Author: bugman
Date: Thu Apr 4 10:59:08 2013
New Revision: 19347
URL: http://svn.gna.org/viewcvs/relax?rev=19347&view=rev
Log:
Updated the relaxation dispersion target function class to handle the recent
changes.
Modified:
branches/relax_disp/specific_analyses/relax_disp.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19347&r1=19346&r2=19347&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Thu Apr 4 10:59:08
2013
@@ -1085,7 +1085,7 @@
print("Unconstrained grid search size: %s (constraints
may decrease this size).\n" % grid_size)
# Initialise the function to minimise.
- model = Dispersion(model=cdp.model,
num_params=self._param_num(spins=spins), num_times=cdp.num_time_pts,
curve_num=cdp.curve_count, values=values, errors=errors,
relax_times=cdp.relax_time_list, cpmg_frqs=cdp.cpmg_frqs_list,
spin_lock_nu1=cdp.spin_lock_nu1_list, scaling_matrix=scaling_matrix)
+ model = Dispersion(model=cdp.model,
num_params=self._param_num(spins=spins), num_spins=spin_num,
num_exp_curves=cdp.curve_count, num_times=cdp.num_time_pts, values=values,
errors=errors, cpmg_frqs=cdp.cpmg_frqs_list,
spin_lock_nu1=cdp.spin_lock_nu1_list, relax_times=cdp.relax_time_list,
scaling_matrix=scaling_matrix)
# Setup the minimisation algorithm when constraints are present.
if constraints and not match('^[Gg]rid', min_algor):
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=19347&r1=19346&r2=19347&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Thu Apr 4 10:59:08
2013
@@ -23,6 +23,9 @@
# Module docstring.
"""Target functions for relaxation dispersion."""
+# Python module imports.
+from numpy import float64, zeros
+
# relax module imports.
from lib.dispersion.equations import fast_2site
from lib.errors import RelaxError
@@ -30,35 +33,64 @@
class Dispersion:
- def __init__(self, model=None, num_params=None, num_times=None,
values=None, sd=None, cpmg_frqs=None, scaling_matrix=None):
+ def __init__(self, model=None, num_params=None, num_spins=None,
num_exp_curves=None, num_times=None, values=None, errors=None,
cpmg_frqs=None, spin_lock_nu1=None, relax_times=None, scaling_matrix=None):
"""Relaxation dispersion target functions for optimisation.
+
+ Models
+ ======
+
+ The following models are currently supported:
+
+ - 'exp_fit': Simple fitting of the exponential curves with
parameters {R2eff, I0},
+ - 'fast 2-site': The 2-site fast exchange equation with
parameters {R2eff, I0, R2, Rex, kex},
+ - 'slow 2-site': The 2-site slow exchange equation with
parameters {R2eff, I0, R2A, kA, dw}.
+
@keyword model: The relaxation dispersion model to fit.
@type model: str
@keyword num_param: The number of parameters in the model.
@type num_param: int
+ @keyword num_spins: The number of spins in the cluster.
+ @type num_spins: int
+ @keyword num_exp_curves: The number of exponential curves.
+ @type num_exp_curves: int
@keyword num_times: The number of relaxation times.
@type num_times: int
- @keyword values: The peak intensities.
- @type values: numpy rank-2 float array
- @keyword sd: The peak intensity errors.
- @type sd: numpy rank-2 float array
- @keyword cpmg_frqs: The CPMG frequencies in Hertz.
+ @keyword values: The peak intensities. The first
dimension is that of the spin cluster (each element corresponds to a
different spin in the block), the second dimension is the exponential curves,
and the third are the relaxation times along the exponential curve.
+ @type values: numpy rank-3 float array
+ @keyword errors: The peak intensity errors. The three
dimensions must correspond to those of the values argument.
+ @type errors: numpy rank-3 float array
+ @keyword cpmg_frqs: The CPMG frequencies in Hertz for each
separate exponential curve. This will be ignored for R1rho experiments.
@type cpmg_frqs: numpy rank-1 float array
+ @keyword spin_lock_nu1: The spin-lock field strengths in Hertz
for each separate exponential curve. This will be ignored for CPMG
experiments.
+ @type spin_lock_nu1: numpy rank-1 float array
+ @keyword relax_times: The relaxation time points in seconds
for the exponential curve.
+ @type relax_times: numpy rank-1 float array
@keyword scaling_matrix: The square and diagonal scaling matrix.
- @type scaling_matrix: numpy rank-2 array
+ @type scaling_matrix: numpy rank-2 float array
"""
+
+ # Check the args.
+ if model not in ['exp_fit', 'fast 2-site', 'slow 2-site']:
+ raise RelaxError("The model '%s' is unknown." % model)
# Store the arguments.
self.num_params = num_params
+ self.num_spins = num_spins
+ self.num_exp_curves = num_exp_curves
self.num_times = num_times
self.values = values
- self.sd = sd
+ self.errors = errors
self.cpmg_frqs = cpmg_frqs
+ self.spin_lock_nu1 = spin_lock_nu1
+ self.relax_times = relax_times
self.scaling_matrix = scaling_matrix
+ # Set up a structure for holding the R2eff and I0 parameters.
+ self.exp_params = zeros((num_exp_curves, 2), float64)
+
# Set up the model.
- if model == 'fast':
+ if model == 'fast 2-site':
self.func = self.func_fast_2site
else:
raise RelaxError("The relaxation dispersion model '%s' is not
supported yet." % model)
r19347 - in /branches/relax_disp: specific_analyses/relax_disp.py target_functions/relax_disp.py