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Commit 4905be1e authored by Tobias Pietzsch's avatar Tobias Pietzsch
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simplify thumbnail generation

parent 3449810b
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src/main/java/bdv/server/CellHandler.java
+ 20
− 16
View file @ 4905be1e
......@@ -12,7 +12,7 @@ import bdv.img.remote.RemoteImageLoaderMetaData;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.util.Thumbnail;
import bdv.util.ThumbnailGenerator;
import com.google.gson.GsonBuilder;
......@@ -94,6 +94,7 @@ public class CellHandler extends ContextHandler
datasetXmlString = buildRemoteDatasetXML( io, spimData, baseUrl );
metadataJson = buildMetadataJsonString( imgLoader, seq );
settingsXmlString = buildSettingsXML( baseFilename );
createThumbnail( spimData, baseFilename );
}
@Override
......@@ -221,21 +222,6 @@ public class CellHandler extends ContextHandler
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";
}
......@@ -301,6 +287,24 @@ public class CellHandler extends ContextHandler
return null;
}
/**
* Create PNG thumbnail file named "{@code <baseFilename>.png}".
*/
private static void createThumbnail( final SpimDataMinimal spimData, final String baseFilename )
{
final File thumbnailFile = new File( baseFilename + ".png" );
final BufferedImage bi = ThumbnailGenerator.makeThumbnail( spimData, baseFilename, 100, 100 );
try
{
ImageIO.write( bi, "png", thumbnailFile );
}
catch ( final IOException e )
{
LOG.warn( "Could not create thumbnail png for dataset \"" + baseFilename + "\"" );
LOG.warn( e.getMessage() );
}
}
/**
* Handle request by sending a UTF-8 string.
*/
......
......
src/main/java/bdv/util/Thumbnail.java deleted 100644 → 0
+ 0
− 205
View file @ 3449810b
package bdv.util;
import bdv.BigDataViewer;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.WrapBasicImgLoader;
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.tools.InitializeViewerState;
import bdv.tools.brightness.ConverterSetup;
import bdv.tools.brightness.MinMaxGroup;
import bdv.tools.brightness.SetupAssignments;
import bdv.tools.transformation.TransformedSource;
import bdv.tools.transformation.XmlIoTransformedSources;
import bdv.viewer.Source;
import bdv.viewer.SourceAndConverter;
import bdv.viewer.state.SourceState;
import bdv.viewer.state.ViewerState;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.sequence.Angle;
import mpicbg.spim.data.sequence.Channel;
import mpicbg.spim.data.sequence.TimePoint;
import net.imglib2.realtransform.AffineTransform3D;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
import javax.imageio.ImageIO;
import java.awt.*;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* Created by moon on 2/5/15.
*/
public class Thumbnail
{
protected final ThumbnailGenerator viewer;
protected final SetupAssignments setupAssignments;
protected ManualTransformation manualTransformation;
protected File proposedSettingsFile;
private static String createSetupName( final BasicViewSetup setup )
{
if ( setup.hasName() )
return setup.getName();
String name = "";
final Angle angle = setup.getAttribute( Angle.class );
if ( angle != null )
name += ( name.isEmpty() ? "" : " " ) + "a " + angle.getName();
final Channel channel = setup.getAttribute( Channel.class );
if ( channel != null )
name += ( name.isEmpty() ? "" : " " ) + "c " + channel.getName();
return name;
}
public Thumbnail( final String xmlFilename, final int width, final int height ) throws SpimDataException, InterruptedException
{
final String thumbnailFile = xmlFilename.replace( ".xml", ".png" );
final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
{
System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );
}
final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
BigDataViewer.initSetups( spimData, converterSetups, sources );
final List< TimePoint > timepoints = seq.getTimePoints().getTimePointsOrdered();
viewer = new ThumbnailGenerator( width, height, sources, timepoints.size() );
manualTransformation = new ManualTransformation( viewer );
setupAssignments = new SetupAssignments( converterSetups, 0, 65535 );
if ( setupAssignments.getMinMaxGroups().size() > 0 )
{
final MinMaxGroup group = setupAssignments.getMinMaxGroups().get( 0 );
for ( final ConverterSetup setup : setupAssignments.getConverterSetups() )
setupAssignments.moveSetupToGroup( setup, group );
}
InitializeViewerState.initTransform( viewer.getWidth(), viewer.getHeight(), viewer.getState() );
if ( !tryLoadSettings( xmlFilename ) )
InitializeViewerState.initBrightness( 0.001, 0.999, viewer.getState(), setupAssignments );
final ViewerState renderState = viewer.getState();
viewer.requestRepaint();
viewer.paint( renderState );
final Image img = viewer.getBufferedImage().getScaledInstance( 100, 100, Image.SCALE_SMOOTH );
final BufferedImage img2 = new BufferedImage( 100, 100, BufferedImage.TYPE_INT_ARGB );
img2.createGraphics().drawImage( img, 0, 0, null );
try
{
ImageIO.write( img2, "png", new File( thumbnailFile ) );
}
catch ( final Exception e )
{
}
}
protected boolean tryLoadSettings( final String xmlFilename )
{
proposedSettingsFile = null;
if ( xmlFilename.endsWith( ".xml" ) )
{
final String settings = xmlFilename.substring( 0, xmlFilename.length() - ".xml".length() ) + ".settings" + ".xml";
proposedSettingsFile = new File( settings );
if ( proposedSettingsFile.isFile() )
{
try
{
loadSettings( settings );
return true;
}
catch ( final Exception e )
{
e.printStackTrace();
}
}
}
return false;
}
protected void loadSettings( final String xmlFilename ) throws IOException, JDOMException
{
final SAXBuilder sax = new SAXBuilder();
final Document doc = sax.build( xmlFilename );
final Element root = doc.getRootElement();
viewer.stateFromXml( root );
setupAssignments.restoreFromXml( root );
manualTransformation.restoreFromXml( root );
viewer.requestRepaint();
}
public static void main( final String[] args )
{
final String fn = args[ 0 ];
try
{
final Thumbnail thumb = new Thumbnail( fn, 800, 600 );
}
catch ( final Exception e )
{
e.printStackTrace();
}
}
public class ManualTransformation
{
protected final ThumbnailGenerator viewer;
protected final XmlIoTransformedSources io;
public ManualTransformation( final ThumbnailGenerator viewer )
{
this.viewer = viewer;
io = new XmlIoTransformedSources();
}
public void restoreFromXml( final Element parent )
{
final Element elem = parent.getChild( io.getTagName() );
final List< TransformedSource< ? > > sources = getTransformedSources();
final List< AffineTransform3D > transforms = io.fromXml( elem ).getTransforms();
if ( sources.size() != transforms.size() )
System.err.println( "failed to load <" + io.getTagName() + "> source and transform count mismatch" );
else
for ( int i = 0; i < sources.size(); ++i )
sources.get( i ).setFixedTransform( transforms.get( i ) );
}
private ArrayList< TransformedSource< ? > > getTransformedSources()
{
final ViewerState state = viewer.getState();
final ArrayList< TransformedSource< ? > > list = new ArrayList< TransformedSource< ? > >();
for ( final SourceState< ? > sourceState : state.getSources() )
{
final Source< ? > source = sourceState.getSpimSource();
if ( TransformedSource.class.isInstance( source ) )
list.add( ( TransformedSource< ? > ) source );
}
return list;
}
}
}
src/main/java/bdv/util/ThumbnailGenerator.java
+ 136
− 184
View file @ 4905be1e
package bdv.util;
import bdv.BigDataViewer;
import bdv.img.cache.Cache;
import bdv.viewer.Interpolation;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import bdv.tools.InitializeViewerState;
import bdv.tools.brightness.ConverterSetup;
import bdv.tools.brightness.SetupAssignments;
import bdv.tools.transformation.TransformedSource;
import bdv.tools.transformation.XmlIoTransformedSources;
import bdv.viewer.Source;
import bdv.viewer.SourceAndConverter;
import bdv.viewer.VisibilityAndGrouping;
import bdv.viewer.render.MultiResolutionRenderer;
import bdv.viewer.state.SourceGroup;
import bdv.viewer.state.SourceState;
import bdv.viewer.state.ViewerState;
import bdv.viewer.state.XmlIoViewerState;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.ui.PainterThread;
import net.imglib2.ui.RenderTarget;
import net.imglib2.ui.TransformListener;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.input.SAXBuilder;
import java.awt.image.BufferedImage;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.CopyOnWriteArrayList;
import static bdv.viewer.VisibilityAndGrouping.Event.*;
import javax.imageio.ImageIO;
/**
* Created by moon on 2/5/15.
*/
public class ThumbnailGenerator implements TransformListener< AffineTransform3D >, VisibilityAndGrouping.UpdateListener
public class ThumbnailGenerator
{
protected final int width;
protected final int height;
/**
* Currently rendered state (visible sources, transformation, timepoint,
* etc.) A copy can be obtained by {@link #getState()}.
* Create a thumbnail image for a dataset. If there is a settings.xml file
* for the dataset, these settings are used for creating the thumbnail.
*
* @param spimData
* the dataset.
* @param baseFilename
* full path of dataset xml file, without the ".xml" extension.
* this is used to derive the name of the settings.xml file.
* @param width
* width of the thumbnail image.
* @param height
* height of the thumbnail image.
* @return thumbnail image
*/
protected final ViewerState state;
public static BufferedImage makeThumbnail( final SpimDataMinimal spimData, final String baseFilename, final int width, final int height )
{
final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
BigDataViewer.initSetups( spimData, converterSetups, sources );
/**
* Renders the current state for the thumbnail.
*/
protected final MultiResolutionRenderer imageRenderer;
final int numTimepoints = spimData.getSequenceDescription().getTimePoints().size();
final ThumbnailGenerator generator = new ThumbnailGenerator( sources, numTimepoints );
final ViewerState state = generator.state;
protected final ThumbnailTarget renderTarget;
final SetupAssignments setupAssignments = new SetupAssignments( converterSetups, 0, 65535 );
final AffineTransform3D initTransform = InitializeViewerState.initTransform( width, height, false, state );
state.setViewerTransform( initTransform );
/**
* Transformation set by the interactive viewer.
*/
protected final AffineTransform3D viewerTransform;
if ( !generator.tryLoadSettings( baseFilename, setupAssignments ) )
InitializeViewerState.initBrightness( 0.001, 0.999, state, setupAssignments );
/**
* Manages visibility and currentness of sources and groups, as well as
* grouping of sources, and display mode.
*/
protected final VisibilityAndGrouping visibilityAndGrouping;
class ThumbnailTarget implements RenderTarget
{
BufferedImage bi;
@Override
public BufferedImage setBufferedImage( final BufferedImage bufferedImage )
{
bi = bufferedImage;
return null;
}
@Override
public int getWidth()
{
return width;
}
@Override
public int getHeight()
{
return height;
}
}
final ThumbnailTarget renderTarget = new ThumbnailTarget();
new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, new Cache.Dummy() ).paint( state );
return renderTarget.bi;
}
/**
* These listeners will be notified about changes to the
* {@link #viewerTransform}. This is done <em>before</em> calling
* {@link #requestRepaint()} so listeners have the chance to interfere.
* Currently rendered state (visible sources, transformation, timepoint,
* etc.)
*/
protected final CopyOnWriteArrayList< TransformListener< AffineTransform3D > > transformListeners;
private final ViewerState state;
/**
* @param sources
......@@ -67,195 +108,106 @@ public class ThumbnailGenerator implements TransformListener< AffineTransform3D
* @param numTimePoints
* number of available timepoints.
*/
public ThumbnailGenerator( final int width, final int height, final List< SourceAndConverter< ? > > sources, final int numTimePoints )
private ThumbnailGenerator( final List< SourceAndConverter< ? > > sources, final int numTimePoints )
{
this.width = width;
this.height = height;
final int numGroups = 10;
final ArrayList< SourceGroup > groups = new ArrayList< SourceGroup >( numGroups );
for ( int i = 0; i < numGroups; ++i )
{
final SourceGroup g = new SourceGroup( "group " + Integer.toString( i + 1 ) );
if ( i < sources.size() )
{
g.addSource( i );
}
groups.add( g );
}
groups.add( new SourceGroup( "" ) );
state = new ViewerState( sources, groups, numTimePoints );
if ( !sources.isEmpty() )
state.setCurrentSource( 0 );
viewerTransform = new AffineTransform3D();
renderTarget = new ThumbnailTarget( width, height );
imageRenderer = new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] {
1 }, 0, false, 1, null, false, new Cache.Dummy() );
visibilityAndGrouping = new VisibilityAndGrouping( state );
visibilityAndGrouping.addUpdateListener( this );
transformListeners = new CopyOnWriteArrayList< TransformListener< AffineTransform3D > >();
}
public BufferedImage getBufferedImage()
private void stateFromXml( final Element parent )
{
return renderTarget.getBufferedImage();
final XmlIoViewerState io = new XmlIoViewerState();
io.restoreFromXml( parent.getChild( io.getTagName() ), state );
}
public void paint( ViewerState state )
private static class ManualTransformation
{
imageRenderer.paint( state );
}
private final ViewerState state ;
/**
* Repaint as soon as possible.
*/
public void requestRepaint()
{
imageRenderer.requestRepaint();
}
private final XmlIoTransformedSources io;
@Override
public synchronized void transformChanged( final AffineTransform3D transform )
public ManualTransformation( final ViewerState state )
{
viewerTransform.set( transform );
state.setViewerTransform( transform );
for ( final TransformListener< AffineTransform3D > l : transformListeners )
l.transformChanged( viewerTransform );
requestRepaint();
this.state = state;
io = new XmlIoTransformedSources();
}
@Override
public void visibilityChanged( final VisibilityAndGrouping.Event e )
public void restoreFromXml( final Element parent )
{
switch ( e.id )
{
case CURRENT_SOURCE_CHANGED:
requestRepaint();
break;
case DISPLAY_MODE_CHANGED:
requestRepaint();
break;
case GROUP_NAME_CHANGED:
requestRepaint();
break;
case VISIBILITY_CHANGED:
requestRepaint();
break;
}
final Element elem = parent.getChild( io.getTagName() );
final List< TransformedSource< ? > > sources = getTransformedSources();
final List< AffineTransform3D > transforms = io.fromXml( elem ).getTransforms();
if ( sources.size() != transforms.size() )
System.err.println( "failed to load <" + io.getTagName() + "> source and transform count mismatch" );
else
for ( int i = 0; i < sources.size(); ++i )
sources.get( i ).setFixedTransform( transforms.get( i ) );
}
private final static double c = Math.cos( Math.PI / 4 );
/**
* Switch to next interpolation mode. (Currently, there are two
* interpolation modes: nearest-neighbor and N-linear.
*/
public synchronized void toggleInterpolation()
{
final Interpolation interpolation = state.getInterpolation();
if ( interpolation == Interpolation.NEARESTNEIGHBOR )
private ArrayList< TransformedSource< ? > > getTransformedSources()
{
state.setInterpolation( Interpolation.NLINEAR );
}
else
final ArrayList< TransformedSource< ? > > list = new ArrayList< TransformedSource< ? > >();
for ( final SourceState< ? > sourceState : state.getSources() )
{
state.setInterpolation( Interpolation.NEARESTNEIGHBOR );
final Source< ? > source = sourceState.getSpimSource();
if ( TransformedSource.class.isInstance( source ) )
list.add( ( TransformedSource< ? > ) source );
}
requestRepaint();
return list;
}
/**
* Set the viewer transform.
*/
public synchronized void setCurrentViewerTransform( final AffineTransform3D viewerTransform )
{
transformChanged( viewerTransform );
}
/**
* Get a copy of the current {@link ViewerState}.
*
* @return a copy of the current {@link ViewerState}.
*/
public synchronized ViewerState getState()
private boolean tryLoadSettings( final String baseFilename, final SetupAssignments setupAssignments )
{
return state.copy();
}
/**
* Add a {@link TransformListener} to notify about viewer transformation
* changes. Listeners will be notified <em>before</em> calling
* {@link #requestRepaint()} so they have the chance to interfere.
*
* @param listener
* the transform listener to add.
* @param index
* position in the list of listeners at which to insert this one.
*/
public void addTransformListener( final TransformListener< AffineTransform3D > listener, final int index )
final String settings = baseFilename + ".settings.xml";
if ( new File( settings ).isFile() )
{
synchronized ( transformListeners )
try
{
final int s = transformListeners.size();
transformListeners.add( index < 0 ? 0 : index > s ? s : index, listener );
listener.transformChanged( viewerTransform );
final SAXBuilder sax = new SAXBuilder();
final Document doc = sax.build( settings );
final Element root = doc.getRootElement();
stateFromXml( root );
setupAssignments.restoreFromXml( root );
new ManualTransformation( state ).restoreFromXml( root );
return true;
}
}
public synchronized void stateFromXml( final Element parent )
catch ( final Exception e )
{
final XmlIoViewerState io = new XmlIoViewerState();
io.restoreFromXml( parent.getChild( io.getTagName() ), state );
e.printStackTrace();
}
public int getWidth()
{
return width;
}
public int getHeight()
{
return height;
return false;
}
public class ThumbnailTarget implements RenderTarget
public static void main( final String[] args )
{
private BufferedImage bi;
int width, height;
public ThumbnailTarget( int width, int height )
final String fn = args[ 0 ];
try
{
this.width = width;
this.height = height;
}
final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( fn );
final String thumbnailFile = fn.replace( ".xml", ".png" );
final BufferedImage bi = makeThumbnail( spimData, fn, 100, 100 );
@Override
public BufferedImage setBufferedImage( final BufferedImage bufferedImage )
try
{
bi = bufferedImage;
return null;
ImageIO.write( bi, "png", new File( thumbnailFile ) );
}
@Override
public int getWidth()
catch ( final Exception e )
{
return width;
}
@Override
public int getHeight()
{
return height;
}
public BufferedImage getBufferedImage()
catch ( final Exception e )
{
return bi;
e.printStackTrace();
}
}
}
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