Mailman 3 May 2013 - 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 volume render/AMRKDtree help
by Renyue Cen 25 Aug '13

25 Aug '13

Hi, I did some simple volume rendering with the following script: volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"], no_ghost=False, tree_type="domain", le=c-0.5*WW, re=c+0.5*WW) cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False, north_vector=L, steady_north=True) cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j)) I got rather strange results in that the pictures look symmetric, which I am pretty sure can not be true. I attach the obtained plot. Note that I am using KD tree and using 32 cores. Your help at your earliest convenience is appreciated. Best, Renyue

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Finding the max density from a checkpoint dump?
by Joseph Smidt 29 May '13

29 May '13

Hey everyone, My Enzo simulation has refined to enough levels that I need to make checkpoint dumps mid-timestep and do YT analysis from there. I can read in the checkpoint dump but when I go to find the max density I get this error: http://pastebin.com/2mNVxNyW Anybody have any idea what is going on and how to fix this? Also, since this dump is in the middle of the W-cycle, I believe the time on the finest grid is different then the root grid. How do I find the time on the finest grid for this checkpoint dump? Thanks. -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931

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Chombo data format - Example load?
by Haig, Christina 29 May '13

29 May '13

Can anyone give me an example script to load an hdf file that is written in the Chombo data format? I've been searching the site, but I can't find any comprehensible documentation about the relatively 'new' feature of being able to read Chombo HDF5. Many Thanks, Christina

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plotting just contours in a slice
by Chris Malone 25 May '13

25 May '13

Hi all, I would like to be able to take a slice through a 3D dataset and then plot just the contours of a single variable within that slice. I do not want to overlay the contours with an annotate_countours method. I know one way about this would be to use the FixedResolutionBuffer of some slice plot to reconstruct a mesh-grid and the data, which can then be used within matplotlib directly to create a contour plot. I was curious if there was a more clever method using yt plot objects? Chris

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PlotCollection questions
by Francia Riesco 22 May '13

22 May '13

Hello Everybody, first I want to thank for every time I got an answer when I write here, I really appreciate it. Now I am writing because I am using PlotCollection (As you can see my code) and I have some questions 1) the plot is coming in cm^3 and I want to change it to kpc^3 is there a way to change it? 2) I am attaching the plot can I change to dot or any different symbol and color? 3) why some plot come "empty"? and also I get this error message /Data has no positive values, and therefore can not be log-scaled./ ----- sphere = pf.h.sphere(c, (250., 'kpc')) # 250. levels = 8 #8 mi, ma = sphere.quantities["Extrema"]("Density")[0] contour_values, connected_sets = sphere.extract_connected_sets("Density", levels, mi, ma) for i in connected_sets: eb = connected_sets[i] print "level " + str(i) + " clmsp# " + str(len(eb)) for j in eb: obj = eb[j] com = obj.quantities["CenterOfMass"]() print com pc = PlotCollection(pf, com) pc.add_profile_object(obj, ["Density", "Temperature"],weight="CellMassMsun") # average T(rho) pc.add_profile_object(obj, ["Density", "CellVolume"], weight=None) # pc.add_profile_object(obj, ["Density", "CellMassMsun"], weight=None) # try: pc.save("sliceplot_300_"+str(i)+"_" +str(j)) except Exception, e: print e continue ----- Thank you in advance!!

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Matplotlib installation failure on OS X
by Paul La Plante 21 May '13

21 May '13

Hi, I am having trouble installing yt on my personal machine using the install script. I downloaded the script from the suggested website (http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh) and attempted to execute it with `bash install_script.sh.' I have tried a few different combinations of install options, but it always seems to fail while building matplotlib. My system is OS X 10.8.3, and gcc version 4.8.0 (installed from MacPorts). I have attached my yt_install.log. Thanks in advance for any help! Best regards, Paul

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Clumps, contours, n_contours
by david collins 21 May '13

21 May '13

Hi, all-- I'm seeing a glitch in the matplotlib countor function, as employed by annotate_clumps. As is, I'm seeing some clumps that are not plotted by the countour plotter unless I bump the number of contours-- I get all the plots if I change the contour line to: self.rv = plot._axes.contour(buff, len(self.clumps)+5, extent=extent,**self.plot_args) instead of self.rv = plot._axes.contour(buff, len(self.clumps)+1, extent=extent,**self.plot_args) Is this a glitch that anyone is aware of? Is there a more general fix? The clump contour is not the only time I've run into this glitch. It seems to happen on large contours, for what that's worth. Thanks! d.

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yt-users May 2013