Fix gradient inversion

[mogres]

Problem

Gradient inversion used distances instead of weights. This could result in unexpected inversion.

Solution

The type of inversion can be specified as an option now. invert: "distance" inverts the scaled distances and invert: "weight" inverts the weights after calculation.

Type of change

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

Change summary:

• add option to specify inversion using weights or distances
• add default values
• update test recipes to visualize inversion
• add credentials file to gitignore

Steps to Verify:

1. pack -r cellpack/tests/recipes/v2/test_mesh_image_gradient.json -c cellpack/tests/packing-configs/test_mesh_config.json
2. Change invert: "weight" to invert: "distance" to visualize alternative inversion.

Screenshots:

Inverting distances:

Inverting weights:

Keyfiles:

1. Gradient.py

[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

[codecov-commenter]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (9105668) 98.52% compared to head (a918184) 98.52%.

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Additional details and impacted files

@@           Coverage Diff           @@
##             main     #196   +/-   ##
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  Coverage   98.52%   98.52%           
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  Files          16       16           
  Lines         476      476           
=======================================
  Hits          469      469           
  Misses          7        7           

Files	Coverage Δ
cellpack/tests/test_gradient_data.py	100.00% <ø> (ø)

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[rugeli]

Looks good to me! I was able to pack the test recipe, however, it's taking a very long time to load the model in Simularium, I'm still waiting to visualize the result.

One question(might not related to this PR):
In terminal logs, the message Packing test_mesh_image_gradient_1.0.0: appeared twice with the first one remaining at 0% progress. Should we make any modifications to address this if one of them is being skipped or something?

[mogres]

@rugeli, were you able to visualize the output? It might help if you change the radius of the primitive_sphere to 1 so that there are fewer grid points to visualize.

As for the progress bar, it gets reprinted/interrupted when something else gets printed to the terminal. The Known pipe types message seems to have reset the bar -- we can look into what causes that message and whether we can prevent it from being displayed.

[rugeli]

@rugeli, were you able to visualize the output? It might help if you change the radius of the primitive_sphere to 1 so that there are fewer grid points to visualize.

As for the progress bar, it gets reprinted/interrupted when something else gets printed to the terminal. The Known pipe types message seems to have reset the bar -- we can look into what causes that message and whether we can prevent it from being displayed.

Thanks for getting back to me! I wasn't able to visualize the output yesterday. I just changed the primitive_sphere to 1, but the simularium has been in loading for the past 20 minutes.

[mogres]

@rugeli the recipe has been updated so you should be able to run it faster and visualize in simularium. Let me know if there are still any issues