Merge pull request #31 from automated-ultramicrotomy/dev

Merge changes from dev

.github/workflows/test.yml

@@ -47,7 +47,7 @@ jobs:
 
 #      - name: Install blosc
 #        run: sudo apt install libblosc-dev
-#      - name: Install xvfb 
-#        run: sudo apt-get install xvfb
+      - name: Install xvfb
+        run: sudo apt-get install xvfb
       - name: Build with maven
-        run: mvn -B package --file pom.xml # for testing with graphics prepend: xvfb-run --auto-servernum
+        run: xvfb-run --auto-servernum mvn -B package --file pom.xml

pom.xml

@@ -8,7 +8,7 @@
 	</parent>
 	<artifactId>crosshair</artifactId>
 	<url>https://github.com/K-Meech/crosshair</url>
-	<version>1.0.3</version>
+	<version>1.0.4</version>
 	<name>Crosshair</name>
 	<description>Assisted 3D targeting via an ultramicrotome</description>
 	<inceptionYear>2020</inceptionYear>
@@ -80,7 +80,7 @@
 
 <!--		<bigdataviewer-core.version>10.2.0</bigdataviewer-core.version>-->
 <!--		<bigdataviewer-vistools.version>1.0.0-beta-28</bigdataviewer-vistools.version>-->
-		<imagej-utils.version>0.6.4-SNAPSHOT</imagej-utils.version>
+		<imagej-utils.version>0.6.4</imagej-utils.version>
 	</properties>
 
 	<repositories>
@@ -111,6 +111,16 @@
 			<groupId>sc.fiji</groupId>
 			<artifactId>3D_Viewer</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.jogamp.gluegen</groupId>
+			<artifactId>gluegen-rt</artifactId>
+			<classifier>${scijava.natives.classifier.gluegen}</classifier>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.jogl</groupId>
+			<artifactId>jogl-all</artifactId>
+			<classifier>${scijava.natives.classifier.jogl}</classifier>
+		</dependency>
 		<dependency>
 			<groupId>de.embl.cba</groupId>
 			<artifactId>imagej-utils</artifactId>
@@ -119,7 +129,7 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter</artifactId>
-            <version>${junit-jupiter.version}</version>
+			<version>${junit-jupiter.version}</version>
             <scope>test</scope>
         </dependency>
 		<dependency>

src/main/java/de/embl/schwab/crosshair/Crosshair.java

@@ -1,13 +1,20 @@
 package de.embl.schwab.crosshair;
 
 import bdv.util.*;
+import bdv.viewer.Source;
 import de.embl.schwab.crosshair.bdv.BdvBehaviours;
 import de.embl.schwab.crosshair.microtome.MicrotomeManager;
+import de.embl.schwab.crosshair.plane.Plane;
 import de.embl.schwab.crosshair.plane.PlaneManager;
 import de.embl.schwab.crosshair.ui.swing.CrosshairFrame;
 import ij3d.Content;
 import ij3d.Image3DUniverse;
+import net.imglib2.img.Img;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.numeric.ARGBType;
+import ij.ImagePlus;
 
+import static de.embl.cba.tables.ij3d.UniverseUtils.addSourceToUniverse;
 import static de.embl.schwab.crosshair.utils.Utils.spaceOutWindows;
 
 // TODO - neaten up code structure, possibly clearer labelling of which coordinate system & units are being used
@@ -33,9 +40,72 @@ public class Crosshair {
 	public static final String block = "block";
 	public static final String image = "image";
 
-	public Crosshair (BdvStackSource bdvStackSource, Image3DUniverse universe, Content imageContent, String unit) {
+	// TODO - make generic? Not just 8 bit
+	private final int min = 0;
+	private final int max = 255;
+	private final float transparency = 0.7f;
+
+	private BdvHandle bdvHandle; // bdvHandle of the BigDataViewer window
+	private Image3DUniverse universe; // universe of the 3D viewer
+	private Content imageContent; // image content displayed in 3D viewer
+	private PlaneManager planeManager;
+	private MicrotomeManager microtomeManager;
+	private String unit; // pixel size unit e.g. mm
+
+	/**
+	 * Open Crosshair from a Source (normally from a bdv style file e.g. hdf5 / n5)
+	 * @param imageSource image source
+	 */
+	public Crosshair(Source<Object> imageSource) {
+
+		BdvStackSource bdvStackSource = BdvFunctions.show(imageSource, 1);
+		Image3DUniverse universe = new Image3DUniverse();
+		universe.show();
+
+		String unit = imageSource.getVoxelDimensions().unit();
+
+		// Set to arbitrary colour
+		ARGBType colour =  new ARGBType( ARGBType.rgba( 0, 0, 0, 0 ) );
+		Content imageContent = addSourceToUniverse(universe, imageSource, 300 * 300 * 300,
+				Content.VOLUME, colour, transparency, min, max );
+		// Reset colour to default for 3D viewer
+		imageContent.setColor(null);
+
+		initialiseCrosshair(bdvStackSource, universe, imageContent, unit);
+	}
+
+	/**
+	 * Open Crosshair from an ImagePlus (normally by pulling current image from ImageJ)
+	 * @param imagePlus image
+	 */
+	public Crosshair(ImagePlus imagePlus) {
+
+		Image3DUniverse universe = new Image3DUniverse();
+		Content imageContent = universe.addContent(imagePlus, Content.VOLUME);
+		imageContent.setTransparency(transparency);
+		universe.show();
+
+		final double pw = imagePlus.getCalibration().pixelWidth;
+		final double ph = imagePlus.getCalibration().pixelHeight;
+		final double pd = imagePlus.getCalibration().pixelDepth;
+		final String unit = imagePlus.getCalibration().getUnit();
+
+		final Img wrap = ImageJFunctions.wrap(imagePlus);
+		BdvStackSource bdvStackSource = BdvFunctions.show(wrap, "raw", Bdv.options()
+				.sourceTransform(pw, ph, pd));
+
+		initialiseCrosshair(bdvStackSource, universe, imageContent, unit);
+	}
+
+	private void initialiseCrosshair(BdvStackSource bdvStackSource, Image3DUniverse universe, Content imageContent, String unit) {
+
+		bdvStackSource.setDisplayRange(min, max);
+
+		this.bdvHandle = bdvStackSource.getBdvHandle();
+		this.imageContent = imageContent;
+		this.universe = universe;
+		this.unit = unit;
 
-		BdvHandle bdvHandle = bdvStackSource.getBdvHandle();
 		imageContent.setLocked(true);
 		imageContent.showPointList(true);
 		universe.getPointListDialog().setVisible(false);
@@ -45,13 +115,37 @@ public Crosshair (BdvStackSource bdvStackSource, Image3DUniverse universe, Conte
 		// Still places so (0,0) of image == (0,0) in global coordinate system, just bounding box is wrapped tight to
 		// only regions of the image > 0
 
-		PlaneManager planeManager = new PlaneManager(bdvStackSource, universe, imageContent);
+		planeManager = new PlaneManager(bdvStackSource, universe, imageContent);
 
-		MicrotomeManager microtomeManager = new MicrotomeManager(planeManager, universe, imageContent, bdvStackSource, unit);
+		microtomeManager = new MicrotomeManager(planeManager, universe, imageContent, bdvStackSource, unit);
 		new BdvBehaviours(bdvHandle, planeManager, microtomeManager);
 
-		CrosshairFrame crosshairFrame = new CrosshairFrame(universe, imageContent, planeManager, microtomeManager, bdvHandle, unit);
+		CrosshairFrame crosshairFrame = new CrosshairFrame(this);
 
 		spaceOutWindows( bdvHandle, crosshairFrame, universe );
 	}
+
+	public BdvHandle getBdvHandle() {
+		return bdvHandle;
+	}
+
+	public Content getImageContent() {
+		return imageContent;
+	}
+
+	public Image3DUniverse getUniverse() {
+		return universe;
+	}
+
+	public MicrotomeManager getMicrotomeManager() {
+		return microtomeManager;
+	}
+
+	public PlaneManager getPlaneManager() {
+		return planeManager;
+	}
+
+	public String getUnit() {
+		return unit;
+	}
 }

src/main/java/de/embl/schwab/crosshair/bdv/BdvBehaviours.java

@@ -15,12 +15,22 @@
 
 import javax.swing.*;
 
+/**
+ * Class to control custom interactions with the BigDataViewer window
+ * For example, clicking to add points or fitting a plane to points
+ */
 public class BdvBehaviours {
 
     private BdvHandle bdvHandle;
     private PlaneManager planeManager;
     private MicrotomeManager microtomeManager;
 
+    /**
+     * Adds custom behaviours to the BigDataViewer window referenced by bdvHandle
+     * @param bdvHandle bdvHandle of the BigDataViewer window
+     * @param planeManager Crosshair plane manager
+     * @param microtomeManager Crosshair microtome manager
+     */
     public BdvBehaviours (BdvHandle bdvHandle, PlaneManager planeManager, MicrotomeManager microtomeManager) {
         this.bdvHandle = bdvHandle;
         this.planeManager = planeManager;

src/main/java/de/embl/schwab/crosshair/bdv/ModeOverlay.java

@@ -5,11 +5,18 @@
 
 import java.awt.*;
 
+/**
+ * Class to display the current Crosshair mode as an overlay on the BigDataViewer window
+ */
 public class ModeOverlay extends BdvOverlay  {
 
     private PlaneManager planeManager;
     private Color colModeText = new Color(255, 255, 255);
 
+    /**
+     * Create a BigDataViewer overlay for the Crosshair mode text
+     * @param planeManager Crosshair plane manager
+     */
     public ModeOverlay( PlaneManager planeManager ) {
         this.planeManager = planeManager;
     }

src/main/java/de/embl/schwab/crosshair/io/IoHelper.java

@@ -4,10 +4,17 @@
 import javax.swing.filechooser.FileNameExtensionFilter;
 import java.io.File;
 
+/**
+ * Class with IO utility functions
+ */
 public class IoHelper {
 
     private static String lastDirPath;
 
+    /**
+     * Opens a file chooser to select a json file
+     * @return filepath of the chosen file
+     */
     public static String chooseOpenFilePath() {
         String filePath = null;
         JFileChooser chooser = new JFileChooser(lastDirPath);
@@ -21,6 +28,10 @@ public static String chooseOpenFilePath() {
         return filePath;
     }
 
+    /**
+     * Opens a file chooser to select where to save a json file
+     * @return filepath to save json
+     */
     public static String chooseSaveFilePath() {
         String filePath = null;
         JFileChooser chooser = new JFileChooser(lastDirPath);