org.eclipse.dawnsci.hdf5.HDF5LazyLoader Maven / Gradle / Ivy

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/*-
 * Copyright 2015 Diamond Light Source Ltd.
 *
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 */

package org.eclipse.dawnsci.hdf5;

import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.util.Arrays;

import org.eclipse.dawnsci.analysis.api.io.ScanFileHolderException;
import org.eclipse.january.IMonitor;
import org.eclipse.january.dataset.DTypeUtils;
import org.eclipse.january.dataset.Dataset;
import org.eclipse.january.dataset.SliceND;
import org.eclipse.january.io.ILazyDynamicLoader;
import org.eclipse.january.io.ILazyLoader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Lazy loader for HDF5 files
 */
public class HDF5LazyLoader implements ILazyLoader, ILazyDynamicLoader, Serializable {
	public static final long serialVersionUID = 5057544213374303912L;
	protected static final Logger logger = LoggerFactory.getLogger(HDF5LazyLoader.class);

	private boolean isReadable;
	private boolean isRemote;
	protected String filePath;
	protected String nodePath;
	protected int[] trueShape;
	protected Class clazz;
	private int isize;
	private boolean extendUnsigned;
	protected String name;
	protected File file;

	/**
	 * @param hostname
	 * @param filename
	 * @param node
	 * @param name
	 * @param trueShape
	 * @param isize
	 * @param dtype
	 * @param extendUnsigned
	 * @deprecated Use {@link #HDF5LazyLoader(String, String, String, String, int[], int, Class, boolean)}
	 */
	@Deprecated
	public HDF5LazyLoader(String hostname, String filename, String node, String name, int[] trueShape, int isize, int dtype,
			boolean extendUnsigned) {
		this(hostname, filename, node, name, trueShape, isize, DTypeUtils.getInterface(dtype), extendUnsigned);
	}

	/**
	 * @param hostname
	 * @param filename
	 * @param node
	 * @param name
	 * @param trueShape
	 * @param isize
	 * @param dtype
	 * @param extendUnsigned
	 */
	public HDF5LazyLoader(String hostname, String filename, String node, String name, int[] trueShape, int isize, final Class clazz,
			boolean extendUnsigned) {
		isRemote = hostname != null && hostname.length() > 0 && !hostname.equals(HDF5Utils.getLocalHostName());
		filePath = filename;
		isReadable = false;
		nodePath = node;
		this.name = name;
		this.trueShape = trueShape;
		this.isize = isize;
		this.clazz = clazz;
		this.extendUnsigned = extendUnsigned;
	}

	@Override
	public boolean isFileReadable() {
		if (!isReadable && !isRemote) { // keep trying if local
			if (file == null) {
				file = new File(filePath);
			}
			isReadable = file.canRead();
		}
		return isReadable;
	}

	@Override
	public String toString() {
		return filePath + ":" + nodePath;
	}

	@Override
	public Dataset getDataset(IMonitor mon, SliceND slice) throws IOException {
		int[] lstart = slice.getStart();
		int[] lstep  = slice.getStep();
		int[] newShape = slice.getShape();
		int[] shape = slice.getSourceShape();
		final int rank = shape.length;

		Dataset d = null;
		try {
			if (!Arrays.equals(trueShape, shape)) {
				final int trank = trueShape.length;
				int[] tstart = new int[trank];
				int[] tsize = new int[trank];
				int[] tstep = new int[trank];

				if (rank > trank) { // shape was extended (from left) then need to translate to true slice
					int j = 0;
					for (int i = 0; i < trank; i++) {
						if (trueShape[i] == 1) {
							tstart[i] = 0;
							tsize[i] = 1;
							tstep[i] = 1;
						} else {
							while (shape[j] == 1 && (rank - j) > (trank - i))
								j++;

							tstart[i] = lstart[j];
							tsize[i] = newShape[j];
							tstep[i] = lstep[j];
							j++;
						}
					}
				} else { // shape was squeezed (and could have been extended again) then need to translate to true slice
					int j = 0;
					while (shape[j] == 1 && j < rank)
						j++;

					for (int i = 0; i < trank; i++) {
						if (trueShape[i] == 1) {
							tstart[i] = 0;
							tsize[i] = 1;
							tstep[i] = 1;
						} else {
							tstart[i] = lstart[j];
							tsize[i] = newShape[j];
							tstep[i] = lstep[j];
							j++;
						}
					}
				}

				d = HDF5Utils.loadDataset(filePath, nodePath, tstart, tsize, tstep, isize, clazz, extendUnsigned);
				d.setShape(newShape); // squeeze shape back
			} else {
				d = HDF5Utils.loadDataset(filePath, nodePath, lstart, newShape, lstep, isize, clazz, extendUnsigned);
			}
			if (d != null) {
				d.setName(name);
			}
			if (mon != null) {
				if (mon.isCancelled()) {
					return d;
				}
				mon.worked(1);
			}
		} catch (Exception e) {
			throw new IOException("Problem loading dataset", e);
		}
		
		return d;
	}

	@Override
	public int[] refreshShape() {
		int[][] shape = null;
		try {
			shape = HDF5Utils.getDatasetShape(filePath, nodePath);
			assert(shape != null);
		} catch (ScanFileHolderException e) {
			logger.error("Problem updating shape", e);
			return null;
		}
		
		trueShape = shape[0];
		return trueShape.clone();
	}
}