Closed BenGros closed 1 month ago
I added the commits I made to fix some things and an example of splitting off the rule..
Code looks good to me, but some documentation could be better. Can you add documentation to briefly describe how to run the .js files? In docs/ or/and using docstring """ """ at the top of the file (as in PEP 257) would be fine.
Also may I ask what's the purpose of the dataset created by testing/create_test_dataset.py? I was looking around but not sure what it's used in. I think it may be good to add a description of this as docstrings as well.
Other .py files can benefit from docstrings as well but I think these two will be most helpful.
Edit: Just saw the issue to add documentation - if it's not part of the PR and will be done in the future then I believe we can merge the PR now.
I can add the documentation for running the js files in this pull request. And the create_test_dataset.py is used to create a subset of a large raw dataset to be able to test the workflow quickly.
@BenGros this looks good to merge now, when you're ready you can do a Squash and Merge to clean the history, and provide a commit message and summarizes the PR.
QC reports are generated for flat-field correction, whole slice viewing and a 3D volume rendered model. These reports are accessible through a locally run HTML file. Also added a script for producing test datasets that are subsets of an original dataset.
The ff correction and whole slice viewing use locally stored images that are created. The 3D viewer generates a JSON file containing the data and generates the model from that.