expt_utils.py 文件源码

def subtract_background_median(z, footprint=19, implementation='scipy'):
    """Remove background using a median filter.

    Parameters
    ----------
    footprint : int
        size of the window that is convoluted with the array to determine
        the median. Should be large enough that it is about 3x as big as the
        size of the peaks.
    implementation: str
        One of 'scipy', 'skimage'. Skimage is much faster, but it messes with
        the data format. The scipy implementation is safer, but slower.

    Returns
    -------
        Pattern with background subtracted as np.array
    """   

    if implementation == 'scipy':
        bg_subtracted = z - ndi.median_filter(z, size=footprint)
    elif implementation == 'skimage':
        selem = morphology.square(footprint)
        # skimage only accepts input image as uint16
        bg_subtracted = z - filters.median(z.astype(np.uint16), selem).astype(z.dtype)
    else:
        raise ValueError("Unknown implementation `{}`".format(implementation))

    return np.maximum(bg_subtracted, 0)