Author: bugman
Date: Mon Jun 17 19:55:44 2013
New Revision: 20186
URL: http://svn.gna.org/viewcvs/relax?rev=20186&view=rev
Log:
Added support for converting between kex and tex, and pA and pB for the
dispersion analysis.
This is performed by the new
specific_analyses.relax_disp.parameters.param_conversion() function.
For this, most of the code from the assemble_param_vector() function has been
shifted into
get_value(), and most of disassemble_param_vector() into set_value(). The
dispersion analysis now
also has a custom sim_init_values() method to handle these parameters.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20186&r1=20185&r2=20186&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Mon Jun 17
19:55:44 2013
@@ -47,7 +47,7 @@
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
from specific_analyses.relax_disp.disp_data import average_intensity,
find_intensity_keys, loop_cluster, loop_frq, loop_frq_point,
loop_frq_point_key, loop_frq_point_time, loop_point, loop_time, relax_time,
return_cpmg_frqs, return_index_from_disp_point, return_index_from_frq,
return_key_from_disp_point_index, return_param_key_from_data,
return_r2eff_arrays, return_spin_lock_nu1, return_value_from_frq_index,
spin_ids_to_containers
-from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
loop_parameters, param_index_to_param_info, param_num
+from specific_analyses.relax_disp.parameters import assemble_param_vector,
assemble_scaling_matrix, disassemble_param_vector, linear_constraints,
loop_parameters, param_conversion, param_index_to_param_info, param_num
from specific_analyses.relax_disp.variables import CPMG_EXP, FIXED_TIME_EXP,
MODEL_LIST_FULL, MODEL_LM63, MODEL_CR72, MODEL_DPL94, MODEL_IT99, MODEL_M61,
MODEL_M61B, MODEL_NOREX, MODEL_R2EFF, R1RHO_EXP, VAR_TIME_EXP
from target_functions.relax_disp import Dispersion
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
@@ -73,7 +73,6 @@
self.return_conversion_factor = self._return_no_conversion_factor
self.return_value = self._return_value_general
self.set_param_values = self._set_param_values_spin
- self.sim_init_values = self._sim_init_values_spin
# Set up the spin parameters.
self.PARAMS.add('intensities', scope='spin', py_type=dict,
grace_string='\\qPeak intensities\\Q')
@@ -1131,6 +1130,7 @@
# Disassemble the parameter vector.
disassemble_param_vector(param_vector=param_vector, spins=spins,
sim_index=sim_index)
+ param_conversion(spins=spins, sim_index=sim_index)
# Monte Carlo minimisation statistics.
if sim_index != None:
@@ -1431,6 +1431,92 @@
spin.select_sim = deepcopy(select_sim)
+ def sim_init_values(self):
+ """Initialise the Monte Carlo parameter values."""
+
+ # Get the parameter object names.
+ param_names = self.data_names(set='params')
+
+ # Add the names of kex-tex pair.
+ pairs = {}
+ pairs['kex'] = 'tex'
+ pairs['tex'] = 'kex'
+
+ # Add the names of pA-pB pair.
+ pairs['pA'] = 'pB'
+ pairs['pB'] = 'pA'
+
+ # Get the minimisation statistic object names.
+ min_names = self.data_names(set='min')
+
+
+ # Test if Monte Carlo parameter values have already been set.
+ #############################################################
+
+ # Loop over the spins.
+ for spin in spin_loop():
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Loop over all the parameter names.
+ for object_name in param_names:
+ # Name for the simulation object.
+ sim_object_name = object_name + '_sim'
+
+
+ # Set the Monte Carlo parameter values.
+ #######################################
+
+ # Loop over the residues.
+ for spin in spin_loop():
+ # Skip deselected residues.
+ if not spin.select:
+ continue
+
+ # Loop over all the data names.
+ for object_name in param_names:
+ # Not a parameter of the model.
+ if not (object_name in spin.params or (object_name in pairs
and pairs[object_name] in spin.params)):
+ continue
+
+ # Name for the simulation object.
+ sim_object_name = object_name + '_sim'
+
+ # Create the simulation object.
+ setattr(spin, sim_object_name, [])
+
+ # Get the simulation object.
+ sim_object = getattr(spin, sim_object_name)
+
+ # Loop over the simulations.
+ for j in range(cdp.sim_number):
+ # The non-simulation value.
+ if object_name not in spin.params:
+ value = deepcopy(getattr(spin, pairs[object_name]))
+ else:
+ value = deepcopy(getattr(spin, object_name))
+
+ # Copy and append the data.
+ sim_object.append(value)
+
+ # Loop over all the minimisation object names.
+ for object_name in min_names:
+ # Name for the simulation object.
+ sim_object_name = object_name + '_sim'
+
+ # Create the simulation object.
+ setattr(spin, sim_object_name, [])
+
+ # Get the simulation object.
+ sim_object = getattr(spin, sim_object_name)
+
+ # Loop over the simulations.
+ for j in range(cdp.sim_number):
+ # Copy and append the data.
+ sim_object.append(deepcopy(getattr(spin, object_name)))
+
+
def sim_pack_data(self, data_id, sim_data):
"""Pack the Monte Carlo simulation data.
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=20186&r1=20185&r2=20186&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Mon Jun 17
19:55:44 2013
@@ -52,49 +52,8 @@
# Loop over the parameters of the cluster.
for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
- # Spin specific parameters.
- if spin_index != None:
- # Set the simulation value.
- if sim_index != None:
- # Get the simulation structure.
- sim_obj = getattr(spins[spin_index], param_name+'_sim')
-
- # Frequency specific parameter.
- if frq_index != None:
- value = sim_obj[sim_index][frq_index]
-
- # Set the normal value.
- else:
- value = sim_obj[sim_index]
-
- # Frequency specific parameter.
- elif frq_index != None:
- obj = getattr(spins[spin_index], param_name)
- if obj == []:
- value = 0.0
- else:
- value = obj[frq_index]
-
- # Set the normal value.
- else:
- value = getattr(spins[spin_index], param_name)
-
- # Cluster specific parameters - use the parameter value from the
first spin.
- else:
- # Set the simulation value.
- if sim_index != None:
- value = getattr(spins[0], param_name+'_sim')[sim_index]
-
- # Set the normal value.
- else:
- value = getattr(spins[0], param_name)
-
- # The R2eff model parameters.
- if key != None:
- if not key in value:
- value = 0.0
- else:
- value = value[key]
+ # Get the value.
+ value = get_value(key=key, spins=spins, sim_index=sim_index,
param_name=param_name, spin_index=spin_index, frq_index=frq_index)
# Add to the vector.
param_vector.append(value)
@@ -189,59 +148,76 @@
for frq in loop_frq():
spin.r2.append(None)
- # Loop over the parameters of the cluster.
+ # Loop over the parameters of the cluster, setting the values.
for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
- # Spin specific parameters.
- if spin_index != None:
- # Get the object.
- if sim_index != None:
- obj = getattr(spins[spin_index], param_name+'_sim')
- else:
- obj = getattr(spins[spin_index], param_name)
-
- # Set the simulation value.
- if sim_index != None:
- # Frequency specific parameter.
- if frq_index != None:
- if key != None:
- obj[sim_index][frq_index][key] =
param_vector[param_index]
- else:
- obj[sim_index][frq_index] = param_vector[param_index]
-
- # Set the normal value.
- else:
- if key != None:
- obj[sim_index][key] = param_vector[param_index]
- else:
- obj[sim_index] = param_vector[param_index]
+ set_value(value=param_vector[param_index], key=key, spins=spins,
sim_index=sim_index, param_name=param_name, spin_index=spin_index,
frq_index=frq_index)
+
+
+def get_value(key=None, spins=None, sim_index=None, param_name=None,
spin_index=None, frq_index=None):
+ """Return the value for the given parameter.
+
+ @keyword key: The key for the R2eff and I0 parameters.
+ @type key: str or None
+ @keyword spins: The list of spin data containers for the block.
+ @type spins: list of SpinContainer instances
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
+ @keyword param_name: The parameter name.
+ @type param_name: str
+ @keyword spin_index: The spin index (for the cluster).
+ @type spin_index: int
+ @keyword frq_index: The frequency index (for parameters with
different values per spectrometer field strength).
+ @type frq_index: int
+ @return: The parameter value.
+ @rtype: float
+ """
+
+ # Spin specific parameters.
+ if spin_index != None:
+ # Set the simulation value.
+ if sim_index != None:
+ # Get the simulation structure.
+ sim_obj = getattr(spins[spin_index], param_name+'_sim')
# Frequency specific parameter.
- elif frq_index != None:
- obj = getattr(spins[spin_index], param_name)
- if key != None:
- obj[frq_index][key] = param_vector[param_index]
- else:
- obj[frq_index] = param_vector[param_index]
+ if frq_index != None:
+ value = sim_obj[sim_index][frq_index]
# Set the normal value.
else:
- if key != None:
- obj[key] = param_vector[param_index]
- else:
- setattr(spins[spin_index], param_name,
param_vector[param_index])
-
- # Cluster specific parameters.
+ value = sim_obj[sim_index]
+
+ # Frequency specific parameter.
+ elif frq_index != None:
+ obj = getattr(spins[spin_index], param_name)
+ if obj == []:
+ value = 0.0
+ else:
+ value = obj[frq_index]
+
+ # Set the normal value.
else:
- # Set the same parameter value for all spins in the cluster.
- for spin in spins:
- # Set the simulation value.
- if sim_index != None:
- sim_obj = getattr(spin, param_name+'_sim')
- sim_obj[sim_index] = param_vector[param_index]
-
- # Set the normal value.
- else:
- setattr(spin, param_name, param_vector[param_index])
+ value = getattr(spins[spin_index], param_name)
+
+ # Cluster specific parameters - use the parameter value from the first
spin.
+ else:
+ # Set the simulation value.
+ if sim_index != None:
+ value = getattr(spins[0], param_name+'_sim')[sim_index]
+
+ # Set the normal value.
+ else:
+ value = getattr(spins[0], param_name)
+
+ # The R2eff model parameters.
+ if key != None:
+ if not key in value:
+ value = 0.0
+ else:
+ value = value[key]
+
+ # Return the value.
+ return value
def linear_constraints(spins=None, scaling_matrix=None):
@@ -459,6 +435,43 @@
yield param, param_index, None, None
+def param_conversion(key=None, spins=None, sim_index=None):
+ """Convert Disassemble the parameter vector.
+
+ @keyword key: The key for the R2eff and I0 parameters.
+ @type key: str or None
+ @keyword spins: The list of spin data containers for the block.
+ @type spins: list of SpinContainer instances
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
+ """
+
+ # Loop over the parameters of the cluster.
+ for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
+ # Get the value.
+ value = get_value(key=key, spins=spins, sim_index=sim_index,
param_name=param_name, spin_index=spin_index, frq_index=frq_index)
+
+ # The pA to pB conversion.
+ if param_name == 'pA':
+ pB = 1.0 - value
+ set_value(value=pB, key=key, spins=spins, sim_index=sim_index,
param_name='pB', spin_index=spin_index, frq_index=frq_index)
+
+ # The pB to pA conversion.
+ if param_name == 'pB':
+ pA = 1.0 - value
+ set_value(value=pA, key=key, spins=spins, sim_index=sim_index,
param_name='pA', spin_index=spin_index, frq_index=frq_index)
+
+ # The kex to tex conversion.
+ if param_name == 'kex':
+ tex = 1.0 / (2.0 * value)
+ set_value(value=tex, key=key, spins=spins, sim_index=sim_index,
param_name='tex', spin_index=spin_index, frq_index=frq_index)
+
+ # The tex to kex conversion.
+ if param_name == 'tex':
+ kex = 1.0 / (2.0 * value)
+ set_value(value=kex, key=key, spins=spins, sim_index=sim_index,
param_name='kex', spin_index=spin_index, frq_index=frq_index)
+
+
def param_index_to_param_info(index=None, spins=None):
"""Convert the given parameter array index to parameter identifying
information.
@@ -517,3 +530,75 @@
# Return the number.
return num
+
+
+def set_value(value=None, key=None, spins=None, sim_index=None,
param_name=None, spin_index=None, frq_index=None):
+ """Return the value for the given parameter.
+
+ @keyword value: The parameter value to set.
+ @type value: float
+ @keyword key: The key for the R2eff and I0 parameters.
+ @type key: str or None
+ @keyword spins: The list of spin data containers for the block.
+ @type spins: list of SpinContainer instances
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
+ @keyword param_name: The parameter name.
+ @type param_name: str
+ @keyword spin_index: The spin index (for the cluster).
+ @type spin_index: int
+ @keyword frq_index: The frequency index (for parameters with
different values per spectrometer field strength).
+ @type frq_index: int
+ """
+
+ # Spin specific parameters.
+ if spin_index != None:
+ # Get the object.
+ if sim_index != None:
+ obj = getattr(spins[spin_index], param_name+'_sim')
+ else:
+ obj = getattr(spins[spin_index], param_name)
+
+ # Set the simulation value.
+ if sim_index != None:
+ # Frequency specific parameter.
+ if frq_index != None:
+ if key != None:
+ obj[sim_index][frq_index][key] = value
+ else:
+ obj[sim_index][frq_index] = value
+
+ # Set the normal value.
+ else:
+ if key != None:
+ obj[sim_index][key] = value
+ else:
+ obj[sim_index] = value
+
+ # Frequency specific parameter.
+ elif frq_index != None:
+ obj = getattr(spins[spin_index], param_name)
+ if key != None:
+ obj[frq_index][key] = value
+ else:
+ obj[frq_index] = value
+
+ # Set the normal value.
+ else:
+ if key != None:
+ obj[key] = value
+ else:
+ setattr(spins[spin_index], param_name, value)
+
+ # Cluster specific parameters.
+ else:
+ # Set the same parameter value for all spins in the cluster.
+ for spin in spins:
+ # Set the simulation value.
+ if sim_index != None:
+ sim_obj = getattr(spin, param_name+'_sim')
+ sim_obj[sim_index] = value
+
+ # Set the normal value.
+ else:
+ setattr(spin, param_name, value)
r20186 - in /branches/relax_disp/specific_analyses/relax_disp: api.py parameters.py