Transcript Collaborative 3D and 4D Visualization in a Distributed Data System

Collaborative 3D and 4D
Visualization in a
Distributed Data
System
Charles Meertens
UNAVCO/GEON
2006 IWCI Meeting, Beijing
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Outline
• GEON IT Approach -overview of 3D/4D Visualization and
backend architecture
• Data access and distribution
• Visualization Elements and considerations for 3D/4D
• GEON Integrative Data Viewer (GEON IDV)
• Future Developments Needed
2006 IWCI Meeting, Beijing
Acknowledgements
Stuart Wier and Greg Bensen, UNAVCO
Don Murray and Jeff McWhirter, Unidata
NSF EAR and ATM
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GEON Cyberinfrastructure (CI) Principles
GEON is based on a service-oriented
architecture (SOA) with support for
“intelligent” search, semantic data
integration, visualization of 4D scientific
datasets, and access to high performance
computing platforms for data analysis and
model execution -- via the GEON Portal.
While focused on Earth Sciences, GEON
cyberinfrastructure is generic and broadly
applicable to a variety of other sciences and
other application domains.
2006 IWCI Meeting, Beijing
GEON Overall Architecture
Data
Physical model
Portal (login, myGEON)
Registration
GEONsearch
Data
Registration
Integration
Services
Services
Indexing
Services
GEONworkbench
Community Modeling
Environment
Workflow Visualization
& Mapping
Services
Services
Modeling
Environment
Core Grid Services
Authentication, monitoring, scheduling, catalog, data transfer,
Replication, collection management, databases
Physical Grid
RedHat Linux, ROCKS, Internet, I2, OptIPuter (planned)
Model results
HPCC
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GEON Visualization (and Data!) Steps
A number of steps were taken to engage community input into the GEON
development process:
Visualization Workshop in San Diego, 2005
- Participants gained an exposure to a number of visualization packages and
related data delivery methods ranging from custom powerful integrated
protocols like GeoFusion, to Open GIS Consortium WMS and OPeNDAP.
- An outcome of this workshop was that major obstacles to effective use of
visualization in Cyberinfrastructure was data interoperability, not lack of
visualization capability. It was recommended that netCDF be used initially
for GEON development.
Data workshop in Boulder, 2006
- Participants from SDSC, Unidata, UNAVCO representing LEAD, GEON, and
CUASHI ITR projects met to discuss data interoperability and find ways to
collaborate on CI related development efforts. This led to implementation of
netCDF into the GEON Grid Portal.
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GEON Visualization Workshop
San Diego Supercomputing Center
Synthesis Center
1-2 March 2005
Meeting Summary: C. Meertens, R. Arrowsmith and C. Baru
and IDV and Geofusion (C.Stein) Demonstrations
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GEON 4D Data Access and Visualization
An ongoing GEON effort is to address 4D (xyzt) representation of earth
science datasets and models in a grid computing environment.
Current desires and approaches include:
•
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Capable volume-time Integrative Visualization tools: Enhancing the
Unidata IDV Java Application for earth science data
4D (and multi-parameter) Data Model: Adopting netCDF (used by IDV
and soon by ESRI). Extensive Common Data Model effort at Unidata
Data Discovery: GeonSearch at the GEON Portal
Data delivery: html, OPeNDAP, OGC (WMS), Interoperable
Automated Data/metadata registration: currently exploring OAI/ADN,
DLESE Data Collection System and webservice, THREDDS (Unidata)
Basically give me the specific types of data I want, for only the specific
time and volume I specify, and in a way that I can find it quickly and
easily use it with any application I desire!
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Data Interoperability
With data interoperability Same data or model => many uses
…but until recently same data + graduate students and programmers => fewer uses!
Jules Verne Voyager
Java Applet -> GMT Server
Versions:
Voyage to Earth
Voyage to the Solar System
Global Strain Rate Map
(GSRM, Kreemer, et. al.
2003).
Jules Verne Voyager, Jr.
EarthScope Voyager, Jr.
Interactive Data Viewer (IDV)
Global and Map versions
Javascript ->data server
Shown are the velocities
from the GSRM and planned
EarthScope sites.
Java Application ->
OPeNDAP Server
Shown are S-wave anomaly
isosurfaces of Ritzwoller, et.
al. 2002 and the GSRM strain
rates using the Global IDV.
OPeNDAP Data Connector
ArcVoyager, ArcMap
C application -> OPeNDAP
Server
Shown is the S-wave velocity
model converted to netCDF
files.
ESRI Application
DLESE/GEON, with UNAVCO
contributions, is building an
education module for the
Earth Exploration Toolbook
And Google!
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UNAVCO/ GEON Data Server
and Visualization Access
UNAVCO/GEON
Data Node
OPeNDAP Server
Example: Seismic
Tomography in NetCDF
format
WMS Server
Example: GPS
Seamless Archive
Postgres/PostGIS
Database
THREDDS/OPeNDAP
Catalog
GEON IDV
WMS Catalog
HTML File
Under development: registration of netCDF files
and OPeNDAP servers into the GEON Portal;
embedded GEONSearch within the IDV
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Other
distributed data
servers
Local File
Why the GEON Integrated Data Viewer?
GEON chose to extend the Unidata IDV as a 3D/4D visualization for solid
earth science applications for a number of reasons.
- First, the IDV was designed within a framework of what is now called
Cyberinfrastructure.
-The IDV combines visualization with access to distributed data systems
and analysis capabilities.
-Powerful 3D-4D visualization
-Embedded mathematical capability using Jython
-Collaboration across internet
-Freely available
-Unidata and UNAVCO support and 10 person years of development
-Scriptable for server-side automation at GEON Portal
- JNLP capable for lauching with Java Webstart
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UNAVCO/GEON IDV Development – Some Samples
geon.unavco.org
Example Below: Geodynamic and
Tomographic models on OPeNDAP
Server. Visualization with IDV.
geon.unavco.org
….Next some GEON IDV Samples
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IDV for Mantle Geodynamics
Mantle Temperature
0.8 T (lower mantle)
0.5 T (Upper mantle)
Whole mantle Convection with geologic plate
motions over 120 million years. Normalized
temperature isosurfaces shown.
McNamara and Zhong (2004)
Lava Lamp analogy? Actually not,
the physics is different….
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Enhancing the IDV for Global Tomography
Map version of the IDV showing the Berkeley global shear wave tomography
model on a 2 degree grid, Mégnin and Romanowicz, 2000. Model data
from this and other models of the Reference Earth Model Project are
directly accessed from the UNAVCO/GEON DODS/OPeNDAP, server
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UNAVCO/GEON Enhancements to Unidata’s IDV
• Earthquakes
• GPS vectors
with error ellipses
• Earthquake
focal mechanisms
• Anisotropy
• Customize
interface for earth
science users
(Dr. Stuart Wier,
UNAVCO)
Ability to show observations and models for your domain is essential
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Data Interoperability: JV Voyager Images in the IDV
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About Data…
Formats: It is desirable to have data in a common format, particularly when
dealing with very large 3D/4D models. Experience so far is that almost no
two formats we get from investigators are the same in the scientific world.
Attributes: Need at minimum basic attributes (x,y,z,t, value(s), uncertainties).
Usually can get this. However, to facilitate integration we likely need to
employ conventions and provide additional information. For example
tomography typically given as an anomaly. We need a reference model to be
reused and integrated.
Georeferencing: Often models are generated only with x,y,z andhe
information to go to latitude, longitude and depth is missing. If lat, long
provided, projections and datums may needed as well.
Boundaries vrs continuum: There are two fundamentally different type of
volume representations. 1) boundaries around volumes of constant value
(e.g. geologic units) and 2) other gridded approximations of a continuum.
Few visualization programs handle both. Same notion applies to time.
Sampling: Data is usually irregularly spaced, models uniformly spaced.
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Why netCDF?
A binary standard was needed for 3D/4D data format. NetCDF provides this
as well as a data delivery protocol and API that is used in the IDV.
- There are not a lot of options other than HDF in the earth science scientific
3D/4D data/model world. NetCDF is a mature, supported standard.
-- NetCDF 4 is including major components of HDF5 into a common data
model.
-- NetCDF is used in a number of applications including the Generic
Mapping Tool (GMT; though in a limited way at the moment), Matlab, GRASS
3D. ESRI and Unidata are working on Arc support for netCDF.
-- NetCDF is a flexible container for data, attributes and georeferencing
information.
-NetCDF is machine-independent
- NetCDF heavily supported in the OPeNDAP data distribution system.
Yellowstone (Smith and others) and the geodynamics of the mantle (McNamara)
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About Data Delivery… UNAVCO/GEON PoP Server
Details: Data, Models, Catalogs, Metadata
Data Access
http
srb
ftp
gridftp
OGC*
UNAVCO/GEON
PoP Data Server
1D/2D/3D/4D
OPeNDAP
Thredds
-Catalog elements
Thredds
Catalog
Digital Library
Metadata elements
OPeNDAP
Data
Servers
-netCDF
-Freeform
(via OAI or DLESE
Webservice)
WMS Catalog
*OGC=WMS/WFS/WCS
Dataset Catalogs and Metadata Access
*OGC: WMS/WCS/WFS
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-Tomography
-GPS data/vectors
-Earthquakes
-Focal Mechanisms
-Strain rate
-Topography
-Image maps
-Geodynamics
-Faults
-Paleogeography
Plus IDV visualization
“Bundles” (.xidv files)
Visualization Elements
To be useful for you, a visualization tool must suit your science
domain. Sounds simple, but as soon as you hit the wall and the tool
does not give you what you need you move on to the next. This is a
fact of life, however, so back to data again…with interoperable data
files and servers using the next tool is not so painful.
Next, what are some earth science visualization elements
we need?
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Visualization Elements - Points
Locations (x,y,z) of a sample or event such as an earthquake
- Draw with dot, sphere, cross
Locations and scalar parameter (x,y,z, value) such as the magnitude of the
earthquake. May want to display uncertainty of location and/or value.
- Draw with dot, sphere, cross
- Indicate value(s) by color, texture, size, intensity
Location and vector (x,y,z, dx,dy,dz) such as GPS velocity
- Draw with vector, but might need conical tip for 3D
- Indicate value with length, vector thickness, might use color
Location and tensor quantity (x,y,z, [ ]) strain and stress; earthquake source
parameter
- Draw with focal mechanisms; anisotropy “flying erasers” (not really
figured out yet.
- Indicate value with color, diameter, orientation of faults on focal sphere
(really not your typical visualization software graphic.
Boils down to being able to draw arbitrary scaled, oriented, colored point
symbols. Hard to do with GIS.
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Visualization Elements – Point Data
Clockwise from top left: Vectors, earthquakes, focal mechanisms, and anisotropy
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Visualization Elements – Lines and Polygons
Lines:
Locations are similar to points but need some interpolation to connect the
dots. Examples are faults mapped on the surface, ray paths, sonde tracks,
etc.
-Draw with a line or curve
Lines plus scalar:
-Draw with line colored with value, dash line, vary thickness
-Draw line with perpendicular variation such as a seismic waveform plotted
in two or three dimensions. Might color in waveform.
Polygons:
Locations like lines, but enclosed regions of constant value. Examples are
geologic units of constant age or lithology; political boundaries. Typical GIS
shapefile feature.
- Draw polygons with lines
- Indicate value by area coloring or texture. Could raise polygon off map like
a histogram. May dash polygon boundary or vary thickness.
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Visualization Elements – Lines and Polygons
Lines:
Polygons:
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Visualization Elements - Surfaces
Surfaces: Maps with relief
Often surfaces such as topographic contour maps with relief are referred to
as “3D”, they are actually 2.5 D surfaces. This is something you quickly
realize when, for example, you try to grid tripod LiDAR data of an
overhanging cliff. Here you get full 3D with multiple values of Z for each x,y.
-Draw with lines, polygons (such as triangular elements)
- Indicate value by coloring and texturing the polygons; can drape raster
over surface, show relief with perspective and illumination. May use
transparency.
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Visualization Elements –Volumes
Volumes: Full 3D objects
Volumes can be rendered with isosurfaces constructed of 3D polygons. The
surface can be colored, textured or made transparent to indicate value or
uncertainty. However, work still needs to be done to effectively show
uncertainty in 3D volume space.
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Visualization Elements – Raster Files
Raster images can come from photographic imagery, multi-spectral
scanning, interferometric SAR, and derived products such as WMS and
ArcGIS map servers, gridded data, etc. A significant barrier to use is geo
referencing the image. Geotif format allows for this in the raw image
specification, but is not widely used. WMS and ArcIMS web mapping can
also serve up this information. Otherwise additional files or metadata are
needed. Rasters can be draped over tomograpy. More recently photographic
images have been applied to full 3D surfaces from tripod LiDAR scans.
Visualization of raster files with vertical orientation is rarely possible.
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Some Ways to “Probe” data with visualization
Get a value of a 3D grid at a particular location in space
Get value and associated metadata of a point such as an earthquake
Generate graphs of values along a line
Generate two dimensional contours along vertical/horizontal cross sections
of 3D grid
Generate isosurfaces of constant value (one at a time, if you wanted to
generate the equivalent of 3D contours you would need transparency)
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Visualization - Integration
Putting it all together. The first step to true integration is to remove the
barriers to accessing and importing the data and then visualization of the
data. Below are some examples of multidimensional data displayed in three
dimensions with the GEON IDV.
Yellowstone (Smith and others) and the geodynamics of the mantle (McNamara)
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4D Visualization Images from GEON IDV
170 ma
90 ma
10 ma
Geodynamics,
paleomagnetics,
Paleogeography
McNamara,
Schettino and
Scotese,
Blakely
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Integration with Visualization
GEON is developing some very sophisticated server-side integration
methods at the GEON Grid Portal. In addition to providing integrated views
of data, the GEON IDV also allow for some advanced client-side integration.
The GEON IDV includes the capability to perform preprogrammed and user
input mathematical operations using Jython.
Examples:
- Calculate the difference between two model grids, even if the source
grids have different sampling in space and different geographic projections.
- Calculate the divergence of a 3D vector field
- Calculate the absolute velocity of a 3D tomographic anomaly grid
using a 1 D reference earth model
- Difference a geodynamic model derived 3D structure with observed
tomographic grid
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Working in the GEON Portal: GEON Search
Search for Resources
Current Types:
ASCII
CUAHSI Data
GMT Raster
GeoTiff
Relational Database
Shapefile
Tool
WMS Service
Web Service
NetCDF
Search Constraints:
Metadata Relation,
Type, Subject, Keyword
Spatial Coverage
Temporal Coverage
Ontology/Concept
Relation
Example of unconstrained search response
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Coming… GEON Search in 4-Dimentions (need depth)
and previews from IDV and WMS
Surface geologic maps (GEON shapefile), WMS imagery,
and OPeNDAP Mantle Tomography
Credits (important!!)
Where did it come from?
Who produced it?
How good is it?
Van der Lee and Nolet
NASA Blue Planet
Geology GEON
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What can still be done?
At a minimum, we want to be able to ingest netCDF 1-4D files into the GEON
Portal, find them using GEON search, and retrieve files for use with the IDV
and other visualization tools. Ideally, additional services volume data will be
provided such as currently supported for GIS.
- Download netCDF file(s) after search
- Generate a jnlp file associated with the netCDF file that can be used to
launch the IDV using Java webstart
- Serve collection of netCDF files after search using OPeNDAP/THREDDS as
a proxy server (could be distributed OPeNDAP servers)
- Integration with other data at GEON Portal using server integration tools.
-Add depth dimension to GEON query bounds
- Add visualization to IDV for viewing 3D grids (e.g. FEM). Add ability to load
in isosurfaces (vrml?). Allow for some simple model generation using
Jython in IDV, not just viewing.
- Upload IDV xidv xml files to Portal to share knowledge (baby steps!)
- WMS GEON server-side slices of 3D volume grids
2006 IWCI Meeting, Beijing
Thank-you!
IDV DEMO
Tomorrow
Image source credits:
Mantle Tomography - Shapiro and Ritzwoller; Megnin and Romanowicz
Geodynamics Model - McNamara and Zhong
Global Strain Rate Map and Plate motions -Kreemer and Holt
2006 IWCI Meeting, Beijing