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'.