Anime API

readms(msname::String)

Read data from Measurement Set.

readobsconfig(configfile::String)

Read YAML configuration file with observation settings in a Dictionary.

readstationinfo(stationfile::String; delim::String=",", ignorerepeated::Bool=false)

Read additional information about stations from CSV file into a DataFrame.

readbandpassinfo(bandpassfile::String; delim::String=",", ignorerepeated::Bool=false)

Read bandpass information from CSV file into a DataFrame.

readalistv5(alistfile::String)

Read in an alist v5 file generated by HOPS.

readalistv6(alistfile::String)

Read in an alist v6 file generated by HOPS.

createmsfromconfig(msname::String, mscreationmode::String, casaanttemplate::String, stationinfo::DataFrame, spw_centrefreq::Array{Float64, 1}, 
spw_bw::Array{Float64, 1}, spw_channels::Array{Int64, 1}, sourcedict::Dict{String, Any}, starttime::String, exposure::Float64, scans::Int64,
scanlengths::Array{Float64, 1}, scanlag::Float64; autocorr::Bool=false, telescopename::String="VLBA", feed::String="perfect R L",
shadowlimit::Float64=1e-6, elevationlimit::String="10deg", stokes::String="RR RL LR LL", delim::String=",", ignorerepeated::Bool=false)

Create Measurement Set from observation parameters and DataFrame containing station information. Requires casatools.

createmsfromconfig(obsconfig, stationinfo::DataFrame)

Alias with fewer arguments for use in pipelines.

createmsfromuvfits(uvfits::String, msname::String, mscreationmode::String; overwrite::Bool=true)

Convert uvfits to MS. Requires casatools and casatasks.

createuvfitsfromms(msname::String, uvfits::String, datacolumn::String; field::String="", spw::String="", antenna::String="",
timerange::String="", overwrite::Bool=true)

Create UVFITS from existing MS. Requires casatasks.

writems(ms::MeasurementSet; h5file::String="")

Write data to MS. Optionally, add weight columns from h5file.

makecasaantennatable(df::DataFrame, casaanttemplate::String; delim::String=",", ignorerepeated::Bool=false)

Create CASA antenna table from the DataFrame df containing station information using casaanttemplate as template. Requires casatools.

addweightcolumns(msname::String, mode::String, sigmaspec::Bool, weightspec::Bool)

Add WEIGHT_SPECTRUM and SIGMA_SPECTRUM columns to existing MS. Requires casatools to be installed.

run_wsclean(msname::String, fitsdir::String, polarized::Bool, channelgroups::Int64, osfactor::Int64)

Compute source coherency matrix using WSClean and populate MS. fitsdir is the directory containing FITS source models, polarized indicates if source model is polarized, and channelgroups is the number of images in frequency. osfactor is the oversampling factor which is a WSClean argument that controls prediction/imaging accuracy.

troposphere!(obs::CjlObservation, h5file::String; absorptionfile::String="", dispersivefile::String="", elevfile::String="")

Umbrella function for tropospheric model. Model is written to HDF5 file.

instrumentalpolarization!(data::Array{Complex{Float32},4}, scanno::Vector{Int32}, times::Vector{Float64},
stationinfo::DataFrame, phasedir::Array{Float64,2}, pos::Array{Float64, 2}, chanfreqvec::Vector{Float64}, polframe::String,
polmode::String, antenna1::Vector{Int32}, antenna2::Vector{Int32}, exposure::Float64, corruptseed::Int; h5file::String="",
elevfile::String="", parangfile::String="")

Compute frequency-varying instrumental polarization (leakage, or "D-Jones" terms) and apply to data; write model to HDF5 file.

instrumentalpolarization!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict; h5file::String="",
elevfile::String="", parangfile::String="")

Alias for use in pipelines.

pointing!(data::Array{Complex{Float32},4}, stationinfo::DataFrame, scanno::Vector{Int32}, chanfreqvec::Vector{Float64}, 
ptgint::Float64, ptgscale::Float64, ptgmode::String, exposure::Float64, times::Vector{Float64}, corruptseed::Int, antenna1::Vector{Int32}, 
antenna2::Vector{Int32}, numchan::Int64; α=1.0, h5file::String="")

Compute pointing model and apply to data; write model to HDF5 file.

pointing!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict; h5file::String="")

Alias with fewer arguments for use in pipelines.

stationgains!(data::Array{Complex{Float32},4}, scanno::Vector{Int32}, times::Vector{Float64}, exposure::Float64, 
stationinfo::DataFrame, mode::String, corruptseed::Int, antenna1::Vector{Int32}, antenna2::Vector{Int32}, numchan::Int64; h5file::String="")

Compute time-variable complex station gains and apply to data; write model to HDF5 file.

stationgains!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict; h5file::String="")

Alias for use in pipelines.

bandpass!(data::Array{Complex{Float32},4}, stationinfo::DataFrame, bandpassinfo::DataFrame, corruptseed::Int,
antenna1::Vector{Int32}, antenna2::Vector{Int32}, numchan::Int64, chanfreqvec::Vector{Float64}; h5file::String="")

Compute the complex bandpass model and apply to data; write model to HDF5 file.

bandpass!(ms::MeasurementSet, stationinfo::DataFrame, bandpassinfo::DataFrame, obsconfig::Dict; h5file::String="")

Alias for use in pipelines.

thermalnoise!(data::Array{Complex{Float32},4}, times::Vector{Float64}, antenna1::Vector{Int32}, antenna2::Vector{Int32},
correff::Float64, exposure::Float64, chanwidth::Float64, corruptseed::Int, sefd::Vector{Float64}; h5file::String="",
noisefile::String="")

Compute per-baseline thermal noise using radiometer equation and apply to data. The actual numerical values are serialized in HDF5 format.

thermalnoise!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict; h5file::String="", noisefile::String="")

Alias for use in pipelines.

genseries1d!(series::Vector{ComplexF32}, mode::String, location::ComplexF32, scale::Float32, driftrate::Float32, nsamples::Int64, rng::AbstractRNG)

Generate a complex-valued Gaussian process 1-D series of length nsamples with the given location, scale, and driftrate parameters. mode determines if "normal" distribution or "gaussian processes" is used to generate the samples.

genseries1d!(series::Vector{Float32}, mode::String, location::Float32, scale::Float32, driftrate::Float32, nsamples::Int64, rng::AbstractRNG)

Generate a Float32-valued Gaussian process 1-D series of length nsamples with the given location, scale, and driftrate parameters. mode determines if "normal" distribution or "gaussian processes" is used to generate the samples.

genseries1d!(series::Vector{Float64}, mode::String, location::Float64, scale::Float64, driftrate::Float64, nsamples::Int64, rng::AbstractRNG)

Generate a Float64-valued Gaussian process 1-D series of length nsamples with the given location, scale, and driftrate parameters. mode determines if "normal" distribution or "gaussian processes" is used to generate the samples.

genseries1d!(series, times, rng::AbstractRNG; μ=0.0, σ=1.0, ρ=1.0)

Generate 1-D series using SE kernel.

genseries1d!(series, times, rng::AbstractRNG, α::Float64; μ=0.0, σ=1.0, ρ=2.0)

Generate 1-D series using RQ kernel.

elevationangle(times::Vector{Float64}, phasedir::Array{Float64,2}, stationinfo::DataFrame, pos::Array{Float64, 2})

Compute elevation angle for all stations in stationinfo for all times using phasedir and pos information.

parallacticangle(times::Vector{Float64}, phasedir::Array{Float64,2}, stationinfo::DataFrame, pos::Array{Float64,2})

Compute parallactic angle for all stations in stationinfo for all times using phasedir and pos information.

plotvis(uvw::Matrix{Float64}, chanfreqvec::Array{Float64,1}, flag::Array{Bool,4}, data::Array{Complex{Float32},4},
numchan::Int64, times::Vector{Float64}; saveprefix="data_")

Plot complex visibilities against time and projected baseline length.

plotuvcov(uvw::Matrix{Float64}, flagrow::Vector{Bool}, chanfreqvec::Vector{Float64}; saveprefix="test_")

Plot uv-coverage of observation.

plotstationgains(h5file::String, scanno::Vector{Int32}, times::Vector{Float64}, exposure::Float64, stationnames::Vector{String3})

Plot complex station gains against time.

plotbandpass(h5file::String, stationnames::Vector{String3}, chanfreqvec::Vector{Float64})

Plot bandpass gains against time.

plotpointingerrors(h5file::String, scanno::Vector{Int32}, stationnames::Vector{String3})

Plot pointing errors.

plotelevationangle(h5file::String, scanno::Vector{Int32}, times::Vector{Float64}, stationnames::Vector{String3})

Plot evolution of station elevation angles during the course of the observation.

plotparallacticangle(h5file::String, scanno::Vector{Int32}, times::Vector{Float64}, stationnames::Vector{String3})

Plot evolution of station parallactic angles during the course of the observation.

plotdterms(h5file::String, stationnames::Vector{String3}, chanfreqvec::Vector{Float64})

Plot frequency-dependent complex instrumental polarization.

plottransmission(h5file::String, stationnames::Vector{String3}, times::Vector{Float64}, chanfreqvec::Vector{Float64})

Plot tropospheric transmission variation with frequency.

plotmeandelays(h5file::String, stationnames::Vector{String3}, times::Vector{Float64}, chanfreqvec::Vector{Float64})

Plot mean delays against time.

struct MeasurementSet{T}

Composite type for storing data from a Measurement Set.

Fields

• name: Measurement Set name

• data: Complex visibility data (MS DATA column)

• flag: Flag array of the same dimensions as data (MS FLAG column)

• flagrow: Flag row Boolean vector (MS FLAG_ROW column)

• antenna1: Antenna 1 in a baseline pair (MS ANTENNA1 column)

• antenna2: Antenna 2 in a baseline pair (MS ANTENNA2 column)

• uvw: uvw coordinates (MS UVW column)

• times: Timestamps (MS TIME column)

• exposure: Integration time

• scanno: Scan numbers (SCAN_NUMBER column in MS)

• numchan: Number of frequency channels

• chanfreqvec: Channel frequencies (Hz) (MS CHAN_FREQ column)

• chanwidth: Width of frequency channel

• phasedir: Direction of phase centre

• pos: Antenna positions in x,y,z coordinates

copymodeltodata(msname::String)

Copy MODEL_DATA to DATA in MS msname.

computeweights!(totalrmsspec::Array{Float32, 4}, totalwtspec::Array{Float32, 4}; h5file::String="")

Compute total rms (sigma) values and inverse-squared visibility weights from thermal+sky noise terms stored in h5file.

run_aatm(ms::MeasurementSet, stationinfo::DataFrame; absorptionfile::String="", dispersivefile::String="")::DataFrame

Run AATM (Bjona Nikolic; Pardo et al. 2001) to compute absorption by and dispersive delay in the troposphere. If AATM is not installed, this function can still accept input absorption and dispersion values in a specific CSV format and populate atm.csv.

compute_transmission!(transmission::Array{Float64, 3}, ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict, atmdf::DataFrame,
elevationmatrix::Array{Float64, 2}, g::HDF5.Group)::Array{Float64, 3}

Compute elevation-dependent (mean) tropospheric transmission given opacity τ and elevation angle θ for each station.

\[e^{-τ/\sin{\theta_{\rm el}}}\]

attenuate!(ms::MeasurementSet, transmission::Array{Float64, 3})

Attenuate the signal as it passes through (mean) troposphere using precomputed transmission values.

\[I = I_0 e^{-τ/\sin{\theta_{\rm el}}}\]

compute_skynoise!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict, atmdf::DataFrame, transmission::Array{Float64, 3}, g::HDF5.Group)

Compute sky contribution to visibility noise using the radiometer equation.

compute_meandelays!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict, atmdf::DataFrame, elevationmatrix::Array{Float64, 2}, g::HDF5.Group)

Compute delays due to (mean) troposphere.

compute_turbulence!(ms::MeasurementSet, stationinfo::DataFrame, obsconfig::Dict, elevationmatrix::Array{Float64, 2}, g::HDF5.Group)

Compute phase delays due to tropospheric turbulence. The time series of phase errors for station p is given by

\[\{{\delta \phi_p(t, \nu)}\} = \frac{1}{\sqrt{\sin({\theta_{\mathrm{el}}(t)})}} \{\delta\phi^{\prime}_p(t)\} \big(\frac{\nu}{\nu_0}\big)\]

where ν is the list of channel frequencies and ν_0 is the reference frequency (lowest in the band).

squaredexponentialkernel(x1, x2; σ=1.0, ρ=1.0)

Generate squared exponential kernel function of the form

\[k_{SE}(x-x') = \sigma^2 e^{-\frac{(x-x')^2}{2\rho^2}}\]

where σ^2 is the variance and ρ is the characteristic length.

rationalquadratickernel(x1, x2; σ=1.0, α=1.0, ρ=2.0)

Generate rational quadratic kernel of the form

\[k_{RQ}(x-x') = \sigma^2 \big(1+\frac{(x-x')^2}{2\alpha\rho^2}\big)^{-\alpha}\]