Provided by: mia-tools_2.4.6-4ubuntu2_amd64 bug

NAME

       ('mia\-2dsegment\-local\-cmeans',) - Run a c-means segmentation of a 2D image.

SYNOPSIS

       mia-2dsegment-local-cmeans -i <in-file> [options]

DESCRIPTION

       mia-2dsegment-local-cmeans  This program runs the segmentation of a 2D image by applying a
       localized c-means approach that helps to overcome intensity inhomogeneities in the  image.
       The  approach  evaluates  a  global  c-means clustering, and then separates the image into
       overlapping regions where more c-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=(input, required); io
                     image to be segmented
                      For supported file types see PLUGINS:2dimage/io

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

              -G --out-global-crisp=(output); io
                     class label image based on global segmentation
                      For supported file types see PLUGINS:2dimage/io

              -C --class-prob=(output); io
                     class  probability  image  file,  filetype  must  support   floating   point
                     multi-frame images
                      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:

                        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

   Parameters
              -g --grid-spacing=15; int in [3, inf)
                     Spacing of the grid used to modulate the intensity inhomogeneities

              -c --cmeans=kmeans:nc=3
                     c-means initializer
                      For supported plugins see PLUGINS:1d/cmeans

              -e --c-means-epsilon=0.0001; float in (0, inf)
                     c-means breaking condition for update tolerance

              -t --relative-cluster-threshold=0.02; double in [0, 1)
                     threshhold to ignore classes when initializing the  local  cmeans  from  the
                     global one.

   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: 1d/cmeans

       even      C-Means  initializer  that  sets the initial class centers as evenly distributed
                 over [0,1], supported parameters are:

                     nc =(required, ulong)
                       Number of classes to use for the fuzzy-cmeans classification.

       kmeans    C-Means initializer that sets the initial  class  centers  by  using  a  k-means
                 classification, supported parameters are:

                     nc =(required, ulong)
                       Number of classes to use for the fuzzy-cmeans classification.

       predefined
                 C-Means  initializer that sets pre-defined values for the initial class centers,
                 supported parameters are:

                     cc =(required, vdouble)
                       Initial class centers fuzzy-cmeans  classification  (normalized  to  range
                       [0,1]).

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-local-cmeans -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'.