CLIJ2 installation check

src/main/java/mosaic/core/detection/FeaturePointDetector.java

@@ -16,7 +16,7 @@ import mosaic.core.imageUtils.convolution.Kernel1D;
 import mosaic.core.imageUtils.convolution.Kernel2D;
 import mosaic.core.imageUtils.convolution.Kernel3D;
 import mosaic.core.utils.DilateImage;
-
+import mosaic.core.utils.DilateImageClij;
 
 /**
  * FeaturePointDetector detects the "real" particles in provided frames.
@@ -35,6 +35,7 @@ public class FeaturePointDetector {
     private float iAbsIntensityThreshold;
     private Mode iThresholdMode = Mode.PERCENTILE_MODE;
     private boolean iUseCLIJ = false;
+    private boolean iIsCLIJavailable = false;
 
     // Internal stuff
     private Vector<Particle> iParticles;
@@ -194,8 +195,13 @@ public class FeaturePointDetector {
     private void pointLocationsEstimation(ImageStack ips) {
         float threshold = findThreshold(ips, iPercentile, iAbsIntensityThreshold);
         /* do a grayscale dilation */
-        final ImageStack dilated_ips = DilateImage.dilate(ips, iRadius, 4, iUseCLIJ);
+
+        final ImageStack dilated_ips = (iIsCLIJavailable && iUseCLIJ) ?
+                DilateImageClij.dilate(ips, iRadius) :
+                DilateImage.dilate(ips, iRadius, 4);
+
         // new StackWindow(new ImagePlus("dilated ", dilated_ips));
+
         iParticles = new Vector<Particle>();
         /* loop over all pixels */
         final int height = ips.getHeight();
@@ -634,7 +640,16 @@ public class FeaturePointDetector {
 
         iUseCLIJ = aUseCLIJ;
 
-        logger.info("Detection options: radius=" + iRadius + " cutoff=" + iCutoff + " percentile=" + iPercentile + " threshold=" + iAbsIntensityThreshold + " mode=" + (absolute ? "THRESHOLD" : "PERCENTILE") + " useCLIJ=" + iUseCLIJ);
+        try {
+            net.haesleinhuepf.clij2.CLIJ2.getInstance();
+            iIsCLIJavailable = true;
+        }
+        catch (final NoClassDefFoundError err) {
+            iIsCLIJavailable = false;
+        }
+
+        logger.info("Detection options: radius=" + iRadius + " cutoff=" + iCutoff + " percentile=" + iPercentile + " threshold=" + iAbsIntensityThreshold + " mode=" + (absolute ? "THRESHOLD" : "PERCENTILE") + " useCLIJ=" + iUseCLIJ + " clijAvailabe=" + iIsCLIJavailable);
+        System.out.println("Detection options: radius=" + iRadius + " cutoff=" + iCutoff + " percentile=" + iPercentile + " threshold=" + iAbsIntensityThreshold + " mode=" + (absolute ? "THRESHOLD" : "PERCENTILE") + " useCLIJ=" + iUseCLIJ + " clijAvailabe=" + iIsCLIJavailable);
 
         // create Mask for Dilation with the user defined radius
         generateDilationMasks(iRadius);

src/main/java/mosaic/core/detection/GUIhelper.java

@@ -70,7 +70,7 @@ public class GUIhelper {
         gd.addNumericField("Per/Abs", fpd.getPercentile() * 100, 3, 7, null);
 
         gd.addCheckbox("Absolute", fpd.getThresholdMode() == FeaturePointDetector.Mode.ABS_THRESHOLD_MODE);
-        gd.addCheckbox("Accelerate_with_CLIJ2 (experimental)", false);
+        gd.addCheckbox("Accelerate_with_CLIJ2 (experimental 2D only)", false);
     }
     
     

src/main/java/mosaic/core/utils/DilateImage.java

@@ -2,12 +2,9 @@ package mosaic.core.utils;
 
 
 import ij.IJ;
-import ij.ImagePlus;
 import ij.ImageStack;
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
-import net.haesleinhuepf.clij2.CLIJ2;
-import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
 import org.apache.log4j.Logger;
 
 import java.util.Vector;
@@ -25,52 +22,33 @@ public class DilateImage {
      * @param ips ImageProcessor to do the dilation with
      * @return the dilated copy of the given <code>ImageProcessor</code>
      */
-    public static ImageStack dilate(ImageStack ips, int radius, int number_of_threads, boolean aUseCLIJ) {
-        if (!aUseCLIJ) {
-            logger.debug("dilate start");
-            final FloatProcessor[] dilated_procs = new FloatProcessor[ips.getSize()];
-            final AtomicInteger z = new AtomicInteger(-1);
-            final Vector<Thread> threadsVector = new Vector<Thread>(number_of_threads);
-            for (int thread_counter = 0; thread_counter < number_of_threads; thread_counter++) {
-                threadsVector.add(new DilateThread(ips, radius, dilated_procs, z));
-            }
-            for (final Thread t : threadsVector) {
-                t.start();
-            }
-            logger.debug("Threads started");
-            for (final Thread t : threadsVector) {
-                try {
-                    t.join();
-                } catch (final InterruptedException ie) {
-                    IJ.showMessage("Calculation interrupted. An error occured in parallel dilation:\n" + ie.getMessage());
-                }
-            }
-            logger.debug("dilate threads done");
-            final ImageStack dilated_ips = new ImageStack(ips.getWidth(), ips.getHeight());
-            for (int s = 0; s < ips.getSize(); s++) {
-                dilated_ips.addSlice(null, dilated_procs[s]);
+    public static ImageStack dilate(ImageStack ips, int radius, int number_of_threads) {
+        logger.debug("dilate start");
+        final FloatProcessor[] dilated_procs = new FloatProcessor[ips.getSize()];
+        final AtomicInteger z = new AtomicInteger(-1);
+        final Vector<Thread> threadsVector = new Vector<Thread>(number_of_threads);
+        for (int thread_counter = 0; thread_counter < number_of_threads; thread_counter++) {
+            threadsVector.add(new DilateThread(ips, radius, dilated_procs, z));
+        }
+        for (final Thread t : threadsVector) {
+            t.start();
+        }
+        logger.debug("Threads started");
+        for (final Thread t : threadsVector) {
+            try {
+                t.join();
+            } catch (final InterruptedException ie) {
+                IJ.showMessage("Calculation interrupted. An error occured in parallel dilation:\n" + ie.getMessage());
             }
-            logger.debug("dilate stop");
-
-            return dilated_ips;
         }
+        logger.debug("dilate threads done");
+        final ImageStack dilated_ips = new ImageStack(ips.getWidth(), ips.getHeight());
+        for (int s = 0; s < ips.getSize(); s++) {
+            dilated_ips.addSlice(null, dilated_procs[s]);
+        }
+        logger.debug("dilate stop");
 
-        // get CLIJ2 instance with default device
-        CLIJ2 clij2 = CLIJ2.getInstance();
-        // push image and create empty one for result (with same parameters as input image)
-        ClearCLBuffer imgBuffer = clij2.push(new ImagePlus("", ips));
-        ClearCLBuffer outBuffer = clij2.create(imgBuffer);
-
-        // Run kernel
-        logger.debug("maximum2dSphere before");
-        clij2.maximum2DSphere(imgBuffer, outBuffer, radius, radius);
-        logger.debug("maximum2dSphere after");
-
-        // Get output and clear CLIJ2 buffers
-        ImagePlus imgRes = clij2.pull(outBuffer);
-        clij2.clear();
-
-        return imgRes.getImageStack();
+        return dilated_ips;
     }
 
     /**

src/main/java/mosaic/core/utils/DilateImageClij.java

+package mosaic.core.utils;
+
+
+import ij.ImagePlus;
+import ij.ImageStack;
+import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
+import net.haesleinhuepf.clij2.CLIJ2;
+import org.apache.log4j.Logger;
+
+public class DilateImageClij {
+    private static final Logger logger = Logger.getLogger(DilateImageClij.class);
+
+    /**
+     * Dilates all values and returns a copy of the input image.
+     * A spherical structuring element of radius <code>radius</code> is used.
+     * Adapted as is from Ingo Oppermann implementation
+     * 
+     * @param ips ImageProcessor to do the dilation with
+     * @return the dilated copy of the given <code>ImageProcessor</code>
+     */
+    public static ImageStack dilate(ImageStack ips, int radius) {
+        // get CLIJ2 instance with default device
+        CLIJ2 clij2 = CLIJ2.getInstance();
+        // push image and create empty one for result (with same parameters as input image)
+        ClearCLBuffer imgBuffer = clij2.push(new ImagePlus("", ips));
+        ClearCLBuffer outBuffer = clij2.create(imgBuffer);
+
+        // Run kernel
+        logger.debug("maximum2dSphere before");
+        clij2.maximum2DSphere(imgBuffer, outBuffer, radius, radius);
+        logger.debug("maximum2dSphere after");
+
+        // Get output and clear CLIJ2 buffers
+        ImagePlus imgRes = clij2.pull(outBuffer);
+        clij2.clear();
+
+        return imgRes.getImageStack();
+    }
+}
+