Example System - Haun and Tononi 2019.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Notebook calculating spectrum of $\\Phi$ values for Haun and Tononi, 2019"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### First generate TPM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Analyzing State =  (0, 0, 0, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 0, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 1, 0, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 0, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 1, 1, 0)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 0, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 1, 0, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 0, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 0, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 0, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 0, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 0, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 0, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 0, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 0, 1, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 0, 1, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (0, 1, 1, 1, 1, 1, 1, 1)\n",
      "Analyzing State =  (1, 1, 1, 1, 1, 1, 1, 1)\n",
      "DONE\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "import pyphi\n",
    "import itertools\n",
    "from pyphi import phi_spectrum\n",
    "\n",
    "\n",
    "## First constuct the TPM\n",
    "n_nodes = 8\n",
    "n_states = 2**8\n",
    "\n",
    "\n",
    "## Function to calculate probality that a given node is ON\n",
    "def get_p_on(j,global_state,z=1/4.,n=5):\n",
    "    if j==0:\n",
    "        W_sum = global_state[j]+0.25*global_state[j+1]\n",
    "    elif j == n_nodes-1:\n",
    "        W_sum = global_state[j] + 0.25*global_state[j-1]\n",
    "    else:\n",
    "        W_sum = global_state[j] + 0.25*global_state[j-1] + 0.25*global_state[j+1]\n",
    "    p_on = W_sum**n/(z+W_sum**n)\n",
    "    return p_on    \n",
    "\n",
    "\n",
    "## Create TPM\n",
    "big_endian_states = itertools.product([0,1],repeat=n_nodes)\n",
    "\n",
    "## Reverse the order so that the states are ordered in little-endian\n",
    "all_states = []\n",
    "for state in big_endian_states:\n",
    "    all_states.append(state[::-1])\n",
    "\n",
    "    \n",
    "## Create a map between indices and states\n",
    "state_index_map = {}\n",
    "index = 0\n",
    "for state in all_states:\n",
    "    state_index_map[index]=state\n",
    "    index = index+1\n",
    "    \n",
    "    \n",
    "## For each state, get the probability of transitioning\n",
    "TPM = np.zeros((n_states,n_states))\n",
    "for i in range(n_states):\n",
    "    current_state = state_index_map[i]\n",
    "    print(\"Analyzing State = \",current_state)\n",
    "        \n",
    "    # Get probality of each node transitioning\n",
    "    node_probs = []\n",
    "    for j in range(n_nodes):\n",
    "        p_on = get_p_on(j,current_state)\n",
    "        p_off = 1 - p_on\n",
    "        node_probs.append([p_off,p_on])\n",
    "        \n",
    "    # Get probability of global state transitions using node transitions\n",
    "    for n in range(n_states):\n",
    "        next_state = state_index_map[n]\n",
    "        transition_prob = 1.0\n",
    "        for m in range(n_nodes):\n",
    "            ## get node_probs at the value of that state\n",
    "            index = next_state[m]\n",
    "            transition_prob = transition_prob*node_probs[m][index]\n",
    "        TPM[i][n] = transition_prob\n",
    "        \n",
    "## Make sure transitions sum to unity\n",
    "for k in range(n_states):\n",
    "    if not np.isclose(np.sum(TPM[k][:]),1.0):\n",
    "        print(\"ERROR TPM NOT SUMMING TO UNITY\")\n",
    "            \n",
    "print(\"DONE\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Build network object and calculate $\\Phi$"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Network =  NodeLabels(('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'))\n"
     ]
    }
   ],
   "source": [
    "# Set up network object\n",
    "network = pyphi.Network(TPM, node_labels=['A','B','C','D','E','F','G','H'])\n",
    "print(\"Network = \",network.node_labels)\n",
    "\n",
    "# Put the system into an initial state\n",
    "state = (0,0,0,0,0,0,0,0)\n",
    "nodes = ['A','B','C','D','E','F','G','H']\n",
    "\n",
    "## Get the requisite Subsystem\n",
    "subsystem = pyphi.Subsystem(network, state, nodes)\n",
    "\n",
    "## Calculate all Phi values\n",
    "display_CES= False  # if True, output will display constellations\n",
    "Phi_Spectrum = phi_spectrum.get_phi_spectrum(subsystem,display_CES)\n",
    "\n",
    "print(\"\\nCuts = \",Phi_Spectrum[0])\n",
    "print(\"\\nPhi Spectrum = \",Phi_Spectrum[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "Phi_MIP = phi_spectrum.get_Phi_MIP(Phi_Spectrum)\n",
    "print(\"Phi MIP = \",Phi_MIP)"
   ]
  }
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