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'uttrs' seeks to interoperate Classes definided using attrs and 'astropy units' in a simple manner.

Project description

Uttrs

uttrs seeks to interoperate Classes definided using attrs and astropy units in a simple manner.

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QuatroPe Build Status Documentation Status License Python 3.8+ PyPI

uttrs is mainly three functions:

  • uttr.ib which generates attributes sensitive to units.
  • uttr.array_accessor which allows access to attributes linked to units, and transform them into numpy arrays.
  • uttr.s a class decorator to automatically add the array_accessor.

Code and issues

The entire source code of is hosted in GitHub https://github.com/quatrope/uttrs/

License

Uttrs is under The BSD-3 License

The BSD 3-clause license allows you almost unlimited freedom with the software so long as you include the BSD copyright and license notice in it (found in Fulltext).

Installation

This is the recommended way to install uttrs.

Installing with pip

Make sure that the Python interpreter can load uttrs code. The most convenient way to do this is to use virtualenv, virtualenvwrapper, and pip.

After setting up and activating the virtualenv, run the following command:

$ pip install uttrs
...

That should be it all.

Installing the development version

If you’d like to be able to update your uttrs code occasionally with the latest bug fixes and improvements, follow these instructions:

Make sure that you have Git installed and that you can run its commands from a shell. (Enter git help at a shell prompt to test this.)

Check out uttrs main development branch like so:

$ git clone https://github.com/quatrope/uttrs
...

This will create a directory uttrs in your current directory.

Then you can proceed to install with the commands

$ cd uttrs
$ pip install -e .
...

Documentation

The full documentation of the project are available in https://uttrs.readthedocs.io/

Contact

For bugs or question please contact

Juan B. Cabral: jbcabral@unc.edu.ar

Quick Start

The following piece of code is an example prototype of a Class representing a Galaxy. The Galaxy contains:

  • three arrays (x, y, z) with particle positions, measured in kiloparsecs (u.kpc).
  • three arrays (vx, vy, vz) for the particle velocities, measured in Km/s (u.kms/u.s).
  • an array (m) of particle masses, expressed in solar masses (u.M_sun).
  • a free text for note taking in notes.

In every case we would like to access to position, velocity and mass of the particles, with and without units (as np.ndarray). Suggested units in the information of the attributes behave like this:

  • If the user makes the class instance without unit specification then default assumed unit is used.
  • If, otherwise, another unit is used as input, it is validated the feasibility of the conversion to default unit.
import uttr

import astropy.units as u

@uttr.s
class Galaxy:
    x = uttr.ib(unit=u.kpc)
    y = uttr.ib(unit=u.kpc)
    z = uttr.ib(unit=u.kpc)

    vx = uttr.ib(unit=u.km/u.s)
    vy = uttr.ib(unit=u.km/u.s)
    vz = uttr.ib(unit=u.km/u.s)

    m = uttr.ib(unit=u.M_sun)

    notes = uttr.ib(converter=str)

Creating a galaxy

>>> import numpy as np
>>> import astropy.units as u

# Creating the particle arrays
>>> x = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)
>>> y = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)
>>> z = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)
>>> vx = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)
>>> vy = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)
>>> vz = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)
>>> m = np.random.randint(1000, 10_000, size=5) + np.random.rand(5)

>>> gal = Galaxy(
...     x = x * u.kpc,  # kpc is the suggested unit
...     y = y * u.mpc,  # milliparsec is equivalent to kpc
...     z = z,  # we assume is the suggested kpc unit
...     vx = vx * (u.km/u.s), # the suggested unit
...     vy = vy * (u.km/u.s), # the suggested unit
...     vz = vz, # the suggested unit
...     m = m * u.M_sun, # the suggested unit
...     notes="a random galaxy made with random numbers")

>>> gal
Galaxy(
    x=<Quantity [5632.35740606, 1363.36235923, 3037.46794044, 2785.45299727, 2515.35793673] kpc>,
    y=<Quantity [4457.3573917 , 2873.54575512, 7979.68745148, 5930.55394614, 5903.63598164] mpc>,
    z=<Quantity [6122.35929872, 3740.22821927, 6859.42245056, 7119.8256744 , 3632.74980958] kpc>,
    vx=<Quantity [7141.40469733, 5713.29552487, 5000.535142  , 9366.36402447, 2967.2546077 ] km / s>,
    vy=<Quantity [8514.83018331, 1362.13309457, 1136.30959053, 1985.49551226, 3286.69029298] km / s>,
    vz=<Quantity [6218.56279077, 2015.04638043, 9919.99579782, 1278.94359767, 7228.21626876] km / s>,
    m=<Quantity [5640.62516958, 4070.66620947, 6106.583697  , 4063.39917315, 3028.85393523] solMass>,
    notes='a random galaxy made with random numbers')

# we can access al the attributes in the traditional python way
>>> gal.x
<Quantity [5632.35740606, 1363.36235923, 3037.46794044, 2785.45299727, 2515.35793673] kpc>

>>> gal.vz  # z is now a km/s
<Quantity [6218.56279077, 2015.04638043, 9919.99579782, 1278.94359767, 7228.21626876] km / s>

# We stored y as mpc (milliparsec)
>>> gal.y
<Quantity [8093.44916403, 2198.55398718, 5464.79397835, 1860.72260272, 3636.64010118] mpc>

Simple interaction with numpy.ndarray

We can access all the same attributes declared with uttr.ib but coerced to the default unit as numpy array.

>>> gal.arr_.y
array([0.00809345, 0.00219855, 0.00546479, 0.00186072, 0.00363664])

The above code is equivalent to

>>> gal.y.to_value(u.kpc)
array([0.00809345, 0.00219855, 0.00546479, 0.00186072, 0.00363664])

Equivalent units errors

If we change the unit to something not equivalent to the default unit declares in uttr.ib an exception is raised.

Lets fot example define x as a kilogram (u.kg)

>>> gal = Galaxy(
...     x = x * u.kg,  # kg is not equivalent to kpc
...     y = y,
...     z = z,
...     vx = vx,
...     vy = vy,
...     vz = vz,
...     m = m,
...     notes="a random galaxy made with random numbers")

ValueError: Unit of attribute 'x' must be equivalent to 'kpc'.Found 'kg'.

References

Astropy

Price-Whelan, Adrian M., et al. "The Astropy project: Building an open-science project and status of the v2. 0 core package." The Astronomical Journal 156.3 (2018): 123.

Project details


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