Welcome to acacia’s documentation!¶
acacia is a Python tool that produces clustered polygons from two rasters. If this seems like a general statement, it’s because it is.
Although originally designed to tak input from our other tool biota, acacia works the same regardless of the data you feed it.
All you need to run acacia are:
- One raster of a given continuous quantity (e.g. biomass in 2010), representing the initial state your your data.
- One raster representing the change between your initial state and the final state of you data (e.g. change in biomass between 2010 and 2015).
Using these 2 rasters, acacia produces polygons of significant negative change, clusters them according to their properties (both geometrical and taken from the rasters) and outputs a shapefile summarizing all these analyses, as well as a few handy figures.
acacia offers the possibility of adding a third input in the form of a shapefile, but we’ll come to it later.
Who do I talk to?¶
Written and maintained by Guillaume Goodwin (g.c.h.goodwin@sms.ed.ac.uk) and Samuel Bowers (sam.bowers@ed.ac.uk).
Contents:¶
Setup instructions¶
Preamble¶
acacia is written in Python and was developped on a Linux platform. Provided you can use Python and can install modules on your computer, it should be possible to run on most OS or a Linux server.
On this page, we explain how to set up your Linux or Windows machine to use acacia.
Note
acacia requires Python 3. It may work with Python 2.7, but it’s best not to try your luck.
Installing Anaconda¶
We recommend running acacia in Anaconda.
If you are using a Linux machine, open a terminal window, change directory to the location you’d like to install Anaconda Python, and run the following commands:
wget https://repo.anaconda.com/archive/Anaconda3-2018.12-Linux-x86_64.sh
bash Anaconda3-2018.12-Linux-x86_64.sh
Once complete, you’ll need to add this version of Python to your .bashrc file as follows (replacing ~/ with your installation directory):
# Substitute root for the path to your system's installation and .bashrc file.
echo 'export PATH="~/anaconda3/bin:$PATH"' >> ~/.bashrc
exec -l $SHELL
If this has functioned, on executing python in a terminal window, you should see the following:
Python 2.7.12 |Anaconda custom (64-bit)| (default, Jul 2 2016, 17:42:40)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>>
For Windows users, go to the Anaconda website ) and download the installer for your version of Windows (64-bit or 32-bit). Once the download is finished, run the installer. This may take a while, but when it is done you will be able to open the Anaconda Prompt, which functions like a linux terminal and has Anaconda conveniently installed.
Setting up your Anaconda environment¶
To ensure you are working with the appropriate version of Python as well as the correct modules, we recommend that you create an Anaconda virtual environment set up for running acacia. This is done by running the following commands in your terminal or the Anaconda prompt (recommended procedure):
conda create -n acacia -c conda-forge python=3.7 tqdm scikit-learn scikit-image pyshp gdal
Note
the GDAL package is notoriously temperamental. If this step fails, try again and add ` openssl=1.0` at the end of the line
Activate the acacia environment whenever opening a new terminal window by running this command:
conda activate acacia
Note
Remember to activate the acacia environment whenever you want to use acacia.
If you are SURE you won’t use anything else than acacia, you can do without virtual environments. In this case, just type:
conda install -c conda-forge python=3.7 tqdm scikit-image pyshp gdal
Acacia is primarily a Graphical User Interface. to use the acacia GUI, you need an extra package called PyQt5. To install it, type:
pip install pyqt5
Installing acacia¶
acacia does not require installation apart from what you’ve already done. Congratulations, you are ready to use acacia!
Graphical User Interface¶
acacia comes in as a Graphical User Interface (GUI). This is the preferred option to use acacia, but of course if you ar handy in Python feel free to extract the script from the file Acacia.py and make it your own.
Using the acacia Graphical User Interface (GUI)¶
The acacia Graphical User Interface (GUI) allows you to use acacia with minimal usage of the command line. In your terminal or the Anaconda prompt (if you’re using Windows), navigate to the folder where you stored acacia by typing:
cd /full/path/to/acacia/
This folder should have a file called Acacia.py.
To open the GUI, type:
python Acacia.py
The GUI window should then open. Now you can use acacia several times with minimal typing.
The acacia window¶
How does acacia work?¶
Making polygons¶
acacia takes values from both input rasters to make polygons of change. In the figure below, the square on the left represents the initial data, and the square on the right represents the change data. If the value of cells in the initial data exceed 10 (Quantity threshold), the cells are selected. However, if less than 5 contiguous cells are selected (Area threshold), then the cells will be discarded. Likewise, if the value of the cells in the change data are high than -3 (Change threshold) and the cells were originally selected in the initial data, then the cells are selected. If less than 2 contiguous cells are selected (Area change), the remaining cell is discarded.
The final selected cells are grouped to form polygons (3 polygons in the example below). Each polygon will be given a set of properties based on the boxes you ticked before running the script.
Making clusters¶
acacia uses a hierarchical clustering method. Based on the properties you selected, it will build a distance matrix between all the polygons It will then select a separation distance to determine between 5 and 10 classes of polygon while ensuring maximum separation between the classes using the ` Davies-Bouldin index <https://en.wikipedia.org/wiki/Davies–Bouldin_index>`_ .
The figures below show examples of clusters and their properties
Using your field data¶
acacia offers the possibility to compare your field data to the data from remote sensing. If you have entered a file for validation data, then acacia will extract properties from your data and compare it to the polygons. It will then fit your data in the most likely class.
The figures below show examples of clusters and their properties compared to field data.
Worked example¶
In this worked example we will try out acacia on merged tiles of biomass and biomass change in North-West Zambia. These files are located in the data/ folder by default.
Preparation¶
First ensure that you’ve followed the setup instructions successfully.
Open a terminal, and use cd to navigate to the location where you’ve stored acacia. Then open the GUI as shown below:
cd /path/to/acacia/
python Acacia.py
You should now see the acacia window on your screen.’ By leaving all your parameters by default, you will obtain about 100 classified polygons. You can then load these polygons into QGIS and check the values of change within them, as shown below:
You can also visualise the clusters by choosing a classified colour scheme for the polygons according to the field ‘cluster’.
You should see something like this (but not exactly this, the subsampling is random).
Note
acacia subsamples the polygons of change by default to avoid crashing your computer. If you are confident your machine can take it, increase the number of elements into the thousands!