feat: export special graphml for yEd

misc/all-graph/02-dump_igraph.py

@@ -82,7 +82,7 @@ def convert_all(json_dir: str, output_dir: str) -> None:
     pool = multiprocessing.Pool()
     for name in sorted(os.listdir(json_dir)):
         json_file = f'{json_dir}/{name}'
-        output_prefix = f"{output_dir}/{name.removesuffix('.json')}"
+        output_prefix = f'{output_dir}/{name.removesuffix('.json')}'
         pool.apply_async(convert_and_dump, args=(json_file, output_prefix))
     pool.close()
     pool.join()

misc/all-graph/03-convert_graphml.py

@@ -2,38 +2,159 @@
 
 from __future__ import annotations
 
+import io
 import os
-import re
+from typing import override
+from abc import ABC, abstractmethod
+
+import numpy as np
 import igraph as ig
 from lxml import etree
+import matplotlib.pyplot as plt
 from dataclasses import dataclass
+import matplotlib.colors as mcolors
 
 
-class GraphML:
+@dataclass(frozen=True)
-    @dataclass(frozen=True)
+class Node:
-    class Node:
+    id: str
-        id: str
+    code: str
-        code: str
+    step: int
-        step: int
 
-    @dataclass(frozen=True)
-    class Edge:
-        src: str  # node id
-        dst: str  # node id
 
+@dataclass(frozen=True)
+class Edge:
+    src: str  # node id
+    dst: str  # node id
+
+
+class Builder(ABC):
+    def __init__(self, _: list[Node]):
+        pass
+
+    @abstractmethod
+    def nsmap(self) -> dict[str | None, str]:
+        pass
+
+    @abstractmethod
+    def build_keys(self) -> list[etree.Element]:
+        pass
+
+    @abstractmethod
+    def build_node(self, node: Node) -> etree.Element:
+        pass
+
+    @abstractmethod
+    def build_edge(self, edge: Edge) -> etree.Element:
+        pass
+
+    @abstractmethod
+    def post_modify(self, content: str) -> str:
+        pass
+
+
+class KlskBuilder(Builder):
+    def __init__(self, _: list[Node]):
+        pass
+
+    @override
+    def nsmap(self) -> dict[str | None, str]:
+        return {
+            None: 'http://graphml.graphdrawing.org/xmlns',
+            'xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+        }
+
+    @override
+    def build_keys(self) -> list[etree.Element]:
+        k_node = etree.Element('key', attrib={
+            'id': 'code',
+            'for': 'node',
+            'attr.name': 'code',
+            'attr.type': 'string'
+        })
+        k_step = etree.Element('key', attrib={
+            'id': 'step',
+            'for': 'node',
+            'attr.name': 'step',
+            'attr.type': 'int'
+        })
+        return [k_node, k_step]
+
+    @override
+    def build_node(self, node: Node) -> etree.Element:
+        node_xml = etree.Element('node', id=node.id)
+        etree.SubElement(node_xml, 'data', key='code').text = node.code
+        etree.SubElement(node_xml, 'data', key='step').text = str(node.step)
+        return node_xml
+
+    @override
+    def build_edge(self, edge: Edge) -> etree.Element:
+        return etree.Element('edge', source=edge.src, target=edge.dst)
+
+    @override
+    def post_modify(self, content: str) -> str:
+        return content
+
+
+class yEdBuilder(KlskBuilder):
+    def __build_colors(self, num: int) -> list[str]:
+        cmap = mcolors.LinearSegmentedColormap.from_list('custom_bwr', ['#0000ff', '#e8daef', '#ff0000'])
+        return [mcolors.to_hex(cmap(x)) for x in np.linspace(0, 1, num)]
+
+    def __init__(self, nodes: list[Node]):
+        max_step = max(x.step for x in nodes)
+        self.__colors = self.__build_colors(max_step + 1)
+        self.__yed_ns = 'http://www.yworks.com/xml/graphml'
+
+    @override
+    def nsmap(self) -> dict[str | None, str]:
+        return {
+            **super().nsmap(),
+            'y': self.__yed_ns
+        }
+
+    @override
+    def build_keys(self) -> list[etree.Element]:
+        k_info = etree.Element('key', attrib={
+            'id': 'info',
+            'for': 'node',
+            'yfiles.type': 'nodegraphics'
+        })
+        return super().build_keys() + [k_info]
+
+    @override
+    def build_node(self, node: Node) -> etree.Element:
+        shape = etree.Element(f'{{{self.__yed_ns}}}ShapeNode')
+        etree.SubElement(shape, f'{{{self.__yed_ns}}}Fill', attrib={'color': self.__colors[node.step]})
+        etree.SubElement(shape, f'{{{self.__yed_ns}}}Shape', attrib={'type': 'ellipse'})
+        etree.SubElement(shape, f'{{{self.__yed_ns}}}Geometry', attrib={'height': '50', 'width': '50'})
+        label = etree.SubElement(shape, f'{{{self.__yed_ns}}}NodeLabel', attrib={'fontSize': '10', 'modelName': 'internal'})
+        label.text = f'{node.code}
({node.step})'
+
+        node_xml = super().build_node(node)
+        node_info = etree.SubElement(node_xml, 'data', attrib={'key': 'info'})
+        node_info.append(shape)
+        return node_xml
+
+    @override
+    def post_modify(self, content: str) -> str:
+        return content.replace('
', '
')
+
+
+class GraphML:
     @dataclass(frozen=True)
     class Graph:
         name: str
-        nodes: list[GraphML.Node]
+        nodes: list[Node]
-        edges: list[GraphML.Edge]
+        edges: list[Edge]
 
     @staticmethod
-    def __load(name: str, graph: ig.Graph) -> GraphML.Graph:
+    def __load_graph(name: str, graph: ig.Graph) -> GraphML.Graph:
         nodes = []
         id_len = len(str(graph.vcount() - 1))
         for index in range(graph.vcount()):
             info = graph.vs[index]
-            nodes.append(GraphML.Node(f'n{index:0{id_len}d}', info['code'], info['step']))
+            nodes.append(Node(f'n{index:0{id_len}d}', info['code'], info['step']))
 
         edges = []
         for n1, n2 in graph.get_edgelist():
@@ -41,74 +162,51 @@ class GraphML:
             node_2 = nodes[n2]
             if node_1.step < node_2.step:
                 node_1, node_2 = node_2, node_1
-            edges.append(GraphML.Edge(node_1.id, node_2.id))
+            edges.append(Edge(node_1.id, node_2.id))
 
         return GraphML.Graph(name, nodes, edges)
 
-    def __init__(self, *graphs: tuple[str, ig.Graph]):
+    def __init__(self, tag: str, graph: ig.Graph):
-        self.__graphs = [self.__load(*x) for x in graphs]
+        self.__graph = self.__load_graph(tag, graph)
-
-    def __dump_node(self, node: Node) -> etree.Element:
-        node_xml = etree.Element('node', id=node.id)
-        etree.SubElement(node_xml, 'data', key='v_code').text = node.code
-        etree.SubElement(node_xml, 'data', key='v_step').text = str(node.step)
-        return node_xml
-
-    def __dump_edge(self, edge: Edge) -> etree.Element:
-        return etree.Element('edge', source=edge.src, target=edge.dst)
 
-    def __dump_graph(self, graph: Graph) -> etree.Element:
+    def __dump_graph(self, graph: Graph, builder: Builder) -> etree.Element:
         graph_xml = etree.Element('graph', id=graph.name, edgedefault='undirected')
         for node in graph.nodes:
-            graph_xml.append(self.__dump_node(node))
+            graph_xml.append(builder.build_node(node))
         for edge in graph.edges:
-            graph_xml.append(self.__dump_edge(edge))
+            graph_xml.append(builder.build_edge(edge))
         return graph_xml
 
-    def save_graph(self, output: str) -> None:
+    def save_graph(self, output: str, builder_t: type[Builder]) -> None:
-        graphml = etree.Element('graphml', nsmap={
+        builder = builder_t(self.__graph.nodes)
-            None: 'http://graphml.graphdrawing.org/xmlns',
+
-            'xsi': 'http://www.w3.org/2001/XMLSchema-instance'
+        graphml = etree.Element('graphml', nsmap=builder.nsmap())
-        })
         graphml.set(
             '{http://www.w3.org/2001/XMLSchema-instance}schemaLocation',
             'http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'
         )
-        etree.SubElement(graphml, 'key', attrib={
+        [graphml.append(x) for x in builder.build_keys()]
-            'id': 'v_code',
+        graphml.append(self.__dump_graph(self.__graph, builder))
-            'for': 'node',
-            'attr.name': 'code',
-            'attr.type': 'string'
-        })
-        etree.SubElement(graphml, 'key', attrib={
-            'id': 'v_step',
-            'for': 'node',
-            'attr.name': 'step',
-            'attr.type': 'int'
-        })
 
-        for graph in self.__graphs:
+        fake_output = io.BytesIO()
-            graphml.append(self.__dump_graph(graph))
         xml_tree = etree.ElementTree(graphml)
-        xml_tree.write(output, pretty_print=True, xml_declaration=True, encoding='utf-8')
+        xml_tree.write(fake_output, pretty_print=True, xml_declaration=True, encoding='utf-8')
-
+        content = fake_output.getvalue().decode('utf-8')
-
+        with open(output, 'w') as fp:
-def to_graphml(inputs: list[tuple[str, str]], output: str) -> None:
+            fp.write(builder.post_modify(content))
-    print(f'Convert into {output}')
-    gml = GraphML(*((x, ig.Graph.Read_Pickle(y)) for x, y in inputs))
-    gml.save_graph(output)
-
 
-def convert_graphs(input_dir: str, output_dir: str) -> None:
-    files = [x.removesuffix('.pkl') for x in os.listdir(input_dir) if x.endswith('.pkl')]
-    tags = sorted(x for x in files if re.match(r'^\d\-\d\d(L|R|M)$', x))
 
-    for tag in tags:
+def to_graphml(tag: str, input: str, output: str, is_yed: bool) -> None:
-        output_file = os.path.join(output_dir, f'{tag}.graphml')
+    print(f'Convert graph {input} into {output}')
-        pkls = sorted(x for x in files if x.startswith(tag))
+    gml = GraphML(tag, ig.Graph.Read_Pickle(input))
-        to_graphml([(x, os.path.join(input_dir, f'{x}.pkl')) for x in pkls], output_file)
+    gml.save_graph(output, yEdBuilder if is_yed else KlskBuilder)
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     os.makedirs('output-gml', exist_ok=True)
-    convert_graphs('output-ig', 'output-gml')
+    os.makedirs('output-yed', exist_ok=True)
+    for name in sorted(os.listdir('output-ig')):
+        name = name.removesuffix('.pkl')
+        tag = name.split('_')[0] if '_' in name else name
+        to_graphml(tag, f'output-ig/{name}.pkl', f'output-gml/{name}.graphml', False)
+        to_graphml(tag, f'output-ig/{name}.pkl', f'output-yed/{name}.graphml', True)