Add hamming distance calculation to bloom filters

Godeps/Godeps.json

@@ -217,6 +217,11 @@
 			"ImportPath": "github.com/mtchavez/jenkins",
 			"Rev": "5a816af6ef21ef401bff5e4b7dd255d63400f497"
 		},
+		{
+			"ImportPath": "github.com/steakknife/hamming",
+			"Comment": "0.0.2-2-g9ad4a62",
+			"Rev": "9ad4a620e3d573267a083c892f2b42a39302153b"
+		},
 		{
 			"ImportPath": "github.com/syndtr/goleveldb/leveldb",
 			"Rev": "87e4e645d80ae9c537e8f2dee52b28036a5dd75e"

Godeps/_workspace/src/github.com/steakknife/hamming/README.md

@@ -0,0 +1,3 @@
+Copyright (c) 2014 Barry Allard
+
+MIT license

Godeps/_workspace/src/github.com/steakknife/hamming/hamming.go

@@ -0,0 +1,38 @@
+package hamming
+
+// SSE4.x PopCnt is 10x slower
+// References: check out Hacker's Delight
+
+const (
+	m1  uint64 = 0x5555555555555555 //binary: 0101...
+	m2  uint64 = 0x3333333333333333 //binary: 00110011..
+	m4  uint64 = 0x0f0f0f0f0f0f0f0f //binary:  4 zeros,  4 ones ...
+	m8  uint64 = 0x00ff00ff00ff00ff //binary:  8 zeros,  8 ones ...
+	m16 uint64 = 0x0000ffff0000ffff //binary: 16 zeros, 16 ones ...
+	m32 uint64 = 0x00000000ffffffff //binary: 32 zeros, 32 ones
+	hff uint64 = 0xffffffffffffffff //binary: all ones
+	h01 uint64 = 0x0101010101010101 //the sum of 256 to the power of 0,1,2,3...
+)
+
+var table = [256]byte{0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4, 1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7, 1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7, 3, 4, 4, 5, 4, 5, 5, 6, 4, 5, 5, 6, 5, 6, 6, 7, 4, 5, 5, 6, 5, 6, 6, 7, 5, 6, 6, 7, 6, 7, 7, 8}
+
+// hamming distance of two uint64's
+func Uint64(x, y uint64) int {
+	return CountBitsUint64(x ^ y)
+}
+
+// hamming distance of two bytes
+func Byte(x, y byte) int {
+	return CountBitsByte(x ^ y)
+}
+
+func CountBitsUint64(x uint64) int {
+	x -= (x >> 1) & m1             // put count of each 2 bits into those 2 bits
+	x = (x & m2) + ((x >> 2) & m2) // put count of each 4 bits into those 4 bits
+	x = (x + (x >> 4)) & m4        // put count of each 8 bits into those 8 bits
+	return int((x * h01) >> 56)    // returns left 8 bits of x + (x<<8) + (x<<16) + (x<<24) + ...
+}
+
+func CountBitsByte(x byte) int {
+	return int(table[x])
+}

Godeps/_workspace/src/github.com/steakknife/hamming/hamming_test.go

@@ -0,0 +1,88 @@
+package hamming
+
+import (
+  "testing"
+)
+
+type testCountBitsUint64Case struct {
+  x uint64
+  n int
+}
+
+type testCountBitsByteCase struct {
+  x byte
+  n int
+}
+
+var testCountBitsByteCases = []testCountBitsByteCase{
+  {0x00, 0},
+  {0x01, 1},
+  {0x02, 1},
+  {0x03, 2},
+  {0xaa, 4},
+  {0x55, 4},
+  {0x7f, 7},
+  {0xff, 8},
+}
+
+var testCountBitsUint64Cases = []testCountBitsUint64Case{
+  {0x00, 0},
+  {0x01, 1},
+  {0x02, 1},
+  {0x03, 2},
+  {0xaa, 4},
+  {0x55, 4},
+  {0x7f, 7},
+  {0xff, 8},
+  {0xffff, 16},
+  {0xffffffff, 32},
+  {0x1ffffffff, 33},
+  {0x3ffffffff, 34},
+  {0x7ffffffff, 35},
+  {0xfffffffff, 36},
+  {0x3fffffffffffffff, 62},
+  {0x7fffffffffffffff, 63},
+  {0xffffffffffffffff, 64},
+}
+
+func TestCountBitByte(t *testing.T) {
+  for _, c := range testCountBitsByteCases {
+    if actualN := CountBitsByte(c.x); actualN != c.n {
+      t.Fatal("CountBitsByte(", c.x, ") = ", actualN, "  != ", c.n)
+    } else {
+      t.Log("CountBitsByte(", c.x, ") == ", c.n)
+    }
+  }
+}
+
+func TestCountBitUint64(t *testing.T) {
+  for _, c := range testCountBitsUint64Cases {
+    if actualN := CountBitsUint64(c.x); actualN != c.n {
+      t.Fatal("CountBitsUint64(", c.x, ") = ", actualN, "  != ", c.n)
+    } else {
+      t.Log("CountBitsUint64(", c.x, ") == ", c.n)
+    }
+  }
+}
+
+func BenchmarkCountBitsUint64(b *testing.B) {
+  j := 0
+  for i := 0; i < b.N; i++ {
+    CountBitsUint64(testCountBitsUint64Cases[j].x)
+    j++
+    if j == len(testCountBitsUint64Cases) {
+      j = 0
+    }
+  }
+}
+
+func BenchmarkCountBitsByte(b *testing.B) {
+  j := 0
+  for i := 0; i < b.N; i++ {
+    CountBitsByte(testCountBitsByteCases[j].x)
+    j++
+    if j == len(testCountBitsByteCases) {
+      j = 0
+    }
+  }
+}

blocks/bloom/filter.go

@@ -6,6 +6,7 @@ import (
 	"errors"
 	// Non crypto hash, because speed
 	"github.com/ipfs/go-ipfs/Godeps/_workspace/src/github.com/mtchavez/jenkins"
+	"github.com/ipfs/go-ipfs/Godeps/_workspace/src/github.com/steakknife/hamming"
 	"hash"
 )
 
@@ -13,6 +14,7 @@ type Filter interface {
 	Add([]byte)
 	Find([]byte) bool
 	Merge(Filter) (Filter, error)
+	HammingDistance(Filter) (int, error)
 }
 
 func NewFilter(size int) Filter {
@@ -100,3 +102,23 @@ func (f *filter) Merge(o Filter) (Filter, error) {
 
 	return nfilt, nil
 }
+
+func (f *filter) HammingDistance(o Filter) (int, error) {
+	casfil, ok := o.(*filter)
+	if !ok {
+		return 0, errors.New("Unsupported filter type")
+	}
+
+	if len(f.filter) != len(casfil.filter) {
+		return 0, errors.New("filter lengths must match!")
+	}
+
+	acc := 0
+
+	// xor together
+	for i := 0; i < len(f.filter); i++ {
+		acc += hamming.Byte(f.filter[i], casfil.filter[i])
+	}
+
+	return acc, nil
+}

blocks/bloom/filter_test.go

@@ -78,3 +78,17 @@ func TestMerge(t *testing.T) {
 		}
 	}
 }
+
+func TestHamming(t *testing.T) {
+	f1 := NewFilter(128)
+	f2 := NewFilter(128)
+
+	f1.Add([]byte("no collision"))
+	f1.Add([]byte("collision? no!"))
+
+	dist, _ := f1.HammingDistance(f2)
+
+	if dist != 6 {
+		t.Fatal("Should have 6 bit difference")
+	}
+}