mia-2dstack-cmeans-presegment(1)


NAME

   mia-2dstack-cmeans-presegment  - Pre-classify the input image series by
   using a c-means estimator

SYNOPSIS

   mia-2dstack-cmeans-presegment -i <in-file>  -o  <out-mask>  -L  <label>
   [options]

DESCRIPTION

   mia-2dstack-cmeans-presegment  This  program  first  evaluates a sparse
   histogram of an input image series, then runs a c-means  classification
   over  the  histogram, and then estimates the mask for one (given) class
   based on class probabilities. This program accepts only images of eight
   or 16 bit integer pixels.

OPTIONS

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

          -p --out-probmap=(output); string
                 Save probability map to this file

          -t --type=png
                 output file name type

          -o --out-mask=(output, required); string
                 output file name base

   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
          -T --histogram-thresh=5; float in [0, 50]
                 Percent of the  extrem  parts  of  the  histogram  to  be
                 collapsed into the respective last histogram bin.

          -C --classes=kmeans:nc=3
                 C-means  class  initializerC-means class initializer  For
                 supported plugins see PLUGINS:1d/cmeans

          -S --seed-threshold=0.95; float in (0, 1)
                 Probability threshold value to consider a pixel  as  seed
                 pixel.

          -L --label=(required); int in [0, 10]
                 Class  label to create the mask fromClass label to create
                 the mask from

   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).

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  program  over images imageXXXX.png with the sparse histogram,
   threshold the lower 30%  bins  (if  available),  run  cmeans  with  two
   classes  on the non-zero pixels and then create the mask for class 1 as
   foregroundXXXX.png.

   mia-2dstack-cmeans-presegment -i imageXXXX.png  -o  foreground  -t  png
          --histogram-tresh=30 --classes 2 --label 1

AUTHOR(s)

   Gert Wollny

COPYRIGHT

   This  software  is Copyright (c) 19992015 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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