Provided by: mia-tools_2.4.6-1_amd64 
NAME
('mia\-2dimagestack\-cmeans',) - Calculate the c-means classification for a series of
images.
SYNOPSIS
mia-2dimagestack-cmeans -i <in-file> -o <out-probmap> [options]
DESCRIPTION
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
OPTIONS
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=(output, required); 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:
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 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).
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
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
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'.