Merge pull request #228 from saalfeldlab/interpolation-painting

Interpolation painting

README.md

@@ -162,6 +162,10 @@ Usage: Paintera [-h] [--default-to-temp-directory] [--print-error-codes]
 | `F` + left click | 2D Flood-fill in current viewer plane with id that was last toggled active (if any) |
 | `Shift` + `F` + left click | Flood-fill with id that was last toggled active (if any) |
 | `N` | Select new, previously unused id |
+| `S` | Enter shape interpolation mode |
+| `1` / `2` | Edit first/second section when previewing interpolated shape |
+| `Enter` | Commit interpolated shape into canvas |
+| `Esc` | Abort shape interpolation mode |
 | `Ctrl` + `C` | Show dialog to commit canvas and/or assignments |
 | `C` | Increment ARGB stream seed by one |
 | `Shift` + `C` | Decrement ARGB stream seed by one |
@@ -174,6 +178,14 @@ Usage: Paintera [-h] [--default-to-temp-directory] [--print-error-codes]
 | `Ctrl` + `Shift` + `N` | Create new label dataset |
 | `Ctrl` + `T` | Threshold raw source (only available if current source is raw source) |
 
+### Shape interpolation mode
+
+The mode is activated by pressing the `S` key when the current source is a label source. Then, you can select the objects in the sections by left/right clicking (scrolling automatically fixes the selection in the current section).
+
+When you're done with selecting the objects in the second section and initiate scrolling, the preview of the interpolated shape will be displayed. If something is not right, you can edit the selection in the first or second section by pressing `1` or `2`, which will update the preview. When the desired result is reached, hit `Enter` to commit the results into the canvas and return back to normal mode.
+
+While in the shape interpolation mode, at any point in time you can hit `Esc` to discard the current state and exit the mode.
+
 ## Data
 
 In [#61](https://github.com/saalfeldlab/paintera/issues/61) we introduced a specification for the data format that Paintera can load through the opener dialog (`Ctrl O`).

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

@@ -36,43 +36,26 @@
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
 import bdv.viewer.ViewerOptions;
-import gnu.trove.list.array.TIntArrayList;
-import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.ReadOnlyBooleanProperty;
 import javafx.beans.property.ReadOnlyDoubleProperty;
-import javafx.beans.property.ReadOnlyObjectProperty;
-import javafx.beans.property.SimpleObjectProperty;
 import javafx.collections.FXCollections;
 import javafx.collections.ListChangeListener;
 import javafx.collections.ObservableList;
 import javafx.scene.Node;
-import javafx.scene.canvas.Canvas;
 import javafx.scene.layout.StackPane;
 import net.imglib2.Interval;
-import net.imglib2.Point;
 import net.imglib2.Positionable;
 import net.imglib2.RealInterval;
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealPoint;
 import net.imglib2.RealPositionable;
-import net.imglib2.algorithm.fill.FloodFill;
-import net.imglib2.algorithm.neighborhood.DiamondShape;
-import net.imglib2.img.array.ArrayImg;
-import net.imglib2.img.array.ArrayImgs;
-import net.imglib2.img.basictypeaccess.array.IntArray;
-import net.imglib2.img.cell.CellGrid;
 import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.ui.TransformListener;
-import net.imglib2.util.Intervals;
-import net.imglib2.view.Views;
-
 import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import java.lang.invoke.MethodHandles;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 import java.util.concurrent.CopyOnWriteArrayList;
@@ -287,6 +270,25 @@ public void displayToGlobalCoordinates(final double x, final double y, final Rea
 		viewerTransform.applyInverse(gPos, lPos);
 	}
 
+	/**
+	 * Set {@code pos} to the display coordinates (x,y,0)<sup>T</sup> transformed into the source coordinate system.
+	 *
+	 * @param pos
+	 * 		is set to the source coordinates at display (x,y,0)<sup>T</sup>.
+	 */
+	public <P extends RealLocalizable & RealPositionable> void displayToSourceCoordinates(
+			final double x,
+			final double y,
+			final AffineTransform3D sourceTransform,
+			final P pos)
+	{
+		pos.setPosition(x, 0);
+		pos.setPosition(y, 1);
+		pos.setPosition(0, 2);
+		displayToGlobalCoordinates(pos);
+		sourceTransform.applyInverse(pos, pos);
+	}
+
 	/**
 	 * Set {@code gPos} to the current mouse coordinates transformed into the global coordinate system.
 	 *
@@ -499,7 +501,7 @@ public ReadOnlyDoubleProperty mouseYProperty()
 	 *                     1. {@code 0 < sceenScales[i] <= 1} for all {@code i}
 	 *                     2. {@code screenScales[i] < screenScales[i - 1]} for all {@code i > 0}
 	 */
-	public void setScreenScales(double[] screenScales)
+	public void setScreenScales(final double[] screenScales)
 	{
 		LOG.debug("Setting screen scales to {}", screenScales);
 		this.renderUnit.setScreenScales(screenScales.clone());

src/main/java/org/janelia/saalfeldlab/fx/ortho/OrthogonalViews.java

@@ -5,9 +5,15 @@
 import java.util.function.Consumer;
 import java.util.function.Function;
 
+import org.janelia.saalfeldlab.paintera.control.navigation.AffineTransformWithListeners;
+import org.janelia.saalfeldlab.paintera.control.navigation.TransformConcatenator;
+import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
+import org.janelia.saalfeldlab.paintera.state.GlobalTransformManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import bdv.cache.CacheControl;
 import bdv.fx.viewer.ViewerPanelFX;
-import bdv.util.volatiles.SharedQueue;
 import bdv.viewer.Interpolation;
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
@@ -16,14 +22,8 @@
 import javafx.event.EventHandler;
 import javafx.event.EventType;
 import javafx.scene.Node;
-import javafx.scene.layout.Pane;
+import javafx.scene.layout.GridPane;
 import net.imglib2.realtransform.AffineTransform3D;
-import org.janelia.saalfeldlab.paintera.control.navigation.AffineTransformWithListeners;
-import org.janelia.saalfeldlab.paintera.control.navigation.TransformConcatenator;
-import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
-import org.janelia.saalfeldlab.paintera.state.GlobalTransformManager;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 /**
  * Wrap a {@link ResizableGridPane2x2} with {@link ViewerPanelFX viewer panels} at top left, top right, and bottom left. Bottom right
@@ -157,7 +157,7 @@ public ResizableGridPane2x2<ViewerPanelFX, ViewerPanelFX, ViewerPanelFX, BR> gri
 	 *
 	 * @return {@link ResizableGridPane2x2#pane()} for the underlying {@link ResizableGridPane2x2}
 	 */
-	public Pane pane()
+	public GridPane pane()
 	{
 		return grid().pane();
 	}

src/main/java/org/janelia/saalfeldlab/fx/ortho/ResizableGridPane2x2.java

@@ -4,7 +4,6 @@
 import javafx.beans.property.SimpleObjectProperty;
 import javafx.scene.Node;
 import javafx.scene.layout.GridPane;
-import javafx.scene.layout.Pane;
 
 /**
  * A wrapper around {@link GridPane} that holds for children organized in a 2x2 grid. The underlying
@@ -62,7 +61,7 @@ public ResizableGridPane2x2(
 	 *
 	 * @return underlying {@link GridPane}
 	 */
-	public Pane pane()
+	public GridPane pane()
 	{
 		return this.grid;
 	}
@@ -149,11 +148,18 @@ public void manage(final GridConstraintsManager manager)
 		manager.manageGrid(this.grid);
 	}
 
+	public Node getNodeAt(final int col, final int row)
+	{
+		for (final Node child : grid.getChildren())
+			if (GridPane.getColumnIndex(child) == col && GridPane.getRowIndex(child) == row)
+				return child;
+		return null;
+	}
+
 	private static void replace(final GridPane grid, final Node oldValue, final Node newValue, final int col, final int
 			row)
 	{
 		grid.getChildren().remove(oldValue);
 		grid.add(newValue, col, row);
 	}
-
 }

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

@@ -4,34 +4,14 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Optional;
 import java.util.concurrent.Executors;
 import java.util.concurrent.ScheduledExecutorService;
 import java.util.concurrent.TimeUnit;
-import java.util.function.*;
+import java.util.function.BiConsumer;
+import java.util.function.LongSupplier;
+import java.util.function.LongUnaryOperator;
+import java.util.function.Supplier;
 
-import bdv.fx.viewer.ViewerPanelFX;
-import bdv.viewer.Source;
-import javafx.animation.KeyFrame;
-import javafx.animation.Timeline;
-import javafx.beans.binding.Bindings;
-import javafx.beans.property.*;
-import javafx.beans.value.ObservableObjectValue;
-import javafx.event.ActionEvent;
-import javafx.event.EventHandler;
-import javafx.scene.Group;
-import javafx.scene.control.*;
-import javafx.scene.control.ScrollPane.ScrollBarPolicy;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.BorderPane;
-import javafx.scene.layout.HBox;
-import javafx.scene.layout.Priority;
-import javafx.scene.layout.Region;
-import javafx.scene.layout.VBox;
-import javafx.scene.paint.Color;
-import javafx.scene.text.Font;
-import javafx.util.Duration;
-import net.imglib2.RealPoint;
 import org.janelia.saalfeldlab.fx.TitledPanes;
 import org.janelia.saalfeldlab.fx.ortho.OrthogonalViews;
 import org.janelia.saalfeldlab.fx.ortho.OrthogonalViews.ViewerAndTransforms;
@@ -57,6 +37,40 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import bdv.fx.viewer.ViewerPanelFX;
+import bdv.viewer.Source;
+import javafx.animation.KeyFrame;
+import javafx.animation.Timeline;
+import javafx.beans.binding.Bindings;
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.LongProperty;
+import javafx.beans.property.ObjectProperty;
+import javafx.beans.property.ReadOnlyBooleanProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.value.ObservableObjectValue;
+import javafx.event.ActionEvent;
+import javafx.event.EventHandler;
+import javafx.scene.Group;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Button;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.Label;
+import javafx.scene.control.ScrollPane;
+import javafx.scene.control.ScrollPane.ScrollBarPolicy;
+import javafx.scene.control.TitledPane;
+import javafx.scene.control.Tooltip;
+import javafx.scene.input.MouseEvent;
+import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
+import javafx.scene.layout.Region;
+import javafx.scene.layout.VBox;
+import javafx.scene.paint.Color;
+import javafx.scene.text.Font;
+import javafx.util.Duration;
+import net.imglib2.RealPoint;
+
 public class BorderPaneWithStatusBars
 {
 
@@ -160,16 +174,29 @@ public BorderPaneWithStatusBars(
 				center.orthogonalViews(),
 				center.viewer3D().meshesGroup(),
 				center.sourceInfo()
-		                                  );
-
-		center.sourceInfo().currentNameProperty().addListener((obs, oldv, newv) -> {
-			currentSourceStatus.textProperty().unbind();
-			Optional.ofNullable(newv).ifPresent(currentSourceStatus.textProperty()::bind);
-		});
+			);
 
 		final SingleChildStackPane sourceDisplayStatus = new SingleChildStackPane();
 		center.sourceInfo().currentState().addListener((obs, oldv, newv) -> sourceDisplayStatus.setChild(newv.getDisplayStatus()));
 
+		// show source name by default, or override it with source status text if any
+		center.sourceInfo().currentState().addListener((obs, oldv, newv) -> {
+			sourceDisplayStatus.setChild(newv.getDisplayStatus());
+			currentSourceStatus.textProperty().unbind();
+			currentSourceStatus.textProperty().bind(Bindings.createStringBinding(
+					() -> {
+						if (newv.statusTextProperty() != null && newv.statusTextProperty().get() != null)
+							return newv.statusTextProperty().get();
+						else if (newv.nameProperty().get() != null)
+							return newv.nameProperty().get();
+						else
+							return null;
+					},
+					newv.nameProperty(),
+					newv.statusTextProperty()
+				));
+		});
+
 		// for positioning the 'show status bar' checkbox on the right
 		final Region valueStatusSpacing = new Region();
 		HBox.setHgrow(valueStatusSpacing, Priority.ALWAYS);
@@ -272,21 +299,25 @@ public BorderPaneWithStatusBars(
 		this.sideBar.setHbarPolicy(ScrollBarPolicy.NEVER);
 		this.sideBar.setVbarPolicy(ScrollBarPolicy.AS_NEEDED);
 		this.sideBar.setVisible(true);
-		this.sideBar.prefWidthProperty().set(250);
+		this.sideBar.prefWidthProperty().set(280);
 		sourceTabs.widthProperty().bind(sideBar.prefWidthProperty());
 		settingsContents.prefWidthProperty().bind(sideBar.prefWidthProperty());
 
 		resizeSideBar = new ResizeOnLeftSide(sideBar, sideBar.prefWidthProperty(), dist -> Math.abs(dist) < 5);
 	}
 
+	public ScrollPane getSideBar()
+	{
+		return sideBar;
+	}
+
 	public void toggleSideBar()
 	{
 		if (pane.getRight() == null)
 		{
 			pane.setRight(sideBar);
 			resizeSideBar.install();
 		}
-
 		else
 		{
 			resizeSideBar.remove();