diff --git a/.gitignore b/.gitignore
index cbacafce2e63531cc4d06db5118df7c7c53cfeba..d358561c28d0de740515edbafc6966af56b99dc4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,7 @@
**/.settings/
**/target/
*.orig
+*.iml
.classpath
.project
.settings
diff --git a/pom.xml b/pom.xml
index 384754f74c3c3047f24276975b7796d153f11806..9f783f4507ed2da6398e304761dc6d6a4a857078 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,13 +5,13 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
- <version>26.0.0</version>
+ <version>28.0.0</version>
<relativePath />
</parent>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer_fiji</artifactId>
- <version>6.0.1-SNAPSHOT</version>
+ <version>6.2.1-SNAPSHOT</version>
<name>BigDataViewer Fiji</name>
<description>Fiji plugins for starting BigDataViewer and exporting data.</description>
@@ -98,6 +98,12 @@
<license.licenseName>gpl_v3</license.licenseName>
<license.copyrightOwners>BigDataViewer developers.</license.copyrightOwners>
+ <imglib2.version>5.9.0</imglib2.version>
+ <imglib2-ij.version>2.0.0-beta-46</imglib2-ij.version>
+ <bigdataviewer-core.version>9.0.3</bigdataviewer-core.version>
+ <spim_data.version>2.2.4</spim_data.version>
+ <ui-behaviour.version>2.0.1</ui-behaviour.version>
+
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>deploy-to-scijava</releaseProfiles>
</properties>
diff --git a/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java b/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
new file mode 100644
index 0000000000000000000000000000000000000000..5fc5e97253ad9b2b4d71f677fb5968fb3cd22b0c
--- /dev/null
+++ b/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
@@ -0,0 +1,565 @@
+package bdv.ij;
+
+import bdv.export.ExportMipmapInfo;
+import bdv.export.ExportScalePyramid.AfterEachPlane;
+import bdv.export.ExportScalePyramid.LoopbackHeuristic;
+import bdv.export.ProgressWriter;
+import bdv.export.ProposeMipmaps;
+import bdv.export.SubTaskProgressWriter;
+import bdv.export.n5.WriteSequenceToN5;
+import bdv.ij.util.PluginHelper;
+import bdv.ij.util.ProgressWriterIJ;
+import bdv.img.imagestack.ImageStackImageLoader;
+import bdv.img.n5.N5ImageLoader;
+import bdv.img.virtualstack.VirtualStackImageLoader;
+import bdv.spimdata.SequenceDescriptionMinimal;
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import fiji.util.gui.GenericDialogPlus;
+import ij.IJ;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.WindowManager;
+import java.awt.Checkbox;
+import java.awt.TextField;
+import java.awt.event.ItemEvent;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import mpicbg.spim.data.SpimDataException;
+import mpicbg.spim.data.generic.sequence.BasicViewSetup;
+import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
+import mpicbg.spim.data.registration.ViewRegistration;
+import mpicbg.spim.data.registration.ViewRegistrations;
+import mpicbg.spim.data.sequence.Channel;
+import mpicbg.spim.data.sequence.FinalVoxelDimensions;
+import mpicbg.spim.data.sequence.TimePoint;
+import mpicbg.spim.data.sequence.TimePoints;
+import net.imglib2.FinalDimensions;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.util.Intervals;
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream;
+import org.janelia.saalfeldlab.n5.Bzip2Compression;
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.GzipCompression;
+import org.janelia.saalfeldlab.n5.Lz4Compression;
+import org.janelia.saalfeldlab.n5.RawCompression;
+import org.janelia.saalfeldlab.n5.XzCompression;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+
+/**
+ * ImageJ plugin to export the current image to xml/n5.
+ *
+ * @author Tobias Pietzsch
+ */
+@Plugin(type = Command.class,
+ menuPath = "Plugins>BigDataViewer>Export Current Image as XML/N5")
+public class ExportImagePlusAsN5PlugIn implements Command
+{
+ public static void main( final String[] args )
+ {
+ new ImageJ();
+ final ImagePlus imp = IJ.openImage( "/Users/pietzsch/workspace/data/confocal-series.tif" );
+ imp.show();
+ new ExportImagePlusAsN5PlugIn().run();
+ }
+
+ @Override
+ public void run()
+ {
+ if ( ij.Prefs.setIJMenuBar )
+ System.setProperty( "apple.laf.useScreenMenuBar", "true" );
+
+ // get the current image
+ final ImagePlus imp = WindowManager.getCurrentImage();
+
+ // make sure there is one
+ if ( imp == null )
+ {
+ IJ.showMessage( "Please open an image first." );
+ return;
+ }
+
+ // check the image type
+ switch ( imp.getType() )
+ {
+ case ImagePlus.GRAY8:
+ case ImagePlus.GRAY16:
+ case ImagePlus.GRAY32:
+ break;
+ default:
+ IJ.showMessage( "Only 8, 16, 32-bit images are supported currently!" );
+ return;
+ }
+
+ // check the image dimensionality
+ if ( imp.getNDimensions() < 2 )
+ {
+ IJ.showMessage( "Image must be at least 2-dimensional!" );
+ return;
+ }
+
+ // get calibration and image size
+ final double pw = imp.getCalibration().pixelWidth;
+ final double ph = imp.getCalibration().pixelHeight;
+ final double pd = imp.getCalibration().pixelDepth;
+ String punit = imp.getCalibration().getUnit();
+ if ( punit == null || punit.isEmpty() )
+ punit = "px";
+ final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions( punit, pw, ph, pd );
+ final int w = imp.getWidth();
+ final int h = imp.getHeight();
+ final int d = imp.getNSlices();
+ final FinalDimensions size = new FinalDimensions( w, h, d );
+
+ // propose reasonable mipmap settings
+ final int maxNumElements = 64 * 64 * 64;
+ final ExportMipmapInfo autoMipmapSettings = ProposeMipmaps.proposeMipmaps(
+ new BasicViewSetup( 0, "", size, voxelSize ),
+ maxNumElements );
+
+ // show dialog to get output paths, resolutions, subdivisions, min-max option
+ final Parameters params = getParameters( autoMipmapSettings );
+ if ( params == null )
+ return;
+
+ final ProgressWriter progressWriter = new ProgressWriterIJ();
+ progressWriter.out().println( "starting export..." );
+
+ // create ImgLoader wrapping the image
+ final TypedBasicImgLoader< ? > imgLoader;
+ final Runnable clearCache;
+ final boolean isVirtual = imp.getStack() != null && imp.getStack().isVirtual();
+ if ( isVirtual )
+ {
+ final VirtualStackImageLoader< ?, ?, ? > il;
+ switch ( imp.getType() )
+ {
+ case ImagePlus.GRAY8:
+ il = VirtualStackImageLoader.createUnsignedByteInstance( imp );
+ break;
+ case ImagePlus.GRAY16:
+ il = VirtualStackImageLoader.createUnsignedShortInstance( imp );
+ break;
+ case ImagePlus.GRAY32:
+ default:
+ il = VirtualStackImageLoader.createFloatInstance( imp );
+ break;
+ }
+ imgLoader = il;
+ clearCache = il.getCacheControl()::clearCache;
+ }
+ else
+ {
+ switch ( imp.getType() )
+ {
+ case ImagePlus.GRAY8:
+ imgLoader = ImageStackImageLoader.createUnsignedByteInstance( imp );
+ break;
+ case ImagePlus.GRAY16:
+ imgLoader = ImageStackImageLoader.createUnsignedShortInstance( imp );
+ break;
+ case ImagePlus.GRAY32:
+ default:
+ imgLoader = ImageStackImageLoader.createFloatInstance( imp );
+ break;
+ }
+ clearCache = () -> {};
+ }
+
+ final int numTimepoints = imp.getNFrames();
+ final int numSetups = imp.getNChannels();
+
+ // create SourceTransform from the images calibration
+ final AffineTransform3D sourceTransform = new AffineTransform3D();
+ sourceTransform.set( pw, 0, 0, 0, 0, ph, 0, 0, 0, 0, pd, 0 );
+
+ // write n5
+ final HashMap< Integer, BasicViewSetup > setups = new HashMap<>( numSetups );
+ for ( int s = 0; s < numSetups; ++s )
+ {
+ final BasicViewSetup setup = new BasicViewSetup( s, String.format( "channel %d", s + 1 ), size, voxelSize );
+ setup.setAttribute( new Channel( s + 1 ) );
+ setups.put( s, setup );
+ }
+ final ArrayList< TimePoint > timepoints = new ArrayList<>( numTimepoints );
+ for ( int t = 0; t < numTimepoints; ++t )
+ timepoints.add( new TimePoint( t ) );
+ final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null );
+
+ Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo;
+ perSetupExportMipmapInfo = new HashMap<>();
+ final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
+ for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() )
+ perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );
+
+ // LoopBackHeuristic:
+ // - If saving more than 8x on pixel reads use the loopback image over
+ // original image
+ // - For virtual stacks also consider the cache size that would be
+ // required for all original planes contributing to a "plane of
+ // blocks" at the current level. If this is more than 1/4 of
+ // available memory, use the loopback image.
+ final long planeSizeInBytes = imp.getWidth() * imp.getHeight() * imp.getBytesPerPixel();
+ final long ijMaxMemory = IJ.maxMemory();
+ final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
+ final LoopbackHeuristic loopbackHeuristic = new LoopbackHeuristic()
+ {
+ @Override
+ public boolean decide( final RandomAccessibleInterval< ? > originalImg, final int[] factorsToOriginalImg, final int previousLevel, final int[] factorsToPreviousLevel, final int[] chunkSize )
+ {
+ if ( previousLevel < 0 )
+ return false;
+
+ if ( Intervals.numElements( factorsToOriginalImg ) / Intervals.numElements( factorsToPreviousLevel ) >= 8 )
+ return true;
+
+ if ( isVirtual )
+ {
+ final long requiredCacheSize = planeSizeInBytes * factorsToOriginalImg[ 2 ] * chunkSize[ 2 ];
+ if ( requiredCacheSize > ijMaxMemory / 4 )
+ return true;
+ }
+
+ return false;
+ }
+ };
+
+ final AfterEachPlane afterEachPlane = new AfterEachPlane()
+ {
+ @Override
+ public void afterEachPlane( final boolean usedLoopBack )
+ {
+ if ( !usedLoopBack && isVirtual )
+ {
+ final long free = Runtime.getRuntime().freeMemory();
+ final long total = Runtime.getRuntime().totalMemory();
+ final long max = Runtime.getRuntime().maxMemory();
+ final long actuallyFree = max - total + free;
+
+ if ( actuallyFree < max / 2 )
+ clearCache.run();
+ }
+ }
+
+ };
+
+ try
+ {
+ WriteSequenceToN5.writeN5File( seq, perSetupExportMipmapInfo,
+ params.compression, params.n5File,
+ loopbackHeuristic, afterEachPlane, numCellCreatorThreads,
+ new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
+
+ // write xml sequence description
+ final N5ImageLoader n5Loader = new N5ImageLoader( params.n5File, null );
+ final SequenceDescriptionMinimal seqh5 = new SequenceDescriptionMinimal( seq, n5Loader );
+
+ final ArrayList< ViewRegistration > registrations = new ArrayList<>();
+ for ( int t = 0; t < numTimepoints; ++t )
+ for ( int s = 0; s < numSetups; ++s )
+ registrations.add( new ViewRegistration( t, s, sourceTransform ) );
+
+ final File basePath = params.seqFile.getParentFile();
+ final SpimDataMinimal spimData = new SpimDataMinimal( basePath, seqh5, new ViewRegistrations( registrations ) );
+
+ new XmlIoSpimDataMinimal().save( spimData, params.seqFile.getAbsolutePath() );
+ progressWriter.setProgress( 1.0 );
+ }
+ catch ( final SpimDataException | IOException e )
+ {
+ throw new RuntimeException( e );
+ }
+ progressWriter.out().println( "done" );
+ }
+
+ protected static class Parameters
+ {
+ final boolean setMipmapManual;
+
+ final int[][] resolutions;
+
+ final int[][] subdivisions;
+
+ final File seqFile;
+
+ final File n5File;
+
+ final Compression compression;
+
+ public Parameters(
+ final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions,
+ final File seqFile, final File n5File,
+ final Compression compression )
+ {
+ this.setMipmapManual = setMipmapManual;
+ this.resolutions = resolutions;
+ this.subdivisions = subdivisions;
+ this.seqFile = seqFile;
+ this.n5File = n5File;
+ this.compression = compression;
+ }
+ }
+
+ static boolean lastSetMipmapManual = false;
+
+ static String lastSubsampling = "";
+
+ static String lastChunkSizes = "";
+
+ static int lastCompressionChoice = 0;
+
+ static boolean lastCompressionDefaultSettings = true;
+
+ static String lastExportPath = "./export.xml";
+
+ protected Parameters getParameters( final ExportMipmapInfo autoMipmapSettings )
+ {
+ while ( true )
+ {
+ final GenericDialogPlus gd = new GenericDialogPlus( "Export for BigDataViewer as XML/N5" );
+
+ gd.addCheckbox( "manual_mipmap_setup", lastSetMipmapManual );
+ final Checkbox cManualMipmap = ( Checkbox ) gd.getCheckboxes().lastElement();
+ gd.addStringField( "Subsampling_factors", lastSubsampling, 25 );
+ final TextField tfSubsampling = ( TextField ) gd.getStringFields().lastElement();
+ gd.addStringField( "N5_chunk_sizes", lastChunkSizes, 25 );
+ final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement();
+
+ gd.addMessage( "" );
+ final String[] compressionChoices = new String[] { "raw (no compression)", "bzip", "gzip", "lz4", "xz" };
+ gd.addChoice( "compression", compressionChoices, compressionChoices[ lastCompressionChoice ] );
+ gd.addCheckbox( "default settings", lastCompressionDefaultSettings );
+
+ gd.addMessage( "" );
+ PluginHelper.addSaveAsFileField( gd, "Export_path", lastExportPath, 25 );
+
+ final String autoSubsampling = ProposeMipmaps.getArrayString( autoMipmapSettings.getExportResolutions() );
+ final String autoChunkSizes = ProposeMipmaps.getArrayString( autoMipmapSettings.getSubdivisions() );
+ gd.addDialogListener( ( dialog, e ) -> {
+ gd.getNextBoolean();
+ gd.getNextString();
+ gd.getNextString();
+ gd.getNextChoiceIndex();
+ gd.getNextBoolean();
+ gd.getNextString();
+ if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cManualMipmap )
+ {
+ final boolean useManual = cManualMipmap.getState();
+ tfSubsampling.setEnabled( useManual );
+ tfChunkSizes.setEnabled( useManual );
+ if ( !useManual )
+ {
+ tfSubsampling.setText( autoSubsampling );
+ tfChunkSizes.setText( autoChunkSizes );
+ }
+ }
+ return true;
+ } );
+
+ tfSubsampling.setEnabled( lastSetMipmapManual );
+ tfChunkSizes.setEnabled( lastSetMipmapManual );
+ if ( !lastSetMipmapManual )
+ {
+ tfSubsampling.setText( autoSubsampling );
+ tfChunkSizes.setText( autoChunkSizes );
+ }
+
+ gd.showDialog();
+ if ( gd.wasCanceled() )
+ return null;
+
+ lastSetMipmapManual = gd.getNextBoolean();
+ lastSubsampling = gd.getNextString();
+ lastChunkSizes = gd.getNextString();
+ lastCompressionChoice = gd.getNextChoiceIndex();
+ lastCompressionDefaultSettings = gd.getNextBoolean();
+ lastExportPath = gd.getNextString();
+
+ // parse mipmap resolutions and cell sizes
+ final int[][] resolutions = PluginHelper.parseResolutionsString( lastSubsampling );
+ final int[][] subdivisions = PluginHelper.parseResolutionsString( lastChunkSizes );
+ if ( resolutions.length == 0 )
+ {
+ IJ.showMessage( "Cannot parse subsampling factors " + lastSubsampling );
+ continue;
+ }
+ if ( subdivisions.length == 0 )
+ {
+ IJ.showMessage( "Cannot parse n5 chunk sizes " + lastChunkSizes );
+ continue;
+ }
+ else if ( resolutions.length != subdivisions.length )
+ {
+ IJ.showMessage( "subsampling factors and n5 chunk sizes must have the same number of elements" );
+ continue;
+ }
+
+ String seqFilename = lastExportPath;
+ if ( !seqFilename.endsWith( ".xml" ) )
+ seqFilename += ".xml";
+ final File seqFile = new File( seqFilename );
+ final File parent = seqFile.getParentFile();
+ if ( parent == null || !parent.exists() || !parent.isDirectory() )
+ {
+ IJ.showMessage( "Invalid export filename " + seqFilename );
+ continue;
+ }
+ final String n5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".n5";
+ final File n5File = new File( n5Filename );
+
+ final Compression compression;
+ switch ( lastCompressionChoice )
+ {
+ default:
+ case 0: // raw (no compression)
+ compression = new RawCompression();
+ break;
+ case 1: // bzip
+ compression = lastCompressionDefaultSettings
+ ? new Bzip2Compression()
+ : getBzip2Settings();
+ break;
+ case 2: // gzip
+ compression = lastCompressionDefaultSettings
+ ? new GzipCompression()
+ : getGzipSettings();
+ break;
+ case 3:// lz4
+ compression = lastCompressionDefaultSettings
+ ? new Lz4Compression()
+ : getLz4Settings();
+ break;
+ case 4:// xz" };
+ compression = lastCompressionDefaultSettings
+ ? new XzCompression()
+ : getXzSettings();
+ break;
+ }
+ if ( compression == null )
+ return null;
+
+ return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, n5File, compression );
+ }
+ }
+
+ static int lastBzip2BlockSize = BZip2CompressorOutputStream.MAX_BLOCKSIZE;
+
+ protected Bzip2Compression getBzip2Settings()
+ {
+ while ( true )
+ {
+ final GenericDialogPlus gd = new GenericDialogPlus( "Bzip2 compression settings" );
+ gd.addNumericField(
+ String.format( "block size (%d-%d)",
+ BZip2CompressorOutputStream.MIN_BLOCKSIZE,
+ BZip2CompressorOutputStream.MAX_BLOCKSIZE ),
+ lastBzip2BlockSize, 0 );
+ gd.addMessage( "as 100k units" );
+
+ gd.showDialog();
+ if ( gd.wasCanceled() )
+ return null;
+
+ lastBzip2BlockSize = ( int ) gd.getNextNumber();
+ if ( lastBzip2BlockSize < BZip2CompressorOutputStream.MIN_BLOCKSIZE || lastBzip2BlockSize > BZip2CompressorOutputStream.MAX_BLOCKSIZE )
+ {
+ IJ.showMessage(
+ String.format( "Block size must be in range [%d, %d]",
+ BZip2CompressorOutputStream.MIN_BLOCKSIZE,
+ BZip2CompressorOutputStream.MAX_BLOCKSIZE ) );
+ continue;
+ }
+ return new Bzip2Compression( lastBzip2BlockSize );
+ }
+ }
+
+ static int lastGzipLevel = 6;
+
+ static boolean lastGzipUseZlib = false;
+
+ protected GzipCompression getGzipSettings()
+ {
+ while ( true )
+ {
+ final GenericDialogPlus gd = new GenericDialogPlus( "Gzip compression settings" );
+ gd.addNumericField( "level (0-9)", lastGzipLevel, 0 );
+ gd.addCheckbox( "use Zlib", lastGzipUseZlib );
+
+ gd.showDialog();
+ if ( gd.wasCanceled() )
+ return null;
+
+ lastGzipLevel = ( int ) gd.getNextNumber();
+ lastGzipUseZlib = gd.getNextBoolean();
+ if ( lastGzipLevel < 0 || lastGzipLevel > 9 )
+ {
+ IJ.showMessage( "Level must be in range [0, 9]" );
+ continue;
+ }
+ return new GzipCompression( lastGzipLevel, lastGzipUseZlib );
+ }
+ }
+
+ static int lastLz4BlockSize = 1 << 16;
+
+ protected Lz4Compression getLz4Settings()
+ {
+ final int COMPRESSION_LEVEL_BASE = 10;
+ final int MIN_BLOCK_SIZE = 64;
+ final int MAX_BLOCK_SIZE = 1 << (COMPRESSION_LEVEL_BASE + 0x0F);
+
+ while ( true )
+ {
+ final GenericDialogPlus gd = new GenericDialogPlus( "LZ4 compression settings" );
+ gd.addNumericField(
+ String.format( "block size (%d-%d)",
+ MIN_BLOCK_SIZE,
+ MAX_BLOCK_SIZE ),
+ lastLz4BlockSize, 0, 8, null );
+
+ gd.showDialog();
+ if ( gd.wasCanceled() )
+ return null;
+
+ lastLz4BlockSize = ( int ) gd.getNextNumber();
+ if ( lastLz4BlockSize < MIN_BLOCK_SIZE || lastLz4BlockSize > MAX_BLOCK_SIZE )
+ {
+ IJ.showMessage( String.format( "Block size must be in range [%d, %d]",
+ MIN_BLOCK_SIZE,
+ MAX_BLOCK_SIZE ) );
+ continue;
+ }
+ return new Lz4Compression( lastLz4BlockSize );
+ }
+ }
+
+ static int lastXzLevel = 6;
+
+ protected XzCompression getXzSettings()
+ {
+ while ( true )
+ {
+ final GenericDialogPlus gd = new GenericDialogPlus( "XZ compression settings" );
+ gd.addNumericField( "level (0-9)", lastXzLevel, 0 );
+ gd.addMessage( "LZMA2 preset level" );
+
+ gd.showDialog();
+ if ( gd.wasCanceled() )
+ return null;
+
+ lastXzLevel = ( int ) gd.getNextNumber();
+ if ( lastXzLevel < 0 || lastXzLevel > 9 )
+ {
+ IJ.showMessage( "Level must be in range [0, 9]" );
+ continue;
+ }
+ return new XzCompression( lastXzLevel );
+ }
+ }
+
+}
diff --git a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
index 1a3c90b3accd850c4726df23aa990ea73cfab0e1..0312a164f4ff7107343bf8ebc2f6312bbda7dc5f 100644
--- a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
@@ -14,16 +14,17 @@ import net.imglib2.FinalDimensions;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.util.Intervals;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;
import bdv.export.ExportMipmapInfo;
+import bdv.export.ExportScalePyramid.AfterEachPlane;
+import bdv.export.ExportScalePyramid.LoopbackHeuristic;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
import bdv.export.SubTaskProgressWriter;
import bdv.export.WriteSequenceToHdf5;
-import bdv.export.WriteSequenceToHdf5.AfterEachPlane;
-import bdv.export.WriteSequenceToHdf5.LoopbackHeuristic;
import bdv.ij.export.imgloader.ImagePlusImgLoader;
import bdv.ij.export.imgloader.ImagePlusImgLoader.MinMaxOption;
import bdv.ij.util.PluginHelper;
@@ -103,7 +104,7 @@ public class ExportImagePlusPlugIn implements Command
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getNSlices();
- final FinalDimensions size = new FinalDimensions( new int[] { w, h, d } );
+ final FinalDimensions size = new FinalDimensions( w, h, d );
// propose reasonable mipmap settings
final ExportMipmapInfo autoMipmapSettings = ProposeMipmaps.proposeMipmaps( new BasicViewSetup( 0, "", size, voxelSize ) );
@@ -177,7 +178,7 @@ public class ExportImagePlusPlugIn implements Command
if ( previousLevel < 0 )
return false;
- if ( WriteSequenceToHdf5.numElements( factorsToOriginalImg ) / WriteSequenceToHdf5.numElements( factorsToPreviousLevel ) >= 8 )
+ if ( Intervals.numElements( factorsToOriginalImg ) / Intervals.numElements( factorsToPreviousLevel ) >= 8 )
return true;
if ( isVirtual )
diff --git a/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java b/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
index 73c9e3a64e212e67ef87ca6df2db021a859a90cb..84066e29e0d087be8403df6602695360fe473c05 100644
--- a/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
+++ b/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
@@ -68,6 +68,7 @@ import mpicbg.spim.io.SPIMConfiguration;
import mpicbg.spim.io.TextFileAccess;
import spimopener.SPIMExperiment;
+@Deprecated
@Plugin(type = Command.class,
menuPath = "Plugins>BigDataViewer>Deprecated>Export Fused Sequence as XML/HDF5")
public class ExportSpimFusionPlugIn implements Command
diff --git a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
index 44bbdf36a75ef6d92fe446551506b6a898f4854c..d7378cb3a133aef2667e174b4cf6d9da61591232 100644
--- a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
+++ b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
@@ -45,6 +45,7 @@ import mpicbg.spim.io.SPIMConfiguration;
import mpicbg.spim.io.TextFileAccess;
import spimopener.SPIMExperiment;
+@Deprecated
@Plugin(type = Command.class,
menuPath = "Plugins>BigDataViewer>Deprecated>Export Spim Sequence as XML/HDF5")
public class ExportSpimSequencePlugIn implements Command
diff --git a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
index 132a981cb9851e965df599b1e254910e5ee05a30..d84afa91d8556557a907028b5509a80107a98589 100644
--- a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
@@ -1,9 +1,13 @@
package bdv.ij;
+import bdv.viewer.ConverterSetups;
+import bdv.viewer.SynchronizedViewerState;
+import bdv.viewer.ViewerState;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import net.imglib2.FinalDimensions;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.ARGBType;
@@ -21,11 +25,9 @@ import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.WrapBasicImgLoader;
import bdv.tools.brightness.ConverterSetup;
-import bdv.tools.brightness.SetupAssignments;
import bdv.viewer.DisplayMode;
import bdv.viewer.SourceAndConverter;
import bdv.viewer.ViewerOptions;
-import bdv.viewer.VisibilityAndGrouping;
import ij.CompositeImage;
import ij.IJ;
import ij.ImageJ;
@@ -132,18 +134,19 @@ public class OpenImagePlusPlugIn implements Command
nTimepoints, cache,
"BigDataViewer", new ProgressWriterIJ(), ViewerOptions.options() );
- final SetupAssignments sa = bdv.getSetupAssignments();
- final VisibilityAndGrouping vg = bdv.getViewer().getVisibilityAndGrouping();
-
- int channelOffset = 0;
- int numActiveChannels = 0;
- for ( ImagePlus imp : imgList )
+ final SynchronizedViewerState state = bdv.getViewer().state();
+ synchronized ( state )
{
- numActiveChannels += transferChannelVisibility( channelOffset, imp,vg );
- transferChannelSettings( channelOffset, imp, sa );
- channelOffset += imp.getNChannels();
+ int channelOffset = 0;
+ int numActiveChannels = 0;
+ for ( ImagePlus imp : imgList )
+ {
+ numActiveChannels += transferChannelVisibility( channelOffset, imp, state );
+ transferChannelSettings( channelOffset, imp, state, bdv.getConverterSetups() );
+ channelOffset += imp.getNChannels();
+ }
+ state.setDisplayMode( numActiveChannels > 1 ? DisplayMode.FUSED : DisplayMode.SINGLE );
}
- vg.setDisplayMode( numActiveChannels > 1 ? DisplayMode.FUSED : DisplayMode.SINGLE );
}
}
@@ -257,19 +260,20 @@ public class OpenImagePlusPlugIn implements Command
/**
* @return number of setups that were set active.
*/
- protected int transferChannelVisibility( int channelOffset, final ImagePlus imp, final VisibilityAndGrouping visibility )
+ protected int transferChannelVisibility( int channelOffset, final ImagePlus imp, final ViewerState state )
{
final int nChannels = imp.getNChannels();
final CompositeImage ci = imp.isComposite() ? ( CompositeImage ) imp : null;
+ final List< SourceAndConverter< ? > > sources = state.getSources();
if ( ci != null && ci.getCompositeMode() == IJ.COMPOSITE )
{
final boolean[] activeChannels = ci.getActiveChannels();
int numActiveChannels = 0;
- for ( int i = 0; i < activeChannels.length; ++i )
+ for ( int i = 0; i < Math.min( activeChannels.length, nChannels ); ++i )
{
- final int setup = channelOffset + i;
- visibility.setSourceActive( setup, activeChannels[ i ] );
- visibility.setCurrentSource( setup );
+ final SourceAndConverter< ? > source = sources.get( channelOffset + i );
+ state.setSourceActive( source, activeChannels[ i ] );
+ state.setCurrentSource( source );
numActiveChannels += activeChannels[ i ] ? 1 : 0;
}
return numActiveChannels;
@@ -278,16 +282,17 @@ public class OpenImagePlusPlugIn implements Command
{
final int activeChannel = imp.getChannel() - 1;
for ( int i = 0; i < nChannels; ++i )
- visibility.setSourceActive( channelOffset + i, i == activeChannel );
- visibility.setCurrentSource( channelOffset + activeChannel );
+ state.setSourceActive( sources.get( channelOffset + i ), i == activeChannel );
+ state.setCurrentSource( sources.get( channelOffset + activeChannel ) );
return 1;
}
}
- protected void transferChannelSettings( int channelOffset, final ImagePlus imp, final SetupAssignments setupAssignments )
+ protected void transferChannelSettings( int channelOffset, final ImagePlus imp, final ViewerState state, final ConverterSetups converterSetups )
{
final int nChannels = imp.getNChannels();
final CompositeImage ci = imp.isComposite() ? ( CompositeImage ) imp : null;
+ final List< SourceAndConverter< ? > > sources = state.getSources();
if ( ci != null )
{
final int mode = ci.getCompositeMode();
@@ -295,7 +300,7 @@ public class OpenImagePlusPlugIn implements Command
for ( int c = 0; c < nChannels; ++c )
{
final LUT lut = ci.getChannelLut( c + 1 );
- final ConverterSetup setup = setupAssignments.getConverterSetups().get( channelOffset + c );
+ final ConverterSetup setup = converterSetups.getConverterSetup( sources.get( channelOffset + c ) );
if ( transferColor )
setup.setColor( new ARGBType( lut.getRGB( 255 ) ) );
setup.setDisplayRange( lut.min, lut.max );
@@ -307,7 +312,7 @@ public class OpenImagePlusPlugIn implements Command
final double displayRangeMax = imp.getDisplayRangeMax();
for ( int i = 0; i < nChannels; ++i )
{
- final ConverterSetup setup = setupAssignments.getConverterSetups().get( channelOffset + i );
+ final ConverterSetup setup = converterSetups.getConverterSetup( sources.get( channelOffset + i ) );
final LUT[] luts = imp.getLuts();
if ( luts.length != 0 )
setup.setColor( new ARGBType( luts[ 0 ].getRGB( 255 ) ) );
diff --git a/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java b/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
index ac4e3d4a77771c4fc5b61fe96e626a984061ae29..b660a7103ada2d6bb29308f7264e70aab5aa8d66 100644
--- a/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
+++ b/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
@@ -29,6 +29,7 @@ import mpicbg.spim.data.generic.sequence.BasicViewSetup;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class FixAbsolutePathsInHdf5Partitions
{
public static void fix( final String xmlFilename ) throws SpimDataException, IOException
diff --git a/src/main/java/bdv/ij/export/FusionResult.java b/src/main/java/bdv/ij/export/FusionResult.java
index 1a57fa72e76961a78342b424ed1ffd7cac0895a1..3b0259441127a9bb81bf742a83e8673a4dc4ad52 100644
--- a/src/main/java/bdv/ij/export/FusionResult.java
+++ b/src/main/java/bdv/ij/export/FusionResult.java
@@ -20,6 +20,7 @@ import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.Dimensions;
import net.imglib2.realtransform.AffineTransform3D;
+@Deprecated
public class FusionResult
{
private final SequenceDescriptionMinimal desc;
diff --git a/src/main/java/bdv/ij/export/Scripting.java b/src/main/java/bdv/ij/export/Scripting.java
index e7f30ae7c10b33d04139e2f04fce84487b3211af..1491f4fe70b8f256ca62f0e018043f78a0bc8746 100644
--- a/src/main/java/bdv/ij/export/Scripting.java
+++ b/src/main/java/bdv/ij/export/Scripting.java
@@ -17,6 +17,7 @@ import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.io.ConfigurationParserException;
import net.imglib2.realtransform.AffineTransform3D;
+@Deprecated
public class Scripting
{
/**
@@ -42,6 +43,7 @@ public class Scripting
* @return an initialized {@link SpimRegistrationSequence} sequence.
* @throws ConfigurationParserException
*/
+ @Deprecated
public static SpimRegistrationSequence createSpimRegistrationSequence(
final String huiskenExperimentXmlFile,
final String channels,
@@ -85,6 +87,7 @@ public class Scripting
* @return an initialized {@link SpimRegistrationSequence} sequence.
* @throws ConfigurationParserException
*/
+ @Deprecated
public static SpimRegistrationSequence createSpimRegistrationSequence(
final String inputDirectory,
final String inputFilePattern,
@@ -108,6 +111,7 @@ public class Scripting
* @param cropOffsetZ
* @return
*/
+ @Deprecated
public static Map< Integer, AffineTransform3D > getFusionTransforms(
final SpimRegistrationSequence spimseq,
final int scale,
@@ -130,6 +134,7 @@ public class Scripting
* @param fusionTransforms
* @return
*/
+ @Deprecated
public static FusionResult createFusionResult(
final SpimRegistrationSequence spimseq,
final String filepath,
@@ -159,6 +164,7 @@ public class Scripting
* is used to generate paths for the partitions.
* @return list of partitions.
*/
+ @Deprecated
public static ArrayList< Partition > split(
final SetupAggregator aggregator,
final int timepointsPerPartition,
diff --git a/src/main/java/bdv/ij/export/SetupAggregator.java b/src/main/java/bdv/ij/export/SetupAggregator.java
index b21d975da3db27e19f48c296a2657a215408b110..4650098e7fe548f8ee2eaeb604fa949d8bddcaca 100644
--- a/src/main/java/bdv/ij/export/SetupAggregator.java
+++ b/src/main/java/bdv/ij/export/SetupAggregator.java
@@ -34,6 +34,7 @@ import net.imglib2.img.cell.CellImg;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class SetupAggregator
{
/**
@@ -80,7 +81,7 @@ public class SetupAggregator
/**
* Add a new {@link BasicViewSetup} to the aggregator.
*
- * Adds a setup of the given source {@link SpimRegistrationSequence} to the
+ * Adds a setup of the given source {@link AbstractSequenceDescription} to the
* aggregator. A reference to the source sequence is kept and the source
* {@link ViewRegistrations} are copied. In the viewer format, every image
* is stored in multiple resolutions. The resolutions are described as int[]
@@ -181,6 +182,7 @@ public class SetupAggregator
* "{32,32,32}, {16,16,8}, {8,8,8}" where each "{...}"
* defines one subdivision.
*/
+ @Deprecated
public void addSetup( final SpimRegistrationSequence sequence, final int setupIndex, final String resolutionsString, final String subdivisionsString )
{
final AbstractSequenceDescription< ?, ?, ? > desc = sequence.getSequenceDescription();
@@ -222,6 +224,7 @@ public class SetupAggregator
* the set of subdivisions to store. each nested int[] array
* defines one subdivision.
*/
+ @Deprecated
public void addSetup( final SpimRegistrationSequence sequence, final int setupIndex, final int[][] resolutions, final int[][] subdivisions )
{
final AbstractSequenceDescription< ?, ?, ? > desc = sequence.getSequenceDescription();
@@ -257,6 +260,7 @@ public class SetupAggregator
* "{32,32,32}, {16,16,8}, {8,8,8}" where each "{...}"
* defines one subdivision.
*/
+ @Deprecated
public void addSetups( final SpimRegistrationSequence sequence, final String resolutionsString, final String subdivisionsString )
{
for ( int s = 0; s < sequence.getSequenceDescription().getViewSetups().size(); ++s )
@@ -286,6 +290,7 @@ public class SetupAggregator
* the set of subdivisions to store. each nested int[] array
* defines one subdivision.
*/
+ @Deprecated
public void addSetups( final SpimRegistrationSequence sequence, final int[][] resolutions, final int[][] subdivisions )
{
for ( int s = 0; s < sequence.getSequenceDescription().getViewSetups().size(); ++s )
@@ -317,6 +322,7 @@ public class SetupAggregator
* "{32,32,32}, {16,16,8}, {8,8,8}" where each "{...}"
* defines one subdivision.
*/
+ @Deprecated
public void addSetups( final FusionResult fusionResult, final String resolutionsString, final String subdivisionsString )
{
final int[][] resolutions = PluginHelper.parseResolutionsString( resolutionsString );
@@ -354,6 +360,7 @@ public class SetupAggregator
* the set of subdivisions to store. each nested int[] array
* defines one subdivision.
*/
+ @Deprecated
public void addSetups( final FusionResult fusionResult, final int[][] resolutions, final int[][] subdivisions )
{
if ( resolutions.length != subdivisions.length )
diff --git a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
index bb0cd223e66181c88f007131678ac62a465a0331..2f2cdfeda09a39c60d832df804877df716aca05c 100644
--- a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
+++ b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
@@ -35,6 +35,7 @@ import net.imglib2.realtransform.AffineTransform3D;
import spim.vecmath.Point3f;
import spimopener.SPIMExperiment;
+@Deprecated
public class SpimRegistrationSequence
{
private final SequenceDescriptionMinimal sequenceDescription;
diff --git a/src/main/java/bdv/ij/export/ViewSetupWrapper.java b/src/main/java/bdv/ij/export/ViewSetupWrapper.java
index ebbb167838e33d821266fcb7b13d0a25295e8f2d..cf1afb839b9f757eeef187846d4bdde747c8169b 100644
--- a/src/main/java/bdv/ij/export/ViewSetupWrapper.java
+++ b/src/main/java/bdv/ij/export/ViewSetupWrapper.java
@@ -13,6 +13,7 @@ import mpicbg.spim.data.sequence.ViewSetup;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class ViewSetupWrapper extends BasicViewSetup
{
private final AbstractSequenceDescription< ?, ?, ? > sourceSequence;
diff --git a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
index 5b01a1dd587d8e59d9b3f947577100656ed6144b..9a0a4c8f35cc26a835bcc28245aae4d5a4da09e7 100644
--- a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
@@ -45,6 +45,7 @@ import net.imglib2.view.Views;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
{
private final String pattern;
diff --git a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
index 8dc85ba386139df45dd5af513d4bde0a2cdaafc0..9e88239e468597cf661afe839966a6f7423f3789 100644
--- a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
@@ -25,6 +25,7 @@ import spimopener.SPIMExperiment;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class HuiskenImageLoader implements BasicImgLoader
{
private final File expFile;
diff --git a/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
index c832d531e349749484db9e5c0fc4fa7de2cc35dc..474351768bff71221fd455ce177ae9bf49b3d51f 100644
--- a/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
@@ -34,6 +34,7 @@ import net.imglib2.type.numeric.integer.UnsignedShortType;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class LegacyStackImageLoader implements LegacyBasicImgLoader< UnsignedShortType >
{
private final ImgOpener opener;
diff --git a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
index e73e7dc90c012b6e6cdef6d7aea11ace53a3a766..adb96918cd89520c6a3ac1ecb9935826f8b468e2 100644
--- a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
@@ -18,6 +18,7 @@ import net.imglib2.type.numeric.integer.UnsignedShortType;
*
* @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
+@Deprecated
public class StackImageLoader extends LegacyBasicImgLoaderWrapper< UnsignedShortType, LegacyStackImageLoader >
{
public StackImageLoader( final HashMap< ViewId, String > filenames, final boolean useImageJOpener )