remove artifacts used for testing

bioimage-io · Oct 27, 2023 · da48ed2 · da48ed2
1 parent 3a71e9a
commit da48ed2
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Showing 3 changed files with 2 additions and 37 deletions.
diff --git a/pom.xml b/pom.xml
@@ -111,14 +111,7 @@
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 	</properties>
-	<!--
-	<repositories>
-		<repository>
-			<id>scijava.public</id>
-			<url>https://maven.scijava.org/content/groups/public</url>
-		</repository>
-	</repositories>
-	-->
+
 	<dependencies>
 		<dependency>
 			<groupId>com.google.code.gson</groupId>
@@ -138,15 +131,5 @@
 			<artifactId>jackson-dataformat-msgpack</artifactId>
 			<version>0.9.5</version>
 		</dependency>
-		<!--
-		<dependency>
-			<groupId>net.imglib2</groupId>
-			<artifactId>imglib2-ij</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>imagej</artifactId>
-		</dependency>
-		-->
 	</dependencies>
 </project>
diff --git a/src/main/java/io/bioimage/modelrunner/model/Model.java b/src/main/java/io/bioimage/modelrunner/model/Model.java
@@ -34,8 +34,6 @@
 import java.util.stream.IntStream;
 import java.util.stream.LongStream;
 
-import ij.IJ;
-import ij.ImagePlus;
 import io.bioimage.modelrunner.bioimageio.bioengine.BioEngineAvailableModels;
 import io.bioimage.modelrunner.bioimageio.bioengine.BioengineInterface;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
@@ -58,7 +56,6 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgs;
-import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.FloatType;
@@ -645,27 +642,13 @@ void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors, Patch
 	public static <T extends NativeType<T> & RealType<T>> void main(String[] args) throws IOException, ModelSpecsException, LoadEngineException, RunModelException, LoadModelException {
 		String mm = "C:\\Users\\angel\\OneDrive\\Documentos\\pasteur\\git\\model-runner-java\\models\\\\EnhancerMitochondriaEM2D_22092023_133921\\";
 		Img<FloatType> im = ArrayImgs.floats(new long[] {1, 1, 512, 512});
-		ImagePlus imp = IJ.openImage(mm + File.separator + "sample_input_0.tif");
-		imp.show();
-		RandomAccessibleInterval<FloatType> wrapImg = ImageJFunctions.convertFloat(imp);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.addDimension(wrapImg, 0, 0);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.addDimension(wrapImg, 0, 0);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 2, 3);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 1, 2);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 0, 1);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 2, 3);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 1, 2);
 		List<Tensor<T>> l = new ArrayList<Tensor<T>>();
-		l.add((Tensor<T>) Tensor.build("input0", "bcyx", wrapImg));
+		l.add((Tensor<T>) Tensor.build("input0", "bcyx", im));
 		Model model = createBioimageioModel(mm);
 		model.loadModel();
 		Map<String, int[]> tilingList = new LinkedHashMap<String, int[]>();
 		tilingList.put("input0", new int[] {1, 1, 256, 256});
 		List<Tensor<T>> out = model.runBioimageioModelOnImgLib2WithTiling(l, tilingList);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.dropSingletonDimensions(out.get(0).getData());
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 0, 2);
-		wrapImg = (RandomAccessibleInterval<FloatType>) Views.permute(wrapImg, 0, 1);
-		ImageJFunctions.show(wrapImg);
 		System.out.println(false);
 	}
 

diff --git a/src/main/java/io/bioimage/modelrunner/tensor/Utils.java b/src/main/java/io/bioimage/modelrunner/tensor/Utils.java
@@ -21,7 +21,6 @@
 
 import net.imglib2.Point;
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.transform.integer.MixedTransform;
 import net.imglib2.type.numeric.NumericType;
 import net.imglib2.type.numeric.RealType;