import mpicbg.spim.data.SpimDataException; //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 mpicbg.spim.data.SpimDataException; //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 mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
private static ContextHandlerCollection createHandlers( final String baseURL, final Map< String, String > dataSet, final String thumbnailsDirectoryName ) throws SpimDataException, IOException
{
	final ContextHandlerCollection handlers = new ContextHandlerCollection();

	for ( final Entry< String, String > entry : dataSet.entrySet() )
	{
		final String name = entry.getKey();
		final String xmlpath = entry.getValue();
		final String context = "/" + name;
		final CellHandler ctx = new CellHandler( baseURL + context + "/", xmlpath, name, thumbnailsDirectoryName );
		ctx.setContextPath( context );
		handlers.addHandler( ctx );
	}

	return handlers;
}
 

import mpicbg.spim.data.SpimDataException; //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 mpicbg.spim.data.SpimDataException; //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 mpicbg.spim.data.SpimDataException; //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 mpicbg.spim.data.SpimDataException; //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.SpimDataException; //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.SpimDataException; //导入依赖的package包/类
public BoundingBoxes fromXml( final Element allBoundingBoxes ) throws SpimDataException
{
	final BoundingBoxes boundingBoxes = super.fromXml( allBoundingBoxes );

	for ( final Element boundingBoxElement : allBoundingBoxes.getChildren( BOUNDINGBOX_TAG ) )
	{
		final String title = boundingBoxElement.getAttributeValue( BOUNDINGBOX_TAG_NAME );

		final int[] min = XmlHelpers.getIntArray( boundingBoxElement, BOUNDINGBOX_TAG_MIN );
		final int[] max = XmlHelpers.getIntArray( boundingBoxElement, BOUNDINGBOX_TAG_MAX );

		boundingBoxes.addBoundingBox( new BoundingBox( title, min, max ) );
	}

	return boundingBoxes;
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
public ViewInterestPoints fromXml( final Element allInterestPointLists, final File basePath, final Map< ViewId, ViewDescription > viewDescriptions ) throws SpimDataException
{
	final ViewInterestPoints viewsInterestPoints = super.fromXml( allInterestPointLists );
	viewsInterestPoints.createViewInterestPoints( viewDescriptions );

	for ( final Element viewInterestPointsElement : allInterestPointLists.getChildren( VIEWINTERESTPOINTSFILE_TAG ) )
	{
		final int timepointId = Integer.parseInt( viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_TIMEPOINT_ATTRIBUTE_NAME ) );
		final int setupId = Integer.parseInt( viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_SETUP_ATTRIBUTE_NAME ) );
		final String label = viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_LABEL_ATTRIBUTE_NAME );
		final String parameters = viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_PARAMETERS_ATTRIBUTE_NAME );

		final String interestPointFileName = viewInterestPointsElement.getTextTrim();

		final ViewId viewId = new ViewId( timepointId, setupId );
		final ViewInterestPointLists collection = viewsInterestPoints.getViewInterestPointLists( viewId );

		// we do not load the interestpoints nor the correspondinginterestpoints, we just do that once it is requested
		final InterestPointList list = new InterestPointList( basePath, new File( interestPointFileName ) );
		list.setParameters( parameters );
		collection.addInterestPointList( label, list );
	}

	return viewsInterestPoints;
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
@Override
public boolean finish()
{
	System.out.println( "finish()" );
	String path = params.getSeqFile().getAbsolutePath();
	try
	{
		new XmlIoSpimData2( "" ).save( spimData, path );

		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + path + "'." );

		// this spimdata object was not modified, we just wrote a new one
		return false;
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + path + "'." );
		e.printStackTrace();
		return false;
	}
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
@Override
public boolean finish()
{
	XmlIoSpimData2 io = new XmlIoSpimData2( "" );

	try
	{
		io.save( spimData, new File( params.getXMLFile() ).getAbsolutePath() );
		
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + io.lastFileName() + "'." );

		// this spimdata object was not modified, we just wrote a new one
		return false;
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + io.lastFileName() + "'." );
		e.printStackTrace();
		return false;
	}
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
public T load( final String xmlFilename ) throws SpimDataException
{
	final SAXBuilder sax = new SAXBuilder();
	Document doc;
	try
	{
		final File file = new File( xmlFilename );
		if ( file.exists() )
			doc = sax.build( file );
		else
			doc = sax.build( xmlFilename );
	}
	catch ( final Exception e )
	{
		throw new SpimDataIOException( e );
	}
	final Element root = doc.getRootElement();

	if ( root.getName() != SPIMDATA_TAG )
		throw new RuntimeException( "expected <" + SPIMDATA_TAG + "> root element. wrong file?" );

	return fromXml( root, new File( xmlFilename ) );
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
/**
	 * TODO
	 *
	 * @param root
	 * @param xmlFile
	 * @return
	 */
	public T fromXml( final Element root, final File xmlFile ) throws SpimDataException
	{
		final T spimData = super.fromXml( root );

//		String version = getVersion( root );

		final File basePath = loadBasePath( root, xmlFile );
		spimData.setBasePath( basePath );

		Element elem = root.getChild( xmlIoSequenceDescription.getTag() );
		if ( elem == null )
			throw new SpimDataIOException( "no <" + xmlIoSequenceDescription.getTag() + "> element found." );
		spimData.setSequenceDescription( xmlIoSequenceDescription.fromXml( elem, basePath ) );

		elem = root.getChild( xmlIoViewRegistrations.getTag() );
		if ( elem == null )
			throw new SpimDataIOException( "no <" + xmlIoViewRegistrations.getTag() + "> element found." );
		spimData.setViewRegistrations( xmlIoViewRegistrations.fromXml( elem ) );

		return spimData;
	}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
/**
 * Create an object from the given element. Unhandled children of the
 * element are stored as associated with the objects {@link Entity#getId()
 * id} and added to any XML element {@link #toXml(Entity) created} for that
 * id.
 */
public T fromXml( final Element elem ) throws SpimDataException
{
	T entity;
	try
	{
		entity = ctor.newInstance();
	}
	catch ( final Exception e )
	{
		throw new SpimDataInstantiationException( "Cannot instantiate Entity " + getEntityClass().getName(), e );
	}
	entity.setId( XmlHelpers.getInt( elem, ID_TAG ) );

	final ArrayList< Element > unhandled = new ArrayList< Element >();
	for ( final Element c : elem.getChildren() )
		if ( !handledTags.contains( c.getName() ) )
			unhandled.add( c.clone() );
	if ( !unhandled.isEmpty() )
		unhandledContent.put( entity.getId(), unhandled );

	return entity;
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
/**
 * Create an object from the given element. Unhandled children of the
 * element are stored and added to any XML element that is
 * {@link #toXml() created}.
 *
 * Calling this method clears all unhandled content from previous
 * invocations.
 */
protected T fromXml( final Element elem ) throws SpimDataException
{
	T entity;
	try
	{
		entity = ctor.newInstance();
	}
	catch ( final Exception e )
	{
		throw new SpimDataInstantiationException( "Cannot instantiate " + ctor.getDeclaringClass().getName(), e );
	}

	unhandledContent.clear();
	for ( final Element c : elem.getChildren() )
		if ( !handledTags.contains( c.getName() ) )
			unhandledContent.add( c.clone() );

	return entity;
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
@Override
public HashMap< Integer, T > fromXml( final Element elem ) throws SpimDataException
{
	// maps attribute name (e.g. "channel") to map from entity id to entity (e.g. id -> Channel)
	final HashMap< String, HashMap< Integer, ? extends Entity > > attributeMap = new HashMap< String, HashMap< Integer, ? extends Entity > >();

	for ( final Element c : elem.getChildren( ATTRIBUTES_TAG ) )
	{
		final String name = c.getAttributeValue( ATTRIBUTES_NAME_ATTRIBUTE_NAME );
		final XmlIoEntityMap< ? > xmlIoAttributes = getXmlIoForAttributeName( name );
		attributeMap.put( name, xmlIoAttributes.fromXml( c ) );
	}

	xmlIoViewSetup.setAttributeMap( attributeMap );
	return super.fromXml( elem );
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
public Element toXml( final T sequenceDescription, final File basePath ) throws SpimDataException
{
	final Element elem = super.toXml();

	final BasicImgLoader imgLoader = sequenceDescription.getImgLoader();
	if ( imgLoader != null )
	{
		final XmlIoBasicImgLoader< ? > imgLoaderIo = ImgLoaders.createXmlIoForImgLoaderClass( imgLoader.getClass() );
		elem.addContent( createImgLoaderElement( imgLoaderIo, imgLoader, basePath ) );
	}

	elem.addContent( xmlIoViewSetups.toXml( sequenceDescription.getViewSetups() ) );

	elem.addContent( xmlIoTimePoints.toXml( sequenceDescription.getTimePoints() ) );

	if ( sequenceDescription.getMissingViews() != null )
		elem.addContent( xmlIoMissingViews.toXml( sequenceDescription.getMissingViews() ) );

	return elem;
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
@Override
public T fromXml( final Element elem ) throws SpimDataException
{
	final T setup = super.fromXml( elem );
	setup.setName( XmlHelpers.getText( elem, NAME_TAG, null ) );
	setup.setSize( XmlHelpers.getDimensions( elem, VIEWSETUP_SIZE_TAG, null ) );
	setup.setVoxelSize( getVoxelDimensions( elem, VIEWSETUP_VOXELSIZE_TAG, null ) );

	final Element as = elem.getChild( VIEWSETUP_ATTRIBUTES_TAG );
	final HashMap< String, Entity > attributes = new HashMap< String, Entity >();
	if ( as != null )
	{
		for ( final Element a : as.getChildren() )
		{
			final String name = a.getName();
			final int id = Integer.parseInt( a.getTextTrim() );
			final Entity attribute = attributeMap.get( name ).get( id );
			attributes.put( name, attribute );
		}
	}
	setup.setAttributes( attributes );

	return setup;
}
 

import mpicbg.spim.data.SpimDataException; //导入依赖的package包/类
@Override
public MissingViews fromXml( final Element elem ) throws SpimDataException
{
	final MissingViews missingViews = super.fromXml( elem );

	final HashSet< ViewId > views = new HashSet< ViewId >();
	for ( final Element c : elem.getChildren( MISSINGVIEW_TAG ) )
	{
		final int t = Integer.parseInt( c.getAttributeValue( MISSINGVIEW_TIMEPOINT_ATTRIBUTE_NAME ) );
		final int s = Integer.parseInt( c.getAttributeValue( MISSINGVIEW_SETUP_ATTRIBUTE_NAME ) );
		views.add( new ViewId( t, s ) );
	}
	missingViews.setMissingViews( views );

	return missingViews;
}