Put uncrustify and uncrustify.cfg in your ~/bin and run this to uncrustify changed lines in your file.

uncrustify_changed_lines.py

#!/usr/bin/env python

import difflib
import subprocess
import shutil
import sys
from os import getcwd
from os.path import normpath, expanduser, join, exists

from git import Repo  # pip install gitpython


path = sys.argv[1]
full_path = normpath(expanduser(join(getcwd(), path)))

repo = Repo(getcwd(), search_parent_directories=True)
no_sha = '0' * 40


def commits_and_lines():
    line_no = 0
    for commit, lines in repo.blame(None, full_path):
        for _ in lines:
            yield commit, line_no
            line_no += 1


def uncommitted_lines():
    for commit, line_no in commits_and_lines():
        if commit.hexsha == no_sha:
            yield line_no


def uncrustify(path):
    subprocess.check_output([
        expanduser('~/bin/uncrustify'),
        '-c',
        expanduser('~/bin/uncrustify.cfg'),
        path,
    ])

    output_path = '%s.uncrustify' % path
    assert exists(output_path), output_path
    return output_path


uls = set(uncommitted_lines())
uncrustified_path = uncrustify(full_path)

lines = list(open(full_path).readlines())
uncrustified_lines = list(open(uncrustified_path).readlines())
matcher = difflib.SequenceMatcher(a=lines, b=uncrustified_lines)

shutil.copy(full_path, full_path + '.bak')


def save():
    with open(full_path, 'w') as f:
        f.write(''.join(lines))

for tag, i1, i2, j1, j2 in reversed(matcher.get_opcodes()):
    if tag == 'equal':
        continue
    if tag == 'replace' and set(range(i1, i2)).issubset(uls):
        lines[i1:i2] = uncrustified_lines[j1:j2]
        save()
    elif tag == 'insert' and i1 in uls:
        lines[i1:i2] = uncrustified_lines[j1:j2]
        save()
    elif tag == 'delete' and set(range(i1, i2)).issubset(uls):
        del lines[i1:i2]
        save()