Re: r13103 - /branches/inversion-recovery/specific_fns/relax_fit.py -- June 17, 2011 - 17:10

Oh, ok, it's a bug.  If I type at the python prompt:

> > > if 'exp_2param_inv_neg':
...  print "a"
...

it will always print 'a'.  A string always evaluates true.  Therefore
the bug is in the lines:

if model == 'exp_2param' or 'exp_2param_neg' or 'exp_2param_inv' or
'exp_2param_inv_neg':

and the elif following.  The last three is evaluating a string, and
does not involve the model variable.  You could instead put all
strings into a list, and ask 'if model in [...]:' to get the correct
behaviour.

Regards,

Edward



On 17 June 2011 17:06, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Ok, running the following works fine:
>
> $ ./relax test_suite/system_tests/scripts/relax_fit.py
>
> but I am not sure why!  Need to look into it more.
>
> Regards,
>
> Edward
>
>
>
> On 17 June 2011 16:49, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > Hmmm, that is not normal.  I will have to have a look.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On 17 June 2011 16:37, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> > > Hi Ed,
> > >
> > > I am currently looking into this and just realized that the system tests
> > > suite still passes without failure, although the option 'exp' is not valid
> > > anymore for function 'relax_fit.select_model()'...
> > >
> > > Any idea why the test does not fail yet (since I kind of deactivated the
> > > option 'exp' and replaced it with 'exp_2param_neg')..?
> > >
> > > Cheers,
> > >
> > >
> > > Séb  :)
> > >
> > >
> > > On 11-06-17 4:14 PM, Edward d'Auvergne wrote:
> > > > Hi Seb,
> > > >
> > > > The changes are looking good.  I would suggest coming up with a simple
> > > > system test for the inversion recovery with some fake peak lists where
> > > > the intensities are from known exponential functions you create
> > > > yourself.  Unless you have some real data in the group.  This would be
> > > > very useful to be sure that the code is fully operational and bug
> > > > free, and remains that way.
> > > >
> > > > Cheers,
> > > >
> > > > Edward
> > > >
> > > >
> > > >
> > > > On 17 June 2011 14:40,<sebastien.morin@xxxxxxxxx>  wrote:
> > > > > Author: semor
> > > > > Date: Fri Jun 17 14:40:30 2011
> > > > > New Revision: 13103
> > > > >
> > > > > URL: http://svn.gna.org/viewcvs/relax?rev=13103&view=rev
> > > > > Log:
> > > > >
> > > > > Modified the specific function 'relax_fit.select_model()' to handle two
> > > > > of the new exponential names.
> > > > >
> > > > > The 'exp' function now is named 'exp_2param_neg' and the 'inv' function,
> > > > > 'exp_3param_inv_neg'.
> > > > >
> > > > >
> > > > > Modified:
> > > > >    branches/inversion-recovery/specific_fns/relax_fit.py
> > > > >
> > > > > Modified: branches/inversion-recovery/specific_fns/relax_fit.py
> > > > > URL:
> > > > > http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/specific_fns/relax_fit.py?rev=13103&r1=13102&r2=13103&view=diff
> > > > >
> > > > > ==============================================================================
> > > > > --- branches/inversion-recovery/specific_fns/relax_fit.py (original)
> > > > > +++ branches/inversion-recovery/specific_fns/relax_fit.py Fri Jun 17
> > > > > 14:40:30 2011
> > > > > @@ -1,6 +1,7 @@
> > > > >
> > > > >  
> > > > > ###############################################################################
> > > > >  #
> > > > >       #
> > > > >  # Copyright (C) 2004-2009 Edward d'Auvergne
> > > > >       #
> > > > > +# Copyright (C) 2011 Sebastien Morin
> > > > >      #
> > > > >  #
> > > > >       #
> > > > >  # This file is part of the program relax.
> > > > >       #
> > > > >  #
> > > > >       #
> > > > > @@ -461,10 +462,12 @@
> > > > >         cdp.relax_times[spectrum_id] = time
> > > > >
> > > > >
> > > > > -    def _select_model(self, model='exp'):
> > > > > +    def _select_model(self, model='exp_2param_neg'):
> > > > >         """Function for selecting the model of the exponential curve.
> > > > >
> > > > > -        @keyword model: The exponential curve type.  Can be one of 
> > > > > 'exp'
> > > > > or 'inv'.
> > > > > +        @keyword model: The exponential curve type.  Can be one of 8
> > > > > functions: 'exp_2param',
> > > > > +                        'exp_2param_neg', 'exp_2param_inv_neg',
> > > > > 'exp_3param', 'exp_3param_neg',
> > > > > +                        'exp_3param_inv', or 'exp_3param_inv_neg'.
> > > > >         @type model:    str
> > > > >         """
> > > > >
> > > > > @@ -480,13 +483,13 @@
> > > > >         if not exists_mol_res_spin_data():
> > > > >             raise RelaxNoSequenceError
> > > > >
> > > > > -        # Two parameter exponential fit.
> > > > > -        if model == 'exp':
> > > > > -            print("Two parameter exponential fit.")
> > > > > +        # Two parameter exponential decay fit.
> > > > > +        if model == 'exp_2param_neg':
> > > > > +            print("Two parameter exponential decay fit.")
> > > > >             params = ['Rx', 'I0']
> > > > >
> > > > >         # Three parameter inversion recovery fit.
> > > > > -        elif model == 'inv':
> > > > > +        elif model == 'exp_3param_inv_neg':
> > > > >             print("Three parameter inversion recovery fit.")
> > > > >             params = ['Rx', 'I0', 'Iinf']
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > relax (http://nmr-relax.com)
> > > > >
> > > > > This is the relax-commits mailing list
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> > >
> > > --
> > > Sébastien Morin, Ph.D.
> > > Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> > > Department of Structural Biology
> > > Biozentrum, Universität Basel
> > > Klingelbergstrasse 70
> > > 4056 Basel
> > > Switzerland