# Changelog
All notable changes to this project will be documented in this file.

## [Unreleased]

## [1.4.0] - 2019-05-23

### Added
- made an option to not save the `lst_array` to uvfits files.
- `conjugate_bls` option to `UVData.get_antenna_redundancies`
- `UVData.conjugate_bls` method to conjugate baselines to get the desired baseline directions.
- `UVData.reorder_blts` method to reorder the data along the blt axis (and optionally also conjugate baselines), and a new `blt_order` optional parameter on UVData objects to track the ordering (including through read/writes).
- `lst_array` is now saved to UVFITS files (even though it's not a standard parameter) so that it doesn't have to be recalculated

### Fixed
- Fixed a bug in how FHD uvw vectors were oriented (and visibilities were conjugated)
- Fixed a bug in `UVData.inflate_by_redundancy` when Nblts is not equal to Nbls * Ntimes.
- Fixed a bug in UVData when reading in an FHD file with a single time integration.
- Fixed a bug in how the longitudinal branch cut was handled in beam interpolation
- Changed the way interpolation splines are saved in UVBeam to fix errors related to polarization selections.
- Python 3: `np.string_` call now uses `keepdims=True` to guard against `antenna_names` being cast as an array.

### Changed
- Testing framework changed from `nose` to `pytest`.
- `uvdata.set_lsts_from_time_array` only calculates lsts for unique elements in `time_array`.

## [1.3.8] - 2019-05-01

### Added
- Optional `x_orientation` parameter to utils functions polstr2num, polnum2str, jstr2num and jnum2str to allow for E/N based polarization strings (rather than just x/y based ones)
- New optional `x_orientation` parameter on UVBeam (paralleling UVData and UVCal), with read/write support in beamfits
- Added `x_orientation` as an optional parameter in read_cst_beam and in cst settings yaml files.
- All str2num or num2str calls on UVData and UVBeam pass the object's x_orientation
- New `UVData.fast_concat` method to allow fast concatenation of UVData objects (or files) along a particular axis.
- Added preliminary `UVFlag` module from hera_qm to pyuvdata. Will eventually promote to `UVBase` object, but for now this is undocumented functionality.

### Deprecated
- Defined 'east' and 'north' as the allowed 'x_orientation' values in UVData and UVCal, Backwards compatiblity support exists for 'E' and 'N' values
- `UVData.order_pols` method in favor of `UVData.reorder_pols`.

### Fixed
- Building pyuvdata on macOS now targets minimum macOS 10.9 if run on macOS 10.9 or above
- Possible bug where `check_variables` dictionary can change size during `read_miriad` call


## [1.3.7] - 2019-04-02

### Added
- Added `add_to_history` kwarg to UVH5.write_uvh5_part
- `_healpix_interp_bilinear` as a new interpolation method in `UVBeam`
- `freq_interpolation_kind` added as an attribute to `UVBeam`
- `tol` added as keyword argument to `UVBeam._interp_freq` which allows for a fast return of `data_array` slice if nearest-neighbor frequencies are all within the distance tolerance.
- `polarizations` added as keyword argument to `UVBeam` interpolation methods.
- Support for a yaml settings file to collect and propagate metadata for CST beam files.

### Changed
- `UVBeam._interp_freq` returns both `interp_data` and `interp_bandpass`, instead of just the former.

### Fixed
- Combining overlapping data along multiple axes (most common when reading in multiple files) no longer errors.


## [1.3.6] - 2019-02-15

### Added
- `keep_all_metadata` keyword for optionally discarding unused metadata when performing a select operation.

### Changed
- Extends `run_acceptability_check` for UVH5 metadata in `check_header` function.

### Fixed
- Antenna numbering bug in redundancy methods. It wasn't using the correct antenna numbers to make baseline indices.
- Redundancy code returns one group if all baselines are redundant. Previously returned each baseline as a separate group
- Redundancy code finds unique baselines along baseline_array without assuming Nblts = Nbls \* Ntimes. Previously assumed Nblts = Nbls \* Ntimes and attempted to slice array.
- "inflate_by_redundancy" method errored when phase_type == phased, due to _set_u_positive using phased uvw coordinates. It now uses ENU frame uvw coordinates.

## [1.3.5] - 2018-12-20

## [1.3.4] - 2018-12-19
### Added
- Methods on UVData objects to compress/inflate data by redundant baselines.
- Convenience functions on UVData for finding redundant baselines (calling the corresponding utils functions)
- memo describing the UVH5 format
- read/write support for uvh5 files with integer datatypes for visibilities
- Option to only do the select on the metadata. This is useful for partially defined objects as in pyuvsim setup or after reading only the metadata from a file.
- support for python3.7

### Changed
- UVdata.get_ENU_antpos() now defaults to using the telescope_location as the center rather than the median antenna position.
- UVBeam.efield_to_pstokes() no longer restricted to healpix coordinates
- latitude and longitude in uvh5 files are written in degrees instead of radians.
- Fixes a bug in redundancy methods for when there are no redundant baselines.

### Fixed
- `_key2inds` now properly reorders polarization axis for conjugated visibilities. This also effects the `get_data` function.
- long strings are saved correctly in miriad files from python3

## [1.3.3] - 2018-11-01
### Added
- option to save splines for reuse in UVBeam.interp function

### Changed
- improve string handling for uvh5 files
- changed top-level import structure to exclude file-specific class (e.g. `UVFITS`, `CALFITS`) and base classes (`UVBase`, `UVParameter`) and to not import utility functions into the top-level namespace

### Deprecated
- Support for UVData objects without antenna_positions. Antenna positions will be required in a future version.

## [1.3.2] - 2018-09-27
### Added
- Utility functions to identify redundant baselines (either by baseline or antenna pair)
- Reading FHD layout files to get antenna positions
- Polarization dict constants and parsing functions in utils.py for mapping between polarization strings and numbers

### Changed
- LST array is now optional in uvh5 files
- polarization string capitalization was unified throughout: use lower case except for Stokes parameters
- integration_time is now a vector of length NBlts instead of a scalar

### Deprecated
- Support for FHD inputs without layout files (containing antenna positions).

### Fixed
- flags are always returned as a boolean array from `UVData.get_flags`
- integration_time, uvw_array and lst_array are now always checked for consistency when adding UVData objects
- consistency checks on baseline lengths now uses the uvw_array tolerances

## [1.3.1] - 2018-07-24

## [1.3] - 2018-07-22
### Added
- compatibility with python 3 (retaining python 2 compatibility)
- generic `UVData.read` method for all input file types, including select on read options
- partial write support for uvh5 file format
- partial read support for uvfits, miriad and uvh5 file formats (including only reading metadata and select on read)
- new uvh5 file format: an HDF5 file standard matched to UVData objects
- new method to calculate uvws from antenna positions
- `UVBeam.get_beam_area` and `UVBeam.get_beam_sq_area` functions to calculate beam integrals, including for pseudo-Stokes beams
- beam interpolation methods, to any set of points and to healpix pixel centers
- a script to renumber antennas for CASA compatiblity if there are fewer than 256 antennas but numbers higher than that
- memo describing the beam fits file format
- method to peak normalize UVBeam objects
- support for reading FHD calibrations into UVCal objects
- support for sky-based calibration metadata in UVCal and the calfits file format
- method to convert E-field beams to power beams
- `UVData.get_ENU_antpos` method to get ENU coordinates from antenna positions
- support for `extra_keywords` on UVCal objects

### Changed
- Major overhaul of phasing code, see the phasing memo in docs/references for more details
- Make all earth location coordinate conversions use same axes order (n_points, 3)
- replaced `ant_pair_nums` keyword in `UVData.select` and partial read methods with `bls` which supports lists like [(0,1,'xx'), (2,3,'yy')]
- extracted miriad wrappers from aipy, removing aipy as a dependency

### Fixed
- Fixed error when combining auto-correlation only and cross-correlation only UVData objects
- Fixed error with the `UVData.select` function using a single antenna name
- Fixed bugs with `UVData.get_data`, `UVData.get_flags`, and `UVData.get_nsamples` for conjugated baseline polarizations
- Fixed a bug that caused a memory error in `UVData.write_uvfits`
- Fixed bugs in interpreting the uvw direction convention for uvfits
- Fixed a bug in reading azimuth locations from CST beam files
- Fixed a bug reading in single frequency uvfits files
- Fixed a bug in reading MWA Cotter measurement sets
- Fixed units errors in cal fits files
- Fixed a serious bug where data was overwritten in the add functions if the axes were out of canonical order
- Fixed scrambled data ordering in add function

## [1.2.1] - 2017-11-09
### Fixed
- Fixed a bug in parsing frequencies from CST file names

## [1.2] - 2017-11-08
### Added
- support doctest in the tutorial
- utility functions for converting between Jones numbers and polarization strings
- support for `antdiam` variable in miriad files
- module for reading a CST file into a UVBeam object
- utility functions for converting to rotated ECEF coordinates from ECEF coordinates
- support reading in a list of calfits files
- include `extra_keywords` to miriad files
- `__add__` method for UVCal objects
- `antenna_diameters` value to UVData objects
- `parse_ants` method on UVData objects
- `x_orientation` value to UVData objects
- "smart slicing" functionality to UVData objects
- convenience methods on UVData objects for easily getting data and metadata
- UVBeam object
- in-place selection for UVData objects
- `total_quality_array` value on UVCal objects
- `__add__` method for UVData objects
- utility functions for converting to local ENU coordinates from ECEF coordinates
- `convert_to_gain` method on UVCal delay-type objects
- read-only support for CASA measurement sets into UVData objects
- `select` method on UVCal objects

### Changed
- antenna names in miriad saved as strings instead of arrays of ASCII hex values

### Fixed
- baseline-time axis mis-ordering in add function
- handling of antenna positions in miriad and uvfits files
- selecting autocorrelation data from UVData objects
- indexing of spectral windows in calfits files
- handling of `total_quality_array` in UVCal objects when selecting a subset of data

## [1.1] - 2017-04-14
(historical information needs to be filled in)