Updates for variable count and size experiments #215
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…to analysis/variable_count_and_size_experiment
…lpack into analysis/variable_count_and_size_experiment
* return count as integer * allow specifying seed list in the recipe
…lpack into fix/parallel_packing_with_simularium
* add sphere mesh objects for tests * add recipe for nested mesh testing
…riable_count_and_size_experiment
Codecov ReportAll modified and coverable lines are covered by tests ✅
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #215 +/- ##
=======================================
Coverage 98.63% 98.63%
=======================================
Files 18 18
Lines 511 511
=======================================
Hits 504 504
Misses 7 7 ☔ View full report in Codecov by Sentry. |
Packing analysis reportAnalysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST
Packing imageDistance analysisExpected minimum distance: 50.00
|
rugeli
approved these changes
Dec 19, 2023
| elif recipe_data.get("randomness_seed") is not None: | ||
| seed_list = recipe_data["randomness_seed"] | ||
| else: | ||
| seed_list = None |
There was a problem hiding this comment.
Nit: should we implement an early return here for seed_list when it's None? So that we don't need to check it again in L274?
…lysis/variable_count_and_size_experiment
meganrm
approved these changes
Jan 10, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Problem
This PR contains updates related to running packing experiments with variable count and size distributions.
Solution
These updates include changes to grid file loading and setting random seeds for packing replicates.
Type of change
Change summary:
number_of_packings > 1, a list of random seeds is generated to match. The random seeds can also be explicitly specified in the recipe itself.Steps to Verify:
pack -r cellpack/tests/recipes/v2/test_variable_count.json -c cellpack/tests/packing-configs/test_variable_count_config.jsonin an activated conda environment