yt-users December 2017

yt-users@python.org

14 participants
20 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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issue with reading pickle files with yt-conda
by Jason Tumlinson 22 Dec '17

22 Dec '17

Hi, I have need for reading some pickle files containing yt array outputs. The files were created by someone else a while ago so I don’t know much about the conditions of their creation. When trying to open them I get the error below. I am asking here because the comment on line 1384 of the traceback seems to point at a yt issue, not something in the file itself. Has anyone encountered this? Is there a workaround? Thanks JT In [3]: f = open(‘file.cpkl', 'rb') In [4]: cPickle.load(f) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-4-1f99de24e8dc> in <module>() ----> 1 cPickle.load(f) /Users/tumlinson/yt-conda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __setstate__(self, state) 1381 """ 1382 super(YTArray, self).__setstate__(state[1:]) -> 1383 unit, lut = state[0] 1384 # need to fix up the lut if the pickle was saved prior to PR #1728 1385 # when the pickle format changed TypeError: 'int' object is not iterable

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Re: [yt-users] cannot SlicePlot() using cut_region() filter on data from yt.load_uniform_grid()
by Dale Braden 11 Dec '17

11 Dec '17

Hi Nathan, Here is a script whose output will show the same problem. I'm using version 3.4.0 -------------------- import yt import numpy as np arr = np.random.random(size=(41,56,47)) data = dict(density = (arr,"g/cm**3")) bbox = np.array([[-4.0,4.2],[-5.5,5.7],[-4.175872,5.22413]]) ds = yt.load_uniform_grid(data, arr.shape, length_unit="cm", bbox=bbox) ad = ds.all_data() print ad.quantities.extrema([("gas", "density")]) den = ad.cut_region(['obj["density"] > 0.0']) print den.quantities.extrema([("gas", "density")]) p = yt.SlicePlot(ds, 'x','density', center="m", data_source=den) ---------------------- thanks for investigating, Dale

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Get particle extent for a non-cosmological simulation
by Jared Coughlin 11 Dec '17

11 Dec '17

Hello! I have a gadget snapshot that was generated from a non-cosmological simulation. This causes yt to ignore the box size parameter. However, when I try to make a plot, yt generally fails because ds.domain_left_edge = ds.domain_right_edge = 0.0. This necessitates that I change those parameters manually. My question is: is there a way to get the domain bounds from the file so that I don't have to set these manually every time? I noticed that if I get the box size wrong, yt complains about particle bounds exceeding the domain bounds, and so I looked a little bit at the code to see if I could figure out how yt was getting these numbers and see if I could just do something similar, but I haven't had a whole lot of luck. It seems that in the compute_morton function there's a pos_x.max and min function, but those are passed in _initialize_index as data having been read from an hdf5 file? I'm not super sure I understand what's going on there, but if anyone has any thoughts, I'd greatly appreciate it. I basically just need the max and min particle positions along each of the x, y, and z directions, but trying ad["Coordinates"] fails unless the bounds are properly set to begin with. Thanks! -Jared

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Unable to open quickstart notebooks #NewUser
by Arpit Kubadia 11 Dec '17

11 Dec '17

Hello. I am new here and was trying to setup yt. I installed yt using virtualenv following the exact steps as mentioned in the github repo. After that I tried to follow the steps on the quickstart page but it failed http://yt-project.org/doc/quickstart/index.html This page. I realised that the path to quickstart on my pc was somewhat different (/yt-git/doc/source/quickstart). So I navigated there and tried running `yt notebook` (as mentioned in the above page) but it failed ModuleNotFoundError: No module named 'notebook' This was the last line How do I run the quickstart process? I am new to opensource community so I dont really know how to setup the tools required Regards, Arpit Kubadia

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cannot SlicePlot() using cut_region() filter on data from yt.load_uniform_grid()
by Dale Braden 10 Dec '17

10 Dec '17

Hello, I have some density data in an unsupported format which I read into yt by means of the yt.load_uniform_grid() function. I want to filter this data by creating a cut_region and then do a SlicePlot on the filtered data. What I find is that no matter how I define the cut_region, the dynamic range of the resulting plot is said to be 0.0, even though the cut region has no values in it which are actually 0.0. I do not have this problem if I use data in a supported format. For example, I can follow the yt tutorial which creates a SlicePlot from a cut_region on the Enzo_64 example dataset. So I wonder if maybe the problem I'm having is due to the fact that when one creates a dataset using load_uniform_grid(), one ends up with a StreamDataset object instead of an object representing a supported format. Here is some relevant output from my session (omitting the code to read in my data from disk): In [8]: data2 = np.array(griddata) In [9]: arr = data2.reshape((41,56,47)) In [10]: data = dict(density = (arr,"g/cm**3")) In [11]: bbox = np.array([[-4.0,4.2],[-5.5,5.7],[-4.175872,5.22413]]) In [12]: ds = yt.load_uniform_grid(data, arr.shape, length_unit="cm", bbox=bbox) yt : [INFO ] 2017-12-09 15:41:20,781 Parameters: current_time = 0.0 yt : [INFO ] 2017-12-09 15:41:20,781 Parameters: domain_dimensions = [41 56 47] yt : [INFO ] 2017-12-09 15:41:20,782 Parameters: domain_left_edge = [-4. -5.5 -4.175872] yt : [INFO ] 2017-12-09 15:41:20,782 Parameters: domain_right_edge = [ 4.2 5.7 5.22413] yt : [INFO ] 2017-12-09 15:41:20,783 Parameters: cosmological_simulation = 0.0 In [13]: ds.find_max('density') yt : [INFO ] 2017-12-09 15:48:16,640 Max Value is 5.14618e+01 at 0.0999999999999996 -0.0000000000000009 -0.0758711276595738 Out[13]: (51.4618 g/cm**3, YTArray([ 1.00000000e-01, -8.88178420e-16, -7.58711277e-02]) code_length) In [14]: ds.find_min('density') yt : [INFO ] 2017-12-09 15:48:53,392 Min Value is 8.71255e-12 at -3.8999999999999999 -5.4000000000000004 -4.0758719787234039 Out[14]: (8.71255e-12 g/cm**3, YTArray([-3.9 , -5.4 , -4.07587198]) code_length) So you can see from find_min() that all data values are > 0.0. I should mention that if I do a SlicePlot on ds.all_data(), it looks fine. But if I try a SlicePlot on a cut_region, even one that essentially duplicates the entire dataset, then there's nothing to plot even though the cut_region does have valid data in it: In [20]: ad = ds.all_data() In [23]: den = ad.cut_region(['obj["density"] > 0.0']) In [24]: print den.quantities.extrema([('gas','density')]) [ 8.71255000e-12 5.14618000e+01] g/cm**3 In [25]: p2 = yt.SlicePlot(ds, 'x','density', center="m", data_source=den) yt : [INFO ] 2017-12-09 15:55:58,155 Max Value is 5.14618e+01 at 0.0999999999999996 -0.0000000000000009 -0.0758711276595738 yt : [INFO ] 2017-12-09 15:55:58,585 xlim = -5.600000 5.600000 yt : [INFO ] 2017-12-09 15:55:58,585 ylim = -4.775872 4.624130 yt : [INFO ] 2017-12-09 15:55:58,586 xlim = -5.600000 5.600000 yt : [INFO ] 2017-12-09 15:55:58,586 ylim = -4.775872 4.624130 yt : [INFO ] 2017-12-09 15:55:58,587 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [WARNING ] 2017-12-09 15:55:58,606 Plot image for field ('gas', 'density') has zero dynamic range. Min = Max = 0.000000. yt : [WARNING ] 2017-12-09 15:55:58,606 Switching to linear colorbar scaling. That first warning message is the problem: zero dynamic range. What's going wrong? best wishes, Dale

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Re: [yt-users] getting real scalar value
by Slavin, Jonathan 08 Dec '17

08 Dec '17

Thanks Matt. Not sure where in the docs something like that might go, but if it's in there, I completely missed it. Jon On Fri, Dec 8, 2017 at 2:10 PM, <yt-users-request(a)lists.spacepope.org> wrote: > > Date: Fri, 8 Dec 2017 09:14:01 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] getting real scalar value > Message-ID: > <CALO3=5HZT53jPgJeFYxhp-0FNU4gTaZo66sp9tqdZyzmkkMAAA@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jon, > > You can see all of these in under ds.parameters, which is populated from > all the non-field values. > > -Matt > > On Fri, Dec 8, 2017 at 9:08 AM, Slavin, Jonathan <jslavin(a)cfa.harvard.edu> > wrote: > > > Hi, > > > > I would like to get the value of the timestep from my FLASH data read in > > by yt. In HDFView I can see the value of 'dt' under 'real scalars'. > Using > > yt to read in the data, though I don't see any way to access it, if it is > > contained in the ds. The field list just shows the grid variables. I can > > get the absolute time via ds.current_time. There are a number of > different > > items at the top level in HDFView, e.g. bflags, block size, sim info, > that > > are not available, as far as I can tell, from the ds object. Am I missing > > something? Is there any way to get yt to read in specific variables like > > dr (under "real scalars")? > > > > Thanks, > > Jon >

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plots with ipython
by Lamberts, Astrid 08 Dec '17

08 Dec '17

Hi all, I'm trying to have a first look at my simulations and when I follow the cookbook for plots, I don't see any plot. I use ipython with: import yt ds=yt.load(mysim) p=yt.ProjectionPlot(ds,"z","density") and no plot appears, even after a p.show(). p.save() saves the plot to a file, but I am looking for a more direct way to look at the data, and I would rather not use jupyter notebooks. How can I proceed? Thanks, Astrid Astrid Lamberts Postdoctoral Researcher TAPIR Group, Caltech

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yt-users December 2017