reorganisation Writing script files + nouvelle illustration

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

% ==========================================
\documentclass[11pt,final,a4paper]{article}
\input{config.tex}
\begin{document}
\bbtkGuide[User's Guide]
% ==========================================


% ==========================================
\newpage
\hrule
\section{Introduction}
Note: pdf version of this User's Guide can be retrieved from the following URL:\\
\url{http://www.creatis.insa-lyon.fr/creatools/documentation}
% ==========================================
\subsection{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}

% ==========================================
\subsubsection{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 these definitions: 
not only the inputs and outputs are of interest but also 
\emph{what the box does!}
Hence, we 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 grouping of black boxes into 
so called {\bf packages}, 
which are \emph{dynamic libraries} that can also 
be queried, in particular about the boxes they provide. 
The package structure then offers a mechanism similar to \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 give 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:  \bbs (the Black Box Script language) and its interpreter
\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 that 
have been written by different persons, using different libraries, etc. 
\end{itemize}


% ==========================================
\hrule
\paragraph{Summary}
%\hrule
A \texttt{black box}:
\begin{itemize}
        \item has a name (this is actually a type name),
        \item has a description and an author, 
        \item belongs to categories (keywords that allow to index it
into automated documentation, and that are specified in the box definition),
        \item has inputs and outputs that in turn have their:
        \begin{itemize}
                \item names,
                \item types (any C++ type),
                \item descriptions, 
        \end{itemize}
        \item does something and can be executed, i.e. outputs are updated according to inputs.
\end{itemize}
A \texttt{package}:
\begin{itemize}
        \item is a ``plug-in'' in the \bbtk framework,
        \item has a name
        \item has a description and an author. 
        \item contains:
        \begin{itemize}
                \item a dynamic library (dll/so/dylib) that contains compiled
black boxes (e.g.: dynamic library name of the package `std' is `bbstd.dll', `libbbstd.so' or `libbbstd.dylib' depending on the platform),
                \item bbs scripts: script-defined boxes, examples, applications,
                \item data: test data, resources.
        \end{itemize}
        \item is automatically documented.
\end{itemize}
\hrule
% ==========================================

% ==========================================
\subsubsection{{\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{"core" 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 visualization and
      interaction).
      %\item {\bf\emph{creaImageIO}}: Provides hight level widgets to read images, including DICOM.
      \item {\bf\emph{itkvtk}}: adaptors permitting to connect \itk boxes to \vtk boxes and conversely.
      \item {\bf\emph{kw}}: widgets based on \texttt{KWWidgets} library (medical-image oriented:
slicer, transfer function editors, etc.).
      \item {\bf\emph{demo}}: some black-box based demos.
      \item {\bf\emph{appli}}: some black-box based standalone applications.
      \item {\bf\emph{toolsbbtk}}: tools for bbtk administration and package development.     
    \end{itemize}
  \item A {\bf\emph{development environment}}, called \bbStudio, which provides:
    \begin{itemize}
      \item An online {\bf\emph{script editor and interpreter}}
      \item A powerful html {\bf\emph{help environment}}, integrating:       
        \begin{itemize}
          \item Online documentation scanning
          \item Retrieving boxes on various criteria
          \item Checking demos and examples
        \end{itemize}
      \end{itemize}
      \item A standalone {\bf\emph{interpreter}}, called \bbins, which allows to 
           execute \bbs scripts.
      \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 \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 \bbc (sorry: Linux only, for the moment) that compiles \texttt{.bbs} scripts into executables.
            \item \bbRegeneratePackageDoc which creates the html documentation of the Package.
            \item \bbRegenerateBoxesLists which creates the html pages of the various lists of all the currenly installed boxes.
            \item \bbPlugPackage which automatically incorporates a new package.                  
         \end{itemize}
      \item A full {\bf\emph{documentation}} that can be printed (pdf), browsed (html) and
      queried through keywords.           
\end{itemize}

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

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

%%\newpage

% ==========================================
\subsection{Content of this guide}
% ==========================================

Read this \texttt{Users' Guide} if you want to learn how to use 
\bbtk development environnement \bbStudio and how to write black box scripts.\\
If your aim is to write your own Packages and Black Boxes, you have to read the
\texttt{Package Developper's Guide}.

% ==========================================
\newpage
\hrule
\section{Getting started with bbStudio}
\label{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.
You'll get something like in figure 
\ref{bbi-fig-bbStudio-gui}
(the exact appearance of \bbStudio is Operating System and \bbtk version dependent).

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

%Let's have a look at the resized window :
\begin{figure}[!ht]
\caption{The bbStudio Development environment interface}
\begin{center}
\includegraphics[width=0.7\textwidth]{bbStudioMainPage.png}
\end{center}
\label{bbi-fig-bbStudio-gui}
\end{figure}

The interface is divided into four parts: \texttt{Files}, \texttt{Messages},
 \texttt{Command}, \texttt{Help}.
It 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.
Feel free to resize/reposition any part you want.
Your preferences will be kept next time you run again \bbStudions. 

%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 is the \bbs script editor (see section \ref{Scripting} to learn about scripting).

If you load a file holding a script, it will be displayed in this area, and you will be
able to modify it, to save it, to save-as it and to run it, using the respective
lower-toolbar buttons (see figure \ref{lowertoolbar}).

\begin{figure}[!ht]
\caption{The 'Files' lower toolbar}
\begin{center}
\includegraphics[width=0.7\textwidth]{lowertoolbar2.png}
\end{center}
\label{lowertoolbar}
\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:\\
\begin{itemize}
\item {\bf\emph{System messages:}} produced by the kernel, in case of a user mistyping, or an execution error.\\
\item {\bf\emph{Script messages:}} produced by the \bbtk equivalent of \texttt{printf} 
or \texttt{std::cout} in user programs.
\end{itemize}


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

You can type here \bbs commands which are executed on the fly.
The buttons are shortcuts to the most frequently used commands.
The command (or button) \texttt{help} permits to print in the \texttt{Message} zone the list of all recognized commands, while the command \texttt{help} \emph{command\_name} provides the help on the selected command.

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

The 'Help' part of \bbStudio is used to browse the html help of \BBTKns. You can find there various guides (see section~\ref{sec:guides}) and detailed information about each black box available (see section~\ref{sec:boxes_help}). They can be browsed alphabetically, by package and by category. Two special categories, demos and examples, are available via direct links (see section~\ref{sec:demos_examples}).


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




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



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

Various levels of help are supplied by \bbStudions.

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


The 'working' area (the left one, as opposed to the (\texttt{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 (\texttt{Messages}) 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.
Command-line help for the black box scripting language \bbs (see section \ref{Scripting}) can be obtained in this zone. \par
As mentioned above, the command (or button) \texttt{help} permits to print in the \texttt{Message} zone the list of all recognized commands, while the command \texttt{help} \emph{command\_name} displays in this zone the help about the selected command.\par
The command \texttt{help} \emph{package\_name} displays in the \texttt{Message} zone a short information about the selected package, provided that this package was previously loaded (Note that you can know which packages were loaded by executing the command \texttt{help packages}). Furthermore, it simultaneously displays in the right zone (\texttt{Help}) the corresponding full html help available.\par
In a similar way, one can obtain the information about any box from the loaded packages, by executing the command \texttt{help} \emph{box\_name}. Note that some boxes may be unavailable if the command \texttt{load} was used to load the package, since this command only loads the boxes in binary. Some boxes are defined in script files. To be sure that all the boxes from the package are loaded the command \texttt{include} is to be preferred.\par
You can also get the list of the objects currently present in the workspace, by executing the command \texttt{help workspace}.

% ==========================================
\subsubsection{Guides}
\label{sec:guides}
% ==========================================

All the guides can be browsed in html version in the \texttt{Help} part of \bbStudions. Their pdf versions (except Doxygen documentation) can be retrieved from:\\
\url{http://www.creatis.insa-lyon.fr/creatools/documentation}

 \begin{itemize}      
     \item {\bf\emph{User's Guide}}: This guide!
     \item {\bf\emph{Package Developer's Guide}}: Step-by-step "How-to" for programmers who want to create their 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 files. Should only concern the kernel developers.
   \end{itemize}
        

  

% ==========================================
\subsubsection{Boxes Help}
\label{sec:boxes_help}
% ==========================================
 Lists of currently available boxes from installed packages, sorted according to the following criteria:
   \begin{itemize} 
    \item {\bf\emph{Alphabetical list}}%: This is the 'zero-level' of retrieving.
    \item {\bf\emph{List by package}}%: The boxes are indexed by package they belong to
    \item {\bf\emph{List by category}}:
     Each box is indexed by a list of keywords, called 'categories', such as '\texttt{read/write}',
     '\texttt{filter}', '\texttt{viewer}', ...
    A given box may belong to more than one \texttt{category}, however some categories are mutually exclusive.
    Standard categories are:
    \begin {itemize}
       \item\texttt{atomic box}/\texttt{complex box}\\
       Any box is either atomic or complex.\\
       The former are 'atomic' units written in C++ and available in binary form.\\
       Any pipeline built up as an assembly of several black boxes (atomic or complex), and described in \bbs script language is itself viewed as a complex black box, and hence tagged as belonging to the latter category.
       \item\texttt{example} / \texttt{demo} / \texttt{application} (see \ref{sec:demos_examples})\\
          These ones are scripts that produce a result when executed (i.e. they
          execute a pipeline), as opposed to the scripts that only define complex boxes but do not instanciate and execute boxes. 
          \begin {itemize}
             \item\texttt{example}: It is just a (simple) example, for programmers, of how to use a given feature. The \texttt{Examples} link on the starting page links to the list of the boxes of this category.
             \item\texttt{demo}: It can be a 'good looking' (a.k.a 'sexy') example of some sophisticated work, done only by using \texttt{bbtk}. The \texttt{Demos} link on the starting page links to the list of the boxes of this category.
             \item\texttt{application}: It is a final application, end-user intended (e.g. association of a DICOM image browser, reader, viewer with some interaction and processing)    
          \end {itemize}
        \item\texttt{widget}: A piece of graphical interface (based on \texttt{wxWidgets}).
        \item\texttt{dicom}: A box related to medical images in Dicom format.
        \item\texttt{viewer}: A box allowing to view something (e.g. an image).
        \item\texttt{read/write}: An I/O-related box.
        \item\texttt{mesh}: A mesh-related box.
        \item\texttt{filter}: A filter, mainly image filters.
        \item\texttt{image}: An image-related box.
        \item\texttt{3D object creator}: A box which creates a 3D object to be injected into a 3D view (e.g. a plane, a surface).
        \item\texttt{math}: Maths of course.
        \item\texttt{misc}: Miscellaneous...       
    \end {itemize}
  Remark that the list of categories is 'auto-extensible': each time a new box is created which belongs to a new category and the boxes list is regenerated, the new category appears in the list, holding the new box. The above list only contains the categories used in the packages provided with current \bbtk release.
    \item {\bf\emph{ List of adaptors}}: The adaptors are a special type of black boxes that are used internally to perform type conversions. Although they are not end user intended, you may see their list. Adaptors belong to the \texttt{adaptor} category.
  \end {itemize}
  For each box, the html \texttt{Help} provides the informations necessary to use it: its name, its purpose, the descriptions of its inputs/outputs and the name of the package (or script file) that is to be loaded. Note that for a given box only the inputs/outputs listed in white cells are of actual interest. The remaining ones, grouped after them in colored cells, are standard (have the same names and purpose) in all atomic boxes. Additionally, for all boxes but the atomic ones (i.e. for all boxes defined in \bbs script language), the corresponding script is available via [\texttt{source}] link. Actually, by clicking on this link, one loads the script into the \texttt{Files} area where it can be analyzed, edited and executed.
  
% ==========================================      
\subsubsection{The Package Browser}
\label{Package_Browser}
% ==========================================

The package browser is a standalone application \texttt{bbPackageBrowser}, which 
dynamically loads and queries the available packages. 
It is thus a smarter tool than the static html documentation.
You can run it independently or from \bbStudio using either the button labeled \texttt{Start Package Browser} of the 'Command' part or the corresponding entry in the menu 'Windows'. 
Note that it may take some time to start because it loads all available 
packages at start.
Its appearance is reproduced in figure \ref{imPackage_Browser}.

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

It allows you to find boxes by use of a multi-criteria filtering principle: 
the boxes listed are the ones the attributes of which match \emph{all} the 
words entered in the 'Filter' part.
You can get the whole description of a given box by clicking on its name.
\\
Warnings: 

\begin{itemize}
\item It is case sensitive, i.e '\texttt{Button}' 
will give different results than '\texttt{button}'.
\item After typing a filtering string, you have to validate it by pressing the 'Enter' key, in order to update the display of the boxes list.
\item A filtering string only needs to match a subpart of the related attribute of a box.
For example, entering 'utt' in the 'Name' attribute will match a box called 'Button'.
\end{itemize}

Attributes:

\begin {itemize}
\item \texttt{Package}: The name of the package to which the box belongs (e.g. \texttt{wxvtk}, \texttt{std}).
\item \texttt{Name}: The name of a box or an application (e.g. \texttt{Reader}, \texttt{example}).
\item \texttt{Description}: A part of the description of a box (e.g. \texttt{3D}, \texttt{image}).
\item \texttt{Category}: The categories of the box (e.g. \texttt{demo}).
\item \texttt{Input/Output Type}: The \CPP type of an input or output (e.g. \texttt{vtkImageData*}, \texttt{std::string}).
\item \texttt{Input/Output Nature}: The \texttt{nature} of an input or output (e.g. \texttt{file name}, \texttt{signal}).
\end {itemize}

%If 'Show widgets' is selected then 


%%\newpage 



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

%\newpage

% ==============================================
\subsection{Running Demos and Examples}
\label{sec:demos_examples}
% ==============================================

As previously mentioned, the links \texttt{Demos} and \texttt{Examples} in the 'Help' part (See figure \ref{HelpContents}), give access to special complex boxes from the respective categories. Here, we use an example, both to illustrate the use of this help and to explain a short \bbs script.\\

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

%\newpage
Select \texttt{Examples} link. You will get a list of examples (See figure \ref{example}).

Note: due to an unfixed bug in Linux, you have to click on 'reload' to get it. \\ 


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


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


Select \texttt{wx::exampleSlider}.
 
\begin{figure}[!ht]
\caption{Html documentation of example 'exampleSlider'}
\begin{center}
\includegraphics[width=0.7\textwidth]{exampleSlider.png}
\end{center}
\label{exampleSlider}
\end{figure}

You can see information about the example and 
the graphical representation of the workflow defined by the script
(the elementary boxes that compose it, and their connections, see figure \ref{exampleSlider}).

Click on \texttt{[source]}, it will be loaded
in the 'Files' part, within the script editor (See figure \ref{exampleSliderSource});

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

Run it, using the 'Files' 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 whether it actually works...

%\newpage

Just a few words on what you saw:
\begin{itemize}
\item{In the source code of the script}:
        \begin{verbatim}
   load std
   load wx
        \end{verbatim}
        These \bbs commands load the packages \texttt{std} and \texttt{wx}
        \begin{verbatim}
   new Slider     slider
   set slider.ReactiveOnTrack 1
        \end{verbatim}
        We create a \texttt{Slider} box called \emph{slider}.

        We tell it to inform anybody that's interested in, that the cursor moved, each time it moved. 
        The default behaviour is to inform only when cursor is released.
        \begin{verbatim}
   new OutputText text
        \end{verbatim}
        We create an \texttt{OutputText} box called \emph{text} 
        (in which slider value will be displayed)

        \begin{verbatim}
   new LayoutLine layout
        \end{verbatim}
        We create a \texttt{LayoutLine} box called \emph{layout},
        a widget box designed to embed other widgets (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. 
        This also produces the execution of the boxes connected to it (the slider, the text).

\item{In the Help part}

        You can see the graphical representation of the workflow (pipeline) created by the script, 
        as in figure \ref{SmallGraph}.


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

        The representation includes 
        both the graphical interface-related pipeline 
        (\emph{slider} and \emph{text} are embedded into \emph{layout})
         and the data processing-related pipeline 
        (\emph{slider} warns \emph{text} immediately when it's modified, 
        \emph{slider} passes \emph{text} its output value)\footnote{Yes, we know : all the arrows                       (graphical interface pipeline arrows and data processing arrows) 
        are blue; using different colors is planned for next release...}.
 
        You can get a much more detailed graph, 
        like in figure  \ref{LargeGraph}, 
        just clicking on the button 
        '\texttt{graph (detailed)}' in the toolbar of the \texttt{Command} part. 

 
        \begin{figure}[!ht]
        \caption{Detailed graphical representation of a pipeline}
        \begin{center}
        \includegraphics[width=0.75\textwidth]{LargeGraph.png}
        \end{center}
        \label{LargeGraph}
        \end{figure} 

\end{itemize}
%\newpage

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

At last, let us have a look at \bbStudio menu (see figure \ref{themenu}).

\begin{figure}[!ht]
\caption{The bbStudio menu}
\begin{center}
\includegraphics[width=0.7\textwidth]{themenu.png}
\end{center}
\label{themenu}
\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 developers to create a new empty package.
        \item{\texttt{Create black box}}:
        Provides a graphical interface to help package developers to create a new empty black box, and add it to an already existing package.   
        \item{\texttt{Plug Package}}:
        Incorporates a package into the list of known packages. Updates the html documentation.
        \item{\texttt{Regenerate package doc}}:
        If a package has changed (e.g. new boxes) this updates the package html documentation.
        \item{\texttt{Regenerate boxes list}}:
        Updates the boxes lists (alphabetical, by package, ...)
        \item{\texttt{Regenerate all}}:
        Regenerates all the packages documentations and the boxes lists (may be long...).
        \item{\texttt{Show last graph}}:
        Shows the last pipeline graph that was generated
     \end {itemize}     
  \item{\texttt{Options}}
     \begin {itemize}
        \item{\texttt{Reset before running}}: Before running a script, all the already created boxes are destroyed, 
        all the already loaded packages are unloaded (this is the recommended option).   
     \end {itemize}     
  \item{\texttt{Windows}}
  User may decide, for any reason of his own, to hide one or more panels:
     \begin {itemize}
        \item{\texttt{Show 'Files' panel}}
        \item{\texttt{Show 'Help' panel}}
        \item{\texttt{Show 'Command' panel}}
        \item{\texttt{Show 'Messages' panel}}
        \item{\texttt{Start Package browser}}: starts the package browser (see \ref{Package_Browser}).
     \end {itemize}     
  \item{\texttt{About}}
     \begin {itemize}
        \item{\texttt{About}}: Info about \texttt{bbStudio}.       
     \end {itemize}     
\end {itemize}




% ==========================================
% ==========================================
% ==========================================
% ==========================================
\newpage
\hrule
\section{Writing black box scripts (\bbsns)}
\label{Scripting}
% ==========================================
% ==========================================
% ==========================================

This section introduces how to write down black box scripts (\bbsns) 
to create and execute pipelines. 

% ==========================================
\subsection{The commands}
% ==========================================
In the sequel the commands entered by the user will be preceded by a prompt (\texttt{>}).
To get started, type in the \texttt{Command} area:
\begin{verbatim}
> help 
\end{verbatim}

you get the following list of the commands recognized by 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 the help on a particular command, type \texttt{help <command name>}, e.g.:
\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 interpreter, including the \texttt{help} command itself! Indeed:
\begin{verbatim}
> help help
\end{verbatim}

gives:
\begin{verbatim}
 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 connections
             of a black box instance.
\end{verbatim}

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


% ==========================================
\subsection{Creating and executing black boxes}
% ==========================================

At start the interpreter 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 interpreter 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},
which is a special type of black box, 
called complex black box, the purpose of which is 
to store other black boxes. 
Any black box you create in \bbStudio is stored 
in \texttt{workspace}  
(see also section \ref{bbi-command-line-app}).

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                   
   Add                     
   ConcatStrings           
   Configuration           
   Div                     
   ExecBbiCommand          
   ExecSystemCommand       
   GetVectorCharElement    
     ...
   MagicBox                
   MakeFileName            
   Mul                     
   MultipleInputs          
   StringRelay             
   StringSelect            
 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. Note that you will get a more detailed information about the package loaded (here \texttt{std}) if you type: 
\begin{verbatim}
> help std
\end{verbatim}

Indeed, each of the items listed is followed by its short description:
\begin{verbatim}
 Package std v1.0.0- laurent.guigues at creatis.insa-lyon.fr
 Basic useful boxes
 Black boxes : 
   ASCII                   : ascii codes sequence to string - ...
   Add                     : Adds its inputs
   ConcatStrings           : String concatenation
   Configuration           : Gets configuration informations
        ...
\end{verbatim}
Additionally, in the right part of the screen ('Help' zone) the corresponding html page is displayed.

Now, if you type:  
\begin{verbatim}
> help Add
\end{verbatim}

\bbStudio displays the appropriate html page in the 'Help' part (see figure : \ref{HelpAdd}), and the following text 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...
                                              executes the box
   'BoxProcessMode' <String>     []       : Sets the processing mode...
                                              (Pipeline | Always |...
   'In1'            <Double>     []       : First number to add
   'In2'            <Double>     []       : Second number to add
 * Outputs : 
   'BoxChange'      <bbtk::VoidS> [signal]: Signals modifications...
   'Out'            <Double>     []       : Result
\end{verbatim}

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

These descriptions 
(provided by the author of the box) include: 
the author(s) of the box (usually e-mail address(es)) and 
the categories to which the box belongs, 
the lists of inputs and outputs of the box.
For each input or output, the help provides 
its \emph{name}, 
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 
include a pipeline graph. 

You can see that  \texttt{Add} boxes have two inputs, 
with name \texttt{In1} and \texttt{In2},
and an output, named \texttt{Out}.

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

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

Here \texttt{'a'} 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} language. The \texttt{new} command allows to create 
an instance of a box type, exactly like \texttt{int i;} in 
a \texttt{C} code declares a variable of type \texttt{int}, the 
name of which is \texttt{i}. 
Of course, like in \texttt{C} Language, you can declare multiple boxes of the 
same type in \bbs.

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}

This means that the user's workspace now contains a black box named \texttt{a},
of type \texttt{std::Add}. If you type:
\begin{verbatim}
> help workspace
\end{verbatim}

You get information about the actual instance \texttt{a} of the box type \texttt{std::Add}. It gives something like this:
\begin{verbatim}
> help a
 Black Box 'a' <std::Add>
  * Inputs : 
     'BoxExecute'     = '? (no adaptor found)'  [Modified]
     'BoxProcessMode' = 'Pipeline'              [Modified]
     'In1'            = '0'                     [Modified]
     'In2'            = '0'                     [Modified]
  * Outputs : 
     'BoxChange'      = '? (no adaptor found)'  [Out-of-date]
     'Out'            = '0'                     [Out-of-date]
\end{verbatim}
Note that the inputs appear as \texttt{[Modified]}, since the code defining the box type includes an initialization of the inputs. On the other hand, the outputs appear as \texttt{[Out-of-date]}, as the box has not yet been executed and therefore its outputs have not been updated. See the second part of this section to learn more about the updating. For a moment, just note that one way to process the box \texttt{a} is to use the command:
\begin{verbatim}
> exec a
\end{verbatim}

This command does not display anything (except if the 
box itself displays something in its processing).
It just processes the box if needed. In our case, the result can be seen as follows:
\begin{verbatim}
> exec a
> help a
 Black Box 'a' <std::Add>
  * Inputs : 
     'BoxExecute'     = '? (no adaptor found)'  [Up-to-date]
     'BoxProcessMode' = 'Pipeline'              [Up-to-date]
     'In1'            = '0'                     [Up-to-date]
     'In2'            = '0'                     [Up-to-date]
  * Outputs : 
     'BoxChange'      = '? (no adaptor found)'  [Up-to-date]
     'Out'            = '0'                     [Up-to-date]
\end{verbatim}
Note the change of status of all the inputs and outputs (\texttt{[Up-to-date]}).
In practice, the command \texttt{exec} is useful 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.

Now, let us set the input \texttt{In1} 
of the \texttt{Add} box \texttt{a} to the value $3.5$ 
by the command:
\begin{verbatim}
> set a.In1 3.5 
\end{verbatim}

Similarly, setting the input \texttt{In2} of \texttt{a} to the value $4.3$
is done with:
\begin{verbatim}
> set a.In2 4.3
\end{verbatim}
 
And you print the output \texttt{Out} of the box \texttt{a} with:
\begin{verbatim}
> print "result=$a.Out$"
result=7.8
\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 these special substrings, the interpreter:
\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 one 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'}. \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}).
\item A particular black box instance (with full description, as well as the values and the status of the inputs/outputs) if you type \texttt{help <box-name>}.
\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}

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

% ==========================================
\subsection{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-deep-box} to get 
more information on pipeline processing.

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

Assume you want to compute a sum of three numbers (e.g. $1+2+3$). 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{ A simple pipeline that adds 3 numbers}
\begin{center}
\includegraphics[width=0.5\textwidth]{1plus2plus3.png}
\end{center}
\label{bbi-fig-connecting-black-boxes-1}
\end{figure}

The \bbs 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}

The first three commands build the pipeline, 
the next three set \texttt{a} and \texttt{b} black boxes' inputs and the last one 
prints the output of the black box \texttt{b}. The pipeline is executed before printing, because the interpreter 'knows' that the box \texttt{b}, the output of which 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 processings 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 arbitrarily long 
chains of boxes (see \ref{bbi-deep-box} 
for details).

Let us consider another, more image-oriented, example :

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

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

> connect fileDialog.Out   reader.In 
> connect reader.Out       viewer.In

> exec viewer
\end{verbatim}

Some explanations: 
\begin{itemize}
        \item The \texttt{include} instructions load the necessary packages.
        \item \texttt{FileSelector} will pop, at run time, a File Selector dialog box that will output the user-selected file name.
        \item \texttt{ImageReader} will read any itk readable file, the name of which is passed as a std::string, and return a pointer on an itk image.
        \item \texttt{Viewer2D} will display a two-dimensional image.
        \item \texttt{connect fileDialog.Out   reader.In} plugs the output of the File Selector (a \texttt{std::string}) to the input of the Image Reader (a \texttt{std::string}, too).
        \item \texttt{connect reader.Out       viewer.In} plugs the output of the Image Reader \\(a \texttt{bbtk::any<bbitk::ImagePointer>} which is a type defined by the
itk package, and which can hold any itk image pointer) to the input of the Viewer (a \texttt{vtkImageData *})
        \item \texttt{exec viewer} processes the Viewer.
\end{itemize}

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

\begin{figure}[!ht]
\caption{\label{bbi-verysimplegraph}(Very) simple Graph of a (very) simple pipeline}
\begin{center}
\includegraphics[width=0.8\textwidth]{bbi-verysimplegraph.png}
\end{center}
\end{figure}
   
Of course, to be able to connect two boxes, 
the output and the input must be compatible. 
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 that has at least one input, called \texttt{In}, 
and at least one output called \texttt{Out} and the role of which 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 retrieve other useful information). In the example above the appropriate adaptor that converts \texttt{bbtk::any<bbitk::ImagePointer>} into \texttt{vtkImageData *} is provided in the package \texttt{itkvtk}.

Most of the useful standard adaptors are provided in the package \texttt{std}. 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 : 
   ASCII                     : ascii codes sequence to string - ...
   Add                       : Adds its inputs
   BoolToString        [DA]  : Converts a Bool (bool) into a string
   CastBoolToChar      [DA]  : Static cast from Bool (bool) to ...
   CastBoolToDouble    [DA]  : Static cast from Bool (bool) to ...
      ...
   CastBoolToUChar     [DA]  : Static cast from Bool (bool) to ...
   CastBoolToUInt      [DA]  : Static cast from Bool (bool) to ...
      ...
   CastUIntToBool      [DA]  : Static cast from UInt (unsigned ...
   CastUIntToChar      [DA]  : Static cast from UInt (unsigned ...
   CastUIntToDouble    [DA]  : Static cast from UInt (unsigned ...
      ...      

\end{verbatim}

In this long list you find many items marked \texttt{[DA]}, which 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 places 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 of \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
% ==========================================

% ==========================================
\subsection{Writing scripts files}
\label{bbi-writing-scripts}
% ==========================================

Now that you know how to connect the existing black boxes, you will soon realize that you want to save and reuse some sequences of commands that you are particularly glad of. In the following subsections you will learn how to write ``simple'' pipeline applications and new complex black boxes built of existing black boxes. 

% ==========================================
\subsubsection{Stand-alone pipeline applications}
\label{sec:pipeline-appli}
% ==========================================

Let us take an example similar to that from section \ref{bbi-connecting-black-boxes}:

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

> new DirectorySelector dirSelect
> new DICOMDirReader  reader 
> new Slider     slider
> new Viewer2D     viewer

> connect dirSelect.Out   reader.In 
> connect reader.Out       viewer.In
> connect slider.Out   viewer.Slice 
> connect slider.BoxChange viewer.BoxExecute
> set slider.ReactiveOnTrack 1

> exec viewer
\end{verbatim}

This is an elementary DICOM-image slicer (fig.~\ref{fig:simpleslicer}) designed to view 3D medical images slice-by-slice. The  image is to be composed of a series of DICOM files contained in a separate directory. The index of the slice to be displayed is selected by means of a slider. The command  \texttt{connect slider.BoxChange viewer.BoxExecute} permits the Viewer to update the display every time the output of the Slider changes. The command \texttt{set slider.ReactiveOnTrack 1} on its turn makes that the output of the Slider changes every time its cursor is moved, while the default behavior is to change only when the mouse-button is released after moving the cursor.\\

\begin{figure}[!ht]
\caption{ Graph of a (very) simple 3D slicer}
\begin{center}
\includegraphics[width=0.8\textwidth]{bbi-simplegraph.png}
\end{center}
\label{fig:simpleslicer}
\end{figure}
   
Despite its simplicity, this application may already be useful. If you want to reuse it, you have to save the \bbs commands in a text file. The conventional (and mandatory) extension for such script files is \texttt{bbs} 
(black box script). For example, our elementary 3D DICOM-image slicer 
can be defined in the following file:

\begin{file}{my\_slicer.bbs}
\begin{verbatim}
# my_slicer.bbs: elementary 3D image slicer"
/*
 the 3D image has to be stored in a separate directory
 as a series of DICOM files representing the 2D slices 
*/

include vtk
include wx
include itk
include wxvtk
include itkvtk

new DirectorySelector dirSelect
new DICOMDirReader reader 
new Slider       slider
new Viewer2D     viewer

connect dirSelect.Out   reader.In 
connect reader.Out       viewer.In
connect slider.Out       viewer.Slice
connect slider.BoxChange viewer.BoxExecute
set slider.ReactiveOnTrack 1

exec viewer
\end{verbatim}
\end{file}

Lines starting with a \texttt{\#} character or with double slash (\texttt{\//\//}) are ignored, they 
are considered as comments by the interpreter. A longer comment can be placed between the marks \texttt{\//*} and \texttt{*\//}. Each of this mark is to be placed alone in a separate line, like in the example.\par

To use this file in \bbStudions, click on the \texttt{include} button, and browse your filestore to find the file. You can also type the command:

\begin{verbatim}
> include my_slicer.bbs
\end{verbatim}

provided that \bbStudio knows the path to the desired \texttt{bbs} file.
See the section \ref{The_configuration_file} to learn about the configuration file and the way to add a new path to it. Note that, if you modify the configuration file, you will have to close \bbStudio and run it again, so that the new configuration be taken into account.

Actually, since the file has the \texttt{bbs} extension, you can omit it and just type:
\begin{verbatim}
> include my_slicer
\end{verbatim}

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

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

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

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

Remind 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 \bbs script file defining this complex black box will be as follows:

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

define Add3
  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}

Explanations:
\begin{itemize}
        \item As we will use \texttt{Add} boxes, we need to load the package \texttt{std}, which is done in the first line.
        \item The command \texttt{define} then starts the definition 
of the complex box type that will be called \texttt{Add3}. 
        \item The next three lines define the pipeline, 
exactly in the same way as outside of a complex box definition. 
        \item The commands \texttt{author}, \texttt{description}, \texttt{input} 
and \texttt{output} are specific to complex boxes definition:
        \begin{itemize}
                \item \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.
                \item \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.
        \end{itemize}
        \item Finally, the \texttt{endefine} command ends the definition of the 
new box type.
\end{itemize}

If you type the command \texttt{include bbAdd3} and then you ask for help 
on the contens of the \texttt{user} package, you get:

\begin{verbatim}
> help user
 Package user - internal
 User defined black boxes
 Black boxes : 
   Add3       : adds three numbers
   workspace  : User's 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:

\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}. Indeed, 
by convention all the 'natural entries' of a box are named \texttt{In}, or \texttt{In}\emph{x} if there is more than one 'natural entry'.
\newline
% ==========================================
\hrule
\paragraph{Summary}
%\hrule
\begin{itemize}
\item The \texttt{define/endefine} commands allow 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{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.result b.In1
  input In1 a.x "first double to add
  input In2 a.y "second double to add
  input In3 a.z "third double to add"
  input In4 b.In2 "fourth double to add"
  output Out b.Out "output"
endefine
\end{verbatim}
\end{file}

Here we kept the \texttt{bbAdd3.bbs} file unchanged, so the inner box of type \texttt{Add3} \texttt{a} has the entries \texttt{x, y, z}, while the entries of the inner box \texttt{b} of type \texttt{Add} are \texttt{In1, In2}.\\
Only the inputs \texttt{x, y, z} of box the \texttt{a} and the input \texttt{In2} of the box \texttt{b} are of interest for the end user, but he/she does not need to care neither about the inner boxes name, nor about the names of their inputs.\\
The author of the complex box has the ability to give these inputs meaningful names (here \texttt{In1, In2, In3, In4}) and to properly document them.

\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 start by \texttt{bb}.
For instance, the package \texttt{wx} will be in the library \texttt{bbwx.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 ending with a \texttt{*\//} are considered as comments by the interpreter.
\end{itemize}

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

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

Command-line applications are those that can be executed by typing, in a console, the name of the application and the values of its parameters. The Linux users are very familiar with this way of working, while the Windows users are not, since they are used to execute the applications by clicking on the corresponding icons. Nevertheless, the command-line execution of the applications is feasible (although not very useful) in Windows. You just need to invoke the black ``console'' available either via \texttt{Start > Execute > cmd}, or via \texttt{Start > Programs > Accessories > Invoke commands}. Furthermore, command-line execution of applications is very useful in both environments in such cases as batches.

So, you already know how to write script files that define complex black boxes 
(with \texttt{define/endefine}), and how to include them in (more) complex black boxes. You can imagine these definitions as though they were a kind of ``functions'' that can be ``called'' by a program (actually, these are rather ``classes'' that can be instanciated, according to the object-oriented programming concepts). The question now is how to write the ``main program'' to be executed directly from the console by typing: 
\begin{verbatim}
> bbi <application-name>
\end{verbatim}
Note that this execution mode invokes the interpreter \texttt{bbi} and passes the name of the application to the interpreter.

Let us think back of the \texttt{workspace} object. 
Remember that it is also 
a \texttt{complex black box}. 
Actually, when you write \bbs commands 
outside of a \texttt{define/}\texttt{endefine} block, 
you progressively define the \texttt{workspace} 
complex black box.
You can think of it as though 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{input} 
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 in the command-line, 
like this:

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

You can also note that, in the command-line context, you can invoke \bbi with 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}

This is particularly useful to learn about the usage of the application, namely about the inputs that are to be set at execution. To improve the help provided, use the \texttt{description} 
and \texttt{author} commands in the script file defining the application:
\\
\\
\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}

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}

Note that for both \texttt{-t} and \texttt{-g} options, 
the input from the user is a \texttt{string} and 
\bbi converts it to the right input type using 
an \texttt{adaptor}, hence the right adaptors must be previously loaded.

% ==========================================
\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
% ==========================================

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

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

Basic graphical interface 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 \bbStudio :
\begin{verbatim}
> include wx 
> new DirectorySelector d
> print $d.Out$
\end{verbatim}

When you hit the \texttt{enter} key after the last line, 
the usual directory-selection window pops up.
When you validate your selection, the directory name you selected, preceded by the corresponding path, is printed by 
the \texttt{print} command.
Note that you can determine a default directory by setting the appropriate input as follows:
\begin{verbatim}
> set d.DefaultDir <directory-name>
\end{verbatim}

Now, 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 ...
 Black boxes : 
   ColourSelector        : Colour Selector dialog (bbfication of ...
   ColourSelectorButton  : A button which displays a colour picke...
   CommandButton         : Button which executes bbi commands
   DirectorySelector     : Pops up a directory selection dialog (...
   FileSelector          : Pops up a file selection dialog for re...
   InputText             : A zone in which the user can enter a t...
   LayoutLine            : LayoutLine widget (wxBoxSizer)
   LayoutSplit           : Widget which splits a window in two fi...
   LayoutTab             : LayoutTab widget (wxNotebook)
   OutputText            : Text zone to be inserted into a window...
   RadioButton           : RadioButton group widget 0-9 entries
   Slider                : Slider widget (wxSlider)
\end{verbatim}

You can reproduce the same experiment as above using for example
a \texttt{FileDialog} rather than a \texttt{DirectorySelector}. 

If you choose to reproduce the experiment with:\\
\texttt{> new InputText t} (or \texttt{new Slider s}),

you will have to precede the command:\\
\texttt{> print \$t.Out\$} (or \texttt{print \$s.Out\$}) 

by the following command:\\
\texttt{> set t.WinDialog true} (or \texttt{set s.WinDialog true} respectively).

This blocks the pipeline until the widget is closed. Also note that the corresponding widgets do not have a validation button. Therefore, you will have to close them by clicking in the appropriate corner.

%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 
% ==========================================
%\subsubsection{Layout widgets}
%\label{bbi-layout-widgets}
% ==========================================

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'' a window into two parts, either horizontally or vertically, 
each part including another widget. 
The initial size of the two parts can be fixed by the input 'Proportion' 
and be adjusted by the user thanks to a ``handle''.

The example \texttt{exampleLayoutSplit} demonstrates its use. 
Run it: it displays a window with two sliders. 
Move the sliders and close the window. 
Now look at the source file to see how this is done:

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

new Slider s1
new Slider s2

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

exec s
\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 ``include'' the sliders in the 
split widget. 
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{layout} 
widgets 
(in \bbStudio 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 box  
to the \texttt{Widget}i input of a layout widget, 
you order to include the widget in the layout.
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} layout widgets in the \texttt{wx} package : 
\begin{itemize} 
\item {the \texttt{LayoutSplit} widget} we just described

\item {the \texttt{LayoutLine} widget} can have multiple children 
(\texttt{Widget1}, \texttt{Widget2},\dots \texttt{Widget9} inputs) 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}.
With only those two layout widgets you can already create 
complex dialog boxes 
(of course layouts can be nested, which leads to tree-like 
structures of widgets). \\
See the script \texttt{exampleComplexLayoutSplit\_In\_LayoutSplit} for an example.

\item {The \texttt{LayoutTab}  widget} arranges its children 
in different pages or 'tabs' (\texttt{wxNotebook}-based).
The label of each page is the name of the widget it contains.

\end{itemize}


%=====> TODO \\


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

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

\subsubsection{Default and mandatory inputs and outputs}
\begin{itemize}
\item Any \texttt{atomic} black box has two default Inputs, which are created by the system :
\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 input was changed (normal pipeline processing).
    \item {\bf\emph{Reactive}}: %bbSetModifiedStatus() calls bbUpdate() \\
                                 Re-processes immediately when \emph{any input} changes.\\
                                 To be more selective, better use 
        '\texttt{connect A.BoxChange B.BoxExecute}'.    
    \item {\bf\emph{Always}}  :% bbUpdate() always calls Process. \\
                                 Usefull for 'sources', that must be processed, even when no input changed (e.g.: FileSelector, ColorSelector)\\
                                 This one is not end user intended (for Package developer only)
  \end{itemize}   
\end{itemize}
\item And one default output :
\begin{itemize}
  \item {\bf\emph{BoxChange}} : Signals any modification of the box. This output may be connected if necessary to the \emph{BoxExecute} 
  input of an other box : each time the boxes changes (e.g. a Slider is moved) the box it is connected to will be forced to update.
\end{itemize}

If you create complex boxes, it is a good idea to define those inputs and outputs to be able 
to force the execution of your complex box or be aware of its changes...

\item Any {\bf 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}

If you define a complex widget box, it is a good idea to define these inputs to be able 
to customize your window settings.

\item Any {\bf widget} box has one mandatory Output :

\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}, then the box  will create its own window (frame or dialog) on execution. If it's connected to the \texttt{Widget}\texttt{\emph{i}} of a \texttt{Layout box}, 
     it will be embedded in its parent window.
\end{itemize}    

If you define a complex widget box, it is a good idea to use this standard name for your window output

\item Any {\bf Layout} box (i.e. \emph{LayoutLine}, \emph{LayoutSplit} or \emph{LayoutTab}) has 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} 

If you define a complex layout box, it is a good idea to use these standard names for your 
sub-windows inputs.

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

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

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


% ==========================================
%\vspace{0.5cm}
\hrule 
\newpage
\section{Using third party Package}
\label{Third_Party_Package}
% ==========================================
% ==========================================
\subsection{Installing a Package}
\label{Installing_a_Package}

% ==========================================
\subsubsection{Linux users}
\label{Installing_a_Package_for_Linux_users}

After compiling a Package, at install time, think of using :
\begin {verbatim}
su - 
make install
\end{verbatim}

and neither :
\begin {verbatim}
su 
make install
\end{verbatim}

nor :
\begin {verbatim}
sudo make install
\end{verbatim}

otherwise package documentation will not be generated. \\

Think of updating your environment variable LD\_LIBRARY\_PATH (in .bashrc in
you're using bash), to add the path to the shared library
libbb\emph{YourNewPackageName}.so


% ==========================================
\subsubsection{Windows users}
\label{Installing_a_Package_for_Windows_users}
% ==========================================
Think of updating your environment variable LD\_LIBRARY\_PATH to add the path to the dynamic library
bb\emph{YourNewPackageName}.dll

% ==========================================
\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 '\texttt{Select
package directory}'. Browse untill you find the install or the build directory,
depending whether you installed the package or not.

\bbStudio will update the configuration file, generate the 'Package
documentation', and update the 'Boxes Lists'.

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/or
one or more directories containing \bbtk scripts (\texttt{.bbs})
you can edit your \bbtk configuration and add the appropriate 
paths, see \ref{The_configuration_file}.

%\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 update the html help of this package,
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 update html boxes lists with the new boxes,
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{include} or \texttt{load} the package, 
within a 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
\newpage
\section{Using black boxes in \CPP programs}
\label{cpp}
% ==========================================

A very useful feature is that you may use any widget 
black box within a \CPP program 
without worrying about writing a \wx main application.\\

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.

The following \CPP code does the same :

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

int main(int argv, char* argc[])
{
  try
    {
      // 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();
    }
}

In this code, we use the headers of the \texttt{bbwx} \CPP library, 
which define the black boxes of the \texttt{wx} package. 

to be continued ...

\end{verbatim}

% ==========================================
\hrule
\newpage
\section{\bbs 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} \bbs pipeline creation and execution related commands.}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline

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

\texttt{newgui} & \texttt{<box-name>} \texttt{<gui-box-name>} &
Automatically creates a graphical user interface with name \texttt{gui-box-name}
for the black box \texttt{box-name} and connects it to the box inputs\\ \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{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{freeze} & 
 Allows to block execution commands while keeping definition commands active (this one is not for end user)\\ \hline 
& \texttt{unfreeze} & 
 Turns back to 'normal' mode (this one is not for end user).\\ \hline 
\end{tabular}
\end{table}
% ==========================================

\newpage

% ==========================================
\subsection{Package related commands}
\label{bbi-reference-package}

\begin{table}[!ht]
\caption{\label{tabbbi-reference-interpreter_1}\bbs package related commands. }% (part 1).}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline


\texttt{include} & \texttt{<package-name>} & 
Loads the package \texttt{package-name} and includes all its complex box definition scripts. \\ \hline 

\texttt{load} & \texttt{<package-name>} & 
Loads the atomic black boxes of package \texttt{package-name}.
Loads the dynamic library but not the complex boxes defined in the scripts shipped with the package. 
Use it only if you know that you won't work with its complex black boxes \\ \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{reset} & - & Deletes all boxes and unloads all packages so 
that the interpreter gets back to its initial state \\ \hline 


\texttt{package} &  \texttt{<package-name>} &  
All complex black boxes definitions until the next \texttt{endpackage} 
will be stored into the package \texttt{package-name}  \\ \hline 

\texttt{endpackage} & - & 
Closes a \texttt{package} command  \\ \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}\bbs intepreter related commands. }% (part 1).}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \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{message}
& - & 
Prints information on available kinds of messages and their current level\\ \hline 

 & \texttt{<kind>} \texttt{<level>} & 
Sets the level of verbosity of the interpreter for the kind of messages 
\texttt{kind} to \texttt{level}.\\ \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{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{graph} & ... & 
Generates the html doc including the pipeline graph for a given complex box \\ \hline

\texttt{index} & ... & 
Generates the html index of currently loaded boxes types \\ \hline

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


\texttt{debug} & \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{quit} & - & Stops the interpretation of the current script\\ \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} \bbs complex black box definition related commands.}
\small
\begin{tabular}{|lcm{6cm}|}
\hline
Command & Parameters & Effect \\ \hline


\texttt{define} & \texttt{<box-type>} [\texttt{<package-name>}] & 
Starts the definition of a complex black box of type
\texttt{box-type}. If \texttt{<package-name>} is provided then includes the 
box in the given package (otherwise it is defined in the current package, 
i.e. \texttt{user} if outside a \texttt{package/endpackage} block). \\ \hline 

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

\texttt{author} & \texttt{<string>} & 
Concatenate the string to the author string 
of the current complex black box.\\ \hline 

\texttt{description} & \texttt{<string>} & 
Concatenate the string to the description of the current complex black box. 
\\ \hline 

\texttt{category} & \texttt{<string>} & 
Specifies the \texttt{categories} of the current complex black box. 
The categories must be separated by semicolons, e.g. "\texttt{widget;image}"\\ \hline 

\texttt{kind} & \texttt{<box kind>} & 
Specifies the \texttt{kind} of the current complex black box 
( ADAPTOR, DEFAULT\_ADAPTOR, WIDGET\_ADAPTOR, DEFAULT\_WIDGET\_ADAPTOR )\\ \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
Note : if outside a \texttt{define/endefine} block then the current complex black box 
is '\texttt{user::workspace}', that is the main program equivalent 
(this is how applications are documented).
This remark holds for all complex black box related commands.








% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
% ==========================================
%\hrule
\newpage
\section{Install and run time issues}
% ==========================================




%%==============================================================================================
%%==============================================================================================
\subsection{\bbtk configuration file}
\label{The_configuration_file}
%%==============================================================================================
%%==============================================================================================

At start, \bbtk applications (\bbStudio, \bbi) try 
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:$\backslash$ Documents and Settings$\backslash$ username}.
\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}


Information on \bbtk configuration is 
obtained in \bbStudio by clicking on the 
\texttt{Config} button of the \texttt{Command} part toolbar.

If you did not installed other packages than the ones 
provided by \bbtk, you get something like :

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

The first line let you know which configuration file is currently used.

You can open this file using \bbStudio menu \texttt{Files$>$Open bbtk Config file}.

You will get something like :

\begin{verbatim}
<?xml version=\"1.0\" encoding=\"iso-8859-1\"?>
<config>
  <bbs_path>     </bbs_path>
  <package_path> </package_path>
  <default_temp_dir> $ </default_temp_dir>
</config>
\end{verbatim}

The \texttt{xml} tags \texttt{bbs\_path} and \texttt{package\_path} 
allow to set additionnal directories in which to search 
for \bbs files and packages dynamic libraries.

For example, if you add the line :
\begin{verbatim}
  <bbs_path> /home/guigues/bbs </bbs_path>
\end{verbatim}

Then the interpreter will search for \bbs in the folder \texttt{/home/guigues/bbs}, 
which allows a command like \texttt{'include bbMyBox.bbs'} to work if 
the folder \texttt{/home/guigues/bbs} contains the file \texttt{bbMyBox.bbs}.

The same, the \texttt{xml} tag \texttt{<package\_path>} let you 
set additional path in which to find a package dynamic library, 
hence allowing to load additionnal packages with the \texttt{'load'} command.

All \bbs and package paths are summmarized in the 
information output when pressing 'Config' in \bbStudio. 
You can see that two \bbs paths are always set :
\begin{itemize}
\item The current directory (\texttt{.})
\item The \bbs folder of \bbtk 
\end{itemize}
Also, two package paths are always set :
\begin{itemize}
\item The current directory (\texttt{.})
\item The libraries folder of \bbtk 
\end{itemize}

Additional paths set in your \texttt{bbtk\_config.xml} are added after those standard paths.
Note that the order displayed is the one in which the folders are searched when 
\texttt{include} or \texttt{load} commands are issued.


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

\subsection{Misc}
\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}



\end{document}