.TH mia\-2dsegmentcropbox 1 "v2.4.7"  "USER COMMANDS"
.SH NAME
mia\-2dsegmentcropbox
\- Evaluate a crop\-box around a manual segmentation.
.SH SYNOPSIS
.B  mia\-2dsegmentcropbox \-i <in\-file> \-o <out\-file> [options]
.SH DESCRIPTION
.B 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.
.SH OPTIONS
.RS
.IP "\-i \-\-in-file=(required, input); string"
input segmentation set

.IP "\-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

.IP "\-o \-\-out-file=(required, output); string"
output segmentation set

.IP "\-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.

.IP "\-e \-\-enlarge=5"
Enlarge the area around the obtained sbounding box by this number of pixels in each direction

.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information

.IP "\-h \-\-help"
print this help

.IP "\-? \-\-usage"
print a short help

.IP "   \-\-version"
print the version number and exit

.RE
.SS Processing
.RS
.IP "   \-\-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).

.RE
.SH 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.
.HP
mia\-2dsegmentcropbox \-i segment.set \-o cropped.set \-e 3
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 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'.