Hi Ed. That was done in 2 commits before.
The lib function just needs to have "replacing checks", replaced with mask functions. Then it is both forward and backward compatible. Best Troels 2014-06-12 14:14 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > This commit seems to be missing the lib.dispersion.tsmfk01 changes > needed to make the model functional. > > Cheers, > > Edward > > > > On 12 June 2014 13:56, <[email protected]> wrote: > > Author: tlinnet > > Date: Thu Jun 12 13:56:12 2014 > > New Revision: 23880 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=23880&view=rev > > Log: > > Large increase in speed for model TSMFK01 by changing target functions > to use multidimensional numpy arrays in calculation. > > > > This is done by restructuring data into multidimensional arrays of > dimension [NE][NS][NM][NO][ND], which are > > number of spins, number of magnetic field strength, number of offsets, > maximum number of dispersion point. > > > > The speed comes from using numpy ufunc operations. > > > > The new version is 2.4X as fast per spin calculation, and 54X as fast > for clustered analysis. > > > > The different in timings for 3 spectrometer frequencies, calculated for > 1 spin or 100 clustered spins with 1000 iterations are: > > > > ---- > > VERSION 3.2.2 > > ---- > > 1 spin: > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1 0.000 0.000 0.262 0.262 <string>:1(<module>) > > 100 spin: > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1 0.000 0.000 25.391 25.391 <string>:1(<module>) > > ---- > > New version > > --- > > > > 1 spin: > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1 0.000 0.000 0.111 0.111 <string>:1(<module>) > > 100 spin: > > ncalls tottime percall cumtime percall filename:lineno(function) > > 1 0.000 0.000 0.468 0.468 <string>:1(<module>) > > > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of > dispersion models for Clustered analysis. > > > > Modified: > > branches/disp_spin_speed/target_functions/relax_disp.py > > > > Modified: branches/disp_spin_speed/target_functions/relax_disp.py > > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23880&r1=23879&r2=23880&view=diff > > > ============================================================================== > > --- branches/disp_spin_speed/target_functions/relax_disp.py > (original) > > +++ branches/disp_spin_speed/target_functions/relax_disp.py Thu Jun > 12 13:56:12 2014 > > @@ -395,7 +395,7 @@ > > self.func = self.func_ns_mmq_3site_linear > > > > # Setup special numpy array structures, for higher dimensional > computation. > > - if model in [MODEL_B14, MODEL_B14_FULL, MODEL_CR72, > MODEL_CR72_FULL]: > > + if model in [MODEL_B14, MODEL_B14_FULL, MODEL_CR72, > MODEL_CR72_FULL, MODEL_TSMFK01]: > > # Get the shape of back_calc structure. > > # If using just one field, or having the same number of > dispersion points, the shape would extend to that number. > > # Shape has to be: [ei][si][mi][oi]. > > @@ -478,7 +478,7 @@ > > if self.missing[ei][si][mi][oi][di]: > > self.has_missing = True > > missing_a[ei][si][mi][oi][di] = 1.0 > > - if model in [MODEL_B14, MODEL_B14_FULL]: > > + if model in [MODEL_B14, MODEL_B14_FULL, > MODEL_TSMFK01]: > > self.power_a[ei][si][mi][oi][di] = > int(round(self.cpmg_frqs[ei][mi][0][di] * self.relax_times[ei][mi])) > > self.tau_cpmg_a[ei][si][mi][oi][di] > = 0.25 / self.cpmg_frqs[ei][mi][0][di] > > > > @@ -1989,29 +1989,22 @@ > > dw = params[self.end_index[0]:self.end_index[1]] > > k_AB = params[self.end_index[1]] > > > > - # Initialise. > > - chi2_sum = 0.0 > > - > > - # Loop over the spins. > > - for si in range(self.num_spins): > > - # Loop over the spectrometer frequencies. > > - for mi in range(self.num_frq): > > - # The R20 index. > > - r20a_index = mi + si*self.num_frq > > - > > - # Convert dw from ppm to rad/s. > > - dw_frq = dw[si] * self.frqs[0][si][mi] > > - > > - # Back calculate the R2eff values. > > - r2eff_TSMFK01(r20a=R20A[r20a_index], dw=dw_frq, > dw_orig=dw, k_AB=k_AB, 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]) > > - > > - # 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]): > > - if self.missing[0][si][mi][0][di]: > > - self.back_calc[0][si][mi][0][di] = > self.values[0][si][mi][0][di] > > - > > - # Calculate and return the chi-squared value. > > - chi2_sum += chi2(self.values[0][si][mi][0], > self.back_calc[0][si][mi][0], self.errors[0][si][mi][0]) > > + # Convert dw from ppm to rad/s. Use the out argument, to pass > directly to structure. > > + multiply( multiply.outer( dw.reshape(self.NE, self.NS), > self.nm_no_nd_struct ), self.frqs_struct, out=self.dw_struct ) > > + > > + # Reshape R20A and R20B to per experiment, spin and frequency. > > + self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, > self.NS, self.NM), self.no_nd_struct ) > > + > > + # Back calculate the R2eff values. > > + r2eff_TSMFK01(r20a=self.r20a_struct, dw=self.dw_struct, > dw_orig=dw, k_AB=k_AB, tcp=self.tau_cpmg_a, back_calc=self.back_calc_a, > num_points=self.num_disp_points_a) > > + > > + # Clean the data for all values, which is left over at the end > of arrays. > > + self.back_calc_a = self.back_calc_a*self.disp_struct > > + > > + ## 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. > > + if self.has_missing: > > + # Replace with values. > > + self.back_calc_a[self.mask_replace_blank.mask] = > self.values_a[self.mask_replace_blank.mask] > > > > # Return the total chi-squared value. > > - return chi2_sum > > + return chi2_rankN(self.values_a, self.back_calc_a, > self.errors_a) > > > > > > _______________________________________________ > > 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
