import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
public List<Pair<? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup > >, ? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup >>>> getComparisons()
{
	final List<Pair<? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup > >, ? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup >>>> res = new ArrayList<>();
	
	// filter first
	final List<BasicViewDescription< ? > > ungroupedElements =
			SpimDataTools.getFilteredViewDescriptions( data.getSequenceDescription(), filters);
	// then group
	final List< Group< BasicViewDescription< ?  > >> groupedElements = 
			Group.combineBy(ungroupedElements, groupingFactors);
	
	// go through possible group pairs
	for (int i = 0; i < groupedElements.size(); ++i)
		for(int j = i+1; j < groupedElements.size(); ++j)
		{
			// we will want to process the pair if:
			// the groups do not differ along an axis along which we want to treat elements individually (e.g. Angle)
			// but they differ along an axis that we want to register (e.g Tile)
			if (!groupsDifferByAny( groupedElements.get( i ), groupedElements.get( j ), axesOfApplication ) 
					&& groupsDifferByAny( groupedElements.get( i ), groupedElements.get( j ), axesOfComparison ))
				res.add(new ValuePair<>(groupedElements.get( i ), groupedElements.get( j )));
		}
	return res;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
public SpimDataFilteringAndGrouping< AS> askUserForFiltering(FilteredAndGroupedExplorerPanel< AS, ?> panel)
{
	List< BasicViewDescription< ? extends BasicViewSetup > > views;
	
	if (panel instanceof GroupedRowWindow)
	{
		Collection< List< BasicViewDescription< ? extends BasicViewSetup > > > selectedRowsGroups = ((GroupedRowWindow)panel).selectedRowsGroups();
		views = selectedRowsGroups.stream().reduce( new ArrayList<>(), (x, y) -> {x.addAll(y); return x;} );
	}
	else
		views = panel.selectedRows();
	
	SpimDataFilteringAndGrouping< AS > res = askUserForFiltering( views );
	return res;
	
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
public SpimDataFilteringAndGrouping< AS> askUserForGrouping( FilteredAndGroupedExplorerPanel< AS, ?> panel)
{
	List< BasicViewDescription< ? extends BasicViewSetup > > views;

	if (panel instanceof GroupedRowWindow)
	{
		Collection< List< BasicViewDescription< ? extends BasicViewSetup > > > selectedRowsGroups = ((GroupedRowWindow)panel).selectedRowsGroups();
		views = selectedRowsGroups.stream().reduce( new ArrayList<>(), (x, y) -> {x.addAll(y); return x;} );
	}
	else
		views = panel.selectedRows();

	final HashSet< Class<? extends Entity> > comparisonsRequested = new HashSet<>();
	if (StitchingExplorerPanel.class.isInstance( panel ) )
	{
		if (!panel.channelsGrouped())
			comparisonsRequested.add( Channel.class );
		if (!panel.illumsGrouped())
			comparisonsRequested.add( Illumination.class );
		if (!panel.tilesGrouped())
			comparisonsRequested.add( Tile.class );
	}
	return askUserForGrouping( views, panel.getTableModel().getGroupingFactors(), comparisonsRequested);
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
@Override
public void selectedViewDescriptions(
		List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions)
{
	//System.out.println( " selection upd " );
	selectedVDs = viewDescriptions;
	
	// sort the selected groups by the view id of the first member
	Collections.sort( selectedVDs, (x, y) -> x.get( 0 ).compareTo( y.get( 0 ) ) );
	
	// hacky solution, wait a bit with update since parent will reset BDV after selection change
	new Timer().schedule(new TimerTask()
	{

		public void run()
		{
			update();
			
		}
	}, 100 );

}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
@Override
public void selectedViewDescriptions(
		List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions)
{
	List<Pair<Group<ViewId>, Group<ViewId>>> res = new ArrayList<>();
	for (int i = 0; i<viewDescriptions.size(); i++)
		for (int j = i+1; j<viewDescriptions.size(); j++)
		{
			Group<ViewId> groupA = new Group<>();
			groupA.getViews().addAll( viewDescriptions.get( i ) );
			Group<ViewId> groupB = new Group<>();
			groupB.getViews().addAll( viewDescriptions.get( j ) );
			res.add( new ValuePair< Group<ViewId>, Group<ViewId> >( groupA, groupB ) );
		}
	setActiveLinks( res );
	
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
protected ArrayList< BasicViewDescription< ? extends BasicViewSetup > > elements()
{
	final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > elementsNew = new ArrayList< BasicViewDescription< ? extends BasicViewSetup > >();

	for ( final TimePoint t : panel.getSpimData().getSequenceDescription().getTimePoints().getTimePointsOrdered() )
		for ( final BasicViewSetup v : panel.getSpimData().getSequenceDescription().getViewSetupsOrdered() )
		{
			final ViewId viewId = new ViewId( t.getId(), v.getId() );
			final BasicViewDescription< ? > viewDesc = panel.getSpimData().getSequenceDescription().getViewDescriptions().get( viewId );

			if ( viewDesc.isPresent() )
				elementsNew.add( viewDesc );
		}

	if ( this.elements == null || this.elements.size() != elementsNew.size() )
		this.elements = elementsNew;

	return elements;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
@Override
public Object getValueAt( final int row, final int column )
{
	final BasicViewDescription< ? extends BasicViewSetup > vd = elements().get( row );

	if ( column == 0 )
		return vd.getTimePoint().getId();
	else if ( column == 1 )
		return vd.getViewSetupId();
	else
	{
		final Entity e = vd.getViewSetup().getAttributes().get( columnNames.get( column ) );

		if ( e instanceof NamedEntity )
			return ((NamedEntity)e).getName() + " (id = " + e.getId() + ")";
		else
			return e.getId() + " (no name available)";
	}
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
private static String createSetupName( final BasicViewSetup setup )
{
	if ( setup.hasName() )
		return setup.getName();

	String name = "";

	final Angle angle = setup.getAttribute( Angle.class );
	if ( angle != null )
		name += ( name.isEmpty() ? "" : " " ) + "a " + angle.getName();

	final Channel channel = setup.getAttribute( Channel.class );
	if ( channel != null )
		name += ( name.isEmpty() ? "" : " " ) + "c " + channel.getName();

	return name;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //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.BasicViewSetup; //导入依赖的package包/类
protected boolean updateProposedMipmaps( final String fusionDirectory, final SPIMConfiguration conf )
{
	final Pair< String, Integer > pair = detectPatternAndNumSlices( new File ( fusionDirectory ), conf.timepoints[0] );
	if ( pair != null )
	{
		final String filenamePattern = pair.getA();
		final int numSlices = pair.getB();
		final String fn = fusionDirectory + "/" + String.format( filenamePattern, conf.timepoints[0], conf.channels[0], 0 );
		final ImagePlus imp = new ImagePlus( fn );
		final int width = imp.getWidth();
		final int height = imp.getHeight();
		imp.close();
		final Dimensions size = new FinalDimensions( new int[] { width, height, numSlices } );
		final VoxelDimensions voxelSize = new FinalVoxelDimensions( "px", 1, 1, 1 );
		final ExportMipmapInfo info = ProposeMipmaps.proposeMipmaps( new BasicViewSetup( 0, "", size, voxelSize ) );
		autoSubsampling = ProposeMipmaps.getArrayString( info.getExportResolutions() );
		autoChunkSizes = ProposeMipmaps.getArrayString( info.getSubdivisions() );
		return true;
	}
	else
		return false;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //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 mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
public static FusionResult create(
		final SpimRegistrationSequence spimseq,
		final String filepath,
		final String filepattern,
		final int numSlices,
		final double sliceValueMin,
		final double sliceValueMax,
		final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
	// add one fused ViewSetup per channel in the SpimRegistrationSequence
	final List< Integer > channels = new ArrayList<>();
	for ( final BasicViewSetup setup : spimseq.getSequenceDescription().getViewSetupsOrdered() )
	{
		final int channel = setup.getAttribute( Channel.class ).getId();
		if ( ! channels.contains( channel ) )
			channels.add( channel );
	}
	final TimePoints timepoints = spimseq.getSequenceDescription().getTimePoints();
	return new FusionResult( filepath, filepattern, channels, timepoints, numSlices, sliceValueMin, sliceValueMax, perTimePointFusionTransforms );
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
public FusionResult(
		final String filepath,
		final String filepattern,
		final TimePoints timepoints,
		final int numSlices,
		final double sliceValueMin,
		final double sliceValueMax,
		final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
	final HashMap< Integer, Integer > setupIdToChannelId = new HashMap<>();
	setupIdToChannelId.put( 0, 0 );
	final ImgLoader fusionLoader = new FusionImageLoader<>( filepath +"/" + filepattern, setupIdToChannelId, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
	final int setupId = 0;
	final String name = "fused";
	final int timepointId = timepoints.getTimePointsOrdered().get( 0 ).getId();
	final Dimensions size = fusionLoader.getSetupImgLoader( setupId ).getImageSize( timepointId );
	final VoxelDimensions voxelSize = fusionLoader.getSetupImgLoader( setupId ).getVoxelSize( timepointId );
	final BasicViewSetup setup = new BasicViewSetup( setupId, name, size, voxelSize );
	desc = new SequenceDescriptionMinimal( timepoints, Entity.idMap( Arrays.asList( setup ) ), fusionLoader, null );
	final ArrayList< ViewRegistration > registrations = new ArrayList<>();
	for ( final TimePoint timepoint : timepoints.getTimePointsOrdered() )
		registrations.add( new ViewRegistration( timepoint.getId(), 0, perTimePointFusionTransforms.get( timepoint.getId() ) ) );
	regs = new ViewRegistrations( registrations );
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
protected String createUniqueName()
{
	long idSum = 1;

	for ( final TimePoint t : getTimePointsToProcess() )
		idSum *= t.getId();

	for ( final BasicViewSetup v : getViewSetupsToProcess() )
		idSum += v.getId();

	long nano = System.nanoTime();
	long millis = System.currentTimeMillis();
	long finalHash = nano + millis + idSum;

	if ( debugRandomClusterHash )
	{
		IOFunctions.println( "idsum=" + idSum );
		IOFunctions.println( "nano=" + nano );
		IOFunctions.println( "millis=" + millis );
		IOFunctions.println( "final=" + finalHash );
	}

	return "" + finalHash;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
@Override
public Object getValueAt( final int row, final int column )
{
	final BasicViewDescription< ? extends BasicViewSetup > vd = elements().get( row );

	if ( column == 0 )
		return vd.getTimePoint().getId();
	else if ( column == 1 )
		return vd.getViewSetupId();
	else if ( column == registrationColumn )
		return this.viewRegistrations.getViewRegistration( vd ).getTransformList().size();
	else if ( column == interestPointsColumn && viewInterestPoints != null )
		return viewInterestPoints.getViewInterestPointLists( vd ).getHashMap().keySet().size();
	else
	{
		final Entity e = vd.getViewSetup().getAttributes().get( columnNames.get( column ) );

		if ( e instanceof NamedEntity )
			return ((NamedEntity)e).getName() + " (id = " + e.getId() + ")";
		else
			return e.getId() + " (no name available)";
	}
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //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.BasicViewSetup; //导入依赖的package包/类
public static Set<Entity> getInstancesOfAttribute(Collection<? extends BasicViewDescription< ? extends BasicViewSetup >> vds, Class<? extends Entity> cl)
{
	Set<Entity> res = new HashSet<>();
	for (BasicViewDescription< ? extends BasicViewSetup > vd : vds)
		if (cl == TimePoint.class)
			res.add( vd.getTimePoint() );
		else
			res.add( vd.getViewSetup().getAttribute( cl ) );
	return res;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
@Override
public void selectedViewDescriptions(
		List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions)
{
	if (viewDescriptions.size() < 1) // nothing selected
	{
		setActiveLinks( new ArrayList<>() );
		return;
	}
	// get pairwise results for first (and only) selected view group
	final HashSet< ViewId > vid = new HashSet<>( viewDescriptions.iterator().next());
	SpimData2.filterMissingViews( parent.getSpimData(), vid );
	ArrayList< PairwiseStitchingResult< ViewId > > pairwiseResults = results.getAllPairwiseResultsForViewId( vid );
	setActiveLinks( pairwiseResults.stream().map( (p) -> p.pair() ).filter( p ->  parent.getSavedFilteringAndGrouping().getComparisons().contains( p )).collect( Collectors.toList() ) );
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
public static int getBDVSourceIndex(final BasicViewSetup vs, final AbstractSpimData< ? > data)
{
	final List< ? extends BasicViewSetup > list = data.getSequenceDescription().getViewSetupsOrdered();

	for ( int i = 0; i < list.size(); ++i )
		if ( list.get( i ).getId() == vs.getId() )
			return i;

	return 0;
}
 

import mpicbg.spim.data.generic.sequence.BasicViewSetup; //导入依赖的package包/类
protected String[] readSetupNames( final AbstractSequenceDescription< ?, ?, ? > sequenceDescriptionMinimal )
{
	final List< ? extends BasicViewSetup > viewSetupsOrdered = sequenceDescriptionMinimal.getViewSetupsOrdered();
	final int numViewSetups = viewSetupsOrdered.size();
	final String[] angles = new String[ numViewSetups ];
	for ( int setup = 0; setup < numViewSetups; setup++ )
	{
		final Angle angle = viewSetupsOrdered.get( setup ).getAttribute( Angle.class );
		angles[ setup ] = "angle " + ( angle == null ? setup : angle.getName() );
	}
	return angles;
}