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Bump to pom-scijava-32.0.0-beta-5 and fix build errors #9

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Aug 19, 2022
Merged

Bump to pom-scijava-32.0.0-beta-5 and fix build errors #9

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10 changes: 2 additions & 8 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>28.0.0</version>
<version>32.0.0-beta-5</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -84,14 +84,8 @@
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

<commons-cli.version>1.2</commons-cli.version>
<commons-cli.version>1.5.0</commons-cli.version>
<stringtemplate.version>3.2.1</stringtemplate.version>

<!-- TODO: Remove these version pins and update the code. -->
<bigdataviewer-core.version>9.0.3</bigdataviewer-core.version>
<imglib2.version>5.9.0</imglib2.version>
<imglib2-cache.version>1.0.0-beta-13</imglib2-cache.version>
<spim_data.version>2.2.4</spim_data.version>
</properties>

<repositories>
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/bdv/server/BigDataServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import mpicbg.spim.data.SpimDataException;

import org.apache.commons.cli.*;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.eclipse.jetty.server.Connector;
import org.eclipse.jetty.server.ConnectorStatistics;
import org.eclipse.jetty.server.Handler;
Expand Down
147 changes: 73 additions & 74 deletions src/main/java/bdv/util/ThumbnailGenerator.java
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Original file line number Diff line number Diff line change
@@ -1,36 +1,34 @@
package bdv.util;

import java.awt.image.BufferedImage;
import java.io.File;
import java.util.ArrayList;
import java.util.List;

import javax.imageio.ImageIO;

import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.input.SAXBuilder;

import bdv.BigDataViewer;
import bdv.cache.CacheControl;
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.tools.transformation.ManualTransformation;
import bdv.viewer.BasicViewerState;
import bdv.viewer.SourceAndConverter;
import bdv.viewer.SynchronizedViewerState;
import bdv.viewer.ViewerState;
import bdv.viewer.render.AccumulateProjectorARGB;
import bdv.viewer.render.MultiResolutionRenderer;
import bdv.viewer.state.SourceGroup;
import bdv.viewer.state.SourceState;
import bdv.viewer.state.ViewerState;
import bdv.viewer.render.RenderTarget;
import bdv.viewer.render.awt.BufferedImageRenderResult;
import bdv.viewer.state.XmlIoViewerState;
import java.awt.image.BufferedImage;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import javax.imageio.ImageIO;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.ui.PainterThread;
import net.imglib2.ui.RenderTarget;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.input.SAXBuilder;

import static bdv.viewer.DisplayMode.SINGLE;
import static bdv.viewer.Interpolation.NEARESTNEIGHBOR;

/**
* Created by moon on 2/5/15.
Expand Down Expand Up @@ -69,17 +67,26 @@ public static BufferedImage makeThumbnail( final SpimDataMinimal spimData, final
if ( !generator.tryLoadSettings( baseFilename, setupAssignments ) )
InitializeViewerState.initBrightness( 0.001, 0.999, state, setupAssignments );

class ThumbnailTarget implements RenderTarget
class ThumbnailTarget implements RenderTarget< BufferedImageRenderResult >
{
BufferedImage bi;
final BufferedImageRenderResult renderResult = new BufferedImageRenderResult();

@Override
public BufferedImage setBufferedImage( final BufferedImage bufferedImage )
public BufferedImageRenderResult getReusableRenderResult()
{
bi = bufferedImage;
return null;
return renderResult;
}

@Override
public BufferedImageRenderResult createRenderResult()
{
return new BufferedImageRenderResult();
}

@Override
public void setRenderResult( final BufferedImageRenderResult renderResult )
{}

@Override
public int getWidth()
{
Expand All @@ -93,15 +100,50 @@ public int getHeight()
}
}
final ThumbnailTarget renderTarget = new ThumbnailTarget();
new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, AccumulateProjectorARGB.factory, new CacheControl.Dummy() ).paint( state );
return renderTarget.bi;
final MultiResolutionRenderer renderer = new MultiResolutionRenderer(
renderTarget, () -> {}, new double[] { 1 }, 0, 1, null, false,
AccumulateProjectorARGB.factory, new CacheControl.Dummy() );
renderer.paint( state );
return renderTarget.renderResult.getBufferedImage();
}

/**
* Initialize ViewerState with the given {@code sources} and {@code numTimepoints}.
* Set up {@code numGroups} SourceGroups named "group 1", "group 2", etc. Add the
* first source to the first group, the second source to the second group etc.
*
* TODO: Setting up groups like this doesn't make a lot of sense. This just
* replicates legacy behaviour. The remaining thing that stands in the way of
* removing it is ViewerState serialization, which assumes that there are always 10
* groups ... m(
*/
private static SynchronizedViewerState setupState( final List< SourceAndConverter< ? > > sources, final int numTimepoints, final int numGroups )
{
final SynchronizedViewerState state = new SynchronizedViewerState( new BasicViewerState() );
state.addSources( sources );
state.setSourcesActive( sources, true );
for ( int i = 0; i < numGroups; ++i ) {
final bdv.viewer.SourceGroup handle = new bdv.viewer.SourceGroup();
state.addGroup( handle );
state.setGroupName( handle, "group " + ( i + 1 ) );
state.setGroupActive( handle, true );
if ( i < sources.size() )
state.addSourceToGroup( sources.get( i ), handle );
}
state.setNumTimepoints( numTimepoints );
state.setInterpolation( NEARESTNEIGHBOR );
state.setDisplayMode( SINGLE );
state.setCurrentSource( sources.isEmpty() ? null : sources.get( 0 ) );
state.setCurrentGroup( numGroups <= 0 ? null : state.getGroups().get( 0 ) );

return state;
}

/**
* Currently rendered state (visible sources, transformation, timepoint,
* etc.)
*/
private final ViewerState state;
private final SynchronizedViewerState state;

/**
* @param sources
Expand All @@ -112,56 +154,14 @@ public int getHeight()
private ThumbnailGenerator( final List< SourceAndConverter< ? > > sources, final int numTimePoints )
{
final int numGroups = 10;
final ArrayList< SourceGroup > groups = new ArrayList< SourceGroup >( numGroups );
for ( int i = 0; i < numGroups; ++i )
groups.add( new SourceGroup( "" ) );

state = new ViewerState( sources, groups, numTimePoints );
if ( !sources.isEmpty() )
state.setCurrentSource( 0 );
state = setupState( sources, numTimePoints, numGroups );
}

private void stateFromXml( final Element parent )
{
final XmlIoViewerState io = new XmlIoViewerState();
io.restoreFromXml( parent.getChild( io.getTagName() ), state );
}

private static class ManualTransformation
{
private final ViewerState state ;

private final XmlIoTransformedSources io;

public ManualTransformation( final ViewerState state )
{
this.state = state;
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 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;
}
final bdv.viewer.state.ViewerState deprecatedState = new bdv.viewer.state.ViewerState( state );
io.restoreFromXml( parent.getChild( io.getTagName() ), deprecatedState );
}

private boolean tryLoadSettings( final String baseFilename, final SetupAssignments setupAssignments )
Expand All @@ -176,7 +176,7 @@ private boolean tryLoadSettings( final String baseFilename, final SetupAssignmen
final Element root = doc.getRootElement();
stateFromXml( root );
setupAssignments.restoreFromXml( root );
new ManualTransformation( state ).restoreFromXml( root );
new ManualTransformation( state.getSources() ).restoreFromXml( root );
return true;
}
catch ( final Exception e )
Expand Down Expand Up @@ -210,5 +210,4 @@ public static void main( final String[] args )
e.printStackTrace();
}
}

}