Author: tlinnet
Date: Fri Jun 13 12:16:52 2014
New Revision: 23928
URL: http://svn.gna.org/viewcvs/relax?rev=23928&view=rev
Log:
Replaced target function for model MP05, to use higher dimensional numpy
array structures.
That makes the model much faster.
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=23928&r1=23927&r2=23928&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun 13
12:16:52 2014
@@ -396,7 +396,7 @@
# Setup special numpy array structures, for higher dimensional
computation.
- test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_M61, MODEL_M61B, MODEL_TAP03, MODEL_TP02,
MODEL_TSMFK01]
+ test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_TAP03,
MODEL_TP02, MODEL_TSMFK01]
if model in test_models + [MODEL_NOREX]:
# Get the shape of back_calc structure.
@@ -1327,37 +1327,25 @@
pA = params[self.end_index[1]]
kex = params[self.end_index[1]+1]
- # Once off parameter conversions.
- pB = 1.0 - pA
-
- # Initialise.
- chi2_sum = 0.0
-
- # Loop over the spins.
- for si in range(self.num_spins):
- # Loop over the spectrometer frequencies.
- for mi in range(self.num_frq):
- # The R20 index.
- r20_index = mi + si*self.num_frq
-
- # Convert dw from ppm to rad/s.
- dw_frq = dw[si] * self.frqs[0][si][mi]
-
- # Loop over the offsets.
- for oi in range(self.num_offsets[0][si][mi]):
- # Back calculate the R1rho values.
- r1rho_MP05(r1rho_prime=R20[r20_index],
omega=self.chemical_shifts[0][si][mi], offset=self.offset[0][si][mi][oi],
pA=pA, pB=pB, dw=dw_frq, kex=kex, R1=self.r1[si, mi],
spin_lock_fields=self.spin_lock_omega1[0][mi][oi],
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]):
- if self.missing[0][si][mi][oi][di]:
- self.back_calc[0][si][mi][oi][di] =
self.values[0][si][mi][oi][di]
-
- # Calculate and return the chi-squared value.
- chi2_sum += chi2(self.values[0][si][mi][oi],
self.back_calc[0][si][mi][oi], self.errors[0][si][mi][oi])
+ # Convert dw from ppm to rad/s. Use the out argument, to pass
directly to structure.
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs_a, out=self.dw_struct )
+
+ # Reshape R20 to per experiment, spin and frequency.
+ self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
+
+ # Back calculate the R1rho values.
+ r1rho_MP05(r1rho_prime=self.r20_struct,
omega=self.chemical_shifts_a, offset=self.offset_a, pA=pA, dw=self.dw_struct,
kex=kex, R1=self.r1_a, spin_lock_fields=self.spin_lock_omega1_a,
spin_lock_fields2=self.spin_lock_omega1_squared_a, 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
+
+ ## 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.
+ if self.has_missing:
+ # Replace with values.
+ self.back_calc_a[self.mask_replace_blank.mask] =
self.values_a[self.mask_replace_blank.mask]
# Return the total chi-squared value.
- return chi2_sum
+ return chi2_rankN(self.values_a, self.back_calc_a, self.errors_a)
def func_mmq_CR72(self, params):
r23928 - /branches/disp_spin_speed/target_functions/relax_disp.py