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Merge branch 'master' of github.com:dlozeve/tda-networks

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This commit is contained in:
Dimitri Lozeve 2018-08-02 15:34:06 +01:00
commit fd4b5c4236
1 changed files with 178 additions and 623 deletions
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sociopatterns.ipynb
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@ -9,7 +9,7 @@
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@ -28,7 +28,7 @@
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@ -45,7 +45,7 @@
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@ -55,7 +55,7 @@
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@ -72,7 +72,7 @@
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@ -81,7 +81,7 @@
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{
"cell_type": "code",
"execution_count": 7,
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"metadata": {},
"outputs": [
{
@ -90,7 +90,7 @@
"'IGRAPH UN-- 10972 415912 -- \\n+ attr: id (v), name (v), id (e), time (e)'"
]
},
"execution_count": 7,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
@ -101,7 +101,7 @@
},
{
"cell_type": "code",
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@ -110,7 +110,7 @@
"76944"
]
},
"execution_count": 8,
"execution_count": 7,
"metadata": {},
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@ -119,27 +119,6 @@
"len(np.unique(g.es[\"time\"]))"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(12, 11), (10, 9), (0, 2), (3, 4), (5, 8), (6, 7), (1, 2, 8)]"
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},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"edges = g.es.select(time_eq=1240916059)\n",
"g.subgraph_edges(edges).maximal_cliques()"
]
},
{
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@ -154,7 +133,7 @@
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@ -193,526 +172,9 @@
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{
"name": "stderr",
"output_type": "stream",
"text": [
"Process ForkPoolWorker-73:\n",
"Process ForkPoolWorker-89:\n",
"Process ForkPoolWorker-90:\n",
"Process ForkPoolWorker-72:\n",
"Process ForkPoolWorker-78:\n",
"Process ForkPoolWorker-79:\n",
"Process ForkPoolWorker-67:\n",
"Process ForkPoolWorker-76:\n",
"Process ForkPoolWorker-81:\n",
"Process ForkPoolWorker-70:\n",
"Process ForkPoolWorker-95:\n",
"Process ForkPoolWorker-68:\n",
"Process ForkPoolWorker-71:\n",
"Process ForkPoolWorker-94:\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"Process ForkPoolWorker-66:\n",
"Process ForkPoolWorker-91:\n",
"Process ForkPoolWorker-65:\n",
"Process ForkPoolWorker-75:\n",
"Process ForkPoolWorker-74:\n",
"Process ForkPoolWorker-96:\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Process ForkPoolWorker-80:\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Process ForkPoolWorker-92:\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
"Traceback (most recent call last):\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3849, in select\n",
" es = es.select(filtered_idxs)\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3753, in select\n",
" es = _igraph.EdgeSeq.select(self, *args)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Process ForkPoolWorker-88:\n",
"KeyboardInterrupt\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
"Process ForkPoolWorker-93:\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
"KeyboardInterrupt\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3849, in select\n",
" es = es.select(filtered_idxs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
"Traceback (most recent call last):\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3849, in select\n",
" es = es.select(filtered_idxs)\n"
]
},
{
"ename": "KeyboardInterrupt",
"evalue": "",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-29-64fed6fd3c57>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mpool\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmultiprocessing\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mPool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprocesses\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmultiprocessing\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcpu_count\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----> 2\u001b[0;31m \u001b[0mcliques\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpool\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclique_subgraph\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/usr/lib/python3.5/multiprocessing/pool.py\u001b[0m in \u001b[0;36mmap\u001b[0;34m(self, func, iterable, chunksize)\u001b[0m\n\u001b[1;32m 258\u001b[0m \u001b[0;32min\u001b[0m \u001b[0ma\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mthat\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mreturned\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 259\u001b[0m '''\n\u001b[0;32m--> 260\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_map_async\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfunc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0miterable\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmapstar\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchunksize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\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 261\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mstarmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0miterable\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchunksize\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[0;32m/usr/lib/python3.5/multiprocessing/pool.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 600\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\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[0;32m--> 602\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 603\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mready\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 604\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mTimeoutError\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/lib/python3.5/multiprocessing/pool.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 597\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 598\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\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[0;32m--> 599\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_event\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 600\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\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[0;32m/usr/lib/python3.5/threading.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 547\u001b[0m \u001b[0msignaled\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_flag\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 548\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0msignaled\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 549\u001b[0;31m \u001b[0msignaled\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_cond\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 550\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0msignaled\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 551\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/lib/python3.5/threading.py\u001b[0m in \u001b[0;36mwait\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 291\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;31m# restore state no matter what (e.g., KeyboardInterrupt)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 292\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mtimeout\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 293\u001b[0;31m \u001b[0mwaiter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0macquire\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 294\u001b[0m \u001b[0mgotit\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 295\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mKeyboardInterrupt\u001b[0m: "
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
"Process ForkPoolWorker-77:\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in <listcomp>\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3753, in select\n",
" es = _igraph.EdgeSeq.select(self, *args)\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3753, in select\n",
" es = _igraph.EdgeSeq.select(self, *args)\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
"Traceback (most recent call last):\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3841, in select\n",
" values = es[attr]\n",
"Process ForkPoolWorker-84:\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in <listcomp>\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
"KeyboardInterrupt\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
"Process ForkPoolWorker-69:\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"Process ForkPoolWorker-86:\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"KeyboardInterrupt\n",
"KeyboardInterrupt\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3841, in select\n",
" values = es[attr]\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
"Process ForkPoolWorker-85:\n",
"Process ForkPoolWorker-82:\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
"Process ForkPoolWorker-83:\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
"KeyboardInterrupt\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
"Traceback (most recent call last):\n",
"KeyboardInterrupt\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
"Process ForkPoolWorker-87:\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
"Traceback (most recent call last):\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
"Traceback (most recent call last):\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 249, in _bootstrap\n",
" self.run()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/usr/lib/python3.5/multiprocessing/process.py\", line 93, in run\n",
" self._target(*self._args, **self._kwargs)\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 119, in worker\n",
" result = (True, func(*args, **kwds))\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in <listcomp>\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
"KeyboardInterrupt\n",
" File \"/usr/lib/python3.5/multiprocessing/pool.py\", line 44, in mapstar\n",
" return list(map(*args))\n",
"KeyboardInterrupt\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
" File \"<ipython-input-13-fb9f2dd39ce0>\", line 2, in clique_subgraph\n",
" return g.subgraph_edges(g.es.select(time_eq=t)).maximal_cliques()\n",
"KeyboardInterrupt\n",
"KeyboardInterrupt\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3846, in select\n",
" filtered_idxs=[i for i, v in enumerate(values) \\\n",
" File \"/home/lozeve/.local/share/virtualenvs/tda-networks--KypeAmE/lib/python3.5/site-packages/igraph/__init__.py\", line 3847, in <listcomp>\n",
" if func(v, value)]\n",
"KeyboardInterrupt\n"
]
}
],
"outputs": [],
"source": [
"pool = multiprocessing.Pool(processes=multiprocessing.cpu_count())\n",
"cliques = pool.map(clique_subgraph, times)"
@ -720,7 +182,7 @@
},
{
"cell_type": "code",
"execution_count": 32,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@ -729,7 +191,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@ -739,23 +201,9 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<3,4,11> 0\n",
"<7,9,10> 0\n",
"<7,8,10> 0\n",
"<5,6,7,8> 0\n",
"<4,8> 0\n",
"<3,5> 0\n",
"<0,1,2> 0\n"
]
}
],
"outputs": [],
"source": [
"maxfilt = d.Filtration(maxcliques)\n",
"for s in maxfilt:\n",
@ -764,7 +212,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@ -773,70 +221,177 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[False,\n",
" False,\n",
" False,\n",
" True,\n",
" False,\n",
" False,\n",
" True,\n",
" False,\n",
" False,\n",
" False,\n",
" True,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" True,\n",
" False,\n",
" True,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False,\n",
" False]"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"presences[-1]"
]
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"[np.argwhere(np.array(p)[1:] ^ np.array(p)[:-1]).flatten().tolist() for p in presences]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Cut into sliding windows"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"duration = 0.1 * (times.max() - times.min())\n",
"duration * np.arange(10)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### TODO overlap"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"def sliding_windows(g, res=0.1, overlap=0):\n",
" times = np.array(g.es[\"time\"])\n",
" duration = res * (times.max() - times.min())\n",
" windows = []\n",
" for i in range(int(1/res)-1):\n",
" edges = g.es.select(time_gt=times.min() + duration*i, time_lt=times.min() + duration*(i+1))\n",
" windows.append(g.subgraph_edges(edges))\n",
" return windows"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"wins = sliding_windows(g, 0.1)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[[], [], [], [], [], [], [2, 3, 5, 6, 9, 10, 17, 18, 19, 20]]"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
"name": "stdout",
"output_type": "stream",
"text": [
"1241607579.0\n",
"1242302279.0\n",
"1242996839.0\n",
"1243691539.0\n",
"1244386179.0\n",
"1244995999.0\n",
"1245775339.0\n",
"1246468459.0\n",
"1247162039.0\n"
]
}
],
"source": [
"[np.argwhere(np.array(p)[1:] ^ np.array(p)[:-1]).flatten().tolist() for p in presences]"
"for i in wins:\n",
" print(max(i.es[\"time\"]))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Zigzag persistence"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Compute the maximal simplicial complex"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"def max_simplicial_complex(g):\n",
" return d.Filtration(g.maximal_cliques())"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"def presence_times(g):\n",
" max_simplicial_complex = d.Filtration(g.cliques())\n",
" filts = []\n",
" for t in np.sort(np.unique(g.es[\"time\"])):\n",
" edges = g.es.select(time_eq=t)\n",
" cliques = g.subgraph_edges(edges).cliques()\n",
" filts.append(d.Filtration(cliques))\n",
" presences = [[s in filt for filt in filts] for s in max_simplicial_complex]\n",
" presences = [np.argwhere(np.array(p)[1:] ^ np.array(p)[:-1]).flatten().tolist() for p in presences]\n",
" return (max_simplicial_complex, presences)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"(f, t) = presence_times(wins[2])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"zz, dgms, cells = d.zigzag_homology_persistence(f, t)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'd' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-1-b3746bc0fac5>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0ms\u001b[0m \u001b[0;32min\u001b[0m \u001b[0md\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mFiltration\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0md\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSimplex\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m2\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[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'd' is not defined"
]
}
],
"source": [
"for s in d.Filtration([d.Simplex((0,1,2))]):\n",
" print(s)"
]
},
{