Author: bugman
Date: Fri Apr 5 16:50:23 2013
New Revision: 19385
URL: http://svn.gna.org/viewcvs/relax?rev=19385&view=rev
Log:
The relaxation dispersion parameter errors from Monte Carlo simulations are
now stored.
Previously MC simulations could run, but the errors were not being calculated
and stored. The
sim_return_param() method was empty. This method is now complete.
In addition the set_error() method has been created for setting the parameter
errors. And the
_exp_curve_key_from_index() and _param_index_to_param_info() auxiliary
methods added to facilitate
data access.
Modified:
branches/relax_disp/specific_analyses/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19385&r1=19384&r2=19385&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Fri Apr 5 16:50:23
2013
@@ -57,7 +57,6 @@
self.data_init = self._data_init_spin
self.return_conversion_factor = self._return_no_conversion_factor
self.return_value = self._return_value_general
- self.set_error = self._set_error_spin
self.set_param_values = self._set_param_values_spin
self.sim_init_values = self._sim_init_values_spin
@@ -494,6 +493,24 @@
# R1rho data.
else:
return cdp.spin_lock_nu1_list.index(key)
+
+
+ def _exp_curve_key_from_index(self, index):
+ """Convert the exponential curve key into the corresponding index.
+
+ @param index: The exponential curve index.
+ @type index: int
+ @return: The exponential curve key - either the CPMG
frequency or R1rho spin-lock field strength.
+ @rtype: float
+ """
+
+ # CPMG data.
+ if cdp.exp_type == 'cpmg':
+ return cdp.cpmg_frqs_list[index]
+
+ # R1rho data.
+ else:
+ return cdp.spin_lock_nu1_list[index]
def _exp_curve_loop(self):
@@ -872,6 +889,51 @@
# The model and parameter names.
spin.model = model
spin.params = params
+
+
+ def _param_index_to_param_info(self, index=None, spins=None):
+ """Convert the given parameter array index to parameter identifying
information.
+
+ The parameter index will be converted to the parameter name, the
relevant spin index in the cluster, and relevant exponential curve key.
+
+ @keyword index: The index of the parameter array.
+ @type index: int
+ @keyword spins: The list of spin data containers for the block.
+ @type spins: list of SpinContainer instances
+ @return: The parameter name, spin cluster index, and
exponential curve key.
+ @rtype: str, int, float
+ """
+
+ # Initialise.
+ param_name = None
+ spin_index = 0
+ curve_key = None
+
+ # The number of spin specific parameters (R2eff and I0 per spin),
times the total number of exponential curves.
+ num = len(spins) * 2 * cdp.curve_count
+
+ # The exponential curve parameters.
+ if index < num:
+ # Even indices are R2eff, odd are I0.
+ if index % 2:
+ param_name = 'i0'
+ else:
+ param_name = 'r2eff'
+
+ # The spin index.
+ spin_index = int(index / 2 / cdp.curve_count)
+
+ # The curve index and key.
+ exp_index = int((index - spin_index * 2) / 2)
+ curve_key = self._exp_curve_key_from_index(exp_index)
+
+ # All other parameters.
+ else:
+ names = self.data_names(set='params')
+ param_name = names[index-num+2]
+
+ # Return the data.
+ return param_name, spin_index, curve_key
def _param_num(self, spins=None):
@@ -1369,6 +1431,42 @@
set_doc.add_paragraph("Only three parameters can be set for either the
slow- or the fast-exchange regime. For the slow-exchange regime, these
parameters include the transversal relaxation rate for state A (R2A), the
exchange rate from state A to state (kA) and the chemical shift difference
between states A and B (dw). For the fast-exchange regime, these include the
transversal relaxation rate (R2), the chemical exchange contribution to R2
(Rex) and the exchange rate (kex). Setting parameters for a non selected
model has no effect.")
+ def set_error(self, model_info, index, error):
+ """Set the parameter errors.
+
+ @param model_info: The spin container originating from model_loop().
+ @type model_info: unknown
+ @param index: The index of the parameter to set the errors for.
+ @type index: int
+ @param error: The error value.
+ @type error: float
+ """
+
+ # Unpack the data.
+ spins, spin_ids = model_info
+
+ # Convert the parameter index.
+ param_name, spin_index, curve_key =
self._param_index_to_param_info(index=index, spins=spins)
+
+ # The parameter error name.
+ err_name = param_name + "_err"
+
+ # The exponential curve parameters.
+ if param_name in ['r2eff', 'i0']:
+ # Initialise if needed.
+ if not hasattr(spins[spin_index], err_name):
+ setattr(spins[spin_index], err_name, {})
+
+ # Set the value.
+ obj = getattr(spins[spin_index], err_name)
+ obj[curve_key] = error
+
+ # All other parameters.
+ else:
+ for spin in spins:
+ setattr(spin, err_name, error)
+
+
def set_selected_sim(self, model_info, select_sim):
"""Set the simulation selection flag.
@@ -1430,6 +1528,38 @@
@rtype: list of float
"""
+ # Unpack the data.
+ spins, spin_ids = model_info
+
+ # No more parameters.
+ total_param_num = self._param_num(spins=spins)
+ if index >= total_param_num:
+ return
+
+ # Convert the parameter index.
+ param_name, spin_index, curve_key =
self._param_index_to_param_info(index=index, spins=spins)
+
+ # The exponential curve parameters.
+ sim_data = []
+ if param_name == 'r2eff':
+ for i in range(cdp.sim_number):
+ sim_data.append(spins[spin_index].r2eff_sim[i][curve_key])
+ elif param_name == 'i0':
+ for i in range(cdp.sim_number):
+ sim_data.append(spins[spin_index].i0_sim[i][curve_key])
+
+ # All other parameters.
+ else:
+ sim_data = getattr(spins[0], param_name + "_sim")
+
+ # Set the sim data to None if empty.
+ if sim_data == []:
+ sim_data = None
+
+ # Return the object.
+ return sim_data
+
+
def sim_return_selected(self, model_info):
"""Return the array of selected simulation flags.
r19385 - /branches/relax_disp/specific_analyses/relax_disp.py