-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
8 changed files
with
747 additions
and
21 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
225 changes: 225 additions & 0 deletions
225
src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/paint/ReplaceLabel.kt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,225 @@ | ||
| package org.janelia.saalfeldlab.paintera.control.actions.paint | ||
|
|
||
| import io.github.oshai.kotlinlogging.KotlinLogging | ||
| import javafx.beans.property.SimpleDoubleProperty | ||
| import javafx.beans.property.SimpleStringProperty | ||
| import javafx.event.ActionEvent | ||
| import javafx.scene.control.ButtonType | ||
| import javafx.scene.control.Dialog | ||
| import kotlinx.coroutines.CoroutineScope | ||
| import kotlinx.coroutines.Dispatchers | ||
| import kotlinx.coroutines.async | ||
| import net.imglib2.FinalInterval | ||
| import net.imglib2.Interval | ||
| import net.imglib2.type.Type | ||
| import net.imglib2.type.numeric.IntegerType | ||
| import net.imglib2.type.numeric.integer.UnsignedLongType | ||
| import net.imglib2.type.volatiles.VolatileUnsignedLongType | ||
| import net.imglib2.util.Intervals | ||
| import net.imglib2.view.IntervalView | ||
| import org.janelia.saalfeldlab.fx.actions.verifyPermission | ||
| import org.janelia.saalfeldlab.fx.extensions.createObservableBinding | ||
| import org.janelia.saalfeldlab.fx.extensions.nonnull | ||
| import org.janelia.saalfeldlab.fx.extensions.nonnullVal | ||
| import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread | ||
| import org.janelia.saalfeldlab.labels.blocks.LabelBlockLookupKey | ||
| import org.janelia.saalfeldlab.paintera.Paintera | ||
| import org.janelia.saalfeldlab.paintera.control.actions.MenuAction | ||
| import org.janelia.saalfeldlab.paintera.control.actions.PaintActionType | ||
| import org.janelia.saalfeldlab.paintera.control.actions.onAction | ||
| import org.janelia.saalfeldlab.paintera.data.mask.MaskInfo | ||
| import org.janelia.saalfeldlab.paintera.data.mask.MaskedSource | ||
| import org.janelia.saalfeldlab.paintera.data.mask.SourceMask | ||
| import org.janelia.saalfeldlab.paintera.data.n5.N5DataSource | ||
| import org.janelia.saalfeldlab.paintera.paintera | ||
| import org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState | ||
| import org.janelia.saalfeldlab.util.convert | ||
| import org.janelia.saalfeldlab.util.grids.LabelBlockLookupAllBlocks | ||
| import org.janelia.saalfeldlab.util.interval | ||
| import kotlin.math.nextUp | ||
| import net.imglib2.type.label.Label as Imglib2Label | ||
|
|
||
| object ReplaceLabel : MenuAction("_Replace or Delete Label...") { | ||
|
|
||
| private val LOG = KotlinLogging.logger { } | ||
|
|
||
| private val state = ReplaceLabelState() | ||
|
|
||
| private val replacementLabelProperty = state.replacementLabel | ||
| private val replacementLabel by replacementLabelProperty.nonnullVal() | ||
|
|
||
| private val activateReplacementProperty = state.activeReplacementLabel.apply { | ||
| subscribe { _, activate -> | ||
| if (activate) | ||
| activateReplacementLabel(0L, replacementLabel) | ||
| else | ||
| activateReplacementLabel(replacementLabel, 0L) | ||
| } | ||
| } | ||
| private val activateReplacement by activateReplacementProperty.nonnull() | ||
|
|
||
| private val progressProperty = SimpleDoubleProperty() | ||
| private val progressTextProperty = SimpleStringProperty() | ||
|
|
||
| init { | ||
| verifyPermission(PaintActionType.Erase, PaintActionType.Background, PaintActionType.Fill) | ||
| onAction(state) { | ||
| showDialog() | ||
| } | ||
| } | ||
|
|
||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.generateReplaceLabelMask(newLabel: Long, vararg fragments: Long) = with(maskedSource) { | ||
| val dataSource = getDataSource(0, 0) | ||
|
|
||
| val fragmentsSet = fragments.toHashSet() | ||
| dataSource.convert(UnsignedLongType(Imglib2Label.INVALID)) { src, target -> | ||
| val value = if (src.integerLong in fragmentsSet) newLabel else Imglib2Label.INVALID | ||
| target.set(value) | ||
| }.interval(dataSource) | ||
| } | ||
|
|
||
|
|
||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.deleteActiveFragment() = replaceActiveFragment(0L) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.deleteActiveSegment() = replaceActiveSegment(0L) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.deleteAllActiveFragments() = replaceAllActiveFragments(0L) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.deleteAllActiveSegments() = replaceAllActiveSegments(0L) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.replaceActiveFragment(newLabel: Long) = replaceLabels(newLabel, activeFragment) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.replaceActiveSegment(newLabel: Long) = replaceLabels(newLabel, *fragmentsForActiveSegment) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.replaceAllActiveFragments(newLabel: Long) = replaceLabels(newLabel, *allActiveFragments) | ||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.replaceAllActiveSegments(newLabel: Long) = replaceLabels(newLabel, *fragmentsForActiveSegment) | ||
|
|
||
|
|
||
| private fun <T : IntegerType<T>> ReplaceLabelState<T>.replaceLabels(newLabel: Long, vararg oldLabels: Long) = with(maskedSource) { | ||
| val blocks = blocksForLabels(0, *oldLabels) | ||
| val replacedLabelMask = generateReplaceLabelMask(newLabel, *oldLabels) | ||
|
|
||
| val sourceMask = SourceMask( | ||
| MaskInfo(0, 0), | ||
| replacedLabelMask, | ||
| replacedLabelMask.convert(VolatileUnsignedLongType(Imglib2Label.INVALID)) { input, output -> | ||
| output.set(input.integerLong) | ||
| output.isValid = true | ||
| }.interval(replacedLabelMask), | ||
| null, | ||
| null | ||
| ) {} | ||
|
|
||
|
|
||
| val numBlocks = blocks.size | ||
| val progressTextBinding = progressProperty.createObservableBinding { | ||
| val blocksDone = (it.doubleValue() * numBlocks).nextUp().toLong().coerceAtMost(numBlocks.toLong()) | ||
| "Blocks: $blocksDone / $numBlocks" | ||
| } | ||
| InvokeOnJavaFXApplicationThread { | ||
| progressTextProperty.unbind() | ||
| progressTextProperty.bind(progressTextBinding) | ||
| } | ||
|
|
||
| setMask(sourceMask) { it == newLabel } | ||
| applyMaskOverIntervals( | ||
| sourceMask, | ||
| blocks, | ||
| progressProperty | ||
| ) { it == newLabel } | ||
|
|
||
| requestRepaintOverIntervals(blocks) | ||
| sourceState.refreshMeshes() | ||
| } | ||
|
|
||
| private fun activateReplacementLabel(current: Long, next: Long) { | ||
| val selectedIds = state.paintContext.selectedIds | ||
| if (current != selectedIds.lastSelection) { | ||
| selectedIds.deactivate(current) | ||
| } | ||
| if (activateReplacement && next > 0L) { | ||
| selectedIds.activateAlso(selectedIds.lastSelection, next) | ||
| } | ||
| } | ||
|
|
||
| fun showDialog() = state.showDialog() | ||
|
|
||
| private fun ReplaceLabelState<*>.showDialog() { | ||
| Dialog<Boolean>().apply { | ||
| isResizable = true | ||
| Paintera.registerStylesheets(dialogPane) | ||
| dialogPane.buttonTypes += ButtonType.APPLY | ||
| dialogPane.buttonTypes += ButtonType.CANCEL | ||
| title = name?.replace("_", "") | ||
|
|
||
| progressTextProperty.unbind() | ||
| progressTextProperty.set("") | ||
|
|
||
| progressProperty.unbind() | ||
| progressProperty.set(0.0) | ||
|
|
||
| val replaceLabelUI = ReplaceLabelUI(state) | ||
| replaceLabelUI.progressBarProperty.bind(progressProperty) | ||
| replaceLabelUI.progressLabelText.bind(progressTextProperty) | ||
|
|
||
| dialogPane.content = replaceLabelUI | ||
| dialogPane.lookupButton(ButtonType.APPLY).also { applyButton -> | ||
| applyButton.disableProperty().bind(paintera.baseView.isDisabledProperty) | ||
| applyButton.cursorProperty().bind(paintera.baseView.node.cursorProperty()) | ||
| applyButton.addEventFilter(ActionEvent.ACTION) { event -> | ||
| event.consume() | ||
| val replacementLabel = state.replacementLabel.value | ||
| val fragmentsToReplace = state.fragmentsToReplace.toLongArray() | ||
| if (replacementLabel != null && replacementLabel >= 0 && fragmentsToReplace.isNotEmpty()) { | ||
| CoroutineScope(Dispatchers.Default).async { | ||
| replaceLabels(replacementLabel, *fragmentsToReplace) | ||
| if (activateReplacement) | ||
| state.sourceState.selectedIds.activate(replacementLabel) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| dialogPane.lookupButton(ButtonType.CANCEL).apply { | ||
| disableProperty().bind(paintContext.dataSource.isApplyingMaskProperty()) | ||
| } | ||
| dialogPane.scene.window.setOnCloseRequest { | ||
| if (paintContext.dataSource.isApplyingMaskProperty().get()) | ||
| it.consume() | ||
| } | ||
| }.show() | ||
| } | ||
|
|
||
| private fun ReplaceLabelState<*>.requestRepaintOverIntervals(sourceIntervals: List<Interval>? = null) { | ||
| val globalInterval = sourceIntervals | ||
| ?.reduce(Intervals::union) | ||
| ?.let { maskedSource.getSourceTransformForMask(MaskInfo(0, 0)).estimateBounds(it) } | ||
|
|
||
| paintera.baseView.orthogonalViews().requestRepaint(globalInterval) | ||
| } | ||
|
|
||
| fun ReplaceLabelState<*>.blocksForLabels(scale0: Int, vararg labels: Long): List<Interval> = with(maskedSource) { | ||
| val blocksFromSource = labels.flatMap { sourceState.labelBlockLookup.read(LabelBlockLookupKey(scale0, it)).toList() } | ||
|
|
||
| /* Read from canvas access (if in canvas) */ | ||
| val cellGrid = getCellGrid(0, scale0) | ||
| val cellIntervals = cellGrid.cellIntervals().randomAccess() | ||
| val cellPos = LongArray(cellGrid.numDimensions()) | ||
| val blocksFromCanvas = labels.flatMap { | ||
| getModifiedBlocks(scale0, it).toArray().map { block -> | ||
| cellGrid.getCellGridPositionFlat(block, cellPos) | ||
| FinalInterval(cellIntervals.setPositionAndGet(*cellPos)) | ||
| } | ||
| } | ||
|
|
||
| return blocksFromSource + blocksFromCanvas | ||
| } | ||
|
|
||
| } | ||
|
|
||
| private fun <T : IntegerType<T>> MaskedSource<T, out Type<*>>.addReplaceMaskAsSource( | ||
| replacedFragmentMask: IntervalView<UnsignedLongType> | ||
| ): ConnectomicsLabelState<UnsignedLongType, VolatileUnsignedLongType> { | ||
| val metadataState = (underlyingSource() as? N5DataSource)?.getMetadataState()!! | ||
| return paintera.baseView.addConnectomicsLabelSource<UnsignedLongType, VolatileUnsignedLongType>( | ||
| replacedFragmentMask, | ||
| metadataState.resolution, | ||
| metadataState.translation, | ||
| 1L, | ||
| "fragmentMask", | ||
| LabelBlockLookupAllBlocks.fromSource(underlyingSource()) | ||
| )!! | ||
| } |
93 changes: 93 additions & 0 deletions
93
src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/paint/ReplaceLabelState.kt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| package org.janelia.saalfeldlab.paintera.control.actions.paint | ||
|
|
||
| import javafx.beans.property.BooleanProperty | ||
| import javafx.beans.property.LongProperty | ||
| import javafx.beans.property.SimpleBooleanProperty | ||
| import javafx.beans.property.SimpleLongProperty | ||
| import javafx.collections.FXCollections | ||
| import javafx.collections.ObservableList | ||
| import javafx.event.Event | ||
| import net.imglib2.type.numeric.IntegerType | ||
| import org.janelia.saalfeldlab.fx.actions.Action | ||
| import org.janelia.saalfeldlab.paintera.control.actions.ActionState | ||
| import org.janelia.saalfeldlab.paintera.control.actions.verify | ||
| import org.janelia.saalfeldlab.paintera.control.modes.PaintLabelMode | ||
| import org.janelia.saalfeldlab.paintera.control.tools.paint.StatePaintContext | ||
| import org.janelia.saalfeldlab.paintera.paintera | ||
| import org.janelia.saalfeldlab.paintera.state.label.ConnectomicsLabelState | ||
|
|
||
| interface ReplaceLabelUIState { | ||
|
|
||
| val activeFragment: Long | ||
| val activeSegment: Long | ||
| val allActiveFragments: LongArray | ||
| val allActiveSegments: LongArray | ||
| val fragmentsForActiveSegment: LongArray | ||
| val fragmentsForAllActiveSegments: LongArray | ||
|
|
||
| val fragmentsToReplace: ObservableList<Long> | ||
| val replacementLabel: LongProperty | ||
| val activeReplacementLabel: BooleanProperty | ||
|
|
||
| fun fragmentsForSegment(segment: Long): LongArray | ||
| fun nextId(): Long | ||
|
|
||
| } | ||
|
|
||
| class ReplaceLabelState<T>() : ActionState(), ReplaceLabelUIState | ||
| where T : IntegerType<T> { | ||
| internal lateinit var sourceState: ConnectomicsLabelState<*, *> | ||
| internal lateinit var paintContext: StatePaintContext<T, *> | ||
|
|
||
| internal val maskedSource | ||
| get() = paintContext.dataSource | ||
|
|
||
| internal val assignment | ||
| get() = paintContext.assignment | ||
|
|
||
| private val selectedIds | ||
| get() = paintContext.selectedIds | ||
|
|
||
| override val activeFragment | ||
| get() = selectedIds.lastSelection | ||
|
|
||
| override val activeSegment | ||
| get() = assignment.getSegment(activeFragment) | ||
|
|
||
| override val fragmentsForActiveSegment: LongArray | ||
| get() = assignment.getFragments(activeSegment).toArray() | ||
|
|
||
| override val allActiveFragments: LongArray | ||
| get() = selectedIds.activeIds.toArray() | ||
|
|
||
| override val allActiveSegments | ||
| get() = allActiveFragments.asSequence() | ||
| .map { assignment.getSegment(it) } | ||
| .toSet() | ||
| .toLongArray() | ||
|
|
||
| override val fragmentsForAllActiveSegments | ||
| get() = allActiveSegments.asSequence() | ||
| .flatMap { assignment.getFragments(it).toArray().asSequence() } | ||
| .toSet() | ||
| .toLongArray() | ||
|
|
||
| override fun fragmentsForSegment(segment: Long): LongArray { | ||
| return assignment.getFragments(segment).toArray() | ||
| } | ||
|
|
||
| override val fragmentsToReplace: ObservableList<Long> = FXCollections.observableArrayList() | ||
| override val replacementLabel: LongProperty = SimpleLongProperty(0L) | ||
| override val activeReplacementLabel = SimpleBooleanProperty(false) | ||
|
|
||
| override fun nextId() = sourceState.nextId() | ||
|
|
||
| override fun <E : Event> Action<E>.verifyState() { | ||
| verify(::sourceState, "Label Source is Active") { paintera.currentSource as? ConnectomicsLabelState<*, *> } | ||
| verify(::paintContext, "Paint Label Mode has StatePaintContext") { PaintLabelMode.statePaintContext as StatePaintContext<T, *> } | ||
|
|
||
| verify("Paint Label Mode is Active") { paintera.currentMode is PaintLabelMode } | ||
| verify("Paintera is not disabled") { !paintera.baseView.isDisabledProperty.get() } | ||
| verify("Mask not in use") { !paintContext.dataSource.isMaskInUseBinding().get() } | ||
| } | ||
| } |
Oops, something went wrong.