Author: tlinnet
Date: Mon Jun 16 20:23:38 2014
New Revision: 24000
URL: http://svn.gna.org/viewcvs/relax?rev=24000&view=rev
Log:
Changed MMQ CR72 to use multi dimensional data.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
Modified: branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/mmq_cr72.py?rev=24000&r1=23999&r2=24000&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/mmq_cr72.py (original)
+++ branches/disp_spin_speed/lib/dispersion/mmq_cr72.py Mon Jun 16 20:23:38
2014
@@ -47,25 +47,26 @@
"""
# Python module imports.
-from numpy import arccosh, array, cos, cosh, isfinite, log, max, sin, sqrt,
sum
+from numpy import arccosh, cos, cosh, isfinite, fabs, log, min, max, sin,
sqrt, sum
+from numpy.ma import fix_invalid, masked_greater_equal, masked_where
-def r2eff_mmq_cr72(r20=None, pA=None, pB=None, dw=None, dwH=None, kex=None,
k_AB=None, k_BA=None, cpmg_frqs=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
+def r2eff_mmq_cr72(r20=None, pA=None, pB=None, dw=None, dwH=None, kex=None,
k_AB=None, k_BA=None, cpmg_frqs=None, inv_tcpmg=None, tcp=None,
back_calc=None):
"""The CR72 model extended to MMQ CPMG data.
This function calculates and stores the R2eff values.
@keyword r20: The R2 value in the absence of exchange.
- @type r20: float
+ @type r20: numpy float array of rank [NS][[NM][NO][ND]
@keyword pA: The population of state A.
@type pA: float
@keyword pB: The population of state B.
@type pB: float
@keyword dw: The chemical exchange difference between states
A and B in rad/s.
- @type dw: float
+ @type dw: numpy float array of rank [NS][[NM][NO][ND]
@keyword dwH: The proton chemical exchange difference between
states A and B in rad/s.
- @type dwH: float
+ @type dwH: numpy float array of rank [NS][[NM][NO][ND]
@keyword kex: The kex parameter value (the exchange rate in
rad/s).
@type kex: float
@keyword k_AB: The rate of exchange from site A to B (rad/s).
@@ -73,23 +74,29 @@
@keyword k_BA: The rate of exchange from site B to A (rad/s).
@type k_BA: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
- @type cpmg_frqs: numpy rank-1 float array
+ @type cpmg_frqs: numpy float array of rank [NS][[NM][NO][ND]
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
- @type inv_tcpmg: float
+ @type inv_tcpmg: numpy float array of rank [NS][[NM][NO][ND]
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
- @type tcp: numpy rank-1 float array
+ @type tcp: numpy float array of rank [NS][[NM][NO][ND]
@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 tcp and back_calc arguments.
- @type num_points: int
- @keyword power: The matrix exponential power array.
- @type power: numpy int16, rank-1 array
+ @type back_calc: numpy float array of rank [NS][[NM][NO][ND]
"""
- # Catch parameter values that will result in no exchange, returning flat
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
- #if (dw == 0.0 and dwH == 0.0) or pA == 1.0 or k_AB == 0.0:
- # back_calc[:] = array([r20]*num_points)
- # return
+ # Flag to tell if values should be replaced if max_etapos in cosh
function is violated.
+ t_dw_dw_H_zero = False
+ t_max_etapos = False
+
+ # Test if pA or kex is zero.
+ if kex == 0.0 or pA == 1.0:
+ back_calc[:] = r20
+ return
+
+ # Test if dw is zero. Wait for replacement, since this is spin specific.
+ if min(fabs(dw)) == 0.0 and min(fabs(dwH)) == 0.0:
+ t_dw_dw_H_zero = True
+ mask_dw_zero = masked_where(dw == 0.0, dw)
+ mask_dw_H_zero = masked_where(dwH == 0.0, dwH)
# Repetitive calculations (to speed up calculations).
dw2 = dw**2
@@ -133,8 +140,10 @@
# Catch math domain error of cosh(val > 710).
# This is when etapos > 710.
if max(etapos) > 700:
- back_calc[:] = array([r20]*num_points)
- return
+ t_max_etapos = True
+ mask_max_etapos = masked_greater_equal(etapos, 700.0)
+ # To prevent math errors, set etapos to 1.
+ etapos[mask_max_etapos.mask] = 1.0
# The full eta - values.
etaneg = etaneg_part / cpmg_frqs
@@ -153,11 +162,21 @@
lambda1 = r20_kex - cpmg_frqs * arccosh(Dpos * cosh(etapos) - Dneg *
cos(etaneg))
# The full formula.
- R2eff = lambda1.real - inv_tcpmg * log(Q)
+ back_calc[:] = lambda1.real - inv_tcpmg * log(Q)
+
+ # Replace data in array.
+ # If eta_pos above 700.
+ if t_max_etapos:
+ back_calc[mask_max_etapos.mask] = r20[mask_max_etapos.mask]
+
+ # Replace data in array.
+ # If dw and dwH is zero.
+ if t_dw_dw_H_zero:
+ back_calc[mask_dw_zero.mask] = r20[mask_dw_zero.mask]
+ back_calc[mask_dw_H_zero.mask] = r20[mask_dw_H_zero.mask]
# 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(R2eff)):
- R2eff = array([1e100]*num_points)
-
- back_calc[:] = R2eff
+ if not isfinite(sum(back_calc)):
+ # Replaces nan, inf, etc. with fill value.
+ fix_invalid(back_calc, copy=False, fill_value=r20)
r24000 - /branches/disp_spin_speed/lib/dispersion/mmq_cr72.py