yt-users March 2020

yt-users@python.org

8 participants
14 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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Question about Projection Plot Color Coding
by sflarkin＠ucsc.edu 12 Jul '20

12 Jul '20

Hello All, I have a question about the Projection plot function in yt. I have a script that plots the smallest mass darkmatter particles of a simulation in all 3 of the 2-d coordinate projections, and overplots the halos found by a halo finder. This script works, and currently plots the colorbar based on the mass in a given 2-d bin as done in some of the basic yt plots included in the website. I am wondering if it is possible to have the color scheme of the particles be based on the squared mass or squared density of the particles in any given 2-d bin, so that the higher density regions are highlighted compared to the background lower density regions. I have included the plotting part of my script below, in case it is helpful. I hope everyone is having a great New Year! ds = yt.load(VELA_snaps[position[0]]) domain_width = float(ds.domain_width.in_units('Mpc/h')[0]) ad = ds.all_data() masses = yt.np.unique(ad[('darkmatter', 'particle_mass')]) #filter out the darkmatter0 particles def mass_filter(pfilter, data): filter = data[(pfilter.filtered_type, 'particle_mass')] == masses[0] return filter yt.add_particle_filter('darkmatter0', function=mass_filter, filtered_type='darkmatter', requires=['particle_mass']) ds.add_particle_filter('darkmatter0') scale = float(ds.scale_factor) fig = plt.figure() grid = AxesGrid(fig, (0.075,0.075,10,5), nrows_ncols = (3, 1), axes_pad = 1.0, label_mode = "L", share_all = False, cbar_location="right", cbar_mode="each", cbar_size="3%", cbar_pad="0%") zoom = 10 x0 = float(consistent.halo_data_sorted[index][0][17]) * scale / domain_width y0 = float(consistent.halo_data_sorted[index][0][18]) * scale / domain_width z0 = float(consistent.halo_data_sorted[index][0][19]) * scale / domain_width center = [x0, y0, z0] a = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_x'), ('darkmatter0', 'particle_position_y'),\ ('darkmatter0', 'particle_mass'), center=center) a.set_unit(('darkmatter0','particle_mass'), 'Msun') a.zoom(zoom) b = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_y'), ('darkmatter0', 'particle_position_z'),\ ('darkmatter0', 'particle_mass'), center=center) b.set_unit(('darkmatter0','particle_mass'), 'Msun') b.zoom(zoom) c = yt.ParticlePlot(ds, ('darkmatter0', 'particle_position_z'), ('darkmatter0', 'particle_position_x'),\ ('darkmatter0', 'particle_mass'), center=center) c.set_unit(('darkmatter0','particle_mass'), 'Msun') c.zoom(zoom) for halos in consistent.halo_data_sorted[index]: x = float(halos[17]) * scale / domain_width y = float(halos[18]) * scale / domain_width z = float(halos[19]) * scale / domain_width r = float(halos[11]) * scale / .7 center = [x, y, z] a.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) b.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) c.annotate_sphere(center, radius=(r, 'kpc'), circle_args={'color':'red'}) index = 0 for letter in [a,b,c]: plot = letter.plots[('darkmatter0', 'particle_mass')] plot.figure = fig plot.axes = grid[index].axes plot.cax = grid.cbar_axes[index] letter._setup_plots() index = index + 1 plt.savefig('{}/CatalogProjectionYT_VELA{}_Scale{}.png'.format(out_dir, VELA_number, str(scale)[2:5]), bbox_inches='tight') plt.close()

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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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create_profile of added field
by Salome Mtchedlidze 31 Mar '20

31 Mar '20

Hello everyone! I am trying to create radial profile of a halo. I can create e.g. temperature, density, B profile but if I add a new field then it does not give me the profile; The code is here: ----------------- ds = yt.load('Dataset') dd = ds.all_data() Halo_ds = "catalog.h5" File = h5py.File(Halo_ds, 'r') n = 0 radius = File["virial_radius"][n]/float(ds.domain_width.in_units("cm")[0]) #code units x = File["particle_position_x"][n]/float(ds.domain_width.in_units("cm")[0]) #Code units y = File["particle_position_y"][n]/float(ds.domain_width.in_units("cm")[0]) z = File["particle_position_z"][n]/float(ds.domain_width.in_units("cm")[0]) center = ds.arr([x, y, z], 'code_length') rvir = radius sph = ds.sphere(center, rvir) #Define new field B = dd['gas','magnetic_field_magnitude'] B_f = B - B.mean() def _B_fluc(field, dd): return (B_f) ds.add_field(("gas", "B_fluc"), function=_B_fluc, units="gauss") prof = yt.create_profile(sph, ["radius"], fields=["B_fluc"], n_bins=64) -------------------------------------- The error is: "Profile fields must have same shape: ('index', 'radius') has shape (6530,) and ('gas', 'B_flucc') has shape (9533574,)." So, I am wondering, is there a way to define this added field only inside the sphere?

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multipanel plot
by Guido granda muñoz 26 Mar '20

26 Mar '20

Hello, I'm trying to do a multipanel plot using yt and matplotlib. I had a problem regarding one of the axis x labels. The problem is described here: https://stackoverflow.com/questions/60859389/unmatching-axes-ticks-and-tick… Have you encountered something similar? Cheers, -- Guido

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Edinburgh yt workshop cancelled
by Britton Smith 23 Mar '20

23 Mar '20

Hi everyone, I think this message will not come as a surprise to anyone. In light of the COVID-19 pandemic, we have decided to cancel the yt user/developer workshop at the University of Edinburgh this summer. There is not yet a specific plan for a workshop at a later date, but we will make a go at having one in summer 2021. In the meantime, we will also look into the possibility of hosting an online yt workshop sometime this summer. Stay safe and stay connected. Britton

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Announcing the 2020 John Hunter Excellence in Plotting Contest
by Madicken Munk 17 Mar '20

17 Mar '20

Dear all, In memory of John Hunter, we are pleased to announce the John Hunter Excellence in Plotting Contest for 2020. This open competition aims to highlight the importance of data visualization to scientific progress and showcase the capabilities of open source software. Participants are invited to submit scientific plots to be judged by a panel. The winning entries will be announced and displayed at SciPy 2020 or announced in the John Hunter Excellence in Plotting Contest website and youtube channel. John Hunter’s family are graciously sponsoring cash prizes for the winners in the following amounts: - 1st prize: $1000 - 2nd prize: $750 - 3rd prize: $500 - Entries must be submitted by June 1st to the form at https://forms.gle/SrexmkDwiAmDc7ej7 - Winners will be announced at Scipy 2020 in Austin, TX or publicly on the John Hunter Excellence in Plotting Contest website and youtube channel - Participants do not need to attend the Scipy conference. - Entries may take the definition of “visualization” rather broadly. Entries may be, for example, a traditional printed plot, an interactive visualization for the web, a dashboard, or an animation. - Source code for the plot must be provided, in the form of Python code and/or a Jupyter notebook, along with a rendering of the plot in a widely used format. The rendering may be, for example, PDF for print, standalone HTML and Javascript for an interactive plot, or MPEG-4 for a video. If the original data can not be shared for reasons of size or licensing, "fake" data may be substituted, along with an image of the plot using real data. - Each entry must include a 300-500 word abstract describing the plot and its importance for a general scientific audience. - Entries will be judged on their clarity, innovation and aesthetics, but most importantly for their effectiveness in communicating a real-world problem. Entrants are encouraged to submit plots that were used during the course of research or work, rather than merely being hypothetical. - SciPy and the John Hunter Excellence in Plotting Contest organizers reserves the right to display any and all entries, whether prize-winning or not, at the conference, use in any materials or on its website, with attribution to the original author(s). - Past entries can be found at https://jhepc.github.io/ - Questions regarding the contest can be sent to jhepc.organizers(a)gmail.com John Hunter Excellence in Plotting Contest Co-Chairs Madicken Munk Nelle Varoquaux

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star formation rate/history
by Robin Eappen 17 Mar '20

17 Mar '20

Hi, Just a quick question on how to read out/plot star formation rate/histories from ramses outputs using yt. I assume the file to be read is the infoxxxx.txt but not sure which module is used to get the SFR/SFH. Thank you

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Placing the Colorbar on top of a yt.Sliceplot plot but labeling and ticks are still right aligned
by bayern50＠gmail.com 15 Mar '20

15 Mar '20

Hello yt-users I am trying to place the Colorbar of a yt.Sliceplot on the top of the image. I was looking at yt examples (under "a few complex plots") and the use of AxesGrid objects. Below is what I used, fig = plt.figure() grid = AxesGrid(fig, 111, nrows_ncols = (1, 1), axes_pad = 1.0, label_mode = "L", share_all = True, cbar_location="top", cbar_mode="single", cbar_size="10%", cbar_pad="2%", ) slc = yt.SlicePlot(ds,'z','density') plot = slc.plots['density'] plot.figure = fig plot.axes = grid[0].axes plot.cax = grid.cbar_axes[0] slc._setup_plots() plt.savefig('testing.png') The Colorbar is placed at the top but the labeling and ticks (of the Colorbar) are still aligned to the right of the Colorbar (as apposed to below the Colorbar). Is there something I'm missing or is there a simpler way to do this? Thank you in advance, Alberto

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yt triage meetings - spring 2020
by Madicken Munk 12 Mar '20

12 Mar '20

Hi yt community, I'd like to start scheduling yt triage meetings for the next few months. If you're interested in yt development, in discussing your recently submitted PR, or you've encountered a bug but you're not sure quite how to start fixing it, then we'd love for you to attend the triage meetings! To be more inclusive to developers a breadth of timezones, we'll alternate triage meeting times every other week. I'll choose one early morning time and afternoon time (based on US central time), which together should cover more developers' availability. If you're interested in attending at all, please respond to the polls I'm sending out! Meetings will be on Fridays. Report your general Friday availability, not just the availability for March 06. Morning meeting poll: http://whenisgood.net/7cbrt49 Afternoon meeting poll: http://whenisgood.net/t3hci7j There are two different polls -- if you know for sure you won't be attending one of the meetings (if you're in Europe and don't like or plan on attending a meeting in the evening, for example), please do not respond to the poll for that time at all and only respond to the one where you plan to attend. Make sure to update the time zone of the poll to be where you're located! These triage meetings will build off of the ones we had in the fall, but I'd like to expand their scope a bit. The first purpose of the meetings will be to do day-to-day yt maintenance work (triage issues, review PRs, respond to issues, etc.), then if we have time the rest of the time can be spent either coworking or talking about where to direct our developer resources over the coming week (which bugs we should focus on fixing, what features need improvement, etc.). We have the yt-4.0 release and yt 3.6 releases on the horizon, so supporting the project moving towards these releases will keep things going! I will pick times for yt triage meetings based on whoever has filled out the poll by Wednesday, March 11th. Our first triage meeting will be on Friday, March 13th (👻)! I'm looking forward to triaging, PRing, and community-ing with you all! -Madicken

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yt-users March 2020