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