FitsHeap.java
package nom.tam.fits;
/*
* #%L
* nom.tam FITS library
* %%
* Copyright (C) 2004 - 2021 nom-tam-fits
* %%
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import java.io.IOException;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
import nom.tam.util.ArrayDataInput;
import nom.tam.util.ArrayDataOutput;
import nom.tam.util.FitsDecoder;
import nom.tam.util.FitsEncoder;
import nom.tam.util.ByteArrayIO;
/**
* This class supports the FITS heap. This is currently used for variable length
* columns in binary tables. The newer implementation of the heap now provides
* proper random access to the byte buffer as of version 1.16.
*
*/
public class FitsHeap implements FitsElement {
/** The minimum stoprage size to allocate for the heap, from which it can grow as necessary */
private static final int MIN_HEAP_CAPACITY = 16384;
// TODO
// AK: In principle we could use ReadWriteAccess interface as the storage, which can be either an in-memory
// array or a buffered file region. The latter could support heaps over 2G, and could reduce memory overhead
// for heap access in some future release...
/** The underlying storage space of the heap */
private ByteArrayIO store;
/** conversion from Java arrays to FITS binary representation */
private FitsEncoder encoder;
/** conversion from FITS binary representation to Java arrays */
private FitsDecoder decoder;
/**
* Construct a new uninitialized FITS heap object.
*/
private FitsHeap() {
}
/**
* Creates a heap of a given initial size. The new heap is initialized with 0's, and
* up to the specified number of bytes are immediately available for reading
* (as zeroes). The heap can grow as needed if more data is written into it.
*
* @throws IllegalArgumentException
* if the size argument is negative.
*
*/
FitsHeap(int size) {
if (size < 0) {
throw new IllegalArgumentException("Illegal size for FITS heap: " + size);
}
ByteArrayIO data = new ByteArrayIO(Math.max(size, MIN_HEAP_CAPACITY));
data.setLength(Math.max(0, size));
setData(data);
encoder = new FitsEncoder(store);
decoder = new FitsDecoder(store);
}
/**
* Sets the underlying data storage for this heap instance. Constructors should
* call this.
*
* @param data the new underlying storage object for this heap instance.
*/
protected void setData(ByteArrayIO data) {
this.store = data;
}
/**
* Add a copy constructor to allow us to duplicate a heap. This would be
* necessary if we wanted to copy an HDU that included variable length
* columns.
*/
FitsHeap copy() {
FitsHeap copy = new FitsHeap();
copy.setData(store.copy());
copy.encoder = new FitsEncoder(copy.store);
copy.decoder = new FitsDecoder(copy.store);
return copy;
}
/**
* Gets data for a Java array from the heap. The array may be a multi-dimensional or a
* heterogenetous array of arrays.
*
* @param offset
* the heap byte offset at which the data begins.
* @param array
* The array to be extracted.
* @throws FitsException
* if the operation failed
*/
public void getData(int offset, Object array) throws FitsException {
try {
store.position(offset);
decoder.readArrayFully(array);
} catch (Exception e) {
throw new FitsException("Error decoding heap area at offset=" + offset + ".", e);
}
}
/**
* Get the file offset of the heap
*/
@Override
public long getFileOffset() {
throw new IllegalStateException("FitsHeap should only be reset from inside its parent, never alone");
}
/**
* Return the size of the heap using the more bean compatible format
*/
@Override
public long getSize() {
return size();
}
/**
* Add some data to the heap.
*/
int putData(Object data) throws FitsException {
long lsize = store.length() + FitsEncoder.computeSize(data);
if (lsize > Integer.MAX_VALUE) {
throw new FitsException("FITS Heap > 2 G");
}
int oldSize = (int) store.length();
try {
store.position(oldSize);
encoder.writeArray(data);
} catch (Exception e) {
throw new FitsException("Unable to write variable column length data", e);
}
return oldSize;
}
@SuppressFBWarnings(value = "RR_NOT_CHECKED", justification = "this read will never return less than the requested length")
@Override
public void read(ArrayDataInput str) throws FitsException {
if (store.length() == 0) {
return;
}
try {
str.readFully(store.getBuffer(), 0, (int) store.length());
} catch (IOException e) {
throw new FitsException("Error reading heap " + e.getMessage(), e);
}
}
@Override
public boolean reset() {
throw new IllegalStateException("FitsHeap should only be reset from inside its parent, never alone");
}
@Override
public void rewrite() throws IOException, FitsException {
throw new FitsException("FitsHeap should only be rewritten from inside its parent, never alone");
}
@Override
public boolean rewriteable() {
return false;
}
/**
* Returns the current heap size.
*
* @return the size of the heap in bytes
*/
public int size() {
return (int) store.length();
}
@Override
public void write(ArrayDataOutput str) throws FitsException {
try {
str.write(store.getBuffer(), 0, (int) store.length());
} catch (IOException e) {
throw new FitsException("Error writing heap:" + e.getMessage(), e);
}
}
}