search

cytomining / DeepProfiler

Morphological profiling using deep learning
Other
104 stars 39 forks source link

Build helper functions #262

Open michaelbornholdt opened 3 years ago

michaelbornholdt commented 3 years ago

Working with millions of files can be a real problem and lead to a lot (!!!) of lost time. Implementing these helper functions will make sure that one can run the big functions (profile, sample-sc, and train) without any errors that cost days of work.

Here is a list of suggestions for the most helpful test functions:

  1. check images: This function simply runs over all lines in the index and checks if the images exist. This prevents the profile command form exiting with an error.

  2. Check sc-metadata.csv This function should run over the sc-metadata file and check if all images exist in the right place. This needs to be run prior to training to prevent crashes during training.

michaelbornholdt commented 2 years ago

@jccaicedo just wanted to check in here. I think the functions exist in the branch and they are still usefull. Maybe we mention them in the Wiki and have them on a side branch? Not sure where to store them.

The checking for black crops is crucial. The other one not so much.