Re: r23834 - /branches/disp_spin_speed/lib/dispersion/cr72.py -- June 11, 2014 - 15:10

Hi,

We should really convert the unit tests to input the higher order
structures.  There is no need to have extra code to handle these
cases, and we do not need backwards compatibility here.  It's better
to change completely and delete the old code for speed.  If a user
would like to directly use the relax library functions, then they can
read the function docstring and work out that dw, R20A, and R20B need
to be higher order structures.

Regards,

Edward



On 11 June 2014 15:06, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> Hi Edward.
>
> It is the unit tests, which fail.
>
> But I can change those.
>
> It is the choice of backwards compatibility and easy import of lib
> function, and easy use of input, that weights higher.
> With those few tests, the function becomes easy to use in 1d all multi d 
> cases.
>
> What do you think?
>
> Best
> Troels
>
> 2014-06-11 15:00 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > Hi Troels,
> >
> > For such changes, do you need to test for r20a being a float?  It is
> > defined as being a numpy array of floats in the docstring, and so it
> > should always be.  Not checking for a value which should never be
> > supplied will simplify the code.
> >
> > Regards,
> >
> > Edward
> >
> > On 11 June 2014 14:54,  <tlinnet@xxxxxxxxxxxxx> wrote:
> > > Author: tlinnet
> > > Date: Wed Jun 11 14:54:37 2014
> > > New Revision: 23834
> > >
> > > URL: http://svn.gna.org/viewcvs/relax?rev=23834&view=rev
> > > Log:
> > > Implemented masked replacement if fact is less that 1.0.
> > >
> > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
> > > models for Clustered analysis.
> > >
> > > Modified:
> > >     branches/disp_spin_speed/lib/dispersion/cr72.py
> > >
> > > Modified: branches/disp_spin_speed/lib/dispersion/cr72.py
> > > URL: 
> > > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/cr72.py?rev=23834&r1=23833&r2=23834&view=diff
> > > ==============================================================================
> > > --- branches/disp_spin_speed/lib/dispersion/cr72.py     (original)
> > > +++ branches/disp_spin_speed/lib/dispersion/cr72.py     Wed Jun 11 
> > > 14:54:37 2014
> > > @@ -93,7 +93,7 @@
> > >
> > >  # Python module imports.
> > >  from numpy import allclose, arccosh, array, cos, cosh, isfinite, isnan, 
> > > fabs, min, max, ndarray, ones, sqrt, sum, zeros
> > > -from numpy.ma import masked_greater_equal, masked_where
> > > +from numpy.ma import masked_greater_equal, masked_less, masked_where
> > >
> > >  # Repetitive calculations (to speed up calculations).
> > >  eta_scale = 2.0**(-3.0/2.0)
> > > @@ -125,6 +125,7 @@
> > >      # Flag to tell if values should be replaced if max_etapos in cosh 
> > > function is violated.
> > >      t_dw_zero = False
> > >      t_max_etapos = False
> > > +    t_min_fact = False
> > >
> > >      # Catch parameter values that will result in no exchange, returning 
> > > flat R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
> > >      # Test if pA or kex is zero.
> > > @@ -182,13 +183,16 @@
> > >      # The arccosh argument - catch invalid values.
> > >      fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
> > >      if min(fact) < 1.0:
> > > -        back_calc[:] = r20_kex
> > > -        return
> > > +        t_min_fact = True
> > > +        mask_min_fact = masked_less(fact, 1.0)
> > > +        # To prevent math errors, set fact to 1.
> > > +        fact[mask_min_etapos.mask] = 1.0
> > >
> > >      # Calculate R2eff.
> > >      R2eff = r20_kex - cpmg_frqs * arccosh( fact )
> > >
> > >      # Replace data in array.
> > > +    # If dw is zero.
> > >      if t_dw_zero:
> > >          if isinstance(r20a, float):
> > >              back_calc[:] = array([r20a]*num_points)
> > > @@ -196,12 +200,21 @@
> > >          else:
> > >              R2eff[mask_dw_zero.mask] = r20a[mask_dw_zero.mask]
> > >
> > > +    # If eta_pos above 700.
> > >      if t_max_etapos:
> > >          if isinstance(r20a, float):
> > >              back_calc[:] = array([r20a]*num_points)
> > >              return
> > >          else:
> > >              R2eff[mask_max_etapos.mask] = r20a[mask_max_etapos.mask]
> > > +
> > > +    # If fact < 1.0
> > > +    if t_min_fact:
> > > +        if isinstance(r20a, float):
> > > +            back_calc[:] = array([r20a]*num_points)
> > > +            return
> > > +        else:
> > > +            R2eff[mask_min_fact.mask] = r20a[mask_min_fact.mask]
> > >
> > >      # Catch errors, taking a sum over array is the fastest way to check 
> > > for
> > >      # +/- inf (infinity) and nan (not a number).
> > >
> > >
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