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Don't stop TrackMate import when a spot is missing. #308

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Jul 1, 2024
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Don't stop TrackMate import when a spot is missing. #308

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12 changes: 12 additions & 0 deletions src/main/java/org/mastodon/mamut/io/importer/trackmate/TrackMateImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -424,6 +424,18 @@ private final class Import extends ModelImporter
final int targetID = Integer.parseInt( edgeEl.getAttributeValue( EDGE_TARGET_ATTRIBUTE ) );
final Spot target = idToSpotIDmap.get( targetID, targetRef );

if ( source == null )
{
// TODO Echo warnings in a logger instead of sysout.
System.out.println( "Could not find spot with ID " + sourceID + " - skipping edge " + sourceID + " → " + targetID );
continue;
}
if ( target == null )
{
System.out.println( "Could not find spot with ID " + targetID + " - skipping edge " + sourceID + " → " + targetID );
continue;
}

// Protect against link time inversion.
final Link link;
if ( source.getTimepoint() < target.getTimepoint() )
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