yt-users October 2017

yt-users@python.org

17 participants
23 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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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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profile plots combining different datasets
by ｔyuta 03 Nov '17

03 Nov '17

Dear yt-users, Hi, I want to ask you about profile plot. I'm analyzing Enzo data, and I'm trying to plot metallicity-cellmass of different 12 datasets into one curve. I can plot 12 curves on one image, but that's not what I want. Does anyone know some good way, or links to documentation? I've attached the 12-curve plot. I want to sum up all the curves to get one curve. Thanks, Y.T.[image: 埋め込み画像 2]

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Integration of a field along line of sight
by tazkera haque 31 Oct '17

31 Oct '17

Dear YT people, I need to do integration of density field along line of sight. I know the ProjectionPlot function plots the integration of a field along line of sight. yt.ProjectionPlot(ds, 'z', 'density, center= 'm') However, I was wondering if it is possible to get the projection as an array (or new field) , so that I can make a ProfilePlot of the integrated field along line of sight and another field ('Mass') In other words, I want to do the following: sp = ds.sphere("max", (200, "kpc")) proj = yt.ProfilePlot(sp, 'Integrated_Density_along_Line_Of_Sight', 'Mass) Thanks Tazkera

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Annotation on profileplots
by ｔyuta 30 Oct '17

30 Oct '17

Dear yt-users, Hi, I want to annotate some lines on 1D profile plots, like on projection plots or slice plots. I looked through the yt documentation, and I found: Callbacks can be applied to plots created with SlicePlot <http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html#y…> , ProjectionPlot <http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html#y…> , OffAxisSlicePlot <http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html#y…>, or OffAxisProjectionPlot <http://yt-project.org/doc/reference/api/yt.visualization.plot_window.html#y…> by calling one of the annotate_ methods that hang off of the plot object. on plot modification page, which means annotate_line method is not effective for profile plots (I actually tried this on profile plots, and it did not work). Is there any good way to annotate lines on 1D profile plots? Also, I want to change the fontsize of numbers and labels on the axes of profileplots. How can I do this? For example, I want to annotate vertical line on density=1e-25, and change the fontsize of "density", "10**-28", ..., "10**-21". Thanks, Y.T. [image: 埋め込み画像 1]

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Plot Callbacks for OffAxis Plots
by Joseph Tomlinson 20 Oct '17

20 Oct '17

Hey yt-users, I am trying to use OffAxis Slice and Projection plots using planes defined by two light rays in Enzo data. I have recently tried added callbacks for visualization of the clumps of gas and star particles but whenever I use annotate_clumps and annotate_particles with OffAxis plots I always get an error saying that they do not have the method. I assume that this is a consequence of how the OffAxis plots are made and there is no easy way around this but I wanted to check to make sure before I give up on OffAxis plots. If you don't understand what I mean here is a short bit of pseudo code to explain. L=[1,1,0] cut = SlicePlot(ds, L, 'Density') cut.annotate_particles((300,'kpc'), ptype=2) AttributeError: 'OffAxisSlicePlot' object has no attribute 'annotate_particles' Thanks, Joe Tomlinson

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Saving and loading Arbitrary grid data
by Li,Qi 19 Oct '17

19 Oct '17

Dear user group, I am trying to smooth particle data output from GIZMO onto an arbitrary grid, then save the object as data set and reload in order to do volume rendering. However I can not handle the reloaded data set. To clarify, I smooth yt sample data — FIRE_M12i_ref11 onto a 64**3 grid, the code is like this: 1 import yt 2 3 ytname='FIRE_M12i_ref11/snapshot_600.hdf5' 4 ds=yt.load(ytname) 5 6 # define the region 7 left = ds.domain_left_edge 8 right = ds.domain_right_edge 9 10 #now create an abitrary grid and save 11 arb = ds.arbitrary_grid(left, right,dims=[64, 64, 64]) 12 13 fn = arb.save_as_dataset(fields=[('PartType0','density')]) 14 15 arb_ds = yt.load('snapshot_600_arbitrary_grid.h5') 16 print arb_ds.field_list And it returns an error: Traceback (most recent call last): File "arbgrid_clean.py", line 16, in <module> print arb_ds.field_list ... ... File "/Users/heavyfat/anaconda/lib/python2.7/site-packages/yt/frontends/ytdata/io.py", line 244, in _initialize_index pos[:,0] = _get_position_array(ptype, f, "x") ValueError: could not broadcast input array from shape (64,64,64) into shape (262144) So, how I can save/load a usable arbitrary grid dataset? Thanks and looking forward to your suggestions. Best regards, Qi

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Yt training workshops
by Nick Gnedin 18 Oct '17

18 Oct '17

Folk, Do you plan any more training workshops/hackatons in the future? I work with a couple of students who would benefit from such, self-learning from the docs is kind of slow. Thanks, Nick Gnedin

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About ProfilePlot
by ｔyuta 18 Oct '17

18 Oct '17

Dear yt-users, Hi, I have a question on ProfilePlot. I want to make profile plot of dark matter density, taking gas density as a bin field, weighted by dark matter mass in the cell.I could make the plot, but the plot looks strange (it looks like chopped in small pieces). Also, I tried other plot changing n_bins like 64,32,16,8,... but they still be "chopped", or sometimes there were no line at all. For comparison, I made a plot weighted by cell_mass (which I don't want), and this look OK. To my understanding, if and only if there is at least 1 cell which fall into each bin, there should be some nonzero value no matter what weight I use, so the range of density which has nonzero dark matter density doesn't depend on the choice of weight field. It seems there is a discrepancy between these two plots. Could you tell me what's wrong with me? I tried on yt example dataset, IsolatedGalaxy/galaxy0030/galaxy0030. I'm working with yt-3.4.0. this is my code: import yt from yt.data_objects.particle_filters import add_particle_filter def stars(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 2 return filter def DMparticles(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 1 return filter add_particle_filter("stars", function=stars, filtered_type='io', requires=["particle_type"]) add_particle_filter("DMparticles", function=DMparticles, filtered_type='io', requires=["particle_type"]) def only_DM(field, data): return data['deposit','DMparticles_density'] def DM_in_cell_mass(field, data): return (data['only_DM_Density']*data['cell_volume']) ds_all=yt.load("~/IsolatedGalaxy/galaxy0030/galaxy0030") ds_all.add_particle_filter('stars') ds_all.add_particle_filter('DMparticles') ds_all.add_field(("gas", "only_DM_Density"), units="g/cm**3", function=only_DM) ds_all.add_field(("gas", "DM_cell_mass"), units="g", function=DM_in_cell_mass) sp = ds_all.sphere([0.5, 0.5, 0.5], (10, "kpc")) lineplot_gas_DM_density_128 = yt.ProfilePlot(sp, "density", [ "only_DM_Density"], weight_field="DM_cell_mass", n_bins=128) lineplot_gas_DM_density_gasweighted_128 = yt.ProfilePlot(sp, "density", [ "only_DM_Density"], weight_field="cell_mass", n_bins=128) lineplot_gas_DM_density_gasweighted_128.save("128_gasweighted") lineplot_gas_DM_density_128.save("128_DMweighted") Sincerely, Y.T.

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yt-users October 2017