SYNOPSIS

mia-2dsegmentcropbox -i <in-file> -o <out-file> [options]

DESCRIPTION

mia-2dsegmentcropbox This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined.

OPTIONS

-i --in-file=(input, required); string

input segmentation set

-p --override-imagepath

Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory

-o --out-file=(output, required); string

output segmentation set

-c --cropped-base=crop

Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.

-e --enlarge=5

Enlarge the area around the obtained sbounding box by this number of pixels in each directionEnlarge the area around the obtained sbounding box by this number of pixels in each direction

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).

EXAMPLE

Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.

mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

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'.