Author: bugman
Date: Tue Jul 29 16:41:17 2014
New Revision: 24814
URL: http://svn.gna.org/viewcvs/relax?rev=24814&view=rev
Log:
Better handling of unset parameters in the frame order optimisation functions.
The specific_analyses.frame_order.optimisation.target_fn_data_setup() and
specific_analyses.frame_order.parameters.assemble_param_vector() function
both now accept the
unset_fail argument. This is set in both the calculate() and minimise() API
methods. When set, a
RelaxError will be raised in the assemble_param_vector() function when a
parameter has not been set
yet. This together with previous changes will prevent the frame order
analysis from using 0.0 as a
starting value for unset parameters.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/api.py
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/api.py?rev=24814&r1=24813&r2=24814&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/api.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/api.py Tue
Jul 29 16:41:17 2014
@@ -125,7 +125,7 @@
"""
# Set up the data structures for the target function.
- param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity)
+ param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity,
unset_fail=True)
# Set up the optimisation target function class.
target_fn = frame_order.Frame_order(model=cdp.model,
init_params=param_vector, full_tensors=full_tensors,
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err,
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs,
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp,
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix[0],
com=com, ave_pos_pivot=ave_pos_pivot, pivot=pivot, pivot_opt=pivot_opt,
num_int_pts=cdp.num_int_pts)
@@ -557,7 +557,7 @@
raise RelaxError("Only the 'simplex' minimisation algorithm is
supported for the relaxation dispersion analysis as function gradients are
not implemented.")
# Set up the data structures for the target function.
- param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity)
+ param_vector, full_tensors, full_in_ref_frame, rdcs, rdc_err,
rdc_weight, rdc_vect, rdc_const, pcs, pcs_err, pcs_weight, atomic_pos, temp,
frq, paramag_centre, com, ave_pos_pivot, pivot, pivot_opt =
target_fn_data_setup(sim_index=sim_index, verbosity=verbosity,
unset_fail=True)
# Get the Processor box singleton (it contains the Processor
instance) and alias the Processor.
processor_box = Processor_box()
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py?rev=24814&r1=24813&r2=24814&view=diff
==============================================================================
---
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
(original)
+++
branches/frame_order_cleanup/specific_analyses/frame_order/optimisation.py
Tue Jul 29 16:41:17 2014
@@ -624,7 +624,7 @@
rdc_index += 1
-def target_fn_data_setup(sim_index=None, verbosity=1, scaling_matrix=None):
+def target_fn_data_setup(sim_index=None, verbosity=1, scaling_matrix=None,
unset_fail=False):
"""Initialise the target function for optimisation or direct calculation.
@keyword sim_index: The index of the simulation to optimise.
This should be None if normal optimisation is desired.
@@ -633,10 +633,12 @@
@type verbosity: int
@keyword scaling_matrix: The diagonal and square scaling matrices.
@type scaling_matrix: numpy rank-2, float64 array or None
+ @keyword unset_fail: A flag which if True will cause a RelaxError
to be raised if the parameter is not set yet.
+ @type unset_fail: bool
"""
# Assemble the parameter vector.
- param_vector = assemble_param_vector(sim_index=sim_index)
+ param_vector = assemble_param_vector(sim_index=sim_index,
unset_fail=unset_fail)
# Determine the base data types (RDCs and/or PCSs).
data_types = base_data_types()
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py?rev=24814&r1=24813&r2=24814&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py
Tue Jul 29 16:41:17 2014
@@ -27,17 +27,20 @@
from numpy import array, float64, zeros
# relax module imports.
+from lib.errors import RelaxError
from specific_analyses.frame_order.data import pivot_fixed
from specific_analyses.frame_order.variables import MODEL_DOUBLE_ROTOR,
MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR,
MODEL_ISO_CONE_TORSIONLESS, MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE,
MODEL_LIST_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE, MODEL_ROTOR
-def assemble_param_vector(sim_index=None):
+def assemble_param_vector(sim_index=None, unset_fail=False):
"""Assemble and return the parameter vector.
- @return: The parameter vector.
- @rtype: numpy rank-1 array
- @keyword sim_index: The Monte Carlo simulation index.
- @type sim_index: int
+ @keyword sim_index: The Monte Carlo simulation index.
+ @type sim_index: int
+ @keyword unset_fail: A flag which if True will cause a RelaxError to
be raised if the parameter is not set yet.
+ @type unset_fail: bool
+ @return: The parameter vector.
+ @rtype: numpy rank-1 array
"""
# Initialise.
@@ -50,13 +53,19 @@
# Loop over all model parameters.
for param_name in cdp.params:
+ # Add the extension.
+ param_name += ext
+
# The parameter does not exist yet.
- if not hasattr(cdp, param_name+ext):
- param_vect.append(None)
- continue
+ if not hasattr(cdp, param_name):
+ if unset_fail:
+ raise RelaxError("The parameter '%s' has not been set." %
param_name)
+ else:
+ param_vect.append(None)
+ continue
# Get the object.
- obj = getattr(cdp, param_name+ext)
+ obj = getattr(cdp, param_name)
# Add it to the parameter vector.
if sim_index == None:
r24814 - in /branches/frame_order_cleanup/specific_analyses/frame_order: api.py optimisation.py parameters.py