Author: bugman
Date: Fri Apr 19 19:52:10 2013
New Revision: 19494
URL: http://svn.gna.org/viewcvs/relax?rev=19494&view=rev
Log:
Shifted the standard deviation code from the Monte Carlo error_analysis()
function to the lib package.
The new function lib.stats.std() is now used to simplify the error_analysis()
function and allow the
code to be reused. This will be useful for expanding the
pipe_control.monte_carlo.error_analysis()
function to handle parameters which are dictionaries, for example as in the
relax_disp branch.
Added:
trunk/lib/stats.py
Modified:
trunk/lib/__init__.py
trunk/pipe_control/monte_carlo.py
Modified: trunk/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/__init__.py?rev=19494&r1=19493&r2=19494&view=diff
==============================================================================
--- trunk/lib/__init__.py (original)
+++ trunk/lib/__init__.py Fri Apr 19 19:52:10 2013
@@ -44,6 +44,7 @@
'regex',
'selection',
'spectral_densities',
+ 'stats',
'structure',
'text',
'warnings'
Added: trunk/lib/stats.py
URL: http://svn.gna.org/viewcvs/relax/trunk/lib/stats.py?rev=19494&view=auto
==============================================================================
--- trunk/lib/stats.py (added)
+++ trunk/lib/stats.py Fri Apr 19 19:52:10 2013
@@ -1,0 +1,85 @@
+###############################################################################
+#
#
+# 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.
+"""Module for calculating simple statistics."""
+
+# Python module imports.
+from math import sqrt
+
+
+def std(values=None, skip=None, dof=1):
+ """Calculate the standard deviation of the given values, skipping values
if asked.
+
+ @keyword values: The list of values to calculate the standard
deviation of.
+ @type values: list of float
+ @keyword skip: An optional list of booleans specifying if a value
should be skipped. The length of this list must match the values. An
element of True will cause the corresponding value to not be included in the
calculation.
+ @type skip: list of bool or None.
+ @keyword dof: The degrees of freedom, whereby the standard
deviation is multipled by 1/(N - dof).
+ @type dof: int
+ @return: The standard deviation.
+ @rtype: float
+ """
+
+ # The total number of points.
+ n = 0
+ for i in range(len(values)):
+ # Skip deselected values.
+ if skip != None and not skip[i]:
+ continue
+
+ # Increment n.
+ n = n + 1
+
+ # Calculate the sum of the values for all points.
+ Xsum = 0.0
+ for i in range(len(values)):
+ # Skip deselected values.
+ if skip != None and not skip[i]:
+ continue
+
+ # Sum.
+ Xsum = Xsum + values[i]
+
+ # Calculate the mean value for all points.
+ if n == 0:
+ Xav = 0.0
+ else:
+ Xav = Xsum / float(n)
+
+ # Calculate the sum part of the standard deviation.
+ sd = 0.0
+ for i in range(len(values)):
+ # Skip deselected values.
+ if skip != None and not skip[i]:
+ continue
+
+ # Sum.
+ sd = sd + (values[i] - Xav)**2
+
+ # Calculate the standard deviation.
+ if n <= 1:
+ sd = 0.0
+ else:
+ sd = sqrt(sd / (float(n) - float(dof)))
+
+ # Return the SD.
+ return sd
Modified: trunk/pipe_control/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/monte_carlo.py?rev=19494&r1=19493&r2=19494&view=diff
==============================================================================
--- trunk/pipe_control/monte_carlo.py (original)
+++ trunk/pipe_control/monte_carlo.py Fri Apr 19 19:52:10 2013
@@ -24,14 +24,14 @@
# Python module imports.
from copy import deepcopy
-from math import sqrt
from numpy import ndarray
from random import gauss
# relax module imports.
+from lib.errors import RelaxError, RelaxNoSequenceError
+from lib import stats
from pipe_control.mol_res_spin import exists_mol_res_spin_data
from pipe_control import pipes
-from lib.errors import RelaxError, RelaxNoSequenceError
from specific_analyses.setup import get_specific_fn
@@ -156,49 +156,9 @@
if param_array == None:
break
- # Simulation parameters with values (ie not None).
+ # SD of simulation parameters with values (ie not None).
if param_array[0] != None:
- # The total number of simulations.
- n = 0
- for i in range(len(param_array)):
- # Skip deselected simulations.
- if not select_sim[i]:
- continue
-
- # Increment n.
- n = n + 1
-
- # Calculate the sum of the parameter value for all
simulations.
- Xsum = 0.0
- for i in range(len(param_array)):
- # Skip deselected simulations.
- if not select_sim[i]:
- continue
-
- # Sum.
- Xsum = Xsum + param_array[i]
-
- # Calculate the mean parameter value for all simulations.
- if n == 0:
- Xav = 0.0
- else:
- Xav = Xsum / float(n)
-
- # Calculate the sum part of the standard deviation.
- sd = 0.0
- for i in range(len(param_array)):
- # Skip deselected simulations.
- if not select_sim[i]:
- continue
-
- # Sum.
- sd = sd + (param_array[i] - Xav)**2
-
- # Calculate the standard deviation.
- if n <= 1:
- sd = 0.0
- else:
- sd = sqrt(sd / (float(n) - 1.0))
+ sd = stats.std(values=param_array, skip=select_sim)
# Simulation parameters with the value None.
else:
r19494 - in /trunk: lib/__init__.py lib/stats.py pipe_control/monte_carlo.py