda beta, x: x[1, :] - beta[0] * x[0, :]**2., implicit=True) odr1 = ODR(data, model, beta0=np.array([1.])) sol1 = odr1.run() odr2 = ODR(data, model, beta0=np.array([1.]), ifixx=fix) sol2 = odr2.run() assert_equal(sol1.beta, sol2.beta)
def _run_odr(self): """Run an ODR regression""" linear = Model(self._modelODR) mydata = Data(ravel(self._datax), ravel(self._datay), 1) myodr = ODR(mydata, linear, beta0=self._guess, maxit=10000) myoutput = myodr.run() self._result = myoutput.beta self._stdev = myoutput.sd_beta self._covar = myoutput.cov_beta self._odr = myoutput
def test_ticket_1253(self): def linear(c, x): return c[0] * x + c[1] c = [2.0, 3.0] x = np.linspace(0, 10) y = linear(c, x) model = Model(linear) data = Data(x, y, wd=1.0, we=1.0) job = ODR(data, model, beta0=[1.0, 1.0]) result = job.run() assert_equal(result.info, 2)
def ODR_Fit(function, x, y, x_err, y_err): print('Fit:\t', function.__name__, '\n') # Create a model for fitting. model = Model(function) # Create a RealData object using our initiated data from above. D = RealData(x, y, sx=x_err, sy=y_err) # Set up ODR with the model and data. odr = ODR(D, model, beta0=[0.7, 0.]) # Run the regression. out = odr.run() # Use the in-built pprint method to give us results. out.pprint() print('\n') return out
def fit_xy(x, y): # Create a model for fitting. linear_model = Model(linear_func) # Create a RealData object using our initiated data from above. data = RealData(x, y) # Set up ODR with the model and data. odr = ODR(data, linear_model, beta0=[0., 1.]) # Run the regression. out = odr.run() return out.beta
def linear_regression(data, err): """Calculate a linear regression using scipy.odr and return fit output.""" print('Fitting with') print(data[:, 0], data[:, 1]) print('and Error') print(err[:, 0], err[:, 1]) beta0 = get_start_values(data) model = Model(linear_model) rdata = RealData(data[:, 0], data[:, 1], sx=err[:, 0], sy=err[:, 1]) # TODO: check different errors fit = ODR(rdata, model, beta0=beta0) output = fit.run() print(output.beta) return output
def odr_inversion(self, initial_guess=None): ''' Just another curve fit/inversion method to find c13, using scipy's ODR class. Does the same job as curve_fit. ''' def odr_forward_model(parameters, xdata): c13, c11, c33, c55, c66, theta = parameters return self.forward_model(xdata, c13, c11, c33, c55, c66, theta) from scipy.odr import ODR, RealData, Model c13_max = np.sqrt(self.c33 * (self.c11 - self.c66)) c13_min = np.sqrt(self.c33 * (self.c11 - 2 * self.c66) + self.c66**2) - self.c66 if not initial_guess: initial_guess = c13_min * 1.1 print(self.c11, self.c33, self.c55, self.c66, self.theta0) print('ok', round(c13_min / 1e9), round(c13_max / 1e9)) parameters = ['c11', 'c33', 'c55', 'c66', 'theta0'] fixed_params = [0, 0, 0, 0, 0] for i, item in enumerate(parameters): if item in self.parameters_to_invert: fixed_params[i] = 1 fixed_params = [ 1, 1, 1, 0, 0, 1 ] #MAKE THIS [1]+fixed_params. I'M FORCING C55 NOT TO BE INVERTED model = Model(odr_forward_model, estimate=[ initial_guess, self.c11, self.c33, self.c55, self.c66, self.theta0 ]) data = RealData(self.group_angles, self.group_vels, sy=self.group_vel_err) fit = ODR(data, model, beta0=[ initial_guess, self.c11, self.c33, self.c55, self.c66, self.theta0 ], ifixb=fixed_params) output = fit.run() best_fit = output.beta errors = output.sd_beta return best_fit, errors