Table of Contents
marcvt, tkmarcvt- format conversion for images collected on marresearch
Image Plate Detectors and marCCD detectors. tkmarcvt is the corresponding
GUI based on the Tcl/Tk package.
marcvt [ -h ] [ --help ] [ -f ] [
--force ] [ -l ] [ --list ] [ -r ] [ --recursive ] [ -s ] [ --swap ] [ -d ] [ --delete
] [ -v ] [ --verbose ] [ -j N ] [ --jump N ] [ -cut CUT ] [ -type TYPE ] [ -x
NX ] [ --xaxis NX ] [ -y NY ] [ --yaxis NY ] [ -o directory ] -out FORMAT or
[ -mar345 ] [ -pck ] [ -image ] [ -cbf ] [ -cif ] [ -raw32 ] [ -raw16 ] [ -raw8
] [ -tiff ] [ -ascii ] file(s)
Additional TIFF file output options: -rainbow -blue -min MIN -max MAX -colors
N
marcvt converts image formats from mar research Imaging
Plate Detector Systems. Supported input formats are: "image" (300 mm uncompressed
images), "pck" (300 mm compressed images), "mar345" (345 mm compressed
images) and images created by the marCCD CCD-detector. marcvt >= 4.0 also supports
CBF/imgCIF formatted images that have been produced by mar programs (marcvt
is NOT intended to be a general utility for handling CBF/imgCIF files).
It is also possible to save binary images into plain ASCII-files. Other supported
formats for output are images containing plain arrays with 8-bit, 16-bit
or 32-bit integers, without headers or trailers. These raw binary data can
easily be read by any other image processing program.
Note, that it is
not possible to obtain a complete image header when converting mar300
formats into the mar345 format, since the new mar345 header store information
that is not used by the mar300 headers.
- -h, --help
- Provides a summary
of the options.
- -l, --list
- Lists the selected files (directories) only, no
output.
- -f, --force
- Forces image output, even if a file with the same name
already exists. The default is to skip output.
- -d, --delete
- Deletes input image
after successful conversion. The default is to keep the input file.
- -r, --recursive
- If the file argument (see below) is a directory, all images in this directory
and its subdirectories will be converted. This is a very fast way of converting
large numbers of images scattered in many directories.
- -s, --swap
- Force swapping
of bytes in input file
- -j, --jump N
- Skip first N bytes of i/p-file
- -x, --xaxis
NX
- No. of elements of fast varying axis in i/p-file
- -y, --yaxis NY
- No. of elements
of slow varying axis in i/p-file
- -type TYPE
- Force input of type TYPE: see
-out
- -cut N
- Cutoff marCCD images to N*N pixels (e.g. 2000)
- -v, --verbose
- Writes
more information to stdout.
- -out FORMAT
- Input images are converted into format
FORMAT. This option is compulsory! Allowed formats are: "mar345", "pck",
"image", "cbf", "cif", "raw32", "raw16", "raw8", "tiff" and "ascii".
- -cbf,
-cif
- Formats "cbf" an "cif" are the new "crystallographic binary file" conventions
created by the CBF/imgCIF committee. "CBF" and "imgCIF" differ by the way
the binary data are encoded. "CBF" uses a binary encoding while "imgCIF"
is ASCII-encoded. When converting into "cbf" and "cif" files, data compression
is always used. Data are stored as 32-bit integers. The details of the formats
are described in http:////ndbserver.rutgers.edu/mmcif/cbf/
- -raw32, -raw16
and -raw8
- Format "raw32" is an array of 32-bit integers, "raw16" only 16-bit
and "raw8" only 8-bit. Note, that values > 16-bit will be truncated to 65535
in "raw16" format. For "raw8", all intensity values will be divided by 256.
Values > 16-bit will also be truncated. The "raw32"-format, however, does not
truncate the data. Saturations will be marked as 999999.
- -tiff
- When producing
TIFF files, data will be modified to give an image with reasonable colors.
By default, the program calculates a minimum and maximum threshold from
a pixel value histogram. Values < minimum will get color white, values > maximum
will get color black. 256 colors shades will be distributed in between the
min. and max. The colorscheme can be altered to give a rainbow spectrum (-rainbow)
or to use shades of blue (-blue) instead of grey. The number of colors may
be altered with option -colors N where N defaults to 256. The min. and max.
threshold may be set explicitely with option -min MIN and -max MAX.
- -o DIRECTORY
- Output images will go into directory DIRECTORY. By default, they will be
in the same directory as the input images.
- files...
- Wild cards are allowed.
If no input format is given by option "-in", the corresponding file name
extension is used to determine the input format.
- marcvt -image
x_001.mar1200
- Converts x_001.mar1200 into x_001.image
- marcvt -o /data -pck -r
/usr/people/mar/data
- Converts all images found in /usr/people/mar/data
and subdirecties into pck format and writes output into directory /data.
- marcvt -cbf *.mar1200
- Converts all images with extension .mar1200 in the current
directory into the corresponding "CBF"-style file. The extension will be
.cbf1200.
mar345_formats, mar300_formats, marpack, marunpack
Claudio
Klein, X-ray Research G.m.b.H., Hamburg, Germany
© Copyright 1997-2000
X-ray Research G.m.b.H., Hamburg, Germany
X-ray Research G.m.b.H. | Phone:
+49 - (40) - 529 884-0 |
Segeberger Chaussee 34 | FAX: +49 - (40) - 529 884-20 |
D-22850
Norderstedt - GERMANY | E-mail: info@marresearch.com |
| http://www.marrresearch.com
|
Table of Contents