Code

feat: avocado protection (🥑)#43

Code

Merged

william-silversmith merged 24 commits intomasterseung-lab/kimimaro:masterfrom wms_avocadosseung-lab/kimimaro:wms_avocadosCopy head branch name to clipboardJun 19, 2020

+41,243-10,722

Commits

Commits on Jun 14, 2020

• wip: writing is_avocado function

  william-silversmith

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  8fc1d97

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• refactor: change conditions at bottom

  william-silversmith

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  6841fbf

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• fix: repair results of refactoring experiment

  william-silversmith

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  26699f7

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• wip: sketching the avocado protection function

  william-silversmith

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  a24b705

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• wip: more complete sketch of avocado protection

  william-silversmith

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  af346ef

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• refactor: change "avocado_protection" to "fix_avocados"

  william-silversmith

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  8e15cae

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• fix: if the box clips the nucleus

  william-silversmith

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  186ddc3

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• feat: improve algorithm to fill in pit

  william-silversmith

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  40df35a

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• fix: compile skeletontricks

  william-silversmith

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  712383d

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• note: we need to deal with the soma acceptance threshold

  william-silversmith

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  2a3bbf6

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Commits on Jun 15, 2020

• fix: handle unchanged, double avocado

  william-silversmith

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  61d97e0

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• fix: now working!

  william-silversmith

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  1fdfa6f

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• fix: strip 0 from remap

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  600a666

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Commits on Jun 16, 2020

• fix: don't scan over black

  william-silversmith

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  77b5d75

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Commits on Jun 17, 2020

• fix: handle case where fruit is processed before pit

  william-silversmith

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  2fe2b66

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• chore: bump fastremap to a fixed version (remap was broken)

  william-silversmith

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  8f40538

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• docs: show how to use fix_avocados

  william-silversmith

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  a49e3fd

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Commits on Jun 18, 2020

• fix: reestablish remapping relationship after fixing avocados

  william-silversmith

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  21ec4c3

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• fix: adjust remapping after modifying segmentation

  william-silversmith

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  e4e5b36

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• perf: reduce size of connected components image

  william-silversmith

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  b0f3d4c

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• feat: handle "dirty" avocados

  william-silversmith

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  faca08b

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• docs: use nicer font for warning

  william-silversmith

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  8ddde2b

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• fix: increase the chance that nucleii are captured

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  b290c24

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Commits on Jun 19, 2020

• fix: make find_objects robust to None types

  william-silversmith

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  c20eae0

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