Merge pull request #531 from saalfeldlab/feat/1.2.0

Feat/1.2.0
saalfeldlab · May 13, 2024 · 74814ec · 74814ec
2 parents aaccbd3 + 59de043
commit 74814ec
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diff --git a/.github/release.yml b/.github/release.yml
@@ -0,0 +1,13 @@
+# .github/release.yml
+
+changelog:
+  categories:
+    - title: Features
+      labels:
+        - '*'
+      exclude:
+        labels:
+          - dependencies
+    - title: Dependencies
+      labels:
+        - dependencies
diff --git a/...b/workflows/maven-build-all-installer.yml → .github/workflows/build-installers.yml b/...b/workflows/maven-build-all-installer.yml → .github/workflows/build-installers.yml
@@ -1,15 +1,12 @@
 # This workflow will build a Java project with Maven
 # For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
 
-name: Build All Installers
+name: Build Installers
 
 on:
-  push:
-    branches: [ master ]
+  workflow_call:
   pull_request:
-    branches: [ master ]
-  workflow_dispatch:
-    branches: [ master ]
+    branches: [master]
 
 env:
   DEV_IDENTITY: BXPZTQZ35S # Your Apple Dev identity, something like BXPZTQZ35S
@@ -21,9 +18,14 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest, macos-14]
     runs-on: ${{ matrix.os }}
-    env:
-      RELEASE_INSTALLERS: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
     steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set Version
+        shell: bash
+        run: |
+          short_version=`git rev-parse --short HEAD`
+          echo "VERSION=$short_version" >> $GITHUB_ENV
       - name: Download Wix
         uses: i3h/download-release-asset@v1
         if: matrix.os == 'windows-latest'
@@ -42,7 +44,7 @@ jobs:
         run: echo "$HOME/target/wix" >> $GITHUB_PATH
         if: matrix.os == 'windows-latest'
       - uses: actions/checkout@v2
-      - name: Set up JDK 17
+      - name: Set up JDK
         uses: actions/setup-java@v2
         with:
           java-version: 18.0.2
@@ -58,14 +60,11 @@ jobs:
           MACOS_CERTIFICATE_PWD: ${{ secrets.MACOS_CERTIFICATE_PWD }}
         if: ${{ env.MACOS_CERTIFICATE == null && (matrix.os == 'macos-latest' || matrix.os == 'macos-14') }}
         run: mvn -B clean install -DskipTests -Pbuild-installer "-Dmatrix.os=${{ matrix.os }}" --file pom.xml
-      - name: Update Automatic Release
-        uses: marvinpinto/action-automatic-releases@latest
-        if: ${{ env.RELEASE_INSTALLERS }}
+
+      - name: Upload Installers
+        uses: actions/upload-artifact@v4
         with:
-          repo_token: "${{ secrets.GITHUB_TOKEN}}"
-          automatic_release_tag: ${{ matrix.os }}
-          prerelease: true
-          title: ${{ matrix.os }} Development Build
-          files: |
+          name: Paintera-${{ matrix.os }}-${{ env.VERSION }}
+          path: |
             ${{ env.DMG_PATH }}
-            ./target/installer-${{ matrix.os }}/*
+            ./target/installer-${{ matrix.os }}/*
diff --git a/.github/workflows/publish-installers.yml b/.github/workflows/publish-installers.yml
@@ -0,0 +1,50 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Publish Installers
+
+on:
+  push:
+    tags: "paintera-*.*.*"
+  workflow_dispatch:
+
+
+
+env:
+  DEV_IDENTITY: BXPZTQZ35S # Your Apple Dev identity, something like BXPZTQZ35S
+  PRIMARY_BUNDLE_ID: org.janelia.saalfeldlab.Paintera # Unique to your app, often the launcher class
+
+jobs:
+  build_installers:
+    name: Build Installers
+    uses: ./.github/workflows/build-installers.yml
+
+  create_release:
+    needs: build_installers
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download Artifacts
+        uses: actions/download-artifact@v4
+      - name: Set Version
+        run: |
+          tag_name=$(echo ${{ github.ref }} | grep -oE "[^/]+$")
+          echo "VERSION=$tag_name" >> $GITHUB_ENV
+      - name: Display structure of downloaded files
+        run: ls -R
+      - name: Rename Artifacts
+        run: |
+          mv Paintera-windows-latest-*/*.msi Paintera-${{ env.VERSION }}-Windows.msi
+          mv Paintera-ubuntu-latest-*/*.deb Paintera-${{ env.VERSION }}_x86_64.deb
+          mv Paintera-macos-latest-*/*.dmg Paintera-${{ env.VERSION }}-MacOS.dmg
+          mv Paintera-macos-14-*/*.dmg Paintera-${{ env.VERSION }}-MacOS-AppleSilicon.dmg
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: Paintera ${{ env.VERSION }}
+          tag_name: ${{ github.ref }}
+          prerelease: false
+          files: |
+            Paintera-${{ env.VERSION }}-Windows.msi
+            Paintera-${{ env.VERSION }}_x86_64.deb
+            Paintera-${{ env.VERSION }}-MacOS.dmg
+            Paintera-${{ env.VERSION }}-MacOS-AppleSilicon.dmg
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>paintera</artifactId>
-	<version>1.1.1-SNAPSHOT</version>
+	<version>1.2.0-SNAPSHOT</version>
 
 	<name>Paintera</name>
 	<description>New Era Painting and annotation tool</description>
@@ -53,7 +53,7 @@
 		<javadoc.skip>true</javadoc.skip>
 		<maven.javadoc.skip>${javadoc.skip}</maven.javadoc.skip>
 
-		<saalfx.version>1.2.0</saalfx.version>
+		<saalfx.version>1.3.0</saalfx.version>
 
 		<janino.version>3.0.7</janino.version>
 		<logback.version>1.4.0</logback.version>

diff --git a/src/main/kotlin/org/janelia/saalfeldlab/fx/ui/ActionBar.kt b/src/main/kotlin/org/janelia/saalfeldlab/fx/ui/ActionBar.kt
@@ -25,7 +25,7 @@ class ActionBar : HBox() {
 		var newGroup : ToggleGroup? = null
 		buttons.forEach { node ->
 			(node as? Toggle)?.apply {
-				toggleGroup = toggleGroup ?: ToggleGroup().also { newGroup = it }
+				toggleGroup = toggleGroup ?: newGroup ?: ToggleGroup().also { newGroup = it }
 			}
 		}
 		toggleGroup = newGroup
@@ -77,7 +77,7 @@ class ActionBar : HBox() {
 
 		fun List<ToolBarItem>.toolBarNodes() = map { item ->
 			item.toolBarButton.apply {
-				this.onAction ?: let {
+				onAction ?: let {
 					userData = item
 				}
 				isFocusTraversable = false

diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/BindingKeys.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/BindingKeys.kt
@@ -103,36 +103,37 @@ private class LateInitNamedKeyCombination(keyCombination: KeyCombination, initNa
 }
 
 enum class LabelSourceStateKeys(lateInitNamedKeyCombo : LateInitNamedKeyCombination) : NamedKeyBinding by lateInitNamedKeyCombo {
-    SELECT_ALL                                        ( CONTROL_DOWN + A),
-    SELECT_ALL_IN_CURRENT_VIEW                        ( CONTROL_DOWN + SHIFT_DOWN + A),
-    LOCK_SEGMENT                                      ( L),
-    NEXT_ID                                           ( N),
-    COMMIT_DIALOG                                     ( C + CONTROL_DOWN),
-    MERGE_ALL_SELECTED                                ( ENTER + CONTROL_DOWN),
-    ARGB_STREAM__INCREMENT_SEED                       ( C),
-    ARGB_STREAM__DECREMENT_SEED                       ( C + SHIFT_DOWN),
-    REFRESH_MESHES                                    ( R),
-    CANCEL                                            ( ESCAPE, "cancel tool / exit mode"),
-    TOGGLE_NON_SELECTED_LABELS_VISIBILITY             ( V + SHIFT_DOWN, "toggle non-selected labels visibility"),
-    SEGMENT_ANYTHING__TOGGLE_MODE                     ( A),
-    PAINT_BRUSH                                       ( SPACE),
-    FILL_2D                                           ( F),
-    FILL_3D                                           ( SHIFT_DOWN + F),
-    CLEAR_CANVAS                                      ( CONTROL_DOWN + SHIFT_DOWN + C),
-    INTERSECT_UNDERLYING_LABEL                        ( SHIFT_DOWN + R),
-    SHAPE_INTERPOLATION__TOGGLE_MODE                  ( S),
-    SHAPE_INTERPOLATION__TOGGLE_PREVIEW               ( CONTROL_DOWN + P),
-    SHAPE_INTERPOLATION__ACCEPT_INTERPOLATION         ( ENTER),
-    SHAPE_INTERPOLATION__SELECT_FIRST_SLICE           ( SHIFT_DOWN + LEFT),
-    SHAPE_INTERPOLATION__SELECT_LAST_SLICE            ( SHIFT_DOWN + RIGHT),
-    SHAPE_INTERPOLATION__SELECT_PREVIOUS_SLICE        ( LEFT),
-    SHAPE_INTERPOLATION__SELECT_NEXT_SLICE            ( RIGHT ),
-    SHAPE_INTERPOLATION__REMOVE_SLICE_1               ( DELETE, "delete current slice "),
-    SHAPE_INTERPOLATION__REMOVE_SLICE_2               ( BACK_SPACE, "delete current slice  "),
-    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICE_LEFT     ( OPEN_BRACKET, "shape interpolation: auto SAM: new slice left" ),
-    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICES_BISECT  ( QUOTE, "shape interpolation: auto SAM: new bisect slices" ),
-    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICE_RIGHT    ( CLOSE_BRACKET, "shape interpolation: auto SAM: new slice right"   ),
-    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICE_HERE     ( SHIFT_DOWN + A, "shape interpolation: auto SAM: new slice at current location"   ),
+    SELECT_ALL                                           ( CONTROL_DOWN + A),
+    SELECT_ALL_IN_CURRENT_VIEW                           ( CONTROL_DOWN + SHIFT_DOWN + A),
+    LOCK_SEGMENT                                         ( L),
+    NEXT_ID                                              ( N),
+    COMMIT_DIALOG                                        ( C + CONTROL_DOWN),
+    MERGE_ALL_SELECTED                                   ( ENTER + CONTROL_DOWN),
+    ARGB_STREAM__INCREMENT_SEED                          ( C),
+    ARGB_STREAM__DECREMENT_SEED                          ( C + SHIFT_DOWN),
+    REFRESH_MESHES                                       ( R),
+    CANCEL                                               ( ESCAPE, "cancel tool / exit mode"),
+    TOGGLE_NON_SELECTED_LABELS_VISIBILITY                ( V + SHIFT_DOWN, "toggle non-selected labels visibility"),
+    SEGMENT_ANYTHING__TOGGLE_MODE                        ( A),
+    PAINT_BRUSH                                          ( SPACE),
+    FILL_2D                                              ( F),
+    FILL_3D                                              ( SHIFT_DOWN + F),
+    CLEAR_CANVAS                                         ( CONTROL_DOWN + SHIFT_DOWN + C),
+    INTERSECT_UNDERLYING_LABEL                           ( SHIFT_DOWN + R),
+    SHAPE_INTERPOLATION__TOGGLE_MODE                     ( S),
+    SHAPE_INTERPOLATION__TOGGLE_PREVIEW                  ( CONTROL_DOWN + P),
+    SHAPE_INTERPOLATION__ACCEPT_INTERPOLATION            ( ENTER),
+    SHAPE_INTERPOLATION__SELECT_FIRST_SLICE              ( SHIFT_DOWN + LEFT),
+    SHAPE_INTERPOLATION__SELECT_LAST_SLICE               ( SHIFT_DOWN + RIGHT),
+    SHAPE_INTERPOLATION__SELECT_PREVIOUS_SLICE           ( LEFT),
+    SHAPE_INTERPOLATION__SELECT_NEXT_SLICE               ( RIGHT ),
+    SHAPE_INTERPOLATION__REMOVE_SLICE_1                  ( DELETE, "delete current slice "),
+    SHAPE_INTERPOLATION__REMOVE_SLICE_2                  ( BACK_SPACE, "delete current slice  "),
+    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICE_LEFT        ( OPEN_BRACKET, "shape interpolation: auto SAM: new slice left" ),
+    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICES_BISECT     ( QUOTE, "shape interpolation: auto SAM: new slice between closest slices" ),
+    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICES_BISECT_ALL ( SHIFT_DOWN + QUOTE, "shape interpolation: auto SAM: new slice between all slices" ),
+    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICE_RIGHT       ( CLOSE_BRACKET, "shape interpolation: auto SAM: new slice right"   ),
+    SHAPE_INTERPOLATION__AUTO_SAM__NEW_SLICE_HERE        ( SHIFT_DOWN + A, "shape interpolation: auto SAM: new slice at current location"   ),
     ;
 
 

diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/config/LoggingConfig.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/config/LoggingConfig.kt
@@ -28,26 +28,23 @@ class LoggingConfig {
 		.apply { addTriggeredListener { _, _, level -> LogUtils.rootLoggerLevel = level } }
 	var rootLoggerLevel: Level by rootLoggerLevelProperty.nonnull()
 
-	val isLoggingEnabledProperty = SimpleBooleanProperty(DEFAULT_IS_LOGGING_ENABLED)
-		.apply {
+	val isLoggingEnabledProperty = SimpleBooleanProperty(DEFAULT_IS_LOGGING_ENABLED).apply {
 			addTriggeredListener { _, _, new ->
 				LogUtils.setLoggingEnabled(new)
 				loggerLevels.forEach { (logger, level) -> LogUtils.setLogLevelFor(logger, level.get()) }
 			}
 		}
 	var isLoggingEnabled: Boolean by isLoggingEnabledProperty.nonnull()
 
-	val isLoggingToConsoleEnabledProperty = SimpleBooleanProperty(DEFAULT_IS_LOGGING_TO_CONSOLE_ENABLED)
-		.apply {
+	val isLoggingToConsoleEnabledProperty = SimpleBooleanProperty(DEFAULT_IS_LOGGING_TO_CONSOLE_ENABLED).apply {
 			addTriggeredListener { _, _, new ->
 				LogUtils.setLoggingToConsoleEnabled(new)
 				loggerLevels.forEach { (logger, level) -> LogUtils.setLogLevelFor(logger, level.get()) }
 			}
 		}
 	var isLoggingToConsoleEnabled: Boolean by isLoggingEnabledProperty.nonnull()
 
-	val isLoggingToFileEnabledProperty = SimpleBooleanProperty(DEFAULT_IS_LOGGING_TO_FILE_ENABLED)
-		.apply {
+	val isLoggingToFileEnabledProperty = SimpleBooleanProperty(DEFAULT_IS_LOGGING_TO_FILE_ENABLED).apply {
 			addTriggeredListener { _, _, new ->
 				LogUtils.setLoggingToFileEnabled(new)
 				loggerLevels.forEach { (logger, level) -> LogUtils.setLogLevelFor(logger, level.get()) }

diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/config/LoggingConfigNode.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/config/LoggingConfigNode.kt
@@ -2,6 +2,7 @@ package org.janelia.saalfeldlab.paintera.config
 
 import ch.qos.logback.classic.Level
 import ch.qos.logback.classic.Logger
+import ch.qos.logback.classic.LoggerContext
 import de.jensd.fx.glyphs.fontawesome.FontAwesomeIcon
 import javafx.beans.InvalidationListener
 import javafx.beans.property.ObjectProperty
@@ -20,10 +21,12 @@ import org.janelia.saalfeldlab.fx.Buttons
 import org.janelia.saalfeldlab.fx.Labels
 import org.janelia.saalfeldlab.fx.TitledPanes
 import org.janelia.saalfeldlab.fx.extensions.TitledPaneExtensions
+import org.janelia.saalfeldlab.fx.ui.MatchSelection
 import org.janelia.saalfeldlab.fx.ui.NamedNode
 import org.janelia.saalfeldlab.paintera.ui.FontAwesome
 import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts
 import org.janelia.saalfeldlab.paintera.util.logging.LogUtils
+import org.slf4j.LoggerFactory
 
 class LoggingConfigNode(private val config: LoggingConfig) {
 
@@ -122,12 +125,25 @@ class LoggingConfigNode(private val config: LoggingConfig) {
 				}
 			}
 		}
+
+		val loggerList = FXCollections.observableArrayList<String>()
+		val updateLoggerList = {
+			(LoggerFactory.getILoggerFactory() as? LoggerContext)?.let {
+				loggerList.setAll(it.loggerList.map { logger -> logger.name }.toList())
+			}
+		}
 		val newLoggerField = TextField("")
-		val newLoggerChoiceBox = logLevelChoiceBox(null)
+		val matcherField = MatchSelection.fuzzyTop(loggerList, { name -> newLoggerField.text = name }, 5)
+		matcherField.emptyBehavior = MatchSelection.EmptyBehavior.MATCH_NONE
+		matcherField.promptText = "Search for Loggers..."
+		matcherField.focusedProperty().addListener { _, _, focused -> if (focused) updateLoggerList() }
+
+		val newLogLevelChoiceBox = logLevelChoiceBox(null)
 		val newLoggerButton = Buttons
-			.withTooltip(null) { config.setLogLevelFor(newLoggerField.text, newLoggerChoiceBox.value) }
+			.withTooltip(null) { config.setLogLevelFor(newLoggerField.text, newLogLevelChoiceBox.value) }
 			.also { it.graphic = FontAwesome[FontAwesomeIcon.PLUS, 2.0] }
 		val listener = InvalidationListener {
+			updateLoggerList()
 			val name = newLoggerField.text
 			val isRootLoggerName = LogUtils.rootLogger.name == name
 			val isExistingLogger = name in keys
@@ -147,11 +163,13 @@ class LoggingConfigNode(private val config: LoggingConfig) {
 			newLoggerField.textProperty().addListener(listener)
 			listener.invalidated(newLoggerField.textProperty())
 			add(newLoggerField, 0, row)
-			add(newLoggerChoiceBox, 1, row)
+			add(newLogLevelChoiceBox, 1, row)
 			add(newLoggerButton, 2, row)
+			add(matcherField, 0, row + 1, GridPane.REMAINING, GridPane.REMAINING)
+			GridPane.setHgrow(matcherField, Priority.ALWAYS)
+			GridPane.setVgrow(matcherField, Priority.ALWAYS)
+			matcherField.maxWidthProperty().bind(widthProperty())
 		}
-
-
 	}
 
 }
diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationController.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationController.kt
@@ -56,6 +56,7 @@ import org.janelia.saalfeldlab.paintera.id.IdService
 import org.janelia.saalfeldlab.paintera.stream.AbstractHighlightingARGBStream
 import org.janelia.saalfeldlab.paintera.stream.HighlightingStreamConverter
 import org.janelia.saalfeldlab.paintera.util.IntervalHelpers
+import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.extendBy
 import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.smallestContainingInterval
 import org.janelia.saalfeldlab.util.*
 import org.slf4j.LoggerFactory
@@ -187,11 +188,9 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 			?.also { repaintInterval ->
 				if (preview) {
 					isBusy = true
-					requestRepaintInterval = repaintInterval union requestRepaintInterval
 					interpolateBetweenSlices(false)
-				} else {
-					requestRepaintAfterTasks(repaintInterval)
 				}
+				requestRepaintAfterTasks(repaintInterval)
 			}
 	}
 
@@ -364,6 +363,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 		Last
 	}
 
+	//TODO Caleb: Controller should not move, let the tool/mode do that
 	fun editSelection(choice: EditSelectionChoice) {
 		val slices = slicesAndInterpolants.slices
 		when (choice) {
@@ -751,7 +751,9 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 			val interpolatedMaskView = interpolant.dataInterpolant
 				.affine(viewerMask.currentGlobalToMaskTransform)
 				.interval(interpolantIntervalSliceInMaskSpace)
-			val fillMaskOverInterval = viewerMask.viewerImg.interval(interpolantIntervalSliceInMaskSpace)
+			val fillMaskOverInterval = viewerMask.viewerImg.apply {
+				extendValue(Label.INVALID)
+			}.interval(interpolantIntervalSliceInMaskSpace)
 
 			LoopBuilder.setImages(interpolatedMaskView, fillMaskOverInterval)
 				.multiThreaded()
@@ -1164,7 +1166,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 			computeBoundingBoxInInitialMask()
 		}
 		val globalBoundingBox: RealInterval?
-			get() = maskBoundingBox?.let { mask.initialGlobalToMaskTransform.inverse().estimateBounds(it) }
+			get() = maskBoundingBox?.let { mask.initialMaskToGlobalWithDepthTransform.estimateBounds(it.extendBy(0.0, 0.0, .5)) }
 
 		private val selectionIntervals: MutableList<Interval> = mutableListOf()