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Handle uncertainties within pandas dataframes and series

Project description

upandas

upandas makes it easy to use quantities with uncertainties in pandas DataFrames and Series.

upandas relies on the excellent uncertainties package, and of course pandas.

# A dataframe with nominal values in columns x and y,
# and their respective uncertainties in u_x, u_y

In [1]: n=3; df = pd.DataFrame({ 'x': randn(n),  'u_x': 0.1*rand(n),
   ...:                   'y': randn(n), 'u_y': 0.1*rand(n) })

In [2]: df
Out[2]:
          x       u_x         y       u_y
0 -1.735288  0.014020 -1.426411  0.093879
1 -0.677756  0.084329 -1.254212  0.034601
2  2.410181  0.054435 -1.611307  0.020315

# Convert col/u_col pairs to uarray columns
In [3]: uf = separate_to_u(df)
In [4]: uf
Out[4]:
                x               y
0  -1.735+/-0.014    -1.43+/-0.09
1    -0.68+/-0.08  -1.254+/-0.035
2     2.41+/-0.05  -1.611+/-0.020

# Operate on columns in the DataFrame as usual,
# but propagate the uncertainties
In [5]: uf['xy2'] = uf['x'] * uf['y']**2
In [6]: uf
Out[6]:
                x               y           xy2
0  -1.735+/-0.014    -1.43+/-0.09    -3.5+/-0.5
1    -0.68+/-0.08  -1.254+/-0.035  -1.07+/-0.15
2     2.41+/-0.05  -1.611+/-0.020   6.26+/-0.21

# Convert back to a conventional dataframe
# for e.g. storage to HDF5.
In [17]: u_to_separate(uf)
Out[17]:
          x       u_x         y       u_y       xy2     u_xy2
0 -1.735288  0.014020 -1.426411  0.093879 -3.530698  0.465620
1 -0.677756  0.084329 -1.254212  0.034601 -1.066143  0.145112
2  2.410181  0.054435 -1.611307  0.020315  6.257576  0.211830

Getting Started

Prerequisites

upandas relies on uncertainties and pandas, but pip will install these if needed.

Installing

pip install upandas

Running the tests

Basic tests are included, using pytest. In the base directory:

pytest tests 

or just make test.

Usage

upandas so far provides only two functions:

  • separate_to_u(df): converts col, u_col pairs to a uarray column col.
  • u_to_separate(df): converts a uarray column col to a pair col, u_col.

If applied to a Series, these functions look at the 'row' index rather than columns.

Built With

Note that as a 'modern' python project and uses pyproject.toml rather than setuptools setup.py.

If you want to develop locally, pull this repository and execute... TBC.

Contributing

Please do send me pull requests!

Versioning

We use SemVer for versioning.

Authors

TODO

  • MultiIndex support.
  • Make ufloats a pandas extensions type, although not clear this is needed.
  • Make uarrays a pandas [https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.api.extensions.ExtensionArray.html#pandas.api.extensions.ExtensionArray] extension array, although again not clear if this is needed.
  • Register pandas custom accessors, so that we can be a bit more pythonic about the conversion: df.u.from_separate()...,
  • ... and df.u.nomnal_values, df.u.std_devs.
  • More tests

License

This project is licensed under the Monash/BSD 2-Clause License - see the LICENSE file for details.

Acknowledgments

Inspired by the extensive support of uncertainties in lyse, as part of the labscript suite.

Project details


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