IN4307 Medical Visualisation Module IDPVI

Transcription

1 IN4307 Medical Visualisation Module IDPVI Dr. Charl P. Botha Week 6, / 38

2 Welcome! Visualisation in Medicine Definition in research, medicine and industry. Learning goals: Function as MedVis engineer / scientist. in4307 is about theory and practice. Course theory based on: Visualization in Medicine, Preim and Bartz, Six modules: 1. IDPVI: Intro,,, VTK, ITK. 2. RAPACP: Representation, Artifacts, Perception, Acquisition, Clinical Practice. 3. IAMV: Image Analysis in Medical Visualisation. 4. VOLVIS: Volume Visualisation. 5. VOLEXP: Volume Exploration. 6. ADVTOP: Advanced Topics. 2 / 38

3 Theory and practice in third quarter. Integrated lectures and exercises. Self-study and homework. Selected self-study papers (questions) and homework exercises will be checked and might contribute to final mark. Project in fourth quarter. Your choice, a number of real-world possibilities will be given. Always first discuss. Submit scientific paper and present your work. Paper specification document, also papers detailing how to write good papers. Course notes. Agile teaching. 3 / 38

4 IDPVI? Basic components needed for the experimental part of the work. 4 / 38

5 Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) 5 / 38

6 Introduction Introduction Challenge: MIA lifecycle What is? Why yet another dataflow application? System description. s and future work. Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) 6 / 38

7 Challenge: MIA lifecycle Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) Need platform to facilitate the MIA lifecycle. 7 / 38

8 Introduction Challenge: MIA lifecycle Delft Visualisation and Image processing Development Environment Cross-platform turn-key rapid prototyping environment for medical visualisation and image processing techniques. Support visual programming. Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) 8 / 38

9 Features Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) Pervasive interaction down to code-level at run-time! VTK, ITK, numpy, matplotlib, statistics, the kitchen sink, all out of the box. Off-line mode for large-scale processing, can be used as black-box by coordination framework, e.g. Nimrod Parameter sweeps Large scale processing (many datasets) Use in production workflow Same software is used for all stages: algorithm prototyping, large-scale processing, and post-process visual analysis. Lovingly dubbed Not Responding by students (32 vs 64) 9 / 38

10 Similar solutions Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Summary AVS, OpenDX, SCIRun, MeVisLab, VisTrails Why? Made for medical vis+ip Introspection Ease of integration Prototyping Hybrid scheduling License. Getting started (ex) 10 / 38

11 Extending: modules Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Algorithm developer: central activity Two requirements for code that needs to be integrated must support data-flow must be callable from (by hook or by crook!) Write class that satisfies module API Drop into modules directory (also at run-time) All encapsulated functionality (VTK, ITK, matplotlib, geometry, etc) in module kits. Summary Getting started (ex) 11 / 38

12 Extending: CodeRunner Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) Insert live code into running network. Pre-module rapid prototyping. Experimentation during learning phase. 12 / 38

13 Summary Introduction Challenge: MIA lifecycle Features BSD open-source virtual laboratory for medvis and ip. Source available, binaries for Win32, Linux, Linux x Used for research, recently integrated in education. Exercises! Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) 13 / 38

14 Getting started (ex) Introduction Challenge: MIA lifecycle Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) 1. Start in Linux by doing: /opt/apps/devide re /dre devide 2. Press F1 for the online help, then go to the Graph Editor section and follow the instructions under A small sample network. 3. Clear the canvas by pressing Ctrl-N. 4. Now build the same network in half the time: (a) Make sure module category ALL is selected. (b) Press Ctrl-F. (c) Typesup in the search box and pressenter. (d) (e) Connect the blocks, press F5. PressESC, then typevw orslice followed byenter. 14 / 38

15 Introduction Data types Control flow, indentation Objects s 15 / 38

16 Introduction Introduction Data types Control flow, indentation Objects Programming language Very high-level Dynamically typed Interpreted Object oriented Ideal for wrapping stuff Great glue s 16 / 38

17 Data types Introduction Data types Control flow, indentation Objects s some integer = 20 some float = 12.2 some string = Hello world! s o m e l i s t = [ some integer, some float, some string ] some tuple = ( some integer, some float, some string ) some tuple = t u p l e ( s o m e l i s t ) # a l t e r n a t i v e l y # watch me s l i c e p r i n t s o m e l i s t [ 0 : 2 ] # e v e r y t h i n g up to j u s t before 2nd item p r i n t s o m e l i s t [ 0 : ] # e v e r y t h i n g up to the end p r i n t some tuple [ 1] # the l a s t item a n o t h e r l i s t = range (10) # 0 to 9 p r i n t a n o t h e r l i s t [6:3: 1] # step reverses d i r e c t i o n # you can t do t h i s some tuple [ 1] = A new s t r i n g # t h i s you can ; m u t a b i l i t y... s o m e l i s t [ 1] = A new s t r i n g 17 / 38

18 Control flow, indentation Introduction Data types Control flow, indentation Objects s some var = 3 some other var = 4 i f some var == 3: p r i n t Hello World! e l i f some other var == 4: p r i n t Good bye World... names = [ Henk, Ernst, Jan, Gert Jan, Gertruida ] for name in names : p r i n t name for i in range ( len ( names ) ) : p r i n t i, names [ i ] i = 0 while i < 10: p r i n t i i += 1 def some function ( some parameter ) : p r i n t some parameter p r i n t t h i s f u n c t i o n ends when the indent changes back some function ( Yoohoo world! ) 18 / 38

19 Objects Introduction Data types Control flow, indentation Objects s # e v e r y t h i n g i n i s an o b j e c t. class some class : def i n i t ( s e l f ) : # t h i s i s the ctor, also note e x p l i c i t s e l f s e l f. i v a r = yoohoo I m home! def s p i l l g u t s ( s e l f ) : p r i n t s e l f. i v a r some object = some class ( ) some object. s p i l l g u t s ( ) import types def r e p l a c e m e n t s p i l l g u t s ( s e l f ) : p r i n t p r i n t I m a v i r u s. p r i n t s e l f. i v a r. upper ( ) replacement # even methods are j u s t c a l l a b l e o b j e c t s some object. s p i l l g u t s = types. MethodType ( r e p l a c e m e n t s p i l l g u t s, some object, some class ) some object. s p i l l g u t s ( ) 19 / 38

20 s Introduction Data types Control flow, indentation comes with the batteries included: standard library contains functionality for almost anything. Work through the tutorial on python.org. Make sure you know how to use the library reference. At the prompt, type: import this Read and absorb... Objects s 20 / 38

21 Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 21 / 38

22 Definition Definition VTK Pipelines Pipelines example Visualization ToolKit: Open-source, object-oriented C++ lib. Hundreds of classes, multi-language wrappings. Defacto standard for SciVis. Marketable skill. Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 22 / 38

23 VTK Pipelines Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 VTK processing is based on two processing pipelines: Visualisation pipeline: process data to prepare for rendering e.g. extract surface from volume Graphics pipeline: render processed data. ITK 23 / 38

24 Pipelines example Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK Start Window:: Shell from the main menu. Open basicvtk1.py with Ctrl-O. Execute with File::Run current edit. Experiment by changing vtkspheresource to vtkarrowsource. import v t k spheresource = v t k. vtkspheresource ( ) spheremapper = v t k. vtkpolydatamapper ( ) spheremapper. SetInput ( spheresource. GetOutput ( ) ) sphereactor = v t k. v t k A c t o r ( ) sphereactor. GetProperty ( ). SetColor ( 1. 0, 0.0, 0. 0 ) sphereactor. SetMapper ( spheremapper ) renderwindow = v t k. vtkrenderwindow ( ) renderer = v t k. vtkrenderer ( ) renderwindow. AddRenderer ( renderer ) renderer. AddActor ( sphereactor ) renderwindow. Render ( ) 24 / 38

25 Adding interaction Run basicvtk2.py in the same way: import v t k Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK spheresource = v t k. vtkspheresource ( ) spheremapper = v t k. vtkpolydatamapper ( ) spheremapper. SetInput ( spheresource. GetOutput ( ) ) sphereactor = v t k. v t k A c t o r ( ) sphereactor. GetProperty ( ). SetColor ( 1. 0, 0.0, 0. 0 ) sphereactor. SetMapper ( spheremapper ) renderwindow = v t k. vtkrenderwindow ( ) renderer = v t k. vtkrenderer ( ) renderwindow. AddRenderer ( renderer ) renderer. AddActor ( sphereactor ) i r e n = v t k. vtkrenderwindowinteractor ( ) i r e n. SetRenderWindow ( renderwindow ) i r e n. I n i t i a l i z e ( ) renderwindow. Render ( ) i r e n. S t a r t ( ) 25 / 38

26 vtkfielddata Definition VTK Pipelines Field data Most basic data container Number of named vtkdataarrays Each array: m tuples of n elements each M assumed constant for all arrays Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 26 / 38

27 vtkdataobject Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 vtkdataobject Encapsulates single vtkfielddata instance Simple pile of data Leads to more interesting things... ITK 27 / 38

28 vtkdataset Definition vtkdataset Still has FieldData instance. Also geometry (points) and topology (cells). PointData and CellData (FieldData children) as attributes. Supports different spatial layouts. VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 28 / 38

29 Exercise: VTK dataset from scratch See exercise on same slide in handouts. Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 29 / 38

30 Execution model, pre-5.0 Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 Streaming, demand-driven consumer.setinput( producer.getoutput() ) consumer.getoutput() request passes to consumer, then to producer.getoutput(), then to producer. Data passes all the way down. Only necessary parts of arbitrarily complex network topologies are executed. In other words: call update() on any downstream part to execute upstream ITK 30 / 38

31 New execution model, post-5.0 Definition VTK Pipelines From a client-programmer POV, much the same c.setinputconnection( 0, p.getoutputport(0) ) Algorithms, Executives, Information objects ProcessRequest(), vtkexecutive, vtkalgorithm Specialised in children: RequestData() Update() Pipelines example Adding interaction vtkfielddata vtkdataobject vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 31 / 38

32 ITK Definition VTK Pipelines Pipelines example Adding interaction vtkfielddata vtkdataobject Insight segmentation and registration toolkit Open source, object-oriented, heavily templated C++ library with hundreds of classes, Tcl and Java interfaces Follows many of the same conventions as VTK VTK and ITK pipelines can be easily connected - Manual pages and downloadable ITK Software Guide WrapITK! vtkdataset Exercise: VTK dataset from scratch Execution model, pre-5.0 New execution model, post-5.0 ITK 32 / 38

33 Summary of IN4307 module IDPVI 33 / 38

34 Summary of IN4307 module IDPVI Main introduction Summary of IN4307 module IDPVI 34 / 38

35 Loading and filtering data (ex) First taste of ITK (ex) Self-study 35 / 38

36 Loading and filtering data (ex) See exercise on same slide in handouts. Loading and filtering data (ex) First taste of ITK (ex) Self-study 36 / 38

37 First taste of ITK (ex) See exercise on same slide in handouts. Loading and filtering data (ex) First taste of ITK (ex) Self-study 37 / 38

38 Self-study Loading and filtering data (ex) First taste of ITK (ex) Self-study Read the System Description section of the paper Hybrid scheduling in the dataflow visualisation environment 1. Work through the tutorial 2. Take a brief look at the contents of the standard library 3. Browse through the VTK class list 4. Browse through the ITK Software Guide 5. Make sure you understand the general structure of the whole software framework. Study some of the examples in more detail to get a feel for how ITK does things. Most examples can be implemented directly in / 38