NAME

       mia-2dsegment-per-pixel-kmeans - Run a k-means segmentation of a 2D image.

SYNOPSIS

       mia-2dsegment-per-pixel-kmeans -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-2dsegment-per-pixel-kmeans  This  program  runs  the  segmentation  of  a  2D image by
       applying a localized k-means approach that helps to overcome intensity inhomogeneities  in
       the  image.  The  approach  evaluates  a global k-means clustering, and then separates the
       image into overlapping regions where more k-means iterations are run  only  including  the
       locally present classes, i.e. the classes that relatively contain more pixels than a given
       threshold.

OPTIONS

   File-IO
              -i --in-file=(required, input); io
                     image to be segmented
                      For supported file types see PLUGINS:2dimage/io

              -o --out-file=(output, required); io
                     class label image based on merging local labels
                      For supported file types see PLUGINS:2dimage/io

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

                        trace ‐ Function call trace
                        debug ‐ Debug output
                        info ‐ Low level messages
                        message ‐ Normal messages
                        warning ‐ Warnings
                        fail ‐ Report test failures
                        error ‐ Report errors
                        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

   Parameters
              -w --window=20; int in [3, inf)
                     Window size around the pixel to be analyzed

              -n --nclasses=3; uint in [2, 127]
                     Number of intensity classes to segment

              -t --relative-cluster-threshold=0.0001; double in [0, 1)
                     Number of intensity classes to segment

   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).

PLUGINS: 2dimage/io

       bmp       BMP  2D-image  input/output support. The plug-in supports reading and writing of
                 binary images and 8-bit gray scale images. read-only  support  is  provided  for
                 4-bit  gray  scale  images.  The color table is ignored and the pixel values are
                 taken as literal gray scale values.

                     Recognized file extensions:  .BMP, .bmp

                     Supported element types:
                       binary data, unsigned 8 bit

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       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

       Run the segmentation on image test.png using three classes, local  regions  of  40  pixels
       (grid width 20 pixels), and a class ignore threshold of 0.01.

       mia-2dsegment-per-pixel-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

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'.