Converters

src/main/java/net/imagej/ops/DefaultOpService.java

@@ -206,7 +206,7 @@ public Object convolve(Object... args) {
 	}
 
 	@Override
-	public Object create(Object... args) {
+	public Object createImg(Object... args) {
 		return run("create", args);
 	}
 

src/main/java/net/imagej/ops/OpService.java

@@ -184,7 +184,7 @@ public interface OpService extends PTService<Op>, ImageJService {
 	Object convolve(Object... args);
 
 	/** Executes the "create" operation on the given arguments. */
-	Object create(Object... args);
+	Object createImg(Object... args);
 
 	/** Executes the "crop" operation on the given arguments. */
 	Object crop(Object... args);

src/main/java/net/imagej/ops/convert/ConvertClip.java

@@ -0,0 +1,25 @@
+package net.imagej.ops.convert;
+
+import net.imagej.ops.Function;
+
+/**
+ * Base interface for "convert-clip" operations.
+ * <p>
+ * Implementing classes should be annotated with:
+ * </p>
+ * 
+ * <pre>
+ * @Plugin(type = Op.class, name = ConvertClip.NAME)
+ * </pre>
+ * 
+ * <p>
+ * Converts some <I> to another <O>. The values are copied. If a value of the
+ * input is lower/higher than the output minimum/maximum, it will be set to the
+ * minimum/maximum of the output.
+ * </p>
+ * 
+ * @author Christian Dietz (University of Konstanz)
+ */
+public interface ConvertClip<I, O> extends Function<I, O> {
+	String NAME = "convert-clip";
+}

src/main/java/net/imagej/ops/convert/ConvertPixScale.java → src/main/java/net/imagej/ops/convert/ConvertClipImg.java

@@ -30,46 +30,40 @@
 
 package net.imagej.ops.convert;
 
+import net.imagej.ops.AbstractOutputFunction;
 import net.imagej.ops.Op;
-import net.imglib2.IterableInterval;
-import net.imglib2.type.numeric.RealType;
+import net.imagej.ops.OpService;
+import net.imglib2.img.Img;
 
+import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 /**
- * @author Martin Horn
+ * Applies a {@link ConvertClip} on an {@link Iterable}.
+ * 
+ * @author Christian Dietz (University of Konstanz)
  */
-@Plugin(type = Op.class, name = Convert.NAME)
-public class ConvertPixScale<I extends RealType<I>, O extends RealType<O>>
-	extends ConvertPix<I, O>
-{
-
-	protected double inMin;
-
-	protected double outMin;
+@Plugin(type = Op.class, name = ConvertClip.NAME, priority = Priority.HIGH_PRIORITY)
+public class ConvertClipImg<T, V> extends
+		AbstractOutputFunction<Img<T>, Img<V>> implements
+		ConvertClip<Img<T>, Img<V>> {
 
-	protected double factor = 0;
-
-	@Override
-	public O compute(final I input, final O output) {
-		output.setReal((input.getRealDouble() - inMin) / factor + outMin);
-		return output;
-	}
+	@Parameter
+	private OpService ops;
 
-	@Override
-	public void checkInput(final I inType, final O outType) {
-		inMin = inType.getMinValue();
-		outMin = outType.getMinValue();
-		factor = (inType.getMaxValue() - inMin) / (outType.getMaxValue() - outMin);
-	}
+	@Parameter
+	private V outType;
 
+	@SuppressWarnings("unchecked")
 	@Override
-	public void checkInput(IterableInterval<I> in) {
-		// nothing to do here
+	public Img<V> createOutput(Img<T> input) {
+		return (Img<V>) ops.createImg(input, outType);
 	}
 
 	@Override
-	public boolean conforms() {
-		return true;
+	protected Img<V> safeCompute(Img<T> input, Img<V> output) {
+		ops.run(ConvertClip.class, output, input);
+		return output;
 	}
 }

src/main/java/net/imagej/ops/convert/ConvertII.java → src/main/java/net/imagej/ops/convert/ConvertClipIterable.java

@@ -33,36 +33,39 @@
 import net.imagej.ops.AbstractFunction;
 import net.imagej.ops.Op;
 import net.imagej.ops.OpService;
-import net.imglib2.IterableInterval;
-import net.imglib2.type.numeric.RealType;
+import net.imagej.ops.map.Map;
 
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 /**
- * @author Martin Horn
+ * Applies a {@link ConvertClip} on an {@link Iterable}.
+ * 
+ * @author Christian Dietz (University of Konstanz)
  */
-@Plugin(type = Op.class, name = Convert.NAME)
-public class ConvertII<I extends RealType<I>, O extends RealType<O>> extends
-	AbstractFunction<IterableInterval<I>, IterableInterval<O>> implements
-	Convert<IterableInterval<I>, IterableInterval<O>>
-{
+@Plugin(type = Op.class, name = ConvertClip.NAME)
+public class ConvertClipIterable<T, V> extends
+		AbstractFunction<Iterable<T>, Iterable<V>> implements
+		ConvertClip<Iterable<T>, Iterable<V>> {
 
 	@Parameter
-	private ConvertPix<I, O> pixConvert;
+	private OpService ops;
 
 	@Parameter
-	private OpService ops;
+	private T outMin;
+
+	@Parameter
+	private V outMax;
 
 	@SuppressWarnings("unchecked")
 	@Override
-	public IterableInterval<O> compute(final IterableInterval<I> input,
-		final IterableInterval<O> output)
-	{
-		pixConvert.checkInput(input.firstElement().createVariable(), output
-			.firstElement().createVariable());
-		pixConvert.checkInput(input);
-		return (IterableInterval<O>) ops.run("map", output, input, pixConvert);
-	}
+	public Iterable<V> compute(final Iterable<T> input, final Iterable<V> output) {
+
+		ConvertClip<T, V> op = (ConvertClip<T, V>) ops.op(ConvertClip.class,
+				outMin, outMax);
 
+		ops.run(Map.class, output, input, op);
+
+		return output;
+	}
 }

src/main/java/net/imagej/ops/convert/ConvertPixClip.java → src/main/java/net/imagej/ops/convert/ConvertClipPixelRT.java

@@ -30,54 +30,41 @@
 
 package net.imagej.ops.convert;
 
+import net.imagej.ops.AbstractFunction;
 import net.imagej.ops.Op;
-import net.imglib2.IterableInterval;
 import net.imglib2.type.numeric.RealType;
 
+import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 /**
- * @author Martin Horn
+ * {@link ConvertClip} implementation for {@link RealType}s.
+ * 
+ * @author Christian Dietz (University of Konstanz)
+ * 
+ * @param <T>
+ * @param <V>
  */
-@Plugin(type = Op.class, name = Convert.NAME)
-public class ConvertPixClip<I extends RealType<I>, O extends RealType<O>>
-	extends ConvertPix<I, O>
-{
-
-	private double outMax;
+@Plugin(type = Op.class, name = ConvertClip.NAME)
+public class ConvertClipPixelRT<T extends RealType<T>, V extends RealType<V>>
+		extends AbstractFunction<T, V> implements ConvertClip<T, V> {
 
+	@Parameter
 	private double outMin;
 
+	@Parameter
+	private double outMax;
+
 	@Override
-	public O compute(final I input, final O output) {
+	public V compute(T input, V output) {
 		final double v = input.getRealDouble();
 		if (v > outMax) {
 			output.setReal(outMax);
-		}
-		else if (v < outMin) {
+		} else if (v < outMin) {
 			output.setReal(outMin);
-		}
-		else {
+		} else {
 			output.setReal(v);
 		}
 		return output;
 	}
-
-	@Override
-	public void checkInput(final I inType, final O outType) {
-		outMax = outType.getMaxValue();
-		outMin = outType.getMinValue();
-
-	}
-
-	@Override
-	public void checkInput(IterableInterval<I> in) {
-		// nothing to do here
-	}
-
-	@Override
-	public boolean conforms() {
-		return true;
-	}
-
 }

src/main/java/net/imagej/ops/convert/ConvertCopy.java

@@ -0,0 +1,23 @@
+package net.imagej.ops.convert;
+
+import net.imagej.ops.Function;
+
+/**
+ * Base interface for "convert-copy" operations.
+ * <p>
+ * Implementing classes should be annotated with:
+ * </p>
+ * 
+ * <pre>
+ * @Plugin(type = Op.class, name = ConvertCopy.NAME)
+ * </pre>
+ * 
+ * <p>
+ * Converts from <I> to <O> by just copying the values.
+ * </p>
+ * 
+ * @author Christian Dietz
+ */
+public interface ConvertCopy<I, O> extends Function<I, O> {
+	String NAME = "convert-copy";
+}

src/main/java/net/imagej/ops/convert/ConvertCopyImg.java

@@ -0,0 +1,71 @@
+/*
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 Board of Regents of the University of
+ * Wisconsin-Madison and University of Konstanz.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imagej.ops.convert;
+
+import net.imagej.ops.AbstractOutputFunction;
+import net.imagej.ops.Op;
+import net.imagej.ops.OpService;
+import net.imagej.ops.create.CreateImg;
+import net.imglib2.img.Img;
+import net.imglib2.type.NativeType;
+
+import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Applies a {@link ConvertCopy} on an {@link Iterable}.
+ * 
+ * @author Christian Dietz (University of Konstanz)
+ */
+@Plugin(type = Op.class, name = ConvertClip.NAME, priority = Priority.HIGH_PRIORITY)
+public class ConvertCopyImg<T, V extends NativeType<V>> extends
+		AbstractOutputFunction<Img<T>, Img<V>> implements
+		ConvertCopy<Img<T>, Img<V>> {
+
+	@Parameter
+	private OpService ops;
+
+	@Parameter
+	private NativeType<V> outType;
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public Img<V> createOutput(Img<T> input) {
+		return (Img<V>) ops.run(CreateImg.class, input, outType);
+	}
+
+	@Override
+	protected Img<V> safeCompute(Img<T> input, Img<V> output) {
+		ops.run(ConvertCopy.class, output, input);
+		return output;
+	}
+}