PASEFHillCentroider.h File Reference

#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <cstddef>
#include <cstdint>
#include <vector>

Include dependency graph for PASEFHillCentroider.h:

Go to the source code of this file.

Classes
struct	Params
struct	Centroid
	One centroided peak produced by hill detection. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.
namespace	OpenMS::Internal
	Namespace used to hide implementation details from users.
namespace	OpenMS::Internal::PASEFHillCentroider

Functions
std::vector< Centroid >	centroidFrame (const double *mz_values, const double *intensities, const double *im_values, std::size_t n, const Params &p, const std::uint32_t *scan_indices=nullptr)

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Class Documentation

OpenMS::Internal::PASEFHillCentroider::Params

struct OpenMS::Internal::PASEFHillCentroider::Params

Parameters for IM-axis hill-based centroiding of one TIMS-PASEF frame. Algorithm modeled on Biosaur2 (linkScanToHills_/splitHills_) but with IM scans within a frame playing the role of consecutive RT spectra.

Collaboration diagram for Params:

Class Members
double	im_group_tolerance = 0.0	Tolerance for treating two flat-input IM values as belonging to the same IM scan. 0.0 means exact equality. TIMS calibration produces discrete IM values per scan index, so exact equality usually works; callers that have float-cast their IM values may want a small epsilon.
Size	max_scan_gap = 0	Maximum number of consecutive empty IM scans a hill is allowed to bridge while linking. 0 (default) = strict consecutive-scan linking (original Biosaur2 behavior). 1 = a single empty scan at the hill's m/z is tolerated; the hill's tail stays "alive" for one extra scan and can still be extended at scan+2. Useful for detector-centroided TIMS-PASEF where ions occasionally fail to register in one IM scan. Note: hill length counts only the scans where the ion was actually observed, not the bridged gap. REQUIRES scan_indices to be passed to centroidFrame(). Without it the helper cannot tell which IM scans are empty (vs. simply absent from the input), and silently treats this as 0 to avoid merging hills across unknown gaps.
Size	min_hill_length = 1	Minimum peaks per hill. Hills shorter than this are dropped. Default 1 is appropriate for TIMS-PASEF data: detector centroiding produces sparse per-scan peaks, and many real ions span only one IM scan in a frame. Empirically, on detector-centroided MS1 frames roughly 75% of peaks have no same-m/z partner in the previous IM scan within 100 ppm — the data is genuinely sparse along the IM axis, not noisy. Raising to 2 (or higher) is appropriate when the caller knows multi-scan hills are typical (e.g. RT-axis hill detection on dense LC-MS data, the original Biosaur2 use case).
double	min_intensity = 0.0	Discard input peaks below this intensity before linking.
double	mz_tol_ppm = 8.0	m/z linking tolerance in ppm. A peak in the next IM scan extends a hill if its m/z is within this tolerance of the previous-scan peak.
double	valley_factor = 1.3	Hill-valley factor (hvf): both (left_max / valley) and (right_max / valley) must exceed this for a valley to split a hill. Smaller values split more aggressively. Biosaur2 default = 1.3.

OpenMS::Internal::PASEFHillCentroider::Centroid

struct OpenMS::Internal::PASEFHillCentroider::Centroid

One centroided peak produced by hill detection.

Collaboration diagram for Centroid:

Class Members
double	im_apex	IM value at the hill's intensity apex.
double	im_lower	minimum IM value covered by the hill
double	im_upper	maximum IM value covered by the hill
double	intensity	summed intensity across the hill
Size	length	number of IM scans contributing to the hill
double	mz	intensity-weighted m/z over the hill
double	mz_lower	minimum m/z value covered by the hill
double	mz_upper	maximum m/z value covered by the hill