nom.tam.fits.FitsHeap Maven / Gradle / Ivy
package nom.tam.fits;
/*
* #%L
* nom.tam FITS library
* %%
* Copyright (C) 2004 - 2015 nom-tam-fits
* %%
* This is free and unencumbered software released into the public domain.
*
* Anyone is free to copy, modify, publish, use, compile, sell, or
* distribute this software, either in source code form or as a compiled
* binary, for any purpose, commercial or non-commercial, and by any
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* of this software dedicate any and all copyright interest in the
* software to the public domain. We make this dedication for the benefit
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* successors. We intend this dedication to be an overt act of
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* software under copyright law.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
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.ArrayFuncs;
import nom.tam.util.BufferedDataInputStream;
import nom.tam.util.BufferedDataOutputStream;
/**
* This class supports the FITS heap. This is currently used for variable length
* columns in binary tables.
*/
public class FitsHeap implements FitsElement {
private static final int MINIMUM_HEAP_SIZE = 16384;
/**
* The storage buffer
*/
private byte[] heap;
/**
* The current used size of the buffer <= heap.length
*/
private int heapSize;
/**
* Our current offset into the heap. When we read from the heap we use a
* byte array input stream. So long as we continue to read further into the
* heap, we can continue to use the same stream, but we need to recreate the
* stream whenever we skip backwards.
*/
private int heapOffset = 0;
/**
* A stream used to read the heap data
*/
private BufferedDataInputStream bstr;
/**
* Create a heap of a given size.
*/
FitsHeap(int size) {
this.heapSize = size;
if (size < 0) {
throw new IllegalArgumentException("Illegal size for FITS heap:" + size);
}
}
private void allocate() {
if (this.heap == null) {
this.heap = new byte[this.heapSize];
}
}
/**
* 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(0);
if (this.heap != null) {
copy.heap = this.heap.clone();
}
copy.heapSize = this.heapSize;
copy.heapOffset = this.heapOffset;
return copy;
}
/**
* Check if the Heap can accommodate a given requirement. If not expand the
* heap.
*/
void expandHeap(int need) {
// Invalidate any existing input stream to the heap.
this.bstr = null;
allocate();
if (this.heapSize + need > this.heap.length) {
int newlen = (this.heapSize + need) * 2;
if (newlen < MINIMUM_HEAP_SIZE) {
newlen = MINIMUM_HEAP_SIZE;
}
byte[] newHeap = new byte[newlen];
System.arraycopy(this.heap, 0, newHeap, 0, this.heapSize);
this.heap = newHeap;
}
}
/**
* Get data from the heap.
*
* @param offset
* The 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 {
allocate();
try {
// Can we reuse the existing byte stream?
if (this.bstr == null || this.heapOffset > offset) {
this.heapOffset = 0;
this.bstr = new BufferedDataInputStream(new ByteArrayInputStream(this.heap));
}
this.bstr.skipAllBytes(offset - this.heapOffset);
this.heapOffset = offset;
this.heapOffset += this.bstr.readLArray(array);
} catch (IOException e) {
throw new FitsException("Error decoding heap area at offset=" + offset + ". Exception: Exception " + 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 = ArrayFuncs.computeLSize(data);
if (lsize > Integer.MAX_VALUE) {
throw new FitsException("FITS Heap > 2 G");
}
int size = (int) lsize;
expandHeap(size);
ByteArrayOutputStream bo = new ByteArrayOutputStream(size);
try {
BufferedDataOutputStream o = new BufferedDataOutputStream(bo);
o.writeArray(data);
o.flush();
o.close();
} catch (IOException e) {
throw new FitsException("Unable to write variable column length data", e);
}
System.arraycopy(bo.toByteArray(), 0, this.heap, this.heapSize, size);
int oldOffset = this.heapSize;
this.heapSize += size;
return oldOffset;
}
/**
* Read the heap
*/
@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 (this.heapSize > 0) {
allocate();
try {
if (str.read(this.heap, 0, this.heapSize) < this.heapSize) {
throw new FitsException("Error reading heap, no more data");
}
} catch (IOException e) {
throw new FitsException("Error reading heap " + e.getMessage(), e);
}
}
this.bstr = null;
}
@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;
}
/**
* @return the size of the Heap
*/
public int size() {
return this.heapSize;
}
/**
* Write the heap
*/
@Override
public void write(ArrayDataOutput str) throws FitsException {
allocate();
try {
str.write(this.heap, 0, this.heapSize);
} catch (IOException e) {
throw new FitsException("Error writing heap:" + e.getMessage(), e);
}
}
}
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