Add neuron reconstruction job backend and frontend part #5922

MichaelBuessemeyer · 2021-12-22T14:37:37Z

This PR adds the necessary parts to the frontend and backend to make the new nuclei reconstruction job of the worker callable.

Open TODOs:

The job needs a description
The job needs an example image

URL of deployed dev instance (used for testing):

https://___.webknossos.xyz

Steps to test:

Enable jobs via yarn enable-jobs.
Open a dataset in view mode.
In the dataset info tab open the processing jobs menu and select the nuclei reconstruction menu entry.
Go to the jobs list and wait for you job to finish.

Issues:

No issue exists in the repo for this

Updated (unreleased) changelog
- I think this is not needed as this feature is still experimental, right?
Ready for review

…-nuclei-reconstruction-job

And disable jobs

…-nuclei-reconstruction-job

MichaelBuessemeyer · 2022-01-10T17:35:42Z

@philippotto I am currently working on making the bounding box of the volume that should be predicted for neurons configurable in the frontend.

The approach I went for is having another select (just like it is right now when the dataset has multiple color layers).
Instead of giving the user the possibility to enter the bounding box via numbers, which I think is quite bothersome, I went for the users bounding boxes. The UI now lets the user select one of the bounding boxes of this annotation. Do you think this is alrighty this way?

I think the advantages are that the user can / must explicitly but quite easy via the bounding box tool, select the volume for the prediction. Therefore the selected volume is first visually displayed to the user so the user can check again whether thats exactly the volume the user wants.
On the other hand, a simple number input that parses 6 numbers is better for automation.
My argument against the simple number input is that this is a UI and it should be more "visual" instead of simply entering numbers. If automation is needed, then this might be a good candidate for wk-libs?

Do you think my arguments make sense and that I chose the right approach?

Thanks for you feedback. 🐱

philippotto · 2022-01-11T09:20:04Z

@MichaelBuessemeyer Sounds great! In the rare (?) scenario that a user happens to have 6 digits in their clipboard, they can always go to the bounding box tab to paste it there. We want to encourage the use of the bounding box tools and therefore it makes sense to reuse that. Good thinking!

…-nuclei-reconstruction-job

MichaelBuessemeyer · 2022-01-13T18:48:29Z

In the rare (?) scenario that a user happens to have 6 digits in their clipboard, they can always go to the bounding box tab to paste it there.

Thanks , thats a very smart solution to that problem 👍

MichaelBuessemeyer

@philippotto I just checked the frontend part of the neuron inferral again. It is now ready for your review. Could you please take over that review? 👀 📝

Random emoji of this post: 🐧

frontend/javascripts/admin/job/job_list_view.js

frontend/javascripts/oxalis/view/right-border-tabs/starting_job_modals.js

MichaelBuessemeyer · 2022-01-24T21:09:20Z

@fm3 could you please check the backend changes?

fm3

Backend looks good 🎉

…nds/webknossos into add-nuclei-reconstruction-job

…-nuclei-reconstruction-job

frontend/javascripts/oxalis/view/components/setting_input_views.js

MichaelBuessemeyer

@philippotto I just finished applying your feedback. I also added the example screenshot for the neuron inferral. Could you please another look on this pr 👀 🏃‍♂️

Random emoji of this post: 🏎️

philippotto · 2022-01-28T12:50:31Z

frontend/javascripts/oxalis/view/right-border-tabs/starting_job_modals.js

@@ -186,8 +187,7 @@ function StartingJobModal(props: StartingJoblModalProps) {
      <br />
      <div style={{ textAlign: "center" }}>
        <img
-          //TODO: get an image
-          src="/assets/images/nuclei_inferral_example.jpg"
+          src={`/assets/images/${_.snakeCase(jobName)}_example.jpg`}


this will make it very hard to search where the file is used. I'd suggest to create a mapping object from jobName to path to make it easier to find. something like this:

const jobNameToImagePath = { "neuron_inferral": "neuron_inferral_example.jpg", ... }

also: the screenshot quality of the new image is quite poor. maybe set the zoom value to 1 to avoid resizing issues? also, I'd hide the "crosshair" in the image.

Thanks for the feedback. I did notice that the image had such a bad resolution. It should be better blazingly sharp 🗡️ now.

…-nuclei-reconstruction-job

frontend/javascripts/oxalis/view/right-border-tabs/starting_job_modals.js

philippotto

Awesome! I could test it and after fixing an issue in vx, it worked very well :) I only left some cosmetic feedback for the UI. Merging this PR is blocked by the worker PR, anyway.

frontend/javascripts/oxalis/view/right-border-tabs/starting_job_modals.js

fm3 · 2022-02-03T13:44:17Z

Sorry I didn’t read through all of the code and comments just now, but quick question: what mechanism are you using to limit this feature to scm team members? the isSuperUser property is not currently exposed in the user json, is it?

philippotto · 2022-02-03T14:04:07Z

Sorry I didn’t read through all of the code and comments just now, but quick question: what mechanism are you using to limit this feature to scm team members? the isSuperUser property is not currently exposed in the user json, is it?

Oh, this is a good point. It's only using activeUser.isAdmin. Could you expose the property?

Co-authored-by: Philipp Otto <[email protected]>

…nds/webknossos into add-nuclei-reconstruction-job

fm3 · 2022-02-03T16:52:57Z

Oh, this is a good point. It's only using activeUser.isAdmin. Could you expose the property?

I added isSuperUser to the user json in 46629d6

MichaelBuessemeyer · 2022-02-10T09:21:21Z

@philippotto Could you please check the change that makes the neuron inferral only available to super users?
I think after that this pr is ready to 🚢 .

philippotto

LGTM :)

…-nuclei-reconstruction-job

…ssos into docs * 'docs' of github.com:scalableminds/webknossos: * 'master' of github.com:scalableminds/webknossos: Split cells via Min Cut (#5885) Clean up backend util package (#6048) Guard against empty saves (#6052) Time tracking: Do not fail on empty timespans list (#6051) Fix clip button changing position (#6050) Include ParamFailure values in error chains (#6045) Fix non-32-aligned bucket requests (#6047) Don't enforce save state when saving is triggered by a timeout and reduce tracing layout analytics event count (#5999) Bump cached-path-relative from 1.0.2 to 1.1.0 (#5994) Volume annotation download: zip with BEST_SPEED (#6036) Sensible scalebar values (#6034) Faster CircleCI builds (#6040) move to Google Analytics 4 (#6031) Fix nightly (fix tokens, upgrade puppeteer) (#6032) Add neuron reconstruction job backend and frontend part (#5922) Allow uploading multi-layer volume annotations (#6028)

* docs: Split cells via Min Cut (#5885) Clean up backend util package (#6048) Guard against empty saves (#6052) Time tracking: Do not fail on empty timespans list (#6051) Fix clip button changing position (#6050) Include ParamFailure values in error chains (#6045) Fix non-32-aligned bucket requests (#6047) Don't enforce save state when saving is triggered by a timeout and reduce tracing layout analytics event count (#5999) Bump cached-path-relative from 1.0.2 to 1.1.0 (#5994) Volume annotation download: zip with BEST_SPEED (#6036) Sensible scalebar values (#6034) Faster CircleCI builds (#6040) move to Google Analytics 4 (#6031) Fix nightly (fix tokens, upgrade puppeteer) (#6032) Add neuron reconstruction job backend and frontend part (#5922) Allow uploading multi-layer volume annotations (#6028)

MichaelBuessemeyer added 5 commits December 22, 2021 14:45

add backend part of new nuclei reconstruction job

b0d50ae

add frontend part of new nuclei reconstruction job

920d07c

fix capitilazation of job name

72a5e4c

Merge branch 'master' of github.com:scalableminds/webknossos into add…

c93a4d6

…-nuclei-reconstruction-job

rename nuclei reconstruction to neuron reconstruction

290633a

daniel-wer changed the title ~~[WIP] Add nuclei reconstruction job backend and frontend part~~ [WIP] Add neuron reconstruction job backend and frontend part Jan 3, 2022

MichaelBuessemeyer added 3 commits January 3, 2022 18:03

fix neuron reconstruction job request path in frontend

bc7d3ce

And disable jobs

rename to neuron inferral

622d54b

Merge branch 'master' of github.com:scalableminds/webknossos into add…

fb05816

…-nuclei-reconstruction-job

MichaelBuessemeyer self-assigned this Jan 6, 2022

MichaelBuessemeyer added frontend new feature labels Jan 6, 2022

MichaelBuessemeyer added 2 commits January 10, 2022 10:27

format backend

ef0f324

WIP: Make bounding box of neuron inferral configurable

17f2fc9

MichaelBuessemeyer added 4 commits January 13, 2022 16:28

Add bounding box selection for neuron inferral job

2d62222

Merge branch 'master' of github.com:scalableminds/webknossos into add…

3e0f253

…-nuclei-reconstruction-job

remove unused import and outdated comment

42d8478

fix css class name

5d63776

Only show neuron inferral job option to admins

8bbe7ff

MichaelBuessemeyer commented Jan 24, 2022

View reviewed changes

small fixes before review

904d52b

MichaelBuessemeyer changed the title ~~[WIP] Add neuron reconstruction job backend and frontend part~~ Add neuron reconstruction job backend and frontend part Jan 24, 2022

Merge branch 'master' into add-nuclei-reconstruction-job

d5a578f

MichaelBuessemeyer marked this pull request as ready for review January 24, 2022 17:45

disable jobs

bbff804

fm3 reviewed Jan 25, 2022

View reviewed changes

MichaelBuessemeyer added 6 commits January 27, 2022 17:03

Merge origin/master into this branch

247146a

add example image for neuron inferral

8abc528

Merge branch 'add-nuclei-reconstruction-job' of github.com:scalablemi…

14387c8

…nds/webknossos into add-nuclei-reconstruction-job

apply review feedback

7720c3a

format backend && add eslintcache to clean script

3558115

Merge branch 'master' of github.com:scalableminds/webknossos into add…

534a585

…-nuclei-reconstruction-job

MichaelBuessemeyer commented Jan 27, 2022

View reviewed changes

frontend/javascripts/oxalis/view/components/setting_input_views.js Show resolved Hide resolved

MichaelBuessemeyer commented Jan 27, 2022

View reviewed changes

philippotto reviewed Jan 28, 2022

View reviewed changes

MichaelBuessemeyer added 2 commits January 31, 2022 10:20

apply pr feedback

6eee2ae

Merge branch 'master' of github.com:scalableminds/webknossos into add…

f21c2f9

…-nuclei-reconstruction-job

philippotto reviewed Feb 3, 2022

View reviewed changes

frontend/javascripts/oxalis/view/right-border-tabs/starting_job_modals.js Outdated Show resolved Hide resolved

philippotto reviewed Feb 3, 2022

View reviewed changes

MichaelBuessemeyer and others added 5 commits February 3, 2022 17:36

Apply suggestions from code review

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Co-authored-by: Philipp Otto <[email protected]>

Merge branch 'master' into add-nuclei-reconstruction-job

32a3f8d

fix formatting

2d76a44

Merge branch 'add-nuclei-reconstruction-job' of github.com:scalablemi…

369ff5f

…nds/webknossos into add-nuclei-reconstruction-job

Include isSuperUser in user json

46629d6

make neuron inferral only available to super users

753b0e3

philippotto approved these changes Feb 10, 2022

View reviewed changes

MichaelBuessemeyer and others added 2 commits February 10, 2022 13:15

Merge branch 'master' of github.com:scalableminds/webknossos into add…

9019ecc

…-nuclei-reconstruction-job

Merge branch 'master' into add-nuclei-reconstruction-job

5267721

MichaelBuessemeyer merged commit e915b3c into master Feb 10, 2022

MichaelBuessemeyer deleted the add-nuclei-reconstruction-job branch February 10, 2022 13:28

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Add neuron reconstruction job backend and frontend part #5922

Add neuron reconstruction job backend and frontend part #5922

MichaelBuessemeyer commented Dec 22, 2021 •

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Add neuron reconstruction job backend and frontend part #5922

Add neuron reconstruction job backend and frontend part #5922

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MichaelBuessemeyer commented Dec 22, 2021 • edited Loading

URL of deployed dev instance (used for testing):

Steps to test:

Issues:

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