yt development - All-sky column density calculation
@ Matthew Turk | Monday, Feb 14, 2011 | 3 minute read | Update at Monday, Feb 14, 2011

This week I added the ability to calculate all-sky column densities. This functionality uses HEALpix to calculate equally-area regions on the sky and then shoots out rays from a central source to some fixed radius, accumulating values of a field along the way. Although so far I’ve only used it to calculate column densities of “Density” it could be used for other values as well, including all- sky weighted averages of quantities.

This works via a new HEALpixCamera object, which accepts an Nside argument (the number of pixels is 12*Nside*Nside) as well as a center and a radius. It’s still a bit rough around the edges, but currently it will work to generate projections over the entire sky.

It’s important to note that the difficulties inherent in sorting bricks radially prevent it from being used for transfer functions that involve any absorption. This means that currently it only works with “ProjectionTransferFunction” as an input.

To generate the projected pixels, we have to create a camera and ask it to cast rays along each pixel. This script will do that:

from yt.mods import *
import as camera
Nside = 32
pf = load('DD0008/galaxy0008')
cam = camera.HEALpixCamera([0.5,0.5,0.5], 0.2, Nside, pf = pf, log_fields = [False])
bitmap = cam.snapshot()

The returned bitmap will, as per usual, be an array of integrated values. Because we’re using the projection transfer function, with the HEALpix camera, it will be an ordered pixel list of shape (12*Nside*Nside, 1, 4) where the first channel is ordered in order of pixels as per the HEALpix notation. We now have to convert this to a regularly gridded set of values, between 0 and 2pi and 0 and pi, for the theta and phi coordinates.

yt provides a helper function to go from pixel ID to angle (as well as a few other things). You can access this helper function in this manner:

import yt.utilities.amr_utils as au
from numpy import pi
phi, theta = na.mgrid[0.0:2*pi:800j, 0:pi:800j]
pixi = au.arr_ang2pix_nest(Nside,
theta.ravel(), phi.ravel())
img = na.log10(bitmap[:,0,0][pixi]).reshape((800,800))

The call to mgrid creates a regularly-spaced mesh of values. We then ask HEALpix what the pixel IDs are that fall into each of these regularly spaced mesh values, and then we apply those pixels in that order. This transformation will, someday, be implicit in the snapshot() call.

At this point we can plot our regularly spaced mesh using one of several projections. We’ll do the Mollweide projection. To do this, we import the appropriate Matplotlib components and plot using the imshow command:

import matplotlib.figure
import matplotlib.backends.backend_agg

fig = matplotlib.figure.Figure((10, 5))
ax = fig.add_subplot(1,1,1,projection='mollweide')
image = ax.imshow(img,
extent=(-pi,pi,-pi/2,pi/2), clip_on=False, aspect=0.5)
cb = fig.colorbar(image, orientation='horizontal')
canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(fig)

As you can see, it’s currently still a bit rough-around-the-edges (the image is below) but it’s on the way to being very useful. In particular, setting Nside higher above should improve the image quality, and adjusting the axis display in matplotlib can remove the latitude and longitude display. There is also currently a bug (which I have reported but not heard back on) in matplotlib related to changing the size of the axes object.

Hopefully soon enough this will be ready to be wrapped more simply into yt, and it can be made available in a more straightforward fashion. For now, paste 1503 includes a full script that will all-sky render and output an image like the one below.


yt extension modules

yt has many extension packages to help you in your scientific workflow! Check these out, or create your own.


ytini is set of tools and tutorials for using yt as a tool inside the 3D visual effects software Houdini or a data pre-processor externally to Houdini.


Trident is a full-featured tool that projects arbitrary sightlines through astrophysical hydrodynamics simulations for generating mock spectral observations of the IGM and CGM.


pyXSIM is a Python package for simulating X-ray observations from astrophysical sources.


Analyze merger tree data from multiple sources. It’s yt for merger trees!


yt_idv is a package for interactive volume rendering with yt! It provides interactive visualization using OpenGL for datasets loaded in yt. It is written to provide both scripting and interactive access.


widgyts is a jupyter widgets extension for yt, backed by rust/webassembly to allow for browser-based, interactive exploration of data from yt.


yt_astro_analysis is the yt extension package for astrophysical analysis.

Make your own!!

Finally, check out our development docs on writing your own yt extensions!

Contributing to the Blog

Are you interested in contributing to the yt blog?

Check out our post on contributing to the blog for a guide!

We welcome contributions from all members of the yt community. Feel free to reach out if you need any help.

the yt data hub

The yt hub at has a ton of resources to check out, whether you have yt installed or not.

The collections host all sorts of data that can be loaded with yt. Some have been used in publications, and others are used as sample frontend data for yt. Maybe there’s data from your simulation software?

The rafts host the yt quickstart notebooks, where you can interact with yt in the browser, without needing to install it locally. Check out some of the other rafts too, like the widgyts release notebooks – a demo of the widgyts yt extension pacakge; or the notebooks from the CCA workshop – a user’s workshop on using yt.

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