Update volume rendering code to work with more modern yt installations #586

jzuhone · 2019-10-17T17:04:45Z

The API for yt's volume rendering has changed completely. This PR updates the volume rendering code for spectral cubes to reflect this.

I haven't tested this yet, so I'm marking it as WIP until I can. In the meantime, I wanted to put it up for @trhunter to play with.

Closes Issue #571.

coveralls · 2019-10-17T17:17:02Z

Coverage decreased (-3.7%) to 84.309% when pulling 72dd5ac on jzuhone:fix_yt_camera into 31b0b51 on radio-astro-tools:master.

jzuhone · 2019-10-17T20:52:26Z

Ok, it runs, but the images are blank. This will probably take a little while to dig out of.

jzuhone · 2019-10-18T14:07:57Z

@keflavich do you have a favorite VR example that we could try out?

keflavich · 2019-10-18T14:13:42Z

Not really... the GRS l=49 data were pretty good though:

https://spectral-cube.readthedocs.io/en/latest/yt_example.html#sketchfab-isosurface-contours

jzuhone · 2019-10-18T14:14:57Z

Is this the L1448_13CO.fits file?

keflavich · 2019-10-18T14:17:04Z

No but that one is totally fine if it looks OK

jzuhone · 2019-10-19T20:30:25Z

So this is working now. But I'd like to add some tests and change the docs before we merge it.

jzuhone · 2019-10-22T15:09:02Z

Hi @keflavich this is ready to go except I cannot get the test data I generated to compare to (as .npz files) to copy correctly when installed. I've tried several of the normal tricks but nothing seems to work. Any idea what's going on here?

keflavich · 2019-10-23T05:59:36Z

in tests/setup_package.py, you need to add *npz

astrofrog · 2020-01-14T11:46:43Z

@jzuhone - would you be able to rebase this? If you don't have time, I'm happy to take over the PR to clean it up.

jzuhone · 2020-01-14T13:12:00Z

@astrofrog I can rebase it. I had trouble getting the tests to pass before, but I'll see what happens now.

astrofrog · 2020-01-15T13:11:16Z

@jzuhone - thanks! When you rebase can you also set the minimum yt version in setup.cfg? If there are any issues with the tests I'm happy to investigate.

keflavich · 2020-04-29T15:42:42Z

The failure last time was related: https://travis-ci.org/github/radio-astro-tools/spectral-cube/jobs/640107285#L635

We'll need another rebase, and maybe another small correction, to get this fixed.

HealthyPear · 2024-10-18T13:35:56Z

If it can help, I tested this PR with a following file from this radio CO survey

in a conda env with

yt                        4.3.1           py310hfd37619_2    conda-forge
yt-idv                    0.4.1                    pypi_0    pypi

with this test code

from spectral_cube import SpectralCube
import yt

input_file = "./FGN00000XXX" # change XXX with your file ID

cube = SpectralCube.read(input_file)

ytcube = cube.to_yt(spectral_factor=0.5)
ds = ytcube.dataset

# add rest of test code from example in the docs of this PR

I also tried directly the interactive renderer (which is what I would like to use together with isosurfaces)

import yt_idv
rc = yt_idv.render_context(height=800, width=800, gui=True)
sg = rc.add_scene(ds, "flux", no_ghost=True)
rc.run()

in both cases I get

yt : [WARNING  ] 2024-10-18 15:31:05,935 Cannot find time
yt : [INFO     ] 2024-10-18 15:31:05,935 Detected these axes: GLON-SFL GLAT-SFL VRAD
yt : [WARNING  ] 2024-10-18 15:31:05,937 No length conversion provided. Assuming 1 = 1 cm.
yt : [WARNING  ] 2024-10-18 15:31:05,937 Assuming 1.0 = 1.0 s
yt : [WARNING  ] 2024-10-18 15:31:05,937 Assuming 1.0 = 1.0 g
yt : [INFO     ] 2024-10-18 15:31:05,963 Parameters: current_time              = 0.0
yt : [INFO     ] 2024-10-18 15:31:05,963 Parameters: domain_dimensions         = [848 848 462]
yt : [INFO     ] 2024-10-18 15:31:05,963 Parameters: domain_left_edge          = [0.5 0.5 0.5]
yt : [INFO     ] 2024-10-18 15:31:05,964 Parameters: domain_right_edge         = [848.5 848.5 231.5]
yt : [INFO     ] 2024-10-18 15:31:05,964 Parameters: cosmological_simulation   = 0
Setting position 1320.0 320.0
yt : [INFO     ] 2024-10-18 15:31:06,406 Adding field flux to the list of fields.
Traceback (most recent call last):
  File "/Users/michele/Software/3D_rendering_radio_data/test_spectral_cube_from_yt.py", line 78, in <module>
    sg = rc.add_scene(ds, "flux", no_ghost=True)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt_idv/rendering_contexts/base_context.py", line 34, in add_scene
    self.scene = SceneGraph.from_ds(ds, field, no_ghost=no_ghost)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt_idv/scene_graph.py", line 271, in from_ds
    scene.add_volume(data_source, field, no_ghost=no_ghost)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt_idv/scene_graph.py", line 61, in add_volume
    self.data_objects[-1].add_data(field_name, no_ghost=no_ghost)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt_idv/scene_data/block_collection.py", line 40, in add_data
    self.data_source.tiles.set_fields([field], [False], no_ghost=no_ghost)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/utilities/amr_kdtree/amr_kdtree.py", line 232, in set_fields
    for b in self.traverse():
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/utilities/amr_kdtree/amr_kdtree.py", line 250, in traverse
    yield self.get_brick_data(node)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/utilities/amr_kdtree/amr_kdtree.py", line 339, in get_brick_data
    vcd = grid.get_vertex_centered_data(
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/data_objects/index_subobjects/grid_patch.py", line 288, in get_vertex_centered_data
    old_field = np.asarray(self[field], dtype="=f8")
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/data_objects/index_subobjects/grid_patch.py", line 75, in __getitem__
    tr = super().__getitem__(key)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/data_objects/data_containers.py", line 235, in __getitem__
    self.get_data(f)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/data_objects/selection_objects/data_selection_objects.py", line 204, in get_data
    read_fluids, gen_fluids = self.index._read_fluid_fields(
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/geometry/geometry_handler.py", line 241, in _read_fluid_fields
    fields_to_return = self.io._read_fluid_selection(
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/frontends/fits/io.py", line 96, in _read_fluid_selection
    ind += g.select(selector, data.astype("float64"), rv[field], ind)
  File "/Users/michele/Software/miniforge3/envs/radio_3d_renderer_yt_pr586/lib/python3.10/site-packages/yt/data_objects/index_subobjects/grid_patch.py", line 413, in select
    dest[offset : offset + count, i] = source[tuple(sl)][np.squeeze(mask)]
IndexError: boolean index did not match indexed array along dimension 2; dimension is 5 but corresponding boolean dimension is 64

jzuhone changed the title ~~[WIP] Update volume rendering code to work with more modern yt installations~~ Update volume rendering code to work with more modern yt installations Oct 22, 2019

jzuhone force-pushed the fix_yt_camera branch from af2928a to 68e7c2b Compare October 23, 2019 13:42

jzuhone added 16 commits January 21, 2020 12:41

Update this code for more modern yt

8a9a7b4

Bug fixes

c7f41d6

This works now, cleaning things up

26e2f9d

Restore this argument, because it won't mess things up

bc43a1b

Add a zoom option

f5b7eee

Version check

67b4852

Make the movie optional so we can run it in a test

dacf756

Update docstrings

da0d805

Update yt tests to include VR

a2a1d13

So I thought I knew what I was doing but I clearly did not

ed878ad

More standard procedure for the vectors

16ccd84

New docs for yt VR

0a37ed1

Fixing test

cbab6f2

Update link

9185143

Fix resolution

d4c40f9

Add in the npz files

f74060c

jzuhone force-pushed the fix_yt_camera branch from fb2a76c to f74060c Compare January 21, 2020 17:50

jzuhone added 3 commits January 21, 2020 12:51

Set minimum yt version

67fffbd

Add this line like the others

3f4fb01

Do these inside with blocks

72dd5ac

HealthyPear mentioned this pull request Oct 17, 2024

yt 3D rendering of radio data from SpectralCubeFITSDataset #925

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update volume rendering code to work with more modern yt installations #586

Update volume rendering code to work with more modern yt installations #586

jzuhone commented Oct 17, 2019

coveralls commented Oct 17, 2019 •

edited

Loading

jzuhone commented Oct 17, 2019

jzuhone commented Oct 18, 2019

keflavich commented Oct 18, 2019

jzuhone commented Oct 18, 2019

keflavich commented Oct 18, 2019

jzuhone commented Oct 19, 2019

jzuhone commented Oct 22, 2019

keflavich commented Oct 23, 2019

astrofrog commented Jan 14, 2020

jzuhone commented Jan 14, 2020

astrofrog commented Jan 15, 2020

keflavich commented Apr 29, 2020

HealthyPear commented Oct 18, 2024

Update volume rendering code to work with more modern yt installations #586

Are you sure you want to change the base?

Update volume rendering code to work with more modern yt installations #586

Conversation

jzuhone commented Oct 17, 2019

coveralls commented Oct 17, 2019 • edited Loading

jzuhone commented Oct 17, 2019

jzuhone commented Oct 18, 2019

keflavich commented Oct 18, 2019

jzuhone commented Oct 18, 2019

keflavich commented Oct 18, 2019

jzuhone commented Oct 19, 2019

jzuhone commented Oct 22, 2019

keflavich commented Oct 23, 2019

astrofrog commented Jan 14, 2020

jzuhone commented Jan 14, 2020

astrofrog commented Jan 15, 2020

keflavich commented Apr 29, 2020

HealthyPear commented Oct 18, 2024

coveralls commented Oct 17, 2019 •

edited

Loading