dimitri/tda-networks
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

New notebooks

Browse source
This commit is contained in:
Dimitri Lozeve 2018-06-14 12:20:40 +01:00
parent 1fb56392a4
commit 6c1efb88d6
5 changed files with 961 additions and 22 deletions
Download patch file Download diff file Expand all files Collapse all files

146
karate.ipynb Normal file
View file

@ -0,0 +1,146 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"autoscroll": false,
"collapsed": false,
"ein.tags": "worksheet-0",
"slideshow": {
"slide_type": "-"
}
},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt\n",
"%matplotlib inline"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"autoscroll": false,
"collapsed": false,
"ein.tags": "worksheet-0",
"slideshow": {
"slide_type": "-"
}
},
"outputs": [],
"source": [
"import igraph as ig\n",
"import dionysus as d"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"karate = ig.read(\"data/karate.gml\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"IGRAPH U--- 34 78 -- \n",
"+ attr: id (v)\n"
]
}
],
"source": [
"ig.summary(karate)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"cl = karate.maximal_cliques()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"5"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"max(map(len, cl))"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"from scipy.spatial.distance import squareform\n",
"dists = np.array(karate.shortest_paths_dijkstra())\n",
"dists = squareform(dists).astype('float64')"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"f = d.fill_rips(dists, 2, 2)\n",
"m = d.homology_persistence(f)\n",
"dgms = d.init_diagrams(m, f)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
}