Restore dependencies of current Fiji - I can release now

RAIHelper: adds the pixeltype in the argument to avoid blocking in Util.getPixelTypeFromRAI RayCastPositionerSliderAdder: adds synchronisation in state update ResampledSource: adapats to change in RAIHelper
bigdataviewer · Jun 7, 2024 · 71e4dc1 · 71e4dc1
1 parent ee30c16
commit 71e4dc1
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Showing 4 changed files with 54 additions and 59 deletions.
diff --git a/pom.xml b/pom.xml
@@ -135,14 +135,16 @@
 		<n5-zstandard.version>1.0.2</n5-zstandard.version>
 		<org.janelia.n5-zstandard.version>${n5-zstandard.version}</org.janelia.n5-zstandard.version>
 
-		<bigwarp.version>9.1.2</bigwarp.version>
+		<bigwarp.version>9.1.0</bigwarp.version>
 		<bigdataviewer-core.version>10.4.13</bigdataviewer-core.version>
 		<bigdataviewer-vistools.version>1.0.0-beta-34</bigdataviewer-vistools.version>
 
-		<ejml-core.version>0.41</ejml-core.version>
-		<ejml-ddense.version>0.41</ejml-ddense.version>
+		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
 
-		<jitk-tps.version>3.0.4</jitk-tps.version>
+		<!--ejml-core.version>0.25</ejml-core.version>
+		<ejml-ddense.version>0.25</ejml-ddense.version-->
+
+		<jitk-tps.version>3.0.3</jitk-tps.version>
 
 	</properties>
 
@@ -197,7 +199,7 @@
 			<version>${bigwarp_fiji.version}</version>
 		</dependency>
 
-		<dependency>
+		<!--dependency>
 			<groupId>org.ejml</groupId>
 			<artifactId>ejml-core</artifactId>
 			<version>${ejml-core.version}</version>
@@ -207,7 +209,7 @@
 			<groupId>org.ejml</groupId>
 			<artifactId>ejml-ddense</artifactId>
 			<version>${ejml-ddense.version}</version>
-		</dependency>
+		</dependency-->
 
 		<!-- Test dependencies -->
 		<dependency>

diff --git a/src/main/java/bdv/util/RAIHelper.java b/src/main/java/bdv/util/RAIHelper.java
@@ -41,18 +41,14 @@
 import net.imglib2.img.cell.CellGrid;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.ARGBType;
-import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.GenericByteType;
 import net.imglib2.type.numeric.integer.GenericIntType;
 import net.imglib2.type.numeric.integer.GenericLongType;
 import net.imglib2.type.numeric.integer.GenericShortType;
 import net.imglib2.type.numeric.real.DoubleType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Intervals;
-import net.imglib2.util.Util;
 import net.imglib2.view.Views;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import static net.imglib2.img.basictypeaccess.AccessFlags.VOLATILE;
 import static net.imglib2.type.PrimitiveType.BYTE;
@@ -69,57 +65,52 @@
 
 public class RAIHelper {
 
-	private static Logger logger = LoggerFactory.getLogger(RAIHelper.class);
-
-	@SuppressWarnings({ "unchecked", "rawtypes" })
 	public static <T extends NativeType<T>> RandomAccessibleInterval<T>
-		wrapAsVolatileCachedCellImg(final RandomAccessibleInterval<T> source,
-			final int[] blockSize, Object objectSource, int timepoint, int level)
+	wrapAsVolatileCachedCellImg(final RandomAccessibleInterval<T> source,
+								final int[] blockSize, Object objectSource, int timepoint, int level, T type)
 	{
 
 		final long[] dimensions = Intervals.dimensionsAsLongArray(source);
 		final CellGrid grid = new CellGrid(dimensions, blockSize);
 
 		final Caches.RandomAccessibleLoader<T> loader =
-			new Caches.RandomAccessibleLoader<>(Views.zeroMin(source));
-
-		final T type = Util.getTypeFromInterval(source);
+				new Caches.RandomAccessibleLoader<>(Views.zeroMin(source));
 
 		final CachedCellImg<T, ?> img;
 		final Cache<Long, Cell<?>> cache = new GlobalLoaderCache(objectSource,
-			timepoint, level).withLoader(LoadedCellCacheLoader.get(grid, loader, type,
+				timepoint, level).withLoader(LoadedCellCacheLoader.get(grid, loader, type,
 				AccessFlags.setOf(VOLATILE)));
 
 		if (GenericByteType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(
-				BYTE, AccessFlags.setOf(VOLATILE)));
+					BYTE, AccessFlags.setOf(VOLATILE)));
 		}
 		else if (GenericShortType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(
-				SHORT, AccessFlags.setOf(VOLATILE)));
+					SHORT, AccessFlags.setOf(VOLATILE)));
 		}
 		else if (GenericIntType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(INT,
-				AccessFlags.setOf(VOLATILE)));
+					AccessFlags.setOf(VOLATILE)));
 		}
 		else if (GenericLongType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(
-				LONG, AccessFlags.setOf(VOLATILE)));
+					LONG, AccessFlags.setOf(VOLATILE)));
 		}
 		else if (FloatType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(
-				FLOAT, AccessFlags.setOf(VOLATILE)));
+					FLOAT, AccessFlags.setOf(VOLATILE)));
 		}
 		else if (DoubleType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(
-				DOUBLE, AccessFlags.setOf(VOLATILE)));
+					DOUBLE, AccessFlags.setOf(VOLATILE)));
 		}
 		else if (ARGBType.class.isInstance(type)) {
 			img = new CachedCellImg(grid, type, cache, ArrayDataAccessFactory.get(INT,
-				AccessFlags.setOf(VOLATILE)));
+					AccessFlags.setOf(VOLATILE)));
 		}
 		else {
-			img = null;
+			throw new UnsupportedOperationException("Cannot resample RAI (wrapAsVolatileCachedCellImg) of pixel type "+type.getClass().getName());
 		}
 
 		return img;

diff --git a/src/main/java/bdv/util/ResampledSource.java b/src/main/java/bdv/util/ResampledSource.java
@@ -256,7 +256,7 @@ public Interpolation originInterpolation() {
 	}
 
 	@Override
-	public RandomAccessibleInterval<T> getSource(int t, int level) {
+	public RandomAccessibleInterval<T> getSource(int t, int level) { // TODO: shouldn't this be synchronized ?
 		if (cache) {
 			if (!cachedRAIs.containsKey(t)) {
 				cachedRAIs.put(t, new ConcurrentHashMap<>());
@@ -275,7 +275,7 @@ public RandomAccessibleInterval<T> getSource(int t, int level) {
 					.dimension(2);
 
 				cachedRAIs.get(t).put(level, RAIHelper.wrapAsVolatileCachedCellImg(
-					nonCached, blockSize, this, t, level));
+					nonCached, blockSize, this, t, level, this.getType()));
 			}
 			return cachedRAIs.get(t).get(level);
 		}

diff --git a/src/main/java/sc/fiji/bdvpg/bdv/navigate/RayCastPositionerSliderAdder.java b/src/main/java/sc/fiji/bdvpg/bdv/navigate/RayCastPositionerSliderAdder.java
@@ -114,41 +114,43 @@ public void run() {
 		bdvh.getViewerPanel().revalidate();
 
 		slider.addChangeListener((e) -> {
-			if (zLocations.size() > 0) {
-				JSlider slider = (JSlider) e.getSource();
-				int newValue = slider.getValue();
-				// Plane : slider.getValue() / slider.getMaximum()
-				if ((currentPosition != newValue) && (newValue != -1)) {
-					// User slider action: needs update of viewer from currentPosition to
-					// newValue
-					currentPosition = newValue;
-					double shiftZ = zLocations.get(currentPosition);
-					// Need to shift z by shiftZ
-
-					AffineTransform3D at3d = new AffineTransform3D();
-
-					// Change the position of the viewer with the new offset
-					bdvh.getViewerPanel().state().getViewerTransform(at3d);
-					double[] currentCenter = BdvHandleHelper
-						.getWindowCentreInCalibratedUnits(bdvh);
-					double[] newCenter = new double[3];
-					newCenter[0] = currentCenter[0] + lastDirection.getDoublePosition(0) *
-						shiftZ;
-					newCenter[1] = currentCenter[1] + lastDirection.getDoublePosition(1) *
-						shiftZ;
-					newCenter[2] = currentCenter[2] + lastDirection.getDoublePosition(2) *
-						shiftZ;
-					bdvh.getViewerPanel().state().setViewerTransform(BdvHandleHelper
-						.getViewerTransformWithNewCenter(bdvh, newCenter));
-
-				} // else: Bdv user movement: no update required
-
+			synchronized (RayCastPositionerSliderAdder.this) {
+				if (zLocations.size() > 0) {
+					JSlider slider = (JSlider) e.getSource();
+					int newValue = slider.getValue();
+					// Plane : slider.getValue() / slider.getMaximum()
+					if ((currentPosition != newValue) && (newValue != -1)) {
+						// User slider action: needs update of viewer from currentPosition to
+						// newValue
+						currentPosition = newValue;
+						double shiftZ = zLocations.get(currentPosition);
+						// Need to shift z by shiftZ
+
+						AffineTransform3D at3d = new AffineTransform3D();
+
+						// Change the position of the viewer with the new offset
+						bdvh.getViewerPanel().state().getViewerTransform(at3d);
+						double[] currentCenter = BdvHandleHelper
+								.getWindowCentreInCalibratedUnits(bdvh);
+						double[] newCenter = new double[3];
+						newCenter[0] = currentCenter[0] + lastDirection.getDoublePosition(0) *
+								shiftZ;
+						newCenter[1] = currentCenter[1] + lastDirection.getDoublePosition(1) *
+								shiftZ;
+						newCenter[2] = currentCenter[2] + lastDirection.getDoublePosition(2) *
+								shiftZ;
+						bdvh.getViewerPanel().state().setViewerTransform(BdvHandleHelper
+								.getViewerTransformWithNewCenter(bdvh, newCenter));
+
+					} // else: Bdv user movement: no update required
+
+				}
 			}
 		});
 
 	}
 
-	public void updatePositions() {
+	public synchronized void updatePositions() {
 
 		// Find origin and direction of ray - center of the bdv window
 		double[] c = BdvHandleHelper.getWindowCentreInCalibratedUnits(bdvh);