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Quick fix: update bbox value in recipes#420

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rugeli merged 2 commits intofeature/example-resultsfrom
update/bbox
Oct 28, 2025
Merged

Quick fix: update bbox value in recipes#420
rugeli merged 2 commits intofeature/example-resultsfrom
update/bbox

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@rugeli
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@rugeli rugeli commented Oct 24, 2025

Problem

In the working group discussion, we wanted to reset the default camera position for certain results to improve the initial view.

Solution

note: this is a quick fix to support several dependent open prs that need a better result view (e.g. readme updates and frontend display). we can revisit camera position or bounding box calculation optimization in the future.

  • updates bounding box value and radius in one_sphere and 3D multi_sphere recipe data

Type of change

  • New feature (non-breaking change which adds functionality)

Steps to Verify:

the current initial position in viewer:
spheres_in_a_box
Screenshot 2025-10-24 at 11 39 52 AM

one_sphere
Screenshot 2025-10-24 at 11 39 17 AM

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Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name Encapsulating radius Average number packed
ext_A 25 236.0

Packing image

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

@rugeli rugeli requested review from meganrm and mogres October 27, 2025 23:50
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Workaround looks good, thanks for adding the fix!

Could we start an issue for using the bbox dimensions to explicitly set the initial camera position in simularium?

@rugeli rugeli changed the base branch from main to feature/example-results October 28, 2025 17:16
@rugeli rugeli merged commit 546e8ff into feature/example-results Oct 28, 2025
11 of 12 checks passed
@rugeli rugeli deleted the update/bbox branch October 28, 2025 17:17
@rugeli rugeli mentioned this pull request Oct 28, 2025
rugeli added a commit that referenced this pull request Oct 29, 2025
* add screenshots to readme

* Quick fix: update bbox value in recipes (#420)

* add randomness_seed to upload and download (#416)

* update bbox value in recipes

* add config option for plot display

* replace result screenshots and update readme

* update docs/index to display images correctly
rugeli added a commit that referenced this pull request Nov 10, 2025
* default upload_results to false

* update config file options

* update schema docs

* propose to remove config files from the packing commands but add a section to explain how configs work

* set open_results_in_browser to false since it's dependent on upload_results

* improve loggings

* add a config file for upload results

* correct option default and log level

* update schema

* add aws db to path

* add a layer to detect non-interactive envs for db selection

* fix readme

* add cellpack website url

* remove unnecessary restriction

* update readme

* add screenshots to readme (#413)

* add screenshots to readme

* Quick fix: update bbox value in recipes (#420)

* add randomness_seed to upload and download (#416)

* update bbox value in recipes

* add config option for plot display

* replace result screenshots and update readme

* update docs/index to display images correctly
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2 participants