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Add support for bitshuffle on visdata
# 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)