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Makes stats cache optional #2135

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Makes stats cache optional #2135

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36 changes: 23 additions & 13 deletions python/tests/test_tree_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,13 @@ def naive_branch_general_stat(


def branch_general_stat(
ts, sample_weights, summary_func, windows=None, polarised=False, span_normalise=True
ts,
sample_weights,
summary_func,
windows=None,
polarised=False,
span_normalise=True,
cache_summary=True,
):
"""
Efficient implementation of the algorithm used as the basis for the
Expand All @@ -200,8 +206,6 @@ def branch_general_stat(
time = ts.tables.nodes.time
parent = np.zeros(ts.num_nodes, dtype=np.int32) - 1
branch_length = np.zeros(ts.num_nodes)
# The value of summary_func(u) for every node.
summary = np.zeros((ts.num_nodes, result_dim))
# The result for the current tree *not* weighted by span.
running_sum = np.zeros(result_dim)

Expand All @@ -211,20 +215,26 @@ def polarised_summary(u):
s += summary_func(total_weight - state[u])
return s

for u in ts.samples():
summary[u] = polarised_summary(u)
# TODO Make this optional and figure out how to cache inline
# The value of summary_func(u) for every node.
# summary = np.zeros((ts.num_nodes, result_dim))
# for u in ts.samples():
# summary[u] = polarised_summary(u)

def summary(u):
return polarised_summary(u)

window_index = 0
for (t_left, t_right), edges_out, edges_in in ts.edge_diffs():
for edge in edges_out:
u = edge.child
running_sum -= branch_length[u] * summary[u]
running_sum -= branch_length[u] * summary(u)
u = edge.parent
while u != -1:
running_sum -= branch_length[u] * summary[u]
running_sum -= branch_length[u] * summary(u)
state[u] -= state[edge.child]
summary[u] = polarised_summary(u)
running_sum += branch_length[u] * summary[u]
# summary(u) = polarised_summary(u)
running_sum += branch_length[u] * summary(u)
u = parent[u]
parent[edge.child] = -1
branch_length[edge.child] = 0
Expand All @@ -233,13 +243,13 @@ def polarised_summary(u):
parent[edge.child] = edge.parent
branch_length[edge.child] = time[edge.parent] - time[edge.child]
u = edge.child
running_sum += branch_length[u] * summary[u]
running_sum += branch_length[u] * summary(u)
u = edge.parent
while u != -1:
running_sum -= branch_length[u] * summary[u]
running_sum -= branch_length[u] * summary(u)
state[u] += state[edge.child]
summary[u] = polarised_summary(u)
running_sum += branch_length[u] * summary[u]
# summary(u) = polarised_summary(u)
running_sum += branch_length[u] * summary(u)
u = parent[u]

# Update the windows
Expand Down