Automatically export GT to CTC file format if provided as TrackMate file.

If the GT is provided as a TrackMate file, we need to export it to
CTC file format to properly use the CTC metrics. This commit does
that but checks first if an existing CTC folder is found in the GT
folder.

Author: tinevez

src/main/java/fiji/plugin/trackmate/helper/ctc/CTCMetricsRunner.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -28,6 +28,9 @@
 import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
+import java.util.Optional;
+import java.util.regex.Pattern;
+import java.util.stream.Stream;
 
 import org.scijava.Context;
 
@@ -40,7 +43,7 @@
 /**
  * Performs tracking and all the CTC metrics measurements with a TrackMate
  * instance.
- * 
+ *
  * @author Jean-Yves Tinevez
  */
 public class CTCMetricsRunner extends MetricsRunner
@@ -54,7 +57,7 @@ public class CTCMetricsRunner extends MetricsRunner
 	/**
 	 * Path to ground truth folder.
 	 */
-	private final String gtPath;
+	private String gtPath;
 
 	public CTCMetricsRunner( final String gtPath, final String saveFolder, final Context context )
 	{
@@ -67,8 +70,43 @@ public CTCMetricsRunner( final String gtPath, final String saveFolder, final Con
 	@Override
 	public TrackingMetrics performMetricsMeasurements( final TrackMate trackmate ) throws MetricsComputationErrorException
 	{
-		batchLogger.log( "Exporting as CTC results.\n" );
+		// Do we have a folder for the ground-truth, or a TrackMate file?
+		if ( gtPath.toLowerCase().endsWith( ".xml" ) )
+		{
+			// Assume it's a TrackMate file, export it to CTC file format.
+			batchLogger.log( "Ground-truth is in the TrackMate file format.\n" );
+
+			final String regexPattern = "\\d{2}_GT";
+			final Pattern pattern = Pattern.compile( regexPattern );
+			try (Stream< Path > paths = Files.list( resultsRootPath ))
+			{
+				final Optional< Path > ctcGTfolder = paths
+						.filter( Files::isDirectory )
+						.filter( path -> pattern.matcher( path.getFileName().toString() ).matches() )
+						.findFirst();
+
+				if ( ctcGTfolder.isPresent() )
+				{
+					batchLogger.log( "Found a GT folder in CTC format: " + ctcGTfolder.get() + "\n" );
+					gtPath = ctcGTfolder.get().toString();
+				}
+				else
+				{
+					batchLogger.log( "Exporting GT file to CTC format.\n" );
+					gtPath = CTCExporter.exportAll( resultsRootPath.toString(), trackmate, ExportType.GOLD_TRUTH, batchLogger );
+					gtPath = Paths.get( gtPath ).getParent().toString();
+				}
+			}
+			catch ( final IOException e )
+			{
+				batchLogger.error( "Error reading the GT parent directory. Stopping."
+						+ "\n" + e.getMessage() );
+				e.printStackTrace();
+				throw new RuntimeException( e );
+			}
+		}
 
+		batchLogger.log( "Exporting test results to CTC format.\n" );
 		final int id = CTCExporter.getAvailableDatasetID( resultsRootPath.toString() );
 		final String resultsFolder = CTCExporter.getExportTrackingDataPath( resultsRootPath.toString(), id, ExportType.RESULTS, trackmate );
 		try