Author: bugman
Date: Tue Nov 24 10:05:30 2009
New Revision: 9892
URL: http://svn.gna.org/viewcvs/relax?rev=9892&view=rev
Log:
Added the methods necessary for the dx.map() user function.
These include:
__assemble_param_vector()
map_bounds()
model_statistics()
return_data_name()
return_units()
Modified:
1.3/specific_fns/frame_order.py
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=9892&r1=9891&r2=9892&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Nov 24 10:05:30 2009
@@ -50,6 +50,22 @@
class Frame_order(Common_functions):
"""Class containing the specific methods of the Frame Order theories."""
+ def __assemble_param_vector(self):
+ """Assemble and return the parameter vector.
+
+ @return: The parameter vector.
+ @rtype: numpy rank-1 array
+ """
+
+ # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
+ if cdp.model == 'rigid':
+ return array([cdp.alpha, cdp.beta, cdp.gamma], float64)
+
+ # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
+ elif cdp.model == 'iso cone':
+ return array([cdp.alpha, cdp.beta, cdp.gamma, cdp.theta_axis,
cdp.phi_axis, cdp.theta_cone], float64)
+
+
def __grid_row(self, incs, lower, upper, dist_type=None):
"""Set up a row of the grid search for a given parameter.
@@ -84,7 +100,7 @@
val = (cos(lower) - cos(upper)) / (incs - 1.0)
for i in range(incs):
v[-i-1] = cos(upper) + float(i) * val
-
+
# Generate the distribution.
row = arccos(v)
@@ -340,21 +356,15 @@
cdp.warning = warning
-
def back_calc(self):
"""Back-calculation of the reduced alignment tensor.
- @return: The peak intensity for the desired
relaxation time.
- @rtype: float
- """
-
- # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
- if cdp.model == 'rigid':
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma], float64)
-
- # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
- elif cdp.model == 'iso cone':
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta_axis, cdp.phi_axis, cdp.theta_cone], float64)
+ @return: The reduced alignment tensors.
+ @rtype: numpy array
+ """
+
+ # Get the parameter vector.
+ param_vector = self.__assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
@@ -384,13 +394,8 @@
def calculate(self, verbosity=None):
"""Calculate the chi-squared value for the current parameter
values."""
- # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
- if cdp.model == 'rigid':
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma], float64)
-
- # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
- elif cdp.model == 'iso cone':
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta_axis, cdp.phi_axis, cdp.theta_cone], float64)
+ # Assemble the parameter vector.
+ param_vector = self.__assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
@@ -741,6 +746,34 @@
# Minimisation.
self.minimise(min_algor='grid', min_options=grid,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+
+
+ def map_bounds(self, param, spin_id=None):
+ """Create bounds for the OpenDX mapping function.
+
+ @param param: The name of the parameter to return the lower
and upper bounds of.
+ @type param: str
+ @param spin_id: The spin identification string (unused).
+ @type spin_id: None
+ @return: The upper and lower bounds of the parameter.
+ @rtype: list of float
+ """
+
+ # Euler angles.
+ if search('^alpha$', param) or search('^beta$', param) or
search('^gamma$', param):
+ return [0.0, 2*pi]
+
+ # Axis spherical coordinate theta.
+ if search('theta[ -_]axis', param):
+ return [0.0, pi]
+
+ # Axis spherical coordinate phi.
+ if search('phi[ -_]axis', param):
+ return [0.0, 2*pi]
+
+ # Cone angle.
+ if search('theta[ -_]cone', param):
+ return [0.0, pi]
def minimise(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, constraints=False, scaling=True,
verbosity=0, sim_index=None):
@@ -784,13 +817,8 @@
# Throw a warning.
warn(RelaxWarning("Constraints are as of yet not implemented -
turning this option off."))
- # The rigid model initial parameter vector (the cone axis angles and
the cone angle).
- if cdp.model == 'rigid':
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma], float64)
-
- # The isotropic cone model initial parameter vector (the cone axis
angles and the cone angle).
- elif cdp.model == 'iso cone':
- param_vector = array([cdp.alpha, cdp.beta, cdp.gamma,
cdp.theta_axis, cdp.phi_axis, cdp.theta_cone], float64)
+ # Assemble the parameter vector.
+ param_vector = self.__assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors(sim_index)
@@ -823,6 +851,42 @@
# Don't return anything, just loop once.
yield None
+
+
+ def model_statistics(self, model_info=None, spin_id=None,
global_stats=None):
+ """Return the k, n, and chi2 model statistics.
+
+ k - number of parameters.
+ n - number of data points.
+ chi2 - the chi-squared value.
+
+
+ @keyword model_info: Unused.
+ @type model_info: None
+ @keyword spin_id: The spin identification string (unused).
+ @type spin_id: None
+ @keyword global_stats: Unused.
+ @type global_stats: None
+ @return: The optimisation statistics, in tuple
format, of the number of
+ parameters (k), the number of data points
(n), and the chi-squared
+ value (chi2).
+ @rtype: tuple of (int, int, float)
+ """
+
+ # Count the number of parameters.
+ param_vector = self.__assemble_param_vector()
+ k = len(param_vector)
+
+ # The number of data points.
+ n = len(cdp.align_tensors.reduction)
+
+ # The chi2 value.
+ if not hasattr(cdp, 'chi2'):
+ raise RelaxError("Statistics are not available, most likely
because the model has not been optimised.")
+ chi2 = cdp.chi2
+
+ # Return the data.
+ return k, n, chi2
def pivot(self, pivot=None):
@@ -873,6 +937,40 @@
self.__update_model()
+ def return_data_name(self, param):
+ """Return a unique identifying string for the Frame order parameter.
+
+ @param param: The Frame order parameter.
+ @type param: str
+ @return: The unique parameter identifying string.
+ @rtype: str
+ """
+
+ # Euler angle alpha.
+ if search('^alpha$', param):
+ return 'alpha'
+
+ # Euler angle beta.
+ if search('^beta$', param):
+ return 'beta'
+
+ # Euler angle gamma.
+ if search('^gamma$', param):
+ return 'gamma'
+
+ # Axis spherical coordinate theta.
+ if search('theta[ -_]axis', param):
+ return 'theta_axis'
+
+ # Axis spherical coordinate phi.
+ if search('phi[ -_]axis', param):
+ return 'phi_axis'
+
+ # Cone angle.
+ if search('theta[ -_]cone', param):
+ return 'theta_cone'
+
+
def return_error(self, index):
"""Return the alignment tensor error structure.
@@ -887,6 +985,36 @@
# Return the errors.
return red_tensor_err
+
+
+ def return_units(self, param, spin=None, spin_id=None):
+ """Return a string representing the parameters units.
+
+ @param param: The name of the parameter to return the units string
for.
+ @type param: str
+ @param spin: The spin container (unused).
+ @type spin: None
+ @param spin_id: The spin identification string (unused).
+ @type spin_id: None
+ @return: The parameter units string.
+ @rtype: str
+ """
+
+ # Euler angles.
+ if search('^alpha$', param) or search('^beta$', param) or
search('^gamma$', param):
+ return 'rad'
+
+ # Axis spherical coordinate theta.
+ if search('theta[ -_]axis', param):
+ return 'rad'
+
+ # Axis spherical coordinate phi.
+ if search('phi[ -_]axis', param):
+ return 'rad'
+
+ # Cone angle.
+ if search('theta[ -_]cone', param):
+ return 'rad'
def select_model(self, model=None):
r9892 - /1.3/specific_fns/frame_order.py