Transcript National Alliance for Medical Image Computing: Namic

NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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)
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
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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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
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•
•
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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!
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
Mrml http://www.slicer.org/mrml
National Alliance for Medical Image Computing
http://na-mic.org
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>
National Alliance for Medical Image Computing
http://na-mic.org
Mrml XML
• Describes the data as it exists on
disk
• Composes the scene by positioning
data elements
• Retains visualization and other state
parameters
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
vtkMrmlNode
National Alliance for Medical Image Computing
http://na-mic.org
Mrml Nodes
• vtkMrmlNode abstract base class
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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
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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;
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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">
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
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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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
$node
– Add your new node to specific spot in the hierarchy
• DevCreateNewCopiedVolume <OrigId>
{Description ""} { VolName ""}
– Create a copy node of existing volume with optional
new name and description
National Alliance for Medical Image Computing
http://na-mic.org
Iterating Through the Mrml
Tree
set nitems [Mrml(dataTree) GetNumberOfItems]
for {set widx 0} {$widx < $nitems} {incr widx} {
set item [Mrml(dataTree) GetNthItem $widx]
puts “$item is a [$item GetClassName]”
}
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
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•
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DevAddButton
DevAddLabel
DevAddFileBrowse
DevInfoWindow, DevErrorWindow, DevWarningWindow…
Etc…
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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)
National Alliance for Medical Image Computing
http://na-mic.org
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 $zIjk 0]
National Alliance for Medical Image Computing
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Progress Bar
• Progress Bar on Lower part of slicer
control window
• For a vtkProcessObject instance X
x AddObserver StartEvent MainStartProgress
x AddObserver ProgressEvent "MainShowProgress x"
x AddObserver EndEvent MainEndProgress
National Alliance for Medical Image Computing
http://na-mic.org
Fiducials Example
proc intensities {vol} {
# Note: does not account for any transforms applied to Volume
catch "m Delete"
vtkMatrix4x4 m
eval m DeepCopy [Volume($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"
}
}
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
Editor Modules
•
•
Similar to Readers, these are managed by Base/tcl/tclmodules/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)
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
Resources
•
•
•
•
•
•
www.slicer.org
www.na-mic.org/Wiki
www.na-mic.org/Bug
www.na-mic.org/Testing
[email protected]
[email protected]
National Alliance for Medical Image Computing
http://na-mic.org
NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Slicer Architecture
Supplement
Adding A New View Option
Nicole Aucoin
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
Adding a new option, con’t
• tcl/tcl-main/MainMrml.tcl:
– MainMrmlBuildTreesVersion2.0: add to
parsing of SceneOptions node, refer to
vtkMrmlSceneOptionsNode C++ code
National Alliance for Medical Image Computing
http://na-mic.org