A static utility to dump the content of a model to a CSV file.

Address https://forum.image.sc/t/error-headlessexception-when-trying-to-save-csv-file-of-tracking-data-from-trackmate-when-running-headlessly/94304/5

src/main/java/fiji/plugin/trackmate/io/CSVExporter.java

@@ -0,0 +1,309 @@
+package fiji.plugin.trackmate.io;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+
+import com.opencsv.CSVWriter;
+
+import fiji.plugin.trackmate.Dimension;
+import fiji.plugin.trackmate.Model;
+import fiji.plugin.trackmate.Spot;
+import fiji.plugin.trackmate.TrackModel;
+import fiji.plugin.trackmate.util.TMUtils;
+
+public class CSVExporter
+{
+
+	/**
+	 * The symbol that will be appended when a value is missing.
+	 */
+	public static final String MISSING_STR = "ø";
+
+	/**
+	 * Exports the spots in the specified model to a CSV file.
+	 * <p>
+	 * The table contains the spots, one spot per line. All the declared spot
+	 * feature values are exported, one feature per column. Additionally, the
+	 * following columns are added:
+	 * <ol start="0">
+	 * <li>The spot ID.
+	 * <li>The spot name.
+	 * <li>The ID of the track the spot belongs to, if any.
+	 * <li>The name of the track the spot belongs to, if any.
+	 * <li>Whether the track the spot belongs to is visible, if any. 1 if
+	 * visible, 0 otherwise.
+	 * </ol>
+	 * 
+	 * The table will have a header on 4 lines containing:
+	 * <ol start="0">
+	 * <li>The feature key.
+	 * <li>The feature name.
+	 * <li>The feature short name.
+	 * <li>The feature unit if any.
+	 * </ol>
+	 * 
+	 * @param csvFile
+	 *            the path of the file to export to.
+	 * @param model
+	 *            the model to export.
+	 * @param visibleOnly
+	 *            if <code>true</code>, only the spots in visible tracks will be
+	 *            exported. Otherwise all spots are exported.
+	 * @throws IOException
+	 *             if something wrong happens while writing to the CSV file.
+	 */
+	public static final void exportSpots( final String csvFile, final Model model, final boolean visibleOnly ) throws IOException
+	{
+		final TrackModel tm = model.getTrackModel();
+		final Set< Integer > trackIDs = tm.trackIDs( visibleOnly );
+		final List< String > features = new ArrayList<>( model.getFeatureModel().getSpotFeatures() );
+
+		// Function to return a feature value.
+		final Map< String, Boolean > isInt = model.getFeatureModel().getSpotFeatureIsInt();
+		final BiFunction< Spot, String, Number > featureVal = ( s, f ) -> {
+			final Double obj = s.getFeature( f );
+			if ( obj == null )
+				return null;
+
+			if ( isInt.getOrDefault( f, Boolean.FALSE ) )
+				return obj.intValue();
+			else
+				return obj;
+		};
+
+		/*
+		 * Extra columns.
+		 */
+
+		// Spot name function.
+		final Function< Spot, String > labelFun = ( s ) -> s.getName();
+		// Spot id function/
+		final Function< Spot, String > idFun = ( s ) -> Integer.toString( s.ID() );
+		// Track id function.
+		final Function< Spot, String > trackIdFun = ( s ) -> {
+			final Integer trackID = tm.trackIDOf( s );
+			if ( trackID == null )
+				return MISSING_STR;
+			else
+				return Integer.toString( trackID );
+		};
+		// Track name function.
+		final Function< Spot, String > trackNameFun = ( s ) -> {
+			final Integer trackID = tm.trackIDOf( s );
+			if ( trackID == null )
+				return MISSING_STR;
+			else
+				return tm.name( trackID );
+		};
+		// Track visibility function.
+		final Function< Spot, String > trackVisiblityFun = ( s ) -> {
+			final Integer trackID = tm.trackIDOf( s );
+			if ( trackID == null || !tm.isVisible( trackID ) )
+				return "0";
+			else
+				return "1";
+		};
+
+		final List< Function< Spot, String > > extraFuns = Arrays.asList( idFun, labelFun, trackIdFun, trackNameFun, trackVisiblityFun );
+		final String[][] extraHeaders = new String[][] {
+				{ "ID", "ID", "ID", "" },
+				{ "LABEL", "Label", "Label", "" },
+				{ "TRACK_ID", "Track ID", "Track ID", "" },
+				{ "TRACK_NAME", "Track name", "Track name", "" },
+				{ "TRACK_VISIBLE", "Track visibility", "Track visibility", "" }
+		};
+
+		try (CSVWriter writer = new CSVWriter( new FileWriter( new File( csvFile ) ),
+				CSVWriter.DEFAULT_SEPARATOR,
+				CSVWriter.NO_QUOTE_CHARACTER,
+				CSVWriter.DEFAULT_ESCAPE_CHARACTER,
+				CSVWriter.DEFAULT_LINE_END ))
+		{
+			// Header.
+			writeHeaderSpots( writer, model, extraHeaders );
+
+			final SpotWriter spotWriter = new SpotWriter( writer, features, featureVal, extraFuns );
+
+			// Spots in tracks.
+			for ( final Integer trackID : trackIDs )
+			{
+				final List< Spot > spots = new ArrayList<>( tm.trackSpots( trackID ) );
+				spots.sort( Spot.frameComparator );
+				for ( final Spot spot : spots )
+					spotWriter.write( spot );
+			}
+
+			// Possibly spots not in tracks.
+			if ( !visibleOnly )
+			{
+				for ( final Spot spot : model.getSpots().iterable( false ) )
+				{
+					if ( tm.trackIDOf( spot ) != null )
+						continue; // Already done abobe.
+
+					spotWriter.write( spot );
+				}
+			}
+		}
+	}
+
+	private static void writeHeaderSpots( final CSVWriter writer, final Model model, final String[][] extra )
+	{
+		final List< String > features = new ArrayList<>( model.getFeatureModel().getSpotFeatures() );
+		final Map< String, String > featureNames = model.getFeatureModel().getSpotFeatureNames();
+		final Map< String, String > featureShortNames = model.getFeatureModel().getSpotFeatureShortNames();
+		final Map< String, String > featureUnits = new HashMap<>();
+		for ( final String feature : features )
+		{
+			final Dimension dimension = model.getFeatureModel().getSpotFeatureDimensions().get( feature );
+			final String units = TMUtils.getUnitsFor( dimension, model.getSpaceUnits(), model.getTimeUnits() );
+			featureUnits.put( feature, units );
+		}
+		writeHeader( writer, features, featureNames, featureShortNames, featureUnits, extra );
+	}
+
+	private static void writeHeader(
+			final CSVWriter writer,
+			final List< String > features,
+			final Map< String, String > featureNames,
+			final Map< String, String > featureShortNames,
+			final Map< String, String > featureUnits,
+			final String[][] extra )
+	{
+
+		final int columnShift = extra.length;
+		final int nCols = columnShift + features.size();
+		final String[] content = new String[ nCols ];
+
+		/*
+		 * Determine whether we can skip 2nd or 3d line, if it's identical to
+		 * the 2nd one (happens when the names are repeated).
+		 */
+
+		boolean skipThirdLine = true;
+		boolean skipSecondLine = true;
+		for ( int i = columnShift; i < content.length; i++ )
+		{
+			final String feature = features.get( i - columnShift );
+			final String name = featureNames.get( features.get( i - columnShift ) );
+			final String shortName = featureShortNames.get( features.get( i - columnShift ) );
+			if ( !feature.equals( name ) )
+				skipSecondLine = false;
+			if ( !name.equals( shortName ) )
+				skipThirdLine = false;
+		}
+
+		// Header 1st line.
+		for ( int i = 0; i < extra.length; i++ )
+			content[ i ] = extra[ i ][ 0 ];
+		for ( int i = columnShift; i < content.length; i++ )
+			content[ i ] = features.get( i - columnShift );
+		writer.writeNext( content );
+
+		// Header 2nd line.
+		if ( !skipSecondLine )
+		{
+			for ( int i = 0; i < extra.length; i++ )
+				content[ i ] = extra[ i ][ 1 ];
+			for ( int i = columnShift; i < content.length; i++ )
+				content[ i ] = featureNames.get( features.get( i - columnShift ) );
+			writer.writeNext( content );
+		}
+
+		// Header 3rd line.
+		if ( !skipThirdLine )
+		{
+			for ( int i = 0; i < extra.length; i++ )
+				content[ i ] = extra[ i ][ 2 ];
+			for ( int i = columnShift; i < content.length; i++ )
+				content[ i ] = featureShortNames.get( features.get( i - columnShift ) );
+			writer.writeNext( content );
+		}
+
+		// Header 4th line.
+		for ( int i = 0; i < extra.length; i++ )
+			content[ i ] = extra[ i ][ 3 ];
+		for ( int i = columnShift; i < content.length; i++ )
+		{
+			final String feature = features.get( i - columnShift );
+			final String units = featureUnits.get( feature );
+			final String unitsStr = ( units == null || units.isEmpty() ) ? "" : "(" + units + ")";
+			content[ i ] = unitsStr;
+		}
+		writer.writeNext( content );
+	}
+
+	private static class SpotWriter
+	{
+
+		private final CSVWriter writer;
+
+		private final List< String > features;
+
+		private final List< Function< Spot, String > > extraFuns;
+
+		private final String[] content;
+
+		private final BiFunction< Spot, String, Number > featureVal;
+
+		private final int columnShift;
+
+		public SpotWriter( final CSVWriter writer, final List< String > features, final BiFunction< Spot, String, Number > featureVal, final List< Function< Spot, String > > extraFuns )
+		{
+			this.writer = writer;
+			this.features = features;
+			this.featureVal = featureVal;
+			this.extraFuns = extraFuns;
+			this.columnShift = extraFuns.size();
+			final int nCols = columnShift + features.size();
+			this.content = new String[ nCols ];
+		}
+
+		public void write( final Spot spot )
+		{
+			for ( int i = 0; i < columnShift; i++ )
+				content[ i ] = extraFuns.get( i ).apply( spot );
+			for ( int i = columnShift; i < content.length; i++ )
+			{
+				final Object val = featureVal.apply( spot, features.get( i - columnShift ) );
+				content[ i ] = ( val == null ) ? MISSING_STR : val.toString();
+			}
+
+			writer.writeNext( content );
+		}
+	}
+
+	public static void main( final String[] args ) throws IOException
+	{
+		final String filename = "samples/FakeTracks.xml";
+		final TmXmlReader reader = new TmXmlReader( new File( filename ) );
+		if ( !reader.isReadingOk() )
+		{
+			System.out.println( reader.getErrorMessage() );
+			return;
+		}
+
+		final String csvFile = filename.replace( ".xml", "-spots_in_tracks.csv" );
+		CSVExporter.exportSpots( csvFile, reader.getModel(), false );
+
+		System.out.println( "Done." );
+		System.out.println( "__________________" );
+		try (BufferedReader br = new BufferedReader( new FileReader( csvFile ) ))
+		{
+			String line;
+			while ( ( line = br.readLine() ) != null )
+				System.out.println( line );
+		}
+	}
+}