pyoifits 0.4.10

Brief intro

Purpose

Read and manipulate Optical Interferometry FITS files version 1 and 2.

For a definition of the standards

• version 2: Duvert at al. (2017), A&A 597, A8 (abstract) (pre-print)
• version 1: Pauls et al. (2005), PASP 117, 1255 (abstract) (pre-print)

Installation

It is packaged as pyoifits.

Site-wide installation will be performed with sudo -H pip3 install pyoifits on unix-like systems. At a user level, within a virtual environment, pip3 install pyoifits.

Short example

Read and merge to OIFITS datasets and tranform to a standard astropy table.

import pyoifits as oifits

data = oifits.openlist(['file1.fits', 'file2.fits'])

tab, corr = data.to_table(correlations='numpy')
obs = tab['observable']
x = tab['value']
dx = tab['error']
cov = corr * np.outer(dx, dx)

There is also a short demo.

Classes and functions

Classes

Classes are in astropy.io.fits tree, they derive either from HDUList (FITS file) or BinTableHDU (FITS table). The end user shouldn't need to manipulate them explicitly as helper functions are provided.

An OIFITS1 object (OIFITS standard version 1, < _OIFITS < astropy.io.fits.HDUList) contains

1. one PrimaryHDU1 object (< astropy.io.fits.PrimaryHDU)
2. several _OITableHDU1 objects (abstract OI table class, < _OITableHDU < astropy.io.fits.BinTableHDU) which can be of the derived types
   • TargetHDU1 (OI_TARGET extrension)
   • ArrayHDU1 (OI_ARRAY extension)
   • WavelengthHDU1 (OI_WAVELENGTH extension, < astropy.io.fits.BinTableHDU)
   • _DataHDU1 (abstract data class, < astropy.io.fits.BinTableHDU)
     • VisHDU1 (OI_VIS extension)
     • Vis2HDU1 (OI_VIS2 extension)
     • T3HDU1 (OI_T3 extension)
3. any other FITS extension

An OIFITS2 object (OIFITS standard version 2, < _OIFITS < astropy.io.fits.HDUList) contains

1. one PrimaryHDU2 object (< astropy.io.fits.PrimaryHDU)
2. several _OITableHDU2 (abstract OI table class, < _OITableHDU < astropy.io.fits.BinTableHDU) which can be of the derived types
   • TargetHDU2 (OI_TARGET extension)
   • ArrayHDU2 (OI_ARRAY extension)
   • WavelengthHDU2 (OI_WAVELENGTH extension)
   • _DataHDU2 (abstract data class)
     • VisHDU2 (OI_VIS extension)
     • Vis2HDU2 (OI_VIS2 extension)
     • T3HDU2 (OI_T3 extension)
     • FluxHDU1 (OI_FLUX extension)
   • CorrHDU1 (OI_CORR extension)
   • InspolHDU1 (OI_INSPOL extension)
3. any other FITS extension

Functions

• Reading and manipulating OIFITS
  • open (open an OIFITS file)
  • openlist (open a list of files and merge them)
  • merge (merge several OIFITS)
  • set_merge_settings (determine how duplicate targets/stations are merged)
• Creating OI tables from scratch
  • new_target_hdu (create an OI_TARGET extension)
  • new_target_hdu_from_simbad
  • new_array_hdu (create an OI_ARRAY extension)
  • new_wavelength_hdu (create an OI_WAVELENGTH extension)
  • new_vis_hdu (create an OI_VIS extension)
  • new_vis2_hdu (create an OI_VIS2 extension)
  • new_t3_hdu (create an OI_T3 extension)
  • new_flux_hdu (create an OI_FLUX extension)

Methods

• _OIFITS (OIFITS1 and OIFITS2)
  • manipulation
    • bin_spectral_channels (downgrade spectral resolution)
    • trim (keep only wavelengths, targets, instruments, ... of interest)
    • to_table (transform to a table with one scalar observable per line)
    • to_version (transform between versions of the OIFITS standard)
  • visualisation
    • visualize (quick plot)
  • data updating
    • verify (check standard compliance and mend if possible)
    • update_primary_header (update primary header using the info in other tables)
    • update_uv (compute spatial frequencies using array data)
  • contents listing
    • get_OITableHDUs
    • get_targetHDU
    • get_arrayHDUs & get_arrayHDU
    • get_wavelengthHDUs & get_wavelengthHDU
    • get_dataHDUs
    • get_visHDUs
    • get_vis2HDUs
    • get_t3HDUs
    • (OIFITS2 only) get_corrHDUs & get_corrHDU
    • (OIFITS2 only) get_fluxHDUs
    • (OIFITS2 only) get_inspolHDUs & get_inspolHDU
• _DataHDU (all classes containing OI data)
  • target information
    • get_target
    • get_dec
    • get_ra
    • get_equinox
    • get_parallax
    • get_pmra
    • get_pmdec
    • get_rv
    • get_skycoord
    • get_spectype
  • wavelength and spatial frequency information
    • get_wave
    • get_band
    • get_uv
    • get_uvw
  • array information
    • get_location
    • get_sta_name
    • get_staenu
    • get_stauvw
    • get_staxyz
    • get_sta_config
    • get_tel_name
    • get_tel_config
  • polarisation information
    • (_DataHDU2 only) get_jones_matrix

Direct data access

Each column of the OI FITS standard can be directly accessed via its standard name, for instance, h.UCOORD or h.VIS2DATA are synonyms to h.data['UCOORD'] and h.data['VIS2DATA'], respectively.

Related projects

• oifits reads an OIFITS file into a table, geared towards the Event Horizon Telescope
• oifits reads and write OIFITS v. 1, mostly geared towards VLTI/MATISSE
• pyhdust has a read/write module for OIFITS version 1

Release notes

0.4

New features:

• Method to_table() optionally returns a correlation matrix GG

0.4.1

Bug fixes:

• WAVELMIN & WAVELMAX FITS keywords have a correct number of significant digits
• EQUINOX FITS keyword now passes verification
• No runtime error when a duplicate INSNAME has to be renamed
• OI data (OI_VIS, OI_VIS2, OI_T3, OI_FLUX) tables merge correctly
• OI_VIS tables with different PHITYP, AMPTYP, AMPORDER, or PHIORDER can no longer be merged
• OI_FLUX tables with different FOV or FOVTYPE can not longer be merged

New features:

• OIFITS1 & OIFITS2 classes have get_visHDUs, get_vis2HDUs, get_T3HDUs methods

0.4.2

New features:

• Method to_table() allows the user to restrict to a subset of target names, instrument setup names, arrays, wavelength range, and/or date range
• OIFITS classes have new method visualize() to plot an interferometric observable as a function of time, baseline length, or spatial frequency.

0.4.3

Bug fixes:

• Successive column renamings no longer lead to KeyError
• fix get_uv
• Typos in this doc

New features:

• Method bin_spectral_channels(R) allows the user to rebin to a given spectral resolution.

0.4.4

• Documentation
• Fixed numerous bugs in get_jones_matrix and InspolHDU1

0.4.5

Bug fixes

• Fixed error in creation of FluxHDU and T3HDU using from_data
• Fixed error in creation of OI tables with non-standard columns using from_data
• Typos in documentation

New features

• New function trim() to keep only wavelengths, instruments, instrumental setups, arrays, targets of interest

0.4.6.

Bug fixes

• Fixed TDIM=1 keyword error when trim() yields N×1 data
• Fixed an issue with astroquery returning str instead of bytes

0.4.7

Bug fixes

• Fixed float format for STAXYZ column in ArrayHDU extension
• verify() can now fix strictly negative errors
• duplicate fits warnings in verify() are now printed

Testing

• A quick test of verify() on a set of JMMC/aspro-generated OIFITS

0.4.8

Bug fixes

• to_version() now runs verify() to produce valid OIFITS if possible
• A quick test of to_version()

0.4.9

Bug fixes

• OIFITS version 2 verification ** verify() now replaces zero and negative TARGET_ID instead of throwing an error ** verify() now masks values and errors (with NULL=NaN) when errors are strictly negative or NULL ** primary header of single-target observations deduces more keywords from data HDUs (BASE_MIN, VIS2ERR, NUM_CHAN, etc.)

0.4.10

• New functions ** new_primary_header to create a primary header
• Bug fixes ** verify() now replaces zero and negative STA_INDEX for OITITS2.