Author: bugman
Date: Thu Apr 11 14:10:28 2013
New Revision: 19455
URL: http://svn.gna.org/viewcvs/relax?rev=19455&view=rev
Log:
Created a basic initial auto-analysis script for relaxation dispersion.
This currently only supports the optimisation of the 'exp_fit' diffusion
model, but has all of the
infrastructure set up to make it easy to add other models.
Added:
branches/relax_disp/auto_analyses/relax_disp.py
Added: branches/relax_disp/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/relax_disp.py?rev=19455&view=auto
==============================================================================
--- branches/relax_disp/auto_analyses/relax_disp.py (added)
+++ branches/relax_disp/auto_analyses/relax_disp.py Thu Apr 11 14:10:28 2013
@@ -1,0 +1,149 @@
+###############################################################################
+#
#
+# Copyright (C) 2013 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""The automatic relaxation dispersion protocol."""
+
+# Python module imports.
+from os import getcwd, sep
+import sys
+
+# relax module imports.
+from lib.text.sectioning import title, subtitle
+from pipe_control.pipes import has_pipe
+from prompt.interpreter import Interpreter
+from status import Status; status = Status()
+
+
+class Relax_disp:
+ def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
models=['exp_fit'], grid_inc=11, mc_sim_num=500):
+ """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
+ """
+
+ # Printout.
+ title(file=sys.stdout, text="Relaxation dispersion auto-analysis")
+
+ # Execution lock.
+ status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
+
+ # Set up the analysis status object.
+ status.init_auto_analysis(pipe_bundle, type='relax_disp')
+ status.current_analysis = pipe_bundle
+
+ # Store the args.
+ self.pipe_name = pipe_name
+ self.pipe_bundle = pipe_bundle
+ self.results_dir = results_dir
+ self.models = models
+ self.grid_inc = grid_inc
+ self.mc_sim_num = mc_sim_num
+
+ # No results directory, so default to the current directory.
+ if not self.results_dir:
+ self.results_dir = getcwd()
+
+ # Data checks.
+ self.check_vars()
+
+ # Load the interpreter.
+ self.interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
+ self.interpreter.populate_self()
+ self.interpreter.on(verbose=False)
+
+ # Execute.
+ self.run()
+
+ # Finish and unlock execution.
+ status.auto_analysis[self.pipe_bundle].fin = True
+ status.current_analysis = None
+ status.exec_lock.release()
+
+
+ def check_vars(self):
+ """Check that the user has set the variables correctly."""
+
+ # The pipe name.
+ if not has_pipe(self.pipe_name):
+ raise RelaxNoPipeError(self.pipe_name)
+
+
+ def exponential_fit(self):
+ """Optimise the simple exponential fit relaxation dispersion
model."""
+
+ # Printout.
+ subtitle(file=sys.stdout, text="Simple exponential curve-fitting")
+
+ # Create the data pipe by copying the base pipe.o
+ self.interpreter.pipe.copy(pipe_from=self.pipe_name,
pipe_to='exp_fit', bundle_to=self.pipe_bundle)
+
+ # Grid search.
+ self.interpreter.grid_search(inc=self.grid_inc)
+
+ # Minimise.
+ self.interpreter.minimise('simplex', constraints=False)
+
+ # Monte Carlo simulations.
+ self.interpreter.monte_carlo.setup(number=self.mc_sim_num)
+ self.interpreter.monte_carlo.create_data()
+ self.interpreter.monte_carlo.initial_values()
+ self.interpreter.minimise('simplex', constraints=False)
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Write out the results.
+ self.write_results()
+
+
+ def run(self):
+ """Execute the auto-analysis."""
+
+ # First optimise the exponential curves to obtain the initial R2eff
values for all other models.
+ self.exponential_fit()
+
+
+ def write_results(self):
+ """Create a set of results, text and Grace files for the current
data pipe."""
+
+ # The directory name.
+ path = self.results_dir + sep + cdp.model
+
+ # Save the results.
+ self.interpreter.results.write(file='results', dir=path, force=True)
+
+ # Save the relaxation dispersion parameters.
+ self.interpreter.value.write(param='rex', file='rex.out', dir=path,
force=True)
+
+ # Create Grace plots of the data.
+ self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr',
dir=path, force=True)
+ self.interpreter.grace.write(x_data_type='res_num',
y_data_type='r2eff', file='r2eff.agr', dir=path, force=True)
+ self.interpreter.grace.write(x_data_type='spin_lock_nu1',
y_data_type='r2eff', file='dispersion_curves.agr', dir=path, force=True)
r19455 - /branches/relax_disp/auto_analyses/relax_disp.py