{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Quickstart example for cancer simulation "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Import modules "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/opt/data/repos/cancer_software\n",
      "Obtaining file:///opt/data/repos/cancer_software\n",
      "Installing collected packages: CaSim\n",
      "  Found existing installation: CaSim 1.0.0\n",
      "    Uninstalling CaSim-1.0.0:\n",
      "      Successfully uninstalled CaSim-1.0.0\n",
      "  Running setup.py develop for CaSim\n",
      "Successfully installed CaSim\n",
      "Note: you may need to restart the kernel to use updated packages.\n",
      "/opt/data/repos/cancer_software/docs/source/include/notebooks\n"
     ]
    }
   ],
   "source": [
    "### Uncomment and execute if the next cell fails with \"module not found\".` Then reload the kernel.\n",
    "# %cd ../../../..\n",
    "# %pip install -e .\n",
    "# %cd -"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# The cancer simulation module.\n",
    "from casim import casim"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#  3rd party modules.\n",
    "import os, shutil\n",
    "from wand.image import Image as WImage"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup parameters "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "parameters=casim.CancerSimulatorParameters(\n",
    "                                matrix_size=20,\n",
    "                                number_of_generations=10,\n",
    "                                division_probability=0.5,\n",
    "                                advantageous_division_probability=0.8,\n",
    "                                death_probability=0.1,\n",
    "                                advantageous_death_probability=0.4,\n",
    "                                mutation_probability=0.2,\n",
    "                                advantageous_mutation_probability=0.8,\n",
    "                                mutations_per_division=10,\n",
    "                                time_of_advantageous_mutation=30000,\n",
    "                                number_of_clonal=2,\n",
    "                                plot_tumour_growth=True,\n",
    "                                export_tumour=True\n",
    "                               )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup the simulation engine. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "if os.path.isdir('out'):\n",
    "    shutil.rmtree('out')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "cancer_sim = casim.CancerSimulator(parameters, seed=1, outdir='out/')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run the simulation "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "text/plain": [
       "<Figure size 432x288 with 0 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "cancer_sim.run()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Display the growth curve. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "image_path=os.path.join(cancer_sim.outdir,'cancer_1', 'simOutput', 'growthCurve.pdf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "img = WImage(filename=image_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<wand.image.Image: 06f6f8f 'PDF' (432x288)>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "display(img)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python [conda env:casim] *",
   "language": "python",
   "name": "conda-env-casim-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}