Module pylars.processing.waveforms

Classes

class waveform_processing

All the things waveforms.

Expand source code

class waveform_processing():
    """All the things waveforms.
    """

    @classmethod
    def get_std_rough(cls, waveform_array: np.ndarray,
                      baseline_samples: int) -> float:
        """Returns the std value of the first self.baseline_samples
        as a good estimate for the std of the baseline.
        """
        std_rough = np.std(waveform_array[:baseline_samples])
        return std_rough

    @classmethod
    def get_baseline_rough(cls, waveform_array: np.ndarray,
                           baseline_samples: int) -> float:
        """Returns the median value of the first self.baseline_samples
        as a good estimate for the baseline.
        """
        baseline_rough = np.median(waveform_array[:baseline_samples])
        return baseline_rough

    @classmethod
    def process_waveform(cls, waveform: np.ndarray, baseline_samples: int,
                         sigma_level: float = 5, negative_polarity: bool = True,
                         baseline_subtracted: bool = False):
        """Main process function on the waveform level. Finds pulses above
        (beelow if negative polarity) threshold and calls pulse level
        processing like area, length and position.

        Args:
            waveform (np.ndarray): ADC counts of the waveform;
            baseline_samples (int): how many samples to take for the
        baseline calculation (at the begining of the waveform);
            sigma_level (float, optional): define threshodl by "sigma_level"
        times the std of the computed baseline. Defaults to 5.

        Returns:
            tuple: areas, lengths, positions
        """

        if baseline_subtracted:
            baseline_rough = 0
        else:
            baseline_rough = cls.get_baseline_rough(waveform, baseline_samples)
        std_rough = cls.get_std_rough(waveform, baseline_samples)

        pulses = pulse_processing.find_pulses_simple(
            waveform, baseline_rough, std_rough, sigma_level,
            negative_polarity=negative_polarity,
            baseline_subtracted=baseline_subtracted)

        # handle case where no pulses were found
        if len(pulses[0]) == 0:
            return [], [], [], []

        areas = pulse_processing.get_all_areas(
            waveform, pulses, baseline_rough,
            negative_polarity=negative_polarity)
        lengths = pulse_processing.get_all_lengths(pulses)
        positions = pulse_processing.get_all_positions(pulses)
        amplitudes = pulse_processing.get_all_amplitudes(
            waveform, pulses, baseline_rough,
            negative_polarity=negative_polarity)

        return areas, lengths, positions, amplitudes

Static methods

def get_baseline_rough(waveform_array: numpy.ndarray, baseline_samples: int) ‑> float

Returns the median value of the first self.baseline_samples as a good estimate for the baseline.

Expand source code

@classmethod
def get_baseline_rough(cls, waveform_array: np.ndarray,
                       baseline_samples: int) -> float:
    """Returns the median value of the first self.baseline_samples
    as a good estimate for the baseline.
    """
    baseline_rough = np.median(waveform_array[:baseline_samples])
    return baseline_rough

def get_std_rough(waveform_array: numpy.ndarray, baseline_samples: int) ‑> float

Returns the std value of the first self.baseline_samples as a good estimate for the std of the baseline.

Expand source code

@classmethod
def get_std_rough(cls, waveform_array: np.ndarray,
                  baseline_samples: int) -> float:
    """Returns the std value of the first self.baseline_samples
    as a good estimate for the std of the baseline.
    """
    std_rough = np.std(waveform_array[:baseline_samples])
    return std_rough

def process_waveform(waveform: numpy.ndarray, baseline_samples: int, sigma_level: float = 5, negative_polarity: bool = True, baseline_subtracted: bool = False)

Main process function on the waveform level. Finds pulses above (beelow if negative polarity) threshold and calls pulse level processing like area, length and position.

Args

waveform : np.ndarray

ADC counts of the waveform;

baseline_samples : int

how many samples to take for the

baseline calculation (at the begining of the waveform); sigma_level (float, optional): define threshodl by "sigma_level" times the std of the computed baseline. Defaults to 5.

Returns

tuple

areas, lengths, positions

Expand source code

@classmethod
def process_waveform(cls, waveform: np.ndarray, baseline_samples: int,
                     sigma_level: float = 5, negative_polarity: bool = True,
                     baseline_subtracted: bool = False):
    """Main process function on the waveform level. Finds pulses above
    (beelow if negative polarity) threshold and calls pulse level
    processing like area, length and position.

    Args:
        waveform (np.ndarray): ADC counts of the waveform;
        baseline_samples (int): how many samples to take for the
    baseline calculation (at the begining of the waveform);
        sigma_level (float, optional): define threshodl by "sigma_level"
    times the std of the computed baseline. Defaults to 5.

    Returns:
        tuple: areas, lengths, positions
    """

    if baseline_subtracted:
        baseline_rough = 0
    else:
        baseline_rough = cls.get_baseline_rough(waveform, baseline_samples)
    std_rough = cls.get_std_rough(waveform, baseline_samples)

    pulses = pulse_processing.find_pulses_simple(
        waveform, baseline_rough, std_rough, sigma_level,
        negative_polarity=negative_polarity,
        baseline_subtracted=baseline_subtracted)

    # handle case where no pulses were found
    if len(pulses[0]) == 0:
        return [], [], [], []

    areas = pulse_processing.get_all_areas(
        waveform, pulses, baseline_rough,
        negative_polarity=negative_polarity)
    lengths = pulse_processing.get_all_lengths(pulses)
    positions = pulse_processing.get_all_positions(pulses)
    amplitudes = pulse_processing.get_all_amplitudes(
        waveform, pulses, baseline_rough,
        negative_polarity=negative_polarity)

    return areas, lengths, positions, amplitudes