Author: bugman
Date: Thu Jun 6 18:26:24 2013
New Revision: 19900
URL: http://svn.gna.org/viewcvs/relax?rev=19900&view=rev
Log:
Reverted r19753 and r19754 - the relax_disp.r2eff_setup user function is now
useless.
The command used was:
svn merge -r19754:r19752 .
Manual editing was required to fix a number of conflicts. The user function
is not necessary as the
errors are now directly calculated rather than simulated using bootstrapping.
.....
r19754 | bugman | 2013-05-28 11:41:25 +0200 (Tue, 28 May 2013) | 6 lines
Changed paths:
M /branches/relax_disp/auto_analyses/relax_disp.py
The relaxation dispersion auto-analysis now handles the Bootstrapping
simulations.
The bootstrap_sim_num argument can now be passed into the auto-analysis,
and the run() method then
executes the relax_disp.r2eff_setup user function.
------------------------------------------------------------------------
r19753 | bugman | 2013-05-28 11:37:19 +0200 (Tue, 28 May 2013) | 6 lines
Changed paths:
M /branches/relax_disp/specific_analyses/relax_disp/__init__.py
M /branches/relax_disp/user_functions/relax_disp.py
Created the relax_disp.r2eff_setup user function.
This is required to set the number of Bootstrapping simulations to use in
the calc user function.
It replaces the hardcoded variable.
.....
Modified:
branches/relax_disp/auto_analyses/relax_disp.py
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/relax_disp.py?rev=19900&r1=19899&r2=19900&view=diff
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (original)
+++ branches/relax_disp/auto_analyses/relax_disp.py Thu Jun 6 18:26:24 2013
@@ -45,25 +45,23 @@
opt_func_tol = 1e-25
opt_max_iterations = int(1e7)
- def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
models=[MODEL_R2EFF], grid_inc=11, mc_sim_num=500, bootstrap_sim_num=100000,
modsel='AIC'):
+ def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
models=[MODEL_R2EFF], grid_inc=11, mc_sim_num=500, modsel='AIC'):
"""Perform a full relaxation dispersion analysis for the given list
of models.
- @keyword pipe_name: The name of the data pipe containing all
of the data for the analysis.
- @type pipe_name: str
- @keyword pipe_bundle: The data pipe bundle to associate all
spawned data pipes with.
- @type pipe_bundle: str
- @keyword results_dir: The directory where results files are
saved.
- @type results_dir: str
- @keyword models: The list of relaxation dispersion models
to optimise.
- @type models: list of str
- @keyword grid_inc: Number of grid search increments.
- @type grid_inc: int
- @keyword mc_sim_num: The number of Monte Carlo simulations to
be used for error analysis at the end of the analysis.
- @type mc_sim_num: int
- @keyword bootstrap_sim_num: The number of Monte Carlo simulations to
be used for error analysis at the end of the analysis.
- @type bootstrap_sim_num: int
- @keyword modsel: The model selection technique to use in
the analysis to determine which model is the best for each spin cluster.
This can currently be one of 'AIC', 'AICc', and 'BIC'.
- @type modsel: str
+ @keyword pipe_name: The name of the data pipe containing all of
the data for the analysis.
+ @type pipe_name: str
+ @keyword pipe_bundle: The data pipe bundle to associate all
spawned data pipes with.
+ @type pipe_bundle: str
+ @keyword results_dir: The directory where results files are saved.
+ @type results_dir: str
+ @keyword models: The list of relaxation dispersion models to
optimise.
+ @type models: list of str
+ @keyword grid_inc: Number of grid search increments.
+ @type grid_inc: int
+ @keyword mc_sim_num: The number of Monte Carlo simulations to be
used for error analysis at the end of the analysis.
+ @type mc_sim_num: int
+ @keyword modsel: The model selection technique to use in the
analysis to determine which model is the best for each spin cluster. This
can currently be one of 'AIC', 'AICc', and 'BIC'.
+ @type modsel: str
"""
# Printout.
@@ -83,7 +81,6 @@
self.models = models
self.grid_inc = grid_inc
self.mc_sim_num = mc_sim_num
- self.bootstrap_sim_num = bootstrap_sim_num
self.modsel = modsel
# No results directory, so default to the current directory.
@@ -188,10 +185,6 @@
# Calculate the R2eff values for the fixed relaxation time
period data types.
if model == MODEL_R2EFF and cdp.exp_type in FIXED_TIME_EXP:
- # Set up the simulation number.
-
self.interpreter.relax_disp.r2eff_setup(sim_num=self.bootstrap_sim_num)
-
- # Calculate the values.
self.interpreter.calc()
# Optimise the model.
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19900&r1=19899&r2=19900&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Thu Jun 6
18:26:24 2013
@@ -776,17 +776,6 @@
add_result_file(type='grace', label='Grace', file=file_path)
- def _r2eff_setup(self, sim_num=100000):
- """Setup the R2eff/R1rho model.
-
- @keyword sim_num: The number of Bootstrapping simulations for
error propagation for the fixed relaxation time period experiments.
- @type sim_num: int
- """
-
- # Set the value.
- cdp.bootstrap_sim_num = sim_num
-
-
def _select_model(self, model=MODEL_R2EFF):
"""Set up the model for the relaxation dispersion analysis.
@@ -958,13 +947,8 @@
if cdp.exp_type not in FIXED_TIME_EXP:
raise RelaxError("The experiment '%s' is not of the fixed
relaxation time period data type, the R2eff/R1rho values cannot be directly
calculated." % cdp.exp_type)
- # Check the simulation number.
- if not hasattr(cdp, 'bootstrap_sim_num'):
- raise RelaxError("The Bootstrapping simulation number has not
been specified, please use the R2eff/R1rho setup user function first.")
-
# Printouts.
print("Calculating the R2eff/R1rho values for fixed relaxation time
period data.")
- print("Error propagation using Bootstrapping with %i simulations." %
cdp.bootstrap_sim_num)
# Loop over the spins.
for spin, spin_id in spin_loop(return_id=True, skip_desel=True):
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=19900&r1=19899&r2=19900&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Thu Jun 6 18:26:24 2013
@@ -393,30 +393,6 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'grace.png'
-# The relax_disp.r2eff_setup user function.
-uf = uf_info.add_uf('relax_disp.r2eff_setup')
-uf.title = "Setup for the R2eff/R1rho model."
-uf.title_short = "R2eff/R1rho model setup."
-uf.add_keyarg(
- name = "sim_num",
- default = 100000,
- min = 3,
- max = 1000000000,
- py_type = "int",
- desc_short = "Bootstrapping simulation number",
- desc = "The number of Bootstrapping simulations for error propagation."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This is used to setup the variables required for
the calculation of the R2eff/R1rho values. Currently only the number of
Bootstrapping simulations for error propagation needs to be given. This is
only required for calculating the R2eff/R1rho values for fixed relaxation
time period data, if full relaxation curves have been collected then this
value will be ignored.")
-uf.backend = relax_disp_obj._r2eff_setup
-uf.menu_text = "&r2eff_setup"
-uf.gui_icon = "oxygen.actions.edit-rename"
-uf.wizard_size = (800, 500)
-uf.wizard_image = ANALYSIS_IMAGE_PATH + 'relax_disp_200x200.png'
-uf.wizard_apply_button = False
-
-
# The relax_disp.relax_time user function.
uf = uf_info.add_uf('relax_disp.relax_time')
uf.title = "Set the relaxation delay time associated with each spectrum."
r19900 - in /branches/relax_disp: auto_analyses/ specific_analyses/relax_disp/ user_functions/