From 3654ca367e9d16b68d0a8f52fb15c88c3aea53e8 Mon Sep 17 00:00:00 2001
From: apister <alexis.pister@inria.fr>
Date: Mon, 28 Jun 2021 14:58:37 +0200
Subject: [PATCH] dynCom Instant Optimal
---
aleclust/clustering/clustering.py | 2 +-
aleclust/globals.py | 2 +-
api.py | 58 +++---
dynCom/dynCom/InstantOptimal.py | 80 +++++++++
dynCom/dynCom/dynCommunities.py | 6 +-
dynCom/dynCom/temporal_trade_off.py | 2 +-
dynCom/notebooks/temporal_trad_off.ipynb | 220 +++++++++++------------
dynCom/notebooks/tiles.ipynb | 160 +++++++++++++++++
dynCom/setup.py | 11 +-
dynCom/tests/conftest.py | 10 +-
dynCom/tests/test_InstantOptimal.py | 10 ++
dynCom/tests/test_temporal_trade_off.py | 12 +-
dynCom/tests/test_utils.py | 8 +-
setup.py | 4 +-
14 files changed, 418 insertions(+), 167 deletions(-)
create mode 100644 dynCom/dynCom/InstantOptimal.py
create mode 100644 dynCom/notebooks/tiles.ipynb
create mode 100644 dynCom/tests/test_InstantOptimal.py
diff --git a/aleclust/clustering/clustering.py b/aleclust/clustering/clustering.py
index b0e92fc..63b24e4 100644
--- a/aleclust/clustering/clustering.py
+++ b/aleclust/clustering/clustering.py
@@ -17,7 +17,7 @@ import aleclust.utility as utility
import aleclust.clustering.communities as nodeClustering
# TODO : Move to metric
-from clustering.attributeCD import attribute_clustering_preprocessing
+from aleclust.clustering.attributeCD import attribute_clustering_preprocessing
METRICS = {
"coverage": community.quality.coverage,
diff --git a/aleclust/globals.py b/aleclust/globals.py
index c479f3b..b5ca9fc 100644
--- a/aleclust/globals.py
+++ b/aleclust/globals.py
@@ -364,7 +364,7 @@ METRICS_PARAMETERS = ["bimodularity_entity_type"]
import dynCom.louvain as dynamic_louvain
DYNAMIC_CDA = {
- "louvain": {
+ "louvain_tdf": {
"description": "Launch the Louvain algorithm at each snapshot, with an initial condition corresponding to the result of the previous timeslot. Use an heuristic to not find a local optimum too fast",
"parameters": {
"resolution": {
diff --git a/api.py b/api.py
index aa42f9e..e12e696 100644
--- a/api.py
+++ b/api.py
@@ -1,12 +1,4 @@
# -*- coding: utf-8 -*-
-from flask import Flask, jsonify, request, send_file
-from flask_socketio import SocketIO, emit, send, Namespace
-from flask_cors import CORS
-from flask import current_app
-
-import requests
-from urllib.parse import urlparse
-from io import BytesIO
import os
import rapidjson
@@ -14,9 +6,18 @@ import copy
import sys
import time
+from flask import Flask, jsonify, request, send_file
+from flask_socketio import SocketIO, emit, send, Namespace
+from flask_cors import CORS
+from flask import current_app
+import requests
+from urllib.parse import urlparse
+from io import BytesIO
import networkx as nx
from networkx.readwrite import json_graph
+from dynCom.InstantOptimal import InstantOptimal
+
import aleclust.processing.preprocessing as preprocessing
import aleclust.utility as utility
import aleclust.dynamiClustering.dynamiClustering as dynamiClustering
@@ -54,14 +55,16 @@ dataPaths = {
@app.route("/", methods=["GET"])
def base():
- message = {"info": INFO,
- "datasets": list(dataPaths.keys()),
- "algorithms": {"unipartite": utility.dict_to_dict_of_strings(
- utility.delete_keys_from_dict(copy.deepcopy(UNIPARTITE_CDA), ["function"])),
- "bipartite": utility.dict_to_dict_of_strings(
- utility.delete_keys_from_dict(copy.deepcopy(BIPARTITE_CDA), ["function"]))},
- "parameters": utility.dict_to_dict_of_strings(PARAMETERS),
- "metrics": list(clustering.METRICS.keys())}
+ message = {
+ "info": INFO,
+ "datasets": list(dataPaths.keys()),
+ "algorithms": {"unipartite": utility.dict_to_dict_of_strings(
+ utility.delete_keys_from_dict(copy.deepcopy(UNIPARTITE_CDA), ["function"])),
+ "bipartite": utility.dict_to_dict_of_strings(
+ utility.delete_keys_from_dict(copy.deepcopy(BIPARTITE_CDA), ["function"]))},
+ "parameters": utility.dict_to_dict_of_strings(PARAMETERS),
+ "metrics": list(clustering.METRICS.keys())
+ }
return jsonify(message)
@@ -111,17 +114,21 @@ def static_clustering_request(flask_request, clustering_algo, dataName=False, dy
def dynamic_clustering_request(flask_request, clustering_algo):
from dynCom import json_read, louvain
json = flask_request.json
- json_parser = PaohJsonParser(json, dynamic=True)
- parameters: Parameters = json_parser.parameters
- parameters.algorithm_list = DYNAMIC_CDA
- # get URL arguments
- args = flask_request.args
- parameters.parse_parameters(clustering_algo, args)
+ if clustering_algo in DYNAMIC_CDA:
+ json_parser = PaohJsonParser(json, dynamic=True)
+ parameters: Parameters = json_parser.parameters
+ parameters.algorithm_list = DYNAMIC_CDA
- dyn_graph = json_parser.own_json_to_graph(dynamic=True)
+ # get URL arguments
+ args = flask_request.args
+ parameters.parse_parameters(clustering_algo, args)
+ dyn_graph = json_parser.own_json_to_graph(dynamic=True)
- model = DYNAMIC_CDA[clustering_algo]["function"](**parameters.clustering_parameters)
+ model = DYNAMIC_CDA[clustering_algo]["function"](**parameters.clustering_parameters)
+ else:
+ dyn_graph = PaohJsonParser.json_to_dyn_graph(json, True)
+ model = InstantOptimal(clustering_algo)
dyn_coms = model.apply(dyn_graph)
dyn_coms_json = dyn_coms.to_json()
@@ -278,4 +285,5 @@ if __name__ == "__main__":
app.run(debug=debug, port=sys.argv[1])
else:
# socketio.run(app, port=10080)
- app.run(debug=debug, port=10080)
+ # app.run(debug=debug, port=10080)
+ app.run(debug=debug, port=10085)
diff --git a/dynCom/dynCom/InstantOptimal.py b/dynCom/dynCom/InstantOptimal.py
new file mode 100644
index 0000000..46a3aa4
--- /dev/null
+++ b/dynCom/dynCom/InstantOptimal.py
@@ -0,0 +1,80 @@
+import networkx as nx
+import dynetx as dn
+from cdlib import algorithms
+from cdlib import TemporalClustering
+from networkx.generators.community import LFR_benchmark_graph
+
+from dynCom import utils, dynCommunities
+
+
+def cdlib_handler(algorithm_name):
+ cdlib_function = algorithms.__dict__[algorithm_name]
+ return cdlib_function
+
+
+def t_com_id_to_com_id(t_com_id):
+ return t_com_id.split("_")[-1]
+
+
+def jaccard(x, y):
+ return len(set(x) & set(y)) / len(set(x) | set(y))
+
+
+class InstantOptimal:
+ def __init__(self, alg_name):
+ self.alg_name = alg_name
+
+ self.dyn_communities = None
+ self.temporal_clustering = None
+ self.snapshot_ids = None
+ self.matches = None
+ self.tcomids_to_comid = None
+ self.com_id = None
+
+ def apply(self, dyn_graph, **kwargs):
+ self.dyn_communities = dynCommunities.DynCommunities(dyn_graph)
+ self.temporal_clustering = TemporalClustering()
+ self.snapshot_ids = dyn_graph.temporal_snapshots_ids()
+
+ for i, snapshot_id in enumerate(self.snapshot_ids):
+ snapshot = utils.dyn_to_nxgraph(dyn_graph.time_slice(snapshot_id))
+ partition = cdlib_handler(self.alg_name)(snapshot, **kwargs)
+ self.temporal_clustering.add_clustering(partition, snapshot_id)
+
+ self.matches = self.temporal_clustering.community_matching(jaccard, two_sided=True)
+ self.matching_step()
+
+ self.save_to_dyn_communities()
+ return self.dyn_communities
+
+ def matching_step(self):
+ self.tcomids_to_comid = {}
+ self.com_id = 0
+ for match in self.matches:
+ similarity = match[2]
+ com_id_t0 = match[0]
+ com_id_t1 = match[1]
+
+ if com_id_t0 in self.tcomids_to_comid:
+ com_id = self.tcomids_to_comid[com_id_t0]
+ else:
+ com_id = self.com_id
+ self.tcomids_to_comid[com_id_t0] = com_id
+ self.com_id += 1
+
+ if similarity > 0.5:
+ self.tcomids_to_comid[com_id_t1] = com_id
+
+ def save_to_dyn_communities(self):
+ for snapshot_id in self.snapshot_ids:
+ for j, com in enumerate(self.temporal_clustering.get_clustering_at(snapshot_id).communities):
+ t_com_id = f"{snapshot_id}_{j}"
+ if t_com_id in self.tcomids_to_comid:
+ com_id = self.tcomids_to_comid[f"{snapshot_id}_{j}"]
+ else:
+ com_id = self.com_id
+ self.com_id += 1
+
+ self.dyn_communities.communities[snapshot_id][com_id] = com
+
+ # print(self.dyn_communities.communities)
diff --git a/dynCom/dynCom/dynCommunities.py b/dynCom/dynCom/dynCommunities.py
index e85a6f2..05d86ae 100644
--- a/dynCom/dynCom/dynCommunities.py
+++ b/dynCom/dynCom/dynCommunities.py
@@ -12,10 +12,11 @@ def dict_to_list_communities(dict_communities):
class DynCommunities:
def __init__(self, dyn_graph=None):
self.dyn_graph = dyn_graph
- self.communities: dict[str, dict[int, list]] = {}
+ # self.communities: dict[str, dict[int, list]] = {} # Time to com to node
+ self.communities: dict[str, dict[int, list]] = defaultdict(dict) # Time to com to node
self.json = None
- self.no_community_label = "None"
+ self.no_community_label = None
def to_json(self):
self.json = {}
@@ -33,4 +34,5 @@ class DynCommunities:
self.json["nodes"] = dict_to_list_communities(nodes_communities)
self.json["graph"] = {}
+
return self.json
diff --git a/dynCom/dynCom/temporal_trade_off.py b/dynCom/dynCom/temporal_trade_off.py
index 60bd2fd..ea0044b 100644
--- a/dynCom/dynCom/temporal_trade_off.py
+++ b/dynCom/dynCom/temporal_trade_off.py
@@ -25,7 +25,7 @@ class GlobalOptUpdate:
self.snapshot_ids = dyn_graph.temporal_snapshots_ids()
for i, snapshot_id in enumerate(self.snapshot_ids):
- print(i, snapshot_id)
+ # print(i, snapshot_id)
snapshot = utils.dyn_to_nxgraph(dyn_graph.time_slice(snapshot_id))
if i == 0:
diff --git a/dynCom/notebooks/temporal_trad_off.ipynb b/dynCom/notebooks/temporal_trad_off.ipynb
index 14b80a0..229a526 100644
--- a/dynCom/notebooks/temporal_trad_off.ipynb
+++ b/dynCom/notebooks/temporal_trad_off.ipynb
@@ -2,61 +2,8 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "1801\n",
- "[(0, 1)]\n",
- "[(0, 2)]\n",
- "[(5, 6)]\n",
- "[(5, 7)]\n",
- "1802\n",
- "[(0, 1)]\n",
- "[(0, 2)]\n",
- "[(0, 3)]\n",
- "[(0, 4)]\n",
- "[(4, 5)]\n",
- "[(5, 6)]\n",
- "[(5, 7)]\n",
- "1803\n",
- "[(0, 1)]\n",
- "[(0, 3)]\n",
- "[(0, 2), (0, 3), (0, 4), (0, 5), (2, 3), (2, 4), (2, 5), (3, 4), (3, 5), (4, 5)]\n",
- "[(0, 5), (0, 6), (5, 6)]\n",
- "[(0, 5), (0, 7), (0, 8), (0, 9), (5, 7), (5, 8), (5, 9), (7, 8), (7, 9), (8, 9)]\n",
- "[(9, 10)]\n",
- "[(10, 11)]\n",
- "[(10, 11), (10, 12), (11, 12)]\n",
- "1804\n",
- "[(0, 10)]\n",
- "[(0, 9), (0, 11), (9, 11)]\n",
- "[(0, 9), (0, 10), (0, 12), (9, 10), (9, 12), (10, 12)]\n",
- "[(2, 3)]\n",
- "[(2, 3), (2, 4), (2, 5), (2, 7), (2, 8), (2, 9), (3, 4), (3, 5), (3, 7), (3, 8), (3, 9), (4, 5), (4, 7), (4, 8), (4, 9), (5, 7), (5, 8), (5, 9), (7, 8), (7, 9), (8, 9)]\n",
- "[(5, 6)]\n",
- "[(5, 7)]\n",
- "[(9, 10)]\n",
- "0 1801\n"
- ]
- },
- {
- "ename": "TypeError",
- "evalue": "'module' object is not callable",
- "output_type": "error",
- "traceback": [
- "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
- "\u001B[0;31mTypeError\u001B[0m Traceback (most recent call last)",
- "\u001B[0;32m<ipython-input-1-b2ac26fc56e7>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[1;32m 4\u001B[0m \u001B[0;32mimport\u001B[0m \u001B[0mjson_read\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 5\u001B[0m \u001B[0;32mimport\u001B[0m \u001B[0mprojection\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m----> 6\u001B[0;31m \u001B[0;32mimport\u001B[0m \u001B[0mlouvain\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 7\u001B[0m \u001B[0;32mimport\u001B[0m \u001B[0mutils\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 8\u001B[0m \u001B[0;32mimport\u001B[0m \u001B[0mtemporal_trade_off\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;32m~/Projects/dynCom/louvain.py\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[1;32m 35\u001B[0m \u001B[0mlouv\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mLouvain\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 36\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 37\u001B[0;31m \u001B[0mp\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mlouv\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mapply\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mgraph_dyn_uni\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 38\u001B[0m \u001B[0;31m#\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 39\u001B[0m \u001B[0;31m# #%%\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;32m~/Projects/dynCom/temporal_trade_off.py\u001B[0m in \u001B[0;36mapply\u001B[0;34m(self, dyn_graph)\u001B[0m\n\u001B[1;32m 32\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 33\u001B[0m \u001B[0;32mif\u001B[0m \u001B[0mi\u001B[0m \u001B[0;34m==\u001B[0m \u001B[0;36m0\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 34\u001B[0;31m \u001B[0mfirst_partition\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0msnapshot_clustering\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0msnapshot\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;32mNone\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 35\u001B[0m \u001B[0;32mcontinue\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 36\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;32m~/Projects/dynCom/louvain.py\u001B[0m in \u001B[0;36msnapshot_clustering\u001B[0;34m(self, snapshot, init_partition)\u001B[0m\n\u001B[1;32m 20\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 21\u001B[0m \u001B[0;32mdef\u001B[0m \u001B[0msnapshot_clustering\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0msnapshot\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0minit_partition\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 22\u001B[0;31m \u001B[0mpartition\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mcommunity_louvain\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0msnapshot\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mpartition\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0minit_partition\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 23\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 24\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;31mTypeError\u001B[0m: 'module' object is not callable"
- ]
- }
- ],
+ "execution_count": 3,
+ "outputs": [],
"source": [
"import rapidjson\n",
"import networkx as nx\n",
@@ -76,7 +23,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 4,
"metadata": {
"collapsed": true
},
@@ -92,48 +39,65 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 5,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "<dynetx.classes.dyngraph.DynGraph at 0x7fd2fbe9cb80>"
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "graph_dyn_uni = projection.projection(graph_dyn)\n",
+ "graph_dyn_uni\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]"
+ },
+ "execution_count": 14,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "graph_dyn_uni.time_slice(1803).nodes()"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "1801\n",
- "[(0, 1)]\n",
- "[(0, 2)]\n",
- "[(5, 6)]\n",
- "[(5, 7)]\n",
- "1802\n",
- "[(0, 1)]\n",
- "[(0, 2)]\n",
- "[(0, 3)]\n",
- "[(0, 4)]\n",
- "[(4, 5)]\n",
- "[(5, 6)]\n",
- "[(5, 7)]\n",
- "1803\n",
- "[(0, 1)]\n",
- "[(0, 3)]\n",
- "[(0, 2), (0, 3), (0, 4), (0, 5), (2, 3), (2, 4), (2, 5), (3, 4), (3, 5), (4, 5)]\n",
- "[(0, 5), (0, 6), (5, 6)]\n",
- "[(0, 5), (0, 7), (0, 8), (0, 9), (5, 7), (5, 8), (5, 9), (7, 8), (7, 9), (8, 9)]\n",
- "[(9, 10)]\n",
- "[(10, 11)]\n",
- "[(10, 11), (10, 12), (11, 12)]\n",
- "1804\n",
- "[(0, 10)]\n",
- "[(0, 9), (0, 11), (9, 11)]\n",
- "[(0, 9), (0, 10), (0, 12), (9, 10), (9, 12), (10, 12)]\n",
- "[(2, 3)]\n",
- "[(2, 3), (2, 4), (2, 5), (2, 7), (2, 8), (2, 9), (3, 4), (3, 5), (3, 7), (3, 8), (3, 9), (4, 5), (4, 7), (4, 8), (4, 9), (5, 7), (5, 8), (5, 9), (7, 8), (7, 9), (8, 9)]\n",
- "[(5, 6)]\n",
- "[(5, 7)]\n",
- "[(9, 10)]\n"
+ "[0, 1, 2, 5, 6, 7, 3, 4, 8, 9, 10, 11, 12]\n"
]
}
],
"source": [
- "graph_dyn_uni = projection.projection(graph_dyn)"
+ "print(graph_dyn_uni.nodes())"
],
"metadata": {
"collapsed": false,
@@ -144,7 +108,7 @@
},
{
"cell_type": "code",
- "execution_count": 85,
+ "execution_count": 40,
"outputs": [],
"source": [
"louv = louvain.Louvain()"
@@ -158,19 +122,16 @@
},
{
"cell_type": "code",
- "execution_count": 86,
+ "execution_count": 41,
"outputs": [
{
- "ename": "TypeError",
- "evalue": "add_nodes_from() missing 1 required positional argument: 'nodes_for_adding'",
- "output_type": "error",
- "traceback": [
- "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
- "\u001B[0;31mTypeError\u001B[0m Traceback (most recent call last)",
- "\u001B[0;32m<ipython-input-86-cbe6fc7cfdad>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[0;32m----> 1\u001B[0;31m \u001B[0mp\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mlouv\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mapply\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mgraph_dyn_uni\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 2\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;32m~/Projects/dynCom/temporal_trade_off.py\u001B[0m in \u001B[0;36mapply\u001B[0;34m(self, dyn_graph)\u001B[0m\n\u001B[1;32m 16\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 17\u001B[0m \u001B[0;32mfor\u001B[0m \u001B[0mi\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0msnapshot_id\u001B[0m \u001B[0;32min\u001B[0m \u001B[0menumerate\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0msnapshot_ids\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 18\u001B[0;31m \u001B[0msnapshot\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mnx\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mGraph\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 19\u001B[0m \u001B[0msnapshot\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0madd_nodes_from\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdyn_graph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mtime_slice\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0msnapshot_id\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mnodes\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 20\u001B[0m \u001B[0;31m# snapshot.add_edges_from(dyn_graph.time_slice(snapshot_id).edges())\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;32m~/Projects/dynCom/utils.py\u001B[0m in \u001B[0;36mdyn_to_nxgraph\u001B[0;34m(dyn_graph)\u001B[0m\n\u001B[1;32m 4\u001B[0m \u001B[0;32mdef\u001B[0m \u001B[0mdyn_to_nxgraph\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdyn_graph\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 5\u001B[0m \u001B[0mgraph\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mnx\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mGraph\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m----> 6\u001B[0;31m \u001B[0mnodes\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mdyn_graph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mnodes\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 7\u001B[0m \u001B[0mgraph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0madd_nodes_from\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mnodes_for_adding\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0mnodes\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 8\u001B[0m \u001B[0mgraph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0madd_edges_from\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdyn_graph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0minteractions\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;31mTypeError\u001B[0m: add_nodes_from() missing 1 required positional argument: 'nodes_for_adding'"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "0 1801\n",
+ "1 1802\n",
+ "2 1803\n",
+ "3 1804\n"
]
}
],
@@ -186,13 +147,36 @@
},
{
"cell_type": "code",
- "execution_count": 80,
+ "execution_count": 42,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{1801: {0: [0, 1, 2], 1: [5, 6, 7]},\n 1802: {0: [0, 1, 2, 3], 1: [4, 5, 6, 7]},\n 1803: {0: [0, 1, 2, 3, 4], 1: [5, 6, 7, 8, 9], 2: [10, 11, 12]},\n 1804: {0: [0, 9, 10, 11, 12], 1: [2, 3, 4, 5, 7, 8, 6]}}"
+ },
+ "execution_count": 42,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "p.communities"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
"outputs": [
{
"data": {
"text/plain": "[1801, 1802, 1803, 1804]"
},
- "execution_count": 80,
+ "execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
@@ -209,13 +193,13 @@
},
{
"cell_type": "code",
- "execution_count": 67,
+ "execution_count": 7,
"outputs": [
{
"data": {
"text/plain": "dynetx.classes.dyngraph.DynGraph"
},
- "execution_count": 67,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
@@ -233,13 +217,13 @@
},
{
"cell_type": "code",
- "execution_count": 68,
+ "execution_count": 8,
"outputs": [
{
"data": {
"text/plain": "[0, 9, 10, 11, 12, 2, 3, 4, 5, 7, 8, 6]"
},
- "execution_count": 68,
+ "execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
@@ -256,19 +240,15 @@
},
{
"cell_type": "code",
- "execution_count": 60,
+ "execution_count": 9,
"outputs": [
{
- "ename": "TypeError",
- "evalue": "add_nodes_from() missing 1 required positional argument: 'nodes_for_adding'",
- "output_type": "error",
- "traceback": [
- "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
- "\u001B[0;31mTypeError\u001B[0m Traceback (most recent call last)",
- "\u001B[0;32m<ipython-input-60-c57278ae38ca>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m\u001B[0m\n\u001B[0;32m----> 1\u001B[0;31m \u001B[0mutils\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mdyn_to_nxgraph\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0msnap\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 2\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;32m~/Projects/dynCom/utils.py\u001B[0m in \u001B[0;36mdyn_to_nxgraph\u001B[0;34m(dyn_graph)\u001B[0m\n\u001B[1;32m 4\u001B[0m \u001B[0;32mdef\u001B[0m \u001B[0mdyn_to_nxgraph\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdyn_graph\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 5\u001B[0m \u001B[0mgraph\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mnx\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mGraph\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m----> 6\u001B[0;31m \u001B[0mnodes\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mdyn_graph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mnodes\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 7\u001B[0m \u001B[0mgraph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0madd_nodes_from\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mnodes_for_adding\u001B[0m\u001B[0;34m=\u001B[0m\u001B[0mnodes\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 8\u001B[0m \u001B[0mgraph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0madd_edges_from\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mdyn_graph\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0minteractions\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
- "\u001B[0;31mTypeError\u001B[0m: add_nodes_from() missing 1 required positional argument: 'nodes_for_adding'"
- ]
+ "data": {
+ "text/plain": "<networkx.classes.graph.Graph at 0x7ffa4527ecd0>"
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
@@ -283,7 +263,7 @@
},
{
"cell_type": "code",
- "execution_count": 65,
+ "execution_count": 10,
"outputs": [],
"source": [
"graph = nx.Graph()"
@@ -297,7 +277,7 @@
},
{
"cell_type": "code",
- "execution_count": 87,
+ "execution_count": 11,
"outputs": [],
"source": [
"graph.add_nodes_from(snap.nodes())"
diff --git a/dynCom/notebooks/tiles.ipynb b/dynCom/notebooks/tiles.ipynb
new file mode 100644
index 0000000..e7c31b8
--- /dev/null
+++ b/dynCom/notebooks/tiles.ipynb
@@ -0,0 +1,160 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "import rapidjson\n",
+ "import networkx as nx\n",
+ "\n",
+ "import json_read\n",
+ "import projection\n",
+ "import louvain\n",
+ "import utils\n",
+ "import temporal_trade_off\n",
+ "from cdlib import algorithms"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "outputs": [],
+ "source": [
+ "fp = \"../data/Marie_Boucher_small.json\"\n",
+ "with open(fp, \"r\", encoding='utf-8') as read_file:\n",
+ " json_data = rapidjson.loads(read_file.read())\n",
+ "\n",
+ "graph_dyn = json_read.paoh_json_reader(json_data)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "<dynetx.classes.dyngraph.DynGraph at 0x7f460f684400>"
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "graph_dyn_uni = projection.projection(graph_dyn)\n",
+ "graph_dyn_uni"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "[('_e_0', 0, '+', 1801), ('_e_0', 1, '+', 1801), ('_e_3', 0, '+', 1801), ('_e_3', 2, '+', 1801), ('_e_17', 5, '+', 1801), ('_e_17', 6, '+', 1801), ('_e_20', 5, '+', 1801), ('_e_20', 7, '+', 1801), ('_e_1', 0, '+', 1802), ('_e_1', 1, '+', 1802), ('_e_4', 0, '+', 1802), ('_e_4', 2, '+', 1802), ('_e_6', 0, '+', 1802), ('_e_6', 3, '+', 1802), ('_e_7', 0, '+', 1802), ('_e_7', 4, '+', 1802), ('_e_16', 4, '+', 1802), ('_e_16', 5, '+', 1802), ('_e_19', 5, '+', 1802), ('_e_19', 6, '+', 1802), ('_e_22', 5, '+', 1802), ('_e_22', 7, '+', 1802), ('_e_2', 0, '+', 1803), ('_e_2', 1, '+', 1803), ('_e_5', 0, '+', 1803), ('_e_5', 3, '+', 1803), ('_e_8', 0, '+', 1803), ('_e_8', 2, '+', 1803), ('_e_8', 3, '+', 1803), ('_e_8', 4, '+', 1803), ('_e_8', 5, '+', 1803), ('_e_9', 0, '+', 1803), ('_e_9', 5, '+', 1803), ('_e_9', 6, '+', 1803), ('_e_10', 0, '+', 1803), ('_e_10', 5, '+', 1803), ('_e_10', 7, '+', 1803), ('_e_10', 8, '+', 1803), ('_e_10', 9, '+', 1803), ('_e_24', 9, '+', 1803), ('_e_24', 10, '+', 1803), ('_e_25', 10, '+', 1803), ('_e_25', 11, '+', 1803), ('_e_26', 10, '+', 1803), ('_e_26', 11, '+', 1803), ('_e_26', 12, '+', 1803), ('_e_11', 0, '+', 1804), ('_e_11', 10, '+', 1804), ('_e_12', 0, '+', 1804), ('_e_12', 11, '+', 1804), ('_e_12', 9, '+', 1804), ('_e_13', 0, '+', 1804), ('_e_13', 9, '+', 1804), ('_e_13', 10, '+', 1804), ('_e_13', 12, '+', 1804), ('_e_14', 2, '+', 1804), ('_e_14', 3, '+', 1804), ('_e_15', 2, '+', 1804), ('_e_15', 3, '+', 1804), ('_e_15', 4, '+', 1804), ('_e_15', 5, '+', 1804), ('_e_15', 7, '+', 1804), ('_e_15', 8, '+', 1804), ('_e_15', 9, '+', 1804), ('_e_18', 5, '+', 1804), ('_e_18', 6, '+', 1804), ('_e_21', 5, '+', 1804), ('_e_21', 7, '+', 1804), ('_e_23', 9, '+', 1804), ('_e_23', 10, '+', 1804)]\n",
+ "[1801, 1802, 1803, 1804]\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(list(graph_dyn.stream_interactions()))\n",
+ "print(graph_dyn.temporal_snapshots_ids())"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 51,
+ "outputs": [],
+ "source": [
+ "coms = algorithms.tiles(graph_dyn_uni, 1)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 52,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "[1, 2, 3, 4, 5]\n",
+ "[]\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(coms.get_observation_ids())\n",
+ "print(coms.get_clustering_at(1).communities)\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "outputs": [],
+ "source": [],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ }
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
\ No newline at end of file
diff --git a/dynCom/setup.py b/dynCom/setup.py
index 20a5af5..335d482 100644
--- a/dynCom/setup.py
+++ b/dynCom/setup.py
@@ -17,7 +17,7 @@ def read(fname):
setup(
name="dynCom",
- version="0.0.1",
+ version="0.0.2",
author="Alexis Pister",
author_email="alexis.pister@inria.fr",
description="Dynamic Graph Clustering Library",
@@ -35,11 +35,12 @@ setup(
# installed or upgraded on the target machine
# install_requires=required,
install_requires=[
- "networkx>=2.3",
- "dynetx==0.2.3"
+ "networkx>=2.5",
+ "dynetx>=0.2.3",
+ "cdlib>=0.2.3"
],
package_data={
# If any package contains *.md, *.txt or *.rst files, include them:
'doc': ['*.md', '*.rst'],
- }
- )
+ }
+)
diff --git a/dynCom/tests/conftest.py b/dynCom/tests/conftest.py
index 47058f5..f063194 100644
--- a/dynCom/tests/conftest.py
+++ b/dynCom/tests/conftest.py
@@ -20,7 +20,7 @@ def graph_dyn_bipartite():
@pytest.fixture(scope="session", params=[marie_boucher_small_fp, "generate"])
-def graph_dyn(request):
+def graphs_dyn(request):
if request.param == "generate":
G = dn.DynGraph(edge_removal=True)
G.add_interactions_from([(1, 2), (2, 3), (10, 11)], t=10)
@@ -33,3 +33,11 @@ def graph_dyn(request):
G = projection.projection(G_bipartite)
return G
+
+@pytest.fixture(scope="session")
+def marie_boucher_graph():
+ json_data = rapidjson.loads(open(marie_boucher_small_fp, "r").read())
+ G_bipartite = json_read.paoh_json_reader(json_data)
+ G = projection.projection(G_bipartite)
+ return G
+
diff --git a/dynCom/tests/test_InstantOptimal.py b/dynCom/tests/test_InstantOptimal.py
new file mode 100644
index 0000000..12ea478
--- /dev/null
+++ b/dynCom/tests/test_InstantOptimal.py
@@ -0,0 +1,10 @@
+from dynCom import InstantOptimal
+
+def test_apply(marie_boucher_graph):
+ model = InstantOptimal.InstantOptimal("louvain")
+ dyn_communities = model.apply(marie_boucher_graph)
+ print(dyn_communities.to_json())
+
+ model = InstantOptimal.InstantOptimal("infomap")
+ dyn_communities = model.apply(marie_boucher_graph)
+ print(dyn_communities.to_json())
diff --git a/dynCom/tests/test_temporal_trade_off.py b/dynCom/tests/test_temporal_trade_off.py
index 28a83a9..f562594 100644
--- a/dynCom/tests/test_temporal_trade_off.py
+++ b/dynCom/tests/test_temporal_trade_off.py
@@ -5,18 +5,20 @@ class TestGlobalOptUpdate:
def test_snapshot_clustering(self):
assert True
- def test_apply(self, graph_dyn):
+ def test_apply(self, graphs_dyn):
louvain_model = louvain.Louvain()
- dyn_communities = louvain_model.apply(graph_dyn)
+ dyn_communities = louvain_model.apply(graphs_dyn)
- assert len(dyn_communities.communities) == len(graph_dyn.temporal_snapshots_ids())
+ assert len(dyn_communities.communities) == len(graphs_dyn.temporal_snapshots_ids())
- for snapshot_id in graph_dyn.temporal_snapshots_ids():
+ for snapshot_id in graphs_dyn.temporal_snapshots_ids():
print(dyn_communities.communities[snapshot_id])
- snapshot = graph_dyn.time_slice(snapshot_id)
+ snapshot = graphs_dyn.time_slice(snapshot_id)
assert len(snapshot) == len([node for com_id, com in dyn_communities.communities[snapshot_id].items() for
node
in com])
+ print(dyn_communities.to_json())
+
def test_save_to_dyn_communities(self):
assert True
diff --git a/dynCom/tests/test_utils.py b/dynCom/tests/test_utils.py
index 31444ed..2ba49d8 100644
--- a/dynCom/tests/test_utils.py
+++ b/dynCom/tests/test_utils.py
@@ -3,10 +3,10 @@ import networkx as nx
from dynCom.utils import dyn_to_nxgraph
-def test_dyn_to_nxgraph(graph_dyn):
- graph = dyn_to_nxgraph(graph_dyn)
+def test_dyn_to_nxgraph(graphs_dyn):
+ graph = dyn_to_nxgraph(graphs_dyn)
assert type(graph) == nx.Graph
- assert set(graph_dyn.nodes()) == set(graph.nodes())
- assert {(u,v) for u, v, t in graph_dyn.interactions()} == set(graph.edges())
+ assert set(graphs_dyn.nodes()) == set(graph.nodes())
+ assert {(u,v) for u, v, t in graphs_dyn.interactions()} == set(graph.edges())
diff --git a/setup.py b/setup.py
index 5970858..885c998 100644
--- a/setup.py
+++ b/setup.py
@@ -40,7 +40,7 @@ setup(
# install_requires=required,
install_requires=[
"python-louvain==0.13",
- "cdlib==0.1.8",
+ "cdlib>=0.1.8",
"docutils==0.15.2",
"pquality==0.0.7",
"bimlpa==0.1.2",
@@ -66,7 +66,7 @@ setup(
"pulp==1.6.10",
"python-rapidjson==0.9.1",
"pytiled-parser==0.9.3",
- "networkx==2.3",
+ "networkx>=2.3",
"requests>=2.22.0",
"scikit-learn",
"pandas",
--
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