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WIP: switch from IJ1 plugins to IJ2 plugins #133

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WIP: switch from IJ1 plugins to IJ2 plugins #133

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12 changes: 8 additions & 4 deletions src/main/java/bdv/ij/ApplyBigwarpPlugin.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,8 @@
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadata;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadataParser;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import bdv.export.ProgressWriter;
import bdv.gui.TransformTypeSelectDialog;
Expand All @@ -63,7 +65,6 @@
import ij.ImageJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.plugin.PlugIn;
import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.FinalInterval;
import net.imglib2.Interval;
Expand All @@ -87,7 +88,10 @@
* Apply a bigwarp transform to a 2d or 3d ImagePlus
*
*/
public class ApplyBigwarpPlugin implements PlugIn
@Plugin(type= Command.class,
menuPath = "Plugins>BigDataViewer>Big Warp Apply"
)
public class ApplyBigwarpPlugin implements Command
{
public static final String TARGET = "Target";
public static final String MOVING = "Moving";
Expand All @@ -103,7 +107,7 @@ public class ApplyBigwarpPlugin implements PlugIn
public static void main( String[] args ) throws IOException
{
new ImageJ();
new ApplyBigwarpPlugin().run( "" );
new ApplyBigwarpPlugin().run();
}

public static boolean validateInput(
Expand Down Expand Up @@ -954,7 +958,7 @@ public static <S, T extends NativeType<T> & NumericType<T>> void runN5Export(
}

@Override
public void run( String arg )
public void run()
{
if ( IJ.versionLessThan( "1.40" ) )
return;
Expand Down
12 changes: 8 additions & 4 deletions src/main/java/bdv/ij/BigWarpImagePlusPlugIn.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@
import java.io.IOException;

import org.janelia.utility.ui.RepeatingReleasedEventsFixer;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import bdv.ij.util.ProgressWriterIJ;
import bigwarp.BigWarp;
Expand All @@ -35,7 +37,6 @@
import ij.ImageJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.plugin.PlugIn;
import mpicbg.spim.data.SpimData;
import mpicbg.spim.data.SpimDataException;

Expand All @@ -46,7 +47,10 @@
* @author Tobias Pietzsch &lt;tobias.pietzsch@gmail.com&gt;
* @author Stephan Saalfeld &lt;saalfelds@janelia.hhmi.org&gt;
*/
public class BigWarpImagePlusPlugIn implements PlugIn
@Plugin(type = Command.class,
menuPath = "Plugins>BigDataViewer>Big Warp"
)
public class BigWarpImagePlusPlugIn implements Command
{

private ImagePlus movingIp;
Expand All @@ -56,11 +60,11 @@ public static void main( final String[] args ) throws IOException
{
new ImageJ();
IJ.run("Boats (356K)");
new BigWarpImagePlusPlugIn().run( null );
new BigWarpImagePlusPlugIn().run();
}

@Override
public void run( final String arg )
public void run()
{
if ( IJ.versionLessThan( "1.40" ) ) return;

Expand Down
12 changes: 8 additions & 4 deletions src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@
import org.janelia.saalfeldlab.n5.ij.N5Exporter;
import org.janelia.saalfeldlab.n5.ij.N5Factory;
import org.janelia.saalfeldlab.n5.imglib2.N5DisplacementField;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import bdv.viewer.SourceAndConverter;
import bigwarp.BigWarpExporter;
Expand All @@ -51,7 +53,6 @@
import ij.ImageJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.plugin.PlugIn;
import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.Cursor;
Expand Down Expand Up @@ -85,7 +86,10 @@
* @author Tobias Pietzsch &lt;tobias.pietzsch@gmail.com&gt;
* @author Stephan Saalfeld &lt;saalfelds@janelia.hhmi.org&gt;
*/
public class BigWarpToDeformationFieldPlugIn implements PlugIn
@Plugin(type= Command.class,
menuPath = "Plugins>BigDataViewer>Big Warp to Displacement field"
)
public class BigWarpToDeformationFieldPlugIn implements Command
{
public static final String[] compressionOptions = new String[] {
N5Exporter.RAW_COMPRESSION,
Expand All @@ -103,7 +107,7 @@ public static void main( final String[] args )
// imp.show();

WindowManager.getActiveWindow();
new BigWarpToDeformationFieldPlugIn().run( null );
new BigWarpToDeformationFieldPlugIn().run();
}

public <T> void runFromBigWarpInstance(
Expand Down Expand Up @@ -165,7 +169,7 @@ public <T> void runFromBigWarpInstance(
}

@Override
public void run( final String arg )
public void run()
{
if ( IJ.versionLessThan( "1.40" ) )
return;
Expand Down
35 changes: 0 additions & 35 deletions src/main/resources/plugins.config
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