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Tip revision: c5a1b463f29b8164cda381e97e3d93a549be4179 authored by Bryna Hazelton on 29 April 2020, 15:53 UTC
Update changelog for new version, minor changelog correction.
Tip revision: c5a1b46
# Changelog
All notable changes to this project will be documented in this file.

## [Unreleased]

## [2.0.2] - 2020-4-29

### Added
- New `_corr_fits` C extension for performing the index and conjugation mapping calculation for read_mwa_corr_fits
- `copy` method to UVCal and UVBeam objects
- `chunks` to `UVH5.write_uvh5` and `UVData.write_uvh5` for HDF5 dataset chunking.
- `multidim_index` to `UVH5.read_uvh5` and `` for multidimensional slicing into HDF5 datasets

### Changed
- Various serialized calculations in,, and to be vectorized with numpy
- Miriad interface was re-written from a hand written CPython interface to a Cython interface which dynamically creates the CPython during package setup/build.
- uvfits, calfits and beamfits files should now be read faster due to a simplified handling of fits header objects, especially when the history is very long.
- The UVData methods `set_drift`, `set_phased`, and `set_unknown_phase_type` have been made private. The public methods will be removed in version 2.2.

## [2.0.1] - 2020-3-24

### Changed
- UVData allows conjugation of metadata only objects.
- Handling of strings in UVFlag files has been made more widely compatible.

### Added
- Option to provide parameters for RectBivariatespline through interp
- `weights_square_array` (optional) parameter on UVFlag - stores sum of squares of weights when converting to waterfall
- `frequency_average` method on UVData to average data along the frequency axis.

### Fixed
- A bug in `select` where baseline-polarization tuples would not be conjugated correctly in `UVData` and `UVFlag`, and select on read for Miriad files.
- `metafits_ppds.fits` files can now be passed to `` without throwing an error.
- UVParameters that are array_like and have NaNs are now properly identified as equal if the NaNs are in the same locations and all non-NaN entries are equal.
- A bug in `` in filling flag and nsample arrays.
- A bug in `UVData.downsample_in_time` in calculating the number of new blts.

## [2.0.0] - 2020-2-12

### Changed
- All references to Python 2 removed from codebase.

### Added
- Routine flagging of MWA coarse band edges and center channels, as well as beginning and end integrations. Only done during `read_mwa_corr_fits`.
- Added a return_weights_square option to `utils.collapse` function, which returns the sum of the squares of the weights.

### Removed
- Previously deprecated code marked for removal in version > 1.5:
 - reading multiple files with file format specific read functions (e.g.  read_mirad). Multi-file reads can only be performed with ``
 - `read_metadata` keyword in various specific read functions (e.g. `read_miriad`)
 - `metadata_only` keyword in `select` and `get_redundancies`
 - `uvdata.miriad.read_miriad_metadata`
 - `phase_center` keyword in `uvdata.read_mwa_corr_fits`
 - `phase_data` keyword in `uvdata.read_mwa_corr_fits`
 - `uvdata.get_antenna_redundancies`
 - `uvdata.get_baseline_redundancies`
 - `uvdata.uvfits.read_uvfits_metadata`
 - `uvdata.uvfits.read_uvfits_data`

## [1.5.0] - 2020-1-15

### Added
- Support for reading the MWA full embedded element beam into a UVBeam object.
- New `time_range` keyword to `select` so exact times don't need to be specified (also added to `read` methods for select on read).
- Support for rephasing phased data including on `read`, `__add__` and `fast_concat` so that files with different phasing can be read in together.
- `sum_vis` and `diff_vis` for summing or differencing visibilities in the data_array.
- `read_mwa_corr_fits` for reading in MWA correlator gpubox files and applying cable corrections.
- `eq_coeffs` for storing equalization coefficients and `remove_eq_coeffs` for removing them.
- `utils.apply_uvflag` for applying UVFlag objects to UVData objects

### Fixed
- Fixed `utils.uvcalibrate` to handle `x_orientation` attribute
- Arrays of file names can now be passed to `read` (not just lists).
- run_check is no longer turned off in `read_uvfits` and `read_uvh5` when `read_data` is False.
- Redundancy finder will now error if any baselines appear in multiple groups.
- A bug in `UVCal` objects that prevented them from properly getting data with `ee`/`nn`-style polarizations.
- a bug in `UVFlag` where `x_orientation` was not set during initialization.
- A bug in `UVCal.read_fhd_cal` that caused calibration solutions to be approximately doubled.
- A bug in UVFlag where polarization array states were not updated when using `force_pol` keyword in `to_antenna` and `to_baseline`
- A bug in UVFlag.to_baseline() where force_pol kwarg did not work for UVData Npols > 1
- `UVData.read_uvfits` no longer breaks if there are non-ascii bytes in antenna names (which CASA sometimes writes).

### Deprecated
- Reading in multiple files (or file sets) using file-type specific read methods (e.g. `read_uvfits`) in favor of the generic `read` method.
- The `phase_center` and `phase_data` keywords to `read_mwa_corr_fits` in favor of `phase_to_pointing_center` and the `phase_center_radec` keyword in the generic `read` method.
- Support for reading only the header (not all the metadata) of uvfits files.
- The `read_uvfits_metadata` and `read_uvfits_data` methods on the UVFITS object.
- The `read_miriad_metadata` method on the Mirad object.

## [1.4.2] - 2019-10-15

### Added
- `copy` method for `UVData`, which can optionally make a copy of just metadata
- `upsample_in_time`, `downsample_in_time`, and `resample_in_time` methods on `UVData` objects
- `utils.uvcalibrate(.., undo=True)` kwarg for undo-ing a calibration.
- `utils.uvcalibrate` updates `UVData.vis_units` if `UVCal.gain_scale` is set.
- `UVCal.gain_scale` non-required attribute
- UVData.get_redundancies method to replace old get_baseline_redundancies and get_antenna_redundancies.
- option for `UVBeam.interp` to return a new beam object.
- `UVFlag` information on Read The Docs

### Changed
- `UVData.phase_to_time` now accepts a float as an input. Assumes float represents a JD.
- Added optional acceptability check for `utils.LatLonAlt_from_XYZ`
- Use `astropy_healpix` rather than `healpy` for HEALPix functionality because `healpy` has a GPL license which is incompatible with ours.
- `h5py` is now a required package instead of an optional one.
- Phasing now supports metadata only `UVData` objects
- utils.get_baseline_redundancies uses scipy pdist functions instead of for loops (faster)
- UVData.get_antenna_redundancies will no longer automatically conjugate baselines.
- UVData.get_baseline_redundancies and UVData.get_antenna_redundancies have been combined.
- `UVFlag` inherits from `UVBase` object.
- `UVFlag` objects can now convert from antenna type to baseline type
- `UVFlag` objects can now be initialized without inputs

### Fixed
- A bug in UVBeam._interp_freq where kind parameter was not passed for real-only beams
- A bug in get_antenna_redundancies for nearly N-S baselines.
- A bug where `conj_pol` could not handle cardinal direction polarizations.
- A bug that gave the wrong error message when calling `UVData.phase_to_time` without an Astropy Time object.

### Deprecated
- UVData.get_baseline_redundancies and UVData.get_antenna_redundancies will be deprecated in version 1.6.1

## [1.4.1] - 2019-08-2

### Added
- `metadata_only` property on `UVData` to automatically detect if data-like arrays are present
- support for combining metadata only objects and reading in multiple files as metadata only
- `utils.uvcalibrate` flag propagation bug fix
- `UVCal.ant2ind` indexing bug fix
- `UVCal.get_*` methods for accessing data arrays with antenna-polarization keys
- `utils.uvcalibrate` for automated calibration of `UVData` by `UVCal`

### Fixed
- Fixed a bug in select that caused bls and antenna_names/numbers to be or'ed rather than and'ed together.
- Fixed a bug where `baseline_to_antnums` could accept a numpy array as input but not other array_like objects.

### Changed
- removed `new_object` keyword from `UVBeam._interp_freq` in favor of new functionality in `UVBeam.interp`

## [1.4.0] - 2019-05-23

### Added
- Option in UVBase.check() to ignore whether required parameters are set.
- 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 init logic in UVFlag.
- 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 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 `` 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 `` 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 `` 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)
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