xcoll 0.3.6__py3-none-any.whl → 0.5.0__py3-none-any.whl

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/docs/advanced/pycpp/numpy.rst

@@ -0,0 +1,463 @@
+.. _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;
+        py::ssize_t itemsize;
+        std::string format;
+        py::ssize_t ndim;
+        std::vector<py::ssize_t> shape;
+        std::vector<py::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 a 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(py::init([](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);
+
+            return 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. This feature requires the :file:`pybind11/numpy.h`
+header to be included. Note that :file:`pybind11/numpy.h` does not depend on
+the NumPy headers, and thus can be used without declaring a build-time
+dependency on NumPy; NumPy>=1.7.0 is a runtime dependency.
+
+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.
+
+There are several methods on arrays; the methods listed below under references
+work, as well as the following functions based on the NumPy API:
+
+- ``.dtype()`` returns the type of the contained values.
+
+- ``.strides()`` returns a pointer to the strides of the array (optionally pass
+  an integer axis to get a number).
+
+- ``.flags()`` returns the flag settings. ``.writable()`` and ``.owndata()``
+  are directly available.
+
+- ``.offset_at()`` returns the offset (optionally pass indices).
+
+- ``.squeeze()`` returns a view with length-1 axes removed.
+
+- ``.view(dtype)`` returns a view of the array with a different dtype.
+
+- ``.reshape({i, j, ...})`` returns a view of the array with a different shape.
+  ``.resize({...})`` is also available.
+
+- ``.index_at(i, j, ...)`` gets the count from the beginning to a given index.
+
+
+There are also several methods for getting references (described below).
+
+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 = static_cast<double *>(buf1.ptr);
+        double *ptr2 = static_cast<double *>(buf2.ptr);
+        double *ptr3 = static_cast<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 (py::ssize_t i = 0; i < r.shape(0); i++)
+            for (py::ssize_t j = 0; j < r.shape(1); j++)
+                for (py::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 (py::ssize_t i = 0; i < r.shape(0); i++)
+            for (py::ssize_t j = 0; j < r.shape(1); j++)
+                for (py::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``:
+
+- ``.ndim()`` returns the number of dimensions
+
+- ``.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.
+In Python 2, the syntactic sugar ``...`` is not available, but the singleton
+``Ellipsis`` (of type ``ellipsis``) can still be used directly.
+
+.. 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)];
+
+.. versionchanged:: 2.6
+   ``py::ellipsis()`` is now also available in Python 2.
+
+Memory view
+===========
+
+For a case when we simply want to provide a direct accessor to C/C++ buffer
+without a concrete class object, we can return a ``memoryview`` object. Suppose
+we wish to expose a ``memoryview`` for 2x4 uint8_t array, we can do the
+following:
+
+.. code-block:: cpp
+
+    const uint8_t buffer[] = {
+        0, 1, 2, 3,
+        4, 5, 6, 7
+    };
+    m.def("get_memoryview2d", []() {
+        return py::memoryview::from_buffer(
+            buffer,                                    // buffer pointer
+            { 2, 4 },                                  // shape (rows, cols)
+            { sizeof(uint8_t) * 4, sizeof(uint8_t) }   // strides in bytes
+        );
+    })
+
+This approach is meant for providing a ``memoryview`` for a C/C++ buffer not
+managed by Python. The user is responsible for managing the lifetime of the
+buffer. Using a ``memoryview`` created in this way after deleting the buffer in
+C++ side results in undefined behavior.
+
+We can also use ``memoryview::from_memory`` for a simple 1D contiguous buffer:
+
+.. code-block:: cpp
+
+    m.def("get_memoryview1d", []() {
+        return py::memoryview::from_memory(
+            buffer,               // buffer pointer
+            sizeof(uint8_t) * 8   // buffer size
+        );
+    })
+
+.. note::
+
+    ``memoryview::from_memory`` is not available in Python 2.
+
+.. versionchanged:: 2.6
+    ``memoryview::from_memory`` added.