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# pyuvdata [](https://circleci.com/gh/RadioAstronomySoftwareGroup/pyuvdata?branch=master) [](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/actions) [](https://dev.azure.com/radioastronomysoftwaregroup/pyuvdata/_build/latest?definitionId=1&branchName=master) [](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvdata) [](https://doi.org/10.21105/joss.00140) pyuvdata defines a pythonic interface to interferometric data sets. Currently pyuvdata supports reading and writing of miriad, uvfits, and uvh5 files and reading of CASA measurement sets and FHD ([Fast Holographic Deconvolution](https://github.com/EoRImaging/FHD)) visibility save files. # Motivation The 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 four major user classes: * UVData: supports interferometric data (visibilities) and associated metadata * UVCal: supports interferometric calibration solutions (antenna-based) and associated metadata (Note that this is a fairly new object, consider it to be a beta version) * UVBeam: supports primary beams (E-field or power) and associated metadata (Note that this is a fairly new object, consider it to be a beta version) * UVFlag: A class to handle the manipulation and combination of flags for data sets. Also can convert raw data quality metrics into flags using thresholding. (This object is very new and experimental. Consider it to be a beta version) ## UVData File standard notes * miriad has been thoroughly tested with aipy-style miriad files and minimally tested with ATCA files * 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 uvfits import does not seem to support >255 antennas. * uvh5 is an HDF5-based file format defined by the HERA collaboration, details in the [uvh5 memo](docs/references/uvh5_memo.pdf). Note that this is a somewhat new format, so it may evolve a bit but we will strive to make future versions backwards compatible with the current format. It is probably not compatible with other interferometric HDF5 files defined by other groups. * 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, details in the [calfits_memo](docs/references/calfits_memo.pdf). Note that this format was recently defined and may change in coming versions, based on user needs. Consider it to be a beta version, but we will strive to make future versions backwards compatible with the current format. * FHD calibration files (read-only support) ## 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) * read support for CST beam text files, with a defined yaml file format for metadata, details here: [cst settings file](docs/cst_settings_yaml.rst) ## Under Development * UVCal: object and calfits file format (beta version) * UVBeam: object and beamfits file format (beta version) * UVFlag: object and HDF5 file format. (beta version) ## Known Issues and Planned Improvements * UVData: phasing (and the accuracy on the uvw coordinates) is only known to be good to 2cm on a 3km baseline (this is limited by the accuracy of the test file, see the [phasing memo](docs/references/phasing.pdf) for more details). * UVData: Multiple spectral windows or multiple sources are not currently supported * UVData: add support for writing CASA measurement sets * UVBeam: support phased-array antenna beams (e.g. MWA beams). * UVFlag: Adding requires a high level knowledge of individual objects. (see [issue #653](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues/653)) For details see the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues). ## Community Guidelines Contributions to this package to add new file formats or address any of the issues in the [issue log](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/issues) are very welcome, as are bug reports and feature requests. Please see our [guide on contributing](.github/CONTRIBUTING.md) # Telescopes pyuvdata has been used with data from the following telescopes. If you use it on data from a telescope we don't have listed here please let us know how it went via an issue! We would like to make pyuvdata generally useful to the community for as many telescopes as possible. * MWA * HERA * PAPER * LWA * ALMA * VLA * ATCA # Versioning We use a `generation.major.minor` version number format. We use the `generation` number for very significant improvements or major rewrites, the `major` number to indicate substantial package changes (intended to be released every 3-4 months) and the `minor` number to release smaller incremental updates (intended to be released approximately monthly and which usually do not include breaking API changes). We do our best to provide a significant period (usually 2 major generations) of deprecation warnings for all breaking changes to the API. We track all changes in our [changelog](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/master/CHANGELOG.md). # Documentation A tutorial with example usage and developer API documentation is hosted on [ReadTheDocs](https://pyuvdata.readthedocs.io). # History pyuvdata was originally developed in the low frequency 21cm community to support the development of and interchange of data between calibration and foreground subtraction pipelines. Particular focus has been paid to supporting drift and phased array modes. # Citation Please cite pyuvdata by citing our JOSS paper: Hazelton et al, (2017), pyuvdata: an interface for astronomical interferometeric datasets in python, Journal of Open Source Software, 2(10), 140, doi:10.21105/joss.00140 [ADS Link](https://ui.adsabs.harvard.edu/abs/2017JOSS....2..140H); [Bibtex entry](http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2017JOSS....2..140H&data_type=BIBTEX&db_key=GEN&nocookieset=1) # Installation Simple installation via conda is available for users, developers should follow the directions under [Developer Installation](#developer-installation) below. For simple installation, the latest stable version is available via conda (preferred: ```conda install -c conda-forge pyuvdata```) or pip (```pip install pyuvdata```). There are some optional dependencies that are required for specific functionality, which will not be installed automatically by conda or pip. See [Dependencies](#dependencies) for details on installing optional dependencies. Note that as of v2, `pyuvdata` is only supported on python 3.6+. ## Dependencies Required: * numpy >= 1.15 * scipy * astropy >= 3.2.3 * h5py * setuptools_scm Optional: * python-casacore (for working with CASA measurement sets) * astropy-healpix (for working with beams in HEALPix formats) * pyyaml (for working with settings files for CST beam files) The numpy and astropy versions are important, so make sure these are up to date. We suggest using conda to install all the dependencies. If you want to install python-casacore and astropy-healpix, you'll need