Mailman 3 December 2018 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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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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3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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Recalculating derived fields in Gadget Binary Dataset
by martincarusso＠gmail.com 31 Dec '18

31 Dec '18

Hi all! Is there any possible way to modify a (non-derived) field in a Gadget Binary Dataset and update the computation of the derived (in particular, deposited) fields to reflect this change? For example, I would like to substract a fixed velocity from all Gas particles (as to account for the Sun's velocity) and recalculate the smoothed velocity fields accordingly. As a reference, modifying the in-disk fields the following way works, but has no effect on the derived_fields: ds = yt.load('path/to/dataset', unit_base = unit_base) for i in range(num_particles): ds.r['Gas', 'Velocities'][i] -= ds.arr([100,100,100], 'code_velocity') #substracting some fixed array Any help would be very much appreciated. Thanks is advance (and happy holidays!) Martin

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REFINEMENT LEVEL FOR PROFILE DATA
by Vadlamani Samhitha 21 Dec '18

21 Dec '18

Is there a way I could know what refinement level yt is accessing my data? For e.g., I plot 1D profiles of density > ts=yt.load([ > "/lunarc/nobackup/users/samvad/FINAL-50-0.5/output/output_00029/info_00029.txt" > , > "/lunarc/nobackup/users/samvad/FINAL-50-0.5/output/output_00037/info_00037.txt" > , > "/lunarc/nobackup/users/samvad/FINAL-50-0.5/output/output_00042/info_00042.txt" > ]) > for ds in ts: ds.define_unit("H", (1.674*10**(-24), "g")) ad=ds.all_data() dens=ad.cut_region(["obj[('gas','density')].in_units('H/cm**3') > 0" ]) > profiles.append(yt.create_profile(ad, ("gas","density"), [("gas", > "cell_mass")], weight_field=None, fractional=True)) My data has highest refinement level of 15 from simulations. However, I'm not sure if this is the same level at which the profiles are being plotted

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Announcing widgyts, the yt widgets package
by Madicken Munk 20 Dec '18

20 Dec '18

Hi all, We’re proud to announce the first release of the yt-widgets package, widgyts, which is a growing collection of Jupyter widgets for use in yt. The package is on PyPI so you can install it with: pip install widgyts This package was designed so that you can interactively explore your data with the goal of making data exploration more accessible to yt users. You can pan, zoom, and update view parameters (like the colormap or the colormap bounds) quickly and learn where interesting features of your data are. We’ve uploaded a couple of demonstration notebooks to give you a feel of the widget, one with IsolatedGalaxy and the others with slices and projections (made using yt) of Britton’s Pop II Prime dataset (thanks for making this dataset available Britton!). You can experiment and play around with the notebooks on the yt hub <https://girder.hub.yt/#raft/5c1ab9f5323d12000134e095>. Alternatively, you can watch <https://www.youtube.com/watch?v=5dl_m_6T2bU> or look at the slides <https://munkm.github.io/2018-07-13-scipy/> from Madicken’s talk at SciPy 2018 about the initial stages of this project. At present, widgyts consists of a few components. The foundational widget is that of a variable-mesh image viewer, using Rust compiled to WebAssembly. The WebAssembly code is used to do the most performant-limiting calculations in the widget, resulting in much higher framerates than pure javascript rendering. Because WebAssembly was designed to interface with javascript, widget features can be built out using standard Python/javascript aspects of Jupyter widgets. You can read a little bit more about WebAssembly here <https://developer.mozilla.org/en-US/docs/WebAssembly> and here <https://medium.com/javascript-scene/what-is-webassembly-the-dawn-of-a-new-e…> if you’d like to learn more about it. Widgyts also currently has a widget that quickly converts data arrays to rgba colormapped arrays, and a tool to set up a standard set of widget controls. This should work in all major browsers in the Jupyter notebook; at present Jupyterlab does not have support for easy distribution of wasm binaries. When able, we will build out support for this widget with Jupyterlab. We’d like to thank the hard work done on other projects to make the development of widgyts possible. In particular, we’d like to thank the Jupyter team and the developers of ipywidgets. We’d also like to thank the rust core team and the wasm-pack developers for their awesome platforms. Thanks for reading! If you’d like to give us any feedback on the widget, please don’t hesitate to reach out via e-mail, slack, or in either the rust <https://github.com/data-exp-lab/rust-yt-tools> or the widgyts <https://github.com/data-exp-lab/widgyts> repository. Madicken Munk, Matthew Turk, and Nathanael Claussen

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Need help reading in the multiple particle hdf5 data from the FLASH code.
by saurabhisreachable＠gmail.com 15 Dec '18

15 Dec '18

Hi, I referred to the relevant part of the documentation about FLASH particle data on, http://yt-project.org/doc/analyzing/particle_trajectories.html and managed to post process a series of data files that have just 1 single particle in it. When I used multiple particles in the simulation, at the step where we do the following, ds = yt.load(my_fns[0]) dd = ds.all_data() indices = dd["particle_index"].astype("int") I got the following error: ~/.local/lib/python3.6/site-packages/yt/frontends/flash/io.py in <listcomp>(.0) 171 self._particle_fields = determine_particle_fields(self._handle) 172 self._position_fields = [self._particle_fields["particle_pos%s" % ax] --> 173 for ax in 'xyz'] 174 self._chunksize = 32**3 175 KeyError: 'particle_posx' I am new to YT in general and facing a difficulty in understanding what's the problem. As per the documentation, the syntax should work for multiple particles. Do you think that it could be FLASH issue? What are the ways you would go about debugging it? Thanks.

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[Rockstar] "cannot import name rockstar interface"
by Andrew Cook 15 Dec '18

15 Dec '18

Hello, I'm trying to run Rockstar Halo Finder using yt 3.5.0 and Enzo 2.5 but I keep getting an error whenever I run it saying it can't import name rockstar interface? Full transcript of the error is below: Traceback (most recent call last): File "rockstar.py", line 4, in <module> from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/analysis_modules/halo_finding/rockstar/api.py", line 16, in <module> from .rockstar import RockstarHaloFinder File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 26, in <module> from . import rockstar_interface ImportError: cannot import name rockstar_interface Many thanks Andy

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Metallicity plots for enzo
by up765045＠myport.ac.uk 10 Dec '18

10 Dec '18

Hi all, I have what is probably quite a basic problem to solve, however I am not very experienced using yt and have only managed basic density and temperature plots. I am having issues plotting metallicity, using this script: from yt import * import sys for i in range(1,len(sys.argv)): ds = load(sys.argv[i]) ds.print_stats() #val, loc = ds.find_max("density") #plot = SlicePlot(ds, 2, ["density","Temperature"] plot = SlicePlot(ds, 2, ("metallicity_fraction"), center= [0.4913024902343750, 0.5008239746093750, 0.4982604980468750], width= (10, 'kpc')) #plot = SlicePlot(ds, 'z', ('all', metallicity),center=[0.4913024902343750, 0.5008239746093750, 0.4982604980468750],width = (10,'kpc')) #plot.set_zlim('all', 1e1, 1e5) plot.annotate_timestamp(corner='upper_left', redshift=True, draw_inset_box=True) #plot.set_cmap(field="Temperature", cmap='hot') plot.save() This script works fine when for plotting density and temperature but I get this error when using the un-commented line above: "_MPL.error: data is of incorrect type (wanted 1D float)" I've been trying to get this to work for a while now so any help would be greatly appreciated. Thanks, Chris Jessop

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