Source code for libpyhat.transform.baseline_code.median

from scipy.signal import medfilt

from libpyhat.transform.baseline_code.common import Baseline




def median_baseline(intensities, window_size=501):
    """Perform median filtering baseline removal.
    Window should be wider than FWHM of the peaks.
    "A Model-free Algorithm for the Removal of Baseline Artifacts"
    Friedrichs 1995
    """
    # Ensure the window size is odd
    if window_size % 2 == 0:
        window_size += 1
    # Enable batch mode
    if intensities.ndim == 2:
        window_size = (1, window_size)
    return medfilt(intensities, window_size)





class MedianFilter(Baseline):
    def __init__(self, window_size=501):
        self.window_size = window_size

    def _fit_many(self, bands, intensities):
        return median_baseline(intensities, window_size=self.window_size)



    def param_ranges(self):
        return {"window_size": (201, 901, "integer")}