NF: read segmentation data from fda files

marksgraham / OCT-Converter

Tools for extracting the raw optical coherence tomography (OCT) and fundus data from proprietary file formats.

https://pypi.org/project/oct-converter/

MIT License

193 stars 70 forks source link

NF: read segmentation data from fda files #95

Closed drombas closed 1 year ago

drombas commented 1 year ago

Closes #94

Changes

Add a read_segmentation method to FDA class
Update fda example

Comments

I had to change the chunk listing to store the position of all @CONTOURINFO chunks as a list
I have noticed that OCTVolumeWithMetaData class supports contour information. Maybe for a next PR?

Happy to make any changes if needed.

marksgraham commented 1 year ago

Hi @drombas

Thanks for this! I'm snowed under with a conference deadline until Friday, so I'll take a proper look at it then.

You're right, there is a contours part of OCTVolume, storing it there would make viewing them easily compatible with the peek method as we've done for e2e here, which would be nice! But we can save for another PR.

drombas commented 1 year ago

Hi @marksgraham. Thanks a lot for your feedback.

I've made the changes. I took the liberty of simplifying the code a bit but feel free to request any changes.