DIA Windows

tdfpy.DiaWindow dataclass

DiaWindow(
    _timsdata: TimsData,
    window_index: int,
    window_group: int,
    scan_num_begin: int,
    scan_num_end: int,
    isolation_mz: float,
    isolation_width: float,
    collision_energy: float,
    frame_id: int,
    rt: float,
    polarity: Polarity,
)

Bases: DiaWindowGroup, _TdfData

A DIA isolation window bound to a specific frame.

Extends DiaWindowGroup with per-frame context (frame_id, rt, polarity). Provides raw and centroided spectrum access and ion mobility conversion properties.

frame_id instance-attribute

frame_id: int

Frame ID this window belongs to.

rt instance-attribute

rt: float

Retention time of the parent frame in seconds.

polarity instance-attribute

polarity: Polarity

Ion polarity.

peaks property

peaks: list[npt.NDArray[np.float64]]

Read raw peaks for this DIA window and return as list of (mz, intensity) arrays.

centroid

centroid(
    mz_tolerance: float = 8,
    mz_tolerance_type: Literal["ppm", "da"] = "ppm",
    im_tolerance: float = 0.05,
    im_tolerance_type: Literal[
        "relative", "absolute"
    ] = "relative",
    min_peaks: int = 3,
    max_peaks: int | None = None,
    noise_filter=None,
    ion_mobility_type: Literal[
        "ccs", "ook0", "voltage"
    ] = "ook0",
) -> np.ndarray

Centroid the spectrum for this DIA window using the specified parameters.

Source code in src/tdfpy/elems.py

def centroid(
    self,
    mz_tolerance: float = 8,
    mz_tolerance_type: Literal["ppm", "da"] = "ppm",
    im_tolerance: float = 0.05,
    im_tolerance_type: Literal["relative", "absolute"] = "relative",
    min_peaks: int = 3,
    max_peaks: int | None = None,
    noise_filter=None,
    ion_mobility_type: Literal["ccs", "ook0", "voltage"] = "ook0",
) -> np.ndarray:
    """Centroid the spectrum for this DIA window using the specified parameters."""
    get_spectrum = partial(
        get_centroided_spectrum,
        self.timsdata,
        frame_id=self.frame_id,
        spectrum_index=None,
        ion_mobility_type=ion_mobility_type,
        mz_tolerance=mz_tolerance,
        mz_tolerance_type=mz_tolerance_type,
        im_tolerance=im_tolerance,
        im_tolerance_type=im_tolerance_type,
        min_peaks=min_peaks,
        max_peaks=max_peaks,
        noise_filter=noise_filter,
    )

    try:
        return get_spectrum(use_numba=True)
    except Exception:
        warnings.warn(
            f"Numba centroiding failed for frame {self.frame_id}. Falling back to Python implementation.",
            UserWarning,
            stacklevel=2,
        )
        return get_spectrum(use_numba=False)

tdfpy.DiaWindowGroup dataclass

DiaWindowGroup(
    window_index: int,
    window_group: int,
    scan_num_begin: int,
    scan_num_end: int,
    isolation_mz: float,
    isolation_width: float,
    collision_energy: float,
)

A DIA isolation window definition (shared across frames in the same group).

Defines the m/z isolation range, mobility scan range, and collision energy for one window within a DIA window group. DiaWindow extends this with per-frame fields (frame_id, rt, polarity).

Field	Type	Description
window_index	int	Index of this window within its group
window_group	int	Window group ID
scan_num_begin	int	First mobility scan (inclusive)
scan_num_end	int	Last mobility scan (inclusive)
isolation_mz	float	Isolation window center m/z
isolation_width	float	Isolation window width in Th
collision_energy	float	Collision energy in eV