yt-users April 2017

yt-users@python.org

17 participants
17 discussions

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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Multiple Projection Multi-panel Appearance
by Ashley Jarvis 27 Apr '17

27 Apr '17

Hi all, I have followed one of the given examples (http://yt-project.org/doc/cookbook/complex_plots.html#mutiple-slice-multipa… <http://yt-project.org/doc/cookbook/complex_plots.html#mutiple-slice-multipa…>) to produce a multi-panel plot from an Enzo data output using AxesGrid in matplotlib. However, the appearance of this plot doesn’t match that of single plots made using yt.ProjectionPlot by itself. I would like the multi-panel plot (https://ibin.co/3KWlDftVLmgR.png <https://ibin.co/3KWlDftVLmgR.png>) to have a similar appearance to this standard projection plot (https://ibin.co/3KWlr0wRQrHT.png <https://ibin.co/3KWlr0wRQrHT.png>). Is there an efficient way of invoking the style settings used by yt in matplotlib, or is it just a matter of individually changing the settings for the font style, font size, axis and tick linewidth, plot resolution, etc. in the plotting script? If the latter, are the default values for these parameters in yt listed somewhere, such that I can change the parameters to these values before plotting? Many thanks, Ashley

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MBH particle coords
by Marco Surace 27 Apr '17

27 Apr '17

Hi all, I'm running an enzo simulation in which I've inserted a Massive Black Hole (MBH) particle. I would like to know the location of it at later times after insertion. Does anyone know how I can use yt to return this information? Best wishes, Marco

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HDF5 TypeError when writing LightRay
by Joseph Tomlinson 25 Apr '17

25 Apr '17

Hi all, I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error. TypeError: Object dtype dtype('O') has no native HDF5 equivalent This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation. I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error. AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str) When using python 2.7 the error is the same but with 'unicode' instead of 'str'. Any help would be greatly appreciated. Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University

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Re: [yt-users] SSLError when trying to update
by Slavin, Jonathan 21 Apr '17

21 Apr '17

Hi Nathan, I just tried again about an hour ago and was able to successfully update. So whatever the problem was, it seems to be fixed now. On a different note, when I do 'conda update anaconda' it asks me if I want to downgrade a whole slew of packages due to dependency conflicts including astropy, matplotlib, numpy, and scipy among others. Any idea what's up with that? I'll ask on the anaconda user's list. Regards, Jon On Fri, Apr 21, 2017 at 2:05 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Fri, 21 Apr 2017 11:52:56 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] SSLError when trying to update > Message-ID: > <CAJXewO=etF-kWGE_VS3-E8s6Dt17h6acjTXFcawF- > gamdC3SHQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hey Jonathan, > > I asked about this in the conda-forge gitter channel and got a response > after a few days: > > No worries, @ngoldbaum. So we package our certificates in a separate > package called ca-certificates. They are just extracted from the certifi > Python package and relocated to allow things like openssl and curl to find > them. This differs from Continuum (or at least last time I checked), which > has them bundled with openssl. The first thing I'd have him check is that > package installed and can Python find them, python -c "import ssl; > print(ssl.get_default_verify_paths())". If the answer is no, then that is > likely a problem. If the answer is yes, then maybe it has something to do > with how this redirection is being handled. > > So you should check to see if a package named ca-certificates is installed > in your conda environment. If it is, you should also check the output of > ssl.get_default_verify_paths(). If it turns out that your python can't > find > the CA certificates store, that's your issue. If it turns out that python > is locating the CA certificates, then this might be due to a bug in how > conda-forge or continuum have decided to handle this issue. > > Unfortunately kind of a headache. I hope you're able to figure this out :) > > -Nathan > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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SSLError when trying to update
by Slavin, Jonathan 21 Apr '17

21 Apr '17

Hi, I have a conda environment set up to use the development branch of yt. When I just now went to update it I got: > conda update -c http://use.yt/with_conda/ -c conda-forge yt Fetching package metadata ............. CondaHTTPError: HTTP None None for url <None> An HTTP error occurred when trying to retrieve this URL. SSLError(SSLError(SSLError(1, u'[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)'),),) I don't get the "None None" bit, but it looks like a problem with the SSL certificate. Or maybe it's something else. Any help would be appreciated. Thanks, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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Real-time histogram presentation based on interactive volume rendered camera properties
by E.M. Dragowsky 20 Apr '17

20 Apr '17

Greetings -- Please forgive the subject line -- it makes sense to me; hopefully after reading the note it will make sense to me+1 or more.... Just last week I became aware of yt, and so this is a question about capabilities: I'm working on a project to aid a researcher with visualizing derived data products (a set of ~5000 histograms) along with volume rendering of simulations performed with Flash (flash.uchicago.edu). This would involve manipulation of the rendered volume data (e.g. temp, density data fields) and coordinated presentation in an inset or separate window from the set of histograms. The active camera view angles from the rendered volume display would be used to select from the histogram set (in this case indexed by 51 polar angle bins and 101 azimuthal angle bins). The key is for the histogram selection to take place as the rendered display is being updated through user interaction -- so as the view is rotated, the histogram updates without having to stop the user actions. Right now, these histograms are created at the end of the simulation. One could imagine a more general case in which the histogram were derived from the volumetric data in real time. Is this a task suited to the current state of yt development? Best regards, ~ Em -- ---------------------------------- E.M. Dragowsky, Ph.D. Research Computing -- UTech Case Western Reserve University (216) 368-0082

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Creating a projection for a derived particle field
by José Mauricio Utreras 19 Apr '17

19 Apr '17

Hi yt users! Does anybody know how to create a projection for particles using another field rather than "particle_mass"? I was using this: proj = ds.proj('density', 2,data_source=disk_dd,method='sum') frb = proj.to_frb(width, res, center=[0.5,0.5,0.5]) M_star=frb[('deposit', 'young_stars_mass')].in_units('Msun') But now I would like to do this with a particle mass field that depends on the characteristic timescales of the particles rather than the default field. Cheers! José Utreras

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Re: [yt-users] SSLError when trying to update
by Slavin, Jonathan 18 Apr '17

18 Apr '17

Yeah, just after I sent that message I tried other conda updates in my other main environment and got the same problem. So it seems to be a we hosting issue as you said. Jon On Tue, Apr 18, 2017 at 3:49 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Tue, 18 Apr 2017 14:49:19 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] SSLError when trying to update > Message-ID: > <CALO3=5Gb_MSy9CEzNihTcN6pp=+61RkHMqsBPHE8zdzcrP0Xzw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jon, > > I think this happens when there are web hosting issues with conda. I think > if you give it a little bit of time it should return to normal. > > -Matt > > On Tue, Apr 18, 2017 at 2:46 PM, Slavin, Jonathan <jslavin(a)cfa.harvard.edu > > > wrote: > > > Hi, > > > > I have a conda environment set up to use the development branch of yt. > > When I just now went to update it I got: > > > conda update -c http://use.yt/with_conda/ -c conda-forge yt > > Fetching package metadata ............. > > > > CondaHTTPError: HTTP None None > > for url <None> > > > > An HTTP error occurred when trying to retrieve this URL. > > SSLError(SSLError(SSLError(1, u'[SSL: CERTIFICATE_VERIFY_FAILED] > > certificate verify failed (_ssl.c:590)'),),) > > > > ?I don't get the "None None" bit, but it looks like a problem with the > SSL > > certificate. Or maybe it's something else. Any help would be > appreciated. > > > > Thanks, > > Jon? > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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yt-users April 2017