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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 1998-2009 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.netcdf3;

import ucar.ma2.*;

import java.io.*;
import java.nio.*;
import java.nio.channels.*;
import java.net.URL;
import java.util.*;


/**
 * use direct channels for bulk reading and writing.
 */

class N3nioCD extends N3iosp {

  protected FileChannel channel;

  public void open(String filename, ucar.nc2.NetcdfFile ncfile, boolean readonly) throws IOException {
    super.open( filename, ncfile, readonly);
    channel = raf.getChannel();
    if (debug) out.println ("Opened file to read:'" + filename+ "', size=" + channel.size());
  }

   /**
    * Read data subset from file for a variable, create primitive array.
    * @param beginOffset: variable's beginning byte offset in file.
    * @param index handles skipping around in the file.
    * @param source from this buye buffer
    * @param dataType dataType of the variable
    * @return primitive array with data read in
    */
  protected Object readData( int beginOffset, Indexer index, DataType dataType) throws IOException {
    int offset = 0;
    int chunk = index.getChunkSize();
    int size = index.getTotalSize();

    if ((dataType == DataType.BYTE) || (dataType == DataType.CHAR)) {
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk);
      byte[] pa = new byte[size];
      while (index.hasNext()) {
        bbuff.clear();
        channel.read(bbuff, (long) beginOffset + index.next());
        bbuff.flip();
        bbuff.get( pa, offset, chunk); // copy into primitive array
        offset += chunk;
      }
      return (dataType == DataType.BYTE) ? pa : (Object) convertByteToChar( pa);

    } else if (dataType == DataType.SHORT) {
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*2);
      ShortBuffer tbuff = bbuff.asShortBuffer(); // typed buffer
      short[] pa = new short[size];
      while (index.hasNext()) {
        bbuff.clear();
        channel.read(bbuff, (long) beginOffset + index.next());
        tbuff.position(0).limit(chunk);
        tbuff.get(pa, offset, chunk); // copy from typed buffer into primitive array
        offset += chunk;
      }
      return pa;

    } else if (dataType == DataType.INT) {
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*4);
      IntBuffer tbuff = bbuff.asIntBuffer(); // typed buffer
      int[] pa = new int[size];
      while (index.hasNext()) {
        bbuff.clear();
        channel.read(bbuff, (long) beginOffset + index.next());
        tbuff.position(0).limit(chunk);
        tbuff.get(pa, offset, chunk); // copy from typed buffer into primitive array
        offset += chunk;
      }
      return pa;

    } else if (dataType == DataType.FLOAT) {
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*4);
      FloatBuffer tbuff = bbuff.asFloatBuffer(); // typed buffer
      float[] pa = new float[size];
      while (index.hasNext()) {
        bbuff.clear();
        channel.read(bbuff, (long) beginOffset + index.next());
        tbuff.position(0).limit(chunk);
        tbuff.get(pa, offset, chunk); // copy from typed buffer into primitive array
        offset += chunk;
      }
      return pa;

    } else if (dataType == DataType.DOUBLE) {
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*8);
      DoubleBuffer tbuff = bbuff.asDoubleBuffer(); // typed buffer
      double[] pa = new double[size];
      while (index.hasNext()) {
        bbuff.clear();
        channel.read(bbuff, (long) beginOffset + index.next());
        tbuff.position(0).limit(chunk);
        tbuff.get(pa, offset, chunk); // copy from typed buffer into primitive array
        offset += chunk;
      }
      return pa;
    }

    throw new IllegalStateException();
  }

  public void create(String filename, ucar.nc2.NetcdfFile ncfile, boolean fill) throws IOException {
    super.create( filename, ncfile, fill);
    channel = raf.getChannel();
    if (debug) out.println ("Opened file to write:'" + filename+ "', size=" + channel.size());
    flush();
  }

   /**
    * Write data subset to file for a variable, create primitive array.
    * @param beginOffset: variable's beginning byte offset in file.
    * @param index handles skipping around in the file.
    * @param source from this buye buffer
    * @param dataType dataType of the variable
    * @return primitive array with data read in
    */
  protected void writeData( Array aa, int beginOffset, Indexer index, DataType dataType) throws IOException {
    int offset = 0;
    int chunk = index.getChunkSize();
    int size = index.getTotalSize();

    if ((dataType == DataType.BYTE) || (dataType == DataType.CHAR)) {
      byte[] pa;
      if (dataType == DataType.BYTE)
         pa = (byte[]) aa.getStorage();
      else {
        char[] cbuff = (char[]) aa.getStorage();
        pa = convertCharToByte( cbuff);
      }
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk);
      while (index.hasNext()) {
        bbuff.clear();
        bbuff.put(pa, offset, chunk); // copy from primitive array to buffer
        bbuff.flip();
        channel.write(bbuff, beginOffset + index.next());
        offset += chunk;
      }
      return;

    } else if (dataType == DataType.SHORT) {
      short[] pa = (short[]) aa.getStorage();
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*2);
      ShortBuffer tbuff = bbuff.asShortBuffer(); // typed buffer
      while (index.hasNext()) {
        tbuff.clear();
        tbuff.put(pa, offset, chunk); // copy from primitive array to typed buffer
        bbuff.clear();
        channel.write(bbuff, beginOffset + index.next());
        offset += chunk;
      }
      return;

    } else if (dataType == DataType.INT) {
      int[] pa = (int[]) aa.getStorage();
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*4);
      IntBuffer tbuff = bbuff.asIntBuffer(); // typed buffer
      while (index.hasNext()) {
        tbuff.clear();
        tbuff.put(pa, offset, chunk); // copy from primitive array to typed buffer
        bbuff.clear();
        channel.write(bbuff, beginOffset + index.next());
        offset += chunk;
      }
      return;

    } else if (dataType == DataType.FLOAT) {
      float[] pa = (float[]) aa.getStorage();
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*4);
      FloatBuffer tbuff = bbuff.asFloatBuffer(); // typed buffer
      while (index.hasNext()) {
        tbuff.clear();
        tbuff.put(pa, offset, chunk); // copy from primitive array to typed buffer
        bbuff.clear();
        channel.write(bbuff, beginOffset + index.next());
        offset += chunk;
      }
      return;

    } else if (dataType == DataType.DOUBLE) {
      double[] pa = (double[]) aa.getStorage();
      ByteBuffer bbuff = ByteBuffer.allocateDirect( chunk*8);
      DoubleBuffer tbuff = bbuff.asDoubleBuffer(); // typed buffer
      while (index.hasNext()) {
        tbuff.clear();
        tbuff.put(pa, offset, chunk); // copy from primitive array to typed buffer
        bbuff.clear();
        channel.write(bbuff, beginOffset + index.next());
        offset += chunk;
      }
      return;
    }

    throw new IllegalStateException();
  }

  public void flush() throws IOException {
    channel.force( false);
  }

  public void close() throws IOException {
    if (!readonly) flush();
    if (channel != null)
      channel.close();
    super.close();
  }


}