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 <[email protected]>:
> 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, <[email protected]> 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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>
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