Py_lectures_05_Errors.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Python-in-the-lab: errors, input/output and best tools I"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import numpy as np\n",
    "import matplotlib.pylab as plt\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Types of exceptions\n",
    "\n",
    "1. try/except\n",
    "2. try/finally\n",
    "3. raise\n",
    "4. assert\n",
    "5. with as"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. try/except\n",
    "**Catch and recover from exceptions raised by Python, or by you**\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# The lines below work, but are error prone\n",
    "filename = \"/home/gf/src/Python/Python-in-the-lab/Bk/F64ac_0.03_time_200.dat\"\n",
    "data = -np.loadtxt(filename)\n",
    "with open(filename) as f:\n",
    "    header = f.readline()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "ename": "OSError",
     "evalue": "/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat not found.",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mOSError\u001b[0m                                   Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-3-33e498a4a448>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[1;31m# The lines below does NOT work, see the error?\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      2\u001b[0m \u001b[0mfilename1\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;34m\"/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat\"\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 3\u001b[1;33m \u001b[0mdata\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m-\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloadtxt\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfilename1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32m~/anaconda3/lib/python3.7/site-packages/numpy/lib/npyio.py\u001b[0m in \u001b[0;36mloadtxt\u001b[1;34m(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin, encoding)\u001b[0m\n\u001b[0;32m    924\u001b[0m             \u001b[0mfname\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mstr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    925\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0m_is_string_like\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfname\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 926\u001b[1;33m             \u001b[0mfh\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mlib\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_datasource\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfname\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'rt'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mencoding\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mencoding\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    927\u001b[0m             \u001b[0mfencoding\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfh\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'encoding'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'latin1'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    928\u001b[0m             \u001b[0mfh\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0miter\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfh\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m~/anaconda3/lib/python3.7/site-packages/numpy/lib/_datasource.py\u001b[0m in \u001b[0;36mopen\u001b[1;34m(path, mode, destpath, encoding, newline)\u001b[0m\n\u001b[0;32m    260\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    261\u001b[0m     \u001b[0mds\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mDataSource\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdestpath\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 262\u001b[1;33m     \u001b[1;32mreturn\u001b[0m \u001b[0mds\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mencoding\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mencoding\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mnewline\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mnewline\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    263\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    264\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m~/anaconda3/lib/python3.7/site-packages/numpy/lib/_datasource.py\u001b[0m in \u001b[0;36mopen\u001b[1;34m(self, path, mode, encoding, newline)\u001b[0m\n\u001b[0;32m    616\u001b[0m                                       encoding=encoding, newline=newline)\n\u001b[0;32m    617\u001b[0m         \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 618\u001b[1;33m             \u001b[1;32mraise\u001b[0m \u001b[0mIOError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"%s not found.\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[0mpath\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    619\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    620\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mOSError\u001b[0m: /home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat not found."
     ]
    }
   ],
   "source": [
    "# The lines below does NOT work, see the error?\n",
    "filename1 = \"/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat\"\n",
    "data = -np.loadtxt(filename1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Can you write a simple routine to check where is the error?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "36 element is different: lab/ - lap/\n"
     ]
    }
   ],
   "source": [
    "if not filename == filename1:\n",
    "    for i, e in enumerate(filename):\n",
    "        e1 = filename1[i]\n",
    "        if not e == e1:\n",
    "            _step = (i>=3) * 2 + i * (i<3)\n",
    "            print(\"%i element is different: %s - %s\" % (i, filename[i-_step:i+_step],filename1[i-_step:i+_step]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### It is not always simple to find the error. And this error is very general and does not tell if it is file or the directory wrong (no file OR directory).\n",
    "\n",
    "### We can at least try to catch the error and elaborate a little bit the problem to better focus on that."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat not found\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    filename = \"/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat\"\n",
    "    data = -np.loadtxt(filename)\n",
    "except OSError: # see the error code above\n",
    "    print(\"%s not found\" % filename)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat not found\n",
      "Error in the directory /home/gf/src/Python/Python-in-the-lap/Bk\n"
     ]
    }
   ],
   "source": [
    "# Can we be more specific?\n",
    "try:\n",
    "    filename = \"/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat\"\n",
    "    data = -np.loadtxt(filename)\n",
    "except OSError:\n",
    "    print(\"%s not found\" %filename)\n",
    "    rootDir, fname = os.path.split(filename)\n",
    "    if not os.path.isdir(rootDir):\n",
    "        print(\"Error in the directory %s\" % rootDir)\n",
    "    elif not os.path.isfile(filename):\n",
    "        print(\"Error in the file %s\" % fname)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Exercise: Find a way to check which subdir gives the problem (i.e. it does not exist)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat not found\n",
      "Error in the directory /home/gf/src/Python/Python-in-the-lap/Bk\n",
      "/home\n",
      "/home/gf\n",
      "/home/gf/src\n",
      "/home/gf/src/Python\n",
      "/home/gf/src/Python/Python-in-the-lap\n",
      "Check folder 'Python-in-the-lap'\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    filename = \"/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat\"\n",
    "    data = -np.loadtxt(filename)\n",
    "except OSError:\n",
    "    print(\"%s not found\" %filename)\n",
    "    rootDir, fname = os.path.split(filename)\n",
    "    if not os.path.isdir(rootDir):\n",
    "        print(\"Error in the directory %s\" % rootDir)\n",
    "        folders = rootDir.split(\"/\")\n",
    "        for i in range(1,len(folders)):\n",
    "            folder = os.path.join(\"/\", *folders[:i+1])\n",
    "            print(folder)\n",
    "            if not os.path.isdir(folder):\n",
    "                print(\"Check folder '%s'\" % folders[i])\n",
    "                break\n",
    "    elif not os.path.isfile(filename):\n",
    "        print(\"Error in the file %s\" % fname)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. try/except/finally\n",
    "**Perform cleanup actions, whether exceptions occur or not**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat not found\n",
      "Give me a new directory: /home/gf\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    filename = \"/home/gf/src/Python/Python-in-the-lap/Bk/F64ac_0.03_time_200.dat\"\n",
    "    data = -np.loadtxt(filename)\n",
    "except OSError:\n",
    "    print(\"%s not found\" %filename)\n",
    "finally:\n",
    "    new_input = input(\"Give me a new directory: \") "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. raise\n",
    "**Trigger an exception manually**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Sometime we can create an error on purpose"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "ename": "OSError",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mOSError\u001b[0m                                   Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-21-e4cefa20d3ea>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[0mi\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m33\u001b[0m\u001b[1;33m;\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      2\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mi\u001b[0m \u001b[1;33m!=\u001b[0m\u001b[1;36m3\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 3\u001b[1;33m     \u001b[1;32mraise\u001b[0m \u001b[0mOSError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mOSError\u001b[0m: "
     ]
    }
   ],
   "source": [
    "i = 33;\n",
    "if i !=3:\n",
    "    raise OSError()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Check the division\n"
     ]
    }
   ],
   "source": [
    "try:\n",
    "    q = 1 / 0\n",
    "    print(q)\n",
    "except ZeroDivisionError:\n",
    "    print(\"Check the division\")\n",
    "    q = 1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 4. assert\n",
    "**Conditional trigger an exception in the code**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def f(x):\n",
    "    assert x < 0, 'x must be negative'\n",
    "    return x**2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "ename": "AssertionError",
     "evalue": "x must be negative",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mAssertionError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-6-281ab0a37d7d>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mf\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32m<ipython-input-5-468805163b0c>\u001b[0m in \u001b[0;36mf\u001b[1;34m(x)\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mf\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mx\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m     \u001b[1;32massert\u001b[0m \u001b[0mx\u001b[0m \u001b[1;33m<\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'x must be negative'\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      3\u001b[0m     \u001b[1;32mreturn\u001b[0m \u001b[0mx\u001b[0m\u001b[1;33m**\u001b[0m\u001b[1;36m2\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mAssertionError\u001b[0m: x must be negative"
     ]
    }
   ],
   "source": [
    "f(1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "f(-1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 5. with/as\n",
    "**Implement context managers**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"README.md\") as f:\n",
    "    data = f.readlines()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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