%
% Complete documentation on the extended LaTeX markup used for Insight
% documentation is available in ``Documenting Insight'', which is part
% of the standard documentation for Insight.  It may be found online
% at:
%
%     http://www.itk.org/

\documentclass{InsightArticle}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%  hyperref should be the last package to be loaded.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[dvips,
bookmarks,
bookmarksopen,
backref,
colorlinks,linkcolor={blue},citecolor={blue},urlcolor={blue},
]{hyperref}
% to be able to use options in graphics
\usepackage{graphicx}
% for pseudo code
\usepackage{listings}
% subfigures
\usepackage{subfigure}


%  This is a template for Papers to the Insight Journal. 
%  It is comparable to a technical report format.

% The title should be descriptive enough for people to be able to find
% the relevant document. 
\title{Consolidated morphology}

% Increment the release number whenever significant changes are made.
% The author and/or editor can define 'significant' however they like.
% \release{0.00}

% At minimum, give your name and an email address.  You can include a
% snail-mail address if you like.
\author{Ga\"etan Lehmann{$^1$} {\small{and}} Richard Beare{$^2$}}
\authoraddress{{$^1$}INRA, UMR 1198; ENVA; CNRS, FRE 2857, Biologie du D\'eveloppement et
Reproduction, Jouy en Josas, F-78350, France\\
{$^2$}Department of Medicine, Monash University, Australia}

\begin{document}
\maketitle

\ifhtml
\chapter*{Front Matter\label{front}}
\fi


\begin{abstract}
\noindent
% The abstract should be a paragraph or two long, and describe the
% scope of the document.
Grayscale dilation and erosion are basic transformations of mathematical
morphology. Used together or with other transformations, they are very useful
tools for image analysis. However, they can be very time consuming, especially
with 3D images, and with large structuring elements. Several algorithms have
been created to decrease the computation time, some of them with some limitations
of shape of structuring element. We have implemented several algorithms, studied
their performance in different conditions, and shown that all of them are more 
efficients than the others in certain conditions.

We finally introduce a new structuring element class and a some meta filter designed to
select the best algorithm depending on the image and the structuring element, and
to smoothely integrate the different algorithms available in the toolkit.

{\em This article is an early version made to describe the FlatStructuringElement class.
The other parts will come later. Be aware that other classes than FlatStructuringElement
are still in development and may produce incorrect results.}
\end{abstract}

\tableofcontents

\section{Introduction}

Several classes can currently be used as structuring element in ITK: \doxygen{Neighborhood}
and some subclass of \doxygen{Neighborhood}. There is several problems with that:
\begin{itemize}
  \item Some class like \doxygen{BinaryBallStructuringElement}
contains some code to generate a structuring element of particular shape
(a ball in that case), but the required call to the method \verb$CreateStructuringElement()$
make it particulary confusing for the beginner
  \item \verb$TPixel$, the first template parameter
of the \doxygen{Neighborhood} class and its subclass is meaning less in that case. It
can be safely set to a different type than the pixel type of the image, and store
only a binary information: inside the neighborhood or outside the neighborhood.
  \item ITK doesn't offer convenient code to visualize the structuring element,
or generate a structuring element from an image
\end{itemize}

The \doxygen{FlatStructuringElement} class provided with this article aims to solve those
problems, and, with the meta filters, to make the integration of the van Herk
/ Gil Werman and Anchor algorithms as transparent as possible.

\section{Algorithms}

 \subsection{Basic algorithm}

 \subsection{Moving histogram algorithm}

 \subsection{van Herk / Gil Werman algorithm}

 \subsection{Anchor algorithm}

\section{Performance}

%  \subsection{Structuring element size}
% 
%  \subsection{Image size}

\section{Implementation}

 \subsection{Basic algorithm}

 \subsection{Moving histogram algorithm}

 \subsection{van Herk / Gil Werman algorithm}

 \subsection{Anchor algorithm}

 \subsection{FlatStructuringElement}

The FlatStructuringElement is implemented as a subclass of \doxygen{Neighborhood}, in order to
keep backward compatibility. However, only the \verb$VDimension$ template parameter has
been kept. The meaning less \verb$TPixel$ of the \doxygen{Neighborhood} class is set to
\verb$bool$ and hidden to the user.

\doxygen{FlatStructuringElement} provides several static methods. Each of them let the user
produce a stucturing element with a given shape:
\begin{itemize}
  \item \verb$Ball()$ generate a ball structuring element. It takes the radius of the structuring
element as parameter.
  \item \verb$Box()$ produce a box structuring element. It takes the radius of the structuring
element as parameter.
  \item \verb$FromImage()$ produce a structuring element from an image. The image is passed
as parameter to the method. A optional parameter can also be passed: the pixel value
to be considered as the foreground value in the image. This value defaults to
\verb$NumericTraits< PixelType >::max()$.
\end{itemize}

The number of available shapes is currently limited. However, the most useful
ones are there, and the ability to generate a structuring element from an
image should let the user easily create the ones he may need.
Also, the infrastructure is there and other methods to generate others shape
can be easily added.

The \verb$GetImage()$ method in \doxygen{FlatStructuringElement} class let the user generate
an image from its structuring element, and thus easily visualize its real
shape. \verb$GetImage()$ is templated over the image type to produce. By default,
the pixels outside the structuring element are set to \verb$NumericTraits< PixelType >::Zero$,
and the pixels inside the structuring element to \verb$NumericTraits< PixelType >::max()$.

The method \verb$GetImage()$ and \verb$FromImage()$ are templated methods. This particularity
make them not available when wrapped in \verb$Python$, \verb$Tcl$ or \verb$Java$. For this usage,
\verb$GetImageUC()$ and \verb$FromImageUC()$ has been created. They provide the same fonctionality
that \verb$GetImage()$ and \verb$FromImage()$, but are limited to the pixel type \verb$unsigned char$, so
they can be not templated. This methods are only there to be used with wrappers
and shouldn't be used in \verb$C++$.

 \subsection{Meta filters}


\section{Usage}

\section{Conclusion}


% \url{http://www.itk.org}
% \code{Insight/Documentation/Style.pdf}
% \section{Principles of Solar Spot Detection}
% \cite{ITKSoftwareGuide}.
% \doxygen{ImageToImageFilter}

% \small \begin{verbatim}
% \end{verbatim} \normalsize


% The {itemize} environment uses a bullet for each \item.  If you want the 
% \item's numbered, use the {enumerate} environment instead.
% \begin{itemize}
%   \item  Insight Toolkit 2.4.
%   \item  CMake 2.2
% \end{itemize}

% \ref{cthead1}

% \begin{figure}[htbp]
% \centering
% \includegraphics{cthead1}
% \caption{The input image.\label{cthead1}}
% \end{figure}


\appendix



\bibliographystyle{plain}
\bibliography{InsightJournal}
\nocite{ITKSoftwareGuide}

\end{document}