toolkits for geoscience visualization dave nadeau, john moreland sdsc

Toolkits forGeoScience Visualization

Dave Nadeau, John Moreland

SDSC

Cyberinfrastructure Summer Institute for GeoscientistsCyberinfrastructure Summer Institute for Geoscientists

Tools for custom visualization

• Lots of great GeoVis tools out there

• What if you need something custom?

– Convert to/from a custom file format

– Analyze and filter data

– Custom visualization and interaction

• Let’s look at some toolkits for building tools


Tools for custom visualization

• Java Image I/O

• GeoTIFF

• Java OpenGL

• GeoTools

• WorldWind

• NetCDF


Java Image I/O

• Sun Java toolkit for image file read/write

– Many formats

• BMP, GIF, PNG, JPEG, JPEG2000, TIFF

– Also use advanced imaging toolkit for filtering

– Standard part of Java

http://java.sun.com/


Java Image I/O example

1. Get an image reader:ImageInputStream stream =

ImageIO.createImageInputStream(file);

Iterator<ImageReader> it =

ImageIO.getImageReaders(stream);

ImageReader reader = it.next();

reader.setInput(stream);



2. Read the image:

3. Display the image:

BufferedImage image = reader.read(0);

ImageIcon icon = new ImageIcon(image);Jlabel label = new Jlabel(icon);frame.add(label,BorderLayout.CENTER);


GeoTIFF

• TIFF image format with Geo tags

– Coordinate space, position, extent

– Readable by TIFF tools (Java Image I/O)

– GeoTIFF metadata adapter understands tags

• Open Source

http://remotesensing.org/geotiff/

http://gelbin.org/code/

• TIFF image format with Geo tags

– Coordinate space, position, extent

– Readable by TIFF tools (Java Image I/O)

– GeoTIFF metadata adapter understands tags

• Open Source

http://remotesensing.org/geotiff/

http://gelbin.org/code/


GeoTIFF example

1. Get a TIFF image reader (same!):ImageInputStream stream =

ImageIO.createImageInputStream(file);

Iterator<ImageReader> it =

ImageIO.getImageReaders(stream);

ImageReader reader = it.next();

reader.setInput(stream);


GeoTIFF example

2. Read the image (same!): :

3. Display the image (same!): :

BufferedImage image = reader.read(0);

ImageIcon icon = new ImageIcon(image);Jlabel label = new Jlabel(icon);frame.add(label,BorderLayout.CENTER);


GeoTIFF example

4. Get the GeoTIFF metadata:IIOMetadata meta = reader.getImageMetadata(0);

GeoTiffIIOMetadataAdapter ameta =

new GeoTiffIIOMetadataAdapter(meta);

String value = ameta.getGeoKey(key);


GeoTIFF example

• Available keys:– GTModelTypeGeoKey

– GTRasterTypeGeoKey

– GTCitationGeoKey

– GeographicTypeGeoKey

– GeogCitationGeoKey

– GeogGeodeticDatumGeoKey

– GeogPrimeMeridianGeoKey

– GeogPrimeMeridianLongGeoKey

– GeogLinearUnitsGeoKey

– GeogLinearUnitSizeGeoKey

– GeogAngularUnitsGeoKey

– GeogAngularUnitsSizeGeoKey

– GeogEllipsoidGeoKey

– GeogSemiMajorAxisGeoKey

– GeogSemiMinorAxisGeoKey

– GeogInvFlatteningGeoKey

– GeogAzimuthUnitsGeoKey

– ProjCenterLongGeoKey

– ProjCenterLatGeoKey

– ProjCenterEastingGeoKey

– ProjCenterNorthingGeoKey

– ProjScaleAtNatOriginGeoKey

– ProjScaleAtCenterGeoKey

– ProjAzimuthAngleGeoKey

– ProjStraightVertPoleLongGeoKey

– VerticalCSTypeGeoKey

– VerticalCitationGeoKey

– VerticalDatumGeoKey

– VerticalUnitsGeoKey

– ProjectedCSTypeGeoKey

– PCSCitationGeoKey

– ProjectionGeoKey

– ProjCoordTransGeoKey

– ProjLinearUnitsGeoKey

– ProjLinearUnitSizeGeoKey

– ProjStdParallel1GeoKey

– ProjStdParallel2GeoKey

– ProjNatOriginLongGeoKey

– ProjNatOriginLatGeoKey

– ProjFalseEastingGeoKey

– ProjFalseNorthingGeoKey

– ProjFalseOriginLongGeoKey

– ProjFalseOriginLatGeoKey

– ProjFalseOriginEastingGeoKey

– ProjFalseOriginNorthingGeoKey


GeoTIFF example


Java OpenGL (JOGL)

• Sun Java toolkit for OpenGL 3D drawing

– Uses native OpenGL to 3D graphics hardware

– Integrates with rest of Java toolkit

– Not part of Java distribution, but easily added

https://jogl.dev.java.net/


Java OpenGL (JOGL)

• Draw points, lines, polygons

• Control point & line size, line patterns,

polygon fill, color, texture

• Control 3D lighting

• All done at hardware speeds


JOGL example: polygons

1. Set a drawing color:

2. Draw a polygon:

gl.glColor3f(r,g,b);

gl.glBegin(GL.GL_POLYGON);

gl.glVertex3f(x,y,z);

...

gl.glEnd();


JOGL example: polygons


1. Create texture from graphics context:

2. Draw shape using texture:gl.glTexCoord2f(s,t);

gl.glVertex3f(x,y,z);

Texture tex= TextureIO.newTexture(file,false);

gl.glEnable(GL.GL_TEXTURE_2D);

tex.bind();

tex.enable();

JOGL example: images


JOGL example: images


GeoTools

• Toolkit implementing OGC GeoAPI

– Read/write many file formats

– Features, images, geometry, coord spaces

– WMS, WFS

– Open source

http://geotools.codehaus.org/


GeoTools example: Shapefile

1. Create a data store to read a file:

2. Get the first feature source:

DataStore dataStore =

FileDataStoreFinder.getDataStore(url);

String[] names = dataStore.getTypeNames();

FeatureSource source =

dataStore.getFeatureSource(names[0]);



3. Create a map context:

4. Add feature source to context:

CoordinateReferenceSystem crs =

CRS.decode(“EPSG:4326”);

DefaultMapContext context =

new DefaultMapContext(crs);

context.addLayer(source,new BasicLineStyle());



5. Draw the map context:MapContextPanel panel = new MapContextPanel();

panel.setContext(context);

frame.add(panel,BorderLayout.CENTER);


NetCDF

• Network Common Data Form

– File format & toolkit to read/write multidimensional data (eg: Volumes)

• Support for many programming languages (such as Java)

– University Corporation for Atmospheric Research (UCAR) / UNAVCO

http://www.unidata.ucar.edu/software/netcdf/


NetCDF

• Variables hold multidimensional data values

– char, byte, short, int, float, double

• Attributes hold meta-data

– Units, names, scale factors, etc.

– Attributes can be global or associated with each

variable


NetcdfFile ncfile = NetcdfFile.open(file);

List variables = ncfile.getVariables();

Variable var = (Variable)variables.get(i);

Array array = var.read();

NetCDF example

1. Open a NetCDF file:

2. Get data variables:


NetCDF example

3. Get variable dimensions:

4. Get voxels:

int rank = var.getRank();

int[] shape = array.getShape();

double voxel =

((ArrayDouble.D3)array).get(i,j,k);


NetCDF example

5. Get global or variable attributes:

6. Get attribute type and value:

List glist = ncfile.getGlobalAttributes();

List vlist = var.getAttributes();

Attribute attrib = vlist.get(i);

DataType type = attrib.getDataType();

Number num = attrib.getNumericValue(i);

String str = attrib.getStringValue(i);


NetCDF example

7. Build an image:BufferedImage image = new BufferedImage(w,h);

int gray = (int)(voxel * 255);

int rgba = (gray<<24) | (gray<<16) ...;

image.setRGB(row,col,rgba);


NetCDF example


NASA World Wind (NWW)

• “Open-Source Google Earth”

– Toolkit (modular library for building applications)

• Versions for .NET (Windows) and Java (Mac, Windows, UNIX)

– Tiled Terrain and Images, WMS, Plug-in Layers, 3D Rendering

(JOGL)

– NASA / ARC (Ames Research Center)

http://worldwind.arc.nasa.gov/


1. Create a canvas:

2. Set a data model:

3. Add canvas to your application interface:

WorldWindGLCanvas c = new WorldWindGLCanvas();

c.setModel( new BasicModel() );

NWW HelloWorldWind example

frame.add( c );


NWW HelloWorldWind output


1. Create a surface image:

2. Make it semi-transparent:

3. Add the image to a renderable layer:

SurfaceImage si = new SurfaceImage( “Map.png”, Sector.fromDegrees(35, 45, -115, -95) );

si.setOpacity( 0.7 );

NWW LayerDemo example

RenderableLayer rl = new RenderableLayer();

rl.addRenderable( si );


4. Get the LayerList from the model:

5. Add our image layer:

LayerList layers = model.getLayers( );

layers.add( layers.size(), rl );

NWW LayerDemo example


NWW LayerDemo output


1. Create a WMS Layer:

2. Get the LayerList from the model:

3. Add the WMS layer:

OpenStreetMapLayer os=newOpenStreetMapLayer();

LayerList layers = model.getLayers( );

NWW WmsDemo example

layers.add( layers.size(), os );


NWW WmsDemo output


Conclusions

• Lot’s of good Java toolkits available…– Image I/O Sun Java Image I/O

– Image filtering Sun Java Advanced Imaging

– GeoTIFF GeoTools, WorldWind, GeoTIFF adapter

– Movie I/O Sun Java Media Framework

– Shapefile I/O GeoTools

– Volume I/O NetCDF, HDF

– Metadata Sun Java Metadata Interface

– GUIs Sun JDK, SwingX

– 3D Sun JOGL, Sun Java3D

– Projections GeoTools, SRI GeoTransform

– GML, WFS GeoTools

– WMS GeoTools, WorldWind

– Net protocols Sun JDK, Apache Commons net, Apache HTTP components

– Web protocols Sun Metro, Apache Web Services

– … lots more …


Open Earth Framework

• Services architecture

– Server-side data management, filtering, pre-processing

– Client-side presentation, interaction

– Java toolkit

• Integrates other toolkits

• Adds missing GeoVis functionality

• In development…

toolkits for geoscience visualization dave nadeau, john moreland sdsc

Documents

bufferedimage image

tiff image reader

new jlabeliconframe

new imageiconimagejlabel

custom file formatanalyze

read0imageicon icon

imageinputstream stream

advanced imaging toolkit