Author: bugman
Date: Wed Jul 23 10:57:23 2014
New Revision: 24671
URL: http://svn.gna.org/viewcvs/relax?rev=24671&view=rev
Log:
The grid search upper and lower bound functions now must accept the incs
argument.
For a few analyses, the number of grid search increments are used to remove
the end point of the
grid, to remove duplicate points due to the circular nature of angles.
Therefore the parameter
object grid_lower() and grid_upper() methods now send the grid increment
number for each parameter
into all grid bound determining functions. The relaxation dispersion and
curve-fitting analyses
have been updated for the change.
Modified:
branches/zooming_grid_search/pipe_control/minimise.py
branches/zooming_grid_search/specific_analyses/parameter_object.py
branches/zooming_grid_search/specific_analyses/relax_disp/api.py
branches/zooming_grid_search/specific_analyses/relax_disp/parameter_object.py
branches/zooming_grid_search/specific_analyses/relax_fit/parameter_object.py
Modified: branches/zooming_grid_search/pipe_control/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/pipe_control/minimise.py?rev=24671&r1=24670&r2=24671&view=diff
==============================================================================
--- branches/zooming_grid_search/pipe_control/minimise.py (original)
+++ branches/zooming_grid_search/pipe_control/minimise.py Wed Jul 23
10:57:23 2014
@@ -292,17 +292,20 @@
elif upper != None:
comment = 'User supplied upper bound'
+ # Alias the number of increments for this parameter.
+ incs = model_inc[-1][i]
+
# The lower bound for this parameter.
if lower != None:
lower_i = lower[i]
else:
- lower_i = param_object.grid_lower(names[i],
model_info=model_info)
+ lower_i = param_object.grid_lower(names[i], incs=incs,
model_info=model_info)
# The upper bound for this parameter.
if upper != None:
upper_i = upper[i]
else:
- upper_i = param_object.grid_upper(names[i],
model_info=model_info)
+ upper_i = param_object.grid_upper(names[i], incs=incs,
model_info=model_info)
# Skip preset values.
if skip_preset and not values[i] in [None, {}, []] and not
isNaN(values[i]):
@@ -321,7 +324,7 @@
model_upper[-1].append(upper_i)
# Add to the data list for printing out.
- data.append([names[i], "%15s" % lower_i, "%15s" % upper_i,
"%15s" % model_inc[-1][i], comment])
+ data.append([names[i], "%15s" % lower_i, "%15s" % upper_i,
"%15s" % incs, comment])
# Printout.
if verbosity:
Modified: branches/zooming_grid_search/specific_analyses/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/parameter_object.py?rev=24671&r1=24670&r2=24671&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/parameter_object.py
(original)
+++ branches/zooming_grid_search/specific_analyses/parameter_object.py Wed
Jul 23 10:57:23 2014
@@ -602,15 +602,17 @@
return self._err[name]
- def grid_lower(self, name, model_info=None):
+ def grid_lower(self, name, incs=None, model_info=None):
"""Return the default lower grid bound for the parameter.
- @param model_info: The model information from the model_loop()
specific API method. If the lower bound is a function, this information is
sent into it.
- @type model_info: int
- @param name: The name of the parameter.
- @type name: str
- @return: The lower bound for the grid search.
- @rtype: int
+ @param name: The name of the parameter.
+ @type name: str
+ @keyword incs: The number of grid search increments. This
is used by some of the bound determining functions.
+ @type incs: int
+ @keyword model_info: The model information from the model_loop()
specific API method. If the lower bound is a function, this information is
sent into it.
+ @type model_info: int
+ @return: The lower bound for the grid search.
+ @rtype: int
"""
# Parameter check.
@@ -618,21 +620,23 @@
# Call any function or method.
if isinstance(self._grid_lower[name], FunctionType) or
isinstance(self._grid_lower[name], MethodType):
- return self._grid_lower[name](model_info)
+ return self._grid_lower[name](incs=incs, model_info=model_info)
# Return the value.
return self._grid_lower[name]
- def grid_upper(self, name, model_info=None):
+ def grid_upper(self, name, incs=None, model_info=None):
"""Return the default upper grid bound for the parameter.
- @param model_info: The model information from the model_loop()
specific API method. If the upper bound is a function, this information is
sent into it.
- @type model_info: int
- @param name: The name of the parameter.
- @type name: str
- @return: The upper bound for the grid search.
- @rtype: int
+ @param name: The name of the parameter.
+ @type name: str
+ @keyword incs: The number of grid search increments. This
is used by some of the bound determining functions.
+ @type incs: int
+ @keyword model_info: The model information from the model_loop()
specific API method. If the upper bound is a function, this information is
sent into it.
+ @type model_info: int
+ @return: The upper bound for the grid search.
+ @rtype: int
"""
# Parameter check.
@@ -640,7 +644,7 @@
# Call any function or method.
if isinstance(self._grid_upper[name], FunctionType) or
isinstance(self._grid_upper[name], MethodType):
- return self._grid_upper[name](model_info)
+ return self._grid_upper[name](incs=incs, model_info=model_info)
# Return the value.
return self._grid_upper[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=24671&r1=24670&r2=24671&view=diff
==============================================================================
--- branches/zooming_grid_search/specific_analyses/relax_disp/api.py
(original)
+++ branches/zooming_grid_search/specific_analyses/relax_disp/api.py Wed
Jul 23 10:57:23 2014
@@ -533,7 +533,7 @@
# Test if the parameter is in the list:
if param_names[i] == param:
- return [self._PARAMS.grid_lower(param, [spin_id]),
self._PARAMS.grid_upper(param, [spin_id])]
+ return [self._PARAMS.grid_lower(param, incs=0,
model_info=[spin_id]), self._PARAMS.grid_upper(param, incs=0,
model_info=[spin_id])]
def minimise(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, constraints=False, scaling_matrix=None,
verbosity=0, sim_index=None, lower=None, upper=None, inc=None):
Modified:
branches/zooming_grid_search/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/relax_disp/parameter_object.py?rev=24671&r1=24670&r2=24671&view=diff
==============================================================================
---
branches/zooming_grid_search/specific_analyses/relax_disp/parameter_object.py
(original)
+++
branches/zooming_grid_search/specific_analyses/relax_disp/parameter_object.py
Wed Jul 23 10:57:23 2014
@@ -29,9 +29,11 @@
from specific_analyses.relax_disp.variables import MODEL_LIST_MMQ, MODEL_M61B
-def dw_lower(model_info):
+def dw_lower(incs=None, model_info=None):
"""Determine the lower grid bound for the dw parameters.
+ @keyword incs: The number of grid search increments.
+ @type incs: int
@keyword model_info: The spin ID strings from the model_loop()
specific API method.
@type model_info: list of str
@return: The lower grid search bound for the dw
parameters.
@@ -50,9 +52,11 @@
return 0.0
-def dwH_lower(model_info):
+def dwH_lower(incs=None, model_info=None):
"""Determine the lower grid bound for the dwH parameters.
+ @keyword incs: The number of grid search increments.
+ @type incs: int
@keyword model_info: The spin ID strings from the model_loop()
specific API method.
@type model_info: list of str
@return: The lower grid search bound for the dwH
parameters.
@@ -71,9 +75,11 @@
return 0.0
-def pA_lower(model_info):
+def pA_lower(incs=None, model_info=None):
"""Determine the lower grid bound for the pA parameter.
+ @keyword incs: The number of grid search increments.
+ @type incs: int
@keyword model_info: The spin containers and the spin ID strings from
the model_loop() specific API method.
@type model_info: list of SpinContainer instances, list of str
@return: The lower grid search bound for the pA parameter.
@@ -92,12 +98,14 @@
return 0.5
-def i0_upper(model_info):
+def i0_upper(incs=None, model_info=None):
"""Find the maximum peak intensity for the cluster.
This is for the grid search upper bound for the I0 parameter.
+ @keyword incs: The number of grid search increments.
+ @type incs: int
@keyword model_info: The spin containers and the spin ID strings from
the model_loop() specific API method.
@type model_info: list of SpinContainer instances, list of str
@return: The maximum peak intensity of all spins and time
points.
Modified:
branches/zooming_grid_search/specific_analyses/relax_fit/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/zooming_grid_search/specific_analyses/relax_fit/parameter_object.py?rev=24671&r1=24670&r2=24671&view=diff
==============================================================================
---
branches/zooming_grid_search/specific_analyses/relax_fit/parameter_object.py
(original)
+++
branches/zooming_grid_search/specific_analyses/relax_fit/parameter_object.py
Wed Jul 23 10:57:23 2014
@@ -30,7 +30,7 @@
from specific_analyses.parameter_object import Param_list
-def i_scaling(model_info):
+def i_scaling(model_info=None):
"""Determine the scaling factor for the peak intensities.
This is for the scaling of the I0 and Iinf parameters during
optimisation. The maximum intensity will be used to scale all values.
@@ -49,12 +49,14 @@
return round_to_next_order(max(spin.peak_intensity.values()))
-def i0(model_info):
+def i0(incs=None, model_info=None):
"""Find the average intensity of the first time point.
This is for the grid search upper bound for the I0 parameter.
+ @keyword incs: The number of grid search increments.
+ @type incs: int
@keyword model_info: The spin container and the spin ID string from
the _model_loop_spin() specific API method.
@type model_info: SpinContainer instance, str
@return: The average peak intensity of the first time
point.
@@ -75,12 +77,14 @@
return average(spin.peak_intensity[id])
-def iinf(model_info):
+def iinf(incs=None, model_info=None):
"""Find the average intensity of the last time point.
This is for the grid search upper bound for the Iinf parameter.
+ @keyword incs: The number of grid search increments.
+ @type incs: int
@keyword model_info: The spin container and the spin ID string from
the _model_loop_spin() specific API method.
@type model_info: SpinContainer instance, str
@return: The average peak intensity of the last time
point.
r24671 - in /branches/zooming_grid_search: pipe_control/ specific_analyses/ specific_analyses/relax_disp/ specific_analyses/...