notebooks/00-jupyter_introduction.ipynb

{
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   "source": [
    "<p><font size=\"6\"><b>Jupyter notebook INTRODUCTION </b></font></p>\n",
    "\n",
    "\n",
    "> *Introduction to GIS scripting*  \n",
    "> *May, 2017*\n",
    "\n",
    "> *© 2017, Stijn Van Hoey (<mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "outputs": [],
   "source": [
    "from IPython.display import Image\n",
    "Image(url='http://python.org/images/python-logo.gif')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "<big><center>To run a cell: push the start triangle in the menu or type **SHIFT + ENTER/RETURN**\n",
    "![](../img/shiftenter.jpg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Notebook cell types"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "We will work in **Jupyter notebooks** during this course. A notebook is a collection of `cells`, that can contain different content:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# Code cell, then we are using python\n",
    "print('Hello DS')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "DS = 10\n",
    "print(DS + 5) # Yes, we advise to use Python 3 (!)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Writing code is what you will do most during this course!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Markdown"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "Text cells, using Markdown syntax. With the syntax, you can make text **bold** or *italic*, amongst many other things..."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "* list\n",
    "* with\n",
    "* items\n",
    "\n",
    "[Link to interesting resources](https://www.youtube.com/watch?v=z9Uz1icjwrM) or images: ![images](https://cdn.meme.am/instances/57388722.jpg)\n",
    "\n",
    "> Blockquotes if you like them\n",
    "> This line is part of the same blockquote."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "Mathematical formulas can also be incorporated (LaTeX it is...)\n",
    "$$\\frac{dBZV}{dt}=BZV_{in} - k_1 .BZV$$\n",
    "$$\\frac{dOZ}{dt}=k_2 .(OZ_{sat}-OZ) - k_1 .BZV$$\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "Or tables:\n",
    "\n",
    "course | points\n",
    " --- | --- \n",
    " Math | 8\n",
    " Chemistry | 4\n",
    "\n",
    "or tables with Latex..\n",
    "\n",
    " Symbool | verklaring\n",
    " --- | --- \n",
    " $BZV_{(t=0)}$      | initiële biochemische zuurstofvraag (7.33 mg.l-1)\n",
    " $OZ_{(t=0)}$\t    | initiële opgeloste zuurstof (8.5 mg.l-1)\n",
    " $BZV_{in}$\t\t  | input BZV(1 mg.l-1.min-1)\n",
    " $OZ_{sat}$\t\t  | saturatieconcentratie opgeloste zuurstof (11 mg.l-1)\n",
    " $k_1$\t\t      | bacteriële degradatiesnelheid (0.3 min-1)\n",
    " $k_2$\t\t      | reäeratieconstante (0.4 min-1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "Code can also be incorporated, but than just to illustrate:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "```python\n",
    "BOT = 12\n",
    "print(BOT)\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "In other words, it is markdown, just as you've written in **`Rmarkdown`** (!)\n",
    "\n",
    "See also: https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## HTML"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "You can also use HTML commands, just check this cell:\n",
    "<h3> html-adapted titel with &#60;h3&#62; </h3> <p></p>\n",
    "<b> Bold text &#60;b&#62; </b> of <i>or italic &#60;i&#62; </i>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "## Headings of different sizes: section\n",
    "### subsection\n",
    "#### subsubsection"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Raw Text"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "Cfr. any text editor"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Notebook handling ESSENTIALS"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Completion: TAB\n",
    "![](../img/tabbutton.jpg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "* The **TAB** button is essential: It provides you all **possible actions** you can do after loading in a library *AND* it is used for **automatic autocompletion**:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "outputs": [],
   "source": [
    "import os\n",
    "os.mkdir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "my_very_long_variable_name = 3"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "my_ + TAB"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Help: SHIFT + TAB\n",
    "![](../img/shift-tab.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true,
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "* The  **SHIFT-TAB** combination is ultra essential to get information/help about the current operation "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "round(3.2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "os.mkdir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# An alternative is to put a question mark behind the command\n",
    "os.mkdir?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "    <b>EXERCISE</b>: \n",
    "<ul>\n",
    "    <li>What happens if you put two question marks behind the command?</li>\n",
    "</ul>\n",
    "</div>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "clear_cell": true,
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# %load ../notebooks/_solutions/00-jupyter_introduction26.py"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## *edit* mode to *command* mode\n",
    "\n",
    "* *edit* mode means you're editing a cell, i.e. with your cursor inside a cell to type content --> <font color=\"green\">green colored side</font>\n",
    "* *command* mode means you're NOT editing(!), i.e. NOT with your cursor inside a cell to type content --> <font color=\"blue\">blue colored side</font>\n",
    "\n",
    "To start editing, click inside a cell or \n",
    "<img src=\"../img/enterbutton.png\" alt=\"Key enter\" style=\"width:150px\">\n",
    "\n",
    "To s stop edting,\n",
    "<img src=\"../img/keyescape.png\" alt=\"Key A\" style=\"width:150px\">"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## new cell A-bove\n",
    "<img src=\"../img/keya.png\" alt=\"Key A\" style=\"width:150px\">\n",
    "\n",
    "Create a new cell above with the key A... when in *command* mode"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## new cell B-elow\n",
    "<img src=\"../img/keyb.png\" alt=\"Key B\" style=\"width:150px\">\n",
    "\n",
    "Create a new cell below with the key B... when in *command* mode"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## CTRL + SHIFT + P"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "Just do it!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Trouble..."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "<div class=\"alert alert-danger\">\n",
    "    <b>NOTE</b>: When you're stuck, or things do crash: \n",
    "    <ul>\n",
    "    <li> first try **Kernel** > **Interrupt** -> you're cell should stop running\n",
    "    <li> if no succes -> **Kernel** > **Restart** -> restart you're notebook\n",
    "    </ul>\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Overload?!?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "<img src=\"../img/toomuch.jpg\" alt=\"Key A\" style=\"width:500px\">\n",
    "<br><br>\n",
    "<center>No stress, just go to </center>\n",
    "<br>\n",
    "<center><p style=\"font-size: 200%;text-align: center;margin:500\">`Help` > `Keyboard shortcuts`</p></center>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "* **Stackoverflow** is really, really, really nice!\n",
    "\n",
    "  http://stackoverflow.com/questions/tagged/python"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "* Google search is with you!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "<big><center>**REMEMBER**: To run a cell: <strike>push the start triangle in the menu or</strike> type **SHIFT + ENTER**\n",
    "![](../img/shiftenter.jpg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# some MAGIC..."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## `%psearch`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "%psearch os.*dir"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## `%%timeit`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "%%timeit\n",
    "\n",
    "mylist = range(1000)\n",
    "for i in mylist:\n",
    "    i = i**2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "%%timeit\n",
    "\n",
    "np.arange(1000)**2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## `%lsmagic`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "%lsmagic"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Let's get started!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "from IPython.display import FileLink, FileLinks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "run_control": {
     "frozen": false,
     "read_only": false
    },
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "FileLinks('.', recursive=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "For now, we will work on the `01-python-introduction.ipynb` notebook, which is a short introduction to some essential basic Python concepts required to start programming in Python. \n",
    "\n",
    "\n",
    "Additional material is available [here](https://github.com/stijnvanhoey/course_python_introduction/tree/master/basic) (largely adopted from the [scientific python notes](http://www.scipy-lectures.org/), which you can explore on your own to get more background on the Python syntax if specific elements would not be clear. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true,
    "run_control": {
     "frozen": false,
     "read_only": false
    }
   },
   "outputs": [],
   "source": []
  }
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