Preprocessing (GUI)

How to prepare spectra before analysis.

Step 0: Early spike masking (automatic)

  • SNID SAGE applies an automatic early spike/outlier masking step before the standard preprocessing pipeline.
  • This is enabled by default in both the GUI and the CLI.
  • In the CLI, you can disable it with --no-spike-masking.
  • The current GUI workflow uses the default automatic behavior rather than exposing a separate user-facing "cosmic-ray cleanup" wizard step.

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

Advanced Preprocessing

Open via: Preprocessing → Advanced Preprocessing

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

Automatic spike-masking controls (CLI)

The automatic step above corresponds to the CLI spike-masking options:

Parameter Default CLI Flag Notes
spike_masking True --no-spike-masking to disable Early spike/outlier masking before smoothing
spike_floor_z 50.0 --spike-floor-z Minimum floor-relative robust z for spike detection
spike_baseline_window 501 --spike-baseline-window Running median baseline window in pixels
spike_baseline_width None --spike-baseline-width Baseline width in wavelength units; overrides pixel window
spike_rel_edge_ratio 2.0 --spike-rel-edge-ratio Center residual must exceed neighboring residuals by this factor
spike_min_separation 2 --spike-min-separation Minimum pixel separation between removed spikes
spike_max_removals None --spike-max-removals Optional cap on spikes removed per spectrum
spike_min_abs_resid None --spike-min-abs-resid Minimum absolute residual required to count as a spike

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