1 % ==========================================
2 \documentclass[11pt,final,a4paper]{article}
5 \title{The Black Box Toolkit\\User's Guide}
7 \author{Laurent Guigues}
9 % ==========================================
11 % ==========================================
17 % ==========================================
19 % ==========================================
21 % ==========================================
23 \section{What is {\bf bbtk} ?}
24 % ==========================================
25 \BBTK(\bbtkns) is a set of tools
26 (\CPP libraries and executables)
27 providing a \CPP framework for the definition
28 of elementary processing \emph{units}, called {\bf black boxes},
29 and the definition and execution of processing \emph{chains}
30 made up of these black boxes.
32 % ==========================================
33 \subsection{The black box philosophy}
34 % ==========================================
35 \href{http://en.wikipedia.org/wiki/Black_box_\%28disambiguation\%29}{Wikipedia}
36 defines a {\bf black box} as
37 \emph{``any component in a system in which only the input and output
38 characteristics are of interest, without regard to its internal mechanism
40 I would add something very important to this definition :
41 not only the inputs and outputs are of interest but also
42 \emph{what the box does} !
43 Hence, I would say that a black box is any \emph{\bf documented}
44 component of a system, letting the user know
45 \emph{\bf what} the box is supposed to do and
46 \emph{\bf how to use it}
47 but not \emph{\bf how it does it}.
49 \BBTK provides a systematic framework
50 to encapsulate (or ``wrap'') any
51 existing \texttt{C} or \CPP processing code into an object
52 (a black box) having a {\bf generic symbolic interface}, where
55 \item{\bf generic} means that the interface is \emph{the same}
56 for all boxes. Hence one does not need to know which particular
57 method allows, say, to set a particular input or
58 get a particular output of the box.
59 One can use a black box in a purely abstract way.
60 \item{\bf symbolic} means that a particular
61 input or output is referenced by a 'name', that is by a symbol
62 which identifies the input or output.
63 It also means that symbolic information (text!) is
64 attached to a box: description of the box, author,
65 description of its inputs and outputs, etc.
68 (in fact, genericity is achieved because the interface is symbolic.
69 I let you think about this\dots)
71 Of course, symbolic data attached to box can be
72 {\bf queried}: what are the inputs/outputs of the box ?
73 what are their type ? their description ? etc.
74 This allows {\bf automatic documentation} of boxes.
76 The abstract definition of black boxes is the most basic
77 aspect of \BBTK architecture.
78 Another key aspect is the groupement of black boxes into
79 so called {\bf packages},
80 which are \emph{dynamic libraries} which can also
81 be queried, in particular about the boxes they provide.
82 The package structure then offers a mechanism which
83 is like a \emph{'plug-in'} mechanism.
84 \BBTK provides the methods to load a package at run-time,
85 and create instances of the boxes it contains.
87 These two mechanisms (black boxes and packages)
88 then gives the way to:
91 \item The definition of an {\bf interpreted language},
92 which allows to manipulate packages and boxes very easily in symbolic way.
93 \BBTK provides one: \bbi (the Black Box Interpreter).
94 \item {\bf Automatic documentation} of existing packages.
95 \texttt{html} documentation of packages is proposed by
99 Finally, these different components allow {\bf efficient}:
102 \item {\bf capitalization and reuse} of existing processing units,
103 including {\bf documentation}
104 \item {\bf testing, prototyping} in a very simple script language
105 \item {\bf inter-operability} between atomic processings which
106 have been written by different persons, using different libraries, etc.
109 % ==========================================
110 \subsection{\bbtk components}
111 % ==========================================
114 \item A \CPP {\bf\emph{library}} - called \bbtk - which defines a framework
115 (abstract classes) to develop black boxes and to store them into
116 dynamic libraries, called black box \emph{packages}.
117 \item Different {\bf\emph{black box packages}}:
119 \item {\bf\emph{std}}: the 'standard' package including basic useful boxes.
120 \item {\bf\emph{wx}}: basic graphical interface elements (widgets: sliders, buttons, etc. based on the \texttt{wxWidgets} library).
121 \item {\bf\emph{itk}}: the basic image processing package, based on the \texttt{itk} library.
122 \item {\bf\emph{vtk}}: the basic image and surfaces processing package, based on the \texttt{vtk} library.
123 \item {\bf\emph{wxvtk}}: widget boxes based on the \texttt{vtk} library.
124 \item {\bf\emph{itkvtk}}: boxes to convert \texttt{itk} structures into \texttt{vtk} structures and conversally.
126 \item A {\bf\emph{Developement environment}}, called bbStudio, which provides
128 \item An online {\bf\emph{script editor}}, called bbed
129 \item A powerfull {\bf\emph{Help environment}}, called bbhelp
132 \item Online documentation scaning
133 \item Retreiving boxes on various criterions
134 \item Checking Demo and examples
137 \item An {\bf\emph{interpreter}}, called \bbi, which allows to
138 load black box packages and to define and execute
139 processing chains by connecting various black boxes of the already loaded packages.
140 \item {\bf\emph{Utilities}}:
142 \item \bbfy generates the \CPP code of a black box from a
143 description file written in \texttt{xml}.
144 %\item \bbdoc generates the html documentation of a black box package
145 %(author, description, description of its black boxes:
146 %author, description, inputs, outputs, and so on).
147 \item \bbCreatePackage allows to create the basic file architecture
148 to start the development of a new black box package.
152 The general architecture of \BBTK
153 is shown in figure \ref{bb-architecture}.
156 \caption{\label{bb-architecture}\BBTK architecture}
158 \includegraphics[width=0.6\textwidth]{bb-architecture.png}
162 % ==========================================
163 \subsection{Structure of this guide}
164 % ==========================================
166 This guide is divided into three parts.
168 The first part (\ref{bbStudio}) is a brief presentation of the very intuitive Development
169 environment, \bbStudio.
171 The second part (\ref{bb0})
172 is devoted to the use of the \emph{black box interpreter} \bbi.
173 This is the highest level of use of the toolkit, which
174 allows to create and execute processing chains by connecting
175 black boxes of existing packages.
177 The third part (\ref{cpp}) explains how to
178 use the black box toolkit framework in \CPP code,
179 typically to develop large applications which
180 involve complex graphical interfaces.
183 % ==========================================
184 % ==========================================
185 % ==========================================
186 % ==========================================
187 % ==========================================
188 % ==========================================
190 \section{The Development environment (bbStudio)}
193 Just run it, typing in a console \texttt{bbed}.
194 You'll get something like in figure
195 \ref{bbi-fig-bbStudio-gui}
196 (the exact appearance of \bbStudio is system and \bbtk version dependent)
199 \caption{\label{bbi-fig-bbStudio-gui}The bbStudio Development environment interface}
201 \includegraphics[width=0.7\textwidth]{bbStudioMainPage.png}
205 All the entries of this Help 'bookmark' are self-explanatory :
208 \item {\bf\emph{Wiki}}: Direct link to the bbtk Wiki (intranet only, right now, www
210 \item {\bf\emph{Demo}}: Link to some demonstrations.
211 \item {\bf\emph{User's Guide}}: Step to step How-to for user who just wants to create his own
212 application, just using already existing boxes.
213 \item {\bf\emph{Package Developper's Guide}}: Step to step How-to for user who wants to create his own
215 \item {\bf\emph{Developper's Guide}}: Sorry, not yet written.
216 \item {\bf\emph{Reference Manual}}: Sorry, not yet written.
217 \item {\bf\emph{Doxygen Documentation}}: Doxygen source browser.
218 \item {\bf\emph{Boxes}}: Box retrieving on various criterions :
220 \item {\bf\emph{By name}}
221 \item {\bf\emph{By package}} (see table : \ref{bbi-list_of_packages})
222 \item {\bf\emph{By category}} (see table :\ref{categories})
223 \item {\bf\emph{Adaptors}} Used internaly to perform type conversions (not end user intended)
228 % ==========================================
230 \caption{\label{bbi-list_of_packages} List of bbtk supplied packages.}
232 \begin{tabular}{|ll||}
234 Package & What it's used for \\ \hline
235 \texttt{std} & : the 'standard' package including basic useful boxes \\ \hline
236 \texttt{wx} & : basic graphical interface elements (widgets: sliders, buttons, etc. based on the \texttt{wxWidgets} library \\ \hline
237 \texttt{itk} & : the basic image processing package, based on the \texttt{itk} library. (without description)\\ \hline
238 \texttt{vtk} & : Prints help on the package \texttt{package-name} and its boxes (with brief description). The package must have been previously loaded\\ \hline
239 \texttt{wxvtk} & : widget boxes based on the \texttt{vtk} library.\\ \hline
240 \texttt{itkvtk} & : boxes to convert \texttt{itk} structures into \texttt{vtk} structures and conversally.\\ \hline
244 % ==========================================
249 % ==========================================
251 \caption{\label{categories} \texttt{Black Box} categories}
253 \begin{tabular}{|ll|}
255 \texttt{Categ name} & : Meaning \\ \hline \\ \hline
256 \texttt{adaptor} & : Adaptor box \\ \hline
257 \texttt{application} & : Final application, end user intended \\ \hline
258 \texttt{atomic box} & : System category.
259 Automatically assigned to Atomic Black Boxes (c++ defined) \\ \hline
260 \texttt{complex box} & : System category.
261 Automatically assigned to Complex Black Boxes (script defined) \\ \hline
262 \texttt{command line} & : Script which defines a command line application (no embedded GUI, but command line imput parameters) \\ \hline
263 \texttt{demo} & : Demonstration \\ \hline
264 \texttt{devel} & : Developer tool (bbCreatePackage.bbs, ...) \\ \hline
265 \texttt{dicom} & : DICOM aware box \\ \hline
266 \texttt{example} & : Example script showing a box use-case \\ \hline
267 \texttt{filter} & : Image processing box \\ \hline
268 \texttt{image} & : Image processing related box \\ \hline
269 \texttt{interaction} & : \\ \hline
270 \texttt{math} & : Mathematical operations\\ \hline
271 \texttt{mesh} & : Mesh processing related box \\ \hline
272 \texttt{misc} & : A box that cannot be put in other category ! \\ \hline
273 \texttt{read/write} & : Box that read or write data from or to disk \\ \hline
274 \texttt{viewer} & : Box which displays some data \\ \hline
275 \texttt{widget} & : Piece of graphical interface \\ \hline
277 \texttt{3D object creator} & : Sophisticated 3D widget \\ \hline
278 \texttt{toolsbbtk} & : Component of bbStudio \\ \hline
286 % ==========================================
287 % ==========================================
288 % ==========================================
289 % ==========================================
290 % ==========================================
291 % ==========================================
293 \section{The script manager}
295 % ==========================================
297 Call it with the bookmark \emph{File}.
301 \caption{\label{bbi-fig-bbStudio-file0}The bbStudio script manager}
303 \includegraphics[width=0.7\textwidth]{bbFile0.png}
307 Using the lower tool bar, you can :
310 \caption{\label{lowertoolbar}The lower tool bar}
312 \includegraphics[width=0.7\textwidth]{lowertoolbar.png}
318 \item {\bf\emph{new}}: Create a newfile to hold a script
319 \item {\bf\emph{open}}: Open a already existing file holding a script
320 \item {\bf\emph{close}}: Close a file holding a script
321 \item {\bf\emph{save}}: Save he current file (if modified)
322 \item {\bf\emph{save as}}: Save he current file under a different name
323 \item {\bf\emph{execute}}: Execute the script you just loaded/modified/written
327 The script language is very simple.
328 Everything is done with only a very few commands (See table \ref{bbi-reference-box}).
329 The philosophy of this part is also very simple:
330 it introduces the \bbi commands using examples,
331 starting with the most simple commands.
332 The first section of this part
333 (\ref{bbi-getting-started})
334 is designed like a tutorial,
335 which progressively introduces all the concepts of \bbi.
336 We suggest you run \bbi and follow the examples,
337 to see how it works in practice.
338 At the end of this section,
339 you will be able to use \bbi and write
340 own black box processing scripts.
343 the section \ref{bbi-more-on}
344 (called \emph{more on...})
345 goes deeper into various issues of \bbi.
346 Read it at your convenience,
347 either linearly to learn more about \bbi,
348 or in random order to get an answer
349 to a particular question.
351 Finally, the section \ref{bbi-reference}
352 summarizes all the commands of \bbi,
353 their parameters and effect.
354 Use it as a reference.
356 % ==========================================
357 \subsection{Getting started}
358 \label{bbi-getting-started}
359 % ==========================================
360 \subsubsection{Creating and executing black boxes}
361 % ==========================================
363 To learn interactivelly the script language features, you can use the black box
365 open a console and type \texttt{bbi}
366 or double click on the application icon.
367 You get a window which looks like the one in figure
368 \ref{bbi-fig-bbi-gui}
369 (the exact appearance of \bbi is system and \bbtk version dependent)
370 \footnote{If you compiled \bbtk without \wx then \bbi does not have a
371 graphical interface but a simple prompt}.
374 \caption{\label{bbi-fig-bbi-gui}The black box interpreter interface}
376 \includegraphics[width=0.7\textwidth]{bbi-gui0.png}
380 The 'Command' tab is subdivided into two parts :
381 one single line zone at the bottom in which you can enter your commands and
382 one multiple line zone in which \bbi prints out the result of your commands.
383 , just using already existing boxes.
385 Try typing in the input zone (in this manual,
386 the commands entered by the user will be preceded by a prompt \textgreater) :
391 you get the list of the commands of the interpreter:
424 To get help on a particular command type \texttt{help <command-name>},
434 Quits the program (during script execution it stops the complete execution)
437 The \texttt{help} command has multiple usages.
438 It is used to get help on almost anything in \bbi !
439 Type \texttt{'help help'} to get help on the \texttt{help} command itself:
444 (2) help <command name>
445 (3) help packages [all]
446 (4) help <package name> [all]
447 (5) help <black box type>
448 (6) help <black box name>
450 (1) Lists all available commands;
451 (2) Prints help on a particular command;
452 (3) Lists the packages loaded and their black boxes.
453 Add 'all' to list adaptors;
454 (4) Prints short help on the black boxes of a package.
455 Add 'all' to include adaptors;
456 (5) Prints full help on a black box type;
457 (6) Prints information on the inputs, outputs and connections of a black box instance.
460 At start \bbi does not know any black box.
461 If you type \texttt{'help packages'}, which is
462 the third form of the \texttt{help} command, you get:
469 which means that \bbi only knows one package
470 (library of black boxes) called \texttt{user}
471 and which contains a black box called \texttt{workspace}.
472 The \texttt{user} package is an internal package to \bbi,
473 which stores user-defined black box types.
474 At start, it already contains
475 one box, called \texttt{workspace}.
476 \texttt{workspace} is a special type of black box,
477 called complex black box, whose purpose is
478 to store other black boxes.
479 Any black box you create in \bbi is stored
480 in \texttt{workspace}
481 (this will be explained in details in sections
482 \ref{bbi-writing-scripts} and
483 \ref{bbi-more-on-complex-black-boxes}).
485 If you type \texttt{'help workspace'}, you get:
488 Complex Black Box <user::workspace>
491 Category(s) : complex box;
497 In the text displayed,
498 the \texttt{user::} prepended to the name \texttt{workspace}
499 means that the box \texttt{workspace}
500 belongs to the \texttt{user} package.
501 Then comes a description and three lines which
502 tell that \texttt{workspace} does not have any input
503 nor output nor boxes yet.
505 In order to let \bbi know of some black boxes,
506 you must load another package.
507 The \texttt{std} package is the ``standard'' package,
508 which contains basic useful black boxes.
520 you get something like:
535 Now \bbi knows the package \texttt{std} and the black boxes it provides,
536 such as the \texttt{'Add'} box, the \texttt{'ConcatStrings'}. Remark that the
537 content of \texttt{std} may vary from one version to another
538 as new black boxes might be added to it.
548 By : laurent.guigues@creatis.insa-lyon.fr
549 Categories : atomic box;math;
551 'BoxExecute' <bbtk::Void> [signal] : Any signal received by this input executes the box
552 'BoxProcessMode' <String> [] : Sets the processing mode of the box (Pipeline | Always | Reactive)
553 'In1' <Double> [] : First number to add
554 'In2' <Double> [] : Second number to add
556 'BoxChange' <bbtk::Void> [signal] : Signals modifications of the box
557 'Out' <Double> [] : Result
561 the \texttt{std::} prepended to the name \texttt{Add}
562 means that the box \texttt{Add}
563 belongs to the \texttt{std} package.
564 Then comes a description
565 (the one which was provided by the author of the box),
566 the author(s) of the box (usually e-mail adress(es)) and
567 the categories to which the box belong.
568 Finally comes the lists of inputs and outputs of the box.
569 For each input or output, \bbi provides
570 its \emph{name} (between quotes, e.g. \texttt{'ProcessMode'}),
571 its \emph{type} (between \texttt{<>}, e.g. \texttt{<Int>})
573 Remark that the box \texttt{Add} is not a 'complex' black box
574 but an 'atomic' box, hence its help does not
575 mention any information concerning possible internal boxes.
577 You can create an \emph{instance} of an \texttt{Add} box by
578 the command \texttt{new}:
583 The \texttt{'a'} at the end is the \emph{name} of the instance,
584 which will be used to reference it later.
585 It is important to distinguish a box \emph{type}
586 and an \emph{instance} of a box type.
587 The \texttt{Add} box of the package \texttt{std} is actually
588 a \emph{box type} , like \texttt{int} is a data type
589 in \texttt{C} langage. The \texttt{new} command allows to create
590 an instance of a box type, exactly like \texttt{int i;} in
591 a \texttt{C} code, it declares a variable of type \texttt{int} whose
593 Of course, like in \texttt{C} Language, you can declare multiple boxes of the
596 After the creation of the box \texttt{a}, type:
603 Complex Black Box <user::workspace>
606 Category(s) : complex box;
613 which means that \bbi workspace now contains a black box named \texttt{a},
614 of type \texttt{std::Add}.
616 Now look back at the help on \texttt{Add} boxes:
617 you can see that this type of box has two inputs,
618 with name \texttt{In1} and \texttt{In2},
619 and an output, with name \texttt{Out}.
621 You can set the input \texttt{In1}
622 of the \texttt{Add} box \texttt{a} to the value $1$
628 Similarly, setting the input \texttt{In2} of \texttt{a} to the value $2$
634 And you print the output \texttt{Out} of the box \texttt{a} with:
636 > print "result=$a.Out$"
640 In the string passed to the \texttt{print} command,
641 each substring enclosed between a couple of \$ is considered
642 as the name of an output of a box.
643 To process this special substrings, \bbi does:
645 \item Processes the box if needed (see below)
646 \item Converts the output of the box to a string if possible
648 \item Substitutes the result in the string to print
649 \item postpone an implicit 'new line' character to the string
653 Box processing is needed if:
655 \item at least input has changed since last processing or
656 \item the input \texttt{'BoxProcessMode'} of the box is set to
657 \texttt{'Always'}, which forces box reprocessing.
660 Note that all boxes have the input \texttt{'BoxProcessMode'}.
662 Another way to process the box \texttt{a} is to issue the command:
667 however this command does not display anything (except if the
668 box itself displays something in its processing).
669 It just processes the box if needed.
670 This command is used to execute boxes that do not have any output,
671 such as boxes that write something to a file or, display a
672 graphical interface, and so on.
680 % ==========================================
685 \item The \texttt{include} command allows to load a package, and the complex black boxes that come with it..
686 \item \texttt{help} gives help on:
688 \item Available commands if you just type \texttt{help}.
689 \item A particular command if you type \texttt{help <command-name>}.
690 \item All available packages and their boxes (without description) if you type \texttt{help packages}.
691 \item A particular package and its boxes (with brief description) if you type \texttt{help <package-name>}.
692 \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}).
694 %\item \texttt{list} displays the list of black box instances created so far (by \texttt{new}).
695 \item \texttt{new} : creates an instance of a black box.
696 \item \texttt{set} : sets the value of an input of a black box.
697 \item In all \bbi, to reference the input called \texttt{i}
698 of a black box called \texttt{b} you must type \texttt{'b.i'}.
699 The same syntax holds for outputs.
700 \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
701 implicit trailing 'new line character' is added at the final string.
702 \item \texttt{exec} : runs the process of a box if needed.
703 \item \texttt{quit} : quits \bbi.
708 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.
709 Wou'll get something like in figure \ref{bbCommandPlusHelp} :
712 \caption{\label{bbCommandPlusHelp}
713 An other way to run the command interpreter}
715 \includegraphics[width=0.5\textwidth]{bbCommandPlusHelp.png}
718 % ==========================================
720 % ==========================================
721 \subsubsection{Connecting black boxes}
722 \label{bbi-connecting-black-boxes}
723 % ==========================================
725 \BBTK allows to create
726 and execute processing chains,
727 also called \emph{pipelines},
728 by connecting black boxes.
729 This section explains how to do it with examples.
730 Read section \ref{bbi-more-on-pipeline-processing} to get
731 more information on pipeline processing.
733 First start \bbi and load the package \texttt{std}:
738 Assume you want to compute $1+2+3$. You can do it by
739 chaining two \texttt{Add} boxes, as shown in figure
740 \ref{bbi-fig-connecting-black-boxes-1}.
743 \caption{\label{bbi-fig-connecting-black-boxes-1}
744 A simple pipeline which adds 3 numbers}
746 \includegraphics[width=0.5\textwidth]{1plus2plus3.png}
751 The \bbi instructions to create and execute this pipeline are:
755 > connect a.Out b.In1
762 You will see the (very expected) result :
767 The first three commands build the pipeline,
768 the next three set \texttt{a} and \texttt{b} black boxes inputs and the last one
769 prints \texttt{b} black boxe output (the pipeline is executed before printing, because the interpretor 'knows' he box \texttt{b},
770 whose output is requested, is not up to date.
772 The command \texttt{'connect a.Out b.In1'} ``plugs'' the output
773 \texttt{Out} of the box \texttt{a} into the input \texttt{In1} of the
775 Once the boxes connected, the processing of the two boxes are chained:
776 getting the output of \texttt{b} requires getting its inputs,
777 hence getting the output of \texttt{a} which is connected to it.
778 This pipeline mechanism can recurse into arbitrary long
779 chains of boxes (see \ref{bbi-more-on-pipeline-processing}
783 Lets' consider an other, more image oriented, example :
791 > new FileSelector fileDialog
792 > new ImageReader reader
794 > new Viewer2D viewer
796 > connect fileDialog.Out reader.In
797 > connect reader.Out viewer.In
798 > connect slider.Out viewer.Slice
799 > connect slider.BoxChange viewer.BoxExecute
804 Some explainations : the \texttt{include} instructions load the necessary packages. \\
806 \texttt{new FileSelector} will pop a File Selector, at run time, that will out the user chosen file name. \\
807 \texttt{new Slider} will pop a Slider, at run time, that will out an integer, used later as a slice number.\\
808 \texttt{new ImageReader} will read any itk readable file, whose name is passed as a std::string, and return a itk::ImagePointer.
809 \texttt{new Viewer2D} display a plane, whose number id specified by an integer.\\
811 \texttt{connect fileDialog.Out reader.In} plugs the output of the File Selector (a std::string) to the input of the reader (a std::string, too).\\
812 \texttt{connect reader.Out viewer.In} plugs the output of the reader (an itk::ImagePointer) to the input of the Viewer (a vtkImageData *)\\
813 \texttt{connect slider.Out viewer.Slice} plugs the output of the slider (an int) to an other output (named Slide) of the viewer.\\
814 \texttt{connect slider.BoxChange viewer.BoxExecute} says the viewer it must re process itself any time the slider is modified.\\
816 \texttt{exec viewer} processes the viewer.
819 This would correspond to the graph in figure \ref{bbi-simplegraph}
823 \caption{\label{bbi-simplegraph}(Very) simple Graph of a (very) simple pipeline}
825 \includegraphics[width=0.8\textwidth]{bbi-simplegraph.png}
829 Of course, to be able to connect two boxes,
830 the output and the input must be compatibles.
831 You can always connect an output to an input of the \emph{same} type,
832 but you can do more, thanks to particular (hidden) black boxes called {\bf adaptors}.
834 An adaptor is a black box which has at least one input, called \texttt{In},
835 and at least one ouput called \texttt{Out} and whose role is to convert
836 a data of the type of \texttt{In}
837 into a data of the type of \texttt{Out} (other inputs or outputs may serve
838 to parameter the adaptor or retreive other usefull information).
840 In \bbi, if you type:
847 Package std v1.0.0 - laurent.guigues@creatis.insa-lyon.fr
848 Basic useful black boxes
850 Add : Adds its inputs
851 Cast<double,float> [DA] : Casts a double into a float
852 Cast<double,int> [DA] : Casts a double into a int
854 Convert<unsigned int,string> [DA] : Converts a unsigned int into a s...
855 Convert<unsigned short,string> [DA] : Converts a unsigned short into a...
856 Print : Prints its input to standard out...
860 The \texttt{Cast<?,?>} and \texttt{Convert<?,?>} boxes are \emph{default adaptors}, which is signaled by the tag \texttt{[DA]} before their descriptions.
862 Once you have loaded the package \texttt{std}, you can
863 plug an output of type \texttt{char} into an input of type \texttt{double}.
864 When \bbi encounters the \texttt{connect} command,
865 it looks for an adequate \emph{adaptor} in the loaded packages.
866 In our case, as the package \texttt{std} provides the
867 \texttt{Cast<char,double>} adaptor, \bbi automatically creates an
868 instance of this adaptor and place it \emph{between}
869 the output and the input you want to connect
870 (however this adaptor is hidden to you,
871 it is embedded into the created connection and does not appear
872 as an existing black box).
873 When the pipeline is processed the
874 adaptor converts the output data into the required input type,
875 in a totally transparent way.
876 In our example, the \texttt{Cast<char,double>} adaptor
877 would simply cast the value of the \texttt{char} into a \texttt{double},
878 however arbitrarily complex type conversion can be done.
881 if two adaptors with the same input and output types exist
882 in the packages loaded,
883 which one is chosen by \bbi at connection ?
884 -> Role of default adaptors
886 Note that the \texttt{set} and \texttt{print} commands of \bbi
887 work with adaptors from \texttt{string} to the type of the input to set
888 or from the type of the output to print to \texttt{string}.
889 Hence in order to \texttt{set} or \texttt{print} values the adequate
890 adaptors must be available in the packages currently loaded.
892 % ==========================================
897 \item The \texttt{connect} command allows to connect two black boxes
898 \item You can connect two black boxes if (and only if):
900 \item The output and the input are of the same type, or
901 \item There is an adaptor black box in the packages loaded which
902 converts data of the output type into data of the input type
904 \item \texttt{help <package name>} does not display the adaptors of the package. To see them use: \texttt{help <package name> all}.
908 % ==========================================
910 % ==========================================
911 \subsubsection{Creating complex black boxes}
912 \label{bbi-complex-black-boxes}
913 % ==========================================
915 Remember the pipeline of figure
916 \ref{bbi-fig-connecting-black-boxes-1}, which
917 computed the sum of three doubles ?
918 You can view it as a whole and define
919 a new black box type, which will be a \emph{complex black box},
920 having three inputs and one output,
921 as shown in figure \ref{bbi-fig-complex-black-box-1}.
924 \caption{\label{bbi-fig-complex-black-box-1}
925 Creating the complex black box \texttt{Add3}}
927 \includegraphics[width=0.5\textwidth]{Add3.png}
931 The \bbi commands to define this complex black box are
941 > connect a.Out b.In1
944 > description "adds 3 doubles"
945 > input x a.In1 "first double to add"
946 > input y a.In2 "second double to add"
947 > input z b.In2 "third double to add"
948 > output result b.Out "output"
955 As we will use \texttt{Add} boxes, we need to load the package \texttt{std}, which is done in first line.
957 The command \texttt{define} then starts the definition
958 of the complex box type, which will be called \texttt{Add3}.
960 The next three lines define the pipeline,
961 exactly in the same way than outside a complex box definition.
963 The commands \texttt{author}, \texttt{description}, \texttt{input}
964 and \texttt{output} are commands specific to complex boxes definition:
966 \texttt{author} and \texttt{description} are used for the documentation
967 of the new box. You can provide multiple \texttt{author} or
968 \texttt{description} commands, the arguments of the commands will
969 be concatenated to produce the final author and description strings.
971 \texttt{input} and \texttt{output} are used to define the inputs and outputs
972 of the new complex box.
973 Their syntax is the same: for each new input/output you need to say
974 to which internal input/output it corresponds and to provide
975 a help string documenting the input/output.
976 In our example, we define that the box \texttt{Add3} has
977 three inputs: \texttt{x}, \texttt{y} and \texttt{z}.
978 The input \texttt{x} corresponds to the input \texttt{In1} of the
979 internal box \texttt{a}.
980 In the same way, the external input \texttt{y}
981 corresponds to the internal input \texttt{a.In2}, and
982 the external input \texttt{In3} to \texttt{b.In2}.
983 The only output of the new box is called \texttt{result}
984 and corresponds to \texttt{b.Out}.
985 The figure \ref{bbi-fig-complex-black-box-1}
986 illustrates the external to internal
987 input/output correspondence.
989 Finally, the \texttt{endefine} command ends the definition of the
992 After this definition, if you ask for help
993 on packages, you get:
1004 The \texttt{user} package now contains a new black box type, called
1005 \texttt{Add3}. If you ask for help on this type of box, you get:
1008 Complex Black Box <user::Add3>
1012 'x' <double>: first double to add
1013 'y' <double>: second double to add
1014 'z' <double>: third double to add
1016 'result' <double>: output
1022 and you can use it like any other box, for example type:
1034 As a side note, we can say that, for consistency reasons, it would have been better to name
1035 \texttt{In1}, \texttt{In2} and \texttt{In3} the inputs of the black box \texttt{Add3},
1036 since all the 'natural entry' of a box is named \texttt{In}, or\texttt{In}x if there are more than one 'natural
1039 % ==========================================
1044 \item The \texttt{define/endefine} commands allows to define complex black box types, i.e. types of black boxes made up of other black boxes.
1045 Inside a \texttt{define/endefine} block:
1047 \item The \texttt{author} and \texttt{description} commands allow to document the new type of box
1048 \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
1049 of internal boxes they correspond.
1053 % ==========================================
1055 % ==========================================
1056 \subsubsection{Writing scripts}
1057 \label{bbi-writing-scripts}
1058 % ==========================================
1060 Once you have defined a new type of complex box, you
1061 may like to reuse it. To do this, you can simply
1062 write the \bbi commands defining the new box
1063 into a text file and afterwards include that file in \bbi.
1064 Doing this, you start writing \bbi scripts.
1065 The conventionnal extension for such scripts is \texttt{bbs}
1067 For consistency reasons, you are requested to prepend \texttt{bb} to the name.
1069 For example, the \texttt{Add3} complex box we previously worked on
1070 can be defined in the \texttt{bbAdd3.bbs} file:
1072 \begin{file}{bbAdd3.bbs}
1074 # Defines the Add3 black box which adds 3 doubles
1080 description "adds 3 doubles"
1086 input x a.In1 "first double to add
1087 input y a.In2 "second double to add
1088 input z b.In2 "third double to add"
1090 output result b.Out "output"
1095 Lines starting with a \texttt{\#} character are ignored, they
1096 are considered as comments by \bbi.
1097 To use this file in \bbi, use the \texttt{include} command:
1100 > include bbAdd3.bbs
1102 Complex Black Box <user::Add3>
1106 'x' <double>: first double to add
1107 'y' <double>: second double to add
1108 'z' <double>: third double to add
1110 'result' <double>: output
1118 If the file has the \texttt{bbs} extension, you can ommit it and just type:
1123 Of course, you can include script files in other script files,
1124 like in the following example:
1126 \begin{file}{bbAdd4.bbs}
1128 # Defines the Add4 black box which adds 4 doubles
1133 description "adds 4 doubles"
1137 input In1 a.In1 "first double to add
1138 input In2 a.In2 "second double to add
1139 input In3 a.In3 "third double to add"
1140 input In4 b.In2 "fourth double to add"
1141 output Out b.Out "output"
1146 % ==========================================
1148 \paragraph{Naming Conventions}
1152 % ==========================================
1156 For consistency reasons, you are requested to prepend \texttt{bb}, and postpone an extention \texttt{.bbs},
1157 to the names of the files that hold a \texttt{complex black box} definition.
1159 For example, the \texttt{Add3} complex box we previously worked on
1160 can be defined in the \texttt{bbAdd3.bbs} file.
1164 % ==========================================
1170 \item The \texttt{include} command allows to include a script file in \bbi.
1171 \item Lines starting with a \texttt{\#} or with a \texttt{\//} are treated as comments in \bbi scripts.
1172 \item Lines between a line starting with a \texttt{\//*} an a line starting with a \texttt{*\//} are treated as comments in \bbi scripts.
1176 % ==========================================
1178 % ==========================================
1179 \subsubsection{Creating command line applications}
1180 \label{bbi-command-line-app}
1181 % ==========================================
1183 Now that you now how to create complex black boxes
1184 (with \texttt{define/endefine}), think
1185 back to the \texttt{workspace} object.
1186 Remember that it is also
1187 a \texttt{complex black box}.
1188 In fact what you are doing when you type \bbi commands
1189 outside a \texttt{define/endefine} block
1190 is to progressively define the \texttt{workspace}
1192 You can think of it like if at start
1193 \bbi was issuing a command \texttt{'define workspace'}
1194 and then letting you define the interior of the box
1197 Remember that the command \texttt{inputs}
1198 allows to define an input of a complex box.
1199 Now, if you use the command \texttt{input}
1200 outside a \texttt{define/endefine} block then
1201 it defines an input of the \texttt{workspace} box,
1202 that is an input of the \emph{main program}.
1203 This input will then be connected to the
1204 parameters that the user passes to the command line.
1206 For example, consider the script:
1208 \begin{file}{add.bbs}
1212 input x a.In1 "first number to add"
1213 input y a.In2 "second number to add"
1218 The third and fourth lines define two inputs \texttt{x}
1219 and \texttt{y}. When you execute this script,
1220 you can pass these two arguments on the command line,
1228 You can also invoke \bbi the option \texttt{-h},
1229 which gives help on the \texttt{workspace} box:
1236 'x' <double>: first number to add
1237 'y' <double>: second number to add
1240 To get a better help, use the \texttt{description}
1241 and \texttt{author} commands:
1243 \begin{file}{add.bbs}
1245 description "Adds two numbers"
1246 author "foo@bar.com"
1249 input x a.In1 "first number to add"
1250 input y a.In2 "second number to add"
1255 Now if you ask for help on the \texttt{add} script, you get:
1262 'x' <double>: first number to add
1263 'y' <double>: second number to add
1266 Rather than getting the inputs of a script
1267 from the command line, you can ask \bbi to
1268 prompt the user for the values, using the \texttt{-t}
1273 x=[the program waits for user answer]2
1274 y=[the program waits for user answer]5
1278 If \bbi is compiled in graphical mode (with \wx),
1279 you can also use the \texttt{-g} commutator.
1280 \bbi then prompts the user in graphical mode,
1281 displaying a dialog box for each input,
1282 like in fig. \ref{bb-input-dialog-box}.
1285 \caption{\label{bb-input-dialog-box}Input dialog box}
1287 \includegraphics[width=0.6\textwidth]{enter-the-value-of-x.png}
1291 % ==========================================
1296 \item The \texttt{input}, \texttt{description} and \texttt{author} commands,
1297 when they are used outside a \texttt{define/endefine} block allow
1298 to define the inputs, description and author of the main program.
1299 \item Inputs of the main program can be passed on the command line
1300 using the syntax \texttt{<input-name>=<value>}.
1301 No white space is allowed, if the value or the input name
1302 contains white spaces, enclose them
1303 between double quotes, e.g. \texttt{"parameter with white spaces = gnu's not unix"}.
1304 \item The \texttt{-h} option of \bbi prints help on the main program.
1305 \item The \texttt{-t} option of \bbi orders the program to prompt for its inputs in text mode.
1306 \item The \texttt{-g} option of \bbi orders the program to prompt for its inputs in graphical mode.
1309 % ==========================================
1311 % ==========================================
1312 \subsubsection{Using graphical interface boxes (widget boxes)}
1314 % ==========================================
1316 % ==========================================
1317 \subsubsection{Overwiew}
1318 \label{bbi-overview}
1319 % ==========================================
1321 If \bbi is compiled in graphical mode
1322 (option \texttt{BUILD\_bbi\_GRAPHICAL} of \cmake, requires \wx),
1323 then you can use special black boxes which are
1324 graphical interface components (widgets).
1325 Basic components are provided in the package \texttt{wx},
1326 such as buttons, sliders, file open/save dialogs, etc.
1328 As first example, type the following commands in \bbi:
1335 When you type \texttt{enter} after the last line,
1336 a window pops up in which you can entrer a text.
1337 When you close the window, the text you entered is printed by
1338 the \texttt{print} command.
1340 Type \texttt{help wx}, you get something like:
1342 Package wx v1.0.0- info-dev@creatis.insa-lyon.fr
1343 Basic graphical interface elements (sliders, buttons ...) based on wxWidgets
1345 ColourSelector : Colour Selector dialog (bbfication of wxColourSele...
1346 ColourSelectorButton : A button which displays a colour picker dialog whe...
1347 CommandButton : Button which executes bbi commands
1348 DirectorySelector : Pops up a directory selection dialog (wxDirDialog)
1349 FileSelector : Pops up a file selection dialog for reading or sav...
1350 InputText : A zone in which the user can enter a text (wxTextC...
1351 LayoutLine : LayoutLine widget (wxBoxSizer)
1352 LayoutSplit : Widget which splits a window in two fixed size par...
1353 LayoutTab : LayoutTab widget (wxNotebook)
1354 OutputText : Text zone to be inserted into a window (wxStaticTe...
1355 RadioButton : RadioButton group widget 0-9 entries
1356 Slider : Slider widget (wxSlider)
1359 You can reproduce the same experiment as above using a
1360 \texttt{Slider} or a \texttt{FileDialog} rather than a \texttt{InputText}.
1361 See the files \texttt{test*.bbs} in the \texttt{scripts/test} directory.
1363 There are two kinds of widgets: ``terminal'' widgets and ``container'' widgets.
1364 The \texttt{InputText}, \texttt{FileDialog} or \texttt{Slider} widgets
1365 are ``terminal'' widgets.
1366 ``container'' widgets are of another kind: they are designed to
1367 contain other widgets in order to build larger dialog boxes.
1368 For example, the \texttt{LayoutSplit} widget is a container which
1369 ``splits'' horizontally a window into two parts,
1370 each part including another widget.
1371 The size of the two parts can be adjusted by the user thanks
1374 The script \texttt{scripts/test/testSplit.bbs} demonstrate its use.
1375 Run it: it displays a window with two sliders.
1376 Move the sliders and close the window.
1377 The final positions of the sliders are printed out.
1378 Now edit the file to see how this is done:
1380 \begin{file}{scripts/test/testSplit.bbs}
1389 connect s1.Widget s.Widget1
1390 connect s2.Widget s.Widget2
1392 print s1=$s1.Out$\\n
1393 print s2=$s2.Out$\\n
1397 First, the two sliders \texttt{s1} and \texttt{s2} are created.
1398 A \texttt{LayoutSplit} box \texttt{s} is also created.
1399 The \texttt{connect} commands then ``includes'' the sliders in the
1400 split ``container''.
1401 The input \texttt{Widget} is common to all widget boxes:
1402 every widget can be inserted into another widget.
1403 The outputs \texttt{Widget1},\texttt{Widget2} are specific of \emph{container}
1405 (in \bbi type \texttt{help Slider}:
1406 you will see the output \texttt{Widget};
1407 type \texttt{help LayoutSplit}:
1408 you will see the inputs \texttt{Widget1} and \texttt{Widget2}
1409 and the output \texttt{Widget}).
1410 When you connect the \texttt{Widget} output of a container
1411 to the \texttt{Widget}i input of a widget,
1412 you order to include the widget in the container.
1413 Of course, the order of connection is important.
1414 In our case, the slider \texttt{s1} is included first,
1415 then the slider \texttt{s2}: \texttt{s1} will be placed
1416 on top of \texttt{s2} (the \texttt{LayoutSplit} box is
1417 implemented that way, but this is arbitrary choice).
1419 Right now, there are only \emph{three} container widgets in the \texttt{wx} package:
1420 the \texttt{LayoutSplit} widget we just described, the \texttt{LayoutLine} , and the \texttt{LayoutTab}
1423 The \texttt{LayoutLine} widget can have multiple children and
1424 divides its window into as much parts as children,
1425 each part of equal size.
1426 The orientation of the \texttt{LayoutSplit} or of the \texttt{LayoutLine} can be changed by the input \texttt{Orientation}.
1427 See the example \texttt{test/testSizer.bbs}.
1428 With only those two containers you can already create
1429 complex dialog boxes (of course containers can be nested, which
1430 leads to tree-like structures of widgets).
1431 See the script \texttt{bbtk/share/bbtk/bbs/wx/appli/ExampleLayoutSplit.bbs} for an example.
1433 The \texttt{LayoutTab} widget is based on the \texttt{wxNotebook.}
1435 One word about a special widget in the package \texttt{wx}:
1436 the \texttt{Button}... to be continued.
1438 % ==========================================
1439 \subsubsection{Deeper in the boxes}
1440 \label{bbi-deep-box}
1441 % ==========================================
1443 Any widget box has two mandatory Outputs :
1446 \item {\bf\emph{Widget}} : that is the \texttt{wxWindow} itself. If it's not connected to the \texttt{Widget}\emph{i} of any \emph{Layout box}, it
1447 will popup. If it's connected to the \texttt{Widget}\texttt{\emph{i}} of any \texttt{Layout box}, it will be embedded in its parent window.
1448 \item {\bf\emph{Boxchange}} : Signals any modification of the box. This output may be connect if necessary to the \emph{BoxExecute} of an other box,
1449 further within the execution pipeline.
1452 Any widget box has two mandatory Inputs :
1454 \item {\bf\emph{BoxExecute}} : Any signal received by this input executes the box
1455 \item {\bf\emph{BoxProcessMode}} : Sets the processing mode of the box :
1457 \item {\bf\emph{Pipeline}} : bbUpdate() calls Process only if Status == MODIFIED (normal pipeline processing)
1458 \item {\bf\emph{Always}} : bbUpdate() always calls Process
1459 \item {\bf\emph{Reactive}} : bbSetModifiedStatus() calls bbUpdate()
1463 Any widget box has five Inputs, that will be dealt with only if the box is not connected to the \emph{Widget}i of any \emph{Layout box} :
1465 \item {\bf\emph{WinHeight}} : Height of the window
1466 \item {\bf\emph{WinWidth}} : Width of the window
1467 \item {\bf\emph{WinTitle}} : Title of the window
1468 \item {\bf\emph{WinClose}} : Any received signal closes the window
1469 \item {\bf\emph{WinHide}} : Any received signal hides the window
1470 \item {\bf\emph{WinDialog}} : When set to 'true', creates a \emph{dialog window}, that blocks the pipeline until it is closed (\emph{modal})
1474 Any \emph{Layout box} (i.e. \emph{LayoutLine}, \emph{LayoutSplit} or \emph{LayoutTab}) has at one or more mandatory Inputs :
1476 \item {\bf\emph{Widget}}\texttt{i} : e.g. a \emph{LayoutSplit} box (Widget which splits a window in two fixed size parts)
1477 has two Input parameters \emph{Widget1} and \emph{Widget2}, used to embed the child windows.
1481 % ==========================================
1482 \subsection{More on ...}
1484 % ==========================================
1486 % ==========================================
1487 \subsubsection{Black box packages}
1488 \label{bbi-more-on-packages}
1489 % ==========================================
1491 There are various others user-intended packages :
1494 It contains some vtk based image processing filters :
1497 \paragraph{AppendPolyData}
1498 Appends one of more polygonal datasets into a single polygonal dataset
1500 \paragraph{ConeSource}
1503 \paragraph{ImageAnisotropicDiffusion3D}
1504 vtkImageAnisotropicDiffusion3D diffuses an volume iteratively. \\
1505 The neighborhood of the diffusion is determined by the instance flags. \\
1506 if 'Faces' is on, the 6 voxels adjoined by faces are included in the neighborhood. \\
1507 If 'Edges' is on the 12 edge connected voxels are included, and if 'Corners' is on, the 8 corner connected voxels are included. \\
1508 'DiffusionFactor' determines how far a pixel value moves toward its neighbors, and is insensitive to the number of neighbors chosen.\\
1509 The diffusion is anisotropic because it only occurs when a gradient measure is below 'GradientThreshold'. \\
1510 Two gradient measures exist and are toggled by the 'GradientMagnitudeThreshold' flag. \\
1511 When 'GradientMagnitudeThreshold' is on, the magnitude of the gradient, computed by central differences, above 'DiffusionThreshold' a voxel is not
1513 The alternative measure examines each neighbor independently.\\
1514 The gradient between the voxel and the neighbor must be below the 'DiffusionThreshold' for diffusion to occur with THAT neighbor.\\
1516 - In : an image (vtkImageData*)\\
1517 - Diffusion : Difference threshold that stops the diffusion\\
1519 - Out : the isosurface mesh (vtkPolyData*)
1521 \paragraph{ImageCharacteristics}
1522 Exports objet sizes, and Spacings
1524 \paragraph{ImageDilateErode3D}
1525 Dilates one value and erodes another.\\
1526 vtkImageDilateErode3D will dilate one value and erode another. \\
1527 It uses an elliptical foot print, and only erodes/dilates on the boundary of the two values. \\
1528 The filter is restricted to the X, Y, and Z axes for now.\\
1529 It can degenerate to a 2 or 1 dimensional filter by setting the kernel size to 1 for a specific axis. \\
1530 (bbfication of vtkImageDilateErode3D) \\
1532 - In : an image (vtkImageData*)\\
1533 - DilateValue : The dilatation value\\
1534 - ErodeValue : The erosion value\\
1536 - Out : the isosurface mesh (vtkPolyData*)
1538 \paragraph{ImageGaussianSmooth}\\
1539 Performs a gaussian convolution of the input image\\
1541 - In : an image (vtkImageData*)\\
1542 - StdDevX : Standard deviation in X direction\\
1543 - StdDevY : Standard deviation in Y direction\\
1545 - Out : the isosurface mesh (vtkPolyData*)
1547 \paragraph{ImagePlanes}
1548 Creates three 3D planes with the input image mapped onto with which the user can interact; \\
1549 The output vtkImagePlaneWidget objects are to be inserted into a 3D scene (e.g. a Viewer3D)
1551 - In : an image (vtkImageData*)\\
1553 - PlaneX : the image plane in X direction (vtkImagePlaneWidget*)\\
1554 - PlaneY : the image plane in Y direction (vtkImagePlaneWidget*)\\
1555 - PlaneY : the image plane in Z direction (vtkImagePlaneWidget*)\\
1558 - Out : the isosurface mesh (vtkPolyData*)
1560 \paragraph{IsoSurfaceExtractor}
1561 Extracts an iso-surface of a 3D image and creates a vtkProp3D object to insert into a 3D scene (e.g. a Viewer3D)
1563 - In : an image (vtkImageData*)\\
1564 - Isovalue : the isosurface value (double)\\
1565 - Colour : Surface colour (vector of 3 doubles)
1567 - Out : the isosurface (vtkProp3D**)
1569 \paragraph{MarchingCubes}
1570 Extracts an iso-surface of an image using the marching cubes algorithm (bbfication of vtkMarchingCubes)\\
1572 - In : an image (vtkImageData*)\\
1573 - Value : the isosurface value (double)\\
1575 - Out : the isosurface mesh (vtkPolyData*)
1577 \paragraph{MIPCreator}
1578 Creates a Maximum Intensity Projection (MIP) view of a 3D image.\\
1580 - In : an image (vtkImageData*)\\
1581 - Scale : the Gray scale scaling (float) \\
1582 - Shift : the Gray scale shift (float) \\
1584 - Out : The MIP object (vtkProp3D*) to be plugged into a 3D Viever
1586 \paragraph{MetaImageReader}
1587 Reads .mhd / .mhd image formats (bbfication of vtkMetaImageReader) \\
1589 - In : the name of the file to be read (std::string)
1591 - Out : The image (vtkImageData*)
1593 \paragraph{SegmentationConnectivity} \\
1594 Segmentation with min max threshold and connectivity \\
1596 - In : an image (vtkImageData*)\\
1597 - PositionXYZ : initial position (std::vector<int>) \\
1598 - ThresholdMinMax : min, max threshold values (std::vector<int>) \\
1600 - Out : The image (vtkImageData*)
1602 \paragraph{SphereSource}
1607 It contains some itk based image processing filters :
1609 \paragraph{BinaryThresholdImageFilter}
1610 Binarizes an image by thresholding (generic bbification of itk::BinaryThresholdImageFilter)
1612 \paragraph{DICOMSeriesFileNames}
1613 Reads a series from a DICOM directory as a 3D itk image
1615 \paragraph{ExtractImageFilter}
1616 Decrease the image size by cropping the image to the selected region bounds (bbification of itk::ExtractImageFilter)
1618 \paragraph{ImageProperties}
1619 Outputs different properties of an image (type, dimension, size, spacing, ...)
1621 \paragraph{ImageRegion}
1622 Creates a generic ImageRegion (bbtk::any) from two vectors providing the index and size of the region.
1623 The dimension D of the actual itk::ImageRegion created is the max of the sizes of Index and Size
1624 (the smallest vector is padded by zeros)
1626 \paragraph{ImageReader}
1627 Generic itk image reader
1629 \paragraph{ImageWriter}
1630 Generic itk image writer
1632 \paragraph{ImageSeriesReader}
1633 Generic itk image series reader.
1635 \paragraph{ResampleImageFilter}
1639 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
1641 Sorry nothing is done, right now for meshes.
1645 It contains two atomic black boxes.
1647 \paragraph{Viewer2D}
1649 - a \textless vtkImageData* \textgreater (In),\\
1650 - an Orientation(0:yz / 1:xz / 2:xy),\\
1651 - an initial slice number (Slice).\\
1653 - a \textless vtkRenderer* \textgreater (Renderer)
1655 \paragraph{Viewer3D}
1657 - up to 5 Input Actors (\textless vtkProp3D* \textgreater),\\
1658 - up to 5 Input Observers (\textless vtkInteractorObserver* \textgreater), \\
1659 - a boolean 'Stereo' option, to use Red-Blue filter
1661 - an Interactor (\textless wxVTKRenderWindowInteractor* \textgreater) with which vtk widgets can interact, \\
1662 - a Renderer (\textless vtkRenderer* \textgreater) to which actors can be added.
1664 It contains too some sophisticated complex black boxes :
1666 \paragraph{IsoSurfaceWithControls}
1667 Image iso-surface extractor (vtk::IsoSurfaceExtractor) with associated control panel (isovalue, opacity and colour)\\
1669 - an initial isovalue (Isovalue)
1670 - an initial opacity (Opacity)
1671 - an initial colour (Colour)
1673 \textless vtkProp3D* \textgreater (In)\\
1675 \paragraph{MIPWithControls}
1676 Maximum Intensity Projection (MIP) creator (vtk::MIPCreator) with associated control panel (shift and scale) \\
1678 - an initial scale (Scale)
1679 - an initial shift (Shift)
1681 \textless vtkProp3D* \textgreater (In)\\
1685 Some boxes are the bbfication of usefull xwWidgets, some other ones are more
1688 \paragraph{ColourSelector} Colour Selector dialog (bbfication of wxColourSelector) \\
1690 \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
1693 \paragraph{ColourSelectorButton} A button which displays a colour picker dialog when clicked \\
1695 \texttt{In} :Initial colour \\
1696 \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
1699 \paragraph{CommandButton} Button which executes bbi commands \\
1701 \texttt{In} : Commands to be executed separated by commas (;). Each single quote (') is replaced by a double quote ("). \\
1702 \texttt{Label} : Label of the button \\
1703 \texttt{Widget} : Output widget \\
1706 \paragraph{DirectorySelector} Pops up a directory selection dialog (wxDirDialog)\\
1708 \texttt{DefaultDir} : The default directory\\
1709 \texttt{Message} : Message to show on the dialog \\
1710 \texttt{Title} : Title of the dialog \\
1711 \texttt{Out} : The directory selected by the user\\
1714 \paragraph{FileSelector} Pops up a file selection dialog for reading or saving (wxFileDialog)\\
1716 \texttt{DefaultDir} : The default directory \\
1717 \texttt{DefaultFile} : The default filename \\
1718 \texttt{Message} : Message to show on the dialog \\
1719 \texttt{OpenSave} : Open for an open dialog (default) / Save for a save dialog\\
1720 \texttt{Title} : Title of the dialog \\
1721 \texttt{Wildcard} : A wildcard, such as "*.*" or "BMP files (*.bmp)|*.bmp|GIF files (*.gif)|*.gif" \\
1722 \texttt{Out} : The file selected by the user \\
1725 \paragraph{InputText} A zone in which the user can enter a text (wxTextCtrl)\\
1727 \texttt{In} : Initial text (default '')\\
1728 \texttt{Title} : Title of the input zone (default '')\\
1729 \texttt{WinTitle} : Title of the window (*)\\
1730 \texttt{Out} :Current text\\
1733 \paragraph{LayoutLine} LayoutLine widget (wxBoxSizer)\\
1735 \texttt{Orientation} Orientation (default V), 0=H=HORIZONTAL , 1=V=VERTICAL \\
1736 \texttt{Widget}1 widget 1 \\
1737 \texttt{Widget2} widget 2 \\
1738 \texttt{Widget3} widget 3 \\
1739 \texttt{Widget4} widget 4 \\
1740 \texttt{Widget5} widget 5 \\
1741 \texttt{Widget6} widget 6 \\
1742 \texttt{Widget7} widget 7 \\
1743 \texttt{Widget8} widget 8 \\
1744 \texttt{Widget9} widget 9\\
1747 \paragraph{LayoutSplit} Widget which splits a window in two fixed size parts (wxSplitterWindow)\\
1749 \texttt{Orientation} : Orientation (default H), 0=H=HORIZONTAL , 1=V=VERTICAL\\
1750 \texttt{Proportion} : Proportion (in percent) of the first children in the window\\
1751 \texttt{Widget1} : Upper or left widget\\
1752 \texttt{Widget2} : Lower or right widget\\
1755 \paragraph{LayoutTDown} Creates a 'T like' complex container : Down {UpLeft, UpRight} \\
1757 \texttt{Widget1} : UpLeft container\\
1758 \texttt{Widget2} : UpRight container\\
1759 \texttt{Widget3} : Down container\\
1770 \paragraph{LayoutTLeft} Creates a 'T like' complex container : Left {RigthUp, RightDown}\\
1772 \texttt{input} Widget1 : "UpLeft container"\\
1773 \texttt{input} Widget2 : "UpRight container"\\
1774 \texttt{input} Wigdet3 : "Down container"\\
1785 \paragraph{LayoutTRight} Creates a 'T like' complex container : Right {LeftUp, LeftDown}\\
1787 \texttt{input} Widget1 currentBox.Widget1 "Up container"\\
1788 \texttt{input} Widget2 down.Widget1 "DownLeft container"\\
1789 \texttt{input} Widget3 down.Widget2 "DownRight container"\\
1800 \paragraph{LayoutTUp} Creates a 'T like' complex container : Up {DownLeft, DownRight} as w1{w2,w3}\\
1802 \texttt{ input} Widget1 currentBox.Widget1 "Up"\\
1803 \texttt{input} Widget2 down.Widget1 "DownLeft"\\
1804 \texttt{input} Widget3 down.Widget2 "DownRight"\\
1815 \paragraph{LayoutTab} LayoutTab widget (wxNotebook)\\
1817 \texttt{Orientation} Orientation (default T), 0=T=TOP , 1=R=RIGHT , 2=B=BOTTON , 3=L=LEFT \\
1818 \texttt{Widget1} widget 1 \\
1819 \texttt{Widget2} widget 2 \\
1820 \texttt{Widget3} widget 3 \\
1821 \texttt{Widget4} widget 4 \\
1822 \texttt{Widget5} widget 5 \\
1823 \texttt{Widget6} widget 6 \\
1824 \texttt{Widget7} widget 7 \\
1825 \texttt{Widget8} widget 8 \\
1826 \texttt{Widget9} widget 9 \\
1829 \paragraph{OutputText} Text zone to be inserted into a window (wxStaticText)\\
1832 \texttt{Title} Title prepended to the text\\
1835 \paragraph{RadioButton} RadioButton group widget 0-9 entries\\
1837 \texttt{In} Set initial item \\
1838 \texttt{In0} option 0\\
1839 \texttt{In1} option 1\\
1840 \texttt{In2} option 2\\
1841 \texttt{In3} option 3\\
1842 \texttt{In4} option 4\\
1843 \texttt{In5} option 5 \\
1844 \texttt{In6} option 6 \\
1845 \texttt{In7} option 7 \\
1846 \texttt{In8} option 8 \\
1847 \texttt{In9} option 9 \\
1848 \texttt{Title} Title of the widget (default '')\\
1849 \texttt{Out} Number of the selected Item
1852 \paragraph{Slider} Slider widget (wxSlider)\\
1854 \texttt{ChangeResolution} Enables the user to change the slider resolution (default FALSE) \\
1855 \texttt{In} Initial slider position(default 0) \\
1856 \texttt{Label} Show slider labels ? (default FALSE) \\
1857 \texttt{Max} Maximum value of the slider (default 500)\\
1858 \texttt{Min} Minimum value of the slider (default 0)\\
1859 \texttt{Orientation} Orientation : (default H) 0=H=HORIZONTAL, 1=V=VERTICAL\\
1860 \texttt{ReactiveOnTrack} Slider sends info when track moves (default 0 = no)\\
1861 \texttt{Title} Title shown above the slider (default '')\\
1864 % ==========================================
1865 \subsubsection{Pipeline processing}
1866 \label{bbi-more-on-pipeline-processing}
1867 % ==========================================
1869 \item the ``control'' mechanism in bbi (switch exec commands, e.g. Button)
1870 \item the role of ProcessMode to update widgets.
1872 % ==========================================
1873 \subsubsection{Complex black boxes}
1874 \label{bbi-more-on-complex-black-boxes}
1875 Creation of complex widgets (containers, contained...)
1877 %\subsubsection{Advanced issues}
1878 %\paragraph{Reducing the number of inputs of a box}
1880 % ==========================================
1881 \subsubsection{Errors}
1882 \label{bbi-more-on-errors}
1884 % ==========================================
1885 \subsubsection{\bbtk configuration file and search pathes}
1886 \label{bbi-more-on-configuration}
1888 At start, \bbi tries to open an \texttt{xml}
1889 configuration file named \texttt{bbtk\_config.xml}.
1892 \item The current directory
1893 \item The subdir \texttt{.bbtk} of the user's home directory.
1895 \item On \texttt{Unix}, the home directory is the
1896 one stored by the environnement variable \texttt{HOME},
1897 typically \texttt{/home/username}.
1898 \item On \texttt{Windows}, the home directory is
1899 the user's profile directory stored by the environnement
1900 variable \texttt{USERPROFILE},
1901 typically \texttt{C:\\...}.
1903 \item If none of these two pathes contains the file then it creates
1904 a new one in the \texttt{.bbtk} directory.
1907 Once created, you can edit the \texttt{bbtk\_config.xml} file located
1908 in your \texttt{.bbtk} directory. It contains:
1910 \begin{file}{bbtk\_config.xml}
1912 <?xml version="1.0" encoding="iso-8859-1"?>
1914 <bbtk_url> http://www.creatis.insa-lyon.fr/software/bbtk </bbtk_url>
1915 <bbs_path> </bbs_path>
1916 <package_path> </package_path>
1917 <data_path> </data_path>
1922 You can add pathes to
1924 \item A custom folder in which to search for \texttt{.bbs} scripts (\texttt{include} command of \bbi) by adding an \texttt{xml} tag:
1925 \texttt{<bbs\_path>complete\_path\_to\_folder<\/bbs\_path>}.
1926 \item A custom folder in which to search for packages (\texttt{load} command of \bbi) by adding an \texttt{xml} tag:
1927 \texttt{<package\_path>complete\_path\_to\_folder<\/package\_path>}.
1930 % ==========================================
1931 \subsection{Language reference}
1932 \label{bbi-reference}
1933 % ==========================================
1939 % ==========================================
1941 \caption{\label{bbi-reference-box}
1942 \bbi pipeline creation and execution related commands.}
1944 \begin{tabular}{|lcm{6cm}|}
1946 Command & Parameters & Effect \\ \hline
1948 \texttt{new} & \texttt{<boxtype>} \texttt{<box-name>}&
1949 Creates a box of type \texttt{boxtype} and name
1953 \texttt{delete} & \texttt{<box-name>} &
1954 Destroys the box named \texttt{box-name}.
1957 \texttt{connect} & \texttt{<box1.output>} \texttt{<box2.input>} &
1959 \texttt{output} of the box named \texttt{box1}
1960 to the input \texttt{input} of the box named \texttt{box2} \\ \hline
1962 \texttt{set} & \texttt{<box.input>} \texttt{<value>} &
1963 Sets the input \texttt{input} of
1964 the box named \texttt{box} to the value \texttt{value}.
1965 There must exist an \texttt{adaptor}
1966 in the packages loaded which converts a \texttt{std::string}
1967 to the type of the input \texttt{input}.
1970 \texttt{print} & \texttt{<string>} &
1971 Prints the string after substituting each token of the form \texttt{\$box.output\$} by the adaptation to string of the value of the
1972 output \texttt{output} of the box named \texttt{box}.
1973 There must exist an \texttt{adaptor}
1974 in the packages loaded which converts
1975 the type of the output \texttt{output}
1976 to a \texttt{std::string}.
1979 \texttt{exec} & \texttt{<box-name>} &
1980 Executes the box named \texttt{box-name}.
1982 connected to its inputs
1983 are also processed recursively (pipeline processing).\\ \hline
1984 \texttt{exec} & \texttt{freeze} &
1985 allows to block execution commands while keeping definition commands active.\\ \hline
1986 \texttt{exec} & \texttt{unfreeze} &
1987 turns back to 'normal' mode.\\ \hline
1990 % ==========================================
1994 % ==========================================
1996 \caption{\label{bbi-reference-interpreter}\bbi intepreter related commands.}
1998 \begin{tabular}{|lcm{6cm}|}
2000 Command & Parameters & Effect \\ \hline
2004 Prints help on available commands \\ \hline
2006 & \texttt{<command-name>} &
2007 Prints help on the command \texttt{command-name} \\ \hline
2009 & \texttt{packages} &
2010 Prints help on available packages and their box types
2011 (without description)\\ \hline
2013 & \texttt{<package-name>} &
2014 Prints help on the package \texttt{package-name} and its boxes
2015 (with brief description).
2016 The package must have been previously loaded
2019 & \texttt{<box-type>} &
2020 Prints help (with full description) on the type of box
2022 The box type must belong to a package which has been previously loaded
2025 \texttt{include} & \texttt{<file-name>} &
2026 Includes and executes the content of the file named \texttt{file-name}
2027 exactly like if you were typing its content at the place were the
2028 \texttt{include} command is.
2031 \texttt{load} & \texttt{<package-name>} &
2032 Loads the package \texttt{package-name}\\ \hline
2034 \texttt{include} & \texttt{<package-name>} &
2035 Loads the package \texttt{package-name} and includes all the complex black boxes that comes with it \\ \hline
2037 \texttt{unload} & \texttt{<package-name>}&
2038 Unloads the package \texttt{package-name}.
2039 The package must have been previously loaded.
2040 No box of a type defined in this package must still exist.
2043 \texttt{message} & \texttt{<category>} \texttt{<level>} &
2044 Sets the level of verbosity of \bbi for the category of messages
2045 \texttt{category} to \texttt{level}.
2046 %See \ref{verbosity}.
2049 \texttt{config} & - & Displays the Configuration parameters\\ \hline
2051 \texttt{reset} & - & Deletes all boxes and unloads all packages so
2052 that \bbi gets back to its initial state \\ \hline
2054 \texttt{quit} & - & Exits the interpreter\\ \hline
2058 % ==========================================
2064 % ==========================================
2066 \caption{\label{bbi-reference-complex-box}
2067 \bbi complex black box definition related commands.}
2069 \begin{tabular}{|lcm{6cm}|}
2071 Command & Parameters & Effect \\ \hline
2074 \texttt{define} & \texttt{<box-type>} &
2075 Starts the definition of a complex black box of type
2076 \texttt{box-type}\\ \hline
2078 \texttt{endefine} & - &
2079 Ends the definition of a complex black box type\\ \hline
2082 \texttt{author} & \texttt{<string>} &
2083 Sets the author(s) of the complex black box currently being defined \\ \hline
2085 \texttt{description} & \texttt{<string>} &
2086 Sets the description of the complex black box currently being defined
2090 \texttt{input} & \texttt{<name>} \texttt{<box.input>} \texttt{<help>} &
2091 Defines a new input for the current complex black box,
2092 named \texttt{name}.
2093 It is defined as corresponding to
2094 the input \texttt{input} of the box \texttt{box}.
2095 \texttt{<help>} is the help string for the new input.
2096 The box \texttt{box} must already have been created in the complex box
2097 and of course have an input named \texttt{input}.
2101 \texttt{output} & \texttt{<name>} \texttt{<box.output>} \texttt{<help>} &
2102 Defines a new output for the current complex black box,
2103 named \texttt{name}.
2104 It is defined as corresponding to
2105 the output \texttt{output} of the box \texttt{box}.
2106 \texttt{<help>} is the help string for the new output.
2107 The box \texttt{box} must already have been created in the complex box and of course have an output named \texttt{output}.
2113 % ==========================================
2118 % ==========================================
2119 \vspace{0.5cm}\hrule
2120 \section{Using black boxes in \CPP programs}
2122 % ==========================================
2131 %\section{Conclusion}