GIS-based visualization and map server efforts in

support of marine fisheries and ecosystem management

Tiffany C. Vance (AFSC) and Christopher Moore (PMEL)

Nazila Merati PMELJason Fabritz OMAOHal Mofjeld PMEL

VRML based visualizations for the Cordell Bank NMS

Using ArcIMS map servers for intra-layer calculations

Java/Java3D and ArcGIS Engine as a framework for a “scientific GIS”

Introduction Visualizations of spatially complicated

datasets are used to enable scientists to understand complex physical and biological processes.

These geo-visualizations are also becoming a way to disseminate the data as a coherent package.

Rather than distributing discrete datasets, • a project can disseminate a view of the data • the recipient has the ability to move through the

data• can add and remove layers • can query to datasets at specific three-

dimensional locations.

VRML based visualizations for the Cordell Bank NMS

Using ArcIMS map servers for intra-layer calculations

Java/Java3D and ArcGIS Engine as a framework for a “scientific GIS”

Project goals

To create interactive visualizations of GIS data for the Sanctuary

To enable viewers to see the Sanctuary as a volume, not a flat map

To test distribution of the visualizations

To test integration of GIS displays and true 3D visualizations

Cordell BankCordell Bank Marine

Sanctuary is a 526-square mile sanctuary located 50 miles northwest of San Francisco. The Sanctuary encompasses Cordell Bank - a pinnacle rising from the seafloor to within 120 feet of the sea surface - and the surrounding waters.

Datasets for the Sanctuary

Bathymetry Physical

characteristics- CTD Hydroacoustic surveryBottom type data SST imagesCoastlines and

boundaries

Visualization of the Sanctuary

Standard tools and plug-ins within browsers (VRML players, animation players such as RealPlayer, javascript tools) to enable users to manipulate the visualizations.

Viewing a visualization

VRML generation - fencelines

Isosurfaces, plumes and vertical fenceline plots created using EVS-Pro. EVS-Pro allows for3-D kriging and fenceline plots

Fenceline of towed instrument data

VRML generation - isosurfaces

3D temperature plumes and isosurfaces created in EVS-Pro are exported and combined with the VRML 2.0 output from ArcScene

(8 degree temperature isosurfaceand CTD cast positions)

Viewing visualizations User loads the visualization into

a VRML-aware web browser Coastline, bathymetry and

topography data in the VRML window.

3-D navigation control in the VRML window

Can load, view and animate data as the scene is rotated and scaled.

Radio-button choices are given for dataset choices

Animation controls appear as time dependent data are loaded.

VRML based visualizations for the Cordell Bank NMS

Using ArcIMS map servers for intra-layer calculations

Java/Java3D and ArcGIS Engine as a framework for a “scientific GIS”

Project goals To create a series of tools to allow

user defined intra and inter-layer calculations and comparisons within the framework of ArcIMS

To allow PMEL to be able to calculate the population at risk from tsunamis

To allow NMML and AFSC to calculate biophysical measures

Background Internet map servers (IMS) are used to

• disseminate information• allow users to perform queries• to extract information • to serve data

All line offices in NOAA are using IMS applications to serve data

A drawback of off-the-shelf map servers is that one cannot do on-the-fly calculations on layers, or between layers

WebMapCalculator architecture

ArcIMS/JSP

Application

HTTP PostWebsite

Server Side calculator

File Access

ShapeFiles

Java Servlet

Application

Calculated Results

Using ArcIMS 4.0.1 on Solaris with JAVA JDK 1.4, Running Image Server, Feature Server and Extract Server

Path to Files

Include Shapefiles in ArcIMS Map Workspace

Demonstration project - tsunami modeling in Puget Sound

PMEL’s Tsunami Inundation Mapping Effort (TIME)

Products for use by emergency managers Involves ingesting data from

• municipalities• NOAA• model output • observational data

Data products are • maps - static and live • data reports produced using GIS analysis

TIME data

Data are disseminated as ArcView projects. Layers include • inundation fields • census products • run up model

results • animations.

Distributed to emergency managers via CD

WebMapCalculator for TIME

   Input: Gridded wave height

data from a tsunami model

Population of Seattle area by day and night

Elevation data Output: A polygon that shows

resulting at-risk population

Output from the IMS Inundation IMS shows

users • inundation results

from model• maximum velocities• day/night populations• natural hazards• shoreline data

Data sources have metadata associated with the layers

Toolkits to be added

RACEBASE dataset of trawl survey data - intra-layer calculations between fisheries datasets and physical oceanography datasets such as water temperature or salinity

NMML - ability to query tracked mammal results to determine swimming speeds, distanced traveled

VRML based visualizations for the Cordell Bank NMS

Using ArcIMS map servers for intra-layer calculations

Java/Java3D and ArcGIS Engine as a framework for a “scientific GIS”

Project Goals To extend the capabilities of ArcGIS to

form the foundation of a “scientific GIS” for fisheries oceanography

To integrate existing oceanographic analytical tools with ArcGIS

To take advantage of visualization tools such as VRML and Java3D to provide truly three-dimensional visualizations

Programming options ArcObjects/VB - limited to single

platform, limitations of VB ArcGIS Engine - platform

independent, cost? Open source GIS tools such as

GRASS, MapServer, PostGIS, GeoTools and VisAD - documentation/support

System Diagram

Algorithms

UNESCO routines for water properties Oceanographic Analyst (ArcView 3.2)

http://www.absc.usgs.gov/glba/gistools/

Matlab tools - SEA-MAT package http://woodshole.er.usgs.gov/operations/sea-mat/

USGS sedx package http://woodshole.er.usgs.gov/staffpages/csherwood/sedx_equations/sedxinfo.html

VTK toolkit - for volume analysis http://public.kitware.com/VTK/

Test Case - Mixed layer depth

www.fd.ntou.edu.tw/5CTemperature201025.doc

The depth to which water is well mixed. This has ramifications for fish and planktonic organisms, also for nutrients.

Surface layer sits above the thermocline. Defined as the layer where the temperature is within 0.5° of the average surface temperature or where the potential density is within 0.125 of the surface average

Conductivity-temperature-depth (CTD) data

Java test case MLD algorithm from VB to Java GeoTools toolkit shapefile reader (Java)

used to read shapefile Created a new application in Java to

calculate the MLD and output a VTK OpenGL window

VTK wrapped in Java Can also display MLD shapefile created in

ArcGIS version

3-D Visualization at PMEL

1. Perspective:1. Perspective:

2. Relative Motion:2. Relative Motion:

3. Stereo:3. Stereo:

Why 3-D?

1. Perspective

High frequency spikes in the bathymetry data are obvious in the 3D plot (right) and are obscured in the 2D plot above.

Calculations of bathymetry gradients to identify regions of internal tide generation would be impacted by these spikes in the bathymetry data.

Bathymetry in Astoria Canyon offshore from the Columbia River outflow in Washington State, in 2D and 3D.

2. Relative Motion (Interaction)

• The ability to judge an object’s distance through the use of relative motion

3. Stereographic Virtual Reality

Fish larvae in a canyon

Stereo gives the scientist true depth perception

Stereo

Stereo

Mono

Mono

Ocean currents

21

ImmersaDesk

A Next Generation Internet (NGI) Testbed

The ImmersaDesk:

• 4’ x 5’ rear projecting screen

• near immersive• 1024 x 768 x 96 Hz• driven by SGI Onyx2

• Two R12000 Processors• 250 MHz• Infinite Reality Graphics

GeoWall

PC-driven projection systemStereoCommodity graphics cardsInexpensiveNOAA-Tech

Hostcomputer

polarizing filter

Projector(R

frame)

Projector(L

frame)

polarizing filter

Polarization-preserving

screen

Supports *any* stereo-equipped software:

vis5d, visAD, stereo VRML viewers, etc.

The GeoWall Approach

Problem:

We’re pushing the computational limits with our models. Even high-end graphics cards aren’t up to the challenge

Let’s look at a real-world example…

PMEL scientist models Gulf of Alaska

Uses NCSA supercomputer cluster to modelLarge domain (540 x 320 x 32) = 5.5 million pointsGenerating files on the order of a terabyte (1000 gigs)

Our models aren’t just run on a linux cluster, they are runon several clusters, connected using Grid technology:

TeraGrid - connecting heterogeneous clusters Myrinet Myrinet

Chicago & LA DTF Core Switch/Routers

SunServer

Federation

7.8 TFPower4

1 TFItanium2

Fibre Channel Fibre Channel

2 TF Itanium29.2 TF Madison

0.5 TF Itanium290 TB

1.5 TF Itanium2/Madison20 TB

DatawulfIA-32

SDSC NCSA

Caltech ArgonneQuadrics

PSC

6TF Alpha EV681.1 TF Alpha EV7

300 TB 300 TB 160 TB

VisAD – Java-based Graphics Tool

VisAD uses Java3D to render 3-D scenes Java provides a Remote Method Invocation (RMI) that allows data to be rendered at each “node” of a cluster, and then stitched together at the client.

host(also a node)

client(PC)

Clusternodes

RMI

internet

*VisAD and RMI framework for parallel rendering by Bill Hibbard: http://www.ssec.wisc.edu/~billh/visad.html

VisAD test program

Viz Clusters: Distributed Rendering with the GeoWall2

• Developed at EVL & SDSC, SCRIPPS

• 15 LCD screens in 3x5 array driven

• by small Linux cluster

• Total resolution: 8000x3600

• Video compositing allows each node to render from distributed file - up to 38 Terabytes of data on the screen!

• Software: JuxtaView, ParaView

• Scalable: Personal GW is 2x2

Future activities

Framework for 3D modeling of environmental factors

Use of Java to handle temporal analyses

Other graphics outputs Integration with ArcIMS site

This work was funded by NOAA’s HPCC program (http://www.cio.noaa.gov/hpcc/) and the Sanctuaries Program (www.sanctuaries.nos.noaa.gov).

For more information about the Pacific Marine Environmental Laboratory's visualization efforts, please visit the PMEL visualization page at http://www.pmel.noaa.gov/vrml/3DViz.html and http://www.pmel.noaa.gov/visualization/.

Questions?