SpimData2 now has a constructor that takes a URI

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/DHM.java

@@ -119,7 +119,7 @@ public SpimData2 createDataset( final String xmlFileName )
 		//viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
 
 		// finally create the SpimData itself based on the sequence description and the view registration
-		final SpimData2 spimData = new SpimData2( meta.getDir(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
+		final SpimData2 spimData = new SpimData2( meta.getDir().toURI(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 
 		return spimData;
 	}

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java

@@ -645,7 +645,7 @@ else if ( aInfoI.axis == 2 )
 		final ViewInterestPoints viewInterestPoints = new ViewInterestPoints();
 		//viewInterestPoints.createViewInterestPoints( sd.getViewDescriptions() );
 
-		SpimData2 data = new SpimData2( new File("/"), sd, vrs, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
+		SpimData2 data = new SpimData2( new File("/").toURI(), sd, vrs, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 		return data;
 	}
 

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/LightSheetZ1.java

@@ -148,7 +148,7 @@ public SpimData2 createDataset( final String xmlFileName )
 		//viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
 
 		// finally create the SpimData itself based on the sequence description and the view registration
-		final SpimData2 spimData = new SpimData2( new File( directory ), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
+		final SpimData2 spimData = new SpimData2( new File( directory ).toURI(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 
 		if ( meta.applyAxis() )
 			Apply_Transformation.applyAxis( spimData );

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/MicroManager.java

@@ -123,7 +123,7 @@ public SpimData2 createDataset( final String xmlFileName )
 		//viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
 
 		// finally create the SpimData itself based on the sequence description and the view registration
-		final SpimData2 spimData = new SpimData2( new File( directory ), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
+		final SpimData2 spimData = new SpimData2( new File( directory ).toURI(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 
 		if ( reader.applyAxis() )
 			Apply_Transformation.applyAxis( spimData );

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/SimView.java

@@ -151,7 +151,7 @@ public SpimData2 createDataset( final String xmlFileName )
 		//viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
 
 		// finally create the SpimData itself based on the sequence description and the view registration
-		final SpimData2 spimData = new SpimData2( new File( directory ), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
+		final SpimData2 spimData = new SpimData2( new File( directory ).toURI(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 
 		return spimData;
 	}

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/StackList.java

@@ -331,7 +331,7 @@ public SpimData2 createDataset( final String xmlFileName )
 		//viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
 
 		// finally create the SpimData itself based on the sequence description and the view registration
-		final SpimData2 spimData = new SpimData2( new File( directory ), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
+		final SpimData2 spimData = new SpimData2( new File( directory ).toURI(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 
 		return spimData;
 	}

src/main/java/net/preibisch/mvrecon/fiji/plugin/fusion/DeconvolutionGUI.java

@@ -73,17 +73,15 @@
 import net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory;
 import net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPUFactory;
 import net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDAFactory;
-import net.preibisch.mvrecon.process.export.AppendSpimData2HDF5;
+import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.export.DisplayImage;
-import net.preibisch.mvrecon.process.export.ExportSpimData2HDF5;
-import net.preibisch.mvrecon.process.export.ExportSpimData2TIFF;
+import net.preibisch.mvrecon.process.export.ExportN5API;
 import net.preibisch.mvrecon.process.export.ImgExport;
 import net.preibisch.mvrecon.process.export.Save3dTIFF;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
 import net.preibisch.mvrecon.process.fusion.FusionTools.ImgDataType;
 import net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjustmentTools;
 import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
-import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 
 public class DeconvolutionGUI implements FusionExportInterface
@@ -97,9 +95,7 @@ public class DeconvolutionGUI implements FusionExportInterface
 
 		staticImgExportAlgorithms.add( new DisplayImage() );
 		staticImgExportAlgorithms.add( new Save3dTIFF( null ) );
-		staticImgExportAlgorithms.add( new ExportSpimData2TIFF() );
-		staticImgExportAlgorithms.add( new ExportSpimData2HDF5() );
-		staticImgExportAlgorithms.add( new AppendSpimData2HDF5() );
+		staticImgExportAlgorithms.add( new ExportN5API() );
 
 		imgExportDescriptions = new String[ staticImgExportAlgorithms.size() ];
 

src/main/java/net/preibisch/mvrecon/fiji/plugin/fusion/QualityGUI.java

@@ -40,14 +40,11 @@
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox;
 import net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools;
-import net.preibisch.mvrecon.process.export.AppendSpimData2HDF5;
+import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.export.DisplayImage;
-import net.preibisch.mvrecon.process.export.ExportSpimData2HDF5;
-import net.preibisch.mvrecon.process.export.ExportSpimData2TIFF;
 import net.preibisch.mvrecon.process.export.ImgExport;
 import net.preibisch.mvrecon.process.export.Save3dTIFF;
 import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
-import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.interestpointregistration.TransformationTools;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 
@@ -89,9 +86,6 @@ public class QualityGUI implements FusionExportInterface
 
 		staticImgExportAlgorithms.add( new DisplayImage() );
 		staticImgExportAlgorithms.add( new Save3dTIFF( null ) );
-		staticImgExportAlgorithms.add( new ExportSpimData2TIFF() );
-		staticImgExportAlgorithms.add( new ExportSpimData2HDF5() );
-		staticImgExportAlgorithms.add( new AppendSpimData2HDF5() );
 
 		imgExportDescriptions = new String[ staticImgExportAlgorithms.size() ];
 

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_HDF5.java

@@ -267,7 +267,7 @@ public static SpimData2 reduceSpimData2( final SpimData2 oldSpimData, final List
 		//TODO: copy PSFs
 
 		final SpimData2 newSpimData = new SpimData2(
-				oldSpimData.getBasePath(),
+				oldSpimData.getBasePathURI(),
 				sequenceDescription,
 				viewRegistrations,
 				viewsInterestPoints,
@@ -288,7 +288,7 @@ public static Pair< SpimData2, List< String > > createXMLObject(
 	{
 		// Re-assemble a new SpimData object containing the subset of viewsetups and timepoints selected
 		final List< String > filesToCopy = new ArrayList< String >();
-		final SpimData2 newSpimData = Resave_TIFF.assemblePartialSpimData2( spimData, viewIds, params.seqFile.getParentFile(), filesToCopy );
+		final SpimData2 newSpimData = Resave_TIFF.assemblePartialSpimData2( spimData, viewIds, params.seqFile.getParentFile().toURI(), filesToCopy );
 		final ArrayList< Partition > partitions = Generic_Resave_HDF5.getPartitions( newSpimData, params );
 
 		final Hdf5ImageLoader hdf5Loader;

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5.java

@@ -28,18 +28,31 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.stream.Collectors;
 
+import org.janelia.saalfeldlab.n5.Compression;
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.N5Writer;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
+
 import bdv.export.ExportMipmapInfo;
 import bdv.export.ProgressWriter;
 import bdv.export.n5.WriteSequenceToN5;
 import bdv.img.n5.N5ImageLoader;
 import ij.ImageJ;
 import ij.plugin.PlugIn;
+import mpicbg.spim.data.SpimData;
 import mpicbg.spim.data.SpimDataException;
+import mpicbg.spim.data.generic.AbstractSpimData;
 import mpicbg.spim.data.sequence.TimePoint;
 import mpicbg.spim.data.sequence.ViewId;
 import mpicbg.spim.data.sequence.ViewSetup;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.type.numeric.real.FloatType;
 import net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML;
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
@@ -120,6 +133,7 @@ public static void resaveN5(
 		}
 		else if ( URITools.isS3( n5Params.n5URI ) || URITools.isGC( n5Params.n5URI ) )
 		{
+			final N5Writer = new N5Factory().openWriter( URITools.appendName( baseDir, baseN5 ) ); // cloud support, avoid dependency hell if it is a local file
 			// TODO: save to cloud
 		}
 
@@ -134,6 +148,44 @@ else if ( URITools.isS3( n5Params.n5URI ) || URITools.isGC( n5Params.n5URI ) )
 		progressWriter.out().println( new Date( System.currentTimeMillis() ) + ": Finished saving " + n5Params.n5URI + " and " + n5Params.xmlURI );
 	}
 
+	public static void createDatasets(
+			final N5Writer n5,
+			final AbstractSpimData<?> data,
+			final int[] blockSize,
+			final int[][] downsamplingFactors,
+			final Compression compression,
+			final Map<Integer, long[]> viewSetupIdToDimensions )
+	{
+		for ( final Entry<Integer, long[]> viewSetup : viewSetupIdToDimensions.entrySet() )
+		{
+			final Object type = data.getSequenceDescription().getImgLoader().getSetupImgLoader( viewSetup.getKey() ).getImageType();
+			final DataType dataType;
+
+			if ( UnsignedShortType.class.isInstance( type ) )
+				dataType = DataType.UINT16;
+			else if ( UnsignedByteType.class.isInstance( type ) )
+				dataType = DataType.UINT8;
+			else if ( FloatType.class.isInstance( type ) )
+				dataType = DataType.FLOAT32;
+			else
+				throw new RuntimeException("Unsupported pixel type: " + type.getClass().getCanonicalName() );
+
+			// TODO: ViewSetupId needs to contain: {"downsamplingFactors":[[1,1,1],[2,2,1]],"dataType":"uint16"}
+			final String n5Dataset = "setup" + viewSetup.getKey();
+
+			System.out.println( "Creating group: " + "'setup" + viewSetup.getKey() + "'" );
+
+			n5.createGroup( n5Dataset );
+
+			System.out.println( "setting attributes for '" + "setup" + viewSetup.getKey() + "'");
+
+			n5.setAttribute( n5Dataset, "downsamplingFactors", downsamplingFactors );
+			n5.setAttribute( n5Dataset, "dataType", dataType );
+			n5.setAttribute( n5Dataset, "blockSize", blockSize );
+			n5.setAttribute( n5Dataset, "dimensions", viewSetup.getValue() );
+			n5.setAttribute( n5Dataset, "compression", compression );
+		}
+	}
 
 	public static void main(String[] args)
 	{

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_TIFF.java

@@ -324,7 +324,7 @@ public static Pair< SpimData2, List< String > > createXMLObject( final SpimData2
 
 		// Re-assemble a new SpimData object containing the subset of viewsetups and timepoints selected
 		final List< String > filesToCopy = new ArrayList< String >();
-		final SpimData2 newSpimData = assemblePartialSpimData2( spimData, viewIds, new File( URITools.removeFilePrefix( params.getXMLPath() ) ).getParentFile(), filesToCopy );
+		final SpimData2 newSpimData = assemblePartialSpimData2( spimData, viewIds, new File( URITools.removeFilePrefix( params.getXMLPath() ) ).getParentFile().toURI(), filesToCopy );
 
 		final StackImgLoaderIJ imgLoader = new StackImgLoaderIJ(
 				new File( URITools.removeFilePrefix( params.getXMLPath() ) ).getParentFile(),
@@ -393,7 +393,7 @@ public static void copyFolder( final File src, final File dest, final List< Stri
 	 * @param basePath - the base path
 	 * @return new SpimData
 	 */
-	public static SpimData2 assemblePartialSpimData2( final SpimData2 spimData, final List< ? extends ViewId > viewIds, final File basePath, final List< String > filesToCopy )
+	public static SpimData2 assemblePartialSpimData2( final SpimData2 spimData, final List< ? extends ViewId > viewIds, final URI basePath, final List< String > filesToCopy )
 	{
 		final TimePoints timepoints;
 

src/main/java/net/preibisch/mvrecon/fiji/spimdata/SpimData2.java

@@ -73,7 +73,8 @@ public class SpimData2 extends SpimData
 	private IntensityAdjustments intensityAdjustments;
 	public boolean gridMoveRequested = false;
 
-	// TODO: only for compatibility with depending packages, remove at some point
+	/*
+	// only for compatibility with depending packages, remove at some point
 	public SpimData2(
 			final File basePath,
 			final SequenceDescription sequenceDescription,
@@ -85,9 +86,10 @@ public SpimData2(
 	{
 		this( basePath, sequenceDescription, viewRegistrations, viewsInterestPoints, boundingBoxes, pointSpreadFunctions, stitchingResults, new IntensityAdjustments() );
 	}
+	*/
 
 	public SpimData2(
-			final File basePath,
+			final URI basePathUri,
 			final SequenceDescription sequenceDescription,
 			final ViewRegistrations viewRegistrations,
 			final ViewInterestPoints viewsInterestPoints,
@@ -96,7 +98,10 @@ public SpimData2(
 			final StitchingResults stitchingResults,
 			final IntensityAdjustments intensityAdjustments )
 	{
-		super( basePath, sequenceDescription, viewRegistrations );
+		super( null, sequenceDescription, viewRegistrations );
+
+		// work-around for the super class not having a constructor for URI
+		this.setBasePathURI(basePathUri);
 
 		this.viewsInterestPoints = viewsInterestPoints;
 		this.boundingBoxes = boundingBoxes;
@@ -523,7 +528,7 @@ public static SpimData2 convert( final SpimData data1 )
 		final StitchingResults sr = new StitchingResults();
 		final IntensityAdjustments ia = new IntensityAdjustments();
 
-		return new SpimData2( data1.getBasePath(), s, vr, vipl, bb, psfs, sr, ia );
+		return new SpimData2( data1.getBasePathURI(), s, vr, vipl, bb, psfs, sr, ia );
 	}
 
 	/**

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyStackImgLoaderIJ.java

@@ -22,40 +22,38 @@
  */
 package net.preibisch.mvrecon.fiji.spimdata.imgloaders;
 
+import java.io.File;
+import java.util.Date;
+
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.gui.GenericDialog;
 import ij.io.Opener;
 import ij.process.ImageProcessor;
-
-import java.io.File;
-import java.util.Date;
-
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.sequence.ViewId;
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.converter.RealUnsignedShortConverter;
 import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
 import net.imglib2.img.array.ArrayImg;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.img.planar.PlanarImg;
-import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.view.Views;
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ;
 import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5;
-import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.Parameters;
+import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5;
 import net.preibisch.mvrecon.fiji.plugin.util.GUIHelper;
-import net.preibisch.mvrecon.process.export.ExportSpimData2HDF5;
+import net.preibisch.mvrecon.process.fusion.FusionTools;
 import util.ImgLib2Tools;
 
 public class LegacyStackImgLoaderIJ extends LegacyStackImgLoader
 {
-	Parameters params = null;
+	ParametersResaveHDF5 params = null;
 
 	public LegacyStackImgLoaderIJ(
 			final File path, final String fileNamePattern,
@@ -132,7 +130,7 @@ public RandomAccessibleInterval< UnsignedShortType > getImage( final ViewId view
 			if ( params == null )
 				return null;
 
-			final double[] minmax = ExportSpimData2HDF5.updateAndGetMinMax( ImageJFunctions.wrapFloat( imp ), params );
+			final double[] minmax = updateAndGetMinMax( ImageJFunctions.wrapFloat( imp ), params );
 			converter = new RealUnsignedShortConverter< FloatType >( minmax[ 0 ], minmax[ 1 ] );
 		}
 		else
@@ -246,7 +244,7 @@ public String toString()
 		return new StackListImageJ().getTitle() + ", ImgFactory=" + getImgFactory().getClass().getSimpleName();
 	}
 
-	protected static Parameters queryParameters()
+	protected static ParametersResaveHDF5 queryParameters()
 	{
 		final GenericDialog gd = new GenericDialog( "Opening 32bit TIFF as 16bit" );
 
@@ -288,6 +286,38 @@ protected static Parameters queryParameters()
 			Generic_Resave_HDF5.defaultMin = Generic_Resave_HDF5.defaultMax = Double.NaN;
 		}
 
-		return new Parameters( false, null, null, null, null, false, false, 0, 0, false, 0, Generic_Resave_HDF5.defaultConvertChoice, Generic_Resave_HDF5.defaultMin, Generic_Resave_HDF5.defaultMax );
+		return new ParametersResaveHDF5( false, null, null, null, null, false, false, 0, 0, false, 0, Generic_Resave_HDF5.defaultConvertChoice, Generic_Resave_HDF5.defaultMin, Generic_Resave_HDF5.defaultMax );
 	}
+
+	public static < T extends RealType< T > > double[] updateAndGetMinMax( final RandomAccessibleInterval< T > img, final ParametersResaveHDF5 params )
+	{
+		double min, max;
+
+		if ( params == null || params.getConvertChoice() == 0 || Double.isNaN( params.getMin() ) || Double.isNaN( params.getMin() ) )
+		{
+			final float[] minmax = FusionTools.minMax( img );
+			min = minmax[ 0 ];
+			max = minmax[ 1 ];
+
+			min = Math.max( 0, min - ((min+max)/2.0) * 0.1 );
+			max = max + ((min+max)/2.0) * 0.1;
+
+			if ( params != null )
+			{
+				params.setMin( min );
+				params.setMax( max );
+			}
+		}
+		else
+		{
+			min = params.getMin();
+			max = params.getMax();
+		}
+
+		IOFunctions.println( "Min intensity for 16bit conversion: " + min );
+		IOFunctions.println( "Max intensity for 16bit conversion: " + max );
+
+		return new double[]{ min, max };
+	}
+
 }

src/main/java/net/preibisch/mvrecon/headless/definedataset/LightSheetZ1.java

@@ -23,6 +23,7 @@
 package net.preibisch.mvrecon.headless.definedataset;
 
 import java.io.File;
+import java.net.URI;
 import java.util.ArrayList;
 
 import mpicbg.spim.data.registration.ViewRegistrations;
@@ -122,7 +123,7 @@ public static SpimData2 createDataset( final String cziFirstFile, final DefineDa
 
 		// finally create the SpimData itself based on the sequence description and the view registration
 		final SpimData2 spimData = new SpimData2(
-				new File( cziFile.getParent() ),
+				new File( cziFile.getParent() ).toURI(),
 				sequenceDescription,
 				viewRegistrations,
 				viewInterestPoints,