C - reading bits from binary file

C file I/O (and C in general) is organized around bytes¹ not bits. So there's generally no way to access specific bits in a file, just bytes.

So if you want to manipulate bits within a file, you need to read the bytes that contain the bits you are interested in and then extract the bits (generally using shifts and masks). If you want to write those bits back, you'll need to repack them into entire bytes.

One way is to have a bit stream abstraction layered on top of a C FILE * that can extract the bits from each byte read (keeping the remaining bits for a later read). Something like:

#include <stdio.h>
#include <limits.h>

struct bit_stream {
    FILE *fp;   // source to read from
    int byte;   // last byte read from fp
    size_t bits;   // how many bits are left in byte;
};

int read_bits(struct bit_stream *bs, size_t size) {
    if (size >= sizeof(int)*CHAR_BIT) {
        fprintf("size %z is too big\n", size);
        exit(1); }
    int rv = 0;
    size_t bits = 0;
    while (bits < size) {
        if (!bs->bits) {
            if ((bs->byte = fgetc(bs->fp)) == EOF)
                return bits ? rv : EOF;
            bs->bits = CHAR_BIT; }
        if (bs->bits > size - bits) {
            size_t extract = size - bits;
            rv |= (bs->byte & ((1U << extract) - 1)) << bits;
            bs->bits -= extract;
            bs->byte >>= extract;
            bits += extract;
        } else {
            rv |= bs->byte << bits;
            bits += bs->bits;
            bs->bits = 0; }
    }
    return rv;
}

int main() {
    struct bit_stream bs = { stdin, 0, 0 };
    int v;
    while ((v = read_bits(&bs, 3) != EOF) {
        printf("%d\n", v);
    }
}

This uses read_bits(&bs, 3) to read the next 3 bits from the file.

¹_{Bytes are pretty much always 8 bits these days, but the C standard still allows for other sizes of bytes, as specified by CHAR_BIT from <limits.h>}