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mehta-lab / waveorder

Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.
BSD 3-Clause "New" or "Revised" License
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`lambda_illu`, `NA_obj`, and `NA_illu` names can be improved #91

Closed talonchandler closed 1 year ago

talonchandler commented 1 year ago

The waveorder_microscopy constructor contains the following lines:

self.lambda_illu = lambda_illu/n_media self.NA_obj = NA_obj/n_media self.NA_illu = NA_illu/n_media which creates confusion when reading the methods and refactoring.

I am planning to make the following changes:

  1. Rename self.lambda_illu to self.lambda_media because lambda_illu/n_media is the wavelength inside the immersion media. It's particularly important to keep track of what media we're in because we have plans to to reconstructions in layered samples (immersion media, water, etc).

  2. Do not change the names ofself.NA_obj and self.NA_illu, but make them true to their names and don't normalize by n_media.

talonchandler commented 1 year ago

The models in alg-dev now use much more descriptive names (numerical_aperture_illumination, numerical_aperture_detection, wavelength_illumination, index_of_refraction_media), so this is solved.