Author: tlinnet
Date: Sun Jun 8 13:14:36 2014
New Revision: 23729
URL: http://svn.gna.org/viewcvs/relax?rev=23729&view=rev
Log:
Removing looping over exp and offset indicies in calc_chi2. They are always
0 anyway.
This brings a little speed.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
----
Profiling.
1000 iterations
100 spins
3 sfrq
('sfrq: ', 600000000.0, 'number of cpmg frq', 15, array([ 2., 6., 10.,
14., 18., 22., 26., 30., 34., 38., 42.,
46., 50., 54., 58.]))
('sfrq: ', 800000000.0, 'number of cpmg frq', 20, array([ 2., 6., 10.,
14., 18., 22., 26., 30., 34., 38., 42.,
46., 50., 54., 58., 62., 66., 70., 74., 78.]))
('sfrq: ', 900000000.0, 'number of cpmg frq', 22, array([ 2., 6., 10.,
14., 18., 22., 26., 30., 34., 38., 42.,
46., 50., 54., 58., 62., 66., 70., 74., 78., 82., 86.]))
('chi2 cluster:', 0.0)
TRUNK
ncalls tottime percall cumtime percall filename:lineno(function)
1000 5.221 0.005 53.578 0.054
relax_disp.py:456(calc_CR72_chi2)
BEFORE
ncalls tottime percall cumtime percall filename:lineno(function)
1000 14.871 0.015 43.084 0.043
relax_disp.py:494(calc_CR72_chi2)
AFTER removing looping over exp and offset indicies. They are always 0.
ncalls tottime percall cumtime percall filename:lineno(function)
1000 12.831 0.013 38.248 0.038
relax_disp.py:494(calc_CR72_chi2)
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=23729&r1=23728&r2=23729&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Sun Jun 8
13:14:36 2014
@@ -508,33 +508,29 @@
@rtype: float
"""
- # Loop over the experiment types.
- for ei in range(self.num_exp):
- # Loop over the spins.
- for si in range(self.num_spins):
- # Loop over the spectrometer frequencies.
- for mi in range(self.num_frq):
- # Loop over the offsets.
- for oi in range(self.num_offsets[ei][si][mi]):
- # Extract number of dispersion points.
- num_disp_points =
self.num_disp_points[ei][si][mi][oi]
-
- # The R20 index.
- r20_index = mi + si*self.num_frq
-
- # Store r20a and r20b values per disp point.
- self.R20A_a[ei][si][mi][oi] = np.array(
[R20A[r20_index]] * self.max_num_disp_points, float64)
- self.R20B_a[ei][si][mi][oi] = np.array(
[R20B[r20_index]] * self.max_num_disp_points, float64)
-
- # Convert dw from ppm to rad/s.
- dw_frq = dw[si] * self.frqs[ei][si][mi]
-
- # Store dw_frq per disp point.
- self.dw_frq_a[ei][si][mi][oi] = np.array( [dw_frq]
* self.max_num_disp_points, float64)
-
- # Store pA and kex per disp point.
- self.pA_a[ei][si][mi][oi] = np.array( [pA] *
self.max_num_disp_points, float64)
- self.kex_a[ei][si][mi][oi] = np.array( [kex] *
self.max_num_disp_points, float64)
+ # Loop over the spins.
+ for si in range(self.num_spins):
+ # Loop over the spectrometer frequencies.
+ for mi in range(self.num_frq):
+ # Extract number of dispersion points.
+ num_disp_points = self.num_disp_points[0][si][mi][0]
+
+ # The R20 index.
+ r20_index = mi + si*self.num_frq
+
+ # Store r20a and r20b values per disp point.
+ self.R20A_a[0][si][mi][0] = np.array( [R20A[r20_index]] *
self.max_num_disp_points, float64)
+ self.R20B_a[0][si][mi][0] = np.array( [R20B[r20_index]] *
self.max_num_disp_points, float64)
+
+ # Convert dw from ppm to rad/s.
+ dw_frq = dw[si] * self.frqs[0][si][mi]
+
+ # Store dw_frq per disp point.
+ self.dw_frq_a[0][si][mi][0] = np.array( [dw_frq] *
self.max_num_disp_points, float64)
+
+ # Store pA and kex per disp point.
+ self.pA_a[0][si][mi][0] = np.array( [pA] *
self.max_num_disp_points, float64)
+ self.kex_a[0][si][mi][0] = np.array( [kex] *
self.max_num_disp_points, float64)
## Back calculate the R2eff values.
r2eff_CR72(r20a=self.R20A_a, r20b=self.R20B_a, pA=self.pA_a,
dw=self.dw_frq_a, kex=self.kex_a, cpmg_frqs=self.cpmg_frqs_a,
back_calc=self.back_calc_a, num_points=self.num_disp_points_a)
@@ -544,26 +540,22 @@
# Now return the values back to the structure of self.back_calc
object.
## 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.
- # Loop over the experiment types.
- for ei in range(self.num_exp):
- # Loop over the spins.
- for si in range(self.num_spins):
- # Loop over the spectrometer frequencies.
- for mi in range(self.num_frq):
- # Loop over the offsets.
- for oi in range(self.num_offsets[ei][si][mi]):
- # Extract number of dispersion points.
- num_disp_points =
self.num_disp_points[ei][si][mi][oi]
-
- self.back_calc[ei][si][mi][oi] =
self.back_calc_a[ei][si][mi][oi][:num_disp_points]
-
-
- for di in
range(self.num_disp_points[ei][si][mi][oi]):
- if self.missing[ei][si][mi][oi][di]:
- self.back_calc[ei][si][mi][oi][di] =
self.values[ei][si][mi][oi][di]
-
- ## Calculate and return the chi-squared value.
- chi2_sum += chi2(self.values[ei][si][mi][oi],
self.back_calc[ei][si][mi][oi], self.errors[ei][si][mi][oi])
+ # Loop over the spins.
+ for si in range(self.num_spins):
+ # Loop over the spectrometer frequencies.
+ for mi in range(self.num_frq):
+ # Extract number of dispersion points.
+ num_disp_points = self.num_disp_points[0][si][mi][0]
+
+ self.back_calc[0][si][mi][0] =
self.back_calc_a[0][si][mi][0][:num_disp_points]
+
+
+ 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]
+
+ ## 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])
# Return the total chi-squared value.
return chi2_sum
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Re: r23729 - /branches/disp_spin_speed/target_functions/relax_disp.py