\name{thresh}

\alias{thresh}
\alias{thresh,Image-method}
\alias{athresh}
\alias{athresh,Image-method}
\alias{cthresh}
\alias{cthresh,Image-method}

\concept{image thresholding}

\title{ Image and color channel thresholding }

\description{
  Functions to threshold images and color channels of images.
}

\usage{

  \S4method{thresh}{Image}(x, w=5, h=5, offset=0.01, ...)
  \S4method{athresh}{Image}(x, w=10, h=10, offset=0, ...)
  \S4method{cthresh}{Image}(x, threshold=0, ...)
  
}

\arguments{

  \item{x}{An object of \code{\linkS4class{Image}}. For \code{thresh} it must be
    in the \code{\link{Grayscale}} mode. }

  \item{w, h}{ Thresholding frame width and height in pixel. } 

  \item{offset}{ Threshold offset from the mean value. }

  \item{threshold}{ Threshold value for channel thresholding (uniform). }

  \item{...}{ Reserved. }

}

\value{

  A new instance of \code{\linkS4class{Image}} in the same color mode as input.
    
}

\details{

  If \code{thresh} and \code{athresh} are adaptive thresholind functions.
  While \code{athresh} can be used on both \code{\link{Grayscale}} and 
  \code{\link{TrueColor}} images, \code{thresh} can only be used on 
  \code{Grayscale} images, however it is significantly faster on them.
  
  The value of \code{offset} in \code{thresh} is on the same scale as data, i.e.
  the default value is selected assuming data in the range \code{[0,1]}. This
  value for \code{athresh} should be selected empirically, as this function
  uses \code{AdaptiveThreshold} of \code{ImageMagick} and the scale of this
  parameter was not documented; the reasonable values are usually in the orders
  of 500, 1000 or avobe (at least to obtain similar thresholding to that of
  0.01 with \code{thresh} on cytomicroscopic images. ).
  
}

\seealso{ \code{
  \linkS4class{Image}, \link{Image}, \link{distmap}, \link{segment}, 
  \link{[,Image-method}
}}

\references{
  \emph{ImageMagick}: \url{http://www.imagemagick.org}.
}

\author{
  Oleg Sklyar, \email{osklyar@ebi.ac.uk},  2005-2007
}

\examples{
  ## see example(watershed)
}

\keyword{manip}