pyemd 2.0.0
A Python wrapper for Ofir Pele and Michael Werman's implementation of the Earth Mover's Distance.
Requires Python: >=3.12

.. image:: https://img.shields.io/github/actions/workflow/status/wmayner/pyemd/build_wheels.yml?style=flat-square&maxAge=86400
    :target: https://github.com/wmayner/pyemd/actions/workflows/build_wheels.yml
    :alt: Build status badge
.. image:: https://img.shields.io/pypi/pyversions/pyemd.svg?style=flat-square&maxAge=86400
    :target: https://pypi.org/project/pyemd/
    :alt: Python versions badge

PyEMD: Fast EMD for Python
==========================

**This library is maintained for backward compatibility only.**

PyEMD v2.0+ is a thin wrapper around `POT (Python Optimal Transport)
<https://pythonot.github.io/>`_. **For new projects, use POT directly**—it
offers the same functionality plus a much broader range of optimal transport
features.

PyEMD continues to be maintained for existing projects that depend on its API.

----

PyEMD computes the `Earth Mover's Distance
<https://en.wikipedia.org/wiki/Earth_mover%27s_distance>`_ (Wasserstein distance)
between histograms using NumPy.


Usage
-----

.. code:: python

    >>> from pyemd import emd
    >>> import numpy as np
    >>> first_histogram = np.array([0.0, 1.0])
    >>> second_histogram = np.array([5.0, 3.0])
    >>> distance_matrix = np.array([[0.0, 0.5],
    ...                             [0.5, 0.0]])
    >>> emd(first_histogram, second_histogram, distance_matrix)
    3.5

You can also get the associated minimum-cost flow:

.. code:: python

    >>> from pyemd import emd_with_flow
    >>> emd_with_flow(first_histogram, second_histogram, distance_matrix)
    (3.5, [[0.0, 0.0], [0.0, 1.0]])

You can also calculate the EMD directly from two arrays of observations:

.. code:: python

    >>> from pyemd import emd_samples
    >>> first_array = [1, 2, 3, 4]
    >>> second_array = [2, 3, 4, 5]
    >>> emd_samples(first_array, second_array, bins=2)
    0.5


API Documentation
-----------------

emd()
~~~~~

.. code:: python

    emd(first_histogram,
        second_histogram,
        distance_matrix,
        extra_mass_penalty=-1.0)

*Arguments:*

- ``first_histogram`` *(array-like)*: A 1D array of length *N*.
- ``second_histogram`` *(array-like)*: A 1D array of length *N*.
- ``distance_matrix`` *(array-like)*: A 2D array of size at least *N* × *N*.
  This defines the underlying metric, or ground distance, by giving the pairwise
  distances between the histogram bins.
  **NOTE: It must represent a metric; there is no warning if it doesn't.**

*Keyword Arguments:*

- ``extra_mass_penalty`` *(float)*: The penalty for extra mass. If you want the
  resulting distance to be a metric, it should be at least half the diameter of
  the space (maximum possible distance between any two points). If you want
  partial matching you can set it to zero (but then the resulting distance is
  not guaranteed to be a metric). The default value is ``-1.0``, which means
  the maximum value in the distance matrix is used.

*Returns:* *(float)* The EMD value.

----

emd_with_flow()
~~~~~~~~~~~~~~~

.. code:: python

    emd_with_flow(first_histogram,
                  second_histogram,
                  distance_matrix,
                  extra_mass_penalty=-1.0)

Arguments are the same as for ``emd()``.

*Returns:* *(tuple(float, list(list(float))))* The EMD value and the associated
minimum-cost flow.

----

emd_samples()
~~~~~~~~~~~~~

.. code:: python

    emd_samples(first_array,
                second_array,
                extra_mass_penalty=-1.0,
                distance='euclidean',
                normalized=True,
                bins='auto',
                range=None)

*Arguments:*

- ``first_array`` *(Iterable)*: An array of samples used to generate a
  histogram.
- ``second_array`` *(Iterable)*: An array of samples used to generate a
  histogram.

*Keyword Arguments:*

- ``extra_mass_penalty`` *(float)*: Same as for ``emd()``.
- ``distance`` *(string or function)*: A string or function implementing
  a metric on a 1D ``np.ndarray``. Defaults to the Euclidean distance.
  Currently limited to 'euclidean' or your own function, which must take
  a 1D array and return a square 2D array of pairwise distances.
- ``normalized`` (*boolean*): If true (default), treat histograms as fractions
  of the dataset. If false, treat histograms as counts. In the latter case the
  EMD will vary greatly by array length.
- ``bins`` *(int or string)*: The number of bins to include in the generated
  histogram. If a string, must be one of the bin selection algorithms accepted
  by ``np.histogram()``. Defaults to ``'auto'``, which gives the maximum of the
  'sturges' and 'fd' estimators.
- ``range`` *(tuple(int, int))*: The lower and upper range of the bins, passed
  to ``numpy.histogram()``. Defaults to the range of the union of
  ``first_array`` and ``second_array``. Note: if the given range is not a
  superset of the default range, no warning will be given.

*Returns:* *(float)* The EMD value between the histograms of ``first_array``
and ``second_array``.

----


Development Setup
-----------------

This project uses `uv <https://docs.astral.sh/uv/>`_ for dependency management.

Quick start::

    # Install uv (if not already installed)
    curl -LsSf https://astral.sh/uv/install.sh | sh

    # Clone and setup
    git clone https://github.com/wmayner/pyemd.git
    cd pyemd
    uv sync --all-extras

    # Install in editable mode
    uv pip install -e .

    # Run tests
    uv run pytest

**Note:** For development workflows, see the ``DEVELOPING.md`` file in the repository.

Dependencies are locked in ``uv.lock`` for reproducibility.


Limitations and Caveats
-----------------------

- ``emd()`` and ``emd_with_flow()``:

  - The ``distance_matrix`` is assumed to represent a metric; there is no check
    to ensure that this is true.

- ``emd_with_flow()``:

  - The flow matrix does not contain the flows to/from the extra mass bin.


Credit
------

- **PyEMD v2.0+** uses the `POT (Python Optimal Transport)
  <https://pythonot.github.io/>`_ library by Rémi Flamary et al.

- **PyEMD v1.x** was a Python wrapper for the `emd_hat
  <https://ofirpele.droppages.com/>`_ C++ implementation by Ofir Pele and
  Michael Werman.


Citation
--------

For PyEMD v2.0+
~~~~~~~~~~~~~~~

If you use PyEMD v2.0 or later, please cite the POT library:

Rémi Flamary et al. POT: Python Optimal Transport. *Journal of Machine Learning
Research*, 22(78):1-8, 2021.

.. code-block:: latex

    @article{flamary2021pot,
      title={POT: Python Optimal Transport},
      author={Flamary, R{\'e}mi and Courty, Nicolas and Gramfort, Alexandre and
              Alaya, Mokhtar Z. and Boisbunon, Aur{\'e}lie and Chambon, Stanislas and
              Chapel, Laetitia and Corenflos, Adrien and Fatras, Kilian and
              Fournier, Nemo and Gautheron, L{\'e}o and Gayraud, Nathalie T.H. and
              Janati, Hicham and Rakotomamonjy, Alain and Redko, Ievgen and
              Rolet, Antoine and Schutz, Antony and Seguy, Vivien and
              Sutherland, Danica J. and Tavenard, Romain and Tong, Alexander and
              Vayer, Titouan},
      journal={Journal of Machine Learning Research},
      volume={22},
      number={78},
      pages={1--8},
      year={2021}
    }

For PyEMD v1.x or the original C++ implementation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If you use PyEMD v1.x, or wish to cite the original C++ algorithm that PyEMD
was built on, please cite the following papers:

Ofir Pele and Michael Werman. Fast and robust earth mover's distances. *Proc.
2009 IEEE 12th Int. Conf. on Computer Vision*, Kyoto, Japan, 2009, pp. 460-467.

.. code-block:: latex

    @INPROCEEDINGS{pele2009,
      title={Fast and robust earth mover's distances},
      author={Pele, Ofir and Werman, Michael},
      booktitle={2009 IEEE 12th International Conference on Computer Vision},
      pages={460--467},
      year={2009},
      month={September},
      organization={IEEE}
    }

Ofir Pele and Michael Werman. A linear time histogram metric for improved SIFT
matching. *Computer Vision - ECCV 2008*, Marseille, France, 2008, pp. 495-508.

.. code-block:: latex

    @INPROCEEDINGS{pele2008,
      title={A linear time histogram metric for improved sift matching},
      author={Pele, Ofir and Werman, Michael},
      booktitle={Computer Vision--ECCV 2008},
      pages={495--508},
      year={2008},
      month={October},
      publisher={Springer}
    }