Author: bugman
Date: Tue Oct 21 18:34:31 2008
New Revision: 7896
URL: http://svn.gna.org/viewcvs/relax?rev=7896&view=rev
Log:
Rewrote the spectrum.error_analysis() user function docstring.
This is still missing 3 sections for error analysis with the volume
integration methods.
Modified:
branches/spectral_errors/prompt/spectrum.py
Modified: branches/spectral_errors/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/spectrum.py?rev=7896&r1=7895&r2=7896&view=diff
==============================================================================
--- branches/spectral_errors/prompt/spectrum.py (original)
+++ branches/spectral_errors/prompt/spectrum.py Tue Oct 21 18:34:31 2008
@@ -88,13 +88,54 @@
def error_analysis(self):
- """Function for calculating the average intensity and standard
deviation of all spectra.
-
-
- Errors of individual spin at a single time point
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- The variance for a single spin at a single time point is calculated
by the formula:
+ """Function for performing an error analysis for peak intensities.
+
+ Description
+ ~~~~~~~~~~~
+
+ This user function must only be called after all peak intensities
have been loaded and all
+ other necessary spectral information set. This includes the
baseplane RMSD and the number
+ of points used in volume integration, both of which are only used if
spectra have not been
+ replicated.
+
+ Six different types of error analysis are supported depending on
whether peak heights or
+ volumes are supplied, whether noise is determined from replicated
spectra or the RMSD of the
+ baseplane noise, and whether all spectra or only a subset have been
duplicated. These are:
+
+
____________________________________________________________________________________________
+ | | |
|
+ | Int type | Noise source | Error scope
|
+
|__________|________________________________________|______________________________________|
+ | | |
|
+ | Heights | RMSD baseplane | One sigma per
peak per spectrum |
+ | | |
|
+ | Heights | Partial duplicate + variance averaging | One sigma for
all peaks, all spectra |
+ | | |
|
+ | Heights | All replicated + variance averaging | One sigma per
replicated spectra set |
+ | | |
|
+ | Volumes | RMSD baseplane | One sigma per
peak per spectrum |
+ | | |
|
+ | Volumes | Partial duplicate + variance averaging | One sigma for
all peaks, all spectra |
+ | | |
|
+ | Volumes | All replicated + variance averaging | One sigma per
replicated spectra set |
+
|__________|________________________________________|______________________________________|
+
+
+ Peak heights with baseplane noise RMSD
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ When none of the spectra have been replicated, then the peak height
errors are calculated
+ using the RMSD of the baseplane noise, the value of which is set by
the
+ spectrum.baseplane_rmsd() user function. This results in a
different error per peak per
+ spectrum. The standard deviation error measure for the peak height,
sigma_I, is set to the
+ RMSD value.
+
+
+ Peak heights with partially replicated spectra
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ When spectra are replicated, the variance for a single spin at a
single replicated spectra
+ set is calculated by the formula
-----
@@ -102,33 +143,32 @@
-----
- where sigma^2 is the variance, sigma is the standard deviation, n is
the total number of
- collected spectra for the time point and i is the corresponding
index, Ii is the peak
- intensity for spectrum i, Iav is the mean over all spectra, ie the
sum of all peak
- intensities divided by n.
-
-
- Averaging of the errors
- ~~~~~~~~~~~~~~~~~~~~~~~
-
- As the value of n in the above equation is always very low, normally
only a couple of
- spectra are collected per time point, the variance of all spins is
averaged for a single
- time point. Although this results in all spins having the same
error, the accuracy of the
- error estimate is significantly improved.
-
-
- Errors across multiple time points
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ where sigma^2 is the variance, sigma is the standard deviation, n is
the size of the
+ replicated spectra set with i being the corresponding index, Ii is
the peak intensity for
+ spectrum i, and Iav is the mean over all spectra i.e. the sum of all
peak intensities
+ divided by n.
+
+ As the value of n in the above equation is always very low since
normally only a couple of
+ spectra are collected per replicated spectra set, the variance of
all spins is averaged for
+ a single replicated spectra set. Although this results in all spins
having the same error,
+ the accuracy of the error estimate is significantly improved.
+
+ If there are in addition to the replicated spectra loaded peak
intensities which only
+ consist of a single spectrum, i.e. not all spectra are replicated,
then the variances of
+ replicated replicated spectra sets will be averaged. This will be
used for the entire
+ experiment so that there will be only a single error value for all
spins and for all
+ spectra.
+
+
+ Peak heights with all spectra replicated
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If all spectra are collected in duplicate (triplicate or higher
number of spectra are
- supported), the each time point will have its own error estimate.
However, if there are
- time points in the series which only consist of a single spectrum,
then the variances of
- replicated time points will be averaged. Hence, for the entire
experiment there will be a
- single error value for all spins and for all time points.
-
- A better approach rather than averaging across all time points would
be to use a form of
- interpolation as the errors across time points generally decreases
for longer time periods.
- This is currently not implemented.
+ supported), the each replicated spectra set will have its own error
estimate. The error
+ for a single peak is calculated as when partially replicated spectra
are collected, and
+ these are again averaged to give a single error per replicated
spectra set. However as all
+ replicated spectra sets will have their own error estimate, variance
averaging across all
+ spectra sets will not be performed.
"""
r7896 - /branches/spectral_errors/prompt/spectrum.py