bionic (1) mia-2dsegment-local-kmeans.1.gz
NAME
('mia\-2dsegment\-local\-kmeans',) - Run a k-means segmentation of a 2D image.
SYNOPSIS
mia-2dsegment-local-kmeans -i <in-file> [options]
DESCRIPTION
mia-2dsegment-local-kmeans This program runs the segmentation of a 2D image by applying a localized k-
means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a
global k-means clustering, and then separates the image into overlapping regions where more k-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
-O --out-file2=(output); io
class label image based on classifying by using the interpolated class centers
For supported file types see PLUGINS:2dimage/io
-D --debug-centers=(output); io
Save the class center images to a debug file (type is double)
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=20; int in [3, inf)
Spacing of the grid used to modulate the intensity inhomogeneities
-n --nclasses=3; uint in [2, 127]
Number of intensity classes to segment
-t --relative-cluster-threshold=0.0001; double in [0, 1)
Number of intensity classes to segment
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: 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-kmeans -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'.