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
> >>>
> >>>
> >>
>
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