Hi Troels, Now that you have converted almost all data structures to numpy arrays, you should change how these are accessed. For example a[1, 1] is cleaner than a[1][1] and is the standard way to index a numpy array. It is also faster:
$ python -m timeit -n 1000 -s "import numpy" "a = numpy.eye(5)" "for i in xrange(10000): a[1][1] = 5.0" 1000 loops, best of 3: 2.2 msec per loop $ python -m timeit -n 1000 -s "import numpy" "a = numpy.eye(5)" "for i in xrange(10000): a[1, 1] = 5.0" 1000 loops, best of 3: 838 usec per loop $ Though this will probably have almost zero effect on the speed of the target function, it will be more correct. Regards, Edward On 16 June 2014 22:11, <[email protected]> wrote: > Author: tlinnet > Date: Mon Jun 16 22:11:40 2014 > New Revision: 24004 > > URL: http://svn.gna.org/viewcvs/relax?rev=24004&view=rev > Log: > Fixed the use of higher dimensional data in mmq 2site sq dq zq. > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion > models for Clustered analysis. > > Modified: > branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py > > Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24004&r1=24003&r2=24004&view=diff > ============================================================================== > --- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original) > +++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Mon Jun 16 > 22:11:40 2014 > @@ -281,26 +281,42 @@ > @type power: numpy int16, rank-1 array > """ > > - # Populate the m1 and m2 matrices (only once per function call for > speed). > - populate_matrix(matrix=m1, R20A=R20A, R20B=R20B, dw=dw, k_AB=k_AB, > k_BA=k_BA) > - populate_matrix(matrix=m2, R20A=R20A, R20B=R20B, dw=-dw, k_AB=k_AB, > k_BA=k_BA) > - > - # Loop over the time points, back calculating the R2eff values. > - for i in range(num_points): > - # The A+/- matrices. > - A_pos = matrix_exponential(m1*tcp[i]) > - A_neg = matrix_exponential(m2*tcp[i]) > - > - # The evolution for one n. > - evol_block = dot(A_pos, dot(A_neg, dot(A_neg, A_pos))) > - > - # The full evolution. > - evol = square_matrix_power(evol_block, power[i]) > - > - # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > - Mx = dot(F_vector, dot(evol, M0)) > - Mx = Mx.real > - if Mx <= 0.0 or isNaN(Mx): > - back_calc[i] = 1e99 > - else: > - back_calc[i] = -inv_tcpmg[i] * log(Mx / pA) > + > + # Extract shape of experiment. > + NS, NM, NO = num_points.shape > + > + # Loop over spins. > + for si in range(NS): > + # Loop over the spectrometer frequencies. > + for mi in range(NM): > + # Loop over offsets: > + for oi in range(NO): > + > + r20a_si_mi_oi = R20A[si][mi][oi][0] > + r20b_si_mi_oi = R20B[si][mi][oi][0] > + dw_si_mi_oi = dw[si][mi][oi][0] > + num_points_si_mi_oi = num_points[si][mi][oi] > + > + # Populate the m1 and m2 matrices (only once per function > call for speed). > + populate_matrix(matrix=m1, R20A=r20a_si_mi_oi , > R20B=r20b_si_mi_oi, dw=dw_si_mi_oi, k_AB=k_AB, k_BA=k_BA) > + populate_matrix(matrix=m2, R20A=r20a_si_mi_oi , > R20B=r20b_si_mi_oi, dw=-dw_si_mi_oi, k_AB=k_AB, k_BA=k_BA) > + > + # Loop over the time points, back calculating the R2eff > values. > + for i in range(num_points_si_mi_oi): > + # The A+/- matrices. > + A_pos = matrix_exponential(m1*tcp[si][mi][oi][i]) > + A_neg = matrix_exponential(m2*tcp[si][mi][oi][i]) > + > + # The evolution for one n. > + evol_block = dot(A_pos, dot(A_neg, dot(A_neg, A_pos))) > + > + # The full evolution. > + evol = square_matrix_power(evol_block, > power[si][mi][oi][i]) > + > + # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > + Mx = dot(F_vector, dot(evol, M0)) > + Mx = Mx.real > + if Mx <= 0.0 or isNaN(Mx): > + back_calc[si][mi][oi][i] = 1e99 > + else: > + back_calc[si][mi][oi][i] = -inv_tcpmg[si][mi][oi][i] > * log(Mx / pA) > > > _______________________________________________ > 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
