Hi Ed.
I would like to collect the grid seach lower and upper bounds into the table
of
specific_analysis/relax_disp/parameter_object.py
This is to make one place, where such details are collected.
And the lower and upper bounds can be extracted for unit tests, and
for example dx.map more easily.
I have worked it out for lower bounds of pA, and tested it.
--- a/specific_analyses/api_base.py
+++ b/specific_analyses/api_base.py
@@ -314,6 +314,22 @@ class API_base(object):
raise RelaxImplementError('grid_search')
+ def grid_lower(self, param):
+ """Return the default lower bounds of paramater for the grid search.
+
+ This basic method will first search for a global parameter
and, if not found, then a spin parameter.
+
+
+ @param param: The specific analysis parameter.
+ @type param: str
+ @return: The default value.
+ @rtype: float
+ """
+
+ # Return the value.
+ return self._PARAMS.grid_lower(param)
+
+
def has_errors(self):
"""Test if errors exist for the current data pipe.
diff --git a/specific_analyses/parameter_object.py
b/specific_analyses/parameter_object.py
index b626a83..8e7abab 100644
--- a/specific_analyses/parameter_object.py
+++ b/specific_analyses/parameter_object.py
@@ -54,6 +54,7 @@ class Param_list(object):
self._scope = {}
self._string = {}
self._defaults = {}
+ self._grid_lowers = {}
self._units = {}
self._desc = {}
self._py_types = {}
@@ -92,7 +93,7 @@ class Param_list(object):
return cls._instance
- def _add(self, name, scope=None, string=None, default=None,
units=None, desc=None, py_type=None, set='all', conv_factor=None,
grace_string=None, err=False, sim=False):
+ def _add(self, name, scope=None, string=None, default=None,
grid_lower=None, units=None, desc=None, py_type=None, set='all',
conv_factor=None, grace_string=None, err=False, sim=False):
"""Add a parameter to the list.
@param name: The name of the parameter. This will
be used as the variable name.
@@ -103,6 +104,8 @@ class Param_list(object):
@type string: None or str
@keyword default: The default value of the parameter.
@type default: anything
+ @keyword grid_lower: The default lower bounds of the grid search.
+ @type grid_lower: float
@keyword units: A string representing the parameters units.
@type units: None or str
@keyword desc: The text description of the parameter.
@@ -134,6 +137,7 @@ class Param_list(object):
self._names.append(name)
self._scope[name] = scope
self._defaults[name] = default
+ self._grid_lowers[name] = grid_lower
self._units[name] = units
self._desc[name] = desc
self._py_types[name] = py_type
@@ -540,6 +544,22 @@ class Param_list(object):
return self._grace_string[name]
+ def grid_lower(self, name):
+ """Return the default lower bounds of paramater for the grid search.
+
+ @param name: The name of the parameter.
+ @type name: str
+ @return: The default value.
+ @rtype: None or str
+ """
+
+ # Parameter check.
+ self.check_param(name)
+
+ # Return the default value.
+ return self._grid_lowers[name]
+
+
def is_spin_param(self, name):
"""Determine whether the given parameter is spin specific.
diff --git a/specific_analyses/relax_disp/optimisation.py
b/specific_analyses/relax_disp/optimisation.py
index a92922e..82bd364 100644
--- a/specific_analyses/relax_disp/optimisation.py
+++ b/specific_analyses/relax_disp/optimisation.py
@@ -38,6 +38,7 @@ from lib.errors import RelaxError
from lib.text.sectioning import subsection
from multi import Memo, Result_command, Slave_command
from pipe_control.mol_res_spin import spin_loop
+from specific_analyses.api import return_api
from specific_analyses.relax_disp.checks import check_disp_points,
check_exp_type, check_exp_type_fixed_time
from specific_analyses.relax_disp.data import average_intensity,
count_spins, find_intensity_keys, has_exponential_exp_type,
has_proton_mmq_cpmg, loop_exp, loop_exp_frq_offset_point,
loop_exp_frq_offset_point_time, loop_frq, loop_offset, loop_time,
pack_back_calc_r2eff, return_cpmg_frqs, return_offset_data,
return_param_key_from_data, return_r1_data, return_r2eff_arrays,
return_spin_lock_nu1
from specific_analyses.relax_disp.parameters import
assemble_param_vector, assemble_scaling_matrix,
disassemble_param_vector, linear_constraints, loop_parameters,
param_conversion, param_num
@@ -296,6 +297,9 @@ def grid_search_setup(spins=None, spin_ids=None,
param_vector=None, lower=None,
elif isinstance(inc, int):
inc = [inc]*n
+ # The specific analysis API object.
+ api = return_api()
+
# Set up the default bounds.
if not lower:
# Init.
@@ -357,7 +361,9 @@ def grid_search_setup(spins=None, spin_ids=None,
param_vector=None, lower=None,
if spins[si].model == MODEL_M61B:
lower.append(0.85)
else:
- lower.append(0.5)
+ #lower.append(0.5)
+ lower.append(api.grid_lower('pA'))
+ #lower.append(api.default_value('pA'))
upper.append(1.0)
# The population of state B (for 3-site exchange).
diff --git a/specific_analyses/relax_disp/parameter_object.py
b/specific_analyses/relax_disp/parameter_object.py
index 936d2b1..21dfe99 100644
--- a/specific_analyses/relax_disp/parameter_object.py
+++ b/specific_analyses/relax_disp/parameter_object.py
@@ -61,7 +61,7 @@ class Relax_disp_params(Param_list):
self._add('r2', scope='spin', default=10.0, desc='The
transversal relaxation rate', set='params', py_type=dict,
grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
self._add('r2a', scope='spin', default=10.0, desc='The
transversal relaxation rate for state A in the absence of exchange',
set='params', py_type=dict, grace_string='\\qR\\s2,A\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
self._add('r2b', scope='spin', default=10.0, desc='The
transversal relaxation rate for state B in the absence of exchange',
set='params', py_type=dict, grace_string='\\qR\\s2,B\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
- self._add('pA', scope='spin', default=0.90, desc='The
population for state A', set='params', py_type=float,
grace_string='\\qp\\sA\\N\\Q', err=True, sim=True)
+ self._add('pA', scope='spin', default=0.90, grid_lower=0.6,
desc='The population for state A', set='params', py_type=float,
grace_string='\\qp\\sA\\N\\Q', err=True, sim=True)
self._add('pB', scope='spin', default=0.5, desc='The
population for state B', set='params', py_type=float,
grace_string='\\qp\\sB\\N\\Q', err=True, sim=True)
self._add('pC', scope='spin', default=0.5, desc='The
population for state C', set='params', py_type=float,
grace_string='\\qp\\sC\\N\\Q', err=True, sim=True)
self._add('phi_ex', scope='spin', default=5.0, desc='The
phi_ex = pA.pB.dw**2 value (ppm^2)', set='params', py_type=float,
grace_string='\\xF\\B\\sex\\N = \\q
p\\sA\\N.p\\sB\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True,
sim=True)
Best
Troels
Proposition for collecting default values of grid seach lower and upper bounds