/* Copyright (C) 2001-2006 Artifex Software, Inc.
   All Rights Reserved.
  
   This software is provided AS-IS with no warranty, either express or
   implied.

   This software is distributed under license and may not be copied, modified
   or distributed except as expressly authorized under the terms of that
   license.  Refer to licensing information at http://www.artifex.com/
   or contact Artifex Software, Inc.,  7 Mt. Lassen Drive - Suite A-134,
   San Rafael, CA  94903, U.S.A., +1(415)492-9861, for further information.
*/

/* $Id: sbwbs.c,v 1.2 2010/07/10 22:02:26 Arabidopsis Exp $ */
/* Burrows/Wheeler block sorting compression filters */
#include "stdio_.h"
#include "memory_.h"
#include <stdlib.h>		/* for qsort */
#include "gdebug.h"
#include "strimpl.h"
#include "sfilter.h"
#include "sbwbs.h"

/* ------ Common code for streams that buffer a block ------ */

private_st_buffered_state();

/* Initialize */
static void
s_buffered_set_defaults(stream_state * st)
{
    stream_buffered_state *const ss = (stream_buffered_state *) st;

    /* Clear pointers */
    ss->buffer = 0;
}
static int
s_buffered_no_block_init(stream_state * st)
{
    stream_buffered_state *const ss = (stream_buffered_state *) st;

    ss->buffer = 0;
    ss->filling = true;
    ss->bpos = 0;
    return 0;
}
static int
s_buffered_block_init(stream_state * st)
{
    stream_buffered_state *const ss = (stream_buffered_state *) st;

    s_buffered_no_block_init(st);
    ss->buffer = gs_alloc_bytes(st->memory, ss->BlockSize, "buffer");
    if (ss->buffer == 0)
	return ERRC;
/****** WRONG ******/
    return 0;
}

/* Continue filling the buffer if needed. */
/* Return 0 if the buffer isn't full yet, 1 if it is full or if */
/* we reached the end of input data. */
/* In the latter case, also set filling = false. */
/* Note that this procedure doesn't take pw as an argument. */
static int
s_buffered_process(stream_state * st, stream_cursor_read * pr, bool last)
{
    stream_buffered_state *const ss = (stream_buffered_state *) st;
    register const byte *p = pr->ptr;
    const byte *rlimit = pr->limit;
    uint count = rlimit - p;
    uint left = ss->bsize - ss->bpos;

    if (!ss->filling)
	return 1;
    if (left < count)
	count = left;
    if_debug3('w', "[w]buffering %d bytes to position %d, last = %s\n",
	      count, ss->bpos, (last ? "true" : "false"));
    memcpy(ss->buffer + ss->bpos, p + 1, count);
    pr->ptr = p += count;
    ss->bpos += count;
    if (ss->bpos == ss->bsize || (p == rlimit && last)) {
	ss->filling = false;
	return 1;
    }
    return 0;
}

/* Release */
static void
s_buffered_release(stream_state * st)
{
    stream_buffered_state *const ss = (stream_buffered_state *) st;

    gs_free_object(st->memory, ss->buffer, "buffer");
}

/* ------ Common code for Burrows/Wheeler block sorting filters ------ */

private_st_BWBS_state();
static void s_BWBS_release(stream_state *);

/* Set default parameter values (actually, just clear pointers). */
static void
s_BWBS_set_defaults(stream_state * st)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;

    s_buffered_set_defaults(st);
    ss->offsets = 0;
}

/* Initialize */
static int
bwbs_init(stream_state * st, uint osize)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;
    int code;

    ss->bsize = ss->BlockSize;
    code = s_buffered_block_init(st);
    if (code != 0)
	return code;
    ss->offsets = (void *)gs_alloc_bytes(st->memory, osize,
					 "BWBlockSort offsets");
    if (ss->offsets == 0) {
	s_BWBS_release(st);
	return ERRC;
/****** WRONG ******/
    }
    ss->I = -1;			/* haven't read I yet */
    return 0;
}

/* Release the filter. */
static void
s_BWBS_release(stream_state * st)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;

    gs_free_object(st->memory, ss->offsets, "BWBlockSort offsets");
    s_buffered_release(st);
}

/* ------ BWBlockSortEncode ------ */

/* Initialize */
static int
s_BWBSE_init(stream_state * st)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;

    return bwbs_init(st, ss->BlockSize * sizeof(int));
}

/* Compare two rotated strings for sorting. */
static stream_BWBS_state *bwbs_compare_ss;
static int
bwbs_compare_rotations(const void *p1, const void *p2)
{
    const byte *buffer = bwbs_compare_ss->buffer;
    const byte *s1 = buffer + *(const int *)p1;
    const byte *s2 = buffer + *(const int *)p2;
    const byte *start1;
    const byte *end;
    int swap;

    if (*s1 != *s2)
	return (*s1 < *s2 ? -1 : 1);
    if (s1 < s2)
	swap = 1;
    else {
	const byte *t = s1;

	s1 = s2;
	s2 = t;
	swap = -1;
    }
    start1 = s1;
    end = buffer + bwbs_compare_ss->N;
    for (s1++, s2++; s2 < end; s1++, s2++)
	if (*s1 != *s2)
	    return (*s1 < *s2 ? -swap : swap);
    s2 = buffer;
    for (; s1 < end; s1++, s2++)
	if (*s1 != *s2)
	    return (*s1 < *s2 ? -swap : swap);
    s1 = buffer;
    for (; s1 < start1; s1++, s2++)
	if (*s1 != *s2)
	    return (*s1 < *s2 ? -swap : swap);
    return 0;
}
/* Sort the strings. */
static void
bwbse_sort(const byte * buffer, uint * indices, int N)
{
    offsets_full Cs;

#define C Cs.v
    /* Sort the strings.  We start with a radix sort. */
    uint sum = 0, j, ch;

    memset(C, 0, sizeof(Cs));
    for (j = 0; j < N; j++)
	C[buffer[j]]++;
    for (ch = 0; ch <= 255; ch++) {
	sum += C[ch];
	C[ch] = sum - C[ch];
    }
    for (j = 0; j < N; j++)
	indices[C[buffer[j]]++] = j;
    /* Now C[ch] = the number of strings that start */
    /* with a character less than or equal to ch. */
    sum = 0;
    /* qsort each bucket produced by the radix sort. */
    for (ch = 0; ch <= 255; sum = C[ch], ch++)
	qsort(indices + sum, C[ch] - sum,
	      sizeof(*indices),
	      bwbs_compare_rotations);
#undef C
}

/* Encode a buffer */
static int
s_BWBSE_process(stream_state * st, stream_cursor_read * pr,
		stream_cursor_write * pw, bool last)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;
    register byte *q = pw->ptr;
    byte *wlimit = pw->limit;
    uint wcount = wlimit - q;
    uint *indices = ss->offsets;

    if (ss->filling) {
	int status, j, N;
	byte *buffer = ss->buffer;
	if (wcount < sizeof(int) * 2)
	        return 1;

	/* Continue filling the buffer. */
	status = s_buffered_process(st, pr, last);
	if (!status)
	    return 0;
	ss->N = N = ss->bpos;
	/* We reverse the string before encoding it, */
	/* so it will come out of the decoder correctly. */
	for (j = N / 2 - 1; j >= 0; j--) {
	    byte *p0 = &buffer[j];
	    byte *p1 = &buffer[N - 1 - j];
	    byte b = *p0;

	    *p0 = *p1;
	    *p1 = b;
	}
	/* Save st in a static, because that's the only way */
	/* we can pass it to the comparison procedure (ugh). */
	bwbs_compare_ss = ss;
	/* Sort the strings. */
	bwbse_sort(buffer, indices, N);
	/* Find the unrotated string. */
	for (j = 0; j < N; j++)
	    if (indices[j] == 0) {
		ss->I = j;
		break;
	    }
	for (j = sizeof(int); --j >= 0;)
	    *++q = (byte) (N >> (j * 8));
	for (j = sizeof(int); --j >= 0;)
	    *++q = (byte) (ss->I >> (j * 8));
	ss->bpos = 0;
    }
    /* We're reading out of the buffer, writing the permuted string. */
    while (q < wlimit && ss->bpos < ss->N) {
	int i = indices[ss->bpos++];

	*++q = ss->buffer[(i == 0 ? ss->N - 1 : i - 1)];
    }
    if (ss->bpos == ss->N) {
	ss->filling = true;
	ss->bpos = 0;
    }
    pw->ptr = q;
    if (q == wlimit)
	return 1;
    return 0;
}

/* Stream template */
const stream_template s_BWBSE_template = {
    &st_BWBS_state, s_BWBSE_init, s_BWBSE_process, sizeof(int) * 2, 1,
    s_BWBS_release, s_BWBS_set_defaults
};

/* ------ BWBlockSortDecode ------ */

#define SHORT_OFFSETS

#ifdef SHORT_OFFSETS

/*
 * Letting S[0..N-1] be the data block before depermutation, we need
 * a table P[0..N-1] that maps the index i to O(S[i],i), where O(c,i) is
 * the number of occurrences of c in S before position i.
 * We observe that for a fixed c, O(c,i) is monotonic with i,
 * and falls in the range 0 .. i; consequently, if 0 <= i <= j,
 * 0 <= O(c,j) - O(c,i) <= j - i.  Proceeding from this observation,
 * rather than allocate an entire int to each entry of P,
 * we construct three tables as follows:
 *      P2[k,c] = O(c,k*65536) for k = 0 .. (N-1)/65536;
 *              each entry requires an int.
 *      P1[k,c] = O(c,k*4096) - P2[k/16,c] for k = 0 .. (N-1)/4096;
 *              each entry falls in the range 0 .. 15*4096 and hence
 *              requires 16 bits.
 *      P0[i] = O(S[i],i) - P1[i/4096,S[i]] for i = 0 .. N-1;
 *              each entry falls in the range 0 .. 4095 and hence
 *              requires 12 bits.
 * Since the value we need in the decompression loop is actually
 * P[i] + C[S[i]], where C[c] is the sum of O(0,N) ... O(c-1,N),
 * we add C[c] into P2[k,c] for all k.
 */
							/*typedef struct { uint v[256]; } offsets_full; *//* in sbwbs.h */
typedef struct {
    bits16 v[256];
} offsets_4k;

#if arch_sizeof_int > 2
#  define ceil_64k(n) (((n) + 0xffff) >> 16)
#else
#  define ceil_64k(n) 1
#endif
#define ceil_4k(n) (((n) + 0xfff) >> 12)
#define offset_space(bsize)\
  (ceil_64k(bsize) * sizeof(offsets_full) +\
   ceil_4k(bsize) * sizeof(offsets_4k) +\
   ((bsize + 1) >> 1) * 3)

#else /* !SHORT_OFFSETS */

#define offset_space(bsize)\
  (bsize * sizeof(int))

#endif /* (!)SHORT_OFFSETS */

/* Initialize */
static int
s_BWBSD_init(stream_state * st)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;
    uint bsize = ss->BlockSize;

    return bwbs_init(st, offset_space(bsize));
}

/* Construct the decoding tables. */

#ifdef SHORT_OFFSETS

static void
bwbsd_construct_offsets(stream_BWBS_state * sst, offsets_full * po64k,
			offsets_4k * po4k, byte * po1, int N)
{
    offsets_full Cs;

#define C Cs.v
    uint i1;
    byte *b = sst->buffer;
    offsets_full *p2 = po64k - 1;
    offsets_4k *p1 = po4k;
    byte *p0 = po1;

    memset(C, 0, sizeof(Cs));
    for (i1 = 0; i1 < ceil_4k(N); i1++, p1++) {
	int j;

	if (!(i1 & 15))
	    *++p2 = Cs;
	for (j = 0; j < 256; j++)
	    p1->v[j] = C[j] - p2->v[j];
	j = (N + 1 - (i1 << 12)) >> 1;
	if (j > 4096 / 2)
	    j = 4096 / 2;
	for (; j > 0; j--, b += 2, p0 += 3) {
	    byte b0 = b[0];
	    uint d0 = C[b0]++ - (p1->v[b0] + p2->v[b0]);
	    byte b1 = b[1];
	    uint d1 = C[b1]++ - (p1->v[b1] + p2->v[b1]);

	    p0[0] = d0 >> 4;
	    p0[1] = (byte) ((d0 << 4) + (d1 >> 8));
	    p0[2] = (byte) d1;
	}
    }
    /* If the block length is odd, discount the extra byte. */
    if (N & 1)
	C[sst->buffer[N]]--;
    /* Compute the cumulative totals in C. */
    {
	int sum = 0, ch;

	for (ch = 0; ch <= 255; ch++) {
	    sum += C[ch];
	    C[ch] = sum - C[ch];
	}
    }
    /* Add the C values back into the 64K table, */
    /* which saves an addition of C[b] in the decoding loop. */
    {
	int i2, ch;

	for (p2 = po64k, i2 = ceil_64k(N); i2 > 0; p2++, i2--)
	    for (ch = 0; ch < 256; ch++)
		p2->v[ch] += C[ch];
    }
#undef C
}

#else /* !SHORT_OFFSETS */

static void
bwbsd_construct_offsets(stream_BWBS_state * sst, int *po, int N)
{
    offsets_full Cs;

#define C Cs.v
    uint i;
    byte *b = sst->buffer;
    int *p = po;

    memset(C, 0, sizeof(Cs));
    for (i = 0; i < N; i++, p++, b++)
	*p = C[*b]++;
    /* Compute the cumulative totals in C. */
    {
	int sum = 0, ch;

	for (ch = 0; ch <= 255; ch++) {
	    sum += C[ch];
	    C[ch] = sum - C[ch];
	}
    }
    /* Add the C values back into the offsets. */
    for (i = 0, b = sst->buffer, p = po; i < N; i++, b++, p++)
	*p += C[*b];
#undef C
}

#endif /* (!)SHORT_OFFSETS */

/* Decode a buffer */
static int
s_BWBSD_process(stream_state * st, stream_cursor_read * pr,
		stream_cursor_write * pw, bool last)
{
    stream_BWBS_state *const ss = (stream_BWBS_state *) st;
    register const byte *p = pr->ptr;
    const byte *rlimit = pr->limit;
    uint count = rlimit - p;
    register byte *q = pw->ptr;
    byte *wlimit = pw->limit;

#ifdef SHORT_OFFSETS
    uint BlockSize = ss->BlockSize;
    offsets_full *po64k = ss->offsets;
    offsets_4k *po4k = (offsets_4k *) (po64k + ceil_64k(BlockSize));
    byte *po1 = (byte *) (po4k + ceil_4k(BlockSize));

#else /* !SHORT_OFFSETS */
    int *po = ss->offsets;

#endif /* (!)SHORT_OFFSETS */

    if (ss->I < 0) {		/* Read block parameters */
	int I, N, j;
	if (count < sizeof(int) * 2)
	        return 0;
	for (N = 0, j = 0; j < sizeof(int); j++)

	    N = (N << 8) + *++p;
	for (I = 0, j = 0; j < sizeof(int); j++)

	    I = (I << 8) + *++p;
	ss->N = N;
	ss->I = I;
	if_debug2('w', "[w]N=%d I=%d\n", N, I);
	pr->ptr = p;
	if (N < 0 || N > ss->BlockSize || I < 0 || I >= N)
	    return ERRC;
	if (N == 0)
	    return EOFC;
	count -= sizeof(int) * 2;

	ss->bpos = 0;
	ss->bsize = N;
    }
    if (ss->filling) {		/* Continue filling the buffer. */
	if (!s_buffered_process(st, pr, last))
	    return 0;
	/* Construct the inverse sort order. */
#ifdef SHORT_OFFSETS
	bwbsd_construct_offsets(ss, po64k, po4k, po1, ss->bsize);
#else /* !SHORT_OFFSETS */
	bwbsd_construct_offsets(ss, po, ss->bsize);
#endif /* (!)SHORT_OFFSETS */
	ss->bpos = 0;
	ss->i = ss->I;
    }
    /* We're reading out of the buffer. */
    while (q < wlimit && ss->bpos < ss->bsize) {
	int i = ss->i;
	byte b = ss->buffer[i];

#ifdef SHORT_OFFSETS
	uint d;
	const byte *pd = &po1[(i >> 1) + i];

	*++q = b;
	if (!(i & 1))
	    d = ((uint) pd[0] << 4) + (pd[1] >> 4);
	else
	    d = ((pd[0] & 0xf) << 8) + pd[1];
	ss->i = po64k[i >> 16].v[b] + po4k[i >> 12].v[b] + d;
#else /* !SHORT_OFFSETS */
	*++q = b;
	ss->i = po[i];
#endif /* (!)SHORT_OFFSETS */
	ss->bpos++;
    }
    if (ss->bpos == ss->bsize) {
	ss->I = -1;
	ss->filling = true;
    }
    pw->ptr = q;
    if (q == wlimit)
	return 1;
    return 0;
}

/* Stream template */
const stream_template s_BWBSD_template = {
    &st_BWBS_state, s_BWBSD_init, s_BWBSD_process, 1, sizeof(int) * 2,
    s_BWBS_release, s_BWBS_set_defaults
};
