Oh, I was a bit too fast (http://thread.gmane.org/gmane.science.nmr.relax.scm/21776/focus=6301). Anyway, there are still a few more:
[edward@localhost disp_spin_speed]$ grep "]\[" lib/dispersion/* Regards, Edward On 17 June 2014 13:07, <[email protected]> wrote: > Author: tlinnet > Date: Tue Jun 17 13:07:42 2014 > New Revision: 24027 > > URL: http://svn.gna.org/viewcvs/relax?rev=24027&view=rev > Log: > More replacing of numpy index. > > 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=24027&r1=24026&r2=24027&view=diff > ============================================================================== > --- branches/disp_spin_speed/target_functions/relax_disp.py (original) > +++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 > 13:07:42 2014 > @@ -263,26 +263,26 @@ > for mi in range(self.NM): > # Fill the frequency. > frq = frqs[ei][si][mi] > - self.frqs[ei, si, mi][:] = frq > - self.frqs_squared[ei, si, mi][:] = frq**2 > + self.frqs[ei, si, mi, :] = frq > + self.frqs_squared[ei, si, mi, :] = frq**2 > frq_H = frqs_H[ei][si][mi] > - self.frqs_H[ei, si, mi][:] = frq_H > + self.frqs_H[ei, si, mi, :] = frq_H > > # Fill the relaxation time. > relax_time = relax_times[ei, mi] > - self.relax_times[ei, si, mi][:] = relax_time > + self.relax_times[ei, si, mi, :] = relax_time > > # Fill r1. > r1_l = r1[si][mi] > - self.r1[ei, si, mi][:] = r1_l > + self.r1[ei, si, mi, :] = r1_l > > # Fill chemical shift. > chemical_shift = chemical_shifts[ei][si][mi] > - self.chemical_shifts[ei, si, mi][:] = chemical_shift > + self.chemical_shifts[ei, si, mi, :] = chemical_shift > > # The inverted relaxation delay. > if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72, > MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, > MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, > MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, > MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, > MODEL_NS_R1RHO_3SITE_LINEAR]: > - self.inv_relax_times[ei, si, mi][:] = 1.0 / > relax_time > + self.inv_relax_times[ei, si, mi, :] = 1.0 / > relax_time > > # The number of offset data points. > if len(offset[ei][si][mi]): > @@ -295,7 +295,7 @@ > if cpmg_frqs != None and len(cpmg_frqs[ei][mi][oi]): > cpmg_frqs_list = cpmg_frqs[ei][mi][oi] > num_disp_points = len(cpmg_frqs_list) > - self.cpmg_frqs[ei, si, mi, oi][:num_disp_points] > = cpmg_frqs_list > + self.cpmg_frqs[ei, si, mi, oi, :num_disp_points] > = cpmg_frqs_list > > for di in range(num_disp_points): > cpmg_frq = cpmg_frqs[ei][mi][oi][di] > @@ -322,9 +322,9 @@ > self.num_disp_points[ei, si, mi, oi] = > num_disp_points > > # Get the values and errors. > - self.values[ei, si, mi, oi][:num_disp_points] = > values[ei][si][mi][oi] > - self.errors[ei, si, mi, oi][:num_disp_points] = > errors[ei][si][mi][oi] > - self.disp_struct[ei, si, mi, oi][:num_disp_points] = > ones(num_disp_points) > + self.values[ei, si, mi, oi, :num_disp_points] = > values[ei][si][mi][oi] > + self.errors[ei, si, mi, oi, :num_disp_points] = > errors[ei][si][mi][oi] > + self.disp_struct[ei, si, mi, oi, :num_disp_points] = > ones(num_disp_points) > > # Loop over dispersion points. > for di in range(num_disp_points): > @@ -790,7 +790,7 @@ > dw_AC_frq = dw_AC[si] * self.frqs[0, si, mi, 0, 0] > > # Loop over the offsets. > - for oi in range(self.num_offsets[0][si, mi]): > + for oi in range(self.num_offsets[0, si, mi]): > # Back calculate the R2eff values for each experiment > type. > ns_r1rho_3site(M0=self.M0, matrix=self.matrix, > r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi, oi, > 0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0], > pA=pA, pB=pB, pC=pC, dw_AB=dw_AB_frq, dw_AC=dw_AC_frq, k_AB=k_AB, k_BA=k_BA, > k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA, > spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi], > relax_time=self.relax_times[0, si, mi, oi], > inv_relax_time=self.inv_relax_times[0, si, mi, oi], > back_calc=self.back_calc[0, si, mi, oi], num_points=self.num_disp_points[0, > si, mi, oi]) > > @@ -1079,8 +1079,8 @@ > > # 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] > + 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]) > @@ -1660,7 +1660,7 @@ > dw_frq = dw[si] * self.frqs[0, si, mi, 0, 0] > > # Loop over the offsets. > - for oi in range(self.num_offsets[0][si, mi]): > + for oi in range(self.num_offsets[0, si, mi]): > # Back calculate the R2eff values. > ns_r1rho_2site(M0=self.M0, matrix=self.matrix, > r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi, oi, > 0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0], > pA=pA, pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA, > spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi], > relax_time=self.relax_times[0, si, mi, oi], > inv_relax_time=self.inv_relax_times[0, si, mi, oi], > back_calc=self.back_calc[0, si, mi, oi], num_points=self.num_disp_points[0, > si, mi, oi]) > > > > _______________________________________________ > 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
