From c46c1b520af0201efa3cc4fb0ed0c235898ab656 Mon Sep 17 00:00:00 2001
From: Curtis Rueden <ctrueden@wisc.edu>
Date: Sat, 25 Feb 2017 14:11:49 -0600
Subject: [PATCH] Convert ImageJ 1.x plugins to SciJava commands
Among other benefits, this allows the plugins to be discovered
efficiently simply by being on the classpath, rather than needing a
plugins.dir system property pointing to a single location with all
the JAR files, which must then be scanned for plugins.config files.
This is a breaking API change, so bumps to major version 4.
---
pom.xml | 2 +-
.../java/bdv/ij/BigDataBrowserPlugIn.java | 11 ++++++----
src/main/java/bdv/ij/BigDataViewerPlugIn.java | 9 +++++---
.../java/bdv/ij/ExportCellVoyagerPlugIn.java | 22 ++++++++++++++-----
.../java/bdv/ij/ExportImagePlusPlugIn.java | 12 ++++++----
.../java/bdv/ij/ExportSpimFusionPlugIn.java | 12 ++++++----
.../java/bdv/ij/ExportSpimSequencePlugIn.java | 12 ++++++----
src/main/java/bdv/ij/ImportPlugIn.java | 11 ++++++----
src/main/java/bdv/ij/OpenImagePlusPlugIn.java | 12 ++++++----
src/main/java/bdv/ij/OpenImarisPlugIn.java | 12 ++++++----
src/main/resources/plugins.config | 20 -----------------
11 files changed, 78 insertions(+), 57 deletions(-)
delete mode 100644 src/main/resources/plugins.config
diff --git a/pom.xml b/pom.xml
index 577ab6f..251c300 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer_fiji</artifactId>
- <version>3.0.2-SNAPSHOT</version>
+ <version>4.0.0-SNAPSHOT</version>
<name>BigDataViewer Fiji</name>
<description>Fiji plugins for starting BigDataViewer and exporting data.</description>
diff --git a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
index 98ce441..f2607f2 100644
--- a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
+++ b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
@@ -27,19 +27,22 @@ import javax.swing.JOptionPane;
import javax.swing.JScrollPane;
import org.apache.commons.lang.StringUtils;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
import bdv.viewer.ViewerOptions;
import ij.IJ;
import ij.ImageJ;
-import ij.plugin.PlugIn;
import mpicbg.spim.data.SpimDataException;
/**
* @author HongKee Moon <moon@mpi-cbg.de>
*/
-public class BigDataBrowserPlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Browse BigDataServer")
+public class BigDataBrowserPlugIn implements Command
{
private final Map< String, ImageIcon > imageMap = new HashMap<>();
@@ -48,7 +51,7 @@ public class BigDataBrowserPlugIn implements PlugIn
public static String serverUrl = "http://";
@Override
- public void run( final String arg )
+ public void run()
{
BufferedImage image = null;
try
@@ -198,6 +201,6 @@ public class BigDataBrowserPlugIn implements PlugIn
public static void main( final String[] args )
{
ImageJ.main( args );
- new BigDataBrowserPlugIn().run( null );
+ new BigDataBrowserPlugIn().run();
}
}
diff --git a/src/main/java/bdv/ij/BigDataViewerPlugIn.java b/src/main/java/bdv/ij/BigDataViewerPlugIn.java
index 0267908..f37c3de 100644
--- a/src/main/java/bdv/ij/BigDataViewerPlugIn.java
+++ b/src/main/java/bdv/ij/BigDataViewerPlugIn.java
@@ -10,18 +10,21 @@ import java.util.concurrent.atomic.AtomicBoolean;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
import bdv.viewer.ViewerOptions;
import ij.Prefs;
-import ij.plugin.PlugIn;
-public class BigDataViewerPlugIn implements PlugIn
+@Plugin(type = Command.class, menuPath = "Plugins>BigDataViewer>Open XML/HDF5")
+public class BigDataViewerPlugIn implements Command
{
static String lastDatasetPath = "./export.xml";
@Override
- public void run( final String arg )
+ public void run()
{
File file = null;
diff --git a/src/main/java/bdv/ij/ExportCellVoyagerPlugIn.java b/src/main/java/bdv/ij/ExportCellVoyagerPlugIn.java
index eaf88e1..0ff922b 100644
--- a/src/main/java/bdv/ij/ExportCellVoyagerPlugIn.java
+++ b/src/main/java/bdv/ij/ExportCellVoyagerPlugIn.java
@@ -14,6 +14,9 @@ import java.io.FilenameFilter;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.export.ProgressWriter;
import bdv.ij.export.tiles.CellVoyagerDataExporter;
import bdv.ij.util.PluginHelper;
@@ -21,9 +24,10 @@ import bdv.ij.util.ProgressWriterIJ;
import fiji.util.gui.GenericDialogPlus;
import ij.IJ;
import ij.ImageJ;
-import ij.plugin.PlugIn;
-public class ExportCellVoyagerPlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Export CellVoyager dataset as XML/HDF5")
+public class ExportCellVoyagerPlugIn implements Command
{
protected static class Parameters
@@ -56,11 +60,18 @@ public class ExportCellVoyagerPlugIn implements PlugIn
static String sourceFolderStr;
+ private String sourcePath;
+
+ public void setSourcePath( final String sourcePath )
+ {
+ this.sourcePath = sourcePath;
+ }
+
@Override
- public void run( final String arg )
+ public void run()
{
- final Parameters params = getParameters( arg );
+ final Parameters params = getParameters( sourcePath );
if ( params == null )
return;
@@ -248,6 +259,7 @@ public class ExportCellVoyagerPlugIn implements PlugIn
final ExportCellVoyagerPlugIn plugin = new ExportCellVoyagerPlugIn();
final File file = new File( "/Users/tinevez/Desktop/Data/1_7_6_1_2/20130703T145244/" );
- plugin.run( file.getAbsolutePath() );
+ plugin.setSourcePath( file.getAbsolutePath() );
+ plugin.run();
}
}
diff --git a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
index 124579b..3297fbc 100644
--- a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
@@ -14,6 +14,9 @@ import net.imglib2.FinalDimensions;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.realtransform.AffineTransform3D;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
@@ -37,7 +40,6 @@ import ij.ImagePlus;
import ij.WindowManager;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.registration.ViewRegistration;
import mpicbg.spim.data.registration.ViewRegistrations;
@@ -51,17 +53,19 @@ import mpicbg.spim.data.sequence.TimePoints;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class ExportImagePlusPlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Export Current Image as XML/HDF5")
+public class ExportImagePlusPlugIn implements Command
{
public static void main( final String[] args )
{
new ImageJ();
IJ.run("Confocal Series (2.2MB)");
- new ExportImagePlusPlugIn().run( null );
+ new ExportImagePlusPlugIn().run();
}
@Override
- public void run( final String arg )
+ public void run()
{
// get the current image
final ImagePlus imp = WindowManager.getCurrentImage();
diff --git a/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java b/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
index e313cde..6f37e87 100644
--- a/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
+++ b/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
@@ -23,6 +23,9 @@ import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.util.Pair;
import net.imglib2.util.ValuePair;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
@@ -47,7 +50,6 @@ import ij.IJ;
import ij.ImagePlus;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
@@ -66,7 +68,9 @@ import mpicbg.spim.io.SPIMConfiguration;
import mpicbg.spim.io.TextFileAccess;
import spimopener.SPIMExperiment;
-public class ExportSpimFusionPlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Export Fused Sequence as XML/HDF5")
+public class ExportSpimFusionPlugIn implements Command
{
static double minValueStatic = 0;
@@ -91,7 +95,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
static String autoChunkSizes = "{16,16,16}";
@Override
- public void run( final String arg0 )
+ public void run()
{
final Parameters params = getParameters();
@@ -1057,6 +1061,6 @@ public class ExportSpimFusionPlugIn implements PlugIn
public static void main(final String[] args)
{
- new ExportSpimFusionPlugIn().run( null );
+ new ExportSpimFusionPlugIn().run();
}
}
diff --git a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
index 39b70b0..b3808ea 100644
--- a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
+++ b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
@@ -15,6 +15,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
@@ -34,7 +37,6 @@ import fiji.util.gui.GenericDialogPlus;
import ij.IJ;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.sequence.TimePoint;
import mpicbg.spim.io.ConfigurationParserException;
@@ -43,10 +45,12 @@ import mpicbg.spim.io.SPIMConfiguration;
import mpicbg.spim.io.TextFileAccess;
import spimopener.SPIMExperiment;
-public class ExportSpimSequencePlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Export Spim Sequence as XML/HDF5")
+public class ExportSpimSequencePlugIn implements Command
{
@Override
- public void run( final String arg0 )
+ public void run()
{
final Parameters params = getParameters();
@@ -713,6 +717,6 @@ public class ExportSpimSequencePlugIn implements PlugIn
Bead_Registration.fileNamePattern = "spim_TL{tt}_Angle{a}.tif";
Bead_Registration.timepoints = "0";
Bead_Registration.angles = "0";
- new ExportSpimSequencePlugIn().run( null );
+ new ExportSpimSequencePlugIn().run();
}
}
diff --git a/src/main/java/bdv/ij/ImportPlugIn.java b/src/main/java/bdv/ij/ImportPlugIn.java
index d333896..2dbe3e3 100644
--- a/src/main/java/bdv/ij/ImportPlugIn.java
+++ b/src/main/java/bdv/ij/ImportPlugIn.java
@@ -13,6 +13,9 @@ import java.util.List;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.numeric.NumericType;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.ViewerImgLoader;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
@@ -24,7 +27,6 @@ import ij.ImagePlus;
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
import ij.measure.Calibration;
-import ij.plugin.PlugIn;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader;
@@ -38,7 +40,8 @@ import mpicbg.spim.data.sequence.VoxelDimensions;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class ImportPlugIn implements PlugIn
+@Plugin(type = Command.class, menuPath = "File>Import>BigDataViewer...")
+public class ImportPlugIn implements Command
{
public static String xmlFile = "";
public static int timepoint = 0;
@@ -59,7 +62,7 @@ public class ImportPlugIn implements PlugIn
}
@Override
- public void run( final String arg0 )
+ public void run()
{
final GenericDialogPlus gd = new GenericDialogPlus( "Import from BigDataViewer file" );
gd.addFileField( "xml file", xmlFile );
@@ -219,6 +222,6 @@ public class ImportPlugIn implements PlugIn
public static void main( final String[] args )
{
new ImageJ();
- new ImportPlugIn().run( null );
+ new ImportPlugIn().run();
}
}
diff --git a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
index 402b6dc..ba26555 100644
--- a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
@@ -8,6 +8,9 @@ import net.imglib2.FinalDimensions;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.ARGBType;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
import bdv.img.imagestack.ImageStackImageLoader;
@@ -25,7 +28,6 @@ import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.WindowManager;
-import ij.plugin.PlugIn;
import ij.process.LUT;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
@@ -41,7 +43,9 @@ import mpicbg.spim.data.sequence.TimePoints;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
-public class OpenImagePlusPlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Open Current Image")
+public class OpenImagePlusPlugIn implements Command
{
public static void main( final String[] args )
{
@@ -49,11 +53,11 @@ public class OpenImagePlusPlugIn implements PlugIn
new ImageJ();
IJ.run("Confocal Series (2.2MB)");
// IJ.run("Fly Brain (1MB)");
- new OpenImagePlusPlugIn().run( null );
+ new OpenImagePlusPlugIn().run();
}
@Override
- public void run( final String arg )
+ public void run()
{
// get the current image
final ImagePlus imp = WindowManager.getCurrentImage();
diff --git a/src/main/java/bdv/ij/OpenImarisPlugIn.java b/src/main/java/bdv/ij/OpenImarisPlugIn.java
index 0e1d450..9db0ce1 100644
--- a/src/main/java/bdv/ij/OpenImarisPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImarisPlugIn.java
@@ -10,6 +10,9 @@ import java.util.concurrent.atomic.AtomicBoolean;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
import bdv.img.imaris.Imaris;
@@ -17,19 +20,20 @@ import bdv.spimdata.SpimDataMinimal;
import bdv.viewer.ViewerOptions;
import ij.ImageJ;
import ij.Prefs;
-import ij.plugin.PlugIn;
-public class OpenImarisPlugIn implements PlugIn
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Open Imaris (experimental)")
+public class OpenImarisPlugIn implements Command
{
static String lastDatasetPath = "";
public static void main( final String[] args )
{
ImageJ.main( args );
- new OpenImarisPlugIn().run( null );
+ new OpenImarisPlugIn().run();
}
@Override
- public void run( final String arg )
+ public void run()
{
File file = null;
diff --git a/src/main/resources/plugins.config b/src/main/resources/plugins.config
deleted file mode 100644
index 2807a76..0000000
--- a/src/main/resources/plugins.config
+++ /dev/null
@@ -1,20 +0,0 @@
-# Name: BigDataViewer
-# Author: Tobias Pietzsch
-# Version: 1.0.0
-
-# A single .jar file can contain multiple plugins, specified in separate lines.
-#
-# The format is: <menu>, "<menu label>", <class name>
-#
-# If something like ("<arg>") is appended to the class name, the setup() method
-# will get that as arg parameter; otherwise arg is simply the empty string.
-
-Plugins>BigDataViewer, "Open XML/HDF5", bdv.ij.BigDataViewerPlugIn
-Plugins>BigDataViewer, "Open Current Image", bdv.ij.OpenImagePlusPlugIn
-Plugins>BigDataViewer, "Browse BigDataServer", bdv.ij.BigDataBrowserPlugIn
-Plugins>BigDataViewer, "Export Current Image as XML/HDF5", bdv.ij.ExportImagePlusPlugIn
-Plugins>BigDataViewer, "Export Spim Sequence as XML/HDF5", bdv.ij.ExportSpimSequencePlugIn
-Plugins>BigDataViewer, "Export Fused Sequence as XML/HDF5", bdv.ij.ExportSpimFusionPlugIn
-Plugins>BigDataViewer, "Export CellVoyager dataset as XML/HDF5", bdv.ij.ExportCellVoyagerPlugIn
-Plugins>BigDataViewer, "Open Imaris (experimental)", bdv.ij.OpenImarisPlugIn
-File>Import, "BigDataViewer...", bdv.ij.ImportPlugIn
\ No newline at end of file
--
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