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Commit 8ec03317 authored by Tobias Pietzsch's avatar Tobias Pietzsch
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Support N5 compression (bzip, gzip, lz4, xz) with custom settings dialogs

parent 5564cdbf
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src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
+ 170
− 11
View file @ 8ec03317
......@@ -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 );
}
}
}
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