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feat: skeletonize (most) autapses and improve cross section analysis #179

Merged
merged 50 commits into from
Aug 14, 2024
Merged

feat: skeletonize (most) autapses and improve cross section analysis #179

merged 50 commits into from
Aug 14, 2024

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william-silversmith
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@william-silversmith
wip(skeletonizing): add support for fixing autapses in graphene volumes
9a6b8c4
@william-silversmith
feat: add support for graphene timestamp
08a8151
@william-silversmith
wip: ensure shape matches atomic chunks
7f2e487
@william-silversmith
fix: add back in xyzrange
2b892c0
@william-silversmith
fix(SkeletonTask): generalize frag_path for windows
dcfc938 
Also interpret bare paths as "file://"
@william-silversmith
fix(SkeletonTask): use agglomerate and timestamp correctly
f3e138f
@william-silversmith
fix: merge error removed cross_sectional_area params
971eb14
@william-silversmith
fix(SkeletonTask): apply timestamp in correct location
a3ab5bb
@william-silversmith
fix: fixup the edges of the vcg with root vcg
86a8a8f
@william-silversmith
feat: remove requirements for a queue parameter
7238b3a
@william-silversmith
redesign: use vol.info to get skeleton path
3392897
@william-silversmith
fix: several errors
6ff5f7e
@william-silversmith
feat: add fix_autapses to cli
9838867
@william-silversmith
fix: compensate for mip levels
cb3e543
@william-silversmith
fix: wrong path joining
3611bc8
@william-silversmith
fix: ensure mesh bounds are rectified after expansion
3bc9755
@william-silversmith
fix: wrong variable name in shard downsample
e6b9174
@william-silversmith
fix(shards/image): fix situation where chunk.z == dataset.z
329db4b
@william-silversmith
wip(skeletonizing): add support for fixing autapses in graphene volumes
6208048
@william-silversmith
feat: add support for graphene timestamp
894b2fa
@william-silversmith
wip: ensure shape matches atomic chunks
3176128
@william-silversmith
fix: add back in xyzrange
91bed59
@william-silversmith
fix(SkeletonTask): generalize frag_path for windows
bc215ce 
Also interpret bare paths as "file://"
@william-silversmith
fix(SkeletonTask): use agglomerate and timestamp correctly
f4a513f
@william-silversmith
fix: merge error removed cross_sectional_area params
2cfed74
@william-silversmith
fix(SkeletonTask): apply timestamp in correct location
548fe0b
@william-silversmith
fix: fixup the edges of the vcg with root vcg
2fb01ac
@william-silversmith
feat: remove requirements for a queue parameter
521c9d2
@william-silversmith
redesign: use vol.info to get skeleton path
f50059b
@william-silversmith
fix: several errors
6f5e094
william-silversmith and others added 16 commits July 24, 2024 01:43
@william-silversmith
feat: add fix_autapses to cli
80ed2c7
@william-silversmith
fix: compensate for mip levels
37e9dc6
@william-silversmith
fix: wrong path joining
fe9267f
@william-silversmith
fix: ensure mesh bounds are rectified after expansion
e7809da
fix: don't import view from CloudVolume
67e18cc
fix: don't import view from cloudvolume
d8da603
@william-silversmith
Merge branch 'wms_autapse' of github.com:seung-lab/igneous into wms_a…
73202cd 
…utapse
@william-silversmith
fix: intelligent frag path resolution
9f9c0b0
@william-silversmith
fix: handle binarization issue in repairing
e028820
@william-silversmith
fix: smart path
52b5bb8
perf: skip downloading the "huge" bbox if no skeletons
12c3117
@william-silversmith
fix: ensure info file uploaded to frag path
be2b462
@william-silversmith
Merge branch 'wms_autapse' of github.com:seung-lab/igneous into wms_a…
1a7b16f 
…utapse
@william-silversmith
fix: check for key
586bdf1
@william-silversmith
feat: support agglomeration for graphene for cross sections
be59802
@william-silversmith
feat: support static root_ids for a graphene volume
32ed272
@william-silversmith william-silversmith added feature documentation Updates to code comments or READMEs CLI Command Line Interface labels Aug 8, 2024
@william-silversmith william-silversmith self-assigned this Aug 8, 2024
@william-silversmith
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This seems to be working OK! So let's merge and iterate from there.

@william-silversmith william-silversmith merged commit 2df3415 into master Aug 14, 2024
5 checks passed
@william-silversmith william-silversmith deleted the wms_autapse branch August 14, 2024 23:43
@william-silversmith william-silversmith added the skeletons Skeleton processing. label Aug 14, 2024
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CLI Command Line Interface documentation Updates to code comments or READMEs feature skeletons Skeleton processing.
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