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Skeletor #35

Merged
merged 74 commits into from Oct 9, 2020
Merged

Skeletor #35

merged 74 commits into from Oct 9, 2020

Commits on Sep 11, 2020

  1. Improved flywire token instructions

    @alexanderbates
    alexanderbates committed Sep 11, 2020
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  2. Merge branch 'master' of https://github.com/jefferis/fafbseg

    @alexanderbates
    alexanderbates committed Sep 11, 2020
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  3. Instructions from I.Taisz on installing cloudvolume and meshparty

    @alexanderbates
    alexanderbates committed Sep 11, 2020
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Commits on Sep 15, 2020

  1. Update .gitignore

    @alexanderbates
    alexanderbates committed Sep 15, 2020
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  2. R wrapper for skeletor pipeline

    @alexanderbates
    alexanderbates committed Sep 15, 2020
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  3. Skeletor documentation

    @alexanderbates
    alexanderbates committed Sep 15, 2020
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  4. Instructions for installing required python modules

    @alexanderbates
    alexanderbates committed Sep 15, 2020
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  5. Merge branch 'master' of https://github.com/jefferis/fafbseg

    @alexanderbates
    alexanderbates committed Sep 15, 2020
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  6. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 15, 2020
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Commits on Sep 16, 2020

  1. Update skeletor.Rd

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  2. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  3. Update installing-cloudvolume-meshparty.Rmd

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  4. Update skeletor.Rd

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  5. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  6. Update installing-cloudvolume-meshparty.Rmd

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  7. Update installing-cloudvolume-meshparty.Rmd

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  8. Add neuronmesh class to skeletor outputs

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  9. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  10. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  11. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  12. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  13. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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  14. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 16, 2020
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Commits on Sep 17, 2020

  1. Update installing-cloudvolume-meshparty.Rmd

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  2. Add heal option to R skeletor pipeline

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  3. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  4. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  5. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  6. Merge branch 'master' into skeletor

    @jefferis
    jefferis committed Sep 17, 2020
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  7. Updates reqquested by Greg 

    *  minus docs/ reversion
    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  8. Merge branch 'skeletor' of https://github.com/jefferis/fafbseg into s… 

    …keletor
    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  9. Option for skeletor to re-root neurons at predicted soma 

    * Soma predicted to be hairballs, optionally outside of a given brain mesh
    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  10. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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  11. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 17, 2020
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Commits on Sep 19, 2020

  1. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 19, 2020
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  2. Revert docs/ to master

    @alexanderbates
    alexanderbates committed Sep 19, 2020
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  3. Update _pkgdown.yml

    @alexanderbates
    alexanderbates committed Sep 19, 2020
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  4. Update skeletor.Rd

    @alexanderbates
    alexanderbates committed Sep 19, 2020
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  5. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 19, 2020
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Commits on Sep 20, 2020

  1. Update skeletor.Rd

    @alexanderbates
    alexanderbates committed Sep 20, 2020
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  2. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 20, 2020
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  3. NEWS polishing

    @jefferis
    jefferis committed Sep 20, 2020
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  4. Merge branch 'master' into skeletor 

    * master:
  NEWS polishing
    @jefferis
    jefferis committed Sep 20, 2020
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  5. revert more changes to docs as requested

    @jefferis
    jefferis committed Sep 20, 2020
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  6. Fix class order 

    * see #35 (comment)
    @jefferis
    jefferis committed Sep 20, 2020
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  7. Pass on brain argument to reroot_hairball

    @jefferis
    jefferis committed Sep 20, 2020
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  8. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 20, 2020
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Commits on Sep 21, 2020

  1. ensure that we use mesh if it exists in skeletor

    @jefferis
    jefferis committed Sep 21, 2020
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  2. Merge remote-tracking branch 'origin/skeletor' into skeletor 

    * origin/skeletor:
  Update flywire-skeleton.R

Conflicts due to double edits by @alexanderbates and me
(but I prefer mine where they clash)
    @jefferis
    jefferis committed Sep 21, 2020
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  3. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Sep 21, 2020
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Commits on Sep 22, 2020

  1. Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor 

    * 'skeletor' of github.com:natverse/fafbseg:
  Update flywire-skeleton.R

Double edits, but nothing significant
    @jefferis
    jefferis committed Sep 22, 2020
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Commits on Sep 23, 2020

  1. only initialise cloudvolume connection if essential 

    * we shouldn't need to do this if we are skeletonising .obj files on disk
    @jefferis
    jefferis committed Sep 23, 2020
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Commits on Sep 28, 2020

  1. Replace WHO with WH0

    @alexanderbates
    alexanderbates committed Sep 28, 2020
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Commits on Oct 1, 2020

  1. Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor 

    * 'skeletor' of github.com:natverse/fafbseg:
  Replace WHO with WH0
    @jefferis
    jefferis committed Oct 1, 2020
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  2. Update skeletor to work with more methods arguments 

    * for skeletonisation and radii calculation
    @alexanderbates
    alexanderbates committed Oct 1, 2020
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  3. Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor 

    * 'skeletor' of github.com:natverse/fafbseg:
  Update skeletor to work with more methods arguments

conflicts due to double edits including in errors where there were logic
changes on both sides that needed integrating
    @jefferis
    jefferis committed Oct 1, 2020
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Commits on Oct 2, 2020

  1. Add theta argument for mesh cleaning w.r.t skeleton

    @alexanderbates
    alexanderbates committed Oct 2, 2020
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Commits on Oct 5, 2020

  1. Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor 

    * 'skeletor' of github.com:natverse/fafbseg:
  Add theta argument for mesh cleaning w.r.t skeleton
    @jefferis
    jefferis committed Oct 5, 2020
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  2. Fix documentation build error

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  3. Add test for skeletor

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  4. Merge branch 'skeletor' of https://github.com/jefferis/fafbseg into s… 

    …keletor
    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  5. Travis update to install python libraries for skeletor

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  6. Update .travis.yml

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  7. Remove travis python install for now

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  8. Update skeletor.Rd

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  9. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  10. Save .obj files in at specified path with skeletor

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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  11. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Oct 5, 2020
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Commits on Oct 6, 2020

  1. Improved handling of temporary save files in skeletor

    @alexanderbates
    alexanderbates committed Oct 6, 2020
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  2. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Oct 6, 2020
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Commits on Oct 8, 2020

  1. Updated skeltor R wrapper for skeletor 0.2.4

    @alexanderbates
    alexanderbates committed Oct 8, 2020
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  2. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Oct 8, 2020
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  3. Update skeletor.Rd

    @alexanderbates
    alexanderbates committed Oct 8, 2020
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  4. Update flywire-skeleton.R

    @alexanderbates
    alexanderbates committed Oct 8, 2020
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