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
