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Make downsampling method configurable #22

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Make downsampling method configurable #22

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218cb42
Add downsampling choice to export hdf5
tischi Feb 7, 2021
ed45eb9
Remove export.n5 folder
tischi Feb 7, 2021
91b0ac3
.gitignore fix
tischi Feb 7, 2021
f40fe4a
Fix version in pom
tischi Feb 7, 2021
cb1697a
Add mode downsampling method
tischi Feb 8, 2021
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5 changes: 5 additions & 0 deletions .gitignore
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Expand Up @@ -10,3 +10,8 @@
.settings
/target
/samples

# IntelliJ
.idea/
*.iml

1 change: 1 addition & 0 deletions pom.xml
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Expand Up @@ -115,6 +115,7 @@
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
<version>10.2.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
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5 changes: 3 additions & 2 deletions src/main/java/bdv/ij/ExportImagePlusAsN5PlugIn.java
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Expand Up @@ -84,8 +84,9 @@ 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();
IJ.run("Confocal Series (2.2MB)");
//final ImagePlus imp = IJ.openImage( "/Users/tischer/Desktop/Desktop/mri-stack-big.tif" );
//imp.show();
new ExportImagePlusAsN5PlugIn().run();
}

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27 changes: 17 additions & 10 deletions src/main/java/bdv/ij/ExportImagePlusPlugIn.java
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Expand Up @@ -31,6 +31,7 @@
import java.util.HashMap;
import java.util.Map;

import bdv.export.*;
import net.imglib2.FinalDimensions;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.realtransform.AffineTransform3D;
Expand All @@ -39,13 +40,8 @@
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.ij.export.imgloader.ImagePlusImgLoader;
import bdv.ij.export.imgloader.ImagePlusImgLoader.MinMaxOption;
import bdv.ij.util.PluginHelper;
Expand Down Expand Up @@ -82,7 +78,10 @@ public class ExportImagePlusPlugIn implements Command
public static void main( final String[] args )
{
new ImageJ();
IJ.run("Confocal Series (2.2MB)");
//IJ.run("Confocal Series (2.2MB)");
final ImagePlus imp = IJ.openImage( "/Users/tischer/Desktop/Desktop/labels-3d-test.tif" );
imp.show();

new ExportImagePlusPlugIn().run();
}

Expand Down Expand Up @@ -243,14 +242,14 @@ public void afterEachPlane( final boolean usedLoopBack )
{
final Partition partition = partitions.get( i );
final ProgressWriter p = new SubTaskProgressWriter( progressWriter, 0, 0.95 * i / partitions.size() );
WriteSequenceToHdf5.writeHdf5PartitionFile( seq, perSetupExportMipmapInfo, params.deflate, partition, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, p );
WriteSequenceToHdf5.writeHdf5PartitionFile( seq, perSetupExportMipmapInfo, params.downsamplingMethod, params.deflate, partition, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, p );
}
WriteSequenceToHdf5.writeHdf5PartitionLinkFile( seq, perSetupExportMipmapInfo, partitions, params.hdf5File );
}
else
{
partitions = null;
WriteSequenceToHdf5.writeHdf5File( seq, perSetupExportMipmapInfo, params.deflate, params.hdf5File, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
WriteSequenceToHdf5.writeHdf5File( seq, perSetupExportMipmapInfo, params.downsamplingMethod, params.deflate, params.hdf5File, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
}

// write xml sequence description
Expand Down Expand Up @@ -285,6 +284,8 @@ protected static class Parameters

final int[][] subdivisions;

final DownsampleBlock.DownsamplingMethod downsamplingMethod;

final File seqFile;

final File hdf5File;
Expand All @@ -305,13 +306,14 @@ protected static class Parameters

public Parameters(
final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions,
final File seqFile, final File hdf5File,
DownsampleBlock.DownsamplingMethod downsamplingMethod, final File seqFile, final File hdf5File,
final MinMaxOption minMaxOption, final double rangeMin, final double rangeMax, final boolean deflate,
final boolean split, final int timepointsPerPartition, final int setupsPerPartition )
{
this.setMipmapManual = setMipmapManual;
this.resolutions = resolutions;
this.subdivisions = subdivisions;
this.downsamplingMethod = downsamplingMethod;
this.seqFile = seqFile;
this.hdf5File = hdf5File;
this.minMaxOption = minMaxOption;
Expand All @@ -330,6 +332,8 @@ public Parameters(

static String lastChunkSizes = "{32,32,4}, {16,16,8}, {8,8,8}";

static DownsampleBlock.DownsamplingMethod lastDownsamplingMethod = DownsampleBlock.DownsamplingMethod.Average;

static int lastMinMaxChoice = 2;

static double lastMin = 0;
Expand Down Expand Up @@ -364,6 +368,7 @@ protected Parameters getParameters( final double impMin, final double impMax, fi
final TextField tfSubsampling = ( TextField ) gd.getStringFields().lastElement();
gd.addStringField( "Hdf5_chunk_sizes", lastChunkSizes, 25 );
final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement();
gd.addChoice( "Subsampling_method", new String[]{ DownsampleBlock.DownsamplingMethod.Average.toString(), DownsampleBlock.DownsamplingMethod.Mode.toString(), DownsampleBlock.DownsamplingMethod.Centre.toString() }, lastDownsamplingMethod.toString() );

gd.addMessage( "" );
final String[] minMaxChoices = new String[] { "Use ImageJ's current min/max setting", "Compute min/max of the (hyper-)stack", "Use values specified below" };
Expand Down Expand Up @@ -402,6 +407,7 @@ public boolean dialogItemChanged( final GenericDialog dialog, final AWTEvent e )
gd.getNextBoolean();
gd.getNextString();
gd.getNextString();
gd.getNextChoice();
gd.getNextChoiceIndex();
gd.getNextNumber();
gd.getNextNumber();
Expand Down Expand Up @@ -459,6 +465,7 @@ else if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED &&
lastSetMipmapManual = gd.getNextBoolean();
lastSubsampling = gd.getNextString();
lastChunkSizes = gd.getNextString();
lastDownsamplingMethod = DownsampleBlock.DownsamplingMethod.valueOf( gd.getNextChoice() );
lastMinMaxChoice = gd.getNextChoiceIndex();
lastMin = gd.getNextNumber();
lastMax = gd.getNextNumber();
Expand Down Expand Up @@ -508,6 +515,6 @@ else if ( lastMinMaxChoice == 1 )
final String hdf5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".h5";
final File hdf5File = new File( hdf5Filename );

return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File, minMaxOption, lastMin, lastMax, lastDeflate, lastSplit, lastTimepointsPerPartition, lastSetupsPerPartition ); }
return new Parameters( lastSetMipmapManual, resolutions, subdivisions, lastDownsamplingMethod, seqFile, hdf5File, minMaxOption, lastMin, lastMax, lastDeflate, lastSplit, lastTimepointsPerPartition, lastSetupsPerPartition ); }
}
}
12 changes: 4 additions & 8 deletions src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
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Expand Up @@ -38,6 +38,7 @@
import java.util.List;
import java.util.Map;

import bdv.export.*;
import net.imglib2.Dimensions;
import net.imglib2.FinalDimensions;
import net.imglib2.realtransform.AffineTransform3D;
Expand All @@ -47,11 +48,6 @@
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
import bdv.export.SubTaskProgressWriter;
import bdv.export.WriteSequenceToHdf5;
import bdv.ij.export.FusionResult;
import bdv.ij.export.SpimRegistrationSequence;
import bdv.ij.export.ViewSetupWrapper;
Expand Down Expand Up @@ -314,7 +310,7 @@ public static void appendToExistingFile( final Parameters params ) throws SpimDa
{
final SubTaskProgressWriter subtaskProgress = new SubTaskProgressWriter( progress, complete, complete + completionStep );
final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
WriteSequenceToHdf5.writeHdf5PartitionFile( fusionSeq, perSetupExportMipmapInfo, params.deflate, partition, null, null, numCellCreatorThreads, subtaskProgress );
WriteSequenceToHdf5.writeHdf5PartitionFile( fusionSeq, perSetupExportMipmapInfo, DownsampleBlock.DownsamplingMethod.Average, params.deflate, partition, null, null, numCellCreatorThreads, subtaskProgress );
complete += completionStep;
}

Expand Down Expand Up @@ -367,13 +363,13 @@ public static void saveAsNewFile( final Parameters params ) throws SpimDataExcep
{
final Partition partition = partitions.get( i );
final ProgressWriter p = new SubTaskProgressWriter( progress, 0, 0.95 * i / partitions.size() );
WriteSequenceToHdf5.writeHdf5PartitionFile( desc, perSetupExportMipmapInfo, params.deflate, partition, null, null, numCellCreatorThreads, p );
WriteSequenceToHdf5.writeHdf5PartitionFile( desc, perSetupExportMipmapInfo, DownsampleBlock.DownsamplingMethod.Average, params.deflate, partition, null, null, numCellCreatorThreads, p );
}
WriteSequenceToHdf5.writeHdf5PartitionLinkFile( desc, perSetupExportMipmapInfo, partitions, params.hdf5File );
}
else
{
WriteSequenceToHdf5.writeHdf5File( desc, perSetupExportMipmapInfo, params.deflate, params.hdf5File, null, null, numCellCreatorThreads, new SubTaskProgressWriter( progress, 0, 0.95 ) );
WriteSequenceToHdf5.writeHdf5File( desc, perSetupExportMipmapInfo, DownsampleBlock.DownsamplingMethod.Average, params.deflate, params.hdf5File, null, null, numCellCreatorThreads, new SubTaskProgressWriter( progress, 0, 0.95 ) );
}

// write xml file
Expand Down
10 changes: 3 additions & 7 deletions src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
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Expand Up @@ -36,14 +36,10 @@
import java.util.List;
import java.util.Map;

import bdv.export.*;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
import bdv.export.SubTaskProgressWriter;
import bdv.export.WriteSequenceToHdf5;
import bdv.ij.export.SpimRegistrationSequence;
import bdv.ij.util.PluginHelper;
import bdv.ij.util.ProgressWriterIJ;
Expand Down Expand Up @@ -115,14 +111,14 @@ public void run()
{
final Partition partition = partitions.get( i );
final ProgressWriter p = new SubTaskProgressWriter( progress, 0, 0.95 * i / partitions.size() );
WriteSequenceToHdf5.writeHdf5PartitionFile( desc, perSetupExportMipmapInfo, params.deflate, partition, null, null, numCellCreatorThreads, p );
WriteSequenceToHdf5.writeHdf5PartitionFile( desc, perSetupExportMipmapInfo, DownsampleBlock.DownsamplingMethod.Average, params.deflate, partition, null, null, numCellCreatorThreads, p );
}
WriteSequenceToHdf5.writeHdf5PartitionLinkFile( desc, perSetupExportMipmapInfo, partitions, params.hdf5File );
}
else
{
partitions = null;
WriteSequenceToHdf5.writeHdf5File( desc, perSetupExportMipmapInfo, params.deflate, params.hdf5File, null, null, numCellCreatorThreads, new SubTaskProgressWriter( progress, 0, 0.95 ) );
WriteSequenceToHdf5.writeHdf5File( desc, perSetupExportMipmapInfo, DownsampleBlock.DownsamplingMethod.Average, params.deflate, params.hdf5File, null, null, numCellCreatorThreads, new SubTaskProgressWriter( progress, 0, 0.95 ) );
}

final Hdf5ImageLoader loader = new Hdf5ImageLoader( params.hdf5File, partitions, null, false );
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/bdv/ij/export/Scripting.java
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Expand Up @@ -26,6 +26,7 @@
import java.util.List;
import java.util.Map;

import bdv.export.DownsampleBlock;
import bdv.export.ExportMipmapInfo;
import bdv.export.WriteSequenceToHdf5;
import bdv.ij.util.PluginHelper;
Expand Down Expand Up @@ -233,7 +234,7 @@ public void writePartition( final int index )
if ( index >= 0 && index < partitions.size() )
{
final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
WriteSequenceToHdf5.writeHdf5PartitionFile( spimData.getSequenceDescription(), perSetupMipmapInfo, deflate, partitions.get( index ), null, null, numCellCreatorThreads, null );
WriteSequenceToHdf5.writeHdf5PartitionFile( spimData.getSequenceDescription(), perSetupMipmapInfo, DownsampleBlock.DownsamplingMethod.Average, deflate, partitions.get( index ), null, null, numCellCreatorThreads, null );
}
}

Expand Down
3 changes: 2 additions & 1 deletion src/main/java/bdv/ij/export/tiles/CellVoyagerDataExporter.java
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Expand Up @@ -27,6 +27,7 @@
import java.util.ArrayList;
import java.util.List;

import bdv.export.DownsampleBlock;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
Expand Down Expand Up @@ -336,7 +337,7 @@ public void export( final File seqFile, final File hdf5File, final int[][] resol
*/

final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
WriteSequenceToHdf5.writeHdf5File( sequenceDescriptionHDF5, resolutions, chunks, true, hdf5File, null, null, numCellCreatorThreads, progressWriter );
WriteSequenceToHdf5.writeHdf5File( sequenceDescriptionHDF5, resolutions, chunks, DownsampleBlock.DownsamplingMethod.Average, true, hdf5File, null, null, numCellCreatorThreads, progressWriter );

/*
* write XML sequence description
Expand Down