Miscellaneous gradient updates #428
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This commit refactors the `Environment.py` file by separating the loading of grid, compartment grids, and mesh store into separate loops. It also clears the triangles_tree cache and resets the grid. Additionally, the `load_object_from_pickle` function has been removed from `utils.py` as it is no longer used.
- Also update the logging of recipe validation to `debug`
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Packing analysis reportAnalysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST
Packing imageDistance analysisExpected minimum distance: 50.00
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rugeli
approved these changes
Nov 10, 2025
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rugeli
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rugeli
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Tested the changes with and without directly editing the test recipe, both worked fine, and the results looked good to me!
meganrm
approved these changes
Nov 13, 2025
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Problem
Closes #427 #396
Solution
Added options to allow zero decay length in gradients. Also added test options in recipe.
Type of change
Steps to Verify:
Check the weights of the zero decay gradient in simularium.
Note
Spheres will still be packed with radial gradient. To pack using the zero decay gradient, edit the recipe.
Screenshots (optional):