Biomedical InformaticsResearch Network

Pipelines & Processing: Tools & Toolkits

David Rex, John Moreland

October 9, 2002

2nd Annual All Hands Meeting

Other Pipelines

Interactive Data/Visualization Pipelines

Data flow graph

Nodegroups

Nodes

Image viewers

Control panel

Other Pipelines - OpenDX

(4) Colorize(4) Colorize

(2) Smooth(2) Smooth(1) View(1) View

(3) Filter(3) Filter

Other Pipelines - Visualization

Utah SCIrun AVS Khoros

Kyma IRIS Explorer

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 API

Tools

API

Modules

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

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 gridManage an N-space data grid

Cache pages for lazy I/OCache pages for lazy I/O

Support specific file formatsSupport specific file formats

Manage file storageManage file storage

Bind a coord. system to dataBind a coord. system to data

Orchestrate filter executionOrchestrate filter execution

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

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

5 13 2467

51 32 4 6 7 8 9

9 8

51 32 4 6 7 8 9

Application

Data Grid Toolkit

Data Management

File Format Handling

SRB, ADR, etc.

Mesh Toolkit

Expression Tree Toolkit

Data Grid Toolkit

Paging Intelligently

Neighborhood-aware paging• Page in nearby cells in N dimensions• Support convolution filtering, rendering, marching-

cubes, ...

0 1 2 3 4

5 6 7 8 9

10 11 12 13 14

15 16 17 18 19

20 21 22 23 24

Current center cellCurrent center cell

Keep neighboring cells Keep neighboring cells paged-in as wellpaged-in as well

Application

Data Grid Toolkit

Data Management

File Format Handling

SRB, ADR, etc.

Mesh Toolkit

Expression Tree Toolkit

Data Grid Toolkit

Filter windowFilter window

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

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

Expression Tree Toolkit

ClientClient

ServerServer

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

Expression Tree Toolkit

Combining Brain Data Sets

RGB to HSIScalar to RGB

Mask by Hue

ScalarScalarCT-scanCT-scan

Color Color CryosectionCryosection

Color Color SegmentationSegmentation

Extract Hue

Composite

512 x 512 x 230512 x 512 x 230 547 x 710 x 672547 x 710 x 672 547 x 710 x 672547 x 710 x 672

Application

Data Grid Toolkit

Data Management

File Format Handling

SRB, ADR, etc.

Mesh Toolkit

Expression Tree Toolkit

Expression Tree Toolkit

Combining Brain Data Sets

Cryosection

Application

Data Grid Toolkit

Data Management

File Format Handling

SRB, ADR, etc.

Mesh Toolkit

Expression Tree Toolkit

Expression Tree Toolkit

CT

Composited

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

PointCloud VISTA

3DTexture

Data-Visualization Pipeline

Get data from disk efficiently

Get data from disk efficiently

Manage data in memory efficiently

Manage data in memory efficiently

Compute on data efficiently

Compute on data efficiently

Visualize data efficiently

Visualize data efficiently

Computation Visualization

Data

SRB ServerSRB Server

MCAT (Metadata)

MCAT (Metadata)

ADR DataCutterADR DataCutter SRB ServerSRB Server

KeLP FloorPlanKeLP FloorPlan

Data

Data Orchestration

. . .

Data-Visualization Pipeline

Get data from disk efficiently

Get data from disk efficiently

Manage data in memory efficiently

Manage data in memory efficiently

Compute on data efficiently

Compute on data efficiently

Visualize data efficiently

Visualize data efficiently

Computation Visualization

Data

Data - Vis Toolkits

Data - Vis Toolkits

Interaction ToolsInteraction Tools

VISTA RendererVISTA Renderer

Data Orchestration

. . .