yt-users April 2013

yt-users@python.org

23 participants
25 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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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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Re: [yt-users] slice plot
by stefano bovino 29 Apr '13

29 Apr '13

Hi Kacper, my minimal resolution is less than 1 AU, the problem seems more related to the Matt's issue. The script is the same as in the yt website, here the link: http://yt-project.org/doc/cookbook/multi_plot_slice_and_proj.py the output of pf.h.find_max("Density") : (1.139355201341093e-11, array([ 0.49722083, 0.50645245, 0.49492896])) Thanks Stefano ---------- Forwarded message ---------- From: Kacper Kowalik <xarthisius.kk(a)gmail.com> Date: Mon, Apr 29, 2013 at 1:35 PM Subject: Re: [yt-users] slice plot To: yt-users(a)lists.spacepope.org On 04/29/2013 01:22 PM, stefano bovino wrote: > Hi all, > when using the following script fromt the yt.project website > multi_plot_slice_and_proj.py< http://yt-project.org/doc/cookbook/multi_plot_slice_and_proj.py>I > have problems if I change the resolution from mpc to pc. > > slc_frb = slc.to_frb((1.0, "mpc"), 512) --> slc_frb = slc.to_frb((1.0, > "pc"), 512) > > I even tried other ways (or scripts) to plot a slice of the density > changing the resolution, but the problem is still there. Do you have any > solution? > > I just would like to create a 9 panels plot with slice of density, H2, and > Temperature with three different width (on the pc scale). Hi Stefano, what is the size of your computational domain or size of the smallest cell you have? You can obtain that information using: yt stats output_filename Cheers, Kacper

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slice plot
by stefano bovino 29 Apr '13

29 Apr '13

Hi all, when using the following script fromt the yt.project website multi_plot_slice_and_proj.py<http://yt-project.org/doc/cookbook/multi_plot_slice_and_proj.py>I have problems if I change the resolution from mpc to pc. slc_frb = slc.to_frb((1.0, "mpc"), 512) --> slc_frb = slc.to_frb((1.0, "pc"), 512) I even tried other ways (or scripts) to plot a slice of the density changing the resolution, but the problem is still there. Do you have any solution? I just would like to create a 9 panels plot with slice of density, H2, and Temperature with three different width (on the pc scale). Thank you in advance.

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ps. here the plot
by stefano bovino 29 Apr '13

29 Apr '13

Sorry, here the plot I obtained. Stefano

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phase objects in the modern era
by David Collins 26 Apr '13

26 Apr '13

Hi, all-- I'm running into problems making phase objects. It looks like the error is in the color bar, and is similar to other errors I get when trying to use PlotCollections. The hash I'm on is 34b95297062b. I'm trying: pf = load(fname) pc = PlotCollection(pf,'c') phase=pc.add_phase_object(pf.h.all_data(),['CellMass', 'x-velocity','CellVolume'],weight=None) min/max are as follows: CellMass: [4.1e-12,1.5e-03] (30631133,) x-velocity: [-7.2e+01,5.5e+01] CellVolume: [1.45e-11,6.0e-08] Is there a more up-to-date manner to do this that doesn't use PlotCollection? Or is there something obvious that I'm missing? It seems to be choking in plot_types.py/__init_colorbar def __init_colorbar(self): temparray = np.ones((self.x_bins.size, self.y_bins.size)) self.norm = matplotlib.colors.Normalize() self.image = self._axes.pcolormesh(self.x_bins, self.y_bins, temparray, shading='flat', norm=self.norm, cmap=self.cmap, rasterized=True) self.colorbar = self._figure.colorbar(self.image, extend='neither', shrink=0.95, format="%0.2e" ) It looks like what's happening is figure.colorbar chokes on the fact that temparray is "ones", so the spacing between elements is zero. This is outside of my yt knowledge, though. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "p14_phase_test.py", line 4, in <module> phase=pc.add_phase_object(pf.h.all_data(),['CellMass','x-velocity','CellVolume']) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py", line 1184, in add_phase_object figure=figure, axes=axes)) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 815, in __init__ self.__init_colorbar() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py", line 834, in __init_colorbar format="%0.2e" ) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py", line 1387, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in draw_all self._config_axes(X, Y) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 409, in _config_axes self.update_ticks() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 345, in update_ticks ticks, ticklabels, offset_string = self._ticker() File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 560, in _ticker ticks = self._locate(b) File "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py", line 808, in _locate z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db FloatingPointError: invalid value encountered in divide

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problem with zoom slice plot
by Latif 26 Apr '13

26 Apr '13

Hi all, I am trying to create a simple slice plot for the central 1 pc of a simulation box of size 1 mpc using the following simplest script. Problem occurs when I set plot width as can be seen in attached plot. I tried stable version of yt as well development fork but did not get any success. Slice works well without any problem if I use pc.add_slice method. Any ideas what is going wrong here. thanks in advance, Cheers Latif SlicePlot(pf, 'x', "Density", width = (800.0, 'kpc')).save()

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Setting zlim
by david collins 25 Apr '13

25 Apr '13

Hi, all-- I'm trying to set the color map and extents for some plots, but it doesn't seem to be taking: If I do field= 'Density' proj = pf.h.proj(ax,field,source=cut_region) pw = proj.to_pw() pw.set_cmap('Density','gray') pw.set_zlim = [0.1,50] pw.save('wtfc.png') pp = ProjectionPlot(pf,0,'Density') pp.set_cmap('Density','gray') pp.set_zlim = [0.1,50] pp.save('wtfd.png') the two plots should have the same range on the color map, but they don't. I tried calls to "refresh" n both pp and pw, but that didn't help. What am I missing? d. -- Sent from my computer.

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cut region vs. projection?
by David Collins 24 Apr '13

24 Apr '13

Hi, all-- Can I hand a cut_region to a projection? I want to make a bunch of projections based on parameters, and don't want to have to instantiate 47 different fields. I'm hoping something like region = pf.h.all_data().cut_region('grid["Density"] > 0.1 and grid["Density"] < 0.2') proj = pf.h.proj(0,"Density",region=cut_region) or something like that. Is that possible? I'm poking around the help and source, but no method immediately popped out at me. Thanks, d.

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yt-users April 2013