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// Copyright ©2015 The Gonum Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package mat
import (
"bytes"
"encoding/binary"
"errors"
"fmt"
"io"
"math"
)
// version is the current on-disk codec version.
const version uint32 = 0x1
// maxLen is the biggest slice/array len one can create on a 32/64b platform.
const maxLen = int64(int(^uint(0) >> 1))
var (
headerSize = binary.Size(storage{})
sizeFloat64 = binary.Size(float64(0))
errWrongType = errors.New("mat: wrong data type")
errTooBig = errors.New("mat: resulting data slice too big")
errTooSmall = errors.New("mat: input slice too small")
errBadBuffer = errors.New("mat: data buffer size mismatch")
errBadSize = errors.New("mat: invalid dimension")
)
// Type encoding scheme:
//
// Type Form Packing Uplo Unit Rows Columns kU kL
// uint8 [GST] uint8 [BPF] uint8 [AUL] bool int64 int64 int64 int64
// General 'G' 'F' 'A' false r c 0 0
// Band 'G' 'B' 'A' false r c kU kL
// Symmetric 'S' 'F' ul false n n 0 0
// SymmetricBand 'S' 'B' ul false n n k k
// SymmetricPacked 'S' 'P' ul false n n 0 0
// Triangular 'T' 'F' ul Diag==Unit n n 0 0
// TriangularBand 'T' 'B' ul Diag==Unit n n k k
// TriangularPacked 'T' 'P' ul Diag==Unit n n 0 0
//
// G - general, S - symmetric, T - triangular
// F - full, B - band, P - packed
// A - all, U - upper, L - lower
// MarshalBinary encodes the receiver into a binary form and returns the result.
//
// Dense is little-endian encoded as follows:
// 0 - 3 Version = 1 (uint32)
// 4 'G' (byte)
// 5 'F' (byte)
// 6 'A' (byte)
// 7 0 (byte)
// 8 - 15 number of rows (int64)
// 16 - 23 number of columns (int64)
// 24 - 31 0 (int64)
// 32 - 39 0 (int64)
// 40 - .. matrix data elements (float64)
// [0,0] [0,1] ... [0,ncols-1]
// [1,0] [1,1] ... [1,ncols-1]
// ...
// [nrows-1,0] ... [nrows-1,ncols-1]
func (m Dense) MarshalBinary() ([]byte, error) {
bufLen := int64(headerSize) + int64(m.mat.Rows)*int64(m.mat.Cols)*int64(sizeFloat64)
if bufLen <= 0 {
// bufLen is too big and has wrapped around.
return nil, errTooBig
}
header := storage{
Form: 'G', Packing: 'F', Uplo: 'A',
Rows: int64(m.mat.Rows), Cols: int64(m.mat.Cols),
Version: version,
}
buf := make([]byte, bufLen)
n, err := header.marshalBinaryTo(bytes.NewBuffer(buf[:0]))
if err != nil {
return buf[:n], err
}
p := headerSize
r, c := m.Dims()
for i := 0; i < r; i++ {
for j := 0; j < c; j++ {
binary.LittleEndian.PutUint64(buf[p:p+sizeFloat64], math.Float64bits(m.at(i, j)))
p += sizeFloat64
}
}
return buf, nil
}
// MarshalBinaryTo encodes the receiver into a binary form and writes it into w.
// MarshalBinaryTo returns the number of bytes written into w and an error, if any.
//
// See MarshalBinary for the on-disk layout.
func (m Dense) MarshalBinaryTo(w io.Writer) (int, error) {
header := storage{
Form: 'G', Packing: 'F', Uplo: 'A',
Rows: int64(m.mat.Rows), Cols: int64(m.mat.Cols),
Version: version,
}
n, err := header.marshalBinaryTo(w)
if err != nil {
return n, err
}
r, c := m.Dims()
var b [8]byte
for i := 0; i < r; i++ {
for j := 0; j < c; j++ {
binary.LittleEndian.PutUint64(b[:], math.Float64bits(m.at(i, j)))
nn, err := w.Write(b[:])
n += nn
if err != nil {
return n, err
}
}
}
return n, nil
}
// UnmarshalBinary decodes the binary form into the receiver.
// It panics if the receiver is a non-empty Dense matrix.
//
// See MarshalBinary for the on-disk layout.
//
// Limited checks on the validity of the binary input are performed:
// - matrix.ErrShape is returned if the number of rows or columns is negative,
// - an error is returned if the resulting Dense matrix is too
// big for the current architecture (e.g. a 16GB matrix written by a
// 64b application and read back from a 32b application.)
// UnmarshalBinary does not limit the size of the unmarshaled matrix, and so
// it should not be used on untrusted data.
func (m *Dense) UnmarshalBinary(data []byte) error {
if !m.IsEmpty() {
panic("mat: unmarshal into non-empty matrix")
}
if len(data) < headerSize {
return errTooSmall
}
var header storage
err := header.unmarshalBinary(data[:headerSize])
if err != nil {
return err
}
rows := header.Rows
cols := header.Cols
header.Version = 0
header.Rows = 0
header.Cols = 0
if (header != storage{Form: 'G', Packing: 'F', Uplo: 'A'}) {
return errWrongType
}
if rows < 0 || cols < 0 {
return errBadSize
}
size := rows * cols
if size == 0 {
return ErrZeroLength
}
if int(size) < 0 || size > maxLen {
return errTooBig
}
if len(data) != headerSize+int(rows*cols)*sizeFloat64 {
return errBadBuffer
}
p := headerSize
m.reuseAsNonZeroed(int(rows), int(cols))
for i := range m.mat.Data {
m.mat.Data[i] = math.Float64frombits(binary.LittleEndian.Uint64(data[p : p+sizeFloat64]))
p += sizeFloat64
}
return nil
}
// UnmarshalBinaryFrom decodes the binary form into the receiver and returns
// the number of bytes read and an error if any.
// It panics if the receiver is a non-empty Dense matrix.
//
// See MarshalBinary for the on-disk layout.
//
// Limited checks on the validity of the binary input are performed:
// - matrix.ErrShape is returned if the number of rows or columns is negative,
// - an error is returned if the resulting Dense matrix is too
// big for the current architecture (e.g. a 16GB matrix written by a
// 64b application and read back from a 32b application.)
// UnmarshalBinary does not limit the size of the unmarshaled matrix, and so
// it should not be used on untrusted data.
func (m *Dense) UnmarshalBinaryFrom(r io.Reader) (int, error) {
if !m.IsEmpty() {
panic("mat: unmarshal into non-empty matrix")
}
var header storage
n, err := header.unmarshalBinaryFrom(r)
if err != nil {
return n, err
}
rows := header.Rows
cols := header.Cols
header.Version = 0
header.Rows = 0
header.Cols = 0
if (header != storage{Form: 'G', Packing: 'F', Uplo: 'A'}) {
return n, errWrongType
}
if rows < 0 || cols < 0 {
return n, errBadSize
}
size := rows * cols
if size == 0 {
return n, ErrZeroLength
}
if int(size) < 0 || size > maxLen {
return n, errTooBig
}
m.reuseAsNonZeroed(int(rows), int(cols))
var b [8]byte
for i := range m.mat.Data {
nn, err := readFull(r, b[:])
n += nn
if err != nil {
if err == io.EOF {
return n, io.ErrUnexpectedEOF
}
return n, err
}
m.mat.Data[i] = math.Float64frombits(binary.LittleEndian.Uint64(b[:]))
}
return n, nil
}
// MarshalBinary encodes the receiver into a binary form and returns the result.
//
// VecDense is little-endian encoded as follows:
//
// 0 - 3 Version = 1 (uint32)
// 4 'G' (byte)
// 5 'F' (byte)
// 6 'A' (byte)
// 7 0 (byte)
// 8 - 15 number of elements (int64)
// 16 - 23 1 (int64)
// 24 - 31 0 (int64)
// 32 - 39 0 (int64)
// 40 - .. vector's data elements (float64)
func (v VecDense) MarshalBinary() ([]byte, error) {
bufLen := int64(headerSize) + int64(v.mat.N)*int64(sizeFloat64)
if bufLen <= 0 {
// bufLen is too big and has wrapped around.
return nil, errTooBig
}
header := storage{
Form: 'G', Packing: 'F', Uplo: 'A',
Rows: int64(v.mat.N), Cols: 1,
Version: version,
}
buf := make([]byte, bufLen)
n, err := header.marshalBinaryTo(bytes.NewBuffer(buf[:0]))
if err != nil {
return buf[:n], err
}
p := headerSize
for i := 0; i < v.mat.N; i++ {
binary.LittleEndian.PutUint64(buf[p:p+sizeFloat64], math.Float64bits(v.at(i)))
p += sizeFloat64
}
return buf, nil
}
// MarshalBinaryTo encodes the receiver into a binary form, writes it to w and
// returns the number of bytes written and an error if any.
//
// See MarshalBainry for the on-disk format.
func (v VecDense) MarshalBinaryTo(w io.Writer) (int, error) {
header := storage{
Form: 'G', Packing: 'F', Uplo: 'A',
Rows: int64(v.mat.N), Cols: 1,
Version: version,
}
n, err := header.marshalBinaryTo(w)
if err != nil {
return n, err
}
var buf [8]byte
for i := 0; i < v.mat.N; i++ {
binary.LittleEndian.PutUint64(buf[:], math.Float64bits(v.at(i)))
nn, err := w.Write(buf[:])
n += nn
if err != nil {
return n, err
}
}
return n, nil
}
// UnmarshalBinary decodes the binary form into the receiver.
// It panics if the receiver is a non-empty VecDense.
//
// See MarshalBinary for the on-disk layout.
//
// Limited checks on the validity of the binary input are performed:
// - matrix.ErrShape is returned if the number of rows is negative,
// - an error is returned if the resulting VecDense is too
// big for the current architecture (e.g. a 16GB vector written by a
// 64b application and read back from a 32b application.)
// UnmarshalBinary does not limit the size of the unmarshaled vector, and so
// it should not be used on untrusted data.
func (v *VecDense) UnmarshalBinary(data []byte) error {
if !v.IsEmpty() {
panic("mat: unmarshal into non-empty vector")
}
if len(data) < headerSize {
return errTooSmall
}
var header storage
err := header.unmarshalBinary(data[:headerSize])
if err != nil {
return err
}
if header.Cols != 1 {
return ErrShape
}
n := header.Rows
header.Version = 0
header.Rows = 0
header.Cols = 0
if (header != storage{Form: 'G', Packing: 'F', Uplo: 'A'}) {
return errWrongType
}
if n == 0 {
return ErrZeroLength
}
if n < 0 {
return errBadSize
}
if int64(maxLen) < n {
return errTooBig
}
if len(data) != headerSize+int(n)*sizeFloat64 {
return errBadBuffer
}
p := headerSize
v.reuseAsNonZeroed(int(n))
for i := range v.mat.Data {
v.mat.Data[i] = math.Float64frombits(binary.LittleEndian.Uint64(data[p : p+sizeFloat64]))
p += sizeFloat64
}
return nil
}
// UnmarshalBinaryFrom decodes the binary form into the receiver, from the
// io.Reader and returns the number of bytes read and an error if any.
// It panics if the receiver is a non-empty VecDense.
//
// See MarshalBinary for the on-disk layout.
// See UnmarshalBinary for the list of sanity checks performed on the input.
func (v *VecDense) UnmarshalBinaryFrom(r io.Reader) (int, error) {
if !v.IsEmpty() {
panic("mat: unmarshal into non-empty vector")
}
var header storage
n, err := header.unmarshalBinaryFrom(r)
if err != nil {
return n, err
}
if header.Cols != 1 {
return n, ErrShape
}
l := header.Rows
header.Version = 0
header.Rows = 0
header.Cols = 0
if (header != storage{Form: 'G', Packing: 'F', Uplo: 'A'}) {
return n, errWrongType
}
if l == 0 {
return n, ErrZeroLength
}
if l < 0 {
return n, errBadSize
}
if int64(maxLen) < l {
return n, errTooBig
}
v.reuseAsNonZeroed(int(l))
var b [8]byte
for i := range v.mat.Data {
nn, err := readFull(r, b[:])
n += nn
if err != nil {
if err == io.EOF {
return n, io.ErrUnexpectedEOF
}
return n, err
}
v.mat.Data[i] = math.Float64frombits(binary.LittleEndian.Uint64(b[:]))
}
return n, nil
}
// storage is the internal representation of the storage format of a
// serialised matrix.
type storage struct {
Version uint32 // Keep this first.
Form byte // [GST]
Packing byte // [BPF]
Uplo byte // [AUL]
Unit bool
Rows int64
Cols int64
KU int64
KL int64
}
// TODO(kortschak): Consider replacing these with calls to direct
// encoding/decoding of fields rather than to binary.Write/binary.Read.
func (s storage) marshalBinaryTo(w io.Writer) (int, error) {
buf := bytes.NewBuffer(make([]byte, 0, headerSize))
err := binary.Write(buf, binary.LittleEndian, s)
if err != nil {
return 0, err
}
return w.Write(buf.Bytes())
}
func (s *storage) unmarshalBinary(buf []byte) error {
err := binary.Read(bytes.NewReader(buf), binary.LittleEndian, s)
if err != nil {
return err
}
if s.Version != version {
return fmt.Errorf("mat: incorrect version: %d", s.Version)
}
return nil
}
func (s *storage) unmarshalBinaryFrom(r io.Reader) (int, error) {
buf := make([]byte, headerSize)
n, err := readFull(r, buf)
if err != nil {
return n, err
}
return n, s.unmarshalBinary(buf[:n])
}
// readFull reads from r into buf until it has read len(buf).
// It returns the number of bytes copied and an error if fewer bytes were read.
// If an EOF happens after reading fewer than len(buf) bytes, io.ErrUnexpectedEOF is returned.
func readFull(r io.Reader, buf []byte) (int, error) {
var n int
var err error
for n < len(buf) && err == nil {
var nn int
nn, err = r.Read(buf[n:])
n += nn
}
if n == len(buf) {
return n, nil
}
if err == io.EOF {
return n, io.ErrUnexpectedEOF
}
return n, err
}
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