Re: [yt-users] Camera Options

21 Apr 2016

      Hi Sushi,

What you need to do this to make use of off-axis slice plot instead of camera; for example, in your code:

L = [1, 0, 0] # View along x axis
north_vector = [0, 0, 1]
slc = yt.SlicePlot(pf, L, “magnetic_field_x", width=(100,'km’), north_vector=north_vector)
slc.annotate_magnetic_field(factor=40, normalize=True)

which gives you the view along x axis. And if you want to rotate the viewing angle by, say 45 degree, you could change the normal vector L to be L = [1, 1, 0], and redo the plotting.

Also, when you load the data, you probably need to change the name “field_x” to be “magnetic_field_x” and so on, so the annotate_magnetic_field function will recognize these names.

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 1:28 PM, Sushilkumar  wrote:
Dear Suoqing Ji:
The fields Bx,By and Bz are already calculated taking into account the rotation. So I am not sure if I need to calculate it again.
What I would like is only change the camera view to a desired angle after I do a slice plot and that is where I am having trouble with?
Thanks in advance.
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Today's Topics:
1. Re: Camera Options (Suoqing Ji)
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Message: 1
Date: Thu, 21 Apr 2016 13:20:32 -0700
From: Suoqing Ji mailto:suoqing@physics.ucsb.edu>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org>
Subject: Re: [yt-users] Camera Options
Message-ID: mailto:FB001F5B-2521-4705-8D31-3166451BCA58@physics.ucsb.edu>
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I see ? that?s a smart way of doing this!
Best wishes,
Suoqing
...
On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:
On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji mailto:suoqing@physics.ucsb.edu mailto:suoqing@physics.ucsb.edu>> wrote:
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
Right, I bet it will work if you do `annotate_velocity()` though.
You should take a look at the definition of the VelocityCallback to see how it handles off-axis slices.
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 <http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing>
...
On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum mailto:nathan12343@gmail.com mailto:nathan12343@gmail.com>> wrote:
On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji mailto:suoqing@physics.ucsb.edu mailto:suoqing@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 <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=fixedre... http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedre... <http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedre... http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedre...>), 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 <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 <http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing>
...
On Apr 21, 2016, at 10:31 AM, Sushilkumar mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@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 <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-render... http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render...>
http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering <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 mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com>> wrote:
Dear Suoqing JI:
Thank you
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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 mailto:suoqing@physics.ucsb.edu mailto:suoqing@physics.ucsb.edu>>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>
Subject: Re: [yt-users] Camera Options
Message-ID: mailto:B885F215-5F0A-49D5-9712-2D8FCEAA1366@physics.ucsb.edu mailto:B885F215-5F0A-49D5-9712-2D8FCEAA1366@physics.ucsb.edu>>
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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-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> <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-render... http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render...> <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... <http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render... http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-render...>>
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 <http://web.physics.ucsb.edu/~suoqing http://web.physics.ucsb.edu/~suoqing>
...
On Apr 15, 2016, at 8:38 AM, Sushilkumar mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@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> <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
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Today's Topics:
1. Inclination problem (Sushilkumar)
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Message: 1
Date: Thu, 31 Mar 2016 22:11:09 -0500
From: Sushilkumar mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com> mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com>>>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
Subject: [yt-users] Inclination problem
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Dear Nathan:
Thank you very much, implementing now
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wrote:
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Today's Topics:
1. Re: Inclination problem (Nathan Goldbaum)
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Message: 1
Date: Thu, 31 Mar 2016 09:50:31 -0500
From: Nathan Goldbaum mailto:nathan12343@gmail.com mailto:nathan12343@gmail.com> mailto:nathan12343@gmail.com mailto:nathan12343@gmail.com>>>
To: Discussion of the yt analysis package
        mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
Subject: Re: [yt-users] Inclination problem
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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> <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 mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com> mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@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, mailto:yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org> mailto:yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org>>>
> wrote:
>
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>> 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" mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu>>>
>> To: Discussion of the yt analysis package
>>         mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
>> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
>>         refinement in HDF5
>> Message-ID:
>>         <
>> CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.com mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.com mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.co...> mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.co... mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%25252B-Ryq5YD-LrYrByDe3Ne7A@mail.gmail....>>>
>> 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@gmail.com mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@gmail.com> mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@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-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...> <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...>>
>> >
>> >
>> >
>>
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...>>
>> >
>> > Best,
>> > Jonah
>> >
>> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>> yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016...><http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016...>>
>> >
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 30 Mar 2016 16:15:30 -0500
>> From: Matthew Turk mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com> mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com>>>
>> To: Discussion of the yt analysis package
>>         mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
>> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
>>         refinement in HDF5
>> Message-ID:
>>         > 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com> mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@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
>> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@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
>> > mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@gmail.com> mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@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-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...> <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...>>
>> >>
>> >>
>> >>
>>
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...>>
>> >>
>> >> Best,
>> >> Jonah
>> >>
>> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>> yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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 mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com> mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com>>>
>> To: Discussion of the yt analysis package
>>         mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
>> Subject: Re: [yt-users] Inclination problem
>> Message-ID:
>>         > joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com mailto:joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com>mailto:joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com mailto:joejr6BBh%25252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@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 mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@gmail.com>mailto:sushil.sush19us@gmail.com mailto:sushil.sush19us@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> <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@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org> mailto:yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org>>
>> >
>> > wrote:
>> >>
>> >> Send yt-users mailing list submissions to
>> >>         yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org> mailto:yt-users-request@lists.spacepope.org mailto:yt-users-request@lists.spacepope.org>>
>> >>
>> >> You can reach the person managing the list at
>> >>         yt-users-owner@lists.spacepope.org mailto:yt-users-owner@lists.spacepope.org mailto:yt-users-owner@lists.spacepope.org> mailto:yt-users-owner@lists.spacepope.org mailto:yt-users-owner@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 mailto:carla.j.bernhardt@gmail.com mailto:carla.j.bernhardt@gmail.com> mailto:carla.j.bernhardt@gmail.com mailto:carla.j.bernhardt@gmail.com>>>
>> >> To: Discussion of the yt analysis package
>> >>         mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
>> >> Subject: Re: [yt-users] gadget onto unigrid
>> >> Message-ID:
>> >>
>> >> mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com>mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com mailto:UhyGS_beuiUMbw7Ag@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> <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 mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com> mailto:matthewturk@gmail.com mailto:matthewturk@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#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-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel...> <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel...>>
>> >> >
>> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
>> >> > mailto:desika.narayanan@gmail.com mailto:desika.narayanan@gmail.com> mailto:desika.narayanan@gmail.com mailto:desika.narayanan@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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016...><http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016...>>
>> >
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 2
>> >> Date: Tue, 29 Mar 2016 08:57:08 -0500
>> >> From: Matthew Turk mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com> mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com>>>
>> >> To: Discussion of the yt analysis package
>> >>         mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>>
>> >> Subject: Re: [yt-users] gadget onto unigrid
>> >> Message-ID:
>> >>
>> >> mailto:P098utA@mail.gmail.com mailto:P098utA@mail.gmail.com>mailto:P098utA@mail.gmail.com mailto:P098utA@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
>> >> mailto:carla.j.bernhardt@gmail.com mailto:carla.j.bernhardt@gmail.com> mailto:carla.j.bernhardt@gmail.com mailto:carla.j.bernhardt@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 mailto:matthewturk@gmail.com mailto:matthewturk@gmail.com> mailto:matthewturk@gmail.com mailto:matthewturk@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#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-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel...> <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... <http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel... http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-sel...>>
>> >> >>
>> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
>> >> >> mailto:desika.narayanan@gmail.com mailto:desika.narayanan@gmail.com> mailto:desika.narayanan@gmail.com mailto:desika.narayanan@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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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 mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@gmail.com> mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@gmail.com>>>
>> To: yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>
>> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
>>         refinement in HDF5
>> Message-ID: <56FC4CA0.4030403@gmail.com mailto:56FC4CA0.4030403@gmail.com mailto:56FC4CA0.4030403@gmail.com> mailto:56FC4CA0.4030403@gmail.com mailto:56FC4CA0.4030403@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-d... http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... <http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...> <http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... <http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...>>
>>
>>
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...><http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...>>
>>
>> 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
>> > mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@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
>> >> mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@gmail.com> mailto:jonah.maxwell.miller@gmail.com mailto:jonah.maxwell.miller@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-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...> <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... <http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...>>
>> >>>
>> >>>
>> >>>
>>
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...> <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... <http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...>>
>> >>>
>> >>> Best,
>> >>> Jonah
>> >>>
>> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
>> yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@cfa.harvard.edu> mailto:yanfei.jiang@cfa.harvard.edu mailto:yanfei.jiang@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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@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> <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@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org>>
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>> Subject: Digest Footer
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>> ------------------------------
>>
>> 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.**"*
>
>
> _______________________________________________
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------------------------------
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.**"*
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End of yt-users Digest, Vol 97, Issue 41
****************************************
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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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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."
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End of yt-users Digest, Vol 98, Issue 27
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-- 
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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