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Java library for reading and writing FITS files. FITS, the Flexible Image Transport System, is the format commonly used in the archiving and transport of astronomical data.
/*
* #%L
* nom.tam FITS library
* %%
* Copyright (C) 1996 - 2024 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
* means.
*
* In jurisdictions that recognize copyright laws, the author or authors
* of this software dedicate any and all copyright interest in the
* software to the public domain. We make this dedication for the benefit
* of the public at large and to the detriment of our heirs and
* successors. We intend this dedication to be an overt act of
* relinquishment in perpetuity of all present and future rights to this
* 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.
* IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
* OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
* ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
* #L%
*/
package nom.tam.util;
import java.io.EOFException;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Array;
import java.nio.Buffer;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import nom.tam.fits.FitsFactory;
import nom.tam.util.type.ElementType;
/**
* Efficient base class for decoding of binary input into Java arrays (primarily for internal use)
*
* @author Attila Kovacs
*
* @since 1.16
*
* @see OutputEncoder
* @see ArrayDataFile
* @see ArrayInputStream
* @see ArrayOutputStream
*/
public abstract class InputDecoder {
/** The buffer size for array translation */
private static final int BUFFER_SIZE = 8 * FitsFactory.FITS_BLOCK_SIZE;
/** bit mask for 1 byte */
private static final int BYTE_MASK = 0xFF;
/** bit mask for a 16-byte integer (a Java short). */
private static final int SHORT_MASK = 0xFFFF;
/** the input providing the binary representation of data */
private InputReader in;
/** the conversion buffer */
private InputBuffer buf;
/**
* Instantiates a new decoder of binary input to Java arrays. To be used by subclass constructors only.
*
* @see #setInput(InputReader)
*/
protected InputDecoder() {
buf = new InputBuffer(BUFFER_SIZE);
}
/**
* Instantiates a new decoder for converting data representations into Java arrays.
*
* @param i the binary input.
*/
public InputDecoder(InputReader i) {
this();
setInput(i);
}
/**
* Sets the input from which to read the binary output.
*
* @param i the new binary input.
*/
protected void setInput(InputReader i) {
in = i;
}
/**
* Returns the buffer that is used for conversion, which can be used to bulk read bytes ahead from the input (see
* {@link InputBuffer#loadBytes(long, int)}) and {@link InputBuffer#loadOne(int)}) before doing conversions to Java
* types locally.
*
* @return the conversion buffer used by this decoder.
*/
protected InputBuffer getInputBuffer() {
return buf;
}
/**
* Makes sure that an elements of the specified size is fully available in the buffer, prompting additional reading
* of the underlying stream as appropriate (but not beyond the limit set by {@link #loadBytes(long, int)}.
*
* @param size the number of bytes we need at once from the buffer
*
* @return true if the requested number of bytes are, or could be made, available.
* Otherwise false.
*
* @throws IOException if there was an underlying IO error, other than the end of file, while trying to fetch
* additional data from the underlying input
*/
boolean makeAvailable(int size) throws IOException {
// TODO Once the deprecated BufferDecoder is retired, this should become
// a private method of InputBuffer (with buf. prefixed removed below).
while (buf.buffer.remaining() < size) {
if (!buf.fetch()) {
return false;
}
}
return true;
}
/**
* Reads one byte from the input. See the contract of {@link InputStream#read()}.
*
* @return the byte, or -1 if at the end of the file.
*
* @throws IOException if an IO error, other than the end-of-file prevented the read.
*/
protected synchronized int read() throws IOException {
return in.read();
}
/**
* Reads bytes into an array from the input. See the contract of {@link InputStream#read(byte[], int, int)}.
*
* @param b the destination array
* @param start the first index in the array to be populated
* @param length the number of bytes to read into the array.
*
* @return the number of bytes successfully read, or -1 if at the end of the file.
*
* @throws IOException if an IO error, other than the end-of-file prevented the read.
*/
protected synchronized int read(byte[] b, int start, int length) throws IOException {
return in.read(b, start, length);
}
/**
* Reads bytes to fill the supplied buffer with the requested number of bytes from the given starting buffer index.
* If not enough bytes are avaialable in the file to deliver the reqauested number of bytes the buffer, an
* {@link EOFException} will be thrown.
*
* @param b the buffer
* @param off the buffer index at which to start reading data
* @param len the total number of bytes to read.
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before the requested number of bytes could all be read.
*/
protected void readFully(byte[] b, int off, int len) throws EOFException, IOException {
while (len > 0) {
int n = read(b, off, len);
if (n < 0) {
throw new EOFException();
}
off += n;
len -= n;
}
}
/**
* Based on {@link #readArray(Object)}, but guaranteeing a complete read of the supplied object or else an
* {@link EOFException} is thrown.
*
* @param o the array, including multi-dimensional, and heterogeneous arrays of arrays.
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error
* @throws IllegalArgumentException if the argument is not a Java array, or is or contains elements that do not have
* supported conversions from binary representation.
*
* @see #readArray(Object)
* @see #readImage(Object)
*/
public void readArrayFully(Object o) throws IOException, IllegalArgumentException {
if (readArray(o) != FitsEncoder.computeSize(o)) {
throw new EOFException("Incomplete array read (FITS encoding).");
}
}
/**
* See the contract of {@link ArrayDataInput#readLArray(Object)}.
*
* @param o an array, to be populated
*
* @return the actual number of bytes read from the input, or -1 if already at the
* end-of-file.
*
* @throws IllegalArgumentException if the argument is not an array or if it contains an element that is not
* supported for decoding.
* @throws IOException if there was an IO error reading from the input
*
* @see #readArrayFully(Object)
*/
public abstract long readArray(Object o) throws IOException, IllegalArgumentException;
/**
* Like {@link #readArrayFully(Object)} but strictly for numerical types only.
*
* @param o An any-dimensional array containing only numerical types
*
* @throws IllegalArgumentException if the argument is not an array or if it contains an element that is not
* supported.
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error
*
* @see #readArrayFully(Object)
*
* @since 1.18
*/
public void readImage(Object o) throws IOException, IllegalArgumentException {
if (o == null) {
return;
}
if (!o.getClass().isArray()) {
throw new IllegalArgumentException("Not an array: " + o.getClass().getName());
}
long size = FitsEncoder.computeSize(o);
if (size == 0) {
return;
}
getInputBuffer().loadBytes(size, 1);
if (getImage(o) != size) {
throw new EOFException("Incomplete image read.");
}
}
private long getImage(Object o) throws IOException, IllegalArgumentException {
int length = Array.getLength(o);
if (length == 0) {
return 0L;
}
if (o instanceof byte[]) {
return buf.get((byte[]) o, 0, length);
}
if (o instanceof short[]) {
return buf.get((short[]) o, 0, length) * Short.BYTES;
}
if (o instanceof int[]) {
return buf.get((int[]) o, 0, length) * Integer.BYTES;
}
if (o instanceof float[]) {
return buf.get((float[]) o, 0, length) * Float.BYTES;
}
if (o instanceof long[]) {
return buf.get((long[]) o, 0, length) * Long.BYTES;
}
if (o instanceof double[]) {
return buf.get((double[]) o, 0, length) * Double.BYTES;
}
if (!(o instanceof Object[])) {
throw new IllegalArgumentException("Not a numerical image type: " + o.getClass().getName());
}
Object[] array = (Object[]) o;
long count = 0L;
// Process multidim arrays recursively.
for (int i = 0; i < length; i++) {
try {
count += getImage(array[i]);
} catch (EOFException e) {
return eofCheck(e, count, -1L);
}
}
return count;
}
/**
* Decides what to do when an {@link EOFException} is encountered after having read some number of bytes from the
* input. The default behavior is to re-throw the exception only if no data at all was obtained from the input,
* otherwise return the non-zero byte count of data that were successfully read. Subclass implementations may
* override this method to adjust if an when {@link EOFException} is thrown upon an incomplete read.
*
* @param e the exception that was thrown, or null.
* @param got the number of elements successfully read
* @param expected the number of elements expected
*
* @return the number of elements successfully read (same as got).
*
* @throws EOFException the rethrown exception, or a new one, as appropriate
*/
long eofCheck(EOFException e, long got, long expected) throws EOFException {
if (got == 0) {
if (e == null) {
throw new EOFException();
}
throw e;
}
return got;
}
/**
*
* The conversion buffer for decoding binary data representation into Java arrays (objects).
*
*
* The buffering is most efficient, if we fist specify how many bytes of input maybe be consumed first (buffered
* from the input), via {@link #loadBytes(long, int)}. After that, we can call the get routines of this class to
* return binary data converted to Java format until we exhaust the specified alotment of bytes.
*
*
*
* // The data we want to retrieve
* double d;
* int i;
* short[] shortArray = new short[100];
* float[] floaTarray = new float[48];
*
* // We convert from the binary format to Java format using
* // the local conversion buffer
* ConversionBuffer buf = getBuffer();
*
* // We can allow the conversion buffer to read enough bytes for all
* // data we want to retrieve:
* buf.loadBytes(FitsIO.BYTES_IN_DOUBLE + FitsIO.BYTES_IN_INT + FitsIO.BYTES_IN_SHORT * shortArray.length
* + FitsIO.BYTES_IN_FLOAT * floatArray.length);
*
* // Now we can get the data with minimal underlying IO calls...
* d = buf.getDouble();
* i = buf.getInt();
*
* for (int i = 0; i < shortArray.length; i++) {
* shortArray[i] = buf.getShort();
* }
*
* for (int i = 0; i < floatArray.length; i++) {
* floatArray[i] = buf.getFloat();
* }
*
*
* In the special case that one needs just a single element (or a few single elements) from the input, rather than
* lots of elements or arrays, one may use {@link #loadOne(int)} instead of {@link #loadBytes(long, int)} to read
* just enough bytes for a single data element from the input before each conversion. For example:
*
*
*
* ConversionBuffer buf = getBuffer();
*
* buf.loadOne(FitsIO.BYTES_IN_FLOAT);
* float f = buf.getFloat();
*
*
* @author Attila Kovacs
*/
protected final class InputBuffer {
/** the byte array in which to buffer data from the input */
private final byte[] data;
/** the buffer wrapped for NIO access */
private final ByteBuffer buffer;
/** The current type-specific view of the buffer or null */
private Buffer view;
/** the number of bytes requested, but not yet buffered */
private long pending = 0;
private InputBuffer(int size) {
data = new byte[size];
buffer = ByteBuffer.wrap(data);
}
/**
* Sets the byte order of the binary data representation from which we are decoding data.
*
* @param order the new byte order
*
* @see #byteOrder()
* @see ByteBuffer#order(ByteOrder)
*/
protected void setByteOrder(ByteOrder order) {
buffer.order(order);
}
/**
* Returns the current byte order of the binary data representation from which we are decoding.
*
* @return the byte order
*
* @see #setByteOrder(ByteOrder)
* @see ByteBuffer#order()
*/
protected ByteOrder byteOrder() {
return buffer.order();
}
private boolean isViewingAs(Class type) {
if (view == null) {
return false;
}
return type.isAssignableFrom(view.getClass());
}
private void assertView(ElementType type) {
if (!isViewingAs(type.bufferClass())) {
view = type.asTypedBuffer(buffer);
}
}
private void rewind() {
buffer.rewind();
view = null;
}
/**
* Set the number of bytes we can buffer from the input for subsequent retrieval from this buffer. The get
* methods of this class will be ensured not to fetch data from the input beyond the requested size.
*
* @param n the number of elements we can read and buffer from the input
* @param size the number of bytes in each elements.
*/
protected void loadBytes(long n, int size) {
rewind();
buffer.limit(0);
pending = n * size;
}
/**
* Loads just a single element of the specified byte size. The element must fit into the conversion buffer, and
* it is up to the caller to ensure that. The method itself does not check.
*
* @param size The number of bytes in the element
*
* @return true if the data was successfully read from the uderlying stream or file,
* otherwise false.
*
* @throws IOException if there was an IO error, other than the end-of-file.
*/
protected boolean loadOne(int size) throws IOException {
pending = size;
rewind();
buffer.limit(0);
return makeAvailable(size);
}
/**
* Reads more data into the buffer from the underlying stream, attempting to fill the buffer if possible.
*
* @return true if data was successfully buffered from the underlying intput or the
* buffer is already full. Otherwise false.
*
* @throws IOException if there as an IO error, other than the end of file, while trying to read more data from
* the underlying input into the buffer.
*/
private boolean fetch() throws IOException {
int remaining = buffer.remaining();
if (remaining > 0) {
System.arraycopy(data, buffer.position(), data, 0, remaining);
}
rewind();
int n = (int) Math.min(pending, data.length - remaining);
n = in.read(data, remaining, n);
if (n < 0) {
return false;
}
buffer.limit(remaining + n);
pending -= n;
return true;
}
/**
* Retrieves a single byte from the buffer. Before data can be retrieved with this method they should be
* 'loaded' into the buffer via {@link #loadOne(int)} or {@link #loadBytes(long, int)}. This method is
* appropriate for retrieving one or a fwew bytes at a time. For bulk input of bytes, you should use
* {@link InputDecoder#read(byte[], int, int)} instead for superior performance.
*
* @return the byte value, or -1 if no more data is available from the buffer or the underlying
* input.
*
* @throws IOException if there as an IO error, other than the end of file, while trying to read more data from
* the underlying input into the buffer.
*
* @see #loadOne(int)
* @see #loadBytes(long, int)
*/
protected int get() throws IOException {
if (makeAvailable(1)) {
view = null;
return buffer.get() & BYTE_MASK;
}
return -1;
}
/**
* Retrieves a 2-byte unsigned integer from the buffer. Before data can be retrieved with this method the should
* be 'loaded' into the buffer via {@link #loadOne(int)} or {@link #loadBytes(long, int)}.
*
* @return the 16-bit integer value, or -1 if no more data is available from the buffer or the
* underlying input.
*
* @throws IOException if there as an IO error, other than the end of file, while trying to read more data from
* the underlying input into the buffer.
*
* @see #loadOne(int)
* @see #loadBytes(long, int)
*/
protected int getUnsignedShort() throws IOException {
if (makeAvailable(Short.BYTES)) {
view = null;
return buffer.getShort() & SHORT_MASK;
}
return -1;
}
/**
* Retrieves a 4-byte integer from the buffer. Before data can be retrieved with this method the should be
* 'loaded' into the buffer via {@link #loadOne(int)} or {@link #loadBytes(long, int)}.
*
* @return the 32-bit integer value.
*
* @throws EOFException if already at the end of file.
* @throws IOException if there as an IO error
*
* @see #loadOne(int)
* @see #loadBytes(long, int)
*/
protected int getInt() throws EOFException, IOException {
if (makeAvailable(Integer.BYTES)) {
view = null;
return buffer.getInt();
}
throw new EOFException();
}
/**
* Retrieves a 8-byte integer from the buffer. Before data can be retrieved with this method the should be
* 'loaded' into the buffer via {@link #loadOne(int)} or {@link #loadBytes(long, int)}.
*
* @return the 64-bit integer value.
*
* @throws EOFException if already at the end of file.
* @throws IOException if there as an IO error
*
* @see #loadOne(int)
* @see #loadBytes(long, int)
*/
protected long getLong() throws EOFException, IOException {
if (makeAvailable(Long.BYTES)) {
view = null;
return buffer.getLong();
}
throw new EOFException();
}
/**
* Retrieves a 4-byte single-precision floating point value from the buffer. Before data can be retrieved with
* this method the shold be 'loaded' into the buffer via {@link #loadOne(int)} or {@link #loadBytes(long, int)}.
*
* @return the 32-bit single-precision floating-point value.
*
* @throws EOFException if already at the end of file.
* @throws IOException if there as an IO error
*
* @see #loadOne(int)
* @see #loadBytes(long, int)
*/
protected float getFloat() throws EOFException, IOException {
if (makeAvailable(Float.BYTES)) {
view = null;
return buffer.getFloat();
}
throw new EOFException();
}
/**
* Retrieves a 8-byte double-precision floating point value from the buffer. Before data can be retrieved with
* this method they should be 'loaded' into the buffer via {@link #loadOne(int)} or
* {@link #loadBytes(long, int)}.
*
* @return the 64-bit double-precision floating-point value.
*
* @throws EOFException if already at the end of file.
* @throws IOException if there as an IO error
*
* @see #loadOne(int)
* @see #loadBytes(long, int)
*/
protected double getDouble() throws EOFException, IOException {
if (makeAvailable(Double.BYTES)) {
view = null;
return buffer.getDouble();
}
throw new EOFException();
}
/**
* Retrieves a sequence of signed bytes from the buffer. Before data can be retrieved with this method the
* should be 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
protected int get(byte[] dst, int from, int n) throws EOFException, IOException {
if (n == 1) {
int i = get();
if (i < 0) {
throw new EOFException();
}
dst[from] = (byte) i;
return 1;
}
view = null;
int got = 0;
while (got < n) {
if (!makeAvailable(1)) {
return (int) eofCheck(null, got, n);
}
int m = Math.min(n - got, buffer.remaining());
buffer.get(dst, from + got, m);
got += m;
}
return got;
}
/**
* Retrieves a sequence of big-endian 16-bit signed integers from the buffer. Before data can be retrieved with
* this method they should be 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
protected int get(short[] dst, int from, int n) throws EOFException, IOException {
if (n == 1 && !isViewingAs(ElementType.SHORT.bufferClass())) {
int i = getUnsignedShort();
if (i < 0) {
throw new EOFException();
}
dst[from] = (short) i;
return 1;
}
return get(ElementType.SHORT, dst, from, n);
}
/**
* Retrieves a sequence of big-endian 32-bit signed integers from the buffer. Before data can be retrieved with
* this method they should be 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
protected int get(int[] dst, int from, int n) throws EOFException, IOException {
if (n == 1 && !isViewingAs(ElementType.INT.bufferClass())) {
dst[from] = getInt();
return 1;
}
return get(ElementType.INT, dst, from, n);
}
/**
* Retrieves a sequence of big-endian 64-bit signed integers from the buffer. Before data can be retrieved with
* this method they should be 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
protected int get(long[] dst, int from, int n) throws EOFException, IOException {
if (n == 1 && !isViewingAs(ElementType.LONG.bufferClass())) {
dst[from] = getLong();
return 1;
}
return get(ElementType.LONG, dst, from, n);
}
/**
* Retrieves a sequence of big-endian 32-bit floating-point values from the buffer. Before data can be retrieved
* with this method they should be 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
protected int get(float[] dst, int from, int n) throws EOFException, IOException {
if (n == 1 && !isViewingAs(ElementType.FLOAT.bufferClass())) {
dst[from] = getFloat();
return 1;
}
return get(ElementType.FLOAT, dst, from, n);
}
/**
* Retrieves a sequence of big-endian 64-bit floating-point values from the buffer. Before data can be retrieved
* with this method they should be 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
protected int get(double[] dst, int from, int n) throws EOFException, IOException {
if (n == 1 && !isViewingAs(ElementType.DOUBLE.bufferClass())) {
dst[from] = getDouble();
return 1;
}
return get(ElementType.DOUBLE, dst, from, n);
}
/**
* Retrieves a sequence of values from the buffer. Before data can be retrieved with this method the should be
* 'loaded' into the buffer via {@link #loadBytes(long, int)}.
*
* @param dst Java array in which to store the retrieved sequence of elements
* @param from the array index for storing the first element retrieved
* @param n the number of elements to retrieve
*
* @return the number of elements successfully retrieved
*
* @throws EOFException if already at the end of file.
* @throws IOException if there was an IO error before, before requested number of bytes could be read
*
* @see #loadBytes(long, int)
*
* @since 1.18
*/
@SuppressWarnings("unchecked")
private int get(ElementType e, Object dst, int from, int n) throws EOFException, IOException {
int got = 0;
while (got < n) {
if (!makeAvailable(e.size())) {
return (int) eofCheck(null, got, n);
}
assertView(e);
int m = Math.min(n - got, view.remaining());
e.getArray((B) view, dst, from + got, m);
buffer.position(buffer.position() + m * e.size());
got += m;
}
return got;
}
}
}
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