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Multi-sem inpainting for wafer 60/61 #210

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Merged
trautmane merged 11 commits into from
Jan 24, 2026
Merged

Multi-sem inpainting for wafer 60/61 #210

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4036d32
Remove deprecated Views.iterable calls
minnerbe Mar 18, 2025
d5ff9b2
Add first conceptually correct version of inpainter (not tested yet)
minnerbe Mar 18, 2025
39ad0af
Fix wrong mask logic and averaging computation
minnerbe Mar 18, 2025
e4d48e2
Use client runner infrastructure in Wafer6061Inpainter
minnerbe Mar 18, 2025
2b78712
Overwrite input dataset's blocks if requested
minnerbe Mar 18, 2025
a8994aa
Use spark (first runnable version)
minnerbe Mar 19, 2025
baa84b0
Extract and fix mask block identification logic
minnerbe Mar 19, 2025
a5f2c1b
Clean up inpainter
minnerbe Mar 19, 2025
69ea993
Fix some errors introduced in transition to spark
minnerbe Mar 19, 2025
1290315
Fix some remaining errors
minnerbe Mar 19, 2025
bb4dc5b
Clean up inpainter and remove test arguments
minnerbe Mar 19, 2025
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2 changes: 1 addition & 1 deletion render-app/src/main/java/org/janelia/alignment/inpainting/InterpolatingZInpainter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ private List<Grid.Block> getBlocksToInpaint() {
final List<Interval> nonEmptyMaskBlocks = new ArrayList<>();
for (final Grid.Block block : maskBlocks) {
final IntervalView<FloatType> pixels = Views.interval(mask, block);
for (final FloatType pixel : Views.iterable(pixels)) {
for (final FloatType pixel : pixels) {
if (pixel.get() > 0) {
nonEmptyMaskBlocks.add(block);
break;
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2 changes: 1 addition & 1 deletion render-app/src/main/java/org/janelia/alignment/inpainting/RayCastingInpainter.java
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Expand Up @@ -50,7 +50,7 @@ private static boolean isInside(final RealLocalizable p, final RealInterval r) {
* @param mask the mask
*/
public void inpaint(final RandomAccessibleInterval<FloatType> img, final RandomAccessibleInterval<FloatType> mask) {
final Cursor<FloatType> imgCursor = Views.iterable(img).localizingCursor();
final Cursor<FloatType> imgCursor = img.localizingCursor();

final RealRandomAccess<FloatType> imageAccess = Views.interpolate(Views.extendBorder(img), new NLinearInterpolatorFactory<>()).realRandomAccess();
final RealRandomAccess<FloatType> maskAccess = Views.interpolate(Views.extendBorder(mask), new NLinearInterpolatorFactory<>()).realRandomAccess();
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