Sonify plugin updates #3269

javerbukh · 2024-11-06T19:12:18Z

Description

This pull request takes the work from james-trayford#3 and moves it into a PR for Jdaviz. There is now a plugin called "Sonify Data" which contains configuration options for sonifying a data cube. There are also options for which speaker the sound will come from, volume, and to start/stop the stream so the spectrum-at-spaxel tool can work as usual after sonifying the cube.

Change log entry

Is a change log needed? If yes, is it added to CHANGES.rst? If you want to avoid merge conflicts,
list the proposed change log here for review and add to CHANGES.rst before merge. If no, maintainer
should add a no-changelog-entry-needed label.
Add Sonify Data plugin which uses the Strauss package to turn a data cube into sound. [Sonify plugin updates #3269]

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
Do the proposed changes follow the STScI Style Guides?
Are tests added/updated as required? If so, do they follow the STScI Style Guides?
Are docs added/updated as required? If so, do they follow the STScI Style Guides?
Did the CI pass? If not, are the failures related?
Is a milestone set? Set this to bugfix milestone if this is a bug fix and needs to be released ASAP; otherwise, set this to the next major release milestone. Bugfix milestone also needs an accompanying backport label.
After merge, any internal documentations need updating (e.g., JIRA, Innerspace)?

- Fix sigcube alignment with other cubes [get rid of transpose] - Add percentile cut option that enables some rough feature isolation without full continuum subtraction - Protect against cubes w/NaNs

…ions

Sonify plugin updates jt

… range

…ch for now, while awaitin PyPI release

Some more functionality tweaks

Jt listener pre merge changes

jdaviz/configs/cubeviz/plugins/cube_listener.py

pllim · 2024-12-12T18:13:53Z

jdaviz/configs/cubeviz/plugins/sonify_data/sonify_data.py:16:1: F841 local variable 'e' is assigned to but never used
jdaviz/configs/cubeviz/plugins/sonify_data/sonify_data.py:21:28: E231 missing whitespace after ','
jdaviz/configs/cubeviz/plugins/sonify_data/sonify_data.py:65:101: E501 line too long (101 > 100 characters)

javerbukh · 2024-12-12T20:59:22Z

The tests pass and run locally but fail on CI because there is no sound device with output. Is there a way we can skip the test in CI? @pllim

pllim · 2024-12-12T22:59:41Z

fail on CI because there is no sound device with output

Can we be sure that every user's machine has a sound device with output? Is it not possible to disable the plugin if such a situation happens (rather than have it fail CI)?

Is there a way we can skip the test in CI?

If you must, yes, you can skip it by checking to see if "CI" env var is set. See https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/store-information-in-variables#default-environment-variables

javerbukh · 2024-12-13T13:55:59Z

jdaviz/configs/cubeviz/plugins/sonify_data/sonify_data.py

+        super().__init__(*args, **kwargs)
+        self._plugin_description = 'Sonify a data cube'
+        self.docs_description = 'Sonify a data cube using the Strauss package.'
+        if not self.has_strauss or sd.default.device[1] < 0:


@pllim This line here will cause the plugin do be disabled if there is not a valid sound output device.

Then why is CI failing? Something is running when it is not supposed to?

Yes, I added a check in vue_sonify_cube() to prevent that from being called.

pllim · 2024-12-13T14:40:37Z

.github/workflows/ci_cron_weekly.yml

+  ci_cron_tests_stable_strauss:
+    name: Python 3.12 with stable versions of dependencies and Strauss
+    runs-on: ubuntu-latest
+    if: (CI == false && (github.repository == 'spacetelescope/jdaviz' && (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' || contains(github.event.pull_request.labels.*.name, 'Extra CI'))))


Now that I see this if here, it does not quite make sense to add a GitHub Actions job and then tell it to never run. Options:

If you still want other tests to run and just to make sure non-strauss stuff does not break when strauss is installed, only skip the failing tests when CI is true. Do not skip the whole job.

If (1) means nothing to you, just remove this whole job from this YAML. It is dead code at this point.

Do I put that skip in the actual test file test_sonify_plugin.py or in this file?

that effectively makes the test useless though, right (unless we occasionally remember to run locally). Is it possible to test that the plugin is disabled because of no sound devices but then still call the internals to generate the sonified cube and assert its contents without ever playing it?

Similar thoughts as Kyle (but less clear) at #3269 (comment)

It would require a non-trivial amount of code moving that should be covered by #3330.

vue_sonify_cube() calls flux_viewer.get_sonified_cube() which requires a device ID because that method creates an instance of CubeListenerData called audified_cube, which does not need a device ID. However, later in the method the sounddevice.OutputStream is created which does need the device ID. I could separate that stream creation from the get_sonified_cube method but that work may be overwritten by #3330 . So is that work worth it to do in this PR if we may do something different down the road? If the answer is yes then I can do that but I wanted to be clear with why I think that effort is covered by #3330.

Given the rush, probably okay to defer unless you think that refactoring is critical here for AAS.

jdaviz/configs/cubeviz/plugins/sonify_data/tests/test_sonify_data.py

javerbukh · 2024-12-13T16:47:12Z

@pllim Looks like the test marked to be skipped if run inside github actions is still being run in the CI. Any suggestions?

pllim · 2024-12-13T18:49:20Z

Pushed a commit to copy over astropy syntax that I know works. 🤞

james-trayford · 2024-12-16T12:43:54Z

IIUC - listener related stuff now compatabile with CI?

So is it just any code formatting, logging, etc now?

pllim · 2024-12-16T15:26:53Z

Still need to insert change log. You can ignore the standalone build.

rosteen

I left a few questions and suggestions. One overarching question: is there a meaningful difference between audification/audified and sonification/sonified? Both are used throughout this code, and if they're being used to mean the same thing we should probably standardize to using only one term.

jdaviz/configs/cubeviz/plugins/viewers.py

jdaviz/configs/cubeviz/plugins/tools.py

pyproject.toml

rosteen

Thanks for the updates, I think this looks good to me now. Re-approving.

kecnry

One small comment that you can take or leave - otherwise looks good to me to merge for now and we can continue to iterate in the follow-up tickets created.

kecnry · 2024-12-19T18:07:08Z

jdaviz/configs/cubeviz/plugins/sonify_data/sonify_data.py

+        self.docs_description = 'Sonify a data cube using the Strauss package.'
+        if not self.has_strauss or sd.default.device[1] < 0:
+            self.disabled_msg = ('To use Sonify Data, install strauss and restart Jdaviz. You '
+                                 'can do this by running `pip install ".[strauss]"` in the command'


should this be updated to pip install strauss now? Back ticks also won't render as code this way... maybe better without them entirely?

Related, I realized that my comment here was never addressed. Right now the instructions are confusing because they don't say that this command has to be run in the Jdaviz root directory, and also aren't applicable if the user is not on a dev install.

The correct syntax is pip install jdaviz[strauss] for end-users.

ref: https://github.com/astropy/astropy/wiki/v7.0.0-RC-testing

Now that strauss is released, can we just suggest pip install strauss or do we want to maintain the ability to pin specific version by suggesting [strauss]?

I'll change it in both places to pip install strauss.

james-trayford · 2024-12-20T10:37:48Z

🎉

javerbukh and others added 25 commits July 31, 2024 17:27

Create audified cube and use with spectrum at spaxel tool

6049d9a

Add Sonify Data plugin and connect to spectrum per spaxel tool

627a34f

Fix errors

9e98b32

Try moving code to mixin

e6d52b4

Move code to viewers.py

0080b2f

Remove print statements

4b01304

Patches:

505f73f

- Fix sigcube alignment with other cubes [get rid of transpose] - Add percentile cut option that enables some rough feature isolation without full continuum subtraction - Protect against cubes w/NaNs

fix np import

89d6fff

add audio frequency range choice and equal loudness normalisation opt…

5c67736

…ions

Create dropdown to select output sound device

d8937c5

Various updates and QOL improvements

75b7ded

Connect volume level in viewer to sonify plugin

9d6844d

add volume attenuation functionality

1d1417c

add sound device switching

6421ee5

feed ELN flag to Image Viewer

352eff9

Merge pull request #18 from james-trayford/sonify-plugin-updates-jt

a7d501e

Sonify plugin updates jt

Enable start stop stream and strauss soft dependency

ceafbb0

Add note to plugin when strauss is not downloaded

a4811e4

Add strauss as soft dependency

2a270ec

Get build devices method working on windows

13f37a8

ensure sound generation always uses the current spectrum-at-spaxel wl…

4a1d628

… range

post rebase clean-up (remove prints and rogue spaces)

a05937d

this syntax seems to work to install strauss on our specific git bran…

0f0eb87

…ch for now, while awaitin PyPI release

Merge pull request #19 from james-trayford/sonify-plugin-updates-jt

a56b26e

Some more functionality tweaks

Update code to be PEP8

18634ea

github-actions bot added cubeviz plugin Label for plugins common to multiple configurations labels Nov 6, 2024

javerbukh added this to the 4.1 milestone Nov 6, 2024

PEP8 fixes

cc51183

javerbukh force-pushed the sonify-plugin-updates branch from 57ee976 to cc51183 Compare November 7, 2024 15:08

James Trayford and others added 2 commits December 12, 2024 17:24

revert change

dc478ce

Merge pull request #23 from james-trayford/jt_listener_mergechanges

e25022f

Jt listener pre merge changes

pllim reviewed Dec 12, 2024

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jdaviz/configs/cubeviz/plugins/cube_listener.py Show resolved Hide resolved

javerbukh commented Dec 13, 2024

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javerbukh added 2 commits December 13, 2024 09:24

Fix codestyle and stop sonify plugin test running on CI

cc81d63

Merge branch 'main' into sonify-plugin-updates

fdef225

pllim reviewed Dec 13, 2024

View reviewed changes

Add test that can run on CI

41b51f6

pllim reviewed Dec 13, 2024

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jdaviz/configs/cubeviz/plugins/sonify_data/tests/test_sonify_data.py Outdated Show resolved Hide resolved

add test to run with CI

a12b687

pllim reviewed Dec 13, 2024

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jdaviz/configs/cubeviz/plugins/sonify_data/tests/test_sonify_data.py Outdated Show resolved Hide resolved

javerbukh added 2 commits December 13, 2024 10:22

Prevent running sonify cube method if disabled_msg is set

908e0af

Use pytest for conditional

4f34615

Update test_sonify_data.py

708024c

Add change log entry

3081c4d

rosteen reviewed Dec 17, 2024

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jdaviz/configs/cubeviz/plugins/viewers.py Outdated Show resolved Hide resolved

jdaviz/configs/cubeviz/plugins/tools.py Outdated Show resolved Hide resolved

pyproject.toml Outdated Show resolved Hide resolved

javerbukh added 2 commits December 17, 2024 14:13

Addres review comments

393031b

Replace audif- with sonif-

853265a

rosteen approved these changes Dec 18, 2024

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kecnry approved these changes Dec 19, 2024

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Change install instructions to pip install strauss

65afcbc

javerbukh merged commit 18a740d into spacetelescope:main Dec 19, 2024
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Sonify plugin updates #3269

Sonify plugin updates #3269

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james-trayford commented Dec 20, 2024

Sonify plugin updates #3269

Sonify plugin updates #3269

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javerbukh commented Nov 6, 2024 • edited Loading

Description

Change log entry

Checklist for package maintainer(s)

pllim commented Dec 12, 2024

javerbukh commented Dec 12, 2024

pllim commented Dec 12, 2024

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javerbukh commented Dec 13, 2024

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james-trayford commented Dec 20, 2024

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