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[ Lecture Notes ]   [ Practical Exercises ]   [ Assignments ]   [ VTK ]   [ PAQ ]  

Lecturer

Taku Komura, JCMB 2701B tkomura [-at-] inf.ed.ac.uk, (0131) 651-3445

Before emailing with a question - please check the module PAQ

Lecture Times

• Tuesday, Friday: 16:10-17:00 DHT 4.01

Syllabus

• Visualisation: definition and motivation.
• System architecture: visualisation pipeline model; synchronisation.
• Data representation: geometric abstractions; volume and surface representations, interpolation.
• Fundamental algorithms: colour mapping; contouring; glyphs; volume rendering.
• Advanced algorithms: flow visualisation, vector visualisation, tensor visualisation
• Information visualisation: networks and trees; document visualisation.
• Current research topics: visualisation of environments; new methods inspired by other disciplines.

Activities

1. 20 lectures on the above syllabus.
2. 2 assessed practical exercises.
3. Additional non-assessed practical exercises (weekly) for familiarisation both with the VTK package in use and the general concepts of the course.

Assessment

Level 10 (UG4) & Level 11 (MSc)

All practical work is covered by the school policy on plagiarism and students are advised to be fully aware of this when submitting practical work.

Course Materials

Lecture handouts will be available on this web site shortly after the lecture. Printed copies are handed out before the lecture and are available in the course pigeon hole (ITO) - please check the pigeon hole first before printing.

• Lecture Notes

  • Lecture 1 VTK - 8th January 2008
      Lecture Note [PDF] VTK tutorial [PDF] VTK cone example [TCL]
      Reading:
    • Online: VTK Design & Implementation Overview;
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - Chapter 3 or The VTK User's Guide - Chapter 3
      Additional URLs (for reference):
    • VTK Manual;  VTK Examples;  More VTK Examples;  VTK - everything else
    • TCL Manual  TCL online tutorial  TCL - Everything else
    • Using VTK and Java on DICE
    
    
  • Lecture 2 Introducing Visualisation - 11th January 2008
      Lecture Note [PDF]
      Reading:
    • Online: Definitions and Rationale for Visualization;
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - Chapter 1
      Additional URLs (for interest):
    • Ordnance Survey 3D map movies;  Google Earth;
    • Vesalius Project - 3D virtual dissection;  3D face models;
    • VIS5D visualisation package;  paraview visualisation package;
    
    
  • Lecture 3 Computer Graphics - 15th January 2008
      Lecture Note [PDF]
    
    
  • Lecture 4 Systems Architecture for Visualisation - 18th January 2008
      Lecture Note [PDF] VTK Quadric example [TCL]
      Reading:
    • Online: "Visualizing a Quadric Function" section of this document
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - Chapter 4
      Additional URLs (for interest):
    • AVS - commerical visualisation package
    • paraview visualisation package (free)
    • Open DX visualisation package (free)
    
    
  • Lecture 5 Data Representation for Visualisation - 20th January 2008
      Lecture Note [PDF] Wind Speed Visualisation [MPG]
      Reading:
    • Online: pixels
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - Chapter 5 (5.1-5.6)
      Additional URLs (for interest):
    • Nasa Scientific Visualization Studio - lots of cool visualisations of global data
    
    
  • Lecture 6 Scalar Algorithms : Colour Mapping - 24th January 2008
      Lecture Note [PDF] Infra-red Movie [AVI]
      Hawaii Example [TCL] [Data]   Reading:
    • Online: RGB; RGB colourspace; Colour Ramping; Grayscale; Colour mapping (ramping) for visualisation
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 3.2 / 6.1 / 6.2
    
    
  • Lecture 7 Scalar Algorithms : Contouring - 27th January 2008
      Lecture Note [PDF] Dividing Cubes Example [TCL] [Data]
      Reading:
    • Online: Marching Cubes overview online tutorial; Dividing Cubes;
    • Supporting Papers: [Lorensen '87] (Marching Cubes); [Cline '88] (Dividing Cubes, abstract only);
      [Hilton '96] (Marching Triangles); [Nielson '91] (Marching Cubes Ambiguity)
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 6.2 / 6.6 (contouring) / 9.1 (Div. Cubes)
      Additional URLs (for interest):
    • Marching Cubes Patent
    • Dividing Cubes Patent
    • Marching Triangles Overview
    
    
  • Lecture 8 Advanced Data Representation - 1st Feburary 2008
      Lecture Note [PDF]
      Reading:
    • Online: Octree (def.); Octree Examples; Cartesian Coordinates;
      Rotation Matrices; interpolation (def); Kd tree demo & tutorial
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 8.1-8.6 8.9 8.10
      Additional URLs (for interest):
    • vtkDataSet class reference
    
    
  • Lecture 9 Contouring & Implicit Modelling - 5th February 2008
      Lecture Note [PDF] Head Contours [TCL] [Data] Hello Text [TCL] [Data]
      Reading:
    • Online: Three-dimensional modeling of human organs and its application to diagnosis and surgical planning [Geiger '93]
         Implicit Surfaces; Constructive Solid Geometry
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 6.5 (Implicit Functions/Modelling + Cutting) 10.1-10.3
      Additional URLs (for interest):
    • Nuages Software
    • The Basics of MRI - J.P. Hornak
    • Image Processing - see Advanced Vision Module
    
    
  • Lecture 10 Volume Rendering - 8th February 2008
      Lecture Note [PDF]
      Volview Examples :
    • Composite with Linear Interpolation [PNG]
    • MIP with Linear Interpolation [PNG]
    • Composite with Nearest Neighbour Interpolation [PNG]
      Reading:
    • Online: Volume Visualization With Ray Casting; Volume rendering techniques
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 7.1 / 7.3 / 7.4
      Additional URLs (for interest):
    • Volview Volume Visualisation Software - demo in lectures (windows only)
    
    
  • Lecture 11 Volume Illumination - 11th February 2008
      Lecture Note [PDF] Vector Field Animation [MPG]
      Reading:
    • Online: Volume Visualization and Rendering;
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 6.3 / 7.8
      Additional URLs (for interest):
    • Hurricane Visualisation @ Nasa
    
    
  • Lecture 12 Vector Field Visualisation : Global View - 15th February 2008
      Lecture Note [PDF] Storm movies [MPG] [MPG] [MPG] [MPG] Streamline VTK example [TCL] [Data]
      Reading:
    • Online: Definition of Streamlines; Streamlines and Streamtubes
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 6.3
      Additional URLs (for interest):
    • Storm Visualisation Examples
    
    
  • Lecture 13 Flow Visualisation - 19st February 2008
      Lecture Note [PDF] Smoke movie [QuickTime] Flow Volume [QuickTime] LIC [GIF] UFLIC [QuickTime]
      Reading:
    • Online: Flow Visualisation - Streamlines, Streaklines, LIC, UFLIC
      
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 9.2
      Additional URLs (for interest):
    • Flow Volumes
    
    
  • Lecture 14 Tensor Visualisation - 22nd February 2008
      Lecture Note [PDF]
      Reading:
    • Online: Tensor Definition; Diffusion tensor imaging; Tensor Glyphs;
          Processing and Visualization of Diffusion Tensor MRI [Westin et al. '02]
          Tensor field visualisation using adaptive filtering of noise fields combined with glyph rendering [Sigfridsson et al. '02]
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 6.4 / 9.3
    
    
  • Lecture 15 Visualisation of "Real" Objects & Environments - 26th Feburary 2008
      Lecture Note [PDF] 3D pineapple example [MPG] laser scanner [WMV]   3D cola bottle scan [MPG] 3D Mosque Model [MPG]
      Reading:
    • Online:     Stereo Vision Overview; Stereo Imaging Intro.; Dense Stereo Matching;
          Range Images (depth maps) 1; Range Images 2;
      Time of Flight Scanners; Triangulation based scanners;
      
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - N/A
      Additional URLs (for interest):
    • Dimensional Imaging Website
    • Wicks & Wilson (Body Scanners) Website
    • 3D Scanners Website
    • The Digital Michelangelo Project
    • The Stanford Cuneiform Tablet Visualization Project
    • The Edinburgh Virtual Environment Centre
    
    
  • Lecture 16 Processing 3D Surface Data - 29th Feburary 2008
      Lecture Note [PDF] ICP Registration A - [MPG] B - [MPG] ICP Result (A & B)- [MPG]
      VTK Decimation Application [TCL] [Required Colour Wheel File] [Face Data]
      Reading:
    • Online: [Schroeder et al. '92] [Besl/McKay '92]
           Laplacian Mesh Smoothing; QSplat
      
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 9.4
    
    
  • Lecture 17 Visualisation of Abstract Information - 4th March 2008
      Lecture Note [PDF] 3D Glyph Example [TCL] [Data]
      Reading:
    • Online: N/A (see additional URLs below)
      
    • Textbook (optional): Schroeder et al (2nd/3rd Edition) - 12.3
      Additional URLs (for interest):
    • Daisy 2000
    • Net Map Analytics
    • Google Earth
    • The London Underground Map - Harry Beck's Design Icon
    • Interactive 3D Visualization for Document Retrieval
    
    
  • Lecture 18 Visualisation : Course Review - 7th March 2008
      Lecture Note [PDF]
    

• Practical Handouts

  • Handout 1 - 8th January 2008 (not assessed)
      [PDF]
      Reading: lecture 1 notes + lecture 1 VTK handout (above)
      Urls: see those given for lecture 1
      Source Code: cone.tcl
    
  • Handout 2 - 25th January 2008 (not assessed)
      [PDF]
      Reading: lecture 2 & 3 notes + lecture 2 VTK handout
      Urls: see those given for lecture 2
      Data: vw_knee.slc neghip.slc
    
  • Handout 3 - 8th March 2008 (not assessed)
      [PDF]
      Urls: MPEG tools; xvidcap
      Reading: handouts 1 and 2
    

• Assignments

  • Assignment 1 - issued 25 January 2008 (weight 50%)
      [PDF]   Data: vw_knee.slc
      xvidcap files: xvidcap.tgz
      mpeg_encode, template file, mpeg_play: mpeg_encode.tgz
    Due : 7th March 2008 at 5pm
    
    
  • Assignment 2 - N.B. different UG4 (level 10) and MSc (level 11) versions
    
    
    • Assignment 2 - UG4 (L10) - issued 29th February 2008 (weight 50%)
        [PDF] Data [glider_gps.vtk glider_map.jpg vtkgps.txt]
      Due : 9th April 2008 at 5pm
      
      
    • Assignment 2 - MSc (L11) - issued 29th February 2008 (weight 50%)
        [PDF] Data [data file directory]
      Due : 9th April 2008 at 5pm
      
      

VTK Software & Documentation

• This course will use the VTK visualisation package which is available on DICE. This is based on the tk/tcl scripting language although interfaces for C++/java/python are also available.
  • Full details of VTK: http://public.kitware.com/VTK/
  • Online VTK documentation (version 5.0)
  • VTK FAQ and example code
• Software for use on home machines/laptops:
  • Download from VTK site
    Use version 5.0. The build under linux can be painful so you are advised to try rpms below if you encounter problems.

Reading List

The following texts are recommended to additionally support the course but are not essential. Most are available from the university library.

• Shroeder, Martin & Lorenson, 'The Visualization Toolkit', 2nd ed., Prentice Hall, 1998. (or 3rd Edition)
• Kitware Inc. Edited by W.J. Shroeder, 'The Visualisation Toolkit User's Guide', Prentice Hall,
• Spence 'Information Visualization', Addison-Wesley, 2001. Good for the topic of information visualisation.

[Visualisation Syllabus Page]

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This page is maintained by the course lecturer, Taku Komura, tkomura@inf.ed.ac.uk, room 2107B JCMB, ext 513445