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karlnicholaskarlnicholas
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Updates for v2 arch
1 parent ac3dd27 commit 983d584

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‎src/main/java/org/hdf5javalib/utils/HdfDisplayCountUtils.java‎

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package org.hdf5javalib.utils;
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import org.hdf5javalib.dataclass.HdfData;
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import org.hdf5javalib.dataclass.HdfFixedPoint;
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import org.hdf5javalib.datasource.TypedDataSource;
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import org.hdf5javalib.hdffile.dataobjects.HdfObjectHeaderPrefix;
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import org.hdf5javalib.hdffile.dataobjects.messages.AttributeMessage;
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import org.hdf5javalib.hdffile.dataobjects.messages.HdfMessage;
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import org.hdf5javalib.hdffile.dataobjects.messages.LinkMessage;
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import org.hdf5javalib.hdfjava.HdfDataFile;
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import org.hdf5javalib.hdfjava.HdfDataset;
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import org.hdf5javalib.hdfjava.HdfFileReader;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.lang.reflect.InvocationTargetException;
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import java.nio.channels.SeekableByteChannel;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.StandardOpenOption;
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import java.util.Arrays;
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import java.util.Comparator;
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import java.util.Optional;
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import java.util.stream.Collectors;
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/**
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* Utility class for displaying HDF5 dataset data and managing attributes.
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* <p>
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* The {@code HdfDisplayUtils} class provides methods to display scalar and vector data
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* from HDF5 datasets using a {@link TypedDataSource}, as well as to create version attributes
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* for datasets. It supports various data types and formats the output for easy inspection,
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* handling both primitive and array types.
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* </p>
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*/
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public class HdfDisplayCountUtils {
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private static final Logger log = LoggerFactory.getLogger(HdfDisplayCountUtils.class);
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public static final String UNDEFINED = "<Undefined>";
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private static final String STREAM_EQUALS = " stream = ";
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public static void displayLinkMessages(HdfObjectHeaderPrefix objectHeader) {
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for( HdfMessage hdfMessage: objectHeader.getHeaderMessages()) {
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if ( hdfMessage instanceof LinkMessage ) {
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LinkMessage linkMessage = (LinkMessage) hdfMessage;
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System.out.println("\tLinkMessage: " + linkMessage.toString());
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}
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}
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}
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// Define a functional interface for actions that may need channel, dataset, and reader
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@FunctionalInterface
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interface FileAction {
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void perform(SeekableByteChannel channel, HdfDataset dataSet, HdfFileReader reader) throws Exception;
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}
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public static String undefinedArrayToString(HdfFixedPoint[] values) {
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if (values == null || values.length == 0) {
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return "Not Present";
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}
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StringBuilder sb = new StringBuilder("[");
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for (int i = 0; i < values.length; i++) {
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sb.append(values[i].isUndefined()?UNDEFINED:values[i].toString() );
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if (i != values.length - 1) {
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sb.append(", ");
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}
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}
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sb.append(']');
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return sb.toString();
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}
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// Generalized method to process the file and apply a custom action per dataset
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private static void processFile(Path filePath, FileAction action) {
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try (SeekableByteChannel channel = Files.newByteChannel(filePath, StandardOpenOption.READ)) {
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HdfFileReader reader = new HdfFileReader(channel).readFile();
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for (HdfDataset dataSet : reader.getDatasets()) {
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System.out.println("{} " + dataSet);
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// log.info("{} ", dataSet);
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action.perform(channel, dataSet, reader);
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}
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} catch (Exception e) {
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log.error("Exception in processFile: {}", filePath, e);
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}
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}
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public static void displayFileAttr(Path filePath) {
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processFile(filePath, (channel, dataSet, reader) -> displayAttributes(dataSet));
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}
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public static void displayFile(Path filePath) {
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processFile(filePath, HdfDisplayCountUtils::displayData);
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}
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public static void displayAttributes(HdfDataset dataSet) throws InvocationTargetException, InstantiationException, IllegalAccessException, IOException {
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for (AttributeMessage message : dataSet.getAttributeMessages()) {
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HdfDataHolder dataHolder = message.getHdfDataHolder();
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if (dataHolder.getDimensionality() == 1) {
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HdfData[] data = dataHolder.getAll(HdfData[].class);
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log.info("Data = {}", Arrays.toString(data));
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} else if (dataHolder.getDimensionality() == 2) {
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HdfData[][] data = dataHolder.getAll(HdfData[][].class);
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for (HdfData[] row : data) {
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log.info("Row = {}", Arrays.toString(row));
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}
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}
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}
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}
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// public static String getDataObjectFullName(HdfDataObject hdfDataObject) {
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// List<String> parents = new ArrayList<>();
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// HdfDataObject currentNode = hdfDataObject;
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// while(currentNode.getParent() != null) {
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// parents.add(currentNode.getObjectName());
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// currentNode = currentNode.getParent().getDataObject();
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// }
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// Collections.reverse(parents);
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// String objectPathString = '/' + currentNode.getObjectName() + String.join("/", parents);
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// return objectPathString;
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// }
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public static void displayData(SeekableByteChannel channel, HdfDataset ds, HdfFileReader reader) throws Exception {
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log.debug("Dataset path: {}", ds.getObjectPath());
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if (ds.hasData()) {
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switch (ds.getDimensionality()) {
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case 0:
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displayScalarData(channel, ds, HdfData.class, reader);
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break;
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case 1:
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displayVectorData(channel, ds, HdfData.class, reader);
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break;
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case 2:
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displayMatrixData(channel, ds, HdfData.class, reader);
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break;
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default:
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displayNDimData(channel, ds, HdfData.class, reader);
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break;
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}
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} else if (ds.isDataset() && ds.getHardLink() != null) {
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log.info("{}: HARDLINK = {} ", ds.getObjectName(), ds.getHardLink());
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}
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}
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/**
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* Displays scalar data from a dataset.
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* <p>
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* Reads and prints the scalar value from the dataset using both direct reading and
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* streaming methods, formatting the output with the dataset name and type information.
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* </p>
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*
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* @param fileChannel the seekable byte channel for reading the HDF5 file
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* @param dataSet the dataset to read from
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* @param clazz the class type of the data
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* @param hdfDataFile the HDF5 file context
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* @param <T> the type of the data
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* @throws IOException if an I/O error occurs
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*/
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public static <T> void displayScalarData(SeekableByteChannel fileChannel, HdfDataset dataSet, Class<T> clazz, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
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TypedDataSource<T> dataSource = new TypedDataSource<>(fileChannel, hdfDataFile, dataSet, clazz);
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// Optional<String> max = dataSource.parallelStreamScalar().map(h->h.toString()).max(Comparator.naturalOrder());
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// System.out.println(dataSet.getObjectPath() + " stream count = " + max.orElse("NO MAX"));
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long count = dataSource.parallelStreamScalar().count();
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System.out.println(dataSet.getObjectPath() + " stream count = " + String.format("%,d", count) + ":" + dataSet.getDatatype().toString());
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}
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/**
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* Displays vector data from a dataset.
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* <p>
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* Reads and prints the vector data from the dataset using both direct reading and
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* streaming methods, formatting the output with type information and a comma-separated
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* list of values.
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* </p>
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*
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* @param fileChannel the seekable byte channel for reading the HDF5 file
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* @param dataSet the dataset to read from
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* @param clazz the class type of the data elements
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* @param hdfDataFile the HDF5 file context
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* @param <T> the type of the data elements
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* @throws IOException if an I/O error occurs
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*/
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public static <T> void displayVectorData(SeekableByteChannel fileChannel, HdfDataset dataSet, Class<T> clazz, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
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TypedDataSource<T> dataSource = new TypedDataSource<>(fileChannel, hdfDataFile, dataSet, clazz);
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// T[] resultArray = dataSource.readVector();
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// log.info("{} read = {}", displayType(clazz, resultArray), displayValue(resultArray));
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// Optional<String> max = dataSource.parallelStreamVector().map(h->h.toString()).max(Comparator.naturalOrder());
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// System.out.println(dataSet.getObjectPath() + " stream count = " + max.orElse("NO MAX"));
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long count = dataSource.parallelStreamVector().count();
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System.out.println(dataSet.getObjectPath() + " stream count = " + String.format("%,d", count) + ":" + dataSet.getDatatype().toString());
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}
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/**
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* Displays vector data from a dataset.
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* <p>
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* Reads and prints the vector data from the dataset using both direct reading and
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* streaming methods, formatting the output with type information and a comma-separated
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* list of values.
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* </p>
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*
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* @param fileChannel the seekable byte channel for reading the HDF5 file
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* @param dataSet the dataset to read from
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* @param clazz the class type of the data elements
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* @param hdfDataFile the HDF5 file context
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* @param <T> the type of the data elements
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* @throws IOException if an I/O error occurs
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*/
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public static <T> void displayMatrixData(SeekableByteChannel fileChannel, HdfDataset dataSet, Class<T> clazz, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
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TypedDataSource<T> dataSource = new TypedDataSource<>(fileChannel, hdfDataFile, dataSet, clazz);
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long count = dataSource.parallelStreamMatrix().count();
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System.out.println(dataSet.getObjectPath() + " stream count = " + String.format("%,d", count) + ":" + dataSet.getDatatype().toString());
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}
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/**
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* Displays vector data from a dataset.
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* <p>
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* Reads and prints the vector data from the dataset using both direct reading and
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* streaming methods, formatting the output with type information and a comma-separated
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* list of values.
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* </p>
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*
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* @param fileChannel the seekable byte channel for reading the HDF5 file
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* @param dataSet the dataset to read from
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* @param clazz the class type of the data elements
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* @param hdfDataFile the HDF5 file context
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* @param <T> the type of the data elements
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* @throws IOException if an I/O error occurs
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*/
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private static <T> void displayNDimData(SeekableByteChannel fileChannel, HdfDataset dataSet, Class<T> clazz, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
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TypedDataSource<T> dataSource = new TypedDataSource<>(fileChannel, hdfDataFile, dataSet, clazz);
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// String readResult = flattenedArrayToString(dataSource.readFlattened(), dataSource.getShape());
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// log.info("read = {}", readResult);
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long count = dataSource.parallelStreamFlattened().count();
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System.out.println(dataSet.getObjectPath() + " stream count = " + String.format("%,d", count) + ":" + dataSet.getDatatype().toString());
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}
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}

‎src/main/java/org/hdf5javalib/utils/HdfDisplayUtils.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ private static void processFile(Path filePath, FileAction action) {
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for (HdfDataset dataSet : reader.getDatasets()) {
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System.out.println("{} " + dataSet);
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// log.info("{} ", dataSet);
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// action.perform(channel, dataSet, reader);
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action.perform(channel, dataSet, reader);
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}
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} catch (Exception e) {
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log.error("Exception in processFile: {}", filePath, e);
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}
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public static void displayFile(Path filePath) {
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processFile(filePath, HdfDisplayUtils::displayData);
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processFile(filePath, HdfDisplayCountUtils::displayData);
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}
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public static void displayAttributes(HdfDataset dataSet) throws InvocationTargetException, InstantiationException, IllegalAccessException, IOException {

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