Animated 3-D Plots in Python

Download/cite the paper here!

In a previous post, I discussed chaos, fractals, and strange attractors. I also showed how to visualize them with static 3-D plots. Here, I’ll demonstrate how to create these animated visualizations using Python and matplotlib. All of my source code is available in this GitHub repo. By the end, we’ll produce animated data visualizations like this, in pure Python:

Animated 3-D Poincare plot of the logistic map's chaotic regime - this is time series data embedded in three dimensional state space Continue reading Animated 3-D Plots in Python

Visualizing Chaos and Randomness

3-D Poincare plot of the logistic map's chaotic regime - this is time series data embedded in three dimensional state space

Download/cite the paper here!

In a previous post, I discussed chaos theory, fractals, and strange attractors – and their implications for knowledge and prediction of systems. I also briefly touched on how phase diagrams (or Poincaré plots) can help us visualize system attractors and differentiate chaotic behavior from true randomness.

In this post (adapted from this paper), I provide more detail on constructing and interpreting phase diagrams. These methods are particularly useful for discovering deterministic chaos in otherwise random-appearing time series data, as they visualize strange attractors. I’m using Python for all of these visualizations and the source code is available in this GitHub repo.

Continue reading Visualizing Chaos and Randomness

Visualizing Summer Travels Part 6: Projecting Spatial Data with Python

This post is part of a series on visualizing data from my summer travels.

I’ve previously discussed visualizing the GPS location data from my summer travels with CartoDB, Leaflet, and Mapbox + Tilemill. I also visualized different aspects of this data set in Python, using the matplotlib plotting library. However, these spatial scatter plots used unprojected lat-long data which looked pretty distorted at European latitudes.

Today I will show how to convert this data into a projected coordinate reference system and plot it again using matplotlib. These projected maps will provide a much more accurate spatial representation of my spatial data and the geographic region. All of my code is available in this GitHub repo, particularly this notebook.

Continue reading Visualizing Summer Travels Part 6: Projecting Spatial Data with Python

Using geopandas on Windows

projected-shapefile-gps-coordinatesThis guide was updated in June 2016 to reflect changes to the dependencies and the ability to install with Python wheels.

I recently went through the exercise of installing geopandas on Windows and getting it to run. Having learned several valuable lessons, I thought I’d share them with the world in case anyone else is trying to get this toolkit working in a Windows environment (also see this GitHub gist I put together).

It seems that pip installing geopandas works fine on Linux and Mac. However, several of its dependencies have C extensions that cause compilation failures with pip on Windows. This guide gets around that issue. For preliminaries, I have this working on Windows 7, 8, and 10. My Python environments are Anaconda, 64-bit, with both Python 2.7 and 3.5. I’m running geopandas version 0.2 with GDAL 2.0.2, Fiona 1.7.0, pyproj 1.9.5.1, and shapely 1.5.16.

Continue reading Using geopandas on Windows

Visualizing Summer Travels Part 5: Python + Matplotlib

This post is part of a series on visualizing data from my summer travels.

I’ve previously discussed visualizing the GPS location data from my summer travels with CartoDB, Leaflet, and Mapbox + Tilemill. Today I will explore visualizing this data set in Python, using the matplotlib plotting library. All of my code is available in this GitHub repo, particularly this notebook.

Continue reading Visualizing Summer Travels Part 5: Python + Matplotlib

Visualizing Summer Travels Part 4: Mapbox + Tilemill

This post is part of a series on visualizing data from my summer travels.

I’ve previously discussed my goals in visualizing GPS data from my summer travels and explored visualizing the data set with CartoDB and with Leaflet. The full OpenPaths location data from my summer travels is available here and I discussed how I reverse-geocoded it here.

Mapbox is a major provider of online web mapping services such as tiled web maps, the Tilemill cartography IDE, and the mapbox.js javascript library. Today I’ll run through how to create an interactive data map in Tilemill’s design studio, export the map as a set of tiles, upload the tileset to Mapbox, and then use a javascript client to display the map on a web page. Our final result will look something like this:

Continue reading Visualizing Summer Travels Part 4: Mapbox + Tilemill

Visualizing Summer Travels Part 3: Leaflet

This post is part of a series on visualizing data from my summer travels.

I’ve previously discussed my goals in visualizing GPS data from my summer travels and explored visualizing the data set with CartoDB. The full OpenPaths location data from my summer travels is available here and I discussed how I reverse-geocoded it here.

Lastly, I reduced the size of this spatial data set so Leaflet can render it more quickly on low-power mobile devices. I discussed why this is important and how to do it with the DBSCAN clustering algorithm and also with the Douglas-Peucker algorithm. The final data set I’ll be working with is available here.

Continue reading Visualizing Summer Travels Part 3: Leaflet

Reducing Spatial Data Set Size with Douglas-Peucker

In a previous post I discussed how to reduce the size of a spatial data set by clustering. Too many data points in a visualization can overwhelm the user and bog down on-the-fly client-side map rendering (for example, with a javascript tool like Leaflet). So, I used the DBSCAN clustering algorithm to reduce my data set from 1,759 rows to 158 spatially-representative points. This series of posts discusses this data set in depth.

Continue reading Reducing Spatial Data Set Size with Douglas-Peucker

Clustering to Reduce Spatial Data Set Size

In this tutorial, I demonstrate how to reduce the size of a spatial data set of GPS latitude-longitude coordinates using Python and its scikit-learn implementation of the DBSCAN clustering algorithm. All my code is in this IPython notebook in this GitHub repo, where you can also find the data.

Traditionally it’s been a problem that researchers did not have enough spatial data to answer useful questions or build compelling visualizations. Today, however, the problem is often that we have too much data. Too many scattered points on a map can overwhelm a viewer looking for a simple narrative. Furthermore, rendering a JavaScript web map (like Leaflet) with millions of data points on a mobile device can swamp the processor and be unresponsive.

Continue reading Clustering to Reduce Spatial Data Set Size

Reverse Geocode a Set of Lat-Long Coordinates to City + Country

This tutorial demonstrates how to reverse geocode a set of latitude-longitude coordinates to city and country using Python and the Google Maps API.

I have previously written about my GPS location data from this summer’s travels. The data set, gathered with the OpenPaths app, contains lat-long coordinates and timestamps. Without city or country data, any visualizations would be very simplistic because all I have is coordinates and timestamps. It would be nice to reverse geocode these coordinates to add city and country data to each point. Then, I could create richer, more informative marker popups that include this new geographical information.

Continue reading Reverse Geocode a Set of Lat-Long Coordinates to City + Country