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List:       relax-devel
Subject:    Re: [bug #5746] TypeError on dx.map() - Bad call to specific.model_free.model_statistics() ?
From:       "Edward d'Auvergne" <edward.dauvergne () domain ! hid>
Date:       2006-04-12 8:09:00
Message-ID: 7f080ed10604120109w77b61123we4e0e710d20f6805 () domain ! hid
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I've reverted the change made at r2462 which was an attempt at fixing
bug #5746 located at
https://gna.org/bugs/?func=detailitem&item_id=5746.

Edward


On 4/12/06, Edward d'Auvergne <edward.dauvergne@domain.hid> wrote:
> Damn. I think that the entire 'self.model_statistics()' function needs
> to be rethought.  The use of the 'instance', 'min_instances', and
> 'num_instances' keyword arguments and the 'global_data' and 'combine'
> variables is very unclear, is not robust, and was not thought out.  It
> was the result of the gradual addition of small changes to the
> function to make the OpenDX mapping and other functions work.
>
> A number of things need to be taken into account.  Firstly for
> model-free analysis, the parameter set type needs to be determined
> using the 'self.determine_param_set_type()' function and the correct
> stats returned.  If the function returns 'all' or 'diff', then the
> instance=0 should return the global stats in self.relax.data.chi2,
> etc.  If the function returns 'mf' or 'local_tm', then the stats of
> the residue corresponding to the 'instance' should be returned.
>
> This algorithm however breaks when running the 'dx.map()' user
> function when trying to map the space of the diffusion tensor
> parameters.  This is what caused the 'combine' variable to be added.
> The reason is because all parameter values are set by the mapping code
> and then the specific 'calculate()' function is executed to generate
> the statistics (the chi-squared value is used in the map).  This
> function does a per residue calculation of the chi-squared value.
>
> The fix could be to modify the 'self.calculate()' function to handle
> the different parameter set types and make the
> 'self.model_statistics()' also behave dependent on the set type.  This
> clean but non-trivial approach is likely to cause breakages.  Another
> option is to sanitise the 'self.model_statistics()' function to handle
> the behaviour of the 'self.calculate()' function.
>
> The data attached to bug #5746 located at
> https://gna.org/bugs/index.php?func=detailitem&item_id=5746 could be
> used for debugging.  To test the OpenDX code, mapping of three spaces
> can be used to probe the different configurations.  These include the
> spheroid parameters {Diso, Da, theta}, model m5, and model tm2.  The
> other test would be to use AIC model selection to select between the
> four types of model-free parameter set.  All these tests could be
> coded into the test suite.  There could also be other parts of the
> program which may fail due to any changes.
>
> Unless someone feels like taking on a huge challenge, I'll work on the
> fix.  As I'm currently trying to add more functionality to the Molmol
> code, it may take me a while to get onto this.  Although I've reopened
> Chris's bug report
> (https://gna.org/bugs/index.php?func=detailitem&item_id=5746), I may
> create a new, more general report with all this info and mark #5746 as
> a duplicate of it.
>
> Edward
>
>
> On 4/11/06, Chris MacRaild <c.a.macraild@domain.hid> wrote:
> >
> > On Tue, 2006-04-11 at 17:03 +1000, Edward d'Auvergne wrote:
> > > I've solved the problem to bug #5746 located at
> > > https://gna.org/bugs/?func=detailitem&item_id=5746.  The issue was
> > > simply an incorrect test in the 'self.model_statistics()' function of
> > > the model-free specific code.  The diff of the fix is:
> > >
> > > Index: specific_fns/model_free.py
> > > ===================================================================
> > > --- specific_fns/model_free.py  (revision 2461)
> > > +++ specific_fns/model_free.py  (working copy)
> > > @@ -2515,7 +2515,7 @@
> > >
> > >          # Sequence specific data.
> > >          # Statistics for a single residue.
> > > -        if not global_stats and not combine:
> > > +        if not global_stats or not combine:
> > >              # Skip unselected residues.model_selection('AIC', run)
> > >              if not self.relax.data.res[self.run][instance].select:
> > >                  return None, None, None
> > >
> >
> > This change breaks model selection of diffusion tensors.
> >
> > If the attached state file is loaded into r2464, and I do eliminate(),
> > model_selection('AIC', 'final') I get:
> >
> > AIC model selection.
> >
> > Instance 0.
> >
> > Run                  Num_params_(k)       Num_data_sets_(n)    Chi2
> > Criterion
> >
> > The model from the run None has been selected.
> >
> >
> >
> > If I revert the above change (by hand), I get the expected behaviour:
> >
> >
> > AIC model selection.
> >
> > Instance 0.
> >
> > Run                  Num_params_(k)       Num_data_sets_(n)    Chi2
> > Criterion
> > sphere               35                   133                  380.01225
> > 450.01225
> > prolate              35                   126                  316.95532
> > 386.95532
> >
> > The model from the run 'prolate' has been selected.
> >
> > Chris
> >
> >
> > _______________________________________________
> > relax (http://nmr-relax.com)
> >
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> >
>


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