% ==========================================
% ==========================================
-\subsubsection{\bbtk components}
+\subsubsection{{\bbtk} components}
% ==========================================
\BBTK includes:
\begin{itemize}
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}.
+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 defined in binary files (dynamic libraries). 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
+
+It is important to note that the black boxes are implemented and have to be used according to the {\bf\emph{object-oriented}} programming principles. This means that you have to make difference between a black box {\bf\emph{type}} and an {\bf\emph{instance}} of the given black box type. The former defines a ``pattern'' (a mold), according to which are formed the actual objects. If you query for help on a black box type, you learn about its purpose, its author, the boxes it contains (if it is a complex black box) and the types of its inputs/outputs. The user-defined black box types belong to the package \texttt{user} and can be listed by use of the command \texttt{help user}. If you query for help on a black box instance, you learn about the values and the state of its inputs/outputs. The currently existing black box instances belong to the complex black box \texttt{workspace} and can be listed by use of the command \texttt{help workspace}.
% ==========================================
\subsubsection{Guides}
\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.
+ \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. 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.
+ 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}
% ==========================================
-\subsection{Creating and executing black boxes}
+\subsection{Creating and executing black box instances}
% ==========================================
At start the interpreter does not know any black box.
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
+Any black box instance you create in \bbStudio is stored
in \texttt{workspace}
(see also section \ref{bbi-command-line-app}).
\end{verbatim}
In the text displayed,
-the \texttt{user::} prepended to the name \texttt{workspace}
+the \texttt{user::} prefixed 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
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.
+which contains basic useful black box types.
To load it, type:
\begin{verbatim}
workspace
\end{verbatim}
-Now the interpreter knows the package \texttt{std} and the black boxes it provides,
+Now the interpreter knows the package \texttt{std} and the black box types 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:
+as new black box types 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}
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}
+Remind that 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
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:
+After the creation of the box instance \texttt{a} the command:
\begin{verbatim}
> help workspace
\end{verbatim}
-you get :
+gives the following result:
\begin{verbatim}
Complex Black Box <user::workspace>
User's workspace
\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
+\item Places an implicit 'new line' character after the string
\end{enumerate}
%\paragraph
> new FileSelector fileDialog
> new ImageReader reader
-> new Slider slider
> new Viewer2D viewer
> connect fileDialog.Out reader.In
> connect reader.Out viewer.In
-> connect slider.Out viewer.Slice
-> connect slider.BoxChange viewer.BoxExecute
+
> exec viewer
\end{verbatim}
\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{Slider} will pop, at run time, a Slider widget that will output an integer number, used later as a slice number.
- \item \texttt{Viewer2D} displays a plane, the number of which is specified by an integer.
- \item \texttt{connect fileDialog.Out reader.In} plugs the output of the File Selector (a \texttt{std::string}) to the input of the reader (a \texttt{std::string}, too).
- \item \texttt{connect reader.Out viewer.In} plugs the output of the reader \\(a \texttt{bbtk::any<bbitk::ImagePointer>} which is a type defined by the
+ \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{connect slider.Out viewer.Slice} plugs the output of the slider (an \texttt{int}) to an other output (named Slide) of the viewer.
- \item \texttt{connect slider.BoxChange viewer.BoxExecute} says the viewer that it must re process itself any time the slider is modified.
-\item \texttt{exec viewer} processes the viewer.
+ \item \texttt{exec viewer} processes the Viewer.
\end{itemize}
-This would correspond to the graph in figure \ref{bbi-simplegraph}
-
+This would correspond to the graph in figure \ref{bbi-verysimplegraph}.
\begin{figure}[!ht]
-\caption{\label{bbi-simplegraph}(Very) simple Graph of a (very) simple pipeline}
+\caption{\label{bbi-verysimplegraph}(Very) simple Graph of a (very) simple pipeline}
\begin{center}
-\includegraphics[width=0.8\textwidth]{bbi-simplegraph.png}
+\includegraphics[width=0.8\textwidth]{bbi-verysimplegraph.png}
\end{center}
\end{figure}
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).
+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}.
-Under \bbStudions, if you type :
+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
% ==========================================
% ==========================================
-\subsection{Creating complex black boxes}
+\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 two empty lines only containing \texttt{\//*} and \texttt{*\//} respectively.
+\end{itemize}
+
+\hrule
+% ==========================================
+
+% ==========================================
+\subsubsection{Creating complex black boxes}
\label{bbi-complex-black-boxes}
% ==========================================
\end{center}
\end{figure}
-The \bbs commands to define this complex black box are
-the following:
+The \bbs script file defining this complex black box will be as follows:
\begin{verbatim}
-> load std
-> define Add3
-> new Add a
-> new Add b
-> connect a.Out b.In1
-> author "myself"
-> description "adds 3 doubles"
-> input x a.In1 "first double to add"
-> input y a.In2 "second double to add"
-> input z b.In2 "third double to add"
-> output result b.Out "output"
-> endefine
+# bbAdd3.bbs: defines the Add3 black box which adds 3 doubles
+
+author "myself"
+description "adds 3 doubles"
+
+load std
+define Add3
+ # 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:
\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 a complex box definition.
+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
+of the new box. They have to be placed at the very beginning of the script file. 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
new box type.
\end{itemize}
-After this definition, if you ask for help
-on packages, you get:
+If you type the command \texttt{include bbAdd3} and then you ask for help
+on the contents of the \texttt{user} package, you get:
+
\begin{verbatim}
-> help packages
-std
- Add
- ...
-user
- Add3
- workspace
+> 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
\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.
+ \item The \texttt{author} and \texttt{description} commands, placed at the very beginning of a script file, allow to document the new type of box.
+ \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
+ \begin{itemize}
+ \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}
\end{itemize}
\hrule
% ==========================================
% ==========================================
-\subsection{Writing scripts files}
-\label{bbi-writing-scripts}
-% ==========================================
-
-Once you have defined a new type of complex box, you
-may like to reuse it. To do this, you can simply
-write the \bbs commands defining the new box
-into a text file and afterwards include that file anywhere you need.
-Doing this, you start writing \bbs scripts.
-The conventional (and mandatory) extension for such scripts is \texttt{bbs}
-(black box script).
-For consistency reasons, you are requested to prepend \texttt{bb} to the name.
-
-For example, the \texttt{Add3} complex box we previously worked on
-can be defined in the \texttt{bbAdd3.bbs} file:
-
-\begin{file}{bbAdd3.bbs}
-\begin{verbatim}
-# Defines the Add3 black box which adds 3 doubles
-load std
-
-define Add3
- # I am the author
- author "myself"
- description "adds 3 doubles"
- # Pipeline creation
- new Add a
- new Add b
- connect a.Out b.In1
- # Inputs definition
- input x a.In1 "first double to add
- input y a.In2 "second double to add
- input z b.In2 "third double to add"
- # Output definition
- output result b.Out "output"
-endefine
-\end{verbatim}
-\end{file}
-
-Lines starting with a \texttt{\#} character or a \texttt{\//\//} character are ignored, they
-are considered as comments by the interpreter.
-To use this file in \bbStudions, click on the \texttt{include} button, and browse your filestore to find the file.
-
-\begin{verbatim}
-> include bbAdd3.bbs
-> help Add3
-Complex Black Box <user::Add3>
- adds 3 doubles
- By : myself
- * Inputs :
- 'x' <double> [] : first double to add
- 'y' <double> [] : second double to add
- 'z' <double> [] : third double to add
- * Outputs :
- 'result' <double> [] : output
- * Boxes :
- 'a' <std::Add>
- 'b' <std::Add>
-\end{verbatim}
-
-If the file has the \texttt{bbs} extension, you can omit it and just type:
-\begin{verbatim}
-> include bbAdd3
-\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.
-
-\subsection{Creating complex black boxes that use complex black boxes}
+\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
+author "myself"
+description "adds 4 doubles"
+include bbAdd3
define Add4
- author "myself"
- description "adds 4 doubles"
new Add3 a
new Add b
connect a.result b.In1
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.
-\subsection{Naming Conventions}
+\subsubsection{Naming Conventions}
\label{bbi-Naming Conventions}
\begin{itemize}
\item
File names :
-For consistency reasons, you are requested to prepend \texttt{bb}, and postpone an extention \texttt{.bbs},
+For consistency reasons, you are requested to prefix \texttt{bb} and place an extension \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
\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
-% ==========================================
% ==========================================
-\subsection{Creating and using command-line applications}
+\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:
+You already know how to write script files that define stand-alone pipeline applications.
+In fact, these applications \emph{can} 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.
+So, what more do you need to know? A command-line application may need some inputs. In order to define them, you need to use the (already known) command \texttt{input}.
+
+To understand the underlying mechanism 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
git://git.creatis.insa-lyon.fr / bbtk.git / blobdiff