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Tobias Pietzsch authoredTobias Pietzsch authored
CellHandler.java 9.41 KiB
package bdv.server;
import bdv.BigDataViewer;
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.RemoteImageLoader;
import bdv.img.remote.RemoteImageLoaderMetaData;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.util.Thumbnail;
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.ContextHandler;
import org.eclipse.jetty.util.log.Log;
import org.jdom2.Document;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
import javax.imageio.ImageIO;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.awt.image.BufferedImage;
import java.io.*;
public class CellHandler extends ContextHandler
{
private static final org.eclipse.jetty.util.log.Logger LOG = Log.getLogger( CellHandler.class );
private final VolatileGlobalCellCache< VolatileShortArray > cache;
private final CacheHints cacheHints;
/**
* Full path of the dataset xml file this {@link CellHandler} is serving.
*/
private final String xmlFilename;
/**
* Full path of the dataset xml file this {@link CellHandler} is serving,
* without the ".xml" suffix.
*/
private final String baseFilename;
private final String dataSetURL;
/**
* Cached dataset XML to be send to and opened by {@link BigDataViewer}
* clients.
*/
private final String datasetXmlString;
/**
* Cached JSON representation of the {@link RemoteImageLoaderMetaData} to be
* send to clients.
*/
private final String metadataJson;
/**
* Cached dataset.settings XML to be send to clients. May be null if no
* settings file exists for the dataset.
*/
private final String settingsXmlString;
public CellHandler( final String baseUrl, final String xmlFilename ) throws SpimDataException, IOException
{
final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
final SpimDataMinimal spimData = io.load( xmlFilename );
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();
cache = imgLoader.getCache();
cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );
// dataSetURL property is used for providing the XML file by replace
// SequenceDescription>ImageLoader>baseUrl
this.xmlFilename = xmlFilename;
baseFilename = xmlFilename.endsWith( ".xml" ) ? xmlFilename.substring( 0, xmlFilename.length() - ".xml".length() ) : xmlFilename;
dataSetURL = baseUrl;
datasetXmlString = buildRemoteDatasetXML( io, spimData, baseUrl );
metadataJson = buildMetadataJsonString( imgLoader, seq );
settingsXmlString = buildSettingsXML( baseFilename );
}
@Override
public void doHandle( final String target, final Request baseRequest, final HttpServletRequest request, final HttpServletResponse response ) throws IOException
{
if ( target.equals( "/settings" ) )
{
if ( settingsXmlString != null )
respondWithString( baseRequest, response, "application/xml", settingsXmlString );
return;
}
if ( target.equals( "/png" ) )
{
provideThumbnail( baseRequest, response );
return;
}
final String cellString = request.getParameter( "p" );
if ( cellString == null )
{
respondWithString( baseRequest, response, "application/xml", datasetXmlString );
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" ) )
{
respondWithString( baseRequest, response, "application/json", metadataJson );
}
}
public void provideThumbnail( final Request baseRequest, final HttpServletResponse response )
{
// Just check it once
final File pngFile = new File( baseFilename + ".png" );
if ( pngFile.exists() )
{
byte[] imageData = null;
try
{
final BufferedImage image = ImageIO.read( pngFile );
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageIO.write( image, "png", baos );
imageData = baos.toByteArray();
}
catch ( final IOException e )
{
e.printStackTrace();
}
if ( imageData != null )
{
response.setContentType( "image/png" );
response.setContentLength( imageData.length );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
try
{
final OutputStream os = response.getOutputStream();
os.write( imageData );
os.close();
}
catch ( final IOException e )
{
return;
}
}
}
else
{
return;
}
}
public String getXmlFile()
{
return xmlFilename;
}
public String getDataSetURL()
{
return dataSetURL;
}
public String getThumbnailUrl()
{
final File pngFile = new File( baseFilename + ".png" );
if ( pngFile.exists() )
return dataSetURL + "png";
// No thumbnail
// Trigger to generate thumbnail here
try
{
final Thumbnail thumb = new Thumbnail( xmlFilename, 800, 600 );
}
catch ( final Exception e )
{
e.printStackTrace();
}
return dataSetURL + "png";
}
public String getDescription()
{
throw new UnsupportedOperationException();
}
/**
* Create a JSON representation of the {@link RemoteImageLoaderMetaData}
* (image sizes and resolutions) provided by the given
* {@link Hdf5ImageLoader}.
*/
private static String buildMetadataJsonString( final Hdf5ImageLoader imgLoader, final SequenceDescriptionMinimal seq )
{
final RemoteImageLoaderMetaData metadata = new RemoteImageLoaderMetaData( imgLoader, seq );
final GsonBuilder gsonBuilder = new GsonBuilder();
gsonBuilder.registerTypeAdapter( AffineTransform3D.class, new AffineTransform3DJsonSerializer() );
gsonBuilder.enableComplexMapKeySerialization();
return gsonBuilder.create().toJson( metadata );
}
/**
* Create a modified dataset XML by replacing the ImageLoader with an
* {@link RemoteImageLoader} pointing to the data we are serving.
*/
private static String buildRemoteDatasetXML( final XmlIoSpimDataMinimal io, final SpimDataMinimal spimData, final String baseUrl ) throws IOException, SpimDataException
{
final SpimDataMinimal s = new SpimDataMinimal( spimData, new RemoteImageLoader( baseUrl, false ) );
final Document doc = new Document( io.toXml( s, s.getBasePath() ) );
final XMLOutputter xout = new XMLOutputter( Format.getPrettyFormat() );
final StringWriter sw = new StringWriter();
xout.output( doc, sw );
return sw.toString();
}
/**
* Read {@code baseFilename.settings.xml} into a string if it exists.
*
* @return contents of {@code baseFilename.settings.xml} or {@code null} if
* that file couldn't be read.
*/
private static String buildSettingsXML( final String baseFilename )
{
final String settings = baseFilename + ".settings.xml";
if ( new File( settings ).exists() )
{
try
{
final SAXBuilder sax = new SAXBuilder();
final Document doc = sax.build( settings );
final XMLOutputter xout = new XMLOutputter( Format.getPrettyFormat() );
final StringWriter sw = new StringWriter();
xout.output( doc, sw );
return sw.toString();
}
catch ( JDOMException | IOException e )
{
LOG.warn( "Could not read settings file \"" + settings + "\"" );
LOG.warn( e.getMessage() );
}
}
return null;
}
/**
* Handle request by sending a UTF-8 string.
*/
private static void respondWithString( final Request baseRequest, final HttpServletResponse response, final String contentType, final String string ) throws IOException
{
response.setContentType( contentType );
response.setCharacterEncoding( "UTF-8" );
response.setStatus( HttpServletResponse.SC_OK );
baseRequest.setHandled( true );
final PrintWriter ow = response.getWriter();
ow.write( string );
ow.close();
}
}