Expand a cell mask by one

expand_mask_by_one.py

def expand_mask_by_one(m):
    """Takes a cell mask np array as input
    and returns with mask expanded by 1
    """
    from skimage.morphology import dilation 
    m2 = m.copy()
    unique_cell_ids = np.sort(np.unique(m.reshape(-1)))
    unique_cell_ids = unique_cell_ids[unique_cell_ids>0]
    
    for cell_id in unique_cell_ids:
        is_cell_id = 1 * (m == cell_id)
        empty = m == 0
        D = dilation(is_cell_id) # new expanded binary bask
        pixels_to_flip = D.astype('bool') & empty # flip expanded pixels that were previously empty
        m2[pixels_to_flip] = cell_id
    return m2