wsDtSegmentation.py 文件源码

def signed_distance_transform(pmap, pmin, minMembraneSize, out_debug_image_dict, ppitch = None):
    """
    Performs a threshold on the given image 'pmap' > pmin, and performs
    a distance transform to the threshold region border for all pixels outside the
    threshold boundaries (positive distances) and also all pixels *inside*
    the boundary (negative distances).

    The result is a signed float32 image.
    """
    # get the thresholded pmap
    binary_membranes = (pmap >= pmin).view(numpy.uint8)

    # delete small CCs
    labeled = vigra.analysis.labelMultiArrayWithBackground(binary_membranes)
    save_debug_image('thresholded membranes', labeled, out_debug_image_dict)
    del binary_membranes

    remove_wrongly_sized_connected_components(labeled, minMembraneSize, in_place=True)
    save_debug_image('filtered membranes', labeled, out_debug_image_dict)

    # perform signed dt on mask
    logger.debug("positive distance transform...")
    if ppitch != None:
        distance_to_membrane = vigra.filters.distanceTransform(labeled, pixel_pitch = ppitch)
    else:
        distance_to_membrane = vigra.filters.distanceTransform(labeled)

    # Save RAM with a sneaky trick:
    # Use distanceTransform in-place, despite the fact that the input and output don't have the same types!
    # (We can just cast labeled as a float32, since uint32 and float32 are the same size.)
    logger.debug("negative distance transform...")
    distance_to_nonmembrane = labeled.view(numpy.float32)
    if ppitch != None:
        vigra.filters.distanceTransform(labeled, background=False, out=distance_to_nonmembrane, pixel_pitch = ppitch)
    else:
        vigra.filters.distanceTransform(labeled, background=False, out=distance_to_nonmembrane, pixel_pitch = ppitch)
    del labeled # Delete this name, not the array

    # Combine the inner/outer distance transforms
    distance_to_nonmembrane[distance_to_nonmembrane>0] -= 1
    distance_to_membrane[:] -= distance_to_nonmembrane

    save_debug_image('distance transform', distance_to_membrane, out_debug_image_dict)
    return distance_to_membrane