Hi, For this change, you don't need to put M0_0 into 'self'. This structure is no longer used and can be removed from the lib.dispersion code. It is best to minimise the number of objects placed into the class instance namespace (self).
Regards, Edward On 25 June 2014 02:14, <[email protected]> wrote: > Author: tlinnet > Date: Wed Jun 25 02:14:42 2014 > New Revision: 24297 > > URL: http://svn.gna.org/viewcvs/relax?rev=24297&view=rev > Log: > For model NS CPMG 2site 3d, the M0 matrix was preformed for higher > dimensionality in init of target function. > > The transposes/rolled axis versions was also initiated. > > 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_cpmg_2site_3d.py > branches/disp_spin_speed/target_functions/relax_disp.py > > Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=24297&r1=24296&r2=24297&view=diff > ============================================================================== > --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py (original) > +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Wed Jun 25 > 02:14:42 2014 > @@ -224,7 +224,7 @@ > return c_mat > > > -def r2eff_ns_cpmg_2site_3D(r180x=None, M0=None, r10a=0.0, r10b=0.0, > r20a=None, r20b=None, pA=None, dw=None, dw_orig=None, kex=None, > inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None): > +def r2eff_ns_cpmg_2site_3D(r180x=None, M0=None, M0_T=None, r10a=0.0, > r10b=0.0, r20a=None, r20b=None, pA=None, dw=None, dw_orig=None, kex=None, > inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None): > """The 2-site numerical solution to the Bloch-McConnell equation. > > This function calculates and stores the R2eff values. > @@ -233,7 +233,9 @@ > @keyword r180x: The X-axis pi-pulse propagator. > @type r180x: numpy float64, rank-2, 7D array > @keyword M0: This is a vector that contains the initial > magnetizations corresponding to the A and B state transverse magnetizations. > - @type M0: numpy float64, rank-1, 7D array > + @type M0: numpy float array of rank > [NE][NS][NM][NO][ND][7][1] > + @keyword M0_T: This is a vector that contains the initial > magnetizations corresponding to the A and B state transverse magnetizations, > where the outer two axis has been swapped for efficient dot operations. > + @type M0_T: numpy float array of rank > [NE][NS][NM][NO][ND][1][7] > @keyword r10a: The R1 value for state A. > @type r10a: float > @keyword r10b: The R1 value for state B. > @@ -281,8 +283,10 @@ > k_AB = pB * kex > > # This is a vector that contains the initial magnetizations > corresponding to the A and B state transverse magnetizations. > - M0[1] = pA > - M0[4] = pB > + M0_T[:, :, :, :, :, 0, 1] = pA > + M0_T[:, :, :, :, :, 0, 4] = pB > + M0[:, :, :, :, :, 1, 0] = pA > + M0[:, :, :, :, :, 4, 0] = pB > > # Extract the total numbers of experiments, number of spins, number of > magnetic field strength, number of offsets, maximum number of dispersion > point. > NE, NS, NM, NO, ND = back_calc.shape > @@ -316,7 +320,7 @@ > r20a_si_mi_di = r20a[0, si, mi, 0, di] > > # Initial magnetisation. > - Mint_i = M0 > + Mint_i = M0[0, si, mi, 0, di] > > # This matrix is a propagator that will evolve the > magnetization with the matrix R for a delay tcp. > evolution_matrix_i = evolution_matrix_mat[0, si, mi, 0, di] > @@ -326,7 +330,7 @@ > Mint_i = dot(evolution_matrix_i, Mint_i) > > # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > - Mx = Mint_i[1] / pA > + Mx = Mint_i[1][0] / pA > if Mx <= 0.0 or isNaN(Mx): > back_calc[0, si, mi, 0, di] = r20a_si_mi_di > else: > > 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=24297&r1=24296&r2=24297&view=diff > ============================================================================== > --- branches/disp_spin_speed/target_functions/relax_disp.py (original) > +++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 25 > 02:14:42 2014 > @@ -400,8 +400,11 @@ > if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: > self.M0 = zeros(3, float64) > if model in [MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL]: > - self.M0 = zeros(7, float64) > - self.M0[0] = 0.5 > + M0_0 = zeros( [self.NE, self.NS, self.NM, self.NO, self.ND,7, > 1], float64) > + M0_0[:, :, :, :, :, 0, 0] = 0.5 > + self.M0 = M0_0 > + # Transpose M0, to prepare for dot operation. Roll the last axis > one back, corresponds to a transpose for the outer two axis. > + self.M0_T = rollaxis(self.M0, 6, 5) > if model in [MODEL_NS_R1RHO_2SITE]: > # Offset of spin-lock from A. > da_mat = self.chemical_shifts - self.offset > @@ -596,7 +599,7 @@ > self.r20b_struct[:] = multiply.outer( R20B.reshape(self.NE, self.NS, > self.NM), self.no_nd_ones ) > > # Back calculate the R2eff values. > - r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, > r20a=self.r20a_struct, r20b=self.r20b_struct, pA=pA, dw=self.dw_struct, > dw_orig=dw, kex=kex, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, > back_calc=self.back_calc, num_points=self.num_disp_points, power=self.power) > + r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, M0_T=self.M0_T, > r20a=self.r20a_struct, r20b=self.r20b_struct, pA=pA, dw=self.dw_struct, > dw_orig=dw, kex=kex, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, > back_calc=self.back_calc, num_points=self.num_disp_points, power=self.power) > > # Clean the data for all values, which is left over at the end of > arrays. > self.back_calc = self.back_calc*self.disp_struct > > > _______________________________________________ > 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
