[yt-users] Camera Options
Suoqing Ji
suoqing at physics.ucsb.edu
Fri Apr 15 10:59:22 PDT 2016
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:
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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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> > 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: 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>
> > >
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> > >
> >
> > ------------------------------
> >
> > 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.**"*
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> ------------------------------
>
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> _______________________________________________
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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."
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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