Merge branch 'master' of https://github.com/bigdataviewer/bigdataviewer-playground

Author: NicoKiaru

pom.xml

@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>38.0.1</version>
+		<version>39.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>bigdataviewer-playground</artifactId>
-	<version>0.10.7-SNAPSHOT</version>
+	<version>0.10.8-SNAPSHOT</version>
 
 	<name>bigdataviewer-playground</name>
 	<description>BigDataViewer Actions and GUI</description>
@@ -121,8 +121,9 @@
 
 		<!-- package version below are not present in the parent pom. A version is needed -->
 		<bigdataviewer-selector.version>0.2.7</bigdataviewer-selector.version>
-		<bigvolumeviewer.version>0.3.3</bigvolumeviewer.version>
+		<bigvolumeviewer.version>0.3.4</bigvolumeviewer.version>
 		<reflections.version>0.10.2</reflections.version> <!-- for test only -->
+		<!--<spim_data.version>2.3.4</spim_data.version>-->
 
 		<!-- package version below are determined by the parent pom but need to be upgraded or temporarily fixed for bugs -->
 
@@ -174,6 +175,12 @@
 			<version>${imglib2-realtransform.version}</version>
 		</dependency>
 
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>spim_data</artifactId>
+			<version>${spim_data.version}</version>
+		</dependency>
+
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>bigwarp_fiji</artifactId>

src/main/java/bdv/util/Procedural3DImageShort.java

@@ -86,6 +86,11 @@ public RealRandomAccessible<UnsignedShortType> getRRA() {
 
 		return new RealRandomAccessible<UnsignedShortType>() {
 
+			@Override
+			public UnsignedShortType getType() {
+				return new UnsignedShortType();
+			}
+
 			@Override
 			public RealRandomAccess<UnsignedShortType> realRandomAccess() {
 				return copy();

src/main/java/sc/fiji/bdvpg/bdv/ManualRegistrationStarter.java

@@ -34,7 +34,6 @@
 import bdv.viewer.SourceAndConverter;
 import net.imglib2.realtransform.AffineTransform3D;
 import bdv.viewer.TransformListener;
-import org.scijava.vecmath.Point3d;
 import sc.fiji.bdvpg.services.SourceAndConverterServices;
 import sc.fiji.bdvpg.sourceandconverter.transform.SourceAffineTransformer;
 
@@ -221,58 +220,65 @@ public static AffineTransform3D ensureOrthoNormalTransform(
 		correctedAffineTransform.set(at3D);
 
 		// Gets three vectors
-		Point3d v1 = new Point3d(at3D.get(0, 0), at3D.get(0, 1), at3D.get(0, 2));
-		Point3d v2 = new Point3d(at3D.get(1, 0), at3D.get(1, 1), at3D.get(1, 2));
+		double v1x = at3D.get(0, 0);
+		double v1y = at3D.get(0, 1);
+		double v1z = at3D.get(0, 2);
+
+		double v2x = at3D.get(1, 0);
+		double v2y = at3D.get(1, 1);
+		double v2z = at3D.get(1,2);
 
 		// 0 - Ensure v1 and v2 have the same norm
-		double normv1 = Math.sqrt(v1.x * v1.x + v1.y * v1.y + v1.z * v1.z);
-		double normv2 = Math.sqrt(v2.x * v2.x + v2.y * v2.y + v2.z * v2.z);
+		double normv1 = Math.sqrt(v1x * v1x + v1y * v1y + v1z * v1z);
+		double normv2 = Math.sqrt(v2x * v2x + v2y * v2y + v2z * v2z);
 
 		// If v1 and v2 do not have the same norm
 		if (Math.abs(normv1 - normv2) / normv1 > 1e-10) {
 			// We make v2 having the norm of v1
-			v2.x = v2.x / normv2 * normv1;
-			v2.y = v2.y / normv2 * normv1;
-			v2.z = v2.z / normv2 * normv1;
+			v2x = v2x / normv2 * normv1;
+			v2y = v2y / normv2 * normv1;
+			v2z = v2z / normv2 * normv1;
 
-			correctedAffineTransform.set(v2.x, 1, 0);
-			correctedAffineTransform.set(v2.y, 1, 1);
-			correctedAffineTransform.set(v2.z, 1, 2);
+			correctedAffineTransform.set(v2x, 1, 0);
+			correctedAffineTransform.set(v2y, 1, 1);
+			correctedAffineTransform.set(v2z, 1, 2);
 		}
 
 		// 1 - Ensure v1 and v2 are perpendicular
 
-		if (Math.abs(v1.x * v2.x + v1.y * v2.y + v1.z * v2.z) / (normv1 *
+		if (Math.abs(v1x * v2x + v1y * v2y + v1z * v2z) / (normv1 *
 			normv2) > (1e-10))
 		{
 			// v1 and v2 not perpendicular enough
 			// Compute the projection of v1 onto v2
-			Point3d u1 = new Point3d(v1.x / normv1, v1.y / normv1, v1.z / normv1);
-			double dotProductNormalized = (u1.x * v2.x + u1.y * v2.y + u1.z * v2.z);
-			v2.x = v2.x - dotProductNormalized * u1.x;
-			v2.y = v2.y - dotProductNormalized * u1.y;
-			v2.z = v2.z - dotProductNormalized * u1.z;
-
-			normv2 = Math.sqrt(v2.x * v2.x + v2.y * v2.y + v2.z * v2.z);
-			v2.x = v2.x / normv2 * normv1;
-			v2.y = v2.y / normv2 * normv1;
-			v2.z = v2.z / normv2 * normv1;
-
-			correctedAffineTransform.set(v2.x, 1, 0);
-			correctedAffineTransform.set(v2.y, 1, 1);
-			correctedAffineTransform.set(v2.z, 1, 2);
+			double u1x = v1x / normv1;
+			double u1y = v1y / normv1;
+			double u1z = v1z / normv1;
+			double dotProductNormalized = (u1x * v2x + u1y * v2y + u1z * v2z);
+			v2x = v2x - dotProductNormalized * u1x;
+			v2y = v2y - dotProductNormalized * u1y;
+			v2z = v2z - dotProductNormalized * u1z;
+
+			normv2 = Math.sqrt(v2x * v2x + v2y * v2y + v2z * v2z);
+			v2x = v2x / normv2 * normv1;
+			v2y = v2y / normv2 * normv1;
+			v2z = v2z / normv2 * normv1;
+
+			correctedAffineTransform.set(v2x, 1, 0);
+			correctedAffineTransform.set(v2y, 1, 1);
+			correctedAffineTransform.set(v2z, 1, 2);
 		}
 
 		// 2 - We now set v3 as the cross product of v1 and v2, no matter what
-		double xr = (v1.y * v2.z - v1.z * v2.y) / normv1;
-		double yr = (v1.z * v2.x - v1.x * v2.z) / normv1;
-		double zr = (v1.x * v2.y - v1.y * v2.x) / normv1;
+		double xr = (v1y * v2z - v1z * v2y) / normv1;
+		double yr = (v1z * v2x - v1x * v2z) / normv1;
+		double zr = (v1x * v2y - v1y * v2x) / normv1;
 
-		Point3d v3orthonormal = new Point3d(xr, yr, zr);
+		//double v3orthonormal = new Point3d(xr, yr, zr);
 
-		correctedAffineTransform.set(v3orthonormal.x, 2, 0);
-		correctedAffineTransform.set(v3orthonormal.y, 2, 1);
-		correctedAffineTransform.set(v3orthonormal.z, 2, 2);
+		correctedAffineTransform.set(xr, 2, 0);
+		correctedAffineTransform.set(yr, 2, 1);
+		correctedAffineTransform.set(zr, 2, 2);
 
 		return correctedAffineTransform;
 

src/main/java/sc/fiji/bdvpg/sourceandconverter/SourceAndConverterHelper.java

@@ -59,7 +59,6 @@
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.volatiles.VolatileARGBType;
 import net.imglib2.util.Intervals;
-import org.scijava.vecmath.Point3d;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import sc.fiji.bdvpg.bdv.BdvHandleHelper;
@@ -946,17 +945,20 @@ public static double getCharacteristicVoxelSize(
 		AffineTransform3D sourceTransform)
 	{ // method also present in resampled source
 		// Gets three vectors
-		Point3d v1 = new Point3d(sourceTransform.get(0, 0), sourceTransform.get(0,
-			1), sourceTransform.get(0, 2));
-		Point3d v2 = new Point3d(sourceTransform.get(1, 0), sourceTransform.get(1,
-			1), sourceTransform.get(1, 2));
-		Point3d v3 = new Point3d(sourceTransform.get(2, 0), sourceTransform.get(2,
-			1), sourceTransform.get(2, 2));
+		double v1x = sourceTransform.get(0, 0);
+		double v1y = sourceTransform.get(0, 1);
+		double v1z = sourceTransform.get(0, 2);
+		double v2x = sourceTransform.get(1, 0);
+		double v2y = sourceTransform.get(1, 1);
+		double v2z = sourceTransform.get(1, 2);
+		double v3x = sourceTransform.get(2, 0);
+		double v3y = sourceTransform.get(2, 1);
+		double v3z = sourceTransform.get(2, 2);
 
 		// 0 - Ensure v1 and v2 have the same norm
-		double a = Math.sqrt(v1.x * v1.x + v1.y * v1.y + v1.z * v1.z);
-		double b = Math.sqrt(v2.x * v2.x + v2.y * v2.y + v2.z * v2.z);
-		double c = Math.sqrt(v3.x * v3.x + v3.y * v3.y + v3.z * v3.z);
+		double a = Math.sqrt(v1x * v1x + v1y * v1y + v1z * v1z);
+		double b = Math.sqrt(v2x * v2x + v2y * v2y + v2z * v2z);
+		double c = Math.sqrt(v3x * v3x + v3y * v3y + v3z * v3z);
 
 		return Math.max(Math.min(a, b), Math.min(Math.max(a, b), c)); // https://stackoverflow.com/questions/1582356/fastest-way-of-finding-the-middle-value-of-a-triple
 	}

src/main/java/sc/fiji/bdvpg/sourceandconverter/importer/VoronoiSourceGetter.java

@@ -122,8 +122,7 @@ public static RandomAccessibleInterval<FloatType> getVoronoiTestLabelImage(
 			randomAccessible, interval);
 
 		if (copyImg) {
-			final ArrayImg<FloatType, ?> labelImageCopy = new ArrayImgFactory(Util
-				.getTypeFromInterval(labelImage)).create(labelImage);
+			final ArrayImg<FloatType, ?> labelImageCopy = new ArrayImgFactory(labelImage.getType()).create(labelImage);
 
 			// Image copied to avoid computing it on the fly
 			// https://github.com/imglib/imglib2-algorithm/blob/47cd6ed5c97cca4b316c92d4d3260086a335544d/src/main/java/net/imglib2/algorithm/util/Grids.java#L221