import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
@SuppressWarnings( "unchecked" )
@Override
public SpimDataMinimal[] load()
{
	SpimDataMinimal spimData = null;
	try
	{
		spimData = new XmlIoSpimDataMinimal().load( xmlPath );

		if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
		{
			System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );
		}

	}
	catch ( final SpimDataException e )
	{
		e.printStackTrace();
	}

	return new SpimDataMinimal[]{ spimData };
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public CellHandler( final String baseUrl, final String xmlFilename, final String datasetName, final String thumbnailsDirectory ) throws SpimDataException, IOException
{
	final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
	final SpimDataMinimal spimData = io.load( xmlFilename );
	final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
	final Hdf5ImageLoader imgLoader = ( Hdf5ImageLoader ) seq.getImgLoader();

	cache = imgLoader.getCacheControl();
	loader = imgLoader.getShortArrayLoader();
	cacheHints = new CacheHints( LoadingStrategy.BLOCKING, 0, false );

	// dataSetURL property is used for providing the XML file by replace
	// SequenceDescription>ImageLoader>baseUrl
	this.xmlFilename = xmlFilename;
	baseFilename = xmlFilename.endsWith( ".xml" ) ? xmlFilename.substring( 0, xmlFilename.length() - ".xml".length() ) : xmlFilename;
	dataSetURL = baseUrl;

	datasetXmlString = buildRemoteDatasetXML( io, spimData, baseUrl );
	metadataJson = buildMetadataJsonString( imgLoader, seq );
	settingsXmlString = buildSettingsXML( baseFilename );
	thumbnailFilename = createThumbnail( spimData, baseFilename, datasetName, thumbnailsDirectory );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
/**
 * Create PNG thumbnail file named "{@code <baseFilename>.png}".
 */
private static String createThumbnail( final SpimDataMinimal spimData, final String baseFilename, final String datasetName, final String thumbnailsDirectory )
{
	final String thumbnailFileName = thumbnailsDirectory + "/" + datasetName + ".png";
	final File thumbnailFile = new File( thumbnailFileName );
	if ( !thumbnailFile.isFile() ) // do not recreate thumbnail if it already exists
	{
		final BufferedImage bi = ThumbnailGenerator.makeThumbnail( spimData, baseFilename, Constants.THUMBNAIL_WIDTH, Constants.THUMBNAIL_HEIGHT );
		try
		{
			ImageIO.write( bi, "png", thumbnailFile );
		}
		catch ( final IOException e )
		{
			LOG.warn( "Could not create thumbnail png for dataset \"" + baseFilename + "\"" );
			LOG.warn( e.getMessage() );
		}
	}
	return thumbnailFileName;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public void exec( final String xmlHDF5Path, final int setupID, final String tgmmPath, final String outputPath, final boolean doCrop, final RealInterval interval, final int tFrom, final int tTo )
{
	SpimDataMinimal spimData;
	try
	{
		spimData = new XmlIoSpimDataMinimal().load( xmlHDF5Path );
	}
	catch ( final SpimDataException e )
	{
		logger.error( "Problem reading the transforms in image data file:\n" + e.getMessage() + "\n" );
		return;
	}
	final Model model = createModel( new File( tgmmPath ), spimData, setupID, interval, tFrom, tTo );
	model.setLogger( logger );
	final Settings settings = createSettings( new File( xmlHDF5Path ) );

	final TrackMate trackmate = new TrackMate( model, settings );
	trackmate.setNumThreads( 1 );
	trackmate.computeSpotFeatures( true );
	trackmate.computeEdgeFeatures( true );
	trackmate.computeTrackFeatures( true );

	save( outputPath, model, settings );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
@Override
public void run( final String ignored )
{
	final File imageFile = askForImageFile();
	if ( null == imageFile ) { return; }

	final File tgmmFolder = askForTGMMFolder();
	if ( null == tgmmFolder ) { return; }

	SpimDataMinimal spimData;
	try
	{
		spimData = new XmlIoSpimDataMinimal().load( imageFile.getAbsolutePath() );
	}
	catch ( final SpimDataException e )
	{
		logger.error( "Problem reading the transforms in image data file:\n" + e.getMessage() + "\n" );
		return;
	}
	final String[] angles = readSetupNames( spimData.getSequenceDescription() );
	final int angleIndex = askForAngle( angles );
	if ( angleIndex < 0 ) { return; }

	final int setupID = spimData.getSequenceDescription().getViewSetupsOrdered().get( angleIndex ).getId();
	launchMamut( imageFile, tgmmFolder, setupID, interval );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public void launchMamut( final File imageFile, final File tgmmFile, final int setupID, final RealInterval interval )
{
	SpimDataMinimal spimData;
	try
	{
		spimData = new XmlIoSpimDataMinimal().load( imageFile.getAbsolutePath() );
	}
	catch ( final SpimDataException e )
	{
		logger.error( "Problem reading the transforms in image data file:\n" + e.getMessage() + "\n" );
		return;
	}
	final Model model = createModel( tgmmFile, spimData, setupID, interval );
	final SourceSettings settings = createSettings();
	new MaMuT( imageFile, model, settings );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
protected Model createModel( final File tgmmFolder, final SpimDataMinimal spimData, final int setupID, final RealInterval interval )
{
	final List< AffineTransform3D > transforms = pickTransform( spimData, setupID );

	final TGMMImporter2 importer = new TGMMImporter2( tgmmFolder, transforms, TGMMImporter2.DEFAULT_PATTERN, logger, interval, 0, Integer.MAX_VALUE );
	if ( !importer.checkInput() || !importer.process() )
	{
		logger.error( importer.getErrorMessage() );
		return new Model();
	}
	final Model model = importer.getResult();

	/*
	 * Hack to set the POSITION_T feature of imported spots.
	 */
	final Settings settings = new Settings();
	settings.dt = 1;
	final TrackMate trackmate = new TrackMate( model, settings );
	final ResetSpotTimeFeatureAction action = new ResetSpotTimeFeatureAction();
	action.execute( trackmate );

	return model;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public static void fix( final String xmlFilename ) throws SpimDataException, IOException
{
	final XmlIoSpimDataMinimal spimDataIo = new XmlIoSpimDataMinimal();
	final SpimDataMinimal spimData = spimDataIo.load( xmlFilename );
	final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
	final Hdf5ImageLoader il = ( Hdf5ImageLoader) seq.getImgLoader();
	final String outfn = il.getHdf5File().getCanonicalPath() + "FIXED";
	final HashMap< Integer, ExportMipmapInfo > perSetupMipmapInfo = new HashMap<>();
	for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() )
	{
		final int setupId = setup.getId();
		final MipmapInfo info = il.getSetupImgLoader( setupId ).getMipmapInfo();
		perSetupMipmapInfo.put( setupId, new ExportMipmapInfo(
				Util.castToInts( info.getResolutions() ),
				info.getSubdivisions() ) );
	}
	final ArrayList< Partition > partitions = il.getPartitions();
	WriteSequenceToHdf5.writeHdf5PartitionLinkFile( seq, perSetupMipmapInfo, partitions, new File( outfn ) );

	System.out.println( "fixed hdf5 master file written to " + outfn );
	System.out.println( "rename it to " + il.getHdf5File().getCanonicalPath() + " to use it." );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public SpimDataMinimal[] loadAll( int startid )
{
	SpimDataMinimal[] out = new SpimDataMinimal[ impList.length ];
	index = startid;
	for( int i = 0; i < impList.length; i++ )
	{
		out[ i ] = load( range( index, impList[ i ].getNChannels() ), impList[ i ] );
		index += impList[ i ].getNChannels();
	}
	return out;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
/**
 * Create a modified dataset XML by replacing the ImageLoader with an
 * {@link RemoteImageLoader} pointing to the data we are serving.
 */
private static String buildRemoteDatasetXML( final XmlIoSpimDataMinimal io, final SpimDataMinimal spimData, final String baseUrl ) throws IOException, SpimDataException
{
	final SpimDataMinimal s = new SpimDataMinimal( spimData, new RemoteImageLoader( baseUrl, false ) );
	final Document doc = new Document( io.toXml( s, s.getBasePath() ) );
	final XMLOutputter xout = new XMLOutputter( Format.getPrettyFormat() );
	final StringWriter sw = new StringWriter();
	xout.output( doc, sw );
	return sw.toString();
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
protected Model createModel( final File tgmmFolder, final SpimDataMinimal spimData, final int setupID, final RealInterval interval, final int tFrom, final int tTo )
{

	final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
	final ViewRegistrations regs = spimData.getViewRegistrations();
	final List< AffineTransform3D > transforms = new ArrayList< AffineTransform3D >( seq.getTimePoints().size() );
	for ( final TimePoint t : seq.getTimePoints().getTimePointsOrdered() )
	{
		transforms.add( regs.getViewRegistration( t.getId(), setupID ).getModel() );
	}

	final TGMMImporter2 importer = new TGMMImporter2( tgmmFolder, transforms, TGMMImporter2.DEFAULT_PATTERN, logger, interval, tFrom, tTo );
	if ( !importer.checkInput() || !importer.process() )
	{
		logger.error( importer.getErrorMessage() );
	}
	final Model model = importer.getResult();

	/*
	 * Hack to set the POSITION_T feature of imported spots.
	 */
	final Settings settings = new Settings();
	settings.dt = 1;
	final TrackMate trackmate = new TrackMate( model, settings );
	final ResetSpotTimeFeatureAction action = new ResetSpotTimeFeatureAction();
	action.execute( trackmate );

	return model;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
protected List< AffineTransform3D > pickTransform( final SpimDataMinimal spimData, final int setupID )
{
	final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
	final ViewRegistrations regs = spimData.getViewRegistrations();
	final List< AffineTransform3D > transforms = new ArrayList< AffineTransform3D >( seq.getTimePoints().size() );
	for ( final TimePoint t : seq.getTimePoints().getTimePointsOrdered() )
	{
		transforms.add( regs.getViewRegistration( t.getId(), setupID ).getModel() );
	}
	return transforms;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
private static SequenceDescriptionMinimal openSequence( final String xmlFilename ) throws SpimDataException
{
	final File f = new File( xmlFilename );
	if ( f.exists() && f.isFile() && f.getName().endsWith( ".xml" ) )
	{
		final SpimDataMinimal spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
		return spimData.getSequenceDescription();
	}
	else
		return null;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public void writeXmlAndLinks() throws SpimDataException
{
	final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
	WriteSequenceToHdf5.writeHdf5PartitionLinkFile( seq, perSetupMipmapInfo, partitions, hdf5File );
	final Hdf5ImageLoader loader = new Hdf5ImageLoader( hdf5File, partitions, null, false );

	new XmlIoSpimDataMinimal().save( new SpimDataMinimal( spimData, loader ), seqFile.getAbsolutePath() );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public static final SpimDataMinimal createSpimData( IFormatReader reader )
{
	Hashtable< String, Object > gmeta = reader.getGlobalMetadata();
	System.out.println( gmeta ); // header stuff here TODO
	
	// get relevant metadata
	double pw = 1.0;
	double ph = 1.0;
	double pd = 1.0;

	if( gmeta.keySet().contains( "XResolution" ))
		pw = ((Double)gmeta.get("XResolution")).doubleValue();

	if( gmeta.keySet().contains( "YResolution" ))
		ph = ((Double)gmeta.get("YResolution")).doubleValue();

	if( gmeta.keySet().contains( "Spacing" ))
		pd = ((Double)gmeta.get("Spacing")).doubleValue();

	int numSetups = 1;
	int numTimepoints = 1;
	int[] ids = new int[]{ 349812342 };
	final File basePath = new File( "." );

	String punit = "px";
	if( gmeta.keySet().contains( "Unit" ))
		punit = (String) gmeta.get( "Unit" );
	
	final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions( punit, pw, ph, pd );
	final long w = ((Long)gmeta.get("ImageWidth")).longValue();
	final long h = ((Long)gmeta.get("ImageLength")).longValue();
	final long d = reader.getSizeZ(); //Long.parseLong( (String)gmeta.get("images") );

	long[] dims = new long[]{ w, h, d };
	final FinalDimensions size = new FinalDimensions( new long[] { w, h, d } );

	// create setups from channels
	final HashMap< Integer, BasicViewSetup > setups = new HashMap< Integer, BasicViewSetup >( numSetups );
	for ( int s = 0; s < numSetups; ++s )
	{
		final BasicViewSetup setup = new BasicViewSetup( ids[ s ], String.format( "channel %d", ids[ s ] + 1 ), size, voxelSize );
		setup.setAttribute( new Channel( ids[ s ] + 1 ) );
		setups.put( ids[ s ], setup );
	}

	// create timepoints
	final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >( numTimepoints );
	for ( int t = 0; t < numTimepoints; ++t )
		timepoints.add( new TimePoint( t ) );

	// create ViewRegistrations from the images calibration
	final AffineTransform3D sourceTransform = new AffineTransform3D();
	sourceTransform.set( 1.0/pw, 0, 0, 0, 0, 1.0/ph, 0, 0, 0, 0, pd, 0 );
	final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
	for ( int t = 0; t < numTimepoints; ++t )
		for ( int s = 0; s < numSetups; ++s )
			registrations.add( new ViewRegistration( t, ids[ s ], sourceTransform ) );

	final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, 
			new DummyImageLoader< FloatType >( new FloatType(), dims ), null );

	SpimDataMinimal spimData = new SpimDataMinimal( basePath, seq, new ViewRegistrations( registrations ) );
	if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
		System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );

	return spimData;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
@SuppressWarnings( "unchecked" )
@Override
public SpimDataMinimal[] load()
{
	return loadAll( 255 );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public final SpimDataMinimal createSpimData()
{
	int numSetups = 1;
	int numTimepoints = 1;
	int[] ids = new int[]{ 349812342 };
	final File basePath = new File( "." );

	double pw = spacingFull[ 0 ];
	double ph = spacingFull[ 1 ];
	double pd = spacingFull[ 2 ];

	double ox = offsetFull[ 0 ] / spacingFull[ 0 ];
	double oy = offsetFull[ 1 ] / spacingFull[ 1 ];
	double oz = offsetFull[ 2 ] / spacingFull[ 2 ];

	String punit = "px";

	final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions( punit, pw, ph, pd );
	final long w = dimsFull[ 0 ];
	final long h = dimsFull[ 1 ];
	final long d = dimsFull[ 2 ];
	final FinalDimensions size = new FinalDimensions( new long[] { w, h, d } );

	// create setups from channels
	final HashMap< Integer, BasicViewSetup > setups = new HashMap< Integer, BasicViewSetup >( numSetups );
	for ( int s = 0; s < numSetups; ++s )
	{
		final BasicViewSetup setup = new BasicViewSetup( ids[ s ], String.format( "channel %d", ids[ s ] + 1 ), size, voxelSize );
		setup.setAttribute( new Channel( ids[ s ] + 1 ) );
		setups.put( ids[ s ], setup );
	}

	// create timepoints
	final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >( numTimepoints );
	for ( int t = 0; t < numTimepoints; ++t )
		timepoints.add( new TimePoint( t ) );

	// create ViewRegistrations from the images calibration
	final AffineTransform3D sourceTransform = new AffineTransform3D();
	sourceTransform.set( pw, 0, 0, ox, 0, ph, 0, oy, 0, 0, pd, oz );
	final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
	for ( int t = 0; t < numTimepoints; ++t )
		for ( int s = 0; s < numSetups; ++s )
			registrations.add( new ViewRegistration( t, ids[ s ], sourceTransform ) );

	final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, 
			new DummyImageLoader< FloatType >( new FloatType(), this ), null );

	SpimDataMinimal spimData = new SpimDataMinimal( basePath, seq, new ViewRegistrations( registrations ) );
	if ( WrapBasicImgLoader.wrapImgLoaderIfNecessary( spimData ) )
		System.err.println( "WARNING:\nOpening <SpimData> dataset that is not suited for interactive browsing.\nConsider resaving as HDF5 for better performance." );

	return spimData;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
/**
 * Create a thumbnail image for a dataset. If there is a settings.xml file
 * for the dataset, these settings are used for creating the thumbnail.
 *
 * @param spimData
 *            the dataset.
 * @param baseFilename
 *            full path of dataset xml file, without the ".xml" extension.
 *            this is used to derive the name of the settings.xml file.
 * @param width
 *            width of the thumbnail image.
 * @param height
 *            height of the thumbnail image.
 * @return thumbnail image
 */
public static BufferedImage makeThumbnail( final SpimDataMinimal spimData, final String baseFilename, final int width, final int height )
{
	final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();
	final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
	BigDataViewer.initSetups( spimData, converterSetups, sources );

	final int numTimepoints = spimData.getSequenceDescription().getTimePoints().size();
	final ThumbnailGenerator generator = new ThumbnailGenerator( sources, numTimepoints );
	final ViewerState state = generator.state;

	final SetupAssignments setupAssignments = new SetupAssignments( converterSetups, 0, 65535 );
	final AffineTransform3D initTransform = InitializeViewerState.initTransform( width, height, false, state );
	state.setViewerTransform( initTransform );

	if ( !generator.tryLoadSettings( baseFilename, setupAssignments ) )
		InitializeViewerState.initBrightness( 0.001, 0.999, state, setupAssignments );

	class ThumbnailTarget implements RenderTarget
	{
		BufferedImage bi;

		@Override
		public BufferedImage setBufferedImage( final BufferedImage bufferedImage )
		{
			bi = bufferedImage;
			return null;
		}

		@Override
		public int getWidth()
		{
			return width;
		}

		@Override
		public int getHeight()
		{
			return height;
		}
	}
	final ThumbnailTarget renderTarget = new ThumbnailTarget();
	new MultiResolutionRenderer( renderTarget, new PainterThread( null ), new double[] { 1 }, 0, false, 1, null, false, AccumulateProjectorARGB.factory, new CacheControl.Dummy() ).paint( state );
	return renderTarget.bi;
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
@Override
public void run()
{
	if ( ij.Prefs.setIJMenuBar )
		System.setProperty( "apple.laf.useScreenMenuBar", "true" );

	final Parameters params = getParameters();

	// cancelled
	if ( params == null )
		return;

	final ProgressWriter progress = new ProgressWriterIJ();
	progress.out().println( "starting export..." );
	final SpimRegistrationSequence sequence = new SpimRegistrationSequence( params.conf );
	final SequenceDescriptionMinimal desc = sequence.getSequenceDescription();

	Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo;
	if ( params.setMipmapManual )
	{
		perSetupExportMipmapInfo = new HashMap<>();
		final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
		for ( final BasicViewSetup setup : desc.getViewSetupsOrdered() )
			perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );
	}
	else
	{
		perSetupExportMipmapInfo = ProposeMipmaps.proposeMipmaps( desc );
	}

	final ArrayList< Partition > partitions;
	final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
	if ( params.split )
	{
		final String xmlFilename = params.seqFile.getAbsolutePath();
		final String basename = xmlFilename.endsWith( ".xml" ) ? xmlFilename.substring( 0, xmlFilename.length() - 4 ) : xmlFilename;
		final List< TimePoint > timepoints = desc.getTimePoints().getTimePointsOrdered();
		final List< BasicViewSetup > setups = desc.getViewSetupsOrdered();
		partitions = Partition.split( timepoints, setups, params.timepointsPerPartition, params.setupsPerPartition, basename );

		for ( int i = 0; i < partitions.size(); ++i )
		{
			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.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 ) );
	}

	final Hdf5ImageLoader loader = new Hdf5ImageLoader( params.hdf5File, partitions, null, false );
	final SequenceDescriptionMinimal sequenceDescription = new SequenceDescriptionMinimal( desc, loader );

	final File basePath = params.seqFile.getParentFile();
	final SpimDataMinimal spimData = new SpimDataMinimal( basePath, sequenceDescription, sequence.getViewRegistrations() );
	try
	{
		new XmlIoSpimDataMinimal().save( spimData, params.seqFile.getAbsolutePath() );
		progress.setProgress( 1.0 );
	}
	catch ( final Exception e )
	{
		progress.err().println( "Failed to write xml file " + params.seqFile );
		e.printStackTrace( progress.err() );
	}
	progress.out().println( "done" );
}
 

import bdv.spimdata.SpimDataMinimal; //导入依赖的package包/类
public static void saveAsNewFile( final Parameters params ) throws SpimDataException
{
	final ProgressWriter progress = new ProgressWriterIJ();
	final XmlIoSpimDataMinimal spimDataIo = new XmlIoSpimDataMinimal();

	final SpimRegistrationSequence spimseq = new SpimRegistrationSequence( params.conf );
	final Map< Integer, AffineTransform3D > fusionTransforms = spimseq.getFusionTransforms( params.cropOffsetX, params.cropOffsetY, params.cropOffsetZ, params.scale );
	final FusionResult fusionResult = FusionResult.create( spimseq, params.fusionDirectory, params.filenamePattern, params.numSlices, params.sliceValueMin, params.sliceValueMax, fusionTransforms );

	// sequence description (no ImgLoader yet)
	final SequenceDescriptionMinimal desc = fusionResult.getSequenceDescription();

	// create ExportMipmapInfos
	final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap<>();
	final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
	for ( final BasicViewSetup setup : desc.getViewSetupsOrdered() )
		perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );

	// create partitions if desired
	final ArrayList< Partition > partitions;
	if ( params.split )
	{
		final String xmlFilename = params.seqFile.getAbsolutePath();
		final String basename = xmlFilename.endsWith( ".xml" ) ? xmlFilename.substring( 0, xmlFilename.length() - 4 ) : xmlFilename;
		final List< TimePoint > timepoints = desc.getTimePoints().getTimePointsOrdered();
		final List< BasicViewSetup > setups = desc.getViewSetupsOrdered();
		partitions = Partition.split( timepoints, setups, params.timepointsPerPartition, params.setupsPerPartition, basename );
	}
	else
		partitions = null;

	// write to hdf5
	final int numCellCreatorThreads = Math.max( 1, PluginHelper.numThreads() - 1 );
	if ( params.split )
	{
		for ( int i = 0; i < partitions.size(); ++i )
		{
			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.writeHdf5PartitionLinkFile( desc, perSetupExportMipmapInfo, partitions, params.hdf5File );
	}
	else
	{
		WriteSequenceToHdf5.writeHdf5File( desc, perSetupExportMipmapInfo, params.deflate, params.hdf5File, null, null, numCellCreatorThreads, new SubTaskProgressWriter( progress, 0, 0.95 ) );
	}

	// write xml file
	final Hdf5ImageLoader loader = new Hdf5ImageLoader( params.hdf5File, partitions, null, false );
	final SequenceDescriptionMinimal sequenceDescription = new SequenceDescriptionMinimal( desc, loader );

	final File basePath = params.seqFile.getParentFile();
	final SpimDataMinimal spimData = new SpimDataMinimal( basePath, sequenceDescription, fusionResult.getViewRegistrations() );
	try
	{
		spimDataIo.save( spimData, params.seqFile.getAbsolutePath() );
		progress.setProgress( 1.0 );
	}
	catch ( final Exception e )
	{
		progress.err().println( "Failed to write xml file " + params.seqFile );
		e.printStackTrace( progress.err() );
	}
}