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Apache Arrow is the universal columnar format and multi-language toolbox for fast data interchange and in-memory analytics

0 0 16 C++
.. Licensed to the Apache Software Foundation (ASF) under one
.. or more contributor license agreements. See the NOTICE file
.. distributed with this work for additional information
.. regarding copyright ownership. The ASF licenses this file
.. to you under the Apache License, Version 2.0 (the
.. "License"); you may not use this file except in compliance
.. with the License. You may obtain a copy of the License at
.. http://www.apache.org/licenses/LICENSE-2.0
.. Unless required by applicable law or agreed to in writing,
.. software distributed under the License is distributed on an
.. "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
.. KIND, either express or implied. See the License for the
.. specific language governing permissions and limitations
.. under the License.
.. currentmodule:: pyarrow
.. cpp:namespace:: arrow
.. _extending:
Using pyarrow from C++ and Cython Code
======================================
pyarrow provides both a Cython and C++ API, allowing your own native code
to interact with pyarrow objects.
C++ API
-------
.. default-domain:: cpp
The Arrow C++ and PyArrow C++ header files are bundled with a pyarrow installation.
To get the absolute path to this directory (like ``numpy.get_include()``), use:
.. code-block:: python
import pyarrow as pa
pa.get_include()
Assuming the path above is on your compiler's include path, the pyarrow API
can be included using the following directive:
.. code-block:: cpp
#include <arrow/python/pyarrow.h>
This will not include other parts of the Arrow API, which you will need
to include yourself (for example ``arrow/api.h``).
When building C extensions that use the Arrow C++ libraries, you must add
appropriate linker flags. We have provided functions ``pa.get_libraries``
and ``pa.get_library_dirs`` which return a list of library names and
likely library install locations (if you installed pyarrow with pip or
conda). These must be included when declaring your C extensions with
setuptools (see below).
.. note::
The PyArrow-specific C++ code is now a part of the PyArrow source tree
and not Arrow C++. That means the header files and ``arrow_python`` library
are not necessarily installed in the same location as that of Arrow C++ and
will no longer be automatically findable by CMake.
Initializing the API
~~~~~~~~~~~~~~~~~~~~
.. function:: int import_pyarrow()
Initialize inner pointers of the pyarrow API. On success, 0 is
returned. Otherwise, -1 is returned and a Python exception is set.
It is mandatory to call this function before calling any other function
in the pyarrow C++ API. Failing to do so will likely lead to crashes.
Wrapping and Unwrapping
~~~~~~~~~~~~~~~~~~~~~~~
pyarrow provides the following functions to go back and forth between
Python wrappers (as exposed by the pyarrow Python API) and the underlying
C++ objects.
.. function:: bool arrow::py::is_array(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Array` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Array` instance.
.. function:: bool arrow::py::is_batch(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`RecordBatch` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.RecordBatch` instance.
.. function:: bool arrow::py::is_buffer(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Buffer` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Buffer` instance.
.. function:: bool arrow::py::is_data_type(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`DataType` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.DataType` instance.
.. function:: bool arrow::py::is_field(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Field` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Field` instance.
.. function:: bool arrow::py::is_scalar(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Scalar` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Scalar` instance.
.. function:: bool arrow::py::is_schema(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Schema` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Schema` instance.
.. function:: bool arrow::py::is_table(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Table` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Table` instance.
.. function:: bool arrow::py::is_tensor(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :class:`Tensor` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.Tensor` instance.
.. function:: bool arrow::py::is_sparse_coo_tensor(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :type:`SparseCOOTensor` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.SparseCOOTensor` instance.
.. function:: bool arrow::py::is_sparse_csc_matrix(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :type:`SparseCSCMatrix` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.SparseCSCMatrix` instance.
.. function:: bool arrow::py::is_sparse_csf_tensor(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :type:`SparseCSFTensor` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.SparseCSFTensor` instance.
.. function:: bool arrow::py::is_sparse_csr_matrix(PyObject* obj)
Return whether *obj* wraps an Arrow C++ :type:`SparseCSRMatrix` pointer;
in other words, whether *obj* is a :py:class:`pyarrow.SparseCSRMatrix` instance.
The following functions expect a pyarrow object, unwrap the underlying
Arrow C++ API pointer, and return it as a :class:`Result` object. An error
may be returned if the input object doesn't have the expected type.
.. function:: Result<std::shared_ptr<Array>> arrow::py::unwrap_array(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Array` pointer from *obj*.
.. function:: Result<std::shared_ptr<RecordBatch>> arrow::py::unwrap_batch(PyObject* obj)
Unwrap and return the Arrow C++ :class:`RecordBatch` pointer from *obj*.
.. function:: Result<std::shared_ptr<Buffer>> arrow::py::unwrap_buffer(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Buffer` pointer from *obj*.
.. function:: Result<std::shared_ptr<DataType>> arrow::py::unwrap_data_type(PyObject* obj)
Unwrap and return the Arrow C++ :class:`DataType` pointer from *obj*.
.. function:: Result<std::shared_ptr<Field>> arrow::py::unwrap_field(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Field` pointer from *obj*.
.. function:: Result<std::shared_ptr<Scalar>> arrow::py::unwrap_scalar(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Scalar` pointer from *obj*.
.. function:: Result<std::shared_ptr<Schema>> arrow::py::unwrap_schema(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Schema` pointer from *obj*.
.. function:: Result<std::shared_ptr<Table>> arrow::py::unwrap_table(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Table` pointer from *obj*.
.. function:: Result<std::shared_ptr<Tensor>> arrow::py::unwrap_tensor(PyObject* obj)
Unwrap and return the Arrow C++ :class:`Tensor` pointer from *obj*.
.. function:: Result<std::shared_ptr<SparseCOOTensor>> arrow::py::unwrap_sparse_coo_tensor(PyObject* obj)
Unwrap and return the Arrow C++ :type:`SparseCOOTensor` pointer from *obj*.
.. function:: Result<std::shared_ptr<SparseCSCMatrix>> arrow::py::unwrap_sparse_csc_matrix(PyObject* obj)
Unwrap and return the Arrow C++ :type:`SparseCSCMatrix` pointer from *obj*.
.. function:: Result<std::shared_ptr<SparseCSFTensor>> arrow::py::unwrap_sparse_csf_tensor(PyObject* obj)
Unwrap and return the Arrow C++ :type:`SparseCSFTensor` pointer from *obj*.
.. function:: Result<std::shared_ptr<SparseCSRMatrix>> arrow::py::unwrap_sparse_csr_matrix(PyObject* obj)
Unwrap and return the Arrow C++ :type:`SparseCSRMatrix` pointer from *obj*.
The following functions take an Arrow C++ API pointer and wrap it in a
pyarray object of the corresponding type. A new reference is returned.
On error, NULL is returned and a Python exception is set.
.. function:: PyObject* arrow::py::wrap_array(const std::shared_ptr<Array>& array)
Wrap the Arrow C++ *array* in a :py:class:`pyarrow.Array` instance.
.. function:: PyObject* arrow::py::wrap_batch(const std::shared_ptr<RecordBatch>& batch)
Wrap the Arrow C++ record *batch* in a :py:class:`pyarrow.RecordBatch` instance.
.. function:: PyObject* arrow::py::wrap_buffer(const std::shared_ptr<Buffer>& buffer)
Wrap the Arrow C++ *buffer* in a :py:class:`pyarrow.Buffer` instance.
.. function:: PyObject* arrow::py::wrap_data_type(const std::shared_ptr<DataType>& data_type)
Wrap the Arrow C++ *data_type* in a :py:class:`pyarrow.DataType` instance.
.. function:: PyObject* arrow::py::wrap_field(const std::shared_ptr<Field>& field)
Wrap the Arrow C++ *field* in a :py:class:`pyarrow.Field` instance.
.. function:: PyObject* arrow::py::wrap_scalar(const std::shared_ptr<Scalar>& scalar)
Wrap the Arrow C++ *scalar* in a :py:class:`pyarrow.Scalar` instance.
.. function:: PyObject* arrow::py::wrap_schema(const std::shared_ptr<Schema>& schema)
Wrap the Arrow C++ *schema* in a :py:class:`pyarrow.Schema` instance.
.. function:: PyObject* arrow::py::wrap_table(const std::shared_ptr<Table>& table)
Wrap the Arrow C++ *table* in a :py:class:`pyarrow.Table` instance.
.. function:: PyObject* arrow::py::wrap_tensor(const std::shared_ptr<Tensor>& tensor)
Wrap the Arrow C++ *tensor* in a :py:class:`pyarrow.Tensor` instance.
.. function:: PyObject* arrow::py::wrap_sparse_coo_tensor(const std::shared_ptr<SparseCOOTensor>& sparse_tensor)
Wrap the Arrow C++ *sparse_tensor* in a :py:class:`pyarrow.SparseCOOTensor` instance.
.. function:: PyObject* arrow::py::wrap_sparse_csc_matrix(const std::shared_ptr<SparseCSCMatrix>& sparse_tensor)
Wrap the Arrow C++ *sparse_tensor* in a :py:class:`pyarrow.SparseCSCMatrix` instance.
.. function:: PyObject* arrow::py::wrap_sparse_csf_tensor(const std::shared_ptr<SparseCSFTensor>& sparse_tensor)
Wrap the Arrow C++ *sparse_tensor* in a :py:class:`pyarrow.SparseCSFTensor` instance.
.. function:: PyObject* arrow::py::wrap_sparse_csr_matrix(const std::shared_ptr<SparseCSRMatrix>& sparse_tensor)
Wrap the Arrow C++ *sparse_tensor* in a :py:class:`pyarrow.SparseCSRMatrix` instance.
Cython API
----------
.. default-domain:: py
The Cython API more or less mirrors the C++ API, but the calling convention
can be different as required by Cython. In Cython, you don't need to
initialize the API as that will be handled automatically by the ``cimport``
directive.
.. note::
Classes from the Arrow C++ API are renamed when exposed in Cython, to
avoid named clashes with the corresponding Python classes. For example,
C++ Arrow arrays have the ``CArray`` type and ``Array`` is the
corresponding Python wrapper class.
Wrapping and Unwrapping
~~~~~~~~~~~~~~~~~~~~~~~
The following functions expect a pyarrow object, unwrap the underlying
Arrow C++ API pointer, and return it. NULL is returned (without setting
an exception) if the input is not of the right type.
.. function:: pyarrow_unwrap_array(obj) -> shared_ptr[CArray]
Unwrap the Arrow C++ :cpp:class:`Array` pointer from *obj*.
.. function:: pyarrow_unwrap_batch(obj) -> shared_ptr[CRecordBatch]
Unwrap the Arrow C++ :cpp:class:`RecordBatch` pointer from *obj*.
.. function:: pyarrow_unwrap_buffer(obj) -> shared_ptr[CBuffer]
Unwrap the Arrow C++ :cpp:class:`Buffer` pointer from *obj*.
.. function:: pyarrow_unwrap_data_type(obj) -> shared_ptr[CDataType]
Unwrap the Arrow C++ :cpp:class:`CDataType` pointer from *obj*.
.. function:: pyarrow_unwrap_field(obj) -> shared_ptr[CField]
Unwrap the Arrow C++ :cpp:class:`Field` pointer from *obj*.
.. function:: pyarrow_unwrap_scalar(obj) -> shared_ptr[CScalar]
Unwrap the Arrow C++ :cpp:class:`Scalar` pointer from *obj*.
.. function:: pyarrow_unwrap_schema(obj) -> shared_ptr[CSchema]
Unwrap the Arrow C++ :cpp:class:`Schema` pointer from *obj*.
.. function:: pyarrow_unwrap_table(obj) -> shared_ptr[CTable]
Unwrap the Arrow C++ :cpp:class:`Table` pointer from *obj*.
.. function:: pyarrow_unwrap_tensor(obj) -> shared_ptr[CTensor]
Unwrap the Arrow C++ :cpp:class:`Tensor` pointer from *obj*.
ARROW-4223: [Python] Support scipy.sparse integration This is to resolve [ARROW-4223](https://issues.apache.org/jira/browse/ARROW-4223). Closes #4779 from rok/ARROW-4223 and squashes the following commits: eca388556 <Rok> Adding type check to from_scipy. d5484bf15 <Rok> Fixing scipy->sparse_tensor tests for dtype=f2. 4d7d2b032 <Rok> Implementing review feedback. 22e864d2d <Rok> Fixing deserialization issue. Rebasing for new tensor type names. 927bf5d0d <Kenta Murata> Add SparseCSRIndex::Make b06429d2c <Kenta Murata> Add SparseCOOIndex::Make 90cbadf5f <Kenta Murata> Extract a common part from ReadSparseTensorPayload and ReadSparseTensor f4d2e1e20 <Rok> Enabling serialization with pydata/sparse. db1fb5a75 <Rok> Applying review feedback for python tests. 2bc253474 <Rok> Re-enabling test_sparse_tensor_coo_components_serialization. 11068eb89 <Rok> Adding from_scipy and to scipy methods to SparseTensorCOO and SparseTensorCSR. b13604d9e <Rok> Temporarily disabling test_sparse_tensor_csr_components_serialization test. 56df620d4 <Kenta Murata> Prevent copying buffers on component serialization of a SparseTensor 958b354ee <Rok> Changes to GetSparseTensorMessage to enable SparseTensor to components serialization. c54f005e9 <Rok> Changes to GetSparseTensorMessage. Enabling comparison for SparseTensor roundtrip test. 247cdbd5d <Rok> Adding scipy.sparse integration. Lead-authored-by: Rok <rok@mihevc.org> Co-authored-by: Kenta Murata <mrkn@mrkn.jp> Signed-off-by: Antoine Pitrou <antoine@python.org>
2019-11-13 10:43:58 +01:00
.. function:: pyarrow_unwrap_sparse_coo_tensor(obj) -> shared_ptr[CSparseCOOTensor]
Unwrap the Arrow C++ :cpp:type:`SparseCOOTensor` pointer from *obj*.
.. function:: pyarrow_unwrap_sparse_csc_matrix(obj) -> shared_ptr[CSparseCSCMatrix]
Unwrap the Arrow C++ :cpp:type:`SparseCSCMatrix` pointer from *obj*.
.. function:: pyarrow_unwrap_sparse_csf_tensor(obj) -> shared_ptr[CSparseCSFTensor]
Unwrap the Arrow C++ :cpp:type:`SparseCSFTensor` pointer from *obj*.
ARROW-4223: [Python] Support scipy.sparse integration This is to resolve [ARROW-4223](https://issues.apache.org/jira/browse/ARROW-4223). Closes #4779 from rok/ARROW-4223 and squashes the following commits: eca388556 <Rok> Adding type check to from_scipy. d5484bf15 <Rok> Fixing scipy->sparse_tensor tests for dtype=f2. 4d7d2b032 <Rok> Implementing review feedback. 22e864d2d <Rok> Fixing deserialization issue. Rebasing for new tensor type names. 927bf5d0d <Kenta Murata> Add SparseCSRIndex::Make b06429d2c <Kenta Murata> Add SparseCOOIndex::Make 90cbadf5f <Kenta Murata> Extract a common part from ReadSparseTensorPayload and ReadSparseTensor f4d2e1e20 <Rok> Enabling serialization with pydata/sparse. db1fb5a75 <Rok> Applying review feedback for python tests. 2bc253474 <Rok> Re-enabling test_sparse_tensor_coo_components_serialization. 11068eb89 <Rok> Adding from_scipy and to scipy methods to SparseTensorCOO and SparseTensorCSR. b13604d9e <Rok> Temporarily disabling test_sparse_tensor_csr_components_serialization test. 56df620d4 <Kenta Murata> Prevent copying buffers on component serialization of a SparseTensor 958b354ee <Rok> Changes to GetSparseTensorMessage to enable SparseTensor to components serialization. c54f005e9 <Rok> Changes to GetSparseTensorMessage. Enabling comparison for SparseTensor roundtrip test. 247cdbd5d <Rok> Adding scipy.sparse integration. Lead-authored-by: Rok <rok@mihevc.org> Co-authored-by: Kenta Murata <mrkn@mrkn.jp> Signed-off-by: Antoine Pitrou <antoine@python.org>
2019-11-13 10:43:58 +01:00
.. function:: pyarrow_unwrap_sparse_csr_matrix(obj) -> shared_ptr[CSparseCSRMatrix]
Unwrap the Arrow C++ :cpp:type:`SparseCSRMatrix` pointer from *obj*.
The following functions take a Arrow C++ API pointer and wrap it in a
pyarray object of the corresponding type. An exception is raised on error.
.. function:: pyarrow_wrap_array(const shared_ptr[CArray]& array) -> object
Wrap the Arrow C++ *array* in a Python :class:`pyarrow.Array` instance.
.. function:: pyarrow_wrap_batch(const shared_ptr[CRecordBatch]& batch) -> object
Wrap the Arrow C++ record *batch* in a Python :class:`pyarrow.RecordBatch` instance.
.. function:: pyarrow_wrap_buffer(const shared_ptr[CBuffer]& buffer) -> object
Wrap the Arrow C++ *buffer* in a Python :class:`pyarrow.Buffer` instance.
.. function:: pyarrow_wrap_data_type(const shared_ptr[CDataType]& data_type) -> object
Wrap the Arrow C++ *data_type* in a Python :class:`pyarrow.DataType` instance.
.. function:: pyarrow_wrap_field(const shared_ptr[CField]& field) -> object
Wrap the Arrow C++ *field* in a Python :class:`pyarrow.Field` instance.
.. function:: pyarrow_wrap_resizable_buffer(const shared_ptr[CResizableBuffer]& buffer) -> object
Wrap the Arrow C++ resizable *buffer* in a Python :class:`pyarrow.ResizableBuffer` instance.
.. function:: pyarrow_wrap_scalar(const shared_ptr[CScalar]& scalar) -> object
Wrap the Arrow C++ *scalar* in a Python :class:`pyarrow.Scalar` instance.
.. function:: pyarrow_wrap_schema(const shared_ptr[CSchema]& schema) -> object
Wrap the Arrow C++ *schema* in a Python :class:`pyarrow.Schema` instance.
.. function:: pyarrow_wrap_table(const shared_ptr[CTable]& table) -> object
Wrap the Arrow C++ *table* in a Python :class:`pyarrow.Table` instance.
.. function:: pyarrow_wrap_tensor(const shared_ptr[CTensor]& tensor) -> object
Wrap the Arrow C++ *tensor* in a Python :class:`pyarrow.Tensor` instance.
.. function:: pyarrow_wrap_sparse_coo_tensor(const shared_ptr[CSparseCOOTensor]& sparse_tensor) -> object
Wrap the Arrow C++ *COO sparse tensor* in a Python :class:`pyarrow.SparseCOOTensor` instance.
.. function:: pyarrow_wrap_sparse_csc_matrix(const shared_ptr[CSparseCSCMatrix]& sparse_tensor) -> object
Wrap the Arrow C++ *CSC sparse tensor* in a Python :class:`pyarrow.SparseCSCMatrix` instance.
.. function:: pyarrow_wrap_sparse_csf_tensor(const shared_ptr[CSparseCSFTensor]& sparse_tensor) -> object
Wrap the Arrow C++ *COO sparse tensor* in a Python :class:`pyarrow.SparseCSFTensor` instance.
.. function:: pyarrow_wrap_sparse_csr_matrix(const shared_ptr[CSparseCSRMatrix]& sparse_tensor) -> object
Wrap the Arrow C++ *CSR sparse tensor* in a Python :class:`pyarrow.SparseCSRMatrix` instance.
Example
~~~~~~~
The following Cython module shows how to unwrap a Python object and call
the underlying C++ object's API.
.. code-block:: python
# distutils: language=c++
from pyarrow.lib cimport *
def get_array_length(obj):
# Just an example function accessing both the pyarrow Cython API
# and the Arrow C++ API
cdef shared_ptr[CArray] arr = pyarrow_unwrap_array(obj)
if arr.get() == NULL:
raise TypeError("not an array")
return arr.get().length()
To build this module, you will need a slightly customized ``setup.py`` file
(this is assuming the file above is named ``example.pyx``):
.. code-block:: python
from setuptools import setup
from Cython.Build import cythonize
import os
import numpy as np
import pyarrow as pa
ext_modules = cythonize("example.pyx")
for ext in ext_modules:
# The Numpy C headers are currently required
ext.include_dirs.append(np.get_include())
ext.include_dirs.append(pa.get_include())
ext.libraries.extend(pa.get_libraries())
ext.library_dirs.extend(pa.get_library_dirs())
if os.name == 'posix':
ext.extra_compile_args.append('-std=c++20')
setup(ext_modules=ext_modules)
Compile the extension:
.. code-block:: bash
python setup.py build_ext --inplace
Building Extensions against PyPI Wheels
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The Python wheels have the Arrow C++ libraries bundled in the top level
``pyarrow/`` install directory. On Linux and macOS, these libraries have an ABI
tag like ``libarrow.so.17`` which means that linking with ``-larrow`` using the
linker path provided by ``pyarrow.get_library_dirs()`` will not work right out
of the box. To fix this, you must run ``pyarrow.create_library_symlinks()``
once as a user with write access to the directory where pyarrow is
installed. This function will attempt to create symlinks like
``pyarrow/libarrow.so``. For example:
.. code-block:: bash
pip install pyarrow
python -c "import pyarrow; pyarrow.create_library_symlinks()"
Toolchain Compatibility (Linux)
"""""""""""""""""""""""""""""""
The Python wheels for Linux are built using the
`PyPA manylinux images <https://quay.io/organization/pypa>`_ which use
the AlmaLinux ``gcc-toolset-12``. In addition to the other notes
above, if you are compiling C++ using these shared libraries, you will need
to make sure you use a compatible toolchain as well or you might see a
segfault during runtime.