Metadata scraping

[elainehoml]

Overview

It would be useful to have a metadata scraping tool to extract parameters from the headers of mrc's, eer's and tiff's for common parameters, e.g., pixel size, bit depth, image dimensions, etc. Where these parameters are not present/incorrect, offer an option for user-defined values.

Context

I guess we could...? Currently it's only one-purpose (for extracting the number of movie frames from EER files) so everything is hard-coded and very specific. But I guess because the headers for TIFFs / MRCs / EERs are different and their representations are different in the metadata, it might be rather difficult to generalise things.

Are there specific parameters you need to extract (regardless of image filetypes)?

More generally, usually image dimensions and bit depth is useful. For AreTomo there's spherical aberration, defocus, kV, dose per tilt, tilt collection scheme, but I'm not sure if these are in the headers or not? Maybe have the option to search for these parameters in the headers and then have users define it if not found. In the meantime maybe we can leave it as user-defined parameters, and I can open a new issue for us to set this up later after having a more thorough think about how we can do this and what we can get out of the headers.

Originally posted by @elainehoml in #24 (comment)