Author: bugman
Date: Tue Nov 24 11:42:53 2009
New Revision: 9902
URL: http://svn.gna.org/viewcvs/relax?rev=9902&view=rev
Log:
Removed assemble_param_vector() and disassemble_param_vector() from the
specific analysis API.
Modified:
1.3/specific_fns/frame_order.py
1.3/specific_fns/model_free/main.py
1.3/specific_fns/model_free/mf_minimise.py
1.3/specific_fns/n_state_model.py
1.3/specific_fns/relax_fit.py
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=9902&r1=9901&r2=9902&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Nov 24 11:42:53 2009
@@ -50,7 +50,7 @@
class Frame_order(API_base):
"""Class containing the specific methods of the Frame Order theories."""
- def __assemble_param_vector(self):
+ def _assemble_param_vector(self):
"""Assemble and return the parameter vector.
@return: The parameter vector.
@@ -364,7 +364,7 @@
"""
# Get the parameter vector.
- param_vector = self.__assemble_param_vector()
+ param_vector = self._assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
@@ -395,7 +395,7 @@
"""Calculate the chi-squared value for the current parameter
values."""
# Assemble the parameter vector.
- param_vector = self.__assemble_param_vector()
+ param_vector = self._assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors()
@@ -818,7 +818,7 @@
warn(RelaxWarning("Constraints are as of yet not implemented -
turning this option off."))
# Assemble the parameter vector.
- param_vector = self.__assemble_param_vector()
+ param_vector = self._assemble_param_vector()
# Get the data structures for optimisation using the tensors as base
data sets.
full_tensors, red_tensors, red_tensor_err, full_in_ref_frame =
self.__minimise_setup_tensors(sim_index)
@@ -874,7 +874,7 @@
"""
# Count the number of parameters.
- param_vector = self.__assemble_param_vector()
+ param_vector = self._assemble_param_vector()
k = len(param_vector)
# The number of data points.
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=9902&r1=9901&r2=9902&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/main.py (original)
+++ 1.3/specific_fns/model_free/main.py Tue Nov 24 11:42:53 2009
@@ -195,7 +195,7 @@
return param_names
- def assemble_param_vector(self, spin=None, spin_id=None, sim_index=None,
model_type=None):
+ def _assemble_param_vector(self, spin=None, spin_id=None,
sim_index=None, model_type=None):
"""Assemble the model-free parameter vector (as numpy array).
If the spin argument is supplied, then the spin_id argument will be
ignored.
@@ -1347,7 +1347,7 @@
spin = None
# Assemble the parameter values and return them.
- return self.assemble_param_vector(spin=spin, sim_index=sim_index,
model_type=model_type)
+ return self._assemble_param_vector(spin=spin, sim_index=sim_index,
model_type=model_type)
def is_spin_param(self, name):
@@ -1896,7 +1896,7 @@
return None, None, None
# Count the number of parameters.
- param_vector = self.assemble_param_vector(spin=spin)
+ param_vector = self._assemble_param_vector(spin=spin)
k = len(param_vector)
# Count the number of data points.
@@ -1908,7 +1908,7 @@
# Global stats.
elif global_stats:
# Count the number of parameters.
- param_vector = self.assemble_param_vector()
+ param_vector = self._assemble_param_vector()
k = len(param_vector)
# Count the number of data points.
Modified: 1.3/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/mf_minimise.py?rev=9902&r1=9901&r2=9902&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/mf_minimise.py (original)
+++ 1.3/specific_fns/model_free/mf_minimise.py Tue Nov 24 11:42:53 2009
@@ -141,7 +141,7 @@
raise RelaxError("Negative error for spin '" +
repr(spin.num) + " " + spin.name + "', calculation not possible.")
# Create the initial parameter vector.
- param_vector = self.assemble_param_vector(spin=spin,
sim_index=sim_index)
+ param_vector = self._assemble_param_vector(spin=spin,
sim_index=sim_index)
# Repackage the spin.
if sim_index == None:
@@ -167,7 +167,7 @@
num_params = [len(spin.params)]
# Repackage the parameter values as a local model (ignore if the
diffusion tensor is not fixed).
- param_values = [self.assemble_param_vector(model_type='mf')]
+ param_values = [self._assemble_param_vector(model_type='mf')]
# Convert to Numeric arrays.
relax_data = [array(spin.relax_data, float64)]
@@ -209,7 +209,7 @@
spin.chi2 = chi2
- def disassemble_param_vector(self, model_type, param_vector=None,
spin=None, spin_id=None, sim_index=None):
+ def _disassemble_param_vector(self, model_type, param_vector=None,
spin=None, spin_id=None, sim_index=None):
"""Disassemble the model-free parameter vector.
@param model_type: The model-free model type. This must be one
of 'mf', 'local_tm',
@@ -865,14 +865,14 @@
# Parameter vector and diagonal scaling.
if min_algor == 'back_calc':
# Create the initial parameter vector.
- param_vector = self.assemble_param_vector(spin=spin,
model_type=model_type)
+ param_vector = self._assemble_param_vector(spin=spin,
model_type=model_type)
# Diagonal scaling.
scaling_matrix = None
else:
# Create the initial parameter vector.
- param_vector = self.assemble_param_vector(spin=spin,
sim_index=sim_index)
+ param_vector = self._assemble_param_vector(spin=spin,
sim_index=sim_index)
# The number of parameters.
num_params = len(param_vector)
@@ -988,7 +988,7 @@
param_vector = dot(scaling_matrix, param_vector)
# Disassemble the parameter vector.
- self.disassemble_param_vector(model_type,
param_vector=param_vector, spin=spin, sim_index=sim_index)
+ self._disassemble_param_vector(model_type,
param_vector=param_vector, spin=spin, sim_index=sim_index)
# Monte Carlo minimisation statistics.
if sim_index != None:
@@ -1205,7 +1205,7 @@
# Repackage the parameter values for minimising just the
diffusion tensor parameters.
if model_type == 'diff':
-
param_values.append(self.assemble_param_vector(model_type='mf'))
+
param_values.append(self._assemble_param_vector(model_type='mf'))
# Convert to numpy arrays.
for k in xrange(len(relax_data)):
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=9902&r1=9901&r2=9902&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Tue Nov 24 11:42:53 2009
@@ -53,7 +53,7 @@
class N_state_model(API_base):
"""Class containing functions for the N-state model."""
- def __assemble_param_vector(self, sim_index=None):
+ def _assemble_param_vector(self, sim_index=None):
"""Assemble all the parameters of the model into a single array.
@param sim_index: The index of the simulation to optimise.
This should be None if
@@ -201,7 +201,7 @@
return list
- def __disassemble_param_vector(self, param_vector=None, data_types=None,
sim_index=None):
+ def _disassemble_param_vector(self, param_vector=None, data_types=None,
sim_index=None):
"""Disassemble the parameter vector and place the values into the
relevant variables.
For the 2-domain N-state model, the parameters are stored in the
probability and Euler angle
@@ -1379,7 +1379,7 @@
self.__update_model()
# Create the initial parameter vector.
- param_vector = self.__assemble_param_vector(sim_index=sim_index)
+ param_vector = self._assemble_param_vector(sim_index=sim_index)
# Determine if alignment tensors or RDCs are to be used.
data_types = self.__base_data_types()
@@ -1444,7 +1444,7 @@
param_vector = dot(scaling_matrix, param_vector)
# Disassemble the parameter vector.
- self.__disassemble_param_vector(param_vector=param_vector,
data_types=data_types, sim_index=sim_index)
+ self._disassemble_param_vector(param_vector=param_vector,
data_types=data_types, sim_index=sim_index)
# Monte Carlo minimisation statistics.
if sim_index != None:
Modified: 1.3/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=9902&r1=9901&r2=9902&view=diff
==============================================================================
--- 1.3/specific_fns/relax_fit.py (original)
+++ 1.3/specific_fns/relax_fit.py Tue Nov 24 11:42:53 2009
@@ -45,7 +45,7 @@
class Relax_fit(API_base):
"""Class containing functions for relaxation curve fitting."""
- def assemble_param_vector(self, spin=None, sim_index=None):
+ def _assemble_param_vector(self, spin=None, sim_index=None):
"""Assemble the exponential curve parameter vector (as a numpy
array).
@keyword spin: The spin data container.
@@ -144,7 +144,7 @@
"""
# Create the initial parameter vector.
- param_vector = self.assemble_param_vector(spin=spin)
+ param_vector = self._assemble_param_vector(spin=spin)
# Create a scaling matrix.
scaling_matrix = self.assemble_scaling_matrix(spin=spin,
scaling=False)
@@ -340,7 +340,7 @@
return 0.0
- def disassemble_param_vector(self, param_vector=None, spin=None,
sim_index=None):
+ def _disassemble_param_vector(self, param_vector=None, spin=None,
sim_index=None):
"""Disassemble the parameter vector.
@keyword param_vector: The parameter vector.
@@ -611,7 +611,7 @@
continue
# Create the initial parameter vector.
- param_vector = self.assemble_param_vector(spin=spin)
+ param_vector = self._assemble_param_vector(spin=spin)
# Diagonal scaling.
scaling_matrix = self.assemble_scaling_matrix(spin=spin,
scaling=scaling)
@@ -703,7 +703,7 @@
param_vector = dot(scaling_matrix, param_vector)
# Disassemble the parameter vector.
- self.disassemble_param_vector(param_vector=param_vector,
spin=spin, sim_index=sim_index)
+ self._disassemble_param_vector(param_vector=param_vector,
spin=spin, sim_index=sim_index)
# Monte Carlo minimisation statistics.
if sim_index != None:
r9902 - in /1.3/specific_fns: frame_order.py model_free/main.py model_free/mf_minimise.py n_state_model.py relax_fit.py