perf: simplify graph combine algorithm

misc/all-graph/04-combine_layout.py

@@ -5,132 +5,97 @@ import igraph as ig
 import multiprocessing
 
 
-def split_layer(graph: ig.Graph, step_a: int, step_b: int) -> tuple[list[set[int]], list[set[int]]]:
+def split_adjacent_layers(graph: ig.Graph, step: int) -> tuple[list[set[int]], list[set[int]]]:
-
+    layouts = graph.vs.select(step_in=[step, step + 1])
-    def extend_from(node: ig.Vertex) -> tuple[set[ig.Vertex], set[ig.Vertex]]:
+    code_map = {x['code']: x.index for x in layouts}
-        assert node['step'] == step_a
+    to_index = lambda iter: {code_map[x['code']] for x in iter}
-
+
-        scan_a2b = True
+    layer_curr, layer_next = [], []
-        union_a, union_b = set(), set()
+    g_focus = graph.subgraph(layouts)
-        curr_set, next_set = set([node]), set()
+    isolated = g_focus.vs.select(_degree=0)
-
+    if isolated:
-        while curr_set:
+        assert {x['step'] for x in isolated} == {step}
-            for layout in curr_set:
+        layer_curr = [to_index(isolated)]
-                for neigh in layout.neighbors():
+        g_focus.delete_vertices(isolated)
-                    if scan_a2b and neigh['step'] == step_b and neigh not in union_b:
+
-                        next_set.add(neigh)
+    for component in g_focus.connected_components():
-                    elif not scan_a2b and neigh['step'] == step_a and neigh not in union_a:
+        component = [g_focus.vs[x] for x in component]
-                        next_set.add(neigh)
+        layer_curr.append(to_index(x for x in component if x['step'] == step))
-
+        layer_next.append(to_index(x for x in component if x['step'] == step + 1))
-            union_a.update(curr_set if scan_a2b else next_set)
+    return layer_curr, layer_next
-            union_b.update(next_set if scan_a2b else curr_set)
+
-            scan_a2b = not scan_a2b
+
-            curr_set = next_set
+def apply_layer_unions(unions_a: list[set[int]], unions_b: list[set[int]]) -> list[set[int]]:
-            next_set = set()
+    layer_data = {x for u in unions_a for x in u}
-
+    assert layer_data == {x for u in unions_b for x in u}
-        return union_a, union_b
+
-
+    unions = []
-    assert step_a + 1 == step_b
+    for curr_union in unions_a:
-
+        for other_union in unions_b:
-    layer_a = set(x for x in graph.vs if x['step'] == step_a)
+            if union := curr_union.intersection(other_union):
-    layer_b = set(x for x in graph.vs if x['step'] == step_b)
+                unions.append(union)
-    layer_num_a, layer_num_b = len(layer_a), len(layer_b)
+                curr_union -= union
-    assert layer_num_a > 0 and layer_num_b > 0
+                other_union -= union
-
+        assert len(curr_union) == 0
-    data_a: list[set[int]] = []
-    data_b: list[set[int]] = []
-    special_set = set()
-    while layer_a:
-        union_a, union_b = extend_from(layer_a.pop())
-        if len(union_b) == 0:
-            assert len(union_a) == 1
-            special_set.update(union_a)
-            continue
-        layer_a -= union_a
-        layer_b -= union_b
-        data_a.append(set(x.index for x in union_a))
-        data_b.append(set(x.index for x in union_b))
-    data_a.append(set(x.index for x in special_set))
-
-    assert len(layer_a) == 0 and len(layer_b) == 0
-    assert sum(len(x) for x in data_a) == layer_num_a
-    assert sum(len(x) for x in data_b) == layer_num_b
-    return data_a, [x for x in data_b if x]
-
-
-def build_multi_set(unions_a: list[set[int]], unions_b: list[set[int]]) -> list[set[int]]:
-    assert set(y for x in unions_a for y in x) == set(y for x in unions_b for y in x)
-
-    release = []
-    for curr in unions_a:
-        for other in unions_b:
-            mid = curr.intersection(other)
-            if mid:
-                release.append(mid)
-                curr -= mid
-                other -= mid
-        assert len(curr) == 0
 
     assert set(len(x) for x in unions_a) == {0}
     assert set(len(x) for x in unions_b) == {0}
-    return release
+    assert layer_data == {x for u in unions for x in u}
+    return unions
 
 
-def do_split(g: ig.Graph) -> ig.Graph:
+def build_all_unions(graph: ig.Graph) -> list[set[int]]:
-    max_step = max(x['step'] for x in g.vs)
+    max_step = max(graph.vs['step'])
-
+    layer_unions = [[{x.index for x in graph.vs if x['step'] == 0}]]
-    layer_data = [[] for _ in range(max_step + 1)]
-    layer_data[0].append([set(x.index for x in g.vs if x['step'] == 0)])
     for step in range(0, max_step):
-        data_a, data_b = split_layer(g, step, step + 1)
+        layer_unions.extend(list(split_adjacent_layers(graph, step)))
-        layer_data[step].append(data_a)
+    layer_unions.append([{x.index for x in graph.vs if x['step'] == max_step}])
-        layer_data[step + 1].append(data_b)
+    assert len(layer_unions) == (max_step + 1) * 2
-    layer_data[max_step].append([set(x.index for x in g.vs if x['step'] == max_step)])
 
-    assert len(layer_data) == max_step + 1
+    all_unions = []
-    assert set(len(x) for x in layer_data) == {2}
+    for idx in range(0, len(layer_unions), 2):
+        all_unions.extend(apply_layer_unions(*layer_unions[idx:idx + 2]))
+    for unions in all_unions:
+        assert len(unions) > 0
+        assert len(set(graph.vs[x]['step'] for x in unions)) == 1
+    return sorted(all_unions, key=lambda u: min(graph.vs[x]['code'] for x in u))
 
-    unions = {}
-    for step in range(0, max_step + 1):
-        layer_unions = build_multi_set(layer_data[step][0], layer_data[step][1])
-        for union in layer_unions:
-            assert len(set(g.vs[x]['step'] for x in union)) == 1
-            codes = [g.vs[x]['code'] for x in union]
-            unions[min(codes)] = union
 
-    assert sorted(y for x in unions.values() for y in x) == list(range(g.vcount()))
+def combine_graph(graph: ig.Graph) -> ig.Graph:
+    unions = build_all_unions(graph)
+    union_idx = sorted((x, idx) for idx, u in enumerate(unions) for x in u)
 
-    combine_info = [-1 for _ in range(g.vcount())]
+    combine_idx = [x for _, x in union_idx]
-    for index, key in enumerate(sorted(unions)):
+    assert len(combine_idx) == graph.vcount()
-        for x in unions[key]:
+    assert set(combine_idx) == set(range(len(unions)))
-            combine_info[x] = index
 
-    assert len(combine_info) == g.vcount()
+    id_len = len(str(len(unions) - 1))
-    assert set(combine_info) == set(range(len(unions)))
+    graph.vs['id'] = [f'U{x:0{id_len}}' for x in combine_idx]
 
-    g.contract_vertices(combine_info, combine_attrs={'step': 'first', 'code': list})
+    graph.contract_vertices(combine_idx, combine_attrs={'id': 'first', 'step': 'first', 'code': list})
-    assert set(x.is_loop() for x in g.es) == {False}
+    assert [int(x.removeprefix('U')) for x in graph.vs['id']] == list(range(len(unions)))
-    g.simplify(multiple=True)
+    assert not any(x.is_loop() for x in graph.es)
-    return g
+    graph.simplify(multiple=True)
+    return graph
 
 
 def do_combine(input: str, output: str) -> None:
     print(f'Start combining: {input}')
-    g = do_split(ig.Graph.Read_Pickle(input))
-    g.write_pickle(output)
 
-    g_mod = g.copy()
+    g_raw = (graph := combine_graph(ig.Graph.Read_Pickle(input))).copy()
-    for x in g_mod.vs:
+    graph.vs['codes'] = graph.vs['code']
-        x['code'] = '+'.join(x['code'])
+    del graph.vs['code']
-    g_mod = do_split(g_mod)
+    graph.write_pickle(output)  # save combined graph
+
+    g_raw.vs['code'] = g_raw.vs['id']  # modify as origin format
+    g_mod = combine_graph(g_raw.copy())
 
-    assert g.vcount() == g_mod.vcount()
+    assert g_raw.vcount() == g_mod.vcount()
-    assert g.ecount() == g_mod.ecount()
+    assert g_raw.ecount() == g_mod.ecount()
-    for index in range(g.vcount()):
+    assert all(x['code'] == [x['id']] for x in g_mod.vs)
-        assert len(g_mod.vs[index]['code']) == 1
+    assert g_raw.vs['step'] == g_mod.vs['step']
-        assert g.vs[index]['step'] == g_mod.vs[index]['step']
+    assert g_raw.vs['code'] == g_mod.vs['id']
-        assert '+'.join(g.vs[index]['code']) == g_mod.vs[index]['code'][0]
+    assert g_raw.isomorphic(g_mod)
-    assert g.isomorphic(g_mod)
 
 
 def combine_all(ig_dir: str, output_dir: str) -> None:
@@ -141,6 +106,6 @@ def combine_all(ig_dir: str, output_dir: str) -> None:
     pool.join()
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     os.makedirs('output-combine', exist_ok=True)
     combine_all('output-ig', 'output-combine')

misc/all-graph/compare.py

@@ -7,14 +7,18 @@ import igraph as ig
 def load_legacy(file: str) -> ig.Graph:
     g = ig.Graph.Read_Pickle(file)
     for node in g.vs:
-        node['code'] = sorted(node['code'])
+        assert sorted(node['code']) == node['code']
+        node['codes'] = node['code']
+    del g.vs['code']
     return g
 
 
 def load_modern(file: str) -> ig.Graph:
     g = ig.Graph.Read_Pickle(file)
+    assert [int(x.removeprefix('U')) for x in g.vs['id']] == list(range(g.vcount()))
     for node in g.vs:
-        assert sorted(node['code']) == sorted(node['code'])
+        assert sorted(node['codes']) == node['codes']
+    del g.vs['id']
     return g
 
 
@@ -26,15 +30,13 @@ def compare(g1: ig.Graph, g2: ig.Graph) -> None:
     assert {len(x.attributes()) for x in g1.es} == {0}
     assert {len(x.attributes()) for x in g2.es} == {0}
 
-    data_a = {min(x['code']): x.attributes() for x in g1.vs}
+    data_a = {min(x['codes']): x.attributes() for x in g1.vs}
-    data_b = {min(x['code']): x.attributes() for x in g2.vs}
+    data_b = {min(x['codes']): x.attributes() for x in g2.vs}
     assert data_a == data_b
 
 
 if __name__ == '__main__':
-    for name in sorted(os.listdir('output-combine')):
+    for name in sorted(os.listdir('output-combine-raw')):
-        if '_' not in name:
+        g1 = load_legacy(f'output-combine-raw/{name}')
-            continue
-        g1 = load_legacy(f'combined/{name.split('_')[1]}')
         g2 = load_modern(f'output-combine/{name}')
         compare(g1, g2)