IN4307 Medical Visualisation Module IDPVI

Transcription

1 IN4307 Medical Visualisation Module IDPVI Dr. Charl P. Botha Week 6, 2012 Course Introduction Logistics Module Introduction DeVIDE 5 Introduction Challenge: MIA lifecycle DeVIDE Features Similar solutions Extending: modules Extending: CodeRunner Summary Getting started (ex) Python 15 Introduction Data types Control flow, indentation Objects Conclusions VTK / ITK 21 Definition VTK Pipelines Pipelines example Adding interaction Data model: vtkfielddata Data model: vtkdataobject Data model: vtkdataset Exercise: VTK dataset from scratch Execution model, pre New execution model, post ITK

2 Conclusion 33 Summary of IN4307 module IDPVI Homework 35 Loading and filtering data (ex) First taste of ITK (ex) Self-study

3 Course Introduction 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, DeVIDE, Python, 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 Logistics 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 Module Introduction IDPVI? Basic components needed for the experimental part of the work. 4 / 38 3

4 DeVIDE 5 / 38 Introduction What is DeVIDE? Why yet another dataflow application? System description. Conclusions and future work. 6 / 38 Challenge: MIA lifecycle Need platform to facilitate the MIA lifecycle. 7 / 38 4

5 DeVIDE Delft Visualisation and Image processing Development Environment Cross-platform turn-key rapid prototyping environment for medical visualisation and image processing techniques. Support visual programming. 8 / 38 Features 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 5

6 Similar solutions AVS, OpenDX, SCIRun, MeVisLab, VisTrails Why DeVIDE? Made for medical vis+ip Introspection Ease of integration Prototyping Python Hybrid scheduling License. 10 / 38 Extending: modules Algorithm developer: central activity Two requirements for code that needs to be integrated must support data-flow must be callable from Python (by hook or by crook!) Write Python class that satisfies module API Drop into modules directory (also at run-time) All encapsulated functionality (VTK, ITK, matplotlib, geometry, etc) in module kits. 11 / 38 Extending: CodeRunner Insert live code into running network. Pre-module rapid prototyping. Experimentation during learning phase. 12 / 38 6

7 Summary 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! 13 / 38 Getting started (ex) 1. Start DeVIDE in Linux by doing: /opt/apps/devide re /dre devide 2. Press F1 for the DeVIDE 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) PressESC, then typevw orslice followed byenter. (e) Connect the blocks, press F5. 14 / 38 Python 15 / 38 Introduction Programming language Very high-level Dynamically typed Interpreted Object oriented Ideal for wrapping stuff Great glue 16 / 38 7

8 Data types 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 some list [ 0 : 2 ] # everything up to j u s t before 2nd item p r i n t some list [ 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 ( 1 0 ) # 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 Control flow, indentation 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: print 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 function ends when the indent changes back some function ( Yoohoo world! ) 18 / 38 8

9 Objects # everything in Python i s an object. 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 replacement 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 ( ) # 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 ( replacement spill guts, some object, some class ) some object. s p i l l g u t s ( ) 19 / 38 Conclusions Python 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 / 38 9

10 VTK / ITK 21 / 38 Definition Visualization ToolKit: Open-source, object-oriented C++ lib. Hundreds of classes, multi-language wrappings. Defacto standard for SciVis. Marketable skill. 22 / 38 10

11 VTK Pipelines 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. 23 / 38 Pipelines example Start Window::Python Shell from the main DeVIDE 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 = vtk. vtkactor ( ) sphereactor. GetProperty ( ). SetColor ( 1. 0, 0.0, 0. 0 ) sphereactor. SetMapper ( spheremapper ) renderwindow = vtk. vtkrenderwindow ( ) renderer = vtk. vtkrenderer ( ) renderwindow. AddRenderer ( renderer ) renderer. AddActor ( sphereactor ) renderwindow. Render ( ) 24 / 38 11

12 Adding interaction Run basicvtk2.py in the same way: import v t k spheresource = v t k. vtkspheresource ( ) spheremapper = v t k. vtkpolydatamapper ( ) spheremapper. SetInput ( spheresource. GetOutput ( ) ) sphereactor = vtk. vtkactor ( ) sphereactor. GetProperty ( ). SetColor ( 1. 0, 0.0, 0. 0 ) sphereactor. SetMapper ( spheremapper ) renderwindow = vtk. vtkrenderwindow ( ) renderer = vtk. vtkrenderer ( ) renderwindow. AddRenderer ( renderer ) renderer. AddActor ( sphereactor ) i r e n = vtk. vtkrenderwindowinteractor ( ) iren. 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 Taking care of the universe You ve just created a foreign event loop inside DeVIDE. This might lead to the universe collapsing. To be on the safe side, stop and restart DeVIDE. note 1 of slide 25 Data model: vtkfielddata Field data Most basic data container Number of named vtkdataarrays Each array: m tuples of n elements each M assumed constant for all arrays 26 / 38 12

13 Data model: vtkdataobject vtkdataobject Encapsulates single vtkfielddata instance Simple pile of data Leads to more interesting things / 38 Data model: vtkdataset vtkdataset Still has FieldData instance. Also geometry (points) and topology (cells). PointData and CellData (FieldData children) as attributes. Supports different spatial layouts. 28 / 38 13

14 Exercise: VTK dataset from scratch 1. Clear the canvas by pressing Ctrl-N. 2. Place a CodeRunner. 3. Switch to the Execute tab in the CodeRunner. 4. Load polytest.py by selecting File::Open file to current edit from the main menu. Click the Apply button. 5. Place a slice3dvwr. 6. Connect the first output of the CodeRunner to the first input of the slice3dvwr. 7. Study the source code that you loaded. Don t forget to execute it. 8. The triangle that appears has only one colour due to the default flat shading mode. Change the shading mode to Phong by doing the following: (a) (b) (c) (d) (e) (f) (g) Click Show Controls on the main slicedvwr 3D view. Select configure the object from the When I click an object in the scene choice at the bottom of the slice3dvwr Controls window. Click on the triangle in the 3D scene. In the VTK pipeline browser that appears, double click on the Property. On the States tab of the newly appeared window, select SetInterpolationToPhong and click on the Apply button. Marvel at the prettiness of your Phong-shaded triangle. Change When I click on an object in the scene back to Do nothing. This part of the interface is indeed quite complex for two reasons: User actions that are often performed are integrated in the simple interface (right click on the object in the object list for an example); With this more complex interface, all VTK flexibility is available. 9. Make changes (for example, add another triangle) to test your comprehension of the VTK polydata that you have created. 29 / 38 Execution model, pre-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: callupdate() on any downstream part to execute upstream 30 / 38 14

15 New execution model, post-5.0 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() 31 / 38 New execution model, post-5.0 Multiple connections per input port possible Pipeline vtkinformation (owned by vtkexecutive) for each output port Pipeline vtkinformationvector (owned by vtkexecutive) for each input port Algorithm, data objects also own their own information objects Default vtkexecutive: Streaming, Demand Driven For more information, read Upgrading to and Understanding the New VTK Pipeline at note 1 of slide 31 15

16 ITK Insight segmentation and registration toolkit Open source, object-oriented, heavily templated C++ library with hundreds of classes Python, 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! 32 / 38 Conclusion 33 / 38 Summary of IN4307 module IDPVI Main introduction DeVIDE Python VTK / ITK 34 / 38 Homework 35 / 38 Loading and filtering data (ex) 1. Load a volume dataset by dragging and dropping pano masked.vti onto the DeVIDE canvas. A vtirdr will automatically be created with the filename already entered. 2. Connect the output of the automatically created vtirdr to the input of a slice3dvwr. 3. Press F5 to execute the network. 4. Visually inspect the data by using the slicer and probing values with your cursor. You can move the slice with the middle mouse button, change the window and level (similar to contrast and brightness) with the right mouse button, and probe the value under the cursor with the left mouse button. Note the cube in the bottom left corner showing the real patient orientation in the scanner. This information can be derived from the DICOM meta-data. 5. Downsample the data by to a quarter by halving the number of samples on both thexandy axes. The resampleimage module is good for this. 6. Write the data to disc in native VTK format by using vtiwrt. 7. If you re working on a 32 bit machine, make available some memory. Clean the canvas with Ctrl-N or File New. Load the downsampled VTI file you just saved by dragging and dropping it onto the DeVIDE canvas. 36 / 38 16

17 First taste of ITK (ex) 1. Convert downsampled data to ITK format with a VTKtoITK, make sure to uncheck its AutoType and click on Apply. 2. Pass data through a gaussianconvolve 3. Use a ITKtoVTK to convert data back to VTK format and add this as the only input to your slice3dvwr. 4. Execute the network. 5. Experiment with the gaussianconvolve parameters. 6. Use three gaussianconvolve modules to implement a standard 3D Gaussian blurring. (Remember that Gaussian kernels are separable.) 37 / 38 Self-study Read the System Description section of the paper Hybrid scheduling in the DeVIDE dataflow visualisation environment a. Work through the Python tutorial b. Take a brief look at the contents of the Python standard library c. Browse through the VTK class list d. Browse through the ITK Software Guide e. 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 DeVIDE. a b c d e 38 / 38 17