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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.
/*
* 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;
import ucar.ma2.Index;
import ucar.ma2.Section;
import ucar.ma2.InvalidRangeException;
/**
* LayoutSegmented has data stored in segments.
* Assume that each segment size is a multiple of elemSize.
*
* @author caron
* @since Dec 31, 2007
*/
public class LayoutSegmented implements Layout {
private long total, done;
private int elemSize; // size of each element
private long[] segPos; // bytes
private long[] segMax, segMin; // bytes
// outer chunk
private IndexChunker chunker;
private IndexChunker.Chunk chunkOuter;
// inner chunk = deal with segmentation
private IndexChunker.Chunk chunkInner = new IndexChunker.Chunk(0,0,0);
private boolean debugNext = false;
/**
* Constructor.
*
* @param segPos starting address of each segment.
* @param segSize number of bytes in each segment. Asume multiple of elemSize
* @param elemSize size of an element in bytes.
* @param srcShape shape of the entire data array.
* @param wantSection the wanted section of data
* @throws ucar.ma2.InvalidRangeException if ranges are misformed
*/
public LayoutSegmented(long[] segPos, int[] segSize, int elemSize, int[] srcShape, Section wantSection) throws InvalidRangeException {
assert segPos.length == segSize.length;
this.segPos = segPos;
int nsegs = segPos.length;
segMin = new long[nsegs];
segMax = new long[nsegs];
long totalElems = 0;
for (int i = 0; i < nsegs; i++) {
assert segPos[i] >= 0;
assert segSize[i] > 0;
assert (segSize[i] % elemSize) == 0;
segMin[i] = totalElems;
totalElems += segSize[i];
segMax[i] = totalElems;
}
assert totalElems >= Index.computeSize(srcShape) * elemSize;
chunker = new IndexChunker(srcShape, wantSection);
this.total = chunker.getTotalNelems();
this.done = 0;
this.elemSize = elemSize;
}
public long getTotalNelems() {
return total;
}
public int getElemSize() {
return elemSize;
}
public boolean hasNext() {
return done < total;
}
///////////////////
private long getFilePos(long elem) {
int segno = 0;
while (elem >= segMax[segno]) segno++;
return segPos[segno] + elem - segMin[segno];
}
// how many more bytes are in this segment ?
private int getMaxBytes(long start) {
int segno = 0;
while (start >= segMax[segno]) segno++;
return (int) (segMax[segno] - start);
}
private int needInner = 0;
private int doneInner = 0;
public Chunk next() {
Chunk result = null;
if (needInner > 0) {
result = nextInner(false, 0);
} else {
result = nextOuter();
int nbytes = getMaxBytes( chunkOuter.getSrcElem() * elemSize);
if (nbytes < result.getNelems() * elemSize)
result = nextInner(true, nbytes);
}
done += result.getNelems();
doneInner += result.getNelems();
needInner -= result.getNelems();
if (debugNext)
System.out.println(" next chunk: " + result);
return result;
}
private Chunk nextInner(boolean first, int nbytes) {
if (first) {
chunkInner.setNelems(nbytes / elemSize);
chunkInner.setDestElem( chunkOuter.getDestElem());
needInner = chunkOuter.getNelems();
doneInner = 0;
} else {
chunkInner.incrDestElem( chunkInner.getNelems()); // increment using last chunks' value
nbytes = getMaxBytes( (chunkOuter.getSrcElem() + doneInner) * elemSize);
nbytes = Math.min(nbytes, needInner * elemSize);
chunkInner.setNelems(nbytes / elemSize); // set this chunk's value
}
chunkInner.setSrcPos( getFilePos( (chunkOuter.getSrcElem() + doneInner) * elemSize));
return chunkInner;
}
public Chunk nextOuter() {
chunkOuter = chunker.next();
long srcPos = getFilePos( chunkOuter.getSrcElem() * elemSize);
chunkOuter.setSrcPos( srcPos);
return chunkOuter;
}
}