Mapper Pipeline Example

mapper_pipeline_example.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Mapper pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tempfile import mkdtemp\n",
    "from shutil import rmtree\n",
    "from joblib import Memory\n",
    "\n",
    "from giotto.mapper.lens import Eccentricity\n",
    "from giotto.mapper.mapper import MapperPipeline\n",
    "\n",
    "import numpy as np\n",
    "from sklearn.decomposition import PCA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create random 2D array\n",
    "n_rows = 20000\n",
    "X = np.c_[np.random.randint(1,11,(n_rows)), np.random.randint(11,21,(n_rows))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "# initialise lenses\n",
    "lens_1 = Eccentricity()\n",
    "lens_2 = Eccentricity()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "# initialise memory\n",
    "cachedir = mkdtemp()\n",
    "memory = Memory(location=cachedir, verbose=10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# initialise pipeline\n",
    "mapper_pipeline = MapperPipeline([('ecc_1', lens_1), ('ecc_2', lens_2)], memory=memory, verbose=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "________________________________________________________________________________\n",
      "[Memory] Calling giotto.mapper.mapper._fit_transform_one...\n",
      "_fit_transform_one(Eccentricity(exponent=inf, metric='euclidean', metric_params={}), array([[ 1, 13],\n",
      "       ...,\n",
      "       [ 3, 15]]), None, None, message_clsname='Pipeline', message='(step 1 of 2) Processing ecc_1')\n",
      "[Pipeline] ............. (step 1 of 2) Processing ecc_1, total=   7.1s\n",
      "________________________________________________fit_transform_one - 7.1s, 0.1min\n",
      "[Pipeline] ............. (step 2 of 2) Processing ecc_2, total=   6.6s\n",
      "CPU times: user 9.44 s, sys: 4.18 s, total: 13.6 s\n",
      "Wall time: 13.7 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "Xt = mapper_pipeline.fit_transform(X)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "MapperPipeline(memory=Memory(location=/var/folders/5s/w9kkkqrx1c503clfqpn_zk280000gn/T/tmpg88e4_zk/joblib),\n",
       "               steps=[('ecc_1',\n",
       "                       Eccentricity(exponent=inf, metric='euclidean',\n",
       "                                    metric_params={})),\n",
       "                      ('ecc_2',\n",
       "                       Eccentricity(exponent=2, metric='euclidean',\n",
       "                                    metric_params={}))],\n",
       "               verbose=True)"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# change one transformer\n",
    "mapper_pipeline.set_params(ecc_2__exponent=2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Memory]29.0s, 0.5min   : Loading _fit_transform_one from /var/folders/5s/w9kkkqrx1c503clfqpn_zk280000gn/T/tmpg88e4_zk/joblib/giotto/mapper/mapper/_fit_transform_one/699a4fdefea0e7672f924df8dc94c4e5\n",
      "___________________________________fit_transform_one cache loaded - 0.0s, 0.0min\n",
      "[Pipeline] ............. (step 2 of 2) Processing ecc_2, total=   6.2s\n",
      "CPU times: user 4.29 s, sys: 1.95 s, total: 6.24 s\n",
      "Wall time: 6.24 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "Xt = mapper_pipeline.fit_transform(X)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "rmtree(cachedir)"
   ]
  },
  {
   "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": "3.7.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}