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rsa fixes and refactors
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@TwFlem
TwFlem committed Dec 6, 2023
1 parent 5ee364b commit 7468d73
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Showing 3 changed files with 76 additions and 65 deletions.
88 changes: 40 additions & 48 deletions bwt/rsa_bitvector.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,68 +5,60 @@ import "math/bits"
// TODO: doc what rsa is, why these DSAs, and why we take in a bit vector
// TODO: clarks select
type rsaBitVector struct {
bv bitvector
totalOnesRank int
jrc []chunk
jrBitsPerChunk int
jrBitsPerSubChunk int
oneSelectMap map[int]int
zeroSelectMap map[int]int
bv bitvector
totalOnesRank int
jrc []chunk
jrSubChunksPerChunk int
jrBitsPerChunk int
jrBitsPerSubChunk int
oneSelectMap map[int]int
zeroSelectMap map[int]int
}

// TODO: talk about why bv should never be modidifed after building the RSA bit vector
func newRSABitVectorFromBitVector(bv bitvector) rsaBitVector {
jacobsonRankChunks, jrBitsPerChunk, jrBitsPerSubChunk, totalOnesRank := buildJacobsonRank(bv)
jacobsonRankChunks, jrSubChunksPerChunk, jrBitsPerSubChunk, totalOnesRank := buildJacobsonRank(bv)
ones, zeros := buildSelectMaps(bv)

return rsaBitVector{
bv: bv,
totalOnesRank: totalOnesRank,
jrc: jacobsonRankChunks,
jrBitsPerChunk: jrBitsPerChunk,
jrBitsPerSubChunk: jrBitsPerSubChunk,
oneSelectMap: ones,
zeroSelectMap: zeros,
bv: bv,
totalOnesRank: totalOnesRank,
jrc: jacobsonRankChunks,
jrSubChunksPerChunk: jrSubChunksPerChunk,
jrBitsPerChunk: jrSubChunksPerChunk * jrBitsPerSubChunk,
jrBitsPerSubChunk: jrBitsPerSubChunk,
oneSelectMap: ones,
zeroSelectMap: zeros,
}
}

func (rsa rsaBitVector) Rank(val bool, i int) int {
c := 0
for j := 0; j < i; j++ {
if rsa.bv.getBit(j) {
c++
if i > rsa.bv.len()-1 {
if val {
return rsa.totalOnesRank
}
return rsa.bv.len() - rsa.totalOnesRank
}

chunkPos := (i / rsa.jrBitsPerChunk)
chunk := rsa.jrc[chunkPos]

subChunkPos := (i % rsa.jrBitsPerChunk) / rsa.jrBitsPerSubChunk
subChunk := chunk.subChunks[subChunkPos]

bitOffset := i % rsa.jrBitsPerSubChunk

bitSet := rsa.bv.getBitSet(chunkPos*rsa.jrSubChunksPerChunk + subChunkPos)

shiftRightAmount := uint64(rsa.jrBitsPerSubChunk - bitOffset)
if val {
return c
remaining := bitSet >> shiftRightAmount
return chunk.onesCumulativeRank + subChunk.onesCumulativeRank + bits.OnesCount64(remaining)
}
return i - c
// if i > rsa.bv.len()-1 {
// if val {
// return rsa.totalOnesRank
// }
// return rsa.bv.len() - rsa.totalOnesRank
// }
//
// chunkPos := (i / rsa.jrBitsPerChunk)
// chunk := rsa.jrc[chunkPos]
//
// subChunkPos := (i % rsa.jrBitsPerChunk) / rsa.jrBitsPerSubChunk
// subChunk := chunk.subChunks[subChunkPos]
//
// bitOffset := i % rsa.jrBitsPerSubChunk
//
// bitSet := rsa.bv.getBitSet(chunkPos*len(rsa.jrc) + subChunkPos)
//
// shiftRightAmount := uint64(rsa.jrBitsPerSubChunk - bitOffset)
// if val {
// remaining := bitSet >> shiftRightAmount
// return chunk.onesCumulativeRank + subChunk.onesCumulativeRank + bits.OnesCount64(remaining)
// }
// remaining := ^bitSet >> shiftRightAmount
//
// // cumulative ranks for 0 should just be the sum of the compliment of cumulative ranks for 1
// return (chunkPos*rsa.jrBitsPerChunk - chunk.onesCumulativeRank) + (subChunkPos*rsa.jrBitsPerSubChunk - subChunk.onesCumulativeRank) + bits.OnesCount64(remaining)
remaining := ^bitSet >> shiftRightAmount

// cumulative ranks for 0 should just be the sum of the compliment of cumulative ranks for 1
return (chunkPos*rsa.jrBitsPerChunk - chunk.onesCumulativeRank) + (subChunkPos*rsa.jrBitsPerSubChunk - subChunk.onesCumulativeRank) + bits.OnesCount64(remaining)
}

func (rsa rsaBitVector) Select(val bool, rank int) (i int, ok bool) {
Expand Down Expand Up @@ -130,7 +122,7 @@ func buildJacobsonRank(inBv bitvector) (jacobsonRankChunks []chunk, numOfSubChun
})
}

return jacobsonRankChunks, numOfSubChunksPerChunk * wordSize, wordSize, totalRank
return jacobsonRankChunks, numOfSubChunksPerChunk, wordSize, totalRank
}

// TODO: talk about how this could be improved memory wise. Talk about how clarks select exists, but keeping it "simple for now" but maybe worth
Expand Down
51 changes: 36 additions & 15 deletions bwt/rsa_bitvector_test.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -164,27 +164,50 @@ func TestRSARank_singleCompleteChunk(t *testing.T) {
}

func TestRSARank_multipleChunks(t *testing.T) {
numBitsToTruncate := 17
initialNumberOfBits := wordSize*15 - numBitsToTruncate
rsa := newTestRSAFromWords(initialNumberOfBits,
rsa := newTestRSAFromWords((8*4+3)*64,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,

0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff,
0x0000000000000000,

0xffffffffffffffff,
0x0000000000000000,
0xffffffffffffffff, // this should end up getting truncated
0xffffffffffffffff,
)

testCases := []rsaRankTestCase{
Expand All @@ -207,7 +230,10 @@ func TestRSARank_multipleChunks(t *testing.T) {

{true, 832, 448}, {false, 832, 384},
{true, 896, 448}, {false, 896, 448},
{true, 896 + wordSize - numBitsToTruncate - 1, 448 + wordSize - numBitsToTruncate - 1}, {false, 896 + wordSize - numBitsToTruncate - 1, 448},

{true, 1024, 512}, {false, 1024, 512},

{true, 2048, 1024}, {false, 2048, 1024},
}

for _, tc := range testCases {
Expand Down Expand Up @@ -310,16 +336,11 @@ func TestRSASelect_notOk(t *testing.T) {

func newTestRSAFromWords(sizeInBits int, wordsToCopy ...uint64) rsaBitVector {
bv := newBitVector(sizeInBits)
for i := 0; i < len(wordsToCopy); i++ {
w := wordsToCopy[i]
for j := 0; j < 64; j++ {
if i*64+j == sizeInBits {
break
}
mask := uint64(1) << uint64(63-j%64)
bit := w&mask != 0
bv.setBit(i*64+j, bit)
}
for i := 0; i < sizeInBits; i++ {
w := wordsToCopy[i/64]
mask := uint64(1) << uint64(63-i%64)
bit := w&mask != 0
bv.setBit(i, bit)
}
return newRSABitVectorFromBitVector(bv)
}
2 changes: 0 additions & 2 deletions bwt/wavelet_test.go
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
package bwt

import (
"fmt"
"strings"
"testing"
)
Expand Down Expand Up @@ -182,7 +181,6 @@ func TestWaveletTree_Access_Reconstruction(t *testing.T) {

for _, str := range testCases {
wt := NewWaveletTreeFromString(str)
fmt.Println(len(str))
actual := ""
for i := 0; i < len(str); i++ {
actual += string(wt.Access(i))
Expand Down

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