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
