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Cache warped source #176

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merged 46 commits into from
Oct 3, 2024
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0fab9b4
perf(wip): toward export of quantized dfields
bogovicj May 29, 2024
2caa065
perf(wip): toward reading and writing quantized transforms
bogovicj May 30, 2024
3a6375d
style: code formatting
bogovicj May 30, 2024
c72e75e
fix: n5 dfield, treat invfield group as inverse
bogovicj Jun 12, 2024
5a3f29a
fix: generic RealComposite compilation issue
bogovicj Jun 12, 2024
8896442
chore: bump n5 artifact versions
bogovicj Jun 14, 2024
f76bcb6
fix: make n5 source loading consistent with n5 viewer
bogovicj Jun 14, 2024
1475201
wip: toward fixing n5 export when an offset exists
bogovicj Jun 27, 2024
fbf62f8
fix: serializing ngff affines
bogovicj Jun 28, 2024
c708e19
fix(wip): toward fixing n5 export
bogovicj Jun 28, 2024
620d35a
feat(wip): more flexible bigwarp exporter
bogovicj Jun 28, 2024
3091d87
fix/perf: use N5Viewer method for opening multiscale data
bogovicj Jul 3, 2024
56ba770
fix: offset typo in ApplyBigWarpPlugin
bogovicj Jul 3, 2024
63ea1c3
fix: correct input/output space for TPS transform export
bogovicj Jul 10, 2024
97eb5c4
style: ApplyBigwarpPlugin formatting
bogovicj Jul 10, 2024
c4433cf
Merge branch 'fix-n5-export' of github.com:saalfeldlab/bigwarp into f…
bogovicj Jul 10, 2024
7197765
Merge branch 'master' into fix-n5-export
bogovicj Jul 10, 2024
295d1af
feat: add BoundingBoxEstimation.estimateInterval
bogovicj Sep 11, 2024
d77bed3
wip: toward caching sources with a fixed transformation
bogovicj Sep 11, 2024
b874dfc
fix: bounding box issue for cached warped source
bogovicj Sep 11, 2024
c8ee1d0
feat: cached fixed-transform source and singleton SharedQueue
bogovicj Sep 11, 2024
839826e
Merge branch 'fix-n5-export' into warpedSourceCaching
bogovicj Sep 12, 2024
0f85352
feat: store on-the-fly transfored source for export and use it
bogovicj Sep 18, 2024
e4587c1
style: misc code style
bogovicj Sep 18, 2024
3ffd97c
fix: bounding box minMaxInterval should not round/floor
bogovicj Sep 19, 2024
4ba6fb7
style: BigWarpInit minor cleanup
bogovicj Sep 19, 2024
450da32
fix: getMovingSourceForExport
bogovicj Sep 27, 2024
90a4f45
test: more helpers in BigWarpTestUtils
bogovicj Sep 27, 2024
60b581c
fix: ImagePlusLoader handles origin
bogovicj Sep 27, 2024
7399f71
fix/test: bigwarp apply with an offset in target fov
bogovicj Sep 27, 2024
091c609
chore(pom): bump imglib2, imglib2-algorithm version
bogovicj Sep 30, 2024
c9edc71
test: BigWarpTestUtils add more helper methods to
bogovicj Sep 30, 2024
5e7dd07
test: add BigWarpTransformCacheTests
bogovicj Sep 30, 2024
ef18e82
fix: ApplyBigWarpPlugin bug in specified physical fov
bogovicj Sep 30, 2024
2312d16
style: be quiet
bogovicj Sep 30, 2024
ca60df9
fix: BitWarpInit allow null target ImagePlus
bogovicj Sep 30, 2024
2d91e4b
fix: ApplyBigwarpPlugin logic that checks what target src can be null
bogovicj Sep 30, 2024
80eadfc
refactor: use imglib2's new getType() method
bogovicj Oct 3, 2024
0358da4
fix: add add NumericType constraint to openAsSourceMulti
bogovicj Oct 3, 2024
65e0707
feat: de-duplicate export code used by UI
bogovicj Oct 3, 2024
02fc95d
feat: remove pixel/physical distinction for landmark fov params
bogovicj Oct 3, 2024
97f3c0d
fix/test: add test of export using landmarks for fov
bogovicj Oct 3, 2024
2c7c41b
chore(pom): clean up pinned versions
bogovicj Oct 3, 2024
7ce37da
fix: add missing dep
bogovicj Oct 3, 2024
a71d024
feat/tes: ApplyBigwarpPlugin expose show option
bogovicj Oct 3, 2024
8106d8f
doc: javadoc fixes
bogovicj Oct 3, 2024
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12 changes: 4 additions & 8 deletions pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -118,11 +118,11 @@
<license.projectName>BigWarp plugin for Fiji.</license.projectName>
<license.excludes>**/resources/*.xml</license.excludes>

<imglib2.version>7.1.0</imglib2.version>
<imglib2.version>7.1.1</imglib2.version>
<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
<imglib2-roi.version>0.15.0</imglib2-roi.version>
<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
<imglib2-algorithm.version>0.15.3</imglib2-algorithm.version>
<imglib2-algorithm.version>0.16.0</imglib2-algorithm.version>
<bigdataviewer-core.version>10.6.0</bigdataviewer-core.version>
<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>

Expand All @@ -131,15 +131,11 @@
<jitk-tps.version>3.0.4</jitk-tps.version>

<n5.version>3.3.0</n5.version>
<n5-imglib2.version>7.0.1</n5-imglib2.version>
<n5-imglib2.version>7.0.2</n5-imglib2.version>
<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
<n5-blosc.version>1.1.1</n5-blosc.version>
<n5-hdf5.version>2.2.0</n5-hdf5.version>
<n5-google-cloud.version>4.1.1</n5-google-cloud.version>
<n5-zarr.version>1.3.5</n5-zarr.version>
<n5-universe.version>1.6.0</n5-universe.version>
<n5-ij.version>4.2.1</n5-ij.version>
<n5-viewer_fiji.version>6.1.1</n5-viewer_fiji.version>
<n5-ij.version>4.2.3</n5-ij.version>

<ejml-core.version>0.41</ejml-core.version>
<ejml-ddense.version>0.41</ejml-ddense.version>
Expand Down
2 changes: 1 addition & 1 deletion scripts/BigWarp_N5.groovy
Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ def makeSources( String n5Base, String[] datasets )

source = new RandomAccessibleIntervalMipmapSource(
images,
Util.getTypeFromInterval(images[0]),
images[0].getType(),
scales,
new mpicbg.spim.data.sequence.FinalVoxelDimensions( "pix", 1, 1, 1),
"source");
Expand Down
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