additional util functions

pom.xml

@@ -8,7 +8,7 @@
 		<version>5.0</version> <relativePath /> </parent> -->
 	<groupId>embl.almf</groupId>
 	<artifactId>AutoMicTools_</artifactId>
-	<version>1.1.29-SNAPSHOT</version>
+	<version>1.1.30-SNAPSHOT</version>
 
 	<name>plugins/AutoMicTools_.jar</name>
 	<description>Collection of tools for automated (feedback) microscopy data acquisition and analysis</description>

src/main/java/automic/geom/Point3D.java

@@ -11,6 +11,14 @@ public class Point3D {
 		z=_z;
 	}
 	
+
+	public Point3D(Integer _xInt, Integer _yInt, Integer _zInt) {
+		x=(_xInt==null)?null:Double.valueOf(_xInt);
+		y=(_yInt==null)?null:Double.valueOf(_yInt);
+		z=(_zInt==null)?null:Double.valueOf(_zInt);
+	}
+
+	
 	public Double getX(){
 		return x;
 	}
@@ -23,6 +31,25 @@ public class Point3D {
 		return z;
 	}
 	
+	public Integer getXInteger(){
+		if (x==null)
+			return null;
+		return x.intValue();
+	}
+	
+	public Integer getYInteger(){
+		if (y==null)
+			return null;
+		return y.intValue();
+	}
+
+	public Integer getZInteger(){
+		if (z==null)
+			return null;
+		return z.intValue();
+	}
+	
+	
 	public void setX(Double _x) {
 		x=_x;
 	}

src/main/java/automic/online/microscope/ZenBlueCommander.java

@@ -179,11 +179,4 @@ public class ZenBlueCommander implements MicroscopeCommanderInterface{
 		_jObject.add(_key, _value);
 	}
 	
-	private static Double getValueFromNonNullArray(double[] _array, int _index) {
-		if (_array==null)
-			return null;
-		return _array[_index];
-	}
-	
-
 }

src/main/java/automic/utils/imagefiles/ImageOpenerWithBioformats.java

@@ -16,6 +16,8 @@ import loci.plugins.in.ImporterOptions;
 
 import java.lang.Exception;
 
+import automic.geom.Point3D;
+
 import java.io.File;
 import java.io.IOException;
 
@@ -197,5 +199,44 @@ public class ImageOpenerWithBioformats {
 		
 		return imgs[0];		
 	}
+	
+	public static Point3D getVoxelSizeUm(String _imageFilePath)throws Exception {
+		
+		ImageReader reader = new ImageReader();
+		IMetadata omeMeta = MetadataTools.createOMEXMLMetadata();
+		reader.setMetadataStore(omeMeta);
+		reader.setId(_imageFilePath);
+		
+		double xSize=omeMeta.getPixelsPhysicalSizeX(0).value().doubleValue();
+		double ySize=omeMeta.getPixelsPhysicalSizeY(0).value().doubleValue();
+		double zSize=omeMeta.getPixelsPhysicalSizeZ(0).value().doubleValue();
+
+		reader.close();
+		
+		return new Point3D(xSize, ySize, zSize);
+	}
+	
+	public static Point3D getVoxelSizeNm(String _imageFilePath) throws Exception {
+		Point3D voxelSizeInUm=getVoxelSizeUm(_imageFilePath);
+		
+		return new Point3D(voxelSizeInUm.getX()*1000, voxelSizeInUm.getY()*1000, voxelSizeInUm.getZ()*1000);
+	}
+	
+	public static Point3D getImageSizePx(String _imageFilePath)throws Exception {
+		
+		ImageReader reader = new ImageReader();
+		IMetadata omeMeta = MetadataTools.createOMEXMLMetadata();
+		reader.setMetadataStore(omeMeta);
+		reader.setId(_imageFilePath);
+		
+		double xSize=omeMeta.getPixelsSizeX(0).getValue();
+		double ySize=omeMeta.getPixelsSizeY(0).getValue();
+		double zSize=omeMeta.getPixelsSizeZ(0).getValue();
+
+		reader.close();
+		
+		return new Point3D(xSize, ySize, zSize);
+	}
+	
 
 }