Merge pull request #502 from cmhulbert/feat/smoothAction

Feat/smooth action

src/main/java/bdv/fx/viewer/ViewerPanelFX.java

@@ -190,7 +190,7 @@ public ViewerPanelFX(
 		transformListeners.add(tf -> Paintera.whenPaintable(getDisplay()::drawOverlays));
 
 		this.state = new ViewerState(numTimepoints, this);
-		state.addListener(obs -> Paintera.whenPaintable(this::requestRepaint));
+		state.addListener(obs -> Paintera.ifPaintable(this::requestRepaint));
 
 		Paintera.whenPaintable(() -> getDisplay().drawOverlays());
 

src/main/java/org/janelia/saalfeldlab/paintera/PainteraCommandLineArgs.java

@@ -76,7 +76,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrWriterIfN5ContainerExists;
+import static org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrGetWriterIfExistsAndWritable;
 
 @Command(name = "Paintera", showDefaultValues = true, resourceBundle = "org.janelia.saalfeldlab.paintera.PainteraCommandLineArgs", usageHelpWidth = 120,
 		parameterListHeading = "%n@|bold,underline Parameters|@:%n",
@@ -649,7 +649,7 @@ private void addToViewer(final PainteraBaseView viewer, final Supplier<String> p
 			for (final String container : containers) {
 				LOG.debug("Adding datasets for container {}", container);
 
-				N5Reader n5Container = getReaderOrWriterIfN5ContainerExists(container);
+				N5Reader n5Container = getReaderOrGetWriterIfExistsAndWritable(container);
 
 				final Predicate<String> datasetFilter = options.useDataset();
 				final ExecutorService es = getDiscoveryExecutorService();

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

@@ -268,9 +268,6 @@ else if (blockOutlineRemoved instanceof Shape3D)
 					((PhongMaterial)meshAdded.getMaterial()).diffuseColorProperty().bind(this.state.premultipliedColor);
 					meshAdded.drawModeProperty().bind(this.state.settings.getDrawModeProperty());
 					meshAdded.cullFaceProperty().bind(this.state.settings.getCullFaceProperty());
-					meshAdded.scaleXProperty().bind(this.state.settings.getInflateProperty());
-					meshAdded.scaleYProperty().bind(this.state.settings.getInflateProperty());
-					meshAdded.scaleZProperty().bind(this.state.settings.getInflateProperty());
 				}
 
 				if (change.getValueAdded().getB() != null) {
@@ -284,9 +281,6 @@ else if (blockOutlineAdded instanceof Shape3D)
 						material = null;
 					if (material instanceof PhongMaterial)
 						((PhongMaterial)material).diffuseColorProperty().bind(this.state.premultipliedColor);
-					blockOutlineAdded.scaleXProperty().bind(this.state.settings.getInflateProperty());
-					blockOutlineAdded.scaleYProperty().bind(this.state.settings.getInflateProperty());
-					blockOutlineAdded.scaleZProperty().bind(this.state.settings.getInflateProperty());
 					blockOutlineAdded.setDisable(true);
 				}
 			}

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

@@ -22,9 +22,9 @@ public class Smooth {
 	 */
 	private static final Logger LOG = LoggerFactory.getLogger(Smooth.class);
 
-	public static final double DEFAULT_LAMBDA = 0.5;
+	public static final double DEFAULT_LAMBDA = 1.0;
 
-	public static final int DEFAULT_ITERATIONS = 3;
+	public static final int DEFAULT_ITERATIONS = 1;
 
 	private static boolean isBoundary(
 			final ArrayList<TIntHashSet> vertexTriangleLUT,

src/main/java/org/janelia/saalfeldlab/paintera/serialization/SourceInfoSerializer.java

@@ -16,7 +16,7 @@
 import org.janelia.saalfeldlab.paintera.serialization.sourcestate.SourceStateSerialization;
 import org.janelia.saalfeldlab.paintera.state.SourceInfo;
 import org.janelia.saalfeldlab.paintera.state.SourceState;
-import org.janelia.saalfeldlab.paintera.state.raw.ConnectomicsRawState;
+import org.janelia.saalfeldlab.util.n5.N5Helpers;
 import org.scijava.plugin.Plugin;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -157,9 +157,11 @@ public static void populate(
 		}
 
 		final SourceState<?, ?>[] sourceStates = new SourceState[numStates];
+		final boolean[] removeState = new boolean[numStates];
 
 		for (int i = 0; i < numStates && Arrays.stream(sourceStates).anyMatch(Objects::isNull); ++i) {
 			for (int k = 0; k < numStates; ++k) {
+				if (removeState[k]) continue;
 				if (sourceStates[k] == null) {
 					final SourceState<?, ?>[] dependencies = IntStream
 							.of(dependsOn[k].toArray())
@@ -180,18 +182,36 @@ public static void populate(
 						@SuppressWarnings("unchecked") final Class<? extends SourceState<?, ?>> clazz = (Class<? extends SourceState<?, ?>>)Class
 								.forName(state.get(STATE_TYPE_KEY).getAsString());
 						LOG.debug("Deserializing state={}, class={}", state, clazz);
-						sourceStates[k] = gson.fromJson(state.get(STATE_KEY), clazz);
+						try {
+							sourceStates[k] = gson.fromJson(state.get(STATE_KEY), clazz);
+						} catch (Exception e) {
+							//noinspection ConstantValue
+							if (e instanceof N5Helpers.RemoveSourceException) {
+								LOG.info("Removing source: {}", stateName);
+								sourceStates[k] = null;
+								removeState[k] = true;
+								continue;
+							} else {
+								throw e;
+							}
+						}
 						logSourceForDependencies.accept(k, sourceStates[k]);
 					}
 				}
 			}
 		}
 
-		if (Arrays.stream(sourceStates).anyMatch(Objects::isNull)) {
-			throw new RuntimeException("Unable to deserialize all source states");
+		final ArrayList<SourceState<?, ?>> states = new ArrayList<>();
+		for (int i = 0; i < sourceStates.length; i++) {
+			final SourceState<?, ?> sourceState = sourceStates[i];
+			if (sourceState == null && !removeState[i])
+				throw new RuntimeException("Unable to deserialize all source states");
+			else if (sourceState != null)
+				states.add(sourceState);
+
 		}
 
-		return sourceStates;
+		return states.toArray(SourceState[]::new);
 
 	}
 

src/main/java/org/janelia/saalfeldlab/paintera/serialization/config/MeshSettingsSerializer.java

@@ -39,8 +39,6 @@ public class MeshSettingsSerializer implements PainteraSerialization.PainteraAda
 
 	private static final String CULL_FACE_KEY = "cullFace";
 
-	private static final String INFLATE_KEY = "inflate";
-
 	private static final String IS_VISIBLE_KEY = "isVisible";
 
 	public static MeshSettings deserializeInto(
@@ -54,7 +52,6 @@ public static MeshSettings deserializeInto(
 		Optional.ofNullable(map.get(SMOOTHING_ITERATIONS_KEY)).map(JsonElement::getAsInt).ifPresent(settings::setSmoothingIterations);
 		Optional.ofNullable(map.get(SMOOTHING_LAMBDA_KEY)).map(JsonElement::getAsDouble).ifPresent(settings::setSmoothingLambda);
 		Optional.ofNullable(map.get(OPACITY_KEY)).map(JsonElement::getAsDouble).ifPresent(settings::setOpacity);
-		Optional.ofNullable(map.get(INFLATE_KEY)).map(JsonElement::getAsDouble).ifPresent(settings::setInflate);
 		Optional.ofNullable(map.get(DRAW_MODE_KEY)).map(el -> (DrawMode)context.deserialize(el, DrawMode.class)).ifPresent(settings::setDrawMode);
 		Optional.ofNullable(map.get(CULL_FACE_KEY)).map(el -> (CullFace)context.deserialize(el, CullFace.class)).ifPresent(settings::setCullFace);
 		Optional.ofNullable(map.get(IS_VISIBLE_KEY)).map(JsonElement::getAsBoolean).ifPresent(settings::setVisible);
@@ -112,9 +109,6 @@ public JsonElement serialize(final MeshSettings src, final Type typeOfSrc, final
 		if (defaults.getOpacity() != src.getOpacityProperty().get())
 			map.addProperty(OPACITY_KEY, src.getOpacityProperty().get());
 
-		if (defaults.getInflate() != src.getInflate())
-			map.addProperty(INFLATE_KEY, src.getInflate());
-
 		if (defaults.isVisible() != src.isVisible())
 			map.addProperty(IS_VISIBLE_KEY, src.isVisible());
 

src/main/java/org/janelia/saalfeldlab/paintera/ui/source/mesh/SegmentMeshExporterDialog.java

@@ -191,8 +191,9 @@ private void createMultiIdsDialog(final ObservableList<Long> ids) {
 		int row = createCommonDialog(contents);
 
 		checkListView.setItems(ids);
-		checkListView.prefHeightProperty()
-				.bind(Bindings.size(checkListView.itemsProperty().get()).multiply(LIST_CELL_HEIGHT));
+		checkListView.getSelectionModel().selectAll();
+		selectAll.setSelected(true);
+		checkListView.prefHeightProperty().bind(Bindings.size(checkListView.itemsProperty().get()).multiply(LIST_CELL_HEIGHT));
 
 		final Button button = new Button("Browse");
 		button.setOnAction(event -> {

src/main/java/org/janelia/saalfeldlab/util/n5/universe/N5FactoryWithCache.java

@@ -59,18 +59,22 @@ public class N5FactoryWithCache extends N5Factory {
 				readerCache.remove(url).close();
 			}
 		} else {
-			readerCache.put(url, super.openReader(url));
+			final N5Reader reader = super.openReader(url);
+			if (reader.getAttribute("/", N5Reader.VERSION_KEY, String.class) != null) {
+				readerCache.put(url, reader);
+			}
 		}
 		return readerCache.get(url);
 	}
 
 	@Override public N5Writer openWriter(String url)  {
 
 		/* Check if writer is valid (it may have been closed by someone) */
-		final N5Reader cachedContainer = writerCache.get(url);
+		final N5Writer cachedContainer = writerCache.get(url);
 		if (cachedContainer != null) {
 			try {
-				cachedContainer.getVersion();
+				/* See if its open, and we still have write permissions */
+				cachedContainer.setAttribute("/", N5Reader.VERSION_KEY, cachedContainer.getVersion().toString());
 			} catch (Exception e) {
 				writerCache.remove(url).close();
 				if (readerCache.get(url) == cachedContainer) {
@@ -79,6 +83,8 @@ public class N5FactoryWithCache extends N5Factory {
 			}
 		} else {
 			final N5Writer n5Writer = super.openWriter(url);
+			/* See if we have write permissions before we declare success */
+			n5Writer.setAttribute("/", N5Reader.VERSION_KEY, n5Writer.getVersion());
 			writerCache.put(url, n5Writer);
 			if (readerCache.get(url) != null) {
 				readerCache.remove(url).close();

src/main/kotlin/org/janelia/saalfeldlab/paintera/config/ScreenScalesConfig.kt

@@ -55,7 +55,7 @@ class ScreenScalesConfig @JvmOverloads constructor(vararg initialScales: Double
 
 	companion object {
 
-		private val DEFAULT_SCREEN_SCALES = doubleArrayOf(1.0, 0.5, 0.25, 0.125, 0.0625)
+		private val DEFAULT_SCREEN_SCALES = doubleArrayOf(0.5, 0.25, 0.125)
 
 		@JvmStatic
 		fun defaultScreenScalesCopy(): DoubleArray {

src/main/kotlin/org/janelia/saalfeldlab/paintera/data/n5/N5HDF5WriterAdapter.kt

@@ -7,7 +7,7 @@ import org.janelia.saalfeldlab.paintera.Paintera.Companion.n5Factory
 import org.janelia.saalfeldlab.paintera.serialization.GsonExtensions
 import org.janelia.saalfeldlab.paintera.serialization.StatefulSerializer
 import org.janelia.saalfeldlab.paintera.state.SourceState
-import org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrWriterIfN5ContainerExists
+import org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrGetWriterIfExistsAndWritable
 import org.janelia.saalfeldlab.util.n5.N5Helpers.getWriterIfN5ContainerExists
 import org.scijava.plugin.Plugin
 import java.lang.reflect.Type
@@ -87,7 +87,7 @@ class N5HDF5ReaderAdapter : StatefulSerializer.SerializerAndDeserializer<N5HDF5R
 	): JsonDeserializer<N5HDF5Reader> = HDF5Deserializer(projectDirectory) { file, overrideBlockSize, defaultBlockSize ->
 		n5Factory.hdf5OverrideBlockSize(overrideBlockSize)
 		n5Factory.hdf5DefaultBlockSize(*(defaultBlockSize ?: intArrayOf()))
-		(getReaderOrWriterIfN5ContainerExists(file) as? N5HDF5Reader) ?: throw hdf5OpenError(file)
+		(getReaderOrGetWriterIfExistsAndWritable(file) as? N5HDF5Reader) ?: throw hdf5OpenError(file)
 	}
 
 	override fun getTargetClass() = N5HDF5Reader::class.java

src/main/kotlin/org/janelia/saalfeldlab/paintera/meshes/MeshSettings.kt

@@ -20,7 +20,6 @@ class MeshSettings @JvmOverloads constructor(
 		val opacity: Double
 		val drawMode: DrawMode
 		val cullFace: CullFace
-		val inflate: Double
 		val isVisible: Boolean
 		val minLabelRatio: Double
 		val levelOfDetail: Int
@@ -45,9 +44,6 @@ class MeshSettings @JvmOverloads constructor(
 			@JvmStatic
 			val cullFace = CullFace.FRONT
 
-			@JvmStatic
-			val inflate = 1.0
-
 			@JvmStatic
 			val isVisible = true
 
@@ -83,7 +79,6 @@ class MeshSettings @JvmOverloads constructor(
 		override var opacity: Double = Defaults.Values.opacity
 		override var drawMode: DrawMode = Defaults.Values.drawMode
 		override var cullFace: CullFace = Defaults.Values.cullFace
-		override var inflate: Double = Defaults.Values.inflate
 		override var isVisible: Boolean = Defaults.Values.isVisible
 		override var minLabelRatio: Double = Defaults.Values.minLabelRatio
 		override var levelOfDetail: Int = Defaults.Values.levelOfDetail
@@ -103,7 +98,6 @@ class MeshSettings @JvmOverloads constructor(
 	val opacityProperty: DoubleProperty = SimpleDoubleProperty(defaults.opacity)
 	val drawModeProperty: ObjectProperty<DrawMode> = SimpleObjectProperty(defaults.drawMode)
 	val cullFaceProperty: ObjectProperty<CullFace> = SimpleObjectProperty(defaults.cullFace)
-	val inflateProperty: DoubleProperty = SimpleDoubleProperty(defaults.inflate)
 	val isVisibleProperty: BooleanProperty = SimpleBooleanProperty(defaults.isVisible)
 	val minLabelRatioProperty: DoubleProperty = SimpleDoubleProperty(defaults.minLabelRatio)
 	val levelOfDetailProperty: IntegerProperty = SimpleIntegerProperty(defaults.levelOfDetail)
@@ -116,7 +110,6 @@ class MeshSettings @JvmOverloads constructor(
 	var opacity by opacityProperty.nonnull()
 	var drawMode by drawModeProperty.nonnull()
 	var cullFace by cullFaceProperty.nonnull()
-	var inflate by inflateProperty.nonnull()
 	var isVisible by isVisibleProperty.nonnull()
 	var minLabelRatio by minLabelRatioProperty.nonnull()
 	var levelOfDetail by levelOfDetailProperty.nonnull()
@@ -147,7 +140,6 @@ class MeshSettings @JvmOverloads constructor(
 		opacity = that.opacity
 		drawMode = that.drawMode
 		cullFace = that.cullFace
-		inflate = that.inflate
 		isVisible = that.isVisible
 	}
 
@@ -171,7 +163,6 @@ class MeshSettings @JvmOverloads constructor(
 		opacityProperty.bind(that.opacityProperty)
 		drawModeProperty.bind(that.drawModeProperty)
 		cullFaceProperty.bind(that.cullFaceProperty)
-		inflateProperty.bind(that.inflateProperty)
 		isVisibleProperty.bind(that.isVisibleProperty)
 	}
 
@@ -186,7 +177,6 @@ class MeshSettings @JvmOverloads constructor(
 		opacityProperty.unbind()
 		drawModeProperty.unbind()
 		cullFaceProperty.unbind()
-		inflateProperty.unbind()
 		isVisibleProperty.unbind()
 	}
 
@@ -201,7 +191,6 @@ class MeshSettings @JvmOverloads constructor(
 		opacityProperty.bindBidirectional(that.opacityProperty)
 		drawModeProperty.bindBidirectional(that.drawModeProperty)
 		cullFaceProperty.bindBidirectional(that.cullFaceProperty)
-		inflateProperty.bindBidirectional(that.inflateProperty)
 		isVisibleProperty.bindBidirectional(that.isVisibleProperty)
 	}
 
@@ -216,7 +205,6 @@ class MeshSettings @JvmOverloads constructor(
 		opacityProperty.unbindBidirectional(that.opacityProperty)
 		drawModeProperty.unbindBidirectional(that.drawModeProperty)
 		cullFaceProperty.unbindBidirectional(that.cullFaceProperty)
-		inflateProperty.unbindBidirectional(that.inflateProperty)
 		isVisibleProperty.unbindBidirectional(that.isVisibleProperty)
 	}
 
@@ -229,7 +217,6 @@ class MeshSettings @JvmOverloads constructor(
 				&& opacity == defaults.opacity
 				&& defaults.drawMode == drawMode
 				&& defaults.cullFace == cullFace
-				&& inflate == defaults.inflate
 				&& isVisible == defaults.isVisible
 	}
 

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

@@ -34,7 +34,6 @@ class MeshSettingsController @JvmOverloads constructor(
 	private val smoothingLambda: DoubleProperty,
 	private val smoothingIterations: IntegerProperty,
 	private val minLabelRatio: DoubleProperty,
-	private val inflate: DoubleProperty,
 	private val drawMode: Property<DrawMode>,
 	private val cullFace: Property<CullFace>,
 	private val isVisible: BooleanProperty,
@@ -51,7 +50,6 @@ class MeshSettingsController @JvmOverloads constructor(
 		meshSettings.smoothingLambdaProperty,
 		meshSettings.smoothingIterationsProperty,
 		meshSettings.minLabelRatioProperty,
-		meshSettings.inflateProperty,
 		meshSettings.drawModeProperty,
 		meshSettings.cullFaceProperty,
 		meshSettings.isVisibleProperty,
@@ -74,10 +72,9 @@ class MeshSettingsController @JvmOverloads constructor(
 				it.slider.valueProperty().bindBidirectional(coarsestScaleLevel)
 			},
 			NumericSliderWithField(0, this.numScaleLevels - 1, finestScaleLevel.value).apply { slider.valueProperty().bindBidirectional(finestScaleLevel) },
-			NumericSliderWithField(0.0, 1.00, .05).apply { slider.valueProperty().bindBidirectional(smoothingLambda) },
-			NumericSliderWithField(0, 10, 5).apply { slider.valueProperty().bindBidirectional(smoothingIterations) },
+			NumericSliderWithField(0.0, 1.00, 1.0).apply { slider.valueProperty().bindBidirectional(smoothingLambda) },
+			NumericSliderWithField(0, 10, 1).apply { slider.valueProperty().bindBidirectional(smoothingIterations) },
 			NumericSliderWithField(0.0, 1.0, 0.5).apply { slider.valueProperty().bindBidirectional(minLabelRatio) },
-			NumericSliderWithField(0.5, 2.0, inflate.value).apply { slider.valueProperty().bindBidirectional(inflate) },
 			ComboBox(FXCollections.observableArrayList(*DrawMode.values())).apply { valueProperty().bindBidirectional(drawMode) },
 			ComboBox(FXCollections.observableArrayList(*CullFace.values())).apply { valueProperty().bindBidirectional(cullFace) })
 	}
@@ -154,7 +151,6 @@ class MeshSettingsController @JvmOverloads constructor(
 			smoothingLambdaSlider: NumericSliderWithField,
 			smoothingIterationsSlider: NumericSliderWithField,
 			minLabelRatioSlider: NumericSliderWithField,
-			inflateSlider: NumericSliderWithField,
 			drawModeChoice: ComboBox<DrawMode>,
 			cullFaceChoice: ComboBox<CullFace>,
 		): GridPane {
@@ -188,7 +184,6 @@ class MeshSettingsController @JvmOverloads constructor(
 				addGridOption("Min label ratio", minLabelRatioSlider, tooltipText)
 			}
 
-			addGridOption("Inflate", inflateSlider, "Inflate Meshes by Factor")
 			addGridOption("Draw Mode", drawModeChoice)
 			addGridOption("Cull Face", cullFaceChoice)
 			return this

src/main/kotlin/org/janelia/saalfeldlab/paintera/state/metadata/MetadataState.kt

@@ -18,7 +18,7 @@ import org.janelia.saalfeldlab.paintera.state.metadata.MetadataState.Companion.i
 import org.janelia.saalfeldlab.util.n5.ImagesWithTransform
 import org.janelia.saalfeldlab.util.n5.N5Data
 import org.janelia.saalfeldlab.util.n5.N5Helpers
-import org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrWriterIfN5ContainerExists
+import org.janelia.saalfeldlab.util.n5.N5Helpers.getReaderOrGetWriterIfExistsAndWritable
 import org.janelia.saalfeldlab.util.n5.metadata.N5PainteraDataMultiScaleGroup
 import java.util.Optional
 
@@ -229,7 +229,7 @@ class MetadataUtils {
 
 		@JvmStatic
 		fun createMetadataState(n5containerAndDataset: String): Optional<MetadataState> {
-			val reader = getReaderOrWriterIfN5ContainerExists(n5containerAndDataset) ?: return Optional.empty()
+			val reader = getReaderOrGetWriterIfExistsAndWritable(n5containerAndDataset) ?: return Optional.empty()
 
 			val n5ContainerState = N5ContainerState(reader)
 			return N5Helpers.parseMetadata(reader).map { treeNode ->
@@ -243,7 +243,7 @@ class MetadataUtils {
 
 		@JvmStatic
 		fun createMetadataState(n5container: String, dataset: String?): Optional<MetadataState> {
-			val reader = getReaderOrWriterIfN5ContainerExists(n5container) ?: return Optional.empty()
+			val reader = getReaderOrGetWriterIfExistsAndWritable(n5container) ?: return Optional.empty()
 
 			val n5ContainerState = N5ContainerState(reader)
 			val metadataRoot = N5Helpers.parseMetadata(reader)