ucar.nc2.stream.NcStreamWriter Maven / Gradle / Ivy
/*
* Copyright 2009-2012 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.stream;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.CDM;
import java.io.ByteArrayOutputStream;
import java.io.OutputStream;
import java.io.IOException;
import java.util.zip.DeflaterOutputStream;
/**
* Write a NetcdfFile to a OutputStream using ncstream protocol
*
* @author caron
* @since Feb 7, 2009
*/
public class NcStreamWriter {
static private long maxChunk = 1 * 1000 * 1000; // 1 MByte
static private int sizeToCache = 100; // when to store a variable's data in the header, ie "immediate" mode
static private int currentVersion = 1;
private NetcdfFile ncfile;
private NcStreamProto.Header header;
private boolean show = false;
public NcStreamWriter(NetcdfFile ncfile, String location) throws IOException {
this.ncfile = ncfile;
NcStreamProto.Group.Builder rootBuilder = NcStream.encodeGroup(ncfile.getRootGroup(), sizeToCache);
NcStreamProto.Header.Builder headerBuilder = NcStreamProto.Header.newBuilder();
headerBuilder.setLocation(location == null ? ncfile.getLocation() : location);
if (ncfile.getTitle() != null) headerBuilder.setTitle(ncfile.getTitle());
if (ncfile.getId() != null) headerBuilder.setId(ncfile.getId());
headerBuilder.setRoot(rootBuilder);
headerBuilder.setVersion(currentVersion);
header = headerBuilder.build();
}
public long sendStart(OutputStream out) throws IOException {
return writeBytes(out, NcStream.MAGIC_START);
}
public long sendEnd(OutputStream out) throws IOException {
return writeBytes(out, NcStream.MAGIC_END);
}
public long sendHeader(OutputStream out) throws IOException {
long size = 0;
//// header message
size += writeBytes(out, NcStream.MAGIC_HEADER);
byte[] b = header.toByteArray();
size += NcStream.writeVInt(out, b.length); // len
if (show) System.out.println("Write Header len=" + b.length);
// payload
size += writeBytes(out, b);
if (show) System.out.println(" header size=" + size);
return size;
}
public long sendData(Variable v, Section section, OutputStream out, boolean deflate) throws IOException, InvalidRangeException {
if (show) System.out.printf(" %s section=%s%n", v.getFullName(), section);
// length of data uncompressed
long uncompressedLength = section.computeSize();
if ((v.getDataType() != DataType.STRING) && (v.getDataType() != DataType.OPAQUE) && !v.isVariableLength())
uncompressedLength *= v.getElementSize(); // nelems for vdata, else nbytes
long size = 0;
size += writeBytes(out, NcStream.MAGIC_DATA); // magic
NcStreamProto.Data dataProto = NcStream.encodeDataProto(v, section, deflate, (int) uncompressedLength);
byte[] datab = dataProto.toByteArray();
size += NcStream.writeVInt(out, datab.length); // dataProto len
size += writeBytes(out, datab); // dataProto
if (v.getDataType() == DataType.SEQUENCE) {
int count = 0;
Structure seq = (Structure) v; // superclass for Sequence, SequenceDS
//coverity[FB.BC_UNCONFIRMED_CAST]
StructureDataIterator iter = seq.getStructureIterator(-1);
try {
while (iter.hasNext()) {
size += writeBytes(out, NcStream.MAGIC_VDATA); // magic
ArrayStructureBB abb = StructureDataDeep.copyToArrayBB(iter.next());
size += NcStream.encodeArrayStructure(abb, out);
count++;
}
} finally {
iter.finish();
}
size += writeBytes(out, NcStream.MAGIC_VEND);
if (show) System.out.printf(" NcStreamWriter sent %d sdata bytes = %d%n", count, size);
return size;
}
// regular arrays
if (deflate) {
ByteArrayOutputStream bout = new ByteArrayOutputStream();
DeflaterOutputStream dout = new DeflaterOutputStream(bout);
v.readToStream(section, dout); // write to internal buffer
// write internal buffer to output stream
dout.close();
int deflatedSize = bout.size();
size += NcStream.writeVInt(out, deflatedSize);
bout.writeTo(out);
size += deflatedSize;
if (show) System.out.printf(" %s proto=%d dataSize=%d len=%d%n", v.getFullName(), datab.length, deflatedSize, uncompressedLength);
} else {
size += NcStream.writeVInt(out, (int) uncompressedLength); // data len or number of objects
if (show) System.out.printf(" %s proto=%d data=%d%n", v.getFullName(), datab.length, uncompressedLength);
size += v.readToStream(section, out); // try to do a direct transfer
}
return size;
}
/* public long sendData(WritableByteChannel out, StructureData sdata) throws IOException {
long size = 0;
ByteBuffer bb = IospHelper.copyToByteBuffer(sdata);
byte[] datab = bb.array();
size += writeBytes(out, NcStream.MAGIC_DATA); // magic
size += NcStream.writeVInt(out, datab.length); // data len
size += writeBytes(out, datab); // data
return size;
} */
private int writeBytes(OutputStream out, byte[] b) throws IOException {
out.write(b);
return b.length;
}
public long streamAll(OutputStream out) throws IOException, InvalidRangeException {
long size = writeBytes(out, NcStream.MAGIC_START);
size += sendHeader(out);
if (show) System.out.printf(" data starts at= %d%n", size);
for (Variable v : ncfile.getVariables()) {
Attribute compressAtt = v.findAttribute(CDM.COMPRESS);
boolean deflate = (compressAtt != null) && compressAtt.isString() && compressAtt.getStringValue().equalsIgnoreCase(CDM.COMPRESS_DEFLATE);
long vsize = v.getSize() * v.getElementSize();
//if (vsize < sizeToCache) continue; // in the header;
if (show) System.out.printf(" var %s len=%d starts at= %d%n", v.getFullName(), vsize, size);
if (vsize > maxChunk) {
size += copyChunks(out, v, maxChunk, deflate);
} else {
size += sendData(v, v.getShapeAsSection(), out, deflate);
}
}
size += writeBytes(out, NcStream.MAGIC_END);
if (show) System.out.printf("total size= %d%n", size);
return size;
}
private long copyChunks(OutputStream out, Variable oldVar, long maxChunkSize, boolean deflate) throws IOException {
long maxChunkElems = maxChunkSize / oldVar.getElementSize();
FileWriter2.ChunkingIndex index = new FileWriter2.ChunkingIndex(oldVar.getShape());
long size = 0;
while (index.currentElement() < index.getSize()) {
try {
int[] chunkOrigin = index.getCurrentCounter();
int[] chunkShape = index.computeChunkShape(maxChunkElems);
size += sendData(oldVar, new Section(chunkOrigin, chunkShape), out, deflate);
index.setCurrentCounter(index.currentElement() + (int) Index.computeSize(chunkShape));
} catch (InvalidRangeException e) {
e.printStackTrace();
throw new IOException(e.getMessage());
}
}
return size;
}
static public void main2(String args[]) throws InvalidRangeException {
int[] totalShape = new int[] {1, 40, 530, 240};
int[] chunkShape = new int[] {1, 1, 530, 240};
FileWriter2.ChunkingIndex index = new FileWriter2.ChunkingIndex(totalShape);
while (index.currentElement() < index.getSize()) {
int[] chunkOrigin = index.getCurrentCounter();
System.out.printf(" %s%n", new Section(chunkOrigin, chunkShape));
index.setCurrentCounter(index.currentElement() + (int) Index.computeSize(chunkShape));
}
}
static public void main(String args[]) throws InvalidRangeException {
long maxChunkElems = maxChunk / 4;
int[] totalShape = new int[] {1, 40, 530, 240};
//int[] chunkShape = new int[] {1, 1, 530, 240};
FileWriter2.ChunkingIndex index = new FileWriter2.ChunkingIndex(totalShape);
while (index.currentElement() < index.getSize()) {
int[] chunkOrigin = index.getCurrentCounter();
int[] chunkShape = index.computeChunkShape(maxChunkElems);
System.out.printf(" %s%n", new Section(chunkOrigin, chunkShape));
index.setCurrentCounter(index.currentElement() + (int) Index.computeSize(chunkShape));
}
}
}
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