This is the command mia-2dsegmentcropbox that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
mia-2dsegmentcropbox - Evaluate a crop-box around a manual segmentation.
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'.
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