diff options
Diffstat (limited to 'astro/fitting/fit_betasbp_cut.py')
| -rwxr-xr-x | astro/fitting/fit_betasbp_cut.py | 32 |
1 files changed, 20 insertions, 12 deletions
diff --git a/astro/fitting/fit_betasbp_cut.py b/astro/fitting/fit_betasbp_cut.py index 9dcf730..2d2931e 100755 --- a/astro/fitting/fit_betasbp_cut.py +++ b/astro/fitting/fit_betasbp_cut.py @@ -11,6 +11,9 @@ # 2015/05/29 # # Changelogs: +# v0.5.1, 2015/06/07, Aaron LI +# * fixed 'dof' calculation with 'n-p-1' +# * fixed 'par_eps' calculation/configuration # v0.5.0, 2015/06/07, Aaron LI # * added 'fit_model_bounds' using 'scipy.optimize.minimize' to # perform function minimization with bounds @@ -33,7 +36,7 @@ # * Support read model initial parameter values from input file. # # TODO: -# * calculate fitting parameter's standard deviation +# * calculate fitting parameter's confidence interval / confidence bounds # * to normalize fitting paramters to be the same order of magnitude # for better minimization # Ref: http://stackoverflow.com/questions/21369139/normalization-for-optimization-in-python @@ -42,7 +45,7 @@ from __future__ import print_function, division -__version__ = "0.5.0" +__version__ = "0.5.1" __date__ = "2015/06/07" import numpy as np @@ -108,7 +111,7 @@ def fit_model(func, xdata, ydata, yerrdata, p0): # the function evaluated at the output parameters fvec = lambda x: func(x, *popt) # degree of freedom - dof = len(xdata) - len(popt) + dof = len(xdata) - len(popt) - 1 # chi squared chisq = np.sum(((ydata - fvec(xdata)) / yerrdata) ** 2) # one standard deviation errors on the parameters @@ -122,10 +125,12 @@ def fit_model(func, xdata, ydata, yerrdata, p0): return (popt, infodict) -def fit_model_bounds(func, xdata, ydata, yerrdata, p0=None, bounds=None, - options=None): +def fit_model_bounds(func, xdata, ydata, yerrdata, p0=None, + bounds=None, options=None): """ - Fit the provided data with the beta model. + Fit the provided data with the beta model, and apply parameter + bounds requirements. + Using 'scipy.optimize.minimize'. Arguments: p0: initial values for the parameters of beta model @@ -142,12 +147,12 @@ def fit_model_bounds(func, xdata, ydata, yerrdata, p0=None, bounds=None, * perr: one standard deviation errors on the parameters """ # objective function to be minimized, required format of 'f(x, *args)' - f = lambda x: calc_chisq(func, xdata, ydata, yerrdata, *x) + f = lambda p: calc_chisq(func, xdata, ydata, yerrdata, *p) # minimize the given function using 'scipy.optimize.minimize' with bounds res = minimize(f, p0, method=MINIMIZE_METHOD, bounds=bounds, options=options) popt = res.x - print("DEBUG: minimization results:\n", res, file=sys.stderr) + #print("DEBUG: minimization results:\n", res, file=sys.stderr) # check minimization results if not res.success: @@ -157,7 +162,7 @@ def fit_model_bounds(func, xdata, ydata, yerrdata, p0=None, bounds=None, # the function evaluated at the output parameters fvec = lambda x: func(x, *popt) # degree of freedom - dof = len(xdata) - len(popt) + dof = len(xdata) - len(popt) - 1 # chi squared chisq = res.fun # one standard deviation errors on the parameters @@ -408,12 +413,15 @@ def main(): # initial values par_0 = np.array([s0_0, rc_0, beta_0, c_0]) # parameter bounds - par_bounds = [(s0_lower, s0_upper), (rc_lower, rc_upper), - (beta_lower, beta_upper), (c_lower, c_upper)] + par_bounds = np.array([(s0_lower, s0_upper), (rc_lower, rc_upper), + (beta_lower, beta_upper), (c_lower, c_upper)]) # set eps for the parameters (required for the minimize method, # otherwise error 'ABNORMAL_TERMINATION_IN_LNSRCH' occurs, which # may due to the different order of magnitude of each parameters) - par_eps = par_0 * 1e-4 + par_eps = np.absolute(par_0) * 1e-3 + par_eps[ par_eps<1e-15 ] = 1e-15 # set par_eps >= 1e-14 + if args.verbose: + print("DEBUG: parameters eps:\n", par_eps, file=sys.stderr) if args.bounds: ## 'fit_model_bounds' to perform fitting with bounds |