mia-2dimagestack-cmeans - Calculate the c-means classification for a series of images.

       Gert Wollny

       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'.

USER COMMANDS                                        v2.4.7                           mia-2dimagestack-cmeans(1)

mia-2dimagestack-cmeans  This  program  first evaluates a sparse histogram of an input image series, then
       runs a c-means classification over the histogram and then writes the probability mapping for thr original
       intensity values

       Run the program over images imageXXXX.png with the sparse histogram, threshold  the  lower  5%  bins  (if
       available), run cmeans with three classes on the non-zero pixels.

       mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3

       mia-2dimagestack-cmeans - Calculate the c-means classification for a series of images.

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

              -o --out-probmap=(required, output); string
                     Save probability map to this file

   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
              -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 initializer
                      For supported plugins see PLUGINS:1d/cmeans

   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).

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]).

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

mia-2dimagestack-cmeans-i<in-file>-o<out-probmap>[options]