/*
* #%L
* BSD implementations of Bio-Formats readers and writers
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package loci.formats.codec;
import java.io.IOException;
import java.util.Arrays;
import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.UnsupportedCompressionException;
/**
* This class implements Nikon decompression. Compression is not yet
* implemented.
*
* Decompression logic is adapted from the jrawio project,
* http://jrawio.dev.java.net
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class NikonCodec extends BaseCodec {
private static final int[] DEFAULT_LINEARIZATION_TABLE = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,
59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,
168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196,
197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210,
211, 212, 213, 214, 215, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226,
227, 228, 230, 231, 232, 233, 234, 235, 236, 238, 239, 240, 241, 242,
243, 245, 246, 247, 248, 249, 251, 252, 253, 254, 255, 257, 258, 259, 261,
262, 263, 264, 266, 267, 268, 270, 271, 272, 274, 275, 276, 278, 279,
280, 282, 283, 285, 286, 287, 289, 290, 292, 293, 295, 296, 298, 300, 303,
307, 311, 315, 319, 323, 328, 332, 336, 341, 345, 349, 354, 358, 362,
367, 371, 376, 381, 385, 390, 394, 399, 404, 409, 413, 418, 423, 428, 433,
437, 442, 447, 452, 457, 462, 467, 472, 477, 483, 488, 493, 498, 503,
508, 514, 519, 524, 530, 535, 540, 546, 551, 557, 562, 568, 574, 579, 585,
590, 596, 602, 608, 613, 619, 625, 631, 637, 642, 648, 654, 660, 666,
672, 679, 685, 691, 697, 703, 709, 716, 722, 728, 735, 741, 747, 754, 760,
767, 773, 780, 786, 793, 799, 806, 813, 819, 826, 833, 840, 846, 853,
860, 867, 874, 881, 888, 895, 902, 909, 916, 923, 930, 937, 944, 952, 959,
966, 973, 981, 988, 995, 1003, 1010, 1017, 1025, 1032, 1040, 1047,
1055, 1063, 1070, 1078, 1085, 1093, 1101, 1109, 1116, 1124, 1132, 1140,
1148, 1156, 1164, 1172, 1180, 1188, 1196, 1204, 1212, 1220, 1228, 1237,
1245, 1253, 1261, 1270, 1278, 1287, 1295, 1303, 1312, 1320, 1329, 1337,
1346, 1355, 1363, 1372, 1381, 1389, 1398, 1407, 1416, 1424, 1433, 1442,
1451, 1460, 1469, 1478, 1487, 1496, 1505, 1514, 1523, 1532, 1541, 1551,
1560, 1569, 1578, 1588, 1597, 1606, 1616, 1625, 1634, 1644, 1653, 1663,
1672, 1682, 1691, 1701, 1711, 1720, 1730, 1740, 1750, 1759, 1769, 1779,
1789, 1799, 1809, 1819, 1829, 1839, 1849, 1859, 1869, 1879, 1889, 1899,
1909, 1920, 1930, 1940, 1951, 1961, 1971, 1982, 1992, 2003, 2013, 2024,
2034, 2045, 2055, 2066, 2077, 2087, 2098, 2109, 2119, 2130, 2141, 2152,
2163, 2174, 2185, 2196, 2207, 2218, 2229, 2240, 2251, 2262, 2273, 2284,
2295, 2306, 2318, 2329, 2340, 2351, 2363, 2374, 2385, 2397, 2408, 2420,
2431, 2443, 2454, 2466, 2478, 2489, 2501, 2513, 2524, 2536, 2548, 2560,
2571, 2583, 2595, 2607, 2619, 2631, 2643, 2655, 2667, 2679, 2691, 2703,
2716, 2728, 2740, 2752, 2765, 2777, 2789, 2802, 2814, 2826, 2839, 2851,
2864, 2876, 2889, 2902, 2914, 2927, 2939, 2952, 2965, 2978, 2990, 3003,
3016, 3029, 3042, 3055, 3068, 3081, 3094, 3107, 3120, 3133, 3146, 3159,
3172, 3185, 3198, 3212, 3225, 3238, 3251, 3265, 3278, 3291, 3305, 3318,
3332, 3345, 3359, 3372, 3386, 3400, 3413, 3427, 3440, 3454, 3468, 3482,
3495, 3509, 3523, 3537, 3551, 3565, 3579, 3593, 3607, 3621, 3635, 3649,
3663, 3677, 3692, 3706, 3720, 3734, 3749, 3763, 3777, 3792, 3806, 3821,
3835, 3850, 3864, 3879, 3893, 3908, 3923, 3937, 3952, 3967, 3981, 3996,
4011, 4026, 4041, 4055, 4070, 4085, 4095
};
private static final short[] LOSSY_DECODER_CONFIGURATION_12 = {
0, 1, 5, 1, 1, 1, 1, 1, 1, 2, 0, 0, 0, 0, 0, 0, 5, 4, 3, 6, 2, 7, 1, 0,
8, 9, 11, 10, 12
};
private static final short[] SPLIT_LOSSY_DECODER_CONFIGURATION_12 = {
0, 1, 5, 1, 1, 1, 1, 1, 1, 2, 0, 0, 0, 0, 0, 0, 0x39, 0x5a, 0x38, 0x27,
0x16, 5, 4, 3, 2, 1, 0, 11, 12, 12
};
private static final short[] LOSSLESS_DECODER_CONFIGURATION_12 = {
0, 1, 4, 2, 3, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 4, 6, 3, 7, 2, 8, 1,
9, 0, 10, 11, 12
};
private static final short[] LOSSY_DECODER_CONFIGURATION_14 = {
0, 1, 4, 3, 1, 1, 1, 1, 1, 2, 0, 0, 0, 0, 0, 0, 5, 6, 4, 7, 8, 3, 9, 2,
1, 0, 10, 11, 12, 13, 14
};
private static final short[] SPLIT_LOSSY_DECODER_CONFIGURATION_14 = {
0, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 0, 0, 0, 0, 0, 8, 0x5c, 0x4b, 0x3a,
0x29, 7, 6, 5, 4, 3, 2, 1, 0, 13, 14
};
private static final short[] LOSSLESS_DECODER_CONFIGURATION_14 = {
0, 1, 4, 2, 2, 3, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 7, 6, 8, 5, 9, 4, 10,
3, 11, 12, 2, 0, 1, 13, 14
};
/* @see Codec#compress(byte[], CodecOptions) */
@Override
public byte[] compress(byte[] data, CodecOptions options)
throws FormatException
{
// TODO: Add compression support.
throw new UnsupportedCompressionException(
"Nikon Compression not currently supported");
}
/**
* The CodecOptions parameter must be an instance of
* {@link NikonCodecOptions}, and should have the following fields set:
* {@link CodecOptions#lossless lossless}
* {@link NikonCodecOptions#vPredictor vPredictor}
* {@link NikonCodecOptions#curve curve}
* {@link NikonCodecOptions#split split}
* {@link CodecOptions#bitsPerSample bitsPerSample}
* {@link CodecOptions#maxBytes maxBytes}
* {@link CodecOptions#width width}
* {@link CodecOptions#height height}
*
* @see Codec#decompress(RandomAccessInputStream, CodecOptions)
*/
@Override
public byte[] decompress(RandomAccessInputStream in, CodecOptions options)
throws FormatException, IOException
{
if (options == null || !(options instanceof NikonCodecOptions)) {
throw new FormatException("Options must be an instanceof " +
"loci.formats.codec.NikonCodecOptions.");
}
NikonCodecOptions nikon = (NikonCodecOptions) options;
HuffmanCodecOptions huffman = new HuffmanCodecOptions();
huffman.bitsPerSample = nikon.bitsPerSample;
huffman.maxBytes = nikon.maxBytes;
if (!nikon.lossless) {
if (nikon.bitsPerSample == 12) {
huffman.table = LOSSY_DECODER_CONFIGURATION_12;
}
else huffman.table = LOSSY_DECODER_CONFIGURATION_14;
}
else {
if (nikon.bitsPerSample == 12) {
huffman.table = LOSSLESS_DECODER_CONFIGURATION_12;
}
else huffman.table = LOSSLESS_DECODER_CONFIGURATION_14;
}
if (nikon.vPredictor == null) {
nikon.vPredictor = new int[] {0, 0, 0, 0};
}
HuffmanCodec huffmanCodec = new HuffmanCodec();
BitWriter out = new BitWriter();
int[] hPredictor = new int[2];
int[] table = nikon.curve == null ? DEFAULT_LINEARIZATION_TABLE :
nikon.curve;
for (int row=0; row<nikon.height; row++) {
if (row == nikon.split) {
if (!nikon.lossless) {
if (nikon.bitsPerSample == 12) {
huffman.table = SPLIT_LOSSY_DECODER_CONFIGURATION_12;
}
else huffman.table = SPLIT_LOSSY_DECODER_CONFIGURATION_14;
Arrays.fill(hPredictor, 0);
}
}
for (int col=0; col<nikon.width; col++) {
int cfaIndex = (2 * (row & 1)) + (col & 1);
int diff = huffmanCodec.getSample(in, huffman);
if (col < 2) {
nikon.vPredictor[cfaIndex] += diff;
hPredictor[col & 1] = nikon.vPredictor[cfaIndex];
}
else {
hPredictor[col & 1] += diff;
}
int index = hPredictor[col & 1];
if (index < 0) index = 0;
if (index >= table.length) {
index = table.length - 1;
}
out.write(table[index], options.bitsPerSample);
}
}
return out.toByteArray();
}
}