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# pyuvdata [![Build Status](https://travis-ci.org/RadioAstronomySoftwareGroup/pyuvdata.svg?branch=master)](https://travis-ci.org/RadioAstronomySoftwareGroup/pyuvdata) [![Coverage Status](https://coveralls.io/repos/github/RadioAstronomySoftwareGroup/pyuvdata/badge.svg?branch=master)](https://coveralls.io/github/RadioAstronomySoftwareGroup/pyuvdata?branch=master) 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 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 (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 new object and is very experimental, consider it to be an alpha version) ## UVData Tested File Paths * uvfits -> miriad * uvfits -> uvh5 * miriad -> uvfits * miriad -> uvh5 * FHD -> uvfits * FHD -> miriad * CASA measurement sets -> miriad * CASA measurement sets -> uvfits * uvh5 -> uvfits * uvh5 -> miriad ## 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. * uvh5 is an HDF5-based file format defined by the HERA collaboration, and will be defined by a memo (coming soon). Note that this is a new format and is very experimental, consider it to be an alpha version. 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, a detailed memo is available here: [calfits_memo](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/master/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 in 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 ## Under Development * UVData: uvh5 file format (alpha version), note that this is probably not compatible with other interferometric HDF5 files defined by other groups. * UVData: phasing was recently updated to use astropy. It has been tested against MWA files and matches to better than 2 cm (5mm if starting from antenna positions rather than the uvws). See the phasing memo in docs/references for more details. * UVCal: object and calfits file format (beta version) * UVBeam: object and beamfits file format (alpha 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 in docs/references for more details). * UVData: Multiple spectral windows or multiple sources are not currently supported * UVData: Add testing against miriad package (currently only tested against aipy derived files) * UVData: Concatenation of multiple datasets is somewhat slow. (see issue #406 for proposed fix) * UVData: add support for writing CASA measurement sets * UVBeam: support reading/writing/combining standard HEALPix FITs files (individual files per frequency, polarization and E-field vector) * UVBeam: support phased-array antenna beams. 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. 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. # 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 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 calibration and foreground subtraction pipelines. Particular focus has been paid to supporting drift and phased array modes. # Installation For simple installation, the latest stable version is available via conda (preferred: ```conda install -c conda-forge pyuvdata```) or pip (```pip install pyuvdata```) ## Optionally install the development version First install the dependencies, see below for package recommendations and extra dependencies for HEALPix beams and CASA measurement set functionalities. Clone the repository using ```git clone https://github.com/RadioAstronomySoftwareGroup/pyuvdata.git``` Navigate into the directory and run ```python setup.py install```. Note that this will attempt to automatically install any missing dependencies. If you use anaconda or another package manager you might prefer to first install the dependencies as described below. To install without dependencies, run ```python setup.py develop --no-deps``` or ```pip install --no-deps``` To compile the binary extension modules such that you can successfully run `import pyuvdata` from the top-level directory of your Git checkout, run: ``` python setup.py build_ext --inplace ``` ## 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, scipy, and optionally h5py, and conda-forge for optionally installing python-casacore and healpy (e.g. ```conda install -c conda-forge python-casacore```). * numpy >= 1.14 * scipy * astropy >= 2.0 * h5py (optional: for reading and writing uvh5 format) * python-casacore (optional: for CASA measurement set reading functionality) * healpy (optional: working with beams in HEALPix formats) ### For CASA 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 do not want to use conda, the casacore c++ libraries are available for ubuntu through the [kern suite](http://kernsuite.info/). On OSX, casacore is available through the [ska-sa brew tap](https://github.com/ska-sa/homebrew-tap). The python-casacore library (with manual install instructions) is available at https://github.com/casacore/python-casacore ### For working with beams in HEALPix formats, install healpy To install via conda, run ```conda install -c conda-forge healpy``` ## 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 functionality from all supported file formats (UVFITS, Miriad, UVH5, FHD, CASA measurement sets) and export to UVFITS, Miriad, and UVH5 formats and can be interacted with directly. Similarly, the primary calibration and beam interfaces are via the UVCal and UVBeam objects. The attributes of the UVData, UVCal and UVBeam objects are described in the uvdata_parameters, uvcal_parameters and uvbeam_parameters descriptions at https://pyuvdata.readthedocs.io or [here](https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/master/docs).