mia-2dimagestack-cmeans - Calculate the c-means classification for
a series of images.
mia-2dimagestack-cmeans -i <in-file> -o
<out-probmap> [options]
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
- -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
- --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
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
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'.