mirror of
https://github.com/gonum/gonum.git
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975d99cd20
This avoids the confusion between Zero() and IsZero() which sounds like they should be related to one another but are not. This makes IsEmpty the counterpart to Reset. Add check for Zero in allMatrix Fixes #1083. Updates #1081.
492 lines
13 KiB
Go
492 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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// 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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// - matrix.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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// 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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// - matrix.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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// 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 MarshalBainry 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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// - matrix.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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// 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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