mioXpektron.pipeline

Functions

run_pipeline(files, *[, ...])

Run the end‑to‑end ToF‑SIMS batch pipeline and return aligned matrices.

Classes

PipelineConfig([use_recalibration, ...])

High-level pipeline configuration for batch ToF‑SIMS processing.

class mioXpektron.pipeline.PipelineConfig(use_recalibration=True, reference_masses=None, output_folder_calibrated='calibrated_spectra', denoise_method='wavelet', denoise_params=None, baseline_method='airpls', baseline_params=None, clip_negative_after_baseline=True, normalization_target=1000000.0, mz_min=None, mz_max=None, mz_tolerance=0.2, mz_rounding_precision=1, max_workers=None, auto_tune=False)

Bases: object

High-level pipeline configuration for batch ToF‑SIMS processing.

Parameters:

• use_recalibration (bool)

• reference_masses (List[float] | None)

• output_folder_calibrated (str)

• denoise_method (str)

• denoise_params (Dict | None)

• baseline_method (str)

• baseline_params (Dict | None)

• clip_negative_after_baseline (bool)

• normalization_target (float)

• mz_min (float | None)

• mz_max (float | None)

• mz_tolerance (float)

• mz_rounding_precision (int)

• max_workers (int | None)

• auto_tune (bool)

use_recalibration: bool = True

reference_masses: List[float] | None = None

output_folder_calibrated: str = 'calibrated_spectra'

denoise_method: str = 'wavelet'

denoise_params: Dict | None = None

baseline_method: str = 'airpls'

baseline_params: Dict | None = None

clip_negative_after_baseline: bool = True

normalization_target: float = 1000000.0

mz_min: float | None = None

mz_max: float | None = None

mz_tolerance: float = 0.2

mz_rounding_precision: int = 1

max_workers: int | None = None

auto_tune: bool = False

mioXpektron.pipeline.run_pipeline(files, *, calib_channels_dict=None, config=None)

Run the end‑to‑end ToF‑SIMS batch pipeline and return aligned matrices.

Steps

1. Optional recalibration (Channel→m/z)

2. Denoising

3. Baseline correction

4. TIC normalization

5. Peak detection and alignment → unified m/z × samples tables

rtype:

(intensity_df, area_df) aligned by m/z across samples.

Parameters:

• files (Sequence[str])

• calib_channels_dict (Dict[str, Sequence[float]] | None)

• config (PipelineConfig | None)

Return type:

Tuple[DataFrame, DataFrame]