Re: r23240 - in /branches/disp_speed: lib/dispersion/cr72.py target_functions/relax_disp.py -- May 20, 2014 - 10:33

Hmmm, maybe a better solution for that system test is to add the check
and fail with a RelaxError.  The solution:

http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?r1=21957&r2=21956&pathrev=21957

is probably not the best.  If we have one
specific_analyses.relax_disp.checks.check_*() function for this, then
we can use it at the start of many different functions in the
specific_analyses.relax_disp package.  The system test could then be
modified to include a self.assertRaises() call.  Note that the save
state file is called 'bug_21460_bad_fields.bz2'
(http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?r1=21954&r2=21953&pathrev=21954),
so it is not a desired state to be in.

Regards,

Edward



On 19 May 2014 15:54, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> Hi Ed.
>
> You are handling this bug here:
> Relax_disp.test_bug_21460_disp_cluster_fail
>
>         """U{Bug #21460<https://gna.org/bugs/?21460>} catch, the
> failure due to a spectrometer frequency having no relaxation data."""
>
> Best
> Troels
>
> 2014-05-19 15:04 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > Hi Troels,
> >
> > I have one suggestion here.  The following check is not necessary:
> >
> > if num_points > 0:
> >
> > This will slow down the code.  Note that this situation should never,
> > ever be reached.  If it is, then we are doing something wrong in the
> > specific_analyses.relax_disp package prior to passing the data into
> > the target function class.  num_points can only be zero if there are
> > no dispersion points in a curve, but then there is no curve!  So we
> > shouldn't supply the target function with information about such a
> > non-existent curve.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> >
> > On 19 May 2014 14:44,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > > Author: tlinnet
> > > Date: Mon May 19 14:44:12 2014
> > > New Revision: 23240
> > >
> > > URL: http://svn.gna.org/viewcvs/relax?rev=23240&view=rev
> > > Log:
> > > Math-domain catching for model CR72.
> > >
> > > task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
> > >
> > > This is to implement catching of math domain errors, before they occur.
> > > These can be found via the --numpy-raise function to the systemtests.
> > >
> > > To make the code look clean, the class object "back_calc" is no longer
> > > being updated per time point, but is updated in the relax_disp target 
> > > function in
> > > one go.
> > >
> > > Modified:
> > >     branches/disp_speed/lib/dispersion/cr72.py
> > >     branches/disp_speed/target_functions/relax_disp.py
> > >
> > > Modified: branches/disp_speed/lib/dispersion/cr72.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/cr72.py?rev=23240&r1=23239&r2=23240&view=diff
> > > ==============================================================================
> > > --- branches/disp_speed/lib/dispersion/cr72.py  (original)
> > > +++ branches/disp_speed/lib/dispersion/cr72.py  Mon May 19 14:44:12 2014
> > > @@ -92,12 +92,12 @@
> > >  """
> > >
> > >  # Python module imports.
> > > -from numpy import arccosh, array, cos, cosh, isfinite, sqrt, sum
> > > +from numpy import arccosh, array, cos, cosh, isfinite, max, sqrt, sum
> > >
> > >  # Repetitive calculations (to speed up calculations).
> > >  eta_scale = 2.0**(-3.0/2.0)
> > >
> > > -def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, 
> > > cpmg_frqs=None, back_calc=None, num_points=None):
> > > +def r2eff_CR72(r20a=None, r20b=None, pA=None, dw=None, kex=None, 
> > > cpmg_frqs=None, num_points=None):
> > >      """Calculate the R2eff values for the CR72 model.
> > >
> > >      See the module docstring for details.
> > > @@ -115,9 +115,7 @@
> > >      @type kex:              float
> > >      @keyword cpmg_frqs:     The CPMG nu1 frequencies.
> > >      @type cpmg_frqs:        numpy rank-1 float array
> > > -    @keyword back_calc:     The array for holding the back calculated 
> > > R2eff values.  Each element corresponds to one of the CPMG nu1 
> > > frequencies.
> > > -    @type back_calc:        numpy rank-1 float array
> > > -    @keyword num_points:    The number of points on the dispersion 
> > > curve, equal to the length of the cpmg_frqs and back_calc arguments.
> > > +    @keyword num_points:    The number of points on the dispersion 
> > > curve, equal to the length of the cpmg_frqs.
> > >      @type num_points:       int
> > >      """
> > >
> > > @@ -151,6 +149,14 @@
> > >      etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs
> > >      etaneg = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2) / cpmg_frqs
> > >
> > > +    # Catch math domain error of cosh(val > 710).
> > > +    # This is when etapos > 710.
> > > +    if num_points > 0:
> > > +        if max(etapos) > 700:
> > > +            R2eff = array([1e100]*num_points)
> > > +
> > > +            return R2eff
> > > +
> > >      # Calculate R2eff.
> > >      R2eff = r20_kex - cpmg_frqs * arccosh( Dpos * cosh(etapos) - Dneg * 
> > > cos(etaneg) )
> > >
> > > @@ -159,6 +165,4 @@
> > >      if not isfinite(sum(R2eff)):
> > >          R2eff = array([1e100]*num_points)
> > >
> > > -    # Parse back the value to update the back_calc class object.
> > > -    for i in range(num_points):
> > > -        back_calc[i] = R2eff[i]
> > > +    return R2eff
> > >
> > > Modified: branches/disp_speed/target_functions/relax_disp.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/branches/disp_speed/target_functions/relax_disp.py?rev=23240&r1=23239&r2=23240&view=diff
> > > ==============================================================================
> > > --- branches/disp_speed/target_functions/relax_disp.py  (original)
> > > +++ branches/disp_speed/target_functions/relax_disp.py  Mon May 19 
> > > 14:44:12 2014
> > > @@ -484,7 +484,7 @@
> > >                  dw_frq = dw[si] * self.frqs[0][si][mi]
> > >
> > >                  # Back calculate the R2eff values.
> > > -                r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], 
> > > pA=pA, dw=dw_frq, kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0], 
> > > back_calc=self.back_calc[0][si][mi][0], 
> > > num_points=self.num_disp_points[0][si][mi][0])
> > > +                self.back_calc[0][si][mi][0] = 
> > > r2eff_CR72(r20a=R20A[r20_index], r20b=R20B[r20_index], pA=pA, dw=dw_frq, 
> > > kex=kex, cpmg_frqs=self.cpmg_frqs[0][mi][0], 
> > > num_points=self.num_disp_points[0][si][mi][0])
> > >
> > >                  # For all missing data points, set the back-calculated 
> > > value to the measured values so that it has no effect on the chi-squared 
> > > value.
> > >                  for di in range(self.num_disp_points[0][si][mi][0]):
> > >
> > >
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