Struct HillsConfig 

pub struct HillsConfig {

    pub min_scans: usize,
    pub max_gap: usize,
    pub split_hills: bool,
    pub split_valley_ratio: f64,
    pub split_sigma_mult: f64,
    pub split_height_frac: f64,
    pub lfc_weight: f64,
    pub gap_fill_enabled: bool,
    pub smoothing_enabled: bool,
    pub smoothing_window: usize,
    pub filter_large_baseline_hills: bool,
    pub large_hill_min_scans: usize,
    pub large_hill_peak_factor: f64,
    pub tic_norm_window: usize,
    pub tic_norm_min_scale: f64,
    pub tic_norm_max_scale: f64,
    pub tic_norm_mode: String,
}

Fields

min_scans: usize

max_gap: usize

split_hills: bool

split_valley_ratio: f64

Persistence: a split between two adjacent peaks is kept only if the valley between them drops to <= this fraction of the SMALLER peak. Scale-free and immune to spike inflation. Default 0.60.

split_sigma_mult: f64

Persistence: absolute notch-depth floor as a multiple of the estimated noise sigma (MAD of the trace’s first difference). Rejects shallow noise notches that the relative test alone would admit on a low baseline. Default 5.0.

split_height_frac: f64

Persistence: minimum peak height as a fraction of the robust (95th-pct) max intensity. Lower catches faint minor co-eluting peaks (e.g. 10:1 duals); higher rejects baseline bumps. Default 0.10.

lfc_weight: f64

Weight for the intensity LFC term in the hill-candidate distance score. 0.0 disables it. Default 0.3; ~0.5 gives intensity consistency roughly half the influence of m/z proximity when selecting which peak extends a hill.

gap_fill_enabled: bool

Linear-interpolate intensity through internal zero-gap scans during hill finalization. Independent of smoothing_enabled. Default false. NOTE: turning this on can create artificial local maxima that the split-hills logic picks up as new peaks — it materially increases final hill count on data with many short gaps.

smoothing_enabled: bool

Apply a running-average filter to the intensity profile during hill finalization. Independent of gap_fill_enabled. Default false.

smoothing_window: usize

Half-width of the running-average window. Total window = 2*smoothing_window+1 scans. 0 = no averaging. Ignored when smoothing_enabled is false.

filter_large_baseline_hills: bool

Drop “large baseline-like” hills before isotope chain assembly. A hill is dropped when its scan length ≥ large_hill_min_scans AND max(unsmoothed) / smoothed_endpoint < large_hill_peak_factor on either end — i.e., the intensity profile lacks a clear apex. Catches column-bleed contaminants, plasticizers, and baseline drift centroids that masquerade as hills. Default false for backward compatibility. Ported from AlphaPept’s filter_hills.

large_hill_min_scans: usize

Minimum scan span for a hill to be considered for the baseline-hill filter. Default 40.

large_hill_peak_factor: f64

Required ratio of max(intensity_profile) to the smoothed endpoint intensity. A clear chromatographic peak easily exceeds this; a flat baseline trace fails. Default 2.0.

tic_norm_window: usize

Pre-detection anomaly normalisation. When > 0, peak intensities in each MS1 scan are scaled by clamp(local_median(reference) / scan_reference, tic_norm_min_scale, tic_norm_max_scale) where the local median is taken over a centred window of tic_norm_window scans. The reference quantity is selected by tic_norm_mode. Defaults to 0 = off.

Use case: brief ESI dropouts / sub-AGC-failure events that the instrument’s automatic gain control didn’t fully compensate. Choosing the window too small (≲ peak FWHM in scans) will flatten real apices, especially in tic mode.

tic_norm_min_scale: f64

tic_norm_max_scale: f64

tic_norm_mode: String

Which per-scan quantity to use as the normalisation reference. “tic” = total ion current (sum of all peak intensities). Heavy- tailed; dominated by a few intense peaks. Real elution apices spike the TIC and get scaled DOWN by the normaliser — apex shapes can be flattened. “median” = median peak intensity per scan. Robust to a few intense peaks: apex elution adds tall peaks but barely moves the median. Dropouts dim everything → median drops → scaling fires only when the whole scan is suppressed. Recommended.

Trait Implementations

impl Clone for HillsConfig

fn clone(&self) -> Self

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for HillsConfig

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for HillsConfig

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for HillsConfig

where HillsConfig: Default,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for HillsConfig

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.