Cleanup pc preprocessing #79
Merged
Conversation
This file contains hidden or 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
fatwir
approved these changes
Dec 13, 2024
Collaborator
fatwir
left a comment
fatwir
left a comment
There was a problem hiding this comment.
I was able to run preprocessing for the PCNA dataset!
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Outdated suggestions cannot be applied.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.
This PR cleans up the preprocessing scripts for generating point clouds for punctate structures after the image_preprocessing is done. Tested on the outputs of the image_preprocessing step.
For the PCNA dataset, run
python src/br/data/preprocessing/pc_preprocessing/pcna --save_path "./make_pcs_test" --preprocessed_manifest "./subpackages/image_preprocessing/tmp_output_pcna/processed/manifest.parquet" --global_path "./subpackages/image_preprocessing/"For nuclear structures from the variance dataset, run
python src/br/data/preprocessing/pc_preprocessing/punctate_nuc.py --save_path "./make_pcs_test" --preprocessed_manifest "./subpackages/image_preprocessing/tmp_output_variance/processed/manifest.parquet" --global_path "./subpackages/image_preprocessing/"For cytoplasmic structures from the variance dataset, run
python src/br/data/preprocessing/pc_preprocessing/punctate_cyto.py --save_path "./make_pcs_test" --preprocessed_manifest "./subpackages/image_preprocessing/tmp_output_variance/processed/manifest.parquet" --global_path "./subpackages/image_preprocessing/"