Author: bugman
Date: Tue Nov 24 12:56:22 2009
New Revision: 9910
URL: http://svn.gna.org/viewcvs/relax?rev=9910&view=rev
Log:
A large number of method and documentation variables to the specific analysis
API.
These include:
default_value_doc
default_value()
grid_search()
minimise()
return_data_name_doc
return_data_name()
return_grace_string()
return_units()
set_doc
sim_pack_data()
Modified:
1.3/specific_fns/api_base.py
Modified: 1.3/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_base.py?rev=9910&r1=9909&r2=9910&view=diff
==============================================================================
--- 1.3/specific_fns/api_base.py (original)
+++ 1.3/specific_fns/api_base.py Tue Nov 24 12:56:22 2009
@@ -30,7 +30,7 @@
class API_base:
"""Base class defining the specific_fns API.
-
+
Most objects are prototype methods, although a few are operational
generic base methods.
"""
@@ -68,7 +68,7 @@
# Not implemented.
raise RelaxImplementError
-
+
def create_mc_data(self, spin_id=None):
"""Prototype method for creating the Monte Carlo data.
@@ -110,8 +110,44 @@
raise RelaxImplementError
+ # Empty documentation string.
+ default_value_doc = ""
+ def default_value(self, param):
+ """Prototype method for returning the default parameter values.
+
+ @param param: The specific analysis parameter.
+ @type param: str
+ @return: The default value.
+ @rtype: float
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def eliminate(self):
"""Dummy method for model elimination."""
+
+
+ def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
+ """Prototype grid search method.
+
+ @keyword lower: The lower bounds of the grid search which
must be equal to the number of parameters in the model.
+ @type lower: array of numbers
+ @keyword upper: The upper bounds of the grid search which
must be equal to the number of parameters in the model.
+ @type upper: array of numbers
+ @keyword inc: The increments for each dimension of the
space for the grid search. The number of elements in the array must equal to
the number of parameters in the model.
+ @type inc: array of int
+ @keyword constraints: If True, constraints are applied during the
grid search (eliminating parts of the grid). If False, no constraints are
used.
+ @type constraints: bool
+ @keyword verbosity: A flag specifying the amount of information
to print. The higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The index of the simulation to apply the
grid search to. If None, the normal model is optimised.
+ @type sim_index: int
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
def has_errors(self):
@@ -162,6 +198,39 @@
return True
+ 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, lower=None, upper=None, inc=None):
+ """Prototype minimisation method.
+
+ @keyword min_algor: The minimisation algorithm to use.
+ @type min_algor: str
+ @keyword min_options: An array of options to be used by the
minimisation algorithm.
+ @type min_options: array of str
+ @keyword func_tol: The function tolerance which, when
reached, terminates optimisation. Setting this to None turns of the check.
+ @type func_tol: None or float
+ @keyword grad_tol: The gradient tolerance which, when
reached, terminates optimisation. Setting this to None turns of the check.
+ @type grad_tol: None or float
+ @keyword max_iterations: The maximum number of iterations for the
algorithm.
+ @type max_iterations: int
+ @keyword constraints: If True, constraints are used during
optimisation.
+ @type constraints: bool
+ @keyword scaling: If True, diagonal scaling is enabled
during optimisation to allow the problem to be better conditioned.
+ @type scaling: bool
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The index of the simulation to optimise.
This should be None if normal optimisation is desired.
+ @type sim_index: None or int
+ @keyword lower: The lower bounds of the grid search
which must be equal to the number of parameters in the model. This optional
argument is only used when doing a grid search.
+ @type lower: array of numbers
+ @keyword upper: The upper bounds of the grid search
which must be equal to the number of parameters in the model. This optional
argument is only used when doing a grid search.
+ @type upper: array of numbers
+ @keyword inc: The increments for each dimension of the
space for the grid search. The number of elements in the array must equal to
the number of parameters in the model. This argument is only used when doing
a grid search.
+ @type inc: array of int
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def model_loop(self):
"""Default generator method for looping over the models.
@@ -230,6 +299,21 @@
return spin.relax_data
+ # Empty documentation string.
+ return_data_name_doc = ""
+ def return_data_name(self, param):
+ """Prototype method for returning a unique identifying string for
the given parameter.
+
+ @param param: The parameter name.
+ @type param: str
+ @return: The unique parameter identifying string.
+ @rtype: str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def return_error(self, spin_id):
"""Return the Ri error structure for the corresponding spin.
@@ -245,6 +329,36 @@
# Return the data.
return spin.relax_error
+
+
+ def return_grace_string(self, param):
+ """Prototype method for returning the Grace string representation of
the parameter
+
+ This is used for axis labelling.
+
+ @param param: The specific analysis parameter.
+ @type param: str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
+ def return_units(self, param, spin=None, spin_id=None):
+ """Prototype method for returning 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.
+ @type spin: SpinContainer instance
+ @param spin_id: The spin identification string (ignored if the spin
container is supplied).
+ @type spin_id: str
+ @return: The parameter units string.
+ @rtype: str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
def return_value(self, spin, param, sim=None):
@@ -332,6 +446,10 @@
return value, error
+ # Empty documentation string.
+ set_doc = ""
+
+
def set_error(self, spin, index, error):
"""Set the parameter errors.
@@ -464,6 +582,19 @@
for j in xrange(cdp.sim_number):
# Copy and append the data.
sim_object.append(deepcopy(getattr(spin, object_name)))
+
+
+ def sim_pack_data(self, spin_id, sim_data):
+ """Pack the Monte Carlo simulation data.
+
+ @param spin_id: The spin identification string, as yielded by
the base_data_loop() generator method.
+ @type spin_id: str
+ @param sim_data: The Monte Carlo simulation data.
+ @type sim_data: list of float
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
def sim_return_chi2(self, spin, index=None):
r9910 - /1.3/specific_fns/api_base.py