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Commit 30881a59 authored by HongKee Moon's avatar HongKee Moon
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Handle multiple datasets with different contexts and XML file provided through http 

For example, if BigDataViewer uses http://localhost:8080/HisYFP-SPIM, it will process the xml file directly and access the remote BigDataServer.
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src/main/java/bdv/server/BigDataServer.java
+ 12
− 108
View file @ 30881a59
package bdv.server; package bdv.server;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import mpicbg.spim.data.SpimDataException;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.realtransform.AffineTransform3D;
import org.eclipse.jetty.server.Request;
import org.eclipse.jetty.server.Server; import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.server.handler.AbstractHandler;
import bdv.img.cache.CacheHints;
import bdv.img.cache.LoadingStrategy;
import bdv.img.cache.VolatileCell;
import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.img.remote.AffineTransform3DJsonSerializer;
import bdv.img.remote.RemoteImageLoaderMetaData;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import com.google.gson.GsonBuilder; import java.util.HashMap;
public class BigDataServer public class BigDataServer
{ {
static HashMap< String, String > dataSet = new HashMap<>();
public static void main( final String[] args ) throws Exception public static void main( final String[] args ) throws Exception
{ {
final String fn = args.length > 0 ? args[ 0 ] : "/Users/pietzsch/Desktop/data/fibsem.xml"; final String fn = args.length > 0 ? args[ 0 ] : "/Users/moon/Projects/git-projects/BigDataViewer/data/HisYFP-SPIM.xml";
dataSet.put( "HisYFP-SPIM", fn );
final int port = args.length > 1 ? Integer.parseInt( args[ 1 ] ) : 8080; final int port = args.length > 1 ? Integer.parseInt( args[ 1 ] ) : 8080;
System.setProperty( "org.eclipse.jetty.util.log.class", "org.eclipse.jetty.util.log.StdErrLog" ); System.setProperty( "org.eclipse.jetty.util.log.class", "org.eclipse.jetty.util.log.StdErrLog" );
final Server server = new Server( port ); final Server server = new Server( port );
server.setHandler( new CellHandler( fn ) );
server.start();
server.join();
}
static class CellHandler extends AbstractHandler
{
private final VolatileGlobalCellCache< VolatileShortArray > cache;
private final String metadataJson; String baseURL = "http://" + server.getURI().getHost() + ":" + port + "/";
private final RemoteImageLoaderMetaData metadata; // System.out.println(baseURL);
private final CacheHints cacheHints; server.setHandler( new DataSetHandler( baseURL, dataSet ) );
server.start();
public CellHandler( final String xmlFilename ) throws SpimDataException server.join();
{
final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
cache = imgLoader.getCache();
metadata = new RemoteImageLoaderMetaData( imgLoader, seq );
final GsonBuilder gsonBuilder = new GsonBuilder();
gsonBuilder.registerTypeAdapter( AffineTransform3D.class, new AffineTransform3DJsonSerializer() );
gsonBuilder.enableComplexMapKeySerialization();
metadataJson = gsonBuilder.create().toJson( metadata );
cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );
}
@Override
public void handle( final String target, final Request baseRequest, final HttpServletRequest request, final HttpServletResponse response ) throws IOException, ServletException
{
final String cellString = request.getParameter( "p" );
if ( cellString == null )
return;
final String[] parts = cellString.split( "/" );
if ( parts[ 0 ].equals( "cell" ) )
{
final int index = Integer.parseInt( parts[ 1 ] );
final int timepoint = Integer.parseInt( parts[ 2 ] );
final int setup = Integer.parseInt( parts[ 3 ] );
final int level = Integer.parseInt( parts[ 4 ] );
VolatileCell< VolatileShortArray > cell = cache.getGlobalIfCached( timepoint, setup, level, index, cacheHints );
if ( cell == null )
{
final int[] cellDims = new int[] {
Integer.parseInt( parts[ 5 ] ),
Integer.parseInt( parts[ 6 ] ),
Integer.parseInt( parts[ 7 ] ) };
final long[] cellMin = new long[] {
Long.parseLong( parts[ 8 ] ),
Long.parseLong( parts[ 9 ] ),
Long.parseLong( parts[ 10 ] ) };
cell = cache.createGlobal( cellDims, cellMin, timepoint, setup, level, index, cacheHints );
}
final short[] data = cell.getData().getCurrentStorageArray();
final byte[] buf = new byte[ 2 * data.length ];
for ( int i = 0, j = 0; i < data.length; i++ )
{
final short s = data[ i ];
buf[ j++ ] = ( byte ) ( ( s >> 8 ) & 0xff );
buf[ j++ ] = ( byte ) ( s & 0xff );
}
response.setContentType( "application/octet-stream" );
response.setContentLength( buf.length );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
final OutputStream os = response.getOutputStream();
os.write( buf );
os.close();
}
else if ( parts[ 0 ].equals( "init" ) )
{
response.setContentType( "application/octet-stream" );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
final PrintWriter ow = response.getWriter();
ow.write( metadataJson );
ow.close();
}
}
} }
} }
src/main/java/bdv/server/CellHandler.java 0 → 100644
+ 153
− 0
View file @ 30881a59
package bdv.server;
import bdv.img.cache.CacheHints;
import bdv.img.cache.LoadingStrategy;
import bdv.img.cache.VolatileCell;
import bdv.img.cache.VolatileGlobalCellCache;
import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.img.remote.AffineTransform3DJsonSerializer;
import bdv.img.remote.RemoteImageLoaderMetaData;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import com.google.gson.GsonBuilder;
import mpicbg.spim.data.SpimDataException;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.realtransform.AffineTransform3D;
import org.eclipse.jetty.server.Request;
import org.eclipse.jetty.server.handler.AbstractHandler;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.input.SAXBuilder;
import org.jdom2.output.XMLOutputter;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
public class CellHandler extends AbstractHandler
{
private final VolatileGlobalCellCache< VolatileShortArray > cache;
private final String metadataJson;
private final RemoteImageLoaderMetaData metadata;
private final CacheHints cacheHints;
private final String xmlFile;
private final String dataSetURL;
public CellHandler( final String baseUrl, final String xmlFilename ) throws SpimDataException
{
final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
cache = imgLoader.getCache();
metadata = new RemoteImageLoaderMetaData( imgLoader, seq );
final GsonBuilder gsonBuilder = new GsonBuilder();
gsonBuilder.registerTypeAdapter( AffineTransform3D.class, new AffineTransform3DJsonSerializer() );
gsonBuilder.enableComplexMapKeySerialization();
metadataJson = gsonBuilder.create().toJson( metadata );
cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );
// dataSetURL property is used for providing the XML file by replace SequenceDescription>ImageLoader>baseUrl
xmlFile = xmlFilename;
dataSetURL = baseUrl;
}
@Override
public void handle( final String target, final Request baseRequest, final HttpServletRequest request, final HttpServletResponse response ) throws IOException, ServletException
{
final String cellString = request.getParameter( "p" );
if ( cellString == null )
return;
final String[] parts = cellString.split( "/" );
if ( parts[ 0 ].equals( "cell" ) )
{
final int index = Integer.parseInt( parts[ 1 ] );
final int timepoint = Integer.parseInt( parts[ 2 ] );
final int setup = Integer.parseInt( parts[ 3 ] );
final int level = Integer.parseInt( parts[ 4 ] );
VolatileCell< VolatileShortArray > cell = cache.getGlobalIfCached( timepoint, setup, level, index, cacheHints );
if ( cell == null )
{
final int[] cellDims = new int[] {
Integer.parseInt( parts[ 5 ] ),
Integer.parseInt( parts[ 6 ] ),
Integer.parseInt( parts[ 7 ] ) };
final long[] cellMin = new long[] {
Long.parseLong( parts[ 8 ] ),
Long.parseLong( parts[ 9 ] ),
Long.parseLong( parts[ 10 ] ) };
cell = cache.createGlobal( cellDims, cellMin, timepoint, setup, level, index, cacheHints );
}
final short[] data = cell.getData().getCurrentStorageArray();
final byte[] buf = new byte[ 2 * data.length ];
for ( int i = 0, j = 0; i < data.length; i++ )
{
final short s = data[ i ];
buf[ j++ ] = ( byte ) ( ( s >> 8 ) & 0xff );
buf[ j++ ] = ( byte ) ( s & 0xff );
}
response.setContentType( "application/octet-stream" );
response.setContentLength( buf.length );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
final OutputStream os = response.getOutputStream();
os.write( buf );
os.close();
}
else if ( parts[ 0 ].equals( "init" ) )
{
response.setContentType( "application/octet-stream" );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
final PrintWriter ow = response.getWriter();
ow.write( metadataJson );
ow.close();
}
}
public void provideXML( final Request baseRequest, final HttpServletResponse response ) throws IOException, ServletException
{
final SAXBuilder sax = new SAXBuilder();
Document doc;
try
{
doc = sax.build( xmlFile );
}
catch ( final Exception e )
{
throw new ServletException( e );
}
final Element root = doc.getRootElement();
final Element SequenceDescription = root.getChild( "SequenceDescription" );
final Element ImageLoader = SequenceDescription.getChild( "ImageLoader" );
ImageLoader.setAttribute( "format", "bdv.remote" );
ImageLoader.removeChild( "hdf5" );
final Element baseUrl = new Element( "baseUrl" );
baseUrl.setText( dataSetURL );
ImageLoader.setContent( baseUrl );
// System.out.println(ImageLoader.getAttribute( "format" ));
// System.out.println(ImageLoader.getValue());
response.setContentType( "application/xml" );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
final PrintWriter ow = response.getWriter();
ow.write( new XMLOutputter().outputString( doc ) );
ow.close();
}
}
\ No newline at end of file
src/main/java/bdv/server/DataSetHandler.java 0 → 100644
+ 46
− 0
View file @ 30881a59
package bdv.server;
import mpicbg.spim.data.SpimDataException;
import org.eclipse.jetty.server.Request;
import org.eclipse.jetty.server.handler.AbstractHandler;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.net.MalformedURLException;
import java.util.HashMap;
public class DataSetHandler extends AbstractHandler
{
final private HashMap< String, CellHandler > cellHandlers;
public DataSetHandler( String baseURL, HashMap< String, String > ds ) throws SpimDataException, MalformedURLException
{
cellHandlers = new HashMap<>();
for ( String dataSet : ds.keySet() )
{
cellHandlers.put( dataSet, new CellHandler( baseURL + dataSet + "/", ds.get( dataSet ) ) );
}
}
@Override
public void handle( final String target, final Request baseRequest, final HttpServletRequest request, final HttpServletResponse response ) throws IOException, ServletException
{
String dsName = target.replace( "/", "" );
if ( cellHandlers.containsKey( dsName ) )
{
if ( request.getParameter( "p" ) != null )
cellHandlers.get( dsName ).handle( target, baseRequest, request, response );
else
// Provide XML file
cellHandlers.get( dsName ).provideXML( baseRequest, response );
}
else
{
return;
}
}
}
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