Merge pull request #18 from qupath/more-accurate-interpolation

More accurate interpolation

Author: Rylern

build.gradle.kts

@@ -4,7 +4,7 @@ plugins {
 }
 
 group = "io.github.qupath"
-version = "0.1.0"
+version = "0.1.1"
 
 repositories {
     mavenCentral()

src/main/java/qupath/ext/imglib2/AccessibleScaler.java

@@ -3,14 +3,14 @@
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.interpolation.InterpolatorFactory;
-import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory;
 import net.imglib2.interpolation.randomaccess.NearestNeighborInterpolatorFactory;
 import net.imglib2.realtransform.AffineGet;
 import net.imglib2.realtransform.RealViews;
 import net.imglib2.realtransform.Scale2D;
 import net.imglib2.realtransform.Translation2D;
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.view.Views;
+import qupath.ext.imglib2.interpolators.LinearInterpolationFactory;
 
 import java.util.Arrays;
 import java.util.stream.LongStream;
@@ -35,15 +35,17 @@ private AccessibleScaler() {
      * @param scale the scale to apply to the first two dimensions of the input {@link RandomAccessibleInterval}. Shouldn't be
      *              less than or equal to 0
      * @return the input if the provided scale is 1, or a new scaled {@link RandomAccessibleInterval} otherwise
-     * @param <T> the type of elements of the random accessible interval
+     * @param <T> the type of elements of the random accessible interval. It must be {@link net.imglib2.type.numeric.ARGBType}
+     *            or an instance of {@link net.imglib2.type.numeric.RealType}, otherwise a {@link IllegalArgumentException}
+     *            will be thrown when accessing the output
      * @throws IllegalArgumentException if the input interval has at least one minimum different from 0, if the provided scale is less
      * than or equal to 0, or if the input interval has less than two dimensions
      */
     public static <T extends NumericType<T>> RandomAccessibleInterval<T> scaleWithLinearInterpolation(
             RandomAccessibleInterval<T> input,
             double scale
     ) {
-        return scale(input, scale, new NLinearInterpolatorFactory<>());
+        return scale(input, scale, new LinearInterpolationFactory<>());
     }
 
     /**

src/main/java/qupath/ext/imglib2/interpolators/ArgbLinearInterpolator.java

@@ -0,0 +1,65 @@
+package qupath.ext.imglib2.interpolators;
+
+import net.imglib2.RandomAccessible;
+import net.imglib2.interpolation.randomaccess.NLinearInterpolator2D;
+import net.imglib2.type.numeric.ARGBType;
+
+/**
+ * A {@link NLinearInterpolator2D} that performs intermediary operations with doubles, to avoid precision errors.
+ */
+class ArgbLinearInterpolator extends NLinearInterpolator2D<ARGBType> {
+
+    /**
+     * Create an instance of this class.
+     *
+     * @param randomAccessible the accessible to interpolate
+     */
+    public ArgbLinearInterpolator(RandomAccessible<ARGBType> randomAccessible) {
+        super(randomAccessible);
+    }
+
+    @Override
+    public ARGBType get()
+    {
+        fillWeights();
+
+        int pixelValue;
+        double red = 0;
+        double green = 0;
+        double blue = 0;
+        double alpha = 0;
+
+        pixelValue = target.get().get();
+        red += ARGBType.red(pixelValue) * weights[0];
+        green += ARGBType.green(pixelValue) * weights[0];
+        blue += ARGBType.blue(pixelValue) * weights[0];
+        alpha += ARGBType.alpha(pixelValue) * weights[0];
+
+        target.fwd(0);
+        pixelValue = target.get().get();
+        red += ARGBType.red(pixelValue) * weights[1];
+        green += ARGBType.green(pixelValue) * weights[1];
+        blue += ARGBType.blue(pixelValue) * weights[1];
+        alpha += ARGBType.alpha(pixelValue) * weights[1];
+
+        target.fwd(1);
+        pixelValue = target.get().get();
+        red += ARGBType.red(pixelValue) * weights[3];
+        green += ARGBType.green(pixelValue) * weights[3];
+        blue += ARGBType.blue(pixelValue) * weights[3];
+        alpha += ARGBType.alpha(pixelValue) * weights[3];
+
+        target.bck(0);
+        pixelValue = target.get().get();
+        red += ARGBType.red(pixelValue) * weights[2];
+        green += ARGBType.green(pixelValue) * weights[2];
+        blue += ARGBType.blue(pixelValue) * weights[2];
+        alpha += ARGBType.alpha(pixelValue) * weights[2];
+
+        target.bck(1);
+
+        accumulator.set(ARGBType.rgba(red, green, blue, alpha));
+
+        return accumulator;
+    }
+}

src/main/java/qupath/ext/imglib2/interpolators/LinearInterpolationFactory.java

@@ -0,0 +1,49 @@
+package qupath.ext.imglib2.interpolators;
+
+import net.imglib2.RandomAccessible;
+import net.imglib2.RealInterval;
+import net.imglib2.RealRandomAccess;
+import net.imglib2.interpolation.InterpolatorFactory;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.numeric.RealType;
+
+/**
+ * An {@link InterpolatorFactory} that implements a 2D linear interpolation.
+ * <p>
+ * This factory can only work with {@link RandomAccessible} that have 2 dimensions and the {@link ARGBType} or {@link RealType}
+ * type. If {@link #create(RandomAccessible)} is called with an invalid {@link RandomAccessible}, an {@link IllegalArgumentException}
+ * is thrown.
+ *
+ * @param <T> the type of {@link RandomAccessible} to interpolate
+ */
+public class LinearInterpolationFactory<T extends NumericType<T>> implements InterpolatorFactory<T, RandomAccessible<T>> {
+
+    @Override
+    @SuppressWarnings({"unchecked", "rawtypes"})
+    public RealRandomAccess<T> create(RandomAccessible randomAccessible) {
+        if (randomAccessible.numDimensions() != 2) {
+            throw new IllegalArgumentException(String.format(
+                    "The provided accessible has not 2 dimensions (found %d)",
+                    randomAccessible.numDimensions()
+            ));
+        }
+
+        Object type = randomAccessible.randomAccess().get();
+        if (type instanceof ARGBType) {
+            return (RealRandomAccess<T>) new ArgbLinearInterpolator(randomAccessible);
+        } else if (type instanceof RealType<?>) {
+            return (RealRandomAccess<T>) new RealLinearInterpolator<>(randomAccessible);
+        } else {
+            throw new IllegalArgumentException(String.format(
+                    "The type of the provided accessible %s is unexpected",
+                    type
+            ));
+        }
+    }
+
+    @Override
+    public RealRandomAccess<T> create(RandomAccessible<T> randomAccessible, RealInterval interval) {
+        return create(randomAccessible);
+    }
+}

src/main/java/qupath/ext/imglib2/interpolators/RealLinearInterpolator.java

@@ -0,0 +1,43 @@
+package qupath.ext.imglib2.interpolators;
+
+import net.imglib2.RandomAccessible;
+import net.imglib2.interpolation.randomaccess.NLinearInterpolator2D;
+import net.imglib2.type.numeric.RealType;
+
+/**
+ * A {@link NLinearInterpolator2D} that performs intermediary operations with doubles, to avoid precision errors.
+ */
+class RealLinearInterpolator<T extends RealType<T>> extends NLinearInterpolator2D<T> {
+
+    /**
+     * Create an instance of this class.
+     *
+     * @param randomAccessible the accessible to interpolate
+     */
+    public RealLinearInterpolator(RandomAccessible<T> randomAccessible) {
+        super(randomAccessible);
+    }
+
+    @Override
+    public T get()
+    {
+        fillWeights();
+
+        double value = target.get().getRealDouble() * weights[0];
+
+        target.fwd(0);
+        value += target.get().getRealDouble() * weights[1];
+
+        target.fwd(1);
+        value += target.get().getRealDouble() * weights[3];
+
+        target.bck(0);
+        value += target.get().getRealDouble() * weights[2];
+
+        target.bck(1);
+
+        accumulator.setReal(value);
+
+        return accumulator;
+    }
+}