Author: tlinnet
Date: Tue Jun 17 13:07:42 2014
New Revision: 24027
URL: http://svn.gna.org/viewcvs/relax?rev=24027&view=rev
Log:
More replacing of numpy index.
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=24027&r1=24026&r2=24027&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17
13:07:42 2014
@@ -263,26 +263,26 @@
for mi in range(self.NM):
# Fill the frequency.
frq = frqs[ei][si][mi]
- self.frqs[ei, si, mi][:] = frq
- self.frqs_squared[ei, si, mi][:] = frq**2
+ self.frqs[ei, si, mi, :] = frq
+ self.frqs_squared[ei, si, mi, :] = frq**2
frq_H = frqs_H[ei][si][mi]
- self.frqs_H[ei, si, mi][:] = frq_H
+ self.frqs_H[ei, si, mi, :] = frq_H
# Fill the relaxation time.
relax_time = relax_times[ei, mi]
- self.relax_times[ei, si, mi][:] = relax_time
+ self.relax_times[ei, si, mi, :] = relax_time
# Fill r1.
r1_l = r1[si][mi]
- self.r1[ei, si, mi][:] = r1_l
+ self.r1[ei, si, mi, :] = r1_l
# Fill chemical shift.
chemical_shift = chemical_shifts[ei][si][mi]
- self.chemical_shifts[ei, si, mi][:] = chemical_shift
+ self.chemical_shifts[ei, si, mi, :] = chemical_shift
# The inverted relaxation delay.
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_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR]:
- self.inv_relax_times[ei, si, mi][:] = 1.0 /
relax_time
+ self.inv_relax_times[ei, si, mi, :] = 1.0 /
relax_time
# The number of offset data points.
if len(offset[ei][si][mi]):
@@ -295,7 +295,7 @@
if cpmg_frqs != None and
len(cpmg_frqs[ei][mi][oi]):
cpmg_frqs_list = cpmg_frqs[ei][mi][oi]
num_disp_points = len(cpmg_frqs_list)
- self.cpmg_frqs[ei, si, mi,
oi][:num_disp_points] = cpmg_frqs_list
+ self.cpmg_frqs[ei, si, mi, oi,
:num_disp_points] = cpmg_frqs_list
for di in range(num_disp_points):
cpmg_frq = cpmg_frqs[ei][mi][oi][di]
@@ -322,9 +322,9 @@
self.num_disp_points[ei, si, mi, oi] =
num_disp_points
# Get the values and errors.
- self.values[ei, si, mi, oi][:num_disp_points] =
values[ei][si][mi][oi]
- self.errors[ei, si, mi, oi][:num_disp_points] =
errors[ei][si][mi][oi]
- self.disp_struct[ei, si, mi, oi][:num_disp_points]
= ones(num_disp_points)
+ self.values[ei, si, mi, oi, :num_disp_points] =
values[ei][si][mi][oi]
+ self.errors[ei, si, mi, oi, :num_disp_points] =
errors[ei][si][mi][oi]
+ self.disp_struct[ei, si, mi, oi, :num_disp_points]
= ones(num_disp_points)
# Loop over dispersion points.
for di in range(num_disp_points):
@@ -790,7 +790,7 @@
dw_AC_frq = dw_AC[si] * self.frqs[0, si, mi, 0, 0]
# Loop over the offsets.
- for oi in range(self.num_offsets[0][si, mi]):
+ for oi in range(self.num_offsets[0, si, mi]):
# Back calculate the R2eff values for each experiment
type.
ns_r1rho_3site(M0=self.M0, matrix=self.matrix,
r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi,
oi, 0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0],
pA=pA, pB=pB, pC=pC, dw_AB=dw_AB_frq, dw_AC=dw_AC_frq, k_AB=k_AB,
k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA,
spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi],
relax_time=self.relax_times[0, si, mi, oi],
inv_relax_time=self.inv_relax_times[0, si, mi, oi],
back_calc=self.back_calc[0, si, mi, oi], num_points=self.num_disp_points[0,
si, mi, oi])
@@ -1079,8 +1079,8 @@
# 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]):
- if self.missing[0, si, mi, 0][di]:
- self.back_calc[0, si, mi, 0][di] = self.values[0,
si, mi, 0][di]
+ if self.missing[0, si, mi, 0, di]:
+ self.back_calc[0, si, mi, 0, di] = self.values[0,
si, mi, 0, di]
# Calculate and return the chi-squared value.
chi2_sum += chi2(self.values[0, si, mi, 0],
self.back_calc[0, si, mi, 0], self.errors[0, si, mi, 0])
@@ -1660,7 +1660,7 @@
dw_frq = dw[si] * self.frqs[0, si, mi, 0, 0]
# Loop over the offsets.
- for oi in range(self.num_offsets[0][si, mi]):
+ for oi in range(self.num_offsets[0, si, mi]):
# Back calculate the R2eff values.
ns_r1rho_2site(M0=self.M0, matrix=self.matrix,
r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi,
oi, 0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0],
pA=pA, pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA,
spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi],
relax_time=self.relax_times[0, si, mi, oi],
inv_relax_time=self.inv_relax_times[0, si, mi, oi],
back_calc=self.back_calc[0, si, mi, oi], num_points=self.num_disp_points[0,
si, mi, oi])
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
relax-commits@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
Re: r24027 - /branches/disp_spin_speed/target_functions/relax_disp.py