mia-2dsegshift(1) 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=(output, required); 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 segmentationshift of segmentation
-k --skip=2
skip frames at the beginningskip 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:
info - Low level messages
trace - Function call trace
fail - Report test failures
warning - Warnings
error - Report errors
debug - Debug output
message - Normal messages
fatal - Report only fatal errors
--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).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

Recognized file extensions: .BMP, .bmp

 
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

 
datapool
Virtual IO to and from the internal data pool

Recognized file extensions: [email protected]

 
dicom
2D image io for DICOM

Recognized file extensions: .DCM, .dcm

 
Supported element types:
signed 16 bit, unsigned 16 bit

 
exr
a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

 
Supported element types:
unsigned 32 bit, floating point 32 bit

 
jpg
a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

 
Supported element types:
unsigned 8 bit

 
png
a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

 
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

 
raw
RAW 2D-image output support

Recognized file extensions: .RAW, .raw

 
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

 
tif
TIFF 2D-image input/output support

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

 
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

 
vista
a 2dimage io plugin for vista images

Recognized file extensions: .V, .VISTA, .v, .vista

 
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

 

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'.