yt-users December 2017

yt-users@python.org

14 participants
18 discussions

by 梁家豪

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

10 months

issue with reading pickle files with yt-conda

by Jason Tumlinson

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

2 years, 3 months

Re: [yt-users] cannot SlicePlot() using cut_region() filter on data from yt.load_uniform_grid()

by Dale Braden

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

2 years, 3 months

Get particle extent for a non-cosmological simulation

by Jared Coughlin

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

2 years, 3 months

Unable to open quickstart notebooks #NewUser

by Arpit Kubadia

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

2 years, 3 months

cannot SlicePlot() using cut_region() filter on data from yt.load_uniform_grid()

by Dale Braden

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

2 years, 3 months

Re: [yt-users] getting real scalar value

by Slavin, Jonathan

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 >

2 years, 3 months

plots with ipython

by Lamberts, Astrid

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

2 years, 3 months

getting real scalar value

by Slavin, Jonathan

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 -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

2 years, 3 months

Re: [yt-users] inconsistent backend when using yt interactively

by Slavin, Jonathan

Thanks Nathan. In fact since sending that message I discovered that it's a simple typo in base_plot_types.py under the visualization directory. qt5agg had been typed as gt5agg. On a related subject, I thought that after doing yt.toggle_interactivity() yt would then send output to a plotting window in the same way that using matplotlib in ipython does. But, at least for me, that doesn't happen. Is the interactivity only for jupyter notebooks? Jon > Message: 2 > Date: Thu, 7 Dec 2017 14:43:11 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] inconsistent backend when using yt > interactively > Message-ID: > <CAJXewOn52fdA4g3EkdP-g4f0dzqy7AWWPXfZn8P9OJqOMz1n4A > @mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Jon, > > This was a bug that got fixed a couple months ago: > > https://github.com/yt-project/yt/commit/d357110d01f63b6e20066703e16dd9 > 79823fb445 > > If you switch to running yt from the git master branch you should be good > to go. > > We're overdo for a bugfix release, which is blocked on me (or someone else > if they're feeling ambitious) figuring out how to adapt the script we used > to use to backport pull requests with hg/bitbucket to git/github. > > Apologies for the trouble, > > Nathan > > On Thu, Dec 7, 2017 at 2:34 PM, Slavin, Jonathan <jslavin(a)cfa.harvard.edu> > wrote: > > > Hi all, > > > > I've been using yt for some time, but mostly as a way to access AMR data > > generated by FLASH. Just now I tried using the (new, I think) > interactive > > plotting capabilities of yt by doing: > > yt.toggle_interactivity() > > ds = yt.load(hdf5_file) > > p2d = yt.plot_2d(ds,'temperature') > > > > When I toggle interactivity I get the message: > > Using matplotlib backend: Qt5Agg > > > > ?but when I try to generate the 2d plot I get a bunch of error messages > > ending with: > > ?/export/slavin/python/anaconda/lib/python2.7/site- > > packages/yt/visualization/base_plot_types.pyc in _set_canvas(self) > > 120 mod = __import__('matplotlib.backends', > > globals(), locals(), > > 121 [backend_dict[key][0]], 0) > > --> 122 submod = getattr(mod, backend_dict[key][0]) > > 123 FigureCanvas = getattr(submod, > > backend_dict[key][1]) > > 124 if len(backend_dict[key]) > 2: > > > > AttributeError: 'module' object has no attribute 'backend_gt5agg' > > > > ?So somehow the backend got changed to, or was assumed? to be, gt5agg > > rather than qt5agg. It's especially weird in that I don't think there > even > > is a gt5agg backend. Seems a mixture of qt5agg and gtkagg. Any ideas? > > > > Jon > > > > -- > > ________________________________________________________ > > Jonathan D. Slavin Harvard-Smithsonian CfA > > jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 > > phone: (617) 496-7981 Cambridge, MA 02138-1516 > > cell: (781) 363-0035 USA > > ________________________________________________________ > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20171207/ebf3f80d/attachment-0001.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 118, Issue 11 > ***************************************** > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

2 years, 3 months

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yt-users December 2017