Check. I am generating R2eff data for 3 fields, and 3 spins, for full model. I will put the data in test_suite/shared_data/dispersion/bug_22146_unpacking_r2a_r2b_cluster
Best Troels 2014-06-06 12:11 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > Right, you have the 2 parameters in the self.num_spins*2 part. And I > forgot about the parameters being different for each field. It would > be good to then have a multi-field and multi-spin cluster system test > to really make sure that relax operates correctly, especially with the > data going into the target function and the subsequently unpacking the > results into the relax data store. For example someone might modify > the loop_parameters() function - this concept could be migrated into > the specific API and converted into a common mechanism for all the > analysis types as it is quite powerful - and they may not know that > the change they just made broke code in the > target_functions.relax_disp module. > > Cheers, > > Edward > > > On 6 June 2014 12:05, Troels Emtekær Linnet <[email protected]> wrote: > > Hi Ed. > > > > The implementations needs: > > R20 = params[:self.end_index[1]].reshape(self.num_spins*2, > > self.num_frq) > > R20A = R20[::2].flatten() > > R20B = R20[1::2].flatten() > > > > > > > > > > > > 2014-06-06 11:55 GMT+02:00 Edward d'Auvergne <[email protected]>: > > > >> The different unpacking implementations can be tested with the timeit > >> Python module to see which is fastest > >> (http://thread.gmane.org/gmane.science.nmr.relax.devel/5937/focus=6010 > ). > >> > >> Cheers, > >> > >> Edward > >> > >> > >> > >> On 6 June 2014 11:53, Edward d'Auvergne <[email protected]> wrote: > >> > Hi, > >> > > >> > In this case, I think 'num_frq' should be fixed to 2. This dimension > >> > corresponds to the parameters R20A and R20B so it is always fixed to > >> > 2. > >> > > >> > Regards, > >> > > >> > Edward > >> > > >> > > >> > > >> > On 6 June 2014 11:51, Troels Emtekær Linnet <[email protected]> > >> > wrote: > >> >> Hi. > >> >> > >> >> Another way is: > >> >> > >> >> ml = params[:end_index[1]].reshape(num_spins*2, num_frq) > >> >> R20A = ml[::2].flatten() > >> >> R20B = ml[1::2].flatten() > >> >> > >> >> > >> >> Best > >> >> Troels > >> >> > >> >> > >> >> > >> >> 2014-06-06 11:39 GMT+02:00 Troels Emtekær Linnet > >> >> <[email protected]>: > >> >> > >> >>> 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
