RFC: add channel_map and version to codebook

[ambrosejcarr]

This PR is a first attempt at adding a version and code_map to the codebook. Note that the diff is much smaller than git makes it appear -- to add properties to the codebook it needed to be converted from an array to an object, which caused it to get shifted up a level.

See examples for the proposed codebook structure.

@berl does this address the concern about being able to detect the channels?

Addresses #3, #10

[berl]

how about "codebook" instead of "codes"? I like the list of codewords being the codebook, but either way is fine with me

[ambrosejcarr]

@berl I like that suggestion. Can you think of a more general term for the codebook.json file now that it also has a channel map? Or is codebook still optimal?

[ttung]

why not do a map of channel name to index val? at least you gain channel name uniqueness as a freebie.

[joshmoore]

I could also see having it as an array. cF. https://github.com/IDR/idr-metadata/blob/403b0817c1c57dd6b509cfb0d0d41bd35ec1b938/idr0006-fong-nuclearbodies/screenA/idr0006-screenA-renderdef.yml

1:
  label: DAPI
  min: 0
  max: 1000
  color: "0000FF"
2:
  label: TRITC
  min: 50,
  max: 800

since an ordering is guaranteed.

[dganguli]

LGTM. @berl @ambrosejcarr is channel_map.json required for the spaceTx pipeline? does it make more sense for this to live in experiment.json?

[berl]

channel_map.json is not strictly required for the pipeline, but it would make some things a little easier to read. E.g. asking to filter images differently based on channel, like [ch in channel_map if ch["channel"] in "488"] differently than images with [ch in channel_map if ch["channel"] in "647"]. or maybe that's just ugly anyway

[ambrosejcarr]

Thanks all for comments. I'm going to wait to land this until we construct the dependency tree between sptx-format, slicedimage, and starfish.

[ttung]

Thanks all for comments. I'm going to wait to land this until we construct the dependency tree between sptx-format, slicedimage, and starfish.

landing post-merge might be a serious PITA.