Add method to combine compensation matrices for Rosetta V2 #366
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alex-l-kong
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HPiyadasa
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May 12, 2023
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Sounds good, gonna merge this PR into |
alex-l-kong
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May 12, 2023
)" This reverts commit 8a51b68.
ngreenwald
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Aug 11, 2023
* Initial commit of Rosetta V2 * PYCODESTYLE * Clarify documentation * Add comments to variables in the notebook * Allow user to list all runs for testing as well * Add option to turn off test set generation for Rosetta V2 * Separate out Rosetta V2 process into a new notebook * Remove run names comment * Clarify comment * Skip percent_norm for Rosetta V2 * Remove comment to set percent_norm to None * Address more comment requests * Add all channels back into V2 * Add a new V2 commercial matrix * Remove timing printouts for Rosetta * Use "Round 2" instead of "v2" * Further disambiguate v2 and Round 2 * Fix format of round 2 Rosetta matrix * Add final_output_channel_names back in * Address documentation and remove timeit imports * Update description * Remove old panel_utils.py * Test ._ removal * Ensure hidden ._ files get deleted * Typo in notebook * Implement scheme to copy uncompensated images from round 1 to round 2 * Make non_output_targets an explicit list to work with io_utils * Documentation fixes * Add scheme to combine compensation files together * Clarify documentation for round 2 compensation combination * Reverting out of compensation, leave that to PR * Re-add compensation scheme * Undo commit, this should be for rosetta_v2_comp * Add method to combine compensation matrices for Rosetta V2 (#366) * Add compensation combination scheme * Fully flesh out Rosetta V2 pipeline * Documentation and variable changes for consistency * Fix comma spacing in subprocess call * Implement less strict run checking for R1R2 Rosetta copying (round two just needs to be a subset of round one) * Implement some notebook QOL changes * Ensure the names of the current_channel and output_channel match that in the example matrix row and column respectively
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What is the purpose of this PR?
Closes #364.
How did you implement your changes
See #364.
Remaining issues
Is asking the user to run section 1 iteratively the best idea?