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Merge pull request #553 from saalfeldlab/feat/1.7.0
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Feat/1.7.0
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@cmhulbert
cmhulbert authored Dec 6, 2024
2 parents cf63e7c + 0cffa24 commit c927f8b
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Showing 11 changed files with 215 additions and 114 deletions.
2 changes: 1 addition & 1 deletion src/main/java/org/janelia/saalfeldlab/paintera/control/actions/LabelActionType.java
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Expand Up @@ -4,7 +4,7 @@

public enum LabelActionType implements ActionType {
Toggle(true),
Append,
Append(true ),
CreateNew,
Lock(true),
Merge,
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71 changes: 45 additions & 26 deletions src/main/java/org/janelia/saalfeldlab/paintera/data/mask/MaskedSource.java
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Expand Up @@ -41,6 +41,7 @@
import javafx.util.Duration;
import javafx.util.Pair;
import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.AbstractInterval;
import net.imglib2.FinalInterval;
import net.imglib2.FinalRealInterval;
import net.imglib2.Interval;
Expand All @@ -66,6 +67,7 @@
import net.imglib2.img.cell.AbstractCellImg;
import net.imglib2.img.cell.CellGrid;
import net.imglib2.interpolation.randomaccess.NearestNeighborInterpolatorFactory;
import net.imglib2.iterator.LocalizingIntervalIterator;
import net.imglib2.loops.LoopBuilder;
import net.imglib2.parallel.TaskExecutor;
import net.imglib2.parallel.TaskExecutors;
Expand Down Expand Up @@ -105,6 +107,8 @@
import org.janelia.saalfeldlab.paintera.data.n5.BlockSpec;
import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts;
import org.janelia.saalfeldlab.paintera.util.IntervalHelpers;
import org.janelia.saalfeldlab.paintera.util.IntervalIterable;
import org.janelia.saalfeldlab.paintera.util.ReusableIntervalIterator;
import org.janelia.saalfeldlab.util.TmpVolatileHelpers;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -1187,36 +1191,51 @@ private static <T extends IntegerType<T>> Set<Long> downsample(
steps
);

/* Views.tiles doesn't preserve intervals, so zeroMin prior to tiling */
final var zeroMinTarget = Views.zeroMin(target);
final var sourceInterval = IntervalHelpers.scale(target, steps, true);
final IntervalView<T> zeroMinSource = Views.zeroMin(Views.interval(source, sourceInterval));
final var tiledSource = Views.tiles(zeroMinSource, steps);

final HashSet<Long> labels = new HashSet<>();
LoopBuilder.setImages(tiledSource, zeroMinTarget)
.forEachChunk(chunk -> {
final TLongLongHashMap maxCounts = new TLongLongHashMap();
chunk.forEachPixel((sourceTile, lowResTarget) -> {
var maxCount = -1L;
var maxId = Label.INVALID;
for (T t : Views.iterable(sourceTile)) {
final long id = t.getIntegerLong();
if (id == Label.INVALID)
continue;
final var curCount = maxCounts.adjustOrPutValue(id, 1, 1);
if (curCount > maxCount) {
maxCount = curCount;
maxId = id;
}
}
lowResTarget.setInteger(maxId);
if (maxId != Label.INVALID)
labels.add(maxId);
maxCounts.clear();
});
return null;
});

final RandomAccess<T> zeroMinSourceRA = zeroMinSource.randomAccess();
final RandomAccess<T> zeroMinTargetRA = zeroMinTarget.randomAccess();

final ReusableIntervalIterator sourceIntervalIterator = new ReusableIntervalIterator(sourceInterval);
final long[] sourcePosMin = new long[zeroMinSource.numDimensions()];
final long[] sourcePosMax = new long[zeroMinSource.numDimensions()];
final var sourceTileInterval = new AbstractInterval(sourcePosMin, sourcePosMax, false) {

};

final TLongLongHashMap maxCounts = new TLongLongHashMap();

var sourceTileIterable = new IntervalIterable(sourceIntervalIterator);
for (long[] targetPos : new IntervalIterable(new LocalizingIntervalIterator(zeroMinTarget))) {
for (int i = 0; i < sourcePosMin.length; i++) {
sourcePosMin[i] = targetPos[i] * steps[i];
sourcePosMax[i] = sourcePosMin[i] + steps[i] - 1;
}
sourceIntervalIterator.resetInterval(sourceTileInterval);

var maxCount = -1L;
var maxId = Label.INVALID;

for (long[] sourcePos : sourceTileIterable) {
final long sourceVal = zeroMinSourceRA.setPositionAndGet(sourcePos).getIntegerLong();
if (sourceVal != Label.INVALID) {
var curCount = maxCounts.adjustOrPutValue(sourceVal, 1, 1);
if (curCount > maxCount) {
maxCount++;
maxId = sourceVal;
}
}
}

final T targetVal = zeroMinTargetRA.setPositionAndGet(targetPos);
targetVal.setInteger(maxId);
labels.add(maxId);
maxCounts.clear();
}
labels.remove(Label.INVALID);
return labels;
}

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2 changes: 1 addition & 1 deletion src/main/java/org/janelia/saalfeldlab/paintera/ui/dialogs/opendialog/VolatileHelpers.java
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Expand Up @@ -39,6 +39,6 @@ public Cell<VolatileLabelMultisetArray> createInvalid(final Long key) throws Exc
}
}

private static final VolatileLabelMultisetArray EMPTY_ACCESS = new VolatileLabelMultisetArray(0, true, new long[]{Label.INVALID});
private static final VolatileLabelMultisetArray EMPTY_ACCESS = new VolatileLabelMultisetArray(0, false, new long[]{Label.INVALID});

}
4 changes: 2 additions & 2 deletions src/main/kotlin/org/janelia/saalfeldlab/paintera/PainteraMainWindow.kt
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Expand Up @@ -117,8 +117,8 @@ class PainteraMainWindow(val gateway: PainteraGateway = PainteraGateway()) {
{ projectDirectory.actualDirectory.absolutePath },
{ indexToState[it] })
val gson = builder.create()
val json = projectDirectory.actualDirectory.absolutePath
.let { Paintera.n5Factory.openReader(it).getAttribute("/", PAINTERA_KEY, JsonElement::class.java) }
val json = projectDirectory.actualDirectory.toURI()
.let { Paintera.n5Factory.openReader(it.toString()).getAttribute("/", PAINTERA_KEY, JsonElement::class.java) }
?.takeIf { it.isJsonObject }
?.asJsonObject
Paintera.n5Factory.gsonBuilder(builder)
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4 changes: 3 additions & 1 deletion src/main/kotlin/org/janelia/saalfeldlab/paintera/cache/SamEmbeddingLoaderCache.kt
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Expand Up @@ -81,7 +81,9 @@ object SamEmbeddingLoaderCache : AsyncCacheWithLoader<RenderUnitState, OnnxTenso

private class NavigationBasedRequestTimer(val viewerAndTransforms: ViewerAndTransforms) : AnimationTimer() {

private val REQUEST_COUNTDOWN = 30 // Unit is pulses of the Animation timer; roughly targets 60 FPS.
companion object {
private const val REQUEST_COUNTDOWN = 15 // Unit is pulses of the Animation timer; roughly targets 60 FPS.
}

private val viewer
get() = viewerAndTransforms.viewer()
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4 changes: 2 additions & 2 deletions src/main/kotlin/org/janelia/saalfeldlab/paintera/config/OrthoSliceConfig.kt
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Expand Up @@ -42,8 +42,8 @@ class OrthoSliceConfig(private val baseConfig: OrthoSliceConfigBase) {
bottomLeftSlice.isVisibleProperty.bind(baseConfig.showBottomLeftProperty().and(enable).and(hasSources).and(isBottomLeftVisible))

listOf(topLeftSlice, topRightSlice, bottomLeftSlice).forEach { slice ->
slice.opacityProperty().bind(baseConfig.opacityProperty())
slice.shadingProperty().bind(baseConfig.shadingProperty())
slice.opacityProperty().bindBidirectional(baseConfig.opacityProperty())
slice.shadingProperty().bindBidirectional(baseConfig.shadingProperty())
}
}
}
15 changes: 14 additions & 1 deletion src/main/kotlin/org/janelia/saalfeldlab/paintera/control/modes/ShapeInterpolationMode.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,10 @@ import org.janelia.saalfeldlab.control.mcu.MCUButtonControl
import org.janelia.saalfeldlab.fx.actions.ActionSet
import org.janelia.saalfeldlab.fx.actions.ActionSet.Companion.installActionSet
import org.janelia.saalfeldlab.fx.actions.ActionSet.Companion.removeActionSet
import org.janelia.saalfeldlab.fx.actions.DragActionSet
import org.janelia.saalfeldlab.fx.actions.NamedKeyBinding
import org.janelia.saalfeldlab.fx.actions.painteraActionSet
import org.janelia.saalfeldlab.fx.actions.painteraDragActionSet
import org.janelia.saalfeldlab.fx.actions.painteraMidiActionSet
import org.janelia.saalfeldlab.fx.midi.MidiButtonEvent
import org.janelia.saalfeldlab.fx.midi.MidiToggleEvent
Expand Down Expand Up @@ -89,7 +91,7 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
old?.viewer()?.apply { modeActions.forEach { removeActionSet(it) } }
}

private val samNavigationRequestListener = ChangeListener { _, _, curViewer ->
private val samNavigationRequestListener = ChangeListener<OrthogonalViews.ViewerAndTransforms?> { _, _, curViewer ->
SamEmbeddingLoaderCache.stopNavigationBasedRequests()
curViewer?.let {
SamEmbeddingLoaderCache.startNavigationBasedRequests(curViewer)
Expand Down Expand Up @@ -221,6 +223,17 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
keyPressEditSelectionAction(EditSelectionChoice.Previous, SHAPE_INTERPOLATION__SELECT_PREVIOUS_SLICE)
keyPressEditSelectionAction(EditSelectionChoice.Next, SHAPE_INTERPOLATION__SELECT_NEXT_SLICE)
},
painteraDragActionSet("drag activate SAM mode with box", PaintActionType.Paint, ignoreDisable = true, consumeMouseClicked = true) {
onDragDetected {
verify("can't trigger box prompt with active tool") { activeTool in listOf(NavigationTool, shapeInterpolationTool, samTool) }
switchTool(samTool)
}
onDrag {
(activeTool as? SamTool)?.apply {
requestBoxPromptPrediction(it)
}
}
},
DeviceManager.xTouchMini?.let { device ->
activeViewerProperty.get()?.viewer()?.let { viewer ->
painteraMidiActionSet("midi paint tool switch actions", device, viewer, PaintActionType.Paint) {
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56 changes: 21 additions & 35 deletions src/main/kotlin/org/janelia/saalfeldlab/paintera/control/paint/FloodFill.kt
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Expand Up @@ -27,22 +27,23 @@ import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.smallestC
import org.janelia.saalfeldlab.util.extendValue
import java.util.concurrent.CancellationException
import java.util.concurrent.atomic.AtomicBoolean
import java.util.function.*
import java.util.function.BooleanSupplier
import java.util.function.Consumer
import java.util.stream.Collectors

class FloodFill<T : IntegerType<T>>(
private val activeViewerProperty: ObservableValue<ViewerPanelFX>,
private val source: MaskedSource<T, *>,
val source: MaskedSource<T, *>,
private val assignment: FragmentSegmentAssignment,
private val requestRepaint: Consumer<Interval>,
val requestRepaint: Consumer<Interval?>,
private val isVisible: BooleanSupplier
) {

fun fillAt(x: Double, y: Double, fillSupplier: (() -> Long?)?): Job {
val fill = fillSupplier?.invoke() ?: let {
return Job().apply {
val reason = CancellationException("Received invalid label -- will not fill.")
LOG.debug(reason) { }
LOG.debug(reason) { }
completeExceptionally(reason)
}
}
Expand All @@ -55,7 +56,7 @@ class FloodFill<T : IntegerType<T>>(
if (!isVisible.asBoolean) {
return Job().apply {
val reason = CancellationException("Selected source is not visible -- will not fill")
LOG.debug(reason) { }
LOG.debug(reason) { }
completeExceptionally(reason)
}
}
Expand Down Expand Up @@ -96,7 +97,7 @@ class FloodFill<T : IntegerType<T>>(
val seedLabel = assignment?.getSegment(seedValue!!.integerLong) ?: seedValue!!.integerLong
if (!Label.regular(seedLabel)) {
val reason = CancellationException("Cannot fill at irregular label: $seedLabel (${Point(seed)})")
LOG.debug(reason) { }
LOG.debug(reason) { }
return Job().apply { completeExceptionally(reason) }
}

Expand All @@ -115,11 +116,13 @@ class FloodFill<T : IntegerType<T>>(
.collect(Collectors.toList<RealInterval>())

val triggerRefresh = AtomicBoolean(false)
var floodFillJob: Job? = null
val accessTracker: AccessBoxRandomAccessible<UnsignedLongType> = object : AccessBoxRandomAccessible<UnsignedLongType>(mask.rai.extendValue(UnsignedLongType(1))) {
val position: Point = Point(sourceAccess.numDimensions())

override fun get(): UnsignedLongType {
if (Thread.currentThread().isInterrupted) throw RuntimeException("Flood Fill Interrupted")
if (floodFillJob?.isCancelled == true || Thread.currentThread().isInterrupted)
throw CancellationException("Flood Fill Canceled")
synchronized(this) {
updateAccessBox()
}
Expand All @@ -136,18 +139,17 @@ class FloodFill<T : IntegerType<T>>(
}
}

val floodFillJob = CoroutineScope(Dispatchers.Default).launch {
floodFillJob = CoroutineScope(Dispatchers.Default).launch {
val fillContext = coroutineContext
InvokeOnJavaFXApplicationThread {
delay(1000)
while (fillContext.isActive) {
awaitPulse()
if (triggerRefresh.get()) {
val repaintInterval = globalToSource.inverse().estimateBounds(accessTracker.createAccessInterval())
requestRepaint.accept(repaintInterval.smallestContainingInterval)
triggerRefresh.set(false)
}
awaitPulse()
awaitPulse()
}
}

Expand All @@ -156,32 +158,16 @@ class FloodFill<T : IntegerType<T>>(
} else {
fillPrimitiveType(data, accessTracker, seed, seedLabel, fill, assignment)
}
}.also {
it.invokeOnCompletion { cause ->
val sourceInterval = accessTracker.createAccessInterval()
val globalInterval = globalToSource.inverse().estimateBounds(sourceInterval).smallestContainingInterval

when (cause) {
null -> {
LOG.trace { "FloodFill has been completed" }
LOG.trace {
"Applying mask for interval ${Intervals.minAsLongArray(sourceInterval).contentToString()} ${Intervals.maxAsLongArray(sourceInterval).contentToString()}"
}
requestRepaint.accept(globalInterval)
source.applyMask(mask, sourceInterval, MaskedSource.VALID_LABEL_CHECK)
}

is CancellationException -> try {
LOG.debug { "FloodFill has been interrupted" }
source.resetMasks()
requestRepaint.accept(globalInterval)
} catch (e: MaskInUse) {
LOG.error(e) {}
}
val sourceInterval = accessTracker.createAccessInterval()
val globalInterval = globalToSource.inverse().estimateBounds(sourceInterval).smallestContainingInterval

else -> requestRepaint.accept(globalInterval)
}
LOG.trace { "FloodFill has been completed" }
LOG.trace {
"Applying mask for interval ${Intervals.minAsLongArray(sourceInterval).contentToString()} ${Intervals.maxAsLongArray(sourceInterval).contentToString()}"
}
requestRepaint.accept(globalInterval)
source.applyMask(mask, sourceInterval, MaskedSource.VALID_LABEL_CHECK)
}
return floodFillJob
}
Expand Down Expand Up @@ -231,7 +217,7 @@ class FloodFill<T : IntegerType<T>>(
) { source, target: UnsignedLongType -> predicate(source, target) }
}

private suspend fun <T : IntegerType<T>> fillPrimitiveType(
private fun <T : IntegerType<T>> fillPrimitiveType(
input: RandomAccessibleInterval<T>,
output: RandomAccessible<UnsignedLongType>,
seed: Localizable,
Expand All @@ -249,7 +235,7 @@ class FloodFill<T : IntegerType<T>>(
seed,
UnsignedLongType(fillLabel),
DiamondShape(1)
) { source, target: UnsignedLongType -> runBlocking { predicate(source, target) } }
) { source, target: UnsignedLongType -> predicate(source, target) }
}

private fun <T : IntegerType<T>> makePredicate(seedLabel: Long, assignment: FragmentSegmentAssignment?): (T, UnsignedLongType) -> Boolean {
Expand Down
27 changes: 20 additions & 7 deletions src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/Fill3DTool.kt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.janelia.saalfeldlab.paintera.control.tools.paint

import de.jensd.fx.glyphs.fontawesome.FontAwesomeIconView
import io.github.oshai.kotlinlogging.KotlinLogging
import javafx.beans.property.SimpleBooleanProperty
import javafx.beans.property.SimpleObjectProperty
import javafx.beans.value.ChangeListener
Expand All @@ -22,6 +23,7 @@ import org.janelia.saalfeldlab.fx.ui.GlyphScaleView
import org.janelia.saalfeldlab.fx.ui.ScaleView
import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread
import org.janelia.saalfeldlab.paintera.LabelSourceStateKeys
import org.janelia.saalfeldlab.paintera.Paintera
import org.janelia.saalfeldlab.paintera.control.ControlUtils
import org.janelia.saalfeldlab.paintera.control.actions.PaintActionType
import org.janelia.saalfeldlab.paintera.control.modes.ToolMode
Expand All @@ -32,6 +34,10 @@ import org.janelia.saalfeldlab.paintera.ui.overlays.CursorOverlayWithText

class Fill3DTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*, *>?>, mode: ToolMode? = null) : PaintTool(activeSourceStateProperty, mode) {

companion object {
private val LOG = KotlinLogging.logger { }
}

override val graphic = { ScaleView().also { it.styleClass += "fill-3d" } }

override val name = "Fill 3D"
Expand All @@ -48,7 +54,7 @@ class Fill3DTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*,
dataSource,
assignment,
{ interval -> paintera.baseView.orthogonalViews().requestRepaint(interval) },
{ activeSourceStateProperty.value?.isVisibleProperty?.get() ?: false }
{ activeSourceStateProperty.value?.isVisibleProperty?.get() == true }
)
}
}
Expand Down Expand Up @@ -101,16 +107,23 @@ class Fill3DTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*,

fillIsRunningProperty.set(true)
fill.fillAt(it!!.x, it.y, statePaintContext?.paintSelection).also { task ->
floodFillTask = task

paintera.baseView.isDisabledProperty.addListener(setFalseAndRemoveListener)
paintera.baseView.disabledPropertyBindings[this] = fillIsRunningProperty

task.invokeOnCompletion { cause ->
fillIsRunningProperty.set(false)
paintera.baseView.disabledPropertyBindings -= this
statePaintContext?.refreshMeshes?.invoke()
floodFillTask = null
floodFillTask = task.apply {
invokeOnCompletion { cause ->
fillIsRunningProperty.set(false)
paintera.baseView.disabledPropertyBindings -= this
cause?.let {
LOG.debug(cause) { "Fill 3D cancelled, resetting mask. " }
statePaintContext?.dataSource?.resetMasks(true)
fill.source.resetMasks()
fill.requestRepaint.accept(null)
}
statePaintContext?.refreshMeshes?.invoke()
floodFillTask = null
}
}
}
}
Expand Down
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