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The NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of scientific data formats.
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/*
 * Copyright 1998-2014 University Corporation for Atmospheric Research/Unidata
 *
 *   Portions of this software were developed by the Unidata Program at the
 *   University Corporation for Atmospheric Research.
 *
 *   Access and use of this software shall impose the following obligations
 *   and understandings on the user. The user is granted the right, without
 *   any fee or cost, to use, copy, modify, alter, enhance and distribute
 *   this software, and any derivative works thereof, and its supporting
 *   documentation for any purpose whatsoever, provided that this entire
 *   notice appears in all copies of the software, derivative works and
 *   supporting documentation.  Further, UCAR requests that the user credit
 *   UCAR/Unidata in any publications that result from the use of this
 *   software or in any product that includes this software. The names UCAR
 *   and/or Unidata, however, may not be used in any advertising or publicity
 *   to endorse or promote any products or commercial entity unless specific
 *   written permission is obtained from UCAR/Unidata. The user also
 *   understands that UCAR/Unidata is not obligated to provide the user with
 *   any support, consulting, training or assistance of any kind with regard
 *   to the use, operation and performance of this software nor to provide
 *   the user with any updates, revisions, new versions or "bug fixes."
 *
 *   THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
 *   IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 *   WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 *   DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
 *   INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
 *   FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 *   NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 *   WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
 */
package ucar.nc2.iosp;

import ucar.ma2.InvalidRangeException;
import ucar.ma2.Section;

import java.io.IOException;
import java.nio.*;

/**
 * For datasets where the data are stored in chunks, and must be processed, eg compressed or filtered.
 * The data is read, processed, and placed in a ByteBuffer. Chunks have an offset into the ByteBuffer.
 * "Tiled" means that all chunks are assumed to be equal size.
 * Chunks do not necessarily cover the array, missing data is possible.
 *
 * @author caron
 * @since Jan 9, 2008
 */
public class LayoutBBTiled implements LayoutBB {
  private Section want;
  private int[] chunkSize; // all chunks assumed to be the same size
  private int elemSize;

  private DataChunkIterator chunkIterator; // iterate across chunks
  private IndexChunkerTiled index = null; // iterate within a chunk

  // track the overall iteration
  private long totalNelems, totalNelemsDone; // total number of elemens

  private static final boolean debug = false, debugIntersection = false;

  /**
   * Constructor.
   *
   * @param chunkIterator iterator over all data chunks
   * @param chunkSize     all chunks assumed to be the same size
   * @param elemSize      size of an element in bytes.
   * @param wantSection   the wanted section of data, contains a List of Range objects. Must be complete.
   * @throws ucar.ma2.InvalidRangeException if section invalid for this variable
   * @throws java.io.IOException            on io error
   */
  public LayoutBBTiled(DataChunkIterator chunkIterator, int[] chunkSize, int elemSize, Section wantSection) throws InvalidRangeException, IOException {
    this.chunkIterator = chunkIterator;
    this.chunkSize = chunkSize;
    this.elemSize = elemSize;
    this.want = wantSection;
    if (debug) System.out.println(" want section="+this.want);

    this.totalNelems = this.want.computeSize();
    this.totalNelemsDone = 0;
  }

  public long getTotalNelems() {
    return totalNelems;
  }

  public int getElemSize() {
    return elemSize;
  }

  private LayoutBBTiled.Chunk next;
  public boolean hasNext() { // have to actually fetch the thing
    if (totalNelemsDone >= totalNelems) return false;

    if ((index == null) || !index.hasNext()) { // get new data node
      try {
        Section dataSection;
        DataChunk dataChunk;

        while (true) { // look for intersecting sections
          if (!chunkIterator.hasNext()) {
            next = null;
            return false;
          }

          // get next dataChunk
          try {
            dataChunk = chunkIterator.next();
          } catch (IOException e) {
            e.printStackTrace();
            next = null;
            return false;
          }

          // make the dataSection for this chunk
          dataSection = new Section(dataChunk.getOffset(), chunkSize);
          if (debugIntersection)
            System.out.println(" test intersecting: " + dataSection + " want: " + want);
          if (dataSection.intersects(want)) // does it intersect ?
            break;
        }

        if (debug)
          System.out.println(" found intersecting dataSection: " + dataSection+" intersect= "+dataSection.intersect(want));

        index = new IndexChunkerTiled(dataSection, want); // new indexer into this chunk
        next = new Chunk( dataChunk.getByteBuffer()); // this does the uncompression

      } catch (InvalidRangeException e) {
        throw new IllegalStateException(e);

      } catch (IOException e) {
        throw new IllegalStateException(e);
      }
    }

    IndexChunker.Chunk chunk = index.next();
    totalNelemsDone += chunk.getNelems();
    next.setDelegate( chunk);

    return true;
  }

  public LayoutBB.Chunk next() throws IOException {
    return next;
  }
  
  public String toString() {
    StringBuilder sbuff = new StringBuilder();
    sbuff.append("want=").append(want).append("; ");
    sbuff.append("chunkSize=[");
    for (int i = 0; i < chunkSize.length; i++) {
      if (i > 0) sbuff.append(",");
      sbuff.append(chunkSize[i]);
    }
    sbuff.append("] totalNelems=").append(totalNelems);
    sbuff.append(" elemSize=").append(elemSize);
    return sbuff.toString();
  }

  /**
   * An iterator over the data chunks.
   */
  static public interface DataChunkIterator {
    public boolean hasNext();
    public DataChunk next() throws IOException;
  }

  /**
   * A data chunk
   */
  static public interface DataChunk {
    public int[] getOffset();
    public ByteBuffer getByteBuffer() throws IOException;
  }

  /**
   * A chunk of data that is contiguous in both the source and destination.
   * Everything is done in elements, not bytes.
   * Read nelems from src at srcPos, store in destination at destPos.
   */
  static private class Chunk implements LayoutBB.Chunk {
    IndexChunker.Chunk delegate;

    private ByteBuffer bb;
    private ShortBuffer sb;
    private IntBuffer ib;
    private LongBuffer longb;
    private FloatBuffer fb;
    private DoubleBuffer db;

    Chunk(ByteBuffer bb) {
      this.bb = bb;
    }

    public void setDelegate(IndexChunker.Chunk delegate) {
      this.delegate = delegate;
    }

    public int getSrcElem() {
      return (int) delegate.getSrcElem();
    }
    public int getNelems() {
      return delegate.getNelems();
    }
    public long getDestElem() {
      return delegate.getDestElem();
    }

    public ByteBuffer getByteBuffer() {
      return bb;
    }

    public ShortBuffer getShortBuffer() {
      if (sb == null) sb = bb.asShortBuffer();
      return sb;
    }

    public IntBuffer getIntBuffer() {
      if (ib == null) ib = bb.asIntBuffer();
      return ib;
    }

    public LongBuffer getLongBuffer() {
      if (longb == null) longb = bb.asLongBuffer();
      return longb;
    }

    public FloatBuffer getFloatBuffer() {
      if (fb == null) fb = bb.asFloatBuffer();
      return fb;
    }

    public DoubleBuffer getDoubleBuffer() {
      if (db == null) db = bb.asDoubleBuffer();
      return db;
    }

    // artifact of overriding Layout
    public long getSrcPos(){
      throw new UnsupportedOperationException();
    }

  }

}