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tlambert03 / nd2

Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction
https://tlambert03.github.io/nd2
BSD 3-Clause "New" or "Revised" License
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Position names are 'None' #78

Closed gatoniel closed 2 years ago

gatoniel commented 2 years ago

Description

I would like to find out the names of the different positions I gave during the experiment. This should be the M-axis in NIS Elements.

What I Did

I guess they should be in

nd2_file.experiment[1].parameters.points[i].name

Where nd2_file.experiment[1] is a XYPosLoop.

However, these values are of type None. In NIS Elements the different positions have names.

tlambert03 commented 2 years ago

Hey @gatoniel, Thanks for the note.

yeah, seems like that would be the place. lemme see what I can find. Do you by chance have a smallish multipoint file where you know what the position names are that you could send me? (I can create one if not). I just loaded a couple files in the actual nis viewer and also couldn't find position names, but I'm not sure if it's just those files...

gatoniel commented 2 years ago

Thakns for the fast reply! @tlambert03 I just send a filesender link to you per e-mail

tlambert03 commented 2 years ago

strange! I can't find it anywhere :joy: ... if it shows up in elements then clearly it's in there, but the NIS SDK doesn't seem to find it naturally (I can't find those strings in the free nis viewer either ... and I'm not at work today to load the files there)

i'll dig around in the binary to see where it might be stored

tlambert03 commented 2 years ago

found it. will try to determine the best way to expose it in the API (and perhaps try to magically inject it into that .experiment attribute

gatoniel commented 2 years ago

Hey, did you have a chance to work out how to expose the position names to the API? If you do not have time for it, could you tell me the details on where to find the names in the nd2-file and where you wish to expose it in the API? I would try to add it myself in a PR.

tlambert03 commented 2 years ago

Hey @gatoniel, sorry for the delay.

I haven't yet exposed it, the code to decode the proper metadata chunk is in this branch: https://github.com/tlambert03/nd2/blob/decodemeta/src/nd2/_nd2decode.py

since i think this is ultimately a bug with the SDK too, I opened an issue with laboratory imaging; it would be ideal if this "just happened correctly" when using the sdk, and it'd be awesome if I didn't have to engineer some workaround for something they'll fix soon. that said, the code isn't terribly far from usable. I'm away this week, so it definitely won't happen for a couple weeks, but i haven't forgotten!

gatoniel commented 2 years ago

Hey @tlambert03 , ok, if they are on it on the SDK side, I will just be patient and wait for it from that side. Thanks for the update.

tlambert03 commented 2 years ago

Hey @gatoniel, I just merged #93 which should fix missing names in nd2_file.experiment[n].parameters.points[i].name ... it also adds a new unstructured_metadata() method that exposes the full header metadata. It's not carefully parsed or structured, but there's good stuff in there. (for the position name, ND2file.experiment will automatically extract position name for you). the 0.4.3 release is building now and it will be ready in 30-60 minutes or so

gatoniel commented 2 years ago

Just tried it out and it works perfectly well for me. Thanks!!!