add possibility of setting eps transformation

bioimage-io · Nov 20, 2024 · fc96c36 · fc96c36
1 parent 0d75458
commit fc96c36
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Showing 5 changed files with 76 additions and 2 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/transformations/BinarizeTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/BinarizeTransformation.java
@@ -30,13 +30,29 @@ public class BinarizeTransformation extends AbstractTensorPixelTransformation
 
 	private static String name = "binarize";
 	private Double threshold;
+	private Double eps = Math.pow(10, -6);
+
 
 	public BinarizeTransformation()
 	{
 		super( name );
 		super.setDoubleUnitaryOperator(v -> ( v >= threshold ) ? 1d : 0d);
 	}
 
+	public void setEps(Object eps) {
+		if (eps instanceof Integer) {
+			this.eps = Double.valueOf((int) eps);
+		} else if (eps instanceof Double) {
+			this.eps = (double) eps;
+		} else if (eps instanceof String) {
+			this.eps = Double.valueOf((String) eps);
+		} else {
+			throw new IllegalArgumentException("'eps' parameter has to be either and instance of "
+					+ Float.class + " or " + Double.class
+					+ ". The provided argument is an instance of: " + eps.getClass());
+		}
+	}
+
 	public void setThreshold(Object threshold) {
 		if (threshold instanceof Integer) {
 			this.threshold = Double.valueOf((int) threshold);

diff --git a/src/main/java/io/bioimage/modelrunner/transformations/ClipTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/ClipTransformation.java
@@ -31,13 +31,28 @@ public class ClipTransformation extends AbstractTensorPixelTransformation
 	private static String name = "clip";
 	private Double min;
 	private Double max;
+	private double eps = Math.pow(10, -6);
 
 	public ClipTransformation()
 	{
 		super(name);
 		super.setDoubleUnitaryOperator(v -> v >= max ? max.doubleValue() : (v < min ? min.doubleValue() : v));
 	}
 
+	public void setEps(Object eps) {
+		if (eps instanceof Integer) {
+			this.eps = Double.valueOf((int) eps);
+		} else if (eps instanceof Double) {
+			this.eps = (double) eps;
+		} else if (eps instanceof String) {
+			this.eps = Double.valueOf((String) eps);
+		} else {
+			throw new IllegalArgumentException("'eps' parameter has to be either and instance of "
+					+ Float.class + " or " + Double.class
+					+ ". The provided argument is an instance of: " + eps.getClass());
+		}
+	}
+
 	public void setMin(Object min) {
 		if (min instanceof Integer) {
 			this.min = Double.valueOf((int) min);

diff --git a/src/main/java/io/bioimage/modelrunner/transformations/ScaleLinearTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/ScaleLinearTransformation.java
@@ -41,12 +41,27 @@ public class ScaleLinearTransformation extends AbstractTensorTransformation
 	private double[] gainArr;
 	private double[] offsetArr;
 	private String axes;
+	private double eps = Math.pow(10, -6);
 
 	public ScaleLinearTransformation()
 	{
 		super( name );
 	}
 
+	public void setEps(Object eps) {
+		if (eps instanceof Integer) {
+			this.eps = Double.valueOf((int) eps);
+		} else if (eps instanceof Double) {
+			this.eps = (double) eps;
+		} else if (eps instanceof String) {
+			this.eps = Double.valueOf((String) eps);
+		} else {
+			throw new IllegalArgumentException("'eps' parameter has to be either and instance of "
+					+ Float.class + " or " + Double.class
+					+ ". The provided argument is an instance of: " + eps.getClass());
+		}
+	}
+
 	public void setGain(Object gain) {
 		if (gain instanceof Integer) {
 			this.gainDouble = Double.valueOf((int) gain);

diff --git a/src/main/java/io/bioimage/modelrunner/transformations/ScaleRangeTransformation.java b/src/main/java/io/bioimage/modelrunner/transformations/ScaleRangeTransformation.java
@@ -47,13 +47,27 @@ public class ScaleRangeTransformation extends AbstractTensorTransformation
 	private String axes;
 	private Mode mode = Mode.PER_SAMPLE;
 	private String tensorName;
-	private float eps = (float) Math.pow(10, -6);
+	private double eps = Math.pow(10, -6);
 
 	public ScaleRangeTransformation()
 	{
 		super( name );
 	}
 
+	public void setEps(Object eps) {
+		if (eps instanceof Integer) {
+			this.eps = Double.valueOf((int) eps);
+		} else if (eps instanceof Double) {
+			this.eps = (double) eps;
+		} else if (eps instanceof String) {
+			this.eps = Double.valueOf((String) eps);
+		} else {
+			throw new IllegalArgumentException("'eps' parameter has to be either and instance of "
+					+ Float.class + " or " + Double.class
+					+ ". The provided argument is an instance of: " + eps.getClass());
+		}
+	}
+
 	public void setMinPercentile(Object minPercentile) {
 		if (minPercentile instanceof Integer) {
 			this.minPercentile = Double.valueOf((int) minPercentile) / 100;

diff --git a/...main/java/io/bioimage/modelrunner/transformations/ZeroMeanUnitVarianceTransformation.java b/...main/java/io/bioimage/modelrunner/transformations/ZeroMeanUnitVarianceTransformation.java
@@ -46,7 +46,7 @@ public class ZeroMeanUnitVarianceTransformation extends AbstractTensorTransforma
 	private double[] stdArr;
 	private Mode mode = Mode.PER_SAMPLE;
 	private String axes;
-	private float eps = (float) Math.pow(10, -6);
+	private double eps = Math.pow(10, -6);
 
 	private static String FIXED_MODE_ERR = "If the mode is 'fixed', the parameters 'mean' and"
 			+ " 'std need to be specified";
@@ -58,6 +58,20 @@ public ZeroMeanUnitVarianceTransformation()
 		super( name );
 	}
 
+	public void setEps(Object eps) {
+		if (eps instanceof Integer) {
+			this.eps = Double.valueOf((int) eps);
+		} else if (eps instanceof Double) {
+			this.eps = (double) eps;
+		} else if (eps instanceof String) {
+			this.eps = Double.valueOf((String) eps);
+		} else {
+			throw new IllegalArgumentException("'eps' parameter has to be either and instance of "
+					+ Float.class + " or " + Double.class
+					+ ". The provided argument is an instance of: " + eps.getClass());
+		}
+	}
+
 	public void setMean(Object mean) {
 		if (mean instanceof Integer) {
 			this.meanDouble = Double.valueOf((int) mean);