[yt-users] transparency and color from two arrays (cont.)

[Nathan Goldbaum]

On Wed, May 17, 2017 at 5:29 AM Matej Tyc <matej.tyc at gmail.com> wrote:

> On 15.5.2017 21:26, Nathan Goldbaum wrote:
>
> On Mon, May 15, 2017 at 2:12 PM, Matěj Týč <matej.tyc at gmail.com> wrote:
>
>> Hello guys,
>>
>
> we're not all guys :)
>
> Actually, guys includes everybody:
> https://en.wiktionary.org/wiki/guys
>

I've had several women tell me that using gendered language like that makes
them feel uncomfortable participating in discussions. That's why I pointed
it out, I want to make sure everyone feels comfortable.



> our research group would like to visualize volume data, where the
>> transfer function is bivariate (see
>>
>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2017-April/008552.html
>> ). We have been struggling with this task, so I would like you to help
>> me understand some of the basic concepts I have come across and that I
>> find confusing.
>>
>> 1. I think that I somehow understand the concept of transfer functions
>> with multiple fields, but I have difficulties of creating a volume
>> source with multiple fields. I have somehow examined the source code,
>> and it seems to me that only the first field is used (judging by
>>
>> https://github.com/yt-project/yt/blob/master/yt/visualization/volume_rendering/render_source.py#L516
>> ).
>
>
> The class you linked to here is for rendering unstructured mesh data. Is
> that what you're trying to do? If so then the advice for how to proceed is
> very different than if you are rendering gridded data.
>
> It is great that you have pointed this out. I think that we have gridded
> data (i.e. a numpy array that corresponds to sampled data). What does it
> mean that render_source is not involved?
>

You will be using a VolumeSource in that case, not a MeshSource. There will
still be a source to be rendered though.

Would be the following snippet OK if I implement the MyCustomTF correctly?
>
> import scipy as sp
> import yt
> import yt.visualization.volume_rendering.api as vr_api
>
> trans = sp.rand(20, 40, 40)
> color = sp.rand(20, 40, 40)
>
> ds = yt.load_uniform_grid(dict(color=color, trans=trans),
>               color.shape)
>
> scene = vr_api.Scene()
>
> source = vr_api.VolumeSource(ds.all_data(), ["color", "trans"])
> source.log_field = False
> source.transfer_function = MyCustomTF(...)
> scene.add_source(source)
>
> scene.add_camera()
> scene.save('render.png')
>

In principle yes.


>
> You are right that each source only renders a single field. If you want to
> render more than one field you will need to create multiple sources.
>
>
>> If I am wrong and it is meaningful and possible to construct a source
>> with multiple fields, could you please provide an example?
>>
>
> Here's an example:
>
>
> https://github.com/yt-project/yt/blob/master/doc/source/cookbook/render_two_fields.py
>
> That said, this is simply compositing two separate volume renderings
> together. A bivariate transfer function is a bit more complex than this.
>
> Transfer function is a property of a volume source, isn't it? So if one
> source means one field, then how can a transfer function access multiple
> fields? At least PlanckTransferFunction uses multiple fields.
>

Good point. You may need to relax that assumption.


> 2. I have no doubts that transfer functions work, but I was unable to
>> find out how are they involved in the integration process. What I came
>> across were the integration routines and they have mentioned that the
>> transfer function is not used:
>>
>> https://github.com/yt-project/yt/blob/master/yt/utilities/lib/ray_integrators.pyx#L235
>> . This is really interesting, how is it in reality?
>>
>
> I believe the low-level routine you want to look at in is
> yt/utlities/lib/image_samplers.pyx, in particular the VolumeRenderSampler.
> The PlaneVoxelIntegration class you linked to here is experimental code
> that is not used elsewhere in yt.
>
> okay, I am happy about this as the code was extremely hard to read. This
> one is somehow easier, although the code still doesn't reveal much intent
> and names of variables are difficult to understand for an outsider. Anyway,
> I will proceed and if I manage to understand it, I may be able to come up
> with some proposals.
>

Feel free to ask questions as you have them.


> 3. You have mentioned the PlanckTransferFunction as a good example of
>> multivariate transfer function.
>> However, doing a Google search, hoping that we will find a code snippet
>> featuring a non-trivial example did not yield any results. Would you be
>> so kind and provide one?
>>
>
> There is no easy example I'm aware of. Making it easier to do the sorts of
> bivariate volume renderings you're trying to do is a longstanding issue.
> I'm not aware of anyone successfully using the machinery in yt for doing
> volume renderings with transfer functions that depend on multiple fields
> since John Wise added the code for the PlanckTransferFunction several years
> ago. That code was not added with any documentation or tests so
> unfortunately it may have bitrot since it was added. Also, in the meantime
> the volume rendering machinery in yt has undergone substantial reworking so
> it's possible that things are just simply broken right now.
>
> We would welcome contributions that make it easier to do the sorts of
> volume renderings you are trying to do. I'm sorry that it's not
> straightforward to do that right now.
>
> As soon as I get this working, I will be happy to submit a PR.
>
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