Volume rendering for octrees #2610

cphyc · 2020-05-27T16:59:25Z

This PR adds support for doing volume rendering for octree-based datasets (e.g. RAMSES). It is built on top of #2425 to provide vertex-centred data (not yet wired though).

It follows the same idea as #2442, but relying instead with an independent octree ray tracer. This has the advantage of making the code much simpler, but generates a bit of code repetition and requires rebuilding an octree.

Currently, it supports the yt API for volume rendering.

Features

support vertex centered data for trilinear interpolation
wire with yt volume rendering API
can handle any geometry, takes care of CPU domains nicely
handle different AMR levels
handle "holes" in the dataset (this means you can use an arbitrary data source for the volume renderer)
Deallocate properly all the stuff (i.e. find the origin of the memory leak)
Possible to improve "aliasing" effect? See image of galaxy in next post.
Merge Octree ghost zones — reloaded #2425 before merging this one.

Demo

import yt
ds = yt.load_sample('output_00080', 'info_00080.txt')
sp = ds.all_data()
sc = yt.create_scene(sp, lens_type='perspective')
source = sc[0]

source.tfh.set_bounds((3e-31, 5e-27))
source.tfh.grey_opacity = True
source.tfh.plot('transfer_function.png', profile_field='density')

sc.save('rendering.png', sigma_clip=4)

Notes on performance

The entire script above takes about 20s to run from end to end. Casting the rays and integrating the transfer function actually only takes 4s on 8 cores (with hyperthreading), 5s on 4 cores and 16s on a single core. The dataset consists of 1,749,455 cells.

cphyc · 2020-05-28T10:53:53Z

After quite a long time working on this, I think this should be ready for review! There's probably ways to make all this cleaner, so don't hesitate!

It is also probably still missing some tests, @matthewturk any suggestion regarding the way to go? Duplicate all 3d rendering tests already happening with grid-based datasets?

cphyc · 2020-05-28T15:11:35Z

There seems to be a compilation issue caused with an older version of gcc used on jenkins. Any guess how to solve this?

neutrinoceros

Didn't have time for a full review, I stopped at 8/40 files. I only have a handful of minor suggestions for those, this seems very well written as usual :)

yt/frontends/ramses/io_utils.pyx

yt/fields/geometric_fields.py

yt/frontends/ramses/data_structures.py

cphyc · 2020-05-29T13:30:38Z

I made some high-res images of a high-resolution galaxy (dx ~ 30pc). It turns out that I had some Fortran/C ordering issues (now fixed in be79cb0) which significantly improves the quality of the image (see images before (top) and after (bottom) the fix).

We can still some grid effects, but they seem "normal" to me.

Performances

Parallelized over 40 cores, each image takes about ~3s to generate (for a resolution of 1024x1024).

Eye-candy

Here's some eye-candy. This shows a galaxy at z=2, with resolution 30pc. Took 10min to render (200frames, 3,168,583 cells).

cphyc · 2020-06-17T15:53:19Z

Converted this to draft because we first need to merge #2425!

cphyc · 2020-07-20T09:50:12Z

There's a massive performance hit that will be resolved by 24a7343 (from #2735). Otherwise I guess it's good to go!

neutrinoceros

I can not honestly pretend I read and reviewed the core cpp part, but for the parts I did read, here are my suggestions. Great stuff as always :)

yt/utilities/lib/image_samplers.pyx

yt/data_objects/octree_subset.py

yt/frontends/ramses/data_structures.py

neutrinoceros · 2020-07-20T14:48:52Z

yt/utilities/lib/pyoctree_raytracing.py

+        RE = np.array([1, 1, 1], dtype=np.float64)
+        depth = data_source.ds.parameters["levelmax"]
+
+        self.octree = CythonOctreeRayTracing(LE, RE, depth)


tbh I find the naming of those classes a bit odd. CythonOctreeRayTracing sounds like the Cython version of OctreeRayTracing, not of a component of the class. But maybe I just don't understand enough of this, it could be absolutely fine.

It is very odd. We should discuss better options. @matthewturk @munkm what's your opinion? The issue is that my implementation is multi-layered, there's a C++ implementation that's wrapped in a cython file that's wrapped in a python file... So we could probably get rid of most of these layers, but which ones?

I changed the naming so that the python file is named octree_raytracing.py, the cython wrapper is _octree_raytracing.p{xd,yx} and the C++ file is _octree_raytracing.hpp.

neutrinoceros · 2020-07-20T14:49:43Z

yt/utilities/lib/pyoctree_raytracing.py

+        ds = data_source.ds
+
+        xyz = np.stack(
+            [data_source[_].to("unitary").value for _ in "x y z".split()], axis=-1


Suggested change

[data_source[_].to("unitary").value for _ in "x y z".split()], axis=-1

[data_source[key].to("unitary").value for key in "xyz"], axis=-1

neutrinoceros · 2020-07-20T15:55:22Z

yt/utilities/lib/image_samplers.pyx

@@ -67,6 +71,10 @@ cdef class ImageSampler:
                  *args, **kwargs):
        cdef int i

+        self.volume_method = kwargs.pop('volume_method', None)
+        if self.volume_method and self.volume_method not in ('KDTree', 'Octree'):


Suggested change

if self.volume_method and self.volume_method not in ('KDTree', 'Octree'):

if self.volume_method not in ('KDTree', 'Octree'):

yt/utilities/lib/image_samplers.pyx

yt/visualization/volume_rendering/render_source.py

neutrinoceros · 2020-07-20T16:01:48Z

yt/visualization/volume_rendering/render_source.py

+            ds = data.ds
+
+            xyz = np.stack(
+                [data[_].to("unitary").value for _ in "x y z".split()], axis=-1


Suggested change

[data[_].to("unitary").value for _ in "x y z".split()], axis=-1

[data[key].to("unitary").value for key in "xyz"], axis=-1

neutrinoceros · 2020-07-20T16:02:39Z

yt/visualization/volume_rendering/render_source.py

-        return image
+        self.zbuffer = zbuffer
+        self.set_sampler(camera)
+        assert self.sampler is not None


Suggested change

assert self.sampler is not None

if self.sampler is None:

raise RuntimeError(message...)

yt/frontends/ramses/data_structures.py

cphyc · 2020-08-03T12:29:37Z

The failing tests are real; I'll have to dig into it.

cphyc · 2020-08-03T14:08:47Z

/rebase

matthewturk · 2020-08-03T15:40:06Z

/rebase

Pull request is not rebaseable

This reverts commit c768d9d for off_axis_projection.py

setup.py

Call function Only support Ndim=3 Drop usage of "using" and rely on typedef instead Use uint8_t instead of u_char Fix platform in appveyor Using uint64_t instead of uint

cphyc · 2020-08-31T09:02:01Z

This is now ready to go!

matthewturk

I think we should do it. One slight reservation is that we're changing the appveyor image,b ut that's not necessarily a big deal.

cphyc · 2020-09-09T14:08:28Z

I think we should do it. One slight reservation is that we're changing the appveyor image, but that's not necessarily a big deal.

I am actually unsure this is still necessary. Let me try using the old one.

cphyc · 2020-09-09T15:30:04Z

I think we should do it. One slight reservation is that we're changing the appveyor image,b ut that's not necessarily a big deal.

I reverted the change of the appveyor image, as it was not necessary anymore!

neutrinoceros · 2020-09-15T05:30:29Z

@yt-fido test this please

cphyc mentioned this pull request May 27, 2020

[WIP] Octree ray tracing #2442

Closed

5 tasks

cphyc changed the title ~~[WIP] Octree raytracing~~ Volume rendering for octress May 28, 2020

cphyc added code frontends Things related to specific frontends new feature Something fun and new! viz: volume rendering labels May 28, 2020

neutrinoceros reviewed May 28, 2020

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cphyc changed the title ~~Volume rendering for octress~~ Volume rendering for octrees May 28, 2020

cphyc mentioned this pull request Jun 1, 2020

SPH and Octree AMR Datasets Failing in volume rendering, OAProj, Interactive Data Viz #1212

Open

cphyc mentioned this pull request Jun 11, 2020

Support vertex centred data #2615

Merged

cphyc added the yt-4.0 feature targeted for the yt-4.0 release label Jun 11, 2020

cphyc marked this pull request as draft June 17, 2020 15:52

cphyc changed the base branch from yt-4.0 to master June 22, 2020 17:24

cphyc force-pushed the indep-octree-raytracing branch 2 times, most recently from 7a39833 to 1817b1b Compare July 2, 2020 19:44

cphyc force-pushed the indep-octree-raytracing branch from 47b367a to 06b8faf Compare July 20, 2020 09:49

cphyc marked this pull request as ready for review July 20, 2020 09:49

neutrinoceros approved these changes Jul 20, 2020

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neutrinoceros reviewed Jul 20, 2020

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yt/frontends/ramses/data_structures.py Outdated Show resolved Hide resolved

cphyc mentioned this pull request Aug 4, 2020

Refactor walk_volume in volume rendering #2809

Draft

5 tasks

cphyc added a commit to cphyc/yt that referenced this pull request Aug 10, 2020

Use retrieve_ghost_zone from yt-project#2610

73e8fbe

cphyc added a commit to cphyc/yt that referenced this pull request Aug 12, 2020

Use retrieve_ghost_zone from yt-project#2610

010b429

cphyc marked this pull request as draft August 12, 2020 08:57

Revert "Start fixing what I broke ..."

55aa3ca

This reverts commit c768d9d for off_axis_projection.py

cphyc marked this pull request as ready for review August 30, 2020 09:06

cphyc added 6 commits August 30, 2020 11:15

More sensible naming conventions

70a597f

Fix pxd imports

d19f845

Fixing isort

acf1032

Import from API

aaf8d88

Get rid of "VolumeSource" invocations

9e11403

Bump image for appveyor

cd8311b

neutrinoceros reviewed Aug 30, 2020

View reviewed changes

setup.py Outdated Show resolved Hide resolved

Fix windows build

748e7ef

Call function Only support Ndim=3 Drop usage of "using" and rely on typedef instead Use uint8_t instead of u_char Fix platform in appveyor Using uint64_t instead of uint

cphyc force-pushed the indep-octree-raytracing branch from f8dc942 to 748e7ef Compare August 30, 2020 17:34

cphyc requested review from matthewturk and munkm and removed request for matthewturk and munkm August 31, 2020 09:02

matthewturk approved these changes Sep 9, 2020

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Revert appveyor image?

a6cf130

Merge branch 'master' into indep-octree-raytracing

d4028e4

neutrinoceros merged commit 987ef35 into yt-project:master Sep 15, 2020

neutrinoceros mentioned this pull request Sep 15, 2020

Rearrange data objects #2828

Merged

cphyc deleted the indep-octree-raytracing branch September 15, 2020 07:51

This was referenced Oct 8, 2020

Fresh yt installation not importing #2892

Closed

Fix GCC 5 Builds #2939

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PaoloSuin mentioned this pull request Feb 2, 2023

find_clump not working on octree-AMR datasets #4322

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Volume rendering for octrees #2610

Volume rendering for octrees #2610

cphyc commented May 27, 2020 •

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neutrinoceros commented Sep 15, 2020

	[data_source[_].to("unitary").value for _ in "x y z".split()], axis=-1
	[data_source[key].to("unitary").value for key in "xyz"], axis=-1

	if self.volume_method and self.volume_method not in ('KDTree', 'Octree'):
	if self.volume_method not in ('KDTree', 'Octree'):

	[data[_].to("unitary").value for _ in "x y z".split()], axis=-1
	[data[key].to("unitary").value for key in "xyz"], axis=-1

	assert self.sampler is not None
	if self.sampler is None:
	raise RuntimeError(message...)

Volume rendering for octrees #2610

Volume rendering for octrees #2610

Conversation

cphyc commented May 27, 2020 • edited Loading

Features

Demo

Notes on performance

cphyc commented May 28, 2020

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Performances

Eye-candy

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