Mailman 3 August 2014 - yt-dev

Issue #879: yt-3.0 docs website (yt_analysis/yt)
by Kenza Arraki 15 Aug '14

15 Aug '14

New issue 879: yt-3.0 docs website https://bitbucket.org/yt_analysis/yt/issue/879/yt-30-docs-website Kenza Arraki: When I visit [3.0 docs](http://yt-project.org/docs/3.0/) with too small a browser window the top options bar collapses into a smaller drop down website. If I click on this button, the menu appears and quickly disappears again before I am able to see or select an option. I have found this using Chrome and Firefox on OSX and Firefox on Ubuntu.

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Next iteration of rockstar development
by Matthew Turk 14 Aug '14

14 Aug '14

Hi all, I've added a card for the next steps for Rockstar here: https://trello.com/c/lqmt2hEz/40-use-yt-fof-rockstar-groups This essentially reduces yt's interaction with Rockstar to just calling "groupies" which does not require any communication on Rockstar's part. The process is now to use yt to identify FOF nodes and then filter them with Rockstar. (In my head, for some reason, I keep thinking of this as "rocketeer.") In that card is a pastebin that includes a working script for doing this with the current state of the yt repo, although I think there's an off-by-one error, and the units might be a bit wrong. Anyway, one nice thing about this is that we can feed in different or additional "filters" instead of Rockstar into this -- for instance, Pfister's isoden method. It also means we can control the domain decomp a bit more in-depth. -Matt

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problem with disk data container and related fields in yt-3.0
by Britton Smith 13 Aug '14

13 Aug '14

Hi all, Some issues seem to have cropped up in the disk data container in yt-3.0. I made a disk object in a periodic simulation in the following way: http://paste.yt-project.org/show/5021/ I then made a project of the "cylindrical_z" field, which yielded the following: http://i.imgur.com/0XSv5Zs.png For reference, the domain is ~45 Mpc in length on a side, so the sphere should be just the object at the bottom, extending a little less than halfway up. I don't know what that top part is about. My guess is that it's an issue with periodicity. Secondly, I made a similar projection of the "cylindrical_r" field, which gave this: http://i.imgur.com/h8SEJp8.png As you can see, it is not symmetric as one would expect. For reference, this is what I get from yt-2.x: http://i.imgur.com/O1xT9MI.png This is what I would expect. Does anyone have any insight on this? Britton

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will yt 2.6 analysis scripts works for yt 3.0 ?
by Reju Sam John 10 Aug '14

10 Aug '14

Dear All, My yt version is --- Version = 2.6.1 Changeset = c7bae05dd4ef --- If I update it to 3.0 with the command: yt update --all , will my old analysis scripts(written for 2.6 ) works? Thank you. -- Reju Sam John

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ARTIO time mapping
by Douglas Harvey Rudd 10 Aug '14

10 Aug '14

Hi all, I've been asked by someone who is using yt to analyze ARTIO data (yes! they exist!). They're interested in the distribution of star particle creation times (BIRTH_TIME in the internal code nomenclature). There is code to do a conversion to age that seems to have been borrowed from the ART frontend, but it's incomplete and incorrect for z > 0, so I'm porting over the c code that we use internally in ART(IO). That's all fine and good, but there's still a residual issue with code_units that I don't quite understand and hoping someone can quickly point me in the right direction. ARTIO defines an attribute time_unit, which is stored in the ARTIO fileset and is the correct code_time -> seconds unit conversion **at the redshift of the snapshot**. The mapping from code time to physical time is non-linear, however, so a code unit defined at a different redshift cannot be simply converted to physical time in cgs using this number (which looks like what happens now). Is there an easy way to override code_unit -> cgs (and other) unit mappings when it's a non-linear function? I can obviously create pre-converted versions of these fields (creation_time and particle_age both defined in seconds), but that doesn't prevent someone from loading ("STAR","BIRTH_TIME") and asking yt to convert it from code units to cgs, and getting the wrong answer: i.e. yt.load("artio dataset").all_data()[("STAR","BIRTH_TIME")].in_cgs() gives nonsensical values. Douglas Rudd Scientific Computing Consultant Research Computing Center drudd(a)uchicago.edu

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coLaboratory Chrome App
by Sam Skillman 08 Aug '14

08 Aug '14

Hi all, Some of you might be interested in a few news bits today: http://googleresearch.blogspot.com/2014/08/doing-data-science-with-colabora… and http://www.symmetrymagazine.org/article/august-2014/open-access-to-the-univ… What's even cooler than the fact that you can now load up an ipython notebook that runs sandboxed in your Chrome browser is that because Matt is the one compiling all these python tools into the Chrome app, we went ahead and included a very recent version of yt 3.0! Then we went a bit further, and baked in thingking ( https://bitbucket.org/zeropy/thingking) and some DarkSky tools, so when you put it all together now anyone and everyone can access data from the DarkSky simulations. If you install the chrome app ( https://chrome.google.com/webstore/detail/colaboratory-notebook/pianggobfjc…) then check out some examples: Dark Sky Examples <https://docs.google.com/folderview?id=0B7ET8zdoN208T1ZRNnk4cUJ0YnM&usp=driv…> We (Matt, Mike Warren, and I) would love to hear feedback if you try things out. I expect there will some growing pains with the interface, but we're all pretty excited about finally getting this out. Congrats to Matt and the Chrome/Jupyter teams! Cheers, Sam

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Issue #878: PlotWindow should fail more gracefully when plotting particle fields (yt_analysis/yt)
by Nathan Goldbaum 07 Aug '14

07 Aug '14

New issue 878: PlotWindow should fail more gracefully when plotting particle fields https://bitbucket.org/yt_analysis/yt/issue/878/plotwindow-should-fail-more-… Nathan Goldbaum: Right now plotting a particle field leads to a crash in the frontend's I/O subsystem when it tries to treat the particle field as if it were a mesh field. We should check whether we're actually plotting a mesh field and then crash gracefully with a nice error message if we detect a particle field. Responsible: ngoldbaum

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Fwd: [yt-svn] commit/yt: 2 new changesets
by Britton Smith 06 Aug '14

06 Aug '14

Oops, I meant to push those changes to my fork. Sorry about that! They are pretty benign changes at least. Britton ---------- Forwarded message ---------- From: <commits-noreply(a)bitbucket.org> Date: Wed, Aug 6, 2014 at 11:14 PM Subject: [yt-svn] commit/yt: 2 new changesets To: yt-svn(a)lists.spacepope.org 2 new commits in yt: https://bitbucket.org/yt_analysis/yt/commits/c8fde451d9c9/ Changeset: c8fde451d9c9 Branch: yt User: brittonsmith Date: 2014-08-07 00:12:46 Summary: Remove obsolete delete. Affected #: 1 file diff -r 6b790e3507a791aeb1a0a801e8e8d7de7e1c56e8 -r c8fde451d9c974cee2808ccf403e07dd26235d9e yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx --- a/yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx +++ b/yt/analysis_modules/halo_finding/rockstar/rockstar_interface.pyx @@ -233,7 +233,6 @@ fi += 1 pi += npart num_p[0] = local_parts - del ds._instantiated_hierarchy del ds cdef class RockstarInterface: https://bitbucket.org/yt_analysis/yt/commits/b5fbf5e597b0/ Changeset: b5fbf5e597b0 Branch: yt User: brittonsmith Date: 2014-08-07 00:13:56 Summary: Fixing bug in halo profiling callback. Affected #: 1 file diff -r c8fde451d9c974cee2808ccf403e07dd26235d9e -r b5fbf5e597b0ca207db496e1e5d131ffc1239338 yt/analysis_modules/halo_analysis/halo_callbacks.py --- a/yt/analysis_modules/halo_analysis/halo_callbacks.py +++ b/yt/analysis_modules/halo_analysis/halo_callbacks.py @@ -225,13 +225,13 @@ # accumulate, if necessary if accumulation: - used = my_profile.used + used = my_profile.used for field in my_profile.field_data: if weight_field is None: my_profile.field_data[field][used] = \ np.cumsum(my_profile.field_data[field][used]) else: - my_weight = my_profile.weight[:, 0] + my_weight = my_profile.weight my_profile.field_data[field][used] = \ np.cumsum(my_profile.field_data[field][used] * my_weight[used]) / \ np.cumsum(my_weight[used]) Repository URL: https://bitbucket.org/yt_analysis/yt/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email. _______________________________________________ yt-svn mailing list yt-svn(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-svn-spacepope.org

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Move sanitization routines into coordinate handlers?
by Matthew Turk 05 Aug '14

05 Aug '14

Hi all, especially Nathan, What do you think about moving the functions: get_sanitized_center get_sanitized_width get_window_parameters get_oblique_window_parameters into the coordinate handler (ds.coordinates)? This would make it easier to implement them more carefully and clearly for the different coordinate systems, like spherical, cylindrical, etc. -Matt

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Anaconda packages have been updated
by Nathan Goldbaum 05 Aug '14

05 Aug '14

The yt conda packages that Continuum Analytics builds for us as part of the anaconda python distribution have just been updated for yt 3.0. Most importantly, there is now a 64 bit Windows build along with the OSX and Linux builds! Right now there are only 64 bit packages, but we should have 32 bit packages soon after fixing an issue that causes test failures on 32 bit builds of yt. If you use conda, you should be able to update yt with "conda update yt". Thanks to Aaron Meurer for helping us out with this yesterday and today.

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