diff --git a/src/main/java/bdv/ij/ApplyBigwarpPlugin.java b/src/main/java/bdv/ij/ApplyBigwarpPlugin.java index 68549c6e..60f14db3 100644 --- a/src/main/java/bdv/ij/ApplyBigwarpPlugin.java +++ b/src/main/java/bdv/ij/ApplyBigwarpPlugin.java @@ -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; @@ -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; @@ -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"; @@ -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( @@ -954,7 +958,7 @@ public static & NumericType> void runN5Export( } @Override - public void run( String arg ) + public void run() { if ( IJ.versionLessThan( "1.40" ) ) return; diff --git a/src/main/java/bdv/ij/BigWarpImagePlusPlugIn.java b/src/main/java/bdv/ij/BigWarpImagePlusPlugIn.java index 8199556a..8fa47dde 100755 --- a/src/main/java/bdv/ij/BigWarpImagePlusPlugIn.java +++ b/src/main/java/bdv/ij/BigWarpImagePlusPlugIn.java @@ -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; @@ -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; @@ -46,7 +47,10 @@ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com> * @author Stephan Saalfeld <saalfelds@janelia.hhmi.org> */ -public class BigWarpImagePlusPlugIn implements PlugIn +@Plugin(type = Command.class, + menuPath = "Plugins>BigDataViewer>Big Warp" +) +public class BigWarpImagePlusPlugIn implements Command { private ImagePlus movingIp; @@ -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; diff --git a/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java b/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java index 3a8cf342..0930471e 100644 --- a/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java +++ b/src/main/java/bdv/ij/BigWarpToDeformationFieldPlugIn.java @@ -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; @@ -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; @@ -85,7 +86,10 @@ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com> * @author Stephan Saalfeld <saalfelds@janelia.hhmi.org> */ -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, @@ -103,7 +107,7 @@ public static void main( final String[] args ) // imp.show(); WindowManager.getActiveWindow(); - new BigWarpToDeformationFieldPlugIn().run( null ); + new BigWarpToDeformationFieldPlugIn().run(); } public void runFromBigWarpInstance( @@ -165,7 +169,7 @@ public void runFromBigWarpInstance( } @Override - public void run( final String arg ) + public void run() { if ( IJ.versionLessThan( "1.40" ) ) return; diff --git a/src/main/resources/plugins.config b/src/main/resources/plugins.config deleted file mode 100644 index e36d3e34..00000000 --- a/src/main/resources/plugins.config +++ /dev/null @@ -1,35 +0,0 @@ -### -# #%L -# BigWarp plugin for Fiji. -# %% -# Copyright (C) 2015 - 2021 Howard Hughes Medical Institute. -# %% -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as -# published by the Free Software Foundation, either version 2 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public -# License along with this program. If not, see -# . -# #L% -### -# Name: BigWarp -# Author: John Bogovic -# Version: 1.0.0 - -# A single .jar file can contain multiple plugins, specified in separate lines. -# -# The format is: , "", -# -# If something like ("") is appended to the class name, the setup() method -# will get that as arg parameter; otherwise arg is simply the empty string. - -Plugins>BigDataViewer, "Big Warp", bdv.ij.BigWarpImagePlusPlugIn -Plugins>BigDataViewer, "Big Warp Apply", bdv.ij.ApplyBigwarpPlugin -Plugins>BigDataViewer, "Big Warp to Displacement field", bdv.ij.BigWarpToDeformationFieldPlugIn