Develop Reference

Matplotlib alternative for 3D scatter plots

I am having a hard time using Matplotlib to visualize reprojection results of my data in 3 dimensions after applying Principle components analysis or Linear discriminant analysis. After doing a scatter plot, I cannot rotate the data or change the point of view while zooming easily (Rotation axis stays the same even after you zoom, and if you zoom too much points just disappear) and every change takes one second to occur. Matplotlib is very useful but for this specific use case it starts to get very frustrating as it probably wasn't designed for such tasks. Is there an alternative to Matplotlib in Python that can handle 3d scatter plots better and where one could fluidly navigate through the cloud?
An example is shown in the next figure. I have drawn spheres around each data cluster corresponding to a specific class and colored overlapping spheres with red. Now I want to see how these sphere intersect. I think the biggest problem with Matplotlib is that it doesn't allow shifting of the whole graph with the mouse, it only allows rotation around a fixed point, which makes things very messy once you zoom a bit.

matplotlib is not quite mature for 3d graphics :
http://matplotlib.org/mpl_toolkits/mplot3d/faq.html
mplot3d was intended to allow users to create simple 3D graphs with the same “look-and-feel” as matplotlib’s 2D plots. Furthermore, users can use the same toolkit that they are already familiar with to generate both their 2D and 3D plots.
I don't think easy navigation in a 3d plot is easily doable (even 3d scaling is not possible without tweaking the lib). mplot3d was not really intended to be a full-fledged 3D graphics library in the beginning, but more a nice addition for people who needed basic 3D and who were acquainted with matplotlib 2D plot structure.
You might want to take a look at MayaVI (which is pretty good) :
MayaVi2 is a very powerful and featureful 3D graphing library. For advanced 3D scenes and excellent rendering capabilities, it is highly recomended to use MayaVi2.
Note that unlike matplotlib, MayaVI is not yet compatible with Python3 (and might not be in the foreseeable future), so you'll need a Python2 installation.

A very good alternative, but not in Python, is the 3D plot from ILNumerics (http://ilnumerics.net/). It is in .NET

Matplotlib works alright for 3D however, not too fast when interactivity is needed:
https://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html
Mayavi is really fast and compatible with Python 3:
https://docs.enthought.com/mayavi/mayavi/mlab.html#id1

Density plots from matlab to matplotlib

Since some years ago I use matlab for my plots (mostly density plots), but now I want to change to matplotlib. I have a problem trying to figure out how to get analogous plots in matplotlib. I have to represent a 2D array. In matlab I used to use the surf function, and then change to view(2) (az=0 and el=90). An example:
surf(X,Y,log10(z),'FaceColor','interp','EdgeColor','none')
view(2)
In matplotlib I have tried some functions, but I have not got the same feeling. m3plot is a computationally expensive toolkit and it is not the same as using surf. imshow does not allow to use log functions in his arguments (like the example), and log values is something mandatory for me. Then it is pcolor, but I can not find a 'FaceColor'-like option to smooth the edges. I would like to know if someone knows what is the best equivalent in matplotlib.
Thank you for your time!

Try installing mayavi which has the surf function (mayavi is a fully-blown 3D visualisation library using hardware acceleration)

Finally, the solution that suits me is to use the routine pcolormesh(). This combined with the option shading='gouraud' interpolates the data and smooth the edges. In addition, it works pretty well with large arrays in comparision with pcolor.

Is there a way to draw primitives in 3D with Python?

I want to draw 3D primitives like spheres, cylinders and planes (patches) in a 3D plot and I would like to be able to interactively rotate, translate and zoom the scene. I want to do that in Python. I'm use to use Matplotlib for 2d graphs but I never worked with 3D graphics with Python.
Any suggestions?
Any link to tutorials?
Any ideas?

If you're used to matplotlib, then mplot3d is probably a good option if it meets your requirements.
Alternatively there is VPython. This allows you greater freedom to create arbitrary objects and manipulate them, but, of course, more to learn.

Plot functions in Python

I am required to use Python for engineering project. Need to create many graphs, including surface plots. In the past I used Matlab for plotting and really liked it. I was wandering if there is a module/package/extension which bring similar capability into Python.
To be more specific, I need piloting for 2 different reasons.
To understand how functions behave. Something quick and dirty would do it.
Publication/presentation. Ability to add labels, legend, grid, customise colour, axis properties etc.

Try matplotlib, it's pretty extensive and has a shell similar to MATLAB / Mathematica.

I suspect matplotlib.pyplot would be right up your alley.

Scientific Plotting in Python

I have a large data set of tuples containing (time of event, latitude, longitude) that I need to visualize. I was hoping to generate a 'movie'-like xy-plot, but was wondering if anyone has a better idea or if there is an easy way to do this in Python?
Thanks in advance for the help,
--Leo

get matplotlib

The easiest option is matplotlib. Two particular solutions that might work for you are:
1) You can generate a series of plots, each a snapshot at a given time. These can either be displayed as a dynamic plot in matplotlib, where the axes stay the same and the data moves around; or you can save the series of plots to separate files and later combine them to make a movie (using a separate application). There a number of examples in the official examples for doing these things.
2) A simple scatter plot, where the colors of the circles changes with time might work well for your data. This is super easy. See this, for example, which produces this figure
alt text http://matplotlib.sourceforge.net/plot_directive/mpl_examples/pylab_examples/ellipse_collection.hires.png

I'd try rpy. All the power of R, from within python.
http://rpy.sourceforge.net/
rpy is awesome.
Check out the CRAN library for animations,
http://cran.r-project.org/web/packages/animation/index.html
Of course, you have to learn a bit about R to do this, but if you're planning to do this kind of thing routinely in future it will be well worth your while to learn.

If you are interested in scientific plotting using Python then have a look at Mlab: http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/mlab.html
It allows you to plot 2d / 3d and animate your data and the quality of the charts is really high.

Enthought's Chaco is designed for interactive/updating plots. the api and such takes a little while to get use to, but once you're there it's a fantastic framework to work with.

I have had reasonable success with Python applications generating SVG with animation features embedded, but this was with a smaller set of elements than what you probably have. For example, if your data is about a seismic event, show a circle that shows up when the event happened and grows in size matching the magnitude of the event. A moving indicator over a timeline is really simple to add.
Kaleidoscope (Opera, others maybe, Safari not) shows lots of pieces moving around and I found inspirational. Lots of other good SVG tutorial content on the site too.

You might want to look at PyQwt. It's a plotting library which works with Qt/PyQt.
Several of the PyQwt examples (in the qt4examples directory) show how to create "moving" / dynamically changing plots -- look at CPUplot.py, MapDemo.py, DataDemo.py.