[yt-users] Camera Options

Suoqing Ji suoqing at physics.ucsb.edu
Thu Apr 21 12:41:40 PDT 2016


Hi Nathan,

I do not have a 3D MHD data at hand, but I’ve tried one with slc.annotate_quiver('velocity_x', 'velocity_y'), which gives the following error:

  File "off_axis.py", line 49, in <module>
    slc.save(pf.basename)
  File "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 76, in newfunc
    args[0].run_callbacks()
  File "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1029, in run_callbacks
    sys.exc_info()[2])
  File "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1025, in run_callbacks
    callback(cbw)
  File "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 352, in __call__
    (xi, yi) = (ds.coordinates.x_axis[ax],
yt.utilities.exceptions.YTPlotCallbackError: annotate_quiver callback failed with the following error: 4

Best wishes,
--
Suoqing JI
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing

> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> 
> 
> 
> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji <suoqing at physics.ucsb.edu <mailto:suoqing at physics.ucsb.edu>> wrote:
> Hi Sushi,
> 
> The quiver/streamline option you’ve used works for 2d plotting but not for volume rendering, so I might suggest to use off-axis slice plot: http://yt-project.org/doc/visualizing/plots.html#off-axis-slices <http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>
> 
> Unfortunately, quiver/streamline does not work (and/or does not work correctly) for off axis slice plot now, but your goal is still achievable via the following steps:
> 
> Are you sure about that? There's a `CuttingQuiverCallback` for off-axis slices. If you do `annotate_magnetic_fields`, it will automatically choose the `CuttingQuiverCallback` for off-axis slices.
>  
> 
> 1. Use fixed resolution buffer to get the off-axis sliced field values including Bx, By and Bz (see this as an example, and replace SlicePlot with OffAxisSlicePlot: http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedresolutionbuffer#multi-plot-slice-and-projections <http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedresolutionbuffer#multi-plot-slice-and-projections>), then you get a 2D array for each field;
> 
> 2. Compute the magnetic field vectors projected onto the rotated viewing plane (perpendicular to your normal vector), based on field values of Bx, By and Bz; now you have two 2D arrays for each components of B field vectors after rotation;
> 
> 3. Use quiver function in matplotlib and plot the B field vectors after rotation, see: http://matplotlib.org/examples/pylab_examples/quiver_demo.html <http://matplotlib.org/examples/pylab_examples/quiver_demo.html>
> 
> Hope this helps! Perhaps there’s an easier way that I do not know...
> 
> Best wishes,
> --
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>
>> On Apr 21, 2016, at 10:31 AM, Sushilkumar <sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> 
>> Dear yt:
>> 
>> I am having trouble with the camera option on yt. 
>> 
>> The google drive link is https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>
>> 
>> I want to change the view of the camera at an angle after the Slice (x-z plane) and Quiver option.
>> 
>> My script is yt_cam_rot.py. Without the camera options I get the desired plot (UniformGridData_Slice.png) but when I use the camera  I get a empty screen. I am not sure where I am going wrong. 
>> 
>> I am using these links for my reference
>> 
>> http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera>
>> http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering <http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>
>> 
>> Thanks in advance
>> 
>>  
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar <sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> Dear Suoqing JI:
>> 
>> Thank you 
>> 
>> On Fri, Apr 15, 2016 at 12:59 PM, <yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>> wrote:
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>> Today's Topics:
>> 
>>    1. Re: Camera Options (Suoqing Ji)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Fri, 15 Apr 2016 10:59:22 -0700
>> From: Suoqing Ji <suoqing at physics.ucsb.edu <mailto:suoqing at physics.ucsb.edu>>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> Subject: Re: [yt-users] Camera Options
>> Message-ID: <B885F215-5F0A-49D5-9712-2D8FCEAA1366 at physics.ucsb.edu <mailto:B885F215-5F0A-49D5-9712-2D8FCEAA1366 at physics.ucsb.edu>>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi Sushi,
>> 
>> I think the off-axis slice/projection plot will meet your requirement best, where the camera orientation is determined by the normal vector:
>> 
>> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices <http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> <http://yt-project.org/doc/visualizing/plots.html#off-axis-slices <http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>
>> http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots <http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> <http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots <http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>>
>> 
>> And of course, if you?re interested in the features provided by volume rendering, it?s also worth a try. This cookbook gives an example of moving a camera; specifically you might want to use the camera.rotation:
>> 
>> http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera> <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera>>
>> 
>> Best wishes,
>> --
>> Suoqing JI
>> Ph.D Candidate
>> Department of Physics
>> University of California, Santa Barbara
>> http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>
>> 
>> > On Apr 15, 2016, at 8:38 AM, Sushilkumar <sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> >
>> > Dear yt:
>> >
>> > I would like to change/customize/rotate my camera angle for my slice plots without rotating the axis.
>> >
>> > What options do I have using yt if I want to move my camera angle by say 45 degrees?
>> >
>> > Can I use the following link or can you suggest me something else
>> > http://yt-project.org/doc/visualizing/volume_rendering.html <http://yt-project.org/doc/visualizing/volume_rendering.html> <http://yt-project.org/doc/visualizing/volume_rendering.html <http://yt-project.org/doc/visualizing/volume_rendering.html>>
>> >
>> > Thanks in advance
>> >
>> >
>> >
>> > On Thu, Mar 31, 2016 at 10:11 PM, <yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org> <mailto:yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>>> wrote:
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>> > Today's Topics:
>> >
>> >    1. Inclination problem (Sushilkumar)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Thu, 31 Mar 2016 22:11:09 -0500
>> > From: Sushilkumar <sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com> <mailto:sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>>>
>> > To: Discussion of the yt analysis package
>> >         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > Subject: [yt-users] Inclination problem
>> > Message-ID:
>> >         <CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg at mail.gmail.com <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg at mail.gmail.com> <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg at mail.gmail.com <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg at mail.gmail.com>>>
>> > Content-Type: text/plain; charset="utf-8"
>> >
>> > Dear Nathan:
>> >
>> > Thank you very much, implementing now
>> >
>> >
>> > On Thu, Mar 31, 2016 at 9:50 AM, <yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org> <mailto:yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>>>
>> > wrote:
>> >
>> > > Send yt-users mailing list submissions to
>> > >         yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > >
>> > > To subscribe or unsubscribe via the World Wide Web, visit
>> > >         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > or, via email, send a message with subject or body 'help' to
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>> > >
>> > > You can reach the person managing the list at
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>> > >
>> > > When replying, please edit your Subject line so it is more specific
>> > > than "Re: Contents of yt-users digest..."
>> > >
>> > >
>> > > Today's Topics:
>> > >
>> > >    1. Re: Inclination problem (Nathan Goldbaum)
>> > >
>> > >
>> > > ----------------------------------------------------------------------
>> > >
>> > > Message: 1
>> > > Date: Thu, 31 Mar 2016 09:50:31 -0500
>> > > From: Nathan Goldbaum <nathan12343 at gmail.com <mailto:nathan12343 at gmail.com> <mailto:nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>>>
>> > > To: Discussion of the yt analysis package
>> > >         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > > Subject: Re: [yt-users] Inclination problem
>> > > Message-ID:
>> > >         <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu=
>> > > DcFZtQ at mail.gmail.com <mailto:DcFZtQ at mail.gmail.com> <mailto:DcFZtQ at mail.gmail.com <mailto:DcFZtQ at mail.gmail.com>>>
>> > > Content-Type: text/plain; charset="utf-8"
>> > >
>> > > Hi SK,
>> > >
>> > > I'm going to reference this example:
>> > >
>> > >
>> > > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines <http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines> <http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines <http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines>>
>> > >
>> > > specifically this snippet:
>> > >
>> > > for stream in streamlines.streamlines:
>> > >     stream = stream[np.all(stream != 0.0, axis=1)]
>> > >     ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1)
>> > >
>> > > Here, the 'stream' object is just a Nx3 numpy array, where N is the number
>> > > of points sampled along the streamline. So each row of the numpy array is
>> > > just the coordinates of the streamline along one direction.
>> > >
>> > > To answer your question, no, there's nothing in yt that will rotate the
>> > > streamlines into a new coordinate system. Fortunately you should be able to
>> > > do it yourself using e.g. an Euler angle rotation matrix. You will need to
>> > > identify the new coordinate system you would like to transform to,
>> > > calculate a 3D rotation matrix, then apply it using matrix multiplication
>> > > (e.g. np.dot, which supports broadcasting) to each coordinate along the
>> > > streamline.
>> > >
>> > > Hope that helps,
>> > >
>> > > Nathan
>> > >
>> > > On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar <sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com> <mailto:sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>>>
>> > > wrote:
>> > >
>> > > > Dear Matt:
>> > > >
>> > > > Pleas correct me if I am wrong but "off axis slices" takes slices of the
>> > > > plot that is already plotted.
>> > > >
>> > > > However, I would like to plot my data in a new coordinate frame
>> > > (x`,y`,z`)
>> > > > which is inclined at an angle of say alpha from the default (x,y,z)
>> > > frame.
>> > > >
>> > > > Or I would like to plot my data in a rotated frame (x`,y`,z`), which is
>> > > > rotated at an angle of alpha from (x,y,z).
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > On Wed, Mar 30, 2016 at 5:01 PM, <yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org> <mailto:yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>>>
>> > > > wrote:
>> > > >
>> > > >> Send yt-users mailing list submissions to
>> > > >>         yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >>
>> > > >> To subscribe or unsubscribe via the World Wide Web, visit
>> > > >>         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> or, via email, send a message with subject or body 'help' to
>> > > >>         yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org> <mailto:yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>>
>> > > >>
>> > > >> You can reach the person managing the list at
>> > > >>         yt-users-owner at lists.spacepope.org <mailto:yt-users-owner at lists.spacepope.org> <mailto:yt-users-owner at lists.spacepope.org <mailto:yt-users-owner at lists.spacepope.org>>
>> > > >>
>> > > >> When replying, please edit your Subject line so it is more specific
>> > > >> than "Re: Contents of yt-users digest..."
>> > > >>
>> > > >>
>> > > >> Today's Topics:
>> > > >>
>> > > >>    1. Re: load spherical polar coordinate data with mesh refinement
>> > > >>       in HDF5 (Jiang, Yanfei)
>> > > >>    2. Re: load spherical polar coordinate data with mesh refinement
>> > > >>       in HDF5 (Matthew Turk)
>> > > >>    3. Re: Inclination problem (Matthew Turk)
>> > > >>    4. Re: load spherical polar coordinate data with mesh refinement
>> > > >>       in HDF5 (Jonah Miller)
>> > > >>
>> > > >>
>> > > >> ----------------------------------------------------------------------
>> > > >>
>> > > >> Message: 1
>> > > >> Date: Wed, 30 Mar 2016 15:49:26 -0400
>> > > >> From: "Jiang, Yanfei" <yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu> <mailto:yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>>
>> > > >> To: Discussion of the yt analysis package
>> > > >>         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
>> > > >>         refinement in HDF5
>> > > >> Message-ID:
>> > > >>         <
>> > > >> CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A at mail.gmail.com <mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A at mail.gmail.com> <mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A at mail.gmail.com <mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A at mail.gmail.com>>>
>> > > >> Content-Type: text/plain; charset="utf-8"
>> > > >>
>> > > >> Hi Jonah,
>> > > >>
>> > > >>    I am able to load the data to yt now using load_amr_grids(). I notice
>> > > >> that it can also set geometry to spherical. This is great. But to make
>> > > >> life
>> > > >> more complicate. Is it possible to let yt know that the grid is
>> > > >> logarithmic? Currently, load_amr_grids() just take left and right edges
>> > > of
>> > > >> each block. I guess yt assumes the grid is uniform between left and
>> > > right
>> > > >> edges. Is it possible to provide arrays of coordinate values for each
>> > > cell
>> > > >> in each block?
>> > > >>
>> > > >> Thanks.
>> > > >>
>> > > >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <
>> > > >> jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com> <mailto:jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com>>> wrote:
>> > > >>
>> > > >> > Hi Yan-Feng,
>> > > >> >
>> > > >> > I haven't tried it, but I think there is functionality for this. You
>> > > can
>> > > >> > use the load_amr_grids() function which can load amr data in
>> > > Cartesian,
>> > > >> > spherical, or polar coordinates. Here's the documentation:
>> > > >> >
>> > > >> >
>> > > >>
>> > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array> <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array>>
>> > > >> >
>> > > >> >
>> > > >> >
>> > > >>
>> > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids>>
>> > > >> >
>> > > >> > Best,
>> > > >> > Jonah
>> > > >> >
>> > > >> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>> > > >> yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu> <mailto:yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>>
>> > > >> > wrote:
>> > > >> >
>> > > >> >> Hi,
>> > > >> >>          I have some data from a new version of Athena simulations.
>> > > It
>> > > >> is
>> > > >> >> in spherical polar coordinate with mesh refinement written in HDF5.
>> > > The
>> > > >> >> data structure is similar to flash data but not the same. Does anyone
>> > > >> have
>> > > >> >> suggestions to load such data to yt directly?
>> > > >> >>
>> > > >> >> Thank you.
>> > > >> >> --
>> > > >> >> Yan-Fei Jiang
>> > > >> >>
>> > > >> >> Einstein Fellow
>> > > >> >> Harvard-Smithsonian Center for Astrophysics
>> > > >> >> 60 Garden Street, Cambridge MA USA 02138
>> > > >> >> _______________________________________________
>> > > >> >> yt-users mailing list
>> > > >> >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>
>> > > >> >
>> > > >> > _______________________________________________
>> > > >> > yt-users mailing list
>> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >
>> > > >> >
>> > > >>
>> > > >>
>> > > >> --
>> > > >> Yan-Fei Jiang
>> > > >>
>> > > >> Einstein Fellow
>> > > >> Harvard-Smithsonian Center for Astrophysics
>> > > >> 60 Garden Street, Cambridge MA USA 02138
>> > > >> -------------- next part --------------
>> > > >> An HTML attachment was scrubbed...
>> > > >> URL: <
>> > > >>
>> > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm> <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm>>
>> > > >> >
>> > > >>
>> > > >> ------------------------------
>> > > >>
>> > > >> Message: 2
>> > > >> Date: Wed, 30 Mar 2016 16:15:30 -0500
>> > > >> From: Matthew Turk <matthewturk at gmail.com <mailto:matthewturk at gmail.com> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>
>> > > >> To: Discussion of the yt analysis package
>> > > >>         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
>> > > >>         refinement in HDF5
>> > > >> Message-ID:
>> > > >>         <CALO3=
>> > > >> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA at mail.gmail.com <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA at mail.gmail.com> <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA at mail.gmail.com <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA at mail.gmail.com>>>
>> > > >> Content-Type: text/plain; charset=UTF-8
>> > > >>
>> > > >> Hi Yanfei,
>> > > >>
>> > > >> This is possible -- but it will also slow some things down.  You can
>> > > >> use the load_hexahedral_mesh function, and there're examples of this.
>> > > >> This takes away some of the optimizations that regular grids can do,
>> > > >> but we're hoping to add them back in shortly.  Like the other
>> > > >> functions it too takes a geometry argument.
>> > > >>
>> > > >> -Matt
>> > > >>
>> > > >> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
>> > > >> <yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu> <mailto:yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>> wrote:
>> > > >> > Hi Jonah,
>> > > >> >
>> > > >> >    I am able to load the data to yt now using load_amr_grids(). I
>> > > notice
>> > > >> > that it can also set geometry to spherical. This is great. But to make
>> > > >> life
>> > > >> > more complicate. Is it possible to let yt know that the grid is
>> > > >> logarithmic?
>> > > >> > Currently, load_amr_grids() just take left and right edges of each
>> > > >> block. I
>> > > >> > guess yt assumes the grid is uniform between left and right edges. Is
>> > > it
>> > > >> > possible to provide arrays of coordinate values for each cell in each
>> > > >> block?
>> > > >> >
>> > > >> > Thanks.
>> > > >> >
>> > > >> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
>> > > >> > <jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com> <mailto:jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com>>> wrote:
>> > > >> >>
>> > > >> >> Hi Yan-Feng,
>> > > >> >>
>> > > >> >> I haven't tried it, but I think there is functionality for this. You
>> > > >> can
>> > > >> >> use the load_amr_grids() function which can load amr data in
>> > > Cartesian,
>> > > >> >> spherical, or polar coordinates. Here's the documentation:
>> > > >> >>
>> > > >> >>
>> > > >> >>
>> > > >>
>> > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array> <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array>>
>> > > >> >>
>> > > >> >>
>> > > >> >>
>> > > >>
>> > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids>>
>> > > >> >>
>> > > >> >> Best,
>> > > >> >> Jonah
>> > > >> >>
>> > > >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>> > > >> yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu> <mailto:yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>>
>> > > >> >> wrote:
>> > > >> >>>
>> > > >> >>> Hi,
>> > > >> >>>          I have some data from a new version of Athena simulations.
>> > > >> It is
>> > > >> >>> in spherical polar coordinate with mesh refinement written in HDF5.
>> > > >> The data
>> > > >> >>> structure is similar to flash data but not the same. Does anyone
>> > > have
>> > > >> >>> suggestions to load such data to yt directly?
>> > > >> >>>
>> > > >> >>> Thank you.
>> > > >> >>> --
>> > > >> >>> Yan-Fei Jiang
>> > > >> >>>
>> > > >> >>> Einstein Fellow
>> > > >> >>> Harvard-Smithsonian Center for Astrophysics
>> > > >> >>> 60 Garden Street, Cambridge MA USA 02138
>> > > >> >>> _______________________________________________
>> > > >> >>> yt-users mailing list
>> > > >> >>> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>
>> > > >> >>
>> > > >> >> _______________________________________________
>> > > >> >> yt-users mailing list
>> > > >> >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>
>> > > >> >
>> > > >> >
>> > > >> >
>> > > >> > --
>> > > >> > Yan-Fei Jiang
>> > > >> >
>> > > >> > Einstein Fellow
>> > > >> > Harvard-Smithsonian Center for Astrophysics
>> > > >> > 60 Garden Street, Cambridge MA USA 02138
>> > > >> >
>> > > >> > _______________________________________________
>> > > >> > yt-users mailing list
>> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >
>> > > >>
>> > > >>
>> > > >> ------------------------------
>> > > >>
>> > > >> Message: 3
>> > > >> Date: Wed, 30 Mar 2016 16:16:22 -0500
>> > > >> From: Matthew Turk <matthewturk at gmail.com <mailto:matthewturk at gmail.com> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>
>> > > >> To: Discussion of the yt analysis package
>> > > >>         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > > >> Subject: Re: [yt-users] Inclination problem
>> > > >> Message-ID:
>> > > >>         <CALO3=5HMB=
>> > > >> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ at mail.gmail.com <mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ at mail.gmail.com> <mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ at mail.gmail.com <mailto:joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ at mail.gmail.com>>>
>> > > >> Content-Type: text/plain; charset=UTF-8
>> > > >>
>> > > >> Hi SK,
>> > > >>
>> > > >> I'm not sure I totally understand, but if you have an inclination
>> > > >> angle you can use this directly in yt in the off axis slices and so
>> > > >> on.  They typically take a vector, but you should be able to convert
>> > > >> one to the other.
>> > > >>
>> > > >> -Matt
>> > > >>
>> > > >> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar <sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com> <mailto:sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>>
>> > > >
>> > > >> wrote:
>> > > >> > Dear yt:
>> > > >> >
>> > > >> > I am trying to numerically solve the region around a pulsar. Now since
>> > > >> > pulsar is an inclined rotator with inclination angle between rotation
>> > > >> axis
>> > > >> > and dipole axis I would like to include in my yt script.
>> > > >> >
>> > > >> > My original code written in FORTRAN incorporated this inclination but
>> > > >> how
>> > > >> > would I incorporate it into my visualization using yt without changing
>> > > >> my
>> > > >> > data.
>> > > >> >
>> > > >> > Could you suggest ways for the same?
>> > > >> >
>> > > >> > The google drive link to my script (streamline.py) and streamline plot
>> > > >> > (streamline_t000.png) is included
>> > > >> >
>> > > >> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>
>> > > >> >
>> > > >> > Thanks in advance
>> > > >> >
>> > > >> > On Tue, Mar 29, 2016 at 12:54 PM, <
>> > > yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org> <mailto:yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>>
>> > > >> >
>> > > >> > wrote:
>> > > >> >>
>> > > >> >> Send yt-users mailing list submissions to
>> > > >> >>         yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >>
>> > > >> >> To subscribe or unsubscribe via the World Wide Web, visit
>> > > >> >>
>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >> or, via email, send a message with subject or body 'help' to
>> > > >> >>         yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org> <mailto:yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>>
>> > > >> >>
>> > > >> >> You can reach the person managing the list at
>> > > >> >>         yt-users-owner at lists.spacepope.org <mailto:yt-users-owner at lists.spacepope.org> <mailto:yt-users-owner at lists.spacepope.org <mailto:yt-users-owner at lists.spacepope.org>>
>> > > >> >>
>> > > >> >> When replying, please edit your Subject line so it is more specific
>> > > >> >> than "Re: Contents of yt-users digest..."
>> > > >> >>
>> > > >> >>
>> > > >> >> Today's Topics:
>> > > >> >>
>> > > >> >>    1. Re: gadget onto unigrid (Carla Bernhardt)
>> > > >> >>    2. Re: gadget onto unigrid (Matthew Turk)
>> > > >> >>
>> > > >> >>
>> > > >> >>
>> > > ----------------------------------------------------------------------
>> > > >> >>
>> > > >> >> Message: 1
>> > > >> >> Date: Tue, 29 Mar 2016 15:55:27 +0200
>> > > >> >> From: Carla Bernhardt <carla.j.bernhardt at gmail.com <mailto:carla.j.bernhardt at gmail.com> <mailto:carla.j.bernhardt at gmail.com <mailto:carla.j.bernhardt at gmail.com>>>
>> > > >> >> To: Discussion of the yt analysis package
>> > > >> >>         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid
>> > > >> >> Message-ID:
>> > > >> >>
>> > > >> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=UhyGS_beuiUMbw7Ag at mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag at mail.gmail.com> <mailto:UhyGS_beuiUMbw7Ag at mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag at mail.gmail.com>>>
>> > > >> >> Content-Type: text/plain; charset="utf-8"
>> > > >> >>
>> > > >> >> Hi All,
>> > > >> >>
>> > > >> >> A follow-up question: In using arbitrary_grid (but with enzo data),
>> > > how
>> > > >> >> does one then extract a field of an arbitrary_grid? I tried
>> > > >> >> arbgrid["density"] as I have done with a smoothed_covering_grid
>> > > object,
>> > > >> >> but
>> > > >> >> it does not work (here is the traceback <
>> > > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0> <http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0>>>
>> > > >> I
>> > > >> >> got).
>> > > >> >>
>> > > >> >> Thanks,
>> > > >> >> Carla
>> > > >> >>
>> > > >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk at gmail.com <mailto:matthewturk at gmail.com> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>:
>> > > >> >>
>> > > >> >> > Hi Desika,
>> > > >> >> >
>> > > >> >> > Yup, this can be done reasonably easily using either the
>> > > >> >> > .arbitrary_grid object (which was designed for this) or the
>> > > interface
>> > > >> >> > to the arbitrary grid that's in the development version, which is
>> > > >> >> > ds.r[ ... ] where the ... is some combination of bounds and steps.
>> > > >> >> >
>> > > >> >> >
>> > > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>>
>> > > >> >> >
>> > > >> >> >
>> > > >> >> >
>> > > >>
>> > > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data> <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data>>
>> > > >> >> >
>> > > >> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
>> > > >> >> > <desika.narayanan at gmail.com <mailto:desika.narayanan at gmail.com> <mailto:desika.narayanan at gmail.com <mailto:desika.narayanan at gmail.com>>> wrote:
>> > > >> >> > > Hi All,
>> > > >> >> > >
>> > > >> >> > > Is it possible to deposit the particles from a gadget data set
>> > > >> onto a
>> > > >> >> > > uniform grid in yt?  Or, could it be possible to trick the octree
>> > > >> >> > deposition
>> > > >> >> > > into doing it by forcing no refinements, but some sort of native
>> > > >> grid
>> > > >> >> > > resolution?
>> > > >> >> > >
>> > > >> >> > > thanks,
>> > > >> >> > > desika
>> > > >> >> > >
>> > > >> >> > >
>> > > >> >> > > _______________________________________________
>> > > >> >> > > yt-users mailing list
>> > > >> >> > > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >> > >
>> > > >> >> > _______________________________________________
>> > > >> >> > yt-users mailing list
>> > > >> >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-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/20160329/e29a03a1/attachment.html <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html> <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html>>
>> > > >> >
>> > > >> >>
>> > > >> >> ------------------------------
>> > > >> >>
>> > > >> >> Message: 2
>> > > >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500
>> > > >> >> From: Matthew Turk <matthewturk at gmail.com <mailto:matthewturk at gmail.com> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>
>> > > >> >> To: Discussion of the yt analysis package
>> > > >> >>         <yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>>
>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid
>> > > >> >> Message-ID:
>> > > >> >>
>> > > >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=P098utA at mail.gmail.com <mailto:P098utA at mail.gmail.com> <mailto:P098utA at mail.gmail.com <mailto:P098utA at mail.gmail.com>>>
>> > > >> >> Content-Type: text/plain; charset=UTF-8
>> > > >> >>
>> > > >> >> Hi Carla,
>> > > >> >>
>> > > >> >> This functionality was recently implemented and is in the development
>> > > >> >> version, but not yet in the stable.  We're hoping for a release very
>> > > >> >> shortly, but you can also try the dev version if you'd like!
>> > > >> >>
>> > > >> >> -Matt
>> > > >> >>
>> > > >> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt
>> > > >> >> <carla.j.bernhardt at gmail.com <mailto:carla.j.bernhardt at gmail.com> <mailto:carla.j.bernhardt at gmail.com <mailto:carla.j.bernhardt at gmail.com>>> wrote:
>> > > >> >> > Hi All,
>> > > >> >> >
>> > > >> >> > A follow-up question: In using arbitrary_grid (but with enzo data),
>> > > >> how
>> > > >> >> > does
>> > > >> >> > one then extract a field of an arbitrary_grid? I tried
>> > > >> >> > arbgrid["density"] as
>> > > >> >> > I have done with a smoothed_covering_grid object, but it does not
>> > > >> work
>> > > >> >> > (here
>> > > >> >> > is the traceback I got).
>> > > >> >> >
>> > > >> >> > Thanks,
>> > > >> >> > Carla
>> > > >> >> >
>> > > >> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk at gmail.com <mailto:matthewturk at gmail.com> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>:
>> > > >> >> >>
>> > > >> >> >> Hi Desika,
>> > > >> >> >>
>> > > >> >> >> Yup, this can be done reasonably easily using either the
>> > > >> >> >> .arbitrary_grid object (which was designed for this) or the
>> > > >> interface
>> > > >> >> >> to the arbitrary grid that's in the development version, which is
>> > > >> >> >> ds.r[ ... ] where the ... is some combination of bounds and steps.
>> > > >> >> >>
>> > > >> >> >>
>> > > >> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>>
>> > > >> >> >>
>> > > >> >> >>
>> > > >> >> >>
>> > > >>
>> > > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data> <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data>>
>> > > >> >> >>
>> > > >> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
>> > > >> >> >> <desika.narayanan at gmail.com <mailto:desika.narayanan at gmail.com> <mailto:desika.narayanan at gmail.com <mailto:desika.narayanan at gmail.com>>> wrote:
>> > > >> >> >> > Hi All,
>> > > >> >> >> >
>> > > >> >> >> > Is it possible to deposit the particles from a gadget data set
>> > > >> onto a
>> > > >> >> >> > uniform grid in yt?  Or, could it be possible to trick the
>> > > octree
>> > > >> >> >> > deposition
>> > > >> >> >> > into doing it by forcing no refinements, but some sort of native
>> > > >> grid
>> > > >> >> >> > resolution?
>> > > >> >> >> >
>> > > >> >> >> > thanks,
>> > > >> >> >> > desika
>> > > >> >> >> >
>> > > >> >> >> >
>> > > >> >> >> > _______________________________________________
>> > > >> >> >> > yt-users mailing list
>> > > >> >> >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >> >> >
>> > > >> >> >> _______________________________________________
>> > > >> >> >> yt-users mailing list
>> > > >> >> >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >> >
>> > > >> >> >
>> > > >> >> >
>> > > >> >> > _______________________________________________
>> > > >> >> > yt-users mailing list
>> > > >> >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >> >
>> > > >> >>
>> > > >> >>
>> > > >> >> ------------------------------
>> > > >> >>
>> > > >> >> Subject: Digest Footer
>> > > >> >>
>> > > >> >> _______________________________________________
>> > > >> >> yt-users mailing list
>> > > >> >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>
>> > > >> >>
>> > > >> >> ------------------------------
>> > > >> >>
>> > > >> >> End of yt-users Digest, Vol 97, Issue 34
>> > > >> >> ****************************************
>> > > >> >
>> > > >> >
>> > > >> >
>> > > >> >
>> > > >> > --
>> > > >> > 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."
>> > > >> >
>> > > >> >
>> > > >> > _______________________________________________
>> > > >> > yt-users mailing list
>> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >
>> > > >>
>> > > >>
>> > > >> ------------------------------
>> > > >>
>> > > >> Message: 4
>> > > >> Date: Wed, 30 Mar 2016 18:01:04 -0400
>> > > >> From: Jonah Miller <jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com> <mailto:jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com>>>
>> > > >> To: yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
>> > > >>         refinement in HDF5
>> > > >> Message-ID: <56FC4CA0.4030403 at gmail.com <mailto:56FC4CA0.4030403 at gmail.com> <mailto:56FC4CA0.4030403 at gmail.com <mailto:56FC4CA0.4030403 at gmail.com>>>
>> > > >> Content-Type: text/plain; charset=windows-1252; format=flowed
>> > > >>
>> > > >> Hi Yanfei,
>> > > >>
>> > > >> To add to Matt's comment. Here is the documentation for using
>> > > >> load_hexahedral_mesh.
>> > > >>
>> > > >>
>> > > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data <http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data> <http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data <http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data>>
>> > > >>
>> > > >>
>> > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html>>
>> > > >>
>> > > >> Best,
>> > > >> Jonah
>> > > >>
>> > > >> On 16-03-30 05:15 PM, Matthew Turk wrote:
>> > > >> > Hi Yanfei,
>> > > >> >
>> > > >> > This is possible -- but it will also slow some things down.  You can
>> > > >> > use the load_hexahedral_mesh function, and there're examples of this.
>> > > >> > This takes away some of the optimizations that regular grids can do,
>> > > >> > but we're hoping to add them back in shortly.  Like the other
>> > > >> > functions it too takes a geometry argument.
>> > > >> >
>> > > >> > -Matt
>> > > >> >
>> > > >> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
>> > > >> > <yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu> <mailto:yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>> wrote:
>> > > >> >> Hi Jonah,
>> > > >> >>
>> > > >> >>     I am able to load the data to yt now using load_amr_grids(). I
>> > > >> notice
>> > > >> >> that it can also set geometry to spherical. This is great. But to
>> > > make
>> > > >> life
>> > > >> >> more complicate. Is it possible to let yt know that the grid is
>> > > >> logarithmic?
>> > > >> >> Currently, load_amr_grids() just take left and right edges of each
>> > > >> block. I
>> > > >> >> guess yt assumes the grid is uniform between left and right edges. Is
>> > > >> it
>> > > >> >> possible to provide arrays of coordinate values for each cell in each
>> > > >> block?
>> > > >> >>
>> > > >> >> Thanks.
>> > > >> >>
>> > > >> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
>> > > >> >> <jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com> <mailto:jonah.maxwell.miller at gmail.com <mailto:jonah.maxwell.miller at gmail.com>>> wrote:
>> > > >> >>> Hi Yan-Feng,
>> > > >> >>>
>> > > >> >>> I haven't tried it, but I think there is functionality for this. You
>> > > >> can
>> > > >> >>> use the load_amr_grids() function which can load amr data in
>> > > >> Cartesian,
>> > > >> >>> spherical, or polar coordinates. Here's the documentation:
>> > > >> >>>
>> > > >> >>>
>> > > >> >>>
>> > > >>
>> > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array> <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array>>
>> > > >> >>>
>> > > >> >>>
>> > > >> >>>
>> > > >>
>> > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids>>
>> > > >> >>>
>> > > >> >>> Best,
>> > > >> >>> Jonah
>> > > >> >>>
>> > > >> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>> > > >> yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu> <mailto:yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>>
>> > > >> >>> wrote:
>> > > >> >>>> Hi,
>> > > >> >>>>           I have some data from a new version of Athena
>> > > simulations.
>> > > >> It is
>> > > >> >>>> in spherical polar coordinate with mesh refinement written in HDF5.
>> > > >> The data
>> > > >> >>>> structure is similar to flash data but not the same. Does anyone
>> > > have
>> > > >> >>>> suggestions to load such data to yt directly?
>> > > >> >>>>
>> > > >> >>>> Thank you.
>> > > >> >>>> --
>> > > >> >>>> Yan-Fei Jiang
>> > > >> >>>>
>> > > >> >>>> Einstein Fellow
>> > > >> >>>> Harvard-Smithsonian Center for Astrophysics
>> > > >> >>>> 60 Garden Street, Cambridge MA USA 02138
>> > > >> >>>> _______________________________________________
>> > > >> >>>> yt-users mailing list
>> > > >> >>>> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>>
>> > > >> >>> _______________________________________________
>> > > >> >>> yt-users mailing list
>> > > >> >>> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>>
>> > > >> >>
>> > > >> >>
>> > > >> >> --
>> > > >> >> Yan-Fei Jiang
>> > > >> >>
>> > > >> >> Einstein Fellow
>> > > >> >> Harvard-Smithsonian Center for Astrophysics
>> > > >> >> 60 Garden Street, Cambridge MA USA 02138
>> > > >> >>
>> > > >> >> _______________________________________________
>> > > >> >> yt-users mailing list
>> > > >> >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >> >>
>> > > >> > _______________________________________________
>> > > >> > yt-users mailing list
>> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >>
>> > > >>
>> > > >>
>> > > >> ------------------------------
>> > > >>
>> > > >> Subject: Digest Footer
>> > > >>
>> > > >> _______________________________________________
>> > > >> yt-users mailing list
>> > > >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >>
>> > > >>
>> > > >> ------------------------------
>> > > >>
>> > > >> End of yt-users Digest, Vol 97, Issue 37
>> > > >> ****************************************
>> > > >>
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > *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.**"*
>> > > >
>> > > >
>> > > > _______________________________________________
>> > > > yt-users mailing list
>> > > > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > > >
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>> > > >
>> > >
>> > > ------------------------------
>> > >
>> > > Subject: Digest Footer
>> > >
>> > > _______________________________________________
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>> > > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> > >
>> > >
>> > > ------------------------------
>> > >
>> > > End of yt-users Digest, Vol 97, Issue 39
>> > > ****************************************
>> > >
>> >
>> >
>> >
>> > --
>> > *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.**"*
>> > -------------- next part --------------
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>> >
>> > ------------------------------
>> >
>> > Subject: Digest Footer
>> >
>> > _______________________________________________
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>> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org> <mailto:yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>>
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
>> >
>> >
>> > ------------------------------
>> >
>> > End of yt-users Digest, Vol 97, Issue 41
>> > ****************************************
>> >
>> >
>> >
>> > --
>> > 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."
>> >
>> > _______________________________________________
>> > yt-users mailing list
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>> ------------------------------
>> 
>> Subject: Digest Footer
>> 
>> _______________________________________________
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>> 
>> 
>> ------------------------------
>> 
>> End of yt-users Digest, Vol 98, Issue 14
>> ****************************************
>> 
>> 
>> 
>> -- 
>> 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."
>> 
>> 
>> 
>> 
>> -- 
>> 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."
>> 
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> 
> 
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