Mailman 3 April 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

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Variance in phase/profiles
by david collins 11 Apr '20

11 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.

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Re: [yt-users] Luminosity within r
by Massimo Gaspari 18 Jul '12

18 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

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problem with fields that use ghost zones
by Britton Smith 30 May '12

30 May '12

Hi everyone, I'm having a problem using fields that use ghost zones. The following simple script: http://paste.yt-project.org/show/2010/ gives this error: http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/ I am working from the tip, but I get the same behavior from yt/2.3. In yt/2.2, everything is working. I am working now to narrow that range down a bit, but does anyone have an idea? Britton

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yt Google+ Hangout Tomorrow
by Sam Skillman 01 May '12

01 May '12

Hi all, Tomorrow we are going to try out a Google Hangout hosted by +yt. This is a chance for you to ask questions or iterate on a particular piece of analysis you'd like to perform. Also feel free to give feedback or just stop by and say hi to us. We'll be starting around 2pm EST tomorrow and there should be several of the yt developers hanging out. Depending on how it goes, we'll consider running one ever so often as a form of office hours or discussion of new capabilities. Anyways, if you have Google+ enabled and you head over and add +yt to your circles at https://plus.google.com/107728486871834552760/posts, you should see the hangout pop up in your feed. We'll also probably send out the link on the irc channel when we get started. I hope to see you there! Sam

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Light Cone + All Sky
by Richard P Wagner 29 Apr '12

29 Apr '12

Hi, I'm looking at the light cone and all sky examples, and I'm wondering how much effort (in human units, not computer time) is required to produce an all sky map based on the "shift and stack" method used for light cone generation. Naively, the answer seems to be based on whether or not the light cone generator projection function could use the HEALpix camera. Is there a simple way to create an all sky map combining several data sets? Thanks, Rick

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Making custom plots consistent with yt's styles
by Christopher Moody 29 Apr '12

29 Apr '12

Hi all, Aesthetically, it'd be nice to make matplotlib plots with a consistent style as yt-made plots so that fonts, sizes, color palettes and so on agree. I imagine that this means I have to find yt's default matplotlib rc, or something analogous, somewhere. Many thanks for the help! chris

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Radial profile of 2D map
by Massimo Gaspari 23 Apr '12

23 Apr '12

Hi guys, suppose I performed a 2D data projection of this form: frb = proj.to_frb(width, res, center=c) how can I obtain the radial profile of this 2D "map" (say frb["Temperature"])?(I have found only how to perform radial profiles of 3D data, setting a certain sphere) Do you have some template? Thanks in advance! Max

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Luminosity within r
by Massimo Gaspari 23 Apr '12

23 Apr '12

Hi guys, I am trying to calculate the (X-ray) luminosity within a sphere of radius r:Lx = sum emissivity *dvol (within r) Suppose I have defined a new derived field XRayEmissivity, dependent on data['Density'] and data['Temperature']. How would you carry out that? I am trying to use BinnedProfile1D. However, it seems that the derived fields are computed only *after* binning, e.g.XRayEmissivity = <Density>**2 * <Temperature>^0.5 I don't want to use the averaged quantities (in each shell). I would like to compute the emissivity point by point, for each leaf block(very important for the luminosity). Is it possible? Thanks, as always! Max

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volume rendering job dies
by Geoffrey So 17 Apr '12

17 Apr '12

Hi all, I'm starting to do some volume rendering of my 800 cube simulation, but the job in the super computer just dies without any kind of error in the logs. The last few lines are: yt : [INFO ] 2012-04-15 16:15:22,264 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. yt : [INFO ] 2012-04-15 16:15:33,307 Max Value is 2.46548e-24 at 0.9743750000000000 0.0193750000000000 0.1781250000000000 in grid EnzoGrid_0442 at level 0 (79, 15, 42) yt : [INFO ] 2012-04-15 16:15:33,309 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. yt : [INFO ] 2012-04-15 16:15:47,133 Max Value is 2.46548e-24 at 0.9743750000000000 0.0193750000000000 0.1781250000000000 in grid EnzoGrid_0442 at level 0 (79, 15, 42) yt : [INFO ] 2012-04-15 16:15:47,135 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. yt : [INFO ] 2012-04-15 16:15:49,839 Max Value is 2.46548e-24 at 0.9743750000000000 0.0193750000000000 0.1781250000000000 in grid EnzoGrid_0442 at level 0 (79, 15, 42) yt : [INFO ] 2012-04-15 16:15:49,841 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. I'm wondering if it is again an memory issue. I ran this job with 16 nodes with 16 cores per node and 4GB per core. This setup is enough memory to do the halo finding, I'm wondering what the memory requirements is for volume rendering, and what's the biggest volume people have done up to date? The script works on my tiny test problem of 64 cube: http://paste.yt-project.org/show/2289/ If this isn't a problem people have with rendering larger volumes than mine, then it might be a machine issue. I haven't moved the data to another super computer, but will try that next if others have done larger volume rendering with no problems at all. From G.S.

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(no subject)
by Nathan Goldbaum 13 Apr '12

13 Apr '12

Hi all, I'm currently analyzing a simulation that contains a disk which is inclined with respect to the simulation box. I've figured out how to make slices through the disk midplane using the cutting plane object but when I try to slice vertically through the disk, I get back images with the disk inclined with respect to the viewing angle. I could fix this if I could control the position angle of the cutting plane but it doesn't look like there is any way to do that currently. Looking at AMRCuttingPlaneBase the docstring says that the cutting plane tries to guess an 'up' direction and that the user cannot set it themselves. Is there a reason for that? Thanks very much for your help, -Nathan Goldbaum

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Enzo file visualization problem
by Abul Latif 06 Apr '12

06 Apr '12

Dear YT users, I am running enzo test problem with MPI. I am unable to visualize the data with YT and it produces following error. If i do not run enzo with MPI (MPICH2) then it works fine. Any ideas, what is going wrong here. Thanks in advance Cheers Latif t : [INFO ] 2012-04-05 17:42:42,770 Parameters: current_time = 7 yt : [INFO ] 2012-04-05 17:42:42,771 Parameters: domain_dimensions = [16 16 16] yt : [INFO ] 2012-04-05 17:42:42,771 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-04-05 17:42:42,771 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2012-04-05 17:42:42,771 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2012-04-05 17:42:42,775 Getting the binary hierarchy Traceback (most recent call last): File "./enzo.py", line 7, in <module> pc=PlotCollection(pf) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 108, in __init__ v,self.c = pf.h.find_max("Density") # @todo: ensure no caching File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 172, in hierarchy self, data_style=self.data_style) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/frontends/enzo/data_structures.py", line 217, in __init__ AMRHierarchy.__init__(self, pf, data_style) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 71, in __init__ self._parse_hierarchy() File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/frontends/enzo/data_structures.py", line 286, in _parse_hierarchy if self._parse_binary_hierarchy(): return File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/frontends/enzo/data_structures.py", line 357, in _parse_binary_hierarchy self.grid_dimensions[:] = f["/ActiveDimensions"][:] ValueError: operands could not be broadcast together with shapes (32,3) (8,3)

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Fwd: SciPy 2012 - The Eleventh Annual Conference on Scientific Computing with Python
by Matthew Turk 04 Apr '12

04 Apr '12

---------- Forwarded message ---------- From: Warren Weckesser <warren.weckesser(a)enthought.com> Date: Wed, Apr 4, 2012 at 5:30 PM Subject: [pydata] SciPy 2012 - The Eleventh Annual Conference on Scientific Computing with Python To: SciPy Users List <scipy-user(a)scipy.org>, scikit-learn-general(a)lists.sourceforge.net, SciPy Developers List <scipy-dev(a)scipy.org>, IPython Development list <ipython-dev(a)scipy.org>, enthought-dev(a)enthought.com, epd-users(a)enthought.com, Discussion of Numerical Python <numpy-discussion(a)scipy.org>, pystatsmodels(a)googlegroups.com, pydata(a)googlegroups.com SciPy 2012, the eleventh annual Conference on Scientific Computing with Python, will be held July 16–21, 2012, in Austin, Texas. At this conference, novel scientific applications and libraries related to data acquisition, analysis, dissemination and visualization using Python are presented. Attended by leading figures from both academia and industry, it is an excellent opportunity to experience the cutting edge of scientific software development. The conference is preceded by two days of tutorials, during which community experts provide training on several scientific Python packages. Following the main conference will be two days of coding sprints. We invite you to give a talk or present a poster at SciPy 2012. The list of topics that are appropriate for the conference includes (but is not limited to): new Python libraries for science and engineering; applications of Python in solving scientific or computational problems; high performance, parallel and GPU computing with Python; use of Python in science education. Specialized Tracks Two specialized tracks run in parallel to the main conference: High Performance Computing with Python Whether your algorithm is distributed, threaded, memory intensive or latency bound, Python is making headway into the problem. We are looking for performance driven designs and applications in Python. Candidates include the use of Python within a parallel application, new architectures, and ways of making traditional applications execute more efficiently. Visualization They say a picture is worth a thousand words--we’re interested in both! Python provides numerous visualization tools that allow scientists to show off their work, and we want to know about any new tools and techniques out there. Come show off your latest graphics, whether it’s an old library with a slick new feature, a new library out to challenge the status quo, or simply a beautiful result. Domain-specific Mini-symposia Mini-symposia on the following topics are also being organized: Computational bioinformatics Meteorology and climatology Astronomy and astrophysics Geophysics Talks, papers and posters We invite you to take part by submitting a talk or poster abstract. Instructions are on the conference website: http://conference.scipy.org/scipy2012/talks.php Selected talks are included as papers in the peer-reviewed conference proceedings, to be published online. Tutorials Tutorials will be given July 16–17. We invite instructors to submit proposals for half-day tutorials on topics relevant to scientific computing with Python. See http://conference.scipy.org/scipy2012/tutorials.php for information about submitting a tutorial proposal. To encourage tutorials of the highest quality, the instructor (or team of instructors) is given a $1,000 stipend for each half day tutorial. Student/Community Scholarships We anticipate providing funding for students and for active members of the SciPy community who otherwise might not be able to attend the conference. See http://conference.scipy.org/scipy2012/student.php for scholarship application guidelines. Be a Sponsor The SciPy conference could not run without the generous support of the institutions and corporations who share our enthusiasm for Python as a tool for science. Please consider sponsoring SciPy 2012. For more information, see http://conference.scipy.org/scipy2012/sponsor/index.php Important dates: Monday, April 30: Talk abstracts and tutorial proposals due. Monday, May 7: Accepted tutorials announced. Monday, May 13: Accepted talks announced. Monday, June 18: Early registration ends. (Price increases after this date.) Sunday, July 8: Online registration ends. Monday-Tuesday, July 16 - 17: Tutorials Wednesday-Thursday, July 18 - July 19: Conference Friday-Saturday, July 20 - July 21: Sprints We look forward to seeing you all in Austin this year! The SciPy 2012 Team http://conference.scipy.org/scipy2012/organizers.php

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