Content-type: text/html
Man page of X-GEN
X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
Index
Return to Main Contents
NAME
X-GEN - imageform
SYNOPSIS
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 beforehand,
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.
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 format.
- -s
-
Output images in Bruker (FRAMBO / SMART) 16-bits-per-pixel format.
- -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 converted 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 filename will be free of appendages.
- -q
-
Suppress diagnostic outputs to stdout and to the
log file almost completely.
- -v
-
Increase the amount of diagnostic output directed to stdout
and the log file from one line per file to about six lines per file.
- -x{val}
-
Re-dimension the detector's width from whatever the
input was to {val}. This option is ignored unless spatial
corrections are being applied, i.e.
imageform -k -x1200 -y1200 does the same thing as imageform -k.
- -y{val}
-
Re-dimension 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 log file.
- USPLINE
-
Input pixel-to-centimeter conversion file.
- FRAMES
-
Index of convertible images.
EXAMPLES
- setenv USPLINE mosaic.uca; imformat
-
Convert all the images in a
directory to MAR image-plate
format
- setenv USPLINE mosaic.uca; imformat -r
-
Convert all the images in a
directory to R-Axis format
- imformat -k ikw.0043 ikw.0372 gru._br
-
Convert images ikw.0043,
ikw.0372, and gru._br into MAR
format, without correcting
for spatial distortion
- imformat -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 variable 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 © 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
-
This document was created by
man2html,
using the manual pages.
Time: 02:08:09 GMT, October 03, 2005