fix: AffineCoordinateTransform constructors

* io for BaseLinearCoordinateTransform
saalfeldlab · Jan 30, 2024 · a62d047 · a62d047
1 parent 20266f2
commit a62d047
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Showing 2 changed files with 40 additions and 10 deletions.
diff --git a/...lfeldlab/n5/universe/metadata/ome/ngff/v05/transformations/AffineCoordinateTransform.java b/...lfeldlab/n5/universe/metadata/ome/ngff/v05/transformations/AffineCoordinateTransform.java
@@ -14,14 +14,13 @@ public AffineCoordinateTransform( BaseLinearCoordinateTransform<AffineGet> ct )
 	}
 
 	public AffineCoordinateTransform( final double[] affine) {
-		super("affine");
-		this.affineFlat = affine;
-		buildTransform(affine );
+		super("affine", affine);
+		buildTransform(affine);
 	}
 
 	public AffineCoordinateTransform( final String name, final String inputSpace, final String outputSpace,
 			final double[] affine) {
-		super("affine", name, inputSpace, outputSpace );
+		super("affine", name, inputSpace, outputSpace, affine );
 		this.affineFlat = affine;
 		buildTransform( affine );
 	}
@@ -36,8 +35,7 @@ public AffineCoordinateTransform(final String name, final N5Reader n5, final Str
 	public AffineCoordinateTransform( final String name, 
 			final String[] inputAxes, final String[] outputAxes,
 			final double[] affine ) {
-		super("affine", name, inputAxes, outputAxes  );
-		this.affineFlat = affine;
+		super("affine", name, inputAxes, outputAxes, affine );
 	}
 
 	public AffineCoordinateTransform( final String name, final String path,

diff --git a/...dlab/n5/universe/metadata/ome/ngff/v05/transformations/BaseLinearCoordinateTransform.java b/...dlab/n5/universe/metadata/ome/ngff/v05/transformations/BaseLinearCoordinateTransform.java
@@ -3,6 +3,7 @@
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.TransformUtils;
 
+import com.google.gson.Gson;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 
@@ -24,6 +25,13 @@ public BaseLinearCoordinateTransform(final String type) {
 		super(type);
 	}
 
+	public BaseLinearCoordinateTransform(final String type, final double[] affineFlat) {
+
+		super(type);
+		this.affineFlat = affineFlat;
+		buildJsonParameter();
+	}
+
 	public BaseLinearCoordinateTransform( final BaseLinearCoordinateTransform<T> other ) {
 		super(other.type, other.path);
 		this.affine = other.affine;
@@ -32,20 +40,38 @@ public BaseLinearCoordinateTransform( final BaseLinearCoordinateTransform<T> oth
 		this.name = other.name;
 		this.input = other.input;
 		this.output = other.output;
+		buildJsonParameter();
 	}
 
-	public BaseLinearCoordinateTransform( final String type, final String name, final String inputSpace, final String outputSpace) {
-		super(type, name, null, inputSpace, outputSpace );
+	public BaseLinearCoordinateTransform(final String type, final String name, final String inputSpace, final String outputSpace) {
+
+		super(type, name, null, inputSpace, outputSpace);
+	}
+
+	public BaseLinearCoordinateTransform(final String type, final String name, final String inputSpace, final String outputSpace, final double[] affineFlat) {
+
+		super(type, name, null, inputSpace, outputSpace);
+		this.affineFlat = affineFlat;
+		buildJsonParameter();
 	}
 
 	public BaseLinearCoordinateTransform(final String type, final String name, final N5Reader n5, final String path,
 			final String inputSpace, final String outputSpace) {
-		super(type, name, path, inputSpace, outputSpace );
+
+		super(type, name, path, inputSpace, outputSpace);
 	}
 
-	public BaseLinearCoordinateTransform( final String type, final String name, 
+	public BaseLinearCoordinateTransform(final String type, final String name,
 			final String[] inputAxes, final String[] outputAxes) {
+
+		super(type, name, null, inputAxes, outputAxes);
+	}
+
+	public BaseLinearCoordinateTransform( final String type, final String name,
+			final String[] inputAxes, final String[] outputAxes, final double[] affineFlat) {
 		super(type, name, null, inputAxes, outputAxes  );
+		this.affineFlat = affineFlat;
+		buildJsonParameter();
 	}
 
 	public BaseLinearCoordinateTransform( final String type, final String name, final String path,
@@ -58,6 +84,12 @@ public JsonElement getJsonParameter() {
 		return affine;
 	}
 
+	protected void buildJsonParameter() {
+
+		if( affineFlat != null )
+			affine = new Gson().toJsonTree(affineFlat);
+	}
+
 	public void interpretParameters() {
 
 		if (!affine.isJsonArray())