1 % # ---------------------------------------------------------------------
3 % # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
5 % # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
6 % # Previous Authors : Laurent Guigues, Jean-Pierre Roux
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27 % ==========================================
28 \documentclass[11pt,final,a4paper]{article}
42 {\Huge Reference Manual}
45 \bbtk version \bbtkVersion
49 Last modified on : September 20 2008 \\
54 Fr\'ed\'eric Cervenansky, Eduardo D\'avila, Laurent Guigues, Jean-Pierre Roux
57 CREATIS, Centre de Recherche en Imagerie M\'edicale \\ CNRS UMR 5220, INSERM U1044\\
59 Universit\'e Claude-Bernard Lyon 1\\
60 http://www.creatis.insa-lyon.fr/site/en/CreatoolsBBTK
67 % ==========================================
69 % ==========================================
77 % ==========================================
79 % ==========================================
81 % ==========================================
86 ---> Should be moved in a 'Reference Manual' ?\\
87 ---> Any suggestion welcome!
89 --> The following is just the concatenation of various parts, removed from different 'manuals', and wainting for
90 their new affectation.
97 \caption{\label{kinds} \texttt{Black Box} kinds}
101 \texttt{Kind name} & : Meaning \\ \hline \\ \hline
102 \texttt{ADAPTOR} & : Adaptor Box \\ \hline
103 \texttt{DEFAULT\_ADAPTOR} & : \\ \hline
104 \texttt{WIDGET\_ADAPTOR} & : \\ \hline
105 \texttt{DEFAULT\_WIDGET\_ADAPTOR} & : \\ \hline
106 \texttt{GUI} & : \\ \hline
107 \texttt{DEFAULT\_GUI} & : \\ \hline
108 \texttt{ALL} & : If kind='ALL' then sets the level for all kinds \\ \hline
115 \bf\emph{Boxes} : Box retrieving on various criterions :
117 \item {\bf\emph{By name}} (Alphabetical list)
118 \item {\bf\emph{By package}} (see table : \ref{bbi-list_of_packages})
119 \item {\bf\emph{By category}} (see table : \ref{categories})
120 \item {\bf\emph{Adaptors}} Used internaly to perform type conversions (not end user intended)
125 % ==========================================
127 \caption{\label{bbi-list_of_packages} List of bbtk supplied packages.}
129 \begin{tabular}{|lp{10cm}|}
131 Package & What it's used for \\ \hline
132 \texttt{std} & : the 'standard' package including basic useful boxes \\ \hline
133 \texttt{wx} & : basic graphical interface elements (widgets : sliders, buttons, etc.) based on the \texttt{wxWidgets} library \\ \hline
134 \itk & : the basic image processing package, based on the \itk library. (without description)\\ \hline
135 \vtk & : prints help on the package \texttt{package-name} and its boxes (with brief description). The package must have been previously loaded\\ \hline
136 \texttt{wxvtk} & : widget boxes based on the \vtk library.\\ \hline
137 \texttt{itkvtk} & : adaptors to convert \itk structures into \vtk structures and conversally.\\ \hline
138 %\texttt{creaImageIO} & : provides high level widgets to read images including DICOM.\\ \hline
139 \texttt{toolsbbtk} & : Tools for bbtk administration and package development.\\ \hline
143 % ==========================================
147 % ==========================================
149 \caption{\label{categories} \texttt{Black Box} categories}
151 \begin{tabular}{|lp{10cm}|}
153 \texttt{Category name} & : Meaning \\ \hline \\ \hline
154 \texttt{adaptor} & : Adaptor box \\ \hline
155 \texttt{application} & : Final application, end user intended \\ \hline
156 \texttt{atomic box} & : System category.
157 Automatically assigned to Atomic Black Boxes (c++ defined) \\ \hline
158 \texttt{complex box} & : System category.
159 Automatically assigned to Complex Black Boxes (script defined) \\ \hline
160 \texttt{command line} & : Script which defines a command line application \\
161 & :(no embedded GUI, but command line imput parameters) \\ \hline
162 \texttt{demo} & : Demonstration \\ \hline
163 \texttt{devel} & : Developer tool (bbCreatePackage.bbs, ...) \\ \hline
164 \texttt{dicom} & : DICOM aware box \\ \hline
165 \texttt{example} & : Example script showing a box use-case \\ \hline
166 \texttt{filter} & : Image processing box \\ \hline
167 \texttt{image} & : Image processing related box \\ \hline
168 \texttt{interaction} & : \\ \hline
169 \texttt{math} & : Mathematical operations \\ \hline
170 \texttt{mesh} & : Mesh processing related box \\ \hline
171 \texttt{misc} & : Box that cannot be put in any other category ! \\ \hline
172 \texttt{read/write} & : Box that read or write data from or to disk \\ \hline
173 \texttt{viewer} & : Box which displays some data \\ \hline
174 \texttt{widget} & : Piece of graphical interface \\ \hline
175 \texttt{3D object creator} & : Sophisticated 3D widget \\ \hline
176 \texttt{toolsbbtk} & : Component of bbStudio \\ \hline
180 % ==========================================
184 % ==========================================
185 \subsubsection{complex black box definition related commands}
186 \label{bbi-reference-black-box-definition}
187 % ==========================================
189 See table \ref{bbi-reference-complex-box}
190 % ==========================================
192 \caption{\label{bbi-reference-complex-box} \bbi complex black box definition related commands.}
194 \begin{tabular}{|lcm{6cm}|}
196 Command & Parameters & Effect \\ \hline
199 \texttt{define} & \texttt{<box-type>} &
200 Starts the definition of a complex black box of type
201 \texttt{box-type}\\ \hline
203 \texttt{endefine} & - &
204 Ends the definition of a complex black box type\\ \hline
206 \texttt{author} & \texttt{<string>} &
207 Sets the author(s) of the complex black box currently being defined \\ \hline
209 \texttt{description} & \texttt{<string>} &
210 Sets the description of the complex black box currently being defined \\ \hline
212 \texttt{input} & \texttt{<name>} \texttt{<box.input>} \texttt{<help>} &
213 Defines a new input for the current complex black box,
215 It is defined as corresponding to
216 the input \texttt{input} of the box \texttt{box}.
218 \texttt{<help>} is the help string for the new input.
219 The box \texttt{box} must already have been created in the complex box
220 and of course have an input named \texttt{input}.\\ \hline
222 \texttt{output} & \texttt{<name>} \texttt{<box.output>} \texttt{<help>} &
223 Defines a new output for the current complex black box,
225 It is defined as corresponding to
226 the output \texttt{output} of the box \texttt{box}.
227 \texttt{<help>} is the help string for the new output.
228 The box \texttt{box} must already have been created in the complex box and of course have an output named \texttt{output}. \\ \hline
234 % ==========================================
235 \subsubsection{Interpreter related commands}
236 \label{bbi-reference-interpreter}
237 % ==========================================
238 See table \ref{tabbbi-reference-interpreter_1} and \ref{tabbbi-reference-interpreter_2}
239 % ==========================================
241 \caption{\label{tabbbi-reference-interpreter_1}\bbi intepreter related commands (part 1).}
243 \begin{tabular}{|lcm{6cm}|}
245 Command & Parameters & Effect \\ \hline
247 \texttt{author} & \texttt{<author-name>} &
248 Adds the string \texttt{<author-name>} to the author information of the black box being defined \\ \hline
250 \texttt{category} & \texttt{<category-name>} &
251 Adds the string \texttt{<category-name>} to the category information of the black box being defined \\ \hline
254 Prints help on available commands \\ \hline
256 & \texttt{<command-name>} &
257 Prints help on the command \texttt{command-name} \\ \hline
259 & \texttt{packages} &
260 Prints help on available packages and their box types
261 (without description)\\ \hline
263 & \texttt{<package-name>} &
264 Prints help on the package \texttt{package-name} and its boxes
265 (with brief description).
266 The package must have been previously loaded \\ \hline
268 & \texttt{<box-type>} &
269 Prints help (with full description) on the type of box
271 The box type must belong to a package which has been previously loaded \\ \hline
273 & \texttt{<debug-directive>} &
275 Prints debug info on living bbtk objects containing the string \texttt{expr} (default expr='').
276 \texttt{-C} checks the factory integrity.
277 \texttt{-D} turns on objects debug info after main ends\\ \hline
279 \texttt{include} & \texttt{<file-name>} &
280 Includes and executes the content of the file named \texttt{file-name}
281 exactly like if you were typing its content at the place were the
282 \texttt{include} command is. \\ \hline
284 \texttt{load} & \texttt{<package-name>} &
285 Loads the package \texttt{package-name} (use it only if you know that you won't work with complex black boxes) \\ \hline
287 \texttt{include} & \texttt{<package-name>} &
288 Loads the package \texttt{package-name} and includes all the complex black boxes that comes with it \\ \hline
290 \texttt{kind} & \texttt{<box kind>} &
291 Specifies the \texttt{kind} of the complex black boxes you are describing \\ \hline
298 % This arbitrary part1/part2 is to avoid to have all the tables at the end of the docoment ...
302 \caption{\label{tabbbi-reference-interpreter_2}\bbi intepreter related commands (part 2).}
304 \begin{tabular}{|lcm{6cm}|}
306 Command & Parameters & Effect \\ \hline
307 \texttt{unload} & \texttt{<package-name>}&
308 Unloads the package \texttt{package-name}.
309 The package must have been previously loaded.
310 No box of a type defined in this package must still exist.\\ \hline
312 \texttt{message} & \texttt{<category>} \texttt{<level>} &
313 Sets the level of verbosity of \bbi for the category of messages
314 \texttt{category} to \texttt{level}.\\ \hline
315 %See \ref{verbosity}.
317 \texttt{config} & - & Displays the Configuration parameters\\ \hline
319 \texttt{reset} & - & Deletes all boxes and unloads all packages so
320 that \bbi gets back to its initial state \\ \hline
322 \texttt{quit} & - & Exits the interpreter (Don't use it under \bbStudions)\\ \hline
331 ---> Should be moved in a 'Reference Manual' ?\\
332 ---> Any suggestion welcome!
335 % ==========================================
336 \subsubsection{Black box packages}
337 \label{bbi-more-on-packages}
338 % ==========================================
340 There are various others user-intended packages :
343 It contains some vtk based image processing filters :
346 \paragraph{AppendPolyData}
347 Appends one of more polygonal datasets into a single polygonal dataset
349 \paragraph{ConeSource}
352 \paragraph{ImageAnisotropicDiffusion3D}
353 vtk\-Image\-Anisotropic\-Diffusion\-3D dif\-fuses a volume iteratively. \\
354 The neighborhood of the diffusion is determined by the instance flags. \\
355 if 'Faces' is on, the 6 voxels adjoined by faces are included in the neighborhood. \\
356 If 'Edges' is on the 12 edge connected voxels are included, and if 'Corners' is on, the 8 corner connected voxels are included. \\
357 'DiffusionFactor' determines how far a pixel value moves toward its neighbors, and is insensitive to the number of neighbors chosen.\\
358 The diffusion is anisotropic because it only occurs when a gradient measure is below 'GradientThreshold'. \\
359 Two gradient measures exist and are toggled by the 'GradientMagnitudeThreshold' flag. \\
360 When 'GradientMagnitudeThreshold' is on, the magnitude of the gradient, computed by central differences, above 'DiffusionThreshold' a voxel is not
362 The alternative measure examines each neighbor independently.\\
363 The gradient between the voxel and the neighbor must be below the 'DiffusionThreshold' for diffusion to occur with THAT neighbor.\\
365 - In : an image (vtkImageData*)\\
366 - Diffusion : Difference threshold that stops the diffusion\\
368 - Out : the isosurface mesh (vtkPolyData*)
370 \paragraph{ImageCharacteristics}
371 Exports objet sizes, and Spacings
373 \paragraph{ImageDilateErode3D}
375 Dilates one value and erodes another.\\
376 vtkImageDilateErode3D will dilate one value and erode another. \\
377 It uses an elliptical foot print, and only erodes/dilates on the boundary of the two values. \\
378 The filter is restricted to the X, Y, and Z axes for now.\\
379 It can degenerate to a 2 or 1 dimensional filter by setting the kernel size to 1 for a specific axis. \\
380 (bbfication of vtkImageDilateErode3D) \\
382 - In : an image (vtkImageData*)\\
383 - DilateValue : The dilatation value\\
384 - ErodeValue : The erosion value\\
386 - Out : the isosurface mesh (vtkPolyData*)
388 \paragraph{ImageGaussianSmooth}
389 Performs a gaussian convolution of the input image\\
391 - In : an image (vtkImageData*)\\
392 - StdDevX : Standard deviation in X direction\\
393 - StdDevY : Standard deviation in Y direction\\
395 - Out : the isosurface mesh (vtkPolyData*)
397 \paragraph{ImagePlanes}
398 Creates three 3D planes with the input image mapped onto with which the user can interact; \\
399 The output vtkImagePlaneWidget objects are to be inserted into a 3D scene (e.g. a Viewer3D)
401 - In : an image (vtkImageData*)\\
403 - PlaneX : the image plane in X direction (vtkImagePlaneWidget*)\\
404 - PlaneY : the image plane in Y direction (vtkImagePlaneWidget*)\\
405 - PlaneY : the image plane in Z direction (vtkImagePlaneWidget*)\\
408 - Out : the isosurface mesh (vtkPolyData*)
410 \paragraph{IsoSurfaceExtractor}
411 Extracts an iso-surface of a 3D image and creates a vtkProp3D object to insert into a 3D scene (e.g. a Viewer3D)
413 - In : an image (vtkImageData*)\\
414 - Isovalue : the isosurface value (double)\\
415 - Colour : Surface colour (vector of 3 doubles)
417 - Out : the isosurface (vtkProp3D**)
419 \paragraph{MIPCreator}
420 Creates a Maximum Intensity Projection (MIP) view of a 3D image.\\
422 - In : an image (vtkImageData*)\\
423 - Scale : the Gray scale scaling (float) \\
424 - Shift : the Gray scale shift (float) \\
426 - Out : The MIP object (vtkProp3D*) to be plugged into a 3D Viever
428 \paragraph{MarchingCubes}
429 Extracts an iso-surface of an image using the marching cubes algorithm (bbfication of vtkMarchingCubes)\\
431 - In : an image (vtkImageData*)\\
432 - Value : the isosurface value (double)\\
434 - Out : the isosurface mesh (vtkPolyData*)
436 \paragraph{MetaImageReader}
437 Reads .mhd / .mhd image formats (bbfication of vtkMetaImageReader) \\
439 - In : the name of the file to be read (std::string)
441 - Out : The image (vtkImageData*)
443 \paragraph{SegmentationConnectivity}
444 Segmentation with min max threshold and connectivity \\
446 - In : an image (vtkImageData*)\\
447 - PositionXYZ : initial position (std::vector<int>) \\
448 - ThresholdMinMax : min, max threshold values (std::vector<int>) \\
450 - Out : The image (vtkImageData*)
452 \paragraph{SphereSource}
457 It contains some itk based image processing filters :
459 \paragraph{BinaryThresholdImageFilter}
460 Binarizes an image by thresholding (generic bbification of itk::BinaryThresholdImageFilter)
463 - In : Input image. Can be any itk::Image<T,D>* \\
464 - InsideValue : Output value for pixels inside thresholds (Double) \\
465 - LowerThreshold : Lower threshold(Double) \\
466 - OutsideValue : Output value for pixels outside thresholds (Double) \\
467 - UpperThreshold : Upper threshold (Double) \\
469 - Out' : Output image. Of the same type and dimension than the input image
471 \paragraph{DICOMSeriesFileNames}
472 Reads a series from a DICOM directory as a 3D itk image
474 \paragraph{ExtractImageFilter}
475 Decrease the image size by cropping the image to the selected region bounds (bbification of itk::ExtractImageFilter)
477 \paragraph{ImageProperties}
478 Outputs different properties of an image (type, dimension, size, spacing, ...)
480 \paragraph{ImageRegion}
481 Creates a generic ImageRegion (bbtk::any) from two vectors providing the index and size of the region.
482 The dimension D of the actual itk::ImageRegion created is the max of the sizes of Index and Size
483 (the smallest vector is padded by zeros)
485 \paragraph{ImageReader}
486 Generic itk image reader
488 \paragraph{ImageWriter}
489 Generic itk image writer
491 \paragraph{ImageSeriesReader}
492 Generic itk image series reader.
494 \paragraph{ResampleImageFilter}
498 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
500 Sorry nothing is done, right now for meshes.
504 It contains two atomic black boxes.
508 - a \textless vtkImageData* \textgreater (In),\\
509 - an Orientation(0:yz / 1:xz / 2:xy),\\
510 - an initial slice number (Slice).\\
512 - a \textless vtkRenderer* \textgreater (Renderer)
516 - up to 5 Input Actors (\textless vtkProp3D* \textgreater),\\
517 - up to 5 Input Observers (\textless vtkInteractorObserver* \textgreater), \\
518 - a boolean 'Stereo' option, to use Red-Blue filter
520 - an Interactor (\textless wxVTKRenderWindowInteractor* \textgreater) with which vtk widgets can interact, \\
521 - a Renderer (\textless vtkRenderer* \textgreater) to which actors can be added.
523 It contains too some sophisticated complex black boxes :
525 \paragraph{IsoSurfaceWidget}
526 Image iso-surface extractor (vtk::IsoSurfaceExtractor) with associated control panel (isovalue, opacity and colour)\\
528 - an initial isovalue (Isovalue)
529 - an initial opacity (Opacity)
530 - an initial colour (Colour)
532 \textless vtkProp3D* \textgreater (In)\\
534 \paragraph{MIPWidget}
535 Maximum Intensity Projection (MIP) creator (vtk::MIPCreator) with associated control panel (shift and scale) \\
537 - an initial scale (Scale)
538 - an initial shift (Shift)
540 \textless vtkProp3D* \textgreater (In)\\
544 Some boxes are the bbfication of usefull xwWidgets, some other ones are more
547 \paragraph{ColourSelector} Colour Selector dialog (bbfication of wxColourSelector) \\
549 \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
552 \paragraph{ColourSelectorButton} A button which displays a colour picker dialog when clicked \\
554 \texttt{In} :Initial colour \\
555 \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
558 \paragraph{CommandButton} Button which executes bbi commands \\
560 \texttt{In} : Commands to be executed separated by commas (;). Each single quote (') is replaced by a double quote ("). \\
561 \texttt{Label} : Label of the button \\
562 \texttt{Widget} : Output widget \\
565 \paragraph{DirectorySelector} Pops up a directory selection dialog (wxDirDialog)\\
567 \texttt{DefaultDir} : The default directory\\
568 \texttt{Message} : Message to show on the dialog \\
569 \texttt{Title} : Title of the dialog \\
570 \texttt{Out} : The directory selected by the user\\
573 \paragraph{FileSelector} Pops up a file selection dialog for reading or saving (wxFileDialog)\\
575 \texttt{DefaultDir} : The default directory \\
576 \texttt{DefaultFile} : The default filename \\
577 \texttt{Message} : Message to show on the dialog \\
578 \texttt{OpenSave} : Open for an open dialog (default) / Save for a save dialog\\
579 \texttt{Title} : Title of the dialog \\
580 \texttt{Wildcard} : A wildcard, such as "*.*" or "BMP files (*.bmp)|*.bmp|GIF files (*.gif)|*.gif" \\
581 \texttt{Out} : The file selected by the user \\
584 \paragraph{InputText} A zone in which the user can enter a text (wxTextCtrl)\\
586 \texttt{In} : Initial text (default '')\\
587 \texttt{Title} : Title of the input zone (default '')\\
588 \texttt{WinTitle} : Title of the window (*)\\
589 \texttt{Out} :Current text\\
592 \paragraph{LayoutLine} LayoutLine widget (wxBoxSizer)\\
594 \texttt{Orientation} Orientation (default V), 0=H=HORIZONTAL , 1=V=VERTICAL \\
595 \texttt{Widget}1 widget 1 \\
596 \texttt{Widget2} widget 2 \\
597 \texttt{Widget3} widget 3 \\
598 \texttt{Widget4} widget 4 \\
599 \texttt{Widget5} widget 5 \\
600 \texttt{Widget6} widget 6 \\
601 \texttt{Widget7} widget 7 \\
602 \texttt{Widget8} widget 8 \\
603 \texttt{Widget9} widget 9\\
606 \paragraph{LayoutSplit} Widget which splits a window in two fixed size parts (wxSplitterWindow)\\
608 \texttt{Orientation} : Orientation (default H), 0=H=HORIZONTAL , 1=V=VERTICAL\\
609 \texttt{Proportion} : Proportion (in percent) of the first children in the window\\
610 \texttt{Widget1} : Upper or left widget\\
611 \texttt{Widget2} : Lower or right widget\\
614 \paragraph{LayoutTDown} Creates a 'T like' complex container : Down {UpLeft, UpRight} \\
616 \texttt{Widget1} : UpLeft container\\
617 \texttt{Widget2} : UpRight container\\
618 \texttt{Widget3} : Down container\\
629 \paragraph{LayoutTLeft} Creates a 'T like' complex container : Left {RigthUp, RightDown}\\
631 \texttt{input} Widget1 : "UpLeft container" \\
632 \texttt{input} Widget2 : "UpRight container" \\
633 \texttt{input} Wigdet3 : "Down container" \\
644 \paragraph{LayoutTRight} Creates a 'T like' complex container : Right {LeftUp, LeftDown}\\
646 \texttt{input} Widget1 currentBox.Widget1 "Up container" \\
647 \texttt{input} Widget2 down.Widget1 "DownLeft container" \\
648 \texttt{input} Widget3 down.Widget2 "DownRight container"\\
659 \paragraph{LayoutTUp} Creates a 'T like' complex container : Up {DownLeft, DownRight} as w1{w2,w3}\\
661 \texttt{ input} Widget1 currentBox.Widget1 "Up" \\
662 \texttt{input} Widget2 down.Widget1 "DownLeft" \\
663 \texttt{input} Widget3 down.Widget2 "DownRight"\\
675 \paragraph{LayoutTab} LayoutTab widget (wxNotebook)\\
677 \texttt{Orientation} Orientation (default T), 0=T=TOP , 1=R=RIGHT , 2=B=BOTTON , 3=L=LEFT \\
678 \texttt{Widget1} widget 1 \\
679 \texttt{Widget2} widget 2 \\
680 \texttt{Widget3} widget 3 \\
681 \texttt{Widget4} widget 4 \\
682 \texttt{Widget5} widget 5 \\
683 \texttt{Widget6} widget 6 \\
684 \texttt{Widget7} widget 7 \\
685 \texttt{Widget8} widget 8 \\
686 \texttt{Widget9} widget 9 \\
689 \paragraph{OutputText} Text zone to be inserted into a window (wxStaticText)\\
692 \texttt{Title} Title prepended to the text\\
695 \paragraph{RadioButton} RadioButton group widget 0-9 entries\\
697 \texttt{In} Set initial item \\
698 \texttt{In0} option 0\\
699 \texttt{In1} option 1\\
700 \texttt{In2} option 2\\
701 \texttt{In3} option 3\\
702 \texttt{In4} option 4\\
703 \texttt{In5} option 5 \\
704 \texttt{In6} option 6 \\
705 \texttt{In7} option 7 \\
706 \texttt{In8} option 8 \\
707 \texttt{In9} option 9 \\
708 \texttt{Title} Title of the widget (default '')\\
709 \texttt{Out} Number of the selected Item
712 \paragraph{Slider} Slider widget (wxSlider)\\
714 \texttt{ChangeResolution} Enables the user to change the slider resolution (default FALSE) \\
715 \texttt{In} Initial slider position(default 0) \\
716 \texttt{Label} Show slider labels ? (default FALSE) \\
717 \texttt{Max} Maximum value of the slider (default 500)\\
718 \texttt{Min} Minimum value of the slider (default 0)\\
719 \texttt{Orientation} Orientation : (default H) 0=H=HORIZONTAL, 1=V=VERTICAL\\
720 \texttt{ReactiveOnTrack} Slider sends info when track moves (default 0 = no)\\
721 \texttt{Title} Title shown above the slider (default '')\\
730 %\section{Conclusion}