/*
* 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
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* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
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* 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
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* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.nc2.iosp.hdf5;
import ucar.ma2.InvalidRangeException;
import ucar.ma2.DataType;
import ucar.ma2.Section;
import ucar.nc2.iosp.LayoutTiled;
import ucar.nc2.iosp.Layout;
import java.io.IOException;
/**
* Iterator to read/write subsets of an array.
* This calculates byte offsets for HD5 chunked datasets.
* Assumes that the data is stored in chunks, indexed by a Btree.
* for unfiltered data only
*
* @author caron
*/
class H5tiledLayout implements Layout {
private LayoutTiled delegate;
private Section want;
private int[] chunkSize; // from the StorageLayout message (exclude the elemSize)
private int elemSize; // last dimension of the StorageLayout message
private boolean debug = false;
/**
* Constructor.
* This is for HDF5 chunked data storage. The data is read by chunk, for efficency.
*
* @param vinfo the vinfo object for this variable
* @param dtype type of data. may be different from v2.
* @param wantSection the wanted section of data, contains a List of Range objects, must be complete
* @throws InvalidRangeException if section invalid for this variable
* @throws java.io.IOException on io error
*/
H5tiledLayout(H5header.Vinfo vinfo, DataType dtype, Section wantSection) throws InvalidRangeException, IOException {
assert vinfo.isChunked;
assert vinfo.btree != null;
// we have to translate the want section into the same rank as the storageSize, in order to be able to call
// Section.intersect(). It appears that storageSize (actually msl.chunkSize) may have an extra dimension, reletive
// to the Variable.
if ((dtype == DataType.CHAR) && (wantSection.getRank() < vinfo.storageSize.length))
this.want = new Section(wantSection).appendRange(1);
else
this.want = wantSection;
// one less chunk dimension, except in the case of char
int nChunkDims = (dtype == DataType.CHAR) ? vinfo.storageSize.length : vinfo.storageSize.length - 1;
this.chunkSize = new int[nChunkDims];
System.arraycopy(vinfo.storageSize, 0, chunkSize, 0, nChunkDims);
this.elemSize = vinfo.storageSize[vinfo.storageSize.length - 1]; // last one is always the elements size
if (debug) System.out.println(" H5tiledLayout: " + this);
// create the data chunk iterator
LayoutTiled.DataChunkIterator iter = vinfo.btree.getDataChunkIterator2( this.want, nChunkDims);
delegate = new LayoutTiled(iter, chunkSize, elemSize, this.want);
}
public long getTotalNelems() {
return delegate.getTotalNelems();
}
public int getElemSize() {
return delegate.getElemSize();
}
public boolean hasNext() {
return delegate.hasNext();
}
public Chunk next() throws IOException {
return delegate.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(getTotalNelems());
sbuff.append(" elemSize=").append(elemSize);
return sbuff.toString();
}
}