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marreference- Subtracts a reference image from a mar image
marreference
[ -h (--help) ] [ -a (--auto) ] [ -f (--force) ] [ -l (--list) ] [ --rec(ursive) ] [
-v (--verbose) ] [ +a (--add) OFFSET ] [ -d (--directory) DIR ] [ -n (--name) NAME
] [ -r (--reference) FILE ] [ -o FILE ] [ -raw ] file1 file2 ...
marreference
subtracts a reference image from a diffraction image. Typical usage is to
correct for special diffraction effects. The reference image should typically
taken with the same experimental conditions (exposure time, beam intensity)
as normal images, but without diffracting samples. After subtraction, the
net difference of the diffracting material will remain in the resulting
image. When subtracting the reference image from the diffraction image,
at least some pixel values may become negative. The program will truncate
all negative values to 0. In order to ensure that all pixel values are positive
an arbitrary OFFSET value may added to all pixels after subtraction.
With option -a (--auto) the OFFSET value is adjusted automatically by determining
the largest negative difference and adding this to all pixels. Since every
image of a series of images may then receive a different OFFSET value,
the automatic procedure may not be desirable to use but rather an arbitrary
but fixed value that leaves all pixels > 0, e.g. a value of 100. The used offset
values will be written into the mar345 image header of the resulting image
and can be found in parameters ADD_A and ADD_B on keyword ADC. Note, that
this information is lost when choosing RAW as image output format.
The
program can apply a given reference file to images of the same pixelsize
but a smaller scan radius. E.g. a reference file taken from the entire plate
(345 mm diameter) and pixelsize 0.15 mm in scanmode 2300 can be applied
to all other scanmodes of pixelsize 0.15 mm, i.e. scanmodes 2000, 1600 and
1200, but not to images collected with a pixelsize of 0.10 mm (scanmodes
3450, 3000, 2400, 1800). Likewise, it is not possible to apply a reference
image collected in mode 1200 to mode 2300! Also, when processing a series
of images using wildcards, the program will adapt the size of the reference
image to the size of the input images in memory. Once the size is reduced,
the program will not be able to automatically augment the memory size. To
process those images, the program will have to be restarted.
The program
accepts wildcards for input images.
- -h, --help
- Provides a summary of
the options.
- -a, --auto
- Automatically determines the largest negative difference
in the resulting image and add this value to all pixels, so all pixels
become > 0.
- +a, --add OFFSET
- After subtraction, add OFFSET to all pixel values
in order to avoid too many truncated negative values.
- -d DIR
- Place output
images in directory DIR. Default is: same directory as input images.
- -f, --force
- Forces image output, even if a file with the same name already exists. The
default is to skip output.
- -l, --list
- Lists the selected files (directories)
only, no output.
- -n, --name NAME
- Root name of output images. Default is: keep
existing root name.
- -o FILE
- Specify name of single output file. Careful when
converting multiple images: they will all have the same name!
- -r, --ref FILE
- Specify name of reference file. This image will be used for subtraction
of all given input images.
- --raw
- Instead of producing a mar345 image output
file, a raw 16-bit array of data is written out without header. This is for
compatibility with other data processing programs.
- --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.
- -v, --verbose
- Writes
more information to stdout.
- file1 file2 ...
- Image files to convert. Wildcards
allowed.
- marreference +a 100 -r ref_001.mar2300 -n out in_???.mar2300
- Subtracts contents of ref_001.mar2300 from all files in_???.mar2300 and produces
output files named out_???.mar2300, where ??? is any 3-digit number. After
subtraction, 100 is added to all pixel values.
mar345_formats
Claudio Klein, marXperts GmbH, Norderstedt, Germany
© Copyright
2016 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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