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Skeletor #35

Merged
merged 74 commits into from Oct 9, 2020
Merged

Skeletor #35

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a7df59d
Improved flywire token instructions
alexanderbates Sep 11, 2020
e2a6ab9
Merge branch 'master' of https://github.com/jefferis/fafbseg
alexanderbates Sep 11, 2020
49893f3
Instructions from I.Taisz on installing cloudvolume and meshparty
alexanderbates Sep 11, 2020
39caa8e
Update .gitignore
alexanderbates Sep 15, 2020
a486961
R wrapper for skeletor pipeline
alexanderbates Sep 15, 2020
bbf03c5
Skeletor documentation
alexanderbates Sep 15, 2020
1e5b06f
Instructions for installing required python modules
alexanderbates Sep 15, 2020
8fb7043
Merge branch 'master' of https://github.com/jefferis/fafbseg
alexanderbates Sep 15, 2020
b58e8bc
Update flywire-skeleton.R
alexanderbates Sep 15, 2020
dab9810
Update skeletor.Rd
alexanderbates Sep 16, 2020
0e86c80
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
618252d
Update installing-cloudvolume-meshparty.Rmd
alexanderbates Sep 16, 2020
d71cd65
Update skeletor.Rd
alexanderbates Sep 16, 2020
9be2cfe
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
000bd53
Update installing-cloudvolume-meshparty.Rmd
alexanderbates Sep 16, 2020
4bcb2a2
Update installing-cloudvolume-meshparty.Rmd
alexanderbates Sep 16, 2020
f2bb8c8
Add neuronmesh class to skeletor outputs
alexanderbates Sep 16, 2020
5e1565b
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
9e0fe8f
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
3c8fb69
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
f3fe4c3
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
68d242f
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
810315e
Update flywire-skeleton.R
alexanderbates Sep 16, 2020
1f93158
Update installing-cloudvolume-meshparty.Rmd
alexanderbates Sep 17, 2020
15acbc1
Add heal option to R skeletor pipeline
alexanderbates Sep 17, 2020
1755b6b
Update flywire-skeleton.R
alexanderbates Sep 17, 2020
6d6ce9d
Update flywire-skeleton.R
alexanderbates Sep 17, 2020
5db44f9
Update flywire-skeleton.R
alexanderbates Sep 17, 2020
1c66fb8
Merge branch 'master' into skeletor
jefferis Sep 17, 2020
3b819f5
Updates reqquested by Greg
alexanderbates Sep 17, 2020
34449a5
Merge branch 'skeletor' of https://github.com/jefferis/fafbseg into s…
alexanderbates Sep 17, 2020
7999c0a
Option for skeletor to re-root neurons at predicted soma
alexanderbates Sep 17, 2020
0bfd5f5
Update flywire-skeleton.R
alexanderbates Sep 17, 2020
4a002bb
Update flywire-skeleton.R
alexanderbates Sep 17, 2020
a707333
Update flywire-skeleton.R
alexanderbates Sep 19, 2020
fefb39f
Revert docs/ to master
alexanderbates Sep 19, 2020
3e43ef5
Update _pkgdown.yml
alexanderbates Sep 19, 2020
07d3449
Update skeletor.Rd
alexanderbates Sep 19, 2020
71a6bd7
Update flywire-skeleton.R
alexanderbates Sep 19, 2020
c6ade05
Update skeletor.Rd
alexanderbates Sep 20, 2020
dbeb4ec
Update flywire-skeleton.R
alexanderbates Sep 20, 2020
31b131f
NEWS polishing
jefferis Sep 20, 2020
a3b208d
Merge branch 'master' into skeletor
jefferis Sep 20, 2020
acb6cfa
revert more changes to docs as requested
jefferis Sep 20, 2020
47278e2
Fix class order
jefferis Sep 20, 2020
d01f23a
Pass on brain argument to reroot_hairball
jefferis Sep 20, 2020
ac1077c
Update flywire-skeleton.R
alexanderbates Sep 20, 2020
d7299b5
ensure that we use mesh if it exists in skeletor
jefferis Sep 21, 2020
5f6cbb7
Merge remote-tracking branch 'origin/skeletor' into skeletor
jefferis Sep 21, 2020
2435fde
Update flywire-skeleton.R
alexanderbates Sep 21, 2020
5501d1e
Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor
jefferis Sep 22, 2020
6ef0c93
only initialise cloudvolume connection if essential
jefferis Sep 23, 2020
8a95f21
Replace WHO with WH0
alexanderbates Sep 28, 2020
a6972d8
Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor
jefferis Oct 1, 2020
6b7635e
Update skeletor to work with more methods arguments
alexanderbates Oct 1, 2020
11afbc5
Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor
jefferis Oct 1, 2020
dd80276
Add theta argument for mesh cleaning w.r.t skeleton
alexanderbates Oct 2, 2020
28f203f
Merge branch 'skeletor' of github.com:natverse/fafbseg into skeletor
jefferis Oct 5, 2020
4886b55
Fix documentation build error
alexanderbates Oct 5, 2020
f10dfd4
Add test for skeletor
alexanderbates Oct 5, 2020
fc7df53
Merge branch 'skeletor' of https://github.com/jefferis/fafbseg into s…
alexanderbates Oct 5, 2020
75eb89e
Travis update to install python libraries for skeletor
alexanderbates Oct 5, 2020
0ff3734
Update .travis.yml
alexanderbates Oct 5, 2020
3179ab4
Remove travis python install for now
alexanderbates Oct 5, 2020
96996e3
Update skeletor.Rd
alexanderbates Oct 5, 2020
d502262
Update flywire-skeleton.R
alexanderbates Oct 5, 2020
55204f6
Save .obj files in at specified path with skeletor
alexanderbates Oct 5, 2020
9d8a939
Update flywire-skeleton.R
alexanderbates Oct 5, 2020
8caa344
Improved handling of temporary save files in skeletor
alexanderbates Oct 6, 2020
f9b6e3d
Update flywire-skeleton.R
alexanderbates Oct 6, 2020
90197b6
Updated skeltor R wrapper for skeletor 0.2.4
alexanderbates Oct 8, 2020
bbd2cc8
Update flywire-skeleton.R
alexanderbates Oct 8, 2020
9ad31f6
Update skeletor.Rd
alexanderbates Oct 8, 2020
a0951bd
Update flywire-skeleton.R
alexanderbates Oct 8, 2020
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4 changes: 1 addition & 3 deletions R/flywire-skeleton.R
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Expand Up @@ -364,8 +364,7 @@ py_skeletor <- function(id,
if(reroot){
neuron = reroot_hairball(neuron, k.soma.search = k.soma.search, radius.soma.search = radius.soma.search, brain = brain)
}
if(mesh3d|save.obj){
if(is.null(mesh)){
if(mesh3d|!is.null(save.obj)){
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@jefferis jefferis Oct 6, 2020 •
edited

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@alexanderbates: as a general rule it is better to use || or && for this kind of logic in if statements as those operators short circuit i.e. they stop evaluating when the value of the expression is certain. So if you do

if(shortcheck() | longcheck())

both are evaluated even if shortcheck() returns TRUE whereas

if(shortcheck() || longcheck())

would stop evaluating if shortcheck() returned TRUE

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If you want convincing, here is some code

fastcheck <- function(x=T) {
  message("fast")
  x
}

slowcheck <- function(x=T) {
  message("slow")
  x
}

message("|| operator")
if(fastcheck() || slowcheck()) {
  message("if!")
} else {
  message("else!")
}


message("| operator")
if(fastcheck() | slowcheck()) {
  message("if!")
} else {
  message("else!")
}

|| operator
fast
if!
| operator
fast
slow
if!

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Thank you, I'll also apply this more generally.

# we need to get python to export it
savedir <- if(!is.null(save.obj)){
save.obj
Expand All @@ -380,7 +379,6 @@ py_skeletor <- function(id,
neuron$mesh3d = mesh
class(neuron) = union("neuronmesh", class(neuron))
}
}
}
neuron$id = id
neuron
Expand Down