import mpicbg.spim.data.sequence.TimePoints; //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.sequence.TimePoints; //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.sequence.TimePoints; //导入依赖的package包/类
/**
 * Creates the {@link TimePoints} for the {@link SpimData} object
 */
protected TimePoints createTimePoints(final SlideBook6MetaData meta) {
    final ArrayList<TimePoint> timepoints = new ArrayList<TimePoint>();

    int firstCapture = defaultCapture;
    int numCaptures = 1;
    if (defaultCapture == -1) {
        firstCapture = 0;
        numCaptures = meta.numCaptures();
    }

    int t = 0;
    for (; t < meta.numTimepoints(firstCapture); ++t)
        timepoints.add(new TimePoint(t));

    return new TimePoints(timepoints);
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public GraphFrame(
		final TimePoints timepoints,
		final JFreeChart chart,
		final int referenceTimePoint,
		final boolean enableReferenceTimePoint,
		final List< SelectTimepointEntry > extraMenuItems,
		final ArrayList< RegistrationStatistics > data )
{
	super();

	mainPanel = new JPanel();
	mainPanel.setLayout( new BorderLayout() );

	updateWithNewChart( timepoints, chart, true, extraMenuItems, data, referenceTimePoint, enableReferenceTimePoint );

	JPanel buttonsPanel = new JPanel();
	mainPanel.add( buttonsPanel, BorderLayout.SOUTH );

	setContentPane( mainPanel );
	validate();
	GUI.center( this );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
MouseListenerTimelapse( final TimePoints timepoints, final ChartPanel panel, final int referenceTimePoint, final boolean enableReferenceTimePoint )
{
	this.timepoints = timepoints;
	this.panel = panel;
	this.referenceTimePoint = referenceTimePoint;
	this.enableReferenceTimePoint = enableReferenceTimePoint;
	
	if ( enableReferenceTimePoint || referenceTimePoint != -1 ) // at least show it if it is not -1
	{
		if ( timepoints != null )
			setReferenceTimepoint( timepoints, referenceTimePoint );

		valueMarker = makeMarker( referenceTimePoint );

		if ( referenceTimePoint >= 0 )
		{
			((XYPlot)panel.getChart().getPlot()).addDomainMarker( valueMarker );
			markerShown = true;
		}
	}
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public static boolean setReferenceTimepoint( final TimePoints timepoints, final int referenceTimePoint )
{
	final TimePoint ref = timepoints.getTimePoints().get( referenceTimePoint );
	if ( ref != null )
	{
		final List< TimePoint > tps = timepoints.getTimePointsOrdered();
		for ( int tp = 0; tp < tps.size(); ++tp )
		{
			if ( tps.get( tp ).getId() == referenceTimePoint )
			{
				Interest_Point_Registration.defaultReferenceTimepointIndex = tp;
				return true;
			}
		}
	}

	return false;
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public SpimRegistrationSequence( final SPIMConfiguration conf )
	{
		this.conf = conf;
		final ArrayList< ViewSetup > setups = createViewSetups( conf );
//		final HashMap< Integer, ViewSetup > setups = Entity.idMap( createViewSetups( conf ) );
		final TimePoints timepoints = createTimePoints( conf );


		final BasicImgLoader imgLoader = createImageLoader( conf, setups );

		viewRegistrations = createViewRegistrations( conf, setups );
		sequenceDescription = new SequenceDescriptionMinimal( timepoints, Entity.idMap( createViewSetups( conf ) ), imgLoader, null );
	}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
protected static TimePoints createTimePoints( final SPIMConfiguration conf )
{
	final ArrayList< TimePoint > timepoints = new ArrayList<>();
	for ( final int tp : conf.timepoints )
		timepoints.add( new TimePoint( tp ) );
	return new TimePoints( timepoints );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public TimePoints readTimePoints()
{
	final Element root = document.getRootElement();
	final int nTimePoints = Integer.parseInt( root.getChild( "TimelapsCondition" ).getChildText( "Iteration" ) );

	final List< TimePoint > timepoints = new ArrayList<>( nTimePoints );
	for ( int i = 0; i < nTimePoints; i++ )
	{
		timepoints.add( new TimePoint( Integer.valueOf( i ) ) );
	}
	return new TimePoints( timepoints );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
protected static String[] assembleTimepoints( final TimePoints timepoints )
{
	final String[] tps = new String[ timepoints.size() ];

	for ( int t = 0; t < tps.length; ++t )
		tps[ t ] = timepoints.getTimePointsOrdered().get( t ).getName();

	return tps;
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
/**
 * Creates the {@link TimePoints} for the {@link SpimData} object
 */
protected TimePoints createTimePoints( final LightSheetZ1MetaData meta )
{
	final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >();

	for ( int t = 0; t < meta.numTimepoints(); ++t )
		timepoints.add( new TimePoint( t ) );

	return new TimePoints( timepoints );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
/**
 * Creates the {@link TimePoints} for the {@link SpimData} object
 */
protected TimePoints createTimePoints( final DHMMetaData meta )
{
	final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >();

	for ( int t = 0; t < meta.getTimepoints().size(); ++t )
		timepoints.add( new TimePoint( Integer.parseInt( meta.getTimepoints().get( t ) ) ) );

	return new TimePoints( timepoints );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
/**
 * Creates the {@link TimePoints} for the {@link SpimData} object
 */
protected TimePoints createTimePoints( MultipageTiffReader meta )
{
	final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >();

	for ( int t = 0; t < meta.numTimepoints(); ++t )
		timepoints.add( new TimePoint( t ) );

	return new TimePoints( timepoints );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
@Override
public SpimData2 createDataset()
{
	// collect all the information
	if ( !queryInformation() )
		return null;
	
	// assemble timepints, viewsetups, missingviews and the imgloader
	final TimePoints timepoints = this.createTimePoints();
	final ArrayList< ViewSetup > setups = this.createViewSetups();
	final MissingViews missingViews = this.createMissingViews();
	
	// instantiate the sequencedescription
	final SequenceDescription sequenceDescription = new SequenceDescription( timepoints, setups, null, missingViews );
	final ImgLoader imgLoader = createAndInitImgLoader( ".", new File( directory ), imgFactory, sequenceDescription );
	sequenceDescription.setImgLoader( imgLoader );

	// get the minimal resolution of all calibrations
	final double minResolution = Apply_Transformation.assembleAllMetaData(
			sequenceDescription,
			sequenceDescription.getViewDescriptions().values() );

	IOFunctions.println( "Minimal resolution in all dimensions over all views is: " + minResolution );
	IOFunctions.println( "(The smallest resolution in any dimension; the distance between two pixels in the output image will be that wide)" );
	
	// create the initial view registrations (they are all the identity transform)
	final ViewRegistrations viewRegistrations = createViewRegistrations( sequenceDescription.getViewDescriptions(), minResolution );
	
	// create the initial view interest point object
	final ViewInterestPoints viewInterestPoints = new ViewInterestPoints();
	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() );

	return spimData;
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
/**
 * Creates the {@link TimePoints} for the {@link SpimData} object
 */
protected TimePoints createTimePoints()
{
	try
	{
		return new TimePointsPattern( timepoints );
	}
	catch ( final ParseException e )
	{
		throw new RuntimeException( e );
	}
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public static void main( String args[] )
{
	final ArrayList< RegistrationStatistics > data = defaultData();
	final ArrayList< TimePoint > tps = new ArrayList< TimePoint >();

	for ( final RegistrationStatistics rs : data )
		tps.add( new TimePoint( rs.getTimePoint() ) );

	final ArrayList< SelectTimepointEntry > items = new ArrayList< SelectTimepointEntry >();
	//items.add( new SelectTimepointEntry( "Select Timepoint", data ) );

	plotData( new TimePoints( tps ), data, getOptimalTimePoint( data ), true, items );
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
synchronized public void updateWithNewChart(
		final TimePoints timepoints,
		final JFreeChart c,
		final boolean setSize,
		final List< SelectTimepointEntry > extraMenuItems,
		final ArrayList< RegistrationStatistics > data,
		final int referenceTimePoint,
		final boolean enableReferenceTimePoint )
{
	if ( chartPanel != null )
		remove( chartPanel );

	chartPanel = null;
	this.chart = c;
	chartPanel = new ChartPanel( c );
	mouseListener = new MouseListenerTimelapse( timepoints, chartPanel, referenceTimePoint, enableReferenceTimePoint );

	chartPanel.addChartMouseListener( mouseListener );

	chartPanel.setMouseWheelEnabled( true );
	chartPanel.setHorizontalAxisTrace( true );
	mainPanel.add( chartPanel, BorderLayout.CENTER );

	// add extra items
	final JPopupMenu menu = chartPanel.getPopupMenu();
	
	if ( extraMenuItems != null )
		for ( final SelectTimepointEntry m : extraMenuItems )
		{
			m.setChartPanel( chartPanel );
			menu.add( new JMenuItem( m ) );
		}

	validate();
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
@SuppressWarnings( { "unchecked", "rawtypes" } )
public T fromXml( final Element elem, final File basePath ) throws SpimDataException
{
	final T sequenceDescription = super.fromXml( elem );

	final HashMap< Integer, V > setups = xmlIoViewSetups.fromXml( elem.getChild( xmlIoViewSetups.getTag() ) );
	sequenceDescription.setViewSetups( setups );

	final TimePoints timepoints = xmlIoTimePoints.fromXml( elem.getChild( xmlIoTimePoints.getTag() ) );
	sequenceDescription.setTimePoints( timepoints );

	final Element missingViewElem = elem.getChild( xmlIoMissingViews.getTag() );
	final MissingViews missingViews = ( missingViewElem == null ) ? null : xmlIoMissingViews.fromXml( missingViewElem );
	sequenceDescription.setMissingViews( missingViews );

	final Element imgLoaderElem = elem.getChild( IMGLOADER_TAG );
	if ( imgLoaderElem != null )
	{
		final String format = imgLoaderElem.getAttributeValue( IMGLOADER_FORMAT_ATTRIBUTE_NAME );
		final XmlIoBasicImgLoader< ? > imgLoaderIo = ImgLoaders.createXmlIoForFormat( format );
		final BasicImgLoader imgLoader = imgLoaderIo.fromXml( imgLoaderElem, basePath, sequenceDescription );
		setImgLoader( ( AbstractSequenceDescription ) sequenceDescription, imgLoader );
	}
	else
		sequenceDescription.setImgLoader( null );

	return sequenceDescription;
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public AbstractSequenceDescription( final TimePoints timepoints, final Map< Integer, ? extends V > setups, final L imgLoader, final MissingViews missingViews )
{
	this.timepoints = timepoints;
	this.setups = setups;
	this.imgLoader = imgLoader;
	this.missingViews = missingViews;
	viewDescriptionsDirty = true;
	viewSetupsOrderedDirty = true;
}
 

import mpicbg.spim.data.sequence.TimePoints; //导入依赖的package包/类
public static TimePoints createTimePoints() throws ParseException
	{
//		final ArrayList< TimePoint > tps = new ArrayList< TimePoint >();
//		tps.add( new TimePoint( 10 ) );
//		tps.add( new TimePoint( 11 ) );
//		tps.add( new TimePoint( 12 ) );
//		tps.add( new TimePoint( 13 ) );
//		final TimePoints timepoints = new TimePoints( tps );
		final TimePoints timepoints = new TimePointsPattern( "1-100:20" );
		return timepoints;
	}