[bbtk.git] / kernel / doc / bbtkUsersGuide / bbtkUsersGuide.tex

% ==========================================
\documentclass[11pt,final,a4paper]{article}
\input{config.tex}



\begin{document}

\begin{center}

{\Large \BBTK}
\vspace{1cm}

{\Huge User's Guide}
\vspace{1cm}

\bbtk version \bbtkVersion
\vspace{0.5cm}


Last modified on : October 16, 2008 \\
Generated on : \today 
\vspace{0.5cm}
\end{center}
\begin{center}
Eduardo D\'avila, Laurent Guigues, Jean-Pierre Roux 
\end{center}
\begin{center}
CREATIS-LRMN, Centre de Recherche en Imagerie Medicale \\ CNRS UMR 5220, INSERM U620\\
INSA Lyon\\
Universit\'e Claude-Bernard Lyon 1
\end{center}

% ==========================================
\tableofcontents
% ==========================================

\listoftables

\listoffigures



% ==========================================
%\section*{Abstract}
% ==========================================
\newpage
% ==========================================
\hrule
\section{What is bbtk ?}
% ==========================================
\BBTK(\bbtkns) is a set of tools 
(\CPP libraries and executables) 
providing a \CPP framework for the definition 
of elementary processing \emph{units}, called {\bf black boxes}, 
and the definition and execution of processing \emph{chains} 
made up of these black boxes. \\
It's a part of the \texttt{Creatools suite} composed mainly of :
\begin{verbatim}
 bbtk
 creaContours
 creaImageIO
 creaLib
 
\end{verbatim}
which depend on the OpenSource libraries: 
\begin{verbatim}
 gdcm 
 itk
 vtk
 wxWidgets
\end{verbatim}

% ==========================================
\subsection{The black box philosophy}
% ==========================================

\href{http://www.answers.com/topic/black-box-theater}{The Answers Dictionary} defines a {\bf black box} as 
\emph{``A device or theoretical construct with known or specified performance characteristics 
but unknown or unspecified constituents and means of operation''} \\
\href{http://en.wikipedia.org/wiki/Black_box_\%28disambiguation\%29}{Wikipedia}
defines a {\bf black box} as 
\emph{``any component in a system in which only the input and output 
characteristics are of interest, without regard to its internal mechanism 
or structure''}. \\
We should merge theese definitions. : 
not only the inputs and outputs are of interest but also 
\emph{what the box does} !
Hence, I would say that a black box is any \emph{\bf documented} 
component of a system, letting the user know  
\emph{\bf what} the box is supposed to do and 
\emph{\bf how to use it}
but not \emph{\bf how it does it}. \\

\BBTK provides a systematic framework 
to encapsulate (or ``wrap'') any 
existing \texttt{C} or \CPP processing code into an object 
(a black box) having a {\bf generic symbolic interface}, where 

\begin{itemize}
\item{\bf generic} means that the interface is \emph{the same} 
for all boxes. Hence one does not need to know which particular 
method allows, say, to set a particular input or 
get a particular output of the box. 
One can use a black box in a purely abstract way. 
\item{\bf symbolic} means that a particular 
input or output is referenced by a 'name', that is by a symbol 
which identifies the input or output. 
It also means that symbolic information (text) is 
attached to a box: description of the box, author, 
description of its inputs and outputs, etc.
\end{itemize}

(Actually, genericity is achieved because the interface is symbolic. 
We let you think about this\dots)

Of course, symbolic data attached to a box may be 
{\bf queried} : what are the inputs/outputs of the box ? 
what are their type ? their description ? etc.
This allows {\bf automatic documentation} of boxes. 

The abstract definition of black boxes is the most basic 
aspect of \BBTK architecture. 
Another key aspect is the groupement of black boxes into 
so called {\bf packages}, 
which are \emph{dynamic libraries} which can also 
be queried, in particular about the boxes they provide. 
The package structure then offers a mechanism which 
is like a \emph{'plug-in'} mechanism.
\BBTK provides the methods to load a package at run-time, 
and create instances of the boxes it contains. 

These two mechanisms (black boxes and packages) 
then gives the way to:

\begin{itemize}
\item The definition of an {\bf interpreted script language}, 
which allows to manipulate packages and boxes very easily in symbolic way. 
\BBTK provides one : \bbi (the Black Box Interpreter). 
\item {\bf Automatic documentation} of existing packages. 
\texttt{html} documentation of packages is proposed by 
\bbStudions.
\end{itemize}

Finally, these different components allow {\bf efficient} :

\begin{itemize}
\item {\bf capitalization and reuse} of existing processing units, 
including {\bf documentation} 
\item {\bf testing, prototyping} in a very simple script language
\item {\bf inter-operability} between atomic processings which 
have been written by different persons, using different libraries, etc. 
\end{itemize}

% ==========================================
\subsection{\bbtk components}
% ==========================================
\BBTK includes :
\begin{itemize}
  \item A \CPP {\bf\emph{library}} - called \bbtk - which defines a framework 
    (abstract classes) to develop black boxes and store them into 
    dynamic libraries, called black box \emph{packages}.
  \item Different {\bf\emph{black box packages}} :
    \begin{itemize}
      \item {\bf\emph{std}} : the 'standard' package including basic useful boxes.
      \item {\bf\emph{wx}} : basic graphical interface elements (widgets : sliders, buttons, etc. based on the \texttt{wxWidgets} library).  
      \item {\bf\emph{itk}} : the basic image processing package, based on the \itk library.
      \item {\bf\emph{vtk}} : the basic images and surfaces processing and visualization package, based on the \vtk library.
      \item {\bf\emph{wxvtk}} : widget boxes based on the \vtk library (2D and 3D vizualization and
      interaction).
      %\item {\bf\emph{creaImageIO}} : Provides hight level widgets to read images, including DICOM.
      \item {\bf\emph{toolsbbtk}} : Tools for bbtk administration and package development..      
    \end{itemize}
  \item A {\bf\emph{Developement environment}}, called \bbStudio, which provides
    \begin{itemize}
      \item An online {\bf\emph{script editor and interpretor}}
      \item A powerful html {\bf\emph{Help environment}}, integrating :       
        \begin{itemize}
          \item Online documentation scaning
          \item Retreiving boxes on various criterions
          \item Checking Demo and examples
        \end{itemize}
      \end{itemize}
      \item An standalone {\bf\emph{interpreter}}, called \bbins, which allows to 
          load black box packages and to define and execute 
          processing chains by connecting various black boxes.
      \item {\bf\emph{Various Development Utilities}} :
         \begin{itemize}
            \item \bbfy generates the \CPP code of a black box from a 
               description file written in \texttt{xml}.
                %\item \bbdoc generates the html documentation of a black box package 
                %(author, description, description of its black boxes : 
                %author, description, inputs, outputs, and so on).
            \item \bbCreatePackage allows to create the basic file architecture 
               to start the development of a new black box package.
            \item \text{bbCreateBlackbox} allows to create the basic file architecture 
               to start the development of a new black box, that will be included in an already existing package.              
            \item \texttt{bbs2cpp} translates a \texttt{.bbs} script into a \CPP file.
            \item \texttt{bbc} that interprets (i.e. : executes) a \texttt{.bbs} script.                  
         \end{itemize}
      \item A full {\bf\emph{documentation}} printable (pdf), browsable (html),
      queryable throught keywords.        
\end{itemize}

The general architecture of \BBTK 
is shown in figure \ref{bb-architecture}.

\begin{figure}[!ht]
\caption{\label{bb-architecture}\BBTK architecture}
\begin{center}
\includegraphics[width=0.6\textwidth]{bb-architecture.png}
\end{center}
\end{figure}

\newpage

% ==========================================
\section{Getting started with bbStudio}
% ==========================================

% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================

% ==========================================
\subsection{The interface}
% ==========================================


%\vspace{0.5cm}\hrule
%\section{The Development environment (bbStudio)}
%\label{bbStudio}

Just run it, typing in a console \bbStudio 
or clicking on its icon or its menu entry.
At start, \bbStudio opens with a very minimal 'How to use' in the middle. \\
Don't forget to read it : it will vanish at the first mouse click. \\
\begin{verbatim}
1) Click on the 'Demo' or 'Examples' link.
2) Select a Demo or an Example
3) Click on the [Source] link : the source file is loaded in bbStudio
4) Click on the 'Run button' (the down arrow at the bottom right
   of the source file).
\end{verbatim}

You'll get something like in figure 
\ref{bbi-fig-bbStudio-gui-start}
(the exact appearance of \bbStudio is Operating System and \bbtk version dependent)

\newpage


\begin{figure}[!ht]
\caption{\label{bbi-fig-bbStudio-gui-start}The bbStudio Development environment interface at start time}
\begin{center}
\includegraphics[width=0.7\textwidth]{bbStudioMainPageStart.png}
\end{center}
\end{figure}


Feel free to resize any part you want.
Your preferences will be kept next time you run again \bbStudio. \\

Let's have a look at the resized window :

\begin{figure}[!ht]
\caption{\label{bbi-fig-bbStudio-gui}The bbStudio Development environment interface}
\begin{center}
\includegraphics[width=0.7\textwidth]{bbStudioMainPage.png}
\end{center}
\end{figure}

You can see four parts : \texttt{Files}, \texttt{Messages},
 \texttt{Command}, \texttt{Help}.\\

The stuff is written using the Advanced User Interface library of wxWidgets
(a.k.a. AUI),
whose 'docking manager' allows windows and toolbars to be floated/docked 
onto a frame.\\
Please don't use this feature at learning time (the snapshots of this document
 wouldn't match with your screen ...)

\subsubsection{'Files' part}
\label{bbi-FilesPart}

It's the .bbs script editor.\\
If you load a file holding a script, it will be displayed here, and you'll be
able to modify it, to save it, to save-as it, to run it, using the
lower toolbar (see figure : \ref{lowertoolbar})

\begin{figure}[!ht]
\caption{\label{lowertoolbar}The lower tool bar}
\begin{center}
\includegraphics[width=0.7\textwidth]{lowertoolbar2.png}
\end{center}
\end{figure}


% \begin{itemize}
%   \item {\bf\emph{New file}} : Create a new file to hold a script
%   \item {\bf\emph{Open file}} : Open an already existing file holding a script 
%   \item {\bf\emph{Close file}} : Close a file holding a script
%   \item {\bf\emph{Save file}} : Save he current file (if modified)
%   \item {\bf\emph{Save file as}} : Save he current file under a different name
%   \item {\bf\emph{Run file}} : Execute the script you just loaded/modified/written
%   \item {\bf\emph{cursor position}} : column number : line number   
% \end{itemize}


\subsubsection{'Messages' part}
\label{bbi-MessagesPart}

Two kinds of messages will be output here:\\
System messages : produced by the kernel, in case of a user mistyping, or an execution error\\
Script messages : produced by the \bbtk equivalent of \texttt{printf} 
or \texttt{std::cout} in user programs

\subsubsection{'Command' part}
\label{bbi-CommandPart}

This is where user will type his requirements.

\subsubsection{'Help Contents' part}
\label{bbi-HelpContentsPart}

The 'Help Contents' part of \bbStudio is used to browse the html help of \BBTK.
All the entries of the starting page are self-explanatory :
 \begin{itemize}
   \item {\bf\emph{Help Contents}}
   \begin{itemize}
     %\item {\bf\emph{Wiki}} : Direct link to the bbtk Wiki (intranet only, right now, www
     %later).
     \item {\bf\emph{Demo}} : Link to some 'sophisticated' demonstrations.
     \item {\bf\emph{Examples}} : Link to some detailed 'How to use' examples
   \end{itemize}
   
   \item {\bf\emph{Guides}}   
   \begin{itemize}      
     \item {\bf\emph{User's Guide}} : Step to step How-to for user who wants to create his own
     application, just using already existing boxes.
     \item {\bf\emph{Package Developper's Guide}} : Step to step How-to for user who wants to create his own
     black boxes.
     \item {\bf\emph{Developper's Guide}} : For bbtk kernel developpers. .
     \item {\bf\emph{Reference Manual}} : 
     \item {\bf\emph{Booklet}} : Vade mecum.    
     \item {\bf\emph{Doxygen Documentation}} : Doxygen source browser.
   \end{itemize}
        
   \item {\bf\emph{Boxes}} : Box retrieving on various criterions :
   \begin{itemize} 
    \item {\bf\emph{ \texttt{By name}}} (Alphabetical list), 
    \item {\bf\emph{    \texttt{By package}}}, 
     \item {\bf\emph{   \texttt{By category}}}.
   \end{itemize} 
   
        A special hidden Box category, called \texttt{{Adaptors}} exists. \\ 
        They are used internaly to perform type conversions. Thought there are not end user intended, you may query them.     

      
 \end{itemize}


% ==========================================




% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================




% ==========================================

\newpage

% ==============================================
\subsection{Running Demo and Examples}
% ==============================================

Run \bbStudio the way you need. \\
In the part 'Help contents' (See figure \ref{HelpContents}), select \texttt{Examples} link.

\begin{figure}[!ht]
\caption{\label{HelpContents}Help Contents}
\begin{center}
\includegraphics[width=0.7\textwidth]{HelpContents.png}
\end{center}
\end{figure}

\newpage

You will be asked to select a Box category (See figure \ref{BoxCategories}); \\ 
Select \texttt{example}.


\begin{figure}[!ht]
\caption{\label{BoxCategories}Box Categories}
\begin{center}
\includegraphics[width=0.7\textwidth]{BoxCategories.png}
\end{center}
\end{figure} 

You will be asked to choose a script (See figure \ref{example}).

\begin{figure}[!ht]
\caption{\label{example}example list}
\begin{center}
\includegraphics[width=0.7\textwidth]{example.png}
\end{center}
\end{figure}



Select \texttt{wx::exampleSlider} (See figure \ref{exampleSlider});
 
\begin{figure}[!ht]
\caption{\label{exampleSlider}example 'exampleSlider'}
\begin{center}
\includegraphics[width=0.7\textwidth]{exampleSlider.png}
\end{center}
\end{figure}

You can see the graphical summary representation of the current script (the elementary boxes that compose it, and their
connections) \\
Click on \texttt{source}, and you'll be able to see the (very simple) script, 
in the 'Files' part, within the script editor (See figure \ref{exampleSliderSource});

\begin{figure}[!ht]
\caption{\label{exampleSliderSource}source code of 'exampleSlider'}
\begin{center}
\includegraphics[width=0.7\textwidth]{exampleSliderSource.png}
\end{center}
\end{figure}

Run it, using the lower toolbar  (see figure : \ref{lowertoolbar})

You'll get something like in figure \ref{execSliderSource}.

\begin{figure}[!ht]
\caption{\label{execSliderSource}execution of 'exampleSlider'}
\begin{center}
\includegraphics[width=0.7\textwidth]{execSliderSource.png}
\end{center}
\end{figure}

Feel free to move the slider, to check it actually works...

\newpage

Just a few words on what you saw :
\begin{itemize}
\item{in the File part} \\
The source code of the script
\begin{verbatim}
   new Slider     slider
     set slider.ReactiveOnTrack 1
\end{verbatim}
We create a \texttt{Slider} called \emph{slider}\\
We tell it to inform anybody that's interested in, that the cursor moved, each time it moved. \\
The deafuault behaviour is to inform, only when cursor is released.
\begin{verbatim}
   new OutputText text
\end{verbatim}
We create a \texttt{OutputText} called \emph{text} 
(in which slider value will be displayed)

\begin{verbatim}
   new LayoutLine layout
\end{verbatim}
We create a \texttt{LayoutLine} called \emph{layout},
a \emph{container} widget, designed to embed other wigets (say, a main window)
\begin{verbatim}
   connect slider.Widget    layout.Widget1
   connect text.Widget      layout.Widget2
\end{verbatim}
We embed \emph{slider} and \emph{text} into  \emph{layout}.
\begin{verbatim}
   connect slider.BoxChange text.BoxExecute
   connect slider.Out       text.In
\end{verbatim}
We tell  \emph{slider} to inform \emph{text} every time it's modified.\\
We tell  \emph{slider} to pass its output value (\texttt{Out} to \emph{text}  input value (\texttt{In})
\begin{verbatim}
   exec layout
\end{verbatim}
We tell \emph{layout} to process itself (it will do it only if it's warned 
that one of its entries was modified since its (own) last processing.

\item{in the Help part}

You can see the graphical representation of the script, as in figure \ref{SmallGraph}.


\begin{figure}[!ht]
\caption{\label{SmallGraph}Graphical representation of a script}
\begin{center}
\includegraphics[width=0.7\textwidth]{SmallGraph.png}
\end{center}
\end{figure}

Both graphical pipe line (\emph{slider} and \emph{text} are embedded into \emph{layout})
 and processing pipe line (\emph{slider} warns \emph{text} immedialtely when it's modified, \emph{slider} passed \emph{text} its new value).\\
 Yes, we know : all the arrows (pipe line arrows and processing arrows) are blue; we are sorry about that...\\
 
 You could get a much more detailled graph, just clicking on the button \\ \texttt{graph (detailled)} in the toolbar of the \texttt{Command} part, like in
 figure  \ref{LargeGraph}.
 
\begin{figure}[!ht]
\caption{\label{LargeGraph}Detailled graphical representation of a script}
\begin{center}
\includegraphics[width=0.75\textwidth]{LargeGraph.png}
\end{center}
\end{figure} 

\end{itemize}
\newpage

% ==============================================
\subsection{Online Help}
% ==============================================

Various levels or help are suplied by \bbStudions.

% ==========================================
\subsubsection{Command line help}
% ==========================================


The 'working' area (the left one, as opposed to the 'help' area, on the right side) is composed of : 
one single line area (\texttt{Command}), at the bottom in which you can enter your commands and 
a multiple line zone in which the Command interpreter prints out the result of your commands.
The upper part contains the script editor; we shall not use it right now, you may reduce it

Try typing in the \texttt{Command} area (in this manual, 
the commands entered by the user will be preceded by a prompt \textgreater) :
\begin{verbatim}
> help 
\end{verbatim}

you get the list of the commands of the interpreter :
\begin{verbatim}
Available commands :
 author
 category
 config
 connect
 debug
 define
 delete
 description
 endefine
 endpackage
 exec
 graph
 help
 include
 index
 input
 kind
 load
 message
 new
 newgui
 output
 package
 print
 quit
 reset
 set
 unload
\end{verbatim}

To get help on a particular command type \texttt{help <command-name>},
for example:
\begin{verbatim}
> help author
\end{verbatim}

gives :
\begin{verbatim}
 usage : author <string>
  Adds the string <string> to the author information of the black box being defined
\end{verbatim}

The \texttt{help} command has multiple usages. 
It is used to get help about almost anything in the interpretor!
Type \texttt{'help help'} to get help on the \texttt{help} command itself :
\begin{verbatim}
> help help
 usage : 
         (1) help 
         (2) help <command name> 
         (3) help packages [all]
         (4) help <package name> [all]
         (5) help <black box type> 
         (6) help <black box name>
  Effect :
         (1) Lists all available commands;
         (2) Prints help on a particular command; 
         (3) Lists the packages loaded and their black boxes.
             Add 'all' to list adaptors; 
         (4) Prints short help on the black boxes of a package.
             Add 'all' to include adaptors; 
         (5) Prints full help on a black box type; 
         (6) Prints information on the inputs, outputs and connectionns
             of a black box instance.
\end{verbatim}

At start the interpretor does not know any black box. 
If you type \texttt{'help packages'}, which is 
the third form of the \texttt{help} command, you get :
\begin{verbatim}
> help packages
user
  workspace
\end{verbatim}

which means that the interpretor only knows one package 
(library of black boxes) called \texttt{user}
and which contains a black box called \texttt{workspace}.
The \texttt{user} package is an internal package of the interpreter, 
which stores user-defined black box types. 
At start, it already contains 
one box, called \texttt{workspace}.
\texttt{workspace} is a special type of black box, 
called complex black box, whose purpose is 
to store other black boxes. 
Any black box you create in \bbStudio is stored 
in \texttt{workspace}  
(this will be explained in details in sections 
\ref{bbi-writing-scripts} and 
\ref{bbi-more-on-complex-black-boxes}). 

If you type \texttt{'help workspace'}, you get :
\begin{verbatim}
> help workspace
 Complex Black Box <user::workspace>
  User's workspace
  By : bbtk
  Category(s) : complex box;
  * No inputs
  * No outputs
  * No boxes
\end{verbatim}

In the text displayed, 
the \texttt{user::} prepended to the name \texttt{workspace} 
means that the box \texttt{workspace} 
belongs to the \texttt{user} package. 
Then comes a description and three lines which 
tell that \texttt{workspace} does not have any input 
nor output nor boxes yet.

In order to let the interpreter know of some black boxes, 
you must load another package. 
The \texttt{std} package is the ``standard'' package, 
which contains basic useful black boxes. 

To load it, type :
\begin{verbatim}
> include std
\end{verbatim}

Then if you type :
\begin{verbatim}
> help packages
\end{verbatim}

you get something like :

\begin{verbatim}

 std
   ASCII                   : ascii codes sequence to string - string to ascii...
   Add                     : Adds its inputs
   ConcatStrings           : String concatenation
   Configuration           : Gets configuration informations
   Div                     : Divides its inputs
   ExecBbiCommand          : Executes bbi commands
   ExecSystemCommand       : Executes system (O.S.) commands
   GetVectorCharElement    : Gets the i-th element from the input vector (std...
     ...
   MagicBox                : Takes *any kind* of data and copies it to its ou...
   MakeFileName            : Makes a kosher file name
   Mul                     : Multiplies its inputs
   MultipleInputs          : This box has multiple Void inputs and one Void o...
   StringRelay             : Just copies the value of its input to its output...
   StringSelect            : Outputs the string set to the ith input Ini (In0...
 user
   workspace 
\end{verbatim}

Now the interpreter knows the package \texttt{std} and the black boxes it provides,
such as the \texttt{Add} box, the \texttt{ConcatStrings} box, and so on. Remark that the 
content of \texttt{std} may vary from one version to another 
as new black boxes might be added to it. 
If you type :  
\begin{verbatim}
> help Add
\end{verbatim}

You'll get a text help, in the 'Message' part :
\begin{verbatim}
Black Box <std::Add>
  Adds its inputs
  By : laurent.guigues@creatis.insa-lyon.fr
  Categories : atomic box;math;
  * Inputs : 
     'BoxExecute'     <bbtk::Void> [signal] : Any signal received by this input 
                                              executes the box
     'BoxProcessMode' <String>     []       : Sets the processing mode of the box 
                                              (Pipeline | Always | Reactive)
     'In1'            <Double>     []       : First number to add
     'In2'            <Double>     []       : Second number to add
  * Outputs : 
     'BoxChange'      <bbtk::VoidS> [signal] : Signals modifications of the box
     'Out'            <Double>     []       : Result
\end{verbatim}

More information about what is a 'box' will be given in the 'Scripting' part of this manual.

% ==========================================
\subsubsection{Guides}
% ==========================================

An html version of all the guides is browsable in the \texttt{Help} part of \bbStudions.
 \begin{itemize}      
     \item {\bf\emph{User's Guide}} : Step to step How-to for user who wants to create his own
     application, just using already existing boxes.
     \item {\bf\emph{Package Developper's Guide}} : Step to step How-to for programmer who wants to create his own
     black boxes/packages.
     \item {\bf\emph{Developper's Guide}} : For bbtk kernel developpers only. (This one is probably not very much
     up-to-date, since we spend more time in developping than writing documentation that's not of user concern).
     \item {\bf\emph{Reference Manual}} : Contains a exaustive description of all the features for all the commands.
     \item {\bf\emph{Booklet}} : Vade mecum.     
     \item {\bf\emph{Doxygen Documentation}} : Doxygen source browser.\\ Automatically generated from source file
     headers. Should concern only the kernel developpers (i.e. : us).
   \end{itemize}
        

   
% ==========================================
\subsubsection{Boxes Help}
% ==========================================
 Box retrieving on various criteria :
   \begin{itemize} 
    \item {\bf\emph{Alphabetical list}} \\ This is the 'zero-level' of retrieving.
    \item {\bf\emph{List by package}} \\ Several packages are supplied with bbtk :
    \begin{itemize}
      \item {\bf\emph{std}} : the 'standard' package including basic useful boxes.
      \item {\bf\emph{wx}} : basic graphical interface elements (widgets : sliders, buttons, etc. based on the \texttt{wxWidgets} library).  
      \item {\bf\emph{itk}} : the basic image processing package, based on the \itk library.
      \item {\bf\emph{vtk}} : the basic images and surfaces processing and vizualization package, based on the \vtk library.
      \item {\bf\emph{wxvtk}} : widget boxes based on the \vtk library (2D and 3D vizualization and
      interaction).
      %\item {\bf\emph{creaImageIO}} : Provides hight level widgets to read images, including DICOM.
      \item {\bf\emph{toolsbbtk}} : Tools for bbtk administration and package development, such as :
         \begin{itemize}
         \item{\texttt{GUICreateBlackBox}} For creating the XML or C++ code for a new black box 
         \item{\texttt{GUICreatePackage}} For creating a new bbtk package file structure on disk (Graphical user interface for the shell script bbCreatePackage)
         \item{\texttt{MakePackageDoc}} For creating the html documentation of a package. The doc is generated at the 'canonical' location. Works both for a build tree or an installed toolkit.         
         \end{itemize}               
    \end{itemize}
    \item {\bf\emph{List by category}}.
    
    
    A given box may belong to more than one \texttt{category}.\\
    You have to consider categories like keywords to index black boxes.\\
    Some of them are mutually exclusive.
    A black box may be :
    \begin {itemize}
       \item{atomic box / complex box}\\
       Whether it's written is C++ or it's an assembly of several black boxes (atomic or complex).\\
       Any box is either atomic ou complex.
       \item{example / demo / application}\\
           These ones are always complex black boxes. 
          \begin {itemize}
             \item{example}\\
             It's just a (simple) example, for programmers, on how to use a given feature.
             \item{demo}\\
             It can be a 'good looking' (a.k.a 'sexy') example on some sophisticated work, done only by using \texttt{bbtk} 
             boxes.      
             \item{application}\\
             It's a Final application, end user intended (e.g. Subscale a huge volume witout loading it in memory, Crop a DICOM image, etc)      
          \end {itemize}
        \item{widget}\\
        Piece of graphical interface (based on \texttt{wxWidgets})
        \item{Dicom}\\
        Dicom medical image related box.
        \item{viewer}
        \item{read/write}
        \item{mesh}
        \item{3D Object creator}
        \item{math}
        \item{misc}              
    \end {itemize}
  \end {itemize}
  
% ==========================================      
\subsubsection{The Package Browser}
\label{Package_Browser}
% ==========================================


You can run it using the tool bar of the 'Command' part. See figure \ref{imPackage_Browser}.

\begin{figure}[!ht]
\caption{\label{imPackage_Browser}The Package Browser}
\begin{center}
\includegraphics[width=0.6\textwidth]{Package_Browser.png}
\end{center}
\end{figure}

It allows you to query informations about what you can find in the packages (boxes and applications), using several criterions
(warning : it's case sensitive, i.e '\texttt{Button}' will give different results than '\texttt{button}' ...)
\begin {itemize}
\item Packages :\\
All the boxes and applications held in a given package (e.g. \texttt{wxvtk}, \texttt{std}, ...)
\item Name :\\
You can query on a subpart of the name of a box or an application (e.g. \texttt{DICOM})
\item Description :\\
You can query on a substring of the description of a box or an application (e.g. \texttt{utton} : user wants to get all
the\texttt{Button} as well as the \texttt{button} )
\item Category :\\
You can query on a sub part of the category name of a box or an application (e.g. \texttt{3D})
\item Input Type :\\
You can query all the boxes or applications that have at least one Input entry of the given type (e.g. \texttt{int})
\item Output Type :\\
You can query all the boxes or applications that have at least one Output entry of the given type (e.g. \texttt{int})
\item Input Nature :\\
You can query all the boxes or applications that have at least one Input entry of the given nature (e.g. \texttt{signal})
\item Output Nature :\\
You can query all the boxes or applications that have at least one Output entry of the given nature (e.g.
\texttt{signal},\texttt{file name})
\end {itemize}


All these criterions are \emph{AND}ed while the query process.\\
You can get the whole description of a given box or application clicking on its name.

\newpage 

% ==============================================
\subsection{The Menu}
% ==============================================

At last, let's have a look at \bbStudio menu.(See figure \ref{themenu})

\begin{figure}[!ht]
\caption{\label{themenu}The bbStudio menu}
\begin{center}
\includegraphics[width=0.7\textwidth]{themenu.png}
\end{center}
\end{figure}

\begin {itemize}
  \item{\texttt{File}}
     \begin {itemize}
        \item{\texttt{Open the bbtk configuration file}}
        \item{\texttt{Quit}}
     \end {itemize}       
  \item{\texttt{Tools}}
     \begin {itemize}
        \item{\texttt{Create package}} :
        Provides a graphical interface to help Package developper to create a new empty package.
        \item{\texttt{Create black box}}
        Provides a graphical interface to help Package developper to create a new empty black box, and add it to an already existing package.   
        \item{\texttt{Show last image graph}}
        \item{\texttt{Regenerate package doc}} :
        if user was supplied new black boxes, and added them to an already existing package, he can update the package documentation, in order to benefit all the features of the Help mechanisms.      
        \item{\texttt{Regenerate boxes list}} :
        if user wants to update only boxes list (quicker)
        \item{\texttt{Regenerate all}}
        User wants to rebuild the whole documentation.     
     \end {itemize}     
  \item{\texttt{Options}}
     \begin {itemize}
        \item{\texttt{Reset before running}} Before running, all the already boxes are destroyed, all the already loaded packages are unloaded (this is the recomended option).   
     \end {itemize}     
  \item{\texttt{Windows}}
  User may decide, for any reason of his own, to hide one or more pannels:
     \begin {itemize}
        \item{\texttt{Show 'Files' panel}}
        \item{\texttt{Show 'Help' panel}}
        \item{\texttt{Show 'Command' panel}}
        \item{\texttt{Show 'Messages' panel}}
        \item{\texttt{Launch Package browser}} The package browser is a stand alone application. This can be achieved, too,
         using the lower tool bar : button \texttt{Start Package Browser}.      
        \item{}     
     \end {itemize}     
  \item{\texttt{About}}
     \begin {itemize}
        \item{\texttt{About}} : Info about \texttt{bbStudio}.       
     \end {itemize}     
\end {itemize}
% ==========================================
\section{bbs scripting}
% ==========================================

% ==========================================
\subsection{Using an already existing script}
% ==========================================

Using the lower toolbar (see figure : \ref{lowertoolbarsmall}), open the file
holding the script.

\begin{figure}[!ht]
\caption{\label{lowertoolbarsmall}The lower tool bar}
\begin{center}
\includegraphics[width=0.7\textwidth]{lowertoolbar.png}
\end{center}
\end{figure}

 You'll see it, in the '\texttt{Files}' part.\\ \\
 You may run it, using the lower toolbar. \\ 
 %\texttt{WARNING :} if the script contains one or more \texttt{LayoutSplit}
% object, you will have to resize the sub windows. \\ \\
 You may modify, save or save-as the current script, using the lower toolbar.\\ \\
 You may have a look at the graphical representation of the pipeline (sorry,
 right now, to modify the pipeline, you have to modify the script; 
 you cannot modify grapically the pipeline; Work in progress...)
  

% ==========================================
\subsection{Inside black boxes}
% ==========================================

After loading the package it belongs to, you can You can create an \emph{instance} of an \texttt{Add} box by 
the command \texttt{new} :

\begin{verbatim}
> new Add a
\end{verbatim}

The \texttt{'a'} at the end is the \emph{name} of the instance, 
which will be used to reference it later. 
It is important to distinguish a box \emph{type} 
and an \emph{instance} of a box type. 
The \texttt{Add} box of the package \texttt{std} is actually 
a \emph{box type} , like \texttt{int} is a data type 
in \texttt{C} langage. The \texttt{new} command allows to create 
an instance of a box type, exactly like \texttt{int i;} in 
a \texttt{C} code, it declares a variable of type \texttt{int} whose 
name is \texttt{i}. 
Of course, like in \texttt{C} Language, you can declare multiple boxes of the 
same type in \bbi. \\

You can ask information about a given black box :\\
In the \texttt{Command part}, type \texttt{help} + black box name, e.g. \\

\begin{verbatim}
> help Add a
\end{verbatim}
Have a look to the 'Help' Part (see figure : \ref{HelpAdd}) :

\begin{figure}[!ht]
\caption{\label{HelpAdd}The html Help}
\begin{center}
\includegraphics[width=0.7\textwidth]{HelpAdd.png}
\end{center}
\end{figure}

The \texttt{std::} prepended to the name \texttt{Add} 
means that the box \texttt{Add} 
belongs to the \texttt{std} package. 
Then comes a description 
(the one which was provided by the author of the box), 
the author(s) of the box (usually e-mail adress(es)) and 
the categories to which the box belongs. 
Finally comes the lists of inputs and outputs of the box.
For each input or output, \bbi provides 
its \emph{name} (between quotes, e.g. \texttt{'ProcessMode'}), 
its \emph{type} (between \texttt{<} and  \texttt{>}, e.g. \texttt{<Int>})
and a description.    
Remark that the box \texttt{Add} is not a 'complex' black box 
but an 'atomic' box, hence its help does not 
mention any information concerning possible internal boxes. 

After the creation of the box \texttt{a}, type :
\begin{verbatim}
> help workspace
\end{verbatim}

you get :
\begin{verbatim}
Complex Black Box <user::workspace>
 User's workspace
 By : bbtk
 Category(s) : complex box;
 * No inputs
 * No outputs
 * Boxes : 
    'a' <std::Add>
\end{verbatim}

which means that \bbi workspace now contains a black box named \texttt{a},
of type \texttt{std::Add}.

Now look back at the help on \texttt{Add} boxes : 
you can see that this type of box has two inputs, 
with name \texttt{In1} and \texttt{In2},
and an output, with name \texttt{Out}.

You can set the input \texttt{In1} 
of the \texttt{Add} box \texttt{a} to the value $1$ 
by the command :
\begin{verbatim}
> set a.In1 1 
\end{verbatim}

Similarly, setting the input \texttt{In2} of \texttt{a} to the value $2$
is done with :
\begin{verbatim}
> set a.In2 2
\end{verbatim}
 
And you print the output \texttt{Out} of the box \texttt{a} with :
\begin{verbatim}
> print "result=$a.Out$"
result=3
\end{verbatim}

In the string passed to the \texttt{print} command, 
each substring enclosed between a couple of \$ is considered 
as the name of an output of a box. 
To process this special substrings, the interpretor :
\begin{enumerate}
\item Processes the box if needed (see below)
\item Converts the output of the box to a string if possible 
(see below)
\item Substitutes the result in the string to print
\item Postpones an implicit 'new line' character to the string
\end{enumerate}

%\paragraph

Box processing is needed if :

\begin{itemize}
\item either at least input has changed since last processing 
\item or the input \texttt{'BoxProcessMode'} of the box is set to 
\texttt{'Always'}, which forces box reprocessing. 
\end{itemize}

Note that all boxes have an input named \texttt{'BoxProcessMode'}.

Another way to process the box \texttt{a} is to issue the command :
\begin{verbatim}
> exec a
\end{verbatim}

however this command does not display anything (except if the 
box itself displays something in its processing).
It just processes the box if needed. 
This command is used to execute boxes that do not have any output,  
such as boxes that write something to a file or, display a 
graphical interface, and so on. \newline

%To exit \bbi, type :
%\begin{verbatim}
%> quit
%Good bye !
%\end{verbatim}



% ==========================================
\hrule

\paragraph{Summary}
%\hrule
\begin{itemize}
\item The \texttt{include} command allows to load a package, and the complex black boxes that come with it..
\item \texttt{help} gives help on :
\begin{itemize} 
\item Available commands if you just type \texttt{help}.
\item A particular command if you type \texttt{help <command-name>}.
\item All available packages and their boxes (without description) if you type \texttt{help packages}.
\item A particular package and its boxes (with brief description) if you type \texttt{help <package-name>}.
\item A particular black box type (with full description) if you type \texttt{help <box-type-name>}. In particular, \texttt{help workspace} displays information on the content of the \texttt{'workspace'} black box, which stores the boxes created by the user (by \texttt{new}).
\end{itemize}
%\item \texttt{list} displays the list of black box instances created so far (by \texttt{new}).
\item \texttt{new} : creates an instance of a black box. 
\item \texttt{set} : sets the value of an input of a black box. 
\item Under any component of  \bbStudions, to reference the input called \texttt{i} 
of a black box called \texttt{b} you must type \texttt{'b.i'}. 
The same syntax holds for outputs.
\item \texttt{print} : prints a string, substituting each substring of the form \$b.o\$ by the value of the output \texttt{o} of the black box \texttt{b}. Note that an
implicit trailing 'new line character' is added at the final string.
\item \texttt{exec} : runs, if needed, the process of a box. 
%\item \texttt{quit} : quits \bbi.
\end{itemize}
\hrule

%\paragraph{Note :}
%A more 'modern' way to proceed is to run \texttt{bbStudio}, drag and drop the  \texttt{Command} bookmark to the lower \texttt{Welcome to bbStudio!} bar.
%Wou'll get something like in figure \ref{bbCommandPlusHelp} :

%\begin{figure}[!ht]
%\caption{\label{bbCommandPlusHelp}
%An other way to run the command interpreter}
%\begin{center}
%\includegraphics[width=0.5\textwidth]{bbCommandPlusHelp.png}
%\end{center}
%\end{figure}

% ==========================================

% ==========================================
\subsubsection{Connecting black boxes}
\label{bbi-connecting-black-boxes}
% ==========================================

\BBTK allows to create 
and execute processing chains, 
also called \emph{pipelines}, 
by connecting black boxes.
This section explains how to do it with examples. 
Read section \ref{bbi-more-on-pipeline-processing} to get 
more information on pipeline processing.

First start \bbStudio and load the package \texttt{std}, typing :
\begin{verbatim}
> include std
\end{verbatim}
in the 'Command' part.

Assume you want to compute $1+2+3$. You can do it by 
chaining two \texttt{Add} boxes, as shown in figure 
\ref{bbi-fig-connecting-black-boxes-1}. 

\begin{figure}[!ht]
\caption{\label{bbi-fig-connecting-black-boxes-1} A simple pipeline which adds 3 numbers}
\begin{center}
\includegraphics[width=0.5\textwidth]{1plus2plus3.png}
\end{center}
\end{figure}


The \bbi instructions to create and execute this pipeline are :
\begin{verbatim}
> new Add a
> new Add b
> connect a.Out b.In1
> set a.In1 1
> set a.In2 2
> set b.In2 3
> print $b.Out$
\end{verbatim}

You will see the (very expected) result :
\begin{verbatim}
6
\end{verbatim}

The first three commands build the pipeline, 
the next three set \texttt{a} and \texttt{b} black boxes inputs and the last one 
prints \texttt{b} black box output (the pipeline is executed before printing, because the interpretor 'knows' the box  \texttt{b}, 
whose output is requested, is not up to date.
 
The command \texttt{'connect a.Out b.In1'} ``plugs'' the output 
\texttt{Out} of the box \texttt{a} into the input \texttt{In1} of the 
box \texttt{b}. 
Once the boxes are connected, the processing of the two boxes are chained :
getting the output of \texttt{b} requires getting its inputs, 
hence getting the output of \texttt{a} which is connected to it. 
This pipeline mechanism can recurse into arbitrary long 
chains of boxes (see \ref{bbi-more-on-pipeline-processing} 
for details).


Lets' consider an other, more image oriented, example :

\begin{verbatim}
> include vtk
> include wx
> include itk
> include wxvtk

> new FileSelector fileDialog
> new ImageReader  reader 
> new Slider       slider
> new Viewer2D     viewer

> connect fileDialog.Out   reader.In 
> connect reader.Out       viewer.In
> connect slider.Out       viewer.Slice
> connect slider.BoxChange viewer.BoxExecute

> exec viewer
\end{verbatim}

Some explainations : the \texttt{include} instructions load the necessary packages. \\

\texttt{new FileSelector} will pop a File Selector, at run time, that will out the user chosen file name. \\
\texttt{new Slider} will pop a Slider, at run time, that will out an integer, used later as a slice number.\\ 
\texttt{new ImageReader} will read any itk readable file, whose name is passed as a std::string, and return a itk::ImagePointer.\\
\texttt{new Viewer2D} display a plane, whose number id specified by an integer.\\
\\
\texttt{connect fileDialog.Out   reader.In} plugs the output of the File Selector (a std::string) to the input of the reader (a std::string, too).\\
\texttt{connect reader.Out       viewer.In} plugs the output of the reader (an itk::ImagePointer) to the input of the Viewer (a vtkImageData *)\\
\texttt{connect slider.Out       viewer.Slice} plugs the output of the slider (an int) to an other output (named Slide) of the viewer.\\
\texttt{connect slider.BoxChange viewer.BoxExecute} says the viewer that it must re process itself any time the slider is modified.\\
\\
\texttt{exec viewer} processes the viewer.


This would correspond to the graph in figure \ref{bbi-simplegraph}


\begin{figure}[!ht]
\caption{\label{bbi-simplegraph}(Very) simple Graph of a (very) simple pipeline}
\begin{center}
\includegraphics[width=0.8\textwidth]{bbi-simplegraph.png}
\end{center}
\end{figure}
   
Of course, to be able to connect two boxes, 
the output and the input must be compatibles. 
You can always connect an output to an input of the \emph{same} type, 
but you can do more, thanks to particular (hidden) black boxes called {\bf adaptors}.

An adaptor is a black box which has at least one input, called \texttt{In}, 
and at least one ouput called \texttt{Out} and whose role is to convert 
a data of the type of \texttt{In} 
into a data of the type of \texttt{Out} (other inputs or outputs may serve 
to parameter the adaptor or retreive other useful information).

Under \bbStudions, if you type :
\begin{verbatim}
> load std
> help std all
\end{verbatim}
you get :
\begin{verbatim}
 Package std v1.0.0 - laurent.guigues@creatis.insa-lyon.fr
 Basic useful black boxes
 Black boxes : 
      ...
   BoolToString        [DA]  : Converts a Bool (bool) into a string
   CastBoolToChar      [DA]  : Static cast from Bool (bool) to Char (signed c...
   CastBoolToDouble    [DA]  : Static cast from Bool (bool) to Double (double...
      ...
   CastBoolToUChar     [DA]  : Static cast from Bool (bool) to UChar (unsigne...
   CastBoolToUInt      [DA]  : Static cast from Bool (bool) to UInt (unsigned...
      ...
   CastUIntToBool      [DA]  : Static cast from UInt (unsigned int) to Bool (...
   CastUIntToChar      [DA]  : Static cast from UInt (unsigned int) to Char (...
   CastUIntToDouble    [DA]  : Static cast from UInt (unsigned int) to Double...
      ...      

\end{verbatim}

\texttt{[DA]}  stands for \emph{default adaptor}.

Once you have loaded the package \texttt{std}, you can 
plug an output of type \texttt{char} into an input of type \texttt{double}. 
When the interpreter encounters the \texttt{connect} command, 
it looks for an adequate \emph{adaptor} in the  loaded packages. 
In our case, as the package \texttt{std} provides the 
\texttt{CastUCharToDouble} adaptor, the interpreter automatically creates an 
instance of this adaptor and place it \emph{between} 
the output and the input you want to connect 
(however this adaptor is hidden to you, 
it is embedded into the created connection and does not appear 
as an existing black box). 
When the pipeline is processed the 
adaptor converts the output data into the required input type, 
in a totally transparent way.
In our example, the \texttt{CastUCharToDouble} adaptor 
would simply cast the value of the \texttt{char} into a \texttt{double}, 
however arbitrarily complex type conversion may be done.\\
\texttt{WARNING} : these adaptors are \texttt{C++ static cast}, i.e., there is, right now',
 no 'intelligent' conversion (only truncation) e.g. think to \texttt{CastDoubleToUChar}!

%\begin{verbatim}
%Question (for info-dev): 
%if two adaptors with the same input and output types exist 
%in two different packages, currenly loaded, 
%which one is chosen by the interpreter at connection time?
%A feature is missing to specify explicitely which one user wants to choose 
%(use a namespace notation ?)
% 
%-> Role of default adaptors
%\end{verbatim}

Note that the \texttt{set} and \texttt{print} commands of interpreter 
work with adaptors from \texttt{string} to the type of the input to set 
or from the type of the output to print to \texttt{string}. 
Hence in order to \texttt{set} or \texttt{print} values the adequate 
adaptors must be available in the packages currently loaded. \\


% ==========================================
\hrule
\paragraph{Summary}
%\hrule
\begin{itemize}
\item The \texttt{connect} command allows to connect two black boxes
\item You can connect two black boxes if (and only if) : 
\begin{itemize}
\item The output and the input are of the same type, or
\item There is an adaptor black box in the packages loaded which 
converts data of the output type into data of the input type
\end{itemize}
\item \texttt{help <package name>} does not display the adaptors of the package. To see them use : \texttt{help <package name> all}.
including adaptors
\end{itemize}
\hrule
% ==========================================

% ==========================================
\subsubsection{Creating complex black boxes}
\label{bbi-complex-black-boxes}
% ==========================================

Remember the pipeline of figure 
\ref{bbi-fig-connecting-black-boxes-1}, which 
computed the sum of three doubles.
You can consider it as a whole and define 
a new black box type, which will be a \emph{complex black box}, 
having three inputs and one output, 
as shown in figure \ref{bbi-fig-complex-black-box-1}.

\begin{figure}[!ht]
\caption{\label{bbi-fig-complex-black-box-1} Creating the complex black box \texttt{Add3}}
\begin{center}
\includegraphics[width=0.5\textwidth]{Add3.png}
\end{center}
\end{figure}

The \bbi commands to define this complex black box are 
the following :

\begin{verbatim}
> load std
>
> define Add3
>
> new Add a
> new Add b
> connect a.Out b.In1
>
> author "myself"
> description "adds 3 doubles"
> input x a.In1 "first double to add"
> input y a.In2 "second double to add"
> input z b.In2 "third double to add"
> output result b.Out "output"
>
> endefine
\end{verbatim}

Explainations :

As we will use \texttt{Add} boxes, we need to load the package \texttt{std}, which is done in first line.

The command \texttt{define} then starts the definition 
of the complex box type, which will be called \texttt{Add3}. 

The next three lines define the pipeline, 
exactly in the same way than outside a complex box definition. 

The commands \texttt{author}, \texttt{description}, \texttt{input} 
and \texttt{output} are commands specific to complex boxes definition :

\texttt{author} and \texttt{description} are used for the documentation 
of the new box. You can provide multiple \texttt{author} or 
\texttt{description} commands, the arguments of the commands will 
be concatenated to produce the final author and description strings.

\texttt{input} and \texttt{output} are used to define the inputs and outputs 
of the new complex box. 
Their syntax is the same : for each new input/output you need to say 
to which internal input/output it corresponds and to provide 
a help string documenting the input/output.
In our example, we define that the box \texttt{Add3} has 
three inputs : \texttt{x}, \texttt{y} and \texttt{z}. 
The input \texttt{x} corresponds to the input \texttt{In1} of the 
internal box \texttt{a}. 
In the same way, the external input \texttt{y} 
corresponds to the internal input \texttt{a.In2}, and 
the external input \texttt{In3} to \texttt{b.In2}. 
The only output of the new box is called \texttt{result}
and corresponds to \texttt{b.Out}. 
The figure \ref{bbi-fig-complex-black-box-1} 
illustrates the external to internal 
input/output correspondence.

Finally, the \texttt{endefine} command ends the definition of the 
new box type.

After this definition, if you ask for help 
on packages, you get :
\begin{verbatim}
> help packages
std
  Add
  ...
user
  Add3
  workspace
\end{verbatim}

The \texttt{user} package now contains a new black box type, called 
\texttt{Add3}. If you ask for help on this type of box, you get :
\begin{verbatim}
> help Add3
Complex Black Box <user::Add3>
 adds 3 doubles
 By : myself
 * Inputs : 
    'x'      <double> : first double to add
    'y'      <double> : second double to add
    'z'      <double> : third double to add
 * Outputs : 
    'result' <double> : output
 * Boxes : 
    'a' <std::Add>
    'b' <std::Add>
\end{verbatim}

and you can use it like any other box, for example type :

\begin{verbatim}
> new Add3 a
> set a.x 1
> set a.y 2
> set a.z 3
> print $a.result$
6
\end{verbatim}


As a side note, we can say that, for consistency reasons, it would have been better to name  
\texttt{In1}, \texttt{In2} and \texttt{In3} the inputs of the black box \texttt{Add3}, 
since all the 'natural entry' of a box is named \texttt{In}, or \texttt{In}\emph{x} if there are more than one  'natural
entry'
.
\newline
% ==========================================
\hrule
\paragraph{Summary}
%\hrule
\begin{itemize}
\item The \texttt{define/endefine} commands allows to define complex black box types, i.e. types of black boxes made up of other black boxes. 
Inside a \texttt{define/endefine} block :
\begin{itemize}
\item The \texttt{author} and \texttt{description} commands allow to document the new type of box
\item The \texttt{input} and \texttt{output} commands allow to define the inputs and outputs of the new type of box, that is to which inputs and outputs 
of internal boxes they correspond.  
\end{itemize}
\end{itemize}
\hrule
% ==========================================

% ==========================================
\subsubsection{Writing scripts}
\label{bbi-writing-scripts}
% ==========================================

Once you have defined a new type of complex box, you 
may like to reuse it. To do this, you can simply 
write the \bbi commands defining the new box 
into a text file and afterwards include that file in \bbins. 
Doing this, you start writing \bbi scripts.
The conventionnal (and mandatory) extension for such scripts is \texttt{bbs} 
(black box script).
For consistency reasons, you are requested to prepend \texttt{bb} to the name.

For example, the \texttt{Add3} complex box we previously worked on 
can be defined in the \texttt{bbAdd3.bbs} file :

\begin{file}{bbAdd3.bbs}
\begin{verbatim}
# Defines the Add3 black box which adds 3 doubles 
load std

define Add3
  # I am the author 
  author "myself"
  description "adds 3 doubles"
  # Pipeline creation
  new Add a
  new Add b
  connect a.Out b.In1
  # Inputs definition
  input x a.In1 "first double to add
  input y a.In2 "second double to add
  input z b.In2 "third double to add"
  # Output definition
  output result b.Out "output"
endefine
\end{verbatim}
\end{file}

Lines starting with a \texttt{\#} character or a \texttt{\//\//} character are ignored, they 
are considered as comments by the interpreter.
To use this file in \bbStudions, click on the \texttt{include} button, and browse your filestore to find the file.

\begin{verbatim}
> include bbAdd3.bbs
> help Add3
Complex Black Box <user::Add3>
 adds 3 doubles
 By : myself
 * Inputs : 
    'x'      <double> : first double to add
    'y'      <double> : second double to add
    'z'      <double> : third double to add
 * Outputs : 
    'result' <double> : output
 * Boxes : 
    'a' <std::Add>
    'b' <std::Add>
>
and so on ...
\end{verbatim}

If the file has the \texttt{bbs} extension, you can ommit it and just type :
\begin{verbatim}
> include Add3
\end{verbatim}

\subsubsection{Creating complex black boxes that use complex black boxes}
\label{bbi-complex-complex-black-boxes}


Of course, you can include script files in other script files, 
like in the following example :

\begin{file}{bbAdd4.bbs}
\begin{verbatim}
# Defines the Add4 black box which adds 4 doubles 
include Add3

define Add4
  author "myself"
  description "adds 4 doubles"
  new Add3 a
  new Add b
  connect a.Out b.In1
  input In1 a.In1 "first double to add
  input In2 a.In2 "second double to add
  input In3 a.In3 "third double to add"
  input In4 b.In2 "fourth double to add"
  output Out b.Out "output"
endefine
\end{verbatim}
\end{file}



\subsubsection{Naming Conventions}
\label{bbi-Naming Conventions}


% ==========================================
%\hrule
%\paragraph{Naming Conventions}
%\hrule

%\hrule
% ==========================================
\begin{itemize}
\item
File names : 
For consistency reasons, you are requested to prepend \texttt{bb}, and postpone an extention \texttt{.bbs},
to the names of the files that hold a \texttt{complex black box} definition.

For example, the \texttt{Add3} complex box we previously worked on 
can be defined in the \texttt{bbAdd3.bbs} file.
\item
Search Paths :
For consistency reasons, the names of dynamic libraries holding the packages must start by \texttt{libbb}.
For instance, the package \texttt{wx} will be in the library \texttt{libbbwx.dll} (Windows) or \texttt{libbbwx.so}
(Linux).


\end{itemize}
% ==========================================
\hrule

\paragraph{Summary}
%\hrule
\begin{itemize}
\item The \texttt{include} command tells the interpreter to include a script file.
\item Lines starting with a \texttt{\#} or with a \texttt{\//\//} are considered as comments by the interpreter.
\item Lines between a line starting with a \texttt{\//*} an a line starting with a \texttt{*\//} are considered as comments by the interpreter.
\end{itemize}

\hrule
% ==========================================

% ==========================================
\subsubsection{Creating command line applications}
\label{bbi-command-line-app}
% ==========================================

Now that you know how to create complex black boxes 
(with \texttt{define/endefine}), think 
back to the \texttt{workspace} object. 
Remember that it is also 
a \texttt{complex black box}. 
Actually, when you type interpreter commands 
outside a \texttt{define/endefine} block, 
you progressively define the \texttt{workspace} 
complex black box.
You can think of it like if at start the interpreter
was issuing a command \texttt{'define workspace'} 
and then letting you define the interior of the box 
\texttt{workspace}.

Remember that the command \texttt{inputs} 
allows to define an input of a complex box. 
Now, if you use the command \texttt{input} 
outside a \texttt{define/endefine} block then 
it defines an input of the \texttt{workspace} box, 
that is an input of the \emph{main program}. 
This input will then be connected to the 
parameters that the user passes to the command line.

For example, consider the script : 

\begin{file}{add.bbs}
\begin{verbatim}
load std
new Add a
input x a.In1 "first number to add"
input y a.In2 "second number to add"
print "x+y=$a.Out$"
\end{verbatim}
\end{file}

The third and fourth lines define two inputs \texttt{x} 
and \texttt{y}. When you execute this script, 
you can pass these two arguments on the command line, 
like this :

\begin{verbatim}
> bbi add x=1 y=1
x+y=2
\end{verbatim}

You can also invoke \bbi the option \texttt{-h}, 
which gives help on the \texttt{workspace} box :

\begin{verbatim}
> bbi add -h
 User's workspace
 By : bbi (internal)
 * Inputs : 
    'x' <double> : first number to add
    'y' <double> : second number to add
\end{verbatim}

To get a better help, use the \texttt{description} 
and \texttt{author} commands :

\begin{file}{add.bbs}
\begin{verbatim}
description "Adds two numbers"
author "foo@bar.com"
load std
new Add a
input x a.In1 "first number to add"
input y a.In2 "second number to add"
print "x+y=$a.Out$"
\end{verbatim}
\end{file}

Now if you ask for help on the \texttt{add} script, you get :

\begin{verbatim}
> bbi add -h
 Adds two numbers
 By : foo@bar.com
 * Inputs : 
    'x' <double> : first number to add
    'y' <double> : second number to add
\end{verbatim}

Rather than getting the inputs of a script 
from the command line, you can ask \bbi to 
prompt the user for the values, using the \texttt{-t}
commutator :

\begin{verbatim}
> bbi add -t
x=[the program waits for user answer]2
y=[the program waits for user answer]5
x+y=7
\end{verbatim}

\bbStudio is always compiled in graphical mode (with \wx), therefore
you can also use the \texttt{-g} commutator. 
\bbi then prompts the user in graphical mode, 
displaying a dialog box for each input,
like in fig. \ref{bb-input-dialog-box}.

\begin{figure}[!ht]
\caption{\label{bb-input-dialog-box}Input dialog box}
\begin{center}
\includegraphics[width=0.6\textwidth]{enter-the-value-of-x.png}
\end{center}
\end{figure}

% ==========================================
\hrule
\paragraph{Summary}
%\hrule
\begin{itemize}
\item The \texttt{input}, \texttt{description} and \texttt{author} commands,
when they are used outside a \texttt{define/endefine} block allow 
to define the inputs, description and author of the main program.
\item Inputs of the main program can be passed on the command line 
using the syntax \texttt{<input-name>=<value>}. 
No white space is allowed, if the value or the input name 
contains white spaces, enclose them 
between double quotes, e.g. \texttt{"parameter with white spaces = gnu's not unix"}.
\item The \texttt{-h} option of \bbi prints help on the main program.
\item The \texttt{-t} option of \bbi orders the program to prompt for its inputs in text mode.
\item The \texttt{-g} option of \bbi orders the program to prompt for its inputs in graphical mode.
\end{itemize}
\hrule
% ==========================================

% ==========================================
\subsubsection{Using graphical interface boxes (widget boxes)}
\label{bbi-widget}
% ==========================================

% ==========================================
\subsubsection{Overwiew}
\label{bbi-overview}
% ==========================================

\bbStudio is always compiled in graphical mode 
(option \texttt{BUILD\_bbi\_GRAPHICAL} of \cmakens, requires \wxns),
then you can use special black boxes which are 
graphical interface components (widgets). 
Basic components are provided in the package \texttt{wx}, 
such as buttons, sliders, file open/save dialogs, etc.

As first example, type the following commands in \bbi :
\begin{verbatim}
> load wx 
> new InputText t
> print $t.Out$\n
\end{verbatim}

When you type \texttt{enter} after the last line, 
a window pops up in which you can entrer a text.
When you close the window, the text you entered is printed by 
the \texttt{print} command.

Type \texttt{help wx}, you get something like :
\begin{verbatim}
 Package wx v1.0.0- info-dev@creatis.insa-lyon.fr
 Basic graphical interface elements (sliders, buttons ...) based on wxWidgets
 Black boxes : 
   ColourSelector        : Colour Selector dialog (bbfication of wxColourSele...
   ColourSelectorButton  : A button which displays a colour picker dialog whe...
   CommandButton         : Button which executes bbi commands
   DirectorySelector     : Pops up a directory selection dialog (wxDirDialog)
   FileSelector          : Pops up a file selection dialog for reading or sav...
   InputText             : A zone in which the user can enter a text (wxTextC...
   LayoutLine            : LayoutLine widget (wxBoxSizer)
   LayoutSplit           : Widget which splits a window in two fixed size par...
   LayoutTab             : LayoutTab widget (wxNotebook)
   OutputText            : Text zone to be inserted into a window (wxStaticTe...
   RadioButton           : RadioButton group widget 0-9 entries
   Slider                : Slider widget (wxSlider)
\end{verbatim}

You can reproduce the same experiment as above using a 
\texttt{Slider} or a \texttt{FileDialog} rather than a \texttt{InputText}.
See the files \texttt{test*.bbs} in the \texttt{scripts/test} directory.


%There are two kinds of widgets : ``terminal'' widgets and ``container'' widgets.
%The \texttt{InputText}, \texttt{FileDialog} or \texttt{Slider} widgets 
%are ``terminal'' widgets. 
%``container'' widgets are of another kind : they are 
There is a special kind of widget, called '\texttt{Layout}', designed to  
contain other widgets in order to build larger dialog boxes. 
For example, the \texttt{LayoutSplit} widget is a container which 
``splits'' horizontally a window into two parts, 
each part including another widget. 
The size of the two parts can be adjusted by the user thanks 
to a ``handle''.

The script \texttt{scripts/test/testSplit.bbs} demonstrate its use. 
Run it : it displays a window with two sliders. 
Move the sliders and close the window. 
The final positions of the sliders are printed out. 
Now edit the file to see how this is done :

\begin{file}{scripts/test/testSplit.bbs}
\begin{verbatim}
load std
load wx

new Slider s1
new Slider s2

new LayoutSplit s
connect  s1.Widget s.Widget1
connect  s2.Widget s.Widget2

print s1=$s1.Out$\\n
print s2=$s2.Out$\\n
\end{verbatim}
\end{file}

First, the two sliders \texttt{s1} and \texttt{s2} are created.
A \texttt{LayoutSplit} box \texttt{s} is also created. 
The \texttt{connect} commands then ``includes'' the sliders in the 
split ``container''. 
The input \texttt{Widget} is common to all widget boxes : 
every widget can be inserted into another widget. 
The outputs \texttt{Widget1},\texttt{Widget2}  are specific of \emph{container} 
widgets 
(in \bbi type \texttt{help Slider} : 
you will see the output \texttt{Widget}; 
type \texttt{help LayoutSplit} : 
you will see the inputs \texttt{Widget1} and \texttt{Widget2} 
and the output \texttt{Widget}). 
When you connect the \texttt{Widget} output of a container 
to the \texttt{Widget}i input of a widget, 
you order to include the widget in the container.
Of course, the order of connection is important. 
In our case, the slider \texttt{s1} is included first, 
then the slider \texttt{s2} : \texttt{s1} will be placed 
on top of \texttt{s2} (the \texttt{LayoutSplit} box is 
implemented that way, but this is arbitrary choice).

Right now, there are only \emph{three} container widgets in the \texttt{wx} package : 
\begin{itemize} 
\item {the \texttt{LayoutSplit} widget} we just described, the \texttt{LayoutLine} , and the \texttt{LayoutTab}
widget. 

\item {the \texttt{LayoutLine} widget} can have multiple children and 
divides its window into as much parts as children, 
each part of equal size. 
The orientation of the \texttt{LayoutSplit} or of the \texttt{LayoutLine}  can be changed by the input \texttt{Orientation}.
See the example \texttt{test/testSizer.bbs}.
With only those two containers you can already create 
complex dialog boxes (of course containers can be nested, which leads to tree-like structures of widgets). \\
See the script \texttt{bbtk/share/bbtk/bbs/wx/appli/ExampleLayoutSplit.bbs} for an example.

\item {The \texttt{LayoutTab}  widget} is based on the \texttt{wxNotebook.}\\
The label of each 'note book' is the name of the object it contains.
\end{itemize}


%=====> TODO \\


%One word about a special widget in the package \texttt{wx} : 
%the \texttt{Button}... to be continued.

% ==========================================
\subsubsection{Deeper in the boxes}
\label{bbi-deep-box}
% ==========================================

Any widget box has two mandatory Inputs :
\begin{itemize}
  \item {\bf\emph{BoxExecute}}     : Any signal received by this input executes the box
  \item {\bf\emph{BoxProcessMode}} : Sets the processing mode of the box :
  \begin{itemize}
    \item {\bf\emph{Pipeline}} : bbBackwardUpdate() calls Process() only if Status == MODIFIED \\
                                 The box executes itself only when an entry was changed (normal pipeline processing).
    \item {\bf\emph{Reactive}} : bbSetModifiedStatus() calls bbUpdate() \\
                                 Warning : Re-processed immediately when \emph{any entry} changed.\\
                                 To be more selective, better use \texttt{connect A.BoxChange \emph{currentBox}.BoxExecute}.    
    \item {\bf\emph{Always}}   : bbUpdate() always calls Process. \\
                                 Usefull for 'sources', that must be processed, even when no entry changed (e.g. : FileSelector, ColorSelector)\\
                                 This one is not end user intended (for Package developer only)
  \end{itemize}   
\end{itemize}

Any widget box has five Inputs, that will be dealt with only if the box is not connected to the \emph{Widget}i of any \emph{Layout box} :  
\begin{itemize}
  \item {\bf\emph{WinHeight}} : Height of the window 
  \item {\bf\emph{WinWidth}}  : Width of the window  
  \item {\bf\emph{WinTitle}}  : Title of the window
  \item {\bf\emph{WinClose}}  : Any received signal closes the window
  \item {\bf\emph{WinHide}}   : Any received signal hides the window
  \item {\bf\emph{WinDialog}} : When set to 'true', creates a \emph{dialog window}, that blocks the pipeline until it is closed (\emph{modal})   
\end{itemize}


Any \emph{Layout box} (i.e. \emph{LayoutLine}, \emph{LayoutSplit} or \emph{LayoutTab}) has at one or more mandatory Inputs :
\begin{itemize}
  \item {\bf\emph{Widget}}\texttt{i} : e.g. a \emph{LayoutSplit} box (Widget which splits a window in two resizeable parts) 
       has two Input parameters \emph{Widget1} and \emph{Widget2}, used to embed the child windows.\\
       e.g. a  \emph{LayoutLine} divides the window in up to 9 (depending on the number of inputs \emph{Widget}i) fixed size parts.  
\end{itemize} 


Any widget box has two mandatory Outputs  :

\begin{itemize}
  \item {\bf\emph{Widget}} : that is the \texttt{wxWindow} itself. If it's not connected to the \texttt{Widget}\emph{i} of any \emph{Layout box}, it
     will popup. If it's connected to the \texttt{Widget}\texttt{\emph{i}} of any \texttt{Layout box}, it will be embedded in its parent window.
  \item {\bf\emph{Boxchange}}  : Signals any modification of the box. This output may be connect if necessary to the \emph{BoxExecute} entry of an other box,
   further within the execution pipeline.
\end{itemize}    



% ==========================================
\subsection{More on ...}
\label{bbi-more-on}
% ==========================================

% ==========================================
%\subsubsection{Black box packages}
%\label{bbi-more-on-packages}
% ==========================================
%There are various others user-intended packages :

%\begin{verbatim}
%---> Were moved in a 'Reference Manual' ?\\
%---> Any suggestion welcome!
%\end{verbatim}

%\begin{itemize}
%\item{vtk} \\
%\item{itk} \\
%\item{...} \\
%\end{itemize}
% ==========================================
\subsubsection{Pipeline processing}
\label{bbi-more-on-pipeline-processing}
% ==========================================
\begin{itemize}
\item the ``control'' mechanism in bbi.

When a box is requested to update itself, it asks (recursively) each one of its inputs if it was modified.\\
In normal pipe-line mode, it will be re-processed if at least one of its imputs was actually modified, as the output of a previous box.

(switch exec commands, e.g. Button)
\item the role of ProcessMode to update widgets.
\end{itemize}
% ==========================================
\subsubsection{Complex black boxes}
\label{bbi-more-on-complex-black-boxes}
Creation of complex widgets (containers, contained...)

You can include script files in other script files, 
like in the following example :


\begin{verbatim}
# Defines the Add4 black box which adds 4 doubles 
include Add3
define Add4
  author "myself"
  description "adds 4 doubles"
  new Add3 a
  new Add b
  connect a.Out b.In1
  input In1 a.In1 "first double to add"
  input In2 a.In2 "second double to add"
  input In3 a.In3 "third double to add"
  input In4 b.In2 "fourth double to add"
  output Out b.Out "output"
endefine
\end{verbatim}

The inner boxes have they own entries (In1, In2, In3 for box a, In1, In2 for box b )\\
Only the inputs In1, In2, In3 of box a and the input In2 of box b is of interest for the end user, but he dosn't want to have to
care neither about the inner boxes name, nor about the names of their Inputs.\\
The writer of the complex box has the ability to give these inputs a meaningfull name !
\begin{verbatim}
  input In3 a.In3 "third double to add"
  input In4 b.In2 "fourth double to add"
\end{verbatim}

%\subsubsection{Advanced issues}
%\paragraph{Reducing the number of inputs of a box}

% ==========================================
%\subsubsection{Errors}
%\label{bbi-more-on-errors}

% ==========================================
\subsubsection{Creating and using your own uninstalled version of bbStudio}
\label{bbi-more-on-your_own_version}

Suppose you want to run your own uninstalled version (say : you downloaded and compiled the
cvs version in order to use a recently commited patch, but you want to be able
to still use the standard version).
 
You have to :
\begin{itemize} 
\item cvs checkout the sources :
\begin{verbatim}
cvs checkout bbtk
\end{verbatim}
\item 
create a build directory
\begin{verbatim}
mkdir buildBBTK
\end{verbatim}
\item cd in the build directory:
\begin{verbatim}
cd buildBBTK
\end{verbatim}
\item run ccmake.
\begin{verbatim}
ccmake ../bbtk
\end{verbatim}

Don't forget to switch ON the flag \texttt{BBTK\_COMPILE\_DEBUG\_MESSAGE} \\
(see figure : \ref{bb-ccmake})

\begin{figure}[!ht]
\caption{\label{bb-ccmake}Running ccmake}
\begin{center}
\includegraphics[width=0.6\textwidth]{ccmake.png}
\end{center}
\end{figure}

\item As usual, type \texttt{c} until there is no longer any area quoted with a * (or highlighted in red)\\
Ask for generation (type \texttt{g} -once is always enough-)

\item Ask for compilation and link.
\begin{verbatim}
make
\end{verbatim}


The dynamic libraries (\texttt{.dll} or \texttt{.so} and the executable programs will be created in the \texttt{bin}
directory of the built tree.

\item choose to install or not your own version.
\begin{verbatim}
make install
\end{verbatim}
Linux users : Don't forget to \texttt{sudo} before.
\end{itemize}
% ==========================================


\newpage



% ==========================================
%\vspace{0.5cm}\hrule \\

\section{Using third party Package}
\label{Third_Party_Package}
% ==========================================
% ==========================================
\subsection{Plugging in a Package}
\label{Plugging_in_a_Package}
% ==========================================

\bbStudio makes it easy for you : in the menu \texttt{Tools} just click on the 
option \texttt{Plug Package}. You will be asked to  to '\texttt{Select
package directory}'. Browse untill you find the the install tree, or the the build tree,
depending whether you installed the package or not.\\

\bbStudio will update the Configuration file, generate the 'Package
documentaion', and update the 'Box List'.\\
You will be able to use the new package just as you did for any other \bbtk
canonical Package.

% ==========================================
\subsection{Hard incorporating of a Package}
\label{Hard_incorporating_of_a_Package}
% ==========================================

If the Package you want to use is supplied in a non standard way (e.g. : you
where given one ore more dynamic libraries (\texttt{.dll} or \texttt{.so}), and
one or more directories containing \bbtk scripts (\texttt{.bbs}), you will have
to proceed to some (simple) manual operations.\\
\texttt{Nota bene} : This way is hightly discouraged !

% ==========================================
\subsubsection{More on the configuration file}
\label{The_configuration_file}
% ==========================================

First, have a glance at the Configuration,  just clicking on \texttt{Config} button of the \texttt{Command} part toolbar.

You'll get something like :

\begin{verbatim}
=============
 Configuration
 =============
 bbtk_config.xml    : [/home/jpr/Creatis/bbtk/binLIN/bin/bbtk_config.xml]
 Documentation Path : [/home/jpr/Creatis/bbtk/binLIN/bin/../share/bbtk/doc]
 Data Path          : [/home/jpr/Creatis/bbtk/binLIN/bin/../share/bbtk/data]
 Temp Directory     : [/home/jpr/Creatis/bbtk/binLIN]
 File Separator     : [/]
 BBS Paths   
 --- [.]
 --- [/home/jpr/Creatis/bbtk/binLIN/bin/../share/bbtk/bbs]
 --- [/home/jpr/Creatis/bbtk/binLIN/share/bbtk/bbs]
 PACKAGE Paths : 
 --- [.]
 --- [/home/jpr/Creatis/bbtk/binLIN/bin]
 --- [/home/jpr/Creatis/bbtk/binLIN/bin/../lib]
 --- [/home/jpr/Creatis/bbtk/binLIN/bin]
 --- [/home/jpr/Creatis/bbtk/binLIN/bin\Debug]
 --- [/home/jpr/Creatis/bbtk/binLIN/bin\Release] 
\end{verbatim}

(depending on who you are, and whether \texttt{bbStudio} is installed or not.)\\

Note the two main parts : \texttt{BBS Paths} and \texttt{PACKAGE Paths}
\subsubsection{How bbStudio uses the Configuration file}
\label{How_bbStudio_uses_the_Configuration_file}


At start, \bbi tries to open an \texttt{xml} 
configuration file named \texttt{bbtk\_config.xml}. 
The search order is 
\begin{enumerate}
\item The current directory
\item The subdir \texttt{.bbtk} of the user's home directory. 
\begin{itemize} 
\item On \texttt{Unix}, the home directory is the
one stored by the environnement variable \texttt{HOME}, 
typically \texttt{/home/username}.
\item On \texttt{Windows}, the home directory is 
the user's profile directory stored by the environnement 
variable \texttt{USERPROFILE}, 
typically \texttt{C:\\...}.
\end{itemize}
\item If none of these two paths contains the file then it creates 
a new one in the \texttt{.bbtk} directory. 
\end{enumerate}


To use a third party Package, you will have to update it.\\

\subsubsection{Modifying the Configuration file}
\label{Modifying_the_Configuration_file}

Just use the \texttt{Open bbtk Config file} option of the \texttt{Files} of the \bbStudio menu.

You will get something like :
\begin{verbatim}
<config>
  <description> Sets the search directories in the build tree </description>
  <url> </url>
  <bbs_path> /home/jpr/Creatis/bbtk/binLIN/share/bbtk/bbs </bbs_path>
  <package_path> /home/jpr/Creatis/bbtk/binLIN/bin </package_path> 
# For windows
  <package_path> /home/jpr/Creatis/bbtk/binLIN/bin\Debug </package_path> 
  <package_path> /home/jpr/Creatis/bbtk/binLIN/bin\Release </package_path> 
#
  <data_path> </data_path>
# 
  <default_temp_dir>  /home/jpr/Creatis/bbtk/binLIN </default_temp_dir>   
</config>
\end{verbatim}

To use a new Package :
\begin{itemize}
\item {}
After the already existing \texttt{xml} tags 
\texttt{bbs\_path}
 (i.e. the lines begining by 
 \texttt{<bbs\_path>} 
 %bbs_path
and ending by 
\texttt{</bbs\_path>}), 
you can add paths to :
\begin{itemize}
\item A custom folder in which to search for \texttt{.bbs} scripts (\texttt{include} command of \bbins) by adding
 an \texttt{xml} tag:\\ 
 \texttt{<bbs\_path>} 
\emph{complete\_path\_to\_scripts\_folder}
\texttt{<\/bbs\_path>}.
\end{itemize}

\item {}
After the already existing tags 
\texttt{package\_path}
 (i.e. the lines begining by 
 \texttt{package\_path} 
 %bbs_path
and ending by 
\texttt{/package\_path}), 
you can add paths to :
\begin{itemize}
\item A custom folder in which to search for packages (the dynamic libraries
 (\texttt{.dll} or \texttt{.so}, called with the \texttt{load} command of \bbins) by adding an \texttt{xml} tag :\\ 
\texttt{<package\_path>} 
\emph{complete\_path\_to\_dynamic\_library\_folder}
\texttt{<\/package\_path>}.
\end{itemize}
\end{itemize}


%\end{itemize}
% ==========================================
\subsection{Updating the documentation}
\label{Updating_the_documentation}
% ==========================================
You may add your own boxes (simple boxes, if you are aware enough in \CPP
language), or complex boxes if you are aware enough in bbtk scripting).

To be able to use the Help tools as well as the features provided by this package,
 you must use the
option \texttt{Regenerate package doc}  in the menu \texttt{Tools} of \texttt{bbStudio}.\\
You'll be prompted for the Package name. Avoid using the \texttt{-a} option (Regenerate all), since it's time consumming.

To benefit the features of Box indexing you must use the
option \texttt{Regenerate Boxes Lists}  in the menu \texttt{Tools} of \texttt{bbStudio}.\\


% ==========================================
\subsection{Using the package}
\label{Using_the_package}
% ==========================================

The only thing you have to do is to \texttt{load} the package, within the script, or from the
\texttt{Command} part, and enjoy the black boxes it contains.

% ==========================================
\subsection{Packages you'll probably want to use }
\label{Packages_you_ll_want_to_use}
% ==========================================
\begin {itemize}
\item{\texttt{creaLib}} \\
a.k.a \texttt{crea}. It's a set of 'low level' utilities, needed by other
packages (an, sure,  useful as well for people that doesn't use bbtkns.

\item{\texttt{creaContours}} \\
Provides sophisticated widgets for managing 3D R.O.I. (Regions of interest)
\item{\texttt{creaImageIO}} \\
Allows browsing, selectionning, ordering directories containing images of almost any type
(including DICOM)
\end {itemize}

\newpage
 
% ==========================================
%\vspace{0.5cm}\hrule \\
\section{Using black boxes in \CPP programs}
\label{cpp}
% ==========================================

A very useful feature is that you may use any black box within a \CPP program without worrying about \texttt{wxWigets} main window.\\

Let's look a the following bbs script :

\begin{verbatim}
# Load the packages
load std
load wx

# Create the Objects
new Slider     slider
new OutputText text
new LayoutLine layout

# Graphical pipeline
connect slider.Widget    layout.Widget1
connect text.Widget      layout.Widget2

# Execution pipeline
connect slider.BoxChange text.BoxExecute
connect slider.Out       text.In

# Go!
exec layout
\end{verbatim}

User wants to create a slider and an output text, within a LayoutLine, and display the slider value in the output text.\\ 
Think about the (little!) nightmare to code the same, in 'raw C++', using wxWidgets.\\

Using the standalone application \texttt{bbc} you just 'convert' the script.

\begin{verbatim}
#include <bbwxSlider.h>
#include <bbwxOutputText.h>
#include <bbtkFactory.h>
#include <bbwxLayoutLine.h>

int main(int argv, char* argc[])
{
      // we need to intanciate a bbtk::Factory to be aware of the adaptors
      bbtk::Factory::Pointer factory = bbtk::Factory::New();
      
      // Load the packages
      // ----------------  
      factory->LoadPackage("std");
      factory->LoadPackage("wx");
      
      // Create the Objects
      // ------------------      
      bbwx::Slider::Pointer     slider   = bbwx::Slider::New("slider");
      bbwx::OutputText::Pointer text     = bbwx::OutputText::New("text");
      bbwx::LayoutLine::Pointer layout   = bbwx::LayoutLine::New("layout");
      
      // Graphical pipeline
      bbtk::Connection::Pointer c1       = bbtk::Connection::New(slider,"Widget",
                                                           layout,"Widget1");
                                                           
      bbtk::Connection::Pointer c2       = bbtk::Connection::New(text,"Widget",
                                                           layout,"Widget2");
                                                                                                                                                                           
      // Execution pipeline
      // ------------------
      
      // We have to pass the 'factory', in order to call automatically an adaptor,
      // if necessary.
      bbtk::Connection::Pointer s2t      = bbtk::Connection::New(slider,"Out",
                                                            text,"In",
                                                            factory);      
       bbtk::Connection::Pointer c3       = bbtk::Connection::New(slider,"BoxChange",
                                                            text,"BoxExecute");      
      layout->bbSetInputWinDialog(true);
      
      // Go!
      // ---     
      layout->bbExecute();

    }
  catch (bbtk::Exception e)
    {
      bbtk::MessageManager::SetMessageLevel("Error",1);
      e.Print();
    }
}
\end{verbatim}

%\bibliography{all}

% ==========================================
\section{Language reference}
\label{bbi-reference}
% ==========================================


% ==========================================
\subsection{Pipeline creation and execution related commands}
\label{bbi-reference-creation-execution}
% ==========================================
 See table \ref{bbi-reference-box}

% ==========================================
\begin{table}[!ht]
\caption{\label{bbi-reference-box} \bbi pipeline creation and execution related commands.}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline

\texttt{new} & \texttt{<boxtype>} \texttt{<box-name>}& 
Creates a box of type \texttt{boxtype} and name  
\texttt{box-name}.\\ \hline

\texttt{delete} & \texttt{<box-name>} & 
Destroys the box named \texttt{box-name}.\\ \hline 

\texttt{connect} & \texttt{<box1.output>} \texttt{<box2.input>} & 
Connects the output 
\texttt{output} of the box named \texttt{box1} 
to the input \texttt{input} of the box named \texttt{box2} \\ \hline 

\texttt{set} & \texttt{<box.input>} \texttt{<value>} &
Sets the input \texttt{input} of 
the box named \texttt{box} to the value \texttt{value}.
An \texttt{adaptor} must exist
in the packages loaded which converts a \texttt{std::string} 
to the type of the input \texttt{input}. \\ \hline 

\texttt{print} & \texttt{<string>} & 
Prints the string after substituting each token of the form \texttt{\$box.output\$} by the adaptation to string of the value of the 
output \texttt{output} of the box named \texttt{box}. 
An \texttt{adaptor} must exist
in the packages loaded which converts 
the type of the output \texttt{output}
to a \texttt{std::string}.
\\ \hline 

\texttt{exec} & \texttt{<box-name>} & 
Executes the box named \texttt{box-name}.
If needed the boxes 
connected to its inputs 
are also processed recursively (pipeline processing).\\ \hline 
\texttt{exec} & \texttt{freeze} & 
 Allows to block execution commands while keeping definition commands active.(This one is not for end user)\\ \hline 
\texttt{exec} & \texttt{unfreeze} & 
 Turns back to 'normal' mode (This one is not for end user).\\ \hline 
\end{tabular}
\end{table}
% ==========================================

\newpage

% ==========================================
\subsection{Interpreter related commands}
\label{bbi-reference-interpreter}
% ==========================================
See table \ref{tabbbi-reference-interpreter_1} and \ref{tabbbi-reference-interpreter_2}
% ==========================================
\begin{table}[!ht]
\caption{\label{tabbbi-reference-interpreter_1}\bbi intepreter related commands (part 1).}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline

\texttt{author} &  \texttt{<author-name>} & 
Adds the string \texttt{<author-name>} to the author information of the black box being defined \\ \hline 

\texttt{category} & \texttt{<category-name>} & 
  Adds the string \texttt{<category-name>} to the category information of the black box being defined \\ \hline 

\texttt{help} & - & 
Prints help on available commands \\ \hline 

& \texttt{<command-name>} & 
Prints help on the command \texttt{command-name} \\ \hline 

& \texttt{packages} & 
Prints help on available packages and their box types 
(without description)\\ \hline 

& \texttt{<package-name>} & 
Prints help on the package \texttt{package-name} and its boxes 
(with brief description). 
The package must have been previously loaded \\ \hline 

& \texttt{<box-type>} & 
Prints help (with full description) on the type of box 
\texttt{box-type}. 
The box type must belong to a package which has been previously loaded \\ \hline 

& \texttt{<debug-directive>} & 
[expr|-C|-D] 
  Prints debug info on living bbtk objects containing the string \texttt{expr} (default expr=''). 
         \texttt{-C} checks the factory integrity.
         \texttt{-D} turns on objects debug info after main ends\\ \hline 

\texttt{include} & \texttt{<file-name>} & 
Includes and executes the content of the file named \texttt{file-name} 
exactly like if you were typing its content at the place were the 
\texttt{include} command is. \\ \hline 

\texttt{load} & \texttt{<package-name>} & 
Loads the package \texttt{package-name} (use it only if you know that you won't work with complex black boxes) \\ \hline 

\texttt{include} & \texttt{<package-name>} & 
Loads the package \texttt{package-name} and includes all the complex black boxes that comes with it \\ \hline 

\texttt{kind} & \texttt{<box kind>} & 
Specifies the \texttt{kind} of the complex black boxes you are describing \\ \hline 
\end{tabular}
\end{table}

%
% This arbitrary part1/part2 is to avoid to have all the tables at the end of the docoment ...
%

\begin{table}[!ht]
\caption{\label{tabbbi-reference-interpreter_2}\bbi intepreter related commands (part 2).}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline
\texttt{unload} & \texttt{<package-name>}& 
Unloads the package \texttt{package-name}. 
The package must have been previously loaded. 
No box of a type defined in this package must still exist.\\ \hline 

\texttt{message} & \texttt{<category>} \texttt{<level>} & 
Sets the level of verbosity of \bbi for the category of messages 
\texttt{category} to \texttt{level}.\\ \hline 
%See \ref{verbosity}.

\texttt{config} & - & Displays the Configuration parameters\\ \hline 

\texttt{reset} & - & Deletes all boxes and unloads all packages so 
that \bbi gets back to its initial state \\ \hline 

\texttt{quit} & - & Exits the interpreter (Don't use it under \bbStudions)\\ \hline 

\end{tabular}
\end{table}
% ==========================================

\newpage

% ==========================================
\subsection{Complex black box definition related commands}
\label{bbi-reference-black-box-definition}
% ==========================================

See table \ref{bbi-reference-complex-box} 
% ==========================================
\begin{table}[!ht]
\caption{\label{bbi-reference-complex-box} \bbi complex black box definition related commands.}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline


\texttt{define} & \texttt{<box-type>} & 
Starts the definition of a complex black box of type  
\texttt{box-type}\\ \hline 

\texttt{endefine} & - & 
Ends the definition of a complex black box type\\ \hline 

\texttt{author} & \texttt{<string>} & 
Sets the author(s) of the complex black box currently being defined \\ \hline 

\texttt{description} & \texttt{<string>} & 
Sets the description of the complex black box currently being defined \\ \hline 

\texttt{input} & \texttt{<name>} \texttt{<box.input>} \texttt{<help>} & 
Defines a new input for the current complex black box, 
named \texttt{name}. 
It is defined as corresponding to 
the input \texttt{input} of the box \texttt{box}.
 
\texttt{<help>} is the help string for the new input.
The box \texttt{box} must already have been created in the complex box 
and of course have an input named \texttt{input}.\\ \hline 

\texttt{output} & \texttt{<name>} \texttt{<box.output>} \texttt{<help>} & 
Defines a new output for the current complex black box, 
named \texttt{name}. 
It is defined as corresponding to 
the output \texttt{output} of the box \texttt{box}. 
\texttt{<help>} is the help string for the new output.
The box \texttt{box} must already have been created in the complex box and of course have an output named \texttt{output}. \\ \hline 


\end{tabular}
\end{table}
% ==========================================

\newpage

\section{Install and run time issues}

\begin {itemize}
\item{make} \\
For some strange reasons (?!?), at \texttt{cmake} time, you may be warned that an error occured while documentation generation.\\
Take it easy, \texttt{make} again!\\

\item{\bbStudio} is written using the Advanced User Interface library of wxWidgets.
If, after some hazardous floating/docking operations onto the frame, you feel
very unhappy with the result, just remove from the hidden directory
\texttt{.bbtk} the file named \texttt{bbStudio.aui}. \\ 

 
\end {itemize}

%\section{Conclusion}


\end{document}