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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 - spots
SYNOPSIS
spots
[-bdquv] [-aval ... ] [fmmin] [fmmax] [ioscut]
DESCRIPTION
"spots" is the functionality within X-GEN that is used to locate and find
the three-dimensional centroids of a set of bright spots in a series of
detector images. At the same time it generates twelve three-dimensional
model profiles. Each of the models corresponds to a particular region of
the detector face, viz. three regions across the top of the image, six
across the middle, and three along the top. spots also, if necessary,
creates the list of pixels on the detector face that are active, i.e.
pixels where reflections can have their intensities measured. This
capacity renders the old "border" functionality within X-GEN unnecessary.
- -b
-
If this Boolean is on, pixels outside the active area of the
detector (as determined in the *border* functionality) will be
excluded from the consideration for the list of bright spots.
- -d
-
Skip the border determination even if the AMASK file (the output of
the operation of determining the border) is missing. Ordinarily this
border determination will be performed if the AMASK file is absent.
- -q
-
If this Boolean is on, a modest amount of additional diagnostics
beyond the default will be written to the XLOG log file and stdout.
- -u
-
Perform the border determination even if the AMASK file
already exists and is readable.
- -v
-
If this Boolean is on, an enormous amount of additional diagnostics
beyond the default will be written to the XLOG log file and stdout.
- -a<val>
-
Search for spots over the first <val> images in the FRAMES
-
index. Thus if the first image called out in the index is image
number 40, and we invoke spots with spots -a20, then images 40
through 59 will be examined. See below for the discussion of the
default image range in the event that this flag is not specified.
- -c<val>
-
If fewer than <val> reflections have been found in the
-
first few images in the data run, keep searching through
additional images until either <val> reflections have been found
or we run out of images. Thus if there are 40 images in a dataset,
and we specify spots -a20 -c500, then if we do not find 500
reflections in the first 20 images, the program will continue to
search through additional images to run the total up to 500.
- -e<val>
-
If this value is provided, it specifies the number of
-
analog-to-digital units per photon (adu/photon, or
"counts per photon") used in calculating the standard deviations.
If no value is provided, a standard value appropriate to the
instrument type is used:
Detector Type adu/photon Detector Type adu/photon
------------- ---------- ---------------------- ----------
FAST 4 Argonne CCD (post '92) 4
Argonne CCD (pre '92) 5 MAR IP (any size) 3
Siemens CCD 4 Mar CCD 1.4
ALL OTHERS 1
- -f<val>
-
This specifies the expected half-width of the spots to be
-
found in the run. This value must be between 1 and 5 inclusive. If
you expect spots to occupy at most 7 frames, the halfwidth is
(7-1)/2=3, and this value can be specified as 3. Default value: 3,
unless the scale factor between between frames and pixels is
greater than 16, in which case the default value is 2.
- -g<val>
-
This specifies a value used in determining the active area
-
of the detector in the event that that is required. The
active-area algorithm works by determining the average count,
<Ci>, on the pixels i on the detector face after the strong
reflections have been flattened out. Then any pixel i for which
the count Ci is less than a certain fraction of <Ci> will be
considered to be an inactive pixel. The fraction in question is
specified with <val>. The default value of this parameter is
detector-dependent, as follows:
Detector type Default g Detector type Default g
--------------------- ---- --------------- ----
Xentronics 0.36 pre-'92 Argonne 0.37
FAST, post'92 ANL 0.40 All IPs 0.37
ADSC Q4 0.41 ADSC Q210, Q315 0.42
Mar CCD, Brandeis CCD 0.38
- -h<val>
-
This value specifies the minimum number of pixels above
-
the local cutoff that must be present in order for a spot to be
counted. Thus if this value is 6 and there are only 5 pixels above
the local cutoff in a given spot, then the spot won't be counted.
Default value: 0.
- -i<val>
-
This defines a minimum total intensity below which a spot will
-
not be output to the CENTROIDS file. Thus if you only wish to consider
spots with I > 5000, specify 5000 here. Note that these intensities
have not been Lorentz/polarization corrected here. Default: 1.
- -k<val>
-
This defines the scale factor relating distances between
-
points in scanning angle to distances between points on the detector
face. If you do not specify a value here, the program will determine
it from the relation between the crystal-to-detector distance, the
detector's geometry, and the stepsize; if not all
those data are available it sets the value to sqrt(10).
- -l<val>
-
This value specifies the fraction of the total number of
-
pixels in a reflection's three-dimensional profile that can lie
more than one standard deviation below the mean background value.
Thus if the mean background count around a spot is 50+/5, then any
pixel with fewer than 45 counts is considered to be below B -
sigma. If there are 400 pixels in the reflection and the fraction
specified is 0.3, then no more than 120 pixels can have fewer than
45 counts in them. The default value for this parameter depends on
the detector type: it is 0.3 for Xentronics, SDMS, and FAST
systems, 0.75 for Bruker CCDs, and 0.5 for all other detectors.
- -m<val>
-
This value specifies how many pixels a centroid is allowed
-
to move between the rough calculation done in the first pass through
the spots and the more precise calculation done in the second pass.
The movement in frames is taken to be half this value. Thus
specifying this value as 3 allows 3 pixels and 1.5 frames of
movement between the centroid calculations. Default value: 2.
- -n<val>
-
This imposes an extra requirement on the profiles, namely
-
that at least one element besides the brightest be at least this
fraction of of the brightest element. Thus specifying 0.1 here
means that the second-largest element must be at least 10% as
large as the largest element. Default value: 0.
- -o<val>
-
This specifies the minimum value of Intensity /
-
sigma(background) for a reflection to be considered for inclusion
in the CENTROIDS output list. This value can be specified either
with this switch or as the third non-switch parameter (below).
The default value is described below under "sigmacut".
- -p<val>
-
This specifies the minimum fraction of the total intensity
-
that must be contained in the center-most three frames of the
profile. Thus if this value is 0.65, we require that 65% of the
total intensity be contained in the center three frames. The
default value of this parameter is 0.6 for SDMS, Xentronics, and
FAST detectors, and 0.65 for all others.
- -s<val>
-
This specifies the fraction of the dark current image that
-
will be subtracted from the ordinary images in analyzing the
latter to find centroids and model profiles. Thus if this value is
taken as 1., we will examine (data frames - 1.0 * dark-current
image). Default value: 0.
- -t<val>
-
This specifies the "shrinkval" during the determination
-
of the active area. This is the number of pixels that the
boundary of the active area should be moved inward from the
boundary calculated directly from the background calculation
(see the -g description, above). The default value for this parameter
depends on the detector dimensions:
Maximum detector default Maximum detector default
dimension shrinkval detector dimension shrinkval
---------------- --------- ------------------ ----------
w <= 512 6 512 < w <= 1024 9
1024 < w <= 2048 16 2048 < w 20
- -w<val>
-
This specifies the expected radius of the spots in pixels.
-
This influences how big an area the spot is checked over, and it
influences how close the spacing between neighbors is allowed to
be. The default value of this parameter depends on the detector
dimensions: it is 4.5 for small detectors, 5.7 for medium-sized
detectors, and 6 for large detectors.
- -x<val>
-
This specifies the horizontal position of the direct beam
-
in X. It governs the choice of where the boundaries between model
profiles will be placed. By default, /spots/ determines this value
from the header of one of the frames, so you only need to specify
a value when you need to overrule what the header says.
- <startfm>
-
specifies the first frame in the range to be examined in
-
obtaining a set of reference reflections. Defaults for this are
discussed below.
- <endfm>
-
specifies the last frame in the range to be examined in
-
obtaining a set of reference reflections. Defaults for this are
discussed below.
- <sigmacut>
-
defines the multiple of sigma(local background) that
-
will be used as the cutoff for the background-corrected counts in
each region. Thus if the local background is 15 and sigma(local
background count) is 5, and this parameter is set to 20, then a
spot will be considered as bright enough to use if it has several
pixels with more than 100 counts in them. The default value is 20
for SDMS, Xentronics, or FAST detectors, and 80 for other types.
The frame range used:
-
If the user does not specify either a frame range, either with
the -a switch or with the first-frame, last-frame parameters,
the program examines the first n images. The value of n is
dependent on the detector type, as follows:
- Detector type
-
# of images Detector type # of images
- SDMS, Xentronics, FAST
-
65 Ancient Argonne CCD 40
- Cornell IP
-
5 Bruker CCD 8
- Other CCDs
-
6 Other IPs 6
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
-
- SYNOPSIS
-
- DESCRIPTION
-
- REPORTING BUGS
-
- COPYRIGHT
-
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Time: 02:08:09 GMT, October 03, 2005