Author: bugman
Date: Tue Mar 1 19:19:47 2011
New Revision: 12675
URL: http://svn.gna.org/viewcvs/relax?rev=12675&view=rev
Log:
Updated the _minimise_data_setup() method for the new relaxation data ID
string design.
The _relax_data_opt_structs() helper method has been created to convert the
new data structures into
the old ones used in the optimisation code of maths_fns.mf.
Modified:
branches/relax_data/specific_fns/model_free/mf_minimise.py
Modified: branches/relax_data/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/specific_fns/model_free/mf_minimise.py?rev=12675&r1=12674&r2=12675&view=diff
==============================================================================
--- branches/relax_data/specific_fns/model_free/mf_minimise.py (original)
+++ branches/relax_data/specific_fns/model_free/mf_minimise.py Tue Mar 1
19:19:47 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -829,16 +829,13 @@
@type spin: SpinContainer instance
@keyword sim_index: The optional MC simulation index.
@type sim_index: int
- @return: An insane tuple. The full tuple is
(relax_data, relax_error,
- equations, param_types, param_values, r,
csa, num_frq, frq, num_ri,
- remap_table, noe_r1_table, ri_labels,
num_params, xh_unit_vectors,
- diff_type, diff_params)
+ @return: An insane tuple. The full tuple is
(ri_data, ri_data_err, equations, param_types, param_values, r, csa, num_frq,
frq, num_ri, remap_table, noe_r1_table, ri_labels, num_params,
xh_unit_vectors, diff_type, diff_params)
@rtype: tuple
"""
# Initialise the data structures for the model-free function.
- relax_data = []
- relax_error = []
+ ri_data = []
+ ri_data_err = []
equations = []
param_types = []
param_values = None
@@ -862,8 +859,8 @@
# Set up the data for the back_calc function.
if min_algor == 'back_calc':
# The data.
- relax_data = [0.0]
- relax_error = [0.000001]
+ ri_data = [0.0]
+ ri_data_err = [0.000001]
equations = [spin.equation]
param_types = [spin.params]
r = [spin.r]
@@ -896,30 +893,33 @@
continue
# Skip spins where there is no data or errors.
- if not hasattr(spin, 'relax_data') or not hasattr(spin,
'relax_error'):
+ if not hasattr(spin, 'ri_data') or not hasattr(spin,
'ri_data_err'):
continue
- # Make sure that the errors are strictly positive numbers.
- for k in xrange(len(spin.relax_error)):
- if spin.relax_error[k] == 0.0:
+ # The relaxation data.
+ for ri_id in cdp.ri_ids:
+ # Make sure that the errors are strictly positive numbers.
+ if spin.ri_data_err[ri_id] == 0.0:
raise RelaxError("Zero error for spin '" +
repr(spin.num) + " " + spin.name + "', minimisation not possible.")
- elif spin.relax_error[k] < 0.0:
+ elif spin.ri_data_err[ri_id] < 0.0:
raise RelaxError("Negative error for spin '" +
repr(spin.num) + " " + spin.name + "', minimisation not possible.")
+ # The relaxation data optimisation structures.
+ data = self._relax_data_opt_structs(spin,
sim_index=sim_index)
+
+ # Append the data.
+ ri_data.append(data[0])
+ ri_data_err.append(data[1])
+ num_frq.append(data[2])
+ num_ri.append(data[3])
+ ri_labels.append(data[4])
+ frq.append(data[5])
+ remap_table.append(data[6])
+ noe_r1_table.append(data[7])
+
# Repackage the data.
- if sim_index == None:
- relax_data.append(spin.relax_data)
- else:
- relax_data.append(spin.relax_sim_data[sim_index])
- relax_error.append(spin.relax_error)
equations.append(spin.equation)
param_types.append(spin.params)
- num_frq.append(spin.num_frq)
- frq.append(spin.frq)
- num_ri.append(spin.num_ri)
- remap_table.append(spin.remap_table)
- noe_r1_table.append(spin.noe_r1_table)
- ri_labels.append(spin.ri_labels)
gx.append(return_gyromagnetic_ratio(spin.heteronuc_type))
gh.append(return_gyromagnetic_ratio(spin.proton_type))
if sim_index == None or model_type == 'diff':
@@ -947,9 +947,9 @@
param_values.append(self._assemble_param_vector(model_type='mf'))
# Convert to numpy arrays.
- for k in xrange(len(relax_data)):
- relax_data[k] = array(relax_data[k], float64)
- relax_error[k] = array(relax_error[k], float64)
+ for k in xrange(len(ri_data)):
+ ri_data[k] = array(ri_data[k], float64)
+ ri_data_err[k] = array(ri_data_err[k], float64)
# Diffusion tensor type.
if model_type == 'local_tm':
@@ -976,7 +976,60 @@
diff_params = [spin.local_tm]
# Return all the data.
- return relax_data, relax_error, equations, param_types,
param_values, r, csa, num_frq, frq, num_ri, remap_table, noe_r1_table,
ri_labels, gx, gh, num_params, xh_unit_vectors, diff_type, diff_params
+ return ri_data, ri_data_err, equations, param_types, param_values,
r, csa, num_frq, frq, num_ri, remap_table, noe_r1_table, ri_labels, gx, gh,
num_params, xh_unit_vectors, diff_type, diff_params
+
+
+ def _relax_data_opt_structs(self, spin, sim_index=None):
+ """Package the relaxation data into the data structures used for
optimisation.
+
+ @param spin: The spin container to extract the data from.
+ @type spin: SpinContainer instance
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
+ @return: The structures ri_data, ri_data_err, num_frq,
num_ri, ri_labels, frq, remap_table, noe_r1_table.
+ @rtype: tuple
+ """
+
+ # Initialise the data.
+ ri_data = []
+ ri_data_err = []
+ ri_labels = []
+ frq = []
+ remap_table = []
+ noe_r1_table = []
+
+ # Loop over the relaxation data.
+ for ri_id in cdp.ri_ids:
+ # The Rx data.
+ ri_data.append(spin.ri_data[ri_id])
+ ri_data_err.append(spin.ri_data_err[ri_id])
+
+ # The labels.
+ ri_labels.append(cdp.ri_types[ri_id])
+
+ # The frequencies.
+ if cdp.frq[ri_id] not in frq:
+ frq.append(cdp.frq[ri_id])
+
+ # The remap table.
+ remap_table.append(frq.index(cdp.frq[ri_id]))
+
+ # The NOE to R1 mapping table.
+ noe_r1_table.append(None)
+
+ # The number of data sets.
+ num_ri = len(cdp.ri_ids)
+
+ # Fill the NOE to R1 mapping table.
+ for i in range(num_ri):
+ # If the data corresponds to 'NOE', try to find if the
corresponding R1 data.
+ if cdp.ri_types[cdp.ri_ids[i]] == 'NOE':
+ for j in range(num_ri):
+ if cdp.ri_types[cdp.ri_ids[j]] == 'R1' and
cdp.frq[cdp.ri_ids[i]] == cdp.frq[cdp.ri_ids[j]]:
+ noe_r1_table[i] = j
+
+ # Return the structures.
+ return ri_data, ri_data_err, len(frq), num_ri, ri_labels, frq,
remap_table, noe_r1_table
def _reset_min_stats(self):
r12675 - /branches/relax_data/specific_fns/model_free/mf_minimise.py