Add more

src/main/java/org/embl/mobie/lib/color/ColorHelper.java

@@ -39,7 +39,6 @@
 public abstract class ColorHelper
 {
 	final static public double goldenRatio = 1.0 / ( 0.5 * Math.sqrt( 5 ) + 0.5 );
-
 	public static final String RANDOM_FROM_GLASBEY = "randomFromGlasbey";
 
 	public static Color getColor( ARGBType argbType )

src/main/java/org/embl/mobie/lib/hcs/HCSDataAdder.java

@@ -30,10 +30,6 @@
 
 import net.thisptr.jackson.jq.internal.misc.Strings;
 import org.embl.mobie.lib.annotation.AnnotatedRegion;
-import org.embl.mobie.lib.hcs.Channel;
-import org.embl.mobie.lib.hcs.Plate;
-import org.embl.mobie.lib.hcs.Site;
-import org.embl.mobie.lib.hcs.Well;
 import org.embl.mobie.lib.serialize.Dataset;
 import org.embl.mobie.lib.serialize.ImageDataSource;
 import org.embl.mobie.lib.serialize.View;
@@ -197,7 +193,7 @@ public void addData( Dataset dataset )
 
 	private String getSiteID( Plate plate, Channel channel, Well well, Site site )
 	{
-		return getWellID( plate, channel, well ) + "-s" + site.getName();
+		return getWellID( plate, channel, well ) + "-s" + site.getId();
 	}
 
 	private String getWellID( Plate plate, Channel channel, Well well )

src/main/java/org/embl/mobie/lib/hcs/OperettaMetadata.java

@@ -1,37 +1,9 @@
-/*-
- * #%L
- * Fiji viewer for MoBIE projects
- * %%
- * Copyright (C) 2018 - 2023 EMBL
- * %%
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 
- * 1. Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- * #L%
- */
 package org.embl.mobie.lib.hcs;
 
-import ij.gui.PointRoi;
-import ij.gui.Roi;
+import ch.epfl.biop.bdv.img.opener.ChannelProperties;
 import mpicbg.spim.data.sequence.FinalVoxelDimensions;
 import mpicbg.spim.data.sequence.VoxelDimensions;
+import org.embl.mobie.lib.color.ColorHelper;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
@@ -41,16 +13,25 @@
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
+import java.awt.*;
 import java.io.File;
 import java.io.IOException;
 import java.util.HashMap;
-
+import java.util.LinkedHashMap;
 
 // one could extract an interface here for the
 // getter methods if this is useful for other data
 public class OperettaMetadata
 {
-	private HashMap< String, Element > filenameToMetadata;
+	private HashMap< String, Element > filenameToImageElement;
+	private HashMap< String, Element > channelIDToElement;
+	private HashMap< String, Integer > filenameToImageIndex;
+	private double dx;
+	private double dy;
+	private String spatialUnit;
+	private int imageSizeX;
+	private int imageSizeY;
+	private int maxIntensity;
 
 	public OperettaMetadata( File xml )
 	{
@@ -76,29 +57,57 @@ private void parse( File xml ) throws ParserConfigurationException, SAXException
 		Document doc = builder.parse( xml );
 		doc.getDocumentElement().normalize();
 
-		final double dx = Double.parseDouble( doc.getElementsByTagName( "ImageResolutionX" ).item( 0 ).getTextContent() );
-		final double dy = Double.parseDouble( doc.getElementsByTagName( "ImageResolutionY" ).item( 0 ).getTextContent() );
-		final String unit = doc.getElementsByTagName( "ImageResolutionX" ).item( 0 ).getAttributes().item( 0 ).getTextContent();
+		dx = Double.parseDouble( doc.getElementsByTagName( "ImageResolutionX" ).item( 0 ).getTextContent() );
+		dy = Double.parseDouble( doc.getElementsByTagName( "ImageResolutionY" ).item( 0 ).getTextContent() );
+		spatialUnit = doc.getElementsByTagName( "ImageResolutionX" ).item( 0 ).getAttributes().item( 0 ).getTextContent();
+
+		// could be channel specific
+		//
+		imageSizeX = Integer.parseInt( doc.getElementsByTagName( "ImageSizeX" ).item( 0 ).getTextContent() );
+		imageSizeY = Integer.parseInt( doc.getElementsByTagName( "ImageSizeY" ).item( 0 ).getTextContent() );
+
+		// could be channel specific
+		//
+		maxIntensity = Integer.parseInt( doc.getElementsByTagName( "MaxIntensity" ).item( 0 ).getTextContent() );
 
-		filenameToMetadata = new HashMap<>();
-		final NodeList fileNames = doc.getElementsByTagName( "URL" );
-		final int numFiles = fileNames.getLength();
-		for ( int i = 0; i < numFiles; i++ )
+		filenameToImageElement = new LinkedHashMap<>();
+		filenameToImageIndex = new LinkedHashMap<>();
+		channelIDToElement = new LinkedHashMap<>();
+
+		final NodeList imageFileNames = doc.getElementsByTagName( "URL" );
+		final int numImages = imageFileNames.getLength();
+		for ( int imageIndex = 0; imageIndex < numImages; imageIndex++ )
 		{
-			final Node item = fileNames.item( i );
+			final Node item = imageFileNames.item( imageIndex );
 			final Element parentNode = (Element) item.getParentNode();
-			filenameToMetadata.put( item.getTextContent(), parentNode );
+			filenameToImageElement.put( item.getTextContent(), parentNode );
+			filenameToImageIndex.put( item.getTextContent(), imageIndex );
+		}
+
+		final NodeList channelIDs = doc.getElementsByTagName( "MaxIntensity" );
+		final int numChannels = channelIDs.getLength();
+		for ( int channelIndex = 0; channelIndex < numChannels; channelIndex++ )
+		{
+			final Node item = channelIDs.item( channelIndex );
+			final Element parentNode = (Element) item.getParentNode();
+			final String channelID = parentNode.getAttributes().item( 0 ).getTextContent();
+			channelIDToElement.put( channelID, parentNode );
 		}
 	}
 
 	public VoxelDimensions getVoxelDimensions( String path )
 	{
-		final Element element = getElement( path );
-		final double imageResolutionX = getDouble( element, "ImageResolutionX" );
-		final double imageResolutionY = getDouble( element, "ImageResolutionY" );
-		final String unit = element.getElementsByTagName( "ImageResolutionX" ).item( 0 ).getAttributes().item( 0 ).getTextContent();
+		// In Operetta 4 and 5 this is not consistently at the same position
+		// thus we just fetch it once globally. Hopefully it is the same for all
+		// images anyway.
+
+		// This only works in Operetta 4
+		//		final Element element = getElement( path );
+		//		final double imageResolutionX = getDouble( element, "ImageResolutionX" );
+		//		final double imageResolutionY = getDouble( element, "ImageResolutionY" );
+		//		final String unit = element.getElementsByTagName( "ImageResolutionX" ).item( 0 ).getAttributes().item( 0 ).getTextContent();
 
-		return new FinalVoxelDimensions( unit, imageResolutionX, imageResolutionY, 1.0 );
+		return new FinalVoxelDimensions( spatialUnit, dx, dy, 1.0 );
 	}
 
 	private double getDouble( Element element, String tag )
@@ -114,10 +123,36 @@ private double getDouble( Element element, String tag )
 		}
 	}
 
-	private Element getElement( String path )
+	private int getInteger( Element element, String tag )
+	{
+		try
+		{
+			return Integer.parseInt( element.getElementsByTagName( tag ).item( 0 ).getTextContent() );
+		}
+		catch ( Exception e )
+		{
+			e.printStackTrace();
+			throw new RuntimeException( e );
+		}
+	}
+
+	private String getString( Element element, String tag )
+	{
+		try
+		{
+			return element.getElementsByTagName( tag ).item( 0 ).getTextContent();
+		}
+		catch ( Exception e )
+		{
+			e.printStackTrace();
+			throw new RuntimeException( e );
+		}
+	}
+
+	private Element getImageElement( String path )
 	{
 		final String filename = new File( path ).getName();
-		final Element element = filenameToMetadata.get( filename );
+		final Element element = filenameToImageElement.get( filename );
 		if ( element == null )
 		{
 			System.err.println("Could not find operetta metadata for " + filename );
@@ -129,15 +164,44 @@ private Element getElement( String path )
 	public boolean contains( String path )
 	{
 		final String filename = new File( path ).getName();
-		return filenameToMetadata.containsKey( filename );
+		return filenameToImageElement.containsKey( filename );
 	}
 
 	public double[] getRealPosition( String path )
 	{
-		final Element element = getElement( path );
+		final Element imageElement = getImageElement( path );
 		return new double[]{
-				getDouble( element, "PositionX" ),
-				-getDouble( element, "PositionY" )
-		  };
+				getDouble( imageElement, "PositionX" ),
+				-getDouble( imageElement, "PositionY" )
+		};
+	}
+
+	public String getColor( String path )
+	{
+		final Element imageElement = getImageElement( path );
+		final String channelID = getString( imageElement, "ChannelID" );
+		final Element channelElement = channelIDToElement.get( channelID );
+		final int mainEmissionWavelength = getInteger( channelElement, "MainEmissionWavelength" );
+
+		final Color color = ChannelProperties.getColorFromWavelength( mainEmissionWavelength );
+		final String string = ColorHelper.getString( ColorHelper.getARGBType( color ) );
+		return string;
+	}
+
+	public int getImageIndex( String path )
+	{
+		return filenameToImageIndex.get( new File( path ).getName() );
+	}
+
+	public double[] getContrastLimits( String path )
+	{
+		// TODO: fetch per channel via channelID of image
+		return new double[]{ 0, maxIntensity };
+	}
+
+	public int[] getSiteDimensions( String path )
+	{
+		// TODO: fetch per channel via channelID of image
+		return new int[]{ imageSizeX, imageSizeY };
 	}
-}
+}