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

X-GEN

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

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