Yeahaa! I realised, that if I wanted to have the systemtests go faster, I should kill this one.
It is nice to see, that systemtest suite just runs faster and faster, the more models i kill. 2014-06-13 10:37 GMT+02:00 Edward d'Auvergne <[email protected]>: > Now this code might be too fast for the user - they may not be fast > enough to even see it in the log files ;) > > Regards, > > Edward > > > On 13 June 2014 10:10, <[email protected]> wrote: > > Author: tlinnet > > Date: Fri Jun 13 10:10:04 2014 > > New Revision: 23908 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=23908&view=rev > > Log: > > Made the NOREX model af faster numpy array calculation. > > > > 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=23908&r1=23907&r2=23908&view=diff > > > ============================================================================== > > --- branches/disp_spin_speed/target_functions/relax_disp.py > (original) > > +++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun > 13 10:10:04 2014 > > @@ -394,8 +394,11 @@ > > if model == MODEL_NS_MMQ_3SITE_LINEAR: > > 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, MODEL_DPL94, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01]: > > + test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72, > MODEL_CR72_FULL, MODEL_DPL94, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01] > > + > > + if model in test_models + [MODEL_NOREX]: > > # 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]. > > @@ -443,8 +446,11 @@ > > self.r20b_struct = deepcopy(zeros_a) > > self.dw_struct = deepcopy(zeros_a) > > > > - # Extract the frequencies to numpy array. > > - self.frqs_a = multiply.outer( > asarray(self.frqs).reshape(self.NE, self.NS, self.NM), self.no_nd_struct ) > > + # Setup special numpy array structures, for higher dimensional > computation. > > + if model in test_models + [MODEL_NOREX]: > > + if model in test_models: > > + # Extract the frequencies to numpy array. > > + self.frqs_a = multiply.outer( > asarray(self.frqs).reshape(self.NE, self.NS, self.NM), self.no_nd_struct ) > > > > if model in MODEL_LIST_CPMG_FULL: > > self.cpmg_frqs_a = deepcopy(ones_a) > > @@ -476,7 +482,7 @@ > > # Extract number of dispersion points. > > num_disp_points = > self.num_disp_points[ei][si][mi][oi] > > > > - if model in MODEL_LIST_CPMG_FULL: > > + if model in MODEL_LIST_CPMG_FULL and model > != MODEL_NOREX: > > # Extract cpmg_frqs and num_disp_points > from lists. > > > self.cpmg_frqs_a[ei][si][mi][oi][:num_disp_points] = > self.cpmg_frqs[ei][mi][oi] > > > self.num_disp_points_a[ei][si][mi][oi][:num_disp_points] = > self.num_disp_points[ei][si][mi][oi] > > @@ -497,7 +503,7 @@ > > 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] > > # For R1rho data. > > - if model in MODEL_LIST_R1RHO_FULL: > > + if model in MODEL_LIST_R1RHO_FULL and > model != MODEL_NOREX: > > > self.disp_struct[ei][si][mi][oi][di] = 1.0 > > > > # Extract the frequencies to numpy > array. > > @@ -511,11 +517,12 @@ > > else: > > > self.num_disp_points_a[ei][si][mi][oi][di] = 0 > > > > + if model in test_models: > > + # Pre calculate frqs structure > > + self.frqs_struct = self.frqs_a * self.disp_struct > > + > > # Make copy of values structure. > > self.back_calc_a = deepcopy(self.values_a) > > - > > - # Pre calculate frqs structure > > - self.frqs_struct = self.frqs_a * self.disp_struct > > > > # Find the numpy mask, which tells where values should be > replaced. > > self.mask_replace_blank = masked_equal(missing_a, 1.0) > > @@ -1465,34 +1472,16 @@ > > # Unpack the parameter values. > > R20 = params > > > > - # Initialise. > > - chi2_sum = 0.0 > > - > > - # Loop over the experiment types. > > - for ei in range(self.num_exp): > > - # 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. > > - r20_index = mi + si*self.num_frq > > - > > - # Loop over the offsets. > > - for oi in range(self.num_offsets[ei][si][mi]): > > - # The R2eff values as R20 values. > > - for di in > range(self.num_disp_points[ei][si][mi][oi]): > > - self.back_calc[ei][si][mi][oi][di] = > R20[r20_index] > > - > > - # 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[ei][si][mi][oi]): > > - if self.missing[ei][si][mi][oi][di]: > > - self.back_calc[ei][si][mi][oi][di] = > self.values[ei][si][mi][oi][di] > > - > > - # Calculate and return the chi-squared value. > > - chi2_sum += chi2(self.values[ei][si][mi][oi], > self.back_calc[ei][si][mi][oi], self.errors[ei][si][mi][oi]) > > + # Reshape R20 to per experiment, spin and frequency. > > + self.back_calc_a[:] = multiply.outer( R20.reshape(self.NE, > self.NS, self.NM), self.no_nd_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) > > > > > > def func_ns_cpmg_2site_3D(self, params): > > > > > > _______________________________________________ > > 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
