Author: tlinnet
Date: Mon Jun 16 19:01:30 2014
New Revision: 23986
URL: http://svn.gna.org/viewcvs/relax?rev=23986&view=rev
Log:
Replaced the temporary structure self.frqs_a to self.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=23986&r1=23985&r2=23986&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Mon Jun 16
19:01:30 2014
@@ -165,6 +165,21 @@
if r1 == None:
raise RelaxError("R1 relaxation rates must be supplied for
the '%s' R1rho off-resonance dispersion model." % model)
+ ### Initialise higher order numpy structures.
+ # Define the shape of all the numpy arrays.
+ self.numpy_array_shape = list( asarray(values).shape )
+
+ # Set the dimensions to paramater.
+ # The total numbers of experiments, number of spins, number of
magnetic field strength, number of offsets, maximum number of dispersion
point.
+ self.NE = self.numpy_array_shape[0]
+ self.NS = self.numpy_array_shape[1]
+ self.NM = self.numpy_array_shape[2]
+ self.NO = self.numpy_array_shape[3]
+ self.ND = self.numpy_array_shape[4]
+
+ # Create special numpy structures.
+ self.no_nd_struct = ones([self.NO, self.ND], float64)
+
# Store the arguments.
self.model = model
self.num_params = num_params
@@ -174,7 +189,7 @@
self.values = values
self.errors = errors
self.missing = missing
- self.frqs = frqs
+ self.frqs = multiply.outer( asarray(frqs).reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
self.frqs_H = frqs_H
self.cpmg_frqs = cpmg_frqs
self.spin_lock_nu1 = spin_lock_nu1
@@ -448,10 +463,6 @@
# Setup special numpy array structures, for higher dimensional
computation.
if model in test_models + [MODEL_NOREX]:
- if model in test_models:
- # Extract the frequencies to numpy array.
- self.frqs_a = multiply.outer(
asarray(self.frqs).reshape(self.NE, self.NS, self.NM), self.no_nd_struct )
-
if model in MODEL_LIST_CPMG_FULL:
self.cpmg_frqs_a = deepcopy(ones_a)
self.phi_ex_struct = deepcopy(zeros_a)
@@ -550,7 +561,7 @@
"""
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, out=self.dw_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
@@ -589,7 +600,7 @@
"""
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, out=self.dw_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
@@ -628,7 +639,7 @@
"""
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, out=self.dw_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
@@ -667,7 +678,7 @@
"""
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, out=self.dw_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
@@ -749,8 +760,8 @@
r20_index = mi + ei*self.num_frq +
si*self.num_frq*self.num_exp
# Convert dw from ppm to rad/s.
- dw_AB_frq = dw_AB[si] * self.frqs[ei][si][mi]
- dw_AC_frq = dw_AC[si] * self.frqs[ei][si][mi]
+ dw_AB_frq = dw_AB[si] * self.frqs[ei][si][mi][0][0]
+ dw_AC_frq = dw_AC[si] * self.frqs[ei][si][mi][0][0]
dwH_AB_frq = dwH_AB[si] * self.frqs_H[ei][si][mi]
dwH_AC_frq = dwH_AC[si] * self.frqs_H[ei][si][mi]
@@ -1028,7 +1039,7 @@
kex = params[self.end_index[1]]
# Convert phi_ex from ppm^2 to (rad/s)^2. Use the out argument, to
pass directly to structure.
- multiply( multiply.outer( phi_ex.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs_a*self.frqs_a, out=self.phi_ex_struct )
+ multiply( multiply.outer( phi_ex.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs*self.frqs, out=self.phi_ex_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 )
@@ -1068,7 +1079,7 @@
tex = params[self.end_index[2]]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, 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 )
@@ -1163,7 +1174,7 @@
kex = params[self.end_index[1]]
# Convert phi_ex from ppm^2 to (rad/s)^2. Use the out argument, to
pass directly to structure.
- multiply( multiply.outer( phi_ex.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs_a*self.frqs_a, out=self.phi_ex_struct )
+ multiply( multiply.outer( phi_ex.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs*self.frqs, out=self.phi_ex_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 )
@@ -1202,7 +1213,7 @@
kex = params[self.end_index[1]]
# Convert phi_ex from ppm^2 to (rad/s)^2. Use the out argument, to
pass directly to structure.
- multiply( multiply.outer( phi_ex.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs_a*self.frqs_a, out=self.phi_ex_struct )
+ multiply( multiply.outer( phi_ex.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs*self.frqs, out=self.phi_ex_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 )
@@ -1242,7 +1253,7 @@
kex = params[self.end_index[1]+1]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, 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 )
@@ -1282,7 +1293,7 @@
kex = params[self.end_index[1]+1]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, 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 )
@@ -1340,7 +1351,7 @@
r20_index = mi + ei*self.num_frq +
si*self.num_frq*self.num_exp
# Convert dw from ppm to rad/s.
- dw_frq = dw[si] * self.frqs[ei][si][mi]
+ dw_frq = dw[si] * self.frqs[ei][si][mi][0][0]
dwH_frq = dwH[si] * self.frqs_H[ei][si][mi]
# Alias the dw frequency combinations.
@@ -1471,7 +1482,7 @@
kex = params[self.end_index[1]+1]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, out=self.dw_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
@@ -1584,7 +1595,7 @@
r20_index = mi + ei*self.num_frq +
si*self.num_frq*self.num_exp
# Convert dw from ppm to rad/s.
- dw_frq = dw[si] * self.frqs[ei][si][mi]
+ dw_frq = dw[si] * self.frqs[ei][si][mi][0][0]
dwH_frq = dwH[si] * self.frqs_H[ei][si][mi]
# Alias the dw frequency combinations.
@@ -1803,7 +1814,7 @@
kex = params[self.end_index[1]+1]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, 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 )
@@ -1843,7 +1854,7 @@
kex = params[self.end_index[1]+1]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, 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 )
@@ -1883,7 +1894,7 @@
k_AB = params[self.end_index[1]]
# 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 )
+ multiply( multiply.outer( dw.reshape(self.NE, self.NS),
self.nm_no_nd_struct ), self.frqs, out=self.dw_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS,
self.NM), self.no_nd_struct )
r23986 - /branches/disp_spin_speed/target_functions/relax_disp.py