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pybind11 ostream example
# Created by https://www.gitignore.io/api/c++,cmake
### C++ ###
# Prerequisites
*.d
# Compiled Object files
*.slo
*.lo
*.o
*.obj
# Precompiled Headers
*.gch
*.pch
# Compiled Dynamic libraries
*.so
*.dylib
*.dll
# Fortran module files
*.mod
*.smod
# Compiled Static libraries
*.lai
*.la
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# Executables
*.exe
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### CMake ###
CMakeCache.txt
CMakeFiles
CMakeScripts
Testing
Makefile
cmake_install.cmake
install_manifest.txt
compile_commands.json
CTestTestfile.cmake
# End of https://www.gitignore.io/api/c++,cmake
cmake_minimum_required(VERSION 3.1)
project(1705_ostream_example)
#find_package(FindPythonInterp REQUIRED)
#find_package(PythonLibs REQUIRED)
#include_directories(${PYTHON_INCLUDE_DIR})
execute_process(
COMMAND python -c "from distutils import sysconfig; print(sysconfig.get_python_inc())"
OUTPUT_VARIABLE PYTHON_INCLUDE_DIR
)
include_directories(${PYTHON_INCLUDE_DIR})
execute_process(
COMMAND python -c "import pybind11; print(pybind11.get_include())"
OUTPUT_VARIABLE PYBIND11_INCLUDE_DIR
)
include_directories(${PYBIND11_INCLUDE_DIR})
include_directories(.)
set (CMAKE_CXX_STANDARD 11)
add_library(ostream_example SHARED
ostream_example.cpp
)
set_target_properties(ostream_example PROPERTIES PREFIX "")
This component utilizes components derived from cctbx, available at
http://cci.lbl.gov/cctbx_sources/boost_adaptbx/python_streambuf.h
*** License agreement ***
cctbx Copyright (c) 2006, The Regents of the University of
California, through Lawrence Berkeley National Laboratory (subject to
receipt of any required approvals from the U.S. Dept. of Energy). All
rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
(1) Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
(2) Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
(3) Neither the name of the University of California, Lawrence Berkeley
National Laboratory, U.S. Dept. of Energy nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
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IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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derivative works thereof, in binary and source code form.
#include <pybind11/pybind11.h>
#include <iostream>
#include <ostream>
#include <pystreambuf.h>
void testprint(std::ostream & o) {
o << "testprint" << std::endl;
}
void testprint_noflush(std::ostream & o) {
o << "testprint_noflush";
}
int testparse(std::istream & i) {
int result;
i >> result;
return result;
}
namespace py = pybind11;
PYBIND11_PLUGIN(ostream_example) {
py::module m("ostream_example");
m.def("testprint", &testprint);
m.def("testprint_noflush", &testprint_noflush);
m.def("testparse", &testparse);
return m.ptr();
}
#pragma once
#include <pybind11/pybind11.h>
#include <streambuf>
#include <iostream>
namespace py = pybind11;
/// A stream buffer getting data from and putting data into a Python file object
/** The aims are as follow:
- Given a C++ function acting on a standard stream, e.g.
\code
void read_inputs(std::istream& input) {
...
input >> something >> something_else;
}
\endcode
and given a piece of Python code which creates a file-like object,
to be able to pass this file object to that C++ function, e.g.
\code
import gzip
gzip_file_obj = gzip.GzipFile(...)
read_inputs(gzip_file_obj)
\endcode
and have the standard stream pull data from and put data into the Python
file object.
- When Python \c read_inputs() returns, the Python object is able to
continue reading or writing where the C++ code left off.
- Operations in C++ on mere files should be competitively fast compared
to the direct use of \c std::fstream.
\b Motivation
- the standard Python library offer of file-like objects (files,
compressed files and archives, network, ...) is far superior to the
offer of streams in the C++ standard library and Boost C++ libraries.
- i/o code involves a fair amount of text processing which is more
efficiently prototyped in Python but then one may need to rewrite
a time-critical part in C++, in as seamless a manner as possible.
\b Usage
This is 2-step:
- a trivial wrapper function
\code
using boost_adaptbx::python::streambuf;
void read_inputs_wrapper(streambuf& input)
{
streambuf::istream is(input);
read_inputs(is);
}
def("read_inputs", read_inputs_wrapper);
\endcode
which has to be written every time one wants a Python binding for
such a C++ function.
- the Python side
\code
from boost.python import streambuf
read_inputs(streambuf(python_file_obj=obj, buffer_size=1024))
\endcode
\c buffer_size is optional. See also: \c default_buffer_size
Note: references are to the C++ standard (the numbers between parentheses
at the end of references are margin markers).
*/
class streambuf : public std::basic_streambuf<char>
{
private:
typedef std::basic_streambuf<char> base_t;
public:
/* The syntax
using base_t::char_type;
would be nicer but Visual Studio C++ 8 chokes on it
*/
typedef base_t::char_type char_type;
typedef base_t::int_type int_type;
typedef base_t::pos_type pos_type;
typedef base_t::off_type off_type;
typedef base_t::traits_type traits_type;
/// The default size of the read and write buffer.
/** They are respectively used to buffer data read from and data written to
the Python file object. It can be modified from Python.
*/
static std::size_t default_buffer_size;
/// Construct from a Python file object
/** if buffer_size is 0 the current default_buffer_size is used.
*/
streambuf(
py::object& python_file_obj,
std::size_t buffer_size_=0)
:
py_read (getattr(python_file_obj, "read", py::none())),
py_write (getattr(python_file_obj, "write", py::none())),
py_seek (getattr(python_file_obj, "seek", py::none())),
py_tell (getattr(python_file_obj, "tell", py::none())),
buffer_size(buffer_size_ != 0 ? buffer_size_ : default_buffer_size),
write_buffer(0),
pos_of_read_buffer_end_in_py_file(0),
pos_of_write_buffer_end_in_py_file(buffer_size),
farthest_pptr(0)
{
assert(buffer_size != 0);
/* Some Python file objects (e.g. sys.stdout and sys.stdin)
have non-functional seek and tell. If so, assign None to
py_tell and py_seek.
*/
if (!py_tell.is_none()) {
try {
py_tell();
}
catch (py::error_already_set& err) {
py_tell = py::none();
py_seek = py::none();
err.restore();
PyErr_Clear();
}
}
if (!py_write.is_none()) {
// C-like string to make debugging easier
write_buffer = new char[buffer_size + 1];
write_buffer[buffer_size] = '\0';
setp(write_buffer, write_buffer + buffer_size); // 27.5.2.4.5 (5)
farthest_pptr = pptr();
}
else {
// The first attempt at output will result in a call to overflow
setp(0, 0);
}
if (!py_tell.is_none()){
off_type py_pos = py_tell().cast<off_type>();
pos_of_read_buffer_end_in_py_file = py_pos;
pos_of_write_buffer_end_in_py_file = py_pos;
}
}
/// Mundane destructor freeing the allocated resources
virtual ~streambuf() {
if (write_buffer) delete[] write_buffer;
}
/// C.f. C++ standard section 27.5.2.4.3
/** It is essential to override this virtual function for the stream
member function readsome to work correctly (c.f. 27.6.1.3, alinea 30)
*/
virtual std::streamsize showmanyc() {
int_type const failure = traits_type::eof();
int_type status = underflow();
if (status == failure) return -1;
return egptr() - gptr();
}
/// C.f. C++ standard section 27.5.2.4.3
virtual int_type underflow() {
int_type const failure = traits_type::eof();
if (py_read.is_none()) {
throw std::invalid_argument(
"That Python file object has no 'read' attribute");
}
read_buffer = py_read(buffer_size);
char *read_buffer_data;
py::ssize_t py_n_read;
if (PYBIND11_BYTES_AS_STRING_AND_SIZE(read_buffer.ptr(),
&read_buffer_data, &py_n_read) == -1) {
setg(0, 0, 0);
throw std::invalid_argument(
"The method 'read' of the Python file object "
"did not return a string.");
}
off_type n_read = (off_type)py_n_read;
pos_of_read_buffer_end_in_py_file += n_read;
setg(read_buffer_data, read_buffer_data, read_buffer_data + n_read);
// ^^^27.5.2.3.1 (4)
if (n_read == 0) return failure;
return traits_type::to_int_type(read_buffer_data[0]);
}
/// C.f. C++ standard section 27.5.2.4.5
virtual int_type overflow(int_type c=traits_type::eof()) {
if (py_write.is_none()) {
throw std::invalid_argument(
"That Python file object has no 'write' attribute");
}
farthest_pptr = std::max(farthest_pptr, pptr());
off_type n_written = (off_type)(farthest_pptr - pbase());
py::bytes chunk(pbase(), n_written);
py_write(chunk);
if (!traits_type::eq_int_type(c, traits_type::eof())) {
py_write(traits_type::to_char_type(c));
n_written++;
}
if (n_written) {
pos_of_write_buffer_end_in_py_file += n_written;
setp(pbase(), epptr());
// ^^^ 27.5.2.4.5 (5)
farthest_pptr = pptr();
}
return traits_type::eq_int_type(
c, traits_type::eof()) ? traits_type::not_eof(c) : c;
}
/// Update the python file to reflect the state of this stream buffer
/** Empty the write buffer into the Python file object and set the seek
position of the latter accordingly (C++ standard section 27.5.2.4.2).
If there is no write buffer or it is empty, but there is a non-empty
read buffer, set the Python file object seek position to the
seek position in that read buffer.
*/
virtual int sync() {
int result = 0;
farthest_pptr = std::max(farthest_pptr, pptr());
if (farthest_pptr && farthest_pptr > pbase()) {
off_type delta = pptr() - farthest_pptr;
int_type status = overflow();
if (traits_type::eq_int_type(status, traits_type::eof())) result = -1;
if (!py_seek.is_none()) py_seek(delta, 1);
}
else if (gptr() && gptr() < egptr()) {
if (!py_seek.is_none()) py_seek(gptr() - egptr(), 1);
}
return result;
}
/// C.f. C++ standard section 27.5.2.4.2
/** This implementation is optimised to look whether the position is within
the buffers, so as to avoid calling Python seek or tell. It is
important for many applications that the overhead of calling into Python
is avoided as much as possible (e.g. parsers which may do a lot of
backtracking)
*/
virtual
pos_type seekoff(off_type off, std::ios_base::seekdir way,
std::ios_base::openmode which= std::ios_base::in
| std::ios_base::out)
{
/* In practice, "which" is either std::ios_base::in or out
since we end up here because either seekp or seekg was called
on the stream using this buffer. That simplifies the code
in a few places.
*/
int const failure = off_type(-1);
if (py_seek.is_none()) {
throw std::invalid_argument(
"That Python file object has no 'seek' attribute");
}
// we need the read buffer to contain something!
if (which == std::ios_base::in && !gptr()) {
if (traits_type::eq_int_type(underflow(), traits_type::eof())) {
return failure;
}
}
// compute the whence parameter for Python seek
int whence;
switch (way) {
case std::ios_base::beg:
whence = 0;
break;
case std::ios_base::cur:
whence = 1;
break;
case std::ios_base::end:
whence = 2;
break;
default:
return failure;
}
// Let's have a go
off_type result;
if (!seekoff_without_calling_python(off, way, which, result)) {
// we need to call Python
if (which == std::ios_base::out) overflow();
if (way == std::ios_base::cur) {
if (which == std::ios_base::in) off -= egptr() - gptr();
else if (which == std::ios_base::out) off += pptr() - pbase();
}
py_seek(off, whence);
result = off_type(py_tell().cast<off_type>());
if (which == std::ios_base::in) underflow();
}
return result;
}
/// C.f. C++ standard section 27.5.2.4.2
virtual
pos_type seekpos(pos_type sp,
std::ios_base::openmode which= std::ios_base::in
| std::ios_base::out)
{
return streambuf::seekoff(sp, std::ios_base::beg, which);
}
private:
py::object py_read, py_write, py_seek, py_tell;
std::size_t buffer_size;
/* This is actually a Python bytes object and the actual read buffer is
its internal data, i.e. an array of characters.
*/
py::bytes read_buffer;
/* A mere array of char's allocated on the heap at construction time and
de-allocated only at destruction time.
*/
char *write_buffer;
off_type pos_of_read_buffer_end_in_py_file,
pos_of_write_buffer_end_in_py_file;
// the farthest place the buffer has been written into
char *farthest_pptr;
bool seekoff_without_calling_python(
off_type off,
std::ios_base::seekdir way,
std::ios_base::openmode which,
off_type & result)
{
// Buffer range and current position
off_type buf_begin, buf_end, buf_cur, upper_bound;
off_type pos_of_buffer_end_in_py_file;
if (which == std::ios_base::in) {
pos_of_buffer_end_in_py_file = pos_of_read_buffer_end_in_py_file;
buf_begin = reinterpret_cast<std::streamsize>(eback());
buf_cur = reinterpret_cast<std::streamsize>(gptr());
buf_end = reinterpret_cast<std::streamsize>(egptr());
upper_bound = buf_end;
}
else if (which == std::ios_base::out) {
pos_of_buffer_end_in_py_file = pos_of_write_buffer_end_in_py_file;
buf_begin = reinterpret_cast<std::streamsize>(pbase());
buf_cur = reinterpret_cast<std::streamsize>(pptr());
buf_end = reinterpret_cast<std::streamsize>(epptr());
farthest_pptr = std::max(farthest_pptr, pptr());
upper_bound = reinterpret_cast<std::streamsize>(farthest_pptr) + 1;
}
else {
std::runtime_error(
"Control flow passes through branch that should be unreachable.");
}
// Sought position in "buffer coordinate"
off_type buf_sought;
if (way == std::ios_base::cur) {
buf_sought = buf_cur + off;
}
else if (way == std::ios_base::beg) {
buf_sought = buf_end + (off - pos_of_buffer_end_in_py_file);
}
else if (way == std::ios_base::end) {
return false;
}
else {
std::runtime_error(
"Control flow passes through branch that should be unreachable.");
}
// if the sought position is not in the buffer, give up
if (buf_sought < buf_begin || buf_sought >= upper_bound) return false;
// we are in wonderland
if (which == std::ios_base::in) gbump(buf_sought - buf_cur);
else if (which == std::ios_base::out) pbump(buf_sought - buf_cur);
result = pos_of_buffer_end_in_py_file + (buf_sought - buf_end);
return true;
}
public:
class istream : public std::istream
{
public:
istream(streambuf& buf) : std::istream(&buf)
{
exceptions(std::ios_base::badbit);
}
~istream() { if (this->good()) this->sync(); }
};
class ostream : public std::ostream
{
public:
ostream(streambuf& buf) : std::ostream(&buf)
{
exceptions(std::ios_base::badbit);
}
~ostream() { if (this->good()) this->flush(); }
};
};
std::size_t streambuf::default_buffer_size = 1024;
struct streambuf_capsule
{
streambuf python_streambuf;
streambuf_capsule(
py::object& python_file_obj,
std::size_t buffer_size=0)
:
python_streambuf(python_file_obj, buffer_size)
{}
};
struct ostream : private streambuf_capsule, streambuf::ostream
{
ostream(
py::object& python_file_obj,
std::size_t buffer_size=0)
:
streambuf_capsule(python_file_obj, buffer_size),
streambuf::ostream(python_streambuf)
{}
~ostream()
{
if (this->good()){
this->flush();
}
}
};
struct istream : private streambuf_capsule, streambuf::istream
{
istream(
py::object& python_file_obj,
std::size_t buffer_size=0)
:
streambuf_capsule(python_file_obj, buffer_size),
streambuf::istream(python_streambuf)
{}
~istream()
{
if (this->good()) {
this->sync();
}
}
};
namespace pybind11 { namespace detail {
template <> struct type_caster<std::istream> {
public:
bool load(handle src, bool) {
if (getattr(src, "read", py::none()).is_none()){
return false;
}
obj = py::reinterpret_borrow<object>(src);
value = std::unique_ptr<istream>(new istream(obj, 0));
return true;
}
protected:
py::object obj;
std::unique_ptr<istream> value;
public:
static PYBIND11_DESCR name() { return type_descr(_("istream")); }
static handle cast(const std::istream *src, return_value_policy policy, handle parent) {
return none().release();
}
operator std::istream*() { return value.get(); }
operator std::istream&() { return *value; }
template <typename _T> using cast_op_type = pybind11::detail::cast_op_type<_T>;
};
template <> struct type_caster<std::ostream> {
public:
bool load(handle src, bool) {
if (getattr(src, "write", py::none()).is_none()){
return false;
}
obj = py::reinterpret_borrow<object>(src);
value = std::unique_ptr<ostream>(new ostream(obj, 0));
return true;
}
protected:
py::object obj;
std::unique_ptr<ostream> value;
public:
static PYBIND11_DESCR name() { return type_descr(_("ostream")); }
static handle cast(const std::ostream *src, return_value_policy policy, handle parent) {
return none().release();
}
operator std::ostream*() { return value.get(); }
operator std::ostream&() { return *value; }
template <typename _T> using cast_op_type = pybind11::detail::cast_op_type<_T>;
};
}} // namespace pybind11::detail
# vim: ai ts=4 sts=4 et sw=4 ft=python
import io
import unittest
class TestOStreamExample(unittest.TestCase):
def test_ostream(self):
import ostream_example
iob = io.BytesIO()
ostream_example.testprint_noflush(iob)
ostream_example.testprint(iob)
assert iob.getvalue() == b"testprint_noflushtestprint\n"
def test_istream(self):
import ostream_example
assert ostream_example.testparse(io.BytesIO(b"4")) == 4
if __name__ == '__main__':
unittest.main()
@cecabert

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commented Aug 3, 2018

Nice example of iostream conversion for pybind11, it is well appreciated :).

However I've noticed that the testparse function fails when it uses std::stream::read instead of operator>>, the return value is just garbage. Moreover when I check what is dumped into the py::bytes read_buffer in the ::underflow function I get the correct value. It seems like there is a synchronisation issue when using read(), any idea how to solve this issue ?

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