[yt-users] Camera Options
Nathan Goldbaum
nathan12343 at gmail.com
Thu Apr 21 12:44:36 PDT 2016
On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji <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
>
> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>
>
> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji <suoqing at physics.ucsb.edu>
> 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
>>
>> 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),
>> 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
>>
>
>> 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
>>
>> On Apr 21, 2016, at 10:31 AM, Sushilkumar <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
>>
>> 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/visualizing/volume_rendering.html#volume-rendering
>>
>> Thanks in advance
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar <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>
>>> wrote:
>>>
>>>> Send yt-users mailing list submissions to
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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>
>>>> To: Discussion of the yt analysis package
>>>> <yt-users at lists.spacepope.org>
>>>> Subject: Re: [yt-users] Camera Options
>>>> Message-ID: <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-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
>>>> >
>>>>
>>>> Best wishes,
>>>> --
>>>> Suoqing JI
>>>> Ph.D Candidate
>>>> Department of Physics
>>>> University of California, Santa Barbara
>>>> http://web.physics.ucsb.edu/~suoqing
>>>>
>>>> > On Apr 15, 2016, at 8:38 AM, Sushilkumar <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>
>>>> >
>>>> > 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>> wrote:
>>>> > Send yt-users mailing list submissions to
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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>>
>>>> > To: Discussion of the yt analysis package
>>>> > <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>>
>>>> > 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>>
>>>> > wrote:
>>>> >
>>>> > > Send yt-users mailing list submissions to
>>>> > > 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>
>>>> > > 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>
>>>> > >
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>>>> > > When replying, please edit your Subject line so it is more specific
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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>>
>>>> > > To: Discussion of the yt analysis package
>>>> > > <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>>
>>>> > > 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
>>>> >
>>>> > >
>>>> > > 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>>
>>>> > > 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>>
>>>> > > > wrote:
>>>> > > >
>>>> > > >> Send yt-users mailing list submissions to
>>>> > > >> 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>
>>>> > > >> 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>
>>>> > > >>
>>>> > > >> You can reach the person managing the list at
>>>> > > >> yt-users-owner at lists.spacepope.org <mailto:
>>>> yt-users-owner at lists.spacepope.org>
>>>> > > >>
>>>> > > >> When replying, please edit your Subject line so it is more
>>>> specific
>>>> > > >> than "Re: Contents of yt-users digest..."
>>>> > > >>
>>>> > > >>
>>>> > > >> Today's Topics:
>>>> > > >>
>>>> > > >> 1. Re: load spherical polar coordinate data with mesh
>>>> refinement
>>>> > > >> in HDF5 (Jiang, Yanfei)
>>>> > > >> 2. Re: load spherical polar coordinate data with mesh
>>>> refinement
>>>> > > >> in HDF5 (Matthew Turk)
>>>> > > >> 3. Re: Inclination problem (Matthew Turk)
>>>> > > >> 4. Re: load spherical polar coordinate data with mesh
>>>> refinement
>>>> > > >> in HDF5 (Jonah Miller)
>>>> > > >>
>>>> > > >>
>>>> > > >>
>>>> ----------------------------------------------------------------------
>>>> > > >>
>>>> > > >> Message: 1
>>>> > > >> Date: Wed, 30 Mar 2016 15:49:26 -0400
>>>> > > >> From: "Jiang, Yanfei" <yanfei.jiang at cfa.harvard.edu <mailto:
>>>> yanfei.jiang at cfa.harvard.edu>>
>>>> > > >> To: Discussion of the yt analysis package
>>>> > > >> <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>>
>>>> > > >> 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>> 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/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>>
>>>> > > >> > 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>
>>>> > > >> >>
>>>> 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>
>>>> > > >> > 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
>>>> >
>>>> > > >> >
>>>> > > >>
>>>> > > >> ------------------------------
>>>> > > >>
>>>> > > >> Message: 2
>>>> > > >> Date: Wed, 30 Mar 2016 16:15:30 -0500
>>>> > > >> From: Matthew Turk <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>>
>>>> > > >> 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>>
>>>> > > >> 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>> 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>> 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/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>>
>>>> > > >> >> 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>
>>>> > > >> >>>
>>>> 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>
>>>> > > >> >>
>>>> 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>
>>>> > > >> > 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>>
>>>> > > >> To: Discussion of the yt analysis package
>>>> > > >> <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>>
>>>> > > >> 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>
>>>> > > >
>>>> > > >> 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>
>>>> > > >> >
>>>> > > >> > 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>
>>>> > > >> >
>>>> > > >> > wrote:
>>>> > > >> >>
>>>> > > >> >> Send yt-users mailing list submissions to
>>>> > > >> >> 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>
>>>> > > >> >> 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>
>>>> > > >> >>
>>>> > > >> >> You can reach the person managing the list at
>>>> > > >> >> 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>>
>>>> > > >> >> To: Discussion of the yt analysis package
>>>> > > >> >> <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>>
>>>> > > >> >> 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>>
>>>> > > >> I
>>>> > > >> >> got).
>>>> > > >> >>
>>>> > > >> >> Thanks,
>>>> > > >> >> Carla
>>>> > > >> >>
>>>> > > >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <
>>>> 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#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>> 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>
>>>> > > >> >> > >
>>>> 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>
>>>> > > >> >> >
>>>> 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
>>>> >
>>>> > > >> >
>>>> > > >> >>
>>>> > > >> >> ------------------------------
>>>> > > >> >>
>>>> > > >> >> Message: 2
>>>> > > >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500
>>>> > > >> >> From: Matthew Turk <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>>
>>>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid
>>>> > > >> >> Message-ID:
>>>> > > >> >>
>>>> > > >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=
>>>> 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>> 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>>:
>>>> > > >> >> >>
>>>> > > >> >> >> 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#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>> 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>
>>>> > > >> >> >> >
>>>> 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>
>>>> > > >> >> >>
>>>> 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>
>>>> > > >> >> >
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>>>> > > >> >> >
>>>> > > >> >>
>>>> > > >> >>
>>>> > > >> >> ------------------------------
>>>> > > >> >>
>>>> > > >> >> Subject: Digest Footer
>>>> > > >> >>
>>>> > > >> >> _______________________________________________
>>>> > > >> >> yt-users mailing list
>>>> > > >> >> yt-users at lists.spacepope.org <mailto:
>>>> yt-users at lists.spacepope.org>
>>>> > > >> >>
>>>> 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>
>>>> > > >> > 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>>
>>>> > > >> To: 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>>
>>>> > > >> 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/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>> 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>> 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/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>>
>>>> > > >> >>> 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>
>>>> > > >> >>>>
>>>> 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>
>>>> > > >> >>>
>>>> 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>
>>>> > > >> >>
>>>> 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>
>>>> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>>>> > > >>
>>>> > > >>
>>>> > > >>
>>>> > > >> ------------------------------
>>>> > > >>
>>>> > > >> Subject: Digest Footer
>>>> > > >>
>>>> > > >> _______________________________________________
>>>> > > >> yt-users mailing list
>>>> > > >> yt-users at lists.spacepope.org <mailto:
>>>> yt-users at lists.spacepope.org>
>>>> > > >> 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
>>>> >
>>>> > > > 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/20160331/b739cfe9/attachment.htm
>>>> <
>>>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/b739cfe9/attachment.htm
>>>> >
>>>> > > >
>>>> > >
>>>> > > ------------------------------
>>>> > >
>>>> > > Subject: Digest Footer
>>>> > >
>>>> > > _______________________________________________
>>>> > > yt-users mailing list
>>>> > > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
>>>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>>>> > >
>>>> > >
>>>> > > ------------------------------
>>>> > >
>>>> > > 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 --------------
>>>> > An HTML attachment was scrubbed...
>>>> > URL: <
>>>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/f4f56e5d/attachment.htm
>>>> <
>>>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/f4f56e5d/attachment.htm
>>>> >>
>>>> >
>>>> > ------------------------------
>>>> >
>>>> > Subject: Digest Footer
>>>> >
>>>> > _______________________________________________
>>>> > yt-users mailing list
>>>> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
>>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>>>> >
>>>> >
>>>> > ------------------------------
>>>> >
>>>> > End of yt-users Digest, Vol 97, Issue 41
>>>> > ****************************************
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > SK2
>>>> >
>>>> > "Claiming that something can move faster than light is a good
>>>> conversation-stopper in physics. People edge away from you in cocktail
>>>> parties; friends never return phone calls. You just don?t mess with Albert
>>>> Einstein."
>>>> >
>>>> > _______________________________________________
>>>> > yt-users mailing list
>>>> > yt-users at lists.spacepope.org
>>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
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>>>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160415/0ccad489/attachment.htm
>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> Subject: Digest Footer
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> End of yt-users Digest, Vol 98, Issue 14
>>>> ****************************************
>>>>
>>>
>>>
>>>
>>> --
>>> *SK2*
>>>
>>> *"**Claiming that something can move faster than light is a good
>>> conversation-stopper in physics. People edge away from you in cocktail
>>> parties; friends never return phone calls. You just don’t mess with Albert
>>> Einstein.**"*
>>>
>>>
>>
>>
>> --
>> *SK2*
>>
>> *"**Claiming that something can move faster than light is a good
>> conversation-stopper in physics. People edge away from you in cocktail
>> parties; friends never return phone calls. You just don’t mess with Albert
>> Einstein.**"*
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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