1 package nom.tam.fits;
2
3 /*
4 * #%L
5 * nom.tam FITS library
6 * %%
7 * Copyright (C) 2004 - 2024 nom-tam-fits
8 * %%
9 * This is free and unencumbered software released into the public domain.
10 *
11 * Anyone is free to copy, modify, publish, use, compile, sell, or
12 * distribute this software, either in source code form or as a compiled
13 * binary, for any purpose, commercial or non-commercial, and by any
14 * means.
15 *
16 * In jurisdictions that recognize copyright laws, the author or authors
17 * of this software dedicate any and all copyright interest in the
18 * software to the public domain. We make this dedication for the benefit
19 * of the public at large and to the detriment of our heirs and
20 * successors. We intend this dedication to be an overt act of
21 * relinquishment in perpetuity of all present and future rights to this
22 * software under copyright law.
23 *
24 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
25 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
26 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
27 * IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
28 * OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
29 * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
30 * OTHER DEALINGS IN THE SOFTWARE.
31 * #L%
32 */
33
34 import java.io.IOException;
35
36 import nom.tam.util.ArrayDataInput;
37 import nom.tam.util.ArrayDataOutput;
38 import nom.tam.util.ByteArrayIO;
39 import nom.tam.util.FitsDecoder;
40 import nom.tam.util.FitsEncoder;
41
42 import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
43
44 /**
45 * Heap for storing variable-length entries in binary tables. FITS binary tables store variable length arrays on a heap,
46 * following the regular array data. The newer implementation of the heap now provides proper random access to the byte
47 * buffer as of version 1.16.
48 */
49 public class FitsHeap implements FitsElement {
50
51 /** The minimum stoprage size to allocate for the heap, from which it can grow as necessary */
52 private static final int MIN_HEAP_CAPACITY = 16384;
53
54 // TODO
55 // AK: In principle we could use ReadWriteAccess interface as the storage, which can be either an in-memory
56 // array or a buffered file region. The latter could support heaps over 2G, and could reduce memory overhead
57 // for heap access in some future release...
58 /** The underlying storage space of the heap */
59 private ByteArrayIO store;
60
61 /** conversion from Java arrays to FITS binary representation */
62 private FitsEncoder encoder;
63
64 /** conversion from FITS binary representation to Java arrays */
65 private FitsDecoder decoder;
66
67 /**
68 * Construct a new uninitialized FITS heap object.
69 */
70 private FitsHeap() {
71 }
72
73 /**
74 * Creates a heap of a given initial size. The new heap is initialized with 0's, and up to the specified number of
75 * bytes are immediately available for reading (as zeroes). The heap can grow as needed if more data is written into
76 * it.
77 *
78 * @throws IllegalArgumentException if the size argument is negative.
79 */
80 FitsHeap(int size) throws IllegalArgumentException {
81 if (size < 0) {
82 throw new IllegalArgumentException("Illegal size for FITS heap: " + size);
83 }
84
85 ByteArrayIO data = new ByteArrayIO(Math.max(size, MIN_HEAP_CAPACITY));
86 data.setLength(Math.max(0, size));
87 setData(data);
88 encoder = new FitsEncoder(store);
89 decoder = new FitsDecoder(store);
90 }
91
92 /**
93 * Sets the underlying data storage for this heap instance. Constructors should call this.
94 *
95 * @param data the new underlying storage object for this heap instance.
96 */
97 protected synchronized void setData(ByteArrayIO data) {
98 store = data;
99 }
100
101 /**
102 * Add a copy constructor to allow us to duplicate a heap. This would be necessary if we wanted to copy an HDU that
103 * included variable length columns.
104 */
105 synchronized FitsHeap copy() {
106 FitsHeap copy = new FitsHeap();
107 synchronized (copy) {
108 copy.setData(store.copy());
109 copy.encoder = new FitsEncoder(copy.store);
110 copy.decoder = new FitsDecoder(copy.store);
111 }
112 return copy;
113 }
114
115 /**
116 * Gets data for a Java array from the heap. The array may be a multi-dimensional array of arrays.
117 *
118 * @param offset the heap byte offset at which the data begins.
119 * @param array The array of primitives to be extracted.
120 *
121 * @throws FitsException if the operation failed
122 */
123 public synchronized void getData(int offset, Object array) throws FitsException {
124 try {
125 store.position(offset);
126 decoder.readArrayFully(array);
127 } catch (Exception e) {
128 throw new FitsException("Error decoding heap area at offset=" + offset + ", size="
129 + FitsEncoder.computeSize(array) + " (heap size " + size() + "): " + e.getMessage(), e);
130 }
131 }
132
133 @Override
134 public long getFileOffset() {
135 throw new IllegalStateException("FitsHeap should only be reset from inside its parent, never alone");
136 }
137
138 @Override
139 public synchronized long getSize() {
140 return size();
141 }
142
143 /**
144 * Puts data to the end of the heap.
145 *
146 * @param data a primitive array object, which may be multidimensional
147 *
148 * @return the number of bytes used by the data.
149 *
150 * @see #putData(Object, long)
151 * @see #getData(int, Object)
152 */
153 synchronized long putData(Object data) throws FitsException {
154 return putData(data, store.length());
155 }
156
157 /**
158 * Puts data onto the heap at a specific heap position.
159 *
160 * @param data a primitive array object, which may be multidimensional
161 * @param pos the byte offset at which the data should begin.
162 *
163 * @return the number of bytes used by the data.
164 *
165 * @see #putData(Object, long)
166 * @see #getData(int, Object)
167 */
168 synchronized long putData(Object data, long pos) throws FitsException {
169 long lsize = pos + FitsEncoder.computeSize(data);
170 if (lsize > Integer.MAX_VALUE) {
171 throw new FitsException("FITS Heap > 2 G");
172 }
173
174 try {
175 store.position(pos);
176 encoder.writeArray(data);
177 } catch (Exception e) {
178 throw new FitsException("Unable to write variable column length data: " + e.getMessage(), e);
179 }
180
181 return store.position() - pos;
182 }
183
184 /**
185 * Copies a segment of data from another heap to the end of this heap
186 *
187 * @param src the heap to source data from
188 * @param offset the byte offset of the data in the source heap
189 * @param len the number of bytes to copy
190 *
191 * @return the position of the copied data in this heap.
192 */
193 synchronized int copyFrom(FitsHeap src, int offset, int len) {
194 int pos = (int) store.length();
195 store.setLength(pos + len);
196 synchronized (src) {
197 System.arraycopy(src.store.getBuffer(), offset, store.getBuffer(), pos, len);
198 }
199 return pos;
200 }
201
202 @SuppressFBWarnings(value = "RR_NOT_CHECKED", justification = "this read will never return less than the requested length")
203 @Override
204 public synchronized void read(ArrayDataInput str) throws FitsException {
205 if (store.length() == 0) {
206 return;
207 }
208
209 try {
210 str.readFully(store.getBuffer(), 0, (int) store.length());
211 } catch (IOException e) {
212 throw new FitsException("Error reading heap " + e.getMessage(), e);
213 }
214 }
215
216 @Override
217 public boolean reset() {
218 throw new IllegalStateException("FitsHeap should only be reset from inside its parent, never alone");
219 }
220
221 @Override
222 public void rewrite() throws IOException, FitsException {
223 throw new FitsException("FitsHeap should only be rewritten from inside its parent, never alone");
224 }
225
226 @Override
227 public boolean rewriteable() {
228 return false;
229 }
230
231 /**
232 * Returns the current heap size.
233 *
234 * @return the size of the heap in bytes
235 */
236 public synchronized int size() {
237 return (int) store.length();
238 }
239
240 @Override
241 public synchronized void write(ArrayDataOutput str) throws FitsException {
242 try {
243 str.write(store.getBuffer(), 0, (int) store.length());
244 } catch (IOException e) {
245 throw new FitsException("Error writing heap:" + e.getMessage(), e);
246 }
247 }
248
249 }