There is no doubt that it is the unpacking of the R20A and R20B in the target function.
I was thinking of creating a function, which do the the unpacking. This unpacking function could then be tested with a unit test? What do you think? Where should I position such a function? Best Troels 2014-06-06 11:26 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > The best way to handle this is to first create a unit test of the > specific_analyses.relax_disp.parameters.disassemble_param_vector() > where the problem is likely to be most easily found. I don't > understand how this could be a problem as the assemble_param_vector() > and disassemble_param_vector() functions both call the same > loop_parameters() function for the ordering of the parameter values! > Maybe the problem is in the unpacking of the parameter vector in the > target functions themselves, for example in the full B14 model: > > > def func_B14_full(self, params): > """Target function for the Baldwin (2014) 2-site exact > solution model for all time scales. > > This assumes that pA > pB, and hence this must be implemented > as a constraint. > > > @param params: The vector of parameter values. > @type params: numpy rank-1 float array > @return: The chi-squared value. > @rtype: float > """ > > # Scaling. > if self.scaling_flag: > params = dot(params, self.scaling_matrix) > > # Unpack the parameter values. > R20A = params[:self.end_index[0]] > R20B = params[self.end_index[0]:self.end_index[1]] > dw = params[self.end_index[1]:self.end_index[2]] > pA = params[self.end_index[2]] > kex = params[self.end_index[2]+1] > > # Calculate and return the chi-squared value. > return self.calc_B14_chi2(R20A=R20A, R20B=R20B, dw=dw, pA=pA, > kex=kex) > > > This R20A and R20B unpacking might be the failure point as this may > not match the loop_parameters() function - which it must! In any > case, having a unit or system test catch the problem would be very > useful for the stability of the dispersion analysis in relax. > > A code example might be useful: > > R20_params = array([1, 2, 3, 4]) > R20A, R20B = transpose(R20_params.reshape(2, 2) > print(R20A) > print(R20B) > > You should see that R20A is [1, 3], and R20B is [2, 4]. This is how > the parameters are handled in the loop_parameters() function which > defines the parameter vector in all parts of relax. There might be a > quicker way to unpack the parameters, but such an idea could be used > for the target functions. > > Cheers, > > Edward > > On 6 June 2014 11:08, Troels E. Linnet <[email protected]> > wrote: > > URL: > > <http://gna.org/bugs/?22146> > > > > Summary: Unpacking of R2A and R2B is performed wrong for > > clustered "full" dispersion models > > Project: relax > > Submitted by: tlinnet > > Submitted on: Fri 06 Jun 2014 09:08:58 AM UTC > > Category: relax's source code > > Specific analysis category: Relaxation dispersion > > Priority: 9 - Immediate > > Severity: 4 - Important > > Status: None > > Assigned to: None > > Originator Name: > > Originator Email: > > Open/Closed: Open > > Release: Repository: trunk > > Discussion Lock: Any > > Operating System: All systems > > > > _______________________________________________________ > > > > Details: > > > > The unpacking of the R2A and R2B parameters in the "full" model is > performed > > wrong. > > This will happen performing a clustered analysis, using one of the "full" > > models. > > > > This bug affect all analysis performed running with a "full" model, with > > clustered residues. > > > > The bug is located in the target function: > > ./target_functions/relax_disp.py > > > > For all the "func_MODEL_full", the unpacking of: > > R20A = params[:self.end_index[0]] > > R20B = params[self.end_index[0]:self.end_index[1]] > > > > This is wrong, since the "params" list, is ordered: > > [spin, spin, spin, [dw], pA, kex], where spin = [nr_frq*r2a, nr_frq*r2b] > > > > This ordering happens in: > > ./specific_analysis/relax_disp/parameters.py > > in the loop_parameters.py > > > > A possible solutions i shown below. > > This alter the unpacking of the parameters. > > > > An example of profiling_cr72.py is attached. > > This can be downloaded, and run in base folder of relax: > > ./profiling_cr72.py . > > > > This is with 3 frq, and 3 spins. > > > > The current implementations would unpack: > > ('R20A', array([ 2., 2., 2., 4., 4., 4., 12., 12., 12.]), > 9) > > ('R20B', array([ 14., 14., 14., 22., 22., 22., 24., 24., 24.]), > 9) > > > > R2A is 2, 12, 22 for the spins 0-3 > > R2B is, 4, 14, 24 for the spins 0-3 > > > > The suggested unpacking loop, unpacks to: > > ('R20A', array([ 2., 2., 2., 12., 12., 12., 22., 22., 22.]), > 9) > > ('R20B', array([ 4., 4., 4., 14., 14., 14., 24., 24., 24.]), > 9) > > > > > > ------- > > from numpy import array, concatenate, delete, index_exp > > import numpy > > > > p = array([ 1.000000000000000e+01, 1.000000000000000e+01, > > 1.100000000000000e+01 > > , 1.100000000000000e+01, 1.000000000000000e+01, 1.000000000000000e+01 > > , 1.100000000000000e+01, 1.100000000000000e+01, 1.000000000000000e+00 > > , 1.000000000000000e+00, 9.000000000000000e-01, 1.000000000000000e+03]) > > > > e = [4, 8, 10] > > > > # Now > > r2a = p[:e[0]] > > print r2a > > r2b = p[e[0]:e[1]] > > print r2b > > dw = p[e[1]:e[2]] > > print dw > > pA = p[e[2]] > > print pA > > kex = p[e[2]+1] > > print kex > > > > print "new" > > ns = 2 > > nf = 2 > > > > ml = p[:e[1]] > > > > R20A = array([]) > > R20B = array([]) > > for i in range(0, ns): > > # Array sorted per [spin, spin, spin], where spin = [nr_frq*r2a, > > nr_frq*r2b] > > spin_AB = ml[:nf*2] > > ml = delete(ml, numpy.s_[:nf*2]) > > R20A = concatenate([R20A, spin_AB[:nf] ]) > > R20B = concatenate([R20B, spin_AB[nf:] ]) > > > > print R20A > > print R20B > > print dw > > print pA > > print kex > > > > > > > > _______________________________________________________ > > > > File Attachments: > > > > > > ------------------------------------------------------- > > Date: Fri 06 Jun 2014 09:08:58 AM UTC Name: profiling_cr72.py Size: > 17kB > > By: tlinnet > > > > <http://gna.org/bugs/download.php?file_id=20938> > > > > _______________________________________________________ > > > > Reply to this item at: > > > > <http://gna.org/bugs/?22146> > > > > _______________________________________________ > > Message sent via/by Gna! > > http://gna.org/ > > > > > > _______________________________________________ > > 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
