correct more errors related to pre and post processing

Author: carlosuc3m

src/main/java/io/bioimage/modelrunner/model/processing/Processing.java

@@ -75,6 +75,7 @@ private void buildPreprocessing() throws IllegalArgumentException, RuntimeExcept
 			for (TransformSpec transformation : preprocessing) {
 				list.add(TransformationInstance.create(transformation));
 			}
+			preMap.put(tt.getName(), list);
 		}
 	}
 
@@ -86,6 +87,7 @@ private void buildPostprocessing() throws IllegalArgumentException, RuntimeExcep
 			for (TransformSpec transformation : preprocessing) {
 				list.add(TransformationInstance.create(transformation));
 			}
+			postMap.put(tt.getName(), list);
 		}
 	}
 
@@ -139,6 +141,8 @@ List<Tensor<R>> preprocess(List<Tensor<T>> tensorList, boolean inplace) {
 			Tensor<T> tt = tensorList.stream().filter(t -> t.getName().equals(ee.getKey())).findFirst().orElse(null);
 			if (tt == null)
 				continue;
+			if (ee.getValue().size() == 0)
+				outputs.add(Cast.unchecked(tt));
 			for (TransformationInstance trans : ee.getValue()) {
 				List<Tensor<R>> outList = trans.run(tt, inplace);
 				outputs.addAll(outList);
@@ -184,6 +188,8 @@ List<Tensor<R>> postprocess(List<Tensor<T>> tensorList, boolean inplace) {
 			Tensor<T> tt = tensorList.stream().filter(t -> t.getName().equals(ee.getKey())).findFirst().orElse(null);
 			if (tt == null)
 				continue;
+			if (ee.getValue().size() == 0)
+				outputs.add(Cast.unchecked(tt));
 			for (TransformationInstance trans : ee.getValue()) {
 				List<Tensor<R>> outList = trans.run(tt, inplace);
 				outputs.addAll(outList);

src/main/java/io/bioimage/modelrunner/model/processing/TransformationInstance.java

@@ -25,6 +25,8 @@
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.lang.reflect.Parameter;
+import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
@@ -34,6 +36,7 @@
 import io.bioimage.modelrunner.transformations.BinarizeTransformation;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
+import net.imglib2.util.Cast;
 
 /**
  * Class that creates an instance able to run the corresponding Bioimage.io processing routine
@@ -116,13 +119,43 @@ List<Tensor<R>> run(Tensor<T> tensor) throws RuntimeException {
 	List<Tensor<R>> run(Tensor<T> tensor, boolean inplace) throws RuntimeException {
 		Method m;
 		try {
-			if (inplace)
-				m = cls.getMethod(RUN_INPLACE_NAME, Tensor.class);
-			else
-				m = cls.getMethod(RUN_NAME, Tensor.class);
-			
-			m.invoke(this.instance, tensor);
-			return null;
+			if (inplace) {
+	            m = cls.getMethod(RUN_INPLACE_NAME, Tensor.class);
+	            m.invoke(this.instance, tensor);
+	            return Collections.singletonList(Cast.unchecked(tensor));
+	        } else {
+	            m = cls.getMethod(RUN_NAME, Tensor.class);
+	            Object result = m.invoke(this.instance, tensor);
+	            
+	            // Handle different possible return types
+	            if (result == null) {
+	                return null;
+	            } else if (result instanceof List<?>) {
+	                // Cast and verify each element is a Tensor<R>
+	                List<?> resultList = (List<?>) result;
+	                List<Tensor<R>> outputList = new ArrayList<>();
+	                
+	                for (Object item : resultList) {
+	                    if (item instanceof Tensor<?>) {
+	                        @SuppressWarnings("unchecked")
+	                        Tensor<R> tensorItem = (Tensor<R>) item;
+	                        outputList.add(tensorItem);
+	                    } else {
+	                        throw new RuntimeException("Invalid return type: Expected Tensor but got " + 
+	                            (item != null ? item.getClass().getName() : "null"));
+	                    }
+	                }
+	                return outputList;
+	            } else if (result instanceof Tensor<?>) {
+	                // Single Tensor result
+	                @SuppressWarnings("unchecked")
+	                Tensor<R> tensorResult = (Tensor<R>) result;
+	                return Collections.singletonList(tensorResult);
+	            } else {
+	                throw new RuntimeException("Unexpected return type: " + 
+	                    (result != null ? result.getClass().getName() : "null"));
+	            }
+	        }
 		} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException 
 				| NoSuchMethodException | SecurityException e) {
 			throw new RuntimeException(Types.stackTrace(e));

src/main/java/io/bioimage/modelrunner/transformations/AbstractTensorTransformation.java

@@ -67,7 +67,8 @@ protected < R extends RealType< R > & NativeType< R > > Tensor< FloatType > make
 		final ImgFactory< FloatType > factory = Util.getArrayOrCellImgFactory( input.getData(), new FloatType() );
 		final Img< FloatType > outputImg = factory.create( input.getData() );
 		RealTypeConverters.copyFromTo(input.getData(), outputImg);
-		final Tensor< FloatType > output = Tensor.build( getName() + '_' + input.getName(), input.getAxesOrderString(), outputImg );
+		// TODO what name final Tensor< FloatType > output = Tensor.build( getName() + '_' + input.getName(), input.getAxesOrderString(), outputImg );
+		final Tensor< FloatType > output = Tensor.build( input.getName(), input.getAxesOrderString(), outputImg );
 		return output;
 	}
 }