/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

/* $Id$ */

package org.apache.pdfbox.filter;

class TIFFFaxDecoder {

    private int bitPointer, bytePointer;
    private byte[] data;
    private int w, h;
    private int fillOrder;

    // Data structures needed to store changing elements for the previous
    // and the current scanline
    private int changingElemSize = 0;
    private int[] prevChangingElems;
    private int[] currChangingElems;

    // Element at which to start search in getNextChangingElement
    private int lastChangingElement = 0;

    private int compression = 2;

    // Variables set by T4Options
    private int uncompressedMode = 0;
    private int fillBits = 0;
    private int oneD;

    static int[] table1 = {
        0x00, // 0 bits are left in first byte - SHOULD NOT HAPPEN
        0x01, // 1 bits are left in first byte
        0x03, // 2 bits are left in first byte
        0x07, // 3 bits are left in first byte
        0x0f, // 4 bits are left in first byte
        0x1f, // 5 bits are left in first byte
        0x3f, // 6 bits are left in first byte
        0x7f, // 7 bits are left in first byte
        0xff  // 8 bits are left in first byte
    };

    static int[] table2 = {
        0x00, // 0
        0x80, // 1
        0xc0, // 2
        0xe0, // 3
        0xf0, // 4
        0xf8, // 5
        0xfc, // 6
        0xfe, // 7
        0xff  // 8
    };

    // Table to be used when fillOrder = 2, for flipping bytes.
    static byte[] flipTable = {
         0,  -128,    64,   -64,    32,   -96,    96,   -32,
        16,  -112,    80,   -48,    48,   -80,   112,   -16,
         8,  -120,    72,   -56,    40,   -88,   104,   -24,
        24,  -104,    88,   -40,    56,   -72,   120,    -8,
         4,  -124,    68,   -60,    36,   -92,   100,   -28,
        20,  -108,    84,   -44,    52,   -76,   116,   -12,
        12,  -116,    76,   -52,    44,   -84,   108,   -20,
        28,  -100,    92,   -36,    60,   -68,   124,    -4,
         2,  -126,    66,   -62,    34,   -94,    98,   -30,
        18,  -110,    82,   -46,    50,   -78,   114,   -14,
        10,  -118,    74,   -54,    42,   -86,   106,   -22,
        26,  -102,    90,   -38,    58,   -70,   122,    -6,
         6,  -122,    70,   -58,    38,   -90,   102,   -26,
        22,  -106,    86,   -42,    54,   -74,   118,   -10,
        14,  -114,    78,   -50,    46,   -82,   110,   -18,
        30,   -98,    94,   -34,    62,   -66,   126,    -2,
         1,  -127,    65,   -63,    33,   -95,    97,   -31,
        17,  -111,    81,   -47,    49,   -79,   113,   -15,
         9,  -119,    73,   -55,    41,   -87,   105,   -23,
        25,  -103,    89,   -39,    57,   -71,   121,    -7,
         5,  -123,    69,   -59,    37,   -91,   101,   -27,
        21,  -107,    85,   -43,    53,   -75,   117,   -11,
        13,  -115,    77,   -51,    45,   -83,   109,   -19,
        29,   -99,    93,   -35,    61,   -67,   125,    -3,
         3,  -125,    67,   -61,    35,   -93,    99,   -29,
        19,  -109,    83,   -45,    51,   -77,   115,   -13,
        11,  -117,    75,   -53,    43,   -85,   107,   -21,
        27,  -101,    91,   -37,    59,   -69,   123,    -5,
         7,  -121,    71,   -57,    39,   -89,   103,   -25,
        23,  -105,    87,   -41,    55,   -73,   119,    -9,
        15,  -113,    79,   -49,    47,   -81,   111,   -17,
        31,   -97,    95,   -33,    63,   -65,   127,    -1,
    };

    // The main 10 bit white runs lookup table
    static short[] white = {
        // 0 - 7
        6430,   6400,   6400,   6400,   3225,   3225,   3225,   3225,
        // 8 - 15
        944,    944,    944,    944,    976,    976,    976,    976,
        // 16 - 23
        1456,   1456,   1456,   1456,   1488,   1488,   1488,   1488,
        // 24 - 31
        718,    718,    718,    718,    718,    718,    718,    718,
        // 32 - 39
        750,    750,    750,    750,    750,    750,    750,    750,
        // 40 - 47
        1520,   1520,   1520,   1520,   1552,   1552,   1552,   1552,
        // 48 - 55
        428,    428,    428,    428,    428,    428,    428,    428,
        // 56 - 63
        428,    428,    428,    428,    428,    428,    428,    428,
        // 64 - 71
        654,    654,    654,    654,    654,    654,    654,    654,
        // 72 - 79
        1072,   1072,   1072,   1072,   1104,   1104,   1104,   1104,
        // 80 - 87
        1136,   1136,   1136,   1136,   1168,   1168,   1168,   1168,
        // 88 - 95
        1200,   1200,   1200,   1200,   1232,   1232,   1232,   1232,
        // 96 - 103
        622,    622,    622,    622,    622,    622,    622,    622,
        // 104 - 111
        1008,   1008,   1008,   1008,   1040,   1040,   1040,   1040,
        // 112 - 119
        44,     44,     44,     44,     44,     44,     44,     44,
        // 120 - 127
        44,     44,     44,     44,     44,     44,     44,     44,
        // 128 - 135
        396,    396,    396,    396,    396,    396,    396,    396,
        // 136 - 143
        396,    396,    396,    396,    396,    396,    396,    396,
        // 144 - 151
        1712,   1712,   1712,   1712,   1744,   1744,   1744,   1744,
        // 152 - 159
        846,    846,    846,    846,    846,    846,    846,    846,
        // 160 - 167
        1264,   1264,   1264,   1264,   1296,   1296,   1296,   1296,
        // 168 - 175
        1328,   1328,   1328,   1328,   1360,   1360,   1360,   1360,
        // 176 - 183
        1392,   1392,   1392,   1392,   1424,   1424,   1424,   1424,
        // 184 - 191
        686,    686,    686,    686,    686,    686,    686,    686,
        // 192 - 199
        910,    910,    910,    910,    910,    910,    910,    910,
        // 200 - 207
        1968,   1968,   1968,   1968,   2000,   2000,   2000,   2000,
        // 208 - 215
        2032,   2032,   2032,   2032,     16,     16,     16,     16,
        // 216 - 223
        10257,  10257,  10257,  10257,  12305,  12305,  12305,  12305,
        // 224 - 231
        330,    330,    330,    330,    330,    330,    330,    330,
        // 232 - 239
        330,    330,    330,    330,    330,    330,    330,    330,
        // 240 - 247
        330,    330,    330,    330,    330,    330,    330,    330,
        // 248 - 255
        330,    330,    330,    330,    330,    330,    330,    330,
        // 256 - 263
        362,    362,    362,    362,    362,    362,    362,    362,
        // 264 - 271
        362,    362,    362,    362,    362,    362,    362,    362,
        // 272 - 279
        362,    362,    362,    362,    362,    362,    362,    362,
        // 280 - 287
        362,    362,    362,    362,    362,    362,    362,    362,
        // 288 - 295
        878,    878,    878,    878,    878,    878,    878,    878,
        // 296 - 303
        1904,   1904,   1904,   1904,   1936,   1936,   1936,   1936,
        // 304 - 311
        -18413, -18413, -16365, -16365, -14317, -14317, -10221, -10221,
        // 312 - 319
        590,    590,    590,    590,    590,    590,    590,    590,
        // 320 - 327
        782,    782,    782,    782,    782,    782,    782,    782,
        // 328 - 335
        1584,   1584,   1584,   1584,   1616,   1616,   1616,   1616,
        // 336 - 343
        1648,   1648,   1648,   1648,   1680,   1680,   1680,   1680,
        // 344 - 351
        814,    814,    814,    814,    814,    814,    814,    814,
        // 352 - 359
        1776,   1776,   1776,   1776,   1808,   1808,   1808,   1808,
        // 360 - 367
        1840,   1840,   1840,   1840,   1872,   1872,   1872,   1872,
        // 368 - 375
        6157,   6157,   6157,   6157,   6157,   6157,   6157,   6157,
        // 376 - 383
        6157,   6157,   6157,   6157,   6157,   6157,   6157,   6157,
        // 384 - 391
        -12275, -12275, -12275, -12275, -12275, -12275, -12275, -12275,
        // 392 - 399
        -12275, -12275, -12275, -12275, -12275, -12275, -12275, -12275,
        // 400 - 407
        14353,  14353,  14353,  14353,  16401,  16401,  16401,  16401,
        // 408 - 415
        22547,  22547,  24595,  24595,  20497,  20497,  20497,  20497,
        // 416 - 423
        18449,  18449,  18449,  18449,  26643,  26643,  28691,  28691,
        // 424 - 431
        30739,  30739, -32749, -32749, -30701, -30701, -28653, -28653,
        // 432 - 439
        -26605, -26605, -24557, -24557, -22509, -22509, -20461, -20461,
        // 440 - 447
        8207,   8207,   8207,   8207,   8207,   8207,   8207,   8207,
        // 448 - 455
        72,     72,     72,     72,     72,     72,     72,     72,
        // 456 - 463
        72,     72,     72,     72,     72,     72,     72,     72,
        // 464 - 471
        72,     72,     72,     72,     72,     72,     72,     72,
        // 472 - 479
        72,     72,     72,     72,     72,     72,     72,     72,
        // 480 - 487
        72,     72,     72,     72,     72,     72,     72,     72,
        // 488 - 495
        72,     72,     72,     72,     72,     72,     72,     72,
        // 496 - 503
        72,     72,     72,     72,     72,     72,     72,     72,
        // 504 - 511
        72,     72,     72,     72,     72,     72,     72,     72,
        // 512 - 519
        104,    104,    104,    104,    104,    104,    104,    104,
        // 520 - 527
        104,    104,    104,    104,    104,    104,    104,    104,
        // 528 - 535
        104,    104,    104,    104,    104,    104,    104,    104,
        // 536 - 543
        104,    104,    104,    104,    104,    104,    104,    104,
        // 544 - 551
        104,    104,    104,    104,    104,    104,    104,    104,
        // 552 - 559
        104,    104,    104,    104,    104,    104,    104,    104,
        // 560 - 567
        104,    104,    104,    104,    104,    104,    104,    104,
        // 568 - 575
        104,    104,    104,    104,    104,    104,    104,    104,
        // 576 - 583
        4107,   4107,   4107,   4107,   4107,   4107,   4107,   4107,
        // 584 - 591
        4107,   4107,   4107,   4107,   4107,   4107,   4107,   4107,
        // 592 - 599
        4107,   4107,   4107,   4107,   4107,   4107,   4107,   4107,
        // 600 - 607
        4107,   4107,   4107,   4107,   4107,   4107,   4107,   4107,
        // 608 - 615
        266,    266,    266,    266,    266,    266,    266,    266,
        // 616 - 623
        266,    266,    266,    266,    266,    266,    266,    266,
        // 624 - 631
        266,    266,    266,    266,    266,    266,    266,    266,
        // 632 - 639
        266,    266,    266,    266,    266,    266,    266,    266,
        // 640 - 647
        298,    298,    298,    298,    298,    298,    298,    298,
        // 648 - 655
        298,    298,    298,    298,    298,    298,    298,    298,
        // 656 - 663
        298,    298,    298,    298,    298,    298,    298,    298,
        // 664 - 671
        298,    298,    298,    298,    298,    298,    298,    298,
        // 672 - 679
        524,    524,    524,    524,    524,    524,    524,    524,
        // 680 - 687
        524,    524,    524,    524,    524,    524,    524,    524,
        // 688 - 695
        556,    556,    556,    556,    556,    556,    556,    556,
        // 696 - 703
        556,    556,    556,    556,    556,    556,    556,    556,
        // 704 - 711
        136,    136,    136,    136,    136,    136,    136,    136,
        // 712 - 719
        136,    136,    136,    136,    136,    136,    136,    136,
        // 720 - 727
        136,    136,    136,    136,    136,    136,    136,    136,
        // 728 - 735
        136,    136,    136,    136,    136,    136,    136,    136,
        // 736 - 743
        136,    136,    136,    136,    136,    136,    136,    136,
        // 744 - 751
        136,    136,    136,    136,    136,    136,    136,    136,
        // 752 - 759
        136,    136,    136,    136,    136,    136,    136,    136,
        // 760 - 767
        136,    136,    136,    136,    136,    136,    136,    136,
        // 768 - 775
        168,    168,    168,    168,    168,    168,    168,    168,
        // 776 - 783
        168,    168,    168,    168,    168,    168,    168,    168,
        // 784 - 791
        168,    168,    168,    168,    168,    168,    168,    168,
        // 792 - 799
        168,    168,    168,    168,    168,    168,    168,    168,
        // 800 - 807
        168,    168,    168,    168,    168,    168,    168,    168,
        // 808 - 815
        168,    168,    168,    168,    168,    168,    168,    168,
        // 816 - 823
        168,    168,    168,    168,    168,    168,    168,    168,
        // 824 - 831
        168,    168,    168,    168,    168,    168,    168,    168,
        // 832 - 839
        460,    460,    460,    460,    460,    460,    460,    460,
        // 840 - 847
        460,    460,    460,    460,    460,    460,    460,    460,
        // 848 - 855
        492,    492,    492,    492,    492,    492,    492,    492,
        // 856 - 863
        492,    492,    492,    492,    492,    492,    492,    492,
        // 864 - 871
        2059,   2059,   2059,   2059,   2059,   2059,   2059,   2059,
        // 872 - 879
        2059,   2059,   2059,   2059,   2059,   2059,   2059,   2059,
        // 880 - 887
        2059,   2059,   2059,   2059,   2059,   2059,   2059,   2059,
        // 888 - 895
        2059,   2059,   2059,   2059,   2059,   2059,   2059,   2059,
        // 896 - 903
        200,    200,    200,    200,    200,    200,    200,    200,
        // 904 - 911
        200,    200,    200,    200,    200,    200,    200,    200,
        // 912 - 919
        200,    200,    200,    200,    200,    200,    200,    200,
        // 920 - 927
        200,    200,    200,    200,    200,    200,    200,    200,
        // 928 - 935
        200,    200,    200,    200,    200,    200,    200,    200,
        // 936 - 943
        200,    200,    200,    200,    200,    200,    200,    200,
        // 944 - 951
        200,    200,    200,    200,    200,    200,    200,    200,
        // 952 - 959
        200,    200,    200,    200,    200,    200,    200,    200,
        // 960 - 967
        232,    232,    232,    232,    232,    232,    232,    232,
        // 968 - 975
        232,    232,    232,    232,    232,    232,    232,    232,
        // 976 - 983
        232,    232,    232,    232,    232,    232,    232,    232,
        // 984 - 991
        232,    232,    232,    232,    232,    232,    232,    232,
        // 992 - 999
        232,    232,    232,    232,    232,    232,    232,    232,
        // 1000 - 1007
        232,    232,    232,    232,    232,    232,    232,    232,
        // 1008 - 1015
        232,    232,    232,    232,    232,    232,    232,    232,
        // 1016 - 1023
        232,    232,    232,    232,    232,    232,    232,    232,
    };

    // Additional make up codes for both White and Black runs
    static short[] additionalMakeup = {
        28679,  28679,  31752,  (short)32777,
        (short)33801,  (short)34825,  (short)35849,  (short)36873,
        (short)29703,  (short)29703,  (short)30727,  (short)30727,
        (short)37897,  (short)38921,  (short)39945,  (short)40969
    };

    // Initial black run look up table, uses the first 4 bits of a code
    static short[] initBlack = {
        // 0 - 7
        3226,  6412,    200,    168,    38,     38,    134,    134,
        // 8 - 15
        100,    100,    100,    100,    68,     68,     68,     68
    };

    //
    static short[] twoBitBlack = {292, 260, 226, 226};   // 0 - 3

    // Main black run table, using the last 9 bits of possible 13 bit code
    static short[] black = {
        // 0 - 7
        62,     62,     30,     30,     0,      0,      0,      0,
        // 8 - 15
        0,      0,      0,      0,      0,      0,      0,      0,
        // 16 - 23
        0,      0,      0,      0,      0,      0,      0,      0,
        // 24 - 31
        0,      0,      0,      0,      0,      0,      0,      0,
        // 32 - 39
        3225,   3225,   3225,   3225,   3225,   3225,   3225,   3225,
        // 40 - 47
        3225,   3225,   3225,   3225,   3225,   3225,   3225,   3225,
        // 48 - 55
        3225,   3225,   3225,   3225,   3225,   3225,   3225,   3225,
        // 56 - 63
        3225,   3225,   3225,   3225,   3225,   3225,   3225,   3225,
        // 64 - 71
        588,    588,    588,    588,    588,    588,    588,    588,
        // 72 - 79
        1680,   1680,  20499,  22547,  24595,  26643,   1776,   1776,
        // 80 - 87
        1808,   1808, -24557, -22509, -20461, -18413,   1904,   1904,
        // 88 - 95
        1936,   1936, -16365, -14317,    782,    782,    782,    782,
        // 96 - 103
        814,    814,    814,    814, -12269, -10221,  10257,  10257,
        // 104 - 111
        12305,  12305,  14353,  14353,  16403,  18451,   1712,   1712,
        // 112 - 119
        1744,   1744,  28691,  30739, -32749, -30701, -28653, -26605,
        // 120 - 127
        2061,   2061,   2061,   2061,   2061,   2061,   2061,   2061,
        // 128 - 135
        424,    424,    424,    424,    424,    424,    424,    424,
        // 136 - 143
        424,    424,    424,    424,    424,    424,    424,    424,
        // 144 - 151
        424,    424,    424,    424,    424,    424,    424,    424,
        // 152 - 159
        424,    424,    424,    424,    424,    424,    424,    424,
        // 160 - 167
        750,    750,    750,    750,   1616,   1616,   1648,   1648,
        // 168 - 175
        1424,   1424,   1456,   1456,   1488,   1488,   1520,   1520,
        // 176 - 183
        1840,   1840,   1872,   1872,   1968,   1968,   8209,   8209,
        // 184 - 191
        524,    524,    524,    524,    524,    524,    524,    524,
        // 192 - 199
        556,    556,    556,    556,    556,    556,    556,    556,
        // 200 - 207
        1552,   1552,   1584,   1584,   2000,   2000,   2032,   2032,
        // 208 - 215
        976,    976,   1008,   1008,   1040,   1040,   1072,   1072,
        // 216 - 223
        1296,   1296,   1328,   1328,    718,    718,    718,    718,
        // 224 - 231
        456,    456,    456,    456,    456,    456,    456,    456,
        // 232 - 239
        456,    456,    456,    456,    456,    456,    456,    456,
        // 240 - 247
        456,    456,    456,    456,    456,    456,    456,    456,
        // 248 - 255
        456,    456,    456,    456,    456,    456,    456,    456,
        // 256 - 263
        326,    326,    326,    326,    326,    326,    326,    326,
        // 264 - 271
        326,    326,    326,    326,    326,    326,    326,    326,
        // 272 - 279
        326,    326,    326,    326,    326,    326,    326,    326,
        // 280 - 287
        326,    326,    326,    326,    326,    326,    326,    326,
        // 288 - 295
        326,    326,    326,    326,    326,    326,    326,    326,
        // 296 - 303
        326,    326,    326,    326,    326,    326,    326,    326,
        // 304 - 311
        326,    326,    326,    326,    326,    326,    326,    326,
        // 312 - 319
        326,    326,    326,    326,    326,    326,    326,    326,
        // 320 - 327
        358,    358,    358,    358,    358,    358,    358,    358,
        // 328 - 335
        358,    358,    358,    358,    358,    358,    358,    358,
        // 336 - 343
        358,    358,    358,    358,    358,    358,    358,    358,
        // 344 - 351
        358,    358,    358,    358,    358,    358,    358,    358,
        // 352 - 359
        358,    358,    358,    358,    358,    358,    358,    358,
        // 360 - 367
        358,    358,    358,    358,    358,    358,    358,    358,
        // 368 - 375
        358,    358,    358,    358,    358,    358,    358,    358,
        // 376 - 383
        358,    358,    358,    358,    358,    358,    358,    358,
        // 384 - 391
        490,    490,    490,    490,    490,    490,    490,    490,
        // 392 - 399
        490,    490,    490,    490,    490,    490,    490,    490,
        // 400 - 407
        4113,   4113,   6161,   6161,    848,    848,    880,    880,
        // 408 - 415
        912,    912,    944,    944,    622,    622,    622,    622,
        // 416 - 423
        654,    654,    654,    654,   1104,   1104,   1136,   1136,
        // 424 - 431
        1168,   1168,   1200,   1200,   1232,   1232,   1264,   1264,
        // 432 - 439
        686,    686,    686,    686,   1360,   1360,   1392,   1392,
        // 440 - 447
        12,     12,     12,     12,     12,     12,     12,     12,
        // 448 - 455
        390,    390,    390,    390,    390,    390,    390,    390,
        // 456 - 463
        390,    390,    390,    390,    390,    390,    390,    390,
        // 464 - 471
        390,    390,    390,    390,    390,    390,    390,    390,
        // 472 - 479
        390,    390,    390,    390,    390,    390,    390,    390,
        // 480 - 487
        390,    390,    390,    390,    390,    390,    390,    390,
        // 488 - 495
        390,    390,    390,    390,    390,    390,    390,    390,
        // 496 - 503
        390,    390,    390,    390,    390,    390,    390,    390,
        // 504 - 511
        390,    390,    390,    390,    390,    390,    390,    390,
    };

    static byte[] twoDCodes = {
        // 0 - 7
        80,     88,     23,     71,     30,     30,     62,     62,
        // 8 - 15
        4,      4,      4,      4,      4,      4,      4,      4,
        // 16 - 23
        11,     11,     11,     11,     11,     11,     11,     11,
        // 24 - 31
        11,     11,     11,     11,     11,     11,     11,     11,
        // 32 - 39
        35,     35,     35,     35,     35,     35,     35,     35,
        // 40 - 47
        35,     35,     35,     35,     35,     35,     35,     35,
        // 48 - 55
        51,     51,     51,     51,     51,     51,     51,     51,
        // 56 - 63
        51,     51,     51,     51,     51,     51,     51,     51,
        // 64 - 71
        41,     41,     41,     41,     41,     41,     41,     41,
        // 72 - 79
        41,     41,     41,     41,     41,     41,     41,     41,
        // 80 - 87
        41,     41,     41,     41,     41,     41,     41,     41,
        // 88 - 95
        41,     41,     41,     41,     41,     41,     41,     41,
        // 96 - 103
        41,     41,     41,     41,     41,     41,     41,     41,
        // 104 - 111
        41,     41,     41,     41,     41,     41,     41,     41,
        // 112 - 119
        41,     41,     41,     41,     41,     41,     41,     41,
        // 120 - 127
        41,     41,     41,     41,     41,     41,     41,     41,
    };

    /**
     * @param fillOrder   The fill order of the compressed data bytes.
     * @param w The width of the image in pixels
     * @param h The height of the image in pixels
     */
    public TIFFFaxDecoder(int fillOrder, int w, int h) 
    {
        this.fillOrder = fillOrder;
        this.w = w;
        this.h = h;

        this.bitPointer = 0;
        this.bytePointer = 0;
        this.prevChangingElems = new int[w + 1];
        this.currChangingElems = new int[w + 1];
    }

    // One-dimensional decoding methods

    public void decode1D(byte[] buffer, byte[] compData,
                         int startX, int height)
    {
        this.data = compData;

        int lineOffset = 0;
        int scanlineStride = (w + 7)/8;

        bitPointer = 0;
        bytePointer = 0;

        for (int i = 0; i < height; i++)
        {
            decodeNextScanline(buffer, lineOffset, startX);
            lineOffset += scanlineStride;
        }
    }

    public void decodeNextScanline(byte[] buffer,
                                   int lineOffset, int bitOffset) {
        int bits = 0, code = 0, isT = 0;
        int current, entry, twoBits;
        boolean isWhite = true;

        // Initialize starting of the changing elements array
        changingElemSize = 0;

        // While scanline not complete
        while (bitOffset < w) {
            while (isWhite) {
                // White run
                current = nextNBits(10);
                entry = white[current];

                // Get the 3 fields from the entry
                isT = entry & 0x0001;
                bits = (entry >>> 1) & 0x0f;

                if (bits == 12) {          // Additional Make up code
                    // Get the next 2 bits
                    twoBits = nextLesserThan8Bits(2);
                    // Consolidate the 2 new bits and last 2 bits into 4 bits
                    current = ((current << 2) & 0x000c) | twoBits;
                    entry = additionalMakeup[current];
                    bits = (entry >>> 1) & 0x07;     // 3 bits 0000 0111
                    code  = (entry >>> 4) & 0x0fff;  // 12 bits
                    bitOffset += code; // Skip white run

                    updatePointer(4 - bits);
                } else if (bits == 0) {     // ERROR
                    throw new RuntimeException("Invalid code encountered.");
                } else if (bits == 15) {    // EOL
                    throw new RuntimeException("EOL encountered in white run.");
                } else {
                    // 11 bits - 0000 0111 1111 1111 = 0x07ff
                    code = (entry >>> 5) & 0x07ff;
                    bitOffset += code;

                    updatePointer(10 - bits);
                    if (isT == 0) {
                        isWhite = false;
                        currChangingElems[changingElemSize++] = bitOffset;
                    }
                }
            }

            // Check whether this run completed one width, if so
            // advance to next byte boundary for compression = 2.
            if (bitOffset == w) {
                if (compression == 2) {
                    advancePointer();
                }
                break;
            }

            while (!isWhite) {
                // Black run
                current = nextLesserThan8Bits(4);
                entry = initBlack[current];

                // Get the 3 fields from the entry
                isT = entry & 0x0001;
                bits = (entry >>> 1) & 0x000f;
                code = (entry >>> 5) & 0x07ff;

                if (code == 100) {
                    current = nextNBits(9);
                    entry = black[current];

                    // Get the 3 fields from the entry
                    isT = entry & 0x0001;
                    bits = (entry >>> 1) & 0x000f;
                    code = (entry >>> 5) & 0x07ff;

                    if (bits == 12) {
                        // Additional makeup codes
                        updatePointer(5);
                        current = nextLesserThan8Bits(4);
                        entry = additionalMakeup[current];
                        bits = (entry >>> 1) & 0x07;     // 3 bits 0000 0111
                        code  = (entry >>> 4) & 0x0fff;  // 12 bits

                        setToBlack(buffer, lineOffset, bitOffset, code);
                        bitOffset += code;

                        updatePointer(4 - bits);
                    } else if (bits == 15) {
                        // EOL code
                        throw new RuntimeException("EOL encountered in black run.");
                    } else {
                        setToBlack(buffer, lineOffset, bitOffset, code);
                        bitOffset += code;

                        updatePointer(9 - bits);
                        if (isT == 0) {
                            isWhite = true;
                            currChangingElems[changingElemSize++] = bitOffset;
                        }
                    }
                } else if (code == 200) {
                    // Is a Terminating code
                    current = nextLesserThan8Bits(2);
                    entry = twoBitBlack[current];
                    code = (entry >>> 5) & 0x07ff;
                    bits = (entry >>> 1) & 0x0f;

                    setToBlack(buffer, lineOffset, bitOffset, code);
                    bitOffset += code;

                    updatePointer(2 - bits);
                    isWhite = true;
                    currChangingElems[changingElemSize++] = bitOffset;
                } else {
                    // Is a Terminating code
                    setToBlack(buffer, lineOffset, bitOffset, code);
                    bitOffset += code;

                    updatePointer(4 - bits);
                    isWhite = true;
                    currChangingElems[changingElemSize++] = bitOffset;
                }
            }

            // Check whether this run completed one width
            if (bitOffset == w) {
                if (compression == 2) {
                    advancePointer();
                }
                break;
            }
        }

        currChangingElems[changingElemSize++] = bitOffset;
    }

    // Two-dimensional decoding methods

    public void decode2D(byte[] buffer,
                         byte[] compData,
                         int startX,
                         int height,
                         long tiffT4Options) {
        this.data = compData;
        compression = 3;

        bitPointer = 0;
        bytePointer = 0;

        int scanlineStride = (w + 7)/8;

        int a0, a1, b1, b2;
        int[] b = new int[2];
        int entry, code, bits;
        boolean isWhite;
        int currIndex = 0;
        int[] temp;

        // fillBits - dealt with this in readEOL
        // 1D/2D encoding - dealt with this in readEOL

        // uncompressedMode - haven't dealt with this yet.


        oneD = (int)(tiffT4Options & 0x01);
        uncompressedMode = (int)((tiffT4Options & 0x02) >> 1);
        fillBits = (int)((tiffT4Options & 0x04) >> 2);

        // The data must start with an EOL code
        if (readEOL() != 1) {
            throw new RuntimeException("First scanline must be 1D encoded.");
        }

        int lineOffset = 0;
        int bitOffset;

        // Then the 1D encoded scanline data will occur, changing elements
        // array gets set.
        decodeNextScanline(buffer, lineOffset, startX);
        lineOffset += scanlineStride;

        for (int lines = 1; lines < height; lines++) {

            // Every line must begin with an EOL followed by a bit which
            // indicates whether the following scanline is 1D or 2D encoded.
            if (readEOL() == 0) {
                // 2D encoded scanline follows

                // Initialize previous scanlines changing elements, and
                // initialize current scanline's changing elements array
                temp = prevChangingElems;
                prevChangingElems = currChangingElems;
                currChangingElems = temp;
                currIndex = 0;

                // a0 has to be set just before the start of this scanline.
                a0 = -1;
                isWhite = true;
                bitOffset = startX;

                lastChangingElement = 0;

                while (bitOffset < w) {
                    // Get the next changing element
                    getNextChangingElement(a0, isWhite, b);

                    b1 = b[0];
                    b2 = b[1];

                    // Get the next seven bits
                    entry = nextLesserThan8Bits(7);

                    // Run these through the 2DCodes table
                    entry = (twoDCodes[entry] & 0xff);

                    // Get the code and the number of bits used up
                    code = (entry & 0x78) >>> 3;
                    bits = entry & 0x07;

                    if (code == 0) {
                        if (!isWhite) {
                            setToBlack(buffer, lineOffset, bitOffset,
                                       b2 - bitOffset);
                        }
                        bitOffset = a0 = b2;

                        // Set pointer to consume the correct number of bits.
                        updatePointer(7 - bits);
                    } else if (code == 1) {
                        // Horizontal
                        updatePointer(7 - bits);

                        // identify the next 2 codes.
                        int number;
                        if (isWhite) {
                            number = decodeWhiteCodeWord();
                            bitOffset += number;
                            currChangingElems[currIndex++] = bitOffset;

                            number = decodeBlackCodeWord();
                            setToBlack(buffer, lineOffset, bitOffset, number);
                            bitOffset += number;
                            currChangingElems[currIndex++] = bitOffset;
                        } else {
                            number = decodeBlackCodeWord();
                            setToBlack(buffer, lineOffset, bitOffset, number);
                            bitOffset += number;
                            currChangingElems[currIndex++] = bitOffset;

                            number = decodeWhiteCodeWord();
                            bitOffset += number;
                            currChangingElems[currIndex++] = bitOffset;
                        }

                        a0 = bitOffset;
                    } else if (code <= 8) {
                        // Vertical
                        a1 = b1 + (code - 5);

                        currChangingElems[currIndex++] = a1;

                        // We write the current color till a1 - 1 pos,
                        // since a1 is where the next color starts
                        if (!isWhite) {
                            setToBlack(buffer, lineOffset, bitOffset,
                                       a1 - bitOffset);
                        }
                        bitOffset = a0 = a1;
                        isWhite = !isWhite;

                        updatePointer(7 - bits);
                    } else {
                        throw new RuntimeException("Invalid code encountered while decoding 2D group 3 compressed data.");
                    }
                }

                // Add the changing element beyond the current scanline for the
                // other color too
                currChangingElems[currIndex++] = bitOffset;
                changingElemSize = currIndex;
            } else {
                // 1D encoded scanline follows
                decodeNextScanline(buffer, lineOffset, startX);
            }

            lineOffset += scanlineStride;
        }
    }

    public synchronized void decodeT6(byte[] buffer,
                                      byte[] compData,
                                      int startX,
                                      int height,
                                      long tiffT6Options,
                                      boolean encodedByteAlign) {
        this.data = compData;
        compression = 4;

        bitPointer = 0;
        bytePointer = 0;

        int scanlineStride = (w + 7)/8;

        int a0, a1, b1, b2;
        int entry, code, bits;
        boolean isWhite;
        int currIndex;
        int[] temp;

        // Return values from getNextChangingElement
        int[] b = new int[2];

        // uncompressedMode - have written some code for this, but this
        // has not been tested due to lack of test images using this optional

        uncompressedMode = (int)((tiffT6Options & 0x02) >> 1);

        // Local cached reference
        int[] cce = currChangingElems;

        // Assume invisible preceding row of all white pixels and insert
        // both black and white changing elements beyond the end of this
        // imaginary scanline.
        changingElemSize = 0;
        cce[changingElemSize++] = w;
        cce[changingElemSize++] = w;

        int lineOffset = 0;
        int bitOffset;

        for (int lines = 0; lines < height; lines++) {
            if (encodedByteAlign && bitPointer != 0)
            {
                bitPointer = 0;
                bytePointer++;
            }            
            // a0 has to be set just before the start of the scanline.
            a0 = -1;
            isWhite = true;

            // Assign the changing elements of the previous scanline to
            // prevChangingElems and start putting this new scanline's
            // changing elements into the currChangingElems.
            temp = prevChangingElems;
            prevChangingElems = currChangingElems;
            cce = currChangingElems = temp;
            currIndex = 0;

            // Start decoding the scanline at startX in the raster
            bitOffset = startX;

            // Reset search start position for getNextChangingElement
            lastChangingElement = 0;

            // Till one whole scanline is decoded
            while (bitOffset < w) {
                // Get the next changing element
                getNextChangingElement(a0, isWhite, b);
                b1 = b[0];
                b2 = b[1];

                // Get the next seven bits
                entry = nextLesserThan8Bits(7);
                // Run these through the 2DCodes table
                entry = (twoDCodes[entry] & 0xff);

                // Get the code and the number of bits used up
                code = (entry & 0x78) >>> 3;
                bits = entry & 0x07;

                if (code == 0) { // Pass
                    // We always assume WhiteIsZero format for fax.
                    if (!isWhite) {
                        setToBlack(buffer, lineOffset, bitOffset,
                                   b2 - bitOffset);
                    }
                    bitOffset = a0 = b2;

                    // Set pointer to only consume the correct number of bits.
                    updatePointer(7 - bits);
                } else if (code == 1) { // Horizontal
                    // Set pointer to only consume the correct number of bits.
                    updatePointer(7 - bits);

                    // identify the next 2 alternating color codes.
                    int number;
                    if (isWhite) {
                        // Following are white and black runs
                        number = decodeWhiteCodeWord();
                        bitOffset += number;
                        cce[currIndex++] = bitOffset;

                        number = decodeBlackCodeWord();
                        setToBlack(buffer, lineOffset, bitOffset, number);
                        bitOffset += number;
                        cce[currIndex++] = bitOffset;
                    } else {
                        // First a black run and then a white run follows
                        number = decodeBlackCodeWord();
                        setToBlack(buffer, lineOffset, bitOffset, number);
                        bitOffset += number;
                        cce[currIndex++] = bitOffset;

                        number = decodeWhiteCodeWord();
                        bitOffset += number;
                        cce[currIndex++] = bitOffset;
                    }

                    a0 = bitOffset;
                } else if (code <= 8) { // Vertical
                    a1 = b1 + (code - 5);
                    cce[currIndex++] = a1;

                    // We write the current color till a1 - 1 pos,
                    // since a1 is where the next color starts
                    if (!isWhite) {
                        setToBlack(buffer, lineOffset, bitOffset,
                                   a1 - bitOffset);
                    }
                    bitOffset = a0 = a1;
                    isWhite = !isWhite;

                    updatePointer(7 - bits);
                } else if (code == 11) {
                    if (nextLesserThan8Bits(3) != 7) {
                        throw new RuntimeException("Invalid code encountered while decoding 2D group 4 compressed data.");
                    }

                    int zeros = 0;
                    boolean exit = false;

                    while (!exit) {
                        while (nextLesserThan8Bits(1) != 1) {
                            zeros++;
                        }

                        if (zeros > 5) {
                            // Exit code

                            // Zeros before exit code
                            zeros = zeros - 6;

                            if (!isWhite && (zeros > 0)) {
                                cce[currIndex++] = bitOffset;
                            }

                            // Zeros before the exit code
                            bitOffset += zeros;
                            if (zeros > 0) {
                                // Some zeros have been written
                                isWhite = true;
                            }

                            // Read in the bit which specifies the color of
                            // the following run
                            if (nextLesserThan8Bits(1) == 0) {
                                if (!isWhite) {
                                    cce[currIndex++] = bitOffset;
                                }
                                isWhite = true;
                            } else {
                                if (isWhite) {
                                    cce[currIndex++] = bitOffset;
                                }
                                isWhite = false;
                            }

                            exit = true;
                        }

                        if (zeros == 5) {
                            if (!isWhite) {
                                cce[currIndex++] = bitOffset;
                            }
                            bitOffset += zeros;

                            // Last thing written was white
                            isWhite = true;
                        } else {
                            bitOffset += zeros;

                            cce[currIndex++] = bitOffset;
                            setToBlack(buffer, lineOffset, bitOffset, 1);
                            ++bitOffset;

                            // Last thing written was black
                            isWhite = false;
                        }

                    }
                } else {
                    throw new RuntimeException("Invalid code encountered while decoding 2D group 4 compressed data.");
                }
            }

            // Add the changing element beyond the current scanline for the
            // other color too
            cce[currIndex++] = bitOffset;

            // Number of changing elements in this scanline.
            changingElemSize = currIndex;

            lineOffset += scanlineStride;
        }
    }

    private void setToBlack(byte[] buffer,
                            int lineOffset, int bitOffset,
                            int numBits) {
        int bitNum = 8*lineOffset + bitOffset;
        int lastBit = bitNum + numBits;

        int byteNum = bitNum >> 3;

        // Handle bits in first byte
        int shift = bitNum & 0x7;
        if (shift > 0) {
            int maskVal = 1 << (7 - shift);
            byte val = buffer[byteNum];
            while (maskVal > 0 && bitNum < lastBit) {
                val |= maskVal;
                maskVal >>= 1;
                ++bitNum;
            }
            buffer[byteNum] = val;
        }

        // Fill in 8 bits at a time
        byteNum = bitNum >> 3;
        while (bitNum < lastBit - 7) {
            buffer[byteNum++] = (byte)255;
            bitNum += 8;
        }

        // Fill in remaining bits
        while (bitNum < lastBit) {
            byteNum = bitNum >> 3;
            buffer[byteNum] |= 1 << (7 - (bitNum & 0x7));
            ++bitNum;
        }
    }

    // Returns run length
    private int decodeWhiteCodeWord() {
        int current, entry, bits, isT, twoBits, code = -1;
        int runLength = 0;
        boolean isWhite = true;

        while (isWhite) {
            current = nextNBits(10);
            entry = white[current];

            // Get the 3 fields from the entry
            isT = entry & 0x0001;
            bits = (entry >>> 1) & 0x0f;

            if (bits == 12) {           // Additional Make up code
                // Get the next 2 bits
                twoBits = nextLesserThan8Bits(2);
                // Consolidate the 2 new bits and last 2 bits into 4 bits
                current = ((current << 2) & 0x000c) | twoBits;
                entry = additionalMakeup[current];
                bits = (entry >>> 1) & 0x07;     // 3 bits 0000 0111
                code = (entry >>> 4) & 0x0fff;   // 12 bits
                runLength += code;
                updatePointer(4 - bits);
            } else if (bits == 0) {     // ERROR
                throw new RuntimeException("Invalid code encountered.");
            } else if (bits == 15) {    // EOL
                throw new RuntimeException("EOL encountered in white run.");
            } else {
                // 11 bits - 0000 0111 1111 1111 = 0x07ff
                code = (entry >>> 5) & 0x07ff;
                runLength += code;
                updatePointer(10 - bits);
                if (isT == 0) {
                    isWhite = false;
                }
            }
        }

        return runLength;
    }

    // Returns run length
    private int decodeBlackCodeWord() {
        int current, entry, bits, isT, code = -1;
        int runLength = 0;
        boolean isWhite = false;

        while (!isWhite) {
            current = nextLesserThan8Bits(4);
            entry = initBlack[current];

            // Get the 3 fields from the entry
            isT = entry & 0x0001;
            bits = (entry >>> 1) & 0x000f;
            code = (entry >>> 5) & 0x07ff;

            if (code == 100) {
                current = nextNBits(9);
                entry = black[current];

                // Get the 3 fields from the entry
                isT = entry & 0x0001;
                bits = (entry >>> 1) & 0x000f;
                code = (entry >>> 5) & 0x07ff;

                if (bits == 12) {
                    // Additional makeup codes
                    updatePointer(5);
                    current = nextLesserThan8Bits(4);
                    entry = additionalMakeup[current];
                    bits = (entry >>> 1) & 0x07;     // 3 bits 0000 0111
                    code  = (entry >>> 4) & 0x0fff;  // 12 bits
                    runLength += code;

                    updatePointer(4 - bits);
                } else if (bits == 15) {
                    // EOL code
                    throw new RuntimeException("EOL encountered in black run.");
                } else {
                    runLength += code;
                    updatePointer(9 - bits);
                    if (isT == 0) {
                        isWhite = true;
                    }
                }
            } else if (code == 200) {
                // Is a Terminating code
                current = nextLesserThan8Bits(2);
                entry = twoBitBlack[current];
                code = (entry >>> 5) & 0x07ff;
                runLength += code;
                bits = (entry >>> 1) & 0x0f;
                updatePointer(2 - bits);
                isWhite = true;
            } else {
                // Is a Terminating code
                runLength += code;
                updatePointer(4 - bits);
                isWhite = true;
            }
        }

        return runLength;
    }

    private int readEOL() {
        if (fillBits == 0) {
            if (nextNBits(12) != 1) {
                throw new RuntimeException("Scanline must begin with EOL.");
            }
        } else if (fillBits == 1) {

            // First EOL code word xxxx 0000 0000 0001 will occur
            // As many fill bits will be present as required to make
            // the EOL code of 12 bits end on a byte boundary.

            int bitsLeft = 8 - bitPointer;

            if (nextNBits(bitsLeft) != 0) {
                throw new RuntimeException("All fill bits preceding EOL code must be 0.");
            }

            // If the number of bitsLeft is less than 8, then to have a 12
            // bit EOL sequence, two more bytes are certainly going to be
            // required. The first of them has to be all zeros, so ensure
            // that.
            if (bitsLeft < 4) {
                if (nextNBits(8) != 0) {
                    throw new RuntimeException("All fill bits preceding EOL code must be 0.");
                }
            }

            // There might be a random number of fill bytes with 0s, so
            // loop till the EOL of 0000 0001 is found, as long as all
            // the bytes preceding it are 0's.
            int n;
            while ((n = nextNBits(8)) != 1) {

                // If not all zeros
                if (n != 0) {
                    throw new RuntimeException("All fill bits preceding EOL code must be 0.");
                }
            }
        }

        // If one dimensional encoding mode, then always return 1
        if (oneD == 0) {
            return 1;
        } else {
            // Otherwise for 2D encoding mode,
            // The next one bit signifies 1D/2D encoding of next line.
            return nextLesserThan8Bits(1);
        }
    }

    private void getNextChangingElement(int a0, boolean isWhite, int[] ret) {
        // Local copies of instance variables
        int[] pce = this.prevChangingElems;
        int ces = this.changingElemSize;

        // If the previous match was at an odd element, we still
        // have to search the preceeding element.
        // int start = lastChangingElement & ~0x1;
        int start = lastChangingElement > 0 ? lastChangingElement - 1 : 0;
        if (isWhite) {
            start &= ~0x1; // Search even numbered elements
        } else {
            start |= 0x1; // Search odd numbered elements
        }

        int i = start;
        for (; i < ces; i += 2) {
            int temp = pce[i];
            if (temp > a0) {
                lastChangingElement = i;
                ret[0] = temp;
                break;
            }
        }

        if (i + 1 < ces) {
            ret[1] = pce[i + 1];
        }
    }

    private int nextNBits(int bitsToGet) {
        byte b, next, next2next;
        int l = data.length - 1;
        int bp = this.bytePointer;

        if (fillOrder == 1) {
            b = data[bp];

            if (bp == l) {
                next = 0x00;
                next2next = 0x00;
            } else if ((bp + 1) == l) {
                next = data[bp + 1];
                next2next = 0x00;
            } else {
                next = data[bp + 1];
                next2next = data[bp + 2];
            }
        } else if (fillOrder == 2) {
            b = flipTable[data[bp] & 0xff];

            if (bp == l) {
                next = 0x00;
                next2next = 0x00;
            } else if ((bp + 1) == l) {
                next = flipTable[data[bp + 1] & 0xff];
                next2next = 0x00;
            } else {
                next = flipTable[data[bp + 1] & 0xff];
                next2next = flipTable[data[bp + 2] & 0xff];
            }
        } else {
            throw new RuntimeException("TIFF_FILL_ORDER tag must be either 1 or 2.");
        }

        int bitsLeft = 8 - bitPointer;
        int bitsFromNextByte = bitsToGet - bitsLeft;
        int bitsFromNext2NextByte = 0;
        if (bitsFromNextByte > 8) {
            bitsFromNext2NextByte = bitsFromNextByte - 8;
            bitsFromNextByte = 8;
        }

        bytePointer++;

        int i1 = (b & table1[bitsLeft]) << (bitsToGet - bitsLeft);
        int i2 = (next & table2[bitsFromNextByte]) >>> (8 - bitsFromNextByte);

        int i3 = 0;
        if (bitsFromNext2NextByte != 0) {
            i2 <<= bitsFromNext2NextByte;
            i3 = (next2next & table2[bitsFromNext2NextByte]) >>>
                (8 - bitsFromNext2NextByte);
            i2 |= i3;
            bytePointer++;
            bitPointer = bitsFromNext2NextByte;
        } else {
            if (bitsFromNextByte == 8) {
                bitPointer = 0;
                bytePointer++;
            } else {
                bitPointer = bitsFromNextByte;
            }
        }

        int i = i1 | i2;
        return i;
    }

    private int nextLesserThan8Bits(int bitsToGet) {
        byte b, next;
        int l = data.length - 1;
        int bp = this.bytePointer;

        if (fillOrder == 1) {
            b = data[bp];
            if (bp == l) {
                next = 0x00;
            } else {
                next = data[bp + 1];
            }
        } else if (fillOrder == 2) {
            b = flipTable[data[bp] & 0xff];
            if (bp == l) {
                next = 0x00;
            } else {
                next = flipTable[data[bp + 1] & 0xff];
            }
        } else {
            throw new RuntimeException("TIFF_FILL_ORDER tag must be either 1 or 2.");
        }

        int bitsLeft = 8 - bitPointer;
        int bitsFromNextByte = bitsToGet - bitsLeft;

        int shift = bitsLeft - bitsToGet;
        int i1, i2;
        if (shift >= 0) {
            i1 = (b & table1[bitsLeft]) >>> shift;
            bitPointer += bitsToGet;
            if (bitPointer == 8) {
                bitPointer = 0;
                bytePointer++;
            }
        } else {
            i1 = (b & table1[bitsLeft]) << (-shift);
            i2 = (next & table2[bitsFromNextByte]) >>> (8 - bitsFromNextByte);

            i1 |= i2;
            bytePointer++;
            bitPointer = bitsFromNextByte;
        }

        return i1;
    }

    // Move pointer backwards by given amount of bits
    private void updatePointer(int bitsToMoveBack) {
        int i = bitPointer - bitsToMoveBack;

        if (i < 0) {
            bytePointer--;
            bitPointer = 8 + i;
        } else {
            bitPointer = i;
        }
    }

    // Move to the next byte boundary
    private boolean advancePointer() {
        if (bitPointer != 0) {
            bytePointer++;
            bitPointer = 0;
        }

        return true;
    }
}

