Added prototype of tiling workflow from the hackathon

src/main/java/net/haesleinhuepf/clijx/faclonheavy/implementations/ThresholdFilter.java

@@ -0,0 +1,39 @@
+package net.haesleinhuepf.clijx.faclonheavy.implementations;
+
+import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
+import net.haesleinhuepf.clijx.faclonheavy.AbstractTileProcessor;
+
+import java.util.Arrays;
+
+/**
+ * An example implementation of an image processing workflow that can be executed on tiles of images.
+ *
+ * @author: Robert Haase
+ */
+public class ThresholdFilter extends AbstractTileProcessor {
+
+    @Override
+    public void accept(ClearCLBuffer input, ClearCLBuffer output) {
+        System.out.println("Start processing on " + clijx.getGPUName() + " image dimensions " + Arrays.toString(input.getDimensions()));
+        long start_time = System.nanoTime();
+
+        // 3d gaussian blur
+        ClearCLBuffer tmpGaussian = clijx.create(input);
+        float sigmaX = 5.0f;
+        float sigmaY = 5.0f;
+        float sigmaZ = 5.0f;
+        clijx.gaussianBlur3D(input, tmpGaussian, sigmaX, sigmaY, sigmaZ);
+
+        // mean threshold
+        ClearCLBuffer tmpThreshold = clijx.create(tmpGaussian);
+        clijx.thresholdMean(tmpGaussian, tmpThreshold);
+        tmpGaussian.close();
+
+        // masked voronoi labelling
+        clijx.maskedVoronoiLabeling(input, tmpThreshold, output);
+        tmpThreshold.close();
+
+        long duration_ms = (System.nanoTime() - start_time) / 1000000;
+        System.out.println("Finished processing on " + clijx.getGPUName() + " after " + duration_ms + " ms");
+    }
+}

src/test/java/net/haesleinhuepf/clijx/faclonheavy/CellCultureTest.java

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+package net.haesleinhuepf.clijx.faclonheavy;
+
+import java.io.IOException;
+
+import net.haesleinhuepf.clijx.faclonheavy.implementations.ThresholdFilter;
+
+import org.janelia.saalfeldlab.i2k2020.ops.CLIJxFilterOp;
+import org.janelia.saalfeldlab.i2k2020.util.Lazy;
+import org.janelia.saalfeldlab.i2k2020.util.N5Factory;
+import org.janelia.saalfeldlab.n5.GzipCompression;
+import org.janelia.saalfeldlab.n5.N5FSWriter;
+import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.converter.Converters;
+import net.imglib2.img.basictypeaccess.AccessFlags;
+import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.view.Views;
+
+/**
+ * Process an image tile-by-tile on multiple GPUs
+ *
+ * This code originates from https://github.com/saalfeldlab/i2k2020-imglib2-advanced/blob/main/src/main/java/org/janelia/saalfeldlab/i2k2020/LazyTutorial3.java
+ *
+ * @author Stephan Saalfeld, Robert Haase
+ */
+public class CellCultureTest {
+
+    public static final void main(final String... args) throws IOException {
+
+        // define location of n5 dataset
+        final N5Reader n5 = N5Factory.openReader("/Users/rossg/Documents/clij-data/n5/cell_culture_crop.n5/data");
+        final RandomAccessibleInterval<FloatType> img = N5Utils.openVolatile(n5, "c3/s0");
+        // convert the input image from any type to FloatType
+        final RandomAccessibleInterval<FloatType> floats = Converters.convert(img, (a, b) -> b.set(a.getRealFloat()), new FloatType());
+
+        // create a pool of clijx instances representing OpenCL contexts executed on different GPUs
+        // specify GPU name and number of threads
+        CLIJxPool pool = CLIJxPool.fromDeviceNames(
+                new String[]{"Intel(R) Iris(TM)"},
+                new int[]{4});
+        System.out.println("CLIJ pool size: " + pool.size());
+        System.out.println("CLIJ pool: \n" + pool.log());
+
+        // create a processor representing the workflow we want to apply to the image
+        final CLIJxFilterOp<FloatType, FloatType> clijxFilter =
+                new CLIJxFilterOp<FloatType, FloatType>(Views.extendMirrorSingle(floats), pool, ThresholdFilter.class, 100, 100, 100);
+
+        final RandomAccessibleInterval<FloatType> filtered = Lazy.generate(
+                img,
+                new int[] {256, 256, 256},
+                new FloatType(),
+                AccessFlags.setOf(AccessFlags.VOLATILE),
+                clijxFilter);
+
+        // save the processed image
+        N5Utils.save(
+                filtered,
+                new N5FSWriter("/Users/rossg/Documents/clij-data/n5/cell_culture_crop.n5"),
+                "filtered/",
+                new int[] {128, 128, 64},
+                new GzipCompression()
+        );
+    }
+}