p2_run_everything.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import datetime\n",
    "\n",
    "from util.util import importstr\n",
    "from util.logconf import logging\n",
    "log = logging.getLogger('nb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def run(app, *argv):\n",
    "    argv = list(argv)\n",
    "    argv.insert(0, '--num-workers=4')  # <1>\n",
    "    log.info(\"Running: {}({!r}).main()\".format(app, argv))\n",
    "    \n",
    "    app_cls = importstr(*app.rsplit('.', 1))  # <2>\n",
    "    app_cls(argv).main()\n",
    "    \n",
    "    log.info(\"Finished: {}.{!r}).main()\".format(app, argv))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import shutil\n",
    "\n",
    "# clean up any old data that might be around.\n",
    "# We don't call this by default because it's destructive, \n",
    "# and would waste a lot of time if it ran when nothing \n",
    "# on the application side had changed.\n",
    "def cleanCache():\n",
    "    shutil.rmtree('data-unversioned/cache')\n",
    "    os.mkdir('data-unversioned/cache')\n",
    "\n",
    "# cleanCache()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "training_epochs = 20\n",
    "experiment_epochs = 10\n",
    "final_epochs = 50\n",
    "\n",
    "training_epochs = 2\n",
    "experiment_epochs = 2\n",
    "final_epochs = 5\n",
    "seg_epochs = 10"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Chapter 11"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch11.prepcache.LunaPrepCacheApp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch11.training.LunaTrainingApp', '--epochs=1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch11.training.LunaTrainingApp', f'--epochs={experiment_epochs}')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Chapter 12"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.prepcache.LunaPrepCacheApp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', '--epochs=1', 'unbalanced')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={training_epochs}', '--balanced', 'balanced')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={experiment_epochs}', '--balanced', '--augment-flip', 'flip')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={experiment_epochs}', '--balanced', '--augment-offset', 'offset')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={experiment_epochs}', '--balanced', '--augment-scale', 'scale')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={experiment_epochs}', '--balanced', '--augment-rotate', 'rotate')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={experiment_epochs}', '--balanced', '--augment-noise', 'noise')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch12.training.LunaTrainingApp', f'--epochs={training_epochs}', '--balanced', '--augmented', 'fully-augmented')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Chapter 13"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch13.prepcache.LunaPrepCacheApp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch13.training.LunaTrainingApp', f'--epochs={final_epochs}', '--balanced', '--augmented', 'final-cls')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "run('p2ch13.train_seg.LunaTrainingApp', f'--epochs={seg_epochs}', '--augmented', 'final-seg')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Chapter 14"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch14.prepcache.LunaPrepCacheApp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "run('p2ch14.training.ClassificationTrainingApp', f'--epochs=100', 'nodule-nonnodule')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "run('p2ch14.training.ClassificationTrainingApp', f'--epochs=40', '--malignant', '--dataset=MalignantLunaDataset',\n",
    "    '--finetune=''data/part2/models/cls_2020-02-06_14.16.55_final-nodule-nonnodule.best.state',\n",
    "    'finetune-head')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "run('p2ch14.training.ClassificationTrainingApp', f'--epochs=40', '--malignant', '--dataset=MalignantLunaDataset',\n",
    "    '--finetune=''data/part2/models/cls_2020-02-06_14.16.55_final-nodule-nonnodule.best.state',\n",
    "    '--finetune-depth=2',\n",
    "    'finetune-depth2')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch14.nodule_analysis.NoduleAnalysisApp', '--run-validation')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "run('p2ch14.nodule_analysis.NoduleAnalysisApp', '--run-validation', '--malignancy-path')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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