Mailman 3 June 2012 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

8 14

Variance in phase/profiles
by david collins 12 Apr '20

12 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

Re: [yt-users] Luminosity within r
by Massimo Gaspari 19 Jul '12

19 Jul '12

Matt, Sam, Eric, Britton, Thank you for all the previous infos (projections and 2D profiles). Now I have a clearer vision of these features. Sam, you are right, the derived field is created before the radial binning.I will let you know if I have further doubts (for sure). As I said to Matt previously, I want to extend my congratulations to all the YT developers.You are doing a great job. Cheers, Max

2 1

scripts from old hub?
by Christine Simpson 07 Jul '12

07 Jul '12

Hi all, Is there a place where the scripts on the old hub migrated to? Thanks Christine

2 2

Error with derived field
by Nathan Butcher 02 Jul '12

02 Jul '12

Hello, I am having trouble using a derived field with a CoveringGrid. I am making fields for dPhi/dx, dPhi/dy, dPhi/dz using the PotentialField from ENZO. The derivative fields do not get passed into the CoveringGrid and get recalculated. This leads to the derivative being zero in areas that were originally in coarse cells. Density and DivV fields were passed to the CoveringGrid properly. As a test I defined a field that was Density^2 and that was passed to the CoveringGrid properly, so I think it is a problem specific to derived fields based on the ENZO-specific PotentialField. I have included the source for my derivative functions. Thank you, Nathan Butcher

2 3

PNG error on YT install
by Carolyn Peruta 30 Jun '12

30 Jun '12

I looked back in the email archive and found this exact same problem from John ZuHone. http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-June/00165… I wiped all png related stuff from the build and set INST_PNGLIB to 0 but I am still getting this error. Any ideas? Notes: OSX 10.7.4 using Apple's gcc 4.2.1 ERROR: Traceback (most recent call last): File "/Users/cperuta/yt-i386/bin/yt", line 9, in <module> load_entry_point('yt==2.3', 'console_scripts', 'yt')() File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg/pkg_resources.py", line 337, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg/pkg_resources.py", line 2281, in load_entry_point return ep.load() File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg/pkg_resources.py", line 1991, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/cperuta/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 26, in <module> from yt.mods import * File "/Users/cperuta/yt-i386/src/yt-hg/yt/mods.py", line 107, in <module> from yt.visualization.api import \ File "/Users/cperuta/yt-i386/src/yt-hg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/Users/cperuta/yt-i386/src/yt-hg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/figure.py", line 18, in <module> from axes import Axes, SubplotBase, subplot_class_factory File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/axes.py", line 14, in <module> import matplotlib.axis as maxis File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/axis.py", line 14, in <module> import matplotlib.text as mtext File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/text.py", line 31, in <module> from matplotlib.backend_bases import RendererBase File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 48, in <module> import matplotlib.textpath as textpath File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/textpath.py", line 9, in <module> from matplotlib.mathtext import MathTextParser File "/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/mathtext.py", line 52, in <module> import matplotlib._png as _png ImportError: dlopen(/Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/_png.so, 2): Symbol not found: _png_set_longjmp_fn Referenced from: /Users/cperuta/yt-i386/lib/python2.7/site-packages/matplotlib/_png.so Expected in: dynamic lookup

4 4

colorbar rasterization
by Christine Simpson 28 Jun '12

28 Jun '12

Hi everyone, I have a question that may be more of a matplotlib question than a yt question, but it's an issue with some yt generated figures I have, so I thought I'd ask it here. I think there was some discussion of this on the list a while ago but I can't find the thread. When I output images that include colorbars in vector formats (like pdf and eps), I get these little lines running across the color bar. It goes away if I output the image in a rasterized format (like png). I wanted to output my images in vector format (as pdfs) so everything looks nice and sharp. I've figured out how to just rasterize the color bar. However, I don't want to rasterize the color bar labels, and the way I've implemented it, the labels get rasterized too. It seems in figure objects (and maybe axes objects?) there is a way to specify the order that items get drawn and/or rasterized (through the zorder and rasterized_zorder keywords); I've played around with this but haven't been able to get it to work. The color bar is a Colorbar object and it doesn't seem like this class allows for adjusting the rasterization order of things. I've pasted an example script here: http://paste.yt-project.org/show/2504/ I'm probably going to give up on this soon, but any advice people have would be greatly appreciated. Christine

3 4

Reason GUI updates
by Matthew Turk 27 Jun '12

27 Jun '12

Hi all, Over the last little while, a few of us have been working to update and improve the GUI for yt, "Reason." These changes were pushed into the main repository this morning. They include a visual refresh, a smaller footprint on disk, and a 3D scene based on XTK. (The camera path editor in the 3D scene is still awaiting some fixes, but the concept is working.) I'd encourage you, if you're on the development branch of yt, to update and give it a shot: yt update yt serve The first time you run this it will tell you to download a package containing the javascript necessary to run, but after that it should run fine. This version also includes the ability to run in parallel on an MPI cluster, but the user interface for that is still being developed. (If you would like to test this out before it's polished up, drop on by IRC or yt-dev.) Any feedback you have would be appreciated. We're going to be pushing for a stable release in the near future. -Matt PS This and a few other things, such as a revised plotting mechanism, were the product of a sprint we had last weekend. The summary is here: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-June/002118.… http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-June/002112.…

1 0

DivV on region
by Elizabeth Tasker 27 Jun '12

27 Jun '12

Hi, Is the field such as DivV (or any field that uses the scheme sl_left = slice(None,-2,None) sl_right = slice(1,-1,None) f = data["x-velocity"][sl_right,1:-1,1:-1]/ds f -= data["x-velocity"][sl_left ,1:-1,1:-1]/ds to average between adjoining cells) valid for objects such as regions, where the cells might not necessarily be adjoining? I'm thinking no... Elizabeth

1 1

how do I use the convert(field) in Field List?
by Geoffrey So 26 Jun '12

26 Jun '12

Hi, I'm trying to plot a projection of the SZ effect, and I'm not sure how the mechanism works. If I do . . . proj = pf.h.proj(0, "SZKinetic", weight_field='Ones') frb = FixedResolutionBuffer(proj, (0.0, 1.0, 0.0, 1.0), (imgres, imgres)) img = frb[field] pylab.imshow( img, interpolation='nearest', origin='lower') After some digging I found the constants defined in yt/utilities/physical_constants.py, but I'm not sure how do I use the convertSZKinetic to get cgs answers (is the field SZKinetic already returned as cgs, if so what is the cgs units?), and what are the units on 0.88 in the following equation? If I know that I can figure out the cgs units. def _convertSZKinetic(data): return 0.88*((sigma_thompson/mh)/clight) From G.S.

2 1