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Slicer Architecture

Slicer Architecture. Steve Pieper, PhD. Overall Goals. Execution Environment Command Line Args Flow of Control, Startup Sequence Data Model Mrml Tree Mrml Nodes Mrml Data Module Architecture Standard Developer Widgets GUI Modules Editor Modules I/O Modules. Execution Environment.

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Slicer Architecture

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  1. Slicer Architecture Steve Pieper, PhD

  2. Overall Goals • Execution Environment • Command Line Args • Flow of Control, Startup Sequence • Data Model • Mrml Tree • Mrml Nodes • Mrml Data • Module Architecture • Standard Developer Widgets • GUI Modules • Editor Modules • I/O Modules

  3. Execution Environment • Slicer runs inside a VTK Tcl/Tk shell • Uses the vtk executable that gets built when Tcl wrapping is enabled for the VTK build or the wish84.exe shell on Windows • vtkSlicerBase is a tcl package that gets pulled in at run time • Each Module is a tcl package • Note that vtkSlicerBase and the Modules can be wrapped for other languages if desired (python, java)

  4. Tcl Packages • Includes Tcl code to be interpreted • Includes compiled C++ code as a shared library (optional) • Can reference and subclass C++ classes from other packages • Package path that can be used to find module-specific logos, data, etc

  5. Command Line Arguments usage: slicer2-<arch> \[options\] \[MRML file name .xml | dir with MRML file\] <arch> is one of win32.exe, solaris-sparc, or linux-x86 \[options\] is one of the following: --help : prints this message and exits --verbose : turns on extra debugging output --no-threads : disables multi threading --no-tkcon : disables tk console --load-dicom <dir> : read dicom files from <dir> --load-analyze <file.hdr> : read analyze file from <file.hdr> --load-freesurfer-volume <COR-.info> : read freesurfer files --load-freesurfer-label-volume <COR-.info> : read freesurfer label files --load-freesurfer-model <file> : read freesurfer model file --load-bxh <file.bxh> : read bxh file from <file.bxh> --script <file.tcl> : script to execute after slicer loads --exec <tcl code> : some code to execute after slicer loads --all-info : print out all of the version info and continue --enable-stereo : set the flag to allow use of frame sequential stereo --old-voxel-shift : start slicer with voxel coords in corner not center of image pixel

  6. Command Line Examples • slicer2-win32.exe mydata.xml • reads Mrml scene file after slicer starts • slicer2-win32.exe –no-threads • good for debugging ThreadedExecute methods • slicer2-win32.exe –load-dicom <dir> • loads all the dicom volumes from a study directory • slicer2-win32.exe –exec set a 100 • executes tcl code on command line after slicer loads • slicer2-win32.exe –script testscript.tcl • runs the tests script after slicer loads • slicer2-win32.exe testscript.tcl • runs the script instead of booting slicer GUI

  7. Bootstrapping • slicer2-win32.exe • essentially the same as calling • slicer2-win32.exe launch.tcl • The launch.tcl script creates a subshell with correct environment variables • Then execs vtk or wish84.exe to start main slicer process with Go.tcl as a startup script

  8. Flow of Control Outline • Base/tcl/Go.tcl is main entry point • Parse command line args • Starts tkcon console • Load vtkSlicerBase and all module packages • Uses tcl ‘package require’ command • Run MainBoot

  9. MainBoot Startup Sequence • Init Slicer Base and Modules • MainInit – sets up base framework, appearance, etc • Create Main Viewer Windows • Call All <Module>Init Procs – set callback procs and defaults • Set up VTK • MainBuildVTK – makes the cube and letters • Call All Module procVTK – module-specific VTK instances • Build GUI • Build Main GUI • Call All Module procGUI – each module is given it’s tab frame • Read Options.xml – per-installation defaults • Read Command Line MRML scene if specified • MainSetup – set view parameter defaults, etc • Enter Main Tcl Event Event Loop

  10. Global Tcl Arrays • Module() • Module(*) – state about modules • Module($m,*) – common state about module $m • <ModuleName>() • an array with the same name as the Module • Internal state of the module, including the variables that are tied to the GUI controls • Volume() and Model() • Two important modules • Volume($id,*), Model($id,*) • SLICER() • Command line argument values and version info • Gui() • Window handles and appearance settings • Anno() • Viewer annotations state and settings

  11. Key VTK Class Instances • Slicer • Instance of vtkMrmlSlicer is “heart” of the volume display process • Mrml(dataTree) – note, this is a class instance of vtkMrmlTree, not an array reference • Hook to the scene data • viewRen • The vtkOpenGLRenderer in the Viewer

  12. Module VTK Class Instance Naming Convention • Name of the Module with variable name in parentheses is used as name of VTK class instance • For Example: catch “SiemensMosaicReader(imageAppend) Delete” vtkImageAppend SiemensMosaicReader(imageAppend) SiemensMosaicReader(imageAppend) SetAppendAxis 2 • Note: delete class instances after use, but it is also good practice to do the catch “<inst> Delete” to make your module re-entrant • Note: the is Not standard Tcl practice – but this is used to avoid namespace conflicts between modules • This convention is widely used in the slicer Tcl code, but it can lead to confusion because the class instances look like Tcl array references. • Be careful!

  13. Mrml Data Model • Tree-structured scene description • Accessible as Mrml(dataTree) • Serialized to XML file • Compiled to VTK class instances in memory for display and manipulation

  14. Mrml http://www.slicer.org/mrml

  15. Mrml XML <?xml version="1.0" standalone='no'?> <!DOCTYPE MRML SYSTEM "mrml20.dtd"> <MRML> <Transform> <Matrix name='manual' matrix='1 0 0 -3 0 1 0 -12 0 0 1 28 0 0 0 1'></Matrix> <Volume name='SPGR' filePattern='%s.%03d' filePrefix='spgr/I' rasToIjkMatrix='0 -1.06667 0 142.187 0 0 -1.06667 98.1333 0.666667 0 0 59.9667 0 0 0 1' rasToVtkMatrix='0 -1.06667 0 142.187 0 0 1.06667 157.867 0.666667 0 0 59.9667 0 0 0 1' positionMatrix='0 0 1 -89.95 -1 0 0 133.3 0 1 0 -148 0 0 0 1' description='LR' colorLUT='0' window='146' level='76' applyThreshold='yes' lowerThreshold='17' upperThreshold='355' imageRange='1 124'></Volume> </Transform> <Volume name='all' filePattern='%s.%03d' filePrefix='labels/all' rasToIjkMatrix='0 -1.06667 0 128 0 0 -1.06667 128 0.666667 0 0 62 0 0 0 1' rasToVtkMatrix='0 -1.06667 0 128 0 0 1.06667 128 0.666667 0 0 62 0 0 0 1' positionMatrix='0 0 1 -93 -1 0 0 120 0 1 0 -120 0 0 0 1' description='LR' colorLUT='-1' labelMap='yes' interpolate='no' window='4' level='1' lowerThreshold='0' upperThreshold='0' imageRange='1 124'></Volume> <Model name='Skin' fileName='models/Skin.vtk' color='Skin' visibility='yes'></Model> <Model name='Ventricles' fileName='models/Ventricles.vtk' color='Ventricles' visibility='yes'></Model> <Model name='Vessels' fileName='models/Vessels.vtk' color='Vessels' visibility='yes'></Model> </MRML>

  16. Mrml XML • Describes the data as it exists on disk • Composes the scene by positioning data elements • Retains visualization and other state parameters

  17. Data Model – the Mrml Tree • Mrml Tree is an in-memory data description corresponding to the mrml xml file • vtkMrmlNode subclasses contain the metadata • Mapping of metadata to run-time state is managed mainly in Tcl • vtkMrmlData subclasses are helpers for classes that need C++ help to efficiently manage runtime state

  18. vtkMrmlNode

  19. Mrml Nodes • vtkMrmlNode abstract base class • int ID; • char *Description; • char *Options; • char *Name; • char *Title; • virtual void Write(ofstream& of, int indent); • IsA vtkObject • Can be subclassed in run time loadable Modules

  20. vtkMrmlModelNode • vtkMrmlModelNode Example Instance Variables // Strings char *ModelID; char *FileName; char *FullFileName; char *Color; // Numbers float Opacity; // Booleans int Visibility; int Clipping; int BackfaceCulling; int ScalarVisibility;

  21. vtkMrmlModelNode - methods vtkMrmlModelNode -- Example Methods SetModelID with 1 arg GetModelID SetFileName with 1 arg GetFileName SetFullFileName with 1 arg GetFullFileName SetColor with 1 arg GetColor SetOpacity with 1 arg GetOpacity VisibilityOn VisibilityOff GetVisibility SetVisibility with 1 arg ClippingOn ClippingOff GetClipping SetClipping with 1 arg BackfaceCullingOn BackfaceCullingOff GetBackfaceCulling SetBackfaceCulling with 1 arg ScalarVisibilityOn ScalarVisibilityOff GetScalarVisibility SetScalarVisibility with 1 arg

  22. vtkMrmlModelNode DTD • XML Representation Example: <Model name='Skin' fileName='models/Skin.vtk' color='Skin' visibility='yes'></Model> • DTD entry from Base/tcl/mrml20.dtd: <!ELEMENT Model (#PCDATA | Fiducials)> <!ATTLIST Model name NMTOKEN "" fileName CDATA #REQUIRED color NMTOKEN "" description CDATA "" opacity NMTOKEN "1.0" visibility (yes | no) "yes" clipping (yes | no) "no" backfaceCulling (yes | no) "yes" scalarVisibility (yes | no) "no" ignore (yes | no) "no" scalarRange NMTOKENS "0 100">

  23. How Mrml Files are Read • MainMrmlReadVersion2.x • In Base/tcl/tcl-main/Parse.tcl • Reads xml file and returns tcl list of nodes and values • MainMrmlBuildTreesVersion2.0 • In Base/tcl/tcl-main/MainMrml.tcl • Converts list into vtkMrmlTree and vtkMrmlNode instances • Modules can define Module($m,procMRMLLoad) to extend Mrml

  24. Compiling the Mrml Tree • MainUpdateMRML • In Base/tcl/tcl-main/Main.tcl • Is called after read or after changes to the Mrml Tree • Invokes Main*UpdateMRML • Models, Volumes, etc • Instances VTK classes, reads data, changes render properties, etc to make scene match the MRML Tree • Keeps Dev* GUI elements in sync with Tree and Selections • Invokes Modules($m,procMRML) for each Module

  25. Rendering • To make the newly updated data visible to the user: • Render3D • Redraw just the 3D view • RenderSlice <s> • Redraw slice view 0, 1, or 2 • RenderSlices • Redraw all slice views • RenderAll • Redraw 3D and Slices

  26. Editing the MrmlTree Examples • MainMrmlAddNode <nodeType> • Creates a new vtkMrmlNode instance and adds it to Mrml(dataTree) and returns nodeId • Use vtkMrmlNode methods to set data • Mrml(dataTree) RemoveItem $node • Remove a node • Mrml(dataTree) InsertAfterItem $nodeBefore $node • Add your new node to specific spot in the hierarchy • DevCreateNewCopiedVolume <OrigId> {Description ""} { VolName ""} • Create a copy node of existing volume with optional new name and description

  27. Iterating Through the Mrml Tree set nitems [Mrml(dataTree) GetNumberOfItems] for {set widx 0} {$widx < $nitems} {incr widx} { set item [Mrml(dataTree) GetNthItem $widx] puts “$item is a [$item GetClassName]” }

  28. Anatomy of A Module • See Modules/vtkCustomModule/tcl/@ModuleName@.tcl.in • For example, Custom • CustomInit • Analogous to a Constructor • CustomBuildGUI • CustomEnter / CustomExit • When user module pane is visible/hidden • Custom* • Any other “Methods” for the Module • These procs Edit the MrmlTree and call MainUpdateMRML and Render

  29. The Shared Dev* Procs • Base/tcl/tcl-shared/Developer.tcl • Interact with MrmlTree • Use standard look and feel conventions • DevAddSelectButton • Automatically updating popup menu for Volumes, Models, etc • Adds entries when objects are created • DevUpdateNodeSelectButton • Updates to currently selected • DevAddButton • DevAddLabel • DevAddFileBrowse • DevInfoWindow, DevErrorWindow, DevWarningWindow… • Etc…

  30. Event Management • The <Module>Enter and <Module>Exit procs can be used to set up custom mouse/keyboard bindings • Base/tcl/tcl-shared/Events.tcl • pushEventManager / popEventManager • Arguments are list of: • Widget, event, callback

  31. Event Example In EMSegmentInit: foreach s $Slice(idList) { set widget $Gui(fSl${s}Win) append EMSegment(eventManager) " \ {$widget <Control-Button-1> {EMSegmentBindingCallback Sample %x %y}}” } In EMSegmentEnter: pushEventManager $EMSegment(eventManager) In EMSegmentExit: pushEventManager $EMSegment(eventManager)

  32. Event Example (continued) EMSegmentBindingCallback calls EMSegmentReadGreyValue $x $y 1 In EMSegmentReadGreyValue: set s $Interactor(s) ;# get the slice window where user clicked scan [MainInteractorXY $s $x $y] "%d %d %d %d" xs ys x y ;# convert to pixels Slicer SetReformatPoint $s $x $y scan [Slicer GetIjkPoint] "%g %g %g" xIjk yIjk zIjk ;# convert to array coords set xIjk [expr int($xIjk)] set yIjk [expr int($yIjk)] set zIjk [expr int($zIjk)] # get the pixel data from the volume set ImageData [Volume($v,vol) GetOutput] set pixel [$ImageData GetScalarComponentAsDouble $xIjk $yIjk $zIjk 0]

  33. Progress Bar • Progress Bar on Lower part of slicer control window • For a vtkProcessObject instance X x AddObserver StartEvent MainStartProgress x AddObserver ProgressEvent "MainShowProgress x" x AddObserver EndEvent MainEndProgress

  34. Fiducials Example proc intensities {vol} { # Note: does not account for any transforms applied to Volume catch "m Delete" vtkMatrix4x4 m eval m DeepCopy [Volume($vol,node) GetRasToVtkMatrix] set ids [FiducialsGetPointIdListFromName default] foreach id $ids { set pt [eval m MultiplyPoint [FiducialsGetPointCoordinates $id] 1] set i [expr int([lindex $pt 0])] set j [expr int([lindex $pt 1])] set k [expr int([lindex $pt 2])] set imageData [Volume($vol,vol) GetOutput] set pixel [$imageData GetScalarComponentAsDouble $i $j $k 0] puts "fiducial $id value $pixel at $i $j $k" } }

  35. Reader Modules Motivation • vtkMrmlVolumeNodes can be created by • User Interface • Reading in XML File • Programmatically • Once the Node exists, the reader proc provides the vtkImageData

  36. Reader Modules • Managed by Base/tcl/tcl-modules/Volumes.tcl • ReaderModule needs an entry point proc named Vol<type>Init • For example: VolGenericInit • This will be invoked by VolumesInit • ReaderModule sets • Volume(readerModules,<type>,procGUI) • to fill in type-specific controls as sub-pane of Volumes Modules • Module(Volumes,readerProc,<type>) • so that MainUpdateMRML has a hook to call the reader when <type> if found in the FileType attribute of a vtkMrmlVolumeNode

  37. Editor Modules Motivation • The Editor manages manually guided segmentation of a • source volume into a working labelmap • Editor Modules add to the palette of tools • Ed(editor) is an instance of vtkImageEditorEffects • Allows you to apply a filtering pipeline to modify the labelmap

  38. Editor Modules • Similar to Readers, these are managed by Base/tcl/tcl-modules/Editor.tcl • Editor Module needs an entry point proc named Ed<type>Init • For example: EdWatershedInit • This will be invoked by EditorInit • EditorModule sets • Ed(<type>,procGUI) • to fill in type-specific controls on the this editor type’s own subframe of the editor • Segmentation is done In the UI control callbacks • Create a vtk (or vtkITK-based) processing pipeline of vtkImageToImageFilter subclasses • Set parameters from UI elements or Slicer data such as Fiducial locations • call Ed(editor) Apply <pipeline start> <pipeline end> • Ed(editor) manages progress bar, updating label map, undo (single)

  39. Conclusions • Slicer provides a usable and extensible application framework for medical image computing research • A significant base code provides a reference for many common coding tasks and user interface paradigms

  40. Resources • www.slicer.org • www.na-mic.org/Wiki • www.na-mic.org/Bug • www.na-mic.org/Testing • slicer-devel@bwh.harvard.edu • slicer-users@bwh.harvard.edu

  41. Slicer Architecture SupplementAdding A New View Option Nicole Aucoin

  42. Adding a new option example To add a new View option, X, to the Scene Options node so can save and restore it via Mrml file: • cxx/vtkMrmlSceneOptionsNode.h • add vtkGet/SetStringMacros(ViewX) • declare char *ViewX • cxx/vtkMrmlSceneOptionsNode.cxx • Add ViewX in constructor, Write, Copy, PrintSelf

  43. Adding a new option, con’t • tcl/tcl-main/MainView.tcl • MainViewInit: add to Module(View,presets) list, set View(X) to same default value. • Add a new proc MainViewSetX, with default arg set to default value • MainViewStorePresets: add setting X's Preset from current value • MainViewRecallPresets: add setting X from preset value

  44. Adding a new option, con’t • tcl/tcl-main/MainOptions.tcl • MainOptionsRetrievePresetValues: set Preset(View,n,X) from the node • MainOptionsUnparsePresets: set the node's X from the Preset

  45. Adding a new option, con’t • tcl/tcl-main/MainMrml.tcl: • MainMrmlBuildTreesVersion2.0: add to parsing of SceneOptions node, refer to vtkMrmlSceneOptionsNode C++ code

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