Author: tlinnet
Date: Mon Jun 16 19:01:32 2014
New Revision: 23987
URL: http://svn.gna.org/viewcvs/relax?rev=23987&view=rev
Log:
Replaced the temporary structure self.cpmg_frqs_a to self.cpmg_frqs, which
works for all target functions
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/target_functions/relax_disp.py
Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23987&r1=23986&r2=23987&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Mon Jun 16
19:01:32 2014
@@ -177,8 +177,12 @@
self.NO = self.numpy_array_shape[3]
self.ND = self.numpy_array_shape[4]
+ # Create zero and one numpy structure.
+ numpy_array_zeros = zeros(self.numpy_array_shape, float64)
+ numpy_array_ones = ones(self.numpy_array_shape, float64)
+
# Create special numpy structures.
- self.no_nd_struct = ones([self.NO, self.ND], float64)
+ self.no_nd_ones = ones([self.NO, self.ND], float64)
# Store the arguments.
self.model = model
@@ -189,9 +193,9 @@
self.values = values
self.errors = errors
self.missing = missing
- self.frqs = multiply.outer( asarray(frqs).reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
+ self.frqs = multiply.outer( asarray(frqs).reshape(self.NE, self.NS,
self.NM), self.no_nd_ones )
self.frqs_H = frqs_H
- self.cpmg_frqs = cpmg_frqs
+ self.cpmg_frqs = deepcopy(numpy_array_ones)
self.spin_lock_nu1 = spin_lock_nu1
self.chemical_shifts = chemical_shifts
self.offset = offset
@@ -229,7 +233,9 @@
for oi in range(self.num_offsets[ei][si][mi]):
self.num_disp_points[ei][si][mi].append([])
if cpmg_frqs != None and len(cpmg_frqs[ei][mi][oi]):
- self.num_disp_points[ei][si][mi][oi] =
len(self.cpmg_frqs[ei][mi][oi])
+ num_disp_points = len(cpmg_frqs[ei][mi][oi])
+ self.num_disp_points[ei][si][mi][oi] =
num_disp_points
+ self.cpmg_frqs[ei][si][mi][oi][:num_disp_points]
= cpmg_frqs[ei][mi][oi]
elif spin_lock_nu1 != None and
len(spin_lock_nu1[ei][mi][oi]):
self.num_disp_points[ei][si][mi][oi] =
len(self.spin_lock_nu1[ei][mi][oi])
else:
@@ -306,7 +312,7 @@
# Normal value.
else:
- self.power[ei][mi][di] =
int(round(self.cpmg_frqs[ei][mi][0][di] * self.relax_times[ei][mi]))
+ self.power[ei][mi][di] =
int(round(self.cpmg_frqs[ei][0][mi][0][di] * self.relax_times[ei][mi]))
# The tau_cpmg times.
self.tau_cpmg = []
@@ -319,7 +325,7 @@
if recalc_tau:
self.tau_cpmg[ei][mi][di] = 0.25 *
self.relax_times[ei][mi] / self.power[ei][mi][di]
else:
- self.tau_cpmg[ei][mi][di] = 0.25 /
self.cpmg_frqs[ei][mi][0][di]
+ self.tau_cpmg[ei][mi][di] = 0.25 /
self.cpmg_frqs[ei][0][mi][0][di]
# Convert the spin-lock data to rad.s^-1.
if spin_lock_nu1 != None:
@@ -464,7 +470,6 @@
# Setup special numpy array structures, for higher dimensional
computation.
if model in test_models + [MODEL_NOREX]:
if model in MODEL_LIST_CPMG_FULL:
- self.cpmg_frqs_a = deepcopy(ones_a)
self.phi_ex_struct = deepcopy(zeros_a)
if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_TSMFK01, MODEL_NS_R1RHO_2SITE,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
@@ -496,7 +501,6 @@
if model in MODEL_LIST_CPMG_FULL and model !=
MODEL_NOREX:
# Extract cpmg_frqs and num_disp_points from
lists.
-
self.cpmg_frqs_a[ei][si][mi][oi][:num_disp_points] =
self.cpmg_frqs[ei][mi][oi]
self.num_disp_points_a[ei][si][mi][oi][:num_disp_points] =
self.num_disp_points[ei][si][mi][oi]
# Make a spin 1/0 file.
@@ -607,7 +611,7 @@
self.r20b_struct[:] = multiply.outer( R20B.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
## Back calculate the R2eff values.
- r2eff_CR72(r20a=self.r20a_struct, r20a_orig=R20A,
r20b=self.r20b_struct, r20b_orig=R20B, pA=pA, dw=self.dw_struct, dw_orig=dw,
kex=kex, cpmg_frqs=self.cpmg_frqs_a, back_calc=self.back_calc_a)
+ r2eff_CR72(r20a=self.r20a_struct, r20a_orig=R20A,
r20b=self.r20b_struct, r20b_orig=R20B, pA=pA, dw=self.dw_struct, dw_orig=dw,
kex=kex, cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc_a)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc_a = self.back_calc_a*self.disp_struct
@@ -1085,7 +1089,7 @@
self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
# Back calculate the R2eff values.
- r2eff_IT99(r20=self.r20_struct, pA=pA, dw=self.dw_struct,
dw_orig=dw, tex=tex, cpmg_frqs=self.cpmg_frqs_a, back_calc=self.back_calc_a)
+ r2eff_IT99(r20=self.r20_struct, pA=pA, dw=self.dw_struct,
dw_orig=dw, tex=tex, cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc_a)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc_a = self.back_calc_a*self.disp_struct
@@ -1180,7 +1184,7 @@
self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
# Back calculate the R2eff values.
- r2eff_LM63(r20=self.r20_struct, phi_ex=self.phi_ex_struct, kex=kex,
cpmg_frqs=self.cpmg_frqs_a, back_calc=self.back_calc_a)
+ r2eff_LM63(r20=self.r20_struct, phi_ex=self.phi_ex_struct, kex=kex,
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc_a)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc_a = self.back_calc_a*self.disp_struct
r23987 - /branches/disp_spin_speed/target_functions/relax_disp.py