import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Create a new HDF5 store for the given file. Annotations will be read from and written to the given group.
 * @param filename
 * @param groupname
 */
public AnnotationsHdf5Store(final String filename, final String groupname, final IdService idService) {

	this.filename = filename;
	this.groupname = groupname;
	this.idService = idService;

	final IHDF5Reader reader = HDF5Factory.openForReading(filename);
	// TODO: following call is deprecated, but what to use instead?
	if (reader.object().hasAttribute("/", "file_format")) {
		fileFormat = Double.parseDouble(reader.string().getAttr("/", "file_format"));
	} else {
		fileFormat = 0.0;
	}

	if (reader.exists(groupname) && reader.hasAttribute(groupname, "offset")) {
		final float[] data = reader.getFloatArrayAttribute(groupname, "offset");
		offset[0] = data[2];
		offset[1] = data[1];
		offset[2] = data[0];
	}

	reader.close();

	System.out.println("AnnotationsHdf5Store: detected file format " + fileFormat);
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load raw data, find maximum raw dimensions
 *
 * @param params
 * @throws IOException
 */
@Override
protected void initRaw( final P params ) throws IOException
{
	System.out.println( "Opening raw from " + params.inFile );
	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFile );

	/* raw pixels */
	Arrays.fill( maxRawDimensions, 0 );
	for ( final String raw : params.raws )
		if ( reader.exists( raw ) )
		{
			final H5UnsignedByteSetupImageLoader rawLoader = new H5UnsignedByteSetupImageLoader( reader, raw, setupId++, cellDimensions, cache );
			raws.add( rawLoader );
			max( maxRawDimensions, Intervals.dimensionsAsLongArray( rawLoader.getVolatileImage( 0, 0 ) ) );
		}
		else
			System.out.println( "no raw dataset '" + raw + "' found" );
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load or initialize canvas
 *
 * @param params
 * @throws IOException
 */
protected void initCanvas( final P params ) throws IOException
{
	System.out.println( "Opening canvas from " + params.inFile );
	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFile );

	/* canvas (to which the brush paints) */
	if ( reader.exists( params.canvas ) )
		canvas = H5Utils.loadUnsignedLong( reader, params.canvas, cellDimensions );
	else
	{
		canvas = new CellImgFactory< LongType >( cellDimensions ).create( maxRawDimensions, new LongType() );
		for ( final LongType t : canvas )
			t.set( Label.TRANSPARENT );
	}

	reader.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load raw data and labels and initialize canvas
 *
 * @param params
 * @throws IOException
 */
protected void initRaw( final P params ) throws IOException
{
	System.out.println( "Opening raw from " + params.inFile );
	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFile );

	/* raw pixels */
	for ( final String raw : params.raws )
	{
		if ( reader.exists( raw ) )
		{
			final H5UnsignedByteSetupImageLoader rawLoader = new H5UnsignedByteSetupImageLoader( reader, raw, setupId++, cellDimensions, cache );
			raws.add( rawLoader );
		}
		else
			System.out.println( "no raw dataset '" + raw + "' found" );
	}
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Initialize ID service.
 *
 * @param params
 * @throws IOException
 */
protected void initIdService( final P params ) throws IOException
{
	/* id */
	idService = new LocalIdService();

	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFile );

	long maxId = 0;
	final Long nextIdObject = H5Utils.loadAttribute( reader, "/", "next_id" );

	reader.close();

	if ( nextIdObject == null )
	{
		for ( final H5LabelMultisetSetupImageLoader labelLoader : labels )
			maxId = maxId( labelLoader, maxId );
	}
	else
		maxId = nextIdObject.longValue() - 1;

	idService.invalidate( maxId );
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Initialize assignments.
 *
 * @param params
 */
protected void initAssignments( final P params )
{
	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFile );

	/* fragment segment assignment */
	assignment = new FragmentSegmentAssignment( idService );
	final TLongLongHashMap lut = H5Utils.loadLongLongLut( reader, params.assignment, 1024 );
	if ( lut != null )
		assignment.initLut( lut );

	/* complete fragments */
	completeFragmentsAssignment = new FragmentAssignment();
	final TLongHashSet set = new TLongHashSet();
	H5Utils.loadLongCollection( set, reader, params.completeFragments, 1024 );

	/* color stream */
	colorStream = new ModalGoldenAngleSaturatedARGBStream( assignment );
	colorStream.setAlpha( 0x20 );

	reader.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
public static SortedMap<Number, Number> importHdf5(String filePath) {

		reader = HDF5Factory.openForReading(filePath);
		double[][] hdf5Data = reader.readDoubleMatrix(DATA_ID);

		SortedMap<Number, Number> data = new TreeMap<>();
		for (int i = 0; i < hdf5Data[0].length; i++) {
			double x = hdf5Data[0][i];
			double y = hdf5Data[1][i];
			Number key = new Double(x);
			Number value = new Double(y);
			data.put(key, value);
		}

		return data;
	}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
@Override
public ArrayList<Sample> parse(String filepath) throws IOException{
    ArrayList<Sample> sampleList = new ArrayList<>();

    IHDF5SimpleReader reader = HDF5Factory.openForReading(filepath);

    // Get number of Samples in File
    String[] sampleIds = reader.readStringArray("/sample/ids");
    String[] observationIds = reader.readStringArray("/observation/ids");
    int[] indptr = reader.readIntArray("/sample/matrix/indptr");
    int[] indices = reader.readIntArray("/sample/matrix/indices");
    float[] data = reader.readFloatArray("/sample/matrix/data");

    // Loop over Samples
    for (int i = 0; i < sampleIds.length ; i++) {

        // Create new Sample
        Sample newSample = new Sample();
        newSample.setSampleId(sampleIds[i]);

        // Add counts to this sample
        for (int j = indptr[i]; j < indptr[i+1]; j++) {
            TaxonNode node = taxonTree.getNodeForID(Integer.parseInt(observationIds[indices[j]]));
            newSample.getTaxa2CountMap().put(node, Math.round(data[j]));
        }

        // Loop over Metadata-Entries
        for (String metaKey: reader.getGroupMembers("/sample/metadata")) {
            System.out.println(metaKey);
            String metaValue = reader.readStringArray("/sample/metadata/" + metaKey)[i];
            newSample.getMetaData().put(metaKey, metaValue);
        }

        sampleList.add(newSample);
    }

    return sampleList;
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Initialize ID service, load max id from file or find max id in labels and
 * canvas.
 *
 * @param params
 * @throws IOException
 */
@Override
protected void initIdService( final P params ) throws IOException
{
	/* id */
	idService = new LocalIdService();

	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFile );

	long maxId = 0;
	final Long nextIdObject = H5Utils.loadAttribute( reader, "/", "next_id" );

	if ( nextIdObject == null )
	{
		for ( final H5LabelMultisetSetupImageLoader labelLoader : labels )
			maxId = maxId( labelLoader, maxId );

		if ( reader.exists( params.canvas ) )
			maxId = maxId( canvas, maxId );
	}
	else
		maxId = nextIdObject.longValue() - 1;

	idService.invalidate( maxId );

	reader.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load labels and create label+canvas compositions.
 *
 * @param params
 * @throws IOException
 */
protected void initLabels( final P params ) throws IOException
{
	System.out.println( "Opening labels from " + params.inFileLabels );
	final IHDF5Reader reader = HDF5Factory.openForReading( params.inFileLabels );

	/* labels */
	for ( final String label : params.labels )
		if ( reader.exists( label ) )
			readLabels( reader, label );
	else
			System.out.println( "no label dataset '" + label + "' found" );
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load an HDF5 float32 dataset into a {@link CellImg} of {@link FloatType}.
 *
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public CellImg< FloatType, ? > loadFloat(
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Reader reader = HDF5Factory.openForReading( file );
	final CellImg< FloatType, ? > target = loadFloat( reader, dataset, cellDimensions );
	reader.close();
	return target;
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load an HDF5 float64 dataset into a {@link CellImg} of {@link DoubleType}.
 *
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public CellImg< DoubleType, ? > loadDouble(
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Reader reader = HDF5Factory.openForReading( file );
	final CellImg< DoubleType, ? > target = loadDouble( reader, dataset, cellDimensions );
	reader.close();
	return target;
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load an HDF5 uint64 dataset into a {@link CellImg} of {@link LongType}.
 *
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public CellImg< LongType, ? > loadUnsignedLong(
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Reader reader = HDF5Factory.openForReading( file );
	final CellImg< LongType, ? > target = loadUnsignedLong( reader, dataset, cellDimensions );
	reader.close();
	return target;
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load an HDF5 uint16 dataset into a {@link CellImg} of {@link UnsignedShortType}.
 *
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public CellImg< UnsignedShortType, ? > loadUnsignedShort(
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Reader reader = HDF5Factory.openForReading( file );
	final CellImg< UnsignedShortType, ? > target = loadUnsignedShort( reader, dataset, cellDimensions );
	reader.close();
	return target;
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Load an HDF5 uint8 dataset into a {@link CellImg} of {@link UnsignedByteType}.
 *
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public CellImg< UnsignedByteType, ? > loadUnsignedByte(
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Reader reader = HDF5Factory.openForReading( file );
	final CellImg< UnsignedByteType, ? > target = loadUnsignedByte( reader, dataset, cellDimensions );
	reader.close();
	return target;
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Save a {@link RandomAccessibleInterval} of {@link UnsignedByteType} into an HDF5
 * uint8 dataset.
 *
 * @param source
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public void saveUnsignedByte(
		final RandomAccessibleInterval< UnsignedByteType > source,
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Writer writer = HDF5Factory.open( file );
	saveUnsignedByte( source, writer, dataset, cellDimensions );
	writer.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Save a {@link RandomAccessibleInterval} of {@link FloatType} into an HDF5
 * float32 dataset.
 *
 * @param source
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public void saveFloat(
		final RandomAccessibleInterval< FloatType > source,
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Writer writer = HDF5Factory.open( file );
	saveFloat( source, writer, dataset, cellDimensions );
	writer.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Save a {@link RandomAccessibleInterval} of {@link DoubleType} into an HDF5
 * float64 dataset.
 *
 * @param source
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public void saveDouble(
		final RandomAccessibleInterval< DoubleType > source,
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Writer writer = HDF5Factory.open( file );
	saveDouble( source, writer, dataset, cellDimensions );
	writer.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Save a {@link RandomAccessibleInterval} of {@link ShortType} into an HDF5
 * uint16 dataset.
 *
 * @param source
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public void saveUnsignedShort(
		final RandomAccessibleInterval< ShortType > source,
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Writer writer = HDF5Factory.open( file );
	saveUnsignedShort( source, writer, dataset, cellDimensions );
	writer.close();
}
 

import ch.systemsx.cisd.hdf5.HDF5Factory; //导入依赖的package包/类
/**
 * Save a {@link RandomAccessibleInterval} of {@link LongType} into an HDF5
 * uint64 dataset.
 *
 * @param source
 * @param file
 * @param dataset
 * @param cellDimensions
 */
static public void saveUnsignedLong(
		final RandomAccessibleInterval< LongType > source,
		final File file,
		final String dataset,
		final int[] cellDimensions )
{
	final IHDF5Writer writer = HDF5Factory.open( file );
	saveUnsignedLong( source, writer, dataset, cellDimensions );
	writer.close();
}