adapt axes to new way of defining them

bioimage-io · Nov 25, 2024 · 721f7b6 · 721f7b6
1 parent 689ad55
commit 721f7b6
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Showing 3 changed files with 63 additions and 8 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/transformations/ScaleLinearTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/ScaleLinearTransformation.java
@@ -20,8 +20,10 @@
 package io.bioimage.modelrunner.transformations;
 
 import java.util.ArrayList;
+import java.util.List;
 
 import io.bioimage.modelrunner.tensor.Tensor;
+import io.bioimage.modelrunner.utils.Constants;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.loops.LoopBuilder;
 import net.imglib2.type.NativeType;
@@ -126,12 +128,29 @@ public void setOffset(Object offset) {
 		}
 	}
 
+	@SuppressWarnings("unchecked")
 	public void setAxes(Object axes) {
 		if (axes instanceof String )
 			this.axes = (String) axes;
-		else
+		else if (axes instanceof List) {
+			this.axes = "";
+			for (Object ax : (List<Object>) axes) {
+				if (!(ax instanceof String))
+					throw new IllegalArgumentException("JDLL does not currently support this axes format. Please "
+							+ "write an issue attaching the rdf.yaml file at: " + Constants.ISSUES_LINK);
+				ax = ax.equals("channel") ? "c" : ax;
+				this.axes += ax;
+			}
+		} else if (axes instanceof String[]) {
+			String[] axesArr = (String[]) axes;
+			this.axes = "";
+			for (String ax : axesArr) {
+				ax = ax.equals("channel") ? "c" : ax;
+				this.axes += ax;
+			}
+		} else
 			throw new IllegalArgumentException("'axes' parameter has to be an instance of " + String.class
-					 + ". The provided argument is " + axes.getClass());
+					 + ", of a String array or of a List of Strings. The provided argument is " + axes.getClass());
 	}
 
 	public void checkRequiredArgs() {

diff --git a/src/main/java/io/bioimage/modelrunner/transformations/ScaleRangeTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/ScaleRangeTransformation.java
@@ -20,9 +20,10 @@
 package io.bioimage.modelrunner.transformations;
 
 import java.util.Arrays;
+import java.util.List;
 
 import io.bioimage.modelrunner.tensor.Tensor;
-
+import io.bioimage.modelrunner.utils.Constants;
 import net.imglib2.Cursor;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessibleInterval;
@@ -96,12 +97,29 @@ public void setMaxPercentile(Object maxPercentile) {
 		}
 	}
 
+	@SuppressWarnings("unchecked")
 	public void setAxes(Object axes) {
 		if (axes instanceof String )
 			this.axes = (String) axes;
-		else
+		else if (axes instanceof List) {
+			this.axes = "";
+			for (Object ax : (List<Object>) axes) {
+				if (!(ax instanceof String))
+					throw new IllegalArgumentException("JDLL does not currently support this axes format. Please "
+							+ "write an issue attaching the rdf.yaml file at: " + Constants.ISSUES_LINK);
+				ax = ax.equals("channel") ? "c" : ax;
+				this.axes += ax;
+			}
+		} else if (axes instanceof String[]) {
+			String[] axesArr = (String[]) axes;
+			this.axes = "";
+			for (String ax : axesArr) {
+				ax = ax.equals("channel") ? "c" : ax;
+				this.axes += ax;
+			}
+		} else
 			throw new IllegalArgumentException("'axes' parameter has to be an instance of " + String.class
-					 + ". The provided argument is " + axes.getClass());
+					 + ", of a String array or of a List of Strings. The provided argument is " + axes.getClass());
 	}
 
 	public void setTensorName(Object tensorName) {

diff --git a/...main/java/io/bioimage/modelrunner/transformations/ZeroMeanUnitVarianceTransformation.java b/...main/java/io/bioimage/modelrunner/transformations/ZeroMeanUnitVarianceTransformation.java
@@ -20,9 +20,10 @@
 package io.bioimage.modelrunner.transformations;
 
 import java.util.ArrayList;
+import java.util.List;
 
 import io.bioimage.modelrunner.tensor.Tensor;
-
+import io.bioimage.modelrunner.utils.Constants;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.array.ArrayImg;
 import net.imglib2.img.array.ArrayImgs;
@@ -135,12 +136,29 @@ public void setStd(Object std) {
 		}
 	}
 
+	@SuppressWarnings("unchecked")
 	public void setAxes(Object axes) {
 		if (axes instanceof String )
 			this.axes = (String) axes;
-		else
+		else if (axes instanceof List) {
+			this.axes = "";
+			for (Object ax : (List<Object>) axes) {
+				if (!(ax instanceof String))
+					throw new IllegalArgumentException("JDLL does not currently support this axes format. Please "
+							+ "write an issue attaching the rdf.yaml file at: " + Constants.ISSUES_LINK);
+				ax = ax.equals("channel") ? "c" : ax;
+				this.axes += ax;
+			}
+		} else if (axes instanceof String[]) {
+			String[] axesArr = (String[]) axes;
+			this.axes = "";
+			for (String ax : axesArr) {
+				ax = ax.equals("channel") ? "c" : ax;
+				this.axes += ax;
+			}
+		} else
 			throw new IllegalArgumentException("'axes' parameter has to be an instance of " + String.class
-					 + ". The provided argument is " + axes.getClass());
+					 + ", of a String array or of a List of Strings. The provided argument is " + axes.getClass());
 	}
 
 	public void setMode(Object mode) {