Mailman 3 May 2015 - yt-users

Re: [yt-users] How to use yt.load_hexahedral_mesh?
by Matthew Turk May 25, 2015

May 25, 2015

Hi Jonah, That's right -- the volume rendering won't work, but slices will. The VR should be working relatively soon, though. -Matt On Sun, May 24, 2015 at 8:47 PM, Jonah Miller <jonah.maxwell.miller(a)gmail.com> wrote: > Oh, I should add that I don't think 3D visualization is possible with > hexahedral meshes at the moment. The pixelizer doesn't support them yet... > At least that's my understanding. If you really need a 3D visualization, you > might want to try transforming your data into a regularly spaced grid (using > another tool) and then loading uniformly spaced data as in this example: > http://yt-project.org/docs/dev/examining/spherical_data.html > > Best, > Jonah > > > On 15-05-24 09:41 PM, Jonah Miller wrote: > > Hi Katharina, Andrew, > > There is a convenience function to create the coordinates and connectivity > arguments: hexahedral_connectivity. This function takes three 1D arrays, > which are the projections of your grid points onto your coordinate axes, > here called x,y, and z. The function then returns the connectivity and > coordinates arrays. > > Here's an example: > http://yt-project.org/docs/dev/examining/loading_data.html#semi-structured-… > > Best, > Jonah > > On 15-05-24 09:35 PM, Andrew Myers wrote: > > Hi Katharina, > > I don't have an example handy, but the "coordinates" and "connectivity" > arguments are arrays you construct that describe the vertices and zones of > the hexahedral mesh you want. The "coordinates" argument is supposed to be a > (N_vertices, 3) - shaped array of floats that has the x, y, and z positions > of all the vertices in the hexahedral mesh. The "connectivity" argument is a > (N_zone, 8) - shaped array of ints that gives, for each zone, the indices of > the 8 vertices that surround it. So for example, if connectivity[0][2] is > '12', then coordinates[12] would give the position coordinate of the third > vertex surrounding the first zone, if that makes sense. > > Once you've constructed those arrays from the information in your dataset > and fed them into "load_hexadral_mesh", yt shouldn't care whether the data > came from an HDF5 file or not. > > -Andrew > > On Sun, May 24, 2015 at 11:46 AM, Katharina Wollenberg > <kwollenberg89(a)gmail.com> wrote: >> >> Hello together, >> >> for visualising a 3D disk from ZEUS-MP HDF5 data in yt, I need to load a >> single spherical polar coordinate grid where x1,x2,x3 are R,T,P and R has >> ratioed zones. For that I want to use the command >> yt.load_hexahedral_mesh(data, connectivity, coordinates, length_unit=None, >> ...) . However, since I am new to yt, I am a little bit stuck right now… >> I am not quite sure what is meant in detail by the arguments connectivity >> and coordinates and how to formulate them in the load_hexahedral_mesh >> command. >> >> Furthermore, do I need to pay particular attention on some commands >> because of using HDF5 data? >> >> If anyone has an example for me, that’d be very helpful! >> >> Thanks a lot! >> >> Katharina Wollenberg >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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How to use yt.load_hexahedral_mesh?
by Katharina Wollenberg May 25, 2015

May 25, 2015

Hello together, for visualising a 3D disk from ZEUS-MP HDF5 data in yt, I need to load a single spherical polar coordinate grid where x1,x2,x3 are R,T,P and R has ratioed zones. For that I want to use the command yt.load_hexahedral_mesh(data, connectivity, coordinates, length_unit=None, ...) . However, since I am new to yt, I am a little bit stuck right now… I am not quite sure what is meant in detail by the arguments connectivity and coordinates and how to formulate them in the load_hexahedral_mesh command. Furthermore, do I need to pay particular attention on some commands because of using HDF5 data? If anyone has an example for me, that’d be very helpful! Thanks a lot! Katharina Wollenberg _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Plot Rotation
by Jason Galyardt May 20, 2015

May 20, 2015

Hi all, Is there a convenient way to rotate a slice or projection plot (with associated axis labels and tick marks) in yt? My simulation domain is long and skinny, and yt automatically plots it with the long edge aligned horizontally; I'd like to rotate these 2D plots by 90 degrees. I've combed through the docs and the only way I can think to do it would be to create a fixed resolution buffer and then manipulate it via matplotlib functions. The camera seems only applicable for 3D (and doesn't paint the axes, so far as I can tell). Any ideas or pointers to docs? Thanks, Jason ---- Jason Galyardt jeg(a)uga.edu Department of Physics and Astronomy University of Georgia _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Enzo Tracer Particle Visualization
by Yuan Li May 19, 2015

May 19, 2015

Hi all, I am trying to make projection plots (e.g. average particle temperature) using Enzo tracer particles. Is there a way of doing this using yt? Thank you! Yuan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Profile Plot range question
by Stephanie Tonnesen May 19, 2015

May 19, 2015

Hi all, I am trying to make a profile plot of a cylindrical radial value. So I politely ask: ds = yt.load("/data/stonnes/dwarf_test_rhopress_extrarot/DD"+sys.argv[1]+"/DD44sMBherlr"+sys.argv[1]) .... my_disk = ds.disk([0.5,0.5,0.5],[0,0,1],(30,"kpc"),(0.1,"kpc")) .... profiles.append(yt.create_profile(my_disk,"cylindrical_r","density",weight_field="cell_mass")) .... plot=yt.ProfilePlot.from_profiles(profiles,labels=labels) plot.set_unit('cylindrical_r','kpc') plot.set_log('cylindrical_r',False) plot.save() And when my box is 96 kpc across, with a root 512 512 512 grid, 2 levels of refinement at 20.0 times initial density, I get what I wanted, a nice profile out to 30 kpc. BUT, when I ask the same thing starting with a lower resolution root grid: 256 256 256, my profile only goes out to 15 kpc! I changed my disk to have a 40 kpc radius and it made no difference. Can anyone tell me why this is happening? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Python Compilation Error while Installing Stable yt on OS X 10.10.3
by Madison Fitzgerald May 18, 2015

May 18, 2015

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Questions on using yt - ENZO simulation data
by Patrick King May 18, 2015

May 18, 2015

Hello yt-users, I am a graduate student working at the University of Virginia, and I would really appreciate some help! I’ve been using yt for a few weeks now to visualize some simulations I’ve run using the ENZO AMR code. I’ve been able to produce several derived fields using the documentation, but I’ve gotten to the point where I need some help with a more advanced usage of the code. Under some approximations, I’ve used yt to determine the Stokes parameters for the radiation field at each grid point. Using yt I can quite easily produce column-averaged plots using projection plot. However, to determine the values I need, I need to actually manipulate the column averaged values. The Stokes parameters give me all the information I need to do this, but these must be column averaged first - I’m essentially using yt to produce values which can be compared to observational data. Can I use projection plot to produce a numpy array that I can manipulate just like in regular python? I’ve been combing the documentation but I can’t find out how to do this. Alternatively, I would like to produce a numpy array from the derived field I calculated and then I can just integrate along columns. Thanks for your help! Patrick King PhD Candidate Department of Astronomy University of Virginia _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] Projection of 2D cylindrical FLASH data
by Ken Shen May 15, 2015

May 15, 2015

Thanks for the suggestions, I'll give them a try! On Fri, May 15, 2015 at 8:18 AM, Roman Yurchak <roman.yurchak(a)crans.org> wrote: > If your observation direction is orthogonal to the revolution axis, you > could also map your 2D cylindrical data to a 2D numpy array (i.e. > re-sample on a uniform grid) and then do a forward Abel transform (the > integral transform to do this particular projection), implemented for > instance in https://github.com/luli/hedp/blob/master/hedp/math/abel.py#L19 > Although, volume rendering approaches would probably be more general and > better integrated with yt. > -- > Roman > > > On 15/05/15 03:27, Suoqing JI wrote: > > One way (imperfect but definitely doable) you might want to try is to > > map 2D cylindrical data into a 3D numpy array, which could be loaded > > by yt.load_uniform_grid and passed into the volume rendering module. > > > > See here: http://yt-project.org/doc/examining/generic_array_data.html > > > > Best wishes, > > -- > > Suoqing JI > > Ph.D Student > > Department of Physics > > University of California, Santa Barbara > > http://web.physics.ucsb.edu/~suoqing > > > >> On May 14, 2015, at 6:01 PM, Nathan Goldbaum <nathan12343(a)gmail.com > >> <mailto:nathan12343@gmail.com>> wrote: > >> > >> > >> > >> On Thu, May 14, 2015 at 5:35 PM, Ken Shen <kenshen(a)astro.berkeley.edu > >> <mailto:kenshen@astro.berkeley.edu>> wrote: > >> > >> I'm really sorry, I can't seem to explain this very clearly in > words! > >> > >> I have 2D axisymmetric data. Let's suppose that I map this to a > >> 3D Cartesian dataset. I'd like to make a 2D plot from this 3D > >> data that consists of integrating the density along rays from the > >> observer through the dataset onto a plane on the other side of the > >> data. Ideally, I'd like to do this with the observer at an > >> arbitrary position with respect to the axes. > >> > >> I haven't done it, but it seems like this is built in to yt's > >> functionality for 3D datasets. But I haven't found how to do it > >> for a 2D axisymmetric dataset. > >> > >> > >> In yt we would call this a volume rendering using rays that are > >> aligned with the cartesian axes and a projection transfer function. > >> > >> I don't think this has been implemented yet, but volume renderings of > >> data with non-cartesian geometries or with unstructured meshes is > >> something we would like to do. > >> > >> > >> > >> Sorry for all the messages! > >> Ken > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> On Thu, May 14, 2015 at 5:28 PM, Michael Zingale > >> <michael.zingale(a)stonybrook.edu > >> <mailto:michael.zingale@stonybrook.edu>> wrote: > >> > >> to be clear here, what Flash calls cylindrical is 2-d > >> axisymmetric, r-z. If I understand what you are asking, you > >> basically want to still have a 2-d plot where each cell is the > >> integral over an annular region as if that cell were rotated > >> about the symmetry axis -- is that right? > >> > >> On Thu, May 14, 2015 at 8:21 PM, Ken Shen > >> <kenshen(a)astro.berkeley.edu > >> <mailto:kenshen@astro.berkeley.edu>> wrote: > >> > >> Hi, sorry I wasn't very clear before. I'd like to make 2D > >> column density plots of my 2D cylindrical data as if my > >> data were 3D cylindrical data with no phi-dependence. > >> > >> (The ProjectionPlot fails for axis = 1 or 3. For axis = > >> 2, it essentially recreates the regular density slice plot.) > >> > >> > >> Thanks, > >> Ken > >> > >> > >> > >> > >> On Thu, May 14, 2015 at 5:00 PM, Matthew Turk > >> <matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>> > wrote: > >> > >> Hi Ken, > >> > >> (I think Suoqing's answer may work as well.) If you > >> want to project > >> along r, z, or theta, you can do a ProjectionPlot (or > >> "ds.proj") and > >> specify "r", "z", or "theta", and the result will be > >> along that axis > >> with the correct path lengths. I think that the "r" > >> direction may be > >> what you're looking for here, i.e., a soup-can label. > >> > >> -Matt > >> > >> On Thu, May 14, 2015 at 6:31 PM, Ken Shen > >> <kenshen(a)astro.berkeley.edu > >> <mailto:kenshen@astro.berkeley.edu>> wrote: > >> > Hi all, I'd like to make column density plots of my > >> 2D cylindrical FLASH > >> > data. Ideally, these would be at arbitrary angles > >> to the z-axis. I'm new > >> > to yt, so I could very well have missed it, but I > >> couldn't seem to find this > >> > in the documentation. Any hints? > >> > > >> > > >> > Thanks, > >> > Ken > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)lists.spacepope.org > >> <mailto:yt-users@lists.spacepope.org> > >> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> <mailto:yt-users@lists.spacepope.org> > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> <mailto:yt-users@lists.spacepope.org> > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> > >> > >> -- > >> Michael Zingale > >> Associate Professor > >> > >> Dept. of Physics & Astronomy • Stony Brook University • Stony > >> Brook, NY 11794-3800 > >> /phone/: 631-632-8225 <tel:631-632-8225> > >> /e-mail/: Michael.Zingale(a)stonybrook.edu > >> <mailto:Michael.Zingale@stonybrook.edu> > >> /web/: http://www.astro.sunysb.edu/mzingale > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Projection of 2D cylindrical FLASH data
by Ken Shen May 15, 2015

May 15, 2015

Hi all, I'd like to make column density plots of my 2D cylindrical FLASH data. Ideally, these would be at arbitrary angles to the z-axis. I'm new to yt, so I could very well have missed it, but I couldn't seem to find this in the documentation. Any hints? Thanks, Ken _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Cython Build Errors in Development Version
by Jason Galyardt May 15, 2015

May 15, 2015

Hi yt Devs, In the latest development version of yt (changeset 23506337f1e8), I'm getting 3 Cython build errors from yt/utilities/lib/pixelization_routines.c to do with the 'faces' variable: yt/utilities/lib/pixelization_routines.pyx:382:14: Assignment to non-lvalue 'faces' yt/utilities/lib/pixelization_routines.pyx:385:14: Assignment to non-lvalue 'faces' yt/utilities/lib/pixelization_routines.pyx:388:14: Assignment to non-lvalue 'faces' This occured when I did the following: python setup.py develop --user --prefix= Is anyone else seeing these errors? I'm using python 2.7.3 and Cython version 0.20.1. If you need more info on my setup, please let me know. Thanks, Jason _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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