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Cache warped source #176

Merged
merged 46 commits into from
Oct 3, 2024
Merged

Cache warped source #176

merged 46 commits into from
Oct 3, 2024

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bogovicj
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@bogovicj bogovicj commented Oct 3, 2024

  • general refactoring
  • better tests of ApplyBigWarpPlugin

bogovicj added 30 commits May 29, 2024 16:46
@bogovicj
perf(wip): toward export of quantized dfields
0fab9b4 
* add a test
@bogovicj
perf(wip): toward reading and writing quantized transforms
2caa065 
* add n5 "format" to exporter
* read from n5 formaat if no fragment given in transform URI
@bogovicj
style: code formatting
3a6375d
@bogovicj
fix: n5 dfield, treat invfield group as inverse
c72e75e
@bogovicj
fix: generic RealComposite compilation issue
5a3f29a
@bogovicj
chore: bump n5 artifact versions
8896442
@bogovicj
fix: make n5 source loading consistent with n5 viewer
f76bcb6
@bogovicj
wip: toward fixing n5 export when an offset exists
1475201
@bogovicj
fix: serializing ngff affines
fbf62f8
@bogovicj
fix(wip): toward fixing n5 export
c708e19
@bogovicj
feat(wip): more flexible bigwarp exporter
620d35a 
* exporter can output a single rai
* when writing to n5 export only active source
* fix physical offset for ngff metadata
@bogovicj
fix/perf: use N5Viewer method for opening multiscale data
3091d87
@bogovicj
fix: offset typo in ApplyBigWarpPlugin
56ba770
@bogovicj
fix: correct input/output space for TPS transform export
63ea1c3
@bogovicj
style: ApplyBigwarpPlugin formatting
97eb5c4
@bogovicj
Merge branch 'fix-n5-export' of github.com:saalfeldlab/bigwarp into f…
c4433cf 
…ix-n5-export
@bogovicj
Merge branch 'master' into fix-n5-export
7197765 
# Conflicts:
#	src/main/java/bdv/gui/sourceList/BigWarpSourceTableModel.java
@bogovicj
feat: add BoundingBoxEstimation.estimateInterval
295d1af 
* for RealIntervals
@bogovicj
wip: toward caching sources with a fixed transformation
d77bed3
@bogovicj
fix: bounding box issue for cached warped source
b874dfc
@bogovicj
feat: cached fixed-transform source and singleton SharedQueue
c8ee1d0
@bogovicj
Merge branch 'fix-n5-export' into warpedSourceCaching
839826e 
# Conflicts:
#	src/main/java/bigwarp/BigWarpInit.java
@bogovicj
feat: store on-the-fly transfored source for export and use it
0f85352
@bogovicj
style: misc code style
e4587c1
@bogovicj
fix: bounding box minMaxInterval should not round/floor
3ffd97c
@bogovicj
style: BigWarpInit minor cleanup
4ba6fb7
@bogovicj
fix: getMovingSourceForExport
450da32
@bogovicj
test: more helpers in BigWarpTestUtils
90a4f45
@bogovicj
fix: ImagePlusLoader handles origin
60b581c
@bogovicj
fix/test: bigwarp apply with an offset in target fov
7399f71 
* ApplyBigwarpPlugin uses physical offset
* add a test
@bogovicj
chore(pom): bump imglib2, imglib2-algorithm version
091c609
@bogovicj
test: BigWarpTestUtils add more helper methods to
c9edc71
@bogovicj
test: add BigWarpTransformCacheTests
5e7dd07
@bogovicj
fix: ApplyBigWarpPlugin bug in specified physical fov
ef18e82
@bogovicj
style: be quiet
2312d16
@bogovicj
fix: BitWarpInit allow null target ImagePlus
ca60df9
@bogovicj
fix: ApplyBigwarpPlugin logic that checks what target src can be null
2d91e4b
@bogovicj
refactor: use imglib2's new getType() method
80eadfc
@bogovicj
fix: add add NumericType constraint to openAsSourceMulti
0358da4
@bogovicj
feat: de-duplicate export code used by UI
65e0707
@bogovicj
feat: remove pixel/physical distinction for landmark fov params
02fc95d
@bogovicj
fix/test: add test of export using landmarks for fov
97f3c0d
@bogovicj
chore(pom): clean up pinned versions
2c7c41b 
* remove those that agree with pom-scijava
@bogovicj
fix: add missing dep
7ce37da
@bogovicj
feat/tes: ApplyBigwarpPlugin expose show option
a71d024 
* dont try to show results in BigWarpApplyTests
@bogovicj
doc: javadoc fixes
8106d8f
@bogovicj bogovicj merged commit e12c269 into master Oct 3, 2024
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This was referenced Oct 3, 2024
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@bogovicj