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This package provides Python bindings to the peak picker from findMF.

Installation

pip install findmfpy

Reference

findmfpy.pick_peaks

pick_peaks(
    mz_arr: numpy.typing.NDArray[numpy.float64],
    int_arr: numpy.typing.NDArray[numpy.float64],
    resolution: float = 10000.0,
    width: float = 2.0,
    int_width: float = 2.0,
    int_threshold: float = 10.0,
    area: bool = True,
    max_peaks: int = 0,
) -> tuple[
    numpy.typing.NDArray[numpy.float64],
    numpy.typing.NDArray[numpy.float64],
]

Picks peaks from a mass spectrum.

Parameters:

Name	Type	Description	Default
mz_arr	numpy.typing.NDArray[numpy.float64]	The m/z array.	required
int_arr	numpy.typing.NDArray[numpy.float64]	The intensity array.	required
resolution	float	The resolution of the instrument.	10000.0
width	float	The width of the peak.	2.0
int_width	float	The width of the intensity.	2.0
int_threshold	float	The intensity threshold.	10.0
area	bool	Whether to calculate the area instead of intensity.	True
max_peaks	int	The maximum number of peaks to return.	0

Returns:

Name	Type	Description
0	numpy.typing.NDArray[numpy.float64]	The m/z array of the peaks.
1	numpy.typing.NDArray[numpy.float64]	The intensity array of the peaks.

findmfpy.pick_peaks_diagnostic

pick_peaks_diagnostic(
    mz_arr: numpy.typing.NDArray[numpy.float64],
    int_arr: numpy.typing.NDArray[numpy.float64],
    resolution: float = 10000.0,
    width: float = 2.0,
    int_width: float = 2.0,
    int_threshold: float = 10.0,
    area: bool = True,
    max_peaks: int = 0,
) -> tuple[
    numpy.typing.NDArray[numpy.float64],
    numpy.typing.NDArray[numpy.float64],
    dict[str, numpy.typing.NDArray[numpy.float64]],
]

Picks peaks from a mass spectrum, and returns some additional diagnostic information of the peak picker.

Parameters:

Name	Type	Description	Default
mz_arr	numpy.typing.NDArray[numpy.float64]	The m/z array.	required
int_arr	numpy.typing.NDArray[numpy.float64]	The intensity array.	required
resolution	float	The resolution of the instrument.	10000.0
width	float	The width of the peak.	2.0
int_width	float	The width of the intensity.	2.0
int_threshold	float	The intensity threshold.	10.0
area	bool	Whether to calculate the area instead of intensity.	True
max_peaks	int	The maximum number of peaks to return.	0

Returns:

Name	Type	Description
0	numpy.typing.NDArray[numpy.float64]	The m/z array of the peaks.
1	numpy.typing.NDArray[numpy.float64]	The intensity array of the peaks.
2	dict[str, numpy.typing.NDArray[numpy.float64]]	Diagnostic information from the peak picker internals.