table of contents
mia-2dsegshift(1) | General Commands Manual | mia-2dsegshift(1) |
NAME¶
mia-2dsegshift - Translate a segmentation by the given amount.
SYNOPSIS¶
mia-2dsegshift -i <in-file> -o <out-file> [options]
DESCRIPTION¶
mia-2dsegshift This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped.
OPTIONS¶
- -i --in-file=(input, required); io
- input segmentation set
For supported file types see PLUGINS:2dimage/io - -o --out-file=(required, output); io
- input segmentation set
For supported file types see PLUGINS:2dimage/io - -g --image-file=crop
- output image filename base
- -S --shift=[0,0]
- shift of segmentation
- -k --skip=2
- skip frames at the beginning
Help & Info¶
- -V --verbose=warning
- verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
- --copyright
- print copyright information
- -h --help
- print this help
- -? --usage
- print a short help
- --version
- print the version number and exit
Processing¶
- --threads=-1
- Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).
PLUGINS: 2dimage/io¶
- bmp
- BMP 2D-image input/output support. The plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The color table is ignored and the pixel values are taken as literal gray scale values.
- datapool
- Virtual IO to and from the internal data pool
- dicom
- 2D image io for DICOM
- exr
- a 2dimage io plugin for OpenEXR images
- jpg
- a 2dimage io plugin for jpeg gray scale images
- png
- a 2dimage io plugin for png images
- raw
- RAW 2D-image output support
- tif
- TIFF 2D-image input/output support
- vista
- a 2dimage io plugin for vista images
EXAMPLE¶
Shift the segmentations of a set segement.set by -20 pixels in horizontal direction and -30 pixels in vertical direction (as if the images where cropped starting at (20,30) and store it in translate.set. The shiftes files are named translatedXXXX.png
mia-2dsegshift -i segment.set -o translate.set -g translated -S "<20,30>"
AUTHOR(s)¶
Gert Wollny
COPYRIGHT¶
This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option '--copyright'.
v2.4.7 | USER COMMANDS |