Mailman 3 April 2015 - yt-users

ad: Open Astrophysics Bookshelf
by Michael Zingale April 23, 2015

April 23, 2015

Dear yt-ers, as many of us teach and train students (or are students), I wanted to draw attention to a new project that I've been working on, the Open Astrophysics Bookshelf. Essentially it is just a github organization where open (CC-licensed) astro texts can be hosted as git repos. The idea is that many of us have our own set of notes, with varying degrees of polish, and by hosting the latex source on github, we can invite other contributors to add to the notes. This would also enable the community to crowdsource new texts of interest to our field, and free us all up from reinventing the wheel. And since everything is openly licensed, anyone can create mash-ups of the content to suit their needs. I have a project page up here where you can read some initial ideas: http://open-astrophysics-bookshelf.github.io/ I've already moved my set of notes on Computational Astrophysical Hydrodynamics there and I've contacted several of our colleagues about hosting their own course notes/texts there as well---hopefully once summer hits, we'll see some new stuff. There is an empty template for a Scientific Computing Cookbook to share tips/techniques and good practices across our field---this latter one is a case where crowdsourcing can hopefully put something nice together. Many people I've spoken to in our field have noted the need for some instructions on computing to new grad students. The way I envision things working is that a book would have a lead author (or authors) who are responsible for the overall flow, tone, etc., and as many contributing authors as want to help out, all of whom would be listed on an author page (and, of course, in the git history). Anyway, that's my ad---if contributing to community-sourced texts or opening up something you've already written for a class interests you, then I hope that you will help out. -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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using yt for non-spatial data
by Carolin Villforth April 23, 2015

April 23, 2015

Hello yt-users, I saw a yt presentation at the Python Astronomy Meeting and am interested to see if yt could be used for non-spatial data. My specific problem is MCMC chains in 19 (or up to 23) dimensional parameter space in which none of the parameters are nuisance parameters. I thought yt could be used to visualize and analyze such data. I tried to load the chain as particles and managed to do so, but am having problems plotting. I pasted the code below. Has anyone used yt for non-spatial data? Cheers, Carolin ----------- In [81]: mcchain.keys() ## a dictionary containing dimensions of the chain Out[81]: ['particle_position_z', 'particle_mass', 'particle_position_x', 'particle_position_y', 'qso'] In [82]: mcyt = yt.load_particles(mcchain) yt : [INFO ] 2015-04-23 09:47:39,235 Parameters: current_time = 0.0 yt : [INFO ] 2015-04-23 09:47:39,235 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2015-04-23 09:47:39,237 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2015-04-23 09:47:39,237 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2015-04-23 09:47:39,238 Parameters: cosmological_simulation = 0.0 In [83]: circle = mcyt.sphere([0.5, 0.5, 0.5], 0.25) yt : [INFO ] 2015-04-23 09:47:45,741 Allocating for 1.000e+04 particles yt : [INFO ] 2015-04-23 09:47:45,763 Identified 7.130e+02 octs yt : [INFO ] 2015-04-23 09:47:45,897 Loading field plugins. yt : [INFO ] 2015-04-23 09:47:45,898 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-04-23 09:47:45,898 Loaded astro (15 new fields) yt : [INFO ] 2015-04-23 09:47:45,898 Loaded cosmology (22 new fields) yt : [INFO ] 2015-04-23 09:47:45,899 Loaded fluid (64 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded fluid_vector (96 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded geometric (112 new fields) yt : [INFO ] 2015-04-23 09:47:45,900 Loaded local (112 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded magnetic_field (120 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded my_plugins (120 new fields) yt : [INFO ] 2015-04-23 09:47:45,901 Loaded species (122 new fields) In [84]: pl=yt.ProjectionPlot(circle, 'x', 'y') --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-84-685c784708ec> in <module>() ----> 1 pl=yt.ProjectionPlot(circle, 'x', 'y') /Users/cvillforth/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/yt/visualization/plot_window.pyc in __init__(self, ds, axis, fields, center, width, axes_unit, weight_field, max_level, origin, fontsize, field_parameters, data_source, method, proj_style, window_size, aspect) 1212 self.ts = ts 1213 ds = self.ds = ts[0] -> 1214 axis = fix_axis(axis, ds) 1215 # proj_style is deprecated, but if someone specifies then it trumps 1216 # method. /Users/cvillforth/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/yt/funcs.pyc in fix_axis(axis, ds) 649 650 def fix_axis(axis, ds): --> 651 return ds.coordinates.axis_id.get(axis, axis) 652 653 def get_image_suffix(name): AttributeError: 'YTSphere' object has no attribute 'coordinates' -------------------------------------------------------------------------------- Dr Carolin Villforth SUPA Advanced Fellow University of St Andrews (SUPA) School of Physics & Astronomy North Haugh, St Andrews, Fife KY16 9SS UK cv21(a)st-andrews.ac.uk Office: 272 phone +44 (0) 1334 46 1612 http://www-star.st-and.ac.uk/~cv21/cv21/Home.html -------------------------------------------------------------------------------- _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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New Python in Astronomy FB Group
by Adam Jacobs April 22, 2015

April 22, 2015

Hi All, I hope this isn't a misuse of the mailing list, but I thought readers of the list would be interested in a newly formed Facebook group all about Python in astronomy: https://www.facebook.com/groups/1596306890613995/ Cheers, Adam -- Adam Jacobs Department of Physics and Astronomy, PhD Candidate Stony Brook University http://astro.sunysb.edu/amjacobs/ _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Question on loading multiple HDF5 files together in one step
by Katharina Wollenberg April 22, 2015

April 22, 2015

Hey together, I have the data for a disk, which I want to visualize, split into 16 HDF5 files. All files have the same structure and ‘columns’ only that the total information of the considered quantities is split over these 16 files. Before I try merging these files into one single file, I was wondering if it is possible with yt to load all the separate files in one step and then use one plot command to visualize the combined corresponding ‘columns’ together in one image. Thanks! Katharina Wollenberg _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Two different setup.py installs
by Junhwan Choi (최준환) April 21, 2015

April 21, 2015

Hi yt user, I have one naive question. I install yt from the yt source with setup.py. There are two different way you can install. 1) python setup.py develop 2) python setup.py build and python setup.py install What is the different between two approach? Strangely, when I install with 1), the yt is installed but it crash when it runs. However, when I install with 2), the yt is installed and the same script run at this time. Is there anyone had a similar experience? Thank you, Junhwan Choi _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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FRB extraction details
by David Collins April 20, 2015

April 20, 2015

Hi, Everybody! If I make an FRB and have the resolution that of the finest zones, how doe the coarser zones get filled? Is it possible for them to be forced to be piecewise-constant sampling of the coarse data? d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Issues with code_length versus physical lengths for positions in x, y, z space
by Devin Silvia April 20, 2015

April 20, 2015

Hi all, I've been trying to do some data analysis of an Enzo dataset to extract information about volumes contained with the virial radius of rockstar identified halos. As a test, I've identified the most massive halo and created sphere at that halo position using a bit of code that looks like this: sp = data_ds.sphere([most_massive.quantities['particle_position_x'], most_massive.quantities['particle_position_y'], most_massive.quantities['particle_position_z']], most_massive.quantities['virial_radius']) Then, when I actually try to use the sphere to analyze data or make plots, it seems like there is something screwy going on with the position information, which you can see if you look at the calculations done here: http://paste.yt-project.org/show/5522/ When you look at the "center" based on a calculation of the positions with respect to the domain, you get a different center than the one that just comes of sp.center in "code_length". Specifically, the "code_length" center values all seem to be off from the actual position of the halo by a factor of 1.4: In [98]: sp.center.in_units("kpc")/data_ds.domain_width.in_units("kpc") / sp.center.d Out[98]: YTArray([ 1.40845077, 1.40845077, 1.40845077]) (dimensionless) I'm not sure where this factor is coming from, but it seems to be buried in some sort of unit conversion step somewhere. Thanks, Devin -- Devin W. Silvia NSF Astronomy and Astrophysics Postdoctoral Fellow Department of Physics and Astronomy Michigan State University www.devinsilvia.com _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Help with volume rendering
by Luc Menard April 15, 2015

April 15, 2015

Hi, I am extremely new to using yt and I have encountered an error while attempting some simple volume rendering. I was using the yt-cookbook script to attempt to make some images, and everything was working fine until I get to the "cam.snapshot()" command. It gives me this error. >>> cam.snapshot("hello.png", double_check = True) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/mnt/home/menardlu/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 764, in snapshot self.initialize_source() File "/mnt/home/menardlu/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 716, in initialize_source self.no_ghost) File "/mnt/home/menardlu/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py", line 178, in initialize_source self.set_fields(fields, log_fields, no_ghost) File "/mnt/home/menardlu/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.py", line 165, in set_fields del self.bricks, self.brick_dimensions AttributeError: bricks Any help would be greatly appreciated. Thank you, Luc Menard _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Periodicity and cutting planes
by Mark Krumholz April 15, 2015

April 15, 2015

Hi YT Users, I’m trying to figure out if there’s a way to get cutting planes to interact with periodicity correctly. I have an ORION data set, and I want to look at a cutting plane in a region that happens to be near a domain boundary. The calculation is periodic, and yt correctly flags it as such. However, when I take a cutting plane that goes off the edge of the computational domain, it doesn’t wrap back around on the other side as it should. Instead, the cells off the domain edge get filled with NaN’s. I have been unable to locate any information in the documentation about whether there is a way to have the cutting plane recognize the periodicity and wrap correctly. Is there a way to do this? Thanks. -- Mark Krumholz _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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install rockstar halo finding in yt(anaconda)
by shuo yuan April 14, 2015

April 14, 2015

Dear yt-users, I just install the yt using anaconda. Can you tell me how to install rockstar halo finding into the yt? The doc http://yt-project.org/doc/analyzing/analysis_modules/halo_finders.html shows a good way the enable rockstar but is not fit for yt built by anaconda. Thanks! Shuo -- ---------------------------------------------------------- *Shuo Yuan* (*袁硕*) Department of Astronomy, Peking University E-mail: yuanshuoastro(a)gmail.com <+yuanshuoastro(a)gmail.com> _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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