How to use the rtree.index.RT_Disk function in Rtree

if len(line) == 0:
        break
      id, lat, lon = line.strip().split(',')
      lat = float(lat)
      lon = float(lon)
      count += 1
      if count % 1000000 == 0:
        print('%d...' % count)
      yield int(id), (lat, lon, lat, lon), None
    

t0 = time.time()
p = rtree.index.Property()
p.filename = 'theindex'
p.overwrite = True
p.storage = rtree.index.RT_Disk
p.dimension = 2

# 17.5 sec
#p.variant = rtree.index.RT_Star
#p.fill_factor = 0.4

# 17.4 sec:
#p.variant = rtree.index.RT_Quadratic
#p.fill_factor = 0.4

# 17.5 sec:
#p.variant = rtree.index.RT_Linear
#p.fill_factor = 0.4

# 34 sec:
#p.leaf_capacity = 1000

def rtree_generator_function():
                c = 0
                centers = np.dstack((sg.center_lon, sg.center_lat))
                for i, axis in enumerate(centers):
                    for j, (x, y) in enumerate(axis):
                        c += 1
                        yield (c, (x, y, x, y), (i, j))

            logger.info("Building Faces (centers) Rtree Topology Cache for {0}".format(self.name))
            _, temp_file = tempfile.mkstemp(suffix='.face')
            start = time.time()
            p = index.Property()
            p.filename = str(temp_file)
            p.overwrite = True
            p.storage   = index.RT_Disk
            p.dimension = 2
            idx = index.Index(p.filename,
                              rtree_generator_function(),
                              properties=p,
                              overwrite=True,
                              interleaved=True)
            idx.close()

            logger.info("Built Faces (centers) Rtree Topology Cache in {0} seconds.".format(time.time() - start))
            shutil.move('{}.dat'.format(temp_file), self.face_tree_data_file)
            shutil.move('{}.idx'.format(temp_file), self.face_tree_index_file)

ug = UGrid.from_nc_dataset(nc=nc)

            def rtree_faces_generator_function():
                for face_idx, node_list in enumerate(ug.faces):
                    nodes = ug.nodes[node_list]
                    xmin, ymin = np.min(nodes, 0)
                    xmax, ymax = np.max(nodes, 0)
                    yield (face_idx, (xmin, ymin, xmax, ymax), face_idx)

            logger.info("Building Faces Rtree Topology Cache for {0}".format(self.name))
            start = time.time()
            _, face_temp_file = tempfile.mkstemp(suffix='.face')
            pf = index.Property()
            pf.filename = str(face_temp_file)
            pf.overwrite = True
            pf.storage   = index.RT_Disk
            pf.dimension = 2
            idx = index.Index(pf.filename,
                              rtree_faces_generator_function(),
                              properties=pf,
                              interleaved=True,
                              overwrite=True)
            idx.close()
            logger.info("Built Faces Rtree Topology Cache in {0} seconds.".format(time.time() - start))
            shutil.move('{}.dat'.format(face_temp_file), self.face_tree_data_file)
            shutil.move('{}.idx'.format(face_temp_file), self.face_tree_index_file)

            def rtree_nodes_generator_function():
                for node_index, (x, y) in enumerate(ug.nodes):
                    yield (node_index, (x, y, x, y), node_index)
            logger.info("Building Nodes Rtree Topology Cache for {0}".format(self.name))
            start = time.time()

overwrite=True)
            idx.close()
            logger.info("Built Faces Rtree Topology Cache in {0} seconds.".format(time.time() - start))
            shutil.move('{}.dat'.format(face_temp_file), self.face_tree_data_file)
            shutil.move('{}.idx'.format(face_temp_file), self.face_tree_index_file)

            def rtree_nodes_generator_function():
                for node_index, (x, y) in enumerate(ug.nodes):
                    yield (node_index, (x, y, x, y), node_index)
            logger.info("Building Nodes Rtree Topology Cache for {0}".format(self.name))
            start = time.time()
            _, node_temp_file = tempfile.mkstemp(suffix='.node')
            pn = index.Property()
            pn.filename = str(node_temp_file)
            pn.overwrite = True
            pn.storage   = index.RT_Disk
            pn.dimension = 2
            idx = index.Index(pn.filename,
                              rtree_nodes_generator_function(),
                              properties=pn,
                              interleaved=True,
                              overwrite=True)
            idx.close()
            logger.info("Built Nodes Rtree Topology Cache in {0} seconds.".format(time.time() - start))
            shutil.move('{}.dat'.format(node_temp_file), self.node_tree_data_file)
            shutil.move('{}.idx'.format(node_temp_file), self.node_tree_index_file)