.TH mia\-2dstack\-cmeans\-presegment 1 "v2.4.7"  "USER COMMANDS"
.SH NAME
mia\-2dstack\-cmeans\-presegment
\- Pre\-classify the input image series by using a c\-means estimator
.SH SYNOPSIS
.B  mia\-2dstack\-cmeans\-presegment \-i <in\-file> \-o <out\-mask> \-L <label> [options]
.SH DESCRIPTION
.B mia\-2dstack\-cmeans\-presegment
This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram, and then estimates the mask for one (given) class based on class probabilities. This program accepts only images of eight or 16 bit integer pixels.
.SH OPTIONS
.SS File-IO
.RS
.IP "\-i \-\-in-file=(input, required); io"
input image(s) to be filtered
 For supported file types see PLUGINS:2dimage/io
.IP "\-p \-\-out-probmap=(output); string"
Save probability map to this file

.IP "\-t \-\-type=png"
output file name type

.IP "\-o \-\-out-mask=(required, output); string"
output file name base

.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information

.IP "\-h \-\-help"
print this help

.IP "\-? \-\-usage"
print a short help

.IP "   \-\-version"
print the version number and exit

.RE
.SS Parameters
.RS
.IP "\-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.

.IP "\-C \-\-classes=kmeans:nc=3"
C\-means class initializer
 For supported plugins see PLUGINS:1d/cmeans
.IP "\-S \-\-seed-threshold=0.95; float in (0, 1)"
Probability threshold value to consider a pixel as seed pixel.

.IP "\-L \-\-label=(required); int in [0, 10]"
Class label to create the mask from

.RE
.SS Processing
.RS
.IP "   \-\-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).

.RE
.SH PLUGINS: 1d/cmeans
.TP 10
.B even
C-Means initializer that sets the initial class centers as evenly distributed over [0,1], supported parameters are: 
.P
.RS 14
.I
nc
=(required, ulong)
.RS 2
Number of classes to use for the fuzzy\-cmeans classification.

.RE
.RE
.TP 10
.B kmeans
C-Means initializer that sets the initial class centers by using a k-means classification, supported parameters are: 
.P
.RS 14
.I
nc
=(required, ulong)
.RS 2
Number of classes to use for the fuzzy\-cmeans classification.

.RE
.RE
.TP 10
.B predefined
C-Means initializer that sets pre-defined values for the initial class centers, supported parameters are: 
.P
.RS 14
.I
cc
=(required, vdouble)
.RS 2
Initial class centers fuzzy\-cmeans classification (normalized to range [0,1]).

.RE
.RE
.SH PLUGINS: 2dimage/io
.TP 10
.B 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.
.P
.RS 14
Recognized file extensions:  .BMP, .bmp
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit
.RE
 
.RE
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
Recognized file extensions:  .@
.RE
 
.TP 10
.B dicom
2D image io for DICOM
.P
.RS 14
Recognized file extensions:  .DCM, .dcm
.RE
 
.RS 14
Supported element types: 
.RS 2
signed 16 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B exr
a 2dimage io plugin for OpenEXR images
.P
.RS 14
Recognized file extensions:  .EXR, .exr
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 32 bit, floating point 32 bit
.RE
 
.RE
.TP 10
.B jpg
a 2dimage io plugin for jpeg gray scale images
.P
.RS 14
Recognized file extensions:  .JPEG, .JPG, .jpeg, .jpg
.RE
 
.RS 14
Supported element types: 
.RS 2
unsigned 8 bit
.RE
 
.RE
.TP 10
.B png
a 2dimage io plugin for png images
.P
.RS 14
Recognized file extensions:  .PNG, .png
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit
.RE
 
.RE
.TP 10
.B raw
RAW 2D-image output support
.P
.RS 14
Recognized file extensions:  .RAW, .raw
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.TP 10
.B tif
TIFF 2D-image input/output support
.P
.RS 14
Recognized file extensions:  .TIF, .TIFF, .tif, .tiff
.RE
 
.RS 14
Supported element types: 
.RS 2
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
.RE
 
.RE
.TP 10
.B vista
a 2dimage io plugin for vista images
.P
.RS 14
Recognized file extensions:  .-, .V, .VISTA, .v, .vista
.RE
 
.RS 14
Supported element types: 
.RS 2
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
.RE
 
.RE
.SH EXAMPLE
Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 30% bins (if available), run cmeans with two classes on the non\-zero pixels and then create the mask for class 1 as foregroundXXXX.png.
.HP
mia\-2dstack\-cmeans\-presegment \-i imageXXXX.png \-o foreground \-t png \-\-histogram\-tresh=30 \-\-classes 2 \-\-label 1
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 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'.