import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
public <T extends RealType<T>> RandomAccessibleInterval< T > aggregate(
		List<RandomAccessibleInterval< T >> rais,
		List<? extends ViewId> vids,
		AbstractSequenceDescription< ?, ? extends BasicViewDescription< ? >, ? > sd
		)
{
	Map<BasicViewDescription< ? >, RandomAccessibleInterval<T>> map = new HashMap<>();
	
	for (int i = 0; i < vids.size(); i++)
	{
		ViewId vid = vids.get( i );
		BasicViewDescription< ? > vd = sd.getViewDescriptions().get( vid );
		map.put( vd, rais.get( i ) );
	}
	
	for (Action< ? > action : actions)
	{
		map = action.aggregate( map );
	}
	
	// return the first RAI still present
	// ideally, there should be only one left
	return map.values().iterator().next();
	
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public LabelblkImageLoader fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
	final String apiUrl = elem.getChildText( "apiUrl" );
	final String nodeId = elem.getChildText( "nodeId" );
	final String dataInstanceId = elem.getChildText( "dataInstanceId" );
	try
	{
		return new LabelblkImageLoader( apiUrl, nodeId, dataInstanceId );
	}
	catch ( Exception e )
	{
		e.printStackTrace();
		return null;
	}
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public DvidMultiscale2dImageLoader fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
	final String apiUrl = elem.getChildText( "apiUrl" );
	final String nodeId = elem.getChildText( "nodeId" );
	final String dataInstanceId = elem.getChildText( "dataInstanceId" );
	try
	{
		return new DvidMultiscale2dImageLoader( apiUrl, nodeId, dataInstanceId );
	}
	catch ( Exception e )
	{
		e.printStackTrace();
		return null;
	}
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public Uint8blkImageLoader fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
	final String apiUrl = elem.getChildText( "apiUrl" );
	final String nodeId = elem.getChildText( "nodeId" );
	final String dataInstanceId = elem.getChildText( "dataInstanceId" );
	try
	{
		return new Uint8blkImageLoader( apiUrl, nodeId, dataInstanceId );
	}
	catch ( final Exception e )
	{
		e.printStackTrace();
		return null;
	}
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
private static void initSetupsARGBTypeNonVolatile(
		final AbstractSpimData< ? > spimData,
		final ARGBType type,
		final List< ConverterSetup > converterSetups,
		final List< SourceAndConverter< ? > > sources )
{
	final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
	for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() )
	{
		final ScaledARGBConverter.ARGB converter = new ScaledARGBConverter.ARGB( 0, 255 );

		final int setupId = setup.getId();
		final String setupName = createSetupName( setup );
		final SpimSource< ARGBType > s = new SpimSource< ARGBType >( spimData, setupId, setupName );

		// Decorate each source with an extra transformation, that can be
		// edited manually in this viewer.
		final TransformedSource< ARGBType > ts = new TransformedSource< ARGBType >( s );
		final SourceAndConverter< ARGBType > soc = new SourceAndConverter< ARGBType >( ts, converter );

		sources.add( soc );
		converterSetups.add( new RealARGBColorConverterSetup( setupId, converter ) );
	}
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
/**
 * Create {@link BigWarpData} from two {@link AbstractSpimData}.
 *
 * @param spimDataP array of moving SpimData
 * @param spimDataQ array of fixed SpimData
 * @return BigWarpData
 */
public static BigWarpData createBigWarpData( final AbstractSpimData< ? > spimDataP, final AbstractSpimData< ? > spimDataQ )
{
	final AbstractSequenceDescription< ?, ?, ? > seqP = spimDataP.getSequenceDescription();
	final AbstractSequenceDescription< ?, ?, ? > seqQ = spimDataQ.getSequenceDescription();

	final ArrayList< ConverterSetup > converterSetups = new ArrayList< ConverterSetup >();

	final ArrayList< SourceAndConverter< ? > > sources = new ArrayList< SourceAndConverter< ? > >();
	BigWarpInit.initSetups( spimDataP, converterSetups, sources );

	int numMovingSources = seqP.getViewSetups().size();
	int numTargetSources = seqQ.getViewSetups().size();

	int[] movingSourceIndices = ImagePlusLoader.range( 0, numMovingSources );
	int[] targetSourceIndices = ImagePlusLoader.range( numMovingSources, numTargetSources );

	/* Load the second source */
	BigWarpInit.initSetups( spimDataQ, converterSetups, sources );

	return new BigWarpData( sources, seqP, seqQ, converterSetups, movingSourceIndices, targetSourceIndices );
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
public static < T extends AbstractSpimData< A >, A extends AbstractSequenceDescription< ?, ?, ? super ImgLoader > > void writeXML(
		final T spimData,
		final XmlIoAbstractSpimData< A, T > io,
		final Parameters params,
		final ProgressWriter progressWriter )
	throws SpimDataException
{
	final A seq = spimData.getSequenceDescription();
	final ArrayList< Partition > partitions = getPartitions( spimData, params );
	final Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader( params.hdf5File, partitions, null, false );
	seq.setImgLoader( hdf5Loader );
	spimData.setBasePath( params.seqFile.getParentFile() );
	try
	{
		if ( !params.onlyRunSingleJob || params.jobId == 0 )
			io.save( spimData, params.seqFile.getAbsolutePath() );
		progressWriter.setProgress( 1.0 );
	}
	catch ( final Exception e )
	{
		progressWriter.err().println( "Failed to write xml file " + params.seqFile );
		e.printStackTrace( progressWriter.err() );
	}
	progressWriter.out().println( "done" );
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
/**
 * For a local initialization without the XML
 * 
 * @param path
 * @param fileNamePattern
 * @param imgFactory
 * @param layoutTP - 0 == one, 1 == one per file, 2 == all in one file
 * @param layoutChannels - 0 == one, 1 == one per file, 2 == all in one file
 * @param layoutIllum - 0 == one, 1 == one per file, 2 == all in one file
 * @param layoutAngles - 0 == one, 1 == one per file, 2 == all in one file
 */
public LegacyStackImgLoader(
		final File path, final String fileNamePattern, final ImgFactory< ? extends NativeType< ? > > imgFactory,
		final int layoutTP, final int layoutChannels, final int layoutIllum, final int layoutAngles,
		final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
	super();
	this.path = path;
	this.fileNamePattern = fileNamePattern;
	this.layoutTP = layoutTP;
	this.layoutChannels = layoutChannels;
	this.layoutIllum = layoutIllum;
	this.layoutAngles = layoutAngles;
	this.sequenceDescription = sequenceDescription;
	
	this.init( imgFactory );
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public MicroManagerImgLoader fromXml(
		final Element elem, File basePath,
		final AbstractSequenceDescription<?, ?, ?> sequenceDescription )
{
	try
	{
		final File path = loadPath( elem, DIRECTORY_TAG, basePath );
		final String masterFile = XmlHelpers.getText( elem, MASTER_FILE_TAG );
		final String container = XmlHelpers.getText( elem, IMGLIB2CONTAINER_PATTERN_TAG );

		if ( container == null )
			System.out.println( "WARNING: No Img implementation defined in XML, using ArrayImg." );
		else if ( !container.toLowerCase().contains( "arrayimg" ) )
			System.out.println( "WARNING: Only ArrayImg supported for MicroManager ImgLoader, using ArrayImg." );

		return new MicroManagerImgLoader( new File( path, masterFile ), sequenceDescription );
	}
	catch ( final Exception e )
	{
		throw new RuntimeException( e );
	}
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
public LegacyDHMImgLoader(
		final File directory,
		final String stackDir,
		final String amplitudeDir,
		final String phaseDir,
		final List< String > timepoints,
		final List< String > zPlanes,
		final String extension,
		final int ampChannelId,
		final int phaseChannelId,
		final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd )
{
	this.directory = directory;
	this.stackDir = stackDir;
	this.amplitudeDir = amplitudeDir;
	this.phaseDir = phaseDir;
	this.timepoints = timepoints;
	this.zPlanes = zPlanes;
	this.extension = extension;
	this.ampChannelId = ampChannelId;
	this.phaseChannelId = phaseChannelId;
	this.sd = sd;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
/**
 * 
 * @param pairs list of potentially overlapping pairs of view groups, this will be modified!
 * @param vrs the view registrations
 * @param sd the sequence description
 * @param <V> view id type
 * @return list of the pairs that were removed
 */
public static <V extends ViewId> List< Pair< Group< V >, Group< V > > > filterNonOverlappingPairs(
		List< Pair<  Group< V >,  Group< V > > > pairs,
		final ViewRegistrations vrs,
		final AbstractSequenceDescription< ?, ? extends BasicViewDescription< ? >, ? > sd
		)
{
	
	final List< Pair<  Group< V >,  Group< V > > > removedPairs = new ArrayList<>();
	
	for (int i = pairs.size() - 1; i >= 0; i--)
	{
		final List<Set<V>> pairAsGroups = new ArrayList<>();
		pairAsGroups.add( pairs.get( i ).getA().getViews() );
		pairAsGroups.add( pairs.get( i ).getB().getViews() );
		
		final BoundingBoxMaximalGroupOverlap< V > ibbd = new BoundingBoxMaximalGroupOverlap< V >(pairAsGroups, sd, vrs);
		BoundingBox bb = ibbd.estimate( "max overlap" );
		
		if (bb == null)
		{
			removedPairs.add( pairs.get( i ) );
			pairs.remove( i );
		}
		
	}
	
	return removedPairs;
	
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
public ExecuteGlobalOpt(
		final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel, 
		final boolean expertMode )
{
	this.panel = panel;
	this.expertMode = expertMode;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
{
	this.panel = panel;

	simpleOptimize.setExplorerWindow( panel );
	expertOptimize.setExplorerWindow( panel );
	return this;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
{
	this.panel = panel;
	return this;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
{
	this.panel = (FilteredAndGroupedExplorerPanel< ?, ? >)panel;
	return this;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
public static ViewSelection< ViewId > getViewSelectionResult(GenericDialog gd, AbstractSequenceDescription< ?, ?, ? > sd)
{
	String choice = gd.getNextChoice();
	if (choice.equals( "Pick brightest" ))
		return new BrightestViewSelection( sd );
	else
		return null;
	
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
{
	if (!wizardMode)
		this.phaseCorrSimple.setExplorerWindow( panel );
	this.phaseCorr.setExplorerWindow( panel );
	this.lucasKanade.setExplorerWindow( panel );
	this.interestPoint.setExplorerWindow( panel );
	return this;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel )
{
	this.panel = panel;
	return this;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
{
	this.stitchingExplorer = panel;
	return this;
}
 

import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; //导入依赖的package包/类
@Override
public JComponent setExplorerWindow(
		ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel)
{
	children.forEach( c -> {
		if (ExplorerWindowSetable.class.isInstance( c ))
			((ExplorerWindowSetable)c).setExplorerWindow( panel );
	} );
	return this;
}