py-pol 1.3.0
Jones and Mueller polarization - Optics
License: MIT license
Keywords: py_pol, optics, polarization, Jones, Stokes, Mueller

========================
Python polarization
========================


.. image:: https://img.shields.io/pypi/dm/py_pol
        :target: https://pypi.org/project/py_pol/

.. image:: https://img.shields.io/pypi/v/py_pol.svg
        :target: https://pypi.org/project/py-pol/


.. image:: https://readthedocs.org/projects/py-pol/badge/?version=latest
        :target: https://py-pol.readthedocs.io/en/master/
        :alt: Documentation Status



* Free software: MIT license
* Documentation: https://py-pol.readthedocs.io/en/master/
* Source code moved to GitHub: https://github.com/JesusDelHoyo/py_pol

.. image:: logo.png
   :width: 75
   :align: right



Features
--------
Py-pol is a Python library for Jones and Stokes-Mueller polarization optics. It has 4 main modules:

    * jones_vector - Light polarization states in Jones formalism (2x1 vectors).

    * jones_matrix - Optical elements polarization properties in Jones formalism (2x2 matrices).

    * stokes - Light polarization states in Mueller-Stokes formalism (4x1 vectors).

    * mueller - Optical elements polarization properties in Mueller-Stokes formalism (4x4 matrices).


Each one has its own class, with multiple methods for generation, operation and parameters extraction.

Examples
--------

Jones formalism
===============

Generating Jones vectors and Matrices

.. code-block:: python

    from py_pol.jones_vector import Jones_vector
    from py_pol.jones_matrix import Jones_matrix
    from py_pol.utils import degrees

    j0 = Jones_vector("j0")
    j0.linear_light(angle=45*degrees)

    m0 = Jones_matrix("m0")
    m0.diattenuator_linear( p1=0.75, p2=0.25, angle=45*degrees)

    m1 = Jones_matrix("m1")
    m1.quarter_waveplate(angle=0 * degrees)

    j1=m1*m0*j0

Extracting information form Jones Vector.

.. code-block:: python

    print(j0,'\n')
    print(j0.parameters)

.. code-block:: python

    j0 = [+0.707; +0.707]

    parameters of j0:
        intensity        : 1.000 arb.u
        alpha            : 45.000 deg
        delay            : 0.000 deg
        azimuth          : 45.000 deg
        ellipticity angle: 0.000 deg
        a, b             : 1.000  0.000
        phase            : 0.000 deg

.. code-block:: python

    print(j1,'\n')
    print(j1.parameters)

.. code-block:: python

        m1 * m0 @45.00 deg * j0 = [+0.530+0.000j; +0.000+0.530j]'

        parameters of m1 * m0 @45.00 deg * j0:
            intensity        : 0.562 arb.u
            alpha            : 45.000 deg
            delay            : 90.000 deg
            azimuth          : 8.618 deg
            ellipticity angle: -45.000 deg
            a, b             : 0.530  0.530
            phase            : 0.000 deg

Extracting information form Jones Matrices.

.. code-block:: python

    print(m0,'\n')
    print(m0.parameters)

.. code-block:: python

        m0 @45.00 deg =
              [+0.500, +0.250]
              [+0.250, +0.500]

        parameters of m0 @45.00 deg:
            is_homogeneous: True
            delay:          0.000 deg
            diattenuation:  0.800


.. code-block:: python


    print(m1,'\n')
    print(m1.parameters)


.. code-block:: python


        m1 =
              [+1+0j, +0+0j]
              [+0+0j, +0+1j]

        parameters of m1:
            is_homogeneous: True
            delay:          90.000 deg
            diattenuation:  0.000




Stokes-Mueller formalism
========================

Generating Stokes vectors and Mueller matrices.


.. code-block:: python


    from py_pol.stokes import Stokes
    from py_pol.mueller import Mueller
    from py_pol.utils import degrees

    j0 = Stokes("j0")
    j0.linear_light(angle=45*degrees)

    m1 = Mueller("m1")
    m1.diattenuator_linear(p1=1, p2=0, angle=0*degrees)

    j1=m1*j0


Extracting information from Stokes vectors.

Determining the intensity of a Stokes vector:

.. code-block:: python

    i1=j0.parameters.intensity()
    print("intensity = {:4.3f} arb. u.".format(i1))


.. code-block:: python

    intensity = 1.000 arb. u.

Determining all the parameters of a Stokes vector:

.. code-block:: python


    print(j0,'\n')
    print(j0.parameters)

.. code-block:: python

        j0 = [ +1;  +0;  +1;  +0]


        parameters of j0:
            intensity             : 1.000 arb. u.
            amplitudes            : E0x 0.707, E0y 0.707, E0_unpol 0.000
            degree polarization   : 1.000
            degree linear pol.    : 1.000
            degree   circular pol.: 0.000
            alpha                 : 45.000 deg
            delay                 : 0.000 deg
            azimuth               : 45.000 deg
            ellipticity  angle    : 0.000 deg
            ellipticity  param    : 0.000
            eccentricity          : 1.000
            polarized vector      : [+1.000; +0.000; +1.000; +0.000]'
            unpolarized vector    : [+0.000; +0.000; +0.000; +0.000]'

.. code-block:: python


    print(j1,'\n')
    print(j1.parameters)

.. code-block:: python

        m1 * j0 = [+0.500; +0.500; +0.000; +0.000]

        parameters of m1 * j0:
            intensity             : 0.500 arb. u.
            amplitudes            : E0x 0.707, E0y 0.000, E0_unpol 0.000
            degree polarization   : 1.000
            degree linear pol.    : 1.000
            degree   circular pol.: 0.000
            alpha                 : 0.000 deg
            delay                 : 0.000 deg
            azimuth               : 0.000 deg
            ellipticity  angle    : 0.000 deg
            ellipticity  param    : 0.000
            eccentricity          : 1.000
            polarized vector      : [+0.500; +0.500; +0.000; +0.000]'
            unpolarized vector    : [+0.000; +0.000; +0.000; +0.000]'




Extracting information from Mueller matrices.

.. code-block:: python

    m2 = Mueller("m2")
    m2.diattenuator_retarder_linear(D=90*degrees, p1=1, p2=0.5, angle=0)
    delay = m2.parameters.retardance()
    print("delay = {:2.1f}Âº".format(delay/degrees))

.. code-block:: python

    delay = 90.0Âº

There is a function in Parameters_Jones_Vector class, .get_all() that will compute all the parameters available and stores in a dictionary .dict_params(). Info about dict parameters can be revised using the print function.


.. code-block:: python

    print(m2,'\n')
    m2.parameters.get_all()
    print(m2.parameters)


.. code-block:: python

        m2 =
          [+0.6250, +0.3750, +0.0000, +0.0000]
          [+0.3750, +0.6250, +0.0000, +0.0000]
          [+0.0000, +0.0000, +0.0000, +0.5000]
          [+0.0000, +0.0000, -0.5000, +0.0000]

      Parameters of m2:
          Transmissions:
              - Mean                  : 62.5 %.
              - Maximum               : 100.0 %.
              - Minimum               : 25.0 %.
          Diattenuation:
              - Total                 : 0.600.
              - Linear                : 0.600.
              - Circular              : 0.000.
          Polarizance:
              - Total                 : 0.600.
              - Linear                : 0.600.
              - Circular              : 0.000.
          Spheric purity              : 0.872.
          Retardance                  : 1.571.
          Polarimetric purity         : 1.000.
          Depolarization degree       : 0.000.
          Depolarization factors:
              - Euclidean distance    : 1.732.
              - Depolarization factor : 0.000.
          Polarimetric purity indices:
              - P1                    : 1.000.
              - P2                    : 1.000.
              - P3                    : 1.000.

There are many types of Mueller matrices. The Check_Mueller calss implements all the checks that can be performed in order to clasify a Mueller matrix. They are stored in the checks field of Mueller class.


.. code-block:: python

    m1 = Mueller("m1")
    m1.diattenuator_linear(p1=1, p2=0.2, angle=0*degrees)
    print(m1,'\n')

    c1 = m1.checks.is_physical()
    c2 = m1.checks.is_homogeneous()
    c3 = m1.checks.is_retarder()
    print('The linear diattenuator is physical: {}; hogeneous: {}; and a retarder: {}.'.format(c1, c2, c3))


.. code-block:: python

    m1 =
      [+0.520, +0.480, +0.000, +0.000]
      [+0.480, +0.520, +0.000, +0.000]
      [+0.000, +0.000, +0.200, +0.000]
      [+0.000, +0.000, +0.000, +0.200]


    The linear diattenuator is physical: True; hogeneous: True; and a retarder: False.

Drawings
========

The modules also allows to obtain graphical representation of polarization.

Drawing polarization ellipse for Jones vectors.

.. image:: ellipse_Jones_1.png
   :width: 600

.. image:: ellipse_Jones_3.png
   :width: 600


Drawing polarization ellipse for Stokes vectors with random distribution due to unpolarized part of light.

.. image:: ellipse_Stokes_1.png
   :width: 600

.. image:: ellipse_Stokes_2.png
   :width: 600

Drawing Stokes vectors in Poincare sphere.

.. image:: poincare2.png
   :width: 600

.. image:: poincare3.png
   :width: 600

.. image:: poincare4.png
   :width: 600


Conventions
-----------
In this module we assume the light is propagated along the z direction. Then, the electric field is defined as:

.. math::

 \overrightarrow{E}(x,y,z)=\left[\begin{array}{c}
 E_{x}(x,y)\\
 E_{y}(x,y)\\
 0
 \end{array}\right]e^{i(kz-\omega t)},

where :math:`E_x` and :math:`E_y` are the two components of the Jones vector. Also, we define the x component as the origin of global phase, so it is 0 when :math:`E_x` is real and positive. In the extraordinary case when :math:`E_x = 0`, the global phase is extracted from the y component. Then, the most general unitary Jones vector can be described as:

.. math::

 E=E_{0}e^{i\Phi}\left[\begin{array}{c}
 \cos(\alpha)\\
 \sin(\alpha)e^{i\delta}
 \end{array}\right]

where :math:`E_0` is the electric field amplitude, :math:`\Phi` is the global phase, and :math:`\alpha` and :math:`\delta` are the characteristic angles of the light state.

This phase convention also affects the description of retarders. For example, a linear retarder with an azimuth of 0Âº for its fast eigenstate will have the following Jones matrix:

.. math::

 J_{R}=\left[\begin{array}{cc}
 1 & 0\\
 0 & e^{-i\Delta}
 \end{array}\right],

where :math:`\Delta` is the retarder retardance.


Authors
-------
.. image:: logoUCM.png
   :width: 125
   :align: right

* Jesus del Hoyo <jhoyo@ucm.es>
* Luis Miguel Sanchez Brea <optbrea@ucm.es>

    **Universidad Complutense de Madrid**,
    Faculty of Physical Sciences,
    Department of Optics
    Plaza de las ciencias 1,
    ES-28040 Madrid (Spain)

Citing
------
* J. Hoyo, L. M. Sanchez-Brea, A. Soria-Garcia, "Open source library for polarimetric calculations "py_pol"", Proc. SPIE 11875, Computational Optics 2021, 1187506 (14 September 2021); doi: 10.1117/12.2597163, https://spie.org/Publications/Proceedings/Paper/10.1117/12.2597163?SSO=1.
* J. del Hoyo, L.M. Sanchez Brea, "py-pol, Python module for polarization optics", https://pypi.org/project/py-pol/ (2019)

References
----------

* D. Goldstein "Polarized light" 2nd edition, Marcel Dekker (1993).

* J. J. Gil, R. Ossikovsky "Polarized light and the Mueller Matrix approach", CRC Press (2016).

* C. Brosseau "Fundamentals of Polarized Light" Wiley (1998).

* R. Martinez-Herrero, P. M. Mejias, G. Piquero "Characterization of partially polarized light fields" Springer series in Optical sciences (2009).

* J. M. Bennet "Handbook of Optics 1" Chapter 5 'Polarization'.

* R. A. Chipman "Handbook of Optics 2" Chapter 2 'Polarimetry'.

* S. Y. Lu and RA Chipman, "Homogeneous and inhomogeneous Jones matrices",  J. Opt. Soc. Am. A 11(2) 766 (1994).




Acknowlegments
--------------
This software was initially developed for the project Retos-ColaboraciÃ³n 2016 "Ecograb" (RTC-2016-5277-5) and "Teluro-AEI" (RTC2019-007113-3) of Ministerio de EconomÃ­a y Competitivdad (Spain) and the European funds for regional development (EU), led by Luis Miguel Sanchez-Brea.


Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

1.3.0
-----------------------
* Adition of ret as variable name for retardance in all retarder creation methods.
* Adition of general, diattenuator_general and retarder_general methods which accept both characteristic angles and azimuth_ellipticity methods.
* Addition of biaxial_material for creating retarders from their ordinary and extraordinary refractive indices.
* Addition of Liquid crystal advanced example using different biaxial layer models.
* Citation file.
* Bug fix of multiplication of elements by arrays.
* Fix in the definition of righ-handed and left-handed in the polarization ellipse representation.
* Other bugfixes.

1.2.0
-----------------------
* Addition of general creation methods that encompases both azimuth_ellipticity and charac_angles methods (which are maintained for retrocompatibility).
* Added ret as parameters of retarders for homogeneity in naming (R is maintained for retrocompatibility).
* New circular diattenuators and retarders methods.
* Limits for alpha, delay, azimuth, ellipticity and retardance values are optional through the force_limits variable in creation methods, which is False by default.
* New liquid crystal advanced exmple.
* Bugfixes.

1.1.4
-----------------------
* bugfix Jones_matrix.parameters.transmission
* Remove the global phase of a diattenuattor before checking if it is a diattenuator
* bugfix Jones_matrix.analysis.decompose_pure
* Include amplitude_phase drawing
* Change the representation origin to 'lower'

1.1.3
-----------------------
* bugfix zeroslike
* bugfix not taking shape = False as flatten the object.

1.1.2
-----------------------
* bugfix Jones_vector.parameters.global_phase

1.1.1
-----------------------
* from_list can also be used with lists of Py_pol objects, lists and tuples. Also, all elemeents may have more than one elemnt.
* minor bugfixes


1.1.0 (2022-3-31)
-------------------
* Added base class Py_pol
* Objects are now iterable
* 3D drawings changed to Plotly
* New density and existence methods


1.0.4 (2022-02-07)
------------------
* Bug fix related to variable limits

1.0.4 (2021-07-19)
------------------
* Bug fixes


1.0.3 (2021-01-22)
------------------
* Bug fixes


1.0.2 (2020-07-04)
--------------------
* Implemented workaround of axis_equal issue.


1.0.0 (2020-06-04)
-------------------
py_pol multidimensional. Alpha state

This is a big overhaul with many changes. All of them are based on the possibility of storing several vector/matrices in the same object. This reduces significantly the time required to perform the same operation to multiple vectors/matrices, using numpy methods instead of for loops. We have calculated that the reduction is around one order of magnitude.

New methods have been introduced. First, methods available for Mueller / Stoes modules have been created also for Jones (when possible). Also, some bugs and errors in the calculations have been solved.

Finally, some method and argument names have been changed to be consistent between different classes. Also, the default value of arguments with the same name have also been unified.

The biggest TO DO we have are tests. Right now, we only have tests for the Jones_vector class. However, we thought that it would be useful to release this version so the community can use it.

NOTE: Due to the change of argument and method names, this version is not compatible with the previous ones.


0.2.2 (2019-09-04)
------------------
* Bug fixes.


0.2.1 (2019-09-04)
------------------
* Bug fixes.
* Solve incidents.
* Start to homogenize structures for both Jones and Stokes.


0.2.0 (2019-05-25)
------------------
pre-alpha state

* Upgrade to Python 3
* Stable version including tests


0.1.5 (2019-02-25)
------------------
* Jones_vector, Jones_matrix, Stokes works.
* Jones_vector: simplify function to represent better Jones vectors.
* tests drawing: Made tests for drawing

* Mueller is in progress.
* Functions = 9/10
* Documentation = 8/10
* Tutorial = 8/10.
* Examples = 8/10.
* Tests = 8/10
* Drawing = 10/10. Finished. Polarization ellipse for Jones and Stokes (partially random). Stokes on PoincarÃ© sphere.


0.1.4 (2019-02-03)
------------------
* bug fixes


0.1.3 (2019-01-22)
------------------
* Fixed axis_equal issue.
* Jones_vector, Jones_matrix, Stokes works.
* Mueller is in progress.
* Functions = 9/10
* Documentation = 8/10
* Tutorial = 7/10.
* Examples = 6/10.
* Drawing = 0/10.


0.1.1 (2018-12-22)
------------------
* First release on PyPI in alpha state.


0.0.0 (2018-11-22)
------------------
First implementation of py_pol.