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marcvt- format conversion for images collected on marresearch Image
Plate Detectors and marCCD detectors.
marcvt [ -h ] [ --help ] [
-f ] [ --force ] [ -l ] [ --list ] [ -r ] [ --recursive ] [ -s ] [ --swap ] [ -d ] [
--delete ] [ -v ] [ --verbose ] [ --flip[v] ] [ -j N ] [ --jump N ] [ --add N ] [
-crop X*Y[+x+y] ] [ -cut CUT ] [ -reduce N ] [ --rotate N ] [ --scale N ]
[ -type TYPE ] [ -x NX ] [ --xaxis NX ] [ -y NY ] [ --yaxis NY ] [ -o directory
] -out FORMAT or [ -mar345 ] [ -pck ] [ -image ] [ -cbf ] [ -cif ] [ -raw32 ]
[ -raw16 ] [ -raw8 ] [ -tiff ] [ -png ] [ -jpg ] [ -ascii ] file(s)
Additional TIFF/PNG/JPG file output options: -rainbow -blue -min MIN -max
MAX -colors N
marcvt converts image formats from marresearch/marXperts
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.
- --add
N
- Add a value of N to all pixels in file.
- -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.
- --crop X*Y[+x+y]
- Crop input image to X*Y pixels with offsets
x and y in horizontal and vertical direction, respectively.
- -cut N
- Cutoff
marCCD images to N*N pixels (e.g. 2000)
- -d, --delete
- Deletes input image after
successful conversion. The default is to keep the input file.
- -f, --force
- Forces
image output, even if a file with the same name already exists. The default
is to skip output.
- --flip[v]
- Flip image horizontally (vertically) on output
- -h, --help
- Provides a summary of the options.
- -j, --jump N
- Skip first N bytes
of i/p-file
- -l, --list
- Lists the selected files (directories) only, no output.
- -o DIRECTORY
- Output images will go into directory DIRECTORY. By default,
they will be in the same directory as the input images.
- -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", "png", and "ascii".
- -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.
- -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.
- -reduce N
- Reduce image size by a factor
of N (integer number), e.g. 5. This is helpful when making thumbnail images
in png/jpg/tiff formats out of diffraction images.
- --rotate N
- Rotate image
counter-/clockwise by N deg.
- -s, --swap
- Force swapping of bytes in input file
- --scale N
- Apply multiplication factor of N to all pixels in file.
- -tiff, -png
and -jpg
- When producing TIFF/PNG/JPG 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.
- -type TYPE
- Force input of type TYPE: see -out
- -v, --verbose
- Writes more information to stdout.
- -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
- 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, marXperts GmbH,
Norderstedt, Germany
© Copyright 2000-2015 marXperts GmbH, Norderstedt,
Germany
marXperts GmbH | Phone: +49 - (40) - 529 884-0 |
Werkstr. 3 | FAX:
+49 - (40) - 529 884-20 |
D-22844 Norderstedt - GERMANY | info@marXperts.com |
| www.marXperts.com |
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