Add prototype for inpainting job for Celegans dataset

render-ws-spark-client/src/main/java/org/janelia/render/client/JrcP3E2D1Lip419Inpainter.java

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+package org.janelia.render.client;
+
+import ij.ImageJ;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.converter.Converters;
+import net.imglib2.img.Img;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.loops.LoopBuilder;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.util.Util;
+import org.janelia.alignment.inpainting.DirectionalStatistic;
+import org.janelia.alignment.inpainting.RandomDirection3D;
+import org.janelia.alignment.inpainting.RayCastingInpainter;
+import org.janelia.render.client.spark.n5.N5Client;
+import org.janelia.saalfeldlab.n5.N5FSReader;
+import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+
+public class JrcP3E2D1Lip419Inpainter {
+
+	// path to the N5 container containing the data and a mask
+	public static final String N5_BASE_PATH = System.getenv("HOME") + "/big-data/streak-correction/jrc_P3-E2-D1-Lip4-19/broken_layers.n5";
+
+	public static void main(final String[] args) {
+		// saveSubStack();
+		doInpainting();
+	}
+
+	@SuppressWarnings("unused")
+	private static void saveSubStack() {
+		final String[] n5ClientArgs = {
+				"--baseDataUrl", "http://renderer-dev.int.janelia.org:8080/render-ws/v1",
+				"--owner", "fibsem",
+				"--project", "jrc_P3_E2_D1_Lip4_19",
+				"--stack", "v1_acquire_trimmed_align_v2",
+				"--n5Path", N5_BASE_PATH,
+				"--n5Dataset", "tissue",
+				"--tileWidth", "2048",
+				"--tileHeight", "2048",
+				"--blockSize", "512,512,128",
+				"--minZ", "14763",
+				"--maxZ", "14805",
+		};
+
+		N5Client.main(n5ClientArgs);
+	}
+
+	@SuppressWarnings("unused")
+	private static void doInpainting() {
+		final DirectionalStatistic directionalStatistic = new RandomDirection3D();
+		final RayCastingInpainter inpainter = new RayCastingInpainter(64, 50, directionalStatistic);
+
+		try (final N5Reader n5 = new N5FSReader(N5_BASE_PATH)) {
+			final RandomAccessibleInterval<UnsignedByteType> tissue = N5Utils.open(n5, "tissue_crop");
+			final RandomAccessibleInterval<UnsignedByteType> mask = N5Utils.open(n5, "mask_crop_v2");
+
+			// convert to float (and copy tissue)
+			final Img<FloatType> tissueFloat = Util.getSuitableImgFactory(tissue, new FloatType()).create(tissue);
+			LoopBuilder.setImages(tissue, tissueFloat).forEachPixel((i, o) -> o.setReal(i.getRealDouble()));
+			final RandomAccessibleInterval<FloatType> maskFloat = Converters.convert(mask, (i, o) -> o.setReal(i.getRealDouble()), new FloatType());
+
+			inpainter.inpaint(tissueFloat, maskFloat);
+
+			new ImageJ();
+			ImageJFunctions.show(tissueFloat, "Tissue");
+			ImageJFunctions.show(maskFloat, "Mask");
+		}
+	}
+
+}