Adds a way to set alpha sources with vanishing edges (L1 alpha). Fix #58

src/main/java/ch/epfl/biop/scijava/command/source/SourceSetAlphaCommand.java

@@ -0,0 +1,52 @@
+package ch.epfl.biop.scijava.command.source;
+
+import bdv.util.source.alpha.AlphaSource;
+import bdv.util.source.alpha.AlphaSourceDistanceL1RAI;
+import bdv.util.source.alpha.AlphaSourceHelper;
+import bdv.viewer.SourceAndConverter;
+import mpicbg.spim.data.sequence.VoxelDimensions;
+import net.imglib2.realtransform.AffineTransform3D;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.vecmath.Point3d;
+import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
+import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand;
+
+@Plugin(type = BdvPlaygroundActionCommand.class, menuPath = ScijavaBdvDefaults.RootMenu+"Sources>Set L1 Alpha Source")
+public class SourceSetAlphaCommand implements Command {
+
+    @Parameter
+    SourceAndConverter<?>[] sources;
+
+    @Override
+    public void run() {
+        for (SourceAndConverter<?> source: sources) {
+
+            double vox_size_x_micrometer, vox_size_y_micrometer, vox_size_z_micrometer;
+
+            VoxelDimensions voxDim = source.getSpimSource().getVoxelDimensions();
+
+            if (voxDim != null) {
+                vox_size_x_micrometer = voxDim.dimension(0);
+                vox_size_y_micrometer = voxDim.dimension(1);
+                vox_size_z_micrometer = voxDim.dimension(2);
+            } else {
+                AffineTransform3D sourceTransform = new AffineTransform3D();
+                source.getSpimSource().getSourceTransform(0,0, sourceTransform); // Assumption: same voxel size for all timepoints, and timepoint 0 exists
+                Point3d v1 = new Point3d(sourceTransform.get(0, 0), sourceTransform.get(0, 1), sourceTransform.get(0, 2));
+                Point3d v2 = new Point3d(sourceTransform.get(1, 0), sourceTransform.get(1, 1), sourceTransform.get(1, 2));
+                Point3d v3 = new Point3d(sourceTransform.get(2, 0), sourceTransform.get(2, 1), sourceTransform.get(2, 2));
+                double a = Math.sqrt(v1.x * v1.x + v1.y * v1.y + v1.z * v1.z);
+                double b = Math.sqrt(v2.x * v2.x + v2.y * v2.y + v2.z * v2.z);
+                double c = Math.sqrt(v3.x * v3.x + v3.y * v3.y + v3.z * v3.z);
+                vox_size_x_micrometer = a;
+                vox_size_y_micrometer = b;
+                vox_size_z_micrometer = c;
+            }
+
+            AlphaSource alpha = new AlphaSourceDistanceL1RAI(source.getSpimSource(), (float) vox_size_x_micrometer,(float) vox_size_y_micrometer, (float) vox_size_z_micrometer);
+            AlphaSourceHelper.setAlphaSource(source, alpha);
+        }
+    }
+}

src/main/java/ch/epfl/biop/sourceandconverter/SourceFuserAndResampler.java

@@ -30,7 +30,7 @@ public class SourceFuserAndResampler<T extends NumericType<T>> implements Runnab
 
     boolean cache;
 
-    int cacheX, cacheY, cacheZ, cacheBounds;
+    int cacheX, cacheY, cacheZ;
 
     int defaultMipMapLevel;
 
@@ -62,7 +62,6 @@ public SourceFuserAndResampler(List<SourceAndConverter<T>> sacs_in,
         this.cacheX = cacheX;
         this.cacheY = cacheY;
         this.cacheZ = cacheZ;
-        this.cacheBounds = cacheBounds;
     }
 
     @Override