DEAfrica_notebooks_template.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### General advice (delete this cell before submitting for review)\n",
    "\n",
    "> * When adding **Products used**, embed the hyperlink to that specific product on the DE Africa Explorer using the `[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",
    "> * Though we have not yet determined if a DE africa docs page will be produced from these notebooks, to faciliate the easy conversion of these notebooks into a docs help page, check the [known issues](https://github.com/GeoscienceAustralia/dea-docs/wiki/Known-issues) for formatting regarding the conversion of notebooks to DE Africa 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",
    "> * The DE Africa Image placed in the title cell will display as long as the notebook is contained in one of the standard directories.\n",
    "It does not work in the highest level directory (hence why it doesn't display in the original template notebook).\n",
    "> * In the final notebook cell, include a set of relevant tags which are used to build the DE Africa User Guide's Tag Index (not yet built, but may be in the future)\n",
    "Use all lower-case (unless the tag is an acronym), separate words with spaces (unless it is the name of an imported module).\n",
    "Ensure the tags cell below is in `Raw` format, rather than `Markdown` or `Code`.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Descriptive title that follows notebook filename <img align=\"right\" src=\"Supplementary_data/DE_Africa_Logo_Stacked_RGB_small.jpg\">\n",
    "\n",
    "* **Products used:** \n",
    "[ls8_usgs_sr_scene](https://explorer.digitalearth.africa/ls8_usgs_sr_scene), \n",
    "[ga_ls8c_wofs_2_annual_summary](ga_ls8c_wofs_2_annual_summary),\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 Digital Earth Africa. \n",
    "For `Beginners_Guide` or `Frequently_Used_Code` notebooks, 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. [Dhu et al. 2017](https://doi.org/10.1080/20964471.2017.1402490))."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Description\n",
    "A _compulsory_ description of the notebook, including a brief overview of how Digital Earth Africa 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": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "\n",
    "import datacube\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import sys\n",
    "import xarray as xr\n",
    "\n",
    "sys.path.append('../Scripts')\n",
    "from dea_plotting import rgb\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Connect to the datacube\n",
    "\n",
    "Connect to the datacube so we can access DEA 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": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dc = datacube.Datacube(app='DEA_notebooks_template')"
   ]
  },
  {
   "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": null,
   "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": null,
   "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": null,
   "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": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Use code comments for low-level documentation of code\n",
    "c = 3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "***\n",
    "\n",
    "## Additional information\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 Africa 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/digitalearthafrica/deafrica-sandbox-notebooks).\n",
    "\n",
    "**Last modified:** January 2020\n",
    "\n",
    "**Compatible datacube version:** "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print(datacube.__version__)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Tags\n",
    "Browse all available tags on the DE Africa User Guide's [Tags Index](https://) (placeholder as this does not exist yet)"
   ]
  },
  {
   "cell_type": "raw",
   "metadata": {
    "raw_mimetype": "text/restructuredtext"
   },
   "source": [
    "**Tags**:  :index:`landsat 8`, :index:`deafrica_plotting`, :index:`rgb`, :index:`NDVI`, :index:`time series`"
   ]
  }
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