Hi Edward. I don't think I will look into this.
I don't think the code should be "chopped" up yet, since there could still be some bugfixing. And I get quite confused with the API setup. Best Troels 2014-08-28 8:53 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > Why not call this user function error_analysis.covariance_matrix? By > using the specific analysis API, you can easily generalise this. It > requires only a few steps, mainly just shifting your existing code > around: > > 1) Rename the user function. > > 2) Have a backend in the new module pipe_control.error_analysis (I > may then merge the pipe_control.monte_carlo module into it for a > general module for all error estimate techniques). A good example of > how to get the specific analysis API and use it is the Monte Carlo > error_analysis() function > (http://www.nmr-relax.com/api/3.2/pipe_control.monte_carlo-pysrc.html#error_analysis). > > 3) Add a new API method to specific_analyses.api_base which, like > most of the others, raises a RelaxImplementError (e.g. > covariance_matrix()). This allows each analysis type to implement it > as desired, and allows the user function to fail cleanly when used on > an analysis that doesn't support it. > > 4) Shift the covariance matrix calculation code of multifit_covar() > into the relax library, maybe in the lib.statistics module. Btw, the > docstring of this function needs a bit of work to allow the API > documentation to be compiled. > > 5) Create the dispersion specific covariance_matrix() method which > obtains the Jacobian and calls the relax library function. This would > just be the estimate_r2eff_err() function converted into a method. > > This is how you add functionality to this API, and it would be a > useful learning exercise. If you know how to control this API, it > will be very powerful when you are adding new features to relax. In > this case, most of your code is unrelated to the dispersion analysis > and it is a perfect example of such an independent and powerful > feature. It would be a rather simple exercise, changing the new > system tests and just shifting the current functions/methods to fit > into this infrastructure. > > Note that the feature of estimating the initial exponential curve > parameters by linearisation is also partly analysis independent as it > is of benefit for the relaxation curve-fitting analysis type as well. > So it could be spun out as a separate user function (maybe > exponential_curve.linear_estimate), use the specific API, and putting > the specific_analyses/relax_disp/estimate_r2eff.py > Exp.estimate_x0_exp() method into the relax library. This too would > be a simple code shifting exercise. > > What do you think? The specific analysis API is one of the most > important design concepts in relax, and being able to control and > extend it will allow new ideas to be added much more quickly. > > Regards, > > Edward > > > On 27 August 2014 20:06, <[email protected]> wrote: >> Author: tlinnet >> Date: Wed Aug 27 20:06:23 2014 >> New Revision: 25347 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=25347&view=rev >> Log: >> Added front-end to the new user function relax_disp.r2eff_err_estimate(), >> which will estimate the R2eff errors >> from a pipe and spins with optimised values of R2eff and i0. >> >> The co-variance matrix can be calculated from the optimised parameters, and >> the Jacobian. >> >> Big care should be taken not to directly trust these results, since the >> errors are quite different compared to the Monte-Carlo simulations. >> >> This implementation, will reach the exact same error estimation as >> scipy.optimize.leastsq. >> >> But with much better control over the data, and insight into the >> calculations. >> >> task #7822(https://gna.org/task/index.php?7822): Implement user function to >> estimate R2eff and associated errors for exponential curve fitting. >> >> Modified: >> trunk/user_functions/relax_disp.py >> >> Modified: trunk/user_functions/relax_disp.py >> URL: >> http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=25347&r1=25346&r2=25347&view=diff >> ============================================================================== >> --- trunk/user_functions/relax_disp.py (original) >> +++ trunk/user_functions/relax_disp.py Wed Aug 27 20:06:23 2014 >> @@ -40,6 +40,7 @@ >> from pipe_control.mol_res_spin import get_spin_ids >> from specific_analyses.relax_disp.catia import catia_execute, catia_input >> from specific_analyses.relax_disp.cpmgfit import cpmgfit_execute, >> cpmgfit_input >> +from specific_analyses.relax_disp.estimate_r2eff import estimate_r2eff_err >> from specific_analyses.relax_disp.data import cpmg_setup, insignificance, >> plot_disp_curves, plot_exp_curves, r2eff_read, r2eff_read_spin, relax_time, >> set_exp_type, r20_from_min_r2eff, spin_lock_field, spin_lock_offset, >> write_disp_curves >> from specific_analyses.relax_disp.data import INTERPOLATE_DISP, >> INTERPOLATE_OFFSET, X_AXIS_DISP, X_AXIS_W_EFF, X_AXIS_THETA, >> Y_AXIS_R2_R1RHO, Y_AXIS_R2_EFF >> from specific_analyses.relax_disp.nessy import nessy_input >> @@ -627,6 +628,50 @@ >> uf.gui_icon = "oxygen.status.object-locked" >> uf.wizard_size = (800, 500) >> uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png' >> + >> + >> +# The relax_disp.r2eff_err_estimate user function. >> +uf = uf_info.add_uf('relax_disp.r2eff_err_estimate') >> +uf.title = "Estimate R2eff errors by the Jacobian matrix." >> +uf.title_short = "Estimate R2eff errors." >> +uf.add_keyarg( >> + name = "spin_id", >> + py_type = "str", >> + arg_type = "spin ID", >> + desc_short = "spin ID to restrict value setting to", >> + desc = "The spin ID string to restrict value setting to.", >> + can_be_none = True >> +) >> +uf.add_keyarg( >> + name = "epsrel", >> + py_type = "float", >> + default = 0.0, >> + desc_short = "parameter to remove linear-dependent columns.", >> + desc = "The parameter to remove linear-dependent columns when J is rank >> deficient.", >> + can_be_none = False >> +) >> +uf.add_keyarg( >> + name = "verbosity", >> + default = 1, >> + py_type = "int", >> + desc_short = "amount of information to print.", >> + desc = "The higher the value, the greater the verbosity.", >> + can_be_none = False >> +) >> +# Description. >> +uf.desc.append(Desc_container()) >> +uf.desc[-1].add_paragraph("This is a new experimental feature from version >> 3.3, and should only be tried out with big care.") >> +uf.desc[-1].add_paragraph("This will estimate R2eff errors by using the >> exponential decay Jacobian matrix 'J' to compute the covariance matrix of >> the best-fit parameters.") >> +uf.desc[-1].add_paragraph("This can be an huge time saving step, when >> performing model fitting in R1rho. Errors of R2eff values, are normally >> estimated by time-consuming Monte-Carlo simulations.") >> +uf.desc[-1].add_paragraph("This method is inspired from the GNU Scientific >> Library (GSL).") >> +uf.desc[-1].add_paragraph("The covariance matrix is given by: covar = Qxx = >> (J^T J)^{-1}.") >> +uf.desc[-1].add_paragraph("Qxx is computed by QR decomposition, Qxx=QR, >> Qxx^-1=R^-1 Q^T. The columns of R which satisfy: |R_{kk}| <= epsrel >> |R_{11}| are considered linearly-dependent and are excluded from the >> covariance matrix (the corresponding rows and columns of the covariance >> matrix are set to zero).") >> +uf.desc[-1].add_paragraph("The parameter 'epsrel' is used to remove >> linear-dependent columns when J is rank deficient.") >> +uf.backend = estimate_r2eff_err >> +uf.menu_text = "&r2eff_err_estimate" >> +uf.gui_icon = "relax.relax_fit" >> +uf.wizard_size = (800, 800) >> +uf.wizard_image = ANALYSIS_IMAGE_PATH + sep + 'blank_150x150.png' >> >> >> # The relax_disp.r2eff_read user function. >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-commits mailing list >> [email protected] >> >> 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 > [email protected] > > 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 [email protected] 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
