Command-Line Interface

AMICAL provides a command-line interface (CLI) to reduce data directly from the terminal.

$ amical -h

usage: amical [-h] {clean,extract,calibrate} ...

positional arguments:
  {clean,extract,calibrate}
    clean               Clean reduced data for NRM extraction.
    extract             Extract the bispectrum from cleaned NRM data.
    calibrate           Calibrate the extracted NRM data with the associated calibrator.

options:
  -h, --help            show this help message and exit

Each of the three subcommands (clean, extract, calibrate) performs one of the main steps discussed in Getting Started.

Below we show the help message for each subcommand.

Cleaning data

$ amical clean -h

usage: amical clean [-h] [--datadir DATADIR] [--outdir OUTDIR] [--isz ISZ] [--r1 R1] [--dr DR] [--apod] [--window WINDOW] [--sky] [--clip] [--kernel KERNEL] [-c] [-p] [-f FILE] [-a]

options:
  -h, --help         show this help message and exit
  --datadir DATADIR  Repository containing the reduced NRM data (default: data/).
  --outdir OUTDIR    Repository to save the cleaned NRM data (as fits files)(default: cleaned/).
  --isz ISZ          Size of the cropped image [pix] (default: None).
  --r1 R1            Radius of the rings to compute background sky [pix] (default: 32).
  --dr DR            Outer radius to compute sky (r2=r1+dr) [pix] (default: 3).
  --apod             Perform apodisation using a super-gaussian function (known as windowing). The gaussian FWHM is set by the parameter `window`.
  --window WINDOW    FWHM used for windowing (used with --apod)(default: 65)
  --sky              Remove sky background using the annulus technique(computed between r1 and r1 + dr)
  --clip             Perform sigma-clipping to reject bad frames (default: False).
  --kernel KERNEL    kernel size used in the applied median filter (to find the center)(default: 3)
  -c, --check        Check the cleaning parameters (plot relevant radius in the image).
  -p, --plot         Plot the diagnostic figures.
  -f, --file FILE    Select the file index to be clean (default allows user selection).
  -a, --all          Clean all data files in --datadir.
~/repos/astro/AMICAL   update-docs ?1                                                                                                                                                                                             amical

Extracting observables

$ amical extract -h

usage: amical extract [-h] [--datadir DATADIR] [--outdir OUTDIR] [--maskname MASKNAME] [--peakmethod {fft,gauss,unique,square}] [--instrum INSTRUM] [--targetname TARGETNAME] [--filtname FILTNAME] [--nwl NWL] [--cutoff CUTOFF]
                      [--diam DIAM] [--fw FW] [--multitri] [--unbias] [--thetadet THETADET] [--scaling SCALING] [--iwl IWL] [--save_to SAVE_TO] [-p] [-e] [-f FILE] [-a]

options:
  -h, --help            show this help message and exit
  --datadir DATADIR     Repository containing the cleaned NRM data (default: cleaned/).
  --outdir OUTDIR       Repository to save the extracted bispectrum (as hdf5 .h5 files)(default: extracted/).
  --maskname MASKNAME   Name of the mask aperture (default: g7).
  --peakmethod {fft,gauss,unique,square}
                        Fourier sampling method (default: fft).
  --instrum INSTRUM     Name of the instrument (if not found in the header).
  --targetname TARGETNAME
                        Name of the target (if not found in the header).
  --filtname FILTNAME   Name of the spectral filter (if not found in the header).
  --nwl NWL             Number of elements to sample the spectral filters (default: 3).
  --cutoff CUTOFF       Cutoff limit between noise and signal for fft method (default: 0.0001).
  --diam DIAM           Diameter of a single aperture (default: 0.8).
  --fw FW               Relative size of the splodge used to compute multiple triangle indices and the fwhm of the 'gauss' technique (default: 0.7).
  --multitri            Compute the CP over multiple triangles (Monnier method).
  --unbias              Unbias the V2 using the Fourier base.
  --thetadet THETADET   Angle [deg] to rotate the mask compare to the detector (if the mask is notperfectly aligned with the detector, e.g.: VLT/VISIR) (default: 0).
  --scaling SCALING     Scaling factor to be applied to match the mask with data (e.g.: VAMPIRES) (default: 1).
  --iwl IWL             Only used for IFU data (e.g.: IFS/SPHERE), select the desired spectral channel to retrieve the appropriate wavelength and mask positions.
  --save_to SAVE_TO     If save_to is set, figures are saved within it as pdf (default: None).
  -p, --plot            Plot the diagnostic figures.
  -e, --expert          Save additional plots.
  -f, --file FILE       Select the file index to be extracted (default allows user selection).
  -a, --all             Extract bispectrum from all data files in --datadir.

Calibrating observables

$ amical calibrate -h

usage: amical calibrate [-h] [--datadir DATADIR] [--outdir OUTDIR] [--clip] [--norm] [--phscorr] [--atmcorr] [-p]

options:
  -h, --help         show this help message and exit
  --datadir DATADIR  Repository containing the extracted bispectrum (default: extracted/).
  --outdir OUTDIR    Repository to save the calibrated oifits files (default: calibrated/).
  --clip             Sigma clipping is performed over the calibrator files (if any) to reject bad observables due to seeing conditions, centering, etc (default: False).
  --norm             CP uncertaintities are normalized by np.sqrt(n_holes/3.) to not over use the non-independant closure phases (default: False).
  --phscorr          Apply a phasor correction due to piston between holes (default: False).
  --atmcorr          Apply a atmospheric correction on V2 from seeing and wind shacking issues (default: False).
  -p, --plot         Plot the calibrated data.