Hi Troels, As I mentioned previously (in the thread at http://thread.gmane.org/gmane.science.nmr.relax.scm/20984), it is good practice to separate the two changes here. I.e. have one commit for the API change, and one commit for the other changes.
Cheers, Edward On 20 May 2014 01:47, <[email protected]> wrote: > Author: tlinnet > Date: Tue May 20 01:47:30 2014 > New Revision: 23246 > > URL: http://svn.gna.org/viewcvs/relax?rev=23246&view=rev > Log: > Math-domain catching for model: 'NS CPMG 2-site expanded'. > > 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/ns_cpmg_2site_expanded.py > branches/disp_speed/target_functions/relax_disp.py > > Modified: branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=23246&r1=23245&r2=23246&view=diff > ============================================================================== > --- branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py > (original) > +++ branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py Tue > May 20 01:47:30 2014 > @@ -235,14 +235,13 @@ > """ > > # Python module imports. > -from math import log > -from numpy import exp, power, sqrt > +from numpy import array, exp, isfinite, power, log, min, sqrt, sum > > # relax module imports. > from lib.float import isNaN > > > -def r2eff_ns_cpmg_2site_expanded(r20=None, pA=None, dw=None, k_AB=None, > k_BA=None, relax_time=None, inv_relax_time=None, tcp=None, back_calc=None, > num_points=None, num_cpmg=None): > +def r2eff_ns_cpmg_2site_expanded(r20=None, pA=None, dw=None, k_AB=None, > k_BA=None, relax_time=None, inv_relax_time=None, tcp=None, num_points=None, > num_cpmg=None): > """The 2-site numerical solution to the Bloch-McConnell equation using > complex conjugate matrices. > > This function calculates and stores the R2eff values. > @@ -264,9 +263,7 @@ > @type inv_relax_time: float > @keyword tcp: The tau_CPMG times (1 / 4.nu1). > @type tcp: 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 tcp and back_calc arguments. > + @keyword num_points: The number of points on the dispersion > curve, equal to the length of the tcp . > @type num_points: int > @keyword num_cpmg: The array of numbers of CPMG blocks. > @type num_cpmg: numpy int16, rank-1 array > @@ -342,7 +339,15 @@ > t116 = power(0.5*(t97_t99 + t112), t115) > t118 = 1.0/t112 > t120 = t97_nt99 + t112 > - t122 = power(0.5*(t97_t99 - t112), t115) > + > + half_t97_t99_m_t112 = 0.5*(t97_t99 - t112) > + # Catch math domain error of power(val < 1.e-7, 40). > + # This is when abs(half_t97_t99_m_t112) < 1.e-7. > + if min(abs(half_t97_t99_m_t112.real)) < 1.e-7: > + R2eff = array([1e100]*num_points) > + return R2eff > + > + t122 = power(half_t97_t99_m_t112, t115) > t127 = 0.5/t108 > t120_t122 = t120*t122 > t139 = 0.5/(k_AB + k_BA) * ((t120_t122 - t113*t116)*t118*k_BA + > (t120_t122 - t116*t120)*t127*t113*t118*k_AB) > @@ -355,8 +360,11 @@ > Mx = intensity / intensity0 > > # Calculate the R2eff using a two-point approximation, i.e. assuming > that the decay is mono-exponential, and store it for each dispersion point. > - for i in range(num_points): > - if Mx[i] <= 0.0 or isNaN(Mx[i]): > - back_calc[i] = 1e99 > - else: > - back_calc[i]= -inv_relax_time * log(Mx[i]) > + R2eff = -inv_relax_time * log(Mx) > + > + # Catch errors, taking a sum over array is the fastest way to check for > + # +/- inf (infinity) and nan (not a number). > + if not isfinite(sum(R2eff)) or min(Mx) <= 0.0 or not isfinite(sum(Mx)): > + R2eff = array([1e100]*num_points) > + > + 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=23246&r1=23245&r2=23246&view=diff > ============================================================================== > --- branches/disp_speed/target_functions/relax_disp.py (original) > +++ branches/disp_speed/target_functions/relax_disp.py Tue May 20 01:47:30 > 2014 > @@ -1480,7 +1480,7 @@ > dw_frq = dw[si] * self.frqs[0][si][mi] > > # Back calculate the R2eff values. > - r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA, > dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=self.relax_times[0][mi], > inv_relax_time=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi], > back_calc=self.back_calc[0][si][mi][0], > num_points=self.num_disp_points[0][si][mi][0], num_cpmg=self.power[0][mi]) > + self.back_calc[0][si][mi][0] = > r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA, dw=dw_frq, k_AB=k_AB, > k_BA=k_BA, relax_time=self.relax_times[0][mi], > inv_relax_time=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi], > num_points=self.num_disp_points[0][si][mi][0], num_cpmg=self.power[0][mi]) > > # 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
