keep iterating

bioimage-io · Aug 6, 2024 · d6aed6f · d6aed6f
1 parent c418a1d
commit d6aed6f
Show file tree

Hide file tree

Showing 8 changed files with 48 additions and 6 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/TileFactory.java b/src/main/java/io/bioimage/modelrunner/bioimageio/TileFactory.java
@@ -11,9 +11,9 @@
 import java.util.stream.IntStream;
 import java.util.stream.LongStream;
 
+import io.bioimage.modelrunner.bioimageio.description.Axis;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
 import io.bioimage.modelrunner.bioimageio.description.TensorSpec;
-import io.bioimage.modelrunner.bioimageio.description.axes.axis.Axis;
 import io.bioimage.modelrunner.tiling.PatchGridCalculator;
 
 public class TileFactory {
@@ -32,10 +32,9 @@ public static TileFactory init(ModelDescriptor descriptor) {
 
 	private long[] getOptimalTileSize(TensorSpec tensor, String inputAxesOrder, long[] dims) {
 		boolean tiling = this.descriptor.isTilingAllowed();
-		int[] halo = descriptor.getTotalHalo();
+		int[] halo = tensor.getAxesInfo().getHaloArr();
 		int[] min = tensor.getMinTileSizeArr();
 		int[] step = tensor.getTileStepArr();
-		double[] scale = tensor.getTileScaleArr();
 
     	long[] patch = new long[inputAxesOrder.length()];
     	String seqSizeAxesUpper = inputAxesOrder.toUpperCase();

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/Axes.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/Axes.java
@@ -18,6 +18,8 @@ public interface Axes {
 
 	public double[] getTileScaleArr();
 
+	public int[] getHaloArr();
+
 	public Axis getAxis(String abreviation);
 
 }
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/AxesV04.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/AxesV04.java
@@ -19,7 +19,7 @@ public class AxesV04 implements Axes {
 
 	private final int[] stepArr;
 
-	private final int[] haloArr;
+	private int[] haloArr;
 
 	private final double[] offsetArr;
 
@@ -118,6 +118,9 @@ public double[] getOffsetArr() {
 	}
 
 	public int[] getHaloArr() {
+		haloArr = new int[this.axesList.size()];
+		for (int i = 0; i < this.axesList.size(); i ++)
+			haloArr[i] = this.axesList.get(i).getHalo();
 		return this.haloArr;
 	}
 

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/AxesV05.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/AxesV05.java
@@ -17,6 +17,8 @@ public class AxesV05 implements Axes {
 
 	private final int[] stepArr;
 
+	private int[] haloArr;
+
 	protected AxesV05(List<Object> axesList) {
 		List<Axis> axesListInit = new ArrayList<Axis>();
 		String order = "";
@@ -61,6 +63,13 @@ public int[] getTileStepArr() {
 		return this.stepArr;
 	}
 
+	public int[] getHaloArr() {
+		haloArr = new int[this.axesList.size()];
+		for (int i = 0; i < this.axesList.size(); i ++)
+			haloArr[i] = this.axesList.get(i).getHalo();
+		return this.haloArr;
+	}
+
 	public double[] getTileScaleArr() {
 		return this.scaleArr;
 	}

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java
@@ -50,6 +50,8 @@ public interface TensorSpec {
 
     public int[] getTileStepArr();
 
+    public int[] getHaloArr();
+
     public double[] getTileScaleArr();
 
     public Axes getAxesInfo();

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV04.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV04.java
@@ -172,4 +172,9 @@ public String getDataType() {
     	// TODO 
     	return this.data.toString();
     }
+
+	@Override
+	public int[] getHaloArr() {
+		return this.axes.getHaloArr();
+	}
 }
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV05.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV05.java
@@ -175,4 +175,9 @@ public String getDataType() {
     	// TODO 
     	return this.data.toString();
     }
+
+	@Override
+	public int[] getHaloArr() {
+		return this.axes.getHaloArr();
+	}
 }
diff --git a/src/main/java/io/bioimage/modelrunner/model/Model.java b/src/main/java/io/bioimage/modelrunner/model/Model.java
@@ -26,6 +26,7 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.MalformedURLException;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -171,7 +172,15 @@ public static Model createDeepLearningModel( String modelFolder, String modelSou
 				&& !engineInfo.getFramework().equals(EngineInfo.getTensorflowKey())
 				&& !engineInfo.getFramework().equals(EngineInfo.getBioimageioTfKey()) )
 			Objects.requireNonNull(modelSource);
-		return new Model( engineInfo, modelFolder, modelSource, null );
+		Model model = new Model( engineInfo, modelFolder, modelSource, null );
+
+		if (Paths.get(modelFolder, Constants.RDF_FNAME).toFile().isFile()) {
+			try {
+				model.descriptor = ModelDescriptorFactory.readFromLocalFile(Paths.get(modelFolder, Constants.RDF_FNAME).toAbsolutePath().toString());
+			} catch (ModelSpecsException | IOException e) {
+			}
+		}
+		return model;
 	}
 
 	/**
@@ -412,7 +421,15 @@ public static Model createDeepLearningModel( String modelFolder, String modelSou
 				&& !engineInfo.getFramework().equals(EngineInfo.getTensorflowKey())
 				&& !engineInfo.getFramework().equals(EngineInfo.getBioimageioTfKey()))
 			Objects.requireNonNull(modelSource);
-		return new Model( engineInfo, modelFolder, modelSource, classLoader );
+		Model model = new Model( engineInfo, modelFolder, modelSource, classLoader );
+
+		if (Paths.get(modelFolder, Constants.RDF_FNAME).toFile().isFile()) {
+			try {
+				model.descriptor = ModelDescriptorFactory.readFromLocalFile(Paths.get(modelFolder, Constants.RDF_FNAME).toAbsolutePath().toString());
+			} catch (ModelSpecsException | IOException e) {
+			}
+		}
+		return model;
 	}
 
 	/**