DaveM@0: {
DaveM@0:  "cells": [
DaveM@0:   {
DaveM@0:    "cell_type": "code",
DaveM@0:    "execution_count": 1,
DaveM@0:    "metadata": {
DaveM@0:     "collapsed": false
DaveM@0:    },
DaveM@0:    "outputs": [],
DaveM@0:    "source": [
DaveM@0:     "from matplotlib import pyplot as plt\n",
DaveM@0:     "from scipy.cluster.hierarchy import dendrogram, linkage, cophenet\n",
DaveM@0:     "from scipy.spatial.distance import pdist\n",
DaveM@1:     "import sklearn \n",
DaveM@0:     "import numpy as np\n",
DaveM@0:     "import csv\n",
DaveM@0:     "\n",
DaveM@0:     "dataFolder = '../data/'\n",
DaveM@0:     "keyFile = 'AdobeNormalised'\n",
DaveM@0:     "datapath = dataFolder + keyFile"
DaveM@0:    ]
DaveM@0:   },
DaveM@0:   {
DaveM@0:    "cell_type": "code",
DaveM@0:    "execution_count": 2,
DaveM@0:    "metadata": {
DaveM@0:     "collapsed": true
DaveM@0:    },
DaveM@0:    "outputs": [],
DaveM@0:    "source": [
DaveM@0:     "X = np.genfromtxt(datapath+'.csv', delimiter = ',', skip_header = 1)\n",
DaveM@0:     "filenames = np.loadtxt(datapath+'_filenames.csv', dtype = str)\n",
DaveM@0:     "labels = np.loadtxt(datapath+'_labels.csv', dtype = str)\n",
DaveM@0:     "features = np.loadtxt(datapath+'_features.csv', dtype = str)\n"
DaveM@0:    ]
DaveM@0:   },
DaveM@0:   {
DaveM@0:    "cell_type": "code",
DaveM@0:    "execution_count": null,
DaveM@0:    "metadata": {
DaveM@0:     "collapsed": false
DaveM@0:    },
DaveM@0:    "outputs": [],
DaveM@0:    "source": [
DaveM@1:     "agglo = cluster.FeatureAgglomeration()\n",
DaveM@1:     "agglo.fit(X)\n",
DaveM@1:     "X_reduced = agglo.transform(X)"
DaveM@0:    ]
DaveM@0:   },
DaveM@0:   {
DaveM@0:    "cell_type": "code",
DaveM@0:    "execution_count": null,
DaveM@0:    "metadata": {
DaveM@0:     "collapsed": false
DaveM@0:    },
DaveM@0:    "outputs": [],
DaveM@0:    "source": [
DaveM@0:     "Z = linkage(X)"
DaveM@0:    ]
DaveM@0:   },
DaveM@0:   {
DaveM@0:    "cell_type": "code",
DaveM@1:    "execution_count": 18,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": false
DaveM@1:    },
DaveM@1:    "outputs": [
DaveM@1:     {
DaveM@1:      "name": "stdout",
DaveM@1:      "output_type": "stream",
DaveM@1:      "text": [
DaveM@1:       "[[  8.51810000e-01   4.00000000e-06   2.46000000e-04 ...,   2.10260000e-02\n",
DaveM@1:       "    1.98220000e-02   1.04000000e-04]\n",
DaveM@1:       " [  9.52275000e-01   7.00000000e-06   1.82600000e-03 ...,   1.79490000e-02\n",
DaveM@1:       "    1.09020000e-02   7.20000000e-05]\n",
DaveM@1:       " [  1.92200000e-03   1.00000000e-06   1.39000000e-04 ...,   2.35900000e-02\n",
DaveM@1:       "    6.93800000e-03   2.61000000e-04]\n",
DaveM@1:       " ..., \n",
DaveM@1:       " [  9.96346000e-01   3.37000000e-04   1.23600000e-03 ...,   5.24103000e-01\n",
DaveM@1:       "    3.36967000e-01   5.39000000e-04]\n",
DaveM@1:       " [  9.99990000e-01   1.00000000e-06   0.00000000e+00 ...,   0.00000000e+00\n",
DaveM@1:       "    0.00000000e+00   0.00000000e+00]\n",
DaveM@1:       " [  9.96624000e-01   6.97000000e-04   2.59300000e-03 ...,   5.24615000e-01\n",
DaveM@1:       "    3.34985000e-01   5.45000000e-04]]\n"
DaveM@1:      ]
DaveM@1:     }
DaveM@1:    ],
DaveM@1:    "source": [
DaveM@1:     "print X"
DaveM@1:    ]
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@1:    "execution_count": 29,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": false
DaveM@1:    },
DaveM@1:    "outputs": [
DaveM@1:     {
DaveM@1:      "name": "stdout",
DaveM@1:      "output_type": "stream",
DaveM@1:      "text": [
DaveM@1:       "(8977, 1536)\n"
DaveM@1:      ]
DaveM@1:     }
DaveM@1:    ],
DaveM@1:    "source": []
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@1:    "execution_count": 42,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": false
DaveM@1:    },
DaveM@1:    "outputs": [
DaveM@1:     {
DaveM@1:      "name": "stdout",
DaveM@1:      "output_type": "stream",
DaveM@1:      "text": [
DaveM@1:       "{'nu_0': 0, 'kappa_0': 0, 'lambda_0': 0, 'mu_0': 0}\n"
DaveM@1:      ]
DaveM@1:     }
DaveM@1:    ],
DaveM@1:    "source": []
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@1:    "execution_count": null,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": true
DaveM@1:    },
DaveM@1:    "outputs": [],
DaveM@1:    "source": [
DaveM@1:     "import pyBHC as bhc\n",
DaveM@1:     "from pyBHC import dists\n",
DaveM@1:     "\n",
DaveM@1:     "mu_init = []\n",
DaveM@1:     "sigma_init = []\n",
DaveM@1:     "S_init = []\n",
DaveM@1:     "cd = dists.NormalFixedCovar(mu_0=mu_init,sigma_0=sigma_init, S=S_init)\n",
DaveM@1:     "\n",
DaveM@1:     "# temp = cd.log_marginal_likelihood(X)\n",
DaveM@1:     "d = bhc.rbhc(X, cd)"
DaveM@1:    ]
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@1:    "execution_count": null,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": true
DaveM@1:    },
DaveM@1:    "outputs": [],
DaveM@1:    "source": [
DaveM@1:     "\n",
DaveM@1:     "\n"
DaveM@1:    ]
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@1:    "execution_count": null,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": true
DaveM@1:    },
DaveM@1:    "outputs": [],
DaveM@1:    "source": []
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@1:    "execution_count": null,
DaveM@1:    "metadata": {
DaveM@1:     "collapsed": true
DaveM@1:    },
DaveM@1:    "outputs": [],
DaveM@1:    "source": []
DaveM@1:   },
DaveM@1:   {
DaveM@1:    "cell_type": "code",
DaveM@0:    "execution_count": null,
DaveM@0:    "metadata": {
DaveM@0:     "collapsed": true
DaveM@0:    },
DaveM@0:    "outputs": [],
DaveM@0:    "source": []
DaveM@0:   }
DaveM@0:  ],
DaveM@0:  "metadata": {
DaveM@0:   "kernelspec": {
DaveM@0:    "display_name": "Python 2",
DaveM@0:    "language": "python",
DaveM@0:    "name": "python2"
DaveM@0:   },
DaveM@0:   "language_info": {
DaveM@0:    "codemirror_mode": {
DaveM@0:     "name": "ipython",
DaveM@0:     "version": 2
DaveM@0:    },
DaveM@0:    "file_extension": ".py",
DaveM@0:    "mimetype": "text/x-python",
DaveM@0:    "name": "python",
DaveM@0:    "nbconvert_exporter": "python",
DaveM@0:    "pygments_lexer": "ipython2",
DaveM@0:    "version": "2.7.10"
DaveM@0:   }
DaveM@0:  },
DaveM@0:  "nbformat": 4,
DaveM@0:  "nbformat_minor": 0
DaveM@0: }