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




\begin{document}
\begin{center}

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

{\Huge Reference Manual}
\vspace{1cm}

\bbtk version 1.0
\vspace{0.5cm}


Last modified on : September 20, 2008 \\
Generated on : \today 
\vspace{0.5cm}

Fantomas, Belphegor
\end{center}

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

\listoftables

\listoffigures



% ==========================================
%\section*{Abstract}
% ==========================================
\newpage
% ==========================================
\hrule


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

\section{aaa}
\subsection{bbb}

\begin{table}[!ht]
\caption{\label{kinds} \texttt{Black Box} kinds}
\small
\begin{tabular}{|ll|}
\hline
\texttt{Kind name}                & : Meaning                         \\ \hline \\ \hline
\texttt{ADAPTOR}                  & : Adaptor Box                     \\ \hline
\texttt{DEFAULT\_ADAPTOR}         & :                                  \\ \hline
\texttt{WIDGET\_ADAPTOR}          & :                                  \\ \hline
\texttt{DEFAULT\_WIDGET\_ADAPTOR} & :                                  \\ \hline
\texttt{GUI}                      & :                                  \\ \hline
\texttt{DEFAULT\_GUI}             & :                                  \\ \hline
\texttt{ALL}                      & : If kind='ALL' then sets the level for all kinds \\ \hline
\end{tabular}
\end{table}



        
   \bf\emph{Boxes} : Box retrieving on various criterions :
      \begin{itemize}
        \item {\bf\emph{By name}} (Alphabetical list)
        \item {\bf\emph{By package}} (see table : \ref{bbi-list_of_packages})
        \item {\bf\emph{By category}} (see table : \ref{categories})
        \item {\bf\emph{Adaptors}} Used internaly to perform type conversions (not end user intended)     
      \end{itemize}



% ==========================================
\begin{table}[!ht]
\caption{\label{bbi-list_of_packages} List of bbtk supplied packages.}
\small
\begin{tabular}{|lp{10cm}|}
\hline
Package         & What it's used for \\ \hline
\texttt{std}    & : the 'standard' package including basic useful boxes \\ \hline 
\texttt{wx}     & : basic graphical interface elements (widgets : sliders, buttons, etc.) based on the \texttt{wxWidgets} library \\ \hline 
\itk    & : the basic image processing package, based on the \itk library. (without description)\\ \hline 
\vtk    & : prints help on the package \texttt{package-name} and its boxes (with brief description). The package must have been previously loaded\\ \hline 
\texttt{wxvtk}  & : widget boxes based on the \vtk library.\\ \hline 
\texttt{itkvtk} & : adaptors to convert \itk structures into \vtk structures and conversally.\\ \hline 
%\texttt{creaImageIO} & : provides high level widgets to read images including DICOM.\\ \hline 
\texttt{toolsbbtk} & : Tools for bbtk administration and package development.\\ \hline 

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



% ==========================================
\begin{table}[!ht]
\caption{\label{categories} \texttt{Black Box} categories}
\small
\begin{tabular}{|lp{10cm}|}
\hline
 \texttt{Category name}  & : Meaning                                          \\ \hline \\ \hline
 \texttt{adaptor}        & : Adaptor box                                      \\ \hline
 \texttt{application}    & : Final application, end user intended             \\ \hline
 \texttt{atomic box}     & : System category.
	       Automatically assigned to Atomic Black Boxes (c++ defined)     \\ \hline
 \texttt{complex box}    & : System category.
	       Automatically assigned to Complex Black Boxes (script defined) \\ \hline  
 \texttt{command line}   & : Script which defines a command line application \\ 
                         & :(no embedded GUI, but command line imput parameters) \\ \hline
 \texttt{demo}           & : Demonstration                             \\ \hline
 \texttt{devel}          & : Developer tool (bbCreatePackage.bbs, ...) \\ \hline
 \texttt{dicom}          & : DICOM aware box                            \\ \hline 
 \texttt{example}        & : Example script showing a box use-case      \\ \hline
 \texttt{filter}         & : Image processing box                       \\ \hline
 \texttt{image}          & : Image processing related box               \\ \hline
 \texttt{interaction}    & :                                            \\ \hline
 \texttt{math}           & : Mathematical operations                    \\ \hline
 \texttt{mesh}           & : Mesh processing related box                 \\ \hline
 \texttt{misc}           & : Box that cannot be put in any other category ! \\ \hline
 \texttt{read/write}     & : Box that read or write data from or to disk  \\ \hline
 \texttt{viewer}         & : Box which displays some data                \\ \hline
 \texttt{widget}         & : Piece of graphical interface                \\ \hline  
 \texttt{3D object creator} & : Sophisticated 3D widget  \\ \hline  
 \texttt{toolsbbtk}         & : Component of bbStudio    \\ \hline  
\end{tabular}
\end{table}

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





\subsection{ccc}

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

% ==========================================
\subsubsection{Black box packages}
\label{bbi-more-on-packages}
% ==========================================

There are various others user-intended packages :
\begin{itemize}
\item{vtk} \\
It contains some vtk based image processing filters :
%   \begin{enumerate}

     \paragraph{AppendPolyData}
     Appends one of more polygonal datasets into a single polygonal dataset 

     \paragraph{ConeSource}
     Creates a Cone 

     \paragraph{ImageAnisotropicDiffusion3D}
vtk\-Image\-Anisotropic\-Diffusion\-3D dif\-fuses a volume iteratively. \\
The neighborhood of the diffusion is determined by the instance flags. \\
if 'Faces' is on, the 6 voxels adjoined by faces are included in the neighborhood. \\
If 'Edges' is on the 12 edge connected voxels are included, and if 'Corners' is on, the 8 corner connected voxels are included. \\
'DiffusionFactor' determines how far a pixel value moves toward its neighbors, and is insensitive to the number of neighbors chosen.\\ 
The diffusion is anisotropic because it only occurs when a gradient measure is below 'GradientThreshold'. \\
Two gradient measures exist and are toggled by the 'GradientMagnitudeThreshold' flag. \\
When 'GradientMagnitudeThreshold' is on, the magnitude of the gradient, computed by central differences, above 'DiffusionThreshold' a voxel is not
modified. \\
The alternative measure examines each neighbor independently.\\ 
The gradient between the voxel and the neighbor must be below the 'DiffusionThreshold' for diffusion to occur with THAT neighbor.\\
     Receives : \\
     - In : an image (vtkImageData*)\\
     - Diffusion : Difference threshold that stops the diffusion\\
     Outputs : \\
     - Out : the isosurface mesh (vtkPolyData*)
     
     \paragraph{ImageCharacteristics}
     Exports objet sizes, and Spacings
     
     \paragraph{ImageDilateErode3D}

     Dilates one value and erodes another.\\ 
     vtkImageDilateErode3D will dilate one value and erode another. \\
     It uses an elliptical foot print, and only erodes/dilates on the boundary of the two values. \\
     The filter is restricted to the X, Y, and Z axes for now.\\ 
     It can degenerate to a 2 or 1 dimensional filter by setting the kernel size to 1 for a specific axis. \\
     (bbfication of vtkImageDilateErode3D) \\
     Receives : \\
     - In : an image (vtkImageData*)\\
     - DilateValue : The dilatation value\\
     - ErodeValue : The erosion value\\
     Outputs : \\
     - Out : the isosurface mesh (vtkPolyData*)     
     
     \paragraph{ImageGaussianSmooth}
     Performs a gaussian convolution of the input image\\
     Receives : \\
     - In : an image (vtkImageData*)\\
     - StdDevX : Standard deviation in X direction\\
     - StdDevY : Standard deviation in Y direction\\
     Outputs : \\
     - Out : the isosurface mesh (vtkPolyData*)       
     
     \paragraph{ImagePlanes}
     Creates three 3D planes with the input image mapped onto with which the user can interact; \\ 
     The output vtkImagePlaneWidget objects are to be inserted into a 3D scene (e.g. a Viewer3D)
     Receives : \\
     - In : an image (vtkImageData*)\\
     Outputs : \\     
     - PlaneX : the image plane in X direction (vtkImagePlaneWidget*)\\
     - PlaneY : the image plane in Y direction (vtkImagePlaneWidget*)\\
     - PlaneY : the image plane in Z direction (vtkImagePlaneWidget*)\\
     
          Outputs : \\
     - Out : the isosurface mesh (vtkPolyData*)  
           
     \paragraph{IsoSurfaceExtractor}
     Extracts an iso-surface of a 3D image and creates a vtkProp3D object to insert into a 3D scene (e.g. a Viewer3D)
     Receives : \\
     - In : an image (vtkImageData*)\\
     - Isovalue : the isosurface value (double)\\
     - Colour : Surface colour (vector of 3 doubles)
     Outputs : \\
     - Out : the isosurface (vtkProp3D**)
     
      \paragraph{MIPCreator}     
     Creates a Maximum Intensity Projection (MIP) view of a 3D image.\\
     Receives : \\
     - In : an image (vtkImageData*)\\
     - Scale : the Gray scale scaling (float) \\
     - Shift : the Gray scale shift (float) \\    
     Ouputs : \\
     - Out : The MIP object (vtkProp3D*) to be plugged into a 3D Viever
    
     \paragraph{MarchingCubes}
     Extracts an iso-surface of an image using the marching cubes algorithm (bbfication of vtkMarchingCubes)\\
     Receives : \\
     - In : an image (vtkImageData*)\\
     - Value : the isosurface value (double)\\
     Outputs : \\
     - Out : the isosurface mesh (vtkPolyData*)

     \paragraph{MetaImageReader}
     Reads .mhd / .mhd image formats (bbfication of vtkMetaImageReader) \\
     Receives : \\
     - In : the name of the file to be read (std::string)
     Outputs :
     - Out : The image (vtkImageData*)     
     
     \paragraph{SegmentationConnectivity}
     Segmentation with min max threshold and connectivity  \\  
     Receives : \\
     - In : an image (vtkImageData*)\\
     - PositionXYZ : initial position (std::vector<int>) \\
     - ThresholdMinMax : min, max threshold values (std::vector<int>) \\
     Outputs : \\
     - Out : The image (vtkImageData*)       
          
     \paragraph{SphereSource}
     Creates a Sphere      
%   \end{enumerate}

\item{itk} \\
It contains some itk based image processing filters :
 
     \paragraph{BinaryThresholdImageFilter}
     Binarizes an image by thresholding (generic bbification of itk::BinaryThresholdImageFilter) 
     Receives : \\ 

      - In :             Input image. Can be any itk::Image<T,D>*    \\
      - InsideValue :    Output value for pixels inside thresholds (Double)    \\
      - LowerThreshold :   Lower threshold(Double)    \\
      - OutsideValue   :   Output value for pixels outside thresholds (Double)    \\
      - UpperThreshold :   Upper threshold (Double)    \\
      Outputs :     \\
      - Out'        : Output image. Of the same type and dimension than the input image
     
     \paragraph{DICOMSeriesFileNames}
     Reads a series from a DICOM directory as a 3D itk image     

     \paragraph{ExtractImageFilter}
     Decrease the image size by cropping the image to the selected region bounds (bbification of itk::ExtractImageFilter)     

     \paragraph{ImageProperties}
     Outputs different properties of an image (type, dimension, size, spacing, ...)      

     \paragraph{ImageRegion}
Creates a generic ImageRegion (bbtk::any) from two vectors providing the index and size of the region. 
The dimension D of the actual itk::ImageRegion created is the max of the sizes of Index and Size 
(the smallest vector is padded by zeros)     

     \paragraph{ImageReader}
Generic itk image reader

     \paragraph{ImageWriter}
Generic itk image writer

     \paragraph{ImageSeriesReader}
Generic itk image series reader.

     \paragraph{ResampleImageFilter}
Resamples an image

\item{itkvtk} \\
It doesn't contain any end user intended box, only adaptors : to convert a generic itkImage to a vtkImageData, and vtkImageData* to a generic itkImage pointer 

Sorry nothing is done, right now for meshes. 

\item{wxvtk} \\

It contains two atomic black boxes.

     \paragraph{Viewer2D} 
     Receives : \\
     - a \textless vtkImageData* \textgreater (In),\\
     - an Orientation(0:yz / 1:xz / 2:xy),\\
     - an initial slice number (Slice).\\
     Outputs :\\
     - a \textless vtkRenderer* \textgreater (Renderer)
     
     \paragraph{Viewer3D} 
     Receives :\\
     - up to 5 Input Actors (\textless vtkProp3D* \textgreater),\\
     - up to 5 Input Observers (\textless vtkInteractorObserver* \textgreater), \\
     - a boolean 'Stereo' option, to use Red-Blue filter     
     Outputs :\\
     - an Interactor (\textless wxVTKRenderWindowInteractor* \textgreater) with which vtk widgets can interact, \\
     - a Renderer (\textless vtkRenderer* \textgreater) to which actors can be added.

It contains too some sophisticated complex black boxes :
 
     \paragraph{IsoSurfaceWithControls} 
     Image iso-surface extractor (vtk::IsoSurfaceExtractor) with associated control panel (isovalue, opacity and colour)\\
     Receives :\\
     - an initial isovalue (Isovalue)
     - an initial opacity  (Opacity)
     - an initial colour   (Colour)
     Outputs :\\
     \textless vtkProp3D* \textgreater (In)\\
      
     \paragraph{MIPWithControls}     
     Maximum Intensity Projection (MIP) creator (vtk::MIPCreator) with associated control panel (shift and scale) \\
    Receives :\\
     - an initial scale (Scale)
     - an initial shift  (Shift) 
     Outputs :\\
     \textless vtkProp3D* \textgreater (In)\\
         
\item{wx} \\

Some boxes are the bbfication of usefull xwWidgets, some other ones are more
sophisticated.

    \paragraph{ColourSelector} Colour Selector dialog (bbfication of wxColourSelector) \\
			%\begin{verbatim}
         \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]' 
			%\end{verbatim}

    \paragraph{ColourSelectorButton} A button which displays a colour picker dialog when clicked \\
			%\begin{verbatim}
          \texttt{In} :Initial colour \\
          \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
			%\end{verbatim} \\

    \paragraph{CommandButton} Button which executes bbi commands \\
			%\begin{verbatim}
          \texttt{In} : Commands to be executed separated by commas (;). Each single quote (') is replaced by a double quote ("). \\
          \texttt{Label} : Label of the button  \\
          \texttt{Widget} : Output widget \\
			%\end{verbatim}

    \paragraph{DirectorySelector} Pops up a directory selection dialog (wxDirDialog)\\
			%\begin{verbatim}
          \texttt{DefaultDir} : The default directory\\
          \texttt{Message} : Message to show on the dialog \\
          \texttt{Title} : Title of the dialog \\
          \texttt{Out} : The directory selected by the user\\
			%\end{verbatim}
 
    \paragraph{FileSelector} Pops up a file selection dialog for reading or saving (wxFileDialog)\\
			%\begin{verbatim}
          \texttt{DefaultDir} : The default directory \\
          \texttt{DefaultFile} : The default filename \\
          \texttt{Message} : Message to show on the dialog \\
          \texttt{OpenSave} : Open for an open dialog (default) / Save for a save dialog\\ 
          \texttt{Title} : Title of the dialog \\
          \texttt{Wildcard} : A wildcard, such as "*.*" or "BMP files (*.bmp)|*.bmp|GIF files (*.gif)|*.gif" \\
          \texttt{Out} : The file selected by the user \\
			%\end{verbatim}

    \paragraph{InputText} A zone in which the user can enter a text (wxTextCtrl)\\
			%\begin{verbatim}
          \texttt{In} : Initial text (default '')\\ 
          \texttt{Title} : Title of the input zone (default '')\\ 
          \texttt{WinTitle} : Title of the window (*)\\
          \texttt{Out} :Current text\\
			%\end{verbatim}

    \paragraph{LayoutLine} LayoutLine widget (wxBoxSizer)\\
			%\begin{verbatim}
          \texttt{Orientation} Orientation (default V), 0=H=HORIZONTAL , 1=V=VERTICAL \\
          \texttt{Widget}1 widget 1 \\
          \texttt{Widget2} widget 2 \\
          \texttt{Widget3} widget 3 \\
          \texttt{Widget4} widget 4 \\
          \texttt{Widget5} widget 5 \\
          \texttt{Widget6} widget 6 \\
          \texttt{Widget7} widget 7 \\
          \texttt{Widget8} widget 8 \\
          \texttt{Widget9} widget 9\\
          %\end{verbatim}    
    
    \paragraph{LayoutSplit} Widget which splits a window in two fixed size parts (wxSplitterWindow)\\ 
			%\begin{verbatim}
          \texttt{Orientation} : Orientation (default H), 0=H=HORIZONTAL , 1=V=VERTICAL\\ 
          \texttt{Proportion} : Proportion (in percent) of the first children in the window\\ 
          \texttt{Widget1} : Upper or left widget\\ 
          \texttt{Widget2} : Lower or right widget\\
			%\end{verbatim}

    \paragraph{LayoutTDown} Creates a 'T like' complex container : Down {UpLeft, UpRight} \\
			%\begin{verbatim}
          \texttt{Widget1} : UpLeft container\\
          \texttt{Widget2} : UpRight container\\ 
          \texttt{Widget3} : Down container\\
                        \begin{verbatim}
//                       ---------------
//                       |      |      |
//                       |  W1  |  W2  |
//                       |-------------|
//                       |             |
//                       |     W3      |
//                       ---------------
			\end{verbatim}
   
    \paragraph{LayoutTLeft} Creates a 'T like' complex container :  Left {RigthUp, RightDown}\\
			%\begin{verbatim}
           \texttt{input}  Widget1 : "UpLeft container"  \\ 
           \texttt{input}  Widget2 : "UpRight container" \\  
           \texttt{input}  Wigdet3 : "Down container"    \\ 
                        \begin{verbatim} 
//                       ---------------
//                       |      |  W2  |
//                       |  W1  |      |
//                       |      |------|
//                       |      |  W3  |
//                       |      |      |
//                       ---------------   
			\end{verbatim}

    \paragraph{LayoutTRight} Creates a 'T like' complex container : Right {LeftUp, LeftDown}\\
			%\begin{verbatim}
          \texttt{input} Widget1 currentBox.Widget1 "Up container"       \\
          \texttt{input} Widget2 down.Widget1       "DownLeft container" \\ 
          \texttt{input} Widget3 down.Widget2       "DownRight container"\\    
                        \begin{verbatim}  
//                       ---------------
//                       |      |      |
//                       |  W1  |      |
//                       |------|  W2  |
//                       |  W3  |      |
//                       |      |      |
//                       ---------------
			\end{verbatim}
  
    \paragraph{LayoutTUp} Creates a 'T like' complex container : Up {DownLeft, DownRight} as w1{w2,w3}\\ 
			%\begin{verbatim} 
          \texttt{ input} Widget1 currentBox.Widget1 "Up"       \\
          \texttt{input} Widget2 down.Widget1        "DownLeft" \\ 
          \texttt{input} Widget3 down.Widget2        "DownRight"\\
     
//             \begin{verbatim}
//                       ----------------
//                       |    W1        |
//                       |              |
//                       |------|-------|
//                       | W3   |  W2   |
//                       |      |       |
//                       ----------------
		\end{verbatim}
			  
    \paragraph{LayoutTab} LayoutTab widget (wxNotebook)\\
			%\begin{verbatim}
          \texttt{Orientation} Orientation (default T), 0=T=TOP , 1=R=RIGHT , 2=B=BOTTON , 3=L=LEFT \\
          \texttt{Widget1} widget 1 \\
          \texttt{Widget2} widget 2 \\
          \texttt{Widget3} widget 3 \\
          \texttt{Widget4} widget 4 \\
          \texttt{Widget5} widget 5 \\
          \texttt{Widget6} widget 6 \\
          \texttt{Widget7} widget 7 \\
          \texttt{Widget8} widget 8 \\
          \texttt{Widget9} widget 9 \\   
%\end{verbatim}
   
    \paragraph{OutputText} 		Text zone to be inserted into a window (wxStaticText)\\
			%\begin{verbatim}
          \texttt{In} Text \\
          \texttt{Title} Title prepended to the text\\   
			%\end{verbatim}
			   
    \paragraph{RadioButton} 		RadioButton group widget 0-9 entries\\
			%\begin{verbatim}
          \texttt{In} Set initial item \\
          \texttt{In0} option 0\\ 
          \texttt{In1} option 1\\ 
          \texttt{In2} option 2\\ 
          \texttt{In3} option 3\\ 
          \texttt{In4} option 4\\ 
          \texttt{In5} option 5 \\
          \texttt{In6} option 6 \\
          \texttt{In7} option 7 \\
          \texttt{In8} option 8 \\
          \texttt{In9} option 9 \\
          \texttt{Title} Title of the widget (default '')\\ 
          \texttt{Out} Number of the selected Item 
			%\end{verbatim}
			   
    \paragraph{Slider} 		Slider widget (wxSlider)\\
			%\begin{verbatim}
          \texttt{ChangeResolution} Enables the user to change the slider resolution (default FALSE) \\
          \texttt{In} Initial slider position(default 0) \\
          \texttt{Label} Show slider labels ? (default FALSE) \\
          \texttt{Max} Maximum value of the slider (default 500)\\ 
          \texttt{Min} Minimum value of the slider (default 0)\\ 
          \texttt{Orientation} Orientation : (default H) 0=H=HORIZONTAL, 1=V=VERTICAL\\ 
          \texttt{ReactiveOnTrack} Slider sends info when track moves (default 0 = no)\\ 
          \texttt{Title} Title shown above the slider (default '')\\     
			%\end{verbatim}
\end{itemize}


%\bibliography{all}



%\section{Conclusion}


\end{document}
