[Users] Query regarding visualisation software/packages

[Annnamalai P S]

Thank you all for taking the time to address my queries. This discussion
thread has been very helpful!

@Gabriele: Thanks again for this detailed answer! This is exactly what I
was hoping to implement and your resources save me a lot of time. I reached
out to get an idea of whether similar code had already been written, and
now that you have shown me these resources, I can focus more on generating
the necessary plots/animations rather than writing the code from scratch.
It has been particularly helpful to see that I won't necessarily be needing
yt as well - the only reason I was keen to find out more was since this is
the first time I have come across this particular package for the purpose
of visualizing volumetric data and wasn't aware of the other packages/tools
I could use.

Kind regards,

On Tue, May 18, 2021 at 12:20 AM Gabriele Bozzola <
bozzola.gabriele at gmail.com> wrote:

> Dear Annamalai,
>
> I don't know much about yt, so the help I can offer is limited and I can
> only point out what you need to be able to do with yt
> to make a video like the one I made. I personally think that yt is not the
> correct tool to use for this kind of plots
> because you need to be able to draw several kinds of structures (curves,
> arrows, meshes, volume rendering), and I am not
> sure what is the level of support for all these different kinds of plots
> in yt. I used mayavi for the example.
>
> 1. Horizons are meshes (typically, 6 partially overlapping meshes). So,
> you need to figure out how to draw meshes
>     with yt. You can learn about how these are represented by kuibit in
> the tutorial on horizons.
>     (https://sbozzolo.github.io/kuibit/tutorials/cactus_horizons.html). I
> report here one of the figures to give an idea
>     of how horizons are represented
> .
> [image: image.png]
>
>   You can obtain the 3D position of all the vertices with the function
> `shape_at_iteration` or `shape_at_time`.
>
> 2. Spins are vectors. You have to find out how to draw arrows in yt. You
> can use the function
>     `ah_origin_at_iteration` to find the center of the horizon at any
> given time, and then you can find the
>     value of the vector you are interested in simply getting the quantity
> with brackets, e.g. h["momentum_x"]
>     would give you a timeseries with the value of the linear momentum
> along the x direction for horizon h.
>     h["momentum_x"](time) is the value of that component at the given
> time, which you can use to draw the
>     arrow.
>
> 3. Orbits are 3D curves. h.ah.centroid_x is a timeseries with the x
> coordinate of the horizon h. You can use this
>     to draw a 3D plot with the orbits. Read tutorial on timeseries for
> more information
>     (https://sbozzolo.github.io/kuibit/tutorials/timeseries.html)
>
> 4. The curvature is the only quantity for which I think it makes sense to
> plot with yt. It is a 3D grid function. Normally,
>     this has all the information about the refinement levels, but you can
> resample everything to a uniform grid.
>     This can be passed to yt as "generic data", as shown here
> https://yt-project.org/doc/examining/generic_array_data.html.
>     For information about grid data, have a look at the relevant tutorial
>     https://sbozzolo.github.io/kuibit/tutorials/grid_data.html.
>
>     When you use mayavi, this can be a 3D contour plot, but it still has
> to be resampled onto an uniform grid.
>
> 5. Gravitational waves are 2D curves that live on a different space
> compared to the main plot. I used matplotlib
>     to draw this (plt.plot(strain)) and then joined the images with
> Pillow. The tutorial on gravitational waves will
>     tell you more about this:
> https://sbozzolo.github.io/kuibit/tutorials/gravitational_waves.html
>
> 6. If you want to have something nice and user-friendly, you can take
> inspiration from the examples in kuibit.
>     These examples are command-line utilities that work out-of-the-box for
> all the simulations. They have a lot
>     of options and other nice features (e.g. tab-completion). Some
> documentation about that is here
>     https://sbozzolo.github.io/kuibit/argparse_helper.html, but the
> examples themselves are great starting points.
>
> My personal recommendation for how you should move forward is to
> familiarize yourself with kuibit first. In this
> email I sketched how you can achieve what you want, but I neglected a ton
> of details. I suspect that it is only after
> you learned the basics of kuibit that this email will make sense. Also,
> you should ask yourself if you really want
> to use yt for this specific use case. If you don't want to, everything I
> described in this email is already implemented
> (with mayavi) and you can simply customize the example that I pointed out
> in the previous email for your needs.
>
> To get started with kuibit, you can read the tutorials,
> https://sbozzolo.github.io/kuibit/#tutorials and this page
> https://sbozzolo.github.io/kuibit/simdir.html. Then, I'd suggest trying
> to re-implement one of the examples on your
> own, for example plot_ah_separation.py (
> https://sbozzolo.github.io/kuibit/examples/bins/plot_ah_separation.html).
> With this, you will gain enough experience to move to the next step and
> make the movie you want to.
>
> Every single function in kuibit is documented. In addition to the examples
> and tutorials, we have two additional
> types of documentation (for a total of four different types):
> - Explanations of the various modules (
> https://sbozzolo.github.io/kuibit/#usage), where you can see how the
> modules
>   should be used and a broad overview on how they are structured and what
> features they provide.
> - Reference and technical details of the APIs (
> https://sbozzolo.github.io/kuibit/#reference-material-classes-functions),
>   where you can see the details of the function signatures, the types
> expected, et cetera.
> You will likely need the latter two forms of documentation when you will
> start writing code with kuibit.
>
> Best,
> Gabriele
>
>
>
> On Mon, May 17, 2021 at 11:05 AM Annnamalai P S <annamalaips.97 at gmail.com>
> wrote:
>
>> Dear Gabriele,
>>
>> Thank you for your reply and for taking the time to point out the
>> resources you felt would be relevant to my current research.
>>
>> I'm currently not very well versed with yt package but am very much
>> interested in the idea that you have suggested. But at the same time I'm
>> new to kuibit as well. If you can share any resources/documentation that
>> helps me to prepare data to be used for yt package that would be great. I
>> hope to create animated volume rendering using yt package like the ones you
>> have created. I also want to set it up as a user friendly and out of the
>> box package that can yield plots for visualization.
>>
>> On Mon, May 17, 2021 at 8:52 PM Gabriele Bozzola <
>> bozzola.gabriele at gmail.com> wrote:
>>
>>> Dear Annamalai,
>>>
>>> I am the author of kuibit, and I would like to highlight that the
>>> package is capable of doing what you are looking for,
>>> including 3D rendering. The package also comes with a lot of examples
>>> that you can immediately use for your
>>> goals. There are already some examples for 2D/3D plots of binary black
>>> holes, and you can see an example of
>>> rendering here:
>>> https://github.com/Sbozzolo/kuibit/tree/experimental/examples
>>> where I rendered a 3D movie with the apparent horizons, magnitude of the
>>> spins, orbits, and gravitational wave
>>> strain. You can produce the same movie for your simulation writing 0
>>> lines of code [1].
>>>
>>> As for yt, kuibit can prepare the data so that it is trivial to use it
>>> with yt (see GitHub issue
>>> https://github.com/Sbozzolo/kuibit/issues/18). I've never used yt and I
>>> don't even know where to start, but if you
>>> are already familiar with it, you'll be able to use it with kuibit in no
>>> time. [2]
>>>
>>> Finally, let me point to the documentation:
>>> https://sbozzolo.github.io/kuibit/. kuibit is thoroughly documented and
>>> there are lots of examples and tutorials that will help you get started.
>>> In addition to that, we have a kuibit user
>>> group chat on Telegram (https://t.me/kuibit) where you can ask
>>> questions if you find that something is not clear.
>>>
>>> Let me know if you have any questions,
>>> Gabriele
>>>
>>>
>>> [1] The code is in the experimental branch, so I would actually not
>>> recommend using it at the moment because it
>>> will break in the future. However, you can still see how it is done
>>> there and use the stable version of kuibit to
>>> achieve a similar result. At this point in time, I would recommend NOT
>>> using the experimental branch.
>>>
>>> [2] In that case, we would love you to contribute back to kuibit :)
>>>
>>> On Mon, May 17, 2021 at 8:05 AM Roland Haas <rhaas at illinois.edu> wrote:
>>>
>>>> Hello Annamalai,
>>>>
>>>> please take a look at our wiki:
>>>>
>>>> https://docs.einsteintoolkit.org/et-docs/Analysis_and_post-processing
>>>>
>>>> Linked in the "Analyzing Data Output by the Einstein Toolkit"
>>>> bullet of "Documentation" section of the wiki at
>>>>
>>>> https://docs.einsteintoolkit.org/et-docs/Main_Page
>>>>
>>>> Please note that yt support is not currently functional since the
>>>> repository linked to no longer exists.
>>>>
>>>> The most functionally complete packages are likely:
>>>>
>>>> * SimulationTools
>>>> * PostCactus
>>>> * Kuibit
>>>>
>>>> For 3d visualization I think you are pretty much limited to VisIt
>>>> unless you convert the HDF5 files into a format understood by other
>>>> packages.
>>>>
>>>> Yours,
>>>> Roland
>>>>
>>>> > Hi Einstein Toolkit users,
>>>> >
>>>> > I'm a relatively new Einstein Toolkit user learning to simulate and
>>>> > visualise binary black hole system mergers. I'm trying to write a
>>>> code to
>>>> > visualise animated trajectories, horizons, gravitational waveforms and
>>>> > curvature of binary system merger using Python matplotlib and
>>>> yt-project
>>>> > packages.
>>>> >
>>>> > Before I proceed, I want to know what are the list of available
>>>> > open-source/commercial visualisation software/packages that can
>>>> produce
>>>> > animated plots(2D and 3D) of binary system merger with data from
>>>> Einstein
>>>> > toolkit output, and get an idea of whether something similar already
>>>> exists.
>>>> >
>>>> >
>>>> > --
>>>> > Best regards,
>>>> > Annamalai P S
>>>>
>>>>
>>>> --
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>>>
>>
>> --
>> Annamalai P S
>>
>

-- 
Annamalai P S
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