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Resolves #4 to bring compatibility with bigdataviewer-core 10.4.12 #6

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Resolves #4 to bring compatibility with bigdataviewer-core 10.4.12 #6

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b57bf41
modified: pom.xml
mhdominguez Mar 3, 2024
bcca2f8
modified: pom.xml
mhdominguez Mar 6, 2024
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24 changes: 19 additions & 5 deletions pom.xml
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Expand Up @@ -5,7 +5,8 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>28.0.0</version>
<version>37.0.0</version>
<relativePath />
</parent>

<groupId>org.janelia.simview</groupId>
Expand Down Expand Up @@ -89,6 +90,7 @@
<additionalparam>-Xdoclint:none</additionalparam>
<klb.version>0.3.6</klb.version>
<!-- <enforcer.skip>true</enforcer.skip> -->
<bigdataviewer-core.version>10.4.12</bigdataviewer-core.version>
</properties>

<repositories>
Expand All @@ -104,18 +106,30 @@
<artifactId>klb</artifactId>
<version>${klb.version}</version>
</dependency>

<!-- BigDataViewer dependencies -->
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>SPIM_Registration</artifactId>
<artifactId>spim_data</artifactId>
</dependency>


<!-- ImgLib2 dependencies -->
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-cache</artifactId>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
</dependency>
<dependency>
<groupId>com.miglayout</groupId>
<artifactId>miglayout</artifactId>
<classifier>swing</classifier>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-ij</artifactId>
</dependency>
</dependencies>

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10 changes: 5 additions & 5 deletions src/main/java/org/janelia/simview/klb/bdv/KlbDownsampler.java
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Expand Up @@ -3,8 +3,8 @@
import bdv.export.Downsample;
import bdv.export.ExportMipmapInfo;
import bdv.export.ProposeMipmaps;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
import mpicbg.spim.data.SpimData;
import mpicbg.spim.data.XmlIoSpimData;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
Expand Down Expand Up @@ -63,9 +63,9 @@ public void process( final File xmlFile, final boolean skipFirst )
this.skipFirst = skipFirst;
final String filePath = xmlFile.getAbsolutePath();

SpimDataMinimal data = null;
SpimData data = null;
try {
data = new XmlIoSpimDataMinimal().load( filePath );
data = new XmlIoSpimData().load( filePath );
} catch ( SpimDataException e ) {
e.printStackTrace();
}
Expand Down Expand Up @@ -244,4 +244,4 @@ public static void main( final String[] args )
new KlbDownsampler().process( new File( filePath ), skipFirst );
}

}
}
3 changes: 2 additions & 1 deletion src/main/java/org/janelia/simview/klb/bdv/KlbImgLoader.java
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Expand Up @@ -16,6 +16,7 @@
import net.imglib2.*;
import net.imglib2.cache.volatiles.CacheHints;
import net.imglib2.cache.volatiles.LoadingStrategy;
import net.imglib2.img.basictypeaccess.DataAccess;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
Expand Down Expand Up @@ -86,7 +87,7 @@ public CacheControl getCacheControl()
}


public class KlbSetupImgLoader< T extends RealType< T > & NativeType< T >, V extends Volatile< T > & NativeType< V >, A > implements ViewerSetupImgLoader< T, V >, MultiResolutionSetupImgLoader< T >
public class KlbSetupImgLoader< T extends RealType< T > & NativeType< T >, V extends Volatile< T > & NativeType< V >, A extends DataAccess > implements ViewerSetupImgLoader< T, V >, MultiResolutionSetupImgLoader< T >
{
private final int viewSetupId;
private final long[] imageSize = new long[ 3 ];
Expand Down
24 changes: 12 additions & 12 deletions src/main/java/org/janelia/simview/klb/bdv/KlbSpimDataAdapter.java
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Expand Up @@ -14,15 +14,15 @@
import java.util.HashMap;
import java.util.List;

import spim.fiji.datasetmanager.MultiViewDatasetDefinition;
import spim.fiji.spimdata.SpimData2;
//import spim.fiji.datasetmanager.MultiViewDatasetDefinition;
import mpicbg.spim.data.SpimData;

/**
* Interfaces a KlbPartitionResolver instance with Fiji's SpimData
* dataset layout description. Can be consumed directly or serialized
* to XML.
*/
public class KlbSpimDataAdapter implements MultiViewDatasetDefinition
public class KlbSpimDataAdapter //implements MultiViewDatasetDefinition
{

private final KlbPartitionResolver resolver;
Expand All @@ -32,20 +32,20 @@ public KlbSpimDataAdapter( final KlbPartitionResolver resolver )
this.resolver = resolver;
}

@Override
//@Override
public String getTitle()
{
return "KLB Dataset";
}

@Override
//@Override
public String getExtendedDescription()
{
return "KLB Dataset";
}

@Override
public SpimData2 createDataset()
//@Override
public SpimData createDataset()
{
// ViewSetups
final long[] imageSize = new long[ 3 ];
Expand Down Expand Up @@ -136,15 +136,15 @@ public SpimData2 createDataset()
}
}

// combine all the above into a SpimData2
return new SpimData2( new File( System.getProperty( "user.home" ) ), seq, new ViewRegistrations( registrations ), null, null );
// combine all the above into a SpimData
return new SpimData( new File( System.getProperty( "user.home" ) ), seq, new ViewRegistrations( registrations ) );
}

@Override
/*@Override
public MultiViewDatasetDefinition newInstance()
{
return new KlbSpimDataAdapter( null );
}
}*/

/**
* Writes the dataset definition to XML.
Expand All @@ -153,7 +153,7 @@ public MultiViewDatasetDefinition newInstance()
*/
public void writeXML( final String filePath ) throws SpimDataException
{
final SpimData2 data = createDataset();
final SpimData data = createDataset();
data.setBasePath( new File( filePath ).getParentFile() );
new XmlIoSpimData().save( data, filePath );
}
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/janelia/simview/klb/bdv/KlbVolatileArrayLoader.java
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Expand Up @@ -5,8 +5,9 @@
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import org.janelia.simview.klb.KLB;
import net.imglib2.img.basictypeaccess.DataAccess;

public abstract class KlbVolatileArrayLoader< T extends RealType< T > & NativeType< T >, V extends Volatile< T > & NativeType< V >, A > implements CacheArrayLoader< A >
public abstract class KlbVolatileArrayLoader< T extends RealType< T > & NativeType< T >, V extends Volatile< T > & NativeType< V >, A extends DataAccess > implements CacheArrayLoader< A >
{
protected final KLB klb = KLB.newInstance();
private final KlbPartitionResolver resolver;
Expand Down
9 changes: 5 additions & 4 deletions src/main/java/org/janelia/simview/klb/bdv/TransformsSpimreg2Simview.java
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Expand Up @@ -23,8 +23,9 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import spim.fiji.spimdata.SpimData2;
import spim.fiji.spimdata.XmlIoSpimData2;
import mpicbg.spim.data.SpimData;
import mpicbg.spim.data.XmlIoSpimData;


@Plugin( type = Command.class, menuPath = "Plugins>Multiview Reconstruction>Convert transforms to SiMView" )
public class TransformsSpimreg2Simview implements Command
Expand Down Expand Up @@ -58,12 +59,12 @@ public void run()
{
log.info( "Converting SPIM Registration transforms to SiMView standard" );

SpimData2 spimData = null;
SpimData spimData = null;
SequenceDescription seq = null;
KlbImgLoader imageLoader = null;
MissingViews missingViews = null;
try {
spimData = new XmlIoSpimData2( null ).load( xmlFile.getAbsolutePath() );
spimData = new XmlIoSpimData().load( xmlFile.getAbsolutePath() );
seq = spimData.getSequenceDescription();
imageLoader = ( KlbImgLoader ) seq.getImgLoader();
missingViews = seq.getMissingViews();
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/janelia/simview/klb/bdv/ui/ViewSetupsConfigDialog.java
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Expand Up @@ -14,7 +14,7 @@
import java.awt.event.*;
import java.io.File;

import spim.fiji.spimdata.SpimData2;
import mpicbg.spim.data.SpimData;

public class ViewSetupsConfigDialog extends JDialog implements ActionListener
{
Expand Down Expand Up @@ -134,7 +134,7 @@ public void actionPerformed( final ActionEvent e )
} else if ( source == viewButton ) {
final KlbPartitionResolver resolver = getResolver();
final KlbSpimDataAdapter spimDataAdapter = new KlbSpimDataAdapter( resolver );
final SpimData2 spimData = spimDataAdapter.createDataset();
final SpimData spimData = spimDataAdapter.createDataset();
BigDataViewer.open( spimData, "", new ProgressWriterConsole(), ViewerOptions.options() );
dispose();
}
Expand Down