Playing around with classification algorithms: Python and QGIS

Thu 23 September 2010

Data visualization is part of my everyday work-flow. More often than not, I’m playing around with my data in a GIS to tease out interesting or informative spatial patterns, or to ensure that I’m getting the results that I’m expecting. As a result, I am constantly trying out different classification schemes to help me generalize spatial patterns, highlight outliers and/or patterns, or just plain mess around with my data.

Unfortunately, QGIS (which has been my primary GIS for several years now) only has had ‘Equal Interval’ and ‘Quantiles’ classification algorithms implemented. While these classification schemes are no doubt useful and revealing when used in the right context, I often need something that better represents the ‘actual’ distribution of values in my data. For this, I usually turn to the Jenks Optimisation (or Natural Breaks) classification. Essentially, this classification algorithm generates class intervals that minimize within group variance, and maximize between group variance. In this way, given a certain number (k) of classes, we arrive at an ‘optimal’ classification of our data into k classes. In the past, I would import my data into R, and calculate class intervals using the very handy classInt package. However, moving data between QGIS and R, while slightly easier using my manageR tool (shameless plug!), is not optimal when all I really want to do is fiddle around with different classification schemes. So I decided to reimplement the Jenks algorithm in Python so that I could do things directly from the Python console in QGIS.

Obviously I didn’t really want to implement this algorithm from scratch, so I had a look at the R code from the classInterval function in the classInt package (ah open source!), as well as the handy Python script from here. Once I had the code in hand, it didn’t take long to have a nice Python script ready to be run on my data directly from within QGIS. While I was at it, I also implemented a few other classification algorithms to play around with, including ‘Equal Interval’, ‘Quantiles’, ‘Standard Deviation’, and R’s ‘Pretty’ algorithm. For those of you who don’t know, R’s pretty algorithm basically computes a sequence of about ‘n+1’ equally spaced ‘round’ values which cover the range of our input data, such that the class breaks are 1, 2 or 5 times a power of 10. The Python script is available here, and has a version of the pretty algorithm based on code from the labeling package.


Classification Jenks Python QGIS R FOSS GIS


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