Re: r25491 - /trunk/specific_analyses/relax_disp/data.py -- September 01, 2014 - 10:37

Ok.

It seems there is no potential error for getting the data.

But I can't find the randomization of R1?

Is this not included?

Best
Troels



2014-09-01 10:20 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:
> Yes.
>
> That was a seriously hard bug to find.
>
> Especially when you consider the MC simulations as the "Golden Standard".
> And then the  "Golden Standard" is wrong...
>
> Ouch.
>
> Should we set the GUI to have exp_sim = -1?
> There is no assumption, that 100000 simulations of exponential fits
> are better than the co-variance.
>
> Btw.
>
> Can we check Monte-Carlo simulations for the dispersion models?
>
> Where is that performed?
>
> Do you randomize only R1rho' or do you also include randomize for R1?
>
> Best
> Troels
>
> 2014-09-01 10:06 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > Hi Troels,
> >
> > Awesome catch!  This is quite a significant bug!  It was introduced in
> > October of last year while trying to fix another bug (r21022 in the
> > relax_disp branch,
> > http://article.gmane.org/gmane.science.nmr.relax.scm/18778).
> > Unfortunately our test suite coverage was not comprehensive enough so
> > the bugfix of r21022 silently introduced this bug.
> >
> > This bug is specific to relaxation dispersion analyses.  And it only
> > affects those who have measured full exponential curves, which would
> > be a lot less than half of all analyses.  It is nevertheless a huge
> > bug!
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> > On 31 August 2014 23:46,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > > Author: tlinnet
> > > Date: Sun Aug 31 23:46:38 2014
> > > New Revision: 25491
> > >
> > > URL: http://svn.gna.org/viewcvs/relax?rev=25491&view=rev
> > > Log:
> > > Correction for catastrophic implementation of Monte-Carlo simulations.
> > >
> > > And wrong implemetented "else if" statement, would add the intensity for 
> > > the simulated intensity together with
> > > the original intensity.
> > >
> > > This means that all intensity values send to minimisation would be twice 
> > > as high than usually.
> > > (If spectra was not replicated.)
> > >
> > > This was discovered for Monte-Carlo simulations of R2eff errors in 
> > > exponential fit.
> > >
> > > The function is restricted to the analysis of errors for exponential fit 
> > > in Relax Dispersion.
> > > Such data are normally restricted to R1rho analysis.
> > >
> > > This will affect all analysis of R1rho data performed until now.
> > > By pure luck, it seems that the effect of this would be that R2eff errors 
> > > are half the value they should be.
> > > A further investigation shows, that for the selected data set, this had a 
> > > minimum on influence on the fitted parameters,
> > > because the chi2 value would be scaled up by a factor 4.
> > >
> > > bug #22554(https://gna.org/bugs/index.php?22554): The distribution of 
> > > intensity with errors in Monte-Carlo simulations are markedly more narrow 
> > > than expected.
> > > task #7822(https://gna.org/task/index.php?7822): Implement user function 
> > > to estimate R2eff and associated errors for exponential curve fitting.
> > >
> > > Modified:
> > >     trunk/specific_analyses/relax_disp/data.py
> > >
> > > Modified: trunk/specific_analyses/relax_disp/data.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/data.py?rev=25491&r1=25490&r2=25491&view=diff
> > > ==============================================================================
> > > --- trunk/specific_analyses/relax_disp/data.py  (original)
> > > +++ trunk/specific_analyses/relax_disp/data.py  Sun Aug 31 23:46:38 2014
> > > @@ -147,7 +147,7 @@
> > >              intensity += spin.peak_intensity_sim[int_keys[i]][sim_index]
> > >
> > >          # Error intensity data.
> > > -        if error:
> > > +        elif error:
> > >              # Error checking.
> > >              if not hasattr(spin, 'peak_intensity_err') or not 
> > > int_keys[i] in spin.peak_intensity_err:
> > >                  raise RelaxError("The peak intensity errors are missing 
> > > the key '%s'." % int_keys[i])
> > >
> > >
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