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nseg->ncomp for swc reader; set assign_groups=True #509

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merged 2 commits into from
Nov 21, 2024

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michaeldeistler
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@michaeldeistler michaeldeistler commented Nov 15, 2024

This PR suggests a few things:

  1. Rename nseg to ncomp when branches are initialized: branch = jx.Branch(comp, ncomp=4)
  2. Rename nseg to ncomp in jx.read_swc(..., ncomp=4)
  3. Rename nseg to ncomp throughout the entire codebase internally
  4. Set max_branch_len=None by default. We now have .set_ncomp(8) to deal with long branches.
  5. Set assign_groups=True by default.

All of these things are also reflected in the SWC tutorial. I also advertise .set_ncomp in the SWC tutorial now.

@jnsbck
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jnsbck commented Nov 20, 2024

I think we might want to move away from nseg altogether anyway, since if will be less confusing for the user. i.e. also change cumsum_nseg, jx.Branch(ncomps=2) etc. accordingly

Will take a look tmr.

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My only high level comment is that we might wanna do this for all nseg. Otherwise good to go from my side.

Also, if we start working with deprecations now, we might wanna think about integrating this into the CI. See #516 for an idea of how to do this.

jaxley/modules/cell.py Outdated Show resolved Hide resolved
@michaeldeistler michaeldeistler force-pushed the rework-swc-tutorial branch 10 times, most recently from 3145a36 to 4716167 Compare November 21, 2024 15:24
@michaeldeistler michaeldeistler merged commit 6e79424 into main Nov 21, 2024
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@michaeldeistler michaeldeistler deleted the rework-swc-tutorial branch November 21, 2024 16:17
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2 participants