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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 - calibrate
SYNOPSIS
calibrate
[-bceghijnopvz] [-aval...] [xcen] [ycen]
DESCRIPTION
"calibrate" creates the mapping from pixels to centimeters and vice
versa. This is ordinarily done by reading in a detector image known as a
"brass plate image", processing its contents, and writing out a binary
file containing both a forward mapping and an inverse mapping. For
detectors that are nearly linear in their geometric response (either
inherently or because the images managed by X-GEN have already had their
nonlinearities mapped away), "calibrate" provides a mechanism for
defining the linear map through the -l and -j options.
OPTIONS
- -b
-
Pixels outside the active area of the detector (as
determined in the "border" or "spots" functionalities) will be
excluded from the list of brass-plate spots used in the mapping
from pixels to centimeters.
- -c
-
Read a list of brass-plate centroids from an ASCII file
with environment variable CALCENTROIDS and use those
instead of finding the centroids in a brass-plate image.
- -e
-
Do _not_ check to see whether a brass-plate fiducial spot
has been excluded from the active-pixel list before using it.
Thus it is the complement of the -b flag.
- -g
-
Force the program to use an actual brass-plate image to do
its job rather than using a linear mapping.
- -h
-
Expect the brass-plate centroids to be arranged in a
hexagonal pattern rather than a rectangular pattern.
- -i
-
Expect that the list of fiducial points found in the
CALCENTROIDS file will be indexed and use those indexings in
setting up the calibration.
- -j
-
Dispense with examining a fiducial image altogether and
simply define a linear mapping from pixels to centimeters using
the information contained in the image header to define the
spacing in cm between fictitious columns and the number of lines
across the detector face. Thus it does a similar operation as
compared to the -l option except that the user does not need to
specify the number of columns or the raster size.
- -n
-
Do not extrapolate its mapping outside the points that are
actually observed until AFTER it has performed the first
inversion of the mapping.
- -o
-
Do not compute a pixel-to-cm mapping at all; instead,
write out an ASCII list of the fiducial-point centroids to
the file with environment-variable name CALCENTROIDS. This file
can then be edited and re-inserted into another run of "calibrate"
using the "read calibration centroids in" Boolean.
- -p
-
Extrapolate out beyond the observed points before
performing the first inversion of the mapping.
This is therefore the converse of the -n option.
- -v
-
Write out large numbers of diagnostics to the XLOG log file
and to stdout during the "calibrate" operation.
- -z
-
Do _not_ write large numbers of diagnostics to the log file.
This is the converse of the -v flag.
- -a<val>
-
This defines the multiple of sigma(local background)
-
that will be used as the cutoff for counts in each region. Thus if
sigma(local background count) in a region is 8 and this switch is
set to 5, then a fiducial spot will be considered as bright enough
to use if it has several pixels with more than 40 counts in them.
Default value: 4 * sqrt(mean count), unless the calibration image
is from a FAST detector, for which it is 0.5 * sqrt(mean count).
- -f<val>
-
This value defines an overall cutoff intensity below which
-
a potential fiducial-point spot won't be considered for inclusion,
independent of the local sigma cutoffs. Thus a value of 8 for this
switch will require that all fiducial spots have several pixels
with at least 8 counts in them, even if the cutoff defined by
sigma(local background) would allow weaker spots. Default value: 0.
- -l<val>
-
If this value is nonzero, "calibrate" will dispense with
-
examining a fiducial image altogether and simply define a linear
mapping from pixels to centimeters in which the value given here
defines the number of COLUMNS of imaginary fiducial spots that
will be created in the analysis. The number of rows will be number
of columns times the ratio of the detector height to the detector
width. Thus on a square detector with this parameter set to 41, we
will create 41 rows and 41 columns of imaginary spots. Default
value: irrelevant if "-l" isn't specified at all; if -l is
specified without an associated numerical value, it is set to 19.
- -m<val>
-
This value specifies the minimum number of pixels above
-
the local cutoff that must be present in order for a fiducial 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: 5.
- -s<val>
-
This specifies the fraction of the dark current image that
-
will be subtracted from the brass-plate image in analyzing the
latter to find fiducial spots. Thus if this value is taken as 1.,
we will examine (fiducial image - 1.0 * dark-current image).
Default value: 0.
- -d<val>
-
This forces the program to treat the Y dimension of the
-
detector to be <val>. This is useful if a subset of the actual
detector face is to be analyzed, so that the dimension given in
the header is inapplicable. Default value: actual Y dimension of
the detector.
- -w<val>
-
This forces the program to treat the X dimension of the
-
detector to be <val>. This is useful if a subset of the actual
detector face is to be analyzed, so that the dimension given in
the header is inapplicable. Default value: actual X dimension of
the detector.
- -x<val>
-
This specifies the spacing in centimeters between COLUMNS
-
of fiducial points in the detector image. Thus if the columns of
holes are 0.254 cm apart on the brass plate, we specify this value
as 0.254. Default value: 0.508.
- -y<val>
-
This specifies the spacing in centimeters between ROWS of
-
fiducial points in the detector image. Thus if the rows of holes
are 0.254 cm apart on the brass plate, we specify this value as
0.254. In the case of an hexagonal grid, this should be specified
as HALF the vertical spacing between points within the same
column. Default value: 0.508.
- xcen, ycen
-
specify the pixel position in (X,Y) of the direct beam when
-
the detector's two-theta value is zero. (X,Y)=(0,0) in the upper
left-hand corner of the detector, with X increasing to the right and Y
increasing down; the view is from the detector toward the crystal.
Default values: half the detector width and height.
EXAMPLES
- calibrate -j
-
Determine the active area of a detector using a
-
linear calibration (constant pixel-to-centimeter values
across the face) at a beam-center position equal to the
middle of the detector:
- calibrate -x0.254 -y0.254 508 513
-
Do a full calibration based on a
-
brass-plate image with the beam center at [508,513], where the
spacing between holes in the brass plate set at 0.254 cm:
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
-
- OPTIONS
-
- EXAMPLES
-
- REPORTING BUGS
-
- COPYRIGHT
-
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Time: 02:08:09 GMT, October 03, 2005