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NAME
X-GEN - imageform
SYNOPSIS
[xgen] imageform [-pmbsrkdqv] [-x{val}] [-y{val}] [filenam]
DESCRIPTION
"imageform" reads in crystallographic detector images created in any
format recognized by the X-GEN package and writes them out in a user-
specified format.
It therefore can be used to convert from one image format to
another.
If the user specifies an X-GEN-style USPLINE file via an environment
variable (see below), it will correct the spatial distortions in the
images before output.
The formats that it knows how to read are:
* Siemens/Nicolet/Xentronics multiwire images
(both the old PCS formats and the FRAMBO formats)
* San Diego Multiwire Systems images
* FAST images
* Bruker/Siemens 1k CCD images
* Bruker/Siemens 2k CCD images
* Bruker/Siemens Mosaic CCD images
* Mar image plate images
* R-Axis image plate images
* MacScience image plate images (2xxx and 3xxx)
* Argonne CCD images (all known formats)
* Fuji raw image plate images
* Mar CCD detector images (all sizes)
Other formats may be added in the future. The formats that it knows
how to output are:
* Siemens/Nicolet/Xentronics multiwire image format
* Bruker/Siemens FRAMBO/SMART format
* Mar image plate format
* R-Axis image plate format
Thus the list of output formats is somewhat shorter than the list of
input formats.
If the user requires the image to be spatially corrected before-
hand,
a file with name or environment variable USPLINE must be present. This
file should be the X-GEN-generated file containing the mapping from
pixels to centimeters and vice versa. IMCA users employing this program
to convert Mosaic CCD images from the IMCA-CAT Bruker system into Mar
or R-Axis formats will receive a copy of the appropriate USPLINE file
along with the executable of the program. Thus if that file is called
mosaic.uca, then to run the program:
% setenv USPLINE ./mosaic.uca
% imageform [args...]
If the user _is_ spatially correcting the images, the program can re-
dimension the images; see below.
This is one of the few X-GEN applications that exists as a standalone
executable in addition to being available from within "xgen" itself.
OPTIONS
-p Output images in PCS format (an old Nicolet format).
-m Output images in Mar image-plate format. This is the default
output format.
-b Output images in Bruker (FRAMBO / SMART) 8-bits-per-pixel for-
mat.
-s Output images in Bruker (FRAMBO / SMART) 16-bits-per-pixel for-
mat.
-r Output images in R-Axis format.
-k Keep the spatial properties of the input image.
By default the spatial correction is applied before output; if the user
does not want the spatial correction applied, this option will suppress
the correction.
-d Do NOT delete the original image before writing out the con-
verted file. Instead, rename the old version by appending ",0"
to the end of the filename, unless <filename>,0 already exists;
in that case, append ",1" to the end. If <filename>,1 already
exists, use ",2", and so on, up through ",99". The output file-
name will be free of appendages.
-q Suppress diagnostic outputs to stdout and to the logfile almost
completely.
-y{val}
Redimension the detector's height from whatever the input was to
{val}. This option is ignored unless spatial corrections are
being applied, as described above.
Processed Files:
The program picks which files to process in any of three ways:
* If the user specifies one or more filenames in the command line,
it will process ONLY the files named.
* If the user does not specify any files in the command line, and
there exists a file with name or environment variable FRAMES,
then it is consulted to define which files to convert. All
images named in the FRAMES file will be converted. Each line in
the FRAMES file will look like
43/data0/ahoward/83071c/data/83071c.0043
i.e. the first five characters in the line are an index value for the
image and the remainder is a filename.
* If the user does not specify any files in the command line, and
the FRAMES file does not exist, then all images in the current
directory will be converted. A file is believed to be an image
if its file extension (the portion of the filename following the
last period) is entirely numeric, is "image", "osc", "stl",
"ipf", or "img", or is "_xy", where x and y are any two letters.
Thus 83071c.0043, george043.img, fred._br, and mydata0387.stl
will all be converted; 135735_235, 135735.stu, and
goody123.0x3will not. These _could_ be converted if they are
explicitly named in a separate run of the imageform program.
Other Files:
XLOG Diagnostic logfile.
USPLINE
Input pixel-to-centimeter conversion file.
FRAMES Index of convertable images.
EXAMPLES
setenv USPLINE mosaic.uca; imageform
Convert all the images in a directory to MAR image-plate format
setenv USPLINE mosaic.uca; imageform -r
Convert all the images in a directory to R-Axis format
imageform -k ikw.0043 ikw.0372 gru._br
Convert images ikw.0043, ikw.0372, and gru._br into MAR format,
without correcting for spatial distortion
imageform -kd ikw.0043 ikw.0372 gru._br
Convert images ikw.0043, ikw.0372, and gru._br into MAR format,
without correcting for spatial distortion, and preserving (not
deleting) the original images.
Diagnostics
Some diagnostics are written to a file with name or environment vari-
able XLOG. Similar diagnostics are written to the standard output.
The amount of information emitted can be increased or decreased with
the -v and -q command-line options, respectively.
Warnings
Specifying non-equal values for "-x" and "-y" options has not been
tested. That is, imageform -x1200 -y1200 is known to work, whereas
imageform -x1200 -y1500 might or might not work.
REPORTING BUGS
Report bugs to Andy Howard at howard@iit.edu or 312-567-5881.
COPYRIGHT
Copyright (C) 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
Version 5.5.5 October 2005 X-GEN(1)
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