Author: bugman
Date: Wed Nov 26 19:42:20 2014
New Revision: 26770
URL: http://svn.gna.org/viewcvs/relax?rev=26770&view=rev
Log:
Shifted the C code Jacobian functions into the new
target_functions.relax_fit_wrapper module.
This shifts all of the relaxation curve-fitting C code access into the
target_functions.relax_fit_wrapper module so that the rest of relax does not
need to handle the C
code. This will allow for new models to be very easily supported, as they
would all be set up in
this target function module.
Modified:
trunk/specific_analyses/relax_disp/estimate_r2eff.py
trunk/specific_analyses/relax_fit/api.py
trunk/target_functions/relax_fit_wrapper.py
Modified: trunk/specific_analyses/relax_disp/estimate_r2eff.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/estimate_r2eff.py?rev=26770&r1=26769&r2=26770&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/estimate_r2eff.py (original)
+++ trunk/specific_analyses/relax_disp/estimate_r2eff.py Wed Nov 26
19:42:20 2014
@@ -44,10 +44,6 @@
from target_functions.chi2 import chi2_rankN, dchi2
from target_functions.relax_fit_wrapper import Relax_fit_opt
-# C modules.
-if C_module_exp_fn:
- from target_functions.relax_fit import jacobian, jacobian_chi2, setup
-
# Scipy installed.
if scipy_module:
# Import leastsq.
@@ -123,10 +119,10 @@
# Initialise data in C code.
scaling_list = [1.0, 1.0]
- setup(num_params=len(param_vector), num_times=len(times),
values=values, sd=errors, relax_times=times, scaling_matrix=scaling_list)
+ model = Relax_fit_opt(num_params=len(param_vector), values=values,
errors=errors, relax_times=times, scaling_matrix=scaling_list)
# Use the direct Jacobian from function.
- jacobian_matrix_exp = transpose(asarray( jacobian(param_vector) ) )
+ jacobian_matrix_exp = transpose(asarray(
model.jacobian(param_vector) ) )
weights = 1. / errors**2
# Get the co-variance
@@ -823,12 +819,12 @@
if E.c_code == True:
if E.chi2_jacobian:
# Use the chi2 Jacobian from C.
- jacobian_matrix_exp = transpose(asarray(
jacobian_chi2(param_vector) ) )
+ jacobian_matrix_exp = transpose(asarray(
model.jacobian_chi2(param_vector) ) )
weights = ones(E.errors.shape)
else:
# Use the direct Jacobian from C.
- jacobian_matrix_exp = transpose(asarray( jacobian(param_vector) ) )
+ jacobian_matrix_exp = transpose(asarray(
model.jacobian(param_vector) ) )
weights = 1. / E.errors**2
elif E.c_code == False:
Modified: trunk/specific_analyses/relax_fit/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_fit/api.py?rev=26770&r1=26769&r2=26770&view=diff
==============================================================================
--- trunk/specific_analyses/relax_fit/api.py (original)
+++ trunk/specific_analyses/relax_fit/api.py Wed Nov 26 19:42:20 2014
@@ -45,10 +45,6 @@
from specific_analyses.relax_fit.parameters import assemble_param_vector,
disassemble_param_vector, linear_constraints
from target_functions.relax_fit_wrapper import Relax_fit_opt
-# C modules.
-if C_module_exp_fn:
- from target_functions.relax_fit import jacobian, setup
-
class Relax_fit(API_base, API_common):
"""Class containing functions for relaxation curve fitting."""
@@ -139,10 +135,10 @@
# Initialise data in C code.
scaling_list = [1.0, 1.0]
- setup(num_params=len(param_vector), num_times=len(times),
values=values, sd=errors, relax_times=times, scaling_matrix=scaling_list)
+ model = Relax_fit_opt(num_params=len(param_vector), values=values,
errors=errors, relax_times=times, scaling_matrix=scaling_list)
# Use the direct Jacobian from function.
- jacobian_matrix_exp = transpose(asarray( jacobian(param_vector) ) )
+ jacobian_matrix_exp = transpose(asarray( model.jacobian(param_vector)
) )
weights = 1. / errors**2
# Return the matrices.
Modified: trunk/target_functions/relax_fit_wrapper.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_fit_wrapper.py?rev=26770&r1=26769&r2=26770&view=diff
==============================================================================
--- trunk/target_functions/relax_fit_wrapper.py (original)
+++ trunk/target_functions/relax_fit_wrapper.py Wed Nov 26 19:42:20 2014
@@ -32,7 +32,7 @@
# C modules.
if C_module_exp_fn:
- from target_functions.relax_fit import setup, func, dfunc, d2func,
back_calc_I
+ from target_functions.relax_fit import jacobian, jacobian_chi2, setup,
func, dfunc, d2func, back_calc_I
class Relax_fit_opt:
@@ -60,6 +60,10 @@
self.func = self.func_wrapper
self.dfunc = self.dfunc_wrapper
self.d2func = self.d2func_wrapper
+
+ # Alias the Jacobian C functions.
+ self.jacobian = jacobian
+ self.jacobian_chi2 = jacobian_chi2
def back_calc_data(self):
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