binary.Read does not handle struct padding as expected - struct

Question

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?

Answer 1

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.)

Answer 2

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 |........|

Answer 3

#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.