Installation Guides
  Installing and Running ArtiSynth on Windows
    1 Overview
    2 Prerequisites
    3 The ArtiSynth installation folder
    4 Installing Java
      4.1 Ensuring the JDK is visible to your system
    5 Installing a Precompiled Release
      5.1 Running from the file browser
      5.2 Running from a terminal window
    6 Installing from GitHub
      6.1 Installation using Eclipse
      6.2 Installation using Git for Windows
    7 Loading and Running Models
      7.1 Other ways to load models
      7.2 Viewing and interacting with models
      7.3 Command line arguments
    8 Creating and Adding Models
      8.1 Model packages
      8.2 Compiling models
      8.3 Finding models in the model menu
    9 Settings and the user configuration folder
    10 Integrating external models
      10.1 Making ArtiSynth visible to the compiler
      10.2 Eclipse development
      10.3 Command line development
      10.4 Making external models visible to ArtiSynth
      10.5 Running from Eclipse
      10.6 Using the external classpath
      10.7 Setting the CLASSPATH environment variable
      10.8 Using the -cp option
    11 Installing artisynth_models
      11.1 Installing a precompiled release
      11.2 Installing from GitHub
        11.2.1 Installation using Eclipse
        11.2.2 Installation using Git for Windows
    12 Updating ArtiSynth
      12.1 Library updates
    13 The Eclipse IDE
      13.1 Installing Eclipse
        13.1.1 Setting Eclipse to use the correct Java JDK
        13.1.2 Preventing excess resource copying
      13.2 Importing external projects
      13.3 Configuring environment variables
        13.3.1 Setting environment variables
      13.4 Command line and JVM arguments
        13.4.1 Setting command line and JVM arguments
      13.5 Adding projects to the build path
      13.6 Adding projects to the ArtiSynth launch configuration
    14 Additional Information
      14.1 Adding Directories to the System Path
        14.1.1 Windows 10
        14.1.2 Windows 8 and earlier
      14.2 Environment variables
        14.2.1 Setting environment variables
        14.2.2 Typical environment settings
        14.2.3 GitBash environment settings
      14.3 ArtiSynth Libraries
      14.4 The EXTCLASSPATH File
      14.5 Quick Git Summary
  Installing and Running ArtiSynth on MacOS
    1 Overview
    2 Prerequisites
    3 The ArtiSynth installation folder
    4 Installing Java
      4.1 Ensuring the JDK is visible to your system
    5 Installing a Precompiled Release
      5.1 Running from the file browser
      5.2 Running from a terminal window
    6 Installing from GitHub
      6.1 Installation using Eclipse
      6.2 Installation using the command line
    7 Loading and Running Models
      7.1 Other ways to load models
      7.2 Viewing and interacting with models
      7.3 Command line arguments
    8 Creating and Adding Models
      8.1 Model packages
      8.2 Compiling models
      8.3 Finding models in the model menu
    9 Settings and the user configuration folder
    10 Integrating external models
      10.1 Making ArtiSynth visible to the compiler
      10.2 Eclipse development
      10.3 Command line development
      10.4 Making external models visible to ArtiSynth
      10.5 Running from Eclipse
      10.6 Using the external classpath
      10.7 Setting the CLASSPATH environment variable
      10.8 Using the -cp option
    11 Installing artisynth_models
      11.1 Installing a precompiled release
      11.2 Installing from GitHub
        11.2.1 Installation using Eclipse
        11.2.2 Installation from the command line
    12 Updating ArtiSynth
      12.1 Library updates
    13 The Eclipse IDE
      13.1 Installing Eclipse
        13.1.1 Setting Eclipse to use the correct Java JDK
        13.1.2 Preventing excess resource copying
      13.2 Importing external projects
      13.3 Configuring environment variables
        13.3.1 Setting environment variables
      13.4 Command line and JVM arguments
        13.4.1 Setting command line and JVM arguments
      13.5 Adding projects to the build path
      13.6 Adding projects to the ArtiSynth launch configuration
    14 Additional Information
      14.1 Adding Directories to the System Path
      14.2 Environment variables
        14.2.1 Example environment set up for bash
        14.2.2 Example environment setup for csh or tcsh
      14.3 ArtiSynth Libraries
      14.4 The EXTCLASSPATH File
      14.5 Quick Git Summary
  Installing and Running ArtiSynth on Linux
    1 Overview
    2 Prerequisites
    3 The ArtiSynth installation folder
    4 Installing Java
      4.1 Ensuring the JDK is visible to your system
    5 Installing a Precompiled Release
      5.1 Running from a terminal window
    6 Installing from GitHub
      6.1 Installation using Eclipse
      6.2 Installation using the command line
    7 Loading and Running Models
      7.1 Other ways to load models
      7.2 Viewing and interacting with models
      7.3 Command line arguments
    8 Creating and Adding Models
      8.1 Model packages
      8.2 Compiling models
      8.3 Finding models in the model menu
    9 Settings and the user configuration folder
    10 Integrating external models
      10.1 Making ArtiSynth visible to the compiler
      10.2 Eclipse development
      10.3 Command line development
      10.4 Making external models visible to ArtiSynth
      10.5 Running from Eclipse
      10.6 Using the external classpath
      10.7 Setting the CLASSPATH environment variable
      10.8 Using the -cp option
    11 Installing artisynth_models
      11.1 Installing a precompiled release
      11.2 Installing from GitHub
        11.2.1 Installation using Eclipse
        11.2.2 Installation from the command line
    12 Updating ArtiSynth
      12.1 Library updates
    13 The Eclipse IDE
      13.1 Installing Eclipse
        13.1.1 Setting Eclipse to use the correct Java JDK
        13.1.2 Preventing excess resource copying
      13.2 Importing external projects
      13.3 Configuring environment variables
        13.3.1 Setting environment variables
      13.4 Command line and JVM arguments
        13.4.1 Setting command line and JVM arguments
      13.5 Adding projects to the build path
      13.6 Adding projects to the ArtiSynth launch configuration
    14 Additional Information
      14.1 Adding Directories to the System Path
      14.2 Environment variables
        14.2.1 Example environment set up for bash
        14.2.2 Example environment setup for csh or tcsh
      14.3 ArtiSynth Libraries
      14.4 The EXTCLASSPATH File
      14.5 Quick Git Summary
  Installing and Running ArtiSynth on Windows
    1 Overview
    2 Prerequisites
    3 The ArtiSynth installation folder
    4 Installing Java
      4.1 Ensuring the JDK is visible to your system
    5 Installing a Precompiled Release
      5.1 Running from the file browser
      5.2 Running from a terminal window
    6 Installing from GitHub
      6.1 Installation using Eclipse
      6.2 Installation using Git for Windows
    7 Loading and Running Models
      7.1 Other ways to load models
      7.2 Viewing and interacting with models
      7.3 Command line arguments
    8 Creating and Adding Models
      8.1 Model packages
      8.2 Compiling models
      8.3 Finding models in the model menu
    9 Settings and the user configuration folder
    10 Integrating external models
      10.1 Making ArtiSynth visible to the compiler
      10.2 Eclipse development
      10.3 Command line development
      10.4 Making external models visible to ArtiSynth
      10.5 Running from Eclipse
      10.6 Using the external classpath
      10.7 Setting the CLASSPATH environment variable
      10.8 Using the -cp option
    11 Installing artisynth_models
      11.1 Installing a precompiled release
      11.2 Installing from GitHub
        11.2.1 Installation using Eclipse
        11.2.2 Installation using Git for Windows
    12 Updating ArtiSynth
      12.1 Library updates
    13 The Eclipse IDE
      13.1 Installing Eclipse
        13.1.1 Setting Eclipse to use the correct Java JDK
        13.1.2 Preventing excess resource copying
      13.2 Importing external projects
      13.3 Configuring environment variables
        13.3.1 Setting environment variables
      13.4 Command line and JVM arguments
        13.4.1 Setting command line and JVM arguments
      13.5 Adding projects to the build path
      13.6 Adding projects to the ArtiSynth launch configuration
    14 Additional Information
      14.1 Adding Directories to the System Path
        14.1.1 Windows 10
        14.1.2 Windows 8 and earlier
      14.2 Environment variables
        14.2.1 Setting environment variables
        14.2.2 Typical environment settings
        14.2.3 GitBash environment settings
      14.3 ArtiSynth Libraries
      14.4 The EXTCLASSPATH File
      14.5 Quick Git Summary
  Installing and Running ArtiSynth on MacOS
    1 Overview
    2 Prerequisites
    3 The ArtiSynth installation folder
    4 Installing Java
      4.1 Ensuring the JDK is visible to your system
    5 Installing a Precompiled Release
      5.1 Running from the file browser
      5.2 Running from a terminal window
    6 Installing from GitHub
      6.1 Installation using Eclipse
      6.2 Installation using the command line
    7 Loading and Running Models
      7.1 Other ways to load models
      7.2 Viewing and interacting with models
      7.3 Command line arguments
    8 Creating and Adding Models
      8.1 Model packages
      8.2 Compiling models
      8.3 Finding models in the model menu
    9 Settings and the user configuration folder
    10 Integrating external models
      10.1 Making ArtiSynth visible to the compiler
      10.2 Eclipse development
      10.3 Command line development
      10.4 Making external models visible to ArtiSynth
      10.5 Running from Eclipse
      10.6 Using the external classpath
      10.7 Setting the CLASSPATH environment variable
      10.8 Using the -cp option
    11 Installing artisynth_models
      11.1 Installing a precompiled release
      11.2 Installing from GitHub
        11.2.1 Installation using Eclipse
        11.2.2 Installation from the command line
    12 Updating ArtiSynth
      12.1 Library updates
    13 The Eclipse IDE
      13.1 Installing Eclipse
        13.1.1 Setting Eclipse to use the correct Java JDK
        13.1.2 Preventing excess resource copying
      13.2 Importing external projects
      13.3 Configuring environment variables
        13.3.1 Setting environment variables
      13.4 Command line and JVM arguments
        13.4.1 Setting command line and JVM arguments
      13.5 Adding projects to the build path
      13.6 Adding projects to the ArtiSynth launch configuration
    14 Additional Information
      14.1 Adding Directories to the System Path
      14.2 Environment variables
        14.2.1 Example environment set up for bash
        14.2.2 Example environment setup for csh or tcsh
      14.3 ArtiSynth Libraries
      14.4 The EXTCLASSPATH File
      14.5 Quick Git Summary
  Installing and Running ArtiSynth on Linux
    1 Overview
    2 Prerequisites
    3 The ArtiSynth installation folder
    4 Installing Java
      4.1 Ensuring the JDK is visible to your system
    5 Installing a Precompiled Release
      5.1 Running from a terminal window
    6 Installing from GitHub
      6.1 Installation using Eclipse
      6.2 Installation using the command line
    7 Loading and Running Models
      7.1 Other ways to load models
      7.2 Viewing and interacting with models
      7.3 Command line arguments
    8 Creating and Adding Models
      8.1 Model packages
      8.2 Compiling models
      8.3 Finding models in the model menu
    9 Settings and the user configuration folder
    10 Integrating external models
      10.1 Making ArtiSynth visible to the compiler
      10.2 Eclipse development
      10.3 Command line development
      10.4 Making external models visible to ArtiSynth
      10.5 Running from Eclipse
      10.6 Using the external classpath
      10.7 Setting the CLASSPATH environment variable
      10.8 Using the -cp option
    11 Installing artisynth_models
      11.1 Installing a precompiled release
      11.2 Installing from GitHub
        11.2.1 Installation using Eclipse
        11.2.2 Installation from the command line
    12 Updating ArtiSynth
      12.1 Library updates
    13 The Eclipse IDE
      13.1 Installing Eclipse
        13.1.1 Setting Eclipse to use the correct Java JDK
        13.1.2 Preventing excess resource copying
      13.2 Importing external projects
      13.3 Configuring environment variables
        13.3.1 Setting environment variables
      13.4 Command line and JVM arguments
        13.4.1 Setting command line and JVM arguments
      13.5 Adding projects to the build path
      13.6 Adding projects to the ArtiSynth launch configuration
    14 Additional Information
      14.1 Adding Directories to the System Path
      14.2 Environment variables
        14.2.1 Example environment set up for bash
        14.2.2 Example environment setup for csh or tcsh
      14.3 ArtiSynth Libraries
      14.4 The EXTCLASSPATH File
      14.5 Quick Git Summary
ArtiSynth Modeling Guide
  Preface
    How to read this guide
  Chapter 1 ArtiSynth Overview
    1.1 System structure
      1.1.1 Model components
      1.1.2 The RootModel
      1.1.3 Component path names
      1.1.4 Model advancement
      1.1.5 MechModel
    1.2 Physics simulation
    1.3 Basic packages
      1.3.1 maspack
      1.3.2 artisynth.core
      1.3.3 artisynth.demos
    1.4 Properties
      1.4.1 Querying and setting property values
      1.4.2 Property handles and paths
      1.4.3 Composite and inheritable properties
    1.5 Creating an application model
      1.5.1 Implementing the build() method
      1.5.2 Making models visible to ArtiSynth
      1.5.3 Loading and running a model
  Chapter 2 Supporting classes
    2.1 Vectors and matrices
    2.2 Rotations and transformations
    2.3 Points and Vectors
    2.4 Spatial vectors and inertias
    2.5 Meshes
      2.5.1 Mesh creation
      2.5.2 Setting normals, colors, and textures
      2.5.3 Automatic creation of normals and hard edges
      2.5.4 Vertex and feature coloring
      2.5.5 Reading and writing mesh files
      2.5.6 Reading and writing normal and texture information
      2.5.7 Constructive solid geometry
    2.6 Reading source relative files
    2.7 Reading and caching remote files
  Chapter 3 Mechanical Models I
    3.1 Springs and particles
      3.1.1 Axial springs and materials
      3.1.2 Example: a simple particle-spring model
      3.1.3 Dynamic, parametric, and attached components
      3.1.4 Custom axial materials
      3.1.5 Damping parameters
    3.2 Rigid bodies
      3.2.1 Frame markers
      3.2.2 Example: a simple rigid body-spring model
      3.2.3 Creating rigid bodies
      3.2.4 Pose and velocity
      3.2.5 Inertia and the surface mesh
      3.2.6 Damping parameters
      3.2.7 Rendering rigid bodies
      3.2.8 Multiple meshes
      3.2.9 Example: a composite rigid body
    3.3 Joints and connectors
      3.3.1 Joints and coordinate frames
      3.3.2 Joint coordinates, constraints, and errors
      3.3.3 Creating Joints
      3.3.4 Working with coordinates
      3.3.5 Example: a simple hinge joint
      3.3.6 Constraint forces
      3.3.7 Compliance and regularization
      3.3.8 Example: an overconstrained linkage
      3.3.9 Rendering joints
    3.4 Joint components
      3.4.1 Hinge Joint
      3.4.2 Slider Joint
      3.4.3 Cylindrical Joint
      3.4.4 Slotted Hinge Joint
      3.4.5 Universal Joint
      3.4.6 Skewed Universal Joint
      3.4.7 Gimbal Joint
      3.4.8 Spherical Joint
      3.4.9 Planar Joint
      3.4.10 Planar Translation Joint
      3.4.11 Solid Joint
      3.4.12 Planar Connector
      3.4.13 Segmented Planar Connector
      3.4.14 Legacy Joints
    3.5 Frame springs
      3.5.1 Frame spring coordinate frames
      3.5.2 Frame materials
      3.5.3 Creating frame springs
      3.5.4 Example: two bodies connected by a frame spring
    3.6 Attachments
      3.6.1 Point attachments
      3.6.2 Example: model with particle attachments
      3.6.3 Frame attachments
      3.6.4 Example: model with frame attachments
  Chapter 4 Mechanical Models II
    4.1 Simulation control properties
      4.1.1 maxStepSize
      4.1.2 integrator
      4.1.3 stabilization
    4.2 Units
      4.2.1 Scaling units
    4.3 Render properties
      4.3.1 Render property taxonomy
      4.3.2 Setting render properties
      4.3.3 Texture mapping
    4.4 Point-to-point muscles
      4.4.1 Muscle materials
      4.4.2 Example: Muscle attached to a rigid body
    4.5 Distance Grids and Components
    4.6 Transforming geometry
      4.6.1 Nonlinear transformations
      4.6.2 Example: the FemModelDeformer class
      4.6.3 Implementation and behavior
      4.6.4 Use in model registration
    4.7 General component arrangements
      4.7.1 Container components
      4.7.2 Example: a net formed from balls and springs
      4.7.3 Adding containers to other models
    4.8 Custom Joints
      4.8.1 Joint constraints
      4.8.2 Unilateral constraint engagement
      4.8.3 Implementing a custom joint
      4.8.4 Implementing a custom coupling
      4.8.5 Example: a simple custom joint
  Chapter 5 Simulation Control
    5.1 Control Panels
      5.1.1 General principles
      5.1.2 Example: Creating a simple control panel
    5.2 Custom properties
      5.2.1 Adding properties to a component
      5.2.2 Example: a visibility property
    5.3 Controllers and monitors
      5.3.1 Implementation
      5.3.2 Example: A controller to move a point
    5.4 Probes
      5.4.1 Numeric probe structure
      5.4.2 Creating probes in code
      5.4.3 Example: probes connected to SimpleMuscle
      5.4.4 Data file format
      5.4.5 Adding probe data in-line
      5.4.6 Numeric monitor probes
      5.4.7 Numeric control probes
    5.5 Application-Defined Menu Items
  Chapter 6 Finite Element Models
    6.1 Overview
      6.1.1 FemModel3d
      6.1.2 Component Structure
        6.1.2.1 Nodes
        6.1.2.2 Elements
        6.1.2.3 Shell elements
        6.1.2.4 Meshes
      6.1.3 Materials
      6.1.4 Boundary conditions
    6.2 FEM model creation
      6.2.1 Factory methods
      6.2.2 Loading external FEM meshes
      6.2.3 Generating from surfaces
      6.2.4 Building elements in code
      6.2.5 Example: a simple beam model
    6.3 FEM Geometry
      6.3.1 Surface meshes
      6.3.2 Embedding geometry within an FEM
      6.3.3 Example: a beam with an embedded sphere
    6.4 Connecting FEM models to other components
      6.4.1 Connecting nodes to rigid bodies or particles
      6.4.2 Example: connecting a beam to a block
      6.4.3 Connecting nodes directly to elements
      6.4.4 Example: connecting two FEMs together
      6.4.5 Finding which nodes to attach
      6.4.6 Example: two bodies connected by an FEM ?spring?
      6.4.7 Nodal-based attachments
      6.4.8 Example: element vs. nodal-based attachments
    6.5 FEM markers
      6.5.1 Example: attaching an FEM beam to a muscle
    6.6 Frame attachments
      6.6.1 Example: attaching frames to an FEM beam
      6.6.2 Adding joints to FEM models
      6.6.3 Example: two FEM beams connected by a joint
    6.7 Incompressibility
      6.7.1 Volume regions and locking
      6.7.2 Hard incompressibility
      6.7.3 Soft incompressibility
      6.7.4 Incompressibility and linear materials
      6.7.5 Using incompressibility in practice
    6.8 Varying and augmenting material behaviors
      6.8.1 Example: FEM sheet with a stiff spine
    6.9 Muscle activated FEM models
      6.9.1 FemMuscleModel
        6.9.1.1 Bundles
        6.9.1.2 Exciters
      6.9.2 Fibre-based muscles
      6.9.3 Material-based muscles
      6.9.4 Example: comparison with two beam examples
    6.10 Fields
      6.10.1 Grid fields
      6.10.2 FEM fields
        6.10.2.1 Nodal fields
        6.10.2.2 Element fields
        6.10.2.3 Sub-element fields
      6.10.3 Mesh fields
        6.10.3.1 Vertex fields
        6.10.3.2 Face fields
      6.10.4 Fields for VectorNd, MatrixNd and Vector3d
      6.10.5 Binding material properties
      6.10.6 Example: FEM with variable stiffness
      6.10.7 Example: specifying FEM muscle directions
    6.11 Rendering and Visualizations
      6.11.1 Example: stress and strain plotting
  Chapter 7 Contact and Collision
    7.1 Enabling collisions
      7.1.1 Collisions between specific bodies
      7.1.2 Default collisions between groups
      7.1.3 Example: collision with a plane
      7.1.4 Collisions for FEM models
      7.1.5 Example: FEM models and rigid bodies
    7.2 Collision behaviors and collidability
      7.2.1 Collision behaviors
      7.2.2 Collidability
    7.3 Collision meshes and compound collidables
      7.3.1 Example: redefining a rigid body collision mesh
      7.3.2 Compound collidables and self-collision
      7.3.3 Example: FEM model with self-collision
      7.3.4 Collidable bodies
      7.3.5 Nested MechModels
    7.4 Implementation
      7.4.1 Contact methods
        7.4.1.1 Contour region
        7.4.1.2 Vertex penetration
        7.4.1.3 Setting the contact method
      7.4.2 Collider types
        7.4.2.1 Collision meshes and signed distance grids
    7.5 Contact rendering
      7.5.1 Example: rendering normals and contours
      7.5.2 Example: rendering a color map
      7.5.3 Example: rendering contact pressures
    7.6 Overconstrained contact
      7.6.1 Constraint reduction
    7.7 Contact regularization
      7.7.1 Compliant contact
      7.7.2 Contact force behaviors
        7.7.2.1 Computing forces based on pressure
      7.7.3 Elastic foundation contact
      7.7.4 Example: elastic foundation contact of a ball in a bowl
      7.7.5 Example: binding EFC properties to fields
    7.8 Monitoring collisions
      7.8.1 Collision responses
      7.8.2 Available information
      7.8.3 Example: monitoring contact forces
    7.9 Tips and limitations
      7.9.1 Contact jitter
      7.9.2 Passing through objects
      7.9.3 Stray vertices
      7.9.4 Coulomb friction and stability
  Chapter 8 Muscle Wrapping and Via Points
    8.1 Via Points
      8.1.1 Example: a muscle with via points
    8.2 Obstacle Wrapping
      8.2.1 Example: wrapping around a cylinder
    8.3 General Surfaces and Distance Grids
      8.3.1 Example: wrapping around a bone
    8.4 Initializing the Wrap Path
      8.4.1 Example: wrapping around a torus
    8.5 Alternate Wrapping Surfaces
      8.5.1 Example: wrapping for a finger joint
    8.6 Tuning the Wrapping Behavior
  Chapter 9 Skinning
    9.1 Implementation
    9.2 Creating a skin mesh
      9.2.1 Example: skinning over rigid bodies
    9.3 Computing weights
      9.3.1 Setting weights explicitly
    9.4 Markers and point attachments
      9.4.1 Markers
      9.4.2 Point attachments
      9.4.3 Example: skinning rigid bodies and FEM models
      9.4.4 Mesh-based markers and attachments
    9.5 Resolution and Limitations
    9.6 Collisions
      9.6.1 Example: collision with a cylinder
    9.7 Application to muscle wrapping
      9.7.1 Example: wrapping for a finger joint
  Chapter 10 DICOM Images
    10.1 The DICOM file format
    10.2 The DICOM classes
      10.2.1 DicomElement
      10.2.2 DicomHeader
      10.2.3 DicomPixelBuffer
      10.2.4 DicomSlice
      10.2.5 DicomImage
    10.3 Loading a DicomImage
      10.3.1 Time-dependent images
      10.3.2 Image formats
    10.4 The DicomViewer
    10.5 DICOM example
  Appendix A Mathematical Review
    A.1 Rotation transforms
    A.2 Rigid transforms
    A.3 Affine transforms
    A.4 Rotational velocity
    A.5 Spatial velocities and forces
    A.6 Spatial inertia
  Bibliography
  Preface
    How to read this guide
  Chapter 1 ArtiSynth Overview
    1.1 System structure
      1.1.1 Model components
      1.1.2 The RootModel
      1.1.3 Component path names
      1.1.4 Model advancement
      1.1.5 MechModel
    1.2 Physics simulation
    1.3 Basic packages
      1.3.1 maspack
      1.3.2 artisynth.core
      1.3.3 artisynth.demos
    1.4 Properties
      1.4.1 Querying and setting property values
      1.4.2 Property handles and paths
      1.4.3 Composite and inheritable properties
    1.5 Creating an application model
      1.5.1 Implementing the build() method
      1.5.2 Making models visible to ArtiSynth
      1.5.3 Loading and running a model
  Chapter 2 Supporting classes
    2.1 Vectors and matrices
    2.2 Rotations and transformations
    2.3 Points and Vectors
    2.4 Spatial vectors and inertias
    2.5 Meshes
      2.5.1 Mesh creation
      2.5.2 Setting normals, colors, and textures
      2.5.3 Automatic creation of normals and hard edges
      2.5.4 Vertex and feature coloring
      2.5.5 Reading and writing mesh files
      2.5.6 Reading and writing normal and texture information
      2.5.7 Constructive solid geometry
    2.6 Reading source relative files
    2.7 Reading and caching remote files
  Chapter 3 Mechanical Models I
    3.1 Springs and particles
      3.1.1 Axial springs and materials
      3.1.2 Example: a simple particle-spring model
      3.1.3 Dynamic, parametric, and attached components
      3.1.4 Custom axial materials
      3.1.5 Damping parameters
    3.2 Rigid bodies
      3.2.1 Frame markers
      3.2.2 Example: a simple rigid body-spring model
      3.2.3 Creating rigid bodies
      3.2.4 Pose and velocity
      3.2.5 Inertia and the surface mesh
      3.2.6 Damping parameters
      3.2.7 Rendering rigid bodies
      3.2.8 Multiple meshes
      3.2.9 Example: a composite rigid body
    3.3 Joints and connectors
      3.3.1 Joints and coordinate frames
      3.3.2 Joint coordinates, constraints, and errors
      3.3.3 Creating Joints
      3.3.4 Working with coordinates
      3.3.5 Example: a simple hinge joint
      3.3.6 Constraint forces
      3.3.7 Compliance and regularization
      3.3.8 Example: an overconstrained linkage
      3.3.9 Rendering joints
    3.4 Joint components
      3.4.1 Hinge Joint
      3.4.2 Slider Joint
      3.4.3 Cylindrical Joint
      3.4.4 Slotted Hinge Joint
      3.4.5 Universal Joint
      3.4.6 Skewed Universal Joint
      3.4.7 Gimbal Joint
      3.4.8 Spherical Joint
      3.4.9 Planar Joint
      3.4.10 Planar Translation Joint
      3.4.11 Solid Joint
      3.4.12 Planar Connector
      3.4.13 Segmented Planar Connector
      3.4.14 Legacy Joints
    3.5 Frame springs
      3.5.1 Frame spring coordinate frames
      3.5.2 Frame materials
      3.5.3 Creating frame springs
      3.5.4 Example: two bodies connected by a frame spring
    3.6 Attachments
      3.6.1 Point attachments
      3.6.2 Example: model with particle attachments
      3.6.3 Frame attachments
      3.6.4 Example: model with frame attachments
  Chapter 4 Mechanical Models II
    4.1 Simulation control properties
      4.1.1 maxStepSize
      4.1.2 integrator
      4.1.3 stabilization
    4.2 Units
      4.2.1 Scaling units
    4.3 Render properties
      4.3.1 Render property taxonomy
      4.3.2 Setting render properties
      4.3.3 Texture mapping
    4.4 Point-to-point muscles
      4.4.1 Muscle materials
      4.4.2 Example: Muscle attached to a rigid body
    4.5 Distance Grids and Components
    4.6 Transforming geometry
      4.6.1 Nonlinear transformations
      4.6.2 Example: the FemModelDeformer class
      4.6.3 Implementation and behavior
      4.6.4 Use in model registration
    4.7 General component arrangements
      4.7.1 Container components
      4.7.2 Example: a net formed from balls and springs
      4.7.3 Adding containers to other models
    4.8 Custom Joints
      4.8.1 Joint constraints
      4.8.2 Unilateral constraint engagement
      4.8.3 Implementing a custom joint
      4.8.4 Implementing a custom coupling
      4.8.5 Example: a simple custom joint
  Chapter 5 Simulation Control
    5.1 Control Panels
      5.1.1 General principles
      5.1.2 Example: Creating a simple control panel
    5.2 Custom properties
      5.2.1 Adding properties to a component
      5.2.2 Example: a visibility property
    5.3 Controllers and monitors
      5.3.1 Implementation
      5.3.2 Example: A controller to move a point
    5.4 Probes
      5.4.1 Numeric probe structure
      5.4.2 Creating probes in code
      5.4.3 Example: probes connected to SimpleMuscle
      5.4.4 Data file format
      5.4.5 Adding probe data in-line
      5.4.6 Numeric monitor probes
      5.4.7 Numeric control probes
    5.5 Application-Defined Menu Items
  Chapter 6 Finite Element Models
    6.1 Overview
      6.1.1 FemModel3d
      6.1.2 Component Structure
        6.1.2.1 Nodes
        6.1.2.2 Elements
        6.1.2.3 Shell elements
        6.1.2.4 Meshes
      6.1.3 Materials
      6.1.4 Boundary conditions
    6.2 FEM model creation
      6.2.1 Factory methods
      6.2.2 Loading external FEM meshes
      6.2.3 Generating from surfaces
      6.2.4 Building elements in code
      6.2.5 Example: a simple beam model
    6.3 FEM Geometry
      6.3.1 Surface meshes
      6.3.2 Embedding geometry within an FEM
      6.3.3 Example: a beam with an embedded sphere
    6.4 Connecting FEM models to other components
      6.4.1 Connecting nodes to rigid bodies or particles
      6.4.2 Example: connecting a beam to a block
      6.4.3 Connecting nodes directly to elements
      6.4.4 Example: connecting two FEMs together
      6.4.5 Finding which nodes to attach
      6.4.6 Example: two bodies connected by an FEM ?spring?
      6.4.7 Nodal-based attachments
      6.4.8 Example: element vs. nodal-based attachments
    6.5 FEM markers
      6.5.1 Example: attaching an FEM beam to a muscle
    6.6 Frame attachments
      6.6.1 Example: attaching frames to an FEM beam
      6.6.2 Adding joints to FEM models
      6.6.3 Example: two FEM beams connected by a joint
    6.7 Incompressibility
      6.7.1 Volume regions and locking
      6.7.2 Hard incompressibility
      6.7.3 Soft incompressibility
      6.7.4 Incompressibility and linear materials
      6.7.5 Using incompressibility in practice
    6.8 Varying and augmenting material behaviors
      6.8.1 Example: FEM sheet with a stiff spine
    6.9 Muscle activated FEM models
      6.9.1 FemMuscleModel
        6.9.1.1 Bundles
        6.9.1.2 Exciters
      6.9.2 Fibre-based muscles
      6.9.3 Material-based muscles
      6.9.4 Example: comparison with two beam examples
    6.10 Fields
      6.10.1 Grid fields
      6.10.2 FEM fields
        6.10.2.1 Nodal fields
        6.10.2.2 Element fields
        6.10.2.3 Sub-element fields
      6.10.3 Mesh fields
        6.10.3.1 Vertex fields
        6.10.3.2 Face fields
      6.10.4 Fields for VectorNd, MatrixNd and Vector3d
      6.10.5 Binding material properties
      6.10.6 Example: FEM with variable stiffness
      6.10.7 Example: specifying FEM muscle directions
    6.11 Rendering and Visualizations
      6.11.1 Example: stress and strain plotting
  Chapter 7 Contact and Collision
    7.1 Enabling collisions
      7.1.1 Collisions between specific bodies
      7.1.2 Default collisions between groups
      7.1.3 Example: collision with a plane
      7.1.4 Collisions for FEM models
      7.1.5 Example: FEM models and rigid bodies
    7.2 Collision behaviors and collidability
      7.2.1 Collision behaviors
      7.2.2 Collidability
    7.3 Collision meshes and compound collidables
      7.3.1 Example: redefining a rigid body collision mesh
      7.3.2 Compound collidables and self-collision
      7.3.3 Example: FEM model with self-collision
      7.3.4 Collidable bodies
      7.3.5 Nested MechModels
    7.4 Implementation
      7.4.1 Contact methods
        7.4.1.1 Contour region
        7.4.1.2 Vertex penetration
        7.4.1.3 Setting the contact method
      7.4.2 Collider types
        7.4.2.1 Collision meshes and signed distance grids
    7.5 Contact rendering
      7.5.1 Example: rendering normals and contours
      7.5.2 Example: rendering a color map
      7.5.3 Example: rendering contact pressures
    7.6 Overconstrained contact
      7.6.1 Constraint reduction
    7.7 Contact regularization
      7.7.1 Compliant contact
      7.7.2 Contact force behaviors
        7.7.2.1 Computing forces based on pressure
      7.7.3 Elastic foundation contact
      7.7.4 Example: elastic foundation contact of a ball in a bowl
      7.7.5 Example: binding EFC properties to fields
    7.8 Monitoring collisions
      7.8.1 Collision responses
      7.8.2 Available information
      7.8.3 Example: monitoring contact forces
    7.9 Tips and limitations
      7.9.1 Contact jitter
      7.9.2 Passing through objects
      7.9.3 Stray vertices
      7.9.4 Coulomb friction and stability
  Chapter 8 Muscle Wrapping and Via Points
    8.1 Via Points
      8.1.1 Example: a muscle with via points
    8.2 Obstacle Wrapping
      8.2.1 Example: wrapping around a cylinder
    8.3 General Surfaces and Distance Grids
      8.3.1 Example: wrapping around a bone
    8.4 Initializing the Wrap Path
      8.4.1 Example: wrapping around a torus
    8.5 Alternate Wrapping Surfaces
      8.5.1 Example: wrapping for a finger joint
    8.6 Tuning the Wrapping Behavior
  Chapter 9 Skinning
    9.1 Implementation
    9.2 Creating a skin mesh
      9.2.1 Example: skinning over rigid bodies
    9.3 Computing weights
      9.3.1 Setting weights explicitly
    9.4 Markers and point attachments
      9.4.1 Markers
      9.4.2 Point attachments
      9.4.3 Example: skinning rigid bodies and FEM models
      9.4.4 Mesh-based markers and attachments
    9.5 Resolution and Limitations
    9.6 Collisions
      9.6.1 Example: collision with a cylinder
    9.7 Application to muscle wrapping
      9.7.1 Example: wrapping for a finger joint
  Chapter 10 DICOM Images
    10.1 The DICOM file format
    10.2 The DICOM classes
      10.2.1 DicomElement
      10.2.2 DicomHeader
      10.2.3 DicomPixelBuffer
      10.2.4 DicomSlice
      10.2.5 DicomImage
    10.3 Loading a DicomImage
      10.3.1 Time-dependent images
      10.3.2 Image formats
    10.4 The DicomViewer
    10.5 DICOM example
  Appendix A Mathematical Review
    A.1 Rotation transforms
    A.2 Rigid transforms
    A.3 Affine transforms
    A.4 Rotational velocity
    A.5 Spatial velocities and forces
    A.6 Spatial inertia
  Bibliography
ArtiSynth User Interface Guide
  1 Introduction
    1.1 User configuration folder
  2 Loading, Simulating and Saving Models
    2.1 Loading from the model menu
    2.2 Loading directly by class
    2.3 Loading from a file
    2.4 Loading recent models
    2.5 Setting a startup model
      2.5.1 Specifying models from the command line
    2.6 Simulating a model
    2.7 Other toolbar controls
    2.8 Saving a model
    2.9 Setting the external classpath
    2.10 The ArtiSynth working folder
  3 The Viewer
    3.1 Viewer Toolbar
    3.2 Viewpoint control
    3.3 Adding additional viewers
    3.4 World coordinate axes
    3.5 Orthographic vs. perspective projection
    3.6 Viewer grid
      3.6.1 Grid units
      3.6.2 Axis labeling
      3.6.3 Grid properties
    3.7 Clipping planes
      3.7.1 Adding and removing
      3.7.2 Moving
      3.7.3 Offsets
      3.7.4 Enabling/disabling
      3.7.5 Slicing mode
      3.7.6 Other features
    3.8 Indicating 3D positions with the mouse
    3.9 Viewer properties
      3.9.1 Viewer-specific properties
    3.10 Mouse Bindings
    3.11 Keyboard shortcuts
  4 Component Navigation and Selection
    4.1 The component hierarchy
      4.1.1 Component names and numbers
      4.1.2 Component path names
    4.2 Navigation panel selection
      4.2.1 Large numbers of nameless components
    4.3 Viewer selection
      4.3.1 Click and box selection
      4.3.2 Elliptic selection
      4.3.3 Selection filtering
    4.4 Selection display
    4.5 Selecting parent and ancestor components
    4.6 Highlighting selected components
  5 Model Manipulation
    5.1 Dragger fixtures
    5.2 Transformer tools
      5.2.1 Constrained transformation
      5.2.2 Transformer repositioning
      5.2.3 Changing the transformer base frame
    5.3 Pull manipulation
    5.4 Marker tool
  6 Editing Properties
    6.1 Property panels
      6.1.1 Inheritable properties
    6.2 Render properties
      6.2.1 Render property settings
  7 The Timeline
    7.1 Probes and waypoints
    7.2 Basic timeline structure
      7.2.1 Play controls
      7.2.2 Tracks
    7.3 Viewing and setting waypoints
      7.3.1 Waypoints
      7.3.2 Breakpoints
      7.3.3 Saving and loading
    7.4 Tracks and probes
      7.4.1 Creating, moving, and deleting tracks
      7.4.2 Muting tracks
      7.4.3 Expanding tracks
      7.4.4 Grouping tracks
    7.5 Numeric probe displays
      7.5.1 Setting the range and display properties
      7.5.2 Visibility control
      7.5.3 Editing and scaling data
      7.5.4 Interpolation control
      7.5.5 Large displays
      7.5.6 Cloning displays and exporting plots
  8 Saving and Loading Probes
    8.1 Saving and loading probe data
    8.2 Exporting numeric probe data
    8.3 Saving and loading all probes
  9 Adding and Editing Numeric Probes
    9.1 Adding output probes
      9.1.1 Creating a simple probe
      9.1.2 General output probes
      9.1.3 Using the probe editor
    9.2 Adding input probes
      9.2.1 Creating a simple probe
      9.2.2 General input probes
      9.2.3 Using the probe editor
    9.3 Setting probe properties
  10 Point Tracing
  11 Settings and Preferences
    11.1 Settings
      11.1.1 Interaction
      11.1.2 Simulation
    11.2 Preferences
    11.3 Layout preferences
  12 Jython Interaction and Scripting
    12.1 Querying ArtiSynth structures and models
    12.2 Object creation and importing classes
    12.3 Running simulations and scripting
    12.4 Using the script menu
    12.5 Selecting a script file
    12.6 Specifying scripts on the command line
    12.7 Built-in functions
  13 Customizing the Model and Script Menus
    13.1 Model menu editor
    13.2 Script menu editor
    13.3 Menu entry types
      13.3.1 Model
      13.3.2 Package
      13.3.3 Demo file
      13.3.4 Script
      13.3.5 Script folder
      13.3.6 Submenu
      13.3.7 Label
      13.3.8 Separator
    13.4 Command line options
    13.5 Demo file text format
    13.6 XML Menu Format
      13.6.1 The root elements
      13.6.2 Model element
      13.6.3 Package element
      13.6.4 DemoFile element
      13.6.5 Script element
      13.6.6 ScriptFolder element
      13.6.7 Submenu element
      13.6.8 Label element
      13.6.9 Separator element
      13.6.10 Hiding elements
  14 Making Movies
    14.1 Recorder tab
      14.1.1 Region to capture
      14.1.2 Record options
      14.1.3 Other options
    14.2 Encoder tab
      14.2.1 Encoder options
      14.2.2 Customizing the encoder command
    14.3 Output size options
    14.4 Advanced tab
    14.5 Saving movie preferences
  15 Control Panels
    15.1 Creating control panels
      15.1.1 Composite property widgets
      15.1.2 Widgets for subproperties
    15.2 Editing control panels
    15.3 Live updating
  16 Component Editing
    16.1 Generic edit operations
      16.1.1 Deletion
      16.1.2 Duplication
      16.1.3 Undo
    16.2 Editing panels
    16.3 Specifying position, orientation, and scaling
    16.4 Editing MechModels
      16.4.1 Adding finite element models
      16.4.2 Adding rigid bodies
      16.4.3 Adding frame markers
      16.4.4 Adding particles
      16.4.5 Adding axial springs and muscles
      16.4.6 Adding rigid body connectors
      16.4.7 Attaching particles to particles
      16.4.8 Attaching particles to rigid bodies
      16.4.9 Collision handling
    16.5 Editing rigid bodies
      16.5.1 Geometry and inertia
    16.6 Editing FEM models
      16.6.1 Adding FEM markers
      16.6.2 Adding muscle bundles
    16.7 Editing muscle bundles
      16.7.1 Adding fibres
      16.7.2 Adding element references
      16.7.3 Automatically setting elements and directions
      16.7.4 Removing fibres and element references
    16.8 Editing muscle exciters
    16.9 Editing root models
  1 Introduction
    1.1 User configuration folder
  2 Loading, Simulating and Saving Models
    2.1 Loading from the model menu
    2.2 Loading directly by class
    2.3 Loading from a file
    2.4 Loading recent models
    2.5 Setting a startup model
      2.5.1 Specifying models from the command line
    2.6 Simulating a model
    2.7 Other toolbar controls
    2.8 Saving a model
    2.9 Setting the external classpath
    2.10 The ArtiSynth working folder
  3 The Viewer
    3.1 Viewer Toolbar
    3.2 Viewpoint control
    3.3 Adding additional viewers
    3.4 World coordinate axes
    3.5 Orthographic vs. perspective projection
    3.6 Viewer grid
      3.6.1 Grid units
      3.6.2 Axis labeling
      3.6.3 Grid properties
    3.7 Clipping planes
      3.7.1 Adding and removing
      3.7.2 Moving
      3.7.3 Offsets
      3.7.4 Enabling/disabling
      3.7.5 Slicing mode
      3.7.6 Other features
    3.8 Indicating 3D positions with the mouse
    3.9 Viewer properties
      3.9.1 Viewer-specific properties
    3.10 Mouse Bindings
    3.11 Keyboard shortcuts
  4 Component Navigation and Selection
    4.1 The component hierarchy
      4.1.1 Component names and numbers
      4.1.2 Component path names
    4.2 Navigation panel selection
      4.2.1 Large numbers of nameless components
    4.3 Viewer selection
      4.3.1 Click and box selection
      4.3.2 Elliptic selection
      4.3.3 Selection filtering
    4.4 Selection display
    4.5 Selecting parent and ancestor components
    4.6 Highlighting selected components
  5 Model Manipulation
    5.1 Dragger fixtures
    5.2 Transformer tools
      5.2.1 Constrained transformation
      5.2.2 Transformer repositioning
      5.2.3 Changing the transformer base frame
    5.3 Pull manipulation
    5.4 Marker tool
  6 Editing Properties
    6.1 Property panels
      6.1.1 Inheritable properties
    6.2 Render properties
      6.2.1 Render property settings
  7 The Timeline
    7.1 Probes and waypoints
    7.2 Basic timeline structure
      7.2.1 Play controls
      7.2.2 Tracks
    7.3 Viewing and setting waypoints
      7.3.1 Waypoints
      7.3.2 Breakpoints
      7.3.3 Saving and loading
    7.4 Tracks and probes
      7.4.1 Creating, moving, and deleting tracks
      7.4.2 Muting tracks
      7.4.3 Expanding tracks
      7.4.4 Grouping tracks
    7.5 Numeric probe displays
      7.5.1 Setting the range and display properties
      7.5.2 Visibility control
      7.5.3 Editing and scaling data
      7.5.4 Interpolation control
      7.5.5 Large displays
      7.5.6 Cloning displays and exporting plots
  8 Saving and Loading Probes
    8.1 Saving and loading probe data
    8.2 Exporting numeric probe data
    8.3 Saving and loading all probes
  9 Adding and Editing Numeric Probes
    9.1 Adding output probes
      9.1.1 Creating a simple probe
      9.1.2 General output probes
      9.1.3 Using the probe editor
    9.2 Adding input probes
      9.2.1 Creating a simple probe
      9.2.2 General input probes
      9.2.3 Using the probe editor
    9.3 Setting probe properties
  10 Point Tracing
  11 Settings and Preferences
    11.1 Settings
      11.1.1 Interaction
      11.1.2 Simulation
    11.2 Preferences
    11.3 Layout preferences
  12 Jython Interaction and Scripting
    12.1 Querying ArtiSynth structures and models
    12.2 Object creation and importing classes
    12.3 Running simulations and scripting
    12.4 Using the script menu
    12.5 Selecting a script file
    12.6 Specifying scripts on the command line
    12.7 Built-in functions
  13 Customizing the Model and Script Menus
    13.1 Model menu editor
    13.2 Script menu editor
    13.3 Menu entry types
      13.3.1 Model
      13.3.2 Package
      13.3.3 Demo file
      13.3.4 Script
      13.3.5 Script folder
      13.3.6 Submenu
      13.3.7 Label
      13.3.8 Separator
    13.4 Command line options
    13.5 Demo file text format
    13.6 XML Menu Format
      13.6.1 The root elements
      13.6.2 Model element
      13.6.3 Package element
      13.6.4 DemoFile element
      13.6.5 Script element
      13.6.6 ScriptFolder element
      13.6.7 Submenu element
      13.6.8 Label element
      13.6.9 Separator element
      13.6.10 Hiding elements
  14 Making Movies
    14.1 Recorder tab
      14.1.1 Region to capture
      14.1.2 Record options
      14.1.3 Other options
    14.2 Encoder tab
      14.2.1 Encoder options
      14.2.2 Customizing the encoder command
    14.3 Output size options
    14.4 Advanced tab
    14.5 Saving movie preferences
  15 Control Panels
    15.1 Creating control panels
      15.1.1 Composite property widgets
      15.1.2 Widgets for subproperties
    15.2 Editing control panels
    15.3 Live updating
  16 Component Editing
    16.1 Generic edit operations
      16.1.1 Deletion
      16.1.2 Duplication
      16.1.3 Undo
    16.2 Editing panels
    16.3 Specifying position, orientation, and scaling
    16.4 Editing MechModels
      16.4.1 Adding finite element models
      16.4.2 Adding rigid bodies
      16.4.3 Adding frame markers
      16.4.4 Adding particles
      16.4.5 Adding axial springs and muscles
      16.4.6 Adding rigid body connectors
      16.4.7 Attaching particles to particles
      16.4.8 Attaching particles to rigid bodies
      16.4.9 Collision handling
    16.5 Editing rigid bodies
      16.5.1 Geometry and inertia
    16.6 Editing FEM models
      16.6.1 Adding FEM markers
      16.6.2 Adding muscle bundles
    16.7 Editing muscle bundles
      16.7.1 Adding fibres
      16.7.2 Adding element references
      16.7.3 Automatically setting elements and directions
      16.7.4 Removing fibres and element references
    16.8 Editing muscle exciters
    16.9 Editing root models
Maspack Reference Manual
  Preface
  Chapter 1 Properties
    1.1 Accessing Properties
      1.1.1 Why Property Handles?
    1.2 Property Ranges
    1.3 Obtaining Property Information
    1.4 Exporting Properties from a Class
      1.4.1 Read-only properties
      1.4.2 Inheriting Properties from a superclass
    1.5 Composite Properties
    1.6 Reading and Writing to Persistent Storage
    1.7 Inheritable Properties
    1.8 Exporting Inheritable Properties
    1.9 Inheritable and Composite Properties
  Chapter 2 Rendering
    2.1 Overview
      2.1.1 Renderables and Viewers
      2.1.2 A Complete Example
    2.2 Viewers
      2.2.1 Render lists
      2.2.2 Prerendering and Rendering
      2.2.3 Viewer renderables and external render lists
      2.2.4 Coordinate frames and view point control
      2.2.5 Lights
    2.3 The Renderer Interface
      2.3.1 Drawing single points and lines
      2.3.2 Drawing single triangles
      2.3.3 Colors and associated attributes
        2.3.3.1 Highlighting
      2.3.4 Drawing using draw mode
      2.3.5 Drawing solid shapes
      2.3.6 Shading and color mixing
      2.3.7 Vertex coloring, and color mixing and interpolation
      2.3.8 Changing the model matrix
      2.3.9 Render properties and RenderProps
        2.3.9.1 Drawing points and lines as 3D solid objects
        2.3.9.2 RenderProps taxonomy
        2.3.9.3 Renderer methods that use RenderProps
      2.3.10 Screen information and 2D rendering
      2.3.11 Depth offsets
      2.3.12 Maintaining the graphics state
      2.3.13 Text rendering
    2.4 Render Objects
      2.4.1 Building a render object
      2.4.2 ?Current? attributes
      2.4.3 Maintaining consistent attributes
      2.4.4 Adding primitives in ?build? mode
      2.4.5 Modifying render objects
      2.4.6 Drawing RenderObjects
      2.4.7 Multiple primitive groups
      2.4.8 Drawing primitive subsets
    2.5 Texture mapping
      2.5.1 Texture mapping properties
      2.5.2 Texturing example using draw mode
      2.5.3 Texturing example using a render object
    2.6 Mesh Renderers
    2.7 Object Selection
      2.7.1 Implementing custom selection
      2.7.2 Selection Events
  Preface
  Chapter 1 Properties
    1.1 Accessing Properties
      1.1.1 Why Property Handles?
    1.2 Property Ranges
    1.3 Obtaining Property Information
    1.4 Exporting Properties from a Class
      1.4.1 Read-only properties
      1.4.2 Inheriting Properties from a superclass
    1.5 Composite Properties
    1.6 Reading and Writing to Persistent Storage
    1.7 Inheritable Properties
    1.8 Exporting Inheritable Properties
    1.9 Inheritable and Composite Properties
  Chapter 2 Rendering
    2.1 Overview
      2.1.1 Renderables and Viewers
      2.1.2 A Complete Example
    2.2 Viewers
      2.2.1 Render lists
      2.2.2 Prerendering and Rendering
      2.2.3 Viewer renderables and external render lists
      2.2.4 Coordinate frames and view point control
      2.2.5 Lights
    2.3 The Renderer Interface
      2.3.1 Drawing single points and lines
      2.3.2 Drawing single triangles
      2.3.3 Colors and associated attributes
        2.3.3.1 Highlighting
      2.3.4 Drawing using draw mode
      2.3.5 Drawing solid shapes
      2.3.6 Shading and color mixing
      2.3.7 Vertex coloring, and color mixing and interpolation
      2.3.8 Changing the model matrix
      2.3.9 Render properties and RenderProps
        2.3.9.1 Drawing points and lines as 3D solid objects
        2.3.9.2 RenderProps taxonomy
        2.3.9.3 Renderer methods that use RenderProps
      2.3.10 Screen information and 2D rendering
      2.3.11 Depth offsets
      2.3.12 Maintaining the graphics state
      2.3.13 Text rendering
    2.4 Render Objects
      2.4.1 Building a render object
      2.4.2 ?Current? attributes
      2.4.3 Maintaining consistent attributes
      2.4.4 Adding primitives in ?build? mode
      2.4.5 Modifying render objects
      2.4.6 Drawing RenderObjects
      2.4.7 Multiple primitive groups
      2.4.8 Drawing primitive subsets
    2.5 Texture mapping
      2.5.1 Texture mapping properties
      2.5.2 Texturing example using draw mode
      2.5.3 Texturing example using a render object
    2.6 Mesh Renderers
    2.7 Object Selection
      2.7.1 Implementing custom selection
      2.7.2 Selection Events
ArtiSynth Reference Manual
  1 Component Hierarchy
    1.1 Model Components
    1.2 Component References
    1.3 Composite Components
    1.4 CompositeComponentBase, ComponentList, and ComponentListImpl
  2 Models
    2.1 Models and State
    2.2 Model Agents
      2.2.1 Probes
      2.2.2 Controllers and monitors
      2.2.3 Models associated with agents
      2.2.4 Model agent state
    2.3 The Root Model
    2.4 Advancing Models in Time
    2.5 Adaptive Stepping
  3 Writing and Scanning Components
    3.1 Writing components
      3.1.1 Writing references
      3.1.2 Writing child components
    3.2 Scanning components
      3.2.1 Scanning references and post-scanning
      3.2.2 Scanning child components
      3.2.3 Post-scanning implementation
      3.2.4 Post-scanning property values
      3.2.5 Invoking the complete scan process
    3.3 File and token structure
    3.4 Debugging
    3.5 Summary
  1 Component Hierarchy
    1.1 Model Components
    1.2 Component References
    1.3 Composite Components
    1.4 CompositeComponentBase, ComponentList, and ComponentListImpl
  2 Models
    2.1 Models and State
    2.2 Model Agents
      2.2.1 Probes
      2.2.2 Controllers and monitors
      2.2.3 Models associated with agents
      2.2.4 Model agent state
    2.3 The Root Model
    2.4 Advancing Models in Time
    2.5 Adaptive Stepping
  3 Writing and Scanning Components
    3.1 Writing components
      3.1.1 Writing references
      3.1.2 Writing child components
    3.2 Scanning components
      3.2.1 Scanning references and post-scanning
      3.2.2 Scanning child components
      3.2.3 Post-scanning implementation
      3.2.4 Post-scanning property values
      3.2.5 Invoking the complete scan process
    3.3 File and token structure
    3.4 Debugging
    3.5 Summary
Interfacing ArtiSynth to MATLAB
  1 Introduction
  2 Requirements and configuration
  3 Starting ArtiSynth
  4 Querying ArtiSynth structures and models
  5 Scripting commands
  6 Java memory limits
  7 Setting the classpath for ArtiSynth
  8 Setting the classpath for models
  9 Connecting to an external MATLAB process
  10 Managing an external MATLAB connection from code
  11 Summary of scripting functions
  1 Introduction
  2 Requirements and configuration
  3 Starting ArtiSynth
  4 Querying ArtiSynth structures and models
  5 Scripting commands
  6 Java memory limits
  7 Setting the classpath for ArtiSynth
  8 Setting the classpath for models
  9 Connecting to an external MATLAB process
  10 Managing an external MATLAB connection from code
  11 Summary of scripting functions
Writing Documentation for ArtiSynth
  1 Introduction
  2 How Documents Are Created
    2.1 Document Source Code Organization
    2.2 Makefile commands to build documents
      2.2.1 Javadocs
      2.2.2 HTML files
      2.2.3 PDF files
      2.2.4 Other Commands
    2.3 Building single HTML files
    2.4 Building sectioned HTML files
    2.5 Building PDF files
    2.6 Installing Documents on the Webserver
  3 LaTeX usage and conventions
    3.1 LaTeXML restrictions
    3.2 Font conventions
    3.3 Code blocks
    3.4 Side blocks
    3.5 Inserting Images
    3.6 Javadoc References
      3.6.1 Class references
      3.6.2 Method references
      3.6.3 How it works
    3.7 References to other ArtiSynth documents
  4 Adding a New Document
    4.1 Creating and Updating the Makefiles
    4.2 Updating the InfoCenter
    4.3 Updating the ArtiSynth website
  5 Images, IDraw and Xfig
  6 Eclipse InfoCenter
  7 External Software Required
    7.1 Installing LaTeXML
  8 Local Customizations
    8.1 setJavadocLinks script
    8.2 fixLatexmlOutput script
  1 Introduction
  2 How Documents Are Created
    2.1 Document Source Code Organization
    2.2 Makefile commands to build documents
      2.2.1 Javadocs
      2.2.2 HTML files
      2.2.3 PDF files
      2.2.4 Other Commands
    2.3 Building single HTML files
    2.4 Building sectioned HTML files
    2.5 Building PDF files
    2.6 Installing Documents on the Webserver
  3 LaTeX usage and conventions
    3.1 LaTeXML restrictions
    3.2 Font conventions
    3.3 Code blocks
    3.4 Side blocks
    3.5 Inserting Images
    3.6 Javadoc References
      3.6.1 Class references
      3.6.2 Method references
      3.6.3 How it works
    3.7 References to other ArtiSynth documents
  4 Adding a New Document
    4.1 Creating and Updating the Makefiles
    4.2 Updating the InfoCenter
    4.3 Updating the ArtiSynth website
  5 Images, IDraw and Xfig
  6 Eclipse InfoCenter
  7 External Software Required
    7.1 Installing LaTeXML
  8 Local Customizations
    8.1 setJavadocLinks script
    8.2 fixLatexmlOutput script
ArtiSynth Coding Standard
  1 Introduction
  2 Cuddle braces and indent by 3
  3 Always used braced blocks
  4 Do not use tabs
  5 Keep line widths to 80 columns
  6 Break lines at the beginning of argument lists
  7 Break lines after assignment operators
  8 Align conditional expressions with the opening parentheses
  9 No space before empty argument lists
  1 Introduction
  2 Cuddle braces and indent by 3
  3 Always used braced blocks
  4 Do not use tabs
  5 Keep line widths to 80 columns
  6 Break lines at the beginning of argument lists
  7 Break lines after assignment operators
  8 Align conditional expressions with the opening parentheses
  9 No space before empty argument lists