Update with 2024 material
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notebooks/02a_Serialization.ipynb
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notebooks/02a_Serialization.ipynb
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{
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"cells": [
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{
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"cell_type": "markdown",
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"source": [
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"# Serialization demo"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%% md\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"outputs": [],
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"source": [
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"import json\n",
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"import numpy as np\n",
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"import pickle"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "markdown",
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"source": [
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"## pickle is simple but can be dangerous"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%% md\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"outputs": [],
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"source": [
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"class SomethingSimple:\n",
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" def __init__(self, foo, bar):\n",
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" self.foo = foo\n",
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" self.bar = bar\n"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"outputs": [
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{
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"data": {
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"text/plain": "(__main__.SomethingSimple, 3, 'two')"
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},
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"execution_count": 3,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"simple = SomethingSimple(foo=3, bar='two')\n",
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"\n",
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"with open('simple.pickle', 'wb') as f:\n",
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" pickle.dump(simple, f)\n",
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"\n",
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"with open('simple.pickle', 'rb') as f:\n",
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" simple_bis = pickle.load(f)\n",
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"\n",
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"type(simple_bis), simple_bis.foo, simple_bis.bar"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"outputs": [],
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"source": [
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"class SomethingSimple:\n",
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" def __init__(self, foo, bla):\n",
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" self.foo = foo\n",
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" self.bla = bla"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"outputs": [
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{
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"data": {
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"text/plain": "{'foo': 3, 'bar': 'two'}"
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},
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"with open('simple.pickle', 'rb') as f:\n",
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" simple_bis = pickle.load(f)\n",
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"\n",
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"simple_bis.__dict__"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "markdown",
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"source": [
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"Even worse when you have a simple class name change"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%% md\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"outputs": [
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{
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"ename": "AttributeError",
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"evalue": "Can't get attribute 'SomethingSimple' on <module '__main__'>",
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"output_type": "error",
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"traceback": [
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"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
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"\u001B[0;31mAttributeError\u001B[0m Traceback (most recent call last)",
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"\u001B[0;32m<ipython-input-6-56e3756749ad>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m()\u001B[0m\n\u001B[1;32m 8\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 9\u001B[0m \u001B[0;32mwith\u001B[0m \u001B[0mopen\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m'simple.pickle'\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m'rb'\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;32mas\u001B[0m \u001B[0mf\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 10\u001B[0;31m \u001B[0msimple_bis\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mpickle\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mload\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mf\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 11\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 12\u001B[0m \u001B[0msimple_bis\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m__dict__\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
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"\u001B[0;31mAttributeError\u001B[0m: Can't get attribute 'SomethingSimple' on <module '__main__'>"
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]
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}
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],
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"source": [
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"# Simulate a name change of the SomethingSimple class\n",
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"del SomethingSimple\n",
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"\n",
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"class Simple:\n",
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" def __init__(self, foo, bar):\n",
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" self.foo = foo\n",
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" self.bar = bar\n",
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"\n",
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"with open('simple.pickle', 'rb') as f:\n",
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" simple_bis = pickle.load(f)\n",
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"\n",
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"simple_bis.__dict__"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "markdown",
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"source": [
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"## JSON is still quite simple, and allows you a closer control"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%% md\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"outputs": [],
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"source": [
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"class SomethingNice:\n",
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"\n",
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" def __init__(self, foo, bar):\n",
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" self.foo = foo\n",
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" self.bar = bar\n",
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"\n",
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" @classmethod\n",
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" def from_json(cls, fname):\n",
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" with open(fname, 'r') as f:\n",
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" dump = json.load(f)\n",
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" return cls(**dump)\n",
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"\n",
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" def to_json(self, fname):\n",
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" with open(fname, 'w') as f:\n",
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" json.dump(self.__dict__, f)\n"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"outputs": [
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{
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"data": {
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"text/plain": "{'foo': 3, 'bar': 'two'}"
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},
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"execution_count": 8,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"so_nice = SomethingNice(foo=3, bar='two')\n",
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"so_nice.__dict__\n"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"{\"foo\": 3, \"bar\": \"two\"}"
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]
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}
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],
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"source": [
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"so_nice.to_json('nice.json')\n",
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"!cat ./nice.json"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"outputs": [
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{
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"data": {
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"text/plain": "{'foo': 3, 'bar': 'two'}"
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},
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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"so_nice_again = SomethingNice.from_json('nice.json')\n",
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"so_nice_again.__dict__"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"outputs": [
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{
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"data": {
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"text/plain": "{'foo': 3, 'bar': array([1.2, 3.4])}"
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},
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"execution_count": 11,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"not_so_nice = SomethingNice(foo=3, bar=np.array([1.2, 3.4]))\n",
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"not_so_nice.__dict__"
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],
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"metadata": {
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"collapsed": false,
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"pycharm": {
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"name": "#%%\n"
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}
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}
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"outputs": [
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{
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"ename": "TypeError",
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"evalue": "Object of type 'ndarray' is not JSON serializable",
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"output_type": "error",
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"traceback": [
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"\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
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"\u001B[0;31mTypeError\u001B[0m Traceback (most recent call last)",
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"\u001B[0;32m<ipython-input-12-e860ef19277d>\u001B[0m in \u001B[0;36m<module>\u001B[0;34m()\u001B[0m\n\u001B[0;32m----> 1\u001B[0;31m \u001B[0mnot_so_nice\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mto_json\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m'not_so_nice.json'\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m",
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"\u001B[0;32m<ipython-input-7-c9b082d8b74f>\u001B[0m in \u001B[0;36mto_json\u001B[0;34m(self, fname)\u001B[0m\n\u001B[1;32m 13\u001B[0m \u001B[0;32mdef\u001B[0m \u001B[0mto_json\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mfname\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 14\u001B[0m \u001B[0;32mwith\u001B[0m \u001B[0mopen\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mfname\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0;34m'w'\u001B[0m\u001B[0;34m)\u001B[0m \u001B[0;32mas\u001B[0m \u001B[0mf\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m---> 15\u001B[0;31m \u001B[0mjson\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mdump\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0m__dict__\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mf\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m",
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"\u001B[0;32m~/miniconda3/envs/bog/lib/python3.6/json/__init__.py\u001B[0m in \u001B[0;36mdump\u001B[0;34m(obj, fp, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, default, sort_keys, **kw)\u001B[0m\n\u001B[1;32m 177\u001B[0m \u001B[0;31m# could accelerate with writelines in some versions of Python, at\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 178\u001B[0m \u001B[0;31m# a debuggability cost\u001B[0m\u001B[0;34m\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 179\u001B[0;31m \u001B[0;32mfor\u001B[0m \u001B[0mchunk\u001B[0m \u001B[0;32min\u001B[0m \u001B[0miterable\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 180\u001B[0m \u001B[0mfp\u001B[0m\u001B[0;34m.\u001B[0m\u001B[0mwrite\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mchunk\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 181\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n",
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"\u001B[0;32m~/miniconda3/envs/bog/lib/python3.6/json/encoder.py\u001B[0m in \u001B[0;36m_iterencode\u001B[0;34m(o, _current_indent_level)\u001B[0m\n\u001B[1;32m 428\u001B[0m \u001B[0;32myield\u001B[0m \u001B[0;32mfrom\u001B[0m \u001B[0m_iterencode_list\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mo\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0m_current_indent_level\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 429\u001B[0m \u001B[0;32melif\u001B[0m \u001B[0misinstance\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mo\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mdict\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 430\u001B[0;31m \u001B[0;32myield\u001B[0m \u001B[0;32mfrom\u001B[0m \u001B[0m_iterencode_dict\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mo\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0m_current_indent_level\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 431\u001B[0m \u001B[0;32melse\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 432\u001B[0m \u001B[0;32mif\u001B[0m \u001B[0mmarkers\u001B[0m \u001B[0;32mis\u001B[0m \u001B[0;32mnot\u001B[0m \u001B[0;32mNone\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
|
||||
"\u001B[0;32m~/miniconda3/envs/bog/lib/python3.6/json/encoder.py\u001B[0m in \u001B[0;36m_iterencode_dict\u001B[0;34m(dct, _current_indent_level)\u001B[0m\n\u001B[1;32m 402\u001B[0m \u001B[0;32melse\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 403\u001B[0m \u001B[0mchunks\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0m_iterencode\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mvalue\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0m_current_indent_level\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 404\u001B[0;31m \u001B[0;32myield\u001B[0m \u001B[0;32mfrom\u001B[0m \u001B[0mchunks\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 405\u001B[0m \u001B[0;32mif\u001B[0m \u001B[0mnewline_indent\u001B[0m \u001B[0;32mis\u001B[0m \u001B[0;32mnot\u001B[0m \u001B[0;32mNone\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 406\u001B[0m \u001B[0m_current_indent_level\u001B[0m \u001B[0;34m-=\u001B[0m \u001B[0;36m1\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
|
||||
"\u001B[0;32m~/miniconda3/envs/bog/lib/python3.6/json/encoder.py\u001B[0m in \u001B[0;36m_iterencode\u001B[0;34m(o, _current_indent_level)\u001B[0m\n\u001B[1;32m 435\u001B[0m \u001B[0;32mraise\u001B[0m \u001B[0mValueError\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0;34m\"Circular reference detected\"\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 436\u001B[0m \u001B[0mmarkers\u001B[0m\u001B[0;34m[\u001B[0m\u001B[0mmarkerid\u001B[0m\u001B[0;34m]\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0mo\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0;32m--> 437\u001B[0;31m \u001B[0mo\u001B[0m \u001B[0;34m=\u001B[0m \u001B[0m_default\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mo\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[0m\u001B[1;32m 438\u001B[0m \u001B[0;32myield\u001B[0m \u001B[0;32mfrom\u001B[0m \u001B[0m_iterencode\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mo\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0m_current_indent_level\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 439\u001B[0m \u001B[0;32mif\u001B[0m \u001B[0mmarkers\u001B[0m \u001B[0;32mis\u001B[0m \u001B[0;32mnot\u001B[0m \u001B[0;32mNone\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
|
||||
"\u001B[0;32m~/miniconda3/envs/bog/lib/python3.6/json/encoder.py\u001B[0m in \u001B[0;36mdefault\u001B[0;34m(self, o)\u001B[0m\n\u001B[1;32m 178\u001B[0m \"\"\"\n\u001B[1;32m 179\u001B[0m raise TypeError(\"Object of type '%s' is not JSON serializable\" %\n\u001B[0;32m--> 180\u001B[0;31m o.__class__.__name__)\n\u001B[0m\u001B[1;32m 181\u001B[0m \u001B[0;34m\u001B[0m\u001B[0m\n\u001B[1;32m 182\u001B[0m \u001B[0;32mdef\u001B[0m \u001B[0mencode\u001B[0m\u001B[0;34m(\u001B[0m\u001B[0mself\u001B[0m\u001B[0;34m,\u001B[0m \u001B[0mo\u001B[0m\u001B[0;34m)\u001B[0m\u001B[0;34m:\u001B[0m\u001B[0;34m\u001B[0m\u001B[0m\n",
|
||||
"\u001B[0;31mTypeError\u001B[0m: Object of type 'ndarray' is not JSON serializable"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"not_so_nice.to_json('not_so_nice.json')"
|
||||
],
|
||||
"metadata": {
|
||||
"collapsed": false,
|
||||
"pycharm": {
|
||||
"name": "#%%\n"
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 13,
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"class SomethingWorking:\n",
|
||||
"\n",
|
||||
" def __init__(self, foo, data):\n",
|
||||
" self.foo = foo\n",
|
||||
" self.data = data\n",
|
||||
"\n",
|
||||
" @classmethod\n",
|
||||
" def from_json(cls, fname):\n",
|
||||
" with open(fname, 'r') as f:\n",
|
||||
" dump = json.load(f)\n",
|
||||
" dump['data'] = np.array(dump['data'])\n",
|
||||
" return cls(**dump)\n",
|
||||
"\n",
|
||||
" def to_json(self, fname):\n",
|
||||
" dump = {\n",
|
||||
" 'foo': self.foo,\n",
|
||||
" 'data': self.data.tolist(),\n",
|
||||
" }\n",
|
||||
" with open(fname, 'w') as f:\n",
|
||||
" json.dump(dump, f)\n"
|
||||
],
|
||||
"metadata": {
|
||||
"collapsed": false,
|
||||
"pycharm": {
|
||||
"name": "#%%\n"
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 14,
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"{\"foo\": 3, \"data\": [[1, 2], [3, 4]]}"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"not_so_nice = SomethingWorking(foo=3, data=np.array([[1, 2], [3,4 ]]))\n",
|
||||
"not_so_nice.to_json('not_so_nice.json')\n",
|
||||
"!cat not_so_nice.json\n"
|
||||
],
|
||||
"metadata": {
|
||||
"collapsed": false,
|
||||
"pycharm": {
|
||||
"name": "#%%\n"
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"outputs": [],
|
||||
"source": [],
|
||||
"metadata": {
|
||||
"collapsed": false,
|
||||
"pycharm": {
|
||||
"name": "#%%\n"
|
||||
}
|
||||
}
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"hide_input": false,
|
||||
"kernelspec": {
|
||||
"display_name": "Python [default]",
|
||||
"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": "3.5.5"
|
||||
},
|
||||
"toc": {
|
||||
"nav_menu": {
|
||||
"height": "12px",
|
||||
"width": "252px"
|
||||
},
|
||||
"navigate_menu": true,
|
||||
"number_sections": true,
|
||||
"sideBar": true,
|
||||
"threshold": 4,
|
||||
"toc_cell": false,
|
||||
"toc_section_display": "block",
|
||||
"toc_window_display": false
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 0
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue