diff --git a/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java b/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
index 911ec379e76044aa67a3486561af2357ee086b3e..2d78bfffccaf33a40bf8debd67d7b7a64e1ca29a 100644
--- a/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
+++ b/src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
@@ -41,9 +41,13 @@ 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;
@@ -243,8 +247,10 @@ public class ExportImagePlusAsN5PlugIn implements Command
try
{
- Compression compression = params.deflate ? new Lz4Compression() : new RawCompression();
- WriteSequenceToN5.writeN5File( seq, perSetupExportMipmapInfo, compression, params.n5File, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
+ 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 );
@@ -280,29 +286,31 @@ public class ExportImagePlusAsN5PlugIn implements Command
final File n5File;
- final boolean deflate;
+ final Compression compression;
public Parameters(
final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions,
final File seqFile, final File n5File,
- final boolean deflate )
+ final Compression compression )
{
this.setMipmapManual = setMipmapManual;
this.resolutions = resolutions;
this.subdivisions = subdivisions;
this.seqFile = seqFile;
this.n5File = n5File;
- this.deflate = deflate;
+ this.compression = compression;
}
}
static boolean lastSetMipmapManual = false;
- static String lastSubsampling = "{1,1,1}, {2,2,1}, {4,4,2}";
+ static String lastSubsampling = "";
- static String lastChunkSizes = "{32,32,4}, {16,16,8}, {8,8,8}";
+ static String lastChunkSizes = "";
- static boolean lastDeflate = true;
+ static int lastCompressionChoice = 0;
+
+ static boolean lastCompressionDefaultSettings = true;
static String lastExportPath = "./export.xml";
@@ -320,7 +328,9 @@ public class ExportImagePlusAsN5PlugIn implements Command
final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement();
gd.addMessage( "" );
- gd.addCheckbox( "use_deflate_compression", lastDeflate );
+ 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 );
@@ -331,6 +341,7 @@ public class ExportImagePlusAsN5PlugIn implements Command
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 )
@@ -362,7 +373,8 @@ public class ExportImagePlusAsN5PlugIn implements Command
lastSetMipmapManual = gd.getNextBoolean();
lastSubsampling = gd.getNextString();
lastChunkSizes = gd.getNextString();
- lastDeflate = gd.getNextBoolean();
+ lastCompressionChoice = gd.getNextChoiceIndex();
+ lastCompressionDefaultSettings = gd.getNextBoolean();
lastExportPath = gd.getNextString();
// parse mipmap resolutions and cell sizes
@@ -397,7 +409,154 @@ public class ExportImagePlusAsN5PlugIn implements Command
final String n5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".n5";
final File n5File = new File( n5Filename );
- return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, n5File, lastDeflate );
+ 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 );
+ }
+ }
+
}