[yt-users] Camera Options
Suoqing Ji
suoqing at physics.ucsb.edu
Thu Apr 21 13:20:32 PDT 2016
I see — that’s a smart way of doing this!
Best wishes,
Suoqing
> On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>
>
> On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji <suoqing at physics.ucsb.edu <mailto:suoqing at 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>
>> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum <nathan12343 at gmail.com <mailto: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
>>>
>>>
>>>
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>>>
>>> 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
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>>> > >
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>>> > > 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
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>>> > > >>
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>>> > > >> 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: 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>>
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>>> > > >> >> >
>>> > > >> >>
>>> > > >> >>
>>> > > >> >> ------------------------------
>>> > > >> >>
>>> > > >> >> 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
>>> > > >>
>>> > > >> _______________________________________________
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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 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>>
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>>> > > >
>>> > >
>>> > > ------------------------------
>>> > >
>>> > > Subject: Digest Footer
>>> > >
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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.**"*
>>> > -------------- next part --------------
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>>> >
>>> > ------------------------------
>>> >
>>> > Subject: Digest Footer
>>> >
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>>> >
>>> >
>>> > ------------------------------
>>> >
>>> > 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."
>>> >
>>> > _______________________________________________
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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
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>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>>
>>
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>>
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>
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