Author: tlinnet
Date: Mon May 26 20:14:01 2014
New Revision: 23434
URL: http://svn.gna.org/viewcvs/relax?rev=23434&view=rev
Log:
Math-domain catching for model M61b.
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To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target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/m61b.py
branches/disp_speed/target_functions/relax_disp.py
Modified: branches/disp_speed/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/m61b.py?rev=23434&r1=23433&r2=23434&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/m61b.py (original)
+++ branches/disp_speed/lib/dispersion/m61b.py Mon May 26 20:14:01 2014
@@ -59,8 +59,10 @@
- U{relaxation dispersion page of the relax
website<http://www.nmr-relax.com/analyses/relaxation_dispersion.html#M61_skew>}.
"""
+# Python module imports.
+from numpy import abs, array, isfinite, min, sum
-def r1rho_M61b(r1rho_prime=None, pA=None, dw=None, kex=None,
spin_lock_fields=None, back_calc=None, num_points=None):
+def r1rho_M61b(r1rho_prime=None, pA=None, dw=None, kex=None,
spin_lock_fields2=None, num_points=None):
"""Calculate the R1rho values for the M61 skew model.
See the module docstring for details.
@@ -76,9 +78,7 @@
@type kex: float
@keyword spin_lock_fields2: The R1rho spin-lock field strengths squared
(in rad^2.s^-2).
@type spin_lock_fields2: numpy rank-1 float array
- @keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to one of the spin-lock fields.
- @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 spin_lock_fields and back_calc arguments.
+ @keyword num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields.
@type num_points: int
"""
@@ -92,20 +92,26 @@
# The numerator.
numer = pA2dw2 * pB * kex
- # Loop over the dispersion points, back calculating the R1rho values.
- for i in range(num_points):
- # Catch zeros (to avoid pointless mathematical operations).
- if numer == 0.0:
- back_calc[i] = r1rho_prime
- continue
+ # Catch zeros (to avoid pointless mathematical operations).
+ # This will result in no exchange, returning flat lines.
+ if numer == 0.0:
+ return array([r1rho_prime]*num_points)
- # Denominator.
- denom = kex2_pA2dw2 + spin_lock_fields2[i]
+ # Denominator.
+ denom = kex2_pA2dw2 + spin_lock_fields2
- # Avoid divide by zero.
- if denom == 0.0:
- back_calc[i] = 1e100
- continue
+ # Catch math domain error of dividing with 0.
+ # This is when denom=0.
+ if min(abs(denom)) == 0:
+ return array([1e100]*num_points)
- # R1rho calculation.
- back_calc[i] = r1rho_prime + numer / denom
+
+ # R1rho calculation.
+ R1rho = r1rho_prime + numer / denom
+
+ # Catch errors, taking a sum over array is the fastest way to check for
+ # +/- inf (infinity) and nan (not a number).
+ if not isfinite(sum(R1rho)):
+ return array([1e100]*num_points)
+
+ return R1rho
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=23434&r1=23433&r2=23434&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Mon May 26 20:14:01
2014
@@ -1210,7 +1210,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R1rho values.
- r1rho_M61b(r1rho_prime=R20[r20_index], pA=pA, dw=dw_frq,
kex=kex, spin_lock_fields2=self.spin_lock_omega1_squared[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] =
r1rho_M61b(r1rho_prime=R20[r20_index], pA=pA, dw=dw_frq, kex=kex,
spin_lock_fields2=self.spin_lock_omega1_squared[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]):
r23434 - in /branches/disp_speed: lib/dispersion/m61b.py target_functions/relax_disp.py