Mailman 3 August 2015 - yt-users

How to get Cell Velocity ?
by Reju Sam John 17 Aug '15

17 Aug '15

Hi all, How to get Cell Velocity from Enzo data? Thank You. -- Reju Sam John

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Installation query
by Sushilkumar 14 Aug '15

14 Aug '15

HI yt I am trying to install yt on my laptop and I got an error which mentioned checking the yt_install.log. But because the file is so extensive I am unable to locate the error. Could you help me with the same? I can email the the yt_install.log file if you need it Thanks in advance -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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gradient field in yt3
by Yuan Li 13 Aug '15

13 Aug '15

Hi all: I am having trouble creating a gradient field in yt3. What I want is the gradient of logP, where logP is defined as: @derived_field(name="logP",units="") def _logP(field,data): return numpy.log(numpy.array(data["gas","pressure"])) Then I add the gradient field: pf.add_gradient_fields(("gas","logP")) which seems to work and I can find it in pf.derived_field_list. But if I try to use it, I get this error message: yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects. Is this because logP does not have a unit? Also, I had another unrelated question about the gradient fields: Can I add the gradient fields globally instead of to a specific dataset? Thanks! Yuan

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volume rendering colorbar issue
by Stephanie Tonnesen 12 Aug '15

12 Aug '15

Hi yt-users, My last attempt was too big to make it to the user list, so I will try again! I am trying to make a volume rendering using --- Version = 3.2-dev Changeset = dc2467c4eae7 (yt) tip --- and basically following this example: http://bender.astro.sunysb.edu/random/vol_rotate.py My problem is that the units are wonky on my colorbar. I input them in my transfer function as cgs, and the peaks seem to be in the right place based on my input range and sample values. Can I get the colorbar to present the density values in cgs? You can see the colorbar and the code attached. Oh, I had to add in the line matplotlib.use('pdf') because I was getting a _tkinter can't find your screen error everytime I tried to add the colorbar. I think it was a matplotlib with my computer problem. Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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display of 2D cylindrical slice
by Slavin, Jonathan 11 Aug '15

11 Aug '15

Hi, As I mentioned in an earlier message, I'm doing FLASH simulations in 2D cylindrical symmetry (r-z). When I use SlicePlot in an ipython notebook, the correct labels for the axes are used but they are incorrectly centered about 0 - when both r and z should start at 0 and go to 36 pc. It's especially odd in that the INFO message printed indicates the correct limits. I suppose I should report that as a bug, but I also wondered about how to change the plotting limits. It seems that the yt.SlicePlot object does not have a set_xlim or set_ylim method. Does anyone know how to do that? 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 ________________________________________________________

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getting slice array
by Slavin, Jonathan 11 Aug '15

11 Aug '15

Hi all, I'm new to using yt, though I'm an experienced python and matplotlib user. I've been doing runs with FLASH and would like to be able to plot the results with matplotlib. I've used yt "interactively" in an ipython notebook and found it a bit cumbersome - e.g. you can't pan and zoom like you can with matplotlib. On the other hand yt has some nice facilities for accessing the data. So my question is, how do I get a slice, such as is plotted using the yt.SlicePlot function, in an array that I can then manipulate, plot, etc.? If I do: ds = yt.load(file) slc = ds.slice(2,0.) d = slc['density'] I have a YTArray that's apparently 1-D: d.shape (138496,) I should mention that this is a 2-D, cylindrically symmetric (r-z) run. Thanks in advance for any help you can offer. Regards, Jon Slavin -- ________________________________________________________ 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 ________________________________________________________

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Re: [yt-users] getting slice array
by Slavin, Jonathan 11 Aug '15

11 Aug '15

Hi Nathan, Thanks! It seems though that the frb cannot be directly passed to matplotlib's imshow, though np.array(frb) can. I would like it in general if yt could provide simpler means of accessing arrays or array-like objects such as are plotted up. There are many reasons for this besides the desire to plot using matplotlib -- e.g. to create plots of ratios of quantities, or to plot scaled variables. Perhaps this is possible now, though it's not obvious from the docs. Regards, Jon On Tue, Aug 11, 2015 at 2:42 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Tue, 11 Aug 2015 13:17:50 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] getting slice array > Message-ID: > <CAJXewOmiymap0uUBy0hL= > zo0Ltf0kG7UErXYFy9dqZseXoapsg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Tue, Aug 11, 2015 at 1:10 PM, Slavin, Jonathan <jslavin(a)cfa.harvard.edu > > > wrote: > > > Hi all, > > > > I'm new to using yt, though I'm an experienced python and matplotlib > > user. I've been doing runs with FLASH and would like to be able to plot > > the results with matplotlib. I've used yt "interactively" in an ipython > > notebook and found it a bit cumbersome - e.g. you can't pan and zoom like > > you can with matplotlib. On the other hand yt has some nice facilities > for > > accessing the data. So my question is, how do I get a slice, such as is > > plotted using the yt.SlicePlot function, in an array that I can then > > manipulate, plot, etc.? If I do: > > ds = yt.load(file) > > slc = ds.slice(2,0.) > > d = slc['density'] > > I have a YTArray that's apparently 1-D: > > d.shape > > (138496,) > > I should mention that this is a 2-D, cylindrically symmetric (r-z) run. > > Thanks in advance for any help you can offer. > > > > If you have a yt plot object (e.g. a SlicePlot or a ProjectionPlot), you > can do: > > slc = yt.SlicePlot(...) > densit_image = slc.frb['density'] > > "frb" here is a FixedResolutionBuffer object which translates the > multiresolution 1-D array you ran into above into a 2D pixelized > representation of your data. > > You can also create a FixedResolutionBuffer object directly: > > http://yt-project.org/docs/dev/analyzing/generating_processed_data.html#d-i… > > The image arrays you get back from a FixedResolutionBuffer object can be > passed directly to e.g. matplotlib's imshow command. > > By the way, Matt Turk has an open pull request to add the interactive > panning and zooming you were looking for: > > > http://yt-project.org/docs/dev/analyzing/generating_processed_data.html#d-i… > > I'm hoping to finish up that pull request soon, since having interactive > plots both in the notebook and using matplotlib's interactive backends is a > common feature request. > -- ________________________________________________________ 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 ________________________________________________________

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volume rendering colorbar issue
by Stephanie Tonnesen 11 Aug '15

11 Aug '15

Hi yt-users, I am trying to make a volume rendering using --- Version = 3.2-dev Changeset = dc2467c4eae7 (yt) tip --- and basically following this example: http://bender.astro.sunysb.edu/random/vol_rotate.py My problem is that the units are wonky on my colorbar. I input them in my transfer function as cgs, and the peaks seem to be in the right place based on my input range and sample values. Can I get the colorbar to present the density values in cgs? You can see the output and the code attached. Oh, I had to add in the line matplotlib.use('pdf') because I was getting a _tkinter can't find your screen error everytime I tried to add the colorbar. I think it was a matplotlib with my computer problem. Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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problems installing rockstar with yt+anaconda
by Brian O'Shea 11 Aug '15

11 Aug '15

Hi folks, I'm using Enzo on Blue Waters, and to get it working I needed to install anaconda and then install yt-3 from source (i.e., by 'hg clone https://bitbucket.org/yt_analysis/yt' and then 'python setup.py develop'). This does not install rockstar by default, unfortunately, and I am having trouble getting rockstar working (although yt itself works great). I've tried to essentially mimic the rockstar portion of the install script for yt-3 (https://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh) by doing the following: > hg clone http://bitbucket.org/MatthewTurk/rockstar > hg pull > hg up -C tip > make lib > cp librockstar.so ~/local_lib/lib/. and then pointing to ~/local_lib/lib with LD_LIBRARY_PATH (using the full path, not the '~/' convention). However, even when I do this I still can't seem to persuade the rockstar interface code in yt to find rockstar. Attempting to import rockstar in a script by: from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder results in this error: ImportError : from .rockstar import RockstarHaloFinder cannot import name rockstar_interface and the script immediately exits. When I look at the directory yt/analysis_modules/halo_finding/rockstar in a version of yt that has been installed from a script, there are some additional .so files (rockstar_groupies.so and rockstar_interface.so) that aren't in my source install, even when I've run 'python setup.py develop' in that directory. I feel like I'm doing something obviously wrong here. Any suggestions? Thanks! --Brian

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annotate_contour takes much longer time to run than expected on some machines
by Bili Dong 10 Aug '15

10 Aug '15

Hi yt-users, I’m using yt-3.2 (Changeset = 329b5039b031 stable). The problem is that the same script that could finish in seconds on my local machine will take much (order of magnitude) longer time to run on the server I’m using. In some cases, it get stuck for hours that I don’t know if it will ever finish. I’ve tracked down the bottleneck to be the `annotate_contour` method. The server should be faster than my local machine. (I’m not exactly sure about how to compare it. But the server is generally much faster in other situations.) For example, for this script (http://paste.yt-project.org/show/5808/ <http://paste.yt-project.org/show/5808/>), on my local machine the output shows: ``` yt : [INFO ] 2015-08-10 14:48:15,401 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [INFO ] 2015-08-10 14:48:15,751 Saving plot snapshot_200_Projection_z_density.png yt : [INFO ] 2015-08-10 14:48:16,716 Saving plot snapshot_200_Projection_z_density.png ``` However, on the server the output shows: ``` yt : [INFO ] 2015-08-10 14:51:25,551 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [INFO ] 2015-08-10 14:51:25,917 Saving plot snapshot_200_Projection_z_density.png yt : [INFO ] 2015-08-10 14:56:21,922 Saving plot snapshot_200_Projection_z_density.png ``` That’s 296 times slower!!! This is likely to be a very specific problem with the server. But I’d like to know if anyone else has encountered similar problems before so I can learn from your experience. For now, I have no idea what could have gone wrong. BTW, I’m using TSCC (http://idi.ucsd.edu/computing/ <http://idi.ucsd.edu/computing/>) at UC San Diego, if you happen to know it. Thanks, Bili

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