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mia-2dsegment-local-cmeans(1) General Commands Manual mia-2dsegment-local-cmeans(1)

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'.
v2.4.6 USER COMMANDS