Open
Description
We need some examples to help illustrate how to use keep_rows and the id_map well. Here's one example (taken from the tests in #2707)
See also #2529
def test_delete_unreferenced_nodes(self):
# 2.00┊ 4 ┊
# ┊ ┏━┻┓ ┊
# 1.00┊ ┃ 3 ┊
# ┊ ┃ ┏┻┓ ┊
# 0.00┊ 0 1 2 ┊
# 0 1
ts = tskit.Tree.generate_balanced(3).tree_sequence
tables = ts.dump_tables()
edges = tables.edges
nodes = tables.nodes
edges.keep_rows(nodes.time[edges.parent] <= 1)
# 2.00┊ ┊
# ┊ ┊
# 1.00┊ 3 ┊
# ┊ ┏┻┓ ┊
# 0.00┊ 0 1 2 ┊
# 0 1
ref_count = np.bincount(edges.child, minlength=len(nodes))
ref_count += np.bincount(edges.parent, minlength=len(nodes))
assert list(ref_count) == [0, 1, 1, 2, 0]
id_map = nodes.keep_rows(ref_count > 0)
assert list(id_map) == [-1, 0, 1, 2, -1]
assert len(nodes) == 3
# Remap the edges IDs
edges.child = id_map[edges.child]
edges.parent = id_map[edges.parent]
ts = tables.tree_sequence()
assert ts.num_trees == 1
assert ts.first().parent_dict == {0: 2, 1: 2}