From b6998f43273da0e2b7db30a026fa4da1e4ac9dc6 Mon Sep 17 00:00:00 2001
From: Stephan Preibisch <stephan.preibisch@gmx.de>
Date: Fri, 18 Oct 2024 15:56:12 -0400
Subject: [PATCH] starting to write analyze error method

---
 .../mvrecon/fiji/plugin/Analyze_Errors.java   | 144 ++++++++++++++++++
 1 file changed, 144 insertions(+)
 create mode 100644 src/main/java/net/preibisch/mvrecon/fiji/plugin/Analyze_Errors.java

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Analyze_Errors.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Analyze_Errors.java
new file mode 100644
index 00000000..b61d25d7
--- /dev/null
+++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Analyze_Errors.java
@@ -0,0 +1,144 @@
+package net.preibisch.mvrecon.fiji.plugin;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+
+import ij.ImageJ;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import mpicbg.spim.data.sequence.ViewId;
+import net.preibisch.legacy.io.IOFunctions;
+import net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML;
+import net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML;
+import net.preibisch.mvrecon.fiji.plugin.util.GUIHelper;
+import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
+import net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools;
+
+public class Analyze_Errors implements PlugIn
+{
+
+	@Override
+	public void run( final String arg0 )
+	{
+		// ask for everything
+		final LoadParseQueryXML result = new LoadParseQueryXML();
+
+		if ( !result.queryXML( "analyze interest point errors", "Analyze", true, true, true, true, true ) )
+			return;
+
+		final SpimData2 data = result.getData();
+		final List< ViewId > viewIds =
+				SpimData2.getAllViewIdsSorted( result.getData(), result.getViewSetupsToProcess(), result.getTimePointsToProcess() );
+
+		final HashMap<String, Double > labelAndWeights = getParameters(data, viewIds);
+	}
+
+	public static void getErrors(
+			final SpimData2 data,
+			final List< ViewId > viewIds )
+	{
+		
+	}
+
+	public static HashMap<String, Double > getParameters(
+			final SpimData2 data,
+			final List< ViewId > viewIds )
+	{
+		final GenericDialog gd = new GenericDialog( "Analyze Interest Point Errors" );
+
+		// check which channels and labels are available and build the choices
+		final String[] labelsRaw = InterestPointTools.getAllInterestPointLabels( data, viewIds );
+
+		if ( labelsRaw.length == 0 )
+		{
+			IOFunctions.printErr( "No interest points available, stopping. Please run Interest Point Detection first" );
+			return null;
+		}
+
+		final String[] labels = new String[ labelsRaw.length + 1 ];
+		for ( int i = 0; i < labelsRaw.length; ++i )
+			labels[ i ] = labelsRaw[ i ];
+		labels[ labelsRaw.length ] = "Select multiple interestpoints [extra dialog]";
+
+		// choose the first label that is complete if possible
+		if ( Interest_Point_Registration.defaultLabel < 0 || Interest_Point_Registration.defaultLabel >= labels.length )
+		{
+			Interest_Point_Registration.defaultLabel = -1;
+
+			for ( int i = 0; i < labels.length; ++i )
+				if ( !labels[ i ].contains( InterestPointTools.warningLabel ) && !labels[ i ].startsWith( "Select multiple interestpoints") )
+				{
+					Interest_Point_Registration.defaultLabel = i;
+					break;
+				}
+
+			if ( Interest_Point_Registration.defaultLabel == -1 )
+				Interest_Point_Registration.defaultLabel = 0;
+		}
+
+		System.out.println( Interest_Point_Registration.defaultLabel );
+
+		gd.addChoice( "Interest_points" , labels, labels[ Interest_Point_Registration.defaultLabel ] );
+		//gd.addCheckbox( "Print sorted results", true );
+		//gd.addCheckbox( "Select & color-code worst pair in GUI", true );
+
+		gd.showDialog();
+
+		if ( gd.wasCanceled() )
+			return null;
+
+		// assemble which label has been selected
+		final int labelChoice = Interest_Point_Registration.defaultLabel = gd.getNextChoiceIndex();
+		//final boolean print = gd.getNextBoolean();
+		//final boolean select = gd.getNextBoolean();
+
+		final HashMap<String, Double > labelAndWeight = new HashMap<>();
+
+		if ( labelChoice < labels.length - 1 )
+		{
+			labelAndWeight.put( InterestPointTools.getSelectedLabel( labels, labelChoice ), 1.0 );
+		}
+		else
+		{
+			final ArrayList< String > labelChoices = Interest_Point_Registration.multipleInterestPointsGUI( labels );
+
+			final GenericDialog gdLabel2 = new GenericDialog( "Select error weights" );
+
+			if ( Interest_Point_Registration.defaultLabelWeights == null || Interest_Point_Registration.defaultLabelWeights.length != labelChoices.size() )
+			{
+				Interest_Point_Registration.defaultLabelWeights = new double[ labelChoices.size() ];
+				Arrays.setAll( Interest_Point_Registration.defaultLabelWeights, d -> 1.0 );
+			}
+			
+			gdLabel2.addMessage( "Weights for interest point labels:", GUIHelper.largefont );
+
+			for ( int i = 0; i < labelChoices.size(); ++i )
+				gdLabel2.addNumericField( labelChoices.get( i ) + " w=", Interest_Point_Registration.defaultLabelWeights[ i ], 2 );
+
+			gdLabel2.showDialog();
+			if ( gdLabel2.wasCanceled() )
+				return null;
+
+			for ( int i = 0; i < labelChoices.size(); ++i )
+			{
+				labelAndWeight.put( labelChoices.get( i ), Interest_Point_Registration.defaultLabelWeights[ i ] = gdLabel2.getNextNumber() );
+				IOFunctions.println( labelChoices.get( i ) + ", weight=" + labelAndWeight.get( labelChoices.get( i ) ) );
+			}
+		}
+
+		return labelAndWeight;
+	}
+
+	public static void main( String[] args )
+	{
+		new ImageJ();
+
+		if ( System.getProperty("os.name").toLowerCase().contains( "mac" ) )
+			GenericLoadParseQueryXML.defaultXMLURI = "/Users/preibischs/SparkTest/Stitching/dataset.xml";
+
+		new Analyze_Errors().run( null );
+	}
+	
+}