Author: tlinnet
Date: Fri Sep 12 11:25:50 2014
New Revision: 25775
URL: http://svn.gna.org/viewcvs/relax?rev=25775&view=rev
Log:
Implemented back-end function to estimate Rx and I0 errors from Jacobian
matrix.
This is to prepare for user funcion in relax_fit, to estimate errors.
Added:
trunk/specific_analyses/relax_fit/estimate_rx_err.py
Modified:
trunk/specific_analyses/relax_fit/__init__.py
Modified: trunk/specific_analyses/relax_fit/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_fit/__init__.py?rev=25775&r1=25774&r2=25775&view=diff
==============================================================================
--- trunk/specific_analyses/relax_fit/__init__.py (original)
+++ trunk/specific_analyses/relax_fit/__init__.py Fri Sep 12 11:25:50
2014
@@ -25,6 +25,7 @@
# The available modules.
__all__ = [
'api',
+ 'estimate_rx_err',
'optimisation',
'parameter_object',
'parameters',
Added: trunk/specific_analyses/relax_fit/estimate_rx_err.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_fit/estimate_rx_err.py?rev=25775&view=auto
==============================================================================
--- trunk/specific_analyses/relax_fit/estimate_rx_err.py (added)
+++ trunk/specific_analyses/relax_fit/estimate_rx_err.py Fri Sep 12
11:25:50 2014
@@ -0,0 +1,157 @@
+###############################################################################
+#
#
+# Copyright (C) 2014 Troels E. Linnet
#
+#
#
+# 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.
+"""Estimation of rx error, from Co-variance matrix."""
+
+# Python module imports.
+from copy import deepcopy
+from numpy import asarray, diag, sqrt, transpose
+import sys
+from warnings import warn
+
+# relax module imports.
+from dep_check import C_module_exp_fn
+from lib.errors import RelaxError
+from lib.statistics import multifit_covar
+from lib.text.sectioning import subsection
+from lib.warnings import RelaxWarning
+from pipe_control.mol_res_spin import generate_spin_string, spin_loop
+
+# C modules.
+if C_module_exp_fn:
+ from target_functions.relax_fit import jacobian, jacobian_chi2, setup
+
+
+def estimate_rx_err(spin_id=None, epsrel=0.0, verbosity=2):
+ """This will estimate the rx and i0 errors from the covariance matrix
Qxx. Qxx is calculated from the Jacobian matrix and the optimised
parameters.
+
+ @keyword spin_id: The spin identification string.
+ @type spin_id: str
+ @param epsrel: Any columns of R which satisfy |R_{kk}| <=
epsrel |R_{11}| are considered linearly-dependent and are excluded from the
covariance matrix, where the corresponding rows and columns of the
covariance matrix are set to zero.
+ @type epsrel: float
+ @keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
+ @type verbosity: int
+ """
+
+ # Check that the C modules have been compiled.
+ if not C_module_exp_fn:
+ raise RelaxError("Relaxation curve fitting is not available. Try
compiling the C modules on your platform.")
+
+ # Perform checks.
+ if not cdp.curve_type == 'exp':
+ raise RelaxError("Only curve type of 'exp' is allowed for error
estimation. Set by: relax_fit.select_model('exp').")
+
+ # Loop over the spins.
+ for cur_spin, mol_name, resi, resn, cur_spin_id in
spin_loop(selection=spin_id, full_info=True, return_id=True,
skip_desel=True):
+ # Generate spin string.
+ spin_string = generate_spin_string(spin=cur_spin,
mol_name=mol_name, res_num=resi, res_name=resn)
+
+ # Raise Error, if not optimised.
+ if not (hasattr(cur_spin, 'rx') and hasattr(cur_spin, 'i0')):
+ raise RelaxError("Spin '%s' does not contain optimised 'rx'
and 'i0' values. Try execute: minimise.execute(min_algor='Newton',
constraints=False)"%(spin_string))
+
+ # Raise warning, if gradient count is 0. This could point to a
lack of minimisation first.
+ if hasattr(cur_spin, 'g_count'):
+ if getattr(cur_spin, 'g_count') == 0.0:
+ text = "Spin %s contains a gradient count of 0.0. Is the
rx parameter optimised? Try execute: minimise.execute(min_algor='Newton',
constraints=False)" %(spin_string)
+ warn(RelaxWarning("%s." % text))
+
+ # Print information.
+ if verbosity >= 1:
+ # Individual spin block section.
+ top = 2
+ if verbosity >= 2:
+ top += 2
+ subsection(file=sys.stdout, text="Estimating rx error for
spin: %s"%spin_string, prespace=top)
+
+ # The keys.
+ keys = list(cur_spin.peak_intensity.keys())
+
+ # The peak intensities and times.
+ values = []
+ errors = []
+ times = []
+ for key in keys:
+ values.append(cur_spin.peak_intensity[key])
+ errors.append(cur_spin.peak_intensity_err[key])
+ times.append(cdp.relax_times[key])
+
+ # Convert to numpy array.
+ values = asarray(values)
+ errors = asarray(errors)
+ times = asarray(times)
+
+ # Extract values.
+ rx = getattr(cur_spin, 'rx')
+ i0 = getattr(cur_spin, 'i0')
+
+ # Pack data
+ param_vector = [rx, i0]
+
+ # Initialise data in C code.
+ scaling_list = [1.0, 1.0]
+ setup(num_params=len(param_vector), num_times=len(times),
values=values, sd=errors, relax_times=times, scaling_matrix=scaling_list)
+
+ # Use the direct Jacobian from function.
+ jacobian_matrix_exp = transpose(asarray( jacobian(param_vector) ) )
+ weights = 1. / errors**2
+
+ # Get the co-variance
+ pcov = multifit_covar(J=jacobian_matrix_exp, weights=weights)
+
+ # To compute one standard deviation errors on the parameters, take
the square root of the diagonal covariance.
+ param_vector_error = sqrt(diag(pcov))
+
+ # Extract values.
+ rx_err, i0_err = param_vector_error
+
+ # Copy rx, to rx_err, if not exists.
+ if not hasattr(cur_spin, 'rx_err'):
+ setattr(cur_spin, 'rx_err', deepcopy(getattr(cur_spin, 'rx')))
+ if not hasattr(cur_spin, 'i0_err'):
+ setattr(cur_spin, 'i0_err', deepcopy(getattr(cur_spin, 'i0')))
+
+ # Set error.
+ cur_spin.rx_err = rx_err
+ cur_spin.i0_err = i0_err
+
+ # Get other relevant information.
+ chi2 = getattr(cur_spin, 'chi2')
+
+ # Print information.
+ print_strings = []
+ if verbosity >= 1:
+ # Add print strings.
+ point_info = "Spin: '%s', with %i time points." %
(spin_string, len(times))
+ print_strings.append(point_info)
+
+ par_info = "rx=%3.3f rx_err=%3.4f, i0=%6.1f, i0_err=%3.4f,
chi2=%3.3f.\n" % ( rx, rx_err, i0, i0_err, chi2)
+ print_strings.append(par_info)
+
+ if verbosity >= 2:
+ time_info = ', '.join(map(str, times))
+ print_strings.append('For time array: '+time_info+'.\n\n')
+
+ # Print info
+ if len(print_strings) > 0:
+ for print_string in print_strings:
+ print(print_string),
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Re: r25775 - in /trunk/specific_analyses/relax_fit: __init__.py estimate_rx_err.py