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Man page of X-GEN
X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
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NAME
X-GEN - reject
DESCRIPTION
"reject" flags certain observations found in a merged set of data as
being outliers. The outliers are noted on the basis of disagreement with
the mean for the reflection involved according to
-
Q = |Iij - gij * <Ij >| / sij ,
where Iij is the intensity of the ith observation of the jth
reflection, gij is the scaling-function value associated with it,
<Ij> is the mean intensity for all observations of reflection j,
and sij is the standard deviation associated with Iij .
Thus if Q is greater than a certain cutoff, an observation will be
flagged for deletion. The cutoff value can be determined several ways,
as described below.
- -a
-
Set up "Curses" menus for looking at difficult cases. This
used to be the default, and no longer is.
- -b
-
This specifies a "batch mode", in which all decisions about
eliminating outliers is performed by the software rather than
leaving any of the decisions up to the user. This is now the
default, but didn't used to be.
- -c
-
This specifies creation of a detailed log file with
environment variable name CHECKREFL into which a
reasonably-formatted list of all the observations of any suspect
reflection are written, together with an accounting of how the
program handles that reflection.
- -g
-
For flagged reflections with exactly two observations,
keep the observation that has the smaller sigma value.
- -i
-
For flagged reflections with exactly two observations,
keep both observations.
- -k
-
For flagged reflections with exactly two observations,
delete both observations.
- -l
-
For flagged reflections with exactly two observations,
keep the observation with the larger intensity.
- -m
-
Inflate the sigmas of all observations by a machine-error
term. This machine-error term is applied only during the
outlier-rejection effort. The extra component of the variance is
set to (0.025 * I) squared.
- -n
-
Separate Bijvoet-related reflections for purposes of
computing mean intensities and calculating deviations from those
means. Thus with this flag on the (3,6,4) reflection will be
treated as independent of the (-3,-6,-4).
- -o
-
Merge Bijvoet-related reflections for purposes of computing
mean intensities and calculating deviations from those means. Thus
with this flag on the (3,6,4) reflection will be treated as
equivalent to the (-3,-6,-4). This is the default behavior of the
program.
- -p
-
If this Boolean is on, observations that had been flagged
for deletion in a previous run of "reject" will remain flagged
this time around. Otherwise these observations will be restored
into consideration.
- -s
-
For flagged reflections with exactly two observations,
when the user is running in Curses (-a) mode, the program will
display both observations and let the user decide how to handle
the reflection.
- -u
-
Do not inflate the observation sigmas with a machine error.
This is the converse of the -m flag.
- -v
-
If this Boolean is on, a moderate amount of additional
diagnostics beyond the default will be written to the XLOG log file
and stdout.
- -f<val>
-
This specifies the approximate fraction of the data that
-
are to be flagged for deletion. Thus if 0.03 is specified here,
then roughly 3% of the observations will be flagged for deletion.
The fraction is always approximate because it is used to establish
the cutoff |I-<I>|/sigma criterion, and the actual number deleted
is obtained from a different algorithm based on that cutoff.
Default: this technique is only exercised if "-f" is specified
with a legal value of <val> (i.e. a value between 0 and 1).
- -q<val>
-
This value specifies the cutoff deviation in (I - <I>) /
-
sigma above which an observation will be considered for deletion.
If no value is specified the program computes a cutoff as a
slowly-increasing function of the number of observations in the
dataset; if the dataset contains 10000 observations the default
cutoff is 3.92; with 200000 it is 4.58.
- -r < h k l >
-
If the program winds up flagging a very large
-
number of observations for deletion, the buffer into which those
observations are put may fill up. Under those circumstances the
program will exit after it has handled as many observations as it
can and will report the last (h,k,l) value that it dealt with. A
subsequent run of reject in which the user specifies that (h,k,l)
value will pick up the remaining data:
-
reject -q5.4 -b -r 8 11 13
-
will begin the process at the (8,11,13) reflection. This feature
has not been extensively tested in recent years and may no longer work.
- -t<val>
-
This value specifies the target Rmerge value (expressed as
-
a fraction, not a percentage) that the algorithm will attempt to
achieve. If the value 0.05 is specified, then the program will set
the cutoff |I-<I>|/sigma criterion such that enough deletions are
done to achieve an Rmerge of 0.05 (5%). As the car manufacturers
would say, your mileage may vary. Default: this technique is only
exercised if "-t" is specified with a legal value of <val> (i.e. a
value between 0 and 1).
REPORTING BUGS
Report bugs to Andy Howard at howard@iit.edu or 312-567-5881.
COPYRIGHT
Copyright © 2002, Illinois Institute of Technology.
See the file 'LICENSE' for information on usage and redistribution
of this file, and for a DISCLAIMER OF ALL WARRANTIES
Index
- NAME
-
- DESCRIPTION
-
- REPORTING BUGS
-
- COPYRIGHT
-
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