Add static utility class for scripting API

src/main/java/mpicbg/stitching/StitchingUtils.java

@@ -0,0 +1,145 @@
+/*-
+ * #%L
+ * Fiji distribution of ImageJ for the life sciences.
+ * %%
+ * Copyright (C) 2007 - 2020 Fiji developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 2 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-2.0.html>.
+ * #L%
+ */
+
+package mpicbg.stitching;
+
+import java.util.ArrayList;
+
+import ij.ImagePlus;
+import mpicbg.models.InvertibleBoundable;
+import mpicbg.models.TranslationModel2D;
+import mpicbg.models.TranslationModel3D;
+import mpicbg.stitching.fusion.Fusion;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.type.numeric.real.FloatType;
+
+/**
+ * 
+ * @author Jan Eglinger
+ *
+ */
+public class StitchingUtils {
+
+	public static final int BLENDING_FUSION = 0;
+	public static final int AVERAGE_FUSION = 1;
+	public static final int MEDIAN_FUSION = 2;
+	public static final int MAX_FUSION = 3;
+	public static final int MIN_FUSION = 4;
+	public static final int OVERLAP_FUSION = 5;
+
+	private StitchingUtils() {
+		// prevent instantiation of static utility class
+	}
+
+	/**
+	 * Compute optimal tile positions from a list of known initial positions
+	 * 
+	 * @param images List of tiles
+	 * @param positions List of known positions
+	 * @param dimensionality 2 or 3
+	 * @param computeOverlap whether to compute the exact tile overlap, or to trust the known coordinates
+	 * @return List of transformation models
+	 */
+	public static ArrayList<InvertibleBoundable> computeStitching(ArrayList<ImagePlus> images, ArrayList<float[]> positions, int dimensionality, boolean computeOverlap) {
+		if (images.size() != positions.size()) {
+			throw new RuntimeException("number of images != number of positions");
+		}
+
+		// Create tile list
+		ArrayList<ImageCollectionElement> elements = new ArrayList<>();
+		float[] pos;
+		for (int i = 0; i < images.size(); i++) {
+			ImageCollectionElement element = new ImageCollectionElement(null, i);
+			element.setDimensionality( dimensionality );
+			element.setModel(dimensionality == 2 ? new TranslationModel2D() : new TranslationModel3D());
+			element.setImagePlus(images.get(i));
+			if (dimensionality == 2) {
+				element.setOffset(positions.get(i));
+			} else {
+				pos = positions.get(i);
+				element.setOffset(new float[] {pos[0], pos[1], 0});
+			}
+			elements.add(element);
+		}
+
+		// Create parameters
+		StitchingParameters params = new StitchingParameters();
+		params.cpuMemChoice = 1; // faster, use more RAM
+		params.dimensionality = dimensionality;
+		params.computeOverlap = computeOverlap;
+		params.checkPeaks = 5;
+		params.subpixelAccuracy = true;
+
+		// Compute stitching
+		ArrayList<ImagePlusTimePoint> tiles = CollectionStitchingImgLib.stitchCollection(elements, params);
+
+		// Extract models
+		ArrayList<InvertibleBoundable> models = new ArrayList<>();
+		for (ImagePlusTimePoint tile : tiles) {
+			models.add((InvertibleBoundable) tile.getModel());
+		}
+		return models;
+	}
+
+	/**
+	 * Fuse a set of tiles, given a set of transformation models and a fusion type
+	 * 
+	 * @param images List of tiles
+	 * @param models List of transformation models
+	 * @param dimensionality 2 or 3
+	 * @param fusionType Type of fusion, one of the following:
+	 * <ul>
+	 *   <li>{@code BLENDING_FUSION}</li>
+	 *   <li>{@code AVERAGE_FUSION}</li>
+	 *   <li>{@code MEDIAN_FUSION}</li>
+	 *   <li>{@code MAX_FUSION}</li>
+	 *   <li>{@code MIN_FUSION}</li>
+	 *   <li>{@code OVERLAP_FUSION}</li>
+	 * </ul>
+	 * @return fused image
+	 */
+	public static ImagePlus fuseTiles(ArrayList<ImagePlus> images, ArrayList<InvertibleBoundable> models, int dimensionality, int fusionType) {
+		switch (images.get(0).getType()) {
+			case ImagePlus.GRAY8:
+				return Fusion.fuse(new UnsignedByteType(), images, models, dimensionality, true, fusionType, null, false, false, false);
+			case ImagePlus.GRAY16:
+				return Fusion.fuse(new UnsignedShortType(), images, models, dimensionality, true, fusionType, null, false, false, false);
+			case ImagePlus.GRAY32:
+				return Fusion.fuse(new FloatType(), images, models, dimensionality, true, fusionType, null, false, false, false);
+			default:
+				throw new RuntimeException("Unknown image type for fusion");
+		}
+	}
+
+	/**
+	 * Fuse a set of tiles, given a set of transformation models
+	 * 
+	 * @param images List of tiles
+	 * @param models List of transformation models
+	 * @param dimensionality 2 or 3
+	 * @return fused image
+	 */
+	public static ImagePlus fuseTiles(ArrayList<ImagePlus> images, ArrayList<InvertibleBoundable> models, int dimensionality) {
+		return fuseTiles(images, models, dimensionality, BLENDING_FUSION);
+	}
+}