CODEWITHSUNDEEP
structgopadding
Derrick Zhang
Derrick Zhang

Reputation: 21501

binary.Read does not handle struct padding as expected

In a recent Go project I need to read a binary data file generated by Python, but due to padding, binary.Read in Go doesn't read it properly. Below is a minimal example of my problem.

The struct I deal with if of the following format

type Index struct{
    A int32
    B int32
    C int32
    D int64
}

As you can see the size of the struct is 4+4+4+8=20, but Python added an extra 4 bytes for alignment. So the size is actually 24.

Below is the runnable Python code I use to write this struct:

#!/usr/bin/env python
# encoding=utf8

import struct

if __name__ == '__main__':
    data = range(1, 13)
    format = 'iiiq' * 3
    content = struct.pack(format, *data)
    with open('index.bin', 'wb') as f:
        f.write(content)

the iiiq format means there are three 32 bit integers and one 64 bit integer in the struct, which is the same with the Index struct I defined earlier. And running this code will generate a file named index.bin of size 72, which equals to 24 * 3.

And below is the Go code I use to read index.bin:

package main

import (
        "encoding/binary"
        "fmt"
        "os"
        "io"
        "unsafe"
)

type Index struct {
        A int32
        B int32
        C int32
        D int64
}

func main() {
        indexSize := unsafe.Sizeof(Index{})
        fp, _ := os.Open("index.bin")
        defer fp.Close()
        info, _ := fp.Stat()
        fileSize := info.Size()
        entryCnt := fileSize / int64(indexSize)
        fmt.Printf("entry cnt: %d\n", entryCnt)

        readSlice := make([]Index, entryCnt)
        reader := io.Reader(fp)
        _ = binary.Read(reader, binary.LittleEndian, &readSlice)
        fmt.Printf("After read:\n%#v\n", readSlice)
}

And this is the output:

entry cnt: 3
After read:
[]main.Index{main.Index{A:1, B:2, C:3, D:17179869184}, main.Index{A:0, B:5, C:6, D:7}, main.Index{A:8, B:0, C:9, D:47244640266}}

Obviously the output is messed up when reading from the Python generated file.

So my question is, how can I read the python generated file(with padding) in Go properly?

Upvotes: 2

Views: 1408

Answers (3)

peterSO
peterSO

Reputation: 166626

For example,

package main

import (
    "bufio"
    "encoding/binary"
    "fmt"
    "io"
    "os"
)

type Index struct {
    A int32
    B int32
    C int32
    D int64
}

func readIndex(r io.Reader) (Index, error) {
    var index Index
    var buf [24]byte
    _, err := io.ReadFull(r, buf[:])
    if err != nil {
        return index, err
    }
    index.A = int32(binary.LittleEndian.Uint32(buf[0:4]))
    index.B = int32(binary.LittleEndian.Uint32(buf[4:8]))
    index.C = int32(binary.LittleEndian.Uint32(buf[8:12]))
    index.D = int64(binary.LittleEndian.Uint64(buf[16:24]))
    return index, nil
}

func main() {
    f, err := os.Open("index.bin")
    if err != nil {
        fmt.Fprintln(os.Stderr, err)
        return
    }
    defer f.Close()
    r := bufio.NewReader(f)
    indexes := make([]Index, 0, 1024)
    for {
        index, err := readIndex(r)
        if err != nil {
            if err == io.EOF {
                break
            }
            fmt.Fprintln(os.Stderr, err)
            return
        }
        indexes = append(indexes, index)
    }
    fmt.Println(indexes)
}

Output:

[{1 2 3 4} {5 6 7 8} {9 10 11 12}]

Input:

00000000  01 00 00 00 02 00 00 00  03 00 00 00 00 00 00 00  |................|
00000010  04 00 00 00 00 00 00 00  05 00 00 00 06 00 00 00  |................|
00000020  07 00 00 00 00 00 00 00  08 00 00 00 00 00 00 00  |................|
00000030  09 00 00 00 0a 00 00 00  0b 00 00 00 00 00 00 00  |................|
00000040  0c 00 00 00 00 00 00 00                           |........|

Upvotes: 1

Derrick Zhang
Derrick Zhang

Reputation: 21501

@Barber's solution is workable, but I found adding a padding field not so comfortable. And I found a better way of doing it.

Below is the new golang read code which works perfectly:

package main

import (
    "fmt"
    "os"
    "io"
    "io/ioutil"
    "unsafe"
)

type Index struct {
    A int32
    B int32
    C int32
    // Pad int32
    D int64
}

func main() {
    indexSize := unsafe.Sizeof(Index{})
    fp, _ := os.Open("index.bin")
    defer fp.Close()
    info, _ := fp.Stat()
    fileSize := info.Size()
    entryCnt := fileSize / int64(indexSize)

    reader := io.Reader(fp)
    allBytes, _ := ioutil.ReadAll(reader)
    readSlice := *((*[]Index)(unsafe.Pointer(&allBytes)))
    realLen := len(allBytes) / int(indexSize)
    readSlice = readSlice[:realLen]
    fmt.Printf("After read:\n%#v\n", readSlice)
}

Output:

After read:
[]main.Index{main.Index{A:1, B:2, C:3, D:4}, main.Index{A:5, B:6, C:7, D:8}, main.Index{A:9, B:10, C:11, D:12}}

This solution needs no explicit padding field.

The essence here is that if you let golang convert the whole bytes to a slice of Index struct, it seems to be able to handle the padding well.

Upvotes: -1

Darshan Rivka Whittle
Darshan Rivka Whittle

Reputation: 34031

You can just pad your Go struct to match:

type Index struct {
    A int32
    B int32
    C int32
    _ int32
    D int64
}

Which produces:

[]main.Index{main.Index{A:1, B:2, C:3, _:0, D:4}, main.Index{A:5, B:6, C:7, _:0, D:8}, main.Index{A:9, B:10, C:11, _:0, D:12}}

binary.Read knows to skip the _ field:

When reading into structs, the field data for fields with blank (_) field names is skipped; i.e., blank field names may be used for padding.

(So the 0 values for _ are not because the padding in the file was set to zero, but because the struct field was initialized to 0 and never changed, and the padding in the file was skipped rather than read.)

Upvotes: 8

Related Questions