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Merge pull request #48 from scijava/scijava/scijava-ops-engine/explicit-op-environment
Rewrite SciJava Ops Engine Ops as Services
2 parents 69e2472 + c9d46d6 commit 72176fd

235 files changed

Lines changed: 5961 additions & 3119 deletions

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‎.gitignore‎

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# IntelliJ #
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.idea/
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.iml
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*.iml

‎imagej/imagej-ops2/pom.xml‎

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<!-- Test scope dependencies -->
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-api</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-api</artifactId>
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<artifactId>junit-jupiter-engine</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>

‎imagej/imagej-ops2/src/main/java/module-info.java‎

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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/eval/DefaultEval.java‎

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@@ -32,7 +32,7 @@
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import java.util.Map;
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import org.scijava.function.Functions;
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import org.scijava.ops.engine.OpService;
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import org.scijava.ops.api.OpEnvironment;
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import org.scijava.ops.spi.Op;
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import org.scijava.plugin.Plugin;
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@@ -48,7 +48,7 @@
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* @see OpEvaluator
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*/
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@Plugin(type = Op.class, name = "eval")
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public class DefaultEval implements Functions.Arity3<String, Map<String, Object>, OpService, Object>
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public class DefaultEval implements Functions.Arity3<String, Map<String, Object>, OpEnvironment, Object>
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{
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/**
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* @return the output
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*/
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@Override
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public Object apply(final String input, final Map<String, Object> vars, final OpService ops) {
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public Object apply(final String input, final Map<String, Object> vars, final OpEnvironment ops) {
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OpEvaluator e = new OpEvaluator(ops);
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if (vars != null) e.setAll(vars);
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return e.evaluate(input);

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/eval/OpEvaluator.java‎

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import java.util.Map;
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import org.scijava.function.Functions;
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import org.scijava.ops.engine.OpService;
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import org.scijava.ops.api.OpEnvironment;
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import org.scijava.ops.engine.util.FunctionUtils;
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import org.scijava.ops.spi.Op;
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import org.scijava.parsington.Operator;
@@ -46,7 +46,6 @@
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import org.scijava.parsington.eval.AbstractStandardStackEvaluator;
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import org.scijava.parsington.eval.Evaluator;
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import org.scijava.types.Nil;
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import org.scijava.types.TypeService;
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/**
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* A Parsington {@link Evaluator} using available {@link Op}s.
@@ -55,12 +54,12 @@
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*/
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public class OpEvaluator extends AbstractStandardStackEvaluator {
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private final OpService ops;
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private final OpEnvironment ops;
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/** Map of Parsington {@link Operator}s to Ops operation names. */
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private final HashMap<Operator, String> opMap;
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63-
public OpEvaluator(final OpService ops) {
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public OpEvaluator(final OpEnvironment ops) {
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this.ops = ops;
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opMap = new HashMap<>();
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@@ -150,13 +149,13 @@ public Object execute(final String opName, final Object... args) {
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Nil<Object> outType = new Nil<>() {};
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// Try executing the op.
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Functions.ArityN<Object> func = FunctionUtils.matchN(ops.env(), opName, outType, inTypes);
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Functions.ArityN<Object> func = FunctionUtils.matchN(ops, opName, outType, inTypes);
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return func.apply(argValues);
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}
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@SuppressWarnings({ "unchecked" })
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private <T> Nil<T> type(Object obj) {
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return (Nil<T>) Nil.of(ops.context().service(TypeService.class).reify(obj));
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return (Nil<T>) Nil.of(ops.genericType(obj));
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}
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/** Gets the op name associated with the given {@link Operator}. */
@@ -411,8 +410,8 @@ public Object execute(final Operator op, final Deque<Object> stack) {
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// Try the base execute, which handles assignment-oriented operations.
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// (NB: super.execute pops the arguments again, so put them back first.)
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for (int i = 0; i < args.length; i++) {
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stack.push(args[i]);
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for (Object arg : args) {
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stack.push(arg);
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}
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final Object result = super.execute(op, stack);
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if (result != null) return result;

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/image/integral/AbstractIntegralImg.java‎

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* The type of the input image.
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* @author Stefan Helfrich (University of Konstanz)
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*/
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@Plugin(type = OpCollection.class)
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public abstract class AbstractIntegralImg<I extends RealType<I>, O extends RealType<O>>
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implements Computers.Arity1<RandomAccessibleInterval<I>, RandomAccessibleInterval<O>> {
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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/labeling/ImgLabelingTypeExtractor.java‎

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‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/types/ImgFactoryTypeExtractor.java‎

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import net.imglib2.img.array.ArrayImg;
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import org.scijava.Priority;
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import org.scijava.types.TypeExtractor;
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import org.scijava.types.TypeService;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.types.TypeExtractor;
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import org.scijava.types.TypeReifier;
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/**
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* {@link TypeExtractor} plugin which operates on {@link ArrayImg} objects.
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*
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* @author Gabriel Selzer
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*/
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@Plugin(type = TypeExtractor.class, priority = Priority.LOW_PRIORITY)
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public class ImgFactoryTypeExtractor implements TypeExtractor<ImgFactory<?>> {
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@Parameter
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private TypeService typeService;
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@Override
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public Type reify(final ImgFactory<?> o, final int n) {
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public Type reify(final TypeReifier t, final ImgFactory<?> o, final int n) {
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if (n != 0)
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throw new IndexOutOfBoundsException();
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return typeService.reify(o.type());
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return t.reify(o.type());
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}
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@Override
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return (Class) ImgFactory.class;
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}
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/**
71+
* Corresponds to org.scijava.Priority.LOW_PRIORITY
72+
*/
73+
@Override
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public double priority() {
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return -100;
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}
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}

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/types/ImgLabelingTypeExtractor.java‎

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import net.imglib2.view.Views;
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import org.scijava.Priority;
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import org.scijava.types.TypeExtractor;
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import org.scijava.types.TypeService;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.types.TypeExtractor;
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import org.scijava.types.TypeReifier;
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/**
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* {@link TypeExtractor} plugin which operates on {@link Iterable} objects.
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*
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* @author Curtis Rueden
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*/
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@Plugin(type = TypeExtractor.class, priority = Priority.LOW_PRIORITY)
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public class ImgLabelingTypeExtractor implements TypeExtractor<ImgLabeling<?, ?>> {
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@Parameter
60-
private TypeService typeService;
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@Override
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public Type reify(final ImgLabeling<?, ?> o, final int n) {
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public Type reify(final TypeReifier t, final ImgLabeling<?, ?> o, final int n) {
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if (n < 0 || n > 1) throw new IndexOutOfBoundsException();
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6661
if(n == 0) {
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// o.firstElement will return a LabelingType
68-
Type labelingType = typeService.reify(o.firstElement());
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Type labelingType = t.reify(o.firstElement());
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// sanity check
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if(!(labelingType instanceof ParameterizedType)) throw new IllegalArgumentException("ImgLabeling is not of a LabelingType");
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// get type arg of labelingType
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ParameterizedType pType = (ParameterizedType) labelingType;
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return pType.getActualTypeArguments()[0];
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}
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// otherwise n == 1
76-
return typeService.reify(Views.iterable(o.getSource()).firstElement());
71+
return t.reify(Views.iterable(o.getSource()).firstElement());
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}
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@Override
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return (Class) ImgLabeling.class;
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}
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/**
81+
* Corresponds to org.scijava.Priority.LOW_PRIORITY
82+
*/
83+
@Override
84+
public double priority() {
85+
return -100;
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}
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}

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/types/LabelingMappingTypeExtractor.java‎

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import net.imglib2.roi.labeling.LabelingMapping;
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import org.scijava.Priority;
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import org.scijava.types.TypeExtractor;
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import org.scijava.types.TypeService;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.types.TypeExtractor;
42+
import org.scijava.types.TypeReifier;
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/**
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* {@link TypeExtractor} plugin which operates on {@link Iterable} objects.
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5251
*
5352
* @author Curtis Rueden
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*/
55-
@Plugin(type = TypeExtractor.class, priority = Priority.LOW_PRIORITY)
5654
public class LabelingMappingTypeExtractor implements TypeExtractor<LabelingMapping<?>> {
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58-
@Parameter
59-
private TypeService typeService;
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@Override
62-
public Type reify(final LabelingMapping<?> o, final int n) {
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public Type reify(final TypeReifier t, final LabelingMapping<?> o, final int n) {
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if (n != 0)
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throw new IndexOutOfBoundsException();
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// determine the type arg of the mapping through looking at the Set of Labels
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// (o.getLabels() returns a Set<T>, which can be reified by another TypeService
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// plugin).
69-
Type labelingMappingSet = typeService.reify(o.getLabels());
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Type labelingMappingSet = t.reify(o.getLabels());
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// sanity check, argType will always be a set so argType should always be a
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// ParameterizedType
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if (!(labelingMappingSet instanceof ParameterizedType))
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return (Class) LabelingMapping.class;
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}
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/**
80+
* Corresponds to org.scijava.Priority.LOW_PRIORITY
81+
*/
82+
@Override
83+
public double priority() {
84+
return -100;
85+
}
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}

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