TGMMImporter2::process() does not allow series that begin on frames o…

…ther than 0 -- even if user sets `tFrom` / `tTo` correctly. Following these changes, importer works correctly. Additional changes were made to ImportTGMMAnnotationPlugin_.java to pass list of timepoints for which affine registration models are available, so those can be properly matched with the incoming TGMM data. modified: src/main/java/fiji/plugin/mamut/ImportTGMMAnnotationPlugin_.java modified: src/main/java/fiji/plugin/mamut/io/TGMMImporter2.java
trackmate-sc · Jun 1, 2021 · 07324c1 · 07324c1
1 parent c74e0d3
commit 07324c1
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Showing 2 changed files with 34 additions and 9 deletions.
diff --git a/src/main/java/fiji/plugin/mamut/ImportTGMMAnnotationPlugin_.java b/src/main/java/fiji/plugin/mamut/ImportTGMMAnnotationPlugin_.java
@@ -424,12 +424,13 @@ protected Model createModel( final File tgmmFolder, final SpimDataMinimal spimDa
 		final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
 		final ViewRegistrations regs = spimData.getViewRegistrations();
 		final List< AffineTransform3D > transforms = new ArrayList<>( seq.getTimePoints().size() );
-		for ( final TimePoint t : seq.getTimePoints().getTimePointsOrdered() )
+		final List< TimePoint > timepoints = seq.getTimePoints().getTimePointsOrdered();
+		for ( final TimePoint t : timepoints )
 		{
 			transforms.add( regs.getViewRegistration( t.getId(), setupID ).getModel() );
 		}
 
-		final TGMMImporter2 importer = new TGMMImporter2( tgmmFolder, transforms, TGMMImporter2.DEFAULT_PATTERN, logger, interval, tFrom, tTo );
+		final TGMMImporter2 importer = new TGMMImporter2( tgmmFolder, transforms, timepoints, TGMMImporter2.DEFAULT_PATTERN, logger, interval, tFrom, tTo );
 		if ( !importer.checkInput() || !importer.process() )
 		{
 			logger.error( importer.getErrorMessage() );

diff --git a/src/main/java/fiji/plugin/mamut/io/TGMMImporter2.java b/src/main/java/fiji/plugin/mamut/io/TGMMImporter2.java
@@ -25,6 +25,7 @@
 import java.io.FilenameFilter;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
@@ -45,6 +46,7 @@
 import fiji.plugin.trackmate.Model;
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.SpotCollection;
+import mpicbg.spim.data.sequence.TimePoint;
 import net.imglib2.RealInterval;
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealPoint;
@@ -97,6 +99,8 @@ public boolean accept( final File folder, final String name )
 
 	private final List< AffineTransform3D > transforms;
 
+	private final List< TimePoint > timepoints;
+
 	private final Logger logger;
 
 	private long processingTime;
@@ -111,11 +115,12 @@ public boolean accept( final File folder, final String name )
 	 * CONSTRUCTORS
 	 */
 
-	public TGMMImporter2( final File file, final List< AffineTransform3D > transforms, final Pattern framePattern, final Logger logger, final RealInterval interval, final int tFrom, final int tTo )
+	public TGMMImporter2( final File file, final List< AffineTransform3D > transforms, final List< TimePoint > timepoints, final Pattern framePattern, final Logger logger, final RealInterval interval, final int tFrom, final int tTo )
 	{
 		this.file = file;
 		this.framePattern = framePattern;
 		this.transforms = transforms;
+		this.timepoints = timepoints;
 		this.logger = logger;
 		this.interval = interval;
 		this.tFrom = tFrom;
@@ -170,7 +175,8 @@ public boolean process()
 		 */
 
 		final File[] xmlFiles = file.listFiles( xmlFilter );
-
+		Arrays.sort(xmlFiles);
+
 		/*
 		 * Extract frame information from filename. It is not stored elsewhere
 		 * so we have to rely on a specific pattern to get it. Note that it is
@@ -194,7 +200,7 @@ public boolean process()
 			try
 			{
 				final int frame = Integer.parseInt( strFrame );
-				frames[ frame ] = i;
+				frames[ i ] = frame;
 			}
 			catch ( final NumberFormatException nfe )
 			{
@@ -221,6 +227,8 @@ public boolean process()
 
 			Map< Integer, Spot > previousSpotID = null;
 			Map< Integer, Spot > currentSpotID;
+			AffineTransform3D transform = transforms.get( 0 );
+			boolean transformNotFound;
 
 			for ( int t = 0; t < frames.length; t++ )
 			{
@@ -229,10 +237,26 @@ public boolean process()
 					continue;
 				}
 
-				logger.log( "Processing frame " + t + ". " );
-				final AffineTransform3D transform = transforms.get( frames[ t ] );
+				logger.log( "Processing frame " + frames[ t ] + ". " );
+				transformNotFound = true;
+
+				for ( int ii = 0; ii < timepoints.size(); ii++ )
+				{
+					if ( timepoints.get( ii ).getId() == frames[ t ] )
+					{
+						transform = transforms.get( ii );
+						transformNotFound = false;
+						break;
+					}
+				}
+
+				if ( transformNotFound )
+				{
+					logger.log( "Unable to find AffineTransform3D for frame " + frames[ t ] + "; using most recently recalled transformation model!" );
+				}
+
 
-				xmlFile = xmlFiles[ frames[ t ] ];
+				xmlFile = xmlFiles[ t ];
 				final Document doc = saxBuilder.build( xmlFile );
 				final Element root = doc.getRootElement();
 				final List< Element > detectionEls = root.getChildren( XML_DETECTION_NAME );
@@ -430,7 +454,7 @@ public boolean process()
 				 * Finished inspecting a frame. Store it in the spot collection.
 				 */
 
-				sc.put( t, spots );
+				sc.put( frames[ t ], spots );
 				previousSpotID = currentSpotID;
 				logger.log( "Found " + spots.size() + " spots.\n" );
 				logger.setProgress( ( double ) t / frames.length );