eo2cube_template.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### General advice (delete this cell before submitting for review)\n",
    "\n",
    "> * This template is adapted from [Geoscience Australias](https://github.com/GeoscienceAustralia/dea-notebooks) published notebooks.\n",
    "> * Remove the \"**Sign up to JupyterHub** to run this notebook interactively from a browser\" header text if the notebook is not eo2cube-compatible.\n",
    "> * Update the **Compatibility** line depending on whether the notebook is compatible or not.\n",
    "> * When adding **Products used**, embed the link to a specific product description, using `[product_name](product url)` syntax.\n",
    "> * When writing in Markdown cells, start each sentence on a **new line**.\n",
    "This makes it easy to see changes through git commits.\n",
    "> * Use proper English in markdown cells and code comments.\n",
    "> * Check the [known issues](https://github.com/GeoscienceAustralia/dea-docs/wiki/Known-issues) for formatting regarding the conversion of notebooks to DEA docs using Sphinx.\n",
    "Things to be aware of:\n",
    "    * Sphinx is highly sensitive to bulleted lists:\n",
    "        * Ensure that there is an empty line between any preceding text and the list\n",
    "        * Only use the `*` bullet (`-` is not recognised)\n",
    "        * Sublists must be indented by 4 spaces\n",
    "    * Two kinds of formatting cannot be used simultaneously:\n",
    "        * Hyperlinked code: \\[\\`code_format\\`](hyperlink) fails\n",
    "        * Bolded code: \\*\\*\\`code_format\\`\\*\\* fails\n",
    "    * Headers must appear in heirachical order (`#`, `##`, `###`, `####`) and there can only be one title (`#`).\n",
    "> * Use the [PEP8 standard](https://www.python.org/dev/peps/pep-0008/) for code. To make sure all code in the notebook is consistent, you can use the `jupyterlab_code_formatter` tool: select each code cell, then click `Edit` and then one of the `Apply X Formatter` options (`YAPF` or `Black` are recommended). This will reformat the code in the cell to a consistent style.\n",
    "> * Additional guidance ?!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img align=\"right\" src=\"/additional_data/banner.png\" style=\"width:1100px;\">"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Descriptive title that follows notebook filename \n",
    "\n",
    "* [**Sign up to the JupyterHub**](https://www.phenocube.org/) to run this notebook interactively from your browser\n",
    "* **Compatibility:** Notebook currently compatible with the Open Data Cube environments of the University of Wuerzburg\n",
    "* **Products used:** \n",
    "[s2a_l2a](https://sentinel.esa.int/web/sentinel/technical-guides/sentinel-2-msi/level-2a/algorithm)\n",
    "\n",
    "* **Special requirements:** An _optional_ description of any special requirements\n",
    "* **Prerequisites:** An _optional_ list of any notebooks that should be run or content that should be understood prior to launching this notebook\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Background\n",
    "An *optional* overview of the scientific, economic or environmental management issue or challenge being addressed by eo2cube, subnational data cubes or earth oservation data cubes in general. This may include information about why the particular technique or approach is useful or required.\n",
    "If you need to cite a scientific paper or link to a website, use a persistent DOI link if possible and link in-text (e.g. [Holzwarth et al. 2020](https://www.mdpi.com/2072-4292/12/21/3570/htm))."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Description\n",
    "A _compulsory_ description of the notebook, including a brief overview of how eo2cube helps to address the problem set out above.\n",
    "It can be good to include a run-down of the tools/methods that will be demonstrated in the notebook:\n",
    "\n",
    "1. First we do this\n",
    "2. Then we do this\n",
    "3. Finally we do this\n",
    "\n",
    "***"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Getting started\n",
    "\n",
    "Provide any particular instructions that the user might need, e.g. To run this analysis, run all the cells in the notebook, starting with the \"Load packages\" cell. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load packages\n",
    "Import Python packages that are used for the analysis.\n",
    "\n",
    "Use standard import commands; some are shown below. \n",
    "Begin with any `iPython` magic commands, followed by standard Python packages, then any additional functionality you need from the `Scripts` directory."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "\n",
    "import sys\n",
    "import datacube\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import xarray as xr\n",
    "\n",
    "sys.path.append('/datacube/data_cube_notebooks/datacube/Scripts')\n",
    "from DEAPlotting import rgb"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Connect to the datacube\n",
    "\n",
    "Connect to the datacube so we can access eo2cube data.\n",
    "The `app` parameter is a unique name for the analysis which is based on the notebook file name."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "dc = datacube.Datacube(app='eo2cube_template',\n",
    "                       config='/home/datacube/.datacube.conf')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Analysis parameters\n",
    "\n",
    "An *optional* section to inform the user of any parameters they'll need to configure to run the notebook:\n",
    "\n",
    "* `param_name_1`: Simple description (e.g. `example_value`). Advice about appropriate values to choose for this parameter.\n",
    "* `param_name_2`: Simple description (e.g. `example_value`). Advice about appropriate values to choose for this parameter.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "param_name_1 = 'example_value'\n",
    "param_name_2 = 'example_value'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Heading 1\n",
    "Use headings to break up key steps/stages of the notebook.\n",
    "\n",
    "Use markdown text for detailed, descriptive text explaining what the code below does and why it is needed.\n",
    "\n",
    "> **Note:** Use this markdown format (sparingly) to draw particular attention to an important point or caveat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Use code comments for low-level documentation of code\n",
    "a = 1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Subheading 1\n",
    "Use subheadings to break up steps within a single section."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Use code comments for low-level documentation of code\n",
    "b = 2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Heading 2\n",
    "Use markdown text for detailed, descriptive text explaining what the code below does and why it is needed."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Use code comments for low-level documentation of code\n",
    "c = 3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Excourses\n",
    "If needed you can give small additional advices if this seems to be useful in the context (e.g. programming related or interesting scientific additions) like:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "***\n",
    "#### **Excourse**:\n",
    "Please take a look at the Zen of Python"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The Zen of Python, by Tim Peters\n",
      "\n",
      "Beautiful is better than ugly.\n",
      "Explicit is better than implicit.\n",
      "Simple is better than complex.\n",
      "Complex is better than complicated.\n",
      "Flat is better than nested.\n",
      "Sparse is better than dense.\n",
      "Readability counts.\n",
      "Special cases aren't special enough to break the rules.\n",
      "Although practicality beats purity.\n",
      "Errors should never pass silently.\n",
      "Unless explicitly silenced.\n",
      "In the face of ambiguity, refuse the temptation to guess.\n",
      "There should be one-- and preferably only one --obvious way to do it.\n",
      "Although that way may not be obvious at first unless you're Dutch.\n",
      "Now is better than never.\n",
      "Although never is often better than *right* now.\n",
      "If the implementation is hard to explain, it's a bad idea.\n",
      "If the implementation is easy to explain, it may be a good idea.\n",
      "Namespaces are one honking great idea -- let's do more of those!\n"
     ]
    }
   ],
   "source": [
    "import this"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### **Excourses end**\n",
    "***"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Adding needed custom functions\n",
    "\n",
    "If a custom function is used, this should be pointed out like this:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### **Needed function**\n",
    "* **Description:** This function greets you when adding your name as string variable."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "def greet(name):\n",
    "    print(\"Hello, \" + name + \". Good morning!\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "An example of the function-usage is optional here. But refer to your custom function using a comment when it is used in the notebook."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Hello, Jon. Good morning!\n"
     ]
    }
   ],
   "source": [
    "greet('Jon')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "***\n",
    "## Additional information\n",
    "\n",
    "<font size=\"2\">This notebook for the usage in the Open Data Cube entities of the [Department of Remote Sensing](http://remote-sensing.org/), [University of Wuerzburg](https://www.uni-wuerzburg.de/startseite/), is adapted from [Geoscience Australia](https://github.com/GeoscienceAustralia/dea-notebooks), published using the Apache License, Version 2.0. Thanks! </font>\n",
    "\n",
    "**License:** The code in this notebook is licensed under the [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0). \n",
    "Digital Earth Australia data is licensed under the [Creative Commons by Attribution 4.0](https://creativecommons.org/licenses/by/4.0/) license.\n",
    "\n",
    "**Contact:** If you need assistance, please post a question on the [Open Data Cube Slack channel](http://slack.opendatacube.org/) or on the [GIS Stack Exchange](https://gis.stackexchange.com/questions/ask?tags=open-data-cube) using the `open-data-cube` tag (you can view previously asked questions [here](https://gis.stackexchange.com/questions/tagged/open-data-cube)).\n",
    "If you would like to report an issue with this notebook, you can file one on [Github](https://github.com/eo2cube).\n",
    "\n",
    "**Last modified:** January 2021\n",
    "\n",
    "**Compatible datacube version:** "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.8.3\n"
     ]
    }
   ],
   "source": [
    "print(datacube.__version__)"
   ]
  }
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