Source code for libpyhat.transform.baseline_code.fabc

import scipy.signal

from libpyhat.transform.baseline_code.common import (
    WhittakerSmoother,
    iterative_threshold,
    Baseline,
)




def fabc_baseline(intensities, dilation_param=50, smoothness_param=1e3):
    """Fully Automatic Baseline Correction, by Carlos Cobas (2006).
    http://www.sciencedirect.com/science/article/pii/S1090780706002266
    """
    cwt = scipy.signal.cwt(intensities, scipy.signal.ricker, (dilation_param,))
    dY = cwt.ravel() ** 2

    is_baseline = iterative_threshold(dY)
    is_baseline[0] = True
    is_baseline[-1] = True

    smoother = WhittakerSmoother(intensities, smoothness_param, deriv_order=1)
    return smoother.smooth(is_baseline)





class FABC(Baseline):
    def __init__(self, dilation_param=50, smoothness_param=1e3):
        self.dilation_param = dilation_param
        self.smoothness_param = smoothness_param

    def _fit_one(self, bands, intensities):
        return fabc_baseline(intensities, self.dilation_param, self.smoothness_param)



    def param_ranges(self):
        return {
            "dilation_param": (1, 100, "integer"),
            "smoothness_param": (1, 1e6, "log"),
        }