X-Git-Url: https://wimlib.net/git/?a=blobdiff_plain;f=src%2Flz_sarray.c;h=881c3c6c15718abd86df6888e51881e193c2ebbf;hb=d6fc4b4b31c5d85847b5f471988e5ce734c31a70;hp=1428ebaac815c5c3b1e79ed65088f8170151408c;hpb=0b655dd071e313311df0333af2522de5bdc264bf;p=wimlib

diff --git a/src/lz_sarray.c b/src/lz_sarray.c
index 1428ebaa..881c3c6c 100644
--- a/src/lz_sarray.c
+++ b/src/lz_sarray.c
@@ -1,7 +1,7 @@
 /*
  * lz_sarray.c
  *
- * Suffix array match-finder for LZ (Lempel-Ziv) compression.
+ * Suffix array match-finder for Lempel-Ziv compression.
  */
 
 /*
@@ -40,89 +40,35 @@
 #include "divsufsort/divsufsort.h"
 #include <string.h>
 
-/* Initialize the suffix array match-finder with the specified parameters.
+/* If ENABLE_LZ_DEBUG is defined, verify that the suffix array satisfies its
+ * definition.
  *
- * After initialization, it can be used for any number of input strings of
- * length less than or equal to @max_window_size.  */
-bool
-lz_sarray_init(struct lz_sarray *mf,
-	       input_idx_t max_window_size,
-	       input_idx_t min_match_len,
-	       input_idx_t max_match_len,
-	       u32 max_matches_to_consider,
-	       u32 max_matches_to_return)
-{
-	mf->max_window_size = max_window_size;
-	mf->min_match_len = min_match_len;
-	mf->max_match_len = max_match_len;
-	mf->max_matches_to_consider = max_matches_to_consider;
-	mf->max_matches_to_return = max_matches_to_return;
-
-	mf->SA = MALLOC(3U * max_window_size * sizeof(mf->SA[0]));
-	if (mf->SA == NULL)
-		return false;
-
-	mf->salink = MALLOC(max_window_size * sizeof(mf->salink[0]));
-	if (mf->salink == NULL)
-		return false;
-
-	return true;
-}
-
-/* Free memory allocated for the suffix array match-finder.  */
-void
-lz_sarray_destroy(struct lz_sarray *mf)
-{
-	FREE(mf->SA);
-	FREE(mf->salink);
-}
-
-/* Initialize the suffix array match-finder for the specified input.  */
-void
-lz_sarray_load_window(struct lz_sarray *mf, const u8 window[],
-		      input_idx_t window_size)
+ * @SA		The constructed suffix array.
+ * @T		The original data.
+ * @found	Temporary 'bool' array of length @n.
+ * @n		Length of the data (length of @SA, @T, and @found arrays).
+ *
+ * WARNING: this is for debug use only as it does not necessarily run in linear
+ * time!!!  */
+static void
+verify_suffix_array(const input_idx_t SA[restrict],
+		    const u8 T[restrict],
+		    bool found[restrict],
+		    input_idx_t n)
 {
-	/* Load variables  */
-	const u8 * const restrict T = window;
-	const input_idx_t n = window_size;
-	const input_idx_t max_match_len = mf->max_match_len;
-	input_idx_t * const restrict SA = mf->SA;
-	input_idx_t * const restrict ISA = mf->ISA = SA + window_size;
-	input_idx_t * const restrict LCP = mf->LCP = ISA + window_size;
-	struct salink * const restrict link = mf->salink;
-
-	/* Compute SA (Suffix Array).  */
-	{
-		/* ISA and link are used as temporary space.  */
-		LZ_ASSERT(mf->max_window_size * sizeof(ISA[0]) >= 256 * sizeof(saidx_t));
-		LZ_ASSERT(mf->max_window_size * 2 * sizeof(link[0]) >= 256 * 256 * sizeof(saidx_t));
-
-		if (sizeof(input_idx_t) == sizeof(saidx_t)) {
-			divsufsort(T, SA, n, (saidx_t*)ISA, (saidx_t*)link);
-		} else {
-			saidx_t sa[n];
-			divsufsort(T, sa, n, (saidx_t*)ISA, (saidx_t*)link);
-			for (input_idx_t i = 0; i < n; i++)
-				SA[i] = sa[i];
-		}
-	}
-
 #ifdef ENABLE_LZ_DEBUG
-
-	LZ_ASSERT(n > 0);
-
-	/* Verify suffix array.  */
-	{
-		bool found[n];
-		ZERO_ARRAY(found);
-		for (input_idx_t r = 0; r < n; r++) {
-			input_idx_t i = SA[r];
-			LZ_ASSERT(i < n);
-			LZ_ASSERT(!found[i]);
-			found[i] = true;
-		}
+	/* Ensure the SA contains exactly one of each i in [0, n - 1].  */
+	for (input_idx_t i = 0; i < n; i++)
+		found[i] = false;
+	for (input_idx_t r = 0; r < n; r++) {
+		input_idx_t i = SA[r];
+		LZ_ASSERT(i < n);
+		LZ_ASSERT(!found[i]);
+		found[i] = true;
 	}
 
+	/* Ensure the suffix with rank r is lexicographically lesser than the
+	 * suffix with rank (r + 1) for all r in [0, n - 2].  */
 	for (input_idx_t r = 0; r < n - 1; r++) {
 
 		input_idx_t i1 = SA[r];
@@ -131,44 +77,77 @@ lz_sarray_load_window(struct lz_sarray *mf, const u8 window[],
 		input_idx_t n1 = n - i1;
 		input_idx_t n2 = n - i2;
 
-		LZ_ASSERT(memcmp(&T[i1], &T[i2], min(n1, n2)) <= 0);
+		int res = memcmp(&T[i1], &T[i2], min(n1, n2));
+		LZ_ASSERT(res < 0 || (res == 0 && n1 < n2));
 	}
-	LZ_DEBUG("Verified SA (len %u)", n);
-#endif /* ENABLE_LZ_DEBUG */
+#endif /* ENABLE_LZ_DEBUG  */
+}
+
+/* Compute the inverse suffix array @ISA from the suffix array @SA in linear
+ * time.
+ *
+ * Whereas the suffix array is a mapping from suffix rank to suffix position,
+ * the inverse suffix array is a mapping from suffix position to suffix rank.
+ */
+static void
+compute_inverse_suffix_array(input_idx_t ISA[restrict],
+			     const input_idx_t SA[restrict],
+			     input_idx_t n)
+{
+	input_idx_t r;
 
-	/* Compute ISA (Inverse Suffix Array)  */
-	for (input_idx_t r = 0; r < n; r++)
+	for (r = 0; r < n; r++)
 		ISA[SA[r]] = r;
+}
 
-	/* Compute LCP (longest common prefix) array.
-	 *
-	 * Algorithm adapted from Kasai et al. 2001: "Linear-Time
-	 * Longest-Common-Prefix Computation in Suffix Arrays and Its
-	 * Applications".  */
-	{
-		input_idx_t h = 0;
-		for (input_idx_t i = 0; i < n; i++) {
-			input_idx_t r = ISA[i];
-			if (r > 0) {
-				input_idx_t j = SA[r - 1];
-
-				input_idx_t lim = min(n - i, n - j);
-
-				while (h < lim && T[i + h] == T[j + h])
-					h++;
-				LCP[r] = h;
-				if (h > 0)
-					h--;
-			}
+
+/* Compute the LCP (Longest Common Prefix) array in linear time.
+ *
+ * LCP[r] will be the length of the longest common prefix between the suffixes
+ * with positions SA[r - 1] and  SA[r].  LCP[0] will be undefined.
+ *
+ * Algorithm adapted from Kasai et al. 2001: "Linear-Time Longest-Common-Prefix
+ * Computation in Suffix Arrays and Its Applications".  Modified slightly to
+ * take into account that with bytes in the real world, there is no unique
+ * symbol at the end of the string.  */
+static void
+compute_lcp_array(input_idx_t LCP[restrict],
+		  const input_idx_t SA[restrict],
+		  const input_idx_t ISA[restrict],
+		  const u8 T[restrict],
+		  input_idx_t n)
+{
+	input_idx_t h, i, r, j, lim;
+
+	h = 0;
+	for (i = 0; i < n; i++) {
+		r = ISA[i];
+		if (r > 0) {
+			j = SA[r - 1];
+			lim = min(n - i, n - j);
+
+			while (h < lim && T[i + h] == T[j + h])
+				h++;
+			LCP[r] = h;
+			if (h > 0)
+				h--;
 		}
 	}
+}
 
+/* If ENABLE_LZ_DEBUG is defined, verify that the LCP (Longest Common Prefix)
+ * array satisfies its definition.
+ *
+ * WARNING: this is for debug use only as it does not necessarily run in linear
+ * time!!!  */
+static void
+verify_lcp_array(input_idx_t LCP[restrict],
+		 const input_idx_t SA[restrict],
+		 const u8 T[restrict],
+		 input_idx_t n)
+{
 #ifdef ENABLE_LZ_DEBUG
-	/* Verify LCP array.  */
 	for (input_idx_t r = 0; r < n - 1; r++) {
-		LZ_ASSERT(ISA[SA[r]] == r);
-		LZ_ASSERT(ISA[SA[r + 1]] == r + 1);
-
 		input_idx_t i1 = SA[r];
 		input_idx_t i2 = SA[r + 1];
 		input_idx_t lcp = LCP[r + 1];
@@ -183,18 +162,36 @@ lz_sarray_load_window(struct lz_sarray *mf, const u8 window[],
 			LZ_ASSERT(T[i1 + lcp] != T[i2 + lcp]);
 	}
 #endif /* ENABLE_LZ_DEBUG */
+}
 
-	/* Compute salink.next and salink.lcpnext.
-	 *
-	 * Algorithm adapted from Crochemore et al. 2009:
-	 * "LPF computation revisited".
-	 *
-	 * Note: we cap lcpnext to the maximum match length so that the
-	 * match-finder need not worry about it later.  */
+/* Initialize the SA link array in linear time.
+ *
+ * This is similar to computing the LPF (Longest Previous Factor) array, which
+ * is addressed in several papers.  In particular the algorithms below are based
+ * on Crochemore et al. 2009: "LPF computation revisited".  However, this
+ * match-finder does not actually compute or use the LPF array per se.  Rather,
+ * this function sets up some information necessary to compute the LPF array,
+ * but later lz_sarray_get_matches() actually uses this information to search
+ * the suffix array directly and can keep searching beyond the first (longest)
+ * match whose length would be placed in the LPF array.  This difference from
+ * the theoretical work is necessary because in many real compression formats
+ * matches take variable numbers of bits to encode, so a decent parser needs to
+ * consider more than just the longest match with unspecified offset.
+ *
+ * Note: We cap the lcpprev and lcpnext values to the maximum match length so
+ * that the match-finder need not worry about it later, in the inner loop.
+ */
+static void
+init_salink(struct salink link[restrict],
+	    const input_idx_t LCP[restrict],
+	    const input_idx_t SA[restrict],
+	    const u8 T[restrict],
+	    input_idx_t n,
+	    input_idx_t max_match_len)
+{
+	/* Compute salink.next and salink.lcpnext.  */
 	link[n - 1].next = ~(input_idx_t)0;
-	link[n - 1].prev = ~(input_idx_t)0;
 	link[n - 1].lcpnext = 0;
-	link[n - 1].lcpprev = 0;
 	for (input_idx_t r = n - 2; r != ~(input_idx_t)0; r--) {
 		input_idx_t t = r + 1;
 		input_idx_t l = LCP[t];
@@ -204,25 +201,11 @@ lz_sarray_load_window(struct lz_sarray *mf, const u8 window[],
 		}
 		link[r].next = t;
 		link[r].lcpnext = min(l, max_match_len);
-		LZ_ASSERT(t == ~(input_idx_t)0 || l <= n - SA[t]);
-		LZ_ASSERT(l <= n - SA[r]);
-		if (t == ~(input_idx_t)0)
-			LZ_ASSERT(l == 0);
-		else
-			LZ_ASSERT(memcmp(&T[SA[r]], &T[SA[t]], l) == 0);
 	}
 
-	/* Compute salink.prev and salink.lcpprev.
-	 *
-	 * Algorithm adapted from Crochemore et al. 2009:
-	 * "LPF computation revisited".
-	 *
-	 * Note: we cap lcpprev to the maximum match length so that the
-	 * match-finder need not worry about it later.  */
+	/* Compute salink.prev and salink.lcpprev.  */
 	link[0].prev = ~(input_idx_t)0;
-	link[0].next = ~(input_idx_t)0;
 	link[0].lcpprev = 0;
-	link[0].lcpnext = 0;
 	for (input_idx_t r = 1; r < n; r++) {
 		input_idx_t t = r - 1;
 		input_idx_t l = LCP[r];
@@ -232,14 +215,251 @@ lz_sarray_load_window(struct lz_sarray *mf, const u8 window[],
 		}
 		link[r].prev = t;
 		link[r].lcpprev = min(l, max_match_len);
-		LZ_ASSERT(t == ~(input_idx_t)0 || l <= n - SA[t]);
-		LZ_ASSERT(l <= n - SA[r]);
-		if (t == ~(input_idx_t)0)
-			LZ_ASSERT(l == 0);
-		else
-			LZ_ASSERT(memcmp(&T[SA[r]], &T[SA[t]], l) == 0);
 	}
+}
+
+/* If ENABLE_LZ_DEBUG is defined, verify the values computed by init_salink().
+ *
+ * WARNING: this is for debug use only as it does not necessarily run in linear
+ * time!!!  */
+static void
+verify_salink(const struct salink link[],
+	      const input_idx_t SA[],
+	      const u8 T[],
+	      input_idx_t n,
+	      input_idx_t max_match_len)
+{
+#ifdef ENABLE_LZ_DEBUG
+	for (input_idx_t r = 0; r < n; r++) {
+		for (input_idx_t prev = r; ; ) {
+			if (prev == 0) {
+				LZ_ASSERT(link[r].prev == ~(input_idx_t)0);
+				LZ_ASSERT(link[r].lcpprev == 0);
+				break;
+			}
+
+			prev--;
+
+			if (SA[prev] < SA[r]) {
+				LZ_ASSERT(link[r].prev == prev);
+				LZ_ASSERT(link[r].lcpprev <= n - SA[prev]);
+				LZ_ASSERT(link[r].lcpprev <= n - SA[r]);
+				LZ_ASSERT(link[r].lcpprev <= max_match_len);
+				LZ_ASSERT(0 == memcmp(&T[SA[prev]],
+						      &T[SA[r]],
+						      link[r].lcpprev));
+				if (link[r].lcpprev < n - SA[prev] &&
+				    link[r].lcpprev < n - SA[r] &&
+				    link[r].lcpprev < max_match_len)
+				{
+					LZ_ASSERT(T[SA[prev] + link[r].lcpprev] !=
+						  T[SA[r] + link[r].lcpprev]);
+				}
+				break;
+			}
+		}
+
+		for (input_idx_t next = r; ; ) {
+			if (next == n - 1) {
+				LZ_ASSERT(link[r].next == ~(input_idx_t)0);
+				LZ_ASSERT(link[r].lcpnext == 0);
+				break;
+			}
+
+			next++;
+
+			if (SA[next] < SA[r]) {
+				LZ_ASSERT(link[r].next == next);
+				LZ_ASSERT(link[r].lcpnext <= n - SA[next]);
+				LZ_ASSERT(link[r].lcpnext <= n - SA[r]);
+				LZ_ASSERT(link[r].lcpnext <= max_match_len);
+				LZ_ASSERT(0 == memcmp(&T[SA[next]],
+						      &T[SA[r]],
+						      link[r].lcpnext));
+				if (link[r].lcpnext < n - SA[next] &&
+				    link[r].lcpnext < n - SA[r] &&
+				    link[r].lcpnext < max_match_len)
+				{
+					LZ_ASSERT(T[SA[next] + link[r].lcpnext] !=
+						  T[SA[r] + link[r].lcpnext]);
+
+				}
+				break;
+			}
+		}
+	}
+#endif
+}
+
+/*
+ * Initialize the suffix array match-finder.
+ *
+ * @mf
+ *	The suffix array match-finder structure to initialize.  This structure
+ *	is expected to be zeroed before this function is called.  In the case
+ *	that this function fails, lz_sarray_destroy() should be called to free
+ *	any memory that may have been allocated.
+ *
+ * @max_window_size
+ *	The maximum window size to support.
+ *
+ *	In the current implementation, the memory needed will be
+ *	(6 * sizeof(input_idx_t) * @max_window_size) bytes.
+ *	For (sizeof(input_idx_t) == 4) that's 24 times the window size.
+ *
+ *	Memory is saved by saving neither the original window nor the LCP
+ *	(Longest Common Prefix) array; otherwise 29 times the window size would
+ *	be required.  (In practice the compressor will likely keep the original
+ *	window around anyway, although based on this property of the
+ *	match-finder it theoretically it could overwrite it with the compressed
+ *	data.)
+ *
+ * @min_match_len
+ *	The minimum length of each match to be found.
+ *
+ * @max_match_len
+ *	The maximum length of each match to be found.
+ *
+ * @max_matches_to_consider
+ *	The maximum number of matches to consider at each position.  This should
+ *	be greater than @max_matches_to_return because @max_matches_to_consider
+ *	counts all the returned matches as well as matches of equal length to
+ *	returned matches that were not returned.  This parameter bounds the
+ *	amount of work the match-finder does at any one position.  This could be
+ *	anywhere from 1 to 100+ depending on the compression ratio and
+ *	performance desired.
+ *
+ * @max_matches_to_return
+ *	Maximum number of matches to return at each position.  Because of the
+ *	suffix array search algorithm, the order in which matches are returned
+ *	will be from longest to shortest, so cut-offs due to this parameter will
+ *	only result in shorter matches being discarded.  This parameter could be
+ *	anywhere from 1 to (@max_match_len - @min_match_len + 1) depending on
+ *	the compression performance desired.  However, making it even moderately
+ *	large (say, greater than 3) may not be very helpful due to the property
+ *	that the matches are returned from longest to shortest.  But the main
+ *	thing to keep in mind is that if the compressor decides to output a
+ *	shorter-than-possible match, ideally it would be best to choose the best
+ *	match of the desired length rather than truncate a longer match to that
+ *	length.
+ *
+ * After initialization, the suffix-array match-finder can be used for any
+ * number of input strings (windows) of length less than or equal to
+ * @max_window_size by successive calls to lz_sarray_load_window().
+ *
+ * Returns %true on success, or %false if sufficient memory could not be
+ * allocated.  See the note for @max_window_size above regarding the needed
+ * memory size.
+ */
+bool
+lz_sarray_init(struct lz_sarray *mf,
+	       input_idx_t max_window_size,
+	       input_idx_t min_match_len,
+	       input_idx_t max_match_len,
+	       u32 max_matches_to_consider,
+	       u32 max_matches_to_return)
+{
+	mf->max_window_size = max_window_size;
+	mf->min_match_len = min_match_len;
+	mf->max_match_len = max_match_len;
+	mf->max_matches_to_consider = max_matches_to_consider;
+	mf->max_matches_to_return = max_matches_to_return;
+
+	/* SA and ISA will share the same storage block.  */
+	mf->SA = MALLOC(2 * max_window_size * sizeof(mf->SA[0]));
+	if (mf->SA == NULL)
+		return false;
 
+	mf->salink = MALLOC(max_window_size * sizeof(mf->salink[0]));
+	if (mf->salink == NULL)
+		return false;
+
+	return true;
+}
+
+u64
+lz_sarray_get_needed_memory(input_idx_t max_window_size)
+{
+	return (u64)6 * sizeof(input_idx_t) * max_window_size;
+}
+
+/*
+ * Prepare the suffix array match-finder to scan the specified window for
+ * matches.
+ *
+ * @mf	Suffix array match-finder previously initialized with lz_sarray_init().
+ *
+ * @T	Window, or "block", in which to find matches.
+ *
+ * @n	Size of window in bytes.  This must be positive and less than or equal
+ *	to the @max_window_size passed to lz_sarray_init().
+ *
+ * This function runs in linear time (relative to @n).
+ */
+void
+lz_sarray_load_window(struct lz_sarray *mf, const u8 T[], input_idx_t n)
+{
+	input_idx_t *ISA, *LCP;
+
+	LZ_ASSERT(n > 0 && n <= mf->max_window_size);
+
+	/* Compute SA (Suffix Array).
+	 *
+	 * divsufsort() needs temporary space --- one array with 256 spaces and
+	 * one array with 65536 spaces.  The implementation has been modified
+	 * from the original to use the provided temporary space instead of
+	 * allocating its own.
+	 *
+	 * We also check at build-time that divsufsort() uses the same integer
+	 * size expected by this code.  Unfortunately, divsufsort breaks if
+	 * 'sa_idx_t' is defined to be a 16-bit integer; however, that would
+	 * limit blocks to only 65536 bytes anyway.  */
+	LZ_ASSERT(mf->max_window_size * sizeof(mf->SA[0])
+		  >= 256 * sizeof(saidx_t));
+	LZ_ASSERT(mf->max_window_size * sizeof(mf->salink[0])
+		  >= 256 * 256 * sizeof(saidx_t));
+	BUILD_BUG_ON(sizeof(input_idx_t) != sizeof(saidx_t));
+
+	divsufsort(T, mf->SA, n, (saidx_t*)&mf->SA[n], (saidx_t*)mf->salink);
+
+	BUILD_BUG_ON(sizeof(bool) > sizeof(mf->salink[0]));
+	verify_suffix_array(mf->SA, T, (bool*)mf->salink, n);
+
+	/* Compute ISA (Inverse Suffix Array) in a preliminary position.
+	 *
+	 * This is just a trick to save memory.  Since LCP is unneeded after
+	 * this function, it can be computed in any available space.  The
+	 * storage for the ISA is the best choice because the ISA can be built
+	 * quickly in salink for now, then re-built in its real location at the
+	 * end.  This is probably worth it because computing the ISA from the SA
+	 * is very fast, and since this match-finder is memory-hungry we'd like
+	 * to save as much memory as possible.  */
+	ISA = (input_idx_t*)mf->salink;
+	compute_inverse_suffix_array(ISA, mf->SA, n);
+
+	/* Compute LCP (Longest Common Prefix) array.  */
+	LCP = mf->SA + n;
+	compute_lcp_array(LCP, mf->SA, ISA, T, n);
+	verify_lcp_array(LCP, mf->SA, T, n);
+
+	/* Initialize suffix array links.  */
+	init_salink(mf->salink, LCP, mf->SA, T, n, mf->max_match_len);
+	verify_salink(mf->salink, mf->SA, T, n, mf->max_match_len);
+
+	/* Compute ISA (Inverse Suffix Array) in its final position.  */
+	ISA = mf->SA + n;
+	compute_inverse_suffix_array(ISA, mf->SA, n);
+
+	/* Save new variables and return.  */
+	mf->ISA = ISA;
 	mf->cur_pos = 0;
 	mf->window_size = n;
 }
+
+/* Free memory allocated for the suffix array match-finder.  */
+void
+lz_sarray_destroy(struct lz_sarray *mf)
+{
+	FREE(mf->SA);
+	FREE(mf->salink);
+}