1. Biomedical Informatics Research Network Pipelines & Processing: Tools & Toolkits David Rex, John Moreland October 9, 2002 2 nd Annual All Hands Meeting

2. Other Pipelines  Interactive Data/Visualization Pipelines Data flow graph Node groups Nodes Image viewers Control panel

3. Other Pipelines - OpenDX (4) Colorize (2) Smooth (1) View (3) Filter

4. Other Pipelines - Visualization Utah SCIrunAVS Khoros KymaIRIS Explorer

5. Scalable Data/Visualization Toolkits  Data flow/pipelining needs good user interface tools Server-side/batch pipelines (eg: LONI Pipeline) Client-side/interactive pipelines (eg: OpenDX, AVS, etc)  Pipelines need command-line tools and/or plug-in modules  Tools and modules will need reusable toolkits/APIs to support common functionality Reusable Components API Tools API Modules

6. Motivation CT Cryosection Classification  Support analysis, filtering, and compositing Larger-than-core (and swap) data sets Multi-modal and time-varying data Multiple data sets simultaneously  And... Do efficient data movement Execute well on parallel architectures Integrate easily w/existing applications & toolkits  Support BIRN project applications

7. Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit Layered Toolkit Architecture Manage an N-space data grid Cache pages for lazy I/O Support specific file formats Manage file storage Bind a coord. system to data Orchestrate filter execution

8. Managing Data Grids  Manage a paged data grid (array-like) An N-dimensional grid of cells Spatial data & time-series Arbitrary cell data content  Handle larger-than-core data Transparently pages data in/out Support from ADR & DataCutter Compressed data (disk & memory) Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit Data Grid Toolkit

9.  Random access (slow) Get/set cells in any order  Structured access (faster) Get/set cells in a pre-defined order  Data-order access (fastest) Get/set cells in the data’s storage order Pre-fetching Intelligently 5132467 513246789 98 513246789 Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit Data Grid Toolkit

10. Paging Intelligently  Neighborhood-aware paging Page in nearby cells in N dimensions Support convolution filtering, rendering, marching-cubes,... 01234 56789 1011121314 1516171819 2021222324 Current center cell Keep neighboring cells paged-in as well Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit Data Grid Toolkit Filter window

11. Using Coordinate Systems  Bind a coordinate system to a data grid Euclidean, cylindrical, spherical, time-series,... Uniform, structured, unstructured  Handle coordinate system-based operations Resampling with interpolation Lazy-evaluation  Multiple file format handlers Application Data Grid Toolkit Data Management File Format Handling SRB,ADR, etc. Mesh Toolkit Expression Tree Toolkit Mesh Toolkit

12. Operating on Data  Define an expression tree for data operations Leaf nodes are data sets, functions,... Interior nodes are composite, filter,... Transforms align overlapping data sets  Execute it to generate samples Client defines the expression Server on big iron executes it Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit Client Server

13. Operating on Expressions  Expressions can be optimized Re-order operators Similar to optimizing compilers & databases  Sample order can be optimized Re-order data accesses for better cache efficiency  Data can be staged & intermediate results cached Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit

14. Combining Brain Data Sets RGB to HSI Scalar to RGB Mask by Hue Scalar CT-scan Color Cryosection Color Segmentation Extract Hue Composite 512 x 512 x 230 547 x 710 x 672 Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit

15. Combining Brain Data Sets Cryosection Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit CT Composited

16. And more toolkits...  Interactive imaging with... Mitsubishi VolumePro cards Point clouds & 3D texture mapping with graphics pipelines  High-quality imaging with VISTA... Application Data Grid Toolkit Data Management File Format Handling SRB, ADR, etc. Mesh Toolkit Expression Tree Toolkit Other Toolkits VolumePro Point Cloud VISTA 3D Texture

17. Data-Visualization Pipeline Get data from disk efficiently Manage data in memory efficiently Compute on data efficiently Visualize data efficiently ComputationVisualization Data SRB Server MCAT (Metadata) ADR DataCutter SRB Server KeLP FloorPlan Data Data Orchestration...

18. Data-Visualization Pipeline Get data from disk efficiently Manage data in memory efficiently Compute on data efficiently Visualize data efficiently ComputationVisualization Data Data - Vis Toolkits Interaction Tools VISTA Renderer Data Orchestration...