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Python tutorials for ENVS3109 (other content online here)

In each workshop, you work through that week's exploratory analysis using Python in an interactive Jupyter Notebook. After an introduction to Python, each week will demonstrate a technique you can use to analyse remote sensing data with an example dataset.

Topic Techniques Data
Introduction to Python syntax and basic usage (see 'software carpentary' below for more) N/A
Image analysis file formats, loading data, colour scales, combining bands, indices MODIS composite imagery
Change Detection thresholds, difference between images, selecting data, means and variance, OPeNDAP LandSat NDVI - 2003 fires
Trend Analysis 'data cubes', reduction to timeseries, time-dim summaries, uneven spacing, plots Vegetation indicies (VOD)
Correlation Analysis more OPeNDAP, statistics in one, two, and three dimensions soil moisture, soil exposure
Combining Vector and Gridded Data selecting subsets, vector data, reporting global streamflow model

Depending on student interest, a number of optional workshops may be organised to cover important tools for writing software (version control with Git, intro to software testing), general data analysis and graphing (how to ditch Excel), and how to use and contribute to open-source projects (plus: what is open source anyway?).

Useful links

  • Anaconda is like Python, but larger: it comes with many scientific packages built-in and makes it far easier to install others. If you want to use Python for science, you should install the latest version of Anaconda - it's available for every operating system and entirely free.

  • Software Carpentry provide excellent introductions to programming for scientists. You can read the material online, or attend a workshop at many scientific conferences.

  • Think Python 2nd ed. is the best introductory Python textbook I've found. And it's entirely free.

  • GitHub provides free hosting and collaboration tools, making it the world's largest repository of open source software. With an account, you can manage your own work using Git - and read the source of or contribute to any of the tools we'll use, from this document to Python itself.

  • The Jupyter project has an incredible list of notable Notebooks which you can read online or download and run for yourself. The Python for Geosciences and Earthpy collections are particularly relevant (in that order).

Using Jupyter Notebooks

Instead of the (many) useful and powerful features, this section just describes how to get the notebooks in this directory running.

  • Have Anaconda installed on the computer. (If you're in an ANU computer lab, it should be)
  • Open a terminal. On Windows, you can open a terminal in any folder by opening it in the file explorer, clicking the address bar, and typing cmd and enter.
  • If you have installed Anaconda at home, type activate remote-sensing (on Windows), or source activate remote-sensing (on OSX or Linux), in the terminal to activate the environment.
  • In the terminal, type jupyter notebook and the notebook homepage will open, and you can navigate to the notebook you want. Alternatively, type jupyter notebook <name of notebook> to open it directly. Note that pressing the tab key completes a partial filename, so you can just type jupyter notebook 1<tab> to open the first notebook.
  • To run a cell in the notebook, press shift-enter when the cell is highlighted.

Note that after the first workshop (intro to Python), you will need to follow the install instructions below.

A brief digression on scientific software

Programming languages and tools are generally classified on a (subjective) spectrum:

  • at a low level, you give detailed instructions and think like a computer
  • at a medium level, you give instructions in a more natural language (which someone else implemented below)
  • at a high level, you simply declare what you want and it happens (thanks to someone else below)

The tradeoff is computer performance (low-level) against human performance (high-level) - and with the speed of modern computers you should generally use the highest-level tools available. Installing existing software avoids the need to reinvent decades of useful functionality.

In Python, the best way to install scientific packages is the conda install tool in Anaconda. Anaconda just like a Python, but bigger - because it's got many science tools by default.

Since we're using some specialist tools for geospatial data, we'll use conda to create a new environment with everything we need (installing too many Python pacakges into one environment leads to dependency hell). Unfortunately the ANU lab computers have an old version of Anaconda that cannot install some packages without admin permissions on Windows, so skip to the next section in class - but follow these instructions at home!

First, check whether the remote-sensing environment already exists by opening a terminal (windows key, then type "cmd" and enter) and running the following command:

conda env list

If remote-sensing isn't in the list, run the following command (remember you can right-click and paste a command):

conda config --append channels conda-forge
conda create --yes --name remote-sensing xarray netcdf4 numpy pandas bottleneck seaborn dask scipy jupyter

Running the notebooks on ANU lab computers

The ANU infocommons computers do have Anaconda installed, which is great. Unfortunately they are using an old and buggy version of the conda tool for creating and managing environments, so we can't use per-user installs. We will therefore use the more generic Python tool pip, which has much weaker checks for compatibility. You should use the instructions above at home, but this works in the labs:

pip install --user xarray
pip install --user netcdf4
pip install --user seaborn

The installed version of pip is also out of date, but you can safely ignore the request to update it. You will get a "kernel not found" warning when opening the notebook, because the remote-sensing environment is missing - just click "continue" to use the root environment ("Python 3" kernel) and it will work.

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