refactor!: abstract mesh export with progress bar

src/main/java/org/janelia/saalfeldlab/paintera/meshes/MeshExporter.java

@@ -2,9 +2,11 @@
 
 import gnu.trove.list.array.TFloatArrayList;
 import gnu.trove.list.array.TIntArrayList;
+import javafx.beans.property.SimpleIntegerProperty;
 import net.imglib2.Interval;
 import net.imglib2.util.Intervals;
 import org.janelia.saalfeldlab.fx.ui.Exceptions;
+import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread;
 import org.janelia.saalfeldlab.paintera.meshes.managed.GetBlockListFor;
 import org.janelia.saalfeldlab.paintera.meshes.managed.GetMeshFor;
 import org.janelia.saalfeldlab.util.HashWrapper;
@@ -14,24 +16,37 @@
 import java.io.IOException;
 import java.lang.invoke.MethodHandles;
 import java.util.*;
+import java.util.concurrent.CancellationException;
 
 public abstract class MeshExporter<T> {
 
+	public final SimpleIntegerProperty blocksProcessed = new SimpleIntegerProperty(0);
+	boolean cancelled = false;
+
 	private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 	public void exportMesh(
 			final GetBlockListFor<T> getBlockListFor,
 			final GetMeshFor<T> getMeshFor,
 			final MeshSettings[] meshSettings,
-			final T[] ids,
+			final List<T> ids,
 			final int scale,
 			final String path) {
 
-		for (int i = 0; i < ids.length; i++) {
-			exportMesh(getBlockListFor, getMeshFor, meshSettings[i], ids[i], scale, path, i != 0);
+		for (int i = 0; i < ids.size(); i++) {
+			exportMesh(getBlockListFor, getMeshFor, meshSettings[i], ids.get(i), scale, path, i != 0);
 		}
 	}
 
-	public void exportMesh(
+	public void cancel() {
+
+		cancelled = true;
+	}
+
+	public boolean isCancelled() {
+		return cancelled;
+	}
+
+	private void exportMesh(
 			final GetBlockListFor<T> getBlockListFor,
 			final GetMeshFor<T> getMeshFor,
 			final MeshSettings meshSettings,
@@ -53,8 +68,8 @@ public void exportMesh(
 		// generate keys from blocks, scaleIndex, and id
 		final List<ShapeKey<T>> keys = new ArrayList<>();
 		for (final Interval block : blocks) {
-			// ignoring simplification iterations parameter
-			// TODO consider smoothing parameters
+			if (cancelled)
+				throw new CancellationException("Mesh Export Cancelled");
 			keys.add(new ShapeKey<>(
 					id,
 					scaleIndex,
@@ -72,8 +87,11 @@ public void exportMesh(
 		final var normals = new TFloatArrayList();
 		final var indices = new TIntArrayList();
 		for (final ShapeKey<T> key : keys) {
+			if (cancelled)
+				throw new CancellationException("Mesh Export Cancelled");
 			PainteraTriangleMesh verticesAndNormals;
 			verticesAndNormals = getMeshFor.getMeshFor(key);
+			InvokeOnJavaFXApplicationThread.invoke(() -> blocksProcessed.set(blocksProcessed.get() + 1));
 			if (verticesAndNormals == null) {
 				continue;
 			}
@@ -86,6 +104,9 @@ public void exportMesh(
 			}
 		}
 
+		if (cancelled)
+			throw new CancellationException("Mesh Export Cancelled");
+
 		try {
 			save(path, id.toString(), vertices.toArray(), normals.toArray(), indices.toArray(), append);
 		} catch (final IOException e) {

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/ExportSourceState.kt

@@ -10,6 +10,7 @@ import net.imglib2.type.NativeType
 import net.imglib2.type.numeric.IntegerType
 import net.imglib2.type.numeric.integer.AbstractIntegerType
 import org.janelia.saalfeldlab.fx.extensions.createObservableBinding
+import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread
 import org.janelia.saalfeldlab.n5.DataType
 import org.janelia.saalfeldlab.n5.DatasetAttributes
 import org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader
@@ -32,7 +33,6 @@ import org.janelia.saalfeldlab.util.convertRAI
 import org.janelia.saalfeldlab.util.interval
 import org.janelia.saalfeldlab.util.n5.N5Helpers.MAX_ID_KEY
 import org.janelia.saalfeldlab.util.n5.N5Helpers.forEachBlockExists
-import java.util.concurrent.atomic.AtomicInteger
 
 class ExportSourceState {
 
@@ -127,7 +127,7 @@ class ExportSourceState {
 		}
 		progressUpdater?.apply {
 			exportJob.invokeOnCompletion { finish() }
-			showAndStart()
+			InvokeOnJavaFXApplicationThread { showAndWait() }
 		}
 	}
 }

src/main/kotlin/org/janelia/saalfeldlab/paintera/meshes/ui/MeshSettingsController.kt

@@ -1,5 +1,6 @@
 package org.janelia.saalfeldlab.paintera.meshes.ui
 
+import io.github.oshai.kotlinlogging.KotlinLogging
 import javafx.beans.property.*
 import javafx.collections.FXCollections
 import javafx.collections.ObservableList
@@ -13,22 +14,33 @@ import javafx.scene.paint.Color
 import javafx.scene.shape.CullFace
 import javafx.scene.shape.DrawMode
 import javafx.stage.Modality
+import kotlinx.coroutines.CoroutineScope
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.async
 import kotlinx.coroutines.javafx.awaitPulse
 import net.imglib2.type.label.LabelMultisetType
 import org.janelia.saalfeldlab.fx.Buttons
 import org.janelia.saalfeldlab.fx.Labels
 import org.janelia.saalfeldlab.fx.extensions.TitledPaneExtensions
+import org.janelia.saalfeldlab.fx.extensions.createNonNullValueBinding
 import org.janelia.saalfeldlab.fx.ui.NamedNode
 import org.janelia.saalfeldlab.fx.ui.NumericSliderWithField
 import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread
 import org.janelia.saalfeldlab.paintera.meshes.MeshExporterObj
 import org.janelia.saalfeldlab.paintera.meshes.MeshInfo
 import org.janelia.saalfeldlab.paintera.meshes.MeshSettings
+import org.janelia.saalfeldlab.paintera.meshes.managed.GetBlockListFor
+import org.janelia.saalfeldlab.paintera.meshes.managed.GetMeshFor
 import org.janelia.saalfeldlab.paintera.meshes.managed.MeshManager
+import org.janelia.saalfeldlab.paintera.meshes.managed.MeshManagerWithAssignmentForSegments
+import org.janelia.saalfeldlab.paintera.meshes.ui.MeshInfoPane.Companion.LOG
 import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts
 import org.janelia.saalfeldlab.paintera.ui.RefreshButton
+import org.janelia.saalfeldlab.paintera.ui.dialogs.AnimatedProgressBarAlert
+import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshExportResult
 import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshExporterDialog
 import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshProgressBar
+import java.util.concurrent.CancellationException
 import kotlin.math.max
 import kotlin.math.min
 
@@ -190,7 +202,7 @@ class MeshSettingsController @JvmOverloads constructor(
 			// min label ratio slider only makes sense for sources of label multiset type
 			if (addMinLabelratioSlider) {
 				val tooltipText = "Min label percentage for a pixel to be filled." + System.lineSeparator() +
-					"0.0 means that a pixel will always be filled if it contains the given label."
+						"0.0 means that a pixel will always be filled if it contains the given label."
 				addGridOption("Min label ratio", minLabelRatioSlider, tooltipText)
 			}
 
@@ -318,14 +330,14 @@ open class MeshInfoPane<T>(private val meshInfo: MeshInfo<T>) : TitledPane(null,
 			val result = exportDialog.showAndWait()
 			if (!result.isPresent) return@setOnAction
 
+			val manager: MeshManager<T> = meshInfo.manager
 			val parameters = result.get()
+			manager.exportMeshWithProgressPopup(parameters)
+
 			val meshExporter = parameters.meshExporter
 
 			val ids = parameters.meshKeys
-			if (ids.isEmpty()) return@setOnAction
-
 			val filePath = parameters.filePath
-			val scale = parameters.scale
 
 			if (meshExporter is MeshExporterObj) {
 				meshExporter.exportMaterial(
@@ -334,19 +346,72 @@ open class MeshInfoPane<T>(private val meshInfo: MeshInfo<T>) : TitledPane(null,
 					arrayOf(meshInfo.manager.getStateFor(ids[0])?.color ?: Color.WHITE)
 				)
 			}
-
-			meshExporter.exportMesh(
-				meshInfo.manager.getBlockListFor,
-				meshInfo.manager.getMeshFor,
-				meshInfo.meshSettings,
-				ids[0],
-				scale,
-				filePath,
-				false
-			)
 		}
 		return exportMeshButton
 	}
+
+	companion object {
+		private val LOG = KotlinLogging.logger { }
+	}
+}
+
+fun <T> MeshManager<T>.exportMeshWithProgressPopup(result : MeshExportResult<T>) {
+	val log = KotlinLogging.logger { }
+	val meshExporter = result.meshExporter
+	val blocksProcessed = meshExporter.blocksProcessed
+	val ids = result.meshKeys
+	if (ids.isEmpty()) return
+	val (getBlocks, getMesh) = when(this) {
+		is MeshManagerWithAssignmentForSegments -> getBlockListForSegment as GetBlockListFor<T> to getMeshForLongKey as GetMeshFor<T>
+		else -> getBlockListFor to getMeshFor
+	}
+	val totalBlocks = ids.sumOf { getBlocks.getBlocksFor(result.scale, it).count() }
+	val labelProp = SimpleStringProperty().apply {
+		bind(blocksProcessed.createNonNullValueBinding { "Blocks processed: ${it}/$totalBlocks" })
+	}
+	val progressProp = SimpleDoubleProperty(0.0).apply {
+		bind(blocksProcessed.createNonNullValueBinding { it.toDouble() / totalBlocks })
+	}
+	val progressUpdater = AnimatedProgressBarAlert(
+		"Export Mesh",
+		"Exporting Mesh",
+		labelProp,
+		progressProp
+	)
+	val exportJob = CoroutineScope(Dispatchers.IO).async {
+		meshExporter.exportMesh(
+			getBlocks,
+			getMesh,
+			ids.map { getSettings(it) }.toTypedArray(),
+			ids,
+			result.scale,
+			result.filePath
+		)
+	}
+	exportJob.invokeOnCompletion { cause ->
+		cause?.let {
+			if (it is CancellationException) {
+				log.info { "Export Mesh Cancelled by User" }
+				progressUpdater.stopAndClose()
+				return@invokeOnCompletion
+			}
+			log.error(it) { "Error exporting meshes" }
+			progressUpdater.stopAndClose()
+			InvokeOnJavaFXApplicationThread {
+				PainteraAlerts.alert(Alert.AlertType.ERROR, true).apply {
+					contentText = "Error exporting meshes\n${it.message}"
+				}.showAndWait()
+			}
+		} ?: progressUpdater.finish()
+	}
+	InvokeOnJavaFXApplicationThread {
+		if (exportJob.isActive) {
+			progressUpdater.showAndWait()
+			if (progressUpdater.cancelled)
+				meshExporter.cancel()
+		}
+
+	}
 }
 
 abstract class MeshInfoList<T : MeshInfo<K>, K>(

src/main/kotlin/org/janelia/saalfeldlab/paintera/state/IntersectingSourceStatePreferencePaneNode.kt

@@ -12,6 +12,7 @@ import org.janelia.saalfeldlab.paintera.meshes.MeshInfo
 import org.janelia.saalfeldlab.paintera.meshes.managed.MeshManagerWithSingleMesh
 import org.janelia.saalfeldlab.paintera.meshes.ui.MeshSettingsController
 import org.janelia.saalfeldlab.paintera.meshes.ui.MeshSettingsController.Companion.addGridOption
+import org.janelia.saalfeldlab.paintera.meshes.ui.exportMeshWithProgressPopup
 import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshExporterDialog
 import org.janelia.saalfeldlab.util.Colors
 
@@ -46,19 +47,12 @@ class IntersectingSourceStatePreferencePaneNode(private val state: IntersectingS
 							val exportDialog = MeshExporterDialog(MeshInfo(key, manager))
 							val result = exportDialog.showAndWait()
 							if (result.isPresent) {
+								manager.exportMeshWithProgressPopup(result.get())
 								result.get().run {
+									if (meshExporter.isCancelled()) return@run
 									(meshExporter as? MeshExporterObj<*>)?.run {
 										exportMaterial(filePath, arrayOf(""), arrayOf(Colors.toColor(state.converter().color)))
 									}
-									meshExporter.exportMesh(
-										manager.getBlockListFor,
-										manager.getMeshFor,
-										manager.getSettings(key),
-										key,
-										scale,
-										filePath,
-										false
-									)
 								}
 							}
 						}

src/main/kotlin/org/janelia/saalfeldlab/paintera/state/LabelSourceStateMeshPaneNode.kt

@@ -1,5 +1,6 @@
 package org.janelia.saalfeldlab.paintera.state
 
+import io.github.oshai.kotlinlogging.KotlinLogging
 import javafx.collections.ObservableList
 import javafx.event.EventHandler
 import javafx.geometry.Insets
@@ -18,14 +19,16 @@ import org.janelia.saalfeldlab.fx.extensions.TitledPaneExtensions.Companion.expa
 import org.janelia.saalfeldlab.fx.extensions.TitledPaneExtensions.Companion.graphicsOnly
 import org.janelia.saalfeldlab.fx.extensions.createNonNullValueBinding
 import org.janelia.saalfeldlab.paintera.data.DataSource
-import org.janelia.saalfeldlab.paintera.meshes.*
+import org.janelia.saalfeldlab.paintera.meshes.GlobalMeshProgressState
+import org.janelia.saalfeldlab.paintera.meshes.MeshExporterObj
+import org.janelia.saalfeldlab.paintera.meshes.MeshInfo
+import org.janelia.saalfeldlab.paintera.meshes.SegmentMeshInfoList
 import org.janelia.saalfeldlab.paintera.meshes.managed.MeshManagerWithAssignmentForSegments
 import org.janelia.saalfeldlab.paintera.meshes.ui.MeshSettingsController
+import org.janelia.saalfeldlab.paintera.meshes.ui.exportMeshWithProgressPopup
 import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts
 import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshExporterDialog
 import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshProgressBar
-import org.slf4j.LoggerFactory
-import java.lang.invoke.MethodHandles
 
 typealias TPE = TitledPaneExtensions
 
@@ -73,25 +76,19 @@ class LabelSourceStateMeshPaneNode(
 				val exportDialog = MeshExporterDialog(meshInfoList.meshInfos as ObservableList<MeshInfo<Long>>)
 				val result = exportDialog.showAndWait()
 				if (result.isPresent) {
+					manager.exportMeshWithProgressPopup(result.get())
 					result.get().run {
+						if (meshExporter.isCancelled()) return@run
+
 						val ids = meshKeys.toTypedArray()
 						val meshSettings = ids.map { manager.getSettings(it) }.toTypedArray()
-
 						(meshExporter as? MeshExporterObj<*>)?.run {
 							val colors: Array<Color> = ids.mapIndexed { idx, it ->
 								val color = manager.getStateFor(it)?.color ?: Color.WHITE
 								color.deriveColor(0.0, 1.0, 1.0, meshSettings[idx].opacity)
 							}.toTypedArray()
 							exportMaterial(filePath, ids.map { it.toString() }.toTypedArray(), colors)
 						}
-						meshExporter.exportMesh(
-							manager.getBlockListForSegment,
-							manager.getMeshForLongKey,
-							meshSettings,
-							ids,
-							scale,
-							filePath
-						)
 					}
 				}
 			}
@@ -131,7 +128,7 @@ class LabelSourceStateMeshPaneNode(
 
 	companion object {
 
-		private val LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass())
+		private val LOG = KotlinLogging.logger { }
 
 		private fun Node.asVBox() = if (this is VBox) this else VBox(this)
 

src/main/kotlin/org/janelia/saalfeldlab/paintera/state/ThresholdingSourceStatePreferencePaneNode.kt

@@ -19,6 +19,7 @@ import org.janelia.saalfeldlab.fx.ui.ObjectField
 import org.janelia.saalfeldlab.paintera.meshes.MeshExporterObj
 import org.janelia.saalfeldlab.paintera.meshes.MeshInfo
 import org.janelia.saalfeldlab.paintera.meshes.ui.MeshSettingsController
+import org.janelia.saalfeldlab.paintera.meshes.ui.exportMeshWithProgressPopup
 import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts
 import org.janelia.saalfeldlab.paintera.ui.source.mesh.MeshExporterDialog
 
@@ -93,19 +94,12 @@ class ThresholdingSourceStatePreferencePaneNode(private val state: ThresholdingS
 				val exportDialog = MeshExporterDialog(MeshInfo(state.meshManager.meshKey, state.meshManager))
 				val result = exportDialog.showAndWait()
 				if (result.isPresent) {
+					state.meshManager.exportMeshWithProgressPopup(result.get())
 					result.get().run {
+						if (meshExporter.isCancelled()) return@run
 						(meshExporter as? MeshExporterObj<*>)?.run {
 							exportMaterial(filePath, arrayOf(""), arrayOf(state.colorProperty().get()))
 						}
-						meshExporter.exportMesh(
-							state.meshManager.getBlockListFor,
-							state.meshManager.getMeshFor,
-							state.meshSettings,
-							state.thresholdBounds,
-							scale,
-							filePath,
-							false
-						)
 					}
 				}
 			}