Mailman 3 June 2017 - 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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[YT-USERS] Incoherence when ploting a slice - from FLASH simulation
by Gabriel RIGON 15 Jul '17

15 Jul '17

Dear all, I recently start to work with yt to analyze my FLASH simulation. The output of those simulation is an hdf5 file. When I try to plot a slice of my simulation, some weird lines appear on it. Here is an example of the python script and the results it leads to. """ import yt ds = yt.load("lasslab_hdf5_plt_cnt_0000.hdf5") yt.SlicePlot(ds, 'z', "dens").show() [cid:972219b9-edbb-4265-81cf-9a07e61cf360] """ Actually they also appear went plotting the results of a frb of a slice (even when I try to plot the x or y coordinate in 2d). Do you have any idea of the reason for such lines, or a solution for my problem? Best regards, Gabriel Rigon

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Streamlines in FLASH
by Benny Tsang 01 Jul '17

01 Jul '17

Hi yt friends, I'm trying to produce 3D streamlines using the AMR data from FLASH following the yt-project tutorial http://yt-project.org/doc/visualizing/streamlines.html. However, the execution was very slow (in particular, at the 'Streamlines' call). The code didn't complete one single streamline after an hour. Here's the excerpt of my code: ————— c = ds.domain_center streamlines = Streamlines(ds, c, 'velx', 'vely', 'velz', length=1.0*pc, get_magnitude=False) streamlines.integrate_through_volume() fig=plt.figure() ax = Axes3D(fig) for stream in streamlines.streamlines: stream = stream[np.all(stream != 0.0, axis=1)] ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1) plt.savefig('streamlines.png') ————— I have two thoughts: 1. My FLASH file is quite large (~10GB). It may just be slow because of the large AMR grid size. Are there any ways to read only the velocities off the grid or only a subsection of the grid? 2. FLASH's octree data structure may be incompatible with the AMRKDTree construction (first step in streamlines creation). In the doc string of AMRKDTree, it says "Not applicable to particle or octree-based datasets.". If it's the case, I may have to find another way out. Thank you very much for your time! Have a great weekend! Best, Benny

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Setting limits on OffAxisProjection plots manually
by Setton, David Jonathan - (davidsetton) 23 Jun '17

23 Jun '17

Hi all, I apologize for bombarding the mailing list this past bit, but hopefully this should be the last question that I have. I'm trying to set aysmmetric units on a projection plot (i.e. xlim=[-10,40] and ylim=[-35,35] in kpc. However, there is not a set_xlim or set_ylim option for off axis projection plots. The idea that I had was to use the pan function. Since my box is 100 kpc in each direction, in code units, I attempted to set the width of my box: #read in my data with the proper north and normal vectors to get the orientation right proj = OffAxisProjectionPlot(ds,normal,'density',center=gal_center,north_vector=north) #this should set the box to be 50 kpc in the x direction and 70 kpc in the y direction proj.set_width((.5,.7)) #pan the box 15 kpc to the right proj.pan((0.15,0)) proj.show() However, when I show the plot, the pan() function has not shifted it at all. Is there a way to manually set the limits to what I need to, or to properly use the pan function? Thanks again for all the help, you guys have been great about getting back to me quickly. Best, David

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Feedback about change to the RAMSES frontend
by Nathan Goldbaum 22 Jun '17

22 Jun '17

Hi all, I'm mailing both yt-users and yt-dev since I don't think there are many ramses users on yt-dev. I'd like some feedback from users of the RAMSES frontend about a pull request I just proposed: https://github.com/yt-project/yt/pull/1463 See the pull request for details, but briefly, I've made it possible to access the 'particle_age' field values for cosmology simulations as they are stored in the ramses outputs. Currently we apply an in-place conversion from conformal time to proper time when we read these data in, and it turns out this conversion makes it difficult to write a particle filter for DM particles that will work for all RAMSES data. The trouble is that if we change the meaning of the particle_age field, this may break the scripts of people who are currently using yt with RAMSES data. Then again, we already made such a change when we added the in-place conversion a year ago. If you have thoughts and opinions about this I'd very much appreciate to hear your comments on github. -Nathan

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unit conversions
by Stephanie Tonnesen 20 Jun '17

20 Jun '17

Hi yt-users! I have what I think should be a relatively simple question. I am trying to make a 3D image of a region of a cosmological simulation, and plot points in the image. I define my region with box(left_edge,right_edge) where left_edge and right_edge are in code units. However, the points that I read in from an earlier file are in cgs units. Since the file was written using yt output, I would like to just let yt do the conversions, but nothing has units attached. I want the 3d image to get everything into the same units. I feel like there are a few ways I could fix this problem--1) tell yt that my points are in cgs units, 2) force the create_scene to be in cgs units, 3) get yt to tell me the conversion factor from code units to cgs units. Unfortunately, I don't know how to do any of these things! Can someone give me some advice on what to do here? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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Cython discrepancy in yt install from source
by Carla Bernhardt 20 Jun '17

20 Jun '17

Dear yt-users, I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython? Here is a piece of the failure report I got: Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt ******************************************** FAILURE REPORT: ******************************************** File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment. ******************************************** ******************************************** Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg

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Overplotting lines and points onto slices and projections
by Setton, David Jonathan - (davidsetton) 20 Jun '17

20 Jun '17

Hi all, I'm a relatively new user to yt, and I've been trying to figure out the best way to overplot some curves onto images generated by OffAxisProjectionPlot and OffAxisSlicePlot routines. My searching through the cookbooks has pointed me towards this page, which seems to indicate that accessing the matplotlib axes and figures are the right way to go about this. Following the example, I've created a density slice plot of my dataset and loaded in my plot in the following way: dens_plot = slice.plots['density'] figure = dens_plot.figure axes = dens_plot.axes colorbar_axes = dens_plot.cax >From here, my next step would be to plot the line I wish to plot using axes.plot(). However, running slice.show() after doing this just shows the original plot and does not contain the plot I've attempted to overplot. I'm sure my misunderstanding comes from not being familiar with how matplotlib works under the hood, but does anybody have any suggestions for the best way to go about doing this? I would also like to plot individual points on a projection plot in the xy-plane at some point, which I would assume has a very similar method. Best, David

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