Hmmm, maybe a better solution for that system test is to add the check and fail with a RelaxError. The solution:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?r1=21957&r2=21956&pathrev=21957 is probably not the best. If we have one specific_analyses.relax_disp.checks.check_*() function for this, then we can use it at the start of many different functions in the specific_analyses.relax_disp package. The system test could then be modified to include a self.assertRaises() call. Note that the save state file is called 'bug_21460_bad_fields.bz2' (http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?r1=21954&r2=21953&pathrev=21954), so it is not a desired state to be in. Regards, Edward On 19 May 2014 15:54, Troels Emtekær Linnet <[email protected]> wrote: > Hi Ed. > > You are handling this bug here: > Relax_disp.test_bug_21460_disp_cluster_fail > > """U{Bug #21460<https://gna.org/bugs/?21460>} catch, the > failure due to a spectrometer frequency having no relaxation data.""" > > Best > Troels > > 2014-05-19 15:04 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Hi Troels, >> >> I have one suggestion here. The following check is not necessary: >> >> if num_points > 0: >> >> This will slow down the code. Note that this situation should never, >> ever be reached. If it is, then we are doing something wrong in the >> specific_analyses.relax_disp package prior to passing the data into >> the target function class. num_points can only be zero if there are >> no dispersion points in a curve, but then there is no curve! So we >> shouldn't supply the target function with information about such a >> non-existent curve. >> >> Regards, >> >> Edward >> >> >> >> >> On 19 May 2014 14:44, <[email protected]> wrote: >>> Author: tlinnet >>> Date: Mon May 19 14:44:12 2014 >>> New Revision: 23240 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=23240&view=rev >>> Log: >>> Math-domain catching for model CR72. >>> >>> task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models. >>> >>> This is to implement catching of math domain errors, before they occur. >>> These can be found via the --numpy-raise function to the systemtests. >>> >>> To make the code look clean, the class object "back_calc" is no longer >>> being updated per time point, but is updated in the relax_disp target >>> function in >>> one go. >>> >>> Modified: >>> branches/disp_speed/lib/dispersion/cr72.py >>> branches/disp_speed/target_functions/relax_disp.py >>> >>> Modified: branches/disp_speed/lib/dispersion/cr72.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23240&r1=23239&r2=23240&view=diff >>> ============================================================================== >>> --- branches/disp_speed/lib/dispersion/cr72.py (original) >>> +++ branches/disp_speed/lib/dispersion/cr72.py Mon May 19 14:44:12 2014 >>> @@ -92,12 +92,12 @@ >>> """ >>> >>> # Python module imports. >>> -from numpy import arccosh, array, cos, cosh, isfinite, sqrt, sum >>> +from numpy import arccosh, array, cos, cosh, isfinite, max, sqrt, sum >>> >>> # Repetitive calculations (to speed up calculations). >>> eta_scale = 2.0**(-3.0/2.0) >>> >>> -def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, >>> cpmg_frqs=None, back_calc=None, num_points=None): >>> +def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, >>> cpmg_frqs=None, num_points=None): >>> """Calculate the R2eff values for the CR72 model. >>> >>> See the module docstring for details. >>> @@ -115,9 +115,7 @@ >>> @type kex: float >>> @keyword cpmg_frqs: The CPMG nu1 frequencies. >>> @type cpmg_frqs: numpy rank-1 float array >>> - @keyword back_calc: The array for holding the back calculated >>> R2eff values. Each element corresponds to one of the CPMG nu1 frequencies. >>> - @type back_calc: numpy rank-1 float array >>> - @keyword num_points: The number of points on the dispersion curve, >>> equal to the length of the cpmg_frqs and back_calc arguments. >>> + @keyword num_points: The number of points on the dispersion curve, >>> equal to the length of the cpmg_frqs. >>> @type num_points: int >>> """ >>> >>> @@ -151,6 +149,14 @@ >>> etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs >>> etaneg = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2) / cpmg_frqs >>> >>> + # Catch math domain error of cosh(val > 710). >>> + # This is when etapos > 710. >>> + if num_points > 0: >>> + if max(etapos) > 700: >>> + R2eff = array([1e100]*num_points) >>> + >>> + return R2eff >>> + >>> # Calculate R2eff. >>> R2eff = r20_kex - cpmg_frqs * arccosh( Dpos * cosh(etapos) - Dneg * >>> cos(etaneg) ) >>> >>> @@ -159,6 +165,4 @@ >>> if not isfinite(sum(R2eff)): >>> R2eff = array([1e100]*num_points) >>> >>> - # Parse back the value to update the back_calc class object. >>> - for i in range(num_points): >>> - back_calc[i] = R2eff[i] >>> + return R2eff >>> >>> Modified: branches/disp_speed/target_functions/relax_disp.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/branches/disp_speed/target_functions/relax_disp.py?rev=23240&r1=23239&r2=23240&view=diff >>> ============================================================================== >>> --- branches/disp_speed/target_functions/relax_disp.py (original) >>> +++ branches/disp_speed/target_functions/relax_disp.py Mon May 19 14:44:12 >>> 2014 >>> @@ -484,7 +484,7 @@ >>> dw_frq = dw[si] * self.frqs[0][si][mi] >>> >>> # Back calculate the R2eff values. >>> - r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], >>> pA=pA, dw=dw_frq, kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0], >>> back_calc=self.back_calc[0][si][mi][0], >>> num_points=self.num_disp_points[0][si][mi][0]) >>> + self.back_calc[0][si][mi][0] = >>> r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq, >>> kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0], >>> num_points=self.num_disp_points[0][si][mi][0]) >>> >>> # For all missing data points, set the back-calculated >>> value to the measured values so that it has no effect on the chi-squared >>> value. >>> for di in range(self.num_disp_points[0][si][mi][0]): >>> >>> >>> _______________________________________________ >>> 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
