Preprocessing (GUI)

Note: This page is a work in progress.

How to prepare spectra before analysis.

Step 0: Cosmic-ray cleanup (new in 0.7.0)

  • Automatically detects and corrects obvious cosmic-ray hits prior to standard preprocessing.
  • Enabled by default in quick preprocessing; can be toggled in the manual wizard.
  • Keeps genuine narrow features by limiting width and amplitude thresholds.

Quick SNID Preprocessing

Purpose Actions When to use
Minimal steps to prepare a spectrum for SNID Log rebinning, optional S-G smoothing, apodization, continuum handling Most cases; fastest path to classification

Manual Preprocessing

Open via: Preprocessing → Manual wizard

Step Control Parameter Default CLI Flag Notes
1. Input and range Wavelength range wmin, wmax None — Leave blank for auto
2. Smoothing Savitzky–Golay window savgol_window 0 --savgol-window 0 disables; typical 11–21
Savitzky–Golay order savgol_order 3 --savgol-order
3. Telluric and sky Remove A-band aband_remove False --aband-remove Masks ~7550–7700 Å
Sky line clipping skyclip False --skyclip
Emission clipping (auto) — — --emclip Uses per-entry/forced z; does not force analysis redshift
Emission clipping z emclip_z -1.0 --emclip-z -1 disables; masking only (does not force z)
Emission width (Å) emwidth 40.0 --emwidth
4. Apodization Apodize percent (%) apodize_percent 10.0 --apodize-percent Typical 5–15%
5. Masks Custom wavelength masks wavelength_masks None --wavelength-masks e.g. 6550:6600 7600:7700

Best practices

  • Inspect S/N before aggressive smoothing
  • Prefer specific masks over broad ranges
  • Keep apodize_percent modest to preserve edges

CLI parity

GUI options map to sage flags:

sage spectrum.dat --output-dir results\
sage spectrum.dat --savgol-window 11 --savgol-order 3
sage spectrum.dat --aband-remove --skyclip
sage spectrum.dat --emclip-z 0.02 --emwidth 40
# In batch, auto emission clipping uses per-row z when present
sage batch --list-csv list.csv --emclip --output-dir results\
sage spectrum.dat --wavelength-masks 6550:6600 7600:7700

See Also