Content-type: text/html Man page of X-GEN


Section: X-GEN Commands (1)
Updated: April 2005
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X-GEN - spots  


spots [-bdquv] [-aval ... ] [fmmin] [fmmax] [ioscut]  


"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.
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.
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.
If this Boolean is on, a modest amount of additional diagnostics beyond the default will be written to the XLOG log file and stdout.
Perform the border determination even if the AMASK file already exists and is readable.
If this Boolean is on, an enormous amount of additional diagnostics beyond the default will be written to the XLOG log file and stdout.
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.
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.
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
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.
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
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.
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.
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).
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.
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.
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.
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".
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.
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.
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
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.
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.
specifies the first frame in the range to be examined in
obtaining a set of reference reflections. Defaults for this are discussed below.
specifies the last frame in the range to be examined in
obtaining a set of reference reflections. Defaults for this are discussed below.
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


Report bugs to Andy Howard at or 312-567-5881.  


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Time: 02:08:09 GMT, October 03, 2005