1 % ==========================================
2 \documentclass[11pt,final,a4paper]{article}
14 {\Huge Reference Manual}
21 Last modified on : September 20, 2008 \\
28 % ==========================================
30 % ==========================================
38 % ==========================================
40 % ==========================================
42 % ==========================================
47 ---> Should be moved in a 'Reference Manual' ?\\
48 ---> Any suggestion welcome!
55 \caption{\label{kinds} \texttt{Black Box} kinds}
59 \texttt{Kind name} & : Meaning \\ \hline \\ \hline
60 \texttt{ADAPTOR} & : Adaptor Box \\ \hline
61 \texttt{DEFAULT\_ADAPTOR} & : \\ \hline
62 \texttt{WIDGET\_ADAPTOR} & : \\ \hline
63 \texttt{DEFAULT\_WIDGET\_ADAPTOR} & : \\ \hline
64 \texttt{GUI} & : \\ \hline
65 \texttt{DEFAULT\_GUI} & : \\ \hline
66 \texttt{ALL} & : If kind='ALL' then sets the level for all kinds \\ \hline
73 \bf\emph{Boxes} : Box retrieving on various criterions :
75 \item {\bf\emph{By name}} (Alphabetical list)
76 \item {\bf\emph{By package}} (see table : \ref{bbi-list_of_packages})
77 \item {\bf\emph{By category}} (see table : \ref{categories})
78 \item {\bf\emph{Adaptors}} Used internaly to perform type conversions (not end user intended)
83 % ==========================================
85 \caption{\label{bbi-list_of_packages} List of bbtk supplied packages.}
87 \begin{tabular}{|lp{10cm}|}
89 Package & What it's used for \\ \hline
90 \texttt{std} & : the 'standard' package including basic useful boxes \\ \hline
91 \texttt{wx} & : basic graphical interface elements (widgets : sliders, buttons, etc.) based on the \texttt{wxWidgets} library \\ \hline
92 \itk & : the basic image processing package, based on the \itk library. (without description)\\ \hline
93 \vtk & : prints help on the package \texttt{package-name} and its boxes (with brief description). The package must have been previously loaded\\ \hline
94 \texttt{wxvtk} & : widget boxes based on the \vtk library.\\ \hline
95 \texttt{itkvtk} & : adaptors to convert \itk structures into \vtk structures and conversally.\\ \hline
96 %\texttt{creaImageIO} & : provides high level widgets to read images including DICOM.\\ \hline
97 \texttt{toolsbbtk} & : Tools for bbtk administration and package development.\\ \hline
101 % ==========================================
105 % ==========================================
107 \caption{\label{categories} \texttt{Black Box} categories}
109 \begin{tabular}{|lp{10cm}|}
111 \texttt{Category name} & : Meaning \\ \hline \\ \hline
112 \texttt{adaptor} & : Adaptor box \\ \hline
113 \texttt{application} & : Final application, end user intended \\ \hline
114 \texttt{atomic box} & : System category.
115 Automatically assigned to Atomic Black Boxes (c++ defined) \\ \hline
116 \texttt{complex box} & : System category.
117 Automatically assigned to Complex Black Boxes (script defined) \\ \hline
118 \texttt{command line} & : Script which defines a command line application \\
119 & :(no embedded GUI, but command line imput parameters) \\ \hline
120 \texttt{demo} & : Demonstration \\ \hline
121 \texttt{devel} & : Developer tool (bbCreatePackage.bbs, ...) \\ \hline
122 \texttt{dicom} & : DICOM aware box \\ \hline
123 \texttt{example} & : Example script showing a box use-case \\ \hline
124 \texttt{filter} & : Image processing box \\ \hline
125 \texttt{image} & : Image processing related box \\ \hline
126 \texttt{interaction} & : \\ \hline
127 \texttt{math} & : Mathematical operations \\ \hline
128 \texttt{mesh} & : Mesh processing related box \\ \hline
129 \texttt{misc} & : Box that cannot be put in any other category ! \\ \hline
130 \texttt{read/write} & : Box that read or write data from or to disk \\ \hline
131 \texttt{viewer} & : Box which displays some data \\ \hline
132 \texttt{widget} & : Piece of graphical interface \\ \hline
133 \texttt{3D object creator} & : Sophisticated 3D widget \\ \hline
134 \texttt{toolsbbtk} & : Component of bbStudio \\ \hline
138 % ==========================================
147 ---> Should be moved in a 'Reference Manual' ?\\
148 ---> Any suggestion welcome!
151 % ==========================================
152 \subsubsection{Black box packages}
153 \label{bbi-more-on-packages}
154 % ==========================================
156 There are various others user-intended packages :
159 It contains some vtk based image processing filters :
162 \paragraph{AppendPolyData}
163 Appends one of more polygonal datasets into a single polygonal dataset
165 \paragraph{ConeSource}
168 \paragraph{ImageAnisotropicDiffusion3D}
169 vtk\-Image\-Anisotropic\-Diffusion\-3D dif\-fuses a volume iteratively. \\
170 The neighborhood of the diffusion is determined by the instance flags. \\
171 if 'Faces' is on, the 6 voxels adjoined by faces are included in the neighborhood. \\
172 If 'Edges' is on the 12 edge connected voxels are included, and if 'Corners' is on, the 8 corner connected voxels are included. \\
173 'DiffusionFactor' determines how far a pixel value moves toward its neighbors, and is insensitive to the number of neighbors chosen.\\
174 The diffusion is anisotropic because it only occurs when a gradient measure is below 'GradientThreshold'. \\
175 Two gradient measures exist and are toggled by the 'GradientMagnitudeThreshold' flag. \\
176 When 'GradientMagnitudeThreshold' is on, the magnitude of the gradient, computed by central differences, above 'DiffusionThreshold' a voxel is not
178 The alternative measure examines each neighbor independently.\\
179 The gradient between the voxel and the neighbor must be below the 'DiffusionThreshold' for diffusion to occur with THAT neighbor.\\
181 - In : an image (vtkImageData*)\\
182 - Diffusion : Difference threshold that stops the diffusion\\
184 - Out : the isosurface mesh (vtkPolyData*)
186 \paragraph{ImageCharacteristics}
187 Exports objet sizes, and Spacings
189 \paragraph{ImageDilateErode3D}
191 Dilates one value and erodes another.\\
192 vtkImageDilateErode3D will dilate one value and erode another. \\
193 It uses an elliptical foot print, and only erodes/dilates on the boundary of the two values. \\
194 The filter is restricted to the X, Y, and Z axes for now.\\
195 It can degenerate to a 2 or 1 dimensional filter by setting the kernel size to 1 for a specific axis. \\
196 (bbfication of vtkImageDilateErode3D) \\
198 - In : an image (vtkImageData*)\\
199 - DilateValue : The dilatation value\\
200 - ErodeValue : The erosion value\\
202 - Out : the isosurface mesh (vtkPolyData*)
204 \paragraph{ImageGaussianSmooth}
205 Performs a gaussian convolution of the input image\\
207 - In : an image (vtkImageData*)\\
208 - StdDevX : Standard deviation in X direction\\
209 - StdDevY : Standard deviation in Y direction\\
211 - Out : the isosurface mesh (vtkPolyData*)
213 \paragraph{ImagePlanes}
214 Creates three 3D planes with the input image mapped onto with which the user can interact; \\
215 The output vtkImagePlaneWidget objects are to be inserted into a 3D scene (e.g. a Viewer3D)
217 - In : an image (vtkImageData*)\\
219 - PlaneX : the image plane in X direction (vtkImagePlaneWidget*)\\
220 - PlaneY : the image plane in Y direction (vtkImagePlaneWidget*)\\
221 - PlaneY : the image plane in Z direction (vtkImagePlaneWidget*)\\
224 - Out : the isosurface mesh (vtkPolyData*)
226 \paragraph{IsoSurfaceExtractor}
227 Extracts an iso-surface of a 3D image and creates a vtkProp3D object to insert into a 3D scene (e.g. a Viewer3D)
229 - In : an image (vtkImageData*)\\
230 - Isovalue : the isosurface value (double)\\
231 - Colour : Surface colour (vector of 3 doubles)
233 - Out : the isosurface (vtkProp3D**)
235 \paragraph{MIPCreator}
236 Creates a Maximum Intensity Projection (MIP) view of a 3D image.\\
238 - In : an image (vtkImageData*)\\
239 - Scale : the Gray scale scaling (float) \\
240 - Shift : the Gray scale shift (float) \\
242 - Out : The MIP object (vtkProp3D*) to be plugged into a 3D Viever
244 \paragraph{MarchingCubes}
245 Extracts an iso-surface of an image using the marching cubes algorithm (bbfication of vtkMarchingCubes)\\
247 - In : an image (vtkImageData*)\\
248 - Value : the isosurface value (double)\\
250 - Out : the isosurface mesh (vtkPolyData*)
252 \paragraph{MetaImageReader}
253 Reads .mhd / .mhd image formats (bbfication of vtkMetaImageReader) \\
255 - In : the name of the file to be read (std::string)
257 - Out : The image (vtkImageData*)
259 \paragraph{SegmentationConnectivity}
260 Segmentation with min max threshold and connectivity \\
262 - In : an image (vtkImageData*)\\
263 - PositionXYZ : initial position (std::vector<int>) \\
264 - ThresholdMinMax : min, max threshold values (std::vector<int>) \\
266 - Out : The image (vtkImageData*)
268 \paragraph{SphereSource}
273 It contains some itk based image processing filters :
275 \paragraph{BinaryThresholdImageFilter}
276 Binarizes an image by thresholding (generic bbification of itk::BinaryThresholdImageFilter)
279 - In : Input image. Can be any itk::Image<T,D>* \\
280 - InsideValue : Output value for pixels inside thresholds (Double) \\
281 - LowerThreshold : Lower threshold(Double) \\
282 - OutsideValue : Output value for pixels outside thresholds (Double) \\
283 - UpperThreshold : Upper threshold (Double) \\
285 - Out' : Output image. Of the same type and dimension than the input image
287 \paragraph{DICOMSeriesFileNames}
288 Reads a series from a DICOM directory as a 3D itk image
290 \paragraph{ExtractImageFilter}
291 Decrease the image size by cropping the image to the selected region bounds (bbification of itk::ExtractImageFilter)
293 \paragraph{ImageProperties}
294 Outputs different properties of an image (type, dimension, size, spacing, ...)
296 \paragraph{ImageRegion}
297 Creates a generic ImageRegion (bbtk::any) from two vectors providing the index and size of the region.
298 The dimension D of the actual itk::ImageRegion created is the max of the sizes of Index and Size
299 (the smallest vector is padded by zeros)
301 \paragraph{ImageReader}
302 Generic itk image reader
304 \paragraph{ImageWriter}
305 Generic itk image writer
307 \paragraph{ImageSeriesReader}
308 Generic itk image series reader.
310 \paragraph{ResampleImageFilter}
314 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
316 Sorry nothing is done, right now for meshes.
320 It contains two atomic black boxes.
324 - a \textless vtkImageData* \textgreater (In),\\
325 - an Orientation(0:yz / 1:xz / 2:xy),\\
326 - an initial slice number (Slice).\\
328 - a \textless vtkRenderer* \textgreater (Renderer)
332 - up to 5 Input Actors (\textless vtkProp3D* \textgreater),\\
333 - up to 5 Input Observers (\textless vtkInteractorObserver* \textgreater), \\
334 - a boolean 'Stereo' option, to use Red-Blue filter
336 - an Interactor (\textless wxVTKRenderWindowInteractor* \textgreater) with which vtk widgets can interact, \\
337 - a Renderer (\textless vtkRenderer* \textgreater) to which actors can be added.
339 It contains too some sophisticated complex black boxes :
341 \paragraph{IsoSurfaceWithControls}
342 Image iso-surface extractor (vtk::IsoSurfaceExtractor) with associated control panel (isovalue, opacity and colour)\\
344 - an initial isovalue (Isovalue)
345 - an initial opacity (Opacity)
346 - an initial colour (Colour)
348 \textless vtkProp3D* \textgreater (In)\\
350 \paragraph{MIPWithControls}
351 Maximum Intensity Projection (MIP) creator (vtk::MIPCreator) with associated control panel (shift and scale) \\
353 - an initial scale (Scale)
354 - an initial shift (Shift)
356 \textless vtkProp3D* \textgreater (In)\\
360 Some boxes are the bbfication of usefull xwWidgets, some other ones are more
363 \paragraph{ColourSelector} Colour Selector dialog (bbfication of wxColourSelector) \\
365 \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
368 \paragraph{ColourSelectorButton} A button which displays a colour picker dialog when clicked \\
370 \texttt{In} :Initial colour \\
371 \texttt{Out} : Colour choosen in format '[0,1] [0,1] [0,1]'
374 \paragraph{CommandButton} Button which executes bbi commands \\
376 \texttt{In} : Commands to be executed separated by commas (;). Each single quote (') is replaced by a double quote ("). \\
377 \texttt{Label} : Label of the button \\
378 \texttt{Widget} : Output widget \\
381 \paragraph{DirectorySelector} Pops up a directory selection dialog (wxDirDialog)\\
383 \texttt{DefaultDir} : The default directory\\
384 \texttt{Message} : Message to show on the dialog \\
385 \texttt{Title} : Title of the dialog \\
386 \texttt{Out} : The directory selected by the user\\
389 \paragraph{FileSelector} Pops up a file selection dialog for reading or saving (wxFileDialog)\\
391 \texttt{DefaultDir} : The default directory \\
392 \texttt{DefaultFile} : The default filename \\
393 \texttt{Message} : Message to show on the dialog \\
394 \texttt{OpenSave} : Open for an open dialog (default) / Save for a save dialog\\
395 \texttt{Title} : Title of the dialog \\
396 \texttt{Wildcard} : A wildcard, such as "*.*" or "BMP files (*.bmp)|*.bmp|GIF files (*.gif)|*.gif" \\
397 \texttt{Out} : The file selected by the user \\
400 \paragraph{InputText} A zone in which the user can enter a text (wxTextCtrl)\\
402 \texttt{In} : Initial text (default '')\\
403 \texttt{Title} : Title of the input zone (default '')\\
404 \texttt{WinTitle} : Title of the window (*)\\
405 \texttt{Out} :Current text\\
408 \paragraph{LayoutLine} LayoutLine widget (wxBoxSizer)\\
410 \texttt{Orientation} Orientation (default V), 0=H=HORIZONTAL , 1=V=VERTICAL \\
411 \texttt{Widget}1 widget 1 \\
412 \texttt{Widget2} widget 2 \\
413 \texttt{Widget3} widget 3 \\
414 \texttt{Widget4} widget 4 \\
415 \texttt{Widget5} widget 5 \\
416 \texttt{Widget6} widget 6 \\
417 \texttt{Widget7} widget 7 \\
418 \texttt{Widget8} widget 8 \\
419 \texttt{Widget9} widget 9\\
422 \paragraph{LayoutSplit} Widget which splits a window in two fixed size parts (wxSplitterWindow)\\
424 \texttt{Orientation} : Orientation (default H), 0=H=HORIZONTAL , 1=V=VERTICAL\\
425 \texttt{Proportion} : Proportion (in percent) of the first children in the window\\
426 \texttt{Widget1} : Upper or left widget\\
427 \texttt{Widget2} : Lower or right widget\\
430 \paragraph{LayoutTDown} Creates a 'T like' complex container : Down {UpLeft, UpRight} \\
432 \texttt{Widget1} : UpLeft container\\
433 \texttt{Widget2} : UpRight container\\
434 \texttt{Widget3} : Down container\\
445 \paragraph{LayoutTLeft} Creates a 'T like' complex container : Left {RigthUp, RightDown}\\
447 \texttt{input} Widget1 : "UpLeft container" \\
448 \texttt{input} Widget2 : "UpRight container" \\
449 \texttt{input} Wigdet3 : "Down container" \\
460 \paragraph{LayoutTRight} Creates a 'T like' complex container : Right {LeftUp, LeftDown}\\
462 \texttt{input} Widget1 currentBox.Widget1 "Up container" \\
463 \texttt{input} Widget2 down.Widget1 "DownLeft container" \\
464 \texttt{input} Widget3 down.Widget2 "DownRight container"\\
475 \paragraph{LayoutTUp} Creates a 'T like' complex container : Up {DownLeft, DownRight} as w1{w2,w3}\\
477 \texttt{ input} Widget1 currentBox.Widget1 "Up" \\
478 \texttt{input} Widget2 down.Widget1 "DownLeft" \\
479 \texttt{input} Widget3 down.Widget2 "DownRight"\\
491 \paragraph{LayoutTab} LayoutTab widget (wxNotebook)\\
493 \texttt{Orientation} Orientation (default T), 0=T=TOP , 1=R=RIGHT , 2=B=BOTTON , 3=L=LEFT \\
494 \texttt{Widget1} widget 1 \\
495 \texttt{Widget2} widget 2 \\
496 \texttt{Widget3} widget 3 \\
497 \texttt{Widget4} widget 4 \\
498 \texttt{Widget5} widget 5 \\
499 \texttt{Widget6} widget 6 \\
500 \texttt{Widget7} widget 7 \\
501 \texttt{Widget8} widget 8 \\
502 \texttt{Widget9} widget 9 \\
505 \paragraph{OutputText} Text zone to be inserted into a window (wxStaticText)\\
508 \texttt{Title} Title prepended to the text\\
511 \paragraph{RadioButton} RadioButton group widget 0-9 entries\\
513 \texttt{In} Set initial item \\
514 \texttt{In0} option 0\\
515 \texttt{In1} option 1\\
516 \texttt{In2} option 2\\
517 \texttt{In3} option 3\\
518 \texttt{In4} option 4\\
519 \texttt{In5} option 5 \\
520 \texttt{In6} option 6 \\
521 \texttt{In7} option 7 \\
522 \texttt{In8} option 8 \\
523 \texttt{In9} option 9 \\
524 \texttt{Title} Title of the widget (default '')\\
525 \texttt{Out} Number of the selected Item
528 \paragraph{Slider} Slider widget (wxSlider)\\
530 \texttt{ChangeResolution} Enables the user to change the slider resolution (default FALSE) \\
531 \texttt{In} Initial slider position(default 0) \\
532 \texttt{Label} Show slider labels ? (default FALSE) \\
533 \texttt{Max} Maximum value of the slider (default 500)\\
534 \texttt{Min} Minimum value of the slider (default 0)\\
535 \texttt{Orientation} Orientation : (default H) 0=H=HORIZONTAL, 1=V=VERTICAL\\
536 \texttt{ReactiveOnTrack} Slider sends info when track moves (default 0 = no)\\
537 \texttt{Title} Title shown above the slider (default '')\\
546 %\section{Conclusion}