Author: tlinnet
Date: Mon May 19 03:20:43 2014
New Revision: 23222
URL: http://svn.gna.org/viewcvs/relax?rev=23222&view=rev
Log:
Huge speed-up for model TAP03.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_tp02_data_to_tap03
13.869s -> 7.263s
This is won by not checking single values in the R1rho array for math domain
errors, but calculating all steps, and in one single round check for finite
values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
Modified:
branches/disp_speed/lib/dispersion/tap03.py
Modified: branches/disp_speed/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/tap03.py?rev=23222&r1=23221&r2=23222&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/tap03.py (original)
+++ branches/disp_speed/lib/dispersion/tap03.py Mon May 19 03:20:43 2014
@@ -60,7 +60,7 @@
"""
# Python module imports.
-from math import atan2, sin, sqrt
+from numpy import arctan2, isfinite, sin, sqrt, sum
def r1rho_TAP03(r1rho_prime=None, omega=None, offset=None, pA=None, pB=None,
dw=None, kex=None, R1=0.0, spin_lock_fields=None, spin_lock_fields2=None,
back_calc=None, num_points=None):
@@ -105,50 +105,42 @@
phi_ex = pA * pB * dw**2
numer = phi_ex * kex
- # Loop over the dispersion points, back calculating the R1rho values.
+ # The factors.
+ da = Wa - offset # Offset of spin-lock from A.
+ db = Wb - offset # Offset of spin-lock from B.
+ d = W - offset # Offset of spin-lock from pop-average.
+
+ # The gamma factor.
+ sigma = pB*da + pA*db
+ sigma2 = sigma**2
+ gamma = 1.0 + phi_ex*(sigma2 - kex2 + spin_lock_fields2) / (sigma2 +
kex2 + spin_lock_fields2)**2
+
+ # Special omega values.
+ waeff2 = gamma*spin_lock_fields2 + da**2 # Effective field at A.
+ wbeff2 = gamma*spin_lock_fields2 + db**2 # Effective field at B.
+ weff2 = gamma*spin_lock_fields2 + d**2 # Effective field at
pop-average.
+
+ # The rotating frame flip angle.
+ theta = arctan2(spin_lock_fields, d)
+ hat_theta = arctan2(sqrt(gamma)*spin_lock_fields, d)
+
+ # Repetitive calculations (to speed up calculations).
+ sin_theta2 = sin(theta)**2
+ hat_sin_theta2 = sin(hat_theta)**2
+ R1_cos_theta2 = R1 * (1.0 - sin_theta2)
+ R1rho_prime_sin_theta2 = r1rho_prime * sin_theta2
+
+ # Denominator.
+ denom = waeff2*wbeff2/weff2 + kex2 - 2.0*hat_sin_theta2*phi_ex + (1.0 -
gamma)*spin_lock_fields2
+
+ # R1rho calculation.
+ R1rho = R1_cos_theta2 + R1rho_prime_sin_theta2 + hat_sin_theta2 * numer
/ denom / gamma
+
+ # 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)):
+ R1rho = array([1e100]*num_points)
+
+ # Parse back the value to update the back_calc class object.
for i in range(num_points):
- # The factors.
- da = Wa - offset # Offset of spin-lock from A.
- db = Wb - offset # Offset of spin-lock from B.
- d = W - offset # Offset of spin-lock from pop-average.
-
- # The gamma factor.
- sigma = pB*da + pA*db
- sigma2 = sigma**2
- gamma = 1.0 + phi_ex*(sigma2 - kex2 + spin_lock_fields2[i]) /
(sigma2 + kex2 + spin_lock_fields2[i])**2
-
- # Bad gamma.
- if gamma < 0.0:
- back_calc[i] = 1e100
- continue
-
- # Special omega values.
- waeff2 = gamma*spin_lock_fields2[i] + da**2 # Effective field at
A.
- wbeff2 = gamma*spin_lock_fields2[i] + db**2 # Effective field at
B.
- weff2 = gamma*spin_lock_fields2[i] + d**2 # Effective field at
pop-average.
-
- # The rotating frame flip angle.
- theta = atan2(spin_lock_fields[i], d)
- hat_theta = atan2(sqrt(gamma)*spin_lock_fields[i], d)
-
- # Repetitive calculations (to speed up calculations).
- sin_theta2 = sin(theta)**2
- hat_sin_theta2 = sin(hat_theta)**2
- R1_cos_theta2 = R1 * (1.0 - sin_theta2)
- R1rho_prime_sin_theta2 = r1rho_prime * sin_theta2
-
- # Catch zeros (to avoid pointless mathematical operations).
- if numer == 0.0:
- back_calc[i] = R1_cos_theta2 + R1rho_prime_sin_theta2
- continue
-
- # Denominator.
- denom = waeff2*wbeff2/weff2 + kex2 - 2.0*hat_sin_theta2*phi_ex +
(1.0 - gamma)*spin_lock_fields2[i]
-
- # Avoid divide by zero.
- if denom == 0.0:
- back_calc[i] = 1e100
- continue
-
- # R1rho calculation.
- back_calc[i] = R1_cos_theta2 + R1rho_prime_sin_theta2 +
hat_sin_theta2 * numer / denom / gamma
+ back_calc[i] = R1rho[i]
r23222 - /branches/disp_speed/lib/dispersion/tap03.py