Minimal fix: set camera position

[rugeli]

Problem

we need to adjust the camera position for simularium results

Solution

• updated camera_z_position in simularium_helper.py per Saurabh's suggestion

• found similar camera position calculation in cellpack/bin/simularium_converter.py, updated that as well for consistency. The code can be DRYer long term

• reverted the bounding_box value in examples/recipes/v2/spheres_in_a_box.json so spheres are packed within the full box as expected

• revised display names and descriptions for editable fields (in firebase)

• result updated in cellPACK Studio, verify the production site or see screenshot (in firebase)

this is the initial view of multiple sphere result, still close to the camera but better than before, and the bounding box is correct

with @mogres

Type of change

• Bug fix (non-breaking change which fixes an issue)

[github-actions]

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

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[ascibisz]

I tested by running this locally as the server with cellpack-client and it looks good!

One question I'll just want to verify before we deploy it to cellpack-server: should we upload new default result files for the recipes in cellpack studio with these camera positions too? Otherwise, you go from a much more zoomed out view to a more zoomed in view when your Re-run completes

[rugeli]

I tested by running this locally as the server with cellpack-client and it looks good!

One question I'll just want to verify before we deploy it to cellpack-server: should we upload new default result files for the recipes in cellpack studio with these camera positions too? Otherwise, you go from a much more zoomed out view to a more zoomed in view when your Re-run completes

Good call! I'll go ahead test the results with smaller windows one more time. If everything looks nice, I'll upload them to /client and make sure the precomputed results in UI updated

[rugeli]

@mogres now z position now uses max_box_dimension so the camera is far enough back to capture the entire packing. Try running some example recipes with different window sizes and let me know if you noticed any issues!

pack -r examples/recipes/v2/spheres_on_a_plane.json -c examples/packing-configs/upload_and_open_result.json
pack -r examples/recipes/v2/endosome.json -c examples/packing-configs/upload_and_open_result.json
pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/upload_and_open_result.json
pack -r examples/recipes/v2/spheres_in_a_box.json -c examples/packing-configs/upload_and_open_result.json

[mogres]

Tested the example packings and the visualizations look good!

Some of them are still maybe a bit too far, but we can adjust the camera position as needed later. For some of our example recipes, we could bump up the number of packed spheres to make it visually more appealing, but that's for another PR.

[mogres]

Good workaround! For the future maybe we can reduce this multiplier or have it as a parameter because some of the packings still look too far away. We also can set the camera x position to 0 instead to avoid hard coded numbers.