If the issue of "fast" is not an issue, then why is an alternative minimisation required? Are you just after the covariance matrix?
Regards, Edward On 25 August 2014 11:16, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: > Hi Edward. > > In this target function, exist the target function whereby > scipy.optimize.leastsq minimises. > > minfx minimises by minimisation of chi2. > > scipy.optimize.leastsq minimises the return of a function which > calculate the array of difference between > function and measured values. > > It will then (I guess) minimise sum squares. > > You could probably make a call to the target function "exponential" instead. > > But I am not so good with C code, and having the code in python makes > it possible for me to bug-fix faster. > > The issue of "fast", does not really come into play here, as a > minimisation takes about 0.02 seconds anyway. > > Best > Troels > > > 2014-08-25 10:33 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >> Hi Troels, >> >> This new target_functions.relax_disp_curve_fit module clashes with the >> C module. It is repetitive, the code already exists in the >> target_functions.relax_fit module. Why is the faster C module not >> being used? >> >> Regards, >> >> Edward >> >> >> >> On 25 August 2014 01:08, <tlin...@nmr-relax.com> wrote: >>> Author: tlinnet >>> Date: Mon Aug 25 01:08:48 2014 >>> New Revision: 25230 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=25230&view=rev >>> Log: >>> Moved the target function for minimisation of exponential fit into the >>> target functions folder. >>> >>> task #7822(https://gna.org/task/index.php?7822): Implement user function to >>> estimate R2eff and associated errors for exponential curve fitting. >>> >>> Added: >>> trunk/target_functions/relax_disp_curve_fit.py >>> - copied, changed from r25229, >>> trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py >>> Removed: >>> trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py >>> Modified: >>> trunk/target_functions/__init__.py >>> >>> trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py >>> trunk/test_suite/shared_data/curve_fitting/profiling/verify_error.py >>> >>> Modified: trunk/target_functions/__init__.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/target_functions/__init__.py?rev=25230&r1=25229&r2=25230&view=diff >>> ============================================================================== >>> --- trunk/target_functions/__init__.py (original) >>> +++ trunk/target_functions/__init__.py Mon Aug 25 01:08:48 2014 >>> @@ -32,5 +32,6 @@ >>> 'mf', >>> 'n_state_model', >>> 'potential', >>> - 'relax_disp' >>> + 'relax_disp', >>> + 'relax_disp_curve_fit' >>> ] >>> >>> Copied: trunk/target_functions/relax_disp_curve_fit.py (from r25229, >>> trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py) >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp_curve_fit.py?p2=trunk/target_functions/relax_disp_curve_fit.py&p1=trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py&r1=25229&r2=25230&rev=25230&view=diff >>> ============================================================================== >>> (empty) >>> >>> Modified: >>> trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py?rev=25230&r1=25229&r2=25230&view=diff >>> ============================================================================== >>> --- >>> trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py >>> (original) >>> +++ >>> trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py >>> Mon Aug 25 01:08:48 2014 >>> @@ -57,7 +57,7 @@ >>> # relax module imports. >>> from status import Status; status = Status() >>> from target_functions.relax_fit import setup, func, dfunc, d2func, >>> back_calc_I >>> -from relax_fit import Exponential >>> +from target_functions.relax_disp_curve_fit import Exponential >>> >>> >>> # Alter setup. >>> >>> Removed: trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py?rev=25229&view=auto >>> ============================================================================== >>> --- trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py >>> (original) >>> +++ trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py >>> (removed) >>> @@ -1,135 +0,0 @@ >>> -############################################################################### >>> -# >>> # >>> -# Copyright (C) 2013-2014 Edward d'Auvergne >>> # >>> -# Copyright (C) 2014 Troels E. Linnet >>> # >>> -# >>> # >>> -# This file is part of the program relax (http://www.nmr-relax.com). >>> # >>> -# >>> # >>> -# This program is free software: you can redistribute it and/or modify >>> # >>> -# it under the terms of the GNU General Public License as published by >>> # >>> -# the Free Software Foundation, either version 3 of the License, or >>> # >>> -# (at your option) any later version. >>> # >>> -# >>> # >>> -# This program is distributed in the hope that it will be useful, >>> # >>> -# but WITHOUT ANY WARRANTY; without even the implied warranty of >>> # >>> -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the >>> # >>> -# GNU General Public License for more details. >>> # >>> -# >>> # >>> -# You should have received a copy of the GNU General Public License >>> # >>> -# along with this program. If not, see <http://www.gnu.org/licenses/>. >>> # >>> -# >>> # >>> -############################################################################### >>> - >>> -# Module docstring. >>> -"""Target functions for relaxation fit.""" >>> - >>> -# Python module imports. >>> -from copy import deepcopy >>> -from numpy import exp, multiply, sum >>> - >>> -# relax module imports. >>> - >>> - >>> -class Exponential: >>> - def __init__(self, num_params=None, num_times=None, values=None, >>> sd=None, relax_times=None, scaling_matrix=None): >>> - """Relaxation dispersion target functions for optimisation. >>> - """ >>> - >>> - # Store variables. >>> - self.num_params = num_params >>> - self.num_times = num_times >>> - self.values = values >>> - self.errors = sd >>> - self.relax_times = relax_times >>> - self.scaling_matrix = scaling_matrix >>> - >>> - # Create the structure for holding the back-calculated R2eff >>> values (matching the dimensions of the values structure). >>> - self.back_calc = deepcopy(self.values) >>> - >>> - # Define function to minimise. >>> - self.func = self.func_exp >>> - self.calc = self.calc_exp >>> - >>> - >>> - def chi2_rankN(self, data, back_calc_vals, errors): >>> - """Function to calculate the chi-squared value for multiple numpy >>> array axis. >>> - >>> - @param data: The multi dimensional vectors of yi values. >>> - @type data: numpy multi dimensional array >>> - @param back_calc_vals: The multi dimensional vectors of yi(theta) >>> values. >>> - @type back_calc_vals: numpy multi dimensional array >>> - @param errors: The multi dimensional vectors of sigma_i >>> values. >>> - @type errors: numpy multi dimensional array >>> - @return: The chi-squared value. >>> - @rtype: float >>> - """ >>> - >>> - # Calculate the chi-squared statistic. >>> - return sum((1.0 / errors * (data - back_calc_vals))**2) >>> - >>> - >>> - def calc_exp(self, times=None, r2eff=None, i0=None): >>> - """Calculate the function values of exponential function. >>> - >>> - @keyword times: The time points. >>> - @type times: float >>> - @keyword r2eff: The effective transversal relaxation rate. >>> - @type r2eff: float >>> - @keyword i0: The initial intensity. >>> - @type i0: float >>> - @return: The function values. >>> - @rtype: float >>> - """ >>> - >>> - # Calculate. >>> - return i0 * exp( -times * r2eff) >>> - >>> - >>> - def calc_exp_chi2(self, r2eff=None, i0=None): >>> - """Calculate the chi-squared value of exponential function. >>> - >>> - >>> - @keyword r2eff: The effective transversal relaxation rate. >>> - @type r2eff: float >>> - @keyword i0: The initial intensity. >>> - @type i0: float >>> - @return: The chi-squared value. >>> - @rtype: float >>> - """ >>> - >>> - # Calculate. >>> - self.back_calc[:] = self.calc_exp(times=self.relax_times, >>> r2eff=r2eff, i0=i0) >>> - >>> - # Return the total chi-squared value. >>> - return self.chi2_rankN(data=self.values, >>> back_calc_vals=self.back_calc, errors=self.errors) >>> - >>> - >>> - def func_exp(self, params): >>> - """Target function for exponential fit. >>> - >>> - @param params: The vector of parameter values. >>> - @type params: numpy rank-1 float array >>> - @return: The chi-squared value. >>> - @rtype: float >>> - """ >>> - >>> - # Unpack the parameter values. >>> - r2eff = params[0] >>> - i0 = params[1] >>> - >>> - # Calculate and return the chi-squared value. >>> - return self.calc_exp_chi2(r2eff=r2eff, i0=i0) >>> - >>> - >>> - def func_exp_general(self, params, xdata, ydata): >>> - """Target function for minimisation with scipy.optimize.leastsq >>> - """ >>> - >>> - return self.calc_exp(xdata, *params) - ydata >>> - >>> - >>> - def func_exp_weighted_general(self, params, xdata, ydata, weights): >>> - """Target function for minimisation with scipy.optimize.leastsq >>> - """ >>> - >>> - return weights * (self.calc_exp(xdata, *params) - ydata) >>> >>> Modified: >>> trunk/test_suite/shared_data/curve_fitting/profiling/verify_error.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/profiling/verify_error.py?rev=25230&r1=25229&r2=25230&view=diff >>> ============================================================================== >>> --- trunk/test_suite/shared_data/curve_fitting/profiling/verify_error.py >>> (original) >>> +++ trunk/test_suite/shared_data/curve_fitting/profiling/verify_error.py >>> Mon Aug 25 01:08:48 2014 >>> @@ -32,7 +32,7 @@ >>> from status import Status; status = Status() >>> >>> # Initial try for Exponential class. >>> -from relax_fit import Exponential >>> +from target_functions.relax_disp_curve_fit import Exponential >>> >>> # Define data path. >>> prev_data_path = status.install_path + >>> sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Kjaergaard_et_al_2013' >>> +sep+ "check_graphs" +sep+ "mc_2000" +sep+ "R2eff" >>> >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-commits mailing list >>> relax-comm...@gna.org >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> relax-devel@gna.org >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
