pyuvdata

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pyuvdata defines a pythonic interface to interferometric data sets. Currently pyuvdata supports reading and writing of miriad and uvfits files and reading of CASA measurement sets and FHD (Fast Holographic Deconvolution) visibility save files.

Motivation

The three main goals are:

  1. To provide a high quality, well documented path to convert between data formats
  2. Support the direct use of datasets from python with minimal software
  3. Provide precise data definition via both human readable code and high quality online documentation

Package Details

pyuvdata has three major user classes:

  • UVData: supports interferometric data (visibilities) and associated metadata
  • UVCal: supports interferometric calibration solutions (antenna-based) and associated metadata
  • UVBeam: supports primary beams (E-field or power) and associated metadata (Note that this is a new object and is very experimental)

UVData Tested File Paths

  • uvfits -> miriad (aipy)
  • miriad (aipy) -> uvfits
  • FHD -> uvfits
  • FHD -> miriad (aipy)
  • CASA measurement sets -> miriad (aipy)
  • CASA measurement sets -> uvfits

UVData File standard notes

  • miriad is supported for aipy-style analysis, further testing is required for use in the miriad package
  • uvfits conforms to AIPS memo 117 (as of May 2015). It is tested against FHD, CASA, and AIPS. However AIPS is limited to <80 antennas and CASA imaging does not seem to support >255 antennas.
  • FHD (read-only support, tested against MWA and PAPER data)
  • CASA measurement sets (read-only support)

UVCal file formats

  • calfits (a new format defined in pyuvdata, detailed memo coming soon). Note that this format was recently defined and may change in coming versions, based on user needs. Consider it to be in a beta version, but we will strive to make future versions backwards compatible with the current format.

UVBeam file formats

  • regularly gridded fits for both E-field and power beams
  • non-standard HEALPix fits for both E-field and power beams (in an ImageHDU rather than a binary table to support frequency, polarization and E-field vector axes)

Known Issues and Planned Improvements

  • UVData: different multiple spectral windows or multiple sources are not currently supported
  • UVData: testing against miriad package
  • UVData: replacing AIPY and pyephem with astropy+NOVAS for time and phase calculations
  • UVData: add support for writing CASA measurement sets
  • UVData: phasing is tested to a part in 10^3, and assumes planar array. Improvements are tracked on Issue #148.
  • UVCal: expand support for calibration solutions: support other formats beyond FITS
  • UVBeam: support reading in native beam model file formats (e.g. CST, HFSS)
  • UVBeam: support reading/writing/combining standard HEALPix FITs files (individual files per frequency, polarization and E-field vector)

For details see the issue log.

Community Guidelines

Contributions to this package to add new file formats or address any of the issues in the issue log are very welcome. Please submit improvements as pull requests against the repo after verifying that the existing tests pass and any new code is well covered by unit tests.

Bug reports or feature requests are also very welcome, please add them to the issue log after verifying that the issue does not already exist. Comments on existing issues are also welcome.

History

pyuvdata was originally developed in the low frequency 21cm community to support the development of calibration and foreground subtraction pipelines. Particular focus has been paid to supporting drift and phased array modes.

Installation

Dependencies

First install dependencies. The numpy and astropy versions are important, so be sure to make sure these are up to date before you install.

For anaconda users, we suggest using conda to install astropy, numpy and scipy and conda-forge for aipy (conda install -c conda-forge aipy).

  • numpy >= 1.10
  • scipy
  • astropy >= 1.2
  • pyephem
  • aipy >= 2.1.5
  • casacore-python (for CASA measurement set reading functionality)

Install pyuvdata

For simple installation, the latest stable version is available via pip using pip install pyuvdata

For measurement set functionality, install python-casacore

python-casacore is required in order to use the measurement set capabilities of pyuvdata. python-casacore requires the casacore c++ libraries. To install via conda, run

conda config --add channels conda-forge

conda install python-casacore (This will install both python-casacore and the casacore c++ libraries as a requirement)

If you don’t want to use conda, the casacore c++ libraries are available for ubuntu through the kern suite. On OSX, casacore is available through the ska-sa brew tap. The python-casacore library (with manual install instructions) is available at https://github.com/casacore/python-casacore

Optionally install the development version

For the development version, clone the repository using git clone https://github.com/HERA-Team/pyuvdata.git

Navigate into the directory and run python setup.py install. Note that this will automatically install any missing dependencies. If you use anaconda or another package manager you might prefer to first install the dependencies as described above.

To install without dependencies, run python setup.py develop --no-deps or pip install --no-deps

Tests

Requires installation of nose package. From the source pyuvdata directory run nosetests pyuvdata.

API

The primary interface to data from python is via the UVData object. It provides import and export functionality to all supported file formats (UVFITS, Miriad, FHD) and can be interacted with directly. The primary calibration interface is via the UVCal object. The attributes of the UVData and UVCal objects are described in the uvdata_parameters and uvcal_parameters descriptions.