Crate dnoise 

dnoise — denoise Bruker timsTOF .d folders with the iterative vertical-IM feature filter (Stage 1 of ALGORITHM.md). Reads via timsrust, re-encodes surviving points as a type-2 tdf_bin, and writes a new .d folder.

Two API tiers are exposed:

• High level — denoise / denoise_with_progress take an input .d and write a filtered output .d, parameterized by FilterParams.
• Low level — FlatFrame plus filter::filter_once / filter::filter_iterated, average::running_average, and the type-2 codec operate on in-memory frames for callers that bring their own I/O.

Example

Run the vertical-IM filter over an in-memory frame:

use dnoise::{FilterParams, FlatFrame, filter_iterated};

// A vertical streak at TOF 1000 across 8 consecutive mobility scans.
let frame = FlatFrame {
    frame_id: 1,
    num_scans: 700,
    scan: (10..18).collect(),
    tof: vec![1000; 8],
    intensity: vec![100; 8],
};
let keep = filter_iterated(&frame, &FilterParams::default());
assert!(keep.iter().all(|&k| k)); // the streak survives

Re-exports

pub use error::DecodeError;

pub use error::DnoiseError;

pub use error::Result;

pub use params::BoxCentroidParams;

pub use params::CropParams;

pub use params::DdaWindowParams;

pub use params::DiaMs1WindowParams;

pub use params::DiaWindowParams;

pub use params::FilterParams;

pub use params::HaloParams;

pub use params::Ms1PolygonParams;

pub use params::MsmsFilterParams;

pub use params::SmoothParams;

pub use params::Stages;

pub use params::WatershedParams;

pub use writer::Calibration;

pub use writer::DecodedFrame;

pub use writer::DenoiseStats;

pub use writer::FrameCtx;

pub use writer::Progress;

pub use writer::RunContext;

pub use writer::RunOptions;

pub use writer::SampleSpec;

pub use writer::denoise;

pub use writer::denoise_with_options;

pub use writer::denoise_with_progress;

pub use writer::process_frame_decoded;

pub use crop::CropGate;

pub use average::running_average;

pub use box_centroid::box_centroid;

pub use dia_ms1::DiaMs1Gate;

pub use dia_ms1::TofScanBox;

pub use dia_window::filter_per_window;

pub use dia_window::in_window_mask;

pub use filter::filter_iterated;

pub use filter::filter_once;

pub use frame::FlatFrame;

pub use halo::horizontal_halo_keep_mask;

pub use msms::combine_and_filter;

pub use polygon::PolygonGate;

pub use smooth::box_average;

pub use watershed::watershed_centroid;

Modules

average

Optional pre-filter smoothing: a centered moving average over the MS1-frame subsequence, applied before the vertical-IM filter (and any downstream centroider). This stage is completely decoupled from the filter — it just produces ordinary FlatFrames that the rest of the pipeline consumes exactly as it consumes raw frames.

box_centroid

Greedy small-box centroider in integer (scan, TOF index) space.

codec

Type-2 tdf_bin frame codec — encode/decode Bruker timsTOF frame records.

config

On-disk run configuration (dnoise.toml), shared by the CLI and the GUI.

crop

Region-of-interest crop (a.k.a. trim): keep only points inside an axis-aligned box in (m/z, 1/K0, intensity) space, plus a retention-time window handled at the frame level by the writer.

dia_ms1

diaPASEF MS1 out-of-window gate.

dia_window

diaPASEF isolation-window handling for MS/MS frames.

error

Error types for the dnoise library.

filter

Stage 1 of ALGORITHM.md: the iterative vertical-IM feature filter.

frame

Flat per-point view of a timsTOF frame in native integer (scan, tof, intensity) space.

halo

Horizontal (m/z-axis) halo filter: remove the weak halo flanking bright ions, left/right only.

msms

ddaPASEF MS/MS denoising (precursor-centric).

params

Tunable parameters for the vertical-IM feature filter (Stage 1 of ALGORITHM.md).

polygon

ddaPASEF/PASEF MS1 selection-polygon gate.

smooth

Box-averaging smoother in integer (scan, TOF index) space.

watershed

Watershed-segmentation centroider in integer (scan, TOF index) space.

writer

Orchestration: copy the source .d, rewrite analysis.tdf_bin with filtered frames (re-encoded as type 2), and fix up the analysis.tdf SQLite database.

Enums

Acquisition

Acquisition scheme of a .d run, detected from the Frames.MsMsType column. Drives the --preset auto gate selection (see the CLI): ddaPASEF wants the MS1 selection-polygon gate, diaPASEF the isolation-window gates.

Functions

detect_acquisition

Detect the acquisition scheme of an input .d folder by inspecting the frame table (MsMsType): 9 anywhere = diaPASEF, else 8 = ddaPASEF, else MS1-only when every frame is MS1, else unknown. A cheap SQLite read, no frame decoding.

tof_half_width_for_ppm

Convert a mass tolerance in ppm to a TOF-index half-width for the vertical filter’s mz_half_width, evaluated at a reference m/z. The timsTOF calibration maps m/z to a fractional TOF index nonlinearly, so a fixed ppm corresponds to a different index width across the mass range; the vertical filter uses one constant index window, so we evaluate the width at ref_mz (defaulting to the midpoint of the acquired m/z range) and round up to at least 1.