mia-2dsegment-local-cmeans - Run a c-means segmentation of a 2D image.

       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-2dsegment-local-cmeans(1)

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. This program implements a 2D prototype of the algorithm described in:

              Dunmore  CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of pale‐
              ontological material. PeerJ 6:e4374.

       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

       mia-2dsegment-local-cmeans - Run a c-means segmentation of a 2D image.

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:

                        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
              -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).

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