Author: bugman
Date: Mon Jul 21 09:14:00 2014
New Revision: 24578
URL: http://svn.gna.org/viewcvs/relax?rev=24578&view=rev
Log:
Updated all of the specific API grid_search() methods to accept the
scaling_matrix argument.
The list of per-model scaling matrices is now created independently of the
analysis type by the
pipe_control.minimise methods for the minimise.calculate,
minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
The argument is also passed into the minimise() API method from the
grid_search() method when that
is used.
Modified:
branches/zooming_grid_search/specific_analyses/frame_order/api.py
branches/zooming_grid_search/specific_analyses/model_free/api.py
branches/zooming_grid_search/specific_analyses/n_state_model/api.py
branches/zooming_grid_search/specific_analyses/relax_disp/api.py
branches/zooming_grid_search/specific_analyses/relax_fit/api.py
Modified: branches/zooming_grid_search/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/frame_order/api.py?rev=24578&r1=24577&r2=24578&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/frame_order/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/frame_order/api.py Mon
Jul 21 09:14:00 2014
@@ -328,21 +328,23 @@
return assemble_param_vector(sim_index=sim_index)
- def grid_search(self, lower=None, upper=None, inc=None,
constraints=False, verbosity=0, sim_index=None):
+ def grid_search(self, lower=None, upper=None, inc=None,
scaling_matrix=None, constraints=False, verbosity=0, sim_index=None):
"""Perform a grid search.
- @keyword lower: The lower bounds of the grid search which
must be equal to the number of parameters in the model.
- @type lower: list of float
- @keyword upper: The upper bounds of the grid search which
must be equal to the number of parameters in the model.
- @type upper: list of float
- @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: int or list 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 Monte Carlo simulation index.
- @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.
+ @type lower: list of float
+ @keyword upper: The upper bounds of the grid search
which must be equal to the number of parameters in the model.
+ @type upper: list of float
+ @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: int or list of int
+ @keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @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 Monte Carlo simulation index.
+ @type sim_index: None or int
"""
# Test if the Frame Order model has been set up.
@@ -480,7 +482,7 @@
indices[j] = 0
# Minimisation.
- self.minimise(min_algor='grid', min_options=pts,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+ self.minimise(min_algor='grid', min_options=pts,
scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity,
sim_index=sim_index)
def map_bounds(self, param, spin_id=None):
Modified: branches/zooming_grid_search/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/model_free/api.py?rev=24578&r1=24577&r2=24578&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/model_free/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/model_free/api.py Mon
Jul 21 09:14:00 2014
@@ -998,32 +998,27 @@
return assemble_param_vector(spin=spin, sim_index=sim_index,
model_type=model_type)
- def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
+ def grid_search(self, lower=None, upper=None, inc=None,
scaling_matrix=None, constraints=True, verbosity=1, sim_index=None):
"""The model-free grid search function.
- @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
+ @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 scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @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
"""
# Minimisation.
- self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+ self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity,
sim_index=sim_index)
def map_bounds(self, param, spin_id=None):
Modified: branches/zooming_grid_search/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/n_state_model/api.py?rev=24578&r1=24577&r2=24578&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/n_state_model/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/n_state_model/api.py Mon
Jul 21 09:14:00 2014
@@ -258,19 +258,21 @@
return mc_data
- def grid_search(self, lower=None, upper=None, inc=None,
constraints=False, verbosity=0, sim_index=None):
+ def grid_search(self, lower=None, upper=None, inc=None,
scaling_matrix=None, constraints=False, verbosity=0, sim_index=None):
"""The grid search function.
- @param 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
- @param 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
- @param 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
- @param constraints: If True, constraints are applied during the grid
search (elinating parts of the grid). If False, no constraints are used.
- @type constraints: bool
- @param verbosity: A flag specifying the amount of information to
print. The higher the value, the greater the verbosity.
- @type verbosity: int
+ @param 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
+ @param 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
+ @param 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 scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @param constraints: If True, constraints are applied during the
grid search (elinating parts of the grid). If False, no constraints are used.
+ @type constraints: bool
+ @param verbosity: A flag specifying the amount of information
to print. The higher the value, the greater the verbosity.
+ @type verbosity: int
"""
# Test if the N-state model has been set up.
@@ -381,7 +383,7 @@
# All other minimisation.
else:
- self.minimise(min_algor='grid', lower=lower, upper=upper,
inc=inc, constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+ self.minimise(min_algor='grid', lower=lower, upper=upper,
inc=inc, scaling_matrix=scaling_matrix, constraints=constraints,
verbosity=verbosity, sim_index=sim_index)
def is_spin_param(self, name):
Modified: branches/zooming_grid_search/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/relax_disp/api.py?rev=24578&r1=24577&r2=24578&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/relax_disp/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/relax_disp/api.py Mon
Jul 21 09:14:00 2014
@@ -466,25 +466,27 @@
return values
- def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
+ def grid_search(self, lower=None, upper=None, inc=None,
scaling_matrix=None, constraints=True, verbosity=1, sim_index=None):
"""The relaxation dispersion curve fitting grid search function.
- @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
+ @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 scaling_matrix: The per-model list of diagonal and
square scaling matrices.
+ @type scaling_matrix: list of numpy rank-2, float64 array or
list of None
+ @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
"""
# Minimisation.
- self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+ self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
scaling_matrix=scaling_matrix, constraints=constraints, verbosity=verbosity,
sim_index=sim_index)
def map_bounds(self, param, spin_id=None):
Modified: branches/zooming_grid_search/specific_analyses/relax_fit/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/relax_fit/api.py?rev=24578&r1=24577&r2=24578&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/relax_fit/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/relax_fit/api.py Mon
Jul 21 09:14:00 2014
@@ -173,20 +173,20 @@
def grid_search(self, lower=None, upper=None, inc=None,
scaling_matrix=None, constraints=True, verbosity=1, sim_index=None):
"""The exponential curve fitting grid search method.
- @keyword lower: The per-model lower bounds of the grid
search which must be equal to the number of parameters in the model.
- @type lower: list of lists of numbers
- @keyword upper: The per-model upper bounds of the grid
search which must be equal to the number of parameters in the model.
- @type upper: list of lists of numbers
- @keyword inc: The per-model 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: list of lists of int
+ @keyword lower: The per-model lower bounds of the grid
search which must be equal to the number of parameters in the model.
+ @type lower: list of lists of numbers
+ @keyword upper: The per-model upper bounds of the grid
search which must be equal to the number of parameters in the model.
+ @type upper: list of lists of numbers
+ @keyword inc: The per-model 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: list of lists of int
@keyword scaling_matrix: The per-model list of diagonal and
square scaling matrices.
@type scaling_matrix: list of numpy rank-2, float64 array or
list of None
- @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
+ @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
"""
# Minimisation.
r24578 - in /branches/zooming_grid_search/specific_analyses: frame_order/ model_free/ n_state_model/ relax_disp/ relax_fit/