Representations of large datasets with Datashader

How to meaningfully visualize millions of points in seconds

Posted by Mario D'Amore on October 3, 2016  Improve this post

Watching Scipy videos always brings interesting findings. In the 2016 edition I found this great introduction to datashader by Dr. James Bednar(@jamesabednar), part of the big Continuum Analytics contribution to the python environment.

At its core, datashader is a highly efficient library to reduce non-gridded data to 2D images using a variety of functions to calculate pixel value. Look at the documentation and these amazing notebooks for further details and examples.

I adapted 1 the nyc_taxi.ipynb notebook that uses ~6M unstructured datapoints to visualize an example planetary dataset.

I cheat a little bit creating an unstructured dataset from MOLA projected images.

I downloaded the MOLA meg016 (16 pixels per degree) data from the PDS and converted each file to csv with 2 :

for i in $(ls *.md )
    do
    base=$( echo $i | cut -d. -f1)
    echo $base
    gdal_translate -of XYZ $i $base.xyz
done

They call it ‘ASCII Gridded XYZ’. Loading all those data brings around 66M points in as tabular data.

Visualizing them could be challenging: honestly all the examples that James did (undersampling, oversampling and/or playing with opacity) are my daily life.

Datashader helps to generate 2D images with some predefined functions to calculate pixel values, like the mean of all data point mapped to a particular bin, the min/max/variance and so on.

I ran all the code on my old 13” Macbook mid 2012, 2.9GHz i7, 16GB of RAM. That is not the brightest machine nowadays, nevertheless it achieved good performance. The funniest thing was that loading all the data with the super pandas library 3 took 30 seconds, when the reduction of all the data on a 800x400 grid with datashader took less then 6 seconds. I’m more than impressed!

Obviously, a more powerful machine achieves better results: on my desktop MacPro ( 32 Cores / 64 GB RAM ) it took an order of magnitude less.

Datashader works pretty well in combination with Bokeh, always from Continuum Analytics. The last cell in the notebook below will produce an interactive plot with live data reduction every time the user pans or zooms.

The only downside I found was the limited set of available functions for the reduction, James opened an issue on github to discuss my proposal. I had in mind something more robust then the mean to handle the noisy dataset that we all know, like the median or density function related characteristics. Sadly, it seems that the current implementation cannot easily accomplish this, mainly due to the extreme optimization and parallelization they use. They agreed that it is interesting and maybe they will add an example for less-then-optimized functions in the future.

Here is the notebook (original link): if you want to run it, please take care of the dependencies and that datashader isn’t pip installable (yet).

  1. someone would define this as “copying”, I would say “tinkering”. 

  2. this needs GDAL installed, present in your PATH, working and all the stuff. 

  3. you are using pandas for tabular data, I hope. 


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