[yt-users] How to re-process a scene?

Fri Sep 16 17:22:20 PDT 2016

Hi Suoqing,

Of course! Here's a link <https://bitbucket.org/yt_analysis/yt/issues/1279>
to the bug report I submitted; I updated it to include your reply. I think
the starting point for new users is going to be adding to the documentation
on the mindset of how these various pieces fit together. As I better learn
how "cameras", "lenses", "scenes" etc. jive together in yt, I'd be happy to
add to sections of the documentation where I got stuck.

If you think that's a good idea, how can I become a supporting editor of
the documentation for http://yt-project.org/doc/? Specifically,
http://yt-project.org/doc/visualizing/volume_rendering.html ?

Scott

Scott Feister, Ph.D.
Postdoctoral Researcher, Flash Center for Computational Science
University of Chicago, Department of Astronomy and Astrophysics

On Fri, Sep 16, 2016 at 6:56 PM, Suoqing Ji <suoqing at physics.ucsb.edu>
wrote:

> Hi Scott,
>
> Just add a bit to Nathan’s comments on volume rendering — previously the
> zooming factor does not change the open angle of perspective lens, that’s
> why you got the same images before and after zooming. I’ve already issued a
> PR here to fix this: https://bitbucket.org/yt_analysis/yt/pull-requests/
> 2381/bugfix-fix-zoom-for-perspective-lens/diff
>
> In addition, if you would like to rotate the camera and keep your focus
> fixed, you could specify the parameter “rot_center” to be your focus (
> http://yt-project.org/docs/dev/reference/api/generated/
> yt.visualization.volume_rendering.camera.Camera.
> rotate.html?highlight=rotate); if not, the default rotation center is the
> camera location. The default rotation center is not set to focus point
> because sometimes people use camera without setting the focus (say, giving
> the camera location and orientation already makes a camera well-defined).
> But we can definitely discuss and think about how to improve this.
>
> Thanks for reporting this!
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> On Sep 16, 2016, at 3:13 PM, Scott Feister <sfeister at gmail.com> wrote:
>
> Hi Nathan,
>
> Thank you so much for this explanation. It gets me off the ground running!
> I appreciate the work you've done to make the volume rendering so amazing;
> these are small final touches. I'll be happy to open a bug report.
>
> Scott
>
>
> Scott Feister, Ph.D.
> Postdoctoral Researcher, Flash Center for Computational Science
> University of Chicago, Department of Astronomy and Astrophysics
>
> On Thu, Sep 15, 2016 at 8:57 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi Scott,
>>
>> So this is really two issues.
>>
>> The first, is that the camera.zoom() function doesn't really zoom in on
>> the image, instead it decreases the "width" the volume rendering region by
>> the zoom factor. This makes a lot of sense for plane-parallel volume
>> renderings (the default), but not so much for perspective lenses as you
>> saw. For a perspective lens you should instead reposition the camera to be
>> closer to the focus to get the same effect.
>>
>> Next, you also saw that manipulating the TransferFunctionHelper object
>> (source.tfh) after you've already done a volume rendering doesn't update
>> the transfer function. That's because the TransferFunctionHelper object is
>> only used to generate the transfer function (source.transfer_function) if
>> it isn't set yet. If it's already set, it reuses it. So in your example the
>> first time you called save(), the VolumeSource saw that no one had manually
>> created a transfer function, and used the TransferFunctionHelper object to
>> build one. Then, when you asked it for the second rendering, it just reused
>> the same one because right now the VolumeSource doesn't track if the
>> TransferFunctionHelper has been updated. To do what you mean, you need to
>> manually set the transfer function to be the one generated by the
>> TransferFunctionHelper:
>>
>> source.tfh.build_transfer_function()
>> source.tfh.setup_default()
>> source.transfer_function = source.tfh.tf
>>
>> After manipulating source.tfh.
>>
>> Using as an example the script from the docs, here's how to make the
>> second image come out as you would expect for the perspective lens:
>>
>> http://paste.yt-project.org/show/6823/
>>
>> Which makes these two images:
>>
>> http://i.imgur.com/gwUTWz1.png (rendering.png)
>> http://i.imgur.com/M1lSz0N.png (rendering2.png)
>>
>> I think we could probably do a better job of detecting that the
>> TransferFunctionHelper has been manipulated and avoid this confusion, if
>> you'd like I invite you to open an issue about this on our issue tracker.
>> One might also argue that the zoom function should adjust the camera
>> position for perspective lenses.
>>
>> Sorry the volume renderer isn't totally intuitive for this use case. I
>> did some work before the yt 3.3.1 release to improve things, but it's still
>> definitely not perfect. I think there's a lot of power there but it also
>> really needs some love from someone who is willing to think about corner
>> cases and interactive workflows.
>>
>> -Nathan
>>
>> On Thu, Sep 15, 2016 at 7:38 PM, Scott Feister <sfeister at gmail.com>
>> wrote:
>>
>>> Hi yt users,
>>>
>>> Hi there! I'm just starting to use yt to make volume renderings of FLASH
>>> simulations. While working through examples, I hit a roadblock, and I've
>>> had some difficulty finding good documentation on the what the
>>> "Scene.save()" function actually does; specifically, why it does different
>>> things on the first and second call. The first example in the user tutorial
>>> page for 3D volume rendering (http://yt-project.org/doc/vis
>>> ualizing/volume_rendering.html) looks something like this:
>>>
>>> ...
>>> *sc = yt.create_scene(ds, lens_type='perspective')*
>>> ...
>>> *source = sc[0]*
>>> *source.tfh.set_bounds((3e-31, 5e-27))*
>>> *...*
>>>
>>> *sc.save('rendering.png', sigma_clip=6.0)*
>>>
>>> And, voila, volume rendering saved to png.
>>>
>>> However, if I naively continue the script to re-render with new settings:
>>> *source.tfh.set_bounds((3e-35, 5e-27))*
>>> *sc.camera.zoom(2.0)*
>>>
>>> *sc.save('rendering2.png', sigma_clip=6.0)*
>>>
>>> I find that none of my new settings are reflected in "rendering2.png" --
>>> it's just a duplicate of "rendering.png"! But if I start again from scratch
>>> with a new scene, the settings take hold. This leaves me (a new user)
>>> scratching my head.
>>>
>>> So here is my question: Once you've created and saved a scene once, how
>>> do you change scene settings like colormap and camera angle?
>>>
>>> Best,
>>>
>>> Scott
>>>
>>>
>>> Scott Feister, Ph.D.
>>> Postdoctoral Researcher, Flash Center for Computational Science
>>> University of Chicago, Department of Astronomy and Astrophysics
>>>
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>>> yt-users mailing list
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>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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