Author: tlinnet
Date: Wed May 28 19:17:19 2014
New Revision: 23566
URL: http://svn.gna.org/viewcvs/relax?rev=23566&view=rev
Log:
Converting back to having back_calc as a function argument to model DPL94:
This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.
The problem is, that many numerical models can't be optimised further, since
they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put
into
a larger numpy array.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Modified:
branches/disp_speed/lib/dispersion/dpl94.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
Modified: branches/disp_speed/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/dpl94.py?rev=23566&r1=23565&r2=23566&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/dpl94.py (original)
+++ branches/disp_speed/lib/dispersion/dpl94.py Wed May 28 19:17:19 2014
@@ -66,7 +66,7 @@
from numpy import abs, array, cos, isfinite, min, sin, sum
-def r1rho_DPL94(r1rho_prime=None, phi_ex=None, kex=None, theta=None, R1=0.0,
spin_lock_fields2=None, num_points=None):
+def r1rho_DPL94(r1rho_prime=None, phi_ex=None, kex=None, theta=None, R1=0.0,
spin_lock_fields2=None, back_calc=None, num_points=None):
"""Calculate the R1rho values for the DPL94 model.
See the module docstring for details.
@@ -84,7 +84,9 @@
@type R1: 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 num_points: The number of points on the dispersion
curve, equal to the length of the spin_lock_fields.
+ @keyword back_calc: The array for holding the back calculated
R1rho values. Each element corresponds to the combination of theta and spin
lock field.
+ @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.
@type num_points: int
"""
@@ -101,7 +103,8 @@
# Catch zeros (to avoid pointless mathematical operations).
# This will result in no exchange, returning flat lines.
if min(numer) == 0.0:
- return R1_R2
+ back_calc[:] = R1_R2
+ return
# Denominator.
denom = kex2 + spin_lock_fields2
@@ -109,9 +112,8 @@
# Catch math domain error of dividing with 0.
# This is when denom =0.
if min(abs(denom)) == 0:
- R1rho = array([1e100]*num_points)
-
- return R1rho
+ back_calc[:] = array([1e100]*num_points)
+ return
# R1rho calculation.
R1rho = R1_R2 + numer / denom
@@ -121,4 +123,4 @@
if not isfinite(sum(R1rho)):
R1rho = array([1e100]*num_points)
- return R1rho
+ back_calc[:] = 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=23566&r1=23565&r2=23566&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Wed May 28 19:17:19
2014
@@ -965,7 +965,7 @@
# Loop over the offsets.
for oi in range(self.num_offsets[0][si][mi]):
# Back calculate the R2eff values.
- self.back_calc[0][si][mi][oi] =
r1rho_DPL94(r1rho_prime=R20[r20_index], phi_ex=phi_ex_scaled, kex=kex,
theta=self.tilt_angles[0][si][mi][oi], R1=self.r1[si, mi],
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][oi],
num_points=self.num_disp_points[0][si][mi][oi])
+ r1rho_DPL94(r1rho_prime=R20[r20_index],
phi_ex=phi_ex_scaled, kex=kex, theta=self.tilt_angles[0][si][mi][oi],
R1=self.r1[si, mi],
spin_lock_fields2=self.spin_lock_omega1_squared[0][mi][oi],
back_calc=self.back_calc[0][si][mi][oi],
num_points=self.num_disp_points[0][si][mi][oi])
# 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][oi]):
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py?rev=23566&r1=23565&r2=23566&view=diff
==============================================================================
--- branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
(original)
+++ branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_dpl94.py
Wed May 28 19:17:19 2014
@@ -56,6 +56,7 @@
# Required data structures.
self.num_points = 11
+ self.R1rho = zeros(self.num_points, float64)
def calc_r1rho(self):
@@ -65,7 +66,7 @@
phi_ex_scaled, spin_lock_omega1_squared =
self.param_conversion(pA=self.pA, dw=self.dw, sfrq=self.sfrq,
spin_lock_nu1=self.spin_lock_nu1)
# Calculate the R1rho values.
- R1rho = r1rho_DPL94(r1rho_prime=self.r1rho_prime,
phi_ex=phi_ex_scaled, kex=self.kex, theta=self.theta, R1=self.r1,
spin_lock_fields2=spin_lock_omega1_squared, num_points=self.num_points)
+ r1rho_DPL94(r1rho_prime=self.r1rho_prime, phi_ex=phi_ex_scaled,
kex=self.kex, theta=self.theta, R1=self.r1,
spin_lock_fields2=spin_lock_omega1_squared, back_calc=self.R1rho,
num_points=self.num_points)
# Compare to function value.
r1rho_no_rex = self.r1 * cos(self.theta)**2 + self.r1rho_prime *
sin(self.theta)**2
@@ -73,10 +74,10 @@
# Check all R1rho values.
if self.kex > 1.e5:
for i in range(self.num_points):
- self.assertAlmostEqual(R1rho[i], r1rho_no_rex[i], 2)
+ self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i], 2)
else:
for i in range(self.num_points):
- self.assertAlmostEqual(R1rho[i], r1rho_no_rex[i])
+ self.assertAlmostEqual(self.R1rho[i], r1rho_no_rex[i])
def param_conversion(self, pA=None, dw=None, sfrq=None,
spin_lock_nu1=None):
r23566 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/