| .. _numpy: |
| |
| NumPy |
| ##### |
| |
| Buffer protocol |
| =============== |
| |
| Python supports an extremely general and convenient approach for exchanging |
| data between plugin libraries. Types can expose a buffer view [#f2]_, which |
| provides fast direct access to the raw internal data representation. Suppose we |
| want to bind the following simplistic Matrix class: |
| |
| .. code-block:: cpp |
| |
| class Matrix { |
| public: |
| Matrix(size_t rows, size_t cols) : m_rows(rows), m_cols(cols) { |
| m_data = new float[rows*cols]; |
| } |
| float *data() { return m_data; } |
| size_t rows() const { return m_rows; } |
| size_t cols() const { return m_cols; } |
| private: |
| size_t m_rows, m_cols; |
| float *m_data; |
| }; |
| |
| The following binding code exposes the ``Matrix`` contents as a buffer object, |
| making it possible to cast Matrices into NumPy arrays. It is even possible to |
| completely avoid copy operations with Python expressions like |
| ``np.array(matrix_instance, copy = False)``. |
| |
| .. code-block:: cpp |
| |
| py::class_<Matrix>(m, "Matrix", py::buffer_protocol()) |
| .def_buffer([](Matrix &m) -> py::buffer_info { |
| return py::buffer_info( |
| m.data(), /* Pointer to buffer */ |
| sizeof(float), /* Size of one scalar */ |
| py::format_descriptor<float>::format(), /* Python struct-style format descriptor */ |
| 2, /* Number of dimensions */ |
| { m.rows(), m.cols() }, /* Buffer dimensions */ |
| { sizeof(float) * m.cols(), /* Strides (in bytes) for each index */ |
| sizeof(float) } |
| ); |
| }); |
| |
| Supporting the buffer protocol in a new type involves specifying the special |
| ``py::buffer_protocol()`` tag in the ``py::class_`` constructor and calling the |
| ``def_buffer()`` method with a lambda function that creates a |
| ``py::buffer_info`` description record on demand describing a given matrix |
| instance. The contents of ``py::buffer_info`` mirror the Python buffer protocol |
| specification. |
| |
| .. code-block:: cpp |
| |
| struct buffer_info { |
| void *ptr; |
| ssize_t itemsize; |
| std::string format; |
| ssize_t ndim; |
| std::vector<ssize_t> shape; |
| std::vector<ssize_t> strides; |
| }; |
| |
| To create a C++ function that can take a Python buffer object as an argument, |
| simply use the type ``py::buffer`` as one of its arguments. Buffers can exist |
| in a great variety of configurations, hence some safety checks are usually |
| necessary in the function body. Below, you can see an basic example on how to |
| define a custom constructor for the Eigen double precision matrix |
| (``Eigen::MatrixXd``) type, which supports initialization from compatible |
| buffer objects (e.g. a NumPy matrix). |
| |
| .. code-block:: cpp |
| |
| /* Bind MatrixXd (or some other Eigen type) to Python */ |
| typedef Eigen::MatrixXd Matrix; |
| |
| typedef Matrix::Scalar Scalar; |
| constexpr bool rowMajor = Matrix::Flags & Eigen::RowMajorBit; |
| |
| py::class_<Matrix>(m, "Matrix", py::buffer_protocol()) |
| .def("__init__", [](Matrix &m, py::buffer b) { |
| typedef Eigen::Stride<Eigen::Dynamic, Eigen::Dynamic> Strides; |
| |
| /* Request a buffer descriptor from Python */ |
| py::buffer_info info = b.request(); |
| |
| /* Some sanity checks ... */ |
| if (info.format != py::format_descriptor<Scalar>::format()) |
| throw std::runtime_error("Incompatible format: expected a double array!"); |
| |
| if (info.ndim != 2) |
| throw std::runtime_error("Incompatible buffer dimension!"); |
| |
| auto strides = Strides( |
| info.strides[rowMajor ? 0 : 1] / (py::ssize_t)sizeof(Scalar), |
| info.strides[rowMajor ? 1 : 0] / (py::ssize_t)sizeof(Scalar)); |
| |
| auto map = Eigen::Map<Matrix, 0, Strides>( |
| static_cast<Scalar *>(info.ptr), info.shape[0], info.shape[1], strides); |
| |
| new (&m) Matrix(map); |
| }); |
| |
| For reference, the ``def_buffer()`` call for this Eigen data type should look |
| as follows: |
| |
| .. code-block:: cpp |
| |
| .def_buffer([](Matrix &m) -> py::buffer_info { |
| return py::buffer_info( |
| m.data(), /* Pointer to buffer */ |
| sizeof(Scalar), /* Size of one scalar */ |
| py::format_descriptor<Scalar>::format(), /* Python struct-style format descriptor */ |
| 2, /* Number of dimensions */ |
| { m.rows(), m.cols() }, /* Buffer dimensions */ |
| { sizeof(Scalar) * (rowMajor ? m.cols() : 1), |
| sizeof(Scalar) * (rowMajor ? 1 : m.rows()) } |
| /* Strides (in bytes) for each index */ |
| ); |
| }) |
| |
| For a much easier approach of binding Eigen types (although with some |
| limitations), refer to the section on :doc:`/advanced/cast/eigen`. |
| |
| .. seealso:: |
| |
| The file :file:`tests/test_buffers.cpp` contains a complete example |
| that demonstrates using the buffer protocol with pybind11 in more detail. |
| |
| .. [#f2] http://docs.python.org/3/c-api/buffer.html |
| |
| Arrays |
| ====== |
| |
| By exchanging ``py::buffer`` with ``py::array`` in the above snippet, we can |
| restrict the function so that it only accepts NumPy arrays (rather than any |
| type of Python object satisfying the buffer protocol). |
| |
| In many situations, we want to define a function which only accepts a NumPy |
| array of a certain data type. This is possible via the ``py::array_t<T>`` |
| template. For instance, the following function requires the argument to be a |
| NumPy array containing double precision values. |
| |
| .. code-block:: cpp |
| |
| void f(py::array_t<double> array); |
| |
| When it is invoked with a different type (e.g. an integer or a list of |
| integers), the binding code will attempt to cast the input into a NumPy array |
| of the requested type. Note that this feature requires the |
| :file:`pybind11/numpy.h` header to be included. |
| |
| Data in NumPy arrays is not guaranteed to packed in a dense manner; |
| furthermore, entries can be separated by arbitrary column and row strides. |
| Sometimes, it can be useful to require a function to only accept dense arrays |
| using either the C (row-major) or Fortran (column-major) ordering. This can be |
| accomplished via a second template argument with values ``py::array::c_style`` |
| or ``py::array::f_style``. |
| |
| .. code-block:: cpp |
| |
| void f(py::array_t<double, py::array::c_style | py::array::forcecast> array); |
| |
| The ``py::array::forcecast`` argument is the default value of the second |
| template parameter, and it ensures that non-conforming arguments are converted |
| into an array satisfying the specified requirements instead of trying the next |
| function overload. |
| |
| Structured types |
| ================ |
| |
| In order for ``py::array_t`` to work with structured (record) types, we first |
| need to register the memory layout of the type. This can be done via |
| ``PYBIND11_NUMPY_DTYPE`` macro, called in the plugin definition code, which |
| expects the type followed by field names: |
| |
| .. code-block:: cpp |
| |
| struct A { |
| int x; |
| double y; |
| }; |
| |
| struct B { |
| int z; |
| A a; |
| }; |
| |
| // ... |
| PYBIND11_MODULE(test, m) { |
| // ... |
| |
| PYBIND11_NUMPY_DTYPE(A, x, y); |
| PYBIND11_NUMPY_DTYPE(B, z, a); |
| /* now both A and B can be used as template arguments to py::array_t */ |
| } |
| |
| The structure should consist of fundamental arithmetic types, ``std::complex``, |
| previously registered substructures, and arrays of any of the above. Both C++ |
| arrays and ``std::array`` are supported. While there is a static assertion to |
| prevent many types of unsupported structures, it is still the user's |
| responsibility to use only "plain" structures that can be safely manipulated as |
| raw memory without violating invariants. |
| |
| Vectorizing functions |
| ===================== |
| |
| Suppose we want to bind a function with the following signature to Python so |
| that it can process arbitrary NumPy array arguments (vectors, matrices, general |
| N-D arrays) in addition to its normal arguments: |
| |
| .. code-block:: cpp |
| |
| double my_func(int x, float y, double z); |
| |
| After including the ``pybind11/numpy.h`` header, this is extremely simple: |
| |
| .. code-block:: cpp |
| |
| m.def("vectorized_func", py::vectorize(my_func)); |
| |
| Invoking the function like below causes 4 calls to be made to ``my_func`` with |
| each of the array elements. The significant advantage of this compared to |
| solutions like ``numpy.vectorize()`` is that the loop over the elements runs |
| entirely on the C++ side and can be crunched down into a tight, optimized loop |
| by the compiler. The result is returned as a NumPy array of type |
| ``numpy.dtype.float64``. |
| |
| .. code-block:: pycon |
| |
| >>> x = np.array([[1, 3],[5, 7]]) |
| >>> y = np.array([[2, 4],[6, 8]]) |
| >>> z = 3 |
| >>> result = vectorized_func(x, y, z) |
| |
| The scalar argument ``z`` is transparently replicated 4 times. The input |
| arrays ``x`` and ``y`` are automatically converted into the right types (they |
| are of type ``numpy.dtype.int64`` but need to be ``numpy.dtype.int32`` and |
| ``numpy.dtype.float32``, respectively). |
| |
| .. note:: |
| |
| Only arithmetic, complex, and POD types passed by value or by ``const &`` |
| reference are vectorized; all other arguments are passed through as-is. |
| Functions taking rvalue reference arguments cannot be vectorized. |
| |
| In cases where the computation is too complicated to be reduced to |
| ``vectorize``, it will be necessary to create and access the buffer contents |
| manually. The following snippet contains a complete example that shows how this |
| works (the code is somewhat contrived, since it could have been done more |
| simply using ``vectorize``). |
| |
| .. code-block:: cpp |
| |
| #include <pybind11/pybind11.h> |
| #include <pybind11/numpy.h> |
| |
| namespace py = pybind11; |
| |
| py::array_t<double> add_arrays(py::array_t<double> input1, py::array_t<double> input2) { |
| py::buffer_info buf1 = input1.request(), buf2 = input2.request(); |
| |
| if (buf1.ndim != 1 || buf2.ndim != 1) |
| throw std::runtime_error("Number of dimensions must be one"); |
| |
| if (buf1.size != buf2.size) |
| throw std::runtime_error("Input shapes must match"); |
| |
| /* No pointer is passed, so NumPy will allocate the buffer */ |
| auto result = py::array_t<double>(buf1.size); |
| |
| py::buffer_info buf3 = result.request(); |
| |
| double *ptr1 = (double *) buf1.ptr, |
| *ptr2 = (double *) buf2.ptr, |
| *ptr3 = (double *) buf3.ptr; |
| |
| for (size_t idx = 0; idx < buf1.shape[0]; idx++) |
| ptr3[idx] = ptr1[idx] + ptr2[idx]; |
| |
| return result; |
| } |
| |
| PYBIND11_MODULE(test, m) { |
| m.def("add_arrays", &add_arrays, "Add two NumPy arrays"); |
| } |
| |
| .. seealso:: |
| |
| The file :file:`tests/test_numpy_vectorize.cpp` contains a complete |
| example that demonstrates using :func:`vectorize` in more detail. |
| |
| Direct access |
| ============= |
| |
| For performance reasons, particularly when dealing with very large arrays, it |
| is often desirable to directly access array elements without internal checking |
| of dimensions and bounds on every access when indices are known to be already |
| valid. To avoid such checks, the ``array`` class and ``array_t<T>`` template |
| class offer an unchecked proxy object that can be used for this unchecked |
| access through the ``unchecked<N>`` and ``mutable_unchecked<N>`` methods, |
| where ``N`` gives the required dimensionality of the array: |
| |
| .. code-block:: cpp |
| |
| m.def("sum_3d", [](py::array_t<double> x) { |
| auto r = x.unchecked<3>(); // x must have ndim = 3; can be non-writeable |
| double sum = 0; |
| for (ssize_t i = 0; i < r.shape(0); i++) |
| for (ssize_t j = 0; j < r.shape(1); j++) |
| for (ssize_t k = 0; k < r.shape(2); k++) |
| sum += r(i, j, k); |
| return sum; |
| }); |
| m.def("increment_3d", [](py::array_t<double> x) { |
| auto r = x.mutable_unchecked<3>(); // Will throw if ndim != 3 or flags.writeable is false |
| for (ssize_t i = 0; i < r.shape(0); i++) |
| for (ssize_t j = 0; j < r.shape(1); j++) |
| for (ssize_t k = 0; k < r.shape(2); k++) |
| r(i, j, k) += 1.0; |
| }, py::arg().noconvert()); |
| |
| To obtain the proxy from an ``array`` object, you must specify both the data |
| type and number of dimensions as template arguments, such as ``auto r = |
| myarray.mutable_unchecked<float, 2>()``. |
| |
| If the number of dimensions is not known at compile time, you can omit the |
| dimensions template parameter (i.e. calling ``arr_t.unchecked()`` or |
| ``arr.unchecked<T>()``. This will give you a proxy object that works in the |
| same way, but results in less optimizable code and thus a small efficiency |
| loss in tight loops. |
| |
| Note that the returned proxy object directly references the array's data, and |
| only reads its shape, strides, and writeable flag when constructed. You must |
| take care to ensure that the referenced array is not destroyed or reshaped for |
| the duration of the returned object, typically by limiting the scope of the |
| returned instance. |
| |
| The returned proxy object supports some of the same methods as ``py::array`` so |
| that it can be used as a drop-in replacement for some existing, index-checked |
| uses of ``py::array``: |
| |
| - ``r.ndim()`` returns the number of dimensions |
| |
| - ``r.data(1, 2, ...)`` and ``r.mutable_data(1, 2, ...)``` returns a pointer to |
| the ``const T`` or ``T`` data, respectively, at the given indices. The |
| latter is only available to proxies obtained via ``a.mutable_unchecked()``. |
| |
| - ``itemsize()`` returns the size of an item in bytes, i.e. ``sizeof(T)``. |
| |
| - ``ndim()`` returns the number of dimensions. |
| |
| - ``shape(n)`` returns the size of dimension ``n`` |
| |
| - ``size()`` returns the total number of elements (i.e. the product of the shapes). |
| |
| - ``nbytes()`` returns the number of bytes used by the referenced elements |
| (i.e. ``itemsize()`` times ``size()``). |
| |
| .. seealso:: |
| |
| The file :file:`tests/test_numpy_array.cpp` contains additional examples |
| demonstrating the use of this feature. |
| |
| Ellipsis |
| ======== |
| |
| Python 3 provides a convenient ``...`` ellipsis notation that is often used to |
| slice multidimensional arrays. For instance, the following snippet extracts the |
| middle dimensions of a tensor with the first and last index set to zero. |
| |
| .. code-block:: python |
| |
| a = # a NumPy array |
| b = a[0, ..., 0] |
| |
| The function ``py::ellipsis()`` function can be used to perform the same |
| operation on the C++ side: |
| |
| .. code-block:: cpp |
| |
| py::array a = /* A NumPy array */; |
| py::array b = a[py::make_tuple(0, py::ellipsis(), 0)]; |